This thesis explores a series of structurally related reagents for formal H-atom transfer reactions. The work builds upon a previous discovery that an aniline-appended cobaltocene complex, upon protonation and reduction, is capable of concerted proton-electron transfer which enables its use as an electrochemical mediator for a variety of unsaturated small molecule reduction reactions. Given its potent reactivity and simple design, the aniline- appended cobaltocene complex is a wonderful platform for structure-function studies, and accordingly, three distinct structure-function relationships are investigated.
\r\n\r\nChapters 2 and 3 examine the reductive component by substituting cobaltocene for a main group reductant of a similar potential, diaryl-o-carborane. The o-carborane can be reduced and protonated to generate an N\u2013H bond with a weak effective bond dissociation free energy of 31 kcal/mol. Crystal structures of the diaryl-o-carborane radical anions are disclosed. The reactivity of the singly reduced, protonated form of the diaryl-o-carborane towards substrates and towards proton reduction is discussed. Then, the synthesis, thermochemistry, and reactivity of a family of o-carborane PCET reagents is described. Cyclic voltammetry using acetophenone reduction as an indicator of concerted proton-electron transfer suggests that the thermochemical perturbations do not categorically change the reactivity.
\r\n\r\nThe second section examines the bridging group that separates the redox and acid/base moieties. Across the series of four complexes, the PCET driving force remains relatively constant while the thermodynamic coupling is varied substantially. Kinetic measurements of PCET reduction reveal that the reaction proceeds by a rate-limiting CPET step in all cases, the rate of which is modestly varied across the series. In particular, the o-phenylene-bridged complex has the fastest PCET rate despite the least driving force, which is attributed to a stabilizing orbital interaction between cobaltocene and the substrate.
\r\n\r\nIn Chapter 5, the synthesis of phosphonium-appended cobaltocene is disclosed as well as its PCET thermochemistry and reactivity with acetophenone. Despite substantially less driving force for PCET than its nitrogen congener, the phosphonium-cobaltocene complex is more reactive.
" }, { "name": "Altshuller, Maria", "degree": "PhD", "year": "2026", "title": "Molecular Mechanisms of DNA Interstrand Cross-Link Repair by the Fanconi Anemia Pathway", "advisor": "Semlow, Daniel R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-194656412", "creators": [ { "name": { "family": "Altshuller", "given": "Maria" }, "id": "Altshuller-Maria", "orcid": "0009-0006-8174-7713", "display_name": "Altshuller, Maria" } ], "advisors": [ { "name": { "family": "Semlow", "given": "Daniel R." }, "id": "Semlow-Daniel-R", "orcid": "0000-0001-6538-9713", "role": "advisor", "display_name": "Semlow, Daniel R." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Dunphy", "given": "William G." }, "id": "Dunphy-W-G", "orcid": "0000-0001-7598-8939", "role": "member", "display_name": "Dunphy, William G." }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Semlow", "given": "Daniel R." }, "id": "Semlow-D-R", "orcid": "0000-0001-6538-9713", "role": "member", "display_name": "Semlow, Daniel R." } ], "option_major": [ "biochem" ], "doi": "10.7907/tqmn-gv72", "abstract": "DNA interstrand cross-links (ICLs), which consist of a covalent link between complementary DNA strands, are among the most cytotoxic lesions that cells encounter, as the ICL blocks strand separation during replication and transcription. The Fanconi anemia (FA) pathway is the primary mechanism through which proliferating cells repair ICLs encountered during DNA replication, and mutations in FA pathway genes cause the inherited bone marrow failure and cancer predisposition syndrome Fanconi anemia. Despite considerable progress in elucidating the molecular mechanism of FA pathway-mediated ICL repair, fundamental questions remain about how specific ICL substrates are processed and how the replication fork dynamics that accompany repair are regulated. This thesis addresses these questions using cell-free extracts prepared from Xenopus laevis eggs, which enable biochemical characterization of ICL repair. We first investigated the repair of ICLs induced by colibactin, a gut microbiome-derived genotoxin implicated in the pathogenesis of colorectal cancer. We demonstrate that the FA pathway is responsible for replication-coupled repair of colibactin-induced ICLs and identify the translesion synthesis polymerases that bypass the unhooked ICL remnant, providing mechanistic insight into how cells process this clinically relevant lesion. We then uncovered a phosphoregulatory axis governing replication fork dynamics during ICL repair, showing that the ataxia-telangiectasia mutated (ATM) kinase promotes nucleolytic resection of reversed fork intermediates through the nucleases EXO1 and DNA2-WRN, and that this resection is constrained by opposing PP2A phosphatase activity. This regulatory mechanism ensures productive fork restoration. Finally, we present preliminary evidence that X-shaped replication intermediates are sufficient to activate FA pathway signaling and ICL unhooking in the absence of ongoing replication, suggesting that these structures may serve as the trigger for FA pathway activation independently of the replisome. Taken together, this work advances our mechanistic understanding of how cells tolerate ICL stress and illuminates regulatory mechanisms that ensure accurate and efficient ICL repair." }, { "name": "Anderson, Robert Lon", "degree": "PhD", "year": "2026", "title": "Methodological Development and Computational Investigations of Metal-Catalyzed Coupling Reactions", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11172025-045827404", "creators": [ { "name": { "family": "Anderson", "given": "Robert Lon" }, "id": "Anderson-Robert-Lon", "orcid": "0009-0000-5568-7768", "display_name": "Anderson, Robert Lon" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zr3d-vz73", "abstract": "Chapter One describes the computational study of the asymmetric arylation of propargylic electrophiles. While previous mechanistic experiments have verified the general scheme of the catalytic cycle, it was still not known what the enantiodetermining step is, or how factors of the ligand and substrate influence reactivity. To answer these questions, a computational study to emulate the entire catalytic cycle was performed. It was determined that radical addition to the nickel catalyst was likely the enantiodetermining step. While the standard substrate and ligand combinations result was well predicted, the computational method was not widely applicable to different ligands. This implies that the catalytic cycle may not go through a discrete radical capture and reductive elimination step, but instead a more concerted process may be operating.
\r\n\r\nChapter Two details the development of the asymmetric cross-coupling between tertiary nucleophiles and secondary electrophiles. Specifically, \u03b1-zincated benzylic nitriles are asymmetrically coupling with secondary alkyl iodides under the influence of a nickel catalyst and iminopyrox ligand. This study represents the first report of such a ligand being use for any asymmetric nickel-catalyzed cross-couplings.
\r\n\r\nChapter Three describes computational work on three separate projects published by coworkers in the Fu lab.
\r\n1) The first section details work on the nickel-catalyzed asymmetric coupling of enynes with secondary racemic electrophiles to accomplish for the first time the simultaneous control of axial and point chirality. The computational work probed the possible steps of rearrangement of the putative nickel-propargyl species into nickel allenyl species, as well as rationalized the different reactivity of the catalyst towards different electrophiles.
\r\n2) The second project was investigations into the photocatalytic coupling of secondary and tertiary electrophiles with secondary amines by copper and a dual-ligand system. The computations shed light on possible C\u2014N coupling mechanisms, as well as rationalized the differing photoactivity of the two CuI complexes present in the system.
\r\n3) The final work supported mechanistic studies into the photocatalytic asymmetric azidation of \u03b1-bromoamides by a copper-phosphine complex. DFT studies were performed to predict EPR spectra which were used to disambiguate the possible CuII species present in solution.
Metabolism encompasses the full network of chemical reactions sustaining life- the creation, utilization, and storage of biologically active small molecules known as metabolites. Understanding how these molecules are organized in space and real time, at the subcellular level, has long been a fundamental bottleneck in advancing our knowledge of cellular metabolism. In recent years, stimulated Raman scattering (SRS) microscopy has emerged as a powerful approach to visualize metabolism directly in living systems, offering high sensitivity, chemical selectivity, and a non-destructive imaging modality uniquely suited to longitudinal studies. Despite these attributes, metabolic imaging with SRS remains in its early stages relative to the well-established fluorescence-based and mass spectrometry imaging methods that dominate the field.
\r\n\r\nTherefore, this thesis aims to push the boundaries of SRS microscopy toward quantitative, spatially resolved metabolomics to enable direct visualization of metabolic activity in living systems. By applying emerging Raman probes across diverse biological systems, this work reveals metabolic vulnerabilities that deepen insight into disease mechanisms and can inform therapeutic development.
\r\n\r\nIn Chapter 1, we introduce metabolic imaging using SRS microscopy and underscore its unique advantages for longitudinal imaging in living biosystems. We cover both label-free (untargeted) and labeled (targeted) approaches using SRS to probe metabolism in situ. We discuss both the advantages and current limitations of SRS microscopy and propose strategies for integrating it with complementary functional \u201c-omics\u201d techniques to gain deeper insight into cellular metabolism.
\r\n\r\nIn Chapter 2, we explore the use of untargeted SRS microscopy to non-invasively characterize the chemical landscape of engineered living materials (ELMs) in real-time. By correlating spectral data with the mechanical properties of genetically modified biofilms, we find multiscale metabolic heterogeneity within these systems. This approach enables quantitative, real-time monitoring of ELMs that would enable improved design in applications spanning biomedicine, sustainability, and responsive materials.
\r\n\r\nIn Chapter 3, we utilize targeted SRS microscopy to tackle critical questions in cardiovascular health with a focus on understanding the metabolic basis of diabetes. In collaboration with the Chen Lab at City of Hope Medical Center and the TeSlaa lab at UCLA, we observe glycogen accumulation in live endothelial cells under diabetic stress. By imaging glutamine and lactate metabolism using Raman probes for the first time in this system, we reveal how intracellular glycogen pools shape early metabolic adaptations in the endothelium during glucose deprivation- providing new insight into the vascular ramifications of hyperglycemia.
\r\n\r\nIn Chapter 4, we introduce MATRIX-SRS (Metabolic Activity TRacing of the trIcarboXylic acid cycle by Stimulated Raman Scattering microscopy), a platform for spatially resolved, quantitative imaging of TCA cycle activity in live cells. By combining deuterium-labeled metabolic probes with hyperspectral stimulated Raman scattering microscopy, we directly visualize and map TCA-associated metabolism at subcellular resolution. We next integrate density functional theory (DFT) with reaction network modeling to develop a robust in situ quantification pipeline in live cells. Using this approach, we identify a global attenuation of TCA activity during epithelial-to-mesenchymal transition (EMT) and, for the first time, achieve absolute quantification of deuterium-labeled biomass in live cells under native and drug-treated conditions, establishing a general framework for live-cell spatial metabolomics.
\r\n\r\nIn Chapter 5, we present MetaboRamics, highly multiplexed metabolic imaging using stimulated Raman for spatial metabolomics in live cells. Through rational probe design, isotope editing, and robust spectral unmixing, we establish a 16-color metabolic palette spanning key pathways alongside endogenous protein, lipid, and redox signals, with organelle-targeted probes enabling spatial interactomics. We apply this high-content platform to EMT to observe a global metabolic rewiring in mesenchymal cells. We further resolve subcellular adaptations under diverse metabolic stress conditions in live epithelial cells. MetaboRamics enables 16-plex, subcellular metabolomics in living systems and opens new avenues for applications in drug discovery and clinical diagnostics.
\r\n\r\nThrough these studies, I demonstrate the power of stimulated Raman imaging for subcellular, spatiotemporal metabolomics to visualize metabolism in living systems and uncover its roles in both health and disease.
" }, { "name": "Chen, Emily Peijia", "degree": "PhD", "year": "2026", "title": "Data-Driven Strategies for the Development of Stereoconvergent Nickel-Catalyzed Cross-Couplings", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112026-182208306", "creators": [ { "name": { "family": "Chen", "given": "Emily Peijia" }, "id": "Chen-Emily-Peijia", "orcid": "0000-0002-6603-9886", "display_name": "Chen, Emily Peijia" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wj2k-d962", "abstract": "Stereoconvergent cross-coupling reactions have emerged in recent decades as powerful methods for the construction of carbon\u2013carbon bonds. Nickel catalysis in particular has been particularly enabling for the formation of C(sp\u00b2)\u2013C(sp\u00b2) bonds. Stereoconvergent reductive and redox-neutral Ni-catalyzed cross-coupling reactions have been useful for the synthesis of pharmaceutically-relevant stereodefined small molecules.
\r\n \r\nHerein we describe our recent efforts in the development of new nickel-catalyzed stereoconvergent cross-coupling reactions. First, the redox-neutral nickel/photoredox dual catalytic coupling of N-heterocyclic trifluoroborates and aryl bromides is described. In collaboration with researchers at Merck, the enantioselective synthesis of N-benzylic heterocycles provides rapid access to pharmaceutically relevant motifs. We next discuss the development of a diastereoselective reductive cross coupling of meso-1,3-cyclobutyl NHP esters with aryl iodides. When chiral bis(oxazoline) ligands are employed, this reaction biases the formation of the cis isomer, prompting the exploration of the scope of the transformation using data science tools. The desire to further increase the yield and diastereoselectivity of this transformation motivated the application of a Bayesian optimizer to efficiently explore the reaction condition space. This optimization campaign led to the identification of new reductive conditions. Finally, the asymmetric coupling of 2-piperidine NHP esters and aryl iodides is described.
" }, { "name": "Chen, Ruby Pengjui", "degree": "PhD", "year": "2026", "title": "Synthesis of Stereoenriched Polycyclic Scaffolds via Palladium Enolates and Progress toward the Total Synthesis of Hypermoin A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112026-194717664", "creators": [ { "name": { "family": "Chen", "given": "Ruby Pengjui" }, "id": "Chen-Ruby-Pengjui", "orcid": "0000-0002-3594-0081", "display_name": "Chen, Ruby Pengjui" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/war0-n433", "abstract": "Research in the Stoltz lab is focused on the synergistic development of novel methodologies for the asymmetric formation of congested stereocenters and natural product total synthesis, while employing computations to aid mechanistic understanding. This thesis describes the development and mechanistic studies of novel asymmetric reactions from Pd enolates and progress toward the total synthesis of hypermoin A.
\r\n\r\nThe first chapter details the development of an enantioselective intramolecular [4+2] cycloaddition from a chiral Pd enolate, allowing formation of highly stereoenriched polycyclic structures. Quantum mechanics calculations, Eyring analysis, and KIE studies allowed further mechanistic understanding of the reaction. The [4+2] cycloaddition was further investigated through molecular dynamics simulations, and studies of cyclohexenone-derived substrates are reported in chapter 2.
\r\n\r\nChapter 3 describes the application of a chiral Pd enolate in an asymmetric intramolecular Michael spirocyclization, forging vicinal quaternary and tertiary stereocenters in a single step. Computational investigations provide mechanistic insights to the stereoselectivity of the process. In chapter 4, a branched-selective asymmetric decarboxylative allylic alkylation reaction is reported. The hypotheses informed by quantum mechanics calculations allow rational ligand design to achieve high regio-, diastereo-, and enantioselectivity in forming vicinal quaternary and tertiary stereocenters.
\r\n\r\nChapter 5 outlines the ongoing progress toward the asymmetric total synthesis of hypermoin A. [2.2.2] bicycle formation through [4+2] cycloaddition or reductive Heck cyclization followed by ring expansion allows formation of a key [3.2.2] bicyclic core, and current efforts are focused on extending this approach to more elaborate substrates.
" }, { "name": "Colazo, Adrian", "degree": "PhD", "year": "2026", "title": "Investigating Single-Cell Metabolism with Advanced Stimulated Raman Scattering Microscopy", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-190520449", "creators": [ { "name": { "family": "Colazo", "given": "Adrian" }, "id": "Colazo-Adrian", "orcid": "0000-0002-0702-0851", "display_name": "Colazo, Adrian" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Morstein", "given": "Johannes" }, "id": "Morstein-Johannes", "orcid": "0000-0002-6940-288X", "role": "member", "display_name": "Morstein, Johannes" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/r9nr-ec20", "abstract": "Stimulated Raman scattering (SRS) microscopy has emerged as a powerful platform for chemically specific imaging in living systems, enabling minimally perturbative visualization of molecular composition and metabolic dynamics at subcellular resolution. However, its potential for metabolomic studies remains limited by intrinsic challenges in sensitivity, multiplexing applications, and quantitative interpretation of metabolized signals. This thesis addresses these limitations through advances in instrumentation, probe palette design, and computational analysis to expand the capabilities of SRS microscopy for metabolic imaging.\r\n\r\nIn Chapter 2, visible enhanced stimulated Raman scattering microscopy via frequency-doubling of picosecond pulses, we develop a new form visible-SRS microscopy (VIS-SRS) microscopy through direct frequency-doubling of narrowband picosecond laser sources for a more practical route to multiplexed VIS-SRS imaging. By shifting excitation into the visible regime with picosecond pulses, this approach enhances Raman scattering cross-sections and improves spatial resolution while simplifying instrumental implementation compared to femtosecond-based VIS-SRS modalities. VIS-SRS holistically provides a new route toward increased sensitivity for imaging low-abundance molecular species and opening new opportunities for electronic pre-resonance imaging of new target analytes.\r\n\r\nIn chapter 3, MetaboRamics: highly multiplexed metabolic imaging using stimulated Raman scattering microscopy for live-cell spatial metabolomics, we introduce a new vibrational palette for live-cell metabolic analysis. By leveraging minimally perturbative, metabolically active probes in combination with label-free contrast and advanced spectral unmixing, MetaboRamics enables super-multiplexed imaging across multiple metabolic pathways. This platform allows high-dimensional characterization of metabolic states and reveals interconnected metabolic rewiring in response to biological perturbations with single-cell and subcellular resolution.\r\n\r\nIn chapter 4, Optical Metabolic Imaging of Tricarboxylic Acid Cycle Activity, we introduce MATRIX-SRS, a framework for quantitative imaging of tricarboxylic acid (TCA) cycle metabolism in living systems. By integrating hyperspectral SRS imaging with density functional theory (DFT)-informed spectral modeling, MATRIX-SRS enables new quantitative insights into metabolized probe signals. This approach allows, for the first time, spatially resolved and absolute quantification of metabolically incorporated species using optical imaging.\r\n\r\n\tTogether, these advances position SRS microscopy as an increasingly powerful platform for metabolic investigations. By improving sensitivity, enabling super-multiplexed spatial metabolomics, and enhancing chemical insight into metabolic activity, this work opens new opportunities to study cellular heterogeneity, metabolic dynamics, and disease-associated metabolic rewiring." }, { "name": "Friesenhahn, Nicholas James", "degree": "PhD", "year": "2026", "title": "Computational Design of Protein-Based Biosensors for Nicotine", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-230448477", "creators": [ { "name": { "family": "Friesenhahn", "given": "Nicholas James" }, "id": "Friesenhahn-Nicholas-James", "orcid": "0000-0002-8129-0171", "display_name": "Friesenhahn, Nicholas James" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "member", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/mw91-pe18", "abstract": "It has been observed that among individual users of nicotine-containing products and between nicotine delivery systems (smoking, vaping, patches, etc.), there is a large degree of variability in the pharmacokinetic profile of nicotine. The time course of [nicotine], [nicotine]t, is crucial to understanding why some nicotine-containing products are addictive, while others aid in smoking cessation via nicotine-replacement therapy. The current methods for measuring [nicotine]t via blood draws and LC-MS analysis are cost-prohibitive for the number of nicotine users, estimated at 1.2 billion globally. To enable [nicotine]t measurements at the necessary scale, we have developed a series of protein-based intensity-based nicotine sensing fluorescent reporters (iNicSnFRs). These sensors are comprised of a nicotine-binding moiety engineered from the OpuBC periplasmic binding protein of Thermoanaerobacter sp. X513 and circularly permuted superfolderGFP. Through a variety of computational protein design and experimental techniques, we discovered mutations that improved the biosensor\u2019s sensitivity, as measured by EC50, 61-fold, from iNicSnFR3a with a 27 \u03bcM EC50 to iNicSnFR12-D72A with a 440 nM EC50. Notably, iNicSnFR12-D72A, with its series-best 11.6 \u03bcM-1 fluorescence response in the linear regime of the dose-response relation, is able to resolve 10 nM nicotine, the lowest [nicotine] measured between smoking and vaping sessions in plasma via the blood draw method. With unparalleled sensitivity and robust thermostability profile, iNicSnFR12-D72A meets many requirements for a sensor to be used in biofluids as a continuous nicotine monitor, an important tool in reducing nicotine addiction and associated morbidity and mortality from tobacco-related diseases." }, { "name": "Gonzalez, Kevin Jaime", "degree": "PhD", "year": "2026", "title": "Strategies and Tactics in Alkaloid Synthesis: Total Synthesis of Strempeliopidine via a Non-Directed Petasis Reaction and Progress Toward the Synthesis of Mitomycin B", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112025-115800167", "creators": [ { "name": { "family": "Gonzalez", "given": "Kevin Jaime" }, "id": "Gonzalez-Kevin-Jaime", "orcid": "0000-0002-4904-590X", "display_name": "Gonzalez, Kevin Jaime" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hakn-7h25", "abstract": "This thesis describes research toward total synthesis of bioactive alkaloids with complex architectures that have demanded for the invention of methodology. Chapter 1 comprehensively reviews the semi-, partial, and total synthesis of heterodimeric monoterpenoid bisindole alkaloid natural products. Chapter 2 describes the enantioselective total synthesis of the bisindole alkaloid strempeliopidine. A convergent strategy featuring a diastereoselective Petasis reaction enabled the synthesis of the natural product and several stereoisomeric analogs. Chapter 3 details the development of a non-directed Petasis reaction inspired by the key step in the synthesis of strempeliopidine. This methodology couples hydroxyindoles with trifluoroborate salts under mild conditions, thereby enabling the synthesis of non-natural heterodimeric bisindole alkaloids. Chapter 4 explores ongoing efforts toward the asymmetric total synthesis of mitomycin B. Chapter 5 covers the development of an enantioselective 1,3-dipolar cycloaddition for the construction of nitrogen-rich spirocycles. A chiral magnesium Lewis acid catalyst facilitated the asymmetric [3+2] cycloaddition between alpha-methylene lactams and diazoacetates or nitrile oxides." }, { "name": "Gross, Benjamin Martin", "degree": "PhD", "year": "2026", "title": "The Total Synthesis of (+)-Ineleganolide, the Lycojapomine Alkaloids, and a New Strategy for Radical Deoxygenation", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112026-184323225", "creators": [ { "name": { "family": "Gross", "given": "Benjamin Martin" }, "id": "Gross-Benjamin-Martin", "orcid": "0000-0002-9124-2317", "display_name": "Gross, Benjamin Martin" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Semlow", "given": "Daniel R." }, "id": "Semlow-D-R", "orcid": "0000-0001-6538-9713", "role": "member", "display_name": "Semlow, Daniel R." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4sc5-0e50", "abstract": "Organic chemistry is an enabling science, that has given scientist the ability to construct and manipulate small molecules. The relationship that bridges the classic study of chemical reactivity and synthesis at the molecular level with the broader field of the life sciences continues to flourish and has expanded its impact tremendously. The study of complex, bioactive small molecules, their synthesis, and the development of new reactions has laid the foundation for many of these advancements to build upon. The contents of this thesis contribute to this goal and hope to be of use for future generations and the development of the field.
\r\n\r\nThe first chapter describes the total synthesis of the furanobutenolide-derived norcembranoid diterpenoid ineleganolide, a secondary metabolite produced by sinularia soft corals. Displaying cytotoxic bioactivity, the chemical structure has intrigued chemists for several decades. We describe a successful synthesis of the natural product in 14 steps, enabled by several unique cascade reactions.
\r\n\r\nThe second chapter details the total synthesis of Lycojapomine A and B, two members of the lycopodium alkaloids. To achieve a practical and concise synthetic route, we developed a photoreaction for the stepwise dearomatization of a pyrrole heterocycle. Building off the simple and easily accessible starting material, we can synthesize each of the complex target molecule in 13 steps.
\r\n\r\nInspired by the previously utilized photochemistry, the third chapter details a new catalytic method for the generation of alkyl radicals directly from alcohols. We achieved this transformation by photo irradiation of a titanium porphyrin catalyst and showcase its ability to deoxygenate several different alcohols, by generation of the carbon-centered radical.
" }, { "name": "Harper, Nathan Andrew", "degree": "PhD", "year": "2026", "title": "Developing New Methods of Quantum Spectroscopy with Nonlinear Integrated Photonics", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09052025-191750417", "creators": [ { "name": { "family": "Harper", "given": "Nathan Andrew" }, "id": "Harper-Nathan-Andrew", "orcid": "0000-0001-8727-0932", "display_name": "Harper, Nathan Andrew" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Marandi", "given": "Alireza" }, "id": "Marandi-A", "orcid": "0000-0002-0470-0050", "role": "member", "display_name": "Marandi, Alireza" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j0x1-5742", "abstract": "Photon pairs produced through spontaneous parametric down-conversion exhibit entanglement in their time-energy degrees of freedom, offering sub-100 fs entanglement times while simultaneously exhibiting a joint energy resolution dictated by that of the continuous-wave pump laser. While entangled photon pairs have found many applications in sensing and imaging, taking advantage of their ultrafast correlations has proven to be more difficult.
\r\n\r\nIn this dissertation, we advance a number of practical aspects of spectroscopy with entangled pairs of photons. First, we show that the ultrafast correlations in photon pairs are useful for fluorescence lifetime measurements, enabling a CW laser to perform time-resolved measurements through a simple heralding scheme. Next, we develop bright, efficient, and single spatial mode sources of entangled photons using thin-film lithium niobate nanophotonics, bringing these devices to the visible and near-IR for the first time. In the process, we develop a source of UV light and investigate the performance of thin-film lithium niobate for evanescent sensing. Finally, we show promising results that two down-conversion processes in the same waveguide can be cascaded to generate entangled photon triplets with high efficiency, enabling pairs of photons to be heralded.
" }, { "name": "Hern\u00e1ndez-Mej\u00edas, \u00c1ngel D.", "degree": "PhD", "year": "2026", "title": "Development of Strategies for Nickel-Catalyzed Asymmetric Reductive Cross-Couplings", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022026-174602521", "creators": [ { "name": { "family": "Hern\u00e1ndez-Mej\u00edas", "given": "\u00c1ngel D." }, "id": "Hern\u00e1ndez-Mej\u00edas-\u00c1ngel-D", "orcid": "0000-0002-1039-4790", "display_name": "Hern\u00e1ndez-Mej\u00edas, \u00c1ngel D." } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6a4p-kp51", "abstract": "Ni-catalyzed asymmetric reductive cross-coupling reactions provide rapid and modular access to enantioenriched building blocks from simple electrophile precursors. Reductive coupling reactions that can diverge via a common organometallic intermediate into two distinct families of enantioenriched products are particularly versatile yet underdeveloped. Here, we describe the development of a bis(oxazoline) ligand that enables the desymmetrization of\u00a0meso-anhydrides. When secondary benzylic electrophiles are employed, doubly stereoselective acyl cross-coupling proceeds to give ketone products with catalyst control over three newly formed stereogenic centers. Alternatively, the use of primary alkyl halides in the presence of an additional halogen atom transfer catalyst results in decarbonylative alkylation to give enantioenriched \u03b2-alkyl acids. Analysis of reaction rates for a range of both catalysts and substrates supports the notion that tuning the different electrophile activation steps with the two catalysts is required for enhanced reaction performance. These studies illustrate how reaction design can diverge a common Ni-acyl intermediate to either acyl or decarbonylative coupling products and highlight how dual ligand systems can be used to engage unactivated alkyl halides in Ni-catalyzed asymmetric reductive coupling." }, { "name": "Hicks, Madeline H.", "degree": "PhD", "year": "2026", "title": "In Situ Spectroscopic Studies of Electrolyte and Organic Films Effects on Electrochemical CO\u2082 Reduction", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272026-160048701", "creators": [ { "name": { "family": "Hicks", "given": "Madeline H." }, "id": "Hicks-Madeline-H", "orcid": "0000-0002-5476-1871", "display_name": "Hicks, Madeline H." } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6rjw-eh78", "abstract": "This thesis employs in-situ spectroscopy and electrochemical techniques to elucidate how electrolyte composition and organic film modification control selectivity in electrochemical CO\u2082 reduction on copper electrodes. The central objective is to establish molecular-level understanding of interfacial phenomena that govern product distributions, with particular focus on disentangling electric field effects from non-electric field contributions of electrolyte cations and on clarifying the role(s) of organic surface coatings. The first chapter motivates the development of selective CO\u2082 reduction technologies and introduces the unique challenges of controlling reaction pathways at copper electrochemical interfaces. Theoretical foundations used in this dissertation are established in the second chapter. The third chapter demonstrates that a local alkaline pH, instead of the presence of cations, is required for CO\u2082 reduction to occur in acidic media. Spectroscopic measurements reveal that enhanced CO\u2082 reduction performance with the addition of cations arises from suppressed H\u207a transport and modified interfacial solvation, motivating the use of transport-modulating organic films. Using organic film-modified copper then yields selective CO\u2082 reduction over hydrogen evolution with low cation concentrations even in strongly acidic (pH 1) electrolyte. The fourth chapter investigates the interplay between electrolyte cations and organic coatings to show that organic films modify transport of reactants and intermediates, amplifying cation effects. Mixed lithium-cesium electrolytes are used, which reveal that organic films reduce the cesium concentration required for selective catalysis not by altering cation accumulation, but by modifying how accumulated cations influence reaction chemistry through changes in water structure and interfacial CO\u2082 and CO populations. The final chapter introduces composite film design to show that film functionality can be tuned via doping provided there is structural control. Amine functionalization is used, which concentrates CO\u2082 at the interface through hydrogen bonding interactions. Composite films with small amine concentrations achieve the highest ethylene selectivity across acidic, neutral, and alkaline electrolytes, demonstrating how tuning of organic coatings via precursor mixing can optimize interfacial properties.
" }, { "name": "Higdon, Nicole Juliet", "degree": "PhD", "year": "2026", "title": "Development of Ion Conducting Polymer Temperature Sensors", "advisor": "Daraio, Chiara", "url": "https://resolver.caltech.edu/CaltechTHESIS:06132025-183938139", "creators": [ { "name": { "family": "Higdon", "given": "Nicole Juliet" }, "id": "Higdon-Nicole-Juliet", "orcid": "0000-0002-5806-1151", "display_name": "Higdon, Nicole Juliet" } ], "advisors": [ { "name": { "family": "Daraio", "given": "Chiara" }, "id": "Daraio-C", "orcid": "0000-0001-5296-4440", "role": "advisor", "display_name": "Daraio, Chiara" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Daraio", "given": "Chiara" }, "id": "Daraio-C", "orcid": "0000-0001-5296-4440", "role": "member", "display_name": "Daraio, Chiara" } ], "option_major": [ "chemistry" ], "doi": "10.7907/avyc-pq77", "abstract": "Improvements to flexible polymer temperature sensors have the potential to substantially improve human health through a variety of devices such as core body temperature sensors, temperature mapping, and IR imaging. In this thesis we examine a novel resistive ion conducting polymer-based temperature sensitive material. This material outperforms vanadium oxide and other leading temperature sensing materials for the temperature range 15-65 \u00b0C allowing for high performance use in medical devices. Unlike conventional materials, this polymer can be readily integrated into flexible devices.
\r\n\r\nIn this thesis we explore both the fundamental science and applications of this material. In Chapter 2 of this thesis, we explore the electrical and chemical properties of this polymer through impedance spectroscopy, Fourier transform infrared spectroscopy, and thermogravimetric analysis. We explore the formation of interpolymer complexes exhibited by this copolymer. We demonstrate its application to temperature mapping and infrared light detection. Chapter 3 explores the effects of water on ion transport within the polymer. Demonstrating that the metal cation is the charge carrier, and that water uptakes primary effect is the lowering of the polymers\u2019 glass transition temperature. Through visible spectroscopy we additionally demonstrate tetrahalocobaltate formation in this and a related polymer. In Chapter 4, we demonstrate an ultra-thin dual heat flux core body temperature sensor leveraging this polymer. We evaluate its response time then verify its functionality by leveraging an agar tissue phantom. We explore the formation of thin film sensors in Chapter 5. We demonstrate a simple sensor with a thin film architecture and discuss in depth the engineering challenges presented by commercialization of this architecture in the context of roll-to-roll fabrication. We demonstrate the sensor is strongly affected by external humidity and develop and demonstrate humidity buffer materials inspired by humidity fixed point salt solutions to address this problem.
\r\n\r\nIn conclusion this thesis provides a window into the mechanism of a novel temperature sensing polymer and explores its commercialization and future applications.
" }, { "name": "Jiang, Chenyu", "degree": "PhD", "year": "2026", "title": "Tug of War between Epoxidation and Ketonization in Electrochemical Alkene Oxidation: Pulling the Rope for Ketonization", "advisor": "Manthiram, Karthish", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282026-051717699", "creators": [ { "name": { "family": "Jiang", "given": "Chenyu" }, "id": "Jiang-Chenyu", "orcid": "0000-0002-3434-3138", "display_name": "Jiang, Chenyu" } ], "advisors": [ { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "advisor", "display_name": "Manthiram, Karthish" } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0fz2-1403", "abstract": "The electrochemical oxidation of organic molecules utilizing renewable electricity has emerged as a sustainable alternative to energy-intensive thermal processes in the chemical industry. This thesis investigates electrochemical oxygen-atom transfer reactions to transform alkenes into value-added products using water as the oxygen source under ambient conditions, with a focus on understanding and controlling the competing pathways between epoxidation and ketonization. Using MnOx as a model electrocatalyst in acetonitrile/water blended electrolytes, a substrate-scope study and complementary kinetic and operando spectroscopic investigations revealed that ketone/epoxide selectivity is influenced by an interplay of alkene electronics, catalyst oxidation states, and the reaction conditions. In particular, ketonization was demonstrated to be selective at lower water content, coinciding with a less oxidized catalyst. Such insights were employed in screening and optimization of Pd-based bimetallic electrocatalysts for the selective ketonization of 1-butene to 2-butanone in aqueous electrolytes, a transformation with industrial relevance that remains underexplored electrochemically. Among the compositions evaluated, bimetallic Pd\u2013Cu catalysts were found to be active for this transformation. Structural and spectroscopic characterization demonstrated that alloying Pd with Cu generates a metallic alloy phase that is preserved under oxidative electrochemical conditions, which is proposed to be responsible for the superior ketonization activity and selectivity. This work establishes key factors governing ketone/epoxide selectivity in alkene electro-oxidation and illustrates the significance of metallic catalyst character in achieving selective ketonization, expanding the product scope and providing a foundation for the rational catalyst design for alkene electro-oxidation." }, { "name": "Klein, Channing K.", "degree": "PhD", "year": "2026", "title": "Development and Exploration of Electrochemical Cascades for Titanium-Mediated Nitrogen Reduction to Ammonia", "advisor": "Manthiram, Karthish", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202026-000057271", "creators": [ { "name": { "family": "Klein", "given": "Channing K." }, "id": "Klein-Channing-K", "orcid": "0000-0002-1593-3896", "display_name": "Klein, Channing K." } ], "advisors": [ { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "advisor", "display_name": "Manthiram, Karthish" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "member", "display_name": "Greer, Julia R." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vs6d-n280", "abstract": "The Haber-Bosch process, invented at the turn of the 19th century, revolutionized agriculture by providing a way to make ammonia\u2014an important component of fertilizer\u2014from nitrogen and hydrogen. It's been estimated that without artificial ammonia synthesis, up to half the population would starve. However, this miracle chemistry comes with costly downsides, responsible for the consumption of an estimated 2% of global energy and for up to 1.6% of global carbon dioxide emissions. Therefore, the development of new methods of ammonia synthesis that are compatible with a greener society is a task of paramount importance. In this thesis, one such method for doing so\u2014an electrochemical cascade reaction involving a plated alkali metal and a homogeneous titanium compound\u2014is developed and explored. Electrochemically-generated sodium naphthalenide in conjunction with titanium isopropoxide is shown to enable a high rate of ammonia synthesis, but low selectivity. By contrast, potassium metal with titanium isopropoxide allows for much higher selectivity at the cost of rate. It is found that the rate-determining step of these reactions is usually electrochemical reductant generation, a powerful discovery that allows for precise tuning of rate via changing applied current density. This spatially-decoupled reaction paradigm is also applied to other alkali metal and transition metal compounds in order to open up a wider chemical space. While much remains unknown about the mechanism of this system, the novel reactivity demonstrated in this work will have immense impacts on the field of sustainable ammonia synthesis." }, { "name": "Lal, Ravi Goel", "degree": "PhD", "year": "2026", "title": "Expanding Enzyme Function Through Data-Guided Evolution", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122026-031420036", "creators": [ { "name": { "family": "Lal", "given": "Ravi Goel" }, "id": "Lal-Ravi-Goel", "orcid": "0000-0001-6943-4147", "display_name": "Lal, Ravi Goel" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Parker", "given": "Joseph" }, "id": "Parker-J", "orcid": "0000-0001-9598-2454", "role": "member", "display_name": "Parker, Joseph" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5zaf-8w29", "abstract": "Through the process of evolution, Nature has optimized enzymes for the chemical transformations which drive biology. The use of enzymes for chemical synthesis is enticing as these privileged catalysts can facilitate reactions in a highly sustainable and selective manner. Directed evolution (DE) is a strategy for engineering proteins to improve a desired function. This approach has been demonstrated to be of great effect for the development of enzymatic activities which have never been naturally observed. These \u2018new-to-nature\u2019 chemistries not only showcase the power of DE to unlock novel functions, but also the potential of biocatalysis to deliver high-value chemical compounds. This thesis details the exploration of new-to-nature biocatalytic reactions of hemoproteins using traditional DE and novel machine learning-assisted directed evolution (MLDE) methods. Chapter I provides an overview of how DE has enabled new-to-nature-biocatalysis, and the challenges associated with developing this novel biocatalytic reactions. In Chapter II, a cytochrome P411 is found to catalyze a carbene-mediated [1,2]-Stevens rearrangement to furnish azetidines via ring expansion, and is engineered to deliver these products with high yield and enantioselectivity. The evolution of this activity is a demonstration of how established DE techniques can be utilized to arrive at enzymes capable of unprecedented chemistry. Chapter III describes efforts towards advancing this ring-expansion chemistry for the synthesis of proline analogs. Though this activity could not be found with existing sequence diversity, several engineering insights were made about protoglobins (small, thermostable hemoproteins). Chapters II and III both highlight challenges associated with DE. In Chapter IV, active-learning assisted directed evolution (ALDE) is introduced as a workflow which leverages MLDE in an iterative fashion to greatly accelerate DE efforts. Alongside simulations on combinatorially complete datasets, ALDE was validated in the wet lab by simultaneously evolving a protoglobin-based cyclopropanation for improved yield and stereoselectivity. Finally, Chapter V describes the use of ALDE to engineer protoglobins with active sites which have been optimized to catalyze a broad scope of nitrene and carbene transfer reactions. This demonstration of enzyme ensemble engineering displays the power of diversity-oriented evolution to provide broad solutions in biocatalysis." }, { "name": "Lee, Wonseok", "degree": "PhD", "year": "2026", "title": "Unraveling Material Behavior with Electron and X-Ray Spectroscopies: From Transient Electronic Responses to Electronic Topological Transitions", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-013727799", "creators": [ { "name": { "family": "Lee", "given": "Wonseok" }, "id": "Lee-Wonseok", "orcid": "0000-0003-1077-0511", "display_name": "Lee, Wonseok" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/q8yy-xb49", "abstract": "Understanding how materials respond to external stimuli requires probes that can resolve coupled electronic, structural, and chemical changes across relevant length, time, and energy scales. This thesis investigates material dynamics and electronic structure using electron and X-ray spectroscopies, with a focus on how photoexcitation and high pressure modify the spectroscopic responses of solids.
\r\n\r\nThe first part of this thesis focuses on ultrafast electron energy-loss spectroscopy as a probe of carrier, thermal, and structural dynamics. This approach is applied to crystalline silicon, where dense photoexcitation produces a transient reshaping of the bulk plasmon. The plasmon redshifts, broadens beyond the zero-loss peak response, and redistributes spectral weight, indicating that dense photoexcitation modifies the full dielectric response rather than simply introducing free carriers. These results show that the transient plasmon response arises from coupled changes in screening, electronic structure, and damping.
\r\n\r\nThe second part investigates pressure-induced electronic topological transitions in cadmium using experimental and theoretical X-ray absorption spectroscopy. First-principles calculations reveal pressure-driven changes in the Fermi surface topology, while core\u2013valence exciton projections connect these transitions to spectral changes at the Cd K edge. These results demonstrate that X-ray absorption spectroscopy can serve as a sensitive probe of electronic topological transitions.
\r\nThe final part investigates resonant self-diffraction of femtosecond extreme ultraviolet pulses in cobalt near the Co M2,3 edge. The observed self-diffraction signal is attributed to resonant changes in the complex refractive index, highlighting the potential of nonlinear extreme ultraviolet spectroscopy for probing ultrafast electronic dynamics at core-level resonances.
\r\n \r\nTogether, these studies demonstrate that electron and X-ray spectroscopies provide powerful and complementary approaches for uncovering material behavior across multiple regimes, from nonequilibrium electronic dynamics to pressure-driven electronic topological transitions and nonlinear light\u2013matter interactions.
" }, { "name": "Li, Rui", "degree": "PhD", "year": "2026", "title": "Efficient Evaluation of Coulomb Interactions for Large-Scale Quantum Chemistry", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-234054998", "creators": [ { "name": { "family": "Li", "given": "Rui" }, "id": "Li-Rui", "orcid": "0009-0002-9029-6847", "display_name": "Li, Rui" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." }, { "name": { "family": "Sharma", "given": "Sandeep" }, "id": "Sharma-Sandeep", "orcid": "0000-0002-6598-8887", "role": "member", "display_name": "Sharma, Sandeep" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vj28-vh82", "abstract": "Evaluating the Coulomb interaction remains a fundamental computational bottleneck in electronic structure theory, dictating the scaling and efficiency of quantum chemical simulations. While recent advancements in graphics processing units (GPUs) offer immense theoretical peak performance, translating traditional, memory-intensive CPU algorithms for evaluating electron repulsion integrals to GPU architectures presents significant challenges due to memory bandwidth limitations and warp divergence.
\r\n\r\nThis thesis presents the development of algorithms to efficiently evaluate Coulomb interactions across diverse chemical systems. Chapter 2 describes the GPU implementation of Coulomb interaction for molecular systems at Hartree-Fock level of theory. Chapter 3 shows how multigrid Gaussian-Plane-Wave algorithm can better utilize GPU compute performance by a two-level parallelization scheme and grid-based screening of orbital pairs in the real space. Chapter 4 illustrates the issues of the original modified Coulomb potential from GFN-xTB in periodic systems, and the effectiveness of a new generalized Ewald summation scheme for the potential in X23 molecular crystal dataset and a range of prototypical bulk semiconductors.
" }, { "name": "Li, Yancheng", "degree": "PhD", "year": "2026", "title": "Characterizing the Lipid II Flippase MurJ as an Antibiotic Target", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-215117772", "creators": [ { "name": { "family": "Li", "given": "Yancheng" }, "id": "Li-Yancheng", "orcid": "0000-0002-7110-2448", "display_name": "Li, Yancheng" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "chair", "display_name": "Newman, Dianne K." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/bqpa-4195", "abstract": "The rapid emergence of antibiotic resistance, coupled with a decline in antibiotic discovery, poses a major threat to global public health and underscores the urgent need for the identification and characterization of new antibiotic targets and mechanisms. The lipid II flippase MurJ, an essential membrane transporter that flips the peptidoglycan precursor lipid II across the cytoplasmic membrane, represents a validated yet unexploited antibiotic target. MurJ has been repeatedly targeted by both bacteriophage-encoded lysis proteins and by small-molecule screening efforts. Distinct single gene lysis protein (Sgls) from small lytic phages have evolved independently to inhibit MurJ, suggesting that MurJ represents a key step for killing bacteria and an evolutionarily validated target. Structural and mechanistic understanding of MurJ has largely been derived from diderm bacteria. However, small molecule compounds that target MurJ have been identified specifically in monoderm pathogens, and the corresponding monoderm MurJ homologs remain uncharacterized. Despite strong validation of MurJ as a potential antibiotic target, the inhibition mechanisms are unknown, limiting efforts to translate this key step into effective therapeutic strategies. In this thesis, we define the inhibition mechanisms of MurJ by Sgls using structural approaches. We show that distinct Sgls converge on a common interface on MurJ and trap MurJ in a periplasm-open conformation. We further identified and structurally characterized a novel MurJ-targeting Sgl from the predicted phage Changjiang3, supporting convergent evolution toward a shared inhibition mechanism. In addition, we determined structures of monoderm MurJ in multiple conformational states, revealing both conserved and divergent features for the transport mechanism across monoderms and diderms. Together, these findings highlight new opportunities for targeting MurJ for the development of novel antimicrobials" }, { "name": "Long, Yueming", "degree": "PhD", "year": "2026", "title": "Data Foundations for Functional Prediction in Enzyme Engineering", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202026-153923569", "creators": [ { "name": { "family": "Long", "given": "Yueming" }, "id": "Long-Yueming", "orcid": "0009-0006-5112-7791", "display_name": "Long, Yueming" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Wittmann", "given": "Bruce J." }, "id": "Wittmann-Bruce-James", "orcid": "0000-0001-8144-9157", "role": "member", "display_name": "Wittmann, Bruce J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rqgx-xv16", "abstract": "Despite transformative progress in protein structure prediction and de novo design, accurate prediction of enzyme function remains elusive. The central barrier is not a lack of sequences or structures, but a lack of learnable, experimentally grounded labels: in enzyme engineering, function is defined by assay context and deployment constraints, yet most available sequence\u2013function datasets are sparse, biased toward successes, incompletely genotyped, and inconsistently annotated. As a result, models that appear strong on curated benchmarks often fail to guide real engineering decisions, especially for new-to-nature transformations and out-of-distribution substrates. This thesis advances a data-centered strategy for functional prediction by building a practical pipeline that turns routine protein engineering experiments into prediction-ready sequence\u2013function records. Chapter 2 establishes the importance of assay-defined, application-relevant labels through a stereodivergent biocatalytic platform for azaspirocycle synthesis, where directed evolution of carbene transferases enables access to azaspiro[2.y]alkane scaffolds with tunable stereochemical outcomes, quantified by deployment-aligned measurements including turnover and enantio- and diastereoselectivity. Chapter 3 develops LevSeq, a high-throughput and cost-effective genotyping and analysis workflow that assigns full-length variant identities at screening scale using dual barcoding and nanopore long reads and reports practical quality-control metrics to prevent silent failure modes and preserve reliable sequence assignment across both hits and non-hits. Chapter 4 introduces EnzEngDB, a curated database and data model that standardizes sequences, reaction context, assay conditions, units, quality metrics, and provenance so datasets can be queried, filtered, and aggregated across campaigns, while retaining negative and neutral outcomes as informative constraints. Chapter 5 closes the loop by using the resulting data substrate to support decision-making in de novo enzyme validation, emphasizing that predictive ranking is currently most reliable within reactions with dense standardized coverage and hypothesize that generalization to unseen reactions will require systematic expansion of assay-defined labels across diverse transformations. Together, these chapters provide the tooling and framework needed to make sequence\u2013function data compounding rather than ephemeral, enabling reliable functional prediction and iterative, model-guided enzyme design." }, { "name": "Luo, Meng (Stella)", "degree": "PhD", "year": "2026", "title": "Polymer Mechanochemistry Using Ultrasound: From Fundamental Reactivity to Controlled Drug Delivery", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212026-163903186", "creators": [ { "name": { "family": "Luo", "given": "Meng (Stella)" }, "id": "Luo-Meng-Stella", "orcid": "0000-0003-4003-7468", "display_name": "Luo, Meng (Stella)" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mnbj-xq97", "abstract": "Polymer mechanochemistry harnesses mechanical force to drive specific chemical transformations in stress-sensitive molecules known as mechanophores. Through judicious chemical design, these force-driven reactions have enabled functional polymeric materials capable of sensing, self-healing, and catalysis. Research in this field encompasses expanding the mechanophore repertoire, elucidating the fundamental principles governing mechanically induced reactivity, and translating force-responsive systems into practical applications.
\r\n \r\nThis thesis advances the field by contributing both fundamental insight and applied functionality in mechanophore activation under ultrasonication, with a particular focus on controlled drug release in biological environments. First, we develop an improved methodology for characterizing mechanophore reactivity, addressing sensitivity limitations in sonication experiments and, combined with computational modeling, revealing underlying principles that govern force-induced bond activation. Separately, we establish a synergistic platform that couples cargo-releasing mechanophores with biocompatible focused ultrasound, enabling controlled release of a fluorophore and a chemotherapeutic agent under physiological conditions. Finally, we demonstrate mechanochemically triggered drug delivery in vivo and validate this process using an inducible protein-expression system as a biological readout, achieving the first constructive modulation of cellular function enabled by covalent polymer mechanochemistry. Together, these studies deepen the fundamental understanding of mechanophore reactivity and illustrate the substantial biomedical potential of mechanochemical approaches using ultrasound activation.
" }, { "name": "Mahajan, Shivansh", "degree": "PhD", "year": "2026", "title": "Mechanistic Studies of ArsA ATPase and ArsB Transporter of the Bacterial Arsenite Efflux System", "advisor": "Clemons, William M.; Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302025-130729385", "creators": [ { "name": { "family": "Mahajan", "given": "Shivansh" }, "id": "Mahajan-Shivansh", "orcid": "0000-0002-3041-7988", "display_name": "Mahajan, Shivansh" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "bioch" ], "doi": "10.7907/xksn-7t38", "abstract": "Arsenic is a notorious metalloid that contaminates the groundwater in several regions worldwide. The trivalent state of arsenic \u2013 arsenite (AsIII) \u2013 is the abundant species of arsenic under reducing conditions of subsurface waters, and is readily mobilized in aqueous environments. This exposes organisms to toxic concentrations of the metalloid. AsIII is particularly toxic to living systems due to its ability to form stable polar covalent bonds with exposed thiol groups, thus disrupting protein structure and function. Arsenic detoxification systems such as efflux pumps, exist in most organisms that confer tolerance to toxic concentrations of arsenicals found in their environment. The ars operon in many bacteria and some archaea confers resistance to AsIII via ArsB, an integral membrane transporter and ArsA, a cytoplasmic P-loop ATPase. These proteins, collectively referred to as the 'ArsAB efflux pump', facilitate toxic AsIII export in an ATP-dependent manner. In addition, ArsB can operate by itself as a proton-coupled secondary transport and confer intermediate levels of AsIII resistance. The mechanisms of this dual mode of AsIII efflux are poorly understood, particularly the molecular events associated with the capture of AsIII from the cytoplasm by ArsA, its transfer to ArsB and subsequent vectorial transport across the membrane. Apart from understanding fundamental mechanisms of toxic metalloid detoxification in living systems, molecular-level investigations of AsIII efflux systems are of broad biotechnological interest for their potential to inform robust and sustainable bioremediation strategies. In this thesis, we elucidate the mechanism of ArsA ATPase and ArsB transporter using structural approaches. We characterized the nucleotide hydrolysis mechanism of ArsA by single particle cryogenic electron microscopy (cryo-EM), outlining various conformational states of the ATPase that modulate the nucleotide-dependent capture and delivery of AsIII for efflux. We show that this mechanism is consistent with the general mechanistic framework of the Intradimeric Walker A (IWA) family of ATPases. Furthermore, overexpression and purification of the membrane transporter ArsB enabled characterization of the first structure of ArsB by cryo-EM, in both apo and AsIII-bound states. Lastly, we show that ArsB enhances steady-state ATPase activity of ArsA, indicating a direct interaction between the two components of the efflux pump. Computational modeling gives some insights into a putative ArsAB interaction interface. While several mechanistic questions remain, the findings reported in this thesis together constitute a foundation for future mechanistic elucidation of the ArsAB efflux system." }, { "name": "Mendes, Jocelyn L.", "degree": "PhD", "year": "2026", "title": "Probing Polaron Design Principles in Iron Oxides with Transient Extreme Ultraviolet Spectroscopy", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292026-142127352", "creators": [ { "name": { "family": "Mendes", "given": "Jocelyn L." }, "id": "Mendes-Jocelyn-L", "orcid": "0000-0003-3850-0724", "display_name": "Mendes, Jocelyn L." } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Falson", "given": "Joseph" }, "id": "Falson-Joseph", "orcid": "0000-0003-3183-9864", "role": "member", "display_name": "Falson, Joseph" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/d8ee-yg54", "abstract": "Long timescale charge separation and high carrier mobilities are necessary for efficient devices. In highly polar transition metal oxide materials, photoexcited polarons remain a bottleneck to realizing highly mobile carriers, while also offering an exciting route for long timescale charge separation. Controlling photoexcited polaron formation in transition metal oxides is therefore necessary. This thesis uses transient extreme ultraviolet (XUV) reflection-absorption spectroscopy and ab initio density functional theory (DFT) and the Bethe\u2013Salpeter equation (BSE) to elucidate photoexcited polaronic dynamics in a series of iron oxide photocatalysts. By systematically varying structure, on-site repulsions, electron\u2013phonon coupling, and exchange interactions, this work identifies the fundamental materials parameters that govern ultrafast polaron formation. The results demonstrate that photoexcited polaron formation can be tuned and, in some cases, suppressed. In CuFeO2, small polarons form on ~100 fs timescales, followed by dynamic delocalization mediated by coherent lattice expansion and charge sharing with surrounding Fe sites. In ErFeO3, frustrated iron-centered octahedra enable favorable exchange pathways, where exchange-mediated charge hopping thermalizes carriers prior to localization as polarons. In GdFeO3, excitation-wavelength-dependent XUV spectroscopy reveals that ligand-to-metal and metal-to-metal charge transfer pathways modulate polaron formation, demonstrating that strong electronic and spin correlations can either suppress or enable polaron formation. In Fe2SiO4 polaron formation is present following metal-to-metal charge transfer. These experimental observables are then mapped onto the Holstein, Hubbard\u2013Holstein, and t-J\u2013Holstein models to define a parameter space for polaron control. These ground-state Hamiltonians act as a ground-state calculable roadmap for materials design parameters based upon measured excited state polaronic dynamics. Together, these studies provide design principles for controlling polaronic behavior in transition metal oxides for photocatalytic, electronic, and quantum materials applications." }, { "name": "Moghadam, Farbod Arya", "degree": "PhD", "year": "2026", "title": "Transition Metal Catalyzed Approaches to the Asymmetric Construction of All-Carbon Quaternary Centers", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06252025-233846076", "creators": [ { "name": { "family": "Moghadam", "given": "Farbod Arya" }, "id": "Moghadam-Farbod-Arya", "orcid": "0009-0005-4442-2349", "display_name": "Moghadam, Farbod Arya" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Demirer", "given": "Gozde S." }, "id": "Demirer-G\u00f6zde-S", "orcid": "0000-0002-3007-1489", "role": "member", "display_name": "Demirer, Gozde S." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/11d1-9b20", "abstract": "In the Stoltz group, chemical research leverages the interplay between methods development and total synthesis, wherein new synthetic technologies enable the pursuit of novel target compounds and challenges encountered during synthetic campaigns inspire the invention of methodologies. Given the stereochemical complexity of natural products and emerging pharmaceuticals, methods development in our group has focused in particular on the asymmetric construction of all-carbon quaternary centers. Herein is described the development of transition metal catalyzed approaches to the formation of such centers with high levels of stereocontrol. Chapter 1 describes the discovery of an Ir-catalyzed asymmetric allylic alkylation reaction efficiently merging linear, trisubstituted allylic electrophiles with prototypical malonate nucleophiles to generate enantioenriched \u03b2-quaternary carbonyl products. The reaction proceeds with low catalyst loadings of iridium and at ambient temperature, marking the first reaction of its kind to be performed under such mild conditions. Appendix 2 highlights recent efforts to develop an Ir-catalyzed process for the doubly stereoselective formation of vicinal quaternary stereocenters. Chapter 2 discloses a more sustainable, Mo-catalyzed alternative to the Ir-catalyzed process in Chapter 1, unveiling thus far unknown reactivity with molybdenum and generating the desired products with outstanding enantioselectivity. This advance was enabled by exhaustive investigation of suitable ligand scaffolds, ultimately leading to the creation of the novel, C1-symmetric ShabyDACH ligand. Chapter 3 discusses the elaboration of a Pd-catalyzed a-vinylation of lactam nucleophiles to forge a-quaternary carbonyls. These products could further be diversified to a range of elusive scaffolds, highlighting their synthetic utility." }, { "name": "Ng, Cai Tong", "degree": "PhD", "year": "2026", "title": "Optimizing Treslin-MTBP for Cryo-EM Analysis", "advisor": "Dunphy, William G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282026-211327832", "creators": [ { "name": { "family": "Ng", "given": "Cai Tong" }, "id": "Ng-Cai-Tong", "orcid": "0000-0002-1082-8667", "display_name": "Ng, Cai Tong" } ], "advisors": [ { "name": { "family": "Dunphy", "given": "William G." }, "id": "Dunphy-W-G", "orcid": "0000-0001-7598-8939", "role": "advisor", "display_name": "Dunphy, William G." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Glover", "given": "David M." }, "id": "Glover-D-M", "orcid": "0000-0003-0956-0103", "role": "member", "display_name": "Glover, David M." }, { "name": { "family": "Dunphy", "given": "William G." }, "id": "Dunphy-W-G", "orcid": "0000-0001-7598-8939", "role": "member", "display_name": "Dunphy, William G." } ], "option_major": [ "biochem" ], "doi": "10.7907/p11y-7r94", "abstract": "DNA replication initiation is a highly regulated process in eukaryotes to maintain genome integrity. Misfiring of the DNA replication machinery from replication origins can result in gene amplification and genome instability. In budding yeast, ORC, Cdc6, Cdt1, and Mcm2-7 assemble on the sites of origins to form the inactive pre-replicative complex. Next, phosphorylation of Sld2 and Sld3 causes them to interact with Dbp11, leading to the recruitment of Cdc45 and GINS to the pre-replicative complex, which results in its activation. The vertebrate homolog of Sld3 is Treslin. Treslin is tightly associated with MTBP throughout the cell cycle, and the complex is essential for DNA replication in metazoan systems, including Xenopus egg extracts and human cells. Here, I aim to understand the mechanism of Treslin-MTBP function by studying its molecular structure. I established purification protocols to produce the Treslin-MTBP complex at high concentration. I then studied the overall structure of the complex using cryo-electron microscopy and obtained reconstructions of the complex at ~20 \u00c5. The reconstructions show that the Treslin-MTBP complex exhibits a large variety of conformations, indicating its intrinsic flexibility. The complex is composed of large, stable domains that can be observed in 2D classes. Using cross-link mass spectrometry, I also showed that Treslin-MTBP transiently binds to Mcm4 in cells, making Mcm4 a potential binding partner for future structural studies of the complex." }, { "name": "Nguyen, Tyler Minh-Hung", "degree": "PhD", "year": "2026", "title": "Infrared Action Spectroscopy of Biomolecules for Planetary Science Applications", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272026-013726453", "creators": [ { "name": { "family": "Nguyen", "given": "Tyler Minh-Hung" }, "id": "Nguyen-Tyler-Minh-Hung", "orcid": "0000-0002-9872-7149", "display_name": "Nguyen, Tyler Minh-Hung" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Brown", "given": "Michael E." }, "id": "Brown-M-E", "orcid": "0000-0002-8255-0545", "role": "member", "display_name": "Brown, Michael E." }, { "name": { "family": "Nemchick", "given": "Deacon J." }, "id": "Nemchick-D-J", "orcid": "0000-0003-4760-4752", "role": "member", "display_name": "Nemchick, Deacon J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jxjd-3b72", "abstract": "The search for extraterrestrial life in our solar system requires the development of novel in situ instrumentation capable of detecting biosignatures in planetary environments and biological samples. This thesis applies infrared (IR) action spectroscopy of mass-selected ions toward this goal, demonstrating the ability to unambiguously characterize planetary-relevant biomolecules in liquid samples for various test cases. Action spectra are generated by plotting a photodissociation yield for biomolecular ions of interest as a function of IR frequency. In Chapter II, I describe the setup and operating procedures of an action spectrometer that uses a quantum cascade laser (QCL) (1000-1600 cm-1) and a Cr:ZnSe/S laser (3300-3800 cm-1), as well as describe general data processing procedures. In Chapter III, I describe the initial demonstration of the relatively compact, QCL-based action spectrometer, highlighting its ability to record action spectra of room temperature, water-tagged amino acids and discern amino acid isomers in mixtures. In Chapter IV, I record the action spectra of planetary-relevant, water-tagged amino acid isomers using the QCL-based instrument. I distinguish between the isomers using a combination of spectrum matching and machine learning methods. In Chapter V, I use the Cr:ZnSe/S laser-based action spectrometer to record multiplexed action spectra of protonated amino acids and nucleosides from bacterial samples, with some trials at lower laser output power than contemporary methods. In Chapter VI, I show progress towards differentiating amino acid enantiomers by recording action spectra of non-covalent chiral tag-amino acid complexes using the Cr:ZnSe/S laser-based action spectrometer. In Chapter VII, I recorded action spectra of additional biomolecules, including small molecules, carbohydrates, and a pigment. Overall, this thesis will aid future development of in situ instruments for astrobiology missions and general analytical applications." }, { "name": "O'Meara, Ryen Logan", "degree": "PhD", "year": "2026", "title": "Towards the Enzymatic Mineralization of Siloxanes", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132026-170731675", "creators": [ { "name": { "family": "O'Meara", "given": "Ryen Logan" }, "id": "O'Meara-Ryen-Logan", "orcid": "0000-0002-3868-0270", "display_name": "O'Meara, Ryen Logan" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Demirer", "given": "Gozde S." }, "id": "Demirer-G\u00f6zde-S", "orcid": "0000-0002-3007-1489", "role": "chair", "display_name": "Demirer, Gozde S." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/a9qm-fv66", "abstract": "Through the synthesis of novel chemical entities, the global chemical industry has contributed significantly to the destabilization of the Earth system. Chapter I outlines the magnitude of this environmental problem and discusses the upsides and drawbacks of three mechanisms used to address it: physicochemical approaches, microbial degradation, and enzymatic bioremediation, specifically highlighting the protein engineering technique of directed evolution in support of the latter. Chapter II then provides an example emblematic of the power directed evolution has by degrading a specific class novel of chemical entities, volatile methylsiloxanes (VMS). VMS are anthropogenic, non-biodegradable chemicals produced at megaton-per-year scale and considered emerging environmental contaminants. We report on the discovery, and subsequent engineering, of cytochrome P450BM3 variants which break silicon\u2013carbon bonds in linear and cyclic VMS, as well as propose a mechanism by which these enzymes catalyze the first known biological Si\u2013C bond cleavage. VMS could not now be considered \u201cbiodegradable,\u201d however, as biodegradation is more appropriately understood as \u201cmineralization,\u201d reducing a compound solely to carbon dioxide, water, and/or inorganics; mineralization is critical because breakdown products of the parent compound may be just as, if not more, problematic than the parent which, for VMS, means their monomeric subunit, dimethylsilanediol (DMSD). Chapter III addresses this shortcoming by describing the discovery of a wild-type enzyme, the sulfite reductase CysI, which can cleave both Si\u2013C bonds of DMSD, representing the capacity for its mineralization. Given the curious nature of a reductase performing oxidative chemistry, the mechanism of CysI was also probed, finding that it has latent NADPH oxidase and peroxygenase activity. Overall, this thesis illustrates how enzymes, and the new-to-nature chemistries imparted by directed evolution, may be the most suitable mechanism for the degradation of novel chemical entities, even potentially mineralizing them." }, { "name": "Osler, Skylar Kathleen", "degree": "PhD", "year": "2026", "title": "Elucidating Fundamental Structure-Property Relationships of Naphthopyran Mechanophores", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292025-144555882", "creators": [ { "name": { "family": "Osler", "given": "Skylar Kathleen" }, "id": "Osler-Skylar-Kathleen", "orcid": "0000-0003-1021-7011", "display_name": "Osler, Skylar Kathleen" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bsm6-p620", "abstract": "Naphthopyran mechanophores have been identified as a privileged class of molecules due to their synthetic accessibility and structural modularity. In response to mechanical force, naphthopyran mechanophores undergo a ring-opening reaction to generate highly colored merocyanine dyes. Force is transduced to naphthopyran small molecules by covalently attached polymer chains, and naphthopyrans that are incorporated into polymeric materials visually report on macroscopic stress and/or strain. The properties of merocyanine dyes produced under mechanical force have been effectively tuned through straightforward structural modifications on various naphthopyran scaffolds. Additionally, the sensitivity of naphthopyran mechanophores toward mechanochemical ring-opening has been modified through targeted molecular design. The studies discussed herein provide insight into the fundamental relationship between the structure of naphthopyran mechanophores and their mechanochromic properties." }, { "name": "Palmer, Levi Daniel", "degree": "PhD", "year": "2026", "title": "Nanoscale Spectroscopic Imaging of Carriers and Heat in Photocatalysts", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192026-182040809", "creators": [ { "name": { "family": "Palmer", "given": "Levi Daniel" }, "id": "Palmer-Levi-Daniel", "orcid": "0000-0002-7228-4263", "display_name": "Palmer, Levi Daniel" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Ardo", "given": "Shane" }, "id": "Ardo-Shane", "orcid": "0000-0001-7162-6826", "role": "member", "display_name": "Ardo, Shane" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h1hh-mf67", "abstract": "Photoexcited carriers (electrons and holes) perform photocatalytic solar energy conversion reactions when they transfer from a solid-state material and into a nearby or surface-adsorbed molecule. For example, light-driven water splitting occurs when molecular hydrogen and oxygen are produced from water because electron transfer drives hydrogen evolution, whereas hole transfer drives oxygen evolution. These photoexcited carriers often get trapped at nanoscale features such as dopants, defects, and grain boundaries, limiting their mobility and potentially reducing photocatalytic efficiency. However, identifying which nanoscale properties hinder solar energy conversion remains a key challenge as this requires a technique that can separately image carriers and photothermal heating on the timescale relevant to photocatalysis. Here, we develop photomodulated electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) to map photocarrier and heat distributions at sub-nanometer length scales. This dissertation presents the experimental and computational developments critical for technique development. We first introduce EELS and the fundamental working principles of ultrafast and optically coupled TEM. We demonstrate the theoretical framework needed to differentiate carriers from photothermal heating in two systems: plasmonic core-shell nanoparticles and crystalline silicon. Then, we apply this method to image photoexcited carriers localized at surface oxygen vacancies and along select nanoparticle facets in water-splitting photocatalysts. We lastly perform optically coupled liquid phase TEM (LPTEM) of similar photocatalytic nanoparticles in carbon film liquid cells, aiming to expand this technique to operando measurements of photocatalysts in their working conditions. Overall, this thesis demonstrates photomodulated STEM-EELS as a tool for imaging photocatalytic structure\u2013function relationships down to the atomic scale." }, { "name": "Qian, Ruilin", "degree": "PhD", "year": "2026", "title": "New Regulatory Mechanisms in SRP Targeting Pathway", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232026-204544790", "creators": [ { "name": { "family": "Qian", "given": "Ruilin" }, "id": "Qian-Ruilin", "orcid": "0009-0001-7138-5556", "display_name": "Qian, Ruilin" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "bioch" ], "doi": "10.7907/tr6n-t650", "abstract": "Cotranslational protein targeting by the signal recognition particle (SRP) is a fundamental and evolutionarily conserved process that ensures accurate delivery of nascent proteins to the endoplasmic reticulum (ER). This pathway requires precise coordination between cargo recognition, targeting complex assembly, and membrane-associated handover, yet how these steps are temporally and mechanistically integrated during ongoing translation remains incompletely understood. In this thesis, I combine steady-state, pre-steady-state, and single-molecule fluorescence approaches to dissect the dynamic regulation of SRP function across distinct stages of the targeting cycle.
\r\n\r\nIn Chapter 1, I investigate how nascent polypeptide elongation modulates SRP activity. Using F\u00f6rster resonance energy transfer (FRET) measurements, I show that increasing nascent chain length enhances dynamic excursions of the signal sequence from SRP, shifting the complex into suboptimal conformations with impaired interaction kinetics with the SRP receptor (SR). Furthermore, the nascent polypeptide-associated complex (NAC) amplifies these effects, further antagonizing SRP function. These findings reveal that nascent chain length and NAC together impose a limited temporal window for efficient cotranslational targeting.
\r\n\r\nIn Chapter 2, I focus on the membrane-associated stages of the SRP pathway and elucidate the mechanism of ribosome\u2013nascent chain complex (RNC) handover to the ER translocation machinery. I demonstrate that SR remodels and partially destabilizes the SRP\u2013RNC complex by inducing signal sequence release and detachment of the SRP GTPase domain from the ribosome, while paradoxically stabilizing the overall complex through multivalent interactions. GTP hydrolysis subsequently disrupts this stabilization to enable cargo transfer. Importantly, the ER membrane selectively stabilizes a pre-handover intermediate with delayed GTP hydrolysis for correct client proteins, thereby providing a time window for continued nascent chain elongation and productive translocation.
\r\n\r\nIn Chapter 3, I explore the expression of the Sec61 complex in insect cells and its reconstitution into nanodiscs to recapitulate the effects of the ER membrane on RNC handover and SRP conformation. Using a copolymer-based method, I successfully purified Sec61-containing nanodiscs comprising all three subunits. However, further assays are required to verify the structural and functional integrity of the reconstituted Sec61 translocon, and additional optimization of the purification strategy is needed.
\r\n\r\nTogether, this work advances our understanding of the molecular mechanisms underlying SRP-dependent cotranslational targeting. In conjunction with prior studies from our laboratory, it contributes to a high-resolution mechanistic model of this pathway. More broadly, it reveals how multiple regulatory layers are temporally coordinated: how SRP selectively rejects RNCs bearing excessively elongated nascent chains to enhance targeting specificity, and how GTPase activity serves as a molecular timer to ensure cargo handover occurs at the appropriate stage of nascent chain elongation.
" }, { "name": "Qin, Ziyang", "degree": "PhD", "year": "2026", "title": "Expanding the Chemical Space of Nitrene Transferases: Biocatalytic Construction of C\u2013N Bonds", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:07052025-063244748", "creators": [ { "name": { "family": "Qin", "given": "Ziyang" }, "id": "Qin-Ziyang", "orcid": "0000-0001-7356-6927", "display_name": "Qin, Ziyang" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5pv2-nr39", "abstract": "The construction of carbon\u2013nitrogen (C\u2013N) bonds is pivotal to the development of pharmaceuticals, agrochemicals, and advanced materials. While traditional synthetic methods offer robust and efficient solutions, biocatalysis has emerged as a powerful, sustainable alternative for constructing these bonds with precise stereochemical control. Yet, the enzymatic repertoire for C\u2013N bond formation remains limited compared to its chemical counterpart. By leveraging directed evolution and enzyme promiscuity, we have traversed beyond natural enzymatic functions and explored the new-to-nature catalytic landscape of enzymes.
\r\n\r\nThis thesis outlines a suite of strategies that expand the enzymatic toolbox for stereoselective C\u2013N bond construction in two main avenues: the functionalization of more challenging C\u2013H bonds and the development of novel nitrene species. Chapter I reviews contemporary chemical and biocatalytic approaches, highlighting how directed evolution can transcend native enzymatic functions to unlock new reactivities.
\r\n\r\nChapter II presents engineered serine-ligated cytochrome P411 variants capable of catalyzing enantioselective propargylic C(sp3)\u2013H amination, granting streamlined access to chiral propargylamines. Chapter III addresses the long-standing challenge of differentiating minimally distinct alkyl groups, methyl and ethyl substituents, by evolving P411 enzymes that perform enantiospecific functionalization of tertiary C\u2013H bonds to construct methyl-ethyl stereocenters with high selectivity.
\r\n\r\n\r\nChapter IV expands the scope of enzymatic nitrene transfer, enabling intramolecular alkyl and aryl nitrene C\u2013H insertions to synthesize chiral pyrrolidines and methyl indolines. Subsequent biocatalytic derivatization of these products affords complex molecules bearing multiple chiral centers, showcasing the potential of biocatalysis to rapidly build molecular complexity. Chapter V introduces engineered protoglobins capable of mediating intermolecular methylnitrene transfer using a simple and stable N-methyl hydroxylamine recursor. This process uniquely achieves the stereoconvergent conversion of both (Z)- and (E)-silyl enol ether isomers, affording enantiopure N-methyl-a-aminoketones, which defies conventional limitations of enzyme specificity.
\r\n\r\nTogether, these efforts address critical gaps in biocatalytic C\u2013N bond formation, establishing broadly applicable platforms for sustainable and stereoselective synthesis of N-containing molecules. The strategies developed herein not only deepen our understanding of heme-dependent enzymes but also lay the foundation for future innovations in biocatalysis and synthetic biology.
" }, { "name": "Radford, Katelyn Margaret", "degree": "PhD", "year": "2026", "title": "Structural and Functional Characterization of Immune System Proteins Using Crystallography and Single Particle Cryo-EM", "advisor": "Chou, Tsui-Fen; Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262026-202448697", "creators": [ { "name": { "family": "Radford", "given": "Katelyn Margaret" }, "id": "Radford-Katelyn-Margaret", "orcid": "0000-0001-8484-7580", "display_name": "Radford, Katelyn Margaret" } ], "advisors": [ { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "co-advisor", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "co-advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Aravin", "given": "Alexei A." }, "id": "Aravin-A-A", "orcid": "0000-0002-6956-8257", "role": "member", "display_name": "Aravin, Alexei A." }, { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "member", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "biochem" ], "doi": "10.7907/5zp5-jd24", "abstract": "Immune system features are ubiquitous across living organisms, and regulate host-pathogen or host-symbiont relationships across domains of life. This thesis explores proteins mediating aspects of immunity in four different systems. First, I explore broadly neutralizing antibodies against the SARS-CoV-2 viral entry protein S. I identified the antibody 11G-12v as belonging to Class 1/4. I additionally found that it shares sequence and structural similarity to a set of previously discovered anti-SARS-CoV-2 RBD antibodies that have a long CDRH3 loop with a YYDRxG motif, which associate with and extend the central beta sheet of the SARS-CoV-2 RBD. Second, I examined the many documented activities of the p97 adapter protein Phospholipase A2 Activating protein in the context of its structure, and considered them in terms of pleiotropy, as some of its functions appear to occur without p97. Third, I solved the crystal structure of the autophagy intiation scaffold FIP200's C-terminal CLAW domain in complex with a 13-amino acid phosphopeptide derived from the TNIP1 FIP200 interacting region, or FIR. This crystal structure supported our understanding of the basis of FIR recognition by CLAW. And finally, I collaborated with the Aravin group and solved five cryo-EM structures of RzAgo, a prokaryotic argonaute protein with two unique N terminal domains. We found that RzAgo forms tetramers to assume an active state, which recapitulates structures previously observed in certain structures of homologous mammalian proteins. However, in its inactive state, RzAgo forms filaments that lock its catalytic sites in a non-catalytic organization. Together, this work demonstrates the contributions of structural biology to studying immune system proteins." }, { "name": "Reich, Natasha D.", "degree": "PhD", "year": "2026", "title": "Template-Free Assembly of Three Dimensional Mesostructures via Polarization Control", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292026-192643507", "creators": [ { "name": { "family": "Reich", "given": "Natasha D." }, "id": "Reich-Natasha-D", "orcid": "0000-0002-8215-792X", "display_name": "Reich, Natasha D." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Carim", "given": "Azhar I." }, "id": "Carim-Azhar-I", "orcid": "0000-0003-3630-6872", "role": "member", "display_name": "Carim, Azhar I." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e1vd-sg75", "abstract": "Plants are inherently sessile and thus exhibit adaptive morphologies to forage for essential resources such as light. For example, palm trees grow with a pronounced tilt towards the time-averaged solar position to optimize light collection. In analogy, electrochemical growth of semiconductor material under illumination can result in spontaneous self-organization. Such inorganic phototropic growth can produce mesostructured deposits consisting of ordered nanoscale features over cm2 areas, despite a lack of lithographic processing, structured light fields, or templating agents (ligands, surfactants, etc.). Precise deposit morphologies are determined by the characteristics of the input illumination. Growth using linearly polarized illumination produces highly anisotropic lamellar arrays with a feature pitch proportional to the wavelength. Abrupt, orthogonal shifts in the polarization direction during growth reorient the direction of the in-plane anisotropy producing woodpile architectures with independently tunable layer heights. Moreover, spatial registration between alternating layers is produced via optical coupling across the intermediary layer. The investigations described herein demonstrate that inorganic phototropic growth enables programmable, high-throughput fabrication of complex three-dimensional lattices that cannot be achieved easily, if at all, via conventional means." }, { "name": "Rezgui, Samir Peter", "degree": "PhD", "year": "2026", "title": "Development of Synthetic Methods to Enable the Synthesis of Pyrroloiminoquinone Alkaloids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-124644565", "creators": [ { "name": { "family": "Rezgui", "given": "Samir Peter" }, "id": "Rezgui-Samir-Peter", "orcid": "0000-0003-4080-9835", "display_name": "Rezgui, Samir Peter" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xmbz-by61", "abstract": "Natural product total synthesis continues to serve as a driving force for inventions in organic chemistry, and is an essential paradigm in the Stoltz group. The content of this thesis reflects this central objective. Chapter 1 focuses on the total synthesis of aleutianamine\u2014 a new pyrroloiminoquinone alkaloid natural product that possesses an unprecedented structure and potent anti-tumor activity. Herein is described a non-biomimetic synthesis that hinges upon the development of a dearomative thiophene arylation to construct the unique [3.3.1] ring system of the natural product. An unconventional ketone installation was then developed to install the alkenyl bromide, and finally, an oxidative amination/thioaminal formation protocol was developed to complete the synthesis. Additionally, a novel Larock/Buchwald\u2013Hartwig annulation/cyclization was developed to access the core of the natural product.
\r\n\t\t\r\nChapter 2 focuses on leveraging the Larock/Buchwald\u2013Hartwig annulation/cyclization developed en route to aleutianamine to access several pyrroloiminoquinone alkaloids in a divergent manner. This strategy led to the shortest synthetic sequences at the time of four pyrroloiminoquinone alkaloids, and the first synthesis of another.
\r\n\t\t\r\nChapter 3 describes the progress toward the total synthesis of atkamine, another pyrroloiminoquinone that has yet to be synthesized, by further leveraging of the Larock/Buchwald\u2013Hartwig annulation/cyclization. The development of additional reaction methodologies were investigated to try and rapidly access the complex bicyclic ring system of this natural product.
\r\n\t\t\r\nFinally, Chapter 4 describes the synthesis of authentic standards to enable investigations of pinene secondary organic aerosols. Access to these standards allowed for the identification and formation mechanism of dimer esters in pinene organic aerosols, which has been a long-standing challenge in the field.
" }, { "name": "Salazar, Matthew", "degree": "PhD", "year": "2026", "title": "Utilizing Mass Transport to Enhance CO\u2082 Conversion to Multi-Carbon Products", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272026-164746670", "creators": [ { "name": { "family": "Salazar", "given": "Matthew" }, "id": "Salazar-Matthew", "orcid": "0009-0002-9643-7276", "display_name": "Salazar, Matthew" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "chair", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/nftx-h654", "abstract": "This thesis focusses on the use of mass transport to improve the selectivity and production rate of electrochemical CO\u2082 reduction to multi-carbon (C\u2082\u208a) products. In the first chapter, the effects of mass transport on CO\u2082 reduction are discussed. Briefly, mass transport has been used to improve the selectivity of CO\u2082 reduction by reducing the transport of proton sources to suppress the competing hydrogen evolution reaction and improve the selectivity towards C\u2082\u208a products by keeping intermediates near the surface. In addition, gas diffusion electrodes (GDEs) have been designed to achieve high current densities by minimizing the diffusion length of CO\u2082 to the catalyst surface. In the second chapter, additive-derived films were studied as an approach to improve the selectivity towards CO\u2082 reduction when using oxygen containing feedstocks, such as flue gas. Oxygen is problematic as it introduces a competing side reaction, the oxygen reduction reaction. The films were able to increase the selectivity towards CO\u2082 reduction by suppressing the transport of oxygen and demonstrated high selectivity towards multi-carbon production when using a simulated flue-gas stream. In the third chapter, a methodology to prepare 3D-printed flow-through electrodes is developed. While GDE can achieve high current densities, they are susceptible to flooding and salt precipitation which can significantly hinder performance. As such, liquid flow-through electrodes are an attractive alternative electrode design to achieve high current densities. A 3D-printed flow-through electrode was fabricated using the methodology and achieved a higher current density compared to a flat plate electrode. The methodology developed in Chapter 3 opens the door to the fabrication of rationally designed flow-through electrodes. In the last chapter, two tandem systems were assembled to convert CO\u2082, water, and sunlight into a butene (C\u2084) and 2-methyl-2-pentenal (C\u2086). A limitation of electrochemical CO\u2082 reduction is that the selectivity towards products with 3-carbon chains (C\u2083\u208a) is relatively low. These devices used a two-step tandem process, where in the first step CO\u2082 is electrochemically reduced to the desired intermediate (ethylene, CO, and/or hydrogen) using a PV-driven electrochemical cell. The gas stream is fed to a photothermocatalytic reactor where the gaseous products are converted to butene (via ethylene dimerization) or 2-methyl-2-pentenal (via ethylene hydroformylation followed by aldol condensation). This chapter highlights the wide range of potential products that can be derived from CO\u2082 and the importance of co-designing of the thermochemical and electrochemical steps." }, { "name": "Samkian, Adrian Eduard", "degree": "PhD", "year": "2026", "title": "Total Synthesis of Hypersampsone M and Studies of Related Polycyclic Polyprenylated Acylphloroglucinol Systems", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08122025-011509478", "creators": [ { "name": { "family": "Samkian", "given": "Adrian Eduard" }, "id": "Samkian-Adrian-Eduard", "orcid": "0000-0002-0068-3572", "display_name": "Samkian, Adrian Eduard" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "orcid": "0000-0001-8586-5641", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hd4h-sk15", "abstract": "Research in the Stoltz group is primarily focused on the total synthesis of complex, bioactive natural products and on the development of reaction methodologies to enable these synthetic endeavors. This thesis focuses on the homoadamantane polycyclic polyprenylated acylphloroglucinol (PPAP) class of natural products, our efforts toward their synthesis, and discoveries made along the way. Chapter 1 describes the completed synthesis of hypersampsone M, while Chapter 2 describes ongoing efforts toward wilsonglucinol G and hypersampsone A. Appendix 5 presents the culmination of optimization studies and unsuccessful routes toward these natural products. Chapter 3 describes selective fragmentations of a-bromocaranones, reactions that were tailored to the synthesis of PPAPs. Chapter 4 discloses the synthesis and characterization of an unexpected, caged side product isolated during an unsuccessful route to the homoadamantane PPAPs. Chapter 5 discusses the development and scope of the key cyclopentene annulation methodology that enabled the installation of the challenging, hindered 5-membered ring on the homoadamantane PPAPs." }, { "name": "Sharp, Kimberly Rhian", "degree": "PhD", "year": "2026", "title": "Efficient Synthetic Transformations Enabled by Group X Catalysis", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-204329271", "creators": [ { "name": { "family": "Sharp", "given": "Kimberly Rhian" }, "id": "Sharp-Kimberly-Rhian", "orcid": "0000-0002-5718-3552", "display_name": "Sharp, Kimberly Rhian" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x572-0721", "abstract": "The development of efficient routes for the synthesis of complex molecules is a central theme of organic chemistry research. Herein, we describe our efforts toward this goal through the demonstration of umpolung strategies for incorporation of nitrogen functionality. Chapter 1 describes nickel-catalyzed N\u2013N cross coupling for the synthesis of hydrazides, tolerant of complex coupling partners. Mechanistic investigation suggests a Ni (I) active catalyst, capable of forming a key nitrenoid intermediate. Chapter 2 details an enolate amidation method, efficiently forming a bond between complex amides and the \u03b1-position of \u03b2-keto esters. Nickelocene catalysis is used, and we hypothesize that it acts as a single electron reductant to form an active N-centered radical species. Appendix 4 conveys initial attempts at producing enantioenriched \u03b1-amidated products with palladium-catalyzed decarboxylative allylic alkylation. Chapter 3 reports our investigations in applying our N\u2013N coupling to the synthesis of the complex indole alkaloid braznitidumine, featuring a hydrazine in its central 10-membered ring. Strategies for the formation of the desired indole coupling partner and the necessary fused imidazolidine-pyran motif are discussed. Chapter 4 outlines our efforts toward the synthesis of hypatulone A, a rearranged polycyclic polyprenylated acylphloroglucinol. We propose a key palladium-catalyzed carbonylative coupling for the formation of the caged core, and detail our efforts toward the synthesis of the requisite bicyclo[3.3.1]nonane." }, { "name": "Shin, Chungkeun", "degree": "PhD", "year": "2026", "title": "Reductive C-C Bond Construction Strategies by Samarium and Nickel Catalysis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-185400251", "creators": [ { "name": { "family": "Shin", "given": "Chungkeun" }, "id": "Shin-Chungkeun", "orcid": "0009-0005-8125-5850", "display_name": "Shin, Chungkeun" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9qzw-c186", "abstract": "Reductive carbon\u2013carbon bond construction is a powerful strategy for rapidly assembling molecular complexity from structurally diverse precursors. Leveraging low-valent or open-shell metal intermediates, reductive catalysis enables efficient bond formation in complex systems. This thesis describes the development and study of reductive catalytic strategies for C\u2013C bond formation using samarium and nickel catalysis.
\r\n\r\nChapter 1 describes the development of a samarium-catalyzed intermolecular reductive cross-coupling of ketones and acrylates enabled by Sm(III)\u2013alkoxide protonolysis. This strategy overcomes a key barrier to Sm(II) catalysis by converting redox-inactive Sm(III)\u2013alkoxide intermediates to redox-active Sm(II) species under mild turnover conditions. Mechanistic insights are provided by electrochemical studies and examination of the solvent\u2013acidity cross-relationship. The modularity of this approach lays the groundwork for more generalized strategies in the future development of reductive Sm catalysis.
\r\n\r\nChapter 2 presents the development of a nickel-catalyzed asymmetric arylation of \u03b1-substituted imides. Two complementary approaches are described, wherein \u03b1-chloroimides are paired with aryl iodides and \u03b1-mesylates are paired with aryl bromides to match the relative rates of imide activation and aryl halides oxidative addition. This methodology provides rapid access to pharmaceutically relevant highly enantioenriched \u03b1-aryl imides.
\r\n\r\nChapter 3 provides an overview of Ni-catalyzed asymmetric C(sp3)\u2013C(sp3) cross-electrophile coupling. This chapter highlights two complementary stereochemical paradigms of stereoconvergent coupling and stereoretentive coupling, with an emphasis on their scope, mechanistic insights, and limitations.
\r\n\r\nChapter 4 discusses efforts toward a Ni-catalyzed stereoretentive\u2013stereoselective decarbonylative C(sp3)\u2013C(sp3) cross-coupling method. This work establishes highly stereoretentive alkylation of enantioenriched pyridyl esters with primary alkyl iodides. Efforts to expand this reactivity to secondary alkyl iodides are then described, with the goal of forging products bearing vicinal stereogenic centers. These studies lay foundation for the future development of reductive asymmetric alkyl\u2013alkyl cross-coupling reactions.
" }, { "name": "Shin, Soyoung", "degree": "PhD", "year": "2026", "title": "Bioinspired Microfluidic Wearable Sensors for Continuous Sweat Sampling and Metabolic Monitoring", "advisor": "Gao, Wei", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142026-143540945", "creators": [ { "name": { "family": "Shin", "given": "Soyoung" }, "id": "Shin-Soyoung", "orcid": "0009-0002-3210-6427", "display_name": "Shin, Soyoung" } ], "advisors": [ { "name": { "family": "Gao", "given": "Wei" }, "id": "Gao-Wei", "orcid": "0000-0002-8503-4562", "role": "advisor", "display_name": "Gao, Wei" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Dabiri", "given": "John O." }, "id": "Dabiri-J-O", "orcid": "0000-0002-6722-9008", "role": "member", "display_name": "Dabiri, John O." }, { "name": { "family": "Gao", "given": "Wei" }, "id": "Gao-Wei", "orcid": "0000-0002-8503-4562", "role": "member", "display_name": "Gao, Wei" } ], "option_major": [ "chemeng" ], "doi": "10.7907/kqhx-h885", "abstract": "Wearable sweat sensors have shown strong potential for noninvasive health monitoring by providing access to dynamic biochemical information. However, continuous monitoring of sweat metabolites remains challenging due to low and variable sweat rates, inefficient sampling, and signal distortion arising from evaporation, contamination, and accumulation. These limitations restrict the accuracy and practical deployment of current wearable systems.
\r\n\r\nIn this thesis, we present bioinspired microfluidic strategies to enable continuous sweat sampling, transport, and metabolic analysis under physiologically relevant conditions. We demonstrate how a Janus interface with asymmetric wettability and geometry enables directional vertical transport at the inlet and outlet, while hierarchical microchannel guides flow across the microfluidic and sensing regions. These design elements enable transport even at low sweat rates while preventing stagnation and backflow, resulting in continuous sweat transport without the need for active pumping. This extends the effective sampling window and reduces the number of sweat induction sessions required.
\r\n\r\nThe platform is integrated with electrochemical sensing modules for real-time detection of metabolites and is further extended toward multiplexed sensing of biomarkers relevant to metabolic health. The system is validated through on-body human studies under stimulated conditions, with initial evaluation during exercise-induced sweating. Overall, the works presented here establish design principles for coupling sweat induction, sampling, and sensing, advancing wearable biofluid technologies for continuous and noninvasive metabolic monitoring.
" }, { "name": "Strong, Christian Santiago", "degree": "PhD", "year": "2026", "title": "Enantioselective Reactions of Palladium Enolates and Progress Toward Mitomycin B", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282026-002052552", "creators": [ { "name": { "family": "Strong", "given": "Christian Santiago" }, "id": "Strong-Christian-Santiago", "orcid": "0000-0003-1349-302X", "display_name": "Strong, Christian Santiago" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gwac-qk95", "abstract": "Research within the Stoltz group encompasses the total synthesis of natural products and the development of useful enantioselective transformations. This thesis overlaps with these domains in that it describes: 1) the development of several stereoselective reactions of Pd enolates and 2) progress toward the total synthesis of mitomycin B. Specifically, Chapter 1 provides historical context for the development of enantioselective reactions of Pd enolates beyond allylic alkylation within our group. Chapter 2 details the development of an enantioselective [4+2] cycloaddition of Pd enolates generated from prenyl \u03b2-ketoesters. Additionally, it describes experimental and computational mechanistic investigations related to the origins of stereoselectivity and the mechanism of catalyst turnover in this transformation. Chapter 3 discloses an enantioselective Michael spirocyclization reaction of Pd enolates as well as a stereoselective intramolecular enone difunctionalization. This method leverages lessons learned from the [4+2] cycloaddition and enables access to a diverse library of stereochemically rich polycycles. Chapter 4 presents our ongoing progress toward the total synthesis of mitomycin B via an isomitomycin approach. Our current strategy involves a key intramolecular nitrile oxide cycloaddition that rapidly constructs a complex framework en route to mitomycin B." }, { "name": "Suarez, Camila Ariana", "degree": "PhD", "year": "2026", "title": "The Use of Abiotic Strategies and C\u2013H Functionalization Toward Natural Product Total Synthesis and Studies Toward CNS-Penetrant Drug Derivatives", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192026-190950627", "creators": [ { "name": { "family": "Suarez", "given": "Camila Ariana" }, "id": "Suarez-Camila-Ariana", "orcid": "0000-0003-1858-000X", "display_name": "Suarez, Camila Ariana" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ed42-3e92", "abstract": "Research in the Stoltz group focuses primarily on total synthesis endeavors and the development of new methodologies for the asymmetric formation of stereocenters in organic chemistry. Herein we describe our efforts in natural product total synthesis campaigns and investigations on the synthesis of small molecule steroid derivatives for the purposes of central nervous system (CNS) targeting treatments. Chapter 1 encompasses our completed and asymmetric total synthesis of (\u2013)-cylindrocyclophane A facilitated by Rh-catalyzed C\u2013H functionalization methodology. We report the use of both a stepwise and a one-pot regio- , enantio-, and diastereoselective macrocyclization to forge a 22-membered paracyclophane framework. Chapter 2 describes the synthesis of bufalin and digitoxigenin derivatives in aim to develop compounds with greater CNS-penetrative properties. We disclose the synthesis of pyridine and pyridone derivatives of bufalin, and stereochemical modifications of the steroid scaffold. Chapter 3 outlines our progress toward a total synthesis of antitumor, antibiotic (+)-cyanocycline A utilizing a modular and convergent approach. We report the exploration of several different synthetic routes toward the natural product, efficient cross-coupling transformations, and current directions toward the naphthyridinomycin alkaloid skeleton." }, { "name": "Sun, Yan", "degree": "PhD", "year": "2026", "title": "Expanding Molecular Designs for Mechanochromic Polymers", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292026-153830830", "creators": [ { "name": { "family": "Sun", "given": "Yan" }, "id": "Sun-Yan", "orcid": "0000-0002-3882-131X", "display_name": "Sun, Yan" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ak8t-kt51", "abstract": "In the field of polymer mechanochemistry, mechanical force is harnessed to promote selective chemical transformations in the stress-sensitive molecules known as mechanophores. Mechanochromic mechanophores, which produce visible optical changes in polymeric materials in response to mechanical force, are particularly attractive for applications in force sensing, damage reporting, and patterning. This dissertation explores new molecular design strategies for mechanochromic polymers, elucidates fundamental understanding of mechanophore reactivity, and develops systems capable of responding to discrete stimuli and exhibiting multistage coloration.
\r\n \r\nUnlike typical angular naphthopyrans that exhibit photochromic and mechanochromic behavior, constitutionally isomeric linear naphthopyrans and 2H-1-benzopyrans are commonly considered non-photochromic at ambient temperature, while their mechanochemical activity has not been studied. In Chapter 1, we demonstrate that linear naphthopyrans incorporating an electron-donating amine substituent do in fact undergo a ring-opening reaction upon photoirradiation with UV light and upon mechanical activation, resulting in pronounced photochromic and mechanochromic behavior. In Chapter 2, we report that the indole-fused 2H-1-benzopyran mechanophore undergoes a ring-opening reaction under force to generate a yellow-colored merocyanine dye, which is further reversibly transformed to a purple-colored dye upon the introduction of acid, enabling a multi-staged coloration.
\r\n\r\nIn contrast to conventional mechanochromic mechanophores, the mechanically gated photoswitching strategy, which decouples mechanochemical activation from the chromogenic response, enables mechanophores with high force-specificity and a high degree of modularity. Chapter 3 describes a mechanically gated 3H-anthra[2,1-b]pyran photoswitch that enables a three-stage coloration process. Mechanochemical activation of the photoinert mechanophore in the polymer generates a yellow-colored 3H-anthrapyran photoswitch, which can subsequently undergo a photochemical ring-opening reaction producing an orange-red colored merocyanine dye. Chapter 4 further expands this concept through the design of a naphthopyran mechanophore bearing a furan\u2013maleimide Diels\u2013Alder adduct whose active photochromism is regulated by mechanical force, providing a new approach to multistate stimuli-responsive polymers.
" }, { "name": "Thompson, Jordan Kenji", "degree": "PhD", "year": "2026", "title": "Development of a Convergent Fragment Coupling Strategy Toward Grayanane Diterpenoids: Enantioselective Synthesis of (+)-Auriculatol A", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152025-191624055", "creators": [ { "name": { "family": "Thompson", "given": "Jordan Kenji" }, "id": "Thompson-Jordan-Kenji", "orcid": "0009-0007-6395-7087", "display_name": "Thompson, Jordan Kenji" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8sth-7196", "abstract": "Total synthesis is a cornerstone of organic chemistry, serving not only as a demonstration of synthetic strategy and innovation but also as a gateway to accessing biologically active natural products that are often scarce or inaccessible from natural sources. Among such natural products, the grayanane diterpenoids represent a structurally complex and medicinally intriguing family of compounds. These molecules, first identified as the active agents in \u201cmad honey,\u201d have a rich history of traditional use and a modern resurgence in medicinal interest due to their activity as sodium channel modulators, carbonic anhydrase inhibitors, and potential analgesics. Grayanotoxin III, in particular, exhibits great pain-relieving properties, positioning it and its analogs as compelling targets for chemical synthesis. Despite their early isolation and full structural elucidation by the early 1960s, the grayananes remain difficult to access in the realm of total synthesis, a testament to their dense stereochemical architecture and unusual [5-7-6-5] fused tetracyclic core.
\r\n\r\nThis work explores synthetic strategies toward the construction of these challenging natural products, with the aim of enabling broader access to their biological potential and deepening our understanding of chemical tools to use in their synthesis. This work introduces complex bond-forming strategies and methods development, with a particular emphasis on nickel catalysis to advance the total synthesis of grayanane diterpenoids. A convergent approach was designed to maximize efficiency at each stage, beginning with the development of a model system to rapidly evaluate \u03b3-functionalization strategies of butenolides or masked butenolide equivalents using siloxyfuran intermediates as a polarity reversal tactic. Key advances include the synthesis of a 5,5-fused butenolide fragment and the discovery and optimization of a unique vinylogous Mukaiyama aldol reaction. Early studies on the diastereoselective 1,4-reduction of butenolides and the development of a nickel-catalyzed \u03b1-enolate arylation reaction are highlighted. Subsequent chapters explore the construction of the 3.2.1 bicycle through a range of innovative transformations, including a Snider radical cascade, palladium-catalyzed decarboxylative Tsuji-Stoltz allylation, and a nickel catalyzed intramolecular carbonyl 1,2-addition. The result of these efforts is a rapid fragment coupling strategy that enables access to the pentacyclic core of auriculatol A through the use of a nickel catalyzed \u03b1-enolate alkenylation reaction using a unique olefin-supported nickel catalyst. In addition to discovering that low-valent olefin-supported nickel catalysts are privileged for \u03b1-enolate arylation and alkenylation, an unexpected 6-membered ring-containing side product was isolated in these reactions, which could have unique mechanistic implications in the area of dehydrogenative catalysis. To follow, detailed investigations into late-stage olefin functionalization and hydrogenation ultimately culminate in the first synthesis of (+)- auriculatol A along with its epimer (+)-9-epi-auriculatol A. Collectively, these studies offer a blueprint for future synthetic approaches to the broader grayanane diterpenoid family and stand as a hallmark achievement for the synthesis of grayanane natural products containing an embedded e ring in an uncommon pentacyclic scaffold.
" }, { "name": "Ton, Thu Nu Minh", "degree": "PhD", "year": "2026", "title": "Electrochemical Carboxylation of Aldehydes with CO\u2082: Mechanistic Insights and Enantioselective Synthesis", "advisor": "Manthiram, Karthish", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262026-184400266", "creators": [ { "name": { "family": "Ton", "given": "Thu Nu Minh" }, "id": "Ton-Thu-Nu-Minh", "orcid": "0000-0003-0134-2435", "display_name": "Ton, Thu Nu Minh" } ], "advisors": [ { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "advisor", "display_name": "Manthiram, Karthish" } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5f9j-mn04", "abstract": "The electrochemical carboxylation of organic substrates with CO\u2082 is a promising strategy for the sustainable synthesis of value-added carboxylic acids, offering mild operating conditions and avoiding the need for highly reactive organometallic reagents. As the electrical grid transitions toward renewable energy sources, electrochemical activation of CO\u2082 is poised to become an increasingly carbon-negative process, further improving the sustainability of chemical manufacturing. Despite these advantages, the scope of electrochemical carboxylation remains limited, and a deeper mechanistic understanding is needed to guide rational improvements in selectivity and efficiency. This thesis addresses these gaps by investigating the electrochemical carboxylation of aldehydes, an underexplored but industrially relevant substrate class, and demonstrating for the first time that this transformation can be performed enantioselectively.
\r\n\r\nFor aromatic aldehydes, electroanalytical and spectroscopic studies support a mechanism in which a substrate-derived ketyl radical couples with CO\u2082 to form the \u03b1-hydroxy carboxylic acid product. EPR spectroscopy provided direct evidence for formation of the ketyl radical intermediate under electrolytic conditions, and kinetic studies identified the coupling step as the rate-determining step. Lewis acidic additives such as MgCl2 were found to play a key role in promoting ketyl radical formation. Extending this chemistry to aliphatic aldehydes revealed that their more negative reduction potentials open an alternative CO\u2082 reduction pathway towards electrochemical carboxylation. However, it was also found that polymerization of the substrate under reductive conditions limits carboxylation selectivity, prompting future works to understand and develop strategies towards mitigating the polymerization pathway.
\r\n\r\nBuilding on this mechanistic foundation, the first enantioselective electrochemical carboxylation of an aldehyde was demonstrated using chiral metal salen complexes as homogeneous catalysts, affording optically active mandelic acid with up to 43% enantiomeric excess. Both the applied potential and metal center identity were found to strongly influence enantioselectivity, pointing to an electronic basis for stereocontrol. Cyclic voltammetry studies further suggest that the most effective catalysts readily undergo reductive activation under the applied conditions, enabling coordination with CO\u2082 to initiate the enantioselective pathway. Taken together, the insights developed in this thesis provide a foundation for the rational design of more selective, efficient, and enantiocontrolled electrochemical CO\u2082 incorporation strategies.
" }, { "name": "Totoiu, Christian Alexander", "degree": "PhD", "year": "2026", "title": "Electron Spin-Based Quantum Sensing in Biomolecular Systems", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042026-032803412", "creators": [ { "name": { "family": "Totoiu", "given": "Christian Alexander" }, "id": "Totoiu-Christian-Alexander", "orcid": "0009-0004-5437-4339", "display_name": "Totoiu, Christian Alexander" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/18jz-mz08", "abstract": "Paramagnetic biomolecules bridge the gap between chemical reactivity through redox processes and quantum mechanics through their inherent electron spins. In this way, they provide a rich set of fundamental systems to elucidate complex electron spin dynamics and investigate their potential effects on native biological functions. Particularly, paramagnetic molecules, via the Zeeman effect, are able to act as molecular quantum bits (qubit) in an external magnetic field by generating a two-level system that operates quantum mechanically. The specificity and synthetic control of molecular spin qubits make them attractive targets for quantum sensing applications. Conventional quantum sensing modalities are often solid-state sensors lacking broad tunability, and magnetic resonance techniques rely on abundant nuclear spins for imaging. Conversely, molecular quantum sensors using electron spins offer chemical tunability of both spin coherences via electronic structure and precise targeting for local chemical microenvironments. Two main classes of quantum sensors are described in this work: organic radical-labeled micelles and paramagnetic metalloproteins. The former can be chemically tuned to target specific areas of interest and are active across broad temperature ranges. The latter are found ubiquitously across the kingdoms of life and offer native sensing targets. Across these systems, the advantages of native biomolecular qubits as quantum sensors were demonstrated alongside the capacity to gain fundamental biophysical insight." }, { "name": "Tsamopoulos, Alexandros", "degree": "PhD", "year": "2026", "title": "Ion Transport and Rheological Behavior in Polymeric Systems", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-074934324", "creators": [ { "name": { "family": "Tsamopoulos", "given": "Alexandros" }, "id": "Tsamopoulos-Alexandros", "orcid": "0009-0003-5924-5512", "display_name": "Tsamopoulos, Alexandros" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Datta", "given": "Sujit" }, "id": "Datta-Sujit-S", "orcid": "0000-0003-2400-1561", "role": "member", "display_name": "Datta, Sujit" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3x2q-xx89", "abstract": "Ion-containing polymers are an important class of soft materials, owing to their applications in electrochemical energy storage, fuel cells, and membrane separations, as well as their rich ion transport and mechanical behavior. Their properties are governed by the interplay of polymer connectivity, ion correlations, segmental dynamics, and viscoelastic response across multiple length and time scales. This thesis examines these couplings using molecular simulations of polymer electrolytes, polymerized ionic liquids, and model polymeric fluids. We first investigate ion transport in salt-doped polymer electrolytes and show how temperature and salt concentration jointly control ionic conductivity through their effect on polymer mobility. We then examine polymerized ionic liquids, focusing on how ion correlations and chain length influence polymer relaxation, Onsager transport coefficients, and ion conductivity. Next, we return to the polymer electrolyte system to study the role of salt in controlling their linear and nonlinear rheological response. Finally, we develop a hydrodynamic framework for the diffusion of anisotropic probes in complex fluids, demonstrating that probe motion is governed by the length-scale-dependent viscous response of the surrounding medium. Overall, the range of systems considered here reflects the broader challenge of understanding ion-containing and polymeric materials." }, { "name": "Varner, Samuel L.", "degree": "PhD", "year": "2026", "title": "Part I: Kinetic Mechanisms and Thermodynamics in Diblock Copolymer Micelles & Part II: Inhomogeneous Thermodynamics of Polar Fluids and Ionic Liquids", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:11032025-231619710", "creators": [ { "name": { "family": "Varner", "given": "Samuel L." }, "id": "Varner-Samuel-L", "orcid": "0000-0002-1365-1027", "display_name": "Varner, Samuel L." } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemeng" ], "doi": "10.7907/p5ca-t067", "abstract": "Part I: Electrolytes are ubiquitous in our world and play essential roles in biology, consumer products, and energy storage. Fundamentally, an electrolyte consists of charged species and a solvent, both of which significantly influence its behavior in the bulk and near interfaces. While it is relatively straightforward to predict charge interactions in a vacuum, the presence of a liquid solvent mediates these interactions in complex and nontrivial ways. Moreover, the interaction of ions with surfaces is highly nuanced and can be strongly affected by the specific chemistry of the ions, solvent, and interface. This is especially relevant in the context of the electric double layer, a subject of scientific inquiry since 1853. Gaining a deeper understanding of these intricate effects and how they govern electrolyte behavior is critical not only for explaining biologically relevant phenomena such as macromolecular complexation, but also for designing batteries and supercapacitors with optimized energy storage performance.
\r\n\r\nThis work presents an analysis of three distinct systems in which the behavior of charged and polar fluids were poorly understood. One area of focus is the effect of introducing non-polar solvents on the charging behavior and energy storage performance of room-temperature ionic liquid supercapacitors, with particular attention to specific surface effects and complex tricritical surface phase behavior. Another topic explored is the entropic origin of ionic interactions in polar solvents, highlighting how entropy is the dominant force driving ion association. Separately, we also investigate the unique surface polarization that arises in asymmetric polar fluids at liquid\u2013vapor interfaces, revealing subtle interfacial phenomena driven solely by molecular asymmetry.
\r\n\r\nPart II: Block copolymers can undergo microphase separation to form a range of ordered nanostructures, including lamellae, lattice-ordered spheres and cylinders, and even network phases. In selective solvents, they self-assemble into micelles, similar to surfactant molecules. However, unlike surfactants, block copolymers often contain hundreds or thousands of repeat units, which significantly slows their dynamics and equilibration. As a result, solutions of diblock copolymer micelles are frequently kinetically trapped far from equilibrium due to large free energy barriers associated with equilibration mechanisms such as chain exchange, micelle fusion, and micelle fission. For applications ranging from viscosity modification and drug delivery to nanoreactors, understanding these kinetic processes is essential. Moreover, developing strategies to achieve consistent and stable micelle size distributions remains a key challenge, particularly in systems far from equilibrium.
\r\n\r\nThis work analyzes the single-chain exchange mechanism in highly segregated copolymer micelles, with particular attention to its chain length dependence, a topic that has been actively debated since the introduction of the Halperin and Alexander theory in 1989. The kinetics of chain exchange are examined under two representative regimes: one involving polymeric solvents, where the micelle core gradually shrinks, and the other involving small-molecule solvents, where the core fully collapses. A combination of simulation and sampling techniques is employed to compare the thermodynamics of the underlying free energy landscape with the actual kinetic pathways of chain escape.
\r\n\r\nThis work also analyzes the kinetic pathways involved in a widely used copolymer micelle preparation technique known as thin film dissolution, or direct dissolution. Mesoscale molecular dynamics simulations are performed to provide a molecular-level picture of micelle formation, starting from both ordered and disordered initial states. In parallel, a mean-field theory is developed to assess how closely the intermediate structures and the final micelles resemble equilibrium configurations.
" }, { "name": "Yang, Jason", "degree": "PhD", "year": "2026", "title": "Artificial Intelligence Methods for Enzyme Engineering", "advisor": "Arnold, Frances Hamilton; Yue, Yisong", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282026-203626843", "creators": [ { "name": { "family": "Yang", "given": "Jason" }, "id": "Yang-Jason", "orcid": "0000-0003-3184-1550", "display_name": "Yang, Jason" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "co-advisor", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Yue", "given": "Yisong" }, "id": "Yue-Yisong", "orcid": "0000-0001-9127-1989", "role": "co-advisor", "display_name": "Yue, Yisong" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Yue", "given": "Yisong" }, "id": "Yue-Yisong", "orcid": "0000-0001-9127-1989", "role": "member", "display_name": "Yue, Yisong" }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "orcid": "0000-0001-5868-348X", "role": "member", "display_name": "Gradinaru, Viviana" } ], "option_major": [ "chemeng" ], "doi": "10.7907/wqhh-dm06", "abstract": "Proteins, such as specialized catalysts called enzymes, offer transformative potential for sustainable chemical synthesis, environmental remediation, and advanced therapeutics. However, engineering proteins for specific industrial or clinical functions remains a formidable challenge due to the expansive and high-dimensional sequence design space. While directed evolution has facilitated significant breakthroughs, the methodology is often constrained by slow iteration cycles and the requirement for a functional starting point. This thesis introduces novel machine learning frameworks, integrated with experimental workflows, to transcend traditional enzyme engineering approaches. We first present Active Learning-Assisted Directed Evolution (ALDE), which employs Bayesian optimization to enable more efficient optimization of protein properties. Afterward, Contrastive Reaction-Enzyme Pretraining (CREEP) is introduced for the annotation and discovery of enzymes with desired \"new-to-nature\" functionalities. Finally, a new paradigm for Steering Generation for Protein Optimization (SGPO) is demonstrated, unifying these two perspectives into a holistic generative framework for efficient protein engineering. Collectively, these innovations advance the transition toward automated, artificial intelligence-driven biomolecular design\u2013unlocking sustainable synthesis, novel therapeutics, and programmable biology at the molecular level." }, { "name": "Yang, Jee Won", "degree": "PhD", "year": "2026", "title": "Engineering Ultrasonic Reporters for Imaging Cellular Enzyme Activity", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012026-215636293", "creators": [ { "name": { "family": "Yang", "given": "Jee Won" }, "id": "Yang-Jee-Won", "orcid": "0000-0002-3257-1823", "display_name": "Yang, Jee Won" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Kennedy", "given": "Mary B." }, "id": "Kennedy-M-B", "orcid": "0000-0003-1369-0525", "role": "member", "display_name": "Kennedy, Mary B." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/b95g-z233", "abstract": "Enzyme activity governs virtually every aspect of cell behavior, from signal transduction and gene regulation to tissue remodeling and disease progression. Yet visualizing when and where specific enzymes act inside living organisms remains a fundamental challenge: optical reporters lack tissue penetration, nuclear imaging requires exogenous radioactive tracers, and MRI-based reporters suffer from low sensitivity. Ultrasound offers a compelling alternative, combining deep tissue penetration, high spatiotemporal resolution, and broad clinical accessibility \u2014 but has historically lacked the genetically encoded molecular reporters needed to connect acoustic contrast to specific cellular activities.
\r\n\r\nGas vesicles (GVs) \u2014 air-filled protein nanostructures derived from buoyant microbes \u2014 have recently bridged this gap, enabling genetically encoded ultrasound contrast and providing initial demonstrations of acoustic biosensing for protease activity and calcium dynamics. However, extending GV-based biosensors to detect diverse enzyme activities in mammalian systems, with the specificity and sensitivity required for biological discovery, has remained an open challenge.
\r\n\r\nThis thesis addresses this challenge by engineering three classes of GV-based acoustic biosensors targeting distinct enzyme families. UReKA (Ultrasonic Reporter of Kinase Activity) is the first genetically encoded ultrasonic reporter of protein kinase A activity, in which phosphorylation of an engineered GvpC substrate motif triggers dissociation from the GV shell and produces a quantitative, reversible increase in nonlinear acoustic contrast in purified GVs and mammalian cells. eUROP (evolved Ultrasound Reporter of Orthogonal Protease) extends this strategy to designed proteolytic activity by combining rational substrate engineering with directed evolution of plum pox virus protease, yielding a low-background, mammalian-compatible acoustic biosensor responsive to constitutive, inducible, and stimulus-driven gene expression. PAINTUR (Protease-Activated Imaging of Nonlinear Tumor Ultrasound Response) extends the platform from intracellular signaling to the extracellular tumor microenvironment, where an MMP9-cleavable GvpC enables acoustic imaging of endogenous protease activity in an orthotopic glioblastoma model while preserving the mechanical robustness needed for deep-tissue ultrasound. Together, these three sensor systems establish GvpC engineering as a generalizable platform for converting enzymatic activity into quantitative, noninvasive acoustic signals, opening new avenues for molecular imaging of cellular function in opaque tissues.
" }, { "name": "Yang, Junjie", "degree": "PhD", "year": "2026", "title": "Scalable Ab Initio Quantum Many-Body Methods for Crystalline Materials", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02062026-212938424", "creators": [ { "name": { "family": "Yang", "given": "Junjie" }, "id": "Yang-Junjie", "orcid": "0000-0002-6726-6538", "display_name": "Yang, Junjie" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Sharma", "given": "Sandeep" }, "id": "Sharma-Sandeep", "orcid": "0000-0002-6598-8887", "role": "member", "display_name": "Sharma, Sandeep" }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/36ns-ht38", "abstract": "Achieving materials-specific predictions for large, realistic molecules and solids with strong electron correlations remains a long-standing challenge in quantum chemistry. This dissertation develops scalable ab initio quantum many-body methods for crystalline materials, demonstrating that rigorous optimization of theoretical approximations and numerical algorithms enables predictive computation even in strongly correlated systems. The work tackles three interconnected challenges, namely describing material-specific properties of strongly correlated superconductors, achieving linear scaling with k-points for large-scale periodic calculations, and establishing reliable methods for electron-phonon interactions. The following chapters address each challenge in turn.
\r\n\r\nChapter 2 demonstrates that ab initio density matrix embedding theory, combined with symmetry-breaking strategies for superconducting order parameters, reproduces experimental trends in cuprate superconductivity, including pressure and layer effects on transition temperatures. By directly solving the electronic Schr\u00f6dinger equation from material structures, these calculations capture multi-orbital covalency effects that simplified model Hamiltonians neglect, revealing their essential role in the spin fluctuations driving pairing. This predictive capability establishes a foundation for efficient computational screening of superconducting materials. Extending these calculations to larger k-point meshes and broader phase diagram explorations, however, demands more efficient computational algorithms.
\r\n\r\nTo overcome this computational bottleneck, Chapter 3 introduces interpolative separable density fitting framework. This development enables thermodynamic limit calculations with up to 1000 k-points, as validated on diamond, carbon dioxide, nickel monoxide, and cuprate systems. Integration with density matrix embedding theory and local natural orbital methods further yields converged ground-state energies from accurate correlated wavefunction methods such as CCSD(T) for crystalline materials in the thermodynamic limit. With computational efficiency established, the remaining challenge lies in extending the theoretical framework beyond purely electronic degrees of freedom.
\r\n\r\nChapter 4 addresses this need by establishing exponential ansatz wavefunctions as competitive approaches for electron-phonon systems. Unlike previous treatments based on perturbation theory, systematic benchmarking of coupled cluster theory and variational Lang-Firsov methods on the Holstein model demonstrates, for the first time, that these approaches accurately describe polaron formation across coupling regimes when combined with appropriate reference state optimization. These results provide a foundation for incorporating phonon effects into ab initio studies of superconducting materials.
\r\n\r\nIn addition to these methodological advances, GPU acceleration and MPI parallelization enhance computational throughput, enabling efficient large-scale calculations. Together, these developments constitute a computational framework for predictive ab initio quantum many-body calculations in crystalline materials, opening new avenues for understanding and designing strongly correlated quantum materials.
" }, { "name": "Ye, Alexandre Z.", "degree": "PhD", "year": "2026", "title": "Investigations of Metal Oxide Photocathode Protection Layers and Interfacial Charge Transfer Rates on Graphene Electrodes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:12052025-204405759", "creators": [ { "name": { "family": "Ye", "given": "Alexandre Z." }, "id": "Ye-Alexandre-Z", "orcid": "0009-0003-4895-0160", "display_name": "Ye, Alexandre Z." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/cx9r-zs82", "abstract": "Coatings of HfO2, Ta2O5, TiO2, and Nb2O5 were evaluated as protection layers for p-InP photocathodes in aqueous acidic electrolytes. Each candidate protection layer was characterized based on several criteria: interfacial conduction of photogenerated electrons, thermodynamic and kinetic stability of the overlayer throughout the relevant potential and pH range for cathodic fuel-forming half-reactions, and inhibition of the primary anodic and/or chemical dissolution processes that limit electrode stability. Both conduction of photogenerated electrons and inhibition of anodic oxidation were evaluated using V3+/2+ in 5.0 M HCl(aq) as a one-electron redox couple with a potential close to that of hydrogen evolution in acidic media. Failure modes due to cathodic plating of metal, as well as anodic dissolution and chemical dissolution processes, were evaluated for photocathodes made from etched p-InP, platinized p-InP, and p-InP photoelectrodes that had been coated with the various oxide films and then platinized for use in photoelectrochemical hydrogen evolution in acidic aqueous electrolytes. Nb2O5 best met all of the previously specified criteria, in contrast, TiO2 was found to be thermodynamically and kinetically unstable in acid over the potential range relevant for the hydrogen evolution and/or CO2 reduction electrochemical half-reactions. The protocols developed in this work are broadly applicable for determining the effectiveness of other materials and semiconductors as protection layers for photocathodes.
\r\n\r\nThe electrochemical charge transfer rate at mechanically exfoliated graphene electrodes have also been investigated to probe the coupling distance into the electrode by which redox species in solution electronically couple. Scanning electrochemical cell microscopy (SECCM) was used to measure the rates of charge transfer and to reduce the effect of graphene defects on the electrochemical measurements. The rates of charge transfer with Co(en)33+/2+, Ru(NH3)63+/2+, and IrCl62-/3- redox couples were determined on graphene with different thicknesses, suggesting a coupling distance of 0.3 nm. However, real coupling distance may differ due to the convoluting effects of surface defects, errors inherent to SECCM, and uncertainty in the thickness of graphene.
" }, { "name": "Yu, Hao", "degree": "PhD", "year": "2026", "title": "The Total Synthesis of Aleutianamine, (\u2013)-Crotonolide D, and (\u2013)-Crotonine G", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222026-182628481", "creators": [ { "name": { "family": "Yu", "given": "Hao" }, "id": "Yu-Hao", "orcid": "0009-0008-6002-6276", "display_name": "Yu, Hao" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/cn84-6g19", "abstract": "The first chapter describes the total synthesis of aleutianamine, a pyrroloiminoquinone alkaloid that displays potent and selective cytotoxicity towards pancreatic cancer PANC-1 cell line (IC\u2085\u2080 = 25 nM). An initial a-thioketone derivatization approach was thwarted by a failed enolate functionalization. A second-generation approach employing palladium-\r\ncatalyzed Barbier addition enabled the successful construction of the [3.3.1]bicyclononane moiety of the natural product, but unsuccessful downstream functionalization and poor material throughput led to the abandonment of this approach. Along the way, a one-pot Larock indolization/Buchwald\u2013Hartwig amination cascade was developed for the synthesis of tricyclic diaminoindole derivatives. Eventually, the total synthesis was accomplished via a\r\nnovel dearomative arylation of an aminothiophene, which allowed rapid access to the molecular skeleton of aleutianamine including the challenging bridgehead sulfide. Following construction of the core, cerium-mediated oxidative amination and palladium-catalyzed decarboxylative pinacol-type rearrangement enabled chemoselective introduction of the C10 aniline and alkenyl bromide, leading to the total synthesis of aleutianamine.
\r\n\r\nThe second chapter details the total synthesis of crotonolide D and crotonine G. The synthetic approach employs a SmI\u2082 mediated ketyl radical cyclization to form the highly congested quaternary carbon at the center of these complex molecules. Following the furan introduction, the core structure of the natural product is constructed via oxidative olefin cleavage to install the unusual C19 and C20 oxidation. Finally, palladium-catalyzed carbonylation, furan oxidation and acid mediated condensation/epimerization completes the synthesis.
" }, { "name": "Zhang, Grace Chen", "degree": "PhD", "year": "2026", "title": "Investigating the Role of a Specific Chondroitin Sulfate Motif in Neuroinflammation and Regeneration", "advisor": "Hsieh-Wilson, Linda Carol", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112025-190323699", "creators": [ { "name": { "family": "Zhang", "given": "Grace Chen" }, "id": "Zhang-Grace-Chen", "orcid": "0000-0002-2044-9230", "display_name": "Zhang, Grace Chen" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda Carol" }, "id": "Hsieh-Wilson-Linda-Carol", "orcid": "0000-0001-5661-1714", "role": "advisor", "display_name": "Hsieh-Wilson, Linda Carol" } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "orcid": "0000-0001-5868-348X", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gkge-0e55", "abstract": "The extracellular matrix (ECM) provides a supportive framework for neurons and glia in the healthy central nervous system (CNS). However, extensive ECM remodeling occurs after CNS insult or injury, and in neuroinflammation. Upregulation and deposition of growth-inhibitory ECM components results in failures in neuronal generation and resolution of harmful inflammation. Chondroitin sulfate proteoglycans (CSPGs), which consist of chondroitin sulfate (CS) polysaccharide chains attached to a core proteoglycan, have been identified as the predominant inhibitory component of this dysregulated ECM, impeding critical repair processes and contributing to prolonged inflammation. Furthermore, CSPGs exert their inhibitory and immunomodulatory effects through their polysaccharide side chains. These CS chains undergo further modification by the addition of sulfate groups, giving rise to various sulfation patterns, or motifs. Recognition of these motifs by protein ligands and cell-surface receptors enable CSPGs to modulate the activity of downstream signaling pathways and regulate neuronal growth and immune processes. Thus, understanding the structure-function relationships of CS glycosaminoglycans (GAGs) will enable development of strategies to promote neuroregeneration and repair after injury and in neurodegenerative diseases.
\r\n\r\nCurrent strategies to target CSPGs and CS GAGs broadly act on all sulfation patterns. This has limited efforts to decode the biological functions of individual sulfation motifs. Herein, we describe our efforts to comprehensively examine the shifts in the CS sulfation composition profile following spinal cord contusion injury. We develop a novel single-chain variable fragment (scFv) selective for the disulfated CS-E motif, and demonstrate its ability to rescue CSPG-mediated inhibition of neurite outgrowth on primary cortical neurons.
\r\n\r\nFurthermore, we provide the first evidence that the CS-E sulfation motif directly modulates\r\nthe activity of microglia, and that 4-O-sulfated CS exacerbates pro-inflammatory immune cell activation and conversion of T cells to a pathogenic phenotype in the experimental autoimmune encephalomyelitis (EAE) model of neuroinflammation. Together, our results contribute toward a greater understanding of the role of ECM components in disease processes and provide insights into the role of specific CS sulfation motifs in neuroinflammation and regeneration.
" }, { "name": "Zhou, Jie", "degree": "PhD", "year": "2026", "title": "A Tale of Two Strategies: Evolving and Engineering Biology Across Scales", "advisor": "Wang, Kaihang", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142026-193956786", "creators": [ { "name": { "family": "Zhou", "given": "Jie" }, "id": "Zhou-Jie", "orcid": "0009-0008-2076-2279", "display_name": "Zhou, Jie" } ], "advisors": [ { "name": { "family": "Wang", "given": "Kaihang" }, "id": "Wang-Kaihang", "orcid": "0000-0001-7657-8755", "role": "advisor", "display_name": "Wang, Kaihang" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Demirer", "given": "Gozde S." }, "id": "Demirer-G\u00f6zde-S", "orcid": "0000-0002-3007-1489", "role": "member", "display_name": "Demirer, Gozde S." }, { "name": { "family": "Wang", "given": "Kaihang" }, "id": "Wang-Kaihang", "orcid": "0000-0001-7657-8755", "role": "member", "display_name": "Wang, Kaihang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/qrag-gm36", "abstract": "Engineering biology at the scale of pathways and genomes requires two core capabilities: the precision to install defined changes and the capacity to generate diversity across large genetic elements. In this thesis, we developed complementary strategies that together span this spectrum. First, we introduced SCOPE (Selective Conjugation-mediated Optimization and Passaging for Evolution), a conjugation-based evolution platform that enables continuous diversification and passaging of replicons ranging from 10 kb to over 500 kb. Extending this approach, SCOPE established genome-to-genome \u201chopping\u201d by evolving CRISPR associated transposase based insertion systems as integrated units, yielding variants with up to 30-fold increased integration efficiency across cargo sizes ranging from 10 kb to 1 Mb. These results illustrate that entire polygenic systems, including genome-editing machines, can be diversified and optimized in vivo. Second, we developed an optimized prime editing framework for E.coli that achieves editing efficiencies above 95% across diverse genomic loci and edit types. Additional intron-based strategies enabled context-dependent template restoration, and together these layers established robust precision editing across diverse loci. Building on this foundation, we created PEACE (Prime Editing Additive Conjugative Engineering), which couples prime editing and conjugative transfer with site-specific recombination to achieve scarless installation of megabase-scale DNA segments across genera. This provides a continuum of editing capabilities ranging from single-nucleotide manipulations to large-scale genomic integrations.
\r\n\r\nTogether, SCOPE and PEACE address two longstanding bottlenecks in microbial genome engineering: the inability to efficiently diversify large genetic elements, and the lack of scalable tools for precise genomic integration. The results presented here suggest that these need not remain fundamental limitations. As the complexity of engineering targets grows, from single enzymes to entire biosynthetic pathways to multi-gene regulatory networks, the field will increasingly require tools that operate at matching scales. This thesis provides a foundation for that shift, offering approaches that are not merely incremental improvements but qualitatively different in the size and complexity of genetic systems they can access.
" }, { "name": "Barlow, Alexandra Nichole", "degree": "PhD", "year": "2025", "title": "The Biochemical and Structural Basis of Get3d\u2019s Role in Photosynthesis", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312025-215903214", "creators": [ { "name": { "family": "Barlow", "given": "Alexandra Nichole" }, "id": "Barlow-Alexandra-Nichole", "orcid": "0000-0001-6515-2396", "display_name": "Barlow, Alexandra Nichole" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "chair", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/wht9-1974", "abstract": "Tail-anchored (TA) membrane proteins, defined by a single C-terminal transmembrane domain, are inserted into the endoplasmic reticulum (ER) membrane via the guided entry of tail-anchored proteins pathway. The central targeting factor of this pathway is Get3, an ATPase that receives TA clients from upstream chaperones and mediates their delivery to the ER. Here, we identify and characterize a unique Get3 homolog, termed Get3d, distinguished by a C-terminal \u03b1-crystallin domain (\u03b1CD). We show that Get3d is conserved across plants and photosynthetic bacteria and demonstrate that it localizes to the chloroplast in plants. We present the X-ray crystal structure of Get3d, revealing unique features including the \u03b1CD and a client-binding chamber in the closed state. Biochemical analyses confirm that Get3d is an active ATPase capable of binding TA proteins in vitro. To investigate its physiological role, we identified the plant-like Get3d homolog in Synechocystis sp. PCC 6803 and generated deletion and complementation strains. Loss of Get3d impairs cell growth and pigment production, and proteomic analyses reveal widespread dysregulation, including up-regulation of transcriptional regulators and down-regulation of redox-associated proteins\u2014suggesting a role in redox homeostasis. Complementation studies show that ATPase activity is necessary for restoring the expression of key photosynthesis-related proteins, while the \u03b1CD is critical for maintaining Get3d protein stability in vivo. Finally, co-immunoprecipitation coupled to mass spectrometry identifies putative Get3d interaction partners enriched in membrane-associated and photosynthetic proteins. Together, these findings establish Get3d as a biochemically distinct and functionally essential member of the Get3 family, with a potential role in redox regulation and photosynthetic homeostasis in diverse photosynthetic organisms." }, { "name": "Bi, Xiaotian", "degree": "PhD", "year": "2025", "title": "Functional Stimulated Raman Imaging for Quantitative Cell Biology with Small Bioorthogonal Tags", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282025-224557158", "creators": [ { "name": { "family": "Bi", "given": "Xiaotian" }, "id": "Bi-Xiaotian", "orcid": "0000-0003-4449-7488", "display_name": "Bi, Xiaotian" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "orcid": "0000-0001-5868-348X", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w2hc-fa62", "abstract": "The development of imaging techniques, particularly optical imaging, has significantly advanced the field of cell biology. Compared to conventional fluorescence imaging, vibrational imaging leverages the intrinsic chemical bond information of molecules, providing multidimensional insights into molecular structures and local environments. So far, stimulated Raman scattering (SRS) microscopy has emerged as a powerful tool for quantitative measurements in biological research. It overcomes several fundamental limitations associated with fluorescence-based techniques and offers high spatial and temporal resolution along with excellent compatibility for live-cell imaging.
\r\n\r\nIn this thesis, I mainly focus on utilizing small bioorthogonal vibrational tags for quantitative investigations in cell biology. These tags, such as alkyne and carbon-deuterium (C-D) bonds, are absent in endogenous biomolecules and smaller than 1 nm in size, enabling minimally perturbative labeling with high molecular specificity. Another key advantage is that the SRS signal scales linearly with bond concentrations, allowing for robust and quantitative analysis. Moreover, because their vibrational modes distinctly reside in the cellular silent region (1800-2700 cm\u207b\u00b9), they provide a high signal-to-background ratio, making them particularly well-suited for quantitative applications in complicated cellular environments.
\r\n\r\nIn Chapter 2, we explored the potential of alkyne-tagged probes to serve as environment-sensitive vibrational sensors, extending their utility beyond imaging markers. We developed a generalizable sensing platform based on hydrogen-deuterium exchange (HDX) at terminal alkynes. This subtle isotopic substitution induces a detectable shift in the alkyne vibrational frequency, allowing for real-time monitoring of exchange kinetics. These kinetics, in turn, provide insight into the chemical structures and local environments. We conducted a comprehensive study of the HDX process through both theoretical analysis and experimental validation. This platform was further applied to detect structural changes in DNA and to indicate pH within live cells, demonstrating the broader applicability of alkyne-tagged Raman probes for local environmental sensing in complex biological systems.
\r\n \r\nIn Chapter 3, we utilized deuterated glutamine to label and study polyglutamine (polyQ) aggregates, a pathological hallmark of Huntington\u2019s disease, in neurons. Traditional imaging approaches typically rely on tagging with bulky fluorescent proteins such as EGFP, which can perturb aggregation behavior with their non-negligible sizes. Through deuterium labeling, we achieved EGFP-free imaging of polyQ aggregates, allowing for a more native characterization with live-cell compatibility. This strategy facilitated quantitative analysis of the aggregate composition and growth dynamics of polyQ aggregates in live neurons. Our results revealed significant variations in polyQ aggregates depending on cell types, subcellular localizations, aggregate sizes, and protein constructs. Notably, we identified a previously unknown type of nuclear aggregates, shedding light on the heterogeneity of polyQ pathology.
\r\n\r\nIn Chapter 4, we applied deuterium-labeled small molecules to study neuronal metabolism and its dynamic interactions with neuronal activity. As neuronal firing requires high and tightly regulated metabolic input, it is critical to understand the coupling between neuronal activity and metabolism for elucidating brain function. Using deuterated glucose and fatty acids, we were able to track their downstream metabolites for metabolism studies with high spatial and temporal resolution via SRS microscopy. In parallel, we employed optogenetic stimulation through Channelrhodopsin to achieve precise control of neuronal activity and also used neurotransmitters for longer-term modulation. By correlating different states of neuronal activation with metabolic flux changes, we gained valuable insights into how neuronal activity dynamically regulated glucose and lipid metabolism, advancing our understanding of neuroenergetic mechanisms in live neurons.
\r\n\r\nThrough these studies, I demonstrate that the integration between small bioorthogonal vibrational tags and the advanced vibrational imaging technique, SRS microscopy, can provide powerful, minimally invasive, and highly quantitative tools for tackling fundamental questions in cell biology with high spatial and temporal resolution.
" }, { "name": "Boyd, Emily A.", "degree": "PhD", "year": "2025", "title": "Reductive Samarium Catalysis Enabled By A Thermochemical Roadmap", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222025-205440915", "creators": [ { "name": { "family": "Boyd", "given": "Emily A." }, "id": "Boyd-Emily-A", "orcid": "0000-0003-0150-5396", "display_name": "Boyd, Emily A." } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7f8x-qg41", "abstract": "Samarium diiodide is a versatile single-electron reductant. Its reactivity is modulated by recruitment of a wide range of additives to its large coordination sphere. Binding of strong Lewis bases produces more potent Sm(II) reductants, while polar protic donors promote net proton-coupled electron transfer to a variety of unsaturated substrates including intermediates of molybdenum-catalyzed nitrogen reduction. However, samarium(II) reagents are used (super)stoichiometrically in all but a few select cases because mild, tunable methods for selective reduction of oxidized samarium(III) products back to the active samarium(III) state were unavailable at the outset of the following studies. Chapter 1 frames the challenge of catalytic samarium turnover in the context of nitrogen fixation. Proton-coupled electron transfer and inner-sphere electron transfer are introduced as two potential catalytic roles for samarium(II), and a strategy for proton-coupled reduction of problematic samarium(III)-alkoxide intermediates to achieve turnover is outlined. Chapter 2 describes a well-defined model system used to construct extended quantitative thermochemical cycles mapping proton transfer, electron transfer, and ligand association at samarium. The samarium(II) complex binds a secondary amide to generate a remarkably potent net hydrogen atom donor. In Chapter 2, this driving force is leveraged in iron-catalyzed nitrogen reduction; the strongly reducing, weakly acidic nature of the samarium reagent leads to selective generation of hydrazine over ammonia (99:1). In Chapter 3, the benchmarked samarium(III)-alkoxide protonolysis thermodynamics inform selection of Br\u00f8nsted acids that can be coupled with a mild reductant (zinc powder or an applied electrochemical potential) to achieve catalytic samarium turnover in reductive coupling of ketones and acrylates to form \u03b3-lactones. Photodriven methods for this samarium-catalyzed transformation are reported in Chapter 5. Finally, in Chapter 6, the hypothesis that samarium(II) might serve as an inner-sphere reductant in nitrogen reduction with transition metal catalysts guides design of conditions for tandem samarium/molybdenum catalysis in electrocatalytic nitrogen reduction to ammonia with the lowest driving force and highest Faradaic efficiency (82%) reported to date for a nonaqueous system at atmospheric pressure." }, { "name": "Bruch, Dorian Wayne", "degree": "PhD", "year": "2025", "title": "Theoretical Modeling of Interactions Between Electrolytes and Surfaces", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:08282024-022514845", "creators": [ { "name": { "family": "Bruch", "given": "Dorian Wayne" }, "id": "Bruch-Dorian-Wayne", "orcid": "0000-0002-3983-4841", "display_name": "Bruch, Dorian Wayne" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/eey8-et93", "abstract": "Electrolytes are ubiquitous in science and engineering and are of active interest, owing to their applications biology, energy storage, colloidal suspensions, and even climate. Near a surface, electrolyte solutions exhibit a plethora of rich thermodynamic and structural phenomena, owing to the interplay of long-ranged electrostatics and nonelectrostatic interactions between ionic species, solvent, and the surface. In this thesis, we present a pedagogical formulation for the thermodynamics of electrolyte solutions near charged surfaces, followed by an examination of interactions and structure of different types of electrolytes near surfaces. Specifically, we investigate the difference between constant surface charge and constant surface potential boundaries in electrolyte solutions, the capacitance applications, double-layer structure, and screening behavior of a zwitterionic polymers, as well as the effect of image charge on structure, capacitance, and forces in simple electrolytes near metal, dielectric, and dielectrically-saturated metal surfaces. We conclude with a Gaussian-fluctuation model for ions with soft-core excluded volume interactions." }, { "name": "Cho, Hyungdo", "degree": "PhD", "year": "2025", "title": "Development of Photoinduced Copper-Catalyzed Amination of Alkyl Electrophiles: Synthesis and Mechanism", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07052024-225058837", "creators": [ { "name": { "family": "Cho", "given": "Hyungdo" }, "id": "Cho-Hyungdo", "orcid": "0000-0001-6109-5742", "display_name": "Cho, Hyungdo" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1008-m865", "abstract": "The formation of carbon-nitrogen (C\u2013N) bonds is crucial in organic chemistry due to the importance of nitrogen-containing functional groups. While traditional nucleophilic substitution reactions, such as SN1, SN2, and SNAr, are limited in scope and efficiency, transition metal-catalyzed versions of these reactions, particularly involving copper, offer a more versatile approach by activating electrophiles and facilitating C\u2013N bond formation via oxidative addition and reductive elimination.
\r\n\r\nCopper-catalyzed C\u2013N couplings have been extensively developed but are primarily effective for aryl electrophiles rather than alkyl electrophiles due to the need for thermal activation, which often leads to undesired side reactions in alkyl electrophiles. The development of photoinduced copper-catalyzed reactions by Fu and Peters addresses these challenges, enabling the activation of alkyl electrophiles without thermal activation.
\r\n\r\nOver the past decade, the Fu group has focused on expanding the scope of this novel approach. The research detailed in this thesis focuses on developing photoinduced copper-catalyzed C\u2013N coupling reactions for more challenging substrates, such as sterically hindered alkyl electrophiles and amines.
\r\n\r\nChapter 2 discusses the photoinduced, enantio-convergent coupling of racemic tertiary alkyl electrophiles with aniline nucleophiles, catalyzed by bisphosphine-copper complexes. The mechanism of this reaction was elucidated using various tools, identifying key copper-based intermediates, including a chiral copper(II)\u2013anilido complex that couples with a tertiary organic radical to form the C\u2013N bond with good enantioselectivity.
\r\n\r\nChapter 3 presents the photoinduced, copper-catalyzed coupling of secondary alkyl amines with secondary or tertiary alkyl bromides to synthesize N-tertiary alkyl amines under mild conditions. This novel reaction provides unique stereoselectivity and compatibility with strained electrophiles, contributing valuable methodologies to the synthesis of bioisosteres and other complex amine structures.
\r\n\r\nOverall, this work broadens the understanding and application of photoinduced copper-catalyzed reactions, offering new pathways for the synthesis of sterically hindered amines.
" }, { "name": "Col\u00f3n, Katsuya Lex", "degree": "PhD", "year": "2025", "title": "In Situ Signal Amplification for Spatial Transcriptomics Using Programmable DNA Assemblies", "advisor": "Cai, Long", "url": "https://resolver.caltech.edu/CaltechThesis:03312025-203601435", "creators": [ { "name": { "family": "Col\u00f3n", "given": "Katsuya Lex" }, "id": "Col\u00f3n-Katsuya-Lex", "orcid": "0000-0002-7347-6128", "display_name": "Col\u00f3n, Katsuya Lex" } ], "advisors": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "advisor", "display_name": "Cai, Long" } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pp5f-pk64", "abstract": "Sequential Fluorescent In Situ Hybridization (seqFISH) has been an invaluable tool in imaging-based spatial transcriptomics, aiding researchers in elucidating spatially-resolved, gene expression patterns in intact tissues and cell culture models. However, methods that rely on smFISH, such as seqFISH, suffer from poor signal-to-noise ratio in certain tissue types or target RNA, require many fluorescently labeled RNA targeting probes which prohibits imaging of small RNA species, and exhibit poor sample throughput due to the need of high magnification objective or long exposure times. Herein, we develop solutions to these limitations by developing and utilizing a robust signal amplification strategy. While various amplification technologies exist, their limitations often hinder broad applicability. Moreover, we desire an amplification platform that is amenable to the denaturing wash conditions used in seqFISH. We will begin Chapter I by discussing the background, technical challenges, and utility of various in situ signal amplification technologies. Chapter II details the exploration and technical limitations of rolling circle amplification (RCA) and branched DNA (bDNA) assembly utilizing ssDNA padlock amplifier strands. Chapter III discusses the design and development of a novel amplification strategy called Signal amPlicAtion by Recursive Crosslinking (SPARC), which builds upon the knowledge gained from Chapter II. We highlight SPARC as a unique photochemical signal amplification method that iteratively deposits amplifier strands near the primary probe target for linear signal amplification. Then, the deposited amplifier strands act as a scaffold for branched DNA assembly, leading to an exponential signal amplification. Through each deposition and assembly step, amplifier strands are photo-crosslinked to the extracellular matrix, forming highly stable DNA nanostructures that can withstand harsh denaturing wash conditions. We demonstrate the utility of SPARC in amplifying signal of both single-molecule transcripts and proteins." }, { "name": "Flesch, Kaylin Nicole", "degree": "PhD", "year": "2025", "title": "Asymmetric Transformations from Palladium Enolates and Progress Toward the Total Synthesis of Hypermoin A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122025-153409748", "creators": [ { "name": { "family": "Flesch", "given": "Kaylin Nicole" }, "id": "Flesch-Kaylin-Nicole", "orcid": "0000-0002-8582-2614", "display_name": "Flesch, Kaylin Nicole" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jfcn-4r24", "abstract": "Research in the Stoltz group is centered around developing new methodologies for the asymmetric formation of stereocenters and the application of these technologies in complex natural product total synthesis. Herein we describe the development of new enantioselective transformations from Pd enolate intermediates and efforts toward the total synthesis of hypermoin A. Chapter 1 reports the development of an asymmetric intramolecular decarboxylative [4+2] cycloaddition from a catalytically generated chiral Pd enolate, forging four contiguous stereocenters in a single transformation. Mechanistic studies including quantum mechanics calculations, Eyring analysis, and KIE studies offer insight into the reaction mechanism. Appendix 2 discloses efforts toward the development of an asymmetric intermolecular decarboxylative double Michael addition. Chapter 2 describes an enantioselective cyclization of Pd enolates and isocyanates to form spirocyclic \u03b3-lactams. This reaction proceeds under mild reaction conditions and utilizes a novel Meldrum\u2019s acid derivative to achieve catalyst turnover, delivering enantioenriched products in up to 97% yield and 96% ee. Chapter 3 outlines the ongoing progress toward the total synthesis of hypermoin A. A [4+2] cycloaddition and ring expansion strategy has been developed in a model system to form the key [3.2.2] bicycle and current efforts are dedicated to the application of this sequence in a more complex setting." }, { "name": "Glisman, Alec Gregory", "degree": "PhD", "year": "2025", "title": "Part I: Multi-Valent Ion Effects on Polyelectrolyte Structure and Thermodynamics & Part II: Hydrodynamic Self-Propulsion", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-204040190", "creators": [ { "name": { "family": "Glisman", "given": "Alec Gregory" }, "id": "Glisman-Alec-Gregory", "orcid": "0000-0001-9677-1958", "display_name": "Glisman, Alec Gregory" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemeng" ], "doi": "10.7907/gf6m-gs53", "abstract": "Part I: Polyelectrolytes are a class of charged polymers that have found widespread utility in water treatment, drug delivery, and scale inhibition, among other applications. For many of these applications, it is crucial to control the phase stability of the polyelectrolyte solution. The long-ranged nature of the electrostatic interactions in polyelectrolyte solutions and the polyelectrolyte's connectivity lead to a rich phase behavior that can be challenging to study, especially in the presence of other ions or surfaces. In scale inhibition applications, polyelectrolytes such as poly(acrylic acid) (PAA) are used to prevent the dissolution of sparingly soluble salts, such as calcium carbonate, in water. While the significant influence of small ions on polyelectrolyte solution phase behavior is recognized, the precise molecular mechanisms driving the resulting phase stability remain largely elusive.
\r\n\r\nPolyelectrolyte theory suggests that a polyelectrolyte's behavior and adsorption properties in solution are strongly tied to the polymer chain conformation and charge distribution, which in turn is influenced by solution ionic strength and ionic valency. Consequently, we expect the polyelectrolyte performance to be highly dependent on the solution conditions and the molecular features of the polyelectrolyte. Previous computational studies have studied general polyelectrolytes in solution with coarse-grained and implicit solvent models and provided insights into the chain conformational transitions. However, they disagree on the mechanisms underlying aqueous polyelectrolytes salting out of suspension and are unable to yield chemically specific insights. We seek to better understand the antiscalant mechanisms of polyelectrolytes using all-atom molecular dynamics to capture solvation and polymer chemistry effects on the mechanisms of polyelectrolytes preventing scale nucleation and slowing growth.
\r\n\r\nThe current work investigates the structure and thermodynamics of polyelectrolytes in bulk solution and at crystalline interfaces with added multi-valent ions. The presence of multi-valent ions, such as Ca2+, can significantly influence polyelectrolyte conformation via ion bridging non-neighboring charged monomers as well as screening the electrostatic interactions. We employ all-atom molecular dynamics simulations to investigate the binding modes of Ca2+ onto a PAA chain, Ca2+\u2013PAA complex aqueous stability, and PAA adsorption onto a crystalline CaCO3 surface. In each of these cases, we find that the balance between ion bridging, electrostatic screening, and water-mediated interactions plays a crucial role in determining the polyelectrolyte's behavior in solution and at an interface.
\r\n\r\n\r\nPart II: Active bodies undergo self-propulsive motion in a fluid medium and span a broad range of length and time scales. Many active systems spontaneously self-organize into visually striking structures: fish schooling, birds flocking, and bacterial colonies growing. Current models of this emergent behavior in the inertial regime are mainly phenomenological and lack consideration of the fluid-mediated interactions between bodies.
\r\n\r\nTo address this limitation, we seek to advance physics-based models of swimmers by explicitly incorporating the fluid mechanical interactions between bodies. We aim to discern the fluid medium's role in group dynamics and determine whether it can reproduce the observed emergent phenomenon without resorting to phenomenologically based interaction rules. To that end, we focus specifically on swimming in high Reynolds number flows, where inertial forces dominate, and draw comparisons to the well-studied low Reynolds number (Stokes) regime. We begin by deriving the equations of motion for a collection of unconstrained spherical particles in potential flow and extend the model to include viscous dissipation and rigid body motion constraints for many bodies with arbitrary kinematics.
\r\n\r\nWe then consider the case of a single swimmer consisting of three linked spheres in potential flow. Through this, we find self-propulsion without needing external forces or momentum transfer via vortex shedding. We compare the inertial swimmer to an identical swimmer in the Stokes regime\u2014where fluid inertia is neglected\u2014and find that the structure of the equations of motion is identical in both flow regimes. Notably, the Stokes hydrodynamics are longer-ranged at leading order, leading to a more significant net displacement of the swimmer after one period of articulation. Finally, our study provides analytical insight into the swimming of a deformable body through an expansion of the non-linear spatial dependence of the hydrodynamic interactions.
" }, { "name": "Gonzalvo i Ulla, Marta", "degree": "PhD", "year": "2025", "title": "Computational Methods for Nucleic Acid Structure Prediction and G Protein-Coupled Receptor Mechanism Investigation", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152025-170540802", "creators": [ { "name": { "family": "Gonzalvo i Ulla", "given": "Marta" }, "id": "Gonzalvo-Ulla-Marta", "orcid": "0009-0005-4235-4282", "display_name": "Gonzalvo i Ulla, Marta" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bxdy-5x58", "abstract": "Molecular dynamics (MD) simulation is a powerful tool to characterize molecular structure. In this thesis, we use MD to solve three problems in biological chemistry: the prediction of secondary nucleic acid structure, the prediction of the structure of a siRNA-based tool, and the understanding of the activation mechanism of the sweet taste receptor.
\r\n\r\nFirst, we use MD to computationally parameterize nucleic acid secondary structure models. Current models are parameterized using experimental data that was limited and time consuming to generate. In this work, we present a workflow to select an ensemble of base pairing reactions using machine learning, perform MD simulations to obtain their free energy and enthalpy profiles, and perform nonlinear regression on the energies and enthalpies to yield thermodynamic nearest neighbor parameters. This computational framework parameterizes secondary structure models with comparable accuracy to experimental data, and can be used to expand the current models to a range of materials and experimental conditions beyond the specific experimental conditions the parameters were originally generated in.
\r\n\r\nNext, we predict the structure of a RNA therapeutic tool, conditionally activated small interfering RNAs (Cond-siRNAs). We evaluate how two structural modifications to the two double helix topology affect the ability of the construct to perform its function in the RNAi pathway, finding that a short sensor overhang and a carbon chain linker between the two duplexes reduce undesired interactions in the structure. We also characterize the structure for a new topology with a single linker between the duplexes, and show how the position of terminal modifiers causes structural distortions and can disrupt its function. These insights will guide the design of Cond-siRNAs and other RNA tools with similar non-canonical modifications.
\r\n\r\nLastly, we investigate the mechanism of activation of the TAS1R2/TAS1R3 sweet taste receptor, coupled to the G protein gustducin. We use metadynamics simulations to estimate the reduction of the free energy of opening the G alpha subunit in the presence of a positive allosteric modulator and steviol glycosides of varying sweetness. We also uncover insights into how the modulator induces the activation of the G alpha, leading to the partial release of GDP; and how the steviol glycosides RebM, RebD and IsoRebM of high sweetness induce an interdomain twist in the Venus Fly Trap domains. These results further our understanding of the activation mechanism of the class C sweet taste receptor and can be used for the development of new sweeteners.
" }, { "name": "He, Tianyi", "degree": "PhD", "year": "2025", "title": "Synthesis and Spectroscopy of Open-Shell Complexes Bearing Unusual M-E (E = N, C) Bonding Motifs and Synthesis of Novel Weakly-Coordinating Anions with Applications in Coordination Chemistry and Electrochemistry", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292025-183641323", "creators": [ { "name": { "family": "He", "given": "Tianyi" }, "id": "He-Tianyi", "orcid": "0000-0002-8191-188X", "display_name": "He, Tianyi" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/27c4-ey05", "abstract": "This dissertation focuses on a diverse range of topics centered around inorganic synthesis, ranging from spectroscopic studies of rare bonding motifs (Chapter 3 and Chapter 4) and applications of novel weakly-coordinating anions in applications in coordination chemistry and electrochemistry (Chapter 1 and Chapter 2). While the projects described herein are distinct in the nature of their execution, the utility and applications of synthetic inorganic chemistry are highlighted in all of the projects.\r\nChapter 1 describes the design principles and the synthesis a novel weakly-coordinating anion based on alkyl or aryl substituted silicates bearing fluorinated pinacolate ligands. A wide range of anions bearing distinct R groups were prepared, enabling facile tuning of anion sterics and solubility. A range of cations invoked in chemical reactivity studies supported by these novel anions was prepared, highlighting the utility of these novel anions in both coordination and catalysis. Cations relevant to electrochemical studies were also accessed, wherein the exceptionally wide stability window for the methyl-substituted variant was demonstrated. Reversible magnesium deposition and stripping supported by these anions were also shown, demonstrating the utility of these novel anions in next-generation battery chemistry applications.\r\nChapter 2 describes efforts towards developing reproducible and stable magnesium deposition and stripping chemistry supported by a novel silicon-based weakly-coordinating anion. Aspects that impact reproducible and stable magnesium electrochemistry described in prior literature were studied in detail. Emphasis was placed on probing the prevalent hypothesis in magnesium electrolyte literature that magnesium alkyl, aryl, and amido additives improve electrochemical performance by acting as water or impurity scavengers. A range of magnesium additives were tested, wherein the identity of the additives was shown to dictate magnesium deposition and stripping behavior. An unconventional magnesium hydrocarbyl species was identified as the active species responsible for improved Mg deposition/stripping performance, highlighting the utility of synthetic inorganic chemistry in elucidating fundamental electrochemistry.\r\nChapter 3 describes the synthesis and the spectroscopy of an unusual molybdenum para-terphenyl diphosphine complex bearing a terminal nitride and a parent amide motif. Detailed continuous wave- and pulse-electron paramagnetic resonance techniques were employed the interrogate the electronic structure of this unusual open-shell motif, revealing significant radical character on the amide motif. On the other hand, the terminal nitride motif showed negligible spin density. With further insight obtained from density functional theory calculations, the high spin density on the terminal amide motif was attributed to significant orbital overlap between the amide nitrogen py orbital with the Mo dxy orbital.\r\nChapter 4 describes the synthetic, spectroscopic, and computational studies of a pentametallic molybdenum-iron-sulfur cluster of MoS3Fe3CMo composition with \u03bc4-carbide and \u03bc2-CO motifs that resembles the lo-CO form of nitrogenase. The cluster was accessed via carbide transfer from a Mo carbide complex supported by a para-terphenyl diphosphine ligand. Different isotopologues of this cluster were accessed by selectively labelling the molybdenum para-terphenyl diphosphine precursor. This cluster displays an S = \u00bd ground spin state amenable for pulse electron paramagnetic resonance spectroscopy. Detailed spectroscopic studies reveal a significantly larger carbide hyperfine interaction than any observed for various states of nitrogenase studied thus far, thereby providing benchmarking information for metal-carbon interactions studied by electron paramagnetic resonance methods.\r\nAppendix A describes the synthesis and preliminary reactivity studies of a heterometallic molybdenum-iron-nickel cubane supported by a bulky bisphenoxide ligand with a central anthracene linker, relevant to the active site of the nickel-iron carbon monoxide dehydrogenase. Preliminary electron paramagnetic resonance studies on this cubane were suggestive of an S = 2 ground state, wherein incorporation of a formal closed-shell nickel site into a trimetallic cluster significantly perturbs the electronic structure.\r\nAppendix B describes efforts towards accessing molybdenum para-terphenyl disphosphine carbyne complexes with no bound carbon monoxide ligands. Preliminary studies on the molybdenum carbyne complexes showed that molybdenum complexes with a terminal carbide and a terminal chloride can be accessed.\r\nAppendix C describes the synthesis and preliminary electrochemical studies of novel dianonic silicates supported by fluorinated pinacolate ligands, wherein magnesium deposition and stripping supported by a novel dianion was demonstrated." }, { "name": "Hicks, Elliot Frederick", "degree": "PhD", "year": "2025", "title": "Stereoselective Synthesis of \u03b1- and \u03b2-Functionalized Carbonyl Derivatives: Allylic Alkylation of Dialkyl Malonates, Total Synthesis of Hunterine A, and Progress Toward the Synthesis of Kuroshine A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102025-162952847", "creators": [ { "name": { "family": "Hicks", "given": "Elliot Frederick" }, "id": "Hicks-Elliot-Frederick", "orcid": "0009-0004-8965-0460", "display_name": "Hicks, Elliot Frederick" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fs03-xy64", "abstract": "Research in the Stoltz group generally focuses on the synthesis of complex molecules enabled by the discovery and application of new synthetic methodologies. The majority of the research described in this thesis encompasses variations on this unifying central theme.
\r\n \r\nChapter 1 focuses on the development of new asymmetric methodology for the synthesis of stereogenic all-carbon quaternary centers through the application of iridium catalysis. A key advance was the use of malonate nucleophiles and bis-alkyl substituted electrophiles, two inputs commonly employed in allylic alkylation chemistry that had yet to be utilized for the synthesis of quaternary carbon centers.
\r\n \r\nChapter 2 describes the development and execution of a synthetic strategy for the asymmetric construction of a rearranged monoterpene indole alkaloid, hunterine A. Key to the assembly of this molecule were an enantioselective desymmetrization, aza-Cope/Mannich rearrangement, azide-alkene dipolar cycloaddition, and regioselective aziridine opening.
\r\n \r\nChapter 3 details an investigation born out of an observation of a regioselective aziridine opening during the course of the synthesis of hunterine A. This research focuses on the synthesis of sterically unbiased fused bicyclic N-aryl aziridines and their reactivity in a variety of ring opening reactions.
\r\n\r\nChapter 4 and Appendix 7 describe ongoing efforts toward the synthesis of Kuroshine A and other highly oxidized zoanthamine alkaloids. The synthetic strategies described focus on evaluating formation of the ABC ring system of the molecule via a masked ortho-benzoquinone cycloaddition.
" }, { "name": "Johansen, Christian Marinelli", "degree": "PhD", "year": "2025", "title": "Catalytic Proton-Coupled Reductions of Dinitrogen and Cyanide", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282025-142549821", "creators": [ { "name": { "family": "Johansen", "given": "Christian Marinelli" }, "id": "Johansen-Christian-Marinelli", "orcid": "0000-0003-0066-4424", "display_name": "Johansen, Christian Marinelli" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jrh7-2a15", "abstract": "This thesis, directly and indirectly, focuses on mechanisms and strategies for the 6H\u207a/6e\u207b reduction of N\u2082 to NH\u2083 (nitrogen reduction; N\u2082R) using well-defined molecular catalysts. In nature, nitrogenases reduce N\u2082 to NH\u2083, but nitrogenases can also reduce cyanide to CH\u2084 and NH\u2083, making CN\u207b and N\u2082 reduction interesting to compare. We describe the highly selective catalytic reduction of CN\u207b to NH\u2083 and CH\u2084 by a mononuclear Fe-catalyst related to Fe-based N\u2082R systems. Mechanistic studies suggest several intermediates, including iron isocyanides (FeCNH), aminocarbynes (FeCNH\u2082), and aminocarbenes (FeC(H)NH\u2082\u207a), allowing a comparison to N\u2082R. We then show the 2H\u207a/2e\u207b equilibration of iron cyanide to the iron aminocarbyne complexes of these early intermediates of catalysis. Such reversible triple bond activations are rare. We show that key to this transformation is the H-bond facilitated multisite proton-coupled electron transfer (MS-PCET).
\r\n\r\nNext, seeking alternative ways to drive N\u2082R, a photodriven approach is explored. The Hantzsch ester (HEH\u2082), a dihydropyridine, is utilized as a 2H\u207a/2e\u207b photoreductant, and when partnered with a suitable catalyst (Mo) and an organic buffer (collidine/collidinium; Col/ColH\u207a) under blue light irradiation allows for photodriven N\u2082R. Catalysis is enhanced by addition of a photoredox catalyst (Ir). This photodriven N\u2082R is thermodynamically comparable to the industrial hydrogenation of N\u2082, but light is used to drive the reaction. Mechanistic studies of the Ir-free conditions show that Col-buffer is essential for transferring H\u207a/e\u207b from HEH\u2082 to N\u2082. An H-bonded pre-association can form between [ColH]\u207a and HEH\u2082, allowing for rapid oxidative quenching of the excited HEH\u2082. Subsequently, the base deprotonates HEH\u2082\u2022\u207a, circumventing back electron transfer. In net ColH\u2022 and HEH\u2022, two potent H-atom donors are generated. This reagent combination is competent for the photoreduction of organic substrates as well. Lessons from this mechanistic study drove the development of photodriven methods for SmIII-to-SmII reduction, an appealing prospect given SmI\u2082 being a potent and selective reductant, including for N\u2082R. HEH\u2082 can serve either as a direct photoreductant or as the reductive quencher for an Ir photoredox catalyst. Both methods for SmI\u2082 generation translate to proof-of-concept photodriven, Sm-catalyzed reductive cross-coupling reactions.
" }, { "name": "Kazmierczak, Nathanael Parker", "degree": "PhD", "year": "2025", "title": "Illuminating Molecular Spin Relaxation Mechanisms through Ligand Field Theory and Physical Inorganic Spectroscopy", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152025-215940051", "creators": [ { "name": { "family": "Kazmierczak", "given": "Nathanael Parker" }, "id": "Kazmierczak-Nathanael-Parker", "orcid": "0000-0002-7822-6769", "display_name": "Kazmierczak, Nathanael Parker" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wysm-z777", "abstract": "Electron spin relaxation is a fundamental process in paramagnetic molecules, and successful development of molecular quantum bits (qubits) for quantum information science hinges on suppressing the rate of spin relaxation. While the relaxation process has been studied since the early 20th century, no consensus has been reached regarding the physical relaxation mechanism in S = 1/2 transition metal molecules. Practical guidelines for designing molecules with slow spin relaxation have likewise remained obscure. This thesis describes the use of ligand field theory and physical inorganic spectroscopy techniques to shed new light on molecular spin relaxation mechanisms, connecting relaxation rates to chemical bonding and transition metal electronic structure. Part 1 (Chapters 2-4) details the use of electron paramagnetic resonance (EPR), magnetic circular dichroism (MCD), and resonance Raman (rR) to interrogate the origins of spin relaxation. Experimental spectroscopic results are analyzed within the context of a model based on group theory, yielding a paradigm referred to as ligand field spin dynamics. Part 2 (Chapters 5-7) describes the development of a new experimental observable, T1 anisotropy, as a novel approach for distinguishing between competing theoretical spin relaxation models. Part 3 (Chapters 8-10) shows how the insights of ligand field spin dynamics and T1 anisotropy have been leveraged to rationally design molecules with slow spin relaxation and other desirable spin dynamics properties. This thesis establishes a framework for controlling the physical process of spin relaxation through distinctly chemical molecular design principles." }, { "name": "Koo, Jin Mo", "degree": "PhD", "year": "2025", "title": "Probing the Biological Interactions of a Therapeutic Small Peptide at the Tissue, Cellular, and Molecular Levels for Treating Retinal Diseases", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292025-043938908", "creators": [ { "name": { "family": "Koo", "given": "Jin Mo" }, "id": "Koo-Jin-Mo", "orcid": "0009-0003-8088-8790", "display_name": "Koo, Jin Mo" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/kye5-xz39", "abstract": "Age-related macular degeneration (AMD) and diabetic retinopathy (DR) are the leading causes of blindness in developed countries, affecting the lives of millions and lowering their quality of life due to limited eyesight. Although these retinal diseases afflict a large portion of the senior population, the current standard of care, primarily antibody injection treatments, merely treats symptoms and fails to address the root causes of diseases.
\r\n\r\nA therapeutic hexapeptide, risuteganib (RSG), designed by Allegro Ophthalmics, LLC., has shown efficacy in treating both angiogenic and inflammatory retinopathies such as wet- and dry-AMD and diabetic macular edema (DME), a progressive form of DR. In the past, many studies sought to identify integrins that demonstrated specific binding affinities to RSG, based on the structural similarity of RSG to the well-known RGD motif. In contrast, Caltech decided to pursue unbiased research directions to unveil the mechanism of action (MOA) of RSG. Following studies from Caltech, UC Irvine, Johns Hopkins University, and Duke University revealed unanticipated features of RSG, suggesting that it has both anti-angiogenic and anti-inflammatory effects and that it can rescue compromised mitochondrial functions in cells under chemically induced oxidative stress. In this thesis, we conducted a series of investigations, progressing from the tissue level to the cellular level and then to the molecular level, to test a hypothesis that may unify these observations.
\r\n\r\nIn Chapter 2, we developed a peptide-directed fluorescent staining method to identify the binding location of RSG-dye conjugate using aged BALB/c to recapitulate features of age-related retinal diseases. We identified crucial parameters that visualized replicable, RSG-specific labeling at the aged RPE layer. Findings from Chapter 2 and past studies laid the groundwork for the multi-layered investigations on the MOA of RSG in subsequent chapters, hinting at the cell type of interest, the need for appropriate stress to tissue or cell, and the importance of limiting RSG probes below clinical dosage. In collaboration with the Kenney lab at UC Irvine, we tested the protective effects of RSG in differentiated ARPE-19 cell model in response to chemically activated hypoxia-inducible factor 1 (HIF-1) signaling pathway (Chapter 3). Sub-clinical dosage of RSG (30 \u00b5M) demonstrated protective effects against chemically elevated HIF-1\u03b1 leading to cell death and compromised mitochondrial membrane integrity. Further, RSG-dye conjugate localized in the mitochondria of differentiated ARPE-19 cells, where partial co-localization with mitochondrial protein, pyruvate dehydrogenase E1 \u03b1 subunit (PDHA1), was observed. In Chapter 4, we developed a luminescence-based in vitro assay to quantify the effect of RSG on the activity of a mitochondrial kinase, pyruvate dehydrogenase kinase 1 (PDHK1). PDHK1 interacts with pyruvate dehydrogenase complex (PDC) which contains PDHA1. PDHK/PDC interaction governs the pyruvate decarboxylation process, thereby serving as a dynamic metabolism switch. Upregulation of PDHK1 decreases PDC activity, which subsequently increases glycolytic flux as an adaptive response against hypoxia, temporarily alleviating oxygen deficiency at the cost of total ATP production per mol glucose. When such response is prolonged in the RPE cells, energy deficiency and compromised homeostasis lead to cell death of not only RPE cells but other crucial retinal cells including the photoreceptor cells. Here, tested RSG concentrations (3.125, 6.25, and 12.5 \u00b5M) did not demonstrate significant inhibition of PDHK1 activity; nevertheless, the devised in vitro assay laid the foundation for a reliable, quantitative assessment of RSG or other inhibitors\u2019 effects on the activity of PDHK1 and its isoforms. Chapter 5 summarized the findings in the previous chapters and suggested future studies that might aid in the continued search for the mechanism of action of RSG.
" }, { "name": "Lee, Brian Chansol", "degree": "PhD", "year": "2025", "title": "Investigation and Control of the Electrode/Electrolyte Interface in Electrochemical Systems", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272025-184257192", "creators": [ { "name": { "family": "Lee", "given": "Brian Chansol" }, "id": "Lee-Brian-Chansol", "orcid": "0000-0002-0898-0838", "display_name": "Lee, Brian Chansol" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "member", "display_name": "Faber, Katherine T." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fz2d-pe37", "abstract": "In electrochemical reactions, the electrode/electrolyte interface is of vital importance, as no reactivity occurs in the bulk electrode or the electrolyte. Often, the interface can be the difference between a successful reaction and a failure. In this thesis, we present three works wherein the electrode/electrolyte interface is studied and controlled to drive desired electrochemical reactivity. A Mg-In alloy is employed for Mg metal batteries to prevent Mg dendrite growth, which can cause cell shorting and failure. By coating the surface of Mg metal electrodes with the Mg-In alloy, the nucleation of Mg dendrites is suppressed and instead the Mg electroalloys into the surface alloy upon reduction, significantly increasing the cell life time. Next, the Li-intercalation material LiTiS\u2082 is studied for use in organic reductive electrosynthesis as counter anodes. Traditional metal sacrificial counter anodes are known to cause issues such as surface passivation, chemical reactivity, and cross-plating at the working electrode, which is deleterious to the desired organic reactivity. It is found that LiTiS\u2082 surface is less reactive in organic electrolytes, reducing both passivation and chemical reactivity. Further, Li\u207a de-intercalated from LiTiS\u2082 oxidation is found to be less susceptible to cross-plating than Zn, a common sacrificial anode. Finally, the effect of electrode material on the electrochemical reduction of \u1d57BuI is studied. Using electrochemical characterization, it is found that the reduction is catalyzed on Au and Ag through adsorption of the initial substrate, as well as the adsorption of the reactive intermediate tBu radical. The catalysis of \u1d57BuI reduction can have meaningful consequences for organic reactivity, driving the desirable generation of the carbanion nucleophile from alkyl halide reactants." }, { "name": "Lee, Dongkwan", "degree": "PhD", "year": "2025", "title": "Bond-Selective Nonlinear Optical Microscopy: From Live Cells to Single- Molecule Imaging", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282025-172449360", "creators": [ { "name": { "family": "Lee", "given": "Dongkwan" }, "id": "Lee-Dongkwan", "orcid": "0000-0001-6091-1349", "display_name": "Lee, Dongkwan" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Lihong" }, "id": "Wang-Lihong", "orcid": "0000-0001-9783-4383", "role": "member", "display_name": "Wang, Lihong" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8qqq-z286", "abstract": "Advances in optical microscopy have revolutionized cell biology, transforming our understanding of cellular processes from static structural observations to dynamic temporal and spatial insights at the single-molecule level. While fluorescence imaging remains the gold standard due to its high sensitivity, specificity, and versatile toolbox, it faces significant limitations, particularly in imaging small molecules that are not inherently fluorescent. Attaching fluorescent tags to these molecules often disrupts their physicochemical properties, highlighting the need for minimally invasive and intrinsic-contrast-based approaches.
\r\n\r\nVibrational spectro-microscopy, which probes the intrinsic vibrational frequencies of chemical bonds, offers a promising solution. Stimulated Raman scattering (SRS) microscopy, a well-established vibrational imaging technique, enhances vibrational excitation by up 10\u2078-fold through stimulated emission amplification, enabling rapid, label-free imaging of biological samples with high specificity.
\r\n \r\nIn the first half of this thesis, we advance SRS microscopy to tackle specific biological challenges and explore new methodological possibilities. To visualize glycogen metabolism, we combined a stable isotope labeling strategy with SRS imaging, achieving high-specificity imaging of glycogen in live cells. This approach was further applied to metabolic phenotyping of patient-derived melanoma cell lines. Additionally, we investigated strategies to photoswitch electronic pre-resonance (epr) SRS probes, which are typically photostable. By inducing electronic transitions that modulate electronic-vibrational coupling, we developed the first genetically encodable photoswitchable epr-SRS probe using a near-infrared fluorescent protein, unlocking new possibilities in Raman imaging.
\r\n\r\nIn the second half of this thesis, we address the limitations of SRS microscopy by developing a novel bond-selective nonlinear optical microscopy technique called bond-selective fluorescence-detected infrared-excited (BonFIRE). BonFIRE introduces a vibration-state-mediated two-photon process as a new vibrational contrast mechanism, overcoming key limitations in sensitivity and speed associated with SRS. By combining the high sensitivity and specificity of fluorescence with the rich chemical information provided by IR absorption-based vibrational contrast, BonFIRE offers a powerful platform for multidimensional insights into biological systems. We envision BonFIRE as a tool to tackle unique challenges that current technologies cannot address, representing a significant step forward in understanding the complex processes that define life.
" }, { "name": "Lin, Li-En", "degree": "PhD", "year": "2025", "title": "Advancing Stimulated Raman Scattering Microscopy through Deep Learning and Gel-Based Tissue Engineering", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:05212025-221836479", "creators": [ { "name": { "family": "Lin", "given": "Li-En" }, "id": "Lin-Li-En", "orcid": "0000-0003-3086-6991", "display_name": "Lin, Li-En" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Van Valen", "given": "David A." }, "id": "Van-Valen-D", "orcid": "0000-0001-7534-7621", "role": "member", "display_name": "Van Valen, David A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9azz-r140", "abstract": "Stimulated Raman scattering (SRS) microscopy is a highly effective label-free imaging method for investigating the molecular composition of biological systems. Its broader use has been held back by spatial resolution, imaging speed, and large-scale tissue imaging compatibility. Breaking these limitations requires an integrated approach beyond the development of optical hardware. This thesis introduces a compilation of techniques that leverage gel-based tissue engineering and deep learning to enhance the capabilities of SRS microscopy.
\r\n \r\nThe first chapter, Gel-Enabled Super-Resolution Label-Free Volumetric Vibrational Imaging, introduces VISTA, a sample-expansion vibrational imaging technique that achieves label-free super-resolution imaging of protein-dense biological structures with resolution as fine as 78 nm. By enabling isotropic expansion and protein retention, VISTA allows for high-throughput, unbiased volumetric imaging without labeling, with further enhancement using deep learning-based component prediction.
\r\n\r\nThe second chapter, High-Resolution Imaging of In Vivo Protein Aggregates, applies VISTA to image amyloid-beta and polyQ aggregates in biological samples with high specificity. Combined with segmentation using convolutional neural networks, this technique is capable of mapping aggregate structure and microenvironments, enabling new insights into neurodegenerative disease pathology.
\r\n\r\nThe third chapter, High-Throughput Volumetric Mapping Facilitated by Active Tissue SHRINK, introduces SHRINK, a hydrogel-based sample shrinkage method that isotropically shrinks tissue while maintaining structural integrity. Active shrinkage enhances imaging throughput and signal sensitivity and enables rapid, large-scale, three-dimensional whole-organ mapping with SRS microscopy.
\r\n\r\nThe fourth chapter, Deep Learning-Augmented Metabolic Profiling in Live Neuronal Cultures, presents a tandem deep learning platform for live-cell metabolic imaging. By integrating a recurrent convolutional neural network and U-Net segmentation model with deuterium-labeled metabolic tracing, this platform enables non-invasive, high-speed profiling of lipid, protein, glucose, and water metabolism in neuronal subtypes under physiological and pathological conditions.
\r\n\r\nThese developments represent multidimensional strategies that expand the application of SRS microscopy to high-resolution, high-throughput, and dynamic imaging in a variety of biological systems. The integration of deep learning and gel-based tissue engineering techniques opens new avenues for SRS microscopy to explore complex biological questions.
" }, { "name": "Luedecke, Kaitlin Mary", "degree": "PhD", "year": "2025", "title": "Elucidating the Role of Transition Metal Electronic Structure in Catalysis and Spin Relaxation", "advisor": "Hadt, Ryan", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192025-180916338", "creators": [ { "name": { "family": "Luedecke", "given": "Kaitlin Mary" }, "id": "Luedecke-Kaitlin-Mary", "orcid": "0000-0002-8163-9417", "display_name": "Luedecke, Kaitlin Mary" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan" }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan" } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Hadt", "given": "Ryan" }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7t77-rd65", "abstract": "Transition metal complexes are the workhorses of physical inorganic chemistry and have diverse applications in catalysis and quantum information science, especially. The primary descriptor of transition metal complexes, and a good predictor of their utility, is their electronic structure. Notably, rigorous characterization of the spin states, oxidation states, excited states, and magnetic properties of these complexes is necessary to gain mechanistic detail for these applications; this thesis focuses on elucidating the role of transition metal electronic structure in catalysis and spin relaxation. Chapter 1 introduces important transition metal electronic structure considerations and motivates these studies. Part I includes Chapters 2\u20134 and considers complexes relevant for CO\u2082 reduction chemistry and cross-coupling reactivity. Chapter 2 investigates the conditions under which a CO\u2082 reduction catalyst, Fe-p-TMA, undergoes speciation changes and characterizes its excited-state identities and lifetimes. Chapter 3 considers the electrochemical conditions under which highly reduced CO reduction products are generated in an iron porphyrin system, and important connections to photocatalysis are made. Chapter 4 compares the excited-state identities and reactivities of prototypical and tethered Ni(II)\u2013bpy aryl halide complexes. Part 2 includes Chapters 5\u20136 and focuses on spin relaxation, a key figure of merit in quantum information science. Chapter 5 investigates the effect of structural distortions in S = \u00bd copper porphyrin systems on their spin-lattice relaxation times, and Chapter 6 moves to identifying the mechanism of spin relaxation in an S = 1 Cr(o-tolyl)\u2084 system. Together, these compiled studies reveal the nuanced roles of transition metal electronic structure in catalysis and spin relaxation and highlight the importance of their characterization for developing optimized systems." }, { "name": "MacKrell, Elliot James", "degree": "PhD", "year": "2025", "title": "Global Analysis of Protein Synthesis and Degradation in Escherichia coli", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06292024-034255793", "creators": [ { "name": { "family": "MacKrell", "given": "Elliot James" }, "id": "MacKrell-Elliot-James", "orcid": "0009-0006-5619-8548", "display_name": "MacKrell, Elliot James" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/n97w-ch36", "abstract": "Protein synthesis and degradation shape the cellular proteome to drive homeostasis and physiological adaptation. Many fundamental aspects of protein regulation have been elucidated through investigation of the Gram-negative bacterium Escherichia coli, which remains a fruitful model organism for uncovering conserved regulatory mechanisms relevant to cell biology, biotechnology, and medicine. Here, we used bioorthogonal noncanonical amino acid tagging (BONCAT) for the time-resolved analysis of protein synthesis and degradation in this organism in several contexts. We profiled protein degradation on a proteome-wide scale in growing and growth-arrested cells, identifying instability in a diverse panel of regulators. Our identifications served as training data in the validation and deployment of a machine learning classifier of in vivo protein stability, which highlighted the role of active degradation in motility and surface adhesion. We then utilized an efficient system of active degradation in this organism to engineer the instability of the mutant methionyl-tRNA synthetase NLL-MetRS for the analysis of protein synthesis in transient physiological states. Destabilized NLL-MetRS variants exhibited half-lives on the order of hours, which improved the fidelity of metabolic labeling in growth-arrested cells. Additionally, we leveraged the sensitivity of BONCAT to investigate protein synthesis in growth-arrested cells expressing a well-studied but controversial member of the widespread toxin-antitoxin family, MazF. Our proteomic profiling suggests this toxin activates several endogenous stress response systems, most notably the cold shock response system. Taken together, these investigations highlight the advantage of time-resolved proteomics in characterizing proteome dynamics." }, { "name": "Mai, Huanghao", "degree": "PhD", "year": "2025", "title": "Advancing Structural Analysis with Computational Methods Development", "advisor": "Nelson, Hosea M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252024-205053475", "creators": [ { "name": { "family": "Mai", "given": "Huanghao" }, "id": "Mai-Huanghao", "orcid": "0000-0003-2278-0768", "display_name": "Mai, Huanghao" } ], "advisors": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "advisor", "display_name": "Nelson, Hosea M." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." } ], "option_major": [ "biochem" ], "doi": "10.7907/4p95-d385", "abstract": "In this thesis, a set of computational methods is developed to extend structural techniques beyond their conventional practice. First, we build in silico simulations and image processing protocols to design a new data acquisition workflow in cryo-electron tomography. This enables in situ visualization of macromolecular complexes at sub-nanometer resolution in a micron-scale field of view. Then, we demonstrate the applicability of a novel machine-learning algorithm in processing small molecule electron diffraction data for the first time. For most molecules tested, the correct ab initio structures can be obtained without the common practice of manual dataset curation. Finally, molecular dynamics simulations using crystallographic structures of protein and drug molecule complexes are performed to investigate the fundamental principles of a ternary binding property. A minimal forcefield with multi-scale coarse-graining enables alchemical free energy calculations at an unconventional size of perturbation while providing physical insight into the role of the drug linker and protein shapes." }, { "name": "Miller, Sophie Eve", "degree": "PhD", "year": "2025", "title": "Time-Resolved Proteomic Analysis in Zebrafish and Cultured Neurons Using Bioorthogonal Noncanonical Amino Acid Tagging", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022025-051628277", "creators": [ { "name": { "family": "Miller", "given": "Sophie Eve" }, "id": "Miller-Sophie-Eve", "orcid": "0000-0001-6805-7036", "display_name": "Miller, Sophie Eve" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Prober", "given": "David A." }, "id": "Prober-D-A", "orcid": "0000-0002-7371-4675", "role": "member", "display_name": "Prober, David A." }, { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "member", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/vdgh-6c46", "abstract": "Temporally and spatially controlled protein synthesis plays a critical role in orchestrating the molecular events underlying behaviors, stress adaptations, and therapeutic responses to drugs. However, traditional proteomic techniques often fail to capture the dynamic changes in protein expression essential for understanding transient biological phenomena. To overcome this limitation, the work presented in this thesis leverages bioorthogonal noncanonical amino acid tagging (BONCAT) coupled with mass spectrometry to perform time-resolved proteomic analyses in zebrafish larvae and cultured neurons.
\r\n\r\nChapter II details the development and validation of BONCAT proteomics in zebrafish, demonstrating that newly synthesized proteins from zebrafish larvae could be reliably labeled, enriched, and identified even over short labeling periods. Proof-of-concept experiments using heat shock revealed that BONCAT proteomics was able to detect changes in expression of proteins known to be induced by heat shock with greater sensitivity than conventional approaches using global proteomics. These results establish BONCAT as a powerful tool for investigating dynamic changes in protein synthesis in zebrafish. In Chapter III, we applied BONCAT to neuronal cultures to profile the proteomic changes induced by sub-anesthetic, antidepressant-relevant doses of ketamine. These studies uncovered rapid alterations in protein synthesis, identifying significantly differentially regulated proteins and pathways involved in synaptic plasticity, cytoskeletal remodeling, cellular signaling, metabolism, and RNA processing. This work provides novel molecular insights into ketamine\u2019s rapid-acting antidepressant effects and further illustrates the utility of BONCAT for capturing early, transient proteomic responses to drug treatment. Finally, in Chapter IV, we explore changes in protein expression in zebrafish larvae underlying circadian rhythms and in response to low-dose ketamine treatment. We observed interesting protein synthesis patterns in both biological contexts, but our findings lacked the statistical significance and reproducibility across experiments required to draw strong biological conclusions from our data. Although methodological refinements are required, our work underscores BONCAT\u2019s potential to elucidate transient proteomic shifts underlying behavioral phenomena and pharmacological interventions in zebrafish.
" }, { "name": "Mirzoyan, Ruben", "degree": "PhD", "year": "2025", "title": "Electron Dynamics in Molecular Qubits and Catalytic Films", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272024-204111663", "creators": [ { "name": { "family": "Mirzoyan", "given": "Ruben" }, "id": "Mirzoyan-Ruben", "orcid": "0000-0002-2334-4012", "display_name": "Mirzoyan, Ruben" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mcq5-js86", "abstract": "Two significant areas within molecular and materials chemistry are explored: spin-phonon coupling in molecular qubits and electrocatalysis in cobalt oxyhydroxide thin films, detailed over four chapters and an appendix. The first chapter reviews advancements in molecular quantum information science, focusing on decoherence mechanisms in transition metal complex-based qubits, and introduces a dynamic ligand field model that categorizes decoherence regimes and designs qubits for various environments. The second chapter develops and enhances a ligand field theory model to quantify spin-phonon interactions in transition metal complexes, correlating theoretical insights with experimental data to improve quantum coherence in molecular qubits. The third chapter investigates the electron transport and dynamic defect states in cobalt-phosphate and cobalt-borate oxyhydroxide films, crucial for understanding their photoexcited states in oxygen evolution catalysis. The fourth chapter presents a novel magneto-electrochemical setup that quantifies magnetoenhancement in electrocatalytic current for water splitting, highlighting the potential of magnetic fields in enhancing electrocatalytic processes. This work provides both a physical inorganic framework and experimental insights for ongoing and future developments in molecular quantum information science and energy conversion." }, { "name": "Morales, Maryann", "degree": "PhD", "year": "2025", "title": "Metal Binding to Nsp1, a SARS-CoV-2 Protein", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302025-004839918", "creators": [ { "name": { "family": "Morales", "given": "Maryann" }, "id": "Morales-Maryann", "orcid": "0000-0002-1778-8901", "display_name": "Morales, Maryann" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "orcid": "0000-0001-8586-5641", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z9m9-yn02", "abstract": "The COVID-19 pandemic, caused by SARS-CoV-2, has underscored the need for novel antiviral strategies beyond vaccines. A key virulence factor in SARS-CoV-2 is nonstructural protein 1 (Nsp1), which suppresses host immune responses by degrading mRNA, inhibiting nuclear export, and binding to the 40S ribosomal subunit to block host translation. Its intrinsically disordered C-terminal domain complicates structure-based drug design, prompting exploration of alternative approaches.
\r\n\r\nThis work investigates the use of transition metal coordination to target disordered regions of Nsp1. Copper(II) and cobalt(III) complexes were examined for their ability to bind histidine residues\u2014particularly H165, critical for ribosome interaction. Biophysical techniques, including fluorescence spectroscopy, EPR, and \u2075\u2079Co NMR, along with computational modeling, were used to characterize binding to Nsp1-derived peptides and the full-length protein.
\r\n\r\nCu(II) displayed pH-dependent coordination through histidine and backbone amides, while oxidized Co(III) complexes formed stable, substitution-inert interactions. Multi-site binding and distinct kinetic profiles were observed. In vitro translation assays showed that metal complexes can affect translation, though selective inhibition of Nsp1 remains challenging.Overall, this work provides a foundation for targeting disordered viral proteins using coordination chemistry.
" }, { "name": "Naragon, Thomas Houser", "degree": "PhD", "year": "2025", "title": "Cuticular Hydrocarbons in Myrmecophiles are a Mechanism of Symbiotic Entrenchment", "advisor": "Parker, Joseph", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-211102729", "creators": [ { "name": { "family": "Naragon", "given": "Thomas Houser" }, "id": "Naragon-Thomas-Houser", "orcid": "0000-0002-5373-4257", "display_name": "Naragon, Thomas Houser" } ], "advisors": [ { "name": { "family": "Parker", "given": "Joseph" }, "id": "Parker-J", "orcid": "0000-0001-9598-2454", "role": "advisor", "display_name": "Parker, Joseph" } ], "committee": [ { "name": { "family": "Chong", "given": "Shasha" }, "id": "Chong-Shasha", "orcid": "0000-0002-5372-311X", "role": "chair", "display_name": "Chong, Shasha" }, { "name": { "family": "Demirer", "given": "G\u00f6zde S." }, "id": "Demirer-G\u00f6zde-S", "orcid": "0000-0002-3007-1489", "role": "member", "display_name": "Demirer, G\u00f6zde S." }, { "name": { "family": "Hong", "given": "Elizabeth J." }, "id": "Hong-Elizabeth-J", "orcid": "0000-0003-3866-418X", "role": "member", "display_name": "Hong, Elizabeth J." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Parker", "given": "Joseph" }, "id": "Parker-J", "orcid": "0000-0001-9598-2454", "role": "member", "display_name": "Parker, Joseph" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s8ng-e309", "abstract": "The velvety tree ant, Liometopum occidentale, hosts three myrmecophilous rove beetles, Sceptobius lativentris, Platyusa sonomae, and Liometoxenus newtonarum. The three beetles independently evolved to mimic the nestmate recognition pheromones of L. occidentale with varying degrees of accuracy. The accuracy of the mimicry determines the degree of integration of the beetles into nests of their host; P. sonomae achieves the least accurate mimicry and is located at the nest periphery, whereas S. lativentris employs the most accurate mimicry and has access to the entirety of the ant nest and its resources. The accuracy of the mimicry was found to be dependent on the mechanism by which it is achieved. P. sonomae synthesizes the pheromone blend de novo and S. lativentris acquires the pheromones from the host ant. The approach taken by S. lativentris is significant, because the class of chemicals used as nestmate recognition pheromones in ants play a more primary role, forming a desiccation barrier that coats the surface of all insects. In the transition into the nests of its hosts, which occurs after the pupal developmental stage, S. lativentris permanently shuts off its production of these anti-desiccation compounds, opting instead to steal them from its host. This high-fidelity mimicry comes at a cost. S. lativentris is locked into an obligate and irreversible dependence on L. occidentale, dying within a day away from its host ant." }, { "name": "Nguyen, Vy Ngoc Mai", "degree": "PhD", "year": "2025", "title": "Structural and Mechanistic Studies of Membrane Protein Biogenesis and Quality Control at the Endoplasmic Reticulum", "advisor": "Voorhees, Rebecca M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282025-222913964", "creators": [ { "name": { "family": "Nguyen", "given": "Vy Ngoc Mai" }, "id": "Nguyen-Vy-Ngoc-Mai", "orcid": "0000-0002-7563-7386", "display_name": "Nguyen, Vy Ngoc Mai" } ], "advisors": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "advisor", "display_name": "Voorhees, Rebecca M." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." } ], "option_major": [ "biochem" ], "doi": "10.7907/ar35-w658", "abstract": "Membrane proteins make up around 30% of the human proteome and carry out essential functions in the cell, including but not limited to signaling, cell adhesion, and metabolic transport. To maintain homeostasis, the eukaryotic cell has evolved complex pathways for membrane protein biogenesis and quality control, as they contain hydrophobic transmembrane domains (TMDs) that can easily aggregate in the aqueous environment of the cytosol causing cellular damage. At the endoplasmic reticulum (ER), the ER membrane protein complex (EMC) co-translationally inserts the first TMD of multipass membrane protein and post-translationally inserts tail-anchored membrane proteins. In this thesis, we are able to show how the EMC can coordinate with the other protein machineries of the multipass translocon (such as the back-of-Sec61/BOS complex) at the ER to accommodate the insertion of diverse multipass membrane protein substrates, depending on the biophysical properties of their N-terminal soluble domain. We also structurally characterize the EMC\u2022BOS holocomplex, highlighting its spatial relation with the other biogenesis factors at the multipass translocon. In addition, this thesis also explores how a novel quality control factor TXNDC15 functions in ER-associated degradation (ERAD) to facilitate degradation of unassembled membrane proteins. We found that TXNDC15 works with the E3 ligase MARCHF6 and recognizes a set of membrane proteins with exposed hydrophobic domain in the ER lumen. Lastly, we were able to also link TXNDC15\u2019s quality control function to its implication in ciliopathies, such as Meckel-Gruber syndrome." }, { "name": "Nimlos, Danika Katherine", "degree": "PhD", "year": "2025", "title": "Development and Characterization of a Table-Top Laser-Produced Plasma Source for In-Situ and Time-Resolved Soft X-Ray Absorption Spectroscopy", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02192025-011837407", "creators": [ { "name": { "family": "Nimlos", "given": "Danika Katherine" }, "id": "Nimlos-Danika-Katherine", "orcid": "0000-0002-5414-0039", "display_name": "Nimlos, Danika Katherine" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "orcid": "0000-0001-9435-0201", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3e9t-xr72", "abstract": "X-ray absorption spectroscopy (XAS) has emerged as an indispensable tool in the fields of carbon capture and conversion, providing element-specific insights into electronic structure, oxidation states, and chemical bonding. Of particular interest are soft X-rays (SXRs), which can probe the X-ray water window, enabling detailed studies of carbon, nitrogen, and transition metal L-edges in aqueous environments. Traditionally, access to this technique and this energy range has been limited to large- scale facilities like synchrotrons and XFELs, which can only serve a small population of users in a given year. Furthermore, more complex techniques such as time-resolved and in-situ XAS are practically inaccessible to the majority of users. This thesis explores the development of a table-top laser-produced plasma (LPP) source based on a gaseous target to extend the reach of XAS techniques into laboratory settings. Such sources offer significant advantages in accessibility, flexibility, and cost, while advances in X-ray optics and detection systems have further enhanced their utility. The research presented here focuses on the utilization of gaseous LPP sources for both in-situ and time-resolved XAS, pushing the boundaries of table-top soft X-ray absorption capabilities.
\r\n\r\nKey achievements include exploration of the lower temporal limit of LPP sources for SXR emission, and the first demonstration of liquid-phase XAS measurements using a gaseous LPP source. Gas-phase measurements were also achieved using the system built in this work. Additionally, a novel UV-pump/SXR-probe technique was developed, enabling future time-resolved studies of charge transfer dynamics in transition metal oxides. These advances pave the way for detailed investigations of photodriven processes, interfaces, and catalytic mechanisms critical to carbon capture and conversion. By improving temporal resolution and expanding the scope of in-situ XAS techniques, this work addresses fundamental challenges in the field, bringing the power of synchrotron-like spectroscopy into everyday laboratories. Ultimately, the results presented here aim to democratize XAS, fostering a broader adoption of this technique in catalysis and materials research.
" }, { "name": "Patheria, Eshaan Salim", "degree": "PhD", "year": "2025", "title": "Multielectron Redox in Lithium-Rich, Industrial-Element Sulfides for High Energy Density Lithium-Ion Battery Cathodes", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032025-064811859", "creators": [ { "name": { "family": "Patheria", "given": "Eshaan Salim" }, "id": "Patheria-Eshaan-Salim", "orcid": "0000-0002-2761-8498", "display_name": "Patheria, Eshaan Salim" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2pdg-hs94", "abstract": "This thesis develops a thermodynamic and electronic framework for lithium-ion battery cathodes and applies it to a new class of high-capacity sulfides composed exclusively of industrially abundant elements.\r\nIt introduces lithium-rich cathodes composed of aluminum, iron, and sulfur that leverage reversible multielectron anion redox, in which the formation and cleavage of sulfur-sulfur bonds enable especially high extents of charge storage.\r\nA core design framework is established linking delithiated-phase stability to accessible electrochemical redox capacity.\r\nThe chemical space is expanded with copper-substituted phases, in which unique copper-sulfur electronic interactions delocalize charge compensation beyond sulfur-sulfur bonds, thereby improving the reversibility of anion redox.\r\nThese materials achieve high energy densities using only industrial elements, offering a promising foundation for next-generation lithium-ion cathodes that address both performance and raw materials constraints.\r\nThus, this thesis advances the long-term goal of building more sustainable energy systems and expanding access to electricity worldwide." }, { "name": "Peng, Linqing", "degree": "PhD", "year": "2025", "title": "Harnessing Locality for Scalable Strongly Correlated Electron Simulations", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312025-001458670", "creators": [ { "name": { "family": "Peng", "given": "Linqing" }, "id": "Peng-Linqing", "orcid": "0000-0001-5682-2407", "display_name": "Peng, Linqing" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6ffe-2j03", "abstract": "Materials-specific predictions of large, realistic molecules and materials with strong electron correlations have been a long-standing challenge in quantum chemistry. This dissertation addresses this challenge by leveraging three forms of physical and mathematical locality\u2014in space, energy, and rank\u2014to develop scalable, efficient, and accurate electronic structure methods.
\r\n\r\nIn Chapter 2, we use quantum embedding theory that exploits the spatial locality of electron correlations and reduces the computational cost of accurate correlated electronic structure methods, enabling accurate ab initio simulation of complicated correlated materials. In this work, we study Kondo physics, a prototypical many-body quantum phenomenon, with a full-cell extension of dynamical mean-field theory (DMFT). Our \\textit{ab initio} simulation of the Kondo correlations systematically converges towards the exact zero-temperature limit, yielding material-specific Kondo temperatures that reproduce the subtle exponential trends observed experimentally and offer new insight into the underlying physics.
\r\n \r\nChapter 3 explores the locality in energy in lanthanide single-ion magnets. Their multi-reference ground and excited states are generally challenging to compute, but fortunately, the states that govern the spin dynamics are local in the energy spectrum. We develop a theoretical protocol to compute their spin Hamiltonian by sampling only relevant states in this reduced Hilbert space, and particularly, the single-reference states accessible by the efficient density functional theory. This method surpasses the prohibitive cost of calculating multi-reference eigenstates, and with its mean-field scaling, enables studying realistic magnets of unprecedentedly large size at an accuracy comparable to the previous state-of-the-art method.
\r\n\r\nChapter 4 focuses on the locality in the rank structure of reduced density matrices (RDMs). The 1- and 2-RDMs are the crucial ingredients in estimating energies and observables in many classical and quantum simulation methods. Their intrinsic low-rank structure makes them compressible and can be exploited to significantly reduce the measurement cost. We analyze both noiseless and noisy measurement scenarios, including shot-noise-limited quantum algorithms, and show that in the context of Gaussian (shot) noise, a low-rank approximate reconstruction of RDMs effectively removes the high-rank noises and reduces the measurement cost by orders of magnitude, therefore enabling larger-scale simulations.
" }, { "name": "Peng, Ruojing", "degree": "PhD", "year": "2025", "title": "Classical Representation and Manipulation of Quantum Many Body States and High Dimensional Data", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01282025-225116139", "creators": [ { "name": { "family": "Peng", "given": "Ruojing" }, "id": "Peng-Ruojing", "orcid": "0000-0002-5293-7503", "display_name": "Peng, Ruojing" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/px31-5g53", "abstract": "This thesis contains several developments in extending the capability of classical simulations for representing and manipulating quantum many-body states and high dimensional data. In Chapter 1, we introduce the different types of problems considered in quantum chemistry (with ab initio molecular Hamiltonian) and condensed matter physics (with lattice model Hamiltonian) as well as a classical scenario of high-dimensional function integration. In each case, we briefly introduce a corresponding anstaz for representing either the quantum many-body wavefunction or the classical high-dimensional integrand, which provides context for more detailed discussion in subsequent chapters.
\r\n\r\nChapter 2 describes a technical improvement on an existing formulation of the coupled cluster method, known as a popular wavefunction ansatz in quantum chemistry, for simulating finite-temperature non-equilibrium ab initio Hamiltonian dynamics. We adapt a technique from zero-temperature dynamics to the non-equilibrium finite-temperature coupled cluster method, thereby restoring conservation laws for 1-particle properties which were previously broken, and stabilizing the numerical behavior of the method for moderate time propagation. We demonstrated the capability of the method on both ab initio molecular systems such as field-driven H2 and electron transport in silicon cell, and model Hamiltonian such as the moderately interacting single impurity Anderson model (SIAM). We were able to perform stable dynamics simulation for sufficient amount of time to extract qualitatively correct physics, such as band population transport in silicon, and Kondo physics in the SIAM.
\r\n\r\nChapter 3 and Chapter 4 introduce developments in tensor network state (TNS) methods for lattice model Hamiltonian. Typically, TNS are constructed to correctly represent the entanglement structure of target physical state, whose computation of e.g., amplitude and expectation value, can only be performed approximately. A representative example is the projected entangled pair state (PEPS) for representing ground states on 2-dimensional lattices. In Chapter 3, we describe several aspects in PEPS (and TNS in general) construction and computation, including approximate contraction and derivative computation, as well as encoding of Abelian symmetry and fermion statistics. We also introduce a change of perspective of TNS ansatz that restores its exact variationality which was hitherto considered only approximate due to the need of approximate contraction. With such new perspective on TNS ansatz, Chapter 4 then focuses on stochastic optimization of TNS using variational Monte Carlo (VMC). In particular, we investigate the convergence behavior of first- and second order update methods under stochastic noise, which was in turn affected by several factors such as sample size, system size, wavefunction quality and variational expressivity of the ansatz. We hope that the developments described in Chapter 3 and Chapter 4 can allow efficient large scale PEPS simulation of highly entangled states on 2-dimensional lattices, such as spin liquids, ground state of fermi-Hubbard model, and phases of uniform electron gas.
\r\n\r\nChapter 5 introduces a constructive approach for representing high dimensional classical functions with tensor network, and perform integration with approximate contraction. Previous attempts of using tensor network for high dimensional integration typically fit a predetermined form of exactly contractable tensor network to the target function, where error is mainly due to the limited expressivity of the tensor network ansatz. On the other hand, our constructive approach is in principle free of representation error for any function that admits polynomial decomposition into small function blocks. The returned tensor network representation is of arbitrary geometry, where the error is mainly due to approximate contraction, which will benefit greatly from new developments in tenor network approximate contraction techniques.
" }, { "name": "Pham, Kim Hoang", "degree": "PhD", "year": "2025", "title": "Application of Ultrafast Spectroscopy Techniques to Probe Correlated Ion Hopping Mechanisms in Solid-State Ion Conductors", "advisor": "Cushing, Scott K.; See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222025-165729471", "creators": [ { "name": { "family": "Pham", "given": "Kim Hoang" }, "id": "Pham-Kim-Hoang", "orcid": "0000-0003-4053-6363", "display_name": "Pham, Kim Hoang" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "co-advisor", "display_name": "Cushing, Scott K." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "co-advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "member", "display_name": "Faber, Katherine T." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/825x-r459", "abstract": "Superionic conductors, or solid-state ion conductors that surpass the ionic con- ductivity of its liquid counterpart, can enable more energy dense batteries, robust artificial ion pumps, and optimized fuel cells. The mechanisms enabling superionic conductivity still remain elusive, though many-body correlations between the mi- grating ions, lattice vibrational modes, and charge screening clouds have all been posited to greatly enhance ionic conduction. Most spectroscopic techniques cannot directly probe and validate the role of such correlations due to their inability to transiently resolve these ultrafast dynamics occurring at picosecond timescales. In this work, we develop an ultrafast technique that measures the time-resolved change in impedance while a light source ranging from UV to THz frequencies selectively excites an ion-coupled correlation. The technique is used to compare the relative changes in impedance of a solid-state Li\u207a conductor Li0.5La0.5TiO3 (LLTO) before and after light excitation to elucidate the role of charge screening clouds, optical phonons, and acoustic phonons on ion migration. From our techniques, we deter- mine that electronic screening and rocking phonon-mode interactions significantly dominate the ion migration pathway of LLTO compared to acoustic phonons. Al- though we only present one case study, our technique can extend to O\u00b2\u207b, H\u207a, or other charge carrier transport phenomena where ultrafast correlations control transport. Furthermore, the temporal relaxation of the measured impedance can distinguish ion transport effects caused by many-body correlations, optical heating, correlation, and memory behavior." }, { "name": "Qian, Michelle Dena", "degree": "PhD", "year": "2025", "title": "Beyond Li: Challenges in Moving Towards Earth-Abundant Battery Materials", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022025-025023583", "creators": [ { "name": { "family": "Qian", "given": "Michelle Dena" }, "id": "Qian-Michelle-Dena", "orcid": "0000-0002-4815-1014", "display_name": "Qian, Michelle Dena" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "orcid": "0000-0002-4571-6884", "role": "chair", "display_name": "Rossman, George Robert" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s5ws-m162", "abstract": "Batteries are a necessary component towards the advancement and proliferation of modern day technology, and are also an essential piece of the transition towards renewable energy. The lithium-ion battery (LIB) is the most common type of rechargeable battery, and the archetype relies on a traditional layered transition metal oxide cathode, organic electrolyte with a lithium salt, and a graphite anode. The design of these cells has been optimized to the point that the energy densities in these batteries are approaching their theoretical capacities. Combined with the supply chain challenges associated with many typical cathode elements and increasing energy demand, this highlights the need for new earth-abundant, high energy density battery technology. This thesis addresses challenges in two such systems: Mg-S and sodium-ion batteries (SIBs). Mg-S batteries suffer from capacity fade related to the polysulfide shuttle effect, which results in loss of active material and passivation of the anode. Here, we demonstrate that the rate of passivation is inversely proportional to the chain length of the polysulfides present in solution, and that passivation can be slowed or even reversed through addition of S\u2088 and the consequent perturbation of existing polysulfide speciation equilibria. SIBs are frequently touted as a \"drop-in\" technology for LIBs due to both systems relying on mobile alkali ions, but SIBs have inherently lower energy densities due to larger Na\u207a ion. In Chapters 3 and 4 we explore anion redox as a method of increasing energy densities in SIBs--Chapter 3 shows that in LiNaFeS\u2082, the charge compensation mechanisms from Li and Na cycling are identical. However, Na\u207a cycling is worsened compared to Li\u207a by structural degradation from the removal and insertion of the bulky Na\u207a ion, emphasizing the differences that exist between optimizing SIB cathode performance compared with that of LIBs. In Chapter 4, we aim to develop structure-property relationships that enable a stronger understanding of anion redox that can be leveraged to design high energy density, multielectron redox cathodes. Through the examination of the electrochemically inactive NaCu1.5Fe0.5S\u2082 and its vacancy-containing derivative NaCu1.125Fe0.625S\u2082, we show that vacancies in the transition metal layer enable redox although the redox is observed occurs on the transition metals. The study also demonstrates potential limitations of ideal model systems and bulk spectroscopic analysis techniques in materials with low degrees of redox.
" }, { "name": "Rosencrans, William Max", "degree": "PhD", "year": "2025", "title": "Mechanisms of Pharmacological and Cellular Regulators of Mitophagy", "advisor": "Chan, David C.; Chou, Tsui-Fen; Youle, Richard", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022025-150650052", "creators": [ { "name": { "family": "Rosencrans", "given": "William Max" }, "id": "Rosencrans-William-Max", "orcid": "0000-0003-1461-8891", "display_name": "Rosencrans, William Max" } ], "advisors": [ { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "advisor", "display_name": "Chan, David C." }, { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "advisor", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Youle", "given": "Richard" }, "id": "Youle-R", "orcid": "0000-0001-9117-5241", "role": "advisor", "display_name": "Youle, Richard" } ], "committee": [ { "name": { "family": "Hay", "given": "Bruce A." }, "id": "Hay-B-A", "orcid": "0000-0002-5486-0482", "role": "chair", "display_name": "Hay, Bruce A." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Chou", "given": "Tsui-Fen" }, "id": "Chou-Tsui-Fen", "orcid": "0000-0003-2410-2186", "role": "member", "display_name": "Chou, Tsui-Fen" }, { "name": { "family": "Youle", "given": "Richard" }, "id": "Youle-Richard", "orcid": "0000-0001-9117-5241", "role": "member", "display_name": "Youle, Richard" } ], "option_major": [ "biochem" ], "doi": "10.7907/zvm6-0682", "abstract": "Autophagy is a highly conserved cellular process that isolates and degrades damaged or unnecessary intracellular structures. Mitochondria, well known as metabolic centers, provide ATP and critical metabolites essential for life. Unchecked mitochondrial damage impairs metabolism, releases immunogenic mitochondrial DNA, and triggers apoptosis. Mitophagy, the selective removal of mitochondria via autophagy, is vital to preventing these harmful outcomes. The PINK1/Parkin pathway detects damaged mitochondria and targets them for mitophagy. Dysfunction in this pathway underlies certain subset Parkinson\u2019s Disease (PD) cases. Efforts to understand the mechanistic basis of this pathway and its regulators provides a pathway to development of potentially disease modifying therapeutics for PD. In this thesis, I characterize the mechanism of action of a series of clinical stage mitophagy activating drugs. We find that these compounds reduce the threshold for which mitochondrial stress initiates mitophagy. However, contrary to reported literature, I demonstrate that these compounds do not directly activate PINK1 or Parkin. Rather, they act as weak mitochondrial toxins sensitizing cells to mitochondrial insult. I reveal that this phenomenon is characteristic of any weak mitochondrial toxin, revealing a potent pitfall for current drug discovery campaigns. Next, I detail a novel endogenous regulator of PINK1/Parkin mitophagy, the immune-related protein TNIP1. We show through a series of cell, biochemistry, and biophysical assays, that TNIP1 competes for autophagy machinery to slow down mitophagy. These data center TNIP1 as a important regulator of autophagic processes, and a unique negative regulator of mitophagy. Finally, I describe a biophysical analysis of the mitochondrial ion channel, VDAC2, critical in apoptosis and PINK1/Parkin pathways. Using a series of single-molecule approaches, I reveal how its structural plasticity regulates its interactions with protein partners. These finding provide a mechanistic basis for understanding its role in disparate cellular processes. I also explore the biological impact of KO of each VDAC isoform on mitochondrial and cell function. Unexpectedly, we find that the lowest expressed isoform, VDAC3, has an outsized impact on mitochondrial function." }, { "name": "Schaus, Lucas Jean Nicolas", "degree": "PhD", "year": "2025", "title": "Studies on Scaling Throughput in Protein Engineering", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08022024-005547280", "creators": [ { "name": { "family": "Schaus", "given": "Lucas Jean Nicolas" }, "id": "Schaus-Lucas-Jean-Nicolas", "orcid": "0000-0002-6094-7402", "display_name": "Schaus, Lucas Jean Nicolas" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/jqng-x012", "abstract": "In this work we present three studies in protein engineering. While all three protein classes that have been targeted for engineering tasks are very different, the studies have a focus on scaling-up the throughput in protein engineering.
\r\n\r\nThe first study concerns machine learning (ML) based antibody humanization techniques. Achieving a reduction of patient anti-drug antibody responses in clinical trials is the goal of antibody humanization. To measure this however, one needs to pass significant scientific, bureaucratic, and financial hurdles, which is very rarely done and especially never at scale. Most existing ML-based antibody humanization techniques claim that they work without providing any experimental evidence. We developed Mousify as an in silico antibody humanization platform to place existing models into one framework for wet-laboratory validation. We demonstrate that even the best models have a fundamental flaw in that they only generate a single antibody. We use Mousify and Markov chains to show that using ML-based antibody humanization models for library generation is not only feasible but produces both stable and functional variants. Learning the lessons from our wet-laboratory experiments, we then developed a variational autoencoder model with properties that hopefully improve the outcomes of antibody humanization experiments.
\r\n \r\nIn the second study, we outline our plans and initial results to develop a bioelectrocatalytic system for the conversion of N2 to ammonia using nitrogenase. Most of the world\u2019s ammonia is used for agricultural purposes and is produced via the environmentally damaging Haber-Bosch process. Engineering nitrogenase for the bioelectrocatalytic production of ammonia is not trivial and a high throughput is not guaranteed. We present preliminary results in how throughput can be increased through diazotrophic pre-selection of nitrogenase variants, as well as a quest to find the ideal starting point for engineering using a combination of ancestral sequence reconstruction and generative protein language models.
\r\n\r\nIn the third and final study we present a directed evolution campaign to evolve protoglobins for the enantioselective catalytic formation of cis-trifluoromethyl substituted cyclopropanes, the first such reaction in both the chemical and biological world. Not only is the enzyme ApePgb LQ capable of efficiently performing carbene insertions into double-bonds, but it also shows a much more diverse substrate scope than similar enantioselective formations of trans-trifluoromethyl substituted cyclopropanes. After demonstrating that ApePgb LQ reactions can be increased to a 1-mmol scale, we investigated the nature of protoglobin cis-selectivity using various computational methods.
" }, { "name": "Schrunk, Erik Tao", "degree": "PhD", "year": "2025", "title": "Biomolecular Engineering of Gas Vesicles with Thiol Functionality", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292025-004444146", "creators": [ { "name": { "family": "Schrunk", "given": "Erik Tao" }, "id": "Schrunk-Erik-Tao", "orcid": "0009-0003-2002-7411", "display_name": "Schrunk, Erik Tao" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Kaihang" }, "id": "Wang-Kaihang", "orcid": "0000-0001-7657-8755", "role": "member", "display_name": "Wang, Kaihang" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/49mr-3744", "abstract": "Therapies involving the administration of engineered cells, such as CAR-T cell therapy and the delivery of genetically modified gut microbes, have enjoyed clinical success and increasing interest in recent years. While these therapies continue to show great promise, the opacity of tissue precludes the use of light in the observation and potential manipulation of these engineered cells as they carry out their functions within the body. To access these cells non-invasively in deep tissue requires the use of imaging modalities that do not involve light, of which ultrasound (US) is especially appealing due to its relatively low cost, safety, and widespread availability. Engineered cells can exhibit US contrast by expressing gas vesicles (GVs), air-filled polymeric proteinaceous nanostructures; GVs have already been used as acoustic reporters for gut colonization, tumor cell activity, and more.
\r\n \r\nWhereas GVs are most notable for their acoustic properties, we set out to further expand the function of GVs by chemically modifying them at the genetic level. Our goals were twofold: we wished to equip the external, solution-facing side of GVs with a unique chemical handle; and we wished to hide a reactive group within the internal, air-facing side of GVs that could only be revealed when the GV structures are irreversibly collapsed. To accomplish both these goals, we chose to incorporate cysteine into the shell of GVs because cysteine\u2019s thiol side chain is chemically unique among all natural amino acids and because wild-type GVs do not contain cysteine in their shells. We set up a cysteine scanning mutant library of the GV shell protein, GvpA/GvpA1, and screened for cysteine-tolerant mutations in the gene. Through this process, we discovered cysteine substitutions that furnished thiol groups facing both the GV exterior and interior.
\r\n\r\nThe GV-exterior-facing cysteines were leveraged to develop a modified GvpA that contains the bioorthogonal six amino acid tetracysteine tag, or TC tag. The TC tag reacts with the membrane-permeable molecule FlAsH, which becomes fluorescent upon reaction. We used TC-tagged GvpA, or tcGvpA, to express GVs in HEK 293T cells, and used confocal microscopy of FlAsH to study those GVs. Notably, we only substituted a small percentage of GvpA to tcGvpA, leaving the rest of the GvpA as wild type; to our knowledge, this is the only report of a polymeric proteinaceous structure that employs this chimeric assembly approach being successfully expressed and labeled with FlAsH. The microscopy results from this study were used to generate three-dimensional renderings that provided insights into the size and positioning of GV clusters expressed within HEK 293T cells.
\r\n\r\nSecond, we identified several interior-facing cysteine mutants to the GV shell protein GvpA1, which we used to develop \u201cSonoCages\u201d: chemical entities whose reactivity is gated by US. We purified GVs with one mutation from our screen, V47C, and reacted them with monobromobimane (mBBr), a fluorogenic, thiol-reactive molecule. The mutant GVs only reacted with mBBr after treatment with US, which collapsed the GVs and exposed their hydrophobic interiors to the bulk solution. Thus, we had developed thiol-bearing SonoCages whose cysteines could only engage in reactions after US-mediated collapse of the GVs\u2014a process we call \u201csono-uncaging\u201d in analogy to photo-uncaging. We further demonstrated the utility of SonoCages by preparing a hydrogel containing SonoCages and mBBr and using US to create fluorescent patterns corresponding to regions of GV collapse.
\r\n \r\nThe work presented in this thesis not only demonstrates the functionalization of the GV interior and exterior, but also establishes a framework through which further modifications can be performed. Whereas we used cysteine as our reactive chemical of choice, other amino acids (including non-canonical amino acids) could be used to explore a much wider library of reactivities. The vast potential of GV chemical modification, along with the amazing results from the rest of the Shapiro Lab and in labs across the world, serves as a reminder that GVs and GV-based technologies are not just a bubble (pun intended)\u2014they are going to be around for a long time.
" }, { "name": "Stegner, Andrea Anna Therese", "degree": "PhD", "year": "2025", "title": "Design and Application of Complexity Generating Strategies and Transformations in Natural Product Synthesis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-173559572", "creators": [ { "name": { "family": "Stegner", "given": "Andrea Anna Therese" }, "id": "Stegner-Andrea-Anna-Therese", "orcid": "0000-0001-9408-3967", "display_name": "Stegner, Andrea Anna Therese" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "https://orcid.org/0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Wilson, Linda C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w4xa-hy67", "abstract": "Rapid and efficient chemical synthesis of complex molecules is critical for enabling studies of their biological function and therapeutic potential. Complexity generation can be achieved by: (1) the development of selective transformations that rapidly construct complex scaffolds from simple precursors, and (2) the application of strategic retrosynthetic disconnections that maximize the efficiency of a synthesis i.e., via convergent fragment coupling strategies. We disclose efforts to address these aims by combining reaction design with the identification of strategic disconnections.
\r\n\r\nToward the first aim, a diastereoselective dearomative pyridine cyclization that forges the tetracyclic core of the matrine-type lupin alkaloids in a single step from commodity feedstocks was developed. This reaction, paired with a C15-selective oxidation cascade and late-stage isomerization, enabled the first total synthesis of (\u2013)-sophoridine and the shortest syntheses to date of (+)-matrine, (+)-isomatrine, (+)-allomatrine, and (+)- isosophoridine.
\r\n\r\nTo address the second aim, a convergent strategy for the synthesis of 6,7-seco-ent- kauranoids via strategic, transition metal-catalyzed C-C bond formation was developed. Both a Ni-catalyzed sp\u00b2\u2013sp\u00b3 and a dual Ni/Pd-catalyzed sp\u00b2\u2013sp\u00b2 coupling were developed and enabled efficient union of complex fragments, the latter yielding 1,3 dienes that underwent divergent annulation reactions to form various complex ring systems. These transformations provided the complete skeleton of isorosthin A and advanced intermediates en route to isodocarpin and secoexertifolin A.
" }, { "name": "Stewart, Christopher Jenkins", "degree": "Masters", "year": "2025", "title": "Dynamics of Charged Polyionic Liquids", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232025-215105217", "creators": [ { "name": { "family": "Stewart", "given": "Christopher Jenkins" }, "id": "Stewart-Christopher-Jenkins", "orcid": "0009-0001-0280-2336", "display_name": "Stewart, Christopher Jenkins" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6js0-8r29", "abstract": "Polymerized ionic liquids (PILs) exhibit complex ion transport dynamics that are central to advancing technology in energy storage and efficient energy conversion. In this work, we probe the behavior of charged polymer systems in the solvent\u2010free limit using a coarse\u2010grained Gaussian core model that explicitly incorporates long\u2010range electrostatic interactions. Our simulations span a wide range of chain lengths, from monomeric units to highly entangled polymers, revealing how both intrachain and interchain interactions govern key properties such as the radius of gyration, relaxation time, and diffusivity. Notably, charged polymers adhere to classical reptation scaling, indicating that electrostatic forces do not inhibit standard polymer melt scaling behavior. We quantify these effects by evaluating both the Onsager transport coefficients and the direct drift response under applied electric fields, thereby linking molecular trajectories to macroscopic ion conductivity.
\r\n\r\nOur findings show that as the chain length increases, the motion of polymerized ions becomes increasingly correlated, a trend that stabilizes ion conductivity despite decreasing diffusivity. This study demonstrates that the complex interplay between correlated motion and cooperative chain dynamics results in a relatively stable conductivity that increases over short chain length, plateaus in the transition regime, before decreasing in the fully entangled regime \u2014 contrary to idealized predictions based solely on diffusivity. By explicitly modeling the microscopic interactions and accounting for both hydrodynamic and electrostatic effects, we provide a physically grounded framework that captures the emergent behavior of these charged systems. In doing so, our work offers a robust platform for the rational design of next-generation PIL electrolytes, distinguishing itself from phenomenological models through clear, simulation-based insights.
" }, { "name": "Stradley, Steven Hartzel", "degree": "PhD", "year": "2025", "title": "Materials and Interfaces to Enable Reversible Mg Electrochemistry for Energy Storage Applications", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152025-202058082", "creators": [ { "name": { "family": "Stradley", "given": "Steven Hartzel" }, "id": "Stradley-Steven-Hartzel", "orcid": "0009-0009-7154-608X", "display_name": "Stradley, Steven Hartzel" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vs2j-ep54", "abstract": "Climate change drives the need for a dramatically increased deployment of electric vehicles and intermittent renewable energy sources. Each of these depends intimately on batteries for range and reliability. Although Li-ion batteries are the current industry standard for electrochemical energy storage, they are based on scarce and unevenly distributed resources. It is thus crucial to develop rechargeable battery chemistries based on more energy dense and resource equitable materials. Orders of magnitude more abundant and energy dense than Li, Mg is an attractive alternative to Li for energy storage. Despite its many attractive properties, deployment of Mg-based chemistries is hindered by a lack of cathode, anode, and electrolyte materials which support Mg electrochemistry and are mutually compatible. This thesis endeavors to deploy new materials to sustain reversible Mg electrochemistry and to understand how certain material properties impact electrochemical performance. First, we investigate new cathode materials based on Earth-abundant transition metal chlorides. These cathodes cycle somewhat reversibly but are prone to rapid capacity fade due to active material dissolution and shuttle. We identify electrolyte modification as a means to combat this fade. Next, we characterize halide-free Mg electrolytes based on weakly coordinating Si-centered anions. These electrolytes display impressively high oxidative stabilities but also relatively high reductive overpotentials and a fatal vulnerability to passivation by H\u2082O. We then consider a class of electrolytes based on B-centered anions with aryl ligands. These systems show exceptionally low reductive overpotentials among halide-free Mg electrolytes. We increase the bulk of the anion and correspondingly observe a slight increase in the reductive overpotential and an enhancement in rate performance. Though this class of compounds shows a low oxidative stability, the structure-property relationships gleaned from it may prove useful in future electrolyte studies. Finally, we deploy Al as an Earth-abundant, high capacity alloying anode for Mg-based batteries. Though the native kinetics for Mg-Al alloying prove too sluggish for practical systems, we use Bi to enhance the alloying kinetics of Al by two orders of magnitude. Though alloying capacity is limited by a large particle size, we present a viable method for enhancing Al alloying kinetics to relevant rates, thereby unlocking a highly desirable material for future studies. Taken together, this work expands the scope of cathode, electrolyte, and anode materials which support reversible Mg electrochemistry. Though imperfect, the lessons we learn from them may inform future design decisions to enable reversible Mg-based batteries." }, { "name": "Sun, Jiace", "degree": "PhD", "year": "2025", "title": "Classical and Quantum Simulation of Chemical and Physical Systems", "advisor": "Miller, Thomas F.; Minnich, Austin J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09022024-211742520", "creators": [ { "name": { "family": "Sun", "given": "Jiace" }, "id": "Sun-Jiace", "orcid": "0000-0002-0566-2084", "display_name": "Sun, Jiace" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "advisor", "display_name": "Minnich, Austin J." } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Chen", "given": "Xie" }, "id": "Chen-Xie", "orcid": "0000-0003-2215-2497", "role": "member", "display_name": "Chen, Xie" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3qp8-q490", "abstract": "Various quantum mechanics effects have been found and widely studied in different microscopic systems, such as quantum nuclear effects and electron correlation in molecular systems, electron-phonon coupling in crystal systems, and quantum Zeno effects in open quantum systems. However, exact numerical simulations require exponentially scaled classical resources. In this thesis, we study these quantum systems by a series of classical or quantum methods, which include semiclassical, ab initio, machine learning, and quantum computing approaches.
\r\n\r\nIn Chapter 2, we develop the molecular-orbital-based machine learning (MOB-ML) method as a general-purpose method to learn molecular electronic structure properties. By preserving physical constraints, including invariance conditions and size consistency, MOB-ML is shown to be able to capture both weak and strong interactions. Furthermore, the Gaussian Process framework is extended for learning both scalar properties such as energies, and linear-response properties like dipole moments with the rotationally equivariant derivative kernel. With these improvements, MOB-ML shows not only significantly higher learning rates for organic molecules, non-covalent interactions, and transition states but also excellent transferability from small systems to large systems.
\r\n\r\nIn Chapter 3, we develop a generalized class of integrators in the thermostatted ring-polymer molecular dynamics (T-RPMD) method, which is a semi-classical quantum dynamics method to capture various types of molecular nuclear quantum effects, including zero point energy, quantum tunneling, and kinetic isotopic effects. Such generalized integrators are carefully designed to be strong stable and dimension-free, which are essential for robust numerical computations. In particular, a so-called \"BCOCB\" integrator is proved to be superior in terms of accuracy and efficiency in the harmonic limit. Such superiority is further verified in strongly anharmonic systems featured by liquid water.
\r\n\r\nIn Chapter 4, we develop an ab initio-based semi-analytical model of electron-phonon scattering to describe the transport and noise behavior in GaAs, which is a widely-used semiconductor. Such a semi-analytical model lifts a few approximations in the standard ab initio calculation of intervalley scatterings, which were believed to be the origin of the failure to capture the nonmonotonic noise phenomena. We find qualitatively unchanged transport and noise properties and agreements on the scattering rates between the photoluminescence experiments. These results indicate the most probable origin of the nonmonotonic noise behavior is the formation of space-charge domains rather than the intervalley scattering.
\r\n\r\nIn Chapter 5, we simulate the challenging measurement-induced phase transitions (MIPT) behavior in quantum many-body systems on a superconducting quantum processor. Due to the intrinsic exponential scaling of the quantum state tomography and post-selection process, traditional simulations of MIPT were limited to a few qubits. With the recently introduced linear cross-entropy benchmarking, such exponential overhead is eliminated, and the correct critical behavior of MIPT is observed on a 22-qubit system. Our work paves the way for the studies of open quantum systems on large-scale near-term quantum devices.
" }, { "name": "Szentkuti, Hannah Kate", "degree": "PhD", "year": "2025", "title": "Anthropogenic Emissions and the Future of Our Atmosphere: I. Cyclohexanol Chemistry and Aerosol Formation in an Environmental Chamber \r\nII. K\u2082CO\u2083-Based Sorbent Development and Testing in a Packed Bed Reactor for CO\u2082 Capture", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-071545991", "creators": [ { "name": { "family": "Szentkuti", "given": "Hannah Kate" }, "id": "Szentkuti-Hannah-Kate", "orcid": "0009-0000-2232-6333", "display_name": "Szentkuti, Hannah Kate" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n0mg-9c43", "abstract": "Chapter 1 presents experimental studies conducted in an environmental chamber, alongside mechanistic modeling, to quantify aerosol formation from the gas-phase pollutant cyclohexanol. The calculated aerosol mass yields, which are higher than measured and predicted values of similar 6-carbon species, indicates the importance of functionalization, and interaction between functional groups (not just carbon number), on aerosol forming potential. Chapter 2 describes the construction and characterization of a mini-industrial scale packed-bed reactor, loaded with K\u2082CO\u2083-impregnated particles for CO\u2082 capture. Chapters 3 and 4 describe the formulation of durable high-capacity K\u2082CO\u2083-based sorbents using wet activated granulation and extrusion spheronization, respectively. In short, capture of point source CO\u2082 via K\u2082CO\u2083 sorbent is demonstrated to be feasible and even economical in the near future.
" }, { "name": "Tong, Zhengjia Jaron", "degree": "PhD", "year": "2025", "title": "Spectroscopic Investigation, Kinetic Analysis, and Ligand Field Theory Rationalization of Catalytic Reactivity for Data-Driven Methodology Development", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212025-074800688", "creators": [ { "name": { "family": "Tong", "given": "Zhengjia Jaron" }, "id": "Tong-Zhengjia-Jaron", "orcid": "0000-0001-9329-8034", "display_name": "Tong, Zhengjia Jaron" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7r55-2431", "abstract": "First-row transition metal catalysis can leverage one or two-electron redox chemistry to catalyze selective C\u2013C bond formation between two stereoelectronically differentiated substrates. Owing to this redox flexibility, many competing reaction pathways could occur, leading to the formation of both desired and undesired products. The electronic structure of the catalytic intermediates and reaction conditions are empirically recognized to modulate product distributions, but identifying the underlying design principle is often challenging. Mechanistic elucidation of the catalytic cycle and spectroscopic elucidation of important factors that influence catalytic reactivity could be beneficial to this endeavor. With the aid of ligand field theory and molecular orbital theory, a direct relationship may be established between the electronic structures of the metal catalysts and the thermodynamic or kinetic parameters of the elementary transformation they catalyze. To this end, this thesis describes the effort of combining spectroscopy, reactivity interpretation, and reaction kinetics to understand Ni-catalyzed reductive alkenylation and acylation of benzylic electrophiles and Cu-catalyzed allylic alkylation of \u03b3-butyric lactone. The research approach and the results described herein are anticipated to aid the emergent effort of data-driven reaction development." }, { "name": "Wang, Jue (Phyllis)", "degree": "PhD", "year": "2025", "title": "Direct Visualization of Cellular Protein Complexes in situ by Fluorescence-Guided Cryo-FIB-SEM and Cryo-ET", "advisor": "Chan, David C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02252025-210356380", "creators": [ { "name": { "family": "Wang", "given": "Jue (Phyllis)" }, "id": "Wang-Jue-Phyllis", "orcid": "0000-0002-5623-0994", "display_name": "Wang, Jue (Phyllis)" } ], "advisors": [ { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "advisor", "display_name": "Chan, David C." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "orcid": "0000-0003-1556-4864", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." } ], "option_major": [ "biochem" ], "doi": "10.7907/rmdd-5t54", "abstract": "Cryogenic electron tomography (cryo-ET) is a technique that can reconstruct three-dimensional volumes of large protein complexes in situ at sub-nanometer resolution. In addition to imaging proteins extracted from cells, cryo-ET also allows direct visualization of macromolecular complexes in their native environment. To reveal molecular details buried deeply inside thick eukaryotic cells, cryogenic focused ion beam milling with scanning electron microscopy (cryo-FIB-SEM) has been established as the leading approach for preparing thin sections of cells suitable for cryo-ET. Recent advances in cryo-FIB-SEM systems integrate fluorescence microscopy (cryo-FM-FIB-SEM) to help direct the milling to specific labeled regions of interest. This method has had success localizing large organelles and protein aggregates. Unfortunately, it is difficult to localize small and rare targets along the optical axis of the cryo-FIB. This thesis work pioneered a customized integrated tri-coincident imaging system (ENZEL) that allows for simultaneous fluorescence imaging and cryo-FIB milling. This novel method allows precise targeting of small and rare structures with a high success rate compared to other systems. To demonstrate the imaging workflow, we applied this approach to visualize the microtubule organizing center (MTOC), a crucial organelle responsible for cell division and cellular transport in mammalian cells. It presents as a single fluorescent punctum expanding approximately 1 \u00b5m in diameter in live cells, making it a challenging target for cryo-FM-FIB-SEM. Our cryo-tomograms resolved the molecular architecture of the MTOC and revealed molecular details at the microtubule nucleation sites. We then used the ENZEL to explore more complicated biological systems. Here we chose the NLRP3 inflammasome, a master mediator of innate immunity colocalized with the MTOC. We captured the first in-situ image of the NLRP3 inflammasome and showed new mechanistic insights that this complex forms a condensate at the MTOC, halting cell division and inducing drastic organelle changes." }, { "name": "Ye, Benjamin Bobin", "degree": "PhD", "year": "2025", "title": "Image Charge Effects Near Solid Surfaces", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:07262024-075858049", "creators": [ { "name": { "family": "Ye", "given": "Benjamin Bobin" }, "id": "Ye-Benjamin-Bobin", "orcid": "0000-0003-0253-6311", "display_name": "Ye, Benjamin Bobin" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "chair", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/fjpq-wn07", "abstract": "Ion\u2013surface interactions underpin fundamental biological and technological processes and hold the key to advancing the performance of modern electrochemical devices, such as electric double-layer capacitors (EDLCs). As such, a comprehensive understanding of the mechanistic details governing these interactions and their effects on the electrical double layer structure and charge transport is crucial. However, accurately modeling ion\u2013surface interactions in theory and simulations remains challenging due to the complexities and computational cost associated with properly treating dielectric discontinuities at ion\u2013surface interfaces. This thesis leverages the efficient method of image charges in coarse-grained molecular dynamics simulations to capture the correct behavior at the ion\u2013surface interface and unravel anomalous phenomena in various charged soft matter systems with conductive metal surfaces. Specifically, we construct a molecular model to demonstrate a spontaneous symmetry breaking transition in room-temperature ionic liquid EDLCs that provides a molecular mechanism for a hysteresis in the capacitance behavior observed experimentally. We also introduce a physically motivated soft-core model, the Gaussian core model with smeared electrostatics (GCMe), which addresses the limitations of traditional hard-core force fields in representing bulky organic ions and their spread charges, while also being orders of magnitude faster. Using GCMe, we then characterize the effects of the polyelectrolyte chain length, electrolyte polarizability, and electrode material on the energy storage of polymerized ionic liquid EDLCs, and the ion adsorption behavior and charging/discharging dynamics in polyelectrolyte EDLCs. Finally, we present MDCraft, an open-source Python assistant designed to streamline computational research workflows by providing tools for simulation setup, data analysis, and visualization. This comprehensive study not only enhances the understanding of ion-surface interactions but also offers practical insights and tools for advancing the design and optimization of systems involving charged species near surfaces, such as next-generation electrochemical energy storage devices." }, { "name": "Zhao, Zhenqi (Steven)", "degree": "PhD", "year": "2025", "title": "Synthesis of Strained Systems via Vinyl Carbocation Intermediates", "advisor": "Nelson, Hosea M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07222024-161123922", "creators": [ { "name": { "family": "Zhao", "given": "Zhenqi (Steven)" }, "id": "Zhao-Zhenqi-Steven", "orcid": "0000-0002-6848-2689", "display_name": "Zhao, Zhenqi (Steven)" } ], "advisors": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "advisor", "display_name": "Nelson, Hosea M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xcmv-0060", "abstract": "Vinyl carbocations are a class of dicoordinated carbocations. Due to their challenging generation, they have been less studied compared to tricoordinated carbocations. This thesis reports multiple novel reactivities involving vinyl carbocation intermediates.
\r\n\r\nThe first chapter reviews methods for generating vinyl carbocations and past reports of vinyl carbocation C\u2013H insertion. It then introduces a field guide to assist researchers in using vinyl carbocation C\u2013H insertion in their synthesis, providing detailed information and optimal reaction conditions developed in our laboratory.
\r\n\r\nThe second chapter describes a catalytic method for forming medium-sized rings via intramolecular Friedel-Crafts reactions of vinyl carbocation intermediates. These reactive species are catalytically generated through the ionization of vinyl toluenesulfonates by a Lewis acidic lithium cation/weakly coordinating anion salt.
\r\n\r\nThe third chapter details selective [2+2] cycloadditions between vinyl carbocations and terminal alkenes, using a LiHMDS-mediated approach. This method allows for the efficient synthesis of strained cyclobutene-containing bicycles under mild conditions, demonstrating the versatile application of vinyl carbocations in constructing complex strained organic structures.
" }, { "name": "Brackney, Helen Maya", "degree": "Senior Thesis", "year": "2024", "title": "Structural Analysis of MurG Interactions with Substrates, Inhibitors, and MraY", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242023-173046393", "creators": [ { "name": { "family": "Brackney", "given": "Helen Maya" }, "id": "Brackney-Helen-Maya", "orcid": "0009-0009-8067-768X", "display_name": "Brackney, Helen Maya" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/y324-9f36", "abstract": "The peptidoglycan layer in bacterial cells is a popular target for antibiotic development. The membrane protein MraY and peripheral membrane protein MurG are part of critical steps in the synthesis of peptidoglycan. Lipid I, a lipid precursor formed by MraY, is recognized by MurG through its soluble domain. Currently, there is no structure of MurG with bound Lipid I, and the residues required for this interaction have not been conclusively defined. Crystallographic methods and Cryo-Electron Microscopy were applied to study the interactions between MurG and the soluble domain of Lipid I by binding Park\u2019s Nucleotide, Lipid II, or a Lipid I analog were used to study the interactions of MurG and MraY with the aforementioned substrates. By adding Park\u2019s Nucleotide, Murgocil, Lipid II, the Lipid I analog, or a combination of the listed additives to concentrated MurG, crystals formed under optimized conditions. We aim to obtain electron-density maps from these techniques to model the structure of MurG." }, { "name": "Bruening, Meaghan Ann", "degree": "PhD", "year": "2024", "title": "Applications of Synthesis in Copolymer Upcycling, Reduction of CO\u2082, Ligand Non-Innocence, and New Weakly-Coordinating Anions", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-222310291", "creators": [ { "name": { "family": "Bruening", "given": "Meaghan Ann" }, "id": "Bruening-Meaghan-Ann", "orcid": "0000-0001-8132-9497", "display_name": "Bruening, Meaghan Ann" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dm7p-vv68", "abstract": "This dissertation focuses on a very diverse series of studies with synthetic applications to organometallic systems supported by a redox non-innocent ligand architecture, \u03b1,\u03c9 diene generation, ionomers for tuning performance of electrochemical CO2 reduction, and design of new weakly coordinating anions.
\r\n\r\nChapter 2 discusses the reactivity of a 9,10-anthracenediyl bis(phenoxide) titanium complex, where the polyaromatic anthracene motif functions as a non-innocent ligand. This enables access to a reduced Ti complex which is competent for oxidative coupling of alkyne and nitrile substrates, and pyrimidines and substituted benzenes can be accessed catalytically. Additional reactivity with oximes and oxidative coupling of alkynes and CO2 is explored.
\r\n\r\nChapter 3 reports a two-step method for generation of a distribution of \u03b1,\u03c9-dienes from ethylene and butadiene. Copolymers are prepared with variable butadiene content, where 1,4-butadiene incorporation ensures the double bonds are in the polymer backbone. Subsequent ethenolysis of the copolymers produces \u03b1,\u03c9-dienes in the C10-C20 range. The conditions can be modified to control product selectivity.
\r\n\r\nChapter 4 presents a series of polystyrene-based ionomers to probe the impact of local [K+] in the Cu electrode microenvironment on CO2R performance (Part A). Partial current density towards C2+ products (|jC2+|) increases with [K+] in ionomer, up to 225 mA cm\u20132. When K+ is replaced with [Me4N]+, performance lowers to the level of bare Cu, highlighting the crucial role of K+ in improving C2+ product selectivity. Molecular dynamics simulations and partial pressure CO2 experiments support enhanced CO2 mass transport with the ionomers. An expanded series of ionomers is presented (Part B), where the incorporation of different neutral comonomers (vinyl biphenyl) and cross-linking monomers (biphenyl and terphenyl) dramatically boosts performance. Direct tends between K+ content and CO2R performance are not observed with the expanded series, highlighting the non-innocent role of the neutral monomer and polymer structure.
\r\n\r\nChapter 5 presents a new, Si-based weakly-coordinating anion. A library of anions bearing a variety of R groups is prepared, enabling facile tuning of sterics and solubility. A range of cations employed in chemical reactivity is supported by these anions, including ether-free alkali cations, Ph3C+, and an ethylene/CO copolymerization catalyst [Pd(dppe)(NCMe)Me]+ (generated by salt metathesis or protonation of a metal-alkyl bond). Electrochemical studies on the [Bu4N]+ variant show an exceptionally wide stability window for the [MeSiF]- anion of 7.5 V in MeCN. The [C6F5SiF]- variant can be readily modified to access additional diverse and/or dianionic variants.
\r\n\r\nChapter 6 discusses the electrochemical performance of a new class of magnesium electrolytes for next-generation batteries. [Mg(DME)3][MeSiF]2 demonstrates remarkable performance with good stability, moderate conditioning, high coulombic efficiency ( > 96%), and high current density ( ~100 mA cm-2). However, the sensitivity of the experiments requires careful study of many parameters including impact of MgR2 additives (identity and concentration), cycling protocol, synthetic route, and the Pt working electrode to understand how the electrochemical performance is impacted. While addition of MgMe2 improves electrochemical performance, it is not inherently required for reversible Mg deposition and stripping. Following an extensive investigation of the cyclic voltammetry (CV) performance of [Mg(DME)3][MeSiF]2, preliminary screening of additional [Mg(DME)3][RSiF]2 variants is discussed.
\r\n\r\nAppendix I discusses the characterization of ethylene/\u03b1-olefin copolymers generated from monometallic and bimetallic Zr catalysts. The decreased polar monomer incorporation for the bimetallic vs. monometallic catalysts is attributed to the steric clash of larger comonomers with the distal metal site in bimetallic catalysts.
\r\n\r\nAppendix II discusses the preparation of bulky anthracene phenoxide ligands for Ti and Ta.
\r\n\r\nAppendix III discusses the preparation of mixed aryl/hydride borates as electrolytes for next-generation Mg batteries.
" }, { "name": "Buenconsejo, Reina S.", "degree": "PhD", "year": "2024", "title": "Clearing the Air: A Chemical Approach to Understanding Secondary Organic Aerosol Formation From Volatile Chemical Products", "advisor": "Seinfeld, John H.; Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302024-161447176", "creators": [ { "name": { "family": "Buenconsejo", "given": "Reina S." }, "id": "Buenconsejo-Reina-S", "orcid": "0000-0002-0162-905X", "display_name": "Buenconsejo, Reina S." } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "co-advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "co-advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6sq5-5m61", "abstract": "Understanding sources of air pollution is critically important as ~7 million premature deaths are associated with poor air quality. A key component of urban air quality is secondary organic aerosol (SOA), a type of particulate matter that contributes smog. SOA is formed via the reactive oxidation of volatile organic chemicals (VOCs), gas-phase compounds often emitted from anthropogenic sources. Historically, SOA formation and VOC emissions have been driven by on-road mobile sources. In recent years, however, other sources, such as consumer and industrial solvents - so called volatile chemical products (VCPs) - have become increasingly more important. SOA also impacts climate change, as particulate matter affects global radiative forcing. \r\n\r\nCharacterizing the chemistry and SOA formation from VCPs can elucidate our understanding of modern urban air pollution, particularly as we try to uncover recent stagnation in air quality. Because VCPs are comprised of hundreds of individual chemical compounds, it is exceedingly difficult to study and characterize each one individually. By contrast, understanding these compounds through a chemistry lens can help to make broader generalizations about larger classes of compounds. \r\n\r\nThis dissertation looks at the chemistry leading to SOA formation from several chemicals that make up VCPs. Specifically, this work looks at benzyl alcohol and ethoxyethanol. These compounds are used in personal care products, cleaning products, architectural coatings and adhesives. Understanding the reactivity of these compounds can help us understand more broadly the chemistry and SOA potential of other chemicals in VCPs that have similar chemical structures." }, { "name": "Buss, Marjorie Theresa", "degree": "PhD", "year": "2024", "title": "Tools for Noninvasive Imaging and Control of Engineered Bacteria In Vivo", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292024-221307093", "creators": [ { "name": { "family": "Buss", "given": "Marjorie Theresa" }, "id": "Buss-Marjorie-Theresa", "orcid": "0000-0002-4266-9197", "display_name": "Buss, Marjorie Theresa" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "chair", "display_name": "Newman, Dianne K." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/mvgg-ch02", "abstract": "Genetically engineered bacteria are promising new cell-based diagnostic and therapeutic agents due to their ability to sense and respond to unique signals, access and interface with hard-to-reach areas of the body, and deliver therapeutics directly to these areas. However, currently tools to noninvasively monitor and control their activity in vivo are limited. Optical imaging methods, which are based on fluorescent and luminescent reporter genes, and optogenetics, which are based on light-activated proteins, are widely used in cell culture and rodent studies. However, these optical methods suffer from the poor penetration depth of light in tissue which limits their use in larger animals or humans. On the other hand, nuclear imaging methods such as PET and SPECT have good imaging depth but rely on radioactive tracers whose synthesis can be complex and exposes patients to radiation. Here I present tools for imaging and control of bacteria that based on non-ionizing forms of energy that easily penetrate tissue: sound waves and magnetic fields.
\r\n\r\nThe first two parts of my thesis focuses on imaging bacteria in vivo with ultrasound, which is a widely available imaging modality that does not use ionizing radiation and has tissue penetration depth of several centimeters. Bacteria can be imaged with ultrasound by expressing acoustic reporter genes (ARGs) which result in the production of gas vesicles (GVs), air-filled protein nanostructures that aquatic microbes use to regulate their buoyancy. However, the first-generation acoustic reporter genes expressed too poorly under in vivo conditions to enable ultrasound imaging of bacteria in therapeutically relevant contexts. Here, we present a new and improved ARG construct that produces high levels of robust gas vesicle expression in the probiotic bacterium E. coli Nissle (EcN), enabling ultrasound imaging of these cells with high sensitivity. This second-generation ARG construct, bARGSer, uses genes derived from Serratia sp. ATCC 39006 and was optimized for plasmid-based expression in EcN. We demonstrate that with bARGSer, we can visualize the spatial distribution of engineered EcN after they home to and colonize tumors upon systemic administration. We also demonstrate that the engineered EcN can be imaged with ultrasound when colonizing the gastrointestinal tract of mice after sensing dietary sugars as well as biomarkers of inflammation. By enabling monitoring of the precise spatial location of engineered probiotic bacteria inside the body, this technology could greatly improve the development and eventual clinical use of this emerging class of microbial cell-based theranostics.
\r\n\r\nThe last part of my thesis focuses on control of bacteria in vivo with magnetic fields. Many bacteria have limited ability to selectively colonize specific targeted regions of the GI tract due to a lack of external control over their location and persistence. Magnetic fields are well suited to provide such control due to their ability to freely penetrate biological tissues, but they are difficult to apply with enough strength to directly manipulate magnetically labeled cells within deep tissue or viscous environments such as in the GI tract. Here, we show that ingestible micron-sized magnetic particles, combined with an externally applied magnetic field, act as in vivo magnetic field gradient amplifiers, enabling the trapping and retention of orally administered probiotic E. coli within the mouse GI tract. This technology improves the ability of these probiotic agents to accumulate at specific locations and stably colonize without antibiotic treatment. By enhancing the ability of GI-targeted cellular agents to be at the right place at the right time, cellular localization assisted by magnetic particles (CLAMP) adds external physical control to an important emerging class of biotherapeutics.
" }, { "name": "Cagan, David Abraham", "degree": "PhD", "year": "2024", "title": "Exploring the Photophysics and Reactivity of Nickel\u2013Bipyridine Cross-Coupling Catalysts", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092024-225449838", "creators": [ { "name": { "family": "Cagan", "given": "David Abraham" }, "id": "Cagan-David-Abraham", "orcid": "0000-0002-4719-2789", "display_name": "Cagan, David Abraham" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/n3xz-6v34", "abstract": "Ni(II)\u2013bipyridine (bpy) aryl halide complexes have been prized for nearly a decade for their catalytic potency to facilitate cross-coupling reactions. To achieve these transformations, the energy from light is leveraged to drive the key catalytic processes. Thus, Ni-mediated photoredox catalysis provides an attractive and sustainable means to replace precious metal catalysts. However, precise mechanistic information regarding how these transformations occur is limited. This thesis thus focuses on a dual experimental and computational analysis of Ni(II)\u2013bpy aryl halide complexes and their photoproducts to provide insight into the specific photophysical and chemical pathways that these catalysts undertake for cross-coupling reactions. The first chapter is a review of the proposed mechanisms presented for Ni-mediated photoredox catalysis. Therein, certain portions of this work are also summarized. The second chapter provides a computational description of the Ni(II) excited states. The third chapter expands on this analysis with experiment, elucidating the photophysical pathway that grants entry into dark Ni(I)/Ni(III) catalytic cycles. Together, chapters two and three show that Ni(II)\u2013bpy aryl halide complexes form low-valent Ni(I)\u2013bpy halide species by an aryl-to-Ni ligand-to-metal charge transfer. Chapter four outlines a method to generate and study these reactive Ni(I)\u2013bpy halide intermediates, identifying their mechanism of C(sp2)\u2013Cl bond activation as nucleophilic aromatic substitution, tunable via the energies of the 3d-orbitals and the effective nuclear charge of Ni. The final chapter finds that these low-valent Ni species are competitive light-absorbers, and it presents a study into their ultrafast photophysics, marking the first of its kind on any Ni(I) complex. The excited-state relaxation dynamics of Ni(I)\u2013bpy halide complexes are well described by vibronic Marcus theory, spanning the normal and inverted regions as a result of simple changes to the bpy substituents. Altogether, these studies have provided a framework to gain electronic structural control over Ni-meditated photoredox catalysis and, thus, guides the use of photonic energy as a sustainable alternative to precious metal catalysis.
" }, { "name": "Chan, Tsam Mang Melinda", "degree": "PhD", "year": "2024", "title": "Asymmetric Total Synthesis of Havellockate and Investigation into Chiral Palladium Enolate: Synthesis, Reactivity, and Applications", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-082931807", "creators": [ { "name": { "family": "Chan", "given": "Tsam Mang Melinda" }, "id": "Chan-Tsam-Mang-Melinda", "orcid": "0000-0002-2495-0110", "display_name": "Chan, Tsam Mang Melinda" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/kb44-n573", "abstract": "Research in the Stoltz group focuses on the synergy of complex natural product synthesis and method development in that we strive to invent new and efficient methodologies that have great synthetic potential in the use for pharmaceuticals and natural products. Herein we describe an asymmetric total synthesis of Havellockate, a polycyclic furanobutenolide-derived cembranoid diterpenoid that exhibits biological activities such as anti-inflammatory, anti-microbial, and cytotoxic. The strategy for this synthesis is highlighted by a convergent Julia\u2013Kocienski olefination, followed by an acylation/intramolecular [4+2] cycloaddition cascade, which furnishes the main core of the natural product in high efficiency.
\r\n\r\nAnother synthetic route toward the total synthesis of Havellocate is presented, using a propargyl ether as a key intermediate. Though the route was unfruitful in compleing the synthesis, the Diels\u2013Alder cascade had significant improvement of yield and stability with this route, and it constitutes tremendous value for the synthesis of other targets within the furanobutenolide-derived natural product family.
\r\n\r\nNext, the synthesis, isolation, and reactivity of a chiral Pd enolate is described. The Pd enolate is arose by an alpha bromo acetophenone oxidative addition complex with Pd2(dba)3 and PHOX ligand. A crystal structure is obtained to show that the enolate is C- bound and highly regioselective. The novelty of this isolation can shine light on the applications of such Pd enolate for future developments.
\r\n\r\nThen, we outlined a Pd-catalyzed asymmetric vinylation of \u03b3-lactams to construct all-carbon quaternary stereocenters. The use of canonically inactive vinyl chloride electrophiles afforded the highest yields and levels of stereoselectivity, and a range of tri-substituted vinyl chlorides were found to be proficient in promoting this transformation. These stereogenically congested products could be further elaborated to functionally rich scaffolds, proving the synthetic utility of this transformation.
\r\n\r\nLastly, we describe the work of organizing the inaugural Day of Inclusion event of CCE. The event was orchestrated by the Diversity in Chemistry Initiative (DICI), aimed to foster cohesion and to inspire concerted efforts towards Diversity, Equity, and Inclusivity (DEI) within the Chemistry and Chemical Engineering (CCE) division at Caltech.
" }, { "name": "Chao, Wen", "degree": "PhD", "year": "2024", "title": "Spectroscopy and Kinetics of Reactive Intermediates in the Atmosphere of Venus: the Catalytic Role of Chlorine Atoms", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202024-220341626", "creators": [ { "name": { "family": "Chao", "given": "Wen" }, "id": "Chao-Wen", "orcid": "0000-0003-0602-1606", "display_name": "Chao, Wen" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "orcid": "0000-0002-4263-2562", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/v9ey-m476", "abstract": "Chlorine chemistry plays essential roles in both industrial and academic fields due to the special reactivity required to initiate or catalyze important reactions in our daily life. For example, Cl atoms are the most common oxidation agents in combustion and are famous for the catalyzed destruction of ozone that eventually leads to the ozone hole.
\r\n\r\nAs terrestrial planets, Venus and Earth\u2019s atmospheres have similar origins but very different evolutions. Compared to Earth, Venus suffers strong water loss in hydrodynamics escape due to its distinct distance from the Sun; as a result, high abundances of chlorine and sulfur species are not trapped in the sea and survive in Venus\u2019 atmosphere. For example, a dense cloud, made with sulfuric acid, has been observed at the middle altitude (50 - 70 km) and the concentration profiles for distinct species (SO\u2082, CO, CO\u2082, O\u2082 ..., etc.) have been measured during the Venus Express mission operated by the European Space Agency. Digging into the discrepancy between the observations and model simulations, a few important questions arose, and further laboratory studies are needed to solve the puzzles, including (1) the unknown UV absorber, (2) the SO\u2082 concentration inversion at high altitude and (3) the extremely low O\u2082 and high CO\u2082 abundances, wherein a reactive chlorine atom is proposed for explaining these phenomena.
\r\n\r\nIn this thesis, we performed the pulsed-laser photolysis experiments with a homemade time-resolved broadband UV-Vis transient-absorption spectroscopy coupled with a temperature- and pressure-controlled flow reactor to study the spectroscopic and kinetic\r\nproperties of key intermediates (ClSO, ClCO and ClCO\u2083) in the oxidation process of sulfur and carbon to ultimately form SO\u2082 and CO\u2082. The recorded spectra are analyzed, and highlevel ab initio calculations were performed to rationalize the electronic structures of target molecules to reveal the catalysis role of Cl atoms. In addition, key reaction rate coefficients\r\n(ClSO + Cl, kClSO+Cl(292 K) = (1.48 \u00b1 0.42)x10-11 cm\u00b3 molecule-1 s-1; ClCO + O\u2082,\r\nkClCO+O\u2082(0) = (9.0 \u00b1 2.3) \u00d7 10-32 cm\u2076 s-1 a cm\u00b3 molecule-1 s-1, and thermodynamic property (Cl + CO \u21cc ClCO, Keq = 1.8 x10-18 molecules cm\u207b\u00b3) have been measured to\r\nfurther assist the model simulations.
\r\n\r\nThis thesis not only offers essential data for model simulations to understand the complex chemistry in Venus' atmosphere but also provide new insights to guide future tasks to explore Venus, e.g. DAVINCI+ and VERITAS by NASA.
" }, { "name": "Csernica, Timothy Andrew", "degree": "PhD", "year": "2024", "title": "Exploring Nature\u2019s Fingerprints with Isotopic Distributions", "advisor": "Eiler, John M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312024-185929614", "creators": [ { "name": { "family": "Csernica", "given": "Timothy Andrew" }, "id": "Csernica-Timothy-Andrew", "orcid": "0000-0002-5273-0721", "display_name": "Csernica, Timothy Andrew" } ], "advisors": [ { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "orcid": "0000-0001-5768-7593", "role": "advisor", "display_name": "Eiler, John M." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "orcid": "0000-0001-5768-7593", "role": "member", "display_name": "Eiler, John M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zt08-jh39", "abstract": "This thesis examines the measurement and interpretation of isotopic distributions and the application of these techniques to forensic questions. Stable isotope abundances are a powerful tool for examining a compound\u2019s history. However, their use is complicated by the fact that 1) isotope substitutions can occur at many positions of a molecule, resulting in a combinatorial increase in possible combinations of isotopes (or isotopologues) with molecule size, and 2) it is difficult to experimentally distinguish between isotopologues, so observational data averages over many isotopologues with distinct properties and histories. We here develop experimental and theoretical strategies to address these questions via observations of the isotopic distributions of small organic compounds obtained by Orbitrap mass spectrometry. In Chapter II, we develop mathematical procedures for manipulating and tracking isotopologues through various experimental designs, allowing us to make precise statements about how observable quantities are affected by underlying physical and chemical processes. Chapters III and IV explore corresponding experimental methods: Chapter III presents a sample introduction technique for the long duration observations required to measure rare, multiply substituted isotopologues, while Chapter IV applies these to observe 146 isotopic properties of methionine, a model analyte. We then explore the use of these Orbitrap methods to applied science problems. In Chapter V, we characterize the 13C and 2H enrichment of methylphosphonic acid, a breakdown product of sarin precursors, and examine the signatures of its synthesis methods. In Chapter VI, we apply these techniques to extraterrestrial, abiotic syntheses of nucleobases, focusing on the chemistry of adenine. These results are interpreted in the context of proposed extraterrestrial syntheses of adenine and other purine nucleobases and used to predict the isotopic distributions of these compounds.
" }, { "name": "Cusumano, Alexander Quinn", "degree": "PhD", "year": "2024", "title": "Asymmetric Pericyclic Transformations from Reactive Palladium Intermediates", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06222023-231753197", "creators": [ { "name": { "family": "Cusumano", "given": "Alexander Quinn" }, "id": "Cusumano-Alexander-Quinn", "orcid": "0000-0002-2914-2008", "display_name": "Cusumano, Alexander Quinn" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/b0wn-wt67", "abstract": "The Pd-catalyzed decarboxylative asymmetric allylic alkylation of enolate nucleophiles is a cornerstone of our groups\u2019 efforts to develop methodologies that directly facilitate the synthesis of stereochemically complex molecular building blocks. This thesis first focuses on our efforts to deepen our mechanistic understanding of these transformations. We then employ our insights as a base from which we expand the scope of the decarboxylative asymmetric allylic alkylation reaction, as well as develop entirely novel reaction paradigms." }, { "name": "Denman, William Thomas Plent", "degree": "PhD", "year": "2024", "title": "The Birth of PICL: New Laboratory Experiments for Understanding Ocean Worlds", "advisor": "Brown, Michael E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01122024-002204703", "creators": [ { "name": { "family": "Denman", "given": "William Thomas Plent" }, "id": "Denman-William-Thomas-Plent", "orcid": "0000-0003-4752-0073", "display_name": "Denman, William Thomas Plent" } ], "advisors": [ { "name": { "family": "Brown", "given": "Michael E." }, "id": "Brown-M-E", "orcid": "0000-0002-8255-0545", "role": "advisor", "display_name": "Brown, Michael E." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Brown", "given": "Michael E." }, "id": "Brown-M-E", "orcid": "0000-0002-8255-0545", "role": "member", "display_name": "Brown, Michael E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/erq7-vb46", "abstract": "A laboratory set up was built analogous to that of the environment of the Galilean system. Previous work has focused on vapor deposition and shied away from bulk samples which more closely resemble the surface of Europa. The focus of this research has been the relationship between laboratory data to observational spectra collected. Data from various telescopes has given an indication of the species which exist on the surface of Europa. Linear spectral modeling has not been effective in identifying these species due to a lack of viable candidates.\r\nChapter II focuses on the instrumentation and sample preparation for the laboratory set up. In Chapter III data is presented on the irradiation of sodium chloride at Europa like conditions and the features that arise with cryogenic irradiation. This data is compared to observational data from HST and provides strong evidence for the presences of sodium chloride (NaCl) on Europa's leading hemisphere. Chapter IV presents FTIR and UV/VIS data for the irradiation of sulfate salts suspected to be present on Europa. This presents one of the first instances of cyrogenic electron irradiation of sulfates compared to new data from JWST. Mechanisms for the trapping of carbon dioxide at both Europa and Ganymede have also been investigated. These experiments are paramount for understanding the composition of Europa\u2019s ocean and can be utilized by the Europa Clipper team. Future experiments involving laboratory spectroscopy of carbon dioxide trapping are also highlighted. The use of cyrogenic gamma irradiation experiments and their feasibility are explored." }, { "name": "Dilanyan, Taleen Gaied", "degree": "PhD", "year": "2024", "title": "Open-Source Custom Beads for Single-Cell Transcriptomics", "advisor": "Pachter, Lior S.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01162024-161326655", "creators": [ { "name": { "family": "Dilanyan", "given": "Taleen Gaied" }, "id": "Dilanyan-Taleen-Gaied", "orcid": "0000-0002-3131-3259", "display_name": "Dilanyan, Taleen Gaied" } ], "advisors": [ { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "advisor", "display_name": "Pachter, Lior S." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "member", "display_name": "Pachter, Lior S." } ], "option_major": [ "chemistry" ], "doi": "10.7907/v52p-gf80", "abstract": "Open-source single-cell genomics technologies have helped democratize single-cell genomics and expedite method development. Methods such as inDrops and Drop-seq for single-cell RNA-seq preceded popular technologies such as the 10x Genomics\u2019 Chromium platform, however despite initial enthusiasm for open-source methods, their popularity has waned. A major reason has been the lack of availability of low-cost, customizable beads, which are essential for microfluidics based single-cell RNA-seq. We address this challenge by introducing a new method for producing barcoded hydrogel beads for single-cell RNA-seq called HiPER (High-throughput PER-barcoded hydrogel beads) that allows for increasing the diversity of barcode sequences, reducing manufacturing cost, and that can be readily adapted to custom applications. HiPER barcodes are decoupled from the capture sequences and can therefore be configured to capture RNA, DNA, or tailored for specific-gene enrichment." }, { "name": "Du, Jiajun", "degree": "PhD", "year": "2024", "title": "Vibrational Imaging for Chemical Biology: from Label-Free to Molecular probes", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:11032023-041429778", "creators": [ { "name": { "family": "Du", "given": "Jiajun" }, "id": "Du-Jiajun", "orcid": "0000-0003-2693-834X", "display_name": "Du, Jiajun" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dm1y-r078", "abstract": "Since the invention of stimulated Raman scattering (SRS) microscopy in 2008, vibrational imaging is increasingly recognized as a powerful tool for biological investigation. As the most suitable far field vibrational imaging modality for live biological studies, SRS microscopy is taking the lead role within its vibrational counterparts with desired sensitivity and image quality. The totally different mechanism of generating vibration signals from fluorescence signals determines the special features of vibrational imaging. Bond vibration originating signals provide inherent optical contrast for every molecule and the quantitative manner allows straightforward quantification. Since the inception, SRS microscopy has achieved large success in label-free imaging. Label-free imaging avoids tedious labeling step and has the least perturbation to the biological samples but with limited sensitivity and specificity. The introducing of labeling starting about 10 years ago opens up a new avenue for SRS microscopy to tackle the fundamental limitations of label-free approaches. Whether to use label-free or molecular probes for SRS microscopy depends on the specific studies. This thesis aims to utilize SRS microscopy (both label-free and minimally labeling) for metabolic study and develop new molecular probes for SRS microscopy.
\r\n\r\nWe start from comparing different vibrational imaging modality and fluorescence imaging and conclude that SRS is the best vibrational imaging technique for biological samples. Then we discuss the features of label-free, bioorthogonal labeling and super-multiplexed SRS imaging. The minimally perturbative triple bond tagging and isotope labeling makes SRS especially suitable for tracking metabolites and accessing metabolic pathways. Furthermore, we also summarize the design principles for functional Raman imaging probe development based on their spectroscopic signatures. (Chapter 1).
\r\n\r\nNon-invasively probing metabolites within single live cells is highly desired but challenging. We explored Raman spectro-microscopy towards spatially-resolved single cell metabolomics, with the specific goal of identifying druggable metabolic susceptibilities from a series of patient-derived melanoma cell lines. The chemical composition analysis of single cell and single organelle lipid droplets identified the fatty acid synthesis pathway and lipid mono-unsaturation as druggable susceptibility. More importantly we revealed that inhibiting lipid mono-unsaturation leads to cellular apoptosis accompanied by the formation of phase-separated intracellular membrane domains. (Chapter 2).
\r\n\r\nNext, we established a first-in-class design of multi-color photoactivatable Raman probes for subcellular imaging and tracking. The fast photochemically generated alkynes from cyclopropenones enable background-free Raman imaging with desired photocontrollable features. After necessary molecule engineering to improve the biocompatibility and sensitivity, we generated organelle-specific probes for targeting mitochondria, lipid droplets, endoplasmic reticulum, and lysosomes. Multiplexed photoactivated imaging and tracking at both subcellular and single-cell levels was also demonstrated to monitor the dynamic migration and interactions of the cellular contents. (Chapter 3).
\r\n\r\nFurther improvement of the Raman signal with molecular probes is a central topic for Raman imaging. Recently developed electronic preresonance (epr) probes boost Raman signals and pushed SRS sensitivity close to that offered by confocal fluorescence microscopy. To guide the development of even stronger Raman probes and fill the final gap between epr-SRS probes and single molecule imaging, the structure-function relationship of epr-SRS probes is indispensable. We therefore used ab initio approach employing the displaced harmonic oscillator (DHO) model for calculating the epr-SRS signals, which proves to provide a consistent agreement between simulated and experimental SRS intensities of various triple-bond bearing epr-SRS probes. The theory also allows us to illustrate how the observed intensity differences between molecular scaffolds stem from the coupling strength between the electronic excitation and the targeted vibrational mode. Utilizing the discovered structure-function relationship of epr-SRS probes, we engineered MARS palette for higher sensitivity. With chemical modification to improve Raman mode displacement or enhance transition dipole moment or adjust detuning, we enhance the signal of alkynyl pyronins and nitrile pyronins, setting the current sensitivity records for small molecule far-field Raman probes. (Chapter 4 and 5).
" }, { "name": "Evans, John Matthew", "degree": "PhD", "year": "2024", "title": "Impact of Interfacial Chemistry on Corrosion, Sensing, and Catalytic Properties of Materials", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202024-184723401", "creators": [ { "name": { "family": "Evans", "given": "John Matthew" }, "id": "Evans-John-Matthew", "orcid": "0000-0002-8721-5316", "display_name": "Evans, John Matthew" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e033-xj27", "abstract": "Interfaces are critical for the development of new technologies spanning applications from energy to sensing. Here, electrochemical and spectroscopic investigations of interfacial chemistry reveal how the sensitivity of chemical vapor sensors can be tuned, how stoichiometry and electrolysis affect the chemical state of a Mn-based oxygen evolution catalyst, and how the presence of barrier protection layers affects the stability of photoanodes in alkaline solution. Additionally, an in-depth discussion of x-ray photoelectron spectroscopy gives advice and insight into this surface-sensitive technique and several practical examples are discussed." }, { "name": "Gao, Shilong", "degree": "PhD", "year": "2024", "title": "Engineering Heme Proteins for C(sp\u00b3)\u2013H Primary Amination", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:08242023-170135027", "creators": [ { "name": { "family": "Gao", "given": "Shilong" }, "id": "Gao-Shilong", "orcid": "0000-0003-2808-6283", "display_name": "Gao, Shilong" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gsmr-b827", "abstract": "Primary amine is one of the most prevalent moieties in synthetic intermediates and pharmaceutical compounds. The preparation of aliphatic primary amines via C\u2212H functionalization would provide direct access to the nitrogen-containing compounds from hydrocarbon substrates. While the enzymatic oxyfunctionalization of C\u2013H bonds is well established, the analogous strategy for nitrogen incorporation is unknown in Nature. Likewise, a synthetic method for selective primary amination of aliphatic C\u2013H bonds remains elusive. Combining chemical intuition and inspiration from Nature, chemists and protein engineers have created new heme-containing enzymes for the C(sp\u00b3)\u2013H primary amination via directed evolution. This thesis describes some of the efforts in the continued pursuit of these new-to-nature reactions. Chapter I discusses directed evolution in the context of biocatalysis, the strategies for introducing new-to-nature chemistry in enzymes, the discovery of nitrene transferases from the cytochrome P450 monooxygenase, and finally, the development of C(sp\u00b3)\u2013H primary aminases. Chapter II details the discovery and engineering of serine-ligated cytochrome P411 enzymes that catalyze the first primary amination of C(sp\u00b3)\u2013H bonds with excellent selectivity, affording a broad scope of enantioenriched primary amines. Chapter III demonstrates that these new-to-nature nitrene transferases were engineered to aminate and amidate unactivated, unbiased C(sp\u00b3)\u2013H bonds with unprecedented selectivity. In Chapter IV, engineered protoglobins are shown to utilize hydroxylamine (NH\u2082OH) for nitrene transfer reactions, including benzylic C\u2013H primary amination and styrene aminohydroxylation. Overall, these new-to-nature reactions can be considered the nitrogen analogs to the C\u2013H oxidation chemistry performed by monooxygenases and peroxygenases. By offering a direct path from saturated precursors, these enzymes present a new biochemical logic for accessing nitrogen-containing compounds. Finally, this work hints at the possible future discovery of natural enzymes that use hydroxylamine precursors for amination chemistry.
" }, { "name": "Goronzy, Isabel Nadine", "degree": "PhD", "year": "2024", "title": "Higher-Order Chromatin States and Nuclear Structures Regulating Gene Expression", "advisor": "Guttman, Mitchell", "url": "https://resolver.caltech.edu/CaltechTHESIS:07272023-175309910", "creators": [ { "name": { "family": "Goronzy", "given": "Isabel Nadine" }, "id": "Goronzy-Isabel-Nadine", "orcid": "0000-0002-6713-9192", "display_name": "Goronzy, Isabel Nadine" } ], "advisors": [ { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "advisor", "display_name": "Guttman, Mitchell" } ], "committee": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "chair", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Chong", "given": "Shasha" }, "id": "Chong-Shasha", "orcid": "0000-0002-5372-311X", "role": "member", "display_name": "Chong, Shasha" }, { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "member", "display_name": "Pachter, Lior S." } ], "option_major": [ "biochem" ], "doi": "10.7907/8gm2-jn84", "abstract": "Although the same genome is present in every cell, each cell type orchestrates a distinct gene expression program, which can be rapidly adapted in response to stimuli. Accordingly, gene regulation is a highly complex, context-specific process that involves the dynamic interplay between numerous regulatory factors. Most methods to study these regulatory factors only measure pairwise interactions between molecules and are limited to mapping one regulatory protein at a time. Consequently, the combinatorial complexity of gene regulation at individual genomic loci and the functional consequence of many regulatory factors remain underexplored. To address this, we have developed new sequencing-based approaches and computational analyses to comprehensively profile, at unprecedented scale, the diverse gene regulatory landscape and directly establish the link between regulatory factors and transcriptional outcomes. In Chapter 2, we present Chromatin Immunoprecipitation Done-In-Parallel (ChIP-DIP), a highly multiplexed method for mapping hundreds of proteins to DNA within a single sample. ChIP-DIP increases the throughput of existing methods by > 100-fold and enables the production of consortium-scale, cell type-specific data within a single lab. Capitalizing on the scale and diversity provided by ChIP-DIP, we uncover unique quantitative combinations of histone modifications that define distinctive classes of regulatory elements. Specifically, we find features distinguishing classes of promoters that correspond to different polymerase activity, transcriptional levels, and gene types and find acetylation patterns distinguishing classes of enhancers that exhibit distinct activity states, induction potential, and regulatory potential. Next, in Chapter 3, we apply RNA-DNA SPRITE (RD-SPRITE), a method for simultaneous measurement of RNA and DNA organization, to investigate the functional relationship between genome structure and transcription. We demonstrate that RD-SPRITE precisely detects individual, nascent pre-mRNAs at their transcriptional locus and, as a result, can be used to assess the 3D genome structure present during active transcription. We find that RNA polymerase II transcription occurs within genomic structures previously thought to be inactive, such as the B compartment and DNA regions near the nucleolus. This suggests that active transcription can occur throughout the nucleus and argues against structural domains that preclude transcription. Overall, our findings highlight the ability of RD-SPRITE to establish a structure-function link. Finally, in Chapter 4, we apply RD-SPRITE to study the transcriptional dependence of nuclear organization. We demonstrate that transcriptional inhibition leads to the loss of high-order structure around multiple RNA-processing bodies \u2014 the nucleolus, the scaRNA hub and the histone locus body \u2014 that are responsible for essential nuclear functions such as RNA processing and gene regulation. These findings suggest a role for RNA and nascent transcription in the formation and maintenance of long-range 3D contacts and critical nuclear compartments. In summary, we have developed new approaches to explore epigenomic and organizational complexity within the mammalian nucleus and have uncovered genome-wide principles of gene regulation.
" }, { "name": "Grayson, Robert Wall", "degree": "PhD", "year": "2024", "title": "Low-Energy Plasma\u2013Surface Interactions at Airless Icy Bodies", "advisor": "Giap, Konstantinos P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-222110855", "creators": [ { "name": { "family": "Grayson", "given": "Robert Wall" }, "id": "Grayson-Robert-Wall", "orcid": "0000-0002-8044-9654", "display_name": "Grayson, Robert Wall" } ], "advisors": [ { "name": { "family": "Giap", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "advisor", "display_name": "Giap, Konstantinos P." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Nordheim", "given": "Thomas A." }, "id": "Nordheim-Thomas-A", "orcid": "0000-0001-5888-4636", "role": "member", "display_name": "Nordheim, Thomas A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/fn7c-k591", "abstract": "Low-energy plasma surface interactions occur in many solar system environments and are especially important in the magnetospheres of gas giants. Within these magnetospheres orbit a catalogue of icy moons, some of which famously host interior liquid-water oceans. They are continuously exposed to a cold, corotating plasma \u201cwind,\u201d resulting in bombardment by heavy reactive ions, with peak number fluxes in the hyperthermal energy regime (10s to 100s of eV). Despite their abundance, these low-energy ions have been mostly overlooked in planetary science because they are poor drivers of radiolysis. In this thesis we take a combined experimental-theoretical approach to understanding the interaction of hyperthermal water group molecules/ions with relevant surfaces, motivated by some specific solar system observations, mostly from the Saturn system.
\r\n \r\nWe begin with experimental case studies of water-group ion scattering on carbonaceous (Chapter 2) and chloride-salt surfaces (Chapter 3), focusing on the emission of secondary negative ions. For carbonaceous surfaces, we detect surprisingly energetic carbon fragments, apparently emitted by near-threshold sputtering processes. The most abundant products (O\u207b, C2\u207b, C2H\u207b) are consistent with mass range for negative PUIs of unknown origin observed near Dione and Rhea. The reported mass ranges, however, have been estimated for pick-up of initially stationary ions, which is a poor assumption for the products we observe. Our experiments with chloride salts (relevant to Jupiter\u2019s moon Europa) are complicated by surface charging but provide kinematic evidence of reactive scattering and single knock-on sputter processes. Specifically, we observe abstraction of Cl from Pt to form chlorine monoxide anions. We then describe a modification of our scattering apparatus to enable exposure of ice targets, developing a one-of-a-kind experimental facility (Chapter 6). Some limited and preliminary results for Ar\u207a and O\u207a bombardment of amorphous water ice follow, which are more revealing of experimental challenges than of surface chemistry and dynamics.
\r\n \r\nOur theoretical efforts include Reactive Molecular Dynamics simulations of collision-induced chemistry in ices using the ReaxFF formalism. These reveal a novel non-radiolytic process (an Eley-Rideal reaction) for formation of molecular oxygen in low-energy (2\u221250 eV) water-group molecule bombardment of crystalline water ice, relevant to the maintenance of O\u2082 exospheres at Saturn\u2019s moons Dione and Rhea (Chapter 4). With the addition of CH\u2084 to the ice (as a clathrate), bombardment results in formation of methanol and formaldehyde at yields as great as 10% and 5%, respectively (Chapter 5). Two mechanisms are observed for methanol synthesis: one a typical radiolysis process and the second a two-step non-radiolytic mechanism. We provide preliminary results for an HCN/CH\u2084/H\u2082O ice target in Chapter 8 to motivate further study of the role that hyperthermal reactive ions play in synthesis of prebiotic organics. Finally, in Chapter 7, we describe a Monte-Carlo model for the production and transport of H\u2082 in the Enceladus due to plasma-surface interactions. Radiolysis by suprathermal electrons is the primary contributor, but the calculated mixing ratio falls several orders of magnitude short of the reported ~1%, which lends credibility to the notion that H\u2082 is being emitted from Enceladus\u2019 internal ocean.
" }, { "name": "He, Manni", "degree": "PhD", "year": "2024", "title": "Entanglement-Enhanced Bioimaging and Sensing", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262024-021912071", "creators": [ { "name": { "family": "He", "given": "Manni" }, "id": "He-Manni", "orcid": "0009-0001-4237-900X", "display_name": "He, Manni" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "chair", "display_name": "Wei, Lu" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Hong", "given": "Elizabeth J." }, "id": "Hong-Elizabeth-J", "orcid": "0000-0003-3866-418X", "role": "member", "display_name": "Hong, Elizabeth J." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3zg0-4135", "abstract": "Studies of entangled light-matter interactions have been gaining momentum because of their potential applications in bioimaging and sensing. Entangled photons are predicted to linearize nonlinear optical processes and offer orders of magnitude of enhancement to the interaction cross sections. To investigate the validity of entanglement-enhanced bioimaging techniques, a continuous wave (CW)-powered, on-chip, broadband entangled light source based on periodically poled lithium tantalate (ppLT) was designed and characterized. This light source achieved femtosecond entangled correlation times comparable to classical ultrafast lasers with an unprecedented power of ~100 nW in near-infrared (NIR), which is a crucial first step toward fully integrated, thin-film lithium niobate (TFLN)-based, visible to NIR entangled photon sources. This light source was then used for subsequent spectroscopy/microscopy experiments to systematically investigate the feasibility of entanglement-enabled microscopy techniques such as entangled two-photon absorption (ETPA) microscopy and entangled fluorescence lifetime measurements. A novel method was developed to measure fluorescence from ETPA using a spectrotemporally resolved Michelson interferometer which is good at eliminating false signals due to one-photon absorption and scattering. Careful experimental attempts at detecting virtual-state mediated ETPA from rhodamine 6G (R6G) and resonance-enhanced ETPA from indocyanine green (ICG) were made, and the ETPA signals were found to be below the instrument detection limits and often masked by one-photon effects such as scattering and linear absorption. Instead, experimental upper bounds were placed on the ETPA cross sections of the studied molecules, with an emphasis on continued improvement of the light source and instrument detection limits. On-chip entangled fluorescence lifetime imaging microscopy (entangled-FLIM) has also been identified as a new future development focus. The feasibility of the technique was demonstrated via a proof-of-principle experiment which measured the fluorescence lifetime of ICG in various solvents. Using entangled photons produced from a CW laser, the lifetime measurement scheme achieved a temporal resolution of 50 ps and a minimum measurable lifetime of 365 ps, which can be used to distinguish most biologically relevant fluorophores in the corresponding wavelength range. This experiment is a critical first step toward scalable, high-throughput, wavelength-multiplexed, and on-chip FLIM or lifetime measurements which could be used in label-free health monitoring technologies." }, { "name": "Heim, Gavin Paul", "degree": "PhD", "year": "2024", "title": "Molecular Tuning of Electrocatalysts for Generation of Commodity Chemicals", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:03302024-040656026", "creators": [ { "name": { "family": "Heim", "given": "Gavin Paul" }, "id": "Heim-Gavin-Paul", "orcid": "0000-0002-9244-6565", "display_name": "Heim, Gavin Paul" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dm95-6856", "abstract": "Improving our understanding of electrocatalytic transformations is envisioned to facilitate society\u2019s implementation of technologies that achieve a net zero carbon footprint. Carbon dioxide is one of the most emitted greenhouse gases, and improvement in CO\u2082 capture technologies along with decreasing costs of renewable energy provide an opportunity to convert this species to value-added chemicals using electrochemical processes. Tuning homogeneous and heterogeneous electrocatalyst performance with well-defined molecular species can render systems more selective and active while also allowing us to readily predict variables crucial in achieving these transformations. This thesis investigates 1) molecular and polymeric species as electrode coatings for enhanced generation of carbon-coupled products and 2) discrete electrocatalyst active sites for formation CO\u2082 reduction products at low overpotentials; generation of highly reduced liquid fuels is observed with molecular electrocatalysts supported on electrodes.\r\nChapter I provides context and background to the contents of this thesis.
\r\n\r\nChapter II discusses novel, polyaromatic molecular additives utilized for low pH CO\u2082 reduction on Cu electrodes. N-phenyl isoquinolinium triflate film facilitates high selectivity for C\u2082+ products in 0.1 M H\u2083PO\u2084/KH\u2082PO\u2084, suggesting enhancement in CO\u2082 mass transport rather than limiting proton carrier diffusion. Improvement in long-term stability and tolerance to lower pH compared to previous films is observed.
\r\n\r\nChapter III reports on a series of polystyrene-based ionomers to probe the effect of local [K\u207a] in the Cu electrode microenvironment on CO\u2082R performance. Partial current density towards C\u2082\u208a products (|jC\u2082\u208a|) increases monotonically with [K\u207a] in ionomer, up to 225 mA cm\u207b\u00b2. Replacing K\u207a with [Me4N]\u207a lowers performance to the level of bare Cu, highlighting the crucial role of K\u207a in improving C\u2082\u208a product selectivity. Molecular dynamics simulations and partial pressure CO\u2082 electrolysis experiments are consistent with enhanced CO\u2082 mass transport due to K\u207a in the film.
\r\n\r\nChapter IV discusses variation of ionomer/polymer structures to maximize CO\u2082R performance. Incorporation of neutral comonomers bearing cross-linking units rich in biphenyl and terphenyl motifs result in high current densities (~270 mA cm\u207b\u00b2) towards C\u2082\u208a products with 82% Faradaic efficiency. The analogous neutral variants (i.e., those lacking the charged comonomer) show comparable |jC\u2082\u208a| to the K\u207a-containing polymers, suggesting a non-innocent role of the aryl-rich polymers in boosting performance.
\r\n\r\nChapter V presents novel four-coordinate, dicationic Co complexes supported on carbon nanotubes capable of generating MeOH from CO\u2082. Electrolysis with CO also leads to formation of MeOH, suggesting a CO-bound complex to be a crucial intermediate in CO\u2082R to MeOH. This work highlights rare examples of molecular systems facilitating multi-electron electrochemical transformations to highly demanded commodity chemicals.
\r\n\r\nChapter VI presents work on molecular electrocatalysts bearing novel polyaromatic ligands that lower the electrocatalytic potential (Ecat) of CO\u2082R by ~310 mV compared to state-of-the-art complexes as determined via cyclic voltammetry. The extended \u03c0 system motif is more proximal to the metal center relative to previously reported nanographene-containing electrocatalysts. Well-defined characterization was obtained via single-crystal X-ray diffraction in addition to solution-state techniques. Density functional theory calculations reveal significant ligand contributions in the frontier orbitals of relevant CO\u2082R intermediates.
\r\n\r\nChapter VII highlights a polycyclic aromatic hydrocarbon (PAH) bearing twelve edge nitrogen atoms. Spectroscopy, electrochemistry, and computational results suggest a significant narrowing of the HOMO-LUMO gap compared to the N-free analogue owing to the electron-deficient extended \u03c0 system imposed by the nitrogen dopants. Changes to absorption and emission spectra from titration of the PAH with metal salts suggest that coordination chemistry provides an additional degree of freedom towards tuning electronic structure. Dramatic changes from addition of trifluoromethanesulfonic acid suggest this material to be a possible pH sensor. This approach in judiciously tuning the band gap of bulk graphene materials via saturation of the nanographene edge sites with nitrogen atoms gives rise to a novel compound with intriguing electronic properties.
\r\n\r\nAppendix A describes systematic attempts in demonstrating cascade electrocatalysis between molecular CO\u2082-to-CO complexes and pyridinium film-modified Cu towards enhanced rates of C\u2082\u208a products formation.
\r\n\r\nAppendix B provides results coupling electrodeposited imidazolium-derived films with pyridinium towards enhanced CO\u2082R to C\u2082\u208a on Cu. While promising performance is achieved, the difficulty in characterizing the films limits the tractability of these systems with respect to their impacts on the microenvironment.
\r\n\r\nAppendix C discusses developing coordination complexes of heteroatom containing polyaromatic hydrocarbons. Several examples characterized via X-ray crystallography are reported.
\r\n\r\nAppendix D shows CO\u2082R data on K\u207a ionomer-coated Au. Elevation in |jCO| is demonstrated as a function of potassium content in the electrode-electrolyte interface provided by the film.
\r\n\r\nAppendix E discusses attempts to determine and CO\u2082 uptake by K\u207a ionomers via solid state NMR spectroscopy.
" }, { "name": "Hickam, Bryce Patrick", "degree": "PhD", "year": "2024", "title": "Exploring How Entangled Photon Correlations Can Enhance Spectroscopy", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08032023-213853772", "creators": [ { "name": { "family": "Hickam", "given": "Bryce Patrick" }, "id": "Hickam-Bryce-Patrick", "orcid": "0000-0003-2120-4769", "display_name": "Hickam, Bryce Patrick" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ez5h-qp07", "abstract": "Quantum light sources consisting of highly correlated or \"entangled\" photon pairs are increasingly becoming popular alternatives to classical light sources to perform microscopy and spectroscopy. Entangled photon pairs can replicate and enhance spectroscopic signals and have practical advantages compared to the pulsed laser systems that are typically utilized to perform these measurements. For instance, entangled photons are inherently low-flux, enabling measurements to be performed without undesired photoeffects, such as sample heating and degredation or nonideal photoinduced sample behavior. In addition, entangled photon sources can be generated and manipulated on much smaller physical footprints than state-of-the-art pulsed laser systems with comparable frequency bandwidths and time resolutions. Together, these capabilities could allow for the development of spectroscopic instruments that do not rely on bulky, expensive pulsed laser systems that necessitate teams of specialists to maintain. In turn, this instrument development could enable more widespread access to exotic forms of atomic and material characterization.
\r\n\r\nDespite a growing body of theoretical work, the field of experimental entangled photon spectroscopy is still nascent and entangled light-matter interactions have yet to be fully characterized in laboratory settings. Here, we investigate entangled photon light-matter interactions towards the goal of developing entangled spectroscopic techniques. A broadband entangled photon source with femtosecond coherence times is designed and characterized to perform these measurements. Using this source and an entangled photon spectrometer, characterization of the entangled photon enhancement to two-photon absorption are attempted by in studies of two different molecular dyes, Rhodamine 6G and zinc tetraphenylporphyrin. The entangled photon two-photon absorption enhancement is determined to be below previously reported values due to the presence of single photon scattering signals. Finally, entangled photons are utilized to replicate fluorescence lifetime measurements using a continuous wave pump laser and the temporal correlations inherent to entangled photon pairs. As the first experimental demonstration of this technique, the fluorescence lifetimes of indocyanine green in three solvent systems are measured.
" }, { "name": "Jones, Christopher Glenn", "degree": "PhD", "year": "2024", "title": "Development of Microcrystal Electron Diffraction Techniques for the Characterization of Small Molecules and Novel Materials", "advisor": "Nelson, Hosea M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11172023-202811116", "creators": [ { "name": { "family": "Jones", "given": "Christopher Glenn" }, "id": "Jones-Christopher-Glenn", "orcid": "0000-0003-4308-1368", "display_name": "Jones, Christopher Glenn" } ], "advisors": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "advisor", "display_name": "Nelson, Hosea M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/cfnr-f362", "abstract": "Traditional techniques for structural analysis, such as X-ray crystallography and Nuclear Magnetic Resonance (NMR), have been invaluable in understanding the composition of various substances. However, these methods often encounter challenges when applied to the analysis of small molecules and certain novel materials, particularly those that cannot form large, high-quality crystals. The research presented here focuses on the evolution and applications of Microcrystal Electron Diffraction (MicroED), a transformative technique that has expanded the boundaries of structural analysis. We trace the developmental trajectory of MicroED, exploring its underlying principles, technological advancements, and comparative advantages over conventional methods. A variety of data from several key studies was collected through a series of experiments utilizing MicroED to analyze a range of substances, from small organic molecules to complex novel materials and innovative inorganic complexes. MicroED offers unprecedented resolution and sensitivity, capable of structural elucidation where other methods fail. In particular, MicroED has been successful in determining the structures of several novel materials and small molecules with applications in areas such as renewable energy, advanced manufacturing, and pharmaceuticals. Furthermore, this technique is highly amenable to integration with other analytical and computational methods, including machine learning algorithms for data interpretation, enhancing its applicability and efficiency. This research contends that MicroED is not merely an alternative but a substantial upgrade to existing methodologies, holding the potential to revolutionize fields as diverse as materials science, chemistry, and medicine." }, { "name": "Jones, Gregory Harrison", "degree": "PhD", "year": "2024", "title": "From Venus to Mars: Spectroscopy and Kinetics of Reactive Intermediates in Planetary Atmospheres", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112023-043755538", "creators": [ { "name": { "family": "Jones", "given": "Gregory Harrison" }, "id": "Jones-Gregory-Harrison", "orcid": "0000-0003-3275-1661", "display_name": "Jones, Gregory Harrison" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "orcid": "0000-0002-4263-2562", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7010-fc76", "abstract": "The spectroscopy and kinetics of reactive intermediates in the atmospheres of Venus, Earth, and Mars were investigated through a combination of experimental and theoretical methods. Vibrational progressions in the A- and B-bands of ClSO were assigned, and predicted spectra matched well with experiment. A new unimolecular mechanism for 3-hydroxy-substituted Criegee intermediates was proposed, and predicted to be competitive with known isomerization pathways. The kinetic isotope effect and temperature dependence of the H + HO\u2082 reaction was calculated using high-level ab initio methods, with implications for the understanding of water loss on Mars." }, { "name": "Ko, Dennis Lok", "degree": "PhD", "year": "2024", "title": "Design and Implementation of a Microparticle Delivery Device for the Cornea", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072024-100209417", "creators": [ { "name": { "family": "Ko", "given": "Dennis Lok" }, "id": "Ko-Dennis-Lok", "orcid": "0000-0001-8700-0844", "display_name": "Ko, Dennis Lok" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "member", "display_name": "Gharib, Morteza" } ], "option_major": [ "chemeng" ], "abstract": "Biolistic drug delivery offers an alternative path for delivering therapeutics into the cornea. Until now, none of the commercially available gene guns are suitable for clinical delivery of therapeutics due to tissue damage caused by high speed gas used to accelerate microparticles. Here, we demonstrated the use of a device that both eliminates the exit gas, only allowing high speed particles through, and one that works in a clinical setting.
\r\n\r\nMicroparticles ranging from 5 to 22 \u03bcm were accelerated and delivered into both the agarose gels and ex vivo corneas. In gels, we found that normalized penetration depth was proportional to particle diameter and density. As the standoff distance between the device and the target increased, more particles were left stranded at the surface, as their penetrating power decreased, and their dispersion from the center of mass on the target increased. The orifice size served to control both the number of particles and the amount of exit gas. Increasing the inlet pressure did not a show significant increase in the penetration depth of microparticles.
\r\n\r\nIn the cornea, we found that we were able to use our device to deliver particles into both the epithelium and the stroma, although only higher density particles were able to enter the stroma. There was little to no damage to the cornea due to particle delivery. If epithelial defects were detected in the cornea due to particle penetration, they were quickly resolved within 30 minutes. Our device demonstrated performance (penetration depth) comparable to previous biolistic delivery methods in the cornea, while also maintaining clinical relevance by eliminating exit gas flow.
" }, { "name": "Korol, Roman", "degree": "PhD", "year": "2024", "title": "Development and Applications of Imaginary Time Path Integral Methods", "advisor": "Goddard, William A., III; Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08212023-205141057", "creators": [ { "name": { "family": "Korol", "given": "Roman" }, "id": "Korol-Roman", "orcid": "0000-0001-9307-6351", "display_name": "Korol, Roman" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "co-advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "orcid": "0000-0001-5768-7593", "role": "member", "display_name": "Eiler, John M." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jy10-rf87", "abstract": "Recent engineering advances have opened up avenues to novel technologies that bridge the gap between the quantum and the classical. In order to understand large-scale quantum systems, a variety of approximate theoretical treatments have been proposed. This thesis focuses on development and applications of path-integral methods, which have enjoyed broad applicability in recent years for exploring nuclear quantum effects in the domains that span physical, bio-, geo-, and materials chemistry.
\r\n\r\nFeynman's path-integral formulation of quantum statistical mechanics offers powerful and widely used strategies for including nuclear quantum effects in complex chemical systems. These strategies are based on the observation that the quantum Boltzmann statistical mechanics of a quantum system is exactly reproduced by the classical Boltzmann statistical mechanics of an isomorphic ring-polymer system. For the numerically exact calculation of quantum Boltzmann statistical properties, the classical Boltzmann distribution of the ring-polymer system can be sampled using Monte Carlo (i.e., path-integral Monte Carlo, or PIMC) or molecular dynamics (PIMD).
\r\n\r\nChapters 1 and 2 of this thesis identify and — with no computational overhead — eliminate the issues in virtually all previous numerical implementations of PIMD that stem from time discretization. The resultant integration scheme requires only a small modification to existing PIMD algorithms and provides accurate statistical and dynamical data in a single-shot simulation with an up to 3-fold increase in the timestep duration.
\r\n\r\nChapter 3 transitions from the PIMD method development to the applications of the related PIMC method to understand equilibrium of stable heavy isotopes (D, 13C, 17, and 18O in small gaseous molecules. We present a collaborative experiment-theory calibration of the temperature dependence of the clumped isotope effect in methane in Chapter 4. We continue in Chapter 5, adding the study of isotopic fractionation between methane, water, and molecular hydrogen. Here we present the first concrete example of the effect of Born-Oppenheimer approximation on PI calculations. Finally, Chapter 6 extends our treatment to ethane and propane. For propane, in addition to multiple clumped isotope effects, there is also a strong site preference for the heavy isotopes to occupy the central (methylene) group.
\r\n\r\nAll the isotopic equilibrium calculations utilize accurate potential energy surfaces and are validated against experimental data in close collaboration with Daniel Stolper's experimental group at Berkeley, representing (to the best of our knowledge) the most accurate reference data available to date.
" }, { "name": "Laubscher, Emily Chiu", "degree": "PhD", "year": "2024", "title": "Deep Learning-Enabled Integrated Measurements of Immune Signaling in Primary Human Macrophages", "advisor": "Van Valen, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222024-204650454", "creators": [ { "name": { "family": "Laubscher", "given": "Emily Chiu" }, "id": "Laubscher-Emily-Chiu", "orcid": "0009-0008-0242-0507", "display_name": "Laubscher, Emily Chiu" } ], "advisors": [ { "name": { "family": "Van Valen", "given": "David A." }, "id": "Van-Valen-D", "orcid": "0000-0001-7534-7621", "role": "advisor", "display_name": "Van Valen, David A." } ], "committee": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "chair", "display_name": "Wei, Lu" }, { "name": { "family": "Chong", "given": "Shasha" }, "id": "Chong-Shasha", "orcid": "0000-0002-5372-311X", "role": "member", "display_name": "Chong, Shasha" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Van Valen", "given": "David A." }, "id": "Van-Valen-D", "orcid": "0000-0001-7534-7621", "role": "member", "display_name": "Van Valen, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hayp-kx45", "abstract": "Examination of biological systems at the single-cell level reveals heterogeneity in both time and space. Single-cell temporal and spatial heterogeneity allow communities of cells to process noisy stimuli and perform complex tasks. We leveraged state-of-the-art imaging technologies to characterize cell-to-cell heterogeneity in responses to environmental stimuli to reveal mechanisms of information transmission. Fluorescent live-cell reporters enable real-time visualization of the activity state of cell signaling proteins. Signaling dynamics allow cells to translate information about environmental stimuli into cellular behaviors. Chapter 2 explores the variety of live-cell reporters designed to characterize the dynamic patterns of activity of key signaling pathways, and covers the development of two live-cell reporters. Spatial transcriptomics assays, on the other hand, excel at capturing heterogeneity in spatial gene expression patterns, which is often required to enable a tissue to perform complex functions. Chapter 3 details the development of Polaris, a deep learning-enabled analysis method for spatial transcriptomics data. Polaris is an assay-agnostic, turnkey solution for analyzing images from spatial transcriptomics experiments, minimizing the time and expertise require to extract biological insights. In chapter 4, we pair dynamic measurements of live-cell reporters with a spatial transcriptomics measurement in an integrated imaging assay in primary human macrophages. This imaging assay revealed transcriptional sub-populations of cells with differing distributions of dynamic immune signaling responses and morphological states.
\r\n\r\nThis work contributes a number of methodological developments, including live- cell reporter expression in primary human macrophages and deep learning-enabled spatial transcriptomics image analysis. Expression of live-cell reporters in primary macrophages will enable the investigation of environmental cues shape macrophages\u2019 cell state, which is highly plastic and shaped by external stimuli. Polaris expedites the analysis of this multi-modal imaging data set, extracting single-cell gene expression values without manual parameter tuning. However, Polaris\u2019 impact extends beyond the scope of this work to the broader spatial biology field as its spot detection and gene decoding capabilities generalize to data sets from a variety of sample types and imaging modalities. Finally, our paired dynamics-spatial transcriptomics imaging assay can be generally applied to characterize information transmission from environmental stimuli through signaling dynamics to the expression of downstream genes for a wide variety of signaling pathways in primary and immortalized cell types.
" }, { "name": "Le, Linh Nguyen Vuong", "degree": "PhD", "year": "2024", "title": "Partial Synthetic Models of the FeMoco Nitrogenase Cluster with Bridging C-Based Ligands", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032024-022957246", "creators": [ { "name": { "family": "Le", "given": "Linh Nguyen Vuong" }, "id": "Le-Linh-Nguyen-Vuong", "orcid": "0000-0003-1451-2675", "display_name": "Le, Linh Nguyen Vuong" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9xgc-d212", "abstract": "Biological N\u2082 reduction to NH\u2083 occurs in microorganisms using the enzyme nitrogenase. This complex system consists of several iron-sulfur clusters, where the active site contains a MFe\u2087S\u2089C cluster (M = Mo, V, Fe) known as FeM cofactor (FeMco). The cluster includes an unusual interstitial carbide ligand, which is rare in both inorganic chemistry and biology. In addition, the role of this motif within the enzyme is not well-understood, and studies on synthetic model complexes are limited due to the absence of any previously reported iron-sulfur cluster systems bearing a carbon-based ligand that bridges the Fe atoms. Thus, this thesis focuses on developing strategies to insert a bridging carbon-based ligand into an iron-sulfur cluster platform.
\r\n \r\nChapter 1 provides a general introduction and overview of complex biologically relevant iron-sulfur clusters and their corresponding synthetic analogs, with focus on NiFe CO dehydrogenase (CODH), acetyl CoA synthase (ACS), [FeFe] hydrogenase, P-cluster, and M-cluster of nitrogenase.
\r\n\r\nChapter 2 discusses the formation of a cluster with a \u03bc\u2083-carbyne ligand resulting from the ring-opening of a bisaminocyclipropenylidene ligand. Electrochemical studies on this system and related species suggest that a chelating \u03bc\u2083-carbyne leads to clusters with highly negative reduction potentials compared to \u03bc\u2083-N or S ligands, suggesting that the interstitial carbide in FeMco may play a role in modulating the redox potential of the cluster to allow for the reduction of difficult substrates like N\u2082.
\r\n\r\nChapter 3 focuses on the binding of CO to the cluster with a \u03bc\u2083-carbyne fragment, resulting in a high level of CO activation at 1851 cm\u207b\u00b9 in the neutral cluster and 1782 cm\u207b\u00b9 in the reduced cluster, Computational studies suggest that the bridging carbyne stabilizes the intermediate spin state at the Fe sites, resulting in more electrons in orbitals that can backbond with CO and greater activation. This suggests that the carbide in FeMco might play a role in modulating the electronic structure at the Fe sites to allow for greater activation of substrates.
\r\n\r\nChapter 4 highlights the synthesis of a cluster bearing a \u03bc\u2084-carbide ligand using a previously reported terminal Mo carbide complex, with a bridging CO ligand that resembles the lo-CO form. The S = 1/2 spin state provides an opportunity to study the metal-carbon interaction by pulse EPR spectroscopy.
\r\n\r\nIn Chapter 5, a cluster ligated by an anthracene-bridged bisphenoxide ligand is described. Upon reduction, the anthracene bridge moves closer to one Fe site and interacts with it in an \u03b7\u00b2 manner. This species can catalyze the electrochemical reduction of proton to form H2, possibly through a protonated cluster intermediate. The studies demonstrate the ability of the cluster to catalyze a biologically relevant reaction, and possibility for future studies on protonated species that have only been proposed in reactions of synthetic iron-sulfur clusters.
" }, { "name": "Lin, Haw-Wei", "degree": "PhD", "year": "2024", "title": "Nonlinear and Multidimensional Terahertz Spectroscopy of Liquids and Crystalline Solids", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01082024-171459002", "creators": [ { "name": { "family": "Lin", "given": "Haw-Wei" }, "id": "Lin-Haw-Wei", "orcid": "0000-0002-5208-7385", "display_name": "Lin, Haw-Wei" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2qt0-mg05", "abstract": "The delocalized and correlated nuclear degrees of freedom in the terahertz (THz) regime strongly influences the room temperature chemical and physical properties of condensed matter systems, yet detailed understanding of the photo-induced dynamics and anharmonicities of the vibrational modes have remained elusive. In hydrogen-bonded liquids, these information facilitates the development of accurate force field models to aid simulations of biological processes of proteins and DNAs. In the field of nonlinear phononics, anharmonic lattice vibrations form the foundation for ultrafast coherent control of material properties, which has become an indispensable technique in the engineering toolbox for quantum materials. In this thesis, we demonstrate the development and application of nonlinear 1D THz Kerr effect (TKE) and 2D THz-THz-Raman (2D-TTR) ultrafast THz spectroscopies, which are specially designed to induce resonant coherent excitations of the correlative nuclear degrees of freedom in liquids and crystalline solids. By analyzing the temporal evolution of the nuclear THz-driven dynamics, insights into the excitation mechanisms, nonlinear coupling interactions, and the dominant source(s) of anharmonicity may be determined. Specifically, we developed a nonlinear imaging method based on the third-order response of electro-optic crystal GaP, which significantly improved the alignment consistency and the signal strength of 2D-TTR spectroscopy. Further, we extended an echelon-based single-shot detection scheme, originally developed in 1D TKE spectroscopy, to 2D-TTR spectroscopy, which led to up to two orders-of-magnitude reduction in acquisition time. Armed with these instrument advancements, we measured 2D-TTR spectra of liquid halogenated methanes with significantly improved signal-to-noise and a larger temporal window, which led to the identification of a novel competing sum-frequency THz excitation pathway. On the other hand, we investigated resonant driven-dynamics of the phonon-polariton modes in semiconductor LiNbO$_3$, which revealed nonlinear coupling interactions between two phonon branches that are attributed to mechanical anharmonicity. In addition, we directly observed photo-induced coherent phonon wavepackets for the layered semiconductors transition metal dichalcogenide using 1D TKE spectroscopy, which are attributed to the sum-frequency excitation pathway. These works highlight the rigorous experimental considerations and careful spectral analysis required to extract essential insight into excitation mechanisms and anharmonic contributions, while avoiding spectral artifacts due to the instrument response function. In order to provide clarity to these often misunderstood spectroscopies in the THz regime, this thesis further summaries the theories behind 1D TKE and 2D-TTR spectroscopies and the lessons we have learned from experimental realization of these exotic instruments and the analysis of complex spectral features." }, { "name": "Liu, Hanwei", "degree": "PhD", "year": "2024", "title": "Engineered Living Material Based on Protein-Mediated Bacterial Assembly", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182024-051357688", "creators": [ { "name": { "family": "Liu", "given": "Hanwei" }, "id": "Liu-Hanwei", "orcid": "0000-0002-4667-1673", "display_name": "Liu, Hanwei" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6cqr-vq43", "abstract": "Engineered Living Materials(ELMs) is a newly emerging field of biotechnology at the interface of synthetic biology and traditional material science. Over the past few years, several kinds of novel ELMs were developed. These materials, derived from organisms including bacteria, fungi and plants, have potential applications in therapeutics, electronics, constructions and environmental remediation. We invented an novel method that enables bacteria to from cohesive thin films through cell surface display of associative proteins. In this thesis, we will first demonstrate that we can genetically encode the mechanical properties of living bacterial films by controlling amino acid sequences of artificial proteins displayed at cell surface. Later, we will show that we can generate bacterial-matrix composite by displaying enzymes and peptides at the cell surface.
\r\n\r\nIn Chapter 1, we review the development of ELMs and existing examples of ELMs. The fundamental definition of ELMs and trends in ELMs development will be presented. Bacterial based ELMs, created either by encapsulating bacteria of interests into a synthetic polymeric matrix or by boosting the natural biosynthetic pathways of biopolymers and mineralization in bacteria will be the major part of discussion. The goal of this chapter is to provide context and background of ELMs research.
\r\n\r\nIn Chapter 2, we discuss the design and preparation method of our own ELM. The process of how we come up with growing bacterial films on perforated polycarbonate membranes and development of suction coating method will be presented. By using model SpyTag-SpyCatcher bacterial assembly system, we unraveled the principles behind making cohesive bacterial films from a single bacterial colony.
\r\n\r\nIn Chapter 3, we discuss controlling bacterial films\u2019 mechanical properties through genetic manipulation. Engineered bacteria displaying artificial unstructured Elastin-like-peptides (ELPs) at cell surface can form cohesive, soft and yielding films with tens of kPa value of Young\u2019s moduli. By merely adding a cysteine at the N-terminal part of the ELP, the engineered bacteria can form relative tough, non-yielding films with 3 times higher Young\u2019s moduli due to formation of intercellular covalent disulfide bond. Apart from having enhanced mechanical strength, such films containing covalent intercellular interactions have abilities to self-heal within 24 hours after being cut into halves.
\r\n\r\nIn chapter 4, we discuss a strategy based on stimulated Raman scattering microscopy to monitor phosphatase-catalyzed mineralization of engineered living bacterial films in situ. Real-time label-free imaging elucidates the mineralization process, quantifies both the organic and inorganic components of the material as functions of time, and reveals spatial heterogeneity at multiple scales. In addition, we correlate the mechanical performance of films with the extent of mineralization.
\r\n\r\nIn chapter 5, we discuss the ability of bacterial protein surface display system to catalyze artificial extracellular matrix formation. We demonstrated that heme-containing peroxidase Apex2 can be fused with autotransporter protein previous described in Chapter 2, 3 and 4, successfully displayed at cell surface and remain functional at catalyzing formation of polymer polyaniline (PANI) in the presence of hydrogen peroxide and aniline monomers at physiological pH. Similarly, by displaying multiple kinds peptide known to mediate silica deposition, we can coat bacteria with silica of different morphologies without reducing the viabilities of bacteria.
\r\n\r\nIn Chapter 6, we discuss the future directions of engineered living materials developed in previous chapters. We propose methods to further improve the mechanical strength of bacterial films, to find \u201csweet-spot\u201d of biomineralization, and to develop artificial hydrophobin.
" }, { "name": "Miao, Kun", "degree": "PhD", "year": "2024", "title": "Stimulated Raman Scattering: a Biophysical Perspective for Imaging Cells and Tissues", "advisor": "Wei, Lu", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312023-053642106", "creators": [ { "name": { "family": "Miao", "given": "Kun" }, "id": "Miao-Kun", "orcid": "0000-0001-6567-3650", "display_name": "Miao, Kun" } ], "advisors": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "advisor", "display_name": "Wei, Lu" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ch88-9173", "abstract": "This thesis explores the utilization of Stimulated Raman Scattering (SRS) microscopy as a novel imaging method in the biomedical field, aiming to overcome the limitations associated with traditional fluorescence-based techniques. Given the drawbacks of fluorescence imaging, such as photobleaching, auto-fluorescence, and the complexity of fluorophore labeling, SRS microscopy emerges as a promising solution. The optical imaging contrast in this method originates from bond vibrations of endogenous biomolecules. Grounded in the principle of Raman scattering, SRS amplifies weak spontaneous Raman transitions through stimulated emission, offering a target-specific, high-speed, and label-free imaging modality that can overcome the challenges of traditional bio-imaging techniques.
\r\n\r\nTo tackle the interference from fluorescent proteins when imaging small proteins of interest, we demonstrated a combination of SRS with selective deuterium labeling for visualizing polyQ aggregates in Huntington's disease. We targeted the C-D vibration on deuterated glutamines, which are metabolically enriched in the polyQ sequence. This allowed us to image Huntingtin aggregates without using fluorescent labels. Our method enables, for the first time, the quantification of protein concentrations and compositional analyses of polyQ and non-polyQ proteins within native Huntingtin aggregates. This novel perspective suggests that aggregates have distinct biophysical roles at different stages of aggregation.
\r\n\r\nIn addition to fluorescent proteins, immunofluorescence is the gold standard for visualizing the location and distribution of proteins within cells or tissues. However, the proper delivery of antibodies is slow and labor-intensive. To overcome this issue, we developed a novel method, Vibrational Imaging of Swelled Tissue and Analysis (VISTA), that combines SRS microscopy with sample expansion to enable label-free super-resolution volumetric imaging in tissues. We developed a unique fixation hydrogel chemistry to maximize protein retention, delipidation, and isotropic expansion in tissue samples. By targeting the bond vibrations from endogenous proteins, VISTA bypasses the limitations of antibody labeling and provides an efficient tool for high-throughput imaging that can be scaled to large-volume clinical samples. The addition of image segmentation methods to VISTA equips it with protein-level specificity similar to immunofluorescence. We further used this technique to study protein aggregates, such as amyloid-\u03b2 plaques in Alzheimer's disease, revealing intricate aggregate structures and polymorphisms absent in conventional fluorescence methods.
\r\n\r\nFinally, as fluorescent biosensors are indispensable tools for studying intracellular dynamics, we worked on extending the utility of SRS microscopy into the realm of sensing. We employed hydrogen-deuterium exchange on alkyne substrates to develop a Raman-based sensing strategy sensitive to subtle variations in local microenvironments. The rate of hydrogen-deuterium exchange changes under different conditions, and the resulting frequency shift from alkyne to deuterated alkyne is captured by SRS microscopy. This new platform enhances the study of chemical environments in various biological structures, marking a pivotal step in integrating imaging and sensing in biophysical research.
" }, { "name": "Michelsen, Jonathan Malte Zschiegner", "degree": "PhD", "year": "2024", "title": "Measuring Charge Carrier and Structural Photodynamics at Solar Energy Material Surfaces Using Transient Extreme Ultraviolet Reflection Spectroscopy", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082024-165921385", "creators": [ { "name": { "family": "Michelsen", "given": "Jonathan Malte Zschiegner" }, "id": "Michelsen-Jonathan-Malte-Zschiegner", "orcid": "0000-0002-7420-5610", "display_name": "Michelsen, Jonathan Malte Zschiegner" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/73h7-kg35", "abstract": "Electronic and vibrational degrees of freedom, and their interactions, control the chemical and physical properties of solids. Core-level spectroscopies, such as transient extreme ultraviolet (XUV) spectroscopy, provide detailed information on the electronic structure and local coordination environment of a material. In this work, we employ transient XUV reflection spectroscopy to measure surface carrier and structural dynamics in solar energy materials. To interpret experimental spectra, excited state valence effects are incorporated into the OCEAN code (Obtaining core excitations from ab initio electronic structure and the NIST Bethe-Salpeter equation solver). The modeling of core-level spectra from first principles enables the extraction of carrier kinetics via the robust assignment of spectral features. Moreover, this thesis explores experimental and theoretical methods for understanding carrier-structural coupling in solids relevant to solar energy applications.
\r\n\r\nSpecifically, we explore the chemical and physical information contained in core-level spectra for various solar energy material systems and present guiding principles for designing a core-level electronic spectroscopy experiments to determine photoexcited carrier and structural dynamics. We report on experimental measurements of ultrafast surface carrier and structural dynamics in photocathodes zinc telluride and copper iron oxide. Further, complementary excited state theory is presented to extract excited state valence dynamics from experimental core-level spectra based on ground state implementations of the Bethe-Salpeter equation.
" }, { "name": "Muthusamy, Anand Kumar", "degree": "PhD", "year": "2024", "title": "Neuropsychiatric Drug Biosensors in Organelles, Cells, Biofluids, & Behaving Animals", "advisor": "Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042024-004047037", "creators": [ { "name": { "family": "Muthusamy", "given": "Anand Kumar" }, "id": "Muthusamy-Anand-Kumar", "orcid": "0000-0003-1041-914X", "display_name": "Muthusamy, Anand Kumar" } ], "advisors": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "orcid": "0000-0001-5868-348X", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1043-8k76", "abstract": "Biology is distinguished in its several levels of spatial organization\u2014from molecular to whole body\u2014that give rise to coherent, goal-related behaviors. Cutting across these layers are definable circuits, each with its own dynamics. These systems should be studied in their natural context to preserve their structure and function. However, quantitative measurements typically demand invasive apparatuses or infrequent, ex vivo measurements. The advent of genetically encoded fluorescent biosensors solves this problem by detecting molecules in situ, read by a microscope or implantable optical probe. These biosensors typically are fusions of a conformational switch and a fluorescent protein. A naturally occurring protein that binds the target of interest typically provides an initial scaffold. However, several molecules, particularly various human-made drugs, do not have similar naturally occurring cognate conformational switches in nature robust enough for this approach.
\r\n\r\nThis work develops and applies the first genetically encoded drug biosensors in cellular and behavioral assays addressing substance abuse disorders. We term these biosensors intensity-based drug-sensing fluorescent reporters or \u201ciDrugSnFRs.\u201d These biosensors are based on a choline-binding periplasmic binding protein (PBP), OpuBC, interrupting a circularly permuted green fluorescent protein (GFP). This work reports a method of optimizing this construct toward the detection of several classes of neural drugs, including nicotinic, SSRIs, ketamine family drugs, and opioids.
\r\n\r\nThe opportunity for continuous monitoring is particularly prominent in brain-body-behavior relationships. For example, a core tenet of behavioral neuropharmacology is the existence of some stereotyped relationship between the time course of a drug and behavioral outcomes such as opioid use disorder. Interindividual variability in pharmacokinetics (PK) complicates the problem of optimized opioid dosing, especially outside the clinic. The problem of personalizing pharmacokinetics is severe in substance use disorders: the patient must receive opioid levels that relieve pain, minimize tolerance and other side effects, and remain within a therapeutic window to maximize adherence. That ideal window is a \u201cmoving target\u201d due to tolerance, changes in metabolism, and stressors.
\r\n\r\nAs an end-to-end study with a preclinical model, the final chapter reports the development of iOpioidSnFRs and their application to the continuous monitoring of fentanyl alongside a computer vision routine to quantify behavior. The fentanyl sensor, iFentanylSnFR2.0, was expressed in the ventral tegmental area of mice and reported [fentanyl] vs. time. This recording is the longest continuous measurement of the brain [drug] alongside behavior (4 hours). We found a stereotypic, repetitive motor pattern that tracked the entire fentanyl time course (2-3 hours) despite variable PK across individuals. This result challenges current models of cellular desensitization and acute tolerance timescales. In a separate experiment, we investigated if this stereotypical pattern impaired mice in a survival task where mice forage for water through a labyrinth maze. Like in the open arena, mice in the maze exhibited circling/stalling for approximately 3 h, to the complete exclusion of successful foraging. Critically, this paradigm offers a normative definition of a deficit, as mice should have a baseline level of successful foraging to survive. We introduce this task to the substance use disorder field as an additional metric for the deficits caused by opioid administration.
\r\n\r\nFinally, this work demonstrates the utility of iOpioidSnFRs in diagnostic tests owing to their suitable aqueous solubility, dynamic range, sensitivity, selectivity, kinetics, and stability after lyophilization. Plate reader assays using iFentanylSnFR2.0, iS-methadoneSnFR, iTapentadolSnFR, and iLevorphanolSnFR provided quantitation across the pharmacologically relevant concentration ranges. These biosensors were also used in a simulated field test using readily available parts: dark box, blue LED strips, band pass filter, and a cellphone camera. This test could be used to determine the presence of a health hazard in the environment (e.g., fentanyl) or determine the exposure level in a person. These results encourage diagnostic and continuous monitoring approaches to personalizing opioid regimens.
" }, { "name": "Orta, Anna Karen", "degree": "PhD", "year": "2024", "title": "Leveraging the \u03a6X174 Protein Antibiotic to Study MraY Structure, Function, and Regulation", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042024-022255958", "creators": [ { "name": { "family": "Orta", "given": "Anna Karen" }, "id": "Orta-Anna-Karen", "orcid": "0000-0002-8526-0383", "display_name": "Orta, Anna Karen" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "chair", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/ggr0-0n72", "abstract": "The overuse of antibiotics has escalated the prevalence of bacterial resistance to existing treatments, posing a significant threat to global health. This rise in antimicrobial resistance (AMR) has spurred research into innovative therapeutic approaches. Among the most promising strategies is the use of viruses of bacteria for 'phage therapy'. This thesis delves into the interplay between antibacterial resistance and peptidoglycan biosynthesis, highlighting the pivotal role of the membrane protein MraY. We present the first structure of MraY from a pathogenic species, revealing its inhibition by the lysis protein from the bacteriophage \u03a6X174, protein E. Additionally, we analyze lipidic interactions with MraY, proposing a previously unexplored allosteric feedback mechanism for regulating its enzymatic activity. Building on these insights, we expand the application of protein E to non-native hosts, offering new avenues for the development of targeted antibiotic interventions. This work not only advances our understanding of the structural and functional dynamics of MraY but also paves the way for novel antibacterial strategies." }, { "name": "Page, Katharine-Rose", "degree": "PhD", "year": "2024", "title": "Using Functional Genomics to Characterize Biogenesis and Quality Control Pathways in the Mammalian ER", "advisor": "Voorhees, Rebecca M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062023-233057820", "creators": [ { "name": { "family": "Page", "given": "Katharine-Rose" }, "id": "Page-Katharine-Rose", "orcid": "0000-0001-8904-1244", "display_name": "Page, Katharine-Rose" } ], "advisors": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "advisor", "display_name": "Voorhees, Rebecca M." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4c7k-yw62", "abstract": "Cells are tasked with ensuring the proper synthesis, localization, and insertion of membrane proteins at the mammalian endoplasmic reticulum (ER). Recent advances have shown that the insertion of transmembrane domains into the ER and the translocation of their associated soluble domains across the ER can be facilitated by members of the Oxa1 superfamily of insertases. The ER membrane protein complex (EMC) contains an Oxa1 insertase that facilitates the co-translational insertion of the first TMD of Nexo proteins, which have their N-terminal soluble domains localized in the ER lumen or extracellular space. Additionally, recent work has described the multipass translocon, a supercomplex at the Sec61 translocation channel that facilitates insertion of multipass membrane proteins. During my PhD and in collaboration with other scientists in the Voorhees lab, I elucidated how the EMC cooperates with the multipass translocon to facilitate biogenesis of multipass membrane proteins. We took a systematic approach, applying a combination of functional genomics, biochemistry, structural biology, and mechanistic cell biology to understand how the biophysical properties of the TMDs and the intervening soluble domains of multipass membrane proteins influence their path into the ER bilayer. We show that the EMC is epistatic with members of the multipass translocon, including the BOS, GEL, and PAT complexes. We structurally characterize the EMC\u2022BOS holocomplex, showing that these complexes directly interact, and that this interaction is mutually exclusive to the interaction of BOS and Sec61. Further, we demonstrate that Nexo proteins that contain a net positive charge in their N-terminal soluble domain are difficult for the EMC to insert and thus also rely on Sec61 or TMCO1, the Oxa1 insertase of the GEL complex, for insertion. We overturn the prevailing model for multipass membrane protein insertion and show that how this diverse class of membrane proteins utilizes the suite of ER biogenesis machinery depends on their distinct biophysical properties. In addition to biogenesis, during my PhD I also studied how the cell surveils multi-subunit complex assembly. I focused on a model ER-resident and obligate complex. These subunits are unstable and degraded in the absence of their binding partner, but how they are recognized for degradation is unknown. I used unbiased functional genomics approaches to identify the quality control components that regulate orphan subunit degradation in the cell. Further, I used proteomics to identify endogenous substrates of this particular ERAD pathway. This work expands upon our understanding of how multi-subunit complexes are regulated by machinery in the cell." }, { "name": "Park, Youngkyu", "degree": "PhD", "year": "2024", "title": "Altering Framework Topology and Heteroatom Distributions of Molecular Sieves by Designed Organic Structure-Directing Agents", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292024-055507772", "creators": [ { "name": { "family": "Park", "given": "Youngkyu" }, "id": "Park-Youngkyu", "orcid": "0000-0001-7328-7565", "display_name": "Park, Youngkyu" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/d1xj-kn25", "abstract": "The growing demand for chemical production combined with the urgent need to mitigate the accelerated climate and environmental changes motivates efforts to create highly efficient and selective catalysts and adsorbents. Zeolites and molecular sieves are a key class of materials for addressing these needs because of their high activity and selectivity with catalytic reactions. Additionally, they can show superior adsorption properties because of their structure and surface polarity that can also give shape selectivity with molecules smaller than ca. 1 nanometer. Further advancements in molecular sieve properties will rely on advancements in preparation methods. To this end, the research results presented here explore synthetic approaches for controlling the framework topology and the heteroatom incorporation within silicate-based molecular sieves by means of the strategic design of their organic structure-directing agents (OSDAs).
\r\n\r\nPart I presents the synthesis of STW-type germanosilicate molecular sieves with high-silica framework compositions and the enrichment of chirality. A chiral OSDA is computationally designed based on the predicted stabilization energy toward the pure-silica STW framework. An improved synthesis route for both enantiomers of the OSDA is developed. The enantiopure OSDA is capable of crystallizing a high-silica STW-type germanosilicate molecular sieve that shows distinct framework compositions from previously reported germanium-rich STW. The enantiomeric enrichment of powdered samples without occluded enantiopure OSDAs is characterized by the dynamical refinement of microcrystal electron diffraction data. The high-silica, enantiomerically enriched STW exhibits the framework stability upon thermal treatment and the enantioselective adsorption of 2-butanol. The results in Part I demonstrate the design strategy of OSDAs for crystallizing stable, enantio-enriched molecular sieves for enantioselective chemical separations and catalysis.
\r\n\r\nIn Part II, the distribution of heteroatoms incorporated within borosilicate molecular sieves is studied with regard to its control by cationic OSDAs. To aid in the characterization of the heteroatom sites within borosilicate molecular sieves, the relationship between the 11B NMR chemical shift and the local geometry of boron within tetrahedrally coordinated silicate frameworks is first investigated. From crystalline borosilicate minerals with highly ordered, tetrahedrally coordinated boron atoms, it is revealed that the chemical shifts from 11B NMR linearly correlate with the local geometric parameters. Further studies on the borosilicate molecular sieves that possess more open space and wider angles suggest that the correlation between the average bond angles and 11B NMR chemical shifts can be employed for the entire class of three-dimensional, crystalline borosilicates. Two structurally similar quaternary ammonium OSDAs with different locations of positive charge are designed and synthesized. MWW-type borosilicate molecular sieves are crystallized by both OSDAs, and the quaternary ammonium moieties in the two OSDAs are found to interact with boron species with significantly different 11B NMR chemical shifts. Using the correlation developed here, the characterization results demonstrate that the heteroatom siting within the molecular sieve framework can be selectively altered by tailoring the OSDA structure in terms of the position of positive charge.
" }, { "name": "Porter, Michael Koizumi", "degree": "PhD", "year": "2024", "title": "Improvement of Microbial Detection and Analysis Techniques in Complex Biological Environments", "advisor": "Ismagilov, Rustem F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292024-020036252", "creators": [ { "name": { "family": "Porter", "given": "Michael Koizumi" }, "id": "Porter-Michael-Koizumi", "orcid": "0000-0002-0777-7563", "display_name": "Porter, Michael Koizumi" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "advisor", "display_name": "Ismagilov, Rustem F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7chb-wk98", "abstract": "Human bodies are home to a vast assortment of microbes, including bacteria, fungi, and viruses. These microbes live within their human hosts, interacting with each other and influencing states of health and disease. Despite their prevalence and importance, studying host-microbe interactions has been limited by the dearth of appropriate tools and approaches, and an underappreciation for the role of biophysics. \r\nThis thesis describes the development and application of novel tools and approaches for studying bacteria, fungi, and viruses to uncover their potential roles in human health and disease.
\r\n\r\nIn my first project, we investigated bacterial aggregation, a phenomenon related to important host-microbe interactions such as biofilm formation and the clearance of pathogens from the gastrointestinal tract. We found that bacteria aggregate in the presence of polymers (such as dietary fiber) via a mechanism that is qualitatively consistent with depletion-type forces under gut-like conditions. Surprisingly, motile bacteria aggregate more than nonmotile bacteria in viscous, high-polymer concentrations due to the higher effective diffusivity and inter-bacterial collisions enabled by motility. These two results give insight on how the foods (such as fiber) that we consume can physically affect the structure of microbes and other matter in the gut.
\r\n\r\nIn my next projects, we investigated viral-load kinetics to understand the best testing modality for early detection of SARS-CoV-2 via a large community-based household transmission study. By collecting longitudinal, paired saliva and nasal-swab specimens from SARS-CoV-2 patients starting from the incident of infection, we quantified the viral-load trajectories of COVID-19-positive participants in each specimen type over time. Our results revealed that viral loads increased quickly and reached a higher peak in nasal-swab specimens, whereas viral loads were detectable earlier but reached a lower maximum in saliva. Both specimen types exhibited a temporal trend whereby viral loads were higher in specimens collected in the morning compared with the evening. In samples where infectious viral titer was measured, we found that the ratio of N gene viral load and infectious viral titer did not remain consistent throughout the course of infection. These three results help us understand the heterogeneity of SARS-CoV-2 disease progression in different individuals, and how the analytical sensitivity of a diagnostic, the specimen type, and time of sampling can be crucial in conducting community surveillance programs during a pandemic. \r\nFinally, we extended and co-validated for fungi a novel sample-preparation method that enriches fungal cells in host-rich samples to enable the first demonstration of deep metagenomic sequencing of fungal communities directly from clinical samples (without a culture step). Our results show that this method depletes host DNA by over 1000-fold by mass, improving taxonomic classification and gene calling, as well as enabling de novo metagenome assembled genome (MAG) assembly in samples dominated by human biomass.
" }, { "name": "Quinn, Laura Katherine", "degree": "PhD", "year": "2024", "title": "Freeze-Cast Porous Ceramics: Tailoring Chemistry and Porosity for Functionality", "advisor": "Faber, Katherine T.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012024-040012207", "creators": [ { "name": { "family": "Quinn", "given": "Laura Katherine" }, "id": "Quinn-Laura-Katherine", "orcid": "0000-0002-6112-028X", "display_name": "Quinn, Laura Katherine" } ], "advisors": [ { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "advisor", "display_name": "Faber, Katherine T." } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "member", "display_name": "Faber, Katherine T." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nj6y-4315", "abstract": "Porous ceramics have been created and utilized in applications ranging from the automotive industry to biomedical research, with the chemical and pore characteristics of these ceramic structures crucial to their function and design. In this work, these intertwined factors are explored for a variety of applications by controlling the chemistry through precursor preparation and heat treatments, and the porosity controlled through freeze casting, a tunable and facile pore-forming technique yielding a range of pore sizes and morphologies. First, shape memory and superelastic behaviors in ceria-doped zirconia are observed by creating porous honeycomb structures that can accommodate the volume change of the martensitic transformation enabling such performance. By controlling dopant concentration, powder morphology, and freezing rate, the martensitic transformation is tracked over multiple cycles and collection volumes in these bulk-scale, polycrystalline zirconia ceramics. Next, transparent porous model sediments are created through heat treatments of freeze-cast synthetic cryolite (Na3AlF6) powder. Fluorescent beads the same size as many bacterial cells are visualized in a range of pore morphologies over both depth and time, and these porous ceramics are deployed in a sedimentary environment and the imaging of the microbial communities contained within and are found to colonize the porous cryolite structures. Alternate porous habitats for bacterial colonization are further created using materials such as iron oxides and carbon nanotubes to produce structures that can act both as electron acceptors and as microbial habitats. Finally, thermally anisotropic Si-based porous ceramics are developed with a potential use in optical devices. Using two contrasting preceramic polymers and both traditional and UV-assisted freeze-casting techniques, porous SiOC is produced from preceramic polymers with differing carbon contents. Together, these examples explore how the chemistry and porosity of porous ceramics can be manipulated to affect the chemical, optical, mechanical, and thermal properties of ceramic structures to best suit the intended function." }, { "name": "Saladi, Shyam Madhukar", "degree": "PhD", "year": "2024", "title": "Some Computer Studies of Membrane Proteins, Molecular Chaperones, and Color", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232023-184021847", "creators": [ { "name": { "family": "Saladi", "given": "Shyam Madhukar" }, "id": "Saladi-Shyam-Madhukar", "orcid": "0000-0001-9701-3059", "display_name": "Saladi, Shyam Madhukar" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "orcid": "0000-0002-5785-7481", "role": "chair", "display_name": "Murray, Richard M." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-0923-3284", "role": "member", "display_name": "Hoelz, Andre" } ], "option_major": [ "biochem" ], "doi": "10.7907/40cw-kn70", "abstract": "This thesis shares a series of stories on seemingly disparate topics united by my efforts and love of computers. Initially, I discuss how the challenge of membrane protein expression provided an initial impetus for research. I channeled efforts towards developing a predictive (machine-learning) model for heterologous overexpression in E. coli. While we made strides to extend this model to other systems (not discussed here), my time was refocused onto questions of more fundamental biochemical interest: the biogenesis of tail-anchored membrane proteins. I built structural, predictive, and phylogenetic models to better understand how the C-terminal domain of co-chaperone Sgt2 functioned, refined the definition of the wider Sti1 family which includes Sgt2-C, and extended our understanding of those features of tail-anchored proteins that determine successful targeting in Yeast and Human cells. I developed a deep phylogeny of Get3, a chaperone involved in tail-anchored protein biogenesis, and helped specifically place Get3 proteins of photosynthesising organisms into evolutionary context. Along the way, I developed a parallel and compelling theme around data visualization, specifically around the use of colormaps across the life sciences. In particular, I built an application to screen and notify preprint authors when their manuscript had poor colormap usage. This was the first time automated software has been used to help authors improve their work at the preprint stage, an area that has grown significantly since my initial work. Finally, I brought together structural biology and data visualization by making perceptually uniform colormaps available in popular molecular visualization software tools to advocate for more thoughtful color usage in the field." }, { "name": "Stanko, Allison Michelle", "degree": "PhD", "year": "2024", "title": "Assembly of Complex Carbocyclic Architectures via Palladium and Nickel-Catalyzed Cyclizations", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292024-194607461", "creators": [ { "name": { "family": "Stanko", "given": "Allison Michelle" }, "id": "Stanko-Allison-Michelle", "orcid": "0000-0003-0576-3739", "display_name": "Stanko, Allison Michelle" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "chair", "display_name": "Nelson, Hosea M." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xx1b-9262", "abstract": "Transition metal catalysis can be leveraged to construct challenging chemical bonds with excellent chemo- and stereoselectivity. Herein we describe the discovery of a novel palladium-catalyzed cascade cyclization and a nickel-catalyzed spirocyclization, enabling the assembly of complex carbocyclic architectures. We begin with an introduction describing notable applications of palladium-catalyzed cascade cyclizations in natural product synthesis, enabling the concurrent formation of C\u2013C and C\u2013N bonds in a single synthetic step.
\r\n\r\nNext, the development of a palladium-catalyzed oxidative Heck/aza-Wacker cascade cyclization is described. This cascade reaction enabled the construction of an all-carbon quaternary center, a C\u2013C bond, and a C\u2013N bond in a single synthetic step. Furthermore, it was employed to build the carbocyclic core of the natural product noraugustamine.
\r\n\r\nThen, we outline the discovery and optimization of an enantioselective nickel-catalyzed \u03b1-spirocyclization of lactones. The established method efficiently and enantioselectively forges 5-, 6-, and 7-membered rings containing all-carbon quaternary centers. This discovery represents an expansion of the synthetic toolkit for enantioselective spirocyclization, providing access to chiral, pharmaceutically relevant spirocyclic products.
\r\n\r\nFinally, we describe a collaborative project with the Su lab at the University of Arizona in the area of polymer synthesis and gas sensing, where we designed a sensor for the selective detection of gaseous nitric oxide. The sensor\u2019s excellent specificity and part-per-trillion level sensitivity was enabled by novel ferrocene-containing polymeric coatings.
" }, { "name": "Stevens, Taylor Anthony", "degree": "PhD", "year": "2024", "title": "Characterization of a Novel Membrane Protein Insertase in the Mitochondrial Outer Membrane", "advisor": "Voorhees, Rebecca M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12092023-142606831", "creators": [ { "name": { "family": "Stevens", "given": "Taylor Anthony" }, "id": "Stevens-Taylor-Anthony", "orcid": "0000-0002-6232-5316", "display_name": "Stevens, Taylor Anthony" } ], "advisors": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "advisor", "display_name": "Voorhees, Rebecca M." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." } ], "option_major": [ "biochem" ], "abstract": "Mitochondria are eukaryotic organelles derived from the endosymbiosis of an ancient bacteria. As a result of their endosymbiotic origin, the mitochondrial proteome is composed of a mixture of ancient bacterial derived genes and others which are unique to eukaryotes. This dual bacterial/eukaryotic protein origin results in a complicated landscape for biogenesis of mitochondrial proteins. This is particularly true for mitochondrial membrane proteins, since mitochondria have both an inner and outer membrane each with unique protein composition. Proteins localized to the outer mitochondrial membrane (OMM) are of particular interest due to their connection to many important physiological pathways in humans. OMM proteins are known to be inserted into the lipid bilayer by the MIM complex in yeast and by ATOM36 in trypanosomes, however it is not known how they are inserted in human cells. In my Ph.D. thesis, I describe the development of improved biochemical tools for protein purification and characterization, and then use them as part of an effort to characterize MTCH2, which we identify as the human gene responsible for OMM protein insertion. After identifying MTCH2 in a genome-wide screen, we use a variety of cell biology and biochemical experiments to show that MTCH2 is both necessary and sufficient for OMM protein insertion. We further show that endogenous OMM proteins are affected by MTCH2 depletion, and that apoptosis, a pathway relying on OMM proteins, is sensitive to MTCH2 modulation. Additional work in my thesis demonstrates that MTCH2 is a deeply conserved gene across metazoans, that other OMM insertases likely evolved independently in separate multi-cellular eukaryotic lineages." }, { "name": "Tong, Xiaoyu", "degree": "PhD", "year": "2024", "title": "Novel Reactivity and Applications of Transition Metal-Catalyzed Nucleophilic Substitution Reactions", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152024-205420698", "creators": [ { "name": { "family": "Tong", "given": "Xiaoyu" }, "id": "Tong-Xiaoyu", "orcid": "0000-0002-1343-6335", "display_name": "Tong, Xiaoyu" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nqkk-2x98", "abstract": "For more than 20 years, the Fu lab has explored the use of transition metal catalysts to enable novel nucleophilic substitution reactions. However, deficiencies in both fundamental reactivity and useful applications persist in this area. The research detailed in this thesis focuses on the development of reactivity and applications of transition metal-catalyzed nucleophilic substitution reactions." }, { "name": "Virgil, Kyle Allan", "degree": "PhD", "year": "2024", "title": "Polarization-Resolved, Oblique Incidence Terahertz Spectroscopy of Highly Uniform 2D Hybrid Perovskite Films", "advisor": "Blake, Geoffrey A.; Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192024-000137690", "creators": [ { "name": { "family": "Virgil", "given": "Kyle Allan" }, "id": "Virgil-Kyle-Allan", "display_name": "Virgil, Kyle Allan" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "orcid": "0000-0001-9435-0201", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dabiri", "given": "John O." }, "id": "Dabiri-J-O", "orcid": "0000-0002-6722-9008", "role": "member", "display_name": "Dabiri, John O." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "orcid": "0000-0001-9435-0201", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cr97-p373", "abstract": "This thesis details the development and optimization of thin film THz transmission measurements to extract spectrally resolved vibrational anisotropy in high quality layered hybrid perovskite materials. After an introduction in Chapter 1, Chapter 2 details the design, construction, and characterization of a terahertz time-domain spectrometer from scratch. Generalized THz propagation models are presented which enable accurate and diverse implementation of THz analysis. In Chapter 3, hybrid perovskite materials are introduced and our efforts towards reliably synthesizing high quality thin film perovskites using spin coating techniques are discussed. We find that optimized thin films are achieved from tailored synthetic conditions which depend on perovskite composition. In Chapter 4, we present our investigation into the elusive yet highly influential THz vibrational properties of 2D hybrid perovskite systems. A novel implementation of oblique-incidence THz transmission measurements reveals previously unseen vibrational excitations which provide valuable insight into the fundamental photodynamics that govern perovskite optoelectronics. We conclude in Chapter 5. This thesis serves to enhance the accessibility of powerful THz spectroscopic techniques as well as support the realization of promising perovskite renewable energy technologies." }, { "name": "Wackelin, Daniel Joseph", "degree": "PhD", "year": "2024", "title": "New to Nature C\u2013C Bond Forming Cyclases: Pushing the Boundaries of Ring Forming Reactions", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:09022023-064950039", "creators": [ { "name": { "family": "Wackelin", "given": "Daniel Joseph" }, "id": "Wackelin-Daniel-Joseph", "orcid": "0000-0001-8189-6985", "display_name": "Wackelin, Daniel Joseph" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemeng" ], "doi": "10.7907/26ag-8c56", "abstract": "Biocatalysts have shown themselves to be extremely powerful for the synthesis of pharmaceuticals, fragrances, and fine chemicals, providing products with high yields and selectivities. Recently, new-to-nature biocatalysis has received increased attention, allowing for the benefits of biocatalysis to be applied to reactions that were previously the sole domain of chemocatalysts. Engineers have begun to develop enzymes that catalyze new-to-nature C\u2013C bond forming cyclisation reactions, which are quite powerful due to their ability to build the carbon skeleton of molecules. Despite this, this class of enzymes is limited in scope. This thesis details the expansion of C\u2013C bond forming cyclases, including expanding the scope of cytochrome P411 cyclopropanation and an intramolecular C\u2013H functionalization strategy for the synthesis of diverse rings. Chapter 1 introduces biocatalysis and its recent applications, especially as they apply to new-to-nature C\u2013C bond forming cyclisation reactions. Chapter 2 shows the development of a cytochrome P411 that catalyzes the enantio- and diastero-specific synthesis of 1,2,3-polysubstituted cyclopropanes. Using directed evolution, this carbene transferase was evolved to react with internal alkenes and build two C\u2013C bonds, expanding the scope and specificity of cyclopropanation reactions. Chapter 3 describes the expansion of this biocatalytic system toward the synthesis of stereoconvergent products, enabling more efficient synthesis from non-diasteropure starting materials. Chapter 4 details the evolution of a cytochrome P411 to perform an intramolecular C\u2013H functionalization using diazo compounds, making a variety of differently sized rings with different molecular geometries. In summary, this work addresses the need for expansion of new-to-nature C\u2013C bond forming cyclisation reactions and provides a guide for expanding new-to-nature reactions to their full potential.
" }, { "name": "Wang, Grace Zimu", "degree": "PhD", "year": "2024", "title": "Chemo-Selective Proteomics for Discovery of Polymicrobial Interactions", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292024-213352165", "creators": [ { "name": { "family": "Wang", "given": "Grace Zimu" }, "id": "Wang-Grace-Zimu", "orcid": "0000-0002-0938-304X", "display_name": "Wang, Grace Zimu" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1vw0-gt98", "abstract": "The future of microbiome research lies in our ability to engineer polymicrobial interactions toward improved host health outcomes, which requires a fundamental molecular understanding of how microbial species sense and respond to ecological competition. Chronic respiratory infection by polymicrobial communities is the leading cause of mortality and morbidity in people living with cystic fibrosis (CF). My thesis work adapts chemo-selective proteomics to dissect molecular mechanisms that drive interspecies dynamics between two notorious opportunistic pathogens dominating chronic CF infection, Pseudomonas aeruginosa and Staphylococcus aureus.
\r\n\r\nIn Chapter 1, I introduce bioorthogonal noncanonical amino acid tagging (BONCAT)-based comparative proteomics, focusing on time-resolved, cell-specific, and cellular state-selective proteomic applications in the dissection of complex microbial systems. In Chapter 2, I discuss a new usage of time-resolved BONCAT\r\nto monitor immediate competition-sensing responses in interbacterial warfare. While coinfection by the Gram-negative Pseudomonas aeruginosa and the Gram-positive Staphylococcus aureus is associated with poor patient outcomes, the interspecies interactions responsible for such decline remain unknown. We\r\ndiscovered that P. aeruginosa senses S. aureus secreted cytotoxic peptides from a distance and preempts potential competition through activation of type six secretion system (T6SS). P. aeruginosa enhances such competition-sensing-induced antagonism through concomitant attraction toward S. aureus peptides, effectively reducing cellular distances between neighboring species and providing a competitive advantage. In Chapter 3, I discuss a new usage of cell-selective BONCAT to target protein synthesis analysis of the lowabundance organism, S. aureus, in a coculture environment predominated by P. aeruginosa. P. aeruginosa robustly outcompetes S. aureus, and conventional shotgun proteomics, which is biased toward highly abundant proteins on principle, could only identify and quantify less than 5% of total protein synthesis by S. aureus in coculture. We demonstrate that chemical enrichment affords a more than 12-fold increase in total protein abundances synthesized by S. aureus. About 50% of protein \u201chits\u201d with statistically significant changes in expression were not detected in pre-enrichment lysates, highlighting BONCAT as a powerful strategy that facilitates high-resolution proteomic analysis of low-abundance organisms in polymicrobial communities.
" }, { "name": "Ware, Skyler Danielle", "degree": "PhD", "year": "2024", "title": "Nonaqueous Electrolyte Design for Energy Storage and Electrosynthesis", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152023-235139391", "creators": [ { "name": { "family": "Ware", "given": "Skyler Danielle" }, "id": "Ware-Skyler-Danielle", "orcid": "0000-0002-3249-1946", "display_name": "Ware, Skyler Danielle" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kx7f-2065", "abstract": "Electrochemically driven metal redox has enabled advances in both academic and industrial processes, including production of metals from their ores, storage of renewable energy in batteries and fuel cells, and greener chemical synthesis conditions. While many electrochemical reactions are performed in aqueous solutions, applications in energy storage and organic synthesis often require extreme applied potentials that lie outside the electrochemical stability window of water or necessitate water-free conditions to prevent undesirable side reactions. Herein, we develop tailored non-aqueous electrolytes for applications in both energy storage and organic electrosynthesis and analyze the effects of electrolyte composition on interfacial and electrochemical reactions. First, a series of highly concentrated solvate electrolytes is developed for Li-S batteries, and interfacial reactivity between the solvate electrolytes and the Li anode is investigated in detail. The addition of a fluoroether cosolvent limits electrolyte decomposition at the Li surface, improving cycling stability and enabling new high-temperature applications. Next, samarium(III)/(II) redox is investigated in a variety of non-aqueous electrolytes to support an electrocatalytic cycle for samarium-mediated carbon-carbon bond formation. The coordination environment of the samarium salt, which can be tuned through anion exchange between the electrolyte and the samarium precursor, strongly affects the reversibility and reducing power of the samarium redox couple. Third, electrolyte additives are studied to increase the desolvation barrier of Zn\u00b2\u207a. When Zn sacrificial anodes are used in organic electrosynthesis, such additives may prevent deleterious cross-plating of Zn\u00b2\u207a at the cathode. Finally, a detailed guide to troubleshooting metal sacrificial anodes is presented with special attention to issues commonly encountered in reductive electrosynthesis." }, { "name": "Watkins, Nicholas Bret", "degree": "PhD", "year": "2024", "title": "Organic Films at the Electrode-Electrolyte Interface in CO\u2082 Reduction", "advisor": "Peters, Jonas C.; Gregoire, John M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272023-154324412", "creators": [ { "name": { "family": "Watkins", "given": "Nicholas Bret" }, "id": "Watkins-Nicholas-Bret", "orcid": "0000-0001-7251-9387", "display_name": "Watkins, Nicholas Bret" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "co-advisor", "display_name": "Peters, Jonas C." }, { "name": { "family": "Gregoire", "given": "John M." }, "id": "Gregoire-J-M", "orcid": "0000-0002-2863-5265", "role": "co-advisor", "display_name": "Gregoire, John M." } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Gregoire", "given": "John M." }, "id": "Gregoire-J-M", "orcid": "0000-0002-2863-5265", "role": "member", "display_name": "Gregoire, John M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7t8e-7j20", "abstract": "This thesis focuses on the use of use high-throughput experimentation and analytical electrochemistry techniques to understand how organic films on (photo)electrode surfaces alter catalyst selectivity. Specifically, the objective has been to deconvolute effects associated with the organic film from the atomic identity of the catalyst, reactant and intermediate concentration polarization effects, and temperature in the context of electrochemical CO\u2082 reduction. The first chapter provides the motivations behind the transformation of CO\u2082 into value-added materials using electricity and the challenges that the field faces. The second chapter introduces the data-driven identification of a scaling relationship between the partial current densities of methane and C\u2082\u208a products among 14 bulk copper bimetallic alloys. This strict dependence represents an intrinsic limitation of selectivity tuning through alloying. However, it can be disrupted to favor C\u2082\u208a products by the presence of an organic additive, highlighting the potential of hybrid organic\u2013inorganic catalysts to tune branching ratios in the CO\u2082R reaction network. The third chapter highlights that with the wide band gap CuGa\u2083Se\u2085 chalcopyrite absorber, organic coatings can not only provide dramatic increases in selectivity toward CO\u2082R products compared to the unmodified system, but also and significantly moderate catalyst corrosion. The fourth chapter unveils a new class of molecular films on polycrystalline copper, derived from aryl diazonium and iodonium salts, that are corrosion resistant even at pH 1 and have the potential for many future electrochemical applications. In the fifth chapter, we demonstrate that increased mass transport at the electrode surface directly resulted in changes to the ethylene and methane Tafel slope values on copper electrodes. These findings emphasize that the apparent Tafel slope reported for any copper system is not necessarily representative of the catalyst\u2019s intrinsic kinetics alone, but also contains information about the cell geometry and electrolyte convective transport. The final chapter investigates the combined effect of organic films, mass transport, and electrode heating on electrocatalysis. We find that we can use surface heating to replace bulk heating, but that the complexity of CO\u2082R prevents predictable behavior. However, the addition of additive films to the electrode surface enables idealized electrochemical CO\u2082 reduction kinetics, and therefore the calculation of important parameters such as the activation energy for C\u2082\u208a product formation." }, { "name": "Zeng, Tian", "degree": "PhD", "year": "2024", "title": "Masked 2-Furylcarbinol Derivatives: A Modular and General Platform for Mechanically Triggered Molecular Release", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012024-065205159", "creators": [ { "name": { "family": "Zeng", "given": "Tian" }, "id": "Zeng-Tian", "orcid": "0000-0001-5957-3442", "display_name": "Zeng, Tian" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2vm9-5415", "abstract": "Stimuli-responsive polymers that undergo chemical transformations when exposed to external stimuli are attractive materials for a wide range of applications, such as targeted drug delivery, sensing, and catalysis. Within the emerging field of polymer mechanochemistry, mechanical force is harnessed to promote productive chemical transformations in stress-responsive molecules known as mechanophores. My research over the past several years has focused on the development of a modular and general mechanophore platform capable of releasing covalently-bound payloads in response to mechanical force. I envision that the further advancement of this design will not only aid in a deeper understanding of the design principles of mechanophores, but also enable new technologies, including non-invasive spatiotemporal delivery of bioactivate small molecules and self-healing materials.
\r\n\r\nChapter 1 reviews the recent process of the development of small molecule-releasing mechanophores and provide an overview of the masked 2-furylcarbinol derivatives we developed that enables a mechanically gated release cascade. Chapter 2 describes our initial demonstration of mechanically gated small molecule release from our mechanophore and the subsequent structural-property investigation to optimize for faster release rates. In Chapter 3, an alternative mechanophore design is introduced that has a shortened synthetic sequence while maintaining a fast release kinetics. In Chapter 4, we address the challenge of low release capacity from previous designs with a novel mechanophore that can be incorporated into multimechanophore polymers. Finally, Chapter 5 demonstrates the use of our modular and general release platform to trigger the depolymerization of a self-immolative polymer.
" }, { "name": "Zhang, Wanji Wendy", "degree": "PhD", "year": "2024", "title": "Efforts Towards C-C Bond Formations: From Ni Catalysis to Transition-Metal Free Electrolysis", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:08212023-202451948", "creators": [ { "name": { "family": "Zhang", "given": "Wanji Wendy" }, "id": "Zhang-Wanji-Wendy", "orcid": "0000-0002-6895-9598", "display_name": "Zhang, Wanji Wendy" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/czam-9x35", "abstract": "The selective construction of C-C bonds has been a critical challenge in modern synthetic organic chemistry. Among the numerous methodologies developed, cross-coupling remains an attractive strategy for direct C-C bond formation. Herein, a diverse range of cross-coupling reactions for C-C bond formations are investigated from different perspectives. First, the mechanism of a Ni/cyano-box-catalyzed asymmetric Suzuki alkynylation is studied. The existing data is consistent with a radical chain pathway that is previously proposed for other Ni-catalyzed enantioselective cross-coupling reactions. Next, moving on from the traditional electrophile-nucleophile cross-couplings, we explore Ni-catalyzed reductive coupling of alkyl halides with internal olefins in the presence of a hydrosilane. With judicious choice of the directing group, hydroalkylation of internal olefins can be achieved with high regio- and enantioselectivity. Following that, an electrochemically driven, transition-metal free cross-electrophile coupling reaction is explored as a greener alternative to constructive C(sp\u00b3)-C(sp\u00b3) bonds. Specifically, we focus on improving the Mg sacrificial anode performance in these electroreductive systems. By carefully choosing the electrolyte composition, we are able to manipulate the metal electrode interfaces for a more effective counter electrode. Finally, Al stripping in ethereal solvents is investigated for its application as a sacrificial anode in reductive electrosynthesis. Inspired by Al corrosion chemistry, we are able to achieve bulk Al stripping in THF-based electrolyte by incorporating halide co-supporting electrolytes.
" }, { "name": "Abundo, Maria Paulene Bernal", "degree": "PhD", "year": "2023", "title": "Ultrasound Controlled Drug Delivery by Acoustically Switchable Hydrogels", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272023-093432414", "creators": [ { "name": { "family": "Abundo", "given": "Maria Paulene Bernal" }, "id": "Abundo-Maria-Paulene-Bernal", "orcid": "0000-0002-5122-6937", "display_name": "Abundo, Maria Paulene Bernal" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Daraio", "given": "Chiara" }, "id": "Daraio-C", "orcid": "0000-0001-5296-4440", "role": "member", "display_name": "Daraio, Chiara" }, { "name": { "family": "Gao", "given": "Wei" }, "id": "Gao-Wei", "orcid": "0000-0002-8503-4562", "role": "member", "display_name": "Gao, Wei" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5rr6-q625", "abstract": "Not only is ultrasound widely used as a diagnostic imaging modality, it can also be focused into deep tissues to perform non-invasive actuation of cells, implants and delivery vehicles and other biological targets. With the addition of gas vesicles (GV), generic hydrogel materials gain the ability to communicate with ultrasound, equipping them with in vivo tracking, targeting and actuation capabilities to safely transport biomolecular cargo. This is possible as GVs function simultaneously as ultrasound contrast agents and steric blockers that can be \"erased\" by an increase in ultrasound pressure to trigger a rapid outflow diffusion of the payload from within the material. We evaluate this concept through in vitro measurements of ultrasound-modulated diffusion and drug release and targeted in vivo release in the lower gastrointestinal tract. Then we demonstrate the use of orally administered hydrogel particles to deliver etanercept in the duodenum to treat gastrointestinal inflammation in a rat model of colitis. Finally, we explore new directions and applications of GV-hydrogel systems, showcasing their potential for deployment in a wide range of biomedical applications.
" }, { "name": "Almhjell, Patrick James", "degree": "PhD", "year": "2023", "title": "Noncanonical Amino Acid Synthesis by Evolved Tryptophan Synthases", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172022-224813021", "creators": [ { "name": { "family": "Almhjell", "given": "Patrick James" }, "id": "Almhjell-Patrick-James", "orcid": "0000-0003-0977-841X", "display_name": "Almhjell, Patrick James" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Wang", "given": "Kaihang" }, "id": "Wang-Kaihang", "orcid": "0000-0001-7657-8755", "role": "chair", "display_name": "Wang, Kaihang" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "biochem" ], "doi": "10.7907/rcvq-dg51", "abstract": "The \u03b2-subunit of tryptophan synthase (TrpB) is responsible for the final step of \u029f-tryptophan biosynthesis in all of known biology. Recognized for this important role and its powerful chemistry, TrpB has more recently been used for the in vitro synthesis of tryptophan analogs and other noncanonical amino acids (ncAAs). This thesis describes some of these efforts as well as the application of TrpB for developing new methods in directed enzyme evolution. Chapter I first establishes important topical background. It begins with a general account of directed enzyme evolution by exploring the emergence of new catalytic functions in natural and laboratory settings, and how this information and chemical intuition can be used to create enzymes for desired reactions. This is followed by a description of the state of the field of ncAA synthesis, with a special focus on biocatalytic approaches using engineered enzymes. Chapters II and III examine targeted engineering campaigns to create enzymes that can efficiently synthesize valuable blue-fluorescent ncAAs such as 4-cyanotryptophan (Chapter II) and \u03b2-(1-azulenyl)-\u029f-alanine (AzAla, Chapter III) from accessible starting materials. In Chapter IV, the native function of TrpB for \u029f-tryptophan biosynthesis is used as a selection pressure to develop an in vivo continuous evolution system. Despite a selection pressure for only \u029f-tryptophan synthesis the orthologous TrpB variants generated by this system have varying promiscuous activities for \u029f-tryptophan analogs, paralleling the sequence-function diversity of natural enzyme homologs. Chapter V describes evSeq, an inexpensive and simple method for sequencing all protein variants generated during an engineering campaign, demonstrated by collecting ~800 TrpB sequence-function data points. Finally, in Chapter VI, directed evolution and chemical intuition are used to convert TrpB from a tryptophan synthase to a novel tyrosine synthase (TyrS). This enzyme can irreversibly and regioselectively alkylate simple phenol analogs to synthesize valuable tyrosine analogs, including the blue-fluorescent ncAA \u03b2-(1-naphthol-4-yl)-\u029f-alanine (NaphAla) and 3-methyl-\u029f-tyrosine at gram scales. Because TyrS synthesizes a primary metabolite, this transformation represents a noncanonical method for the biosynthesis of \u029f-tyrosine. This is the first example of a feasible new route for de novo aromatic amino acid biosynthesis, which occurs through a universally conserved set of chemistry across all of life. In total, the work described here expands the fields of chemical synthesis and synthetic biology by presenting new enzymes\u2014and methods for producing these enzymes\u2014that are capable of synthesizing important amino acids in vitro and in vivo.
" }, { "name": "Alshafei, Faisal H.", "degree": "PhD", "year": "2023", "title": "Enhancing the Ethylene and Propylene Selectivities in the Methanol-to-Olefins Reaction by Exploiting the Intricate Relationship between Framework Topology and Acidity", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142023-055704455", "creators": [ { "name": { "family": "Alshafei", "given": "Faisal H." }, "id": "Alshafei-Faisal-H", "orcid": "0000-0003-1808-1374", "display_name": "Alshafei, Faisal H." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "member", "display_name": "Manthiram, Karthish" }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/btcj-w948", "abstract": "This thesis describes and presents results from several related projects within the theme of molecular sieve synthesis and catalysis. The early part of the thesis focuses on understanding the link between cage size/dimension and acidity (i.e., acid site density and strength) in the methanol-to-olefins (MTO) reaction. This relationship between cage size and acidity, once identified and investigated, is exploited in the latter parts of the thesis to rationally design materials that are able to steer the light olefins product distribution toward either more ethylene or propylene in a significant improvement over SAPO-34 (CHA), the commercial catalyst.
\r\n \r\nIn Chapters 2, 44 zeolites and silicoaluminophosphates (SAPOs) belonging to five frameworks (AEI, CHE, LEV, SWY, and ERI) with a wide range of Si/Al=4-31 and Si/(Al+P)=0.04-0.3, are synthesized and characterized using a myriad of techniques. Their MTO behavior is then systematically investigated to rationalize the effect of cage dimensions on the olefins product distribution as a function of acid site density and strength. The results from this study show that changes in acid site density and strength play a secondary role to the dominating influence of cage architecture on product distribution in AEI- and CHA-type molecular sieves. Decreasing the cage size, in going from AEI and CHA to LEV, SWY, and ERI, however, results in substantial changes in the ethylene-to-propylene ratio (E/P) as a function of acidity. These changes are attributed to differences in the identity and concentration of the hydrocarbon-pool (HP) species that form, particularly in early stages of the reaction.
\r\n \r\nIn Chapters 3 and 4, ERI-type molecular sieves (e.g., SSZ-98, UZM-12, ERI-type zeolites, and SAPO-17) are thoroughly investigated as promising methanol-to-ethylene materials due to their narrow cage size. Specifically, numerous ERI-type molecular sieves are synthesized using several organic structure-directing agents (OSDAs) with varied Si/Al or Si/T-atoms ratios. The list of ERI-related materials synthesized and tested in MTO included a new disordered SAPO, denoted as CIT-16P, which upon thermal treatment in air transforms to SAPO-17 (ERI). The reaction results show that decreasing the Si/Al (or increasing the Si/T) ratio, irrespective of other material properties, improves the E/P of ERI-type molecular sieves (E/P=1.1-1.9) over CHA-type molecular sieves (E/P=0.82-0.85) in MTO. Dissolution-extraction experiments reveal that the rapid formation of cyclic intermediates and the shift in their composition toward less-methylated methylbenzenes and methylnaphthalenes are found to be key to enhancing the ethylene selectivity in ERI-type molecular sieves.
\r\n \r\nIn Chapter 5, several SAT-type molecular sieves are investigated as promising methanol-to-propylene catalysts. This effort entails the synthesis of CIT-17, an SAT SAPO-type molecular sieve, which is isostructural to STA-2 (MgAPO-SAT). Following the successful synthesis of CIT-17, the MTO behavior of several SAT-type molecular sieves (MgAPO, CoAPO, and SAPO) are investigated in MTO. The combination of low acidity of CIT-17 and unique structural features of the narrow SAT-cage lead to a catalytic pathway and mechanism that predominantly favors propylene (propylene-to-ethylene ratios (P/E) of 2-4.2; propylene selectivity of 40-50%). Indeed, CIT-17 achieves one of the highest P/E ratio values reported for this class of materials.
" }, { "name": "Balzer, Christopher James", "degree": "PhD", "year": "2023", "title": "Polyelectrolytes Near Solid Surfaces", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162023-233932300", "creators": [ { "name": { "family": "Balzer", "given": "Christopher James" }, "id": "Balzer-Christopher-James-J", "orcid": "0000-0002-9767-8437", "display_name": "Balzer, Christopher James" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Frischknecht", "given": "Amalie L." }, "id": "Frischknecht-Amalie-L", "orcid": "0000-0003-2112-2587", "role": "member", "display_name": "Frischknecht, Amalie L." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/kga2-1820", "abstract": "Polyelectrolytes are ubiquitous in nature and in the products we use daily. The combination of their connectivity and charge lead to many useful properties in solution and near surfaces. Electrostatic forces dominate much of the behavior of charged species near solid surfaces; however, nonelectrostatic forces arising ion specific interactions or from varying polymer chemistry play an important role in tuning electrolyte and polyelectrolyte properties. The balance of these forces depends on factors like the salt concentration, solution pH, and properties of the surface. The current work outlines the thermodynamics of charged systems and investigates the structure and phase behavior of polyelectrolytes near solid surfaces. In particular, the work covers the thermodynamic aspects of preferential adsorption of small ions in electric double layers, polyelectrolyte adsorption, polymer-mediated interactions of surfaces using strong and weak electrolytes, surface phase transitions and contact angles of complex coacervates on solid surfaces, complexation-induced conformational phase transitions of polyelectrolyte brushes, and electro-swelling of weak polyelectrolyte brushes. The wide variety of problems addressed here reflects the variety of applications of polyelectrolytes and contexts in which polyelectrolytes appear.
" }, { "name": "Barber, Ross William", "degree": "PhD", "year": "2023", "title": "Mechanophore Strategies for the Development of Polymers with Mechanically Gated Responsive Behavior", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092023-013609857", "creators": [ { "name": { "family": "Barber", "given": "Ross William" }, "id": "Barber-Ross-William", "orcid": "0000-0003-0434-847X", "display_name": "Barber, Ross William" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "co-chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wgnw-zq30", "abstract": "The development of mechanically sensitive molecules has recently enabled mechanical force to induce specific changes in polymeric materials. This document details efforts in the development of such mechanophores in which mechanical activation is used to gate the desired functional responses.
\r\n\r\nChapter 1 is an introduction to polymer mechanochemistry and delineates the state of the field as it relates to color changing mechanophores used for damage detection. Special emphasis is placed on a system developed by our lab in which mechanical force gates the photoresponsive behavior of a diarylethene molecular switch.
\r\n\r\nChapter 2 details the design of a new mechanically gated photoswitch whose synthesis and activity are improved from the previous iteration. The modular design enables a late-stage synthetic intermediate to be differentiated into a small library of masked photoswitches that produce unique colors following mechanical activation and ultraviolet irradiation. Notably, these mechanophores show activity in solution phase experiments as well as in bulk polymeric materials.
" }, { "name": "Barth, Alexandra Teresa", "degree": "PhD", "year": "2023", "title": "Electronic Structure and Reactivity of Metal Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12282022-061839565", "creators": [ { "name": { "family": "Barth", "given": "Alexandra Teresa" }, "id": "Barth-Alexandra-Teresa", "orcid": "0000-0002-1813-4029", "display_name": "Barth, Alexandra Teresa" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/k66v-1c93", "abstract": "Transition metals are at the core of addressing global energy needs. Functioning as catalysts, these systems have long demonstrated competency to promote thermodynamically challenging reactions, lowering energetic barriers and facilitating desired transformations with applied light or potential. Employing infrared, visible, ultraviolet, and x-ray spectroscopy, chemists are afforded insight into the electronic structures of transition metal complexes, investigating ligand field strengths and metal-ligand interactions. Addition of time-resolved techniques affords resolution of dynamic processes in molecular species, such as electron transfer pathways.
\r\n\r\nChapter 1 reviews the electronic structure and reactivity of homoleptic tungsten(0) arylisocyanides W(CNAr)\u2086 to provide the foundation for much of this work.
\r\n\r\nIn Chapter 2, application of W(CNAr)\u2086 species for one- and two-photon photoredox catalysis are explored. The two-photon absorption cross-sections of W(CNAr)\u2086 are remarkably large (\u03b4\u2088\u2081\u2080 = 180\u20131900 GM) and enable these photocatalysts to operate under excitation from visible or near infrared light. Photoredox activity is evaluated via base-promoted homolytic aromatic substitution (BHAS) reaction of thermodynamically challenging substrates. In Chapter 3, solvent perturbations enhance visible light-activated BHAS catalysis from W(CNAr)\u2086. Increased solvent dielectric (benzene to 1,2-difluorobenzene) and solvated electrolyte combine to increase *W(CNAr)\u2086 quenching rates up to one order of magnitude with greater cage-escape yields.
\r\n\r\nIn Chapter 4, the electronic structure of linear gold(I) arylisocyanide complexes ([Au(CNDipp-R)\u2082]\u207a; CNDipp = 2,6-diisopropylphenylisocyanide) are assigned using insights from UV-visible spectroscopy and time-dependent density functional theory (TD-DFT) calculations. In Chapter 5, the electronic structure of Fe(II) and Co(II) quaterpyridine photo-/electro-catalysts for CO\u2082 reduction are evaluated using UV-visible-NIR, \u00b9H NMR, M\u00f6ssbauer, and infrared spectra. Assignment of the absorption transitions are supported by TD-DFT calculations.
" }, { "name": "Breunig, Stephanie Lynne", "degree": "PhD", "year": "2023", "title": "Incorporation of Non-Canonical Proline Residues into Proteins Expressed in Escherichia coli", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222023-030948313", "creators": [ { "name": { "family": "Breunig", "given": "Stephanie Lynne" }, "id": "Breunig-Stephanie-Lynne", "orcid": "0000-0002-8665-6363", "display_name": "Breunig, Stephanie Lynne" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8nj2-v152", "abstract": "Non-canonical proline residues expand the chemical space about proline, while maintaining some conformational properties of the canonical residue. The translational machinery of Escherichia coli can accommodate close structural analogs of proline, which has enabled the production of recombinant proteins that contain non-canonical residues at proline positions. However, proline mutagenesis in E. coli is restricted to a relatively small set of proline variants, and protein science and engineering efforts utilizing non-canonical proline residues are limited.
\r\n\r\nThis thesis aims to expand the scope of proline analogs that can be accepted by E. coli, and demonstrate the utility of proline mutagenesis in modifying and studying protein behavior. In Chapter II, we describe the incorporation of three aliphatic proline residues into recombinantly-produced insulin, and find that these modest modifications at ProB28 alter the biophysical properties of the therapeutic protein. In particular, the addition of an exocyclic olefin at B28 accelerated insulin fibril formation, while 4-methyl substituents increased the rate of dissociation from the pharmaceutically-formulated insulin hexamer. We expand our proline mutagenesis approach to monomeric insulins in Chapter III. 4-fluorinated proline analogs replaced ProB29 of the fast-acting insulin lispro; 4S-fluorination of ProB29 slowed fibril formation. Chapter IV describes the incorporation of the photo-activatable proline analog \"photo-proline\" into proteins expressed in E. coli, and Chapter V discusses our efforts to engineer the E. coli prolyl-tRNA synthetase to accommodate more diverse proline substrates. Together, this work expands the proline analogs accessible to recombinant expression in E. coli, and demonstrates their use in probing and engineering the biophysical properties of proteins.
" }, { "name": "Casselman, Tyler Daniel", "degree": "PhD", "year": "2023", "title": "Unveiling Incipient Reactivity via Tandem Hydrosilylation Reaction Cascades and the Progress Toward the Total Synthesis of (\u2013)-Cylindrocyclophane A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-191413115", "creators": [ { "name": { "family": "Casselman", "given": "Tyler Daniel" }, "id": "Casselman-Tyler-Daniel", "orcid": "0000-0002-1691-3969", "display_name": "Casselman, Tyler Daniel" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/92b3-2d90", "abstract": "The two pillars of synthetic organic chemistry, reaction methodology development and total synthesis of complex natural products, has remained the focus of chemical research for synthetic chemists since their fundamental inception. In particular, harnessing the reactivity of unstable, but useful, chemical intermediates through telescoping reaction conditions is emerging as an attractive approach to rapidly access complex molecular architecture from readily available building blocks. Herein is described two unique reaction methodologies relying on tandem hydrosilylation reaction cascades to synthesis saturated N-heterocyclic products in a stereoselective manner. We have developed a diastereoselective Mannich reaction combining \u03b1-substituted-\u03b3-lactam pronucleophiles with N-silyl imine electrophiles generated in situ via catalytic hydrosilylation of aryl nitriles. Additionally, we have developed a tandem hydrosilylation, enantioselective allylic alkylation reaction of substituted pyridines to yield chiral tetrahydropyridine products. This serves as the first example of using hydrosilylation of pyridines to generate enamine nucleophiles that can undergo an asymmetric allylic alkylation reaction. The final portion of this thesis describes the progress toward a total synthesis of (\u2013)-cylindrocyclophane using C\u2013H functionalization logic. We were able to access the necessary [7.7]-paracyclophane core in 8 steps from a feedstock aryl diazoacetate compound and n-hexene. Through functional group manipulations, we were able to advance this paracyclophane core to an intermediate possessing the exact stereocenters and carbon framework in (\u2013)-cylindrocyclophane A. We are currently modeling the necessary deoxygenation needed to advance this intermediate and complete the total synthesis.
" }, { "name": "Chittur, Priya K.", "degree": "PhD", "year": "2023", "title": "A Millifluidic Bulge Test for Multiscale Properties of Engineered Biofilms", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08282022-230140735", "creators": [ { "name": { "family": "Chittur", "given": "Priya K." }, "id": "Chittur-Priya-K", "orcid": "0000-0002-9409-4671", "display_name": "Chittur, Priya K." } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "orcid": "0000-0002-2912-0001", "role": "member", "display_name": "Ravichandran, Guruswami" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e1yv-mr74", "abstract": "Biofilms \u2013 communities of bacterial cells associated with their extracellular polymeric matrices \u2013 are complex materials whose features span many length scales, ranging from bulk cohesive material properties, to mesoscale structural and compositional heterogeneity, down to the microscopic cellular morphology and cell-cell interaction chemistry.
\r\n\r\nHere, we demonstrate a tool to study the mechanical properties of biofilms across length scales from the mesoscale (0.2 mm) to the bulk (1 mm) using a simplified model system based on genetically engineered E. coli. Using a custom millifluidic device that suspends a 3 mm dia. biofilm across a support, we impose tunable hydrostatic pressure drops in the Pa-kPa range across the biofilm. The resulting deformation of the film through an aperture is visualized with optical coherence tomography and used to estimate bulk and mesoscale mechanical properties of the film. Our method requires only microliters of material, causes minimal disruption to the film structure, and allows for estimates of both average properties as well as local heterogeneity as a function of cell-cell interaction chemistry and biofilm damage and healing. In the final chapter we introduce other model biofilm systems for their unique optical and mechanical properties.
" }, { "name": "Cui, Zhi-Hao", "degree": "PhD", "year": "2023", "title": "Towards Ab Initio Simulations of High-Temperature Superconductivity", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11022022-092201743", "creators": [ { "name": { "family": "Cui", "given": "Zhi-Hao" }, "id": "Cui-Zhi-Hao", "orcid": "0000-0002-7389-4063", "display_name": "Cui, Zhi-Hao" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Yeh", "given": "Nai-Chang" }, "id": "Yeh-Nai-Chang", "orcid": "0000-0002-1826-419X", "role": "member", "display_name": "Yeh, Nai-Chang" }, { "name": { "family": "Bernardi", "given": "Marco" }, "id": "Bernardi-Marco", "orcid": "0000-0001-7289-9666", "role": "member", "display_name": "Bernardi, Marco" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/y2qf-1f77", "abstract": "High-temperature superconductors have been discovered for more than three decades. Nonetheless, the theoretical understanding of their microscopic properties remains unclear with substantial difficulties in linking the observed phenomena to material composition and structures. This thesis aims to establish a theoretical hierarchy (from lattice models to realistic materials) for faithful simulations of high temperature superconductivity.
\r\n\r\nWe start with the lattice models of superconductors by using quantum embedding theory, whose self-consistency allows magnetic and superconducting phases to emerge. We extended the density matrix embedding theory (DMET) with improved self-consistency algorithms and determined the ground-state phase diagrams for both one-band [Chap. 3] the three-band Hubbard models [Chap. 4]. In particular, in the three-band model, we explored the atomic-scale nature of the antiferromagnetic and superconducting orders for different model parametrizations, and highlighted the role of the oxygen degrees of freedom beyond the one-band picture.
\r\n\r\nTo go beyond the models, we therefore extended the original theory [DMET and dynamical mean-field theory (DMFT)] to ab initio realistic solids [Chap. 5]. The methods, namely the full-cell quantum embedding, are distinct from other embedding schemes in three aspects: (i) all local orbitals in a unit cell are included in the embedding problem whereas the bath orbitals are truncated according the atomic valence characters; (ii) The embedding Hamiltonian is of full quartic fermionic form rather simplified Hubbard like Hamiltonians; (iii) Many-body quantum chemistry solvers such as coupled cluster (CC) are used to generate embedding density matrix and Green\u2019s functions. As demonstrated across a variety of semiconducting and insulating materials, the full-cell quantum embedding provides accurate energy, equation of state, spin-spin correlation functions and excited-state band structures.
\r\n\r\nWe then applied our ab initio quantum embedding methods to the parent state of a series of cuprate superconductors [Chap. 6]. We uncovered microscopic trends in the electron correlations and revealed the link between the material composition and magnetic energy scales via a many-body picture of excitation processes involving the buffer layers. We found the competition between the in-plane superexchange and the CuO\u2082-buffer layer excitations, which explains the magnetic coupling difference among a series of superconducting materials.
\r\n\r\nFinally, we investigated the doped cuprates, where the superconducting orders enter into the phase diagram [Chap. 7]. We generalized our ab initio framework to allow the particle-number symmetry breaking states such that the superconducting orders can spontaneously emerge during the self-consistency. We showed that the d-wave superconducting magnitude increases with the pressure applied to crystals and the trend connects to the superexchange coupling J . Furthermore, we also studied the layer effect on superconductivity. Unlike the pressure effect, the layer effect between different compounds is affected by more factors - both magnetic coupling J and charge distribution matters. The work provides a promising route to study the material-specific physics in high-temperature superconductivity.
\r\n\r\nThe aforementioned applications also relied on (i) the development and adaptation of many-body solvers, including the CC singles and doubles (CCSD) with Newton-Krylov method for better numerical convergence, and active-space quantum chemistry techniques with large-scale density matrix renormalization group. (ii) projection-based orbital localizations for metallic systems, frozen core techniques and symmetry adaptations. These contents are discussed in Chap. 2 and Appendices, including their efficient implementation and parallelization.
\r\n\r\nIn the concluding remarks [Chap. 8], we summarized the current status and limitations of the high-temperature superconductivity studies. In addition, we proposed several possible directions to address the challenges in electronic correlation and atomic modelling of other exotic phases from an ab initio perspective.
" }, { "name": "Dibrell, Sara Elise", "degree": "PhD", "year": "2023", "title": "Development of Oxidation and Transition Metal-Mediated Reactions and Application to Natural Product Synthesis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282023-211208336", "creators": [ { "name": { "family": "Dibrell", "given": "Sara Elise" }, "id": "Dibrell-Sara-Elise", "orcid": "0000-0003-0332-1101", "display_name": "Dibrell, Sara Elise" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ve4j-tw63", "abstract": "Expedient access to complex molecules via chemical synthesis is important for assessing their biological activity and medicinal properties. In one approach, convergent joining of fragments of similar size and complexity is followed by minimal scaffold tailoring steps to rapidly access natural products. This strategy hinges on the ability to (1) tailor peripheral oxidation, ideally via creative redox transformations, and (2) forge strategic bonds within a complex scaffold through C\u2013C bond formation. We disclose efforts to address these aims by developing broadly useful chemical tools and applying them to the preparation of bioactive natural products.
\r\n\r\nToward the first aim, we investigated unusual oxidative reactivity mediated by selenium dioxide. To address the second aim, we developed nickel-catalyzed reductive cross-coupling reactions to study: catalyst-controlled enantioselectivity in the preparation of medicinally relevant small molecules, substrate-controlled stereoselectivity, and selectivity for ring formation. The latter studies enabled the exploration of transition metal-mediated cyclization as a convergent annulation strategy toward the rearranged isoryanodane diterpene (+)-cassiabudanol A, as well as the formal synthesis of the macrocyclic cytotoxin (\u2013)-cylindrocyclophane F.
" }, { "name": "Dowling, Jacqueline Anne", "degree": "PhD", "year": "2023", "title": "Long-Duration Energy Storage in Reliable Wind and Solar Electricity Systems", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042023-203620894", "creators": [ { "name": { "family": "Dowling", "given": "Jacqueline Anne" }, "id": "Dowling-Jacqueline-Anne", "orcid": "0000-0001-5642-8960", "display_name": "Dowling, Jacqueline Anne" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gyzn-4n98", "abstract": "Several U.S. states mandate zero-carbon electricity systems based primarily on renewable technologies, such as wind and solar. Reliable and affordable electricity systems based on these variable resources may depend on the ability to store large quantities of low-cost energy over long timescales. This thesis combines techno-economic analysis with materials chemistry to advance long-duration energy storage in reliable wind and solar electricity systems. Our macro-energy model incorporated multi-decadal weather datasets and revealed unique long-duration energy storage roles, such as seasonal and multi-year storage, that increase the affordability of wind- and solar-based electricity, informing technology investments and policy. We find that low-cost energy storage, such as underground hydrogen, is valuable even if the charge/discharge cost is expensive. In U.S. wind and solar systems, hydrogen energy storage and conversion capital cost improvements are more valuable than efficiency improvements. Low-cost earth-abundant catalysts may be acceptable replacements for precious metal catalysts in proton exchange membrane electrolyzers despite lower efficiency for storage applications in wind and solar systems. We synthesized earth-abundant manganese antimony oxide catalysts via a new chemical vapor deposition route and assessed their long-term electrochemical durability for oxygen evolution. Multi-day tests confirmed the activity-stability tradeoff across the Mn:Sb composition space." }, { "name": "Dutka, Przemys\u0142aw", "degree": "PhD", "year": "2023", "title": "Cryo-ET Reveals Molecular Details of Multi-Megadalton Bacterial Protein Complexes", "advisor": "Shapiro, Mikhail G.; Jensen, Grant J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092023-163511031", "creators": [ { "name": { "family": "Dutka", "given": "Przemys\u0142aw" }, "id": "Dutka-Przemys\u0142aw", "orcid": "0000-0003-3819-1618", "display_name": "Dutka, Przemys\u0142aw" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "orcid": "0000-0003-1556-4864", "role": "co-advisor", "display_name": "Jensen, Grant J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "orcid": "0000-0003-1556-4864", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "biochem" ], "doi": "10.7907/87jm-7v06", "abstract": "Cryo-electron tomography (cryo-ET) is a powerful method for investigating the 3D structure of intact cells, organelles, and complex protein macromolecules that cannot be crystallized or are too heterogenous for single-particle cryo-electron microscopy (cryo-EM). However, obtaining high- resolution cryo-ET structures for many biologically important targets is still a challenge. To address this challenge, cryo-ET can be combined with other methods, including X-ray crystallography, single-particle cryo-EM, structure predictions, cross-linking mass spectrometry, biochemistry, and evolutionary analysis to produce integrative models. Recently, with the development of AI-based tools such as AlphaFold2, structure prediction has played an increasingly important role in integrative modeling. The combination of cryo-ET and structure prediction in particular has provided unprecedented insights into the ultrastructure of cellular components. This thesis focuses on two bacterial multi-megadalton protein complexes which are difficult to study by classical structural biology approaches: gas vesicles (GVs) and the Legionella pneumophila Dot/Icm type IV secretion system (T4SS). GVs are gas-filled protein nanostructures that regulate the position of certain microorganisms in water and consequently their access to sunlight and nutrients. Here, we investigate the mechanical properties of GVs and reveal the molecular structure of GVs and its implication for the assembly mechanism. The Dot/Icm T4SS is a macromolecular complex formed by approximately 27 proteins, utilized by L. pneumophila to hijack the host cell's biology for its replication purposes. A nearly-complete integrative model of this complex provides crucial insights into its structural organization and its evolution from conjugation to secretion, as well as the transportation of substrates into the host cell.
" }, { "name": "Dutton, Sarah Emily", "degree": "PhD", "year": "2023", "title": "Chirped Pulse Rotational Spectroscopy of Small Molecule Clusters", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04172023-221653165", "creators": [ { "name": { "family": "Dutton", "given": "Sarah Emily" }, "id": "Dutton-Sarah-Emily", "orcid": "0000-0002-9587-5971", "display_name": "Dutton, Sarah Emily" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "chair", "display_name": "Wei, Lu" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/dxsp-c265", "abstract": "Despite the ubiquity of water and alcohol mixtures in every realm of science, the hydrogen bond network governing the unique properties of these mixtures is still under investigation. To aid in the determination of hydrogen bond energetics and dynamics in alcohol and water mixtures, herein a ground up approach studying small alcohol:water clusters is presented. Novel instrumentation for chirped pulse Fourier-transform microwave spectroscopy was developed, and subsequently benchmarked against the detection and characterization of ethanol and water trimers. From there, cluster size was gradually increased, first studying ethanol and water tetramers, then switching to methanol for larger cluster studies of pentamers and hexamers. Throughout this thesis, the over-arching questions as to microaggregation in clusters and trends in geometry and relative energy ordering were investigated, and evidence supporting the facile mixing of small alcohols and water is presented at the few-molecule cluster scale. In the final studies of methanol and water hexamers, the first `3-dimensional' bonding motifs of methanol and water clusters are observed, marking the transition from the planar conformers of small clusters to the complex and higher cooperativity bonding patterns in larger clusters and in bulk mixtures." }, { "name": "Friedman, Andrew Collin", "degree": "PhD", "year": "2023", "title": "Scalable Fabrication of Micro-Architected Water Filtering Membranes", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-223752519", "creators": [ { "name": { "family": "Friedman", "given": "Andrew Collin" }, "id": "Friedman-Andrew-Collin", "display_name": "Friedman, Andrew Collin" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "member", "display_name": "Greer, Julia R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/rktj-2v55", "abstract": "Polymer-based filtration devices are predominantly mass manufactured via mechanical spinning or electrospinning of heated polymer materials or fiberglass to create a randomly oriented fibrous network. This technique, while effective at producing materials necessary for traditional filtering applications, fails to afford control over morphology, both macro- and microscopically. The filtering material produced often relies exclusively on its randomly assembled porosity (and occasionally on its surface charge) to capture materials from filtered fluids but provides little means for targeted analyte capture without bulk surface coating or functionalization. This thesis seeks to demonstrate a unique approach to filtration membrane manufacture via a novel high-throughput holographic lithography and contact lithography process in the visible spectrum that utilizes a customized negative-tone photoresist inherently capable of localized surface modification.
\r\n\r\nThis thesis first describes the development of a large-scale holographic lithography process, from conceptualization to implementation, and demonstrates its efficacy by examining produced materials. A phase metasurface mask is utilized to produce a periodic intensity distribution of incident photons. This mask is irradiated at 0.23-0.25 W via linear raster scanning of a 2.2 mm diameter 532 nm laser at 1.5 mm/s and a scan offset of 0.4 mm to produce a homogeneous exposure profile in visible-light sensitized SU-8 negative-tone photoresist. Subsequent photoresist development results in 30\u201340 \u00b5m-thick nano-architected sheets with 2.1 \u00d7 2.4 cm\u00b2 lateral dimensions and ~500 nm-wide struts organized in layered 3D brick-and-mortar-like patterns to result in ~50\u201370% porosity. Scanning electron micrographs of cross-sectioned materials reveal how pattern morphology varies with cure depth, and furthermore how the lack of complete porosity disqualifies this material for application as a membrane filter.
\r\n\r\nThis thesis subsequently focuses on the development of a novel glycidyl methacrylate (GMA)-based negative-tone photoresist for implementation in the previously described lithography system to produce materials more amenable to functional membrane filter production. GMA is polymerized with a photo-caged aminated monomer, 2-((((2-nitrobenzyl)oxy)carbonyl)amino)ethyl 2-methyloxirane-2-carboxylate (ONBAMA) via free radical polymerization (FRP) and atom-transfer radical polymerization (ATRP) to produce ~30 kDa statistical co-polymers at an 85:15 monomer ratio, respectively. These linear co-polymers are then mixed with a photoacid generator (PAG) to produce a 532 nm sensitized negative-tone photoresist. Pre- and post-exposure bake temperatures are selected via glass-transition temperature identification (~62 \u00b0C) with differential scanning calorimetry (DSC) experiments, and cure depth varying with optical exposure dose is examined via establishment of contrast curves. The photoresist is then utilized in the previously described lithography system to produce square arrays of ~25 um circular holes, and the resulting films are characterized via optical and scanning electron microscopy.
\r\n\r\nThis thesis concludes with an examination of the poly(GMA-rand-ONBAMA) films implemented as water-permeable filtration membranes. Efficacy of surface functionalization and solution capture explored via amine deprotection and subsequent tagging with fluorescein isothiocyanate (FITC) dye. The presence and intensity uniformity of tagged samples are examined via confocal microscopy. Transmission of water is justified analytical examination and phenomenologically demonstrated via droplet loading of supported membranes with methylene blue-dyed water. Results are preliminary but indicate potential application of manufactured films as water filters.
\r\n\r\nIn summary, this thesis provides a foundation for the development of nano- and micro-architected materials at large scale and details its implementation for the design and preliminary testing of a GMA-based photoresist for water filtering membrane manufacture. Future research on optimizing photoresist design for mechanical stability could enable utilization of similar membranes for protein capture from biological fluids for use in diagnostic tools and assay automation.
" }, { "name": "Gan, Quan", "degree": "PhD", "year": "2023", "title": "Synthesis of Cyclic Polymers by Ring Expansion and Ring Opening Metathesis Polymerization", "advisor": "Grubbs, Robert H.; Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03232023-190331423", "creators": [ { "name": { "family": "Gan", "given": "Quan" }, "id": "Gan-Quan", "orcid": "0000-0001-5908-4163", "display_name": "Gan, Quan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/g9em-gt08", "abstract": "Cyclic polymers are topologically interesting and envisioned as a lubricant material. However, scalable synthesis of pure cyclic polymers remains elusive. The most straightforward way is to recover a used catalyst after the synthesis of cyclic polymers and reuse it. Unfortunately, this is demanding because of the catalyst\u2019s vulnerability and inseparability from polymers, which reduce the practicality of the process. In Chapter 1 we describe a continuous circular process, where polymerization, polymer separation, and catalyst recovery happen in situ, to dispense a pure cyclic polymer after bulk ring-expansion metathesis polymerization of cyclopentene. This process is enabled by introducing silica-supported ruthenium catalysts and newly designed glassware. Different depolymerization kinetics of the cyclic polymer from its linear analogue are also discussed. This process minimizes manual labour, maximizes the security of vulnerable catalysts and guarantees the purity of cyclic polymers, thereby showcasing a prototype of a scalable access to cyclic polymers with increased turnovers (\u2265415,000) of precious catalysts.
\r\n\r\n\u03b1-Oxygenated Z-olefins are ubiquitous in biologically active molecules and serve as versatile handles for organic synthesis, but their syntheses are often tedious and less selective. In Chapter 2 we report the efficient Z-selective metathesis of various terminal acrylates and allyl alcohols, which enables facile and selective construction of high value-added \u03b1-oxygenated Z-olefins from readily available feedstock chemicals. These challenging metathesis transformations are enabled by novel cyclometalated Ru-carbene-nitrate complexes bearing bulky-yet-flexible side arms, whose assembly was unlocked by new organometallic syntheses.
\r\n\r\nEfficient separation of macrocyclic polyolefins from reaction mixtures of ring-opening metathesis polymerization is crucial for their application in materials science, drug delivery, and for the mechanistic study of the reaction mechanism. In Chapter 3, we present a facile method for obtaining topologically pure macrocyclic fractions by modifying chain ends using enyne metathesis chemistry and introducing polar functional groups into linear polymer chains through the addition of polar monomers. Nonpolar cyclic polyolefins are then readily separated using silica gel chromatography. The purity of the cyclic fractions was verified using multiple techniques, including gel permeation chromatography, nuclear magnetic resonance spectroscopy, and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. We investigate the reaction factors affecting the yield and molecular weight of macrocycles during ring-opening metathesis polymerization of cyclooctadiene and discuss macrocycle formation in the ring-opening metathesis polymerization of cyclooctene, cyclopentene, and norbornene. Our work offers crucial insights into the synthesis and separation of macrocycles.
" }, { "name": "Gorin, Gennady", "degree": "PhD", "year": "2023", "title": "Stochastic Foundations for Single-Cell RNA Sequencing", "advisor": "Pachter, Lior S.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-194724728", "creators": [ { "name": { "family": "Gorin", "given": "Gennady" }, "id": "Gorin-Gennady", "orcid": "0000-0001-6097-2029", "display_name": "Gorin, Gennady" } ], "advisors": [ { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "advisor", "display_name": "Pachter, Lior S." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Chong", "given": "Shasha" }, "id": "Chong-Shasha", "orcid": "0000-0002-5372-311X", "role": "member", "display_name": "Chong, Shasha" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "member", "display_name": "Pachter, Lior S." } ], "option_major": [ "chemeng" ], "doi": "10.7907/jn6n-x368", "abstract": "Single-cell RNA sequencing, which quantifies cell transcriptomes, has seen widespread adoption, accompanied by proliferation of analysis methods. However, there has been relatively little systematic investigation of its best practices and their underlying assumptions, leading to challenges and discrepancies in interpretation. I present a set of generic, principled strategies for modeling the biological and technical components of sequencing experiments and use case studies to motivate their application to sequencing data.
" }, { "name": "Hsieh, Hao-Hsuan", "degree": "PhD", "year": "2023", "title": "Coordination Between Mammalian Nascent Protein Targeting and Cotranslational Chaperones", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252022-075028264", "creators": [ { "name": { "family": "Hsieh", "given": "Hao-Hsuan" }, "id": "Hsieh-Hao-Hsuan", "orcid": "0000-0001-9629-5832", "display_name": "Hsieh, Hao-Hsuan" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x61p-vf31", "abstract": "Protein biogenesis starts with ribosome synthesizing nascent polypeptide chain. Ribosome is a major hub for multiple pathways including membrane targeting, chaperones, chemical modification, and quality control. All these pathways need to coordinate with each other spatially on the ribosomal surface and temporally within the translation elongation window. Accumulating data start to point to more intricate interaction and coordination between different pathways beyond the simple competition traditionally presumed.
\r\n\r\nIn Chapter 1, I demonstrate the coordination between a cotranslational chaperone, NAC, and the ER targeting machinery, SRP. NAC and SRP can bind to the same ribosome simultaneously despite overlapping binding sites, allowing NAC to change conformation of SRP specifically to the NC sequences. This allostery enhances the specificity of SRP-SR association, explaining the long-observed effect of NAC modulating ER targeting specificity.
\r\n\r\nIn Chapter 2, I dig deeper into the mechanism of NAC regulating SRP. Based on cryo-EM structures, NAC domain sits on top of the ribosomal tunnel exit, potentially sensing the identity of NC, and is anchored by positively charged NAC\u03b2 N-terminal tail. NAC-UBA domain is the key to recruiting SRP and coordinating the substrate handover to SRP.
\r\n\r\nIn Chapter 3, I focus on the cotranslational HSP40/HSP70 system of RAC. Ribosome binding of RAC stimulates its cochaperone activity to activate HSP70 ATP hydrolysis. Ribosome sensing by RAC is related to the NBD of HSPA14. RAC-stimulated HSP70 engagement to NC keeps it in a folding-competent unfolded state before HSP70 dissociation.
\r\n\r\nTaken together, this study advances the experimental and theoretical tools to studying cotranslational pathways associated with the mammalian ribosome and demonstrates the interesting question of coordination between cotranslational pathways.
" }, { "name": "Huang, Shan", "degree": "PhD", "year": "2023", "title": "DNA-Guided Genome Manipulation in Escherichia coli", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072022-205043055", "creators": [ { "name": { "family": "Huang", "given": "Shan" }, "id": "Huang-Shan", "orcid": "0000-0002-4436-3327", "display_name": "Huang, Shan" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Wang", "given": "Kaihang" }, "id": "Wang-Kaihang", "orcid": "0000-0001-7657-8755", "role": "member", "display_name": "Wang, Kaihang" }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3yab-jg50", "abstract": "Argonaute proteins (Agos) were initially discovered in eukaryotes as key players in RNA interference (RNAi) pathways and later found in prokaryotes. Some prokaryotic argonautes (pAgos) have been shown to mediate nucleic acid-guided cleavage of DNA targets, reminiscent of the nucleic acid-guided DNase activity of the CRISPR/Cas9 system. It has been postulated that pAgo variants might be used as a novel genome-editing tool. However, genome manipulation induced by pAgo-mediated DNA cleavage has never been established. To demonstrate that pAgo-mediated DNA cleavage can introduce genomic mutations in Escherichia coli, we first created a recombination system and showed that CbAgo, a pAgo from Clostridium butyricum, can be directed by plasmid-encoded guide sequences to cleave the genome target site and induce chromosome recombination between downstream direct repeat sequences. Results from testing different pAgo variants suggest that the recombination rate correlates well with pAgo DNA cleavage activity, and the mechanistic study suggests the recombination involves DSB generation and RecBCD processing. In RecA-deficient E. coli strain, guide-directed CbAgo cleavage on chromosomes severely impairs cell growth, which can be utilized as counter-selection to assist Lambda-Red recombineering. These findings demonstrate the guide-directed cleavage of pAgo on the host genome is mutagenic and can lead to different outcomes according to the function of the host DNA repair machinery. Furthermore, we created a dCbAgo-based deaminase and showed that it can not only act as a random mutagen in vivo but also has the potential to be directed by plasmid-encoded guide sequences. We anticipate the novel DNA-guided interference by pAgo only or by its fusion protein to be useful in broader genetic manipulation. My work of engineering fluorescent protein-based nicotine biosensors via computational design and experimental evolution is also described in the thesis.
" }, { "name": "Hui, Yue", "degree": "PhD", "year": "2023", "title": "Applications of Genetically Engineered Bacillus subtilis in Biocatalysis and Functional Materials", "advisor": "Tirrell, David", "url": "https://resolver.caltech.edu/CaltechTHESIS:07272022-064642720", "creators": [ { "name": { "family": "Hui", "given": "Yue" }, "id": "Hui-Yue", "orcid": "0000-0002-0354-0382", "display_name": "Hui, Yue" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David" }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David" } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/cdja-ck19", "abstract": "Bacillus subtilis is a gram-positive model bacterium that forms endospores as a response to nutrient limitation and other environmental stresses. The B. subtilis spore contains a dehydrated core, where the bacterial genome is safely stored, and multilayer proteinaceous coats, protecting the spore from various physical and chemical insults. Because of the outstanding resilience of the B. subtilis spore, it has attracted increasing interest for application in biotechnology. In this thesis, we demonstrate the utilization of genetically engineered B. subtilis cells and spores for heterologous protein display and functional material synthesis and characterization.
\r\n\r\nIn Chapter 1, we review the fundamentals of sporulation and germination in B. subtilis. We highlight notable biotechnological applications of native and engineered B. subtilis spores in recent years. We also discuss limitations associated with prior studies that inspire us to pursue the work in this thesis.
\r\n\r\nIn Chapter 2, we describe the T7 RNA polymerase (RNAP) enabled high density protein display on B. subtilis spores (TIED) method. The TIED constructs employ a coat protein promoter \u2013 PcotG, PcotV, or PcotZ \u2013 to drive the expression of the T7 RNAP. Target proteins are fused to the C-terminus of a spore crust protein \u2013 CotY or CotZ \u2013 and subjected to amplification by the T7 promoter. We prepare the endogenous constructs in which coat protein promoters directly regulate fusion protein expression for comparison with TIED. In addition, we develop a supplementary procedure to harvest spores before mother cell lysis, further improving the loading density of the target proteins. We verify the performance of the TIED architectures with a fluorescent reporter protein, mWasabi. Together with the early harvest protocol, the TIED method substantially enhances the total expression level and loading density of the crust-mWasabi fusion proteins relative to the endogenous expression system, as evidenced by bulk fluorescence measurements and microscopy.
\r\n\r\nIn Chapter 3, we implement the TIED architectures described in Chapter 2 for enzyme display on B. subtilis spores. We demonstrate the spore-based biocatalyst platform with three enzymes \u2013 lipase A and lipase B secreted by vegetative B. subtilis, and an engineered peroxidase, APEX2. We manifest that TIED enables massive accumulation of all three enzymes on the spore surface, with loading densities in the range of 106-107 enzymes per spore. Further, TIED-enzymes show comparable catalytic performance to the respective free-form enzymes, enhanced catalytic activity in methanol, and increased temperature stability. We conduct Michaelis-Menten studies to elucidate the kinetic characteristics of TIED-enzymes and their free form counterparts. Finally, we demonstrate that TIED-enzymes are not only recyclable, but also fully renewable after loss of activity through induction of germination and sporulation, demonstrating the potential for perpetual regeneration of the immobilized biocatalysts.
\r\n\r\nIn Chapter 4, we describe a new class of living composite materials (LCMs), in which genetically engineered B. subtilis cells and spores are effectively crosslinked into the surrounding polymeric scaffold. The resulting LCMs can be dried to yield portable materials. When re-immersed in aqueous media, entrapped cells and spores in previously- dried LCMs exhibit metabolic activity, including synthesis and secretion of recombinant proteins. Notably, we show that the scaffold based on photopolymerization of N-(hydroxymethyl) acrylamide (NHMAA) achieves effective cellular confinement, showing no evidence of cellular leakage over a period of 72 hours. We envision that the design principles elucidated in this work can provide a promising route to functional living materials engineered for biomedical and other applications.
" }, { "name": "Husic, Corey Christopher", "degree": "PhD", "year": "2023", "title": "Strategies for the Mechanically Triggered Release of Small Molecules", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04242023-215416950", "creators": [ { "name": { "family": "Husic", "given": "Corey Christopher" }, "id": "Husic-Corey-Christopher", "orcid": "0000-0003-0248-7484", "display_name": "Husic, Corey Christopher" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0add-6n09", "abstract": "The development of force-responsive molecules called mechanophores is a central component of the field of polymer mechanochemistry. Mechanophores enable the design and fabrication of polymers for a variety of applications ranging from sensing to self-healing materials. Nevertheless, an insufficient understanding of structure\u2013activity relationships limits experimental development, and thus computation is necessary to guide structural design. Herein, we use the constrained geometries simulate external force (CoGEF) method to evaluate a library of covalent mechanophores using density functional theory (DFT). We use these results to identify key parameters that accurately predict experimentally determined mechanochemical reactivity.
\r\n \r\nPolymers that release small molecules upon external stimulation are promising for a wide range of applications, including sensing, catalysis, and drug delivery. Mechanophores are uniquely suited to enable molecular release with excellent selectivity and control. We have designed a general platform for mechanically gated small molecule release that leverages a latent 2-furylcarbinol species masked as a mechanically labile Diels\u2013Alder adduct. Here, we describe the computationally guided design of metastable 2-furylcarbinol derivatives through the prediction of activation energy values and construction of structure\u2013activity relationships. These results enable a molecular release platform suitable for a wide scope of cargo molecules across a broad range of chemical environments.
" }, { "name": "Ifkovits, Zachary Philip", "degree": "PhD", "year": "2023", "title": "Strategies for Enabling Stable and Efficient (Photo)Electrochemical Water Splitting", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132023-220300179", "creators": [ { "name": { "family": "Ifkovits", "given": "Zachary Philip" }, "id": "Ifkovits-Zachary-Philip", "orcid": "0000-0003-2538-0794", "display_name": "Ifkovits, Zachary Philip" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jt8t-w739", "abstract": "The electrolysis of water splits H\u2082O into its constituent parts, generating H\u2082 fuel and O\u2082 as a by-product. Although electrolysis has been known since late 1700s and has a consistently expanding industrial capacity, several barriers still exist to its widespread utilization as a clean method of generating hydrogen for industrial uses or as a grid-scale energy storage chemical. Among these, the materials and costs constraints surrounding the use of precious metal catalysts and expenses associated with balance-of-system costs are of primary importance. In this thesis, the first point is addressed by utilizing earth-abundant catalysts for chemical, electrochemical, and photoelectrochemical water splitting reactions. Specifically, MnySb1-yOx catalysts were synthesized for use as both cerium-mediated chemical water oxidation catalysts and as electrochemical water oxidation catalysts, furthering steps towards removing Ir from industrial electrolysis devices. Addition of Sb was shown to stabilize reactive Mn centers in these configurations, offering enhanced stability over pure Mn oxide catalysts. Reduction of electrolyzer balance-of-system costs were addressed in this thesis through the integration of multiple components of a solar-powered electrolysis system into a single, integrated photoelectrochemical water splitting device. Specifically, electrodeposition conditions were shown to affect the spontaneous mesostructuring of Ni-P hydrogen evolution catalysts on silicon photocathodes, leading to enhanced transmission of light to the semiconductor substrate. Furthermore, Y\u2082SiO\u2085 protective layers were shown to mitigate the corrosion of Si photocathodes in alkaline environments, an electrochemical environment known to be destructive towards silicon." }, { "name": "Kerkovius, Jeffrey Kevan", "degree": "PhD", "year": "2023", "title": "Total Synthesis of Lupin Alkaloids, Diterpenoid Alkaloids, and Progress Towards the Myrsinane Diterpenes", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012023-171716967", "creators": [ { "name": { "family": "Kerkovius", "given": "Jeffrey Kevan" }, "id": "Kerkovius-Jeffrey-Kevan", "orcid": "0000-0001-5692-0285", "display_name": "Kerkovius, Jeffrey Kevan" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/y6rd-nm97", "abstract": "The interplay between total synthesis and methodology is a driver of innovation in organic synthesis. Challenging bond formations in complex systems necessitate the development ever more robust new reactions, which intern can enable more efficient syntheses. The need for powerful synthetic organic chemistry can\u2019t be understated because of its utility in applications such as medicine, petrochemicals, plastics, and agrichemicals.
\r\n\r\nHerein, we present how total synthesis drives innovation in organic chemistry. First, a novel cyclization reaction between pyridine and glutaryl chloride is discussed, which has enabled the synthesis of seven lupin alkaloids. Next, the development of a convergent fragment coupling tactic based upon the semi-pinacol rearrangement is evaluated for its generality inspired by the total synthesis of several C19 diterpenoid alkaloids. Lastly, a convergent fragment coupling approach is applied to the total synthesis of falcatin A based upon a Mukaiyama Michael tandem Mukaiyama aldol reaction.
" }, { "name": "Kim, Alexia Nahyun", "degree": "PhD", "year": "2023", "title": "Enantioselective Syntheses of Tetrahydroisoquinolines (THIQs) via Iridium-Catalyzed Asymmetric Hydrogenation and Progress Toward the Total Synthesis of (+)-Cyanocycline A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-190747966", "creators": [ { "name": { "family": "Kim", "given": "Alexia Nahyun" }, "id": "Kim-Alexia-Nahyun", "orcid": "0000-0002-4060-8892", "display_name": "Kim, Alexia Nahyun" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4xty-8711", "abstract": "Described herein are two reviews and three projects related to the asymmetric syntheses of tetrahydroisoquinoline (THIQs) alkaloids, and the progress toward the total synthesis of (+)-cyanocycline A. In Chapter 1, a review of the development of asymmetric methodologies for the preparation of enantioenriched N-heteroarenes is detailed. In Chapter 2, the development of an iridium-catalyzed enantio- and diastereoselective hydrogenation of 1,3-disubstituted isoquinolines to achieve cis-THIQs is reported. Chapter 3 describes the iridium-catalyzed asymmetric hydrogenation of 1,3-disubstituted isoquinolines that can afford trans-THIQs in a single transformation. Preliminary mechanistic insights to the iridium-catalyzed asymmetric hydrogenation method using deuterium experiments are detailed.
\r\n\r\nChapter 4 details a comprehensive review of the advances in the total syntheses of complex THIQ alkaloids from 2000 \u2013 2020, ranging from simple benzyl THIQ natural products to complex THIQ alkaloids such as Ecteinascidin-743. In Chapter 5, efforts toward the total synthesis of (+)-cyanocycline A are described, harnessing a non- biomimetic synthetic route through a convergent cross-coupling of two heterocyclic fragments followed by a global hydrogenation event.
" }, { "name": "Kim, Hojin", "degree": "PhD", "year": "2023", "title": "New Long End-Associative Polymers for Mist Control in I. Aqueous Solutions and II. Hydrocarbon Solvents", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08252022-035254306", "creators": [ { "name": { "family": "Kim", "given": "Hojin" }, "id": "Kim-Hojin", "orcid": "0000-0002-0257-7300", "display_name": "Kim, Hojin" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/rsx9-qt39", "abstract": "Ultralong linear polymers are well known to be useful in a variety of applications such as mist control, drag reduction, and agricultural spray drift control. However, the application of ultralong linear polymers is limited by shear degradation of the ultralong polymer chains that occurs under strong flow conditions. To overcome the issue of shear degradation, our group previously designed long end-associative polymers that can self-assemble into megasupramolecules (Mw > 2000 kg/mol) in low polarity solvents like jet fuel. The previously developed long end associative polymers had polycyclooctadiene backbones (1,4 polybutadiene) with carboxylic acid or tertiary amine end groups that associated via hydrogen bonding. They were shear degradation resistant and used as mist-control agents that provided fire-protection to jet fuel at concentrations as low as 0.3wt%.
\r\n\r\nBuilding upon the previous work, this thesis describes efforts toward expanding the applicability of long end-associative polymers. We first describe the design and synthesis of water-soluble long end-associative polymers for agricultural spray mist-control. We synthesized telechelic polyacrylamides using reversible addition fragmentation chain transfer (RAFT) polymerization. We explored two types of associations that can form stable supramolecules in water: host-guest interactions between adamantane and beta-cyclodextrin (Chapter 1), and metal-ligand association between terpyridine and transition metal ions (Chapter 2). Careful optimization of polymerization conditions allowed the synthesis of ultra-high molecular weight telechelic polyacrylamides with narrow polydispersity. We found that the terpyridine functionalized polyacrylamides with Mw 820 kg/mol could assemble into megasupramolecules (Mw > 2000 kg/mol) upon addition of Fe(II) or Ni(II).
\r\n\r\nIn Chapters 3 and 4, we return to long end-associative polymers in hydrocarbon solvents. In Chapter 3, we tackle the issue of poor solubility of the previous generation of associative PCODs in a highly nonpolar solvent, PAO. In Chapter 4, we develop a new generation of end groups for improved solubility and ease of synthesis.
\r\n\r\nFinally in Chapter 5, we discuss polyDODT (poly(3,6-dioxa-1,8-octanedithiol)), a polydisulfide that tends to form a mixture of linear and cyclic species. We present new methods to detect the presence of linear species in the mixture, as well as an alternative synthesis route for synthesis of polyDODT.
" }, { "name": "Kim, Seong Shik (Steve)", "degree": "PhD", "year": "2023", "title": "Design Rules for Multi-Electron Systems in Next-Generation Batteries: From Mg Electrode-Electrolyte Interface to Anion Redox Activation in Li-Rich Sulfides", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032023-004803929", "creators": [ { "name": { "family": "Kim", "given": "Seong Shik (Steve)" }, "id": "Kim-Seong-Shik-Steve", "orcid": "0000-0003-2604-6392", "display_name": "Kim, Seong Shik (Steve)" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemeng" ], "doi": "10.7907/v52j-t589", "abstract": "Li-ion batteries (LIBs) have revolutionized the modern world, powering portable electronic devices and more recently realizing electrification of transportation. With more technological advancements that further improved the performance, LIBs also play an important role as one of the most promising energy storage systems in transforming into renewable energy sources and achieving net zero emissions. However, state-of-the-art intercalation-based LIBs are beginning to mature and reach their theoretical capacity limits. To further improve the electrochemical performance of batteries and meet growing demands of energy storage applications, there have been growing efforts to increase the energy density beyond the limits of conventional LIBs. In this thesis, we examine two examples of multi-electron systems\u2013Mg electrolytes and Li-rich sulfide cathode materials\u2013to gain insights and establish design principles.
\r\n\r\nFirst, we explore the magnesium aluminum chloride complex (MACC) electrolyte to study the role of the electrode-electrolyte interface in Mg charge transfer. We demonstrate that MACC electrolyte which normally requires electrolytic conditioning can be chemically activated by the small addition of Mg(HMDS)\u2082. Solution-phase characterization reveals that Mg(HMDS)\u2082 helps prevent the formation of passivating film on the Mg surface by scavenging trace amounts of H\u2082O. Mg(HMDS)\u2082 also reacts with MACC to form free Cl\u207b which decorates the Mg surface which facilitates Mg electrodeposition and stripping.
\r\n\r\nNext, we investigate three different alkali-rich sulfides-LiNaFeS\u2082, LiNaCoS\u2082, and Li1.33-1.33zTi0.67+0.33zVaczS\u2082 - to probe the role of electronic and physical structure in governing reversible anion redox. We demonstrate that cryomilling LiNaFeS\u2082 mitigates particle fracturing by increasing microstrain and reducing crystallite size. Isostructural LiNaCoS\u2082 exhibits more covalent interactions between the transition metal-d and S-p states compared to LiNaFeS\u2082, but undergoes an irreversible conversion reaction. Lastly, Li\u2082TiS\u2083 exhibits no electrochemical activity, but introducing cationic vacancies in Li1.33-1.33zTi0.67+0.33zVaczS\u2082 activates S oxidation. Li1.33-1.33zTi0.67+0.33zVaczS\u2082 is studied further to study first-cycle activation and voltage hysteresis in Li-rich sulfides.
" }, { "name": "Klein, Isabel McMillan", "degree": "PhD", "year": "2023", "title": "Understanding the Origins of Photoexcited XUV Spectra", "advisor": "Cushing, Scott K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12132022-201432142", "creators": [ { "name": { "family": "Klein", "given": "Isabel McMillan" }, "id": "Klein-Isabel-McMillan", "orcid": "0000-00016134-6732", "display_name": "Klein, Isabel McMillan" } ], "advisors": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "advisor", "display_name": "Cushing, Scott K." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s8qe-4s74", "abstract": "A full measurement of photoexcited dynamics, from excitation to recombination, is required to understand the photochemical processes at the heart of solar energy materials and devices. Measuring these complete dynamics is often unachievable with a single experimental tool. Transient X-ray spectroscopies, however, have proven to be powerful techniques as they can separately measure electron and hole dynamics, as well as vibrational and structural modes, all with elemental specificity. The interpretation of these measurements is still challenging, as the core-hole created following a core-level transition distorts the measured spectrum. This thesis aims to develop complementary experimental and computational techniques to measure and interpret transient X-ray spectra. Initially, the measured photoexcited dynamics of ZnTe and CuFeO\u2082, which reveal polaron formation and lattice coupling, as well as electron and hole kinetics and band gap dynamics, are presented. Following this experimental work, we develop an ab initio computational method for modeling transient X-ray and extreme ultraviolet (XUV) spectra. The ab initio method is a Bethe-Salpeter equation (BSE) approach based on the previously developed Obtaining Core Excitations from Ab initio electronic structure and the NIST BSE solver (OCEAN) code. Building on the foundations of the OCEAN code, we incorporate photoexcited states for a range of transition metal oxides and demonstrate the method\u2019s ability to simulate the effects of state filling, isotropic thermal expansion and polaron states on XUV absorption spectra. Importantly, our method is also able to fully decompose the calculated spectra into the constituent components of the X-ray transition Hamiltonian, providing further insight into the origins and nature of spectral features. The XUV absorption spectra for the ground, photoexcited, and polaron states of \u03b1-Fe\u2082O\u2083, as well as for the ground, photoexcited, and thermally expanded states of other first row transition metal oxides \u2013 TiO\u2082, \u03b1-Cr\u2082O\u2083, \u03b2-MnO\u2082, Co\u2083O\u2084, NiO, CuO, and ZnO \u2013 are calculated to demonstrate the accuracy of our approach. This method is easily generalized to K, L, M, and N edges to provide a general approach for analyzing transient X-ray absorption or reflection data.
" }, { "name": "Kuintzle, Rachael Christine", "degree": "PhD", "year": "2023", "title": "Diversity in Notch Ligand-Receptor Signaling Interactions", "advisor": "Elowitz, Michael B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302023-215054202", "creators": [ { "name": { "family": "Kuintzle", "given": "Rachael Christine" }, "id": "Kuintzle-Rachael-Christine", "orcid": "0000-0002-1035-4983", "display_name": "Kuintzle, Rachael Christine" } ], "advisors": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "advisor", "display_name": "Elowitz, Michael B." } ], "committee": [ { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "chair", "display_name": "Pachter, Lior S." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "orcid": "0000-0003-4274-1862", "role": "member", "display_name": "Bronner, Marianne E." }, { "name": { "family": "Hay", "given": "Bruce A." }, "id": "Hay-B-A", "orcid": "0000-0002-5486-0482", "role": "member", "display_name": "Hay, Bruce A." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "member", "display_name": "Elowitz, Michael B." } ], "option_major": [ "biochem" ], "doi": "10.7907/w8gj-jb92", "abstract": "The ability to understand and predict signaling between different cell types is a major challenge in biology. The Notch pathway enables direct signaling through membrane-bound ligands and receptors, and is used in diverse contexts. While its canonical molecular signaling mechanism is well characterized, its many-to-many interacting pathway components, the complexity of their expression patterns, and the presence of same-cell (cis) as well as inter-cellular (trans) receptor-ligand interactions, have made it difficult to predict how a given cell will signal to others. Here, we use a cell-based approach, with Chinese hamster ovary (CHO-K1) cells and C2C12 mouse myoblasts, to systematically characterize trans-activation, cis-inhibition, and cis-activation efficiencies for the essential receptors (Notch1 and Notch2) and activating ligands (Dll1, Dll4, Jag1, and Jag2), in the presence of Lunatic Fringe (Lfng) or the enzymatically dead Lfng D289E mutant. All ligands trans-activate Notch1 and Notch2, except for Jag1, which competitively inhibits Notch1 signaling, and whose Notch1 binding strength is potentiated by Lfng. For Notch1, cis-activation is generally weaker than trans-activation, but for Notch2, cis-activation by Delta ligands is much stronger than trans-activation, and Notch2 cis-activation by Jag1 is similar in strength to trans-activation. Cis-inhibition is associated with weak cis-activation, as Dll1 and Dll4 do not cis-inhibit Notch2. Lfng expression potentiates trans-activation of both Notch1 and Notch2 by the Delta ligands and weakens trans-activation of both receptors by the Jagged ligands. The map of receptor-ligand-Fringe interaction outcomes revealed here should help guide rational perturbation and control of the Notch pathway." }, { "name": "Lawniczak, James Joseph", "degree": "PhD", "year": "2023", "title": "Computational Investigations of Organometallic Catalysis", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08042022-183527205", "creators": [ { "name": { "family": "Lawniczak", "given": "James Joseph" }, "id": "Lawniczak-James-Joseph", "orcid": "0000-0003-1898-9809", "display_name": "Lawniczak, James Joseph" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/aepb-jm46", "abstract": "Organometallic catalysis facilitates the synthesis of diverse products ranging from polyolefin materials to pharmaceutical compounds, and catalyst performance depends in part on the design of the ligand scaffold. Towards computational ligand design, quantum mechanical methods more fully capture chemical reactivity in comparison to classical methods, but are more computationally demanding. Free energy calculations of key elementary steps of the catalytic cycle permit the computational prediction of catalyst performance and allow modifications of the ligand structure to be explored. In the dissertation, experimental and computational investigations of organometallic catalysis focuses on rational ligand design. Embedding techniques such as embedded mean field theory (EMFT) and quantum mechanics/molecular mechanics (QM/MM) are leveraged in free energy calculations to allow for the reduction of wall-clock times of energy calculations and trajectory sampling. The organometallic systems investigated include Group IV polyolefin catalysts capable of co-polymerization and enantioselective cross-coupling nickel catalysts. Additionally, experimental methodology development is discussed for a nickel-catalyzed cross-coupling of alkynyl nucleophiles to tertiary electrophiles.
" }, { "name": "Ling, Bill", "degree": "PhD", "year": "2023", "title": "Acoustic Biomolecules for Diagnostic Ultrasound Imaging", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312023-220301021", "creators": [ { "name": { "family": "Ling", "given": "Bill" }, "id": "Ling-Bill", "orcid": "0000-0002-1276-7204", "display_name": "Ling, Bill" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Chan", "given": "Warren C. W." }, "id": "Chan-Warren-C-W", "orcid": "0000-0001-5435-4785", "role": "member", "display_name": "Chan, Warren C. W." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/va8g-tb47", "abstract": "Nanotechnology has enabled significant breakthroughs in the early detection and treatment of disease, but many of these advances rely on expensive and less-accessible imaging modalities. Ultrasound, on the other hand, is a noninvasive imaging modality that stands out for its universal availability, cost-effectiveness, and safety. However, harnessing the benefits of nanomaterials for ultrasound has been challenging due to the size and stability constraints of typical ultrasound contrast agents. Recently, an innovative solution has emerged in the form of gas vesicles (GVs), a class of air-filled protein nanostructures found in certain aquatic microbes. These promising next-generation ultrasound contrast agents offer a crucial bridge between nanotechnology and ultrasonography.
\r\n\r\nIn this thesis, we investigate the in vivo behavior of GVs, explore their potential applications as nanodiagnostic agents, and consider key factors for their future clinical deployment. In Chapter 2, we examine the interactions of GVs with blood components, focusing on imaging performance and immunogenicity. In Chapter 3, we show that intravenously injected GVs are cleared by liver-resident macrophages and subsequently undergo lysosomal degradation. We leverage this finding to develop an ultrasound-based method for visualizing cellular degradative processes and demonstrate its potential as a liver disease diagnostic. In Chapter 4, we introduce bicone GVs, the smallest known ultrasound contrast agent. We show that these sub-80 nm particles can penetrate tumors, deliver potent ultrasound-induced mechanical effects, and are readily engineered for molecular targeting, extended circulation time, and payload conjugation.
\r\n\r\nTogether, these findings highlight the tremendous potential of GVs as injectable nanomaterials for ultrasound imaging, laying the foundation for future studies to further refine the design and application of these agents.
" }, { "name": "Liu, Xinyan", "degree": "PhD", "year": "2023", "title": "Bioorthogonal Noncanonical Amino Acid Tagging for Understanding Bacterial Persistence", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272022-063655097", "creators": [ { "name": { "family": "Liu", "given": "Xinyan" }, "id": "Liu-Xinyan", "orcid": "0000-0003-3258-5720", "display_name": "Liu, Xinyan" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Orphan", "given": "Victoria J." }, "id": "Orphan-V-J", "orcid": "0000-0002-5374-6178", "role": "member", "display_name": "Orphan, Victoria J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/q6bx-kt39", "abstract": "Phenotypic heterogeneity in populations of isogenic bacterial cells includes variations in metabolic rates and responses to antibiotic treatment. In particular, sub-populations of \u201cpersister\u201d cells exhibit increased antibiotic tolerance. Understanding the mechanisms that underlie bacterial persistence would constitute an important step toward preventing and treating chronic infections. On the other hand, bacteria often have multiple molecular mechanisms to adapt to fluctuating environments. Understanding these mechanisms, and their redundancy, requires examinations in depth at the molecular level. This thesis describes a time- and cell state-selective proteome-labeling approach that enables researchers to investigate heterogeneous systems and molecular redundancy.
\r\n\r\nIn Chapter 1, we review the concept of bacterial persistence. The definition of bacterial persistence is introduced. Both the differences and connections between bacterial persistence and resistance are covered. In particular, we discuss research related to Pseudomonas aeruginosa (P. aeruginosa), an important opportunistic pathogen found in many cystic fibrosis patients. State-of-the-art technologies to investigate bacterial persistence are discussed, and we conclude that advanced tools are needed to advance research on bacterial persistence further.
\r\n\r\nIn Chapter 2, we highlight the concept of bioorthogonal noncanonical amino acid tagging (BONCAT). BONCAT is a powerful tool developed in the Tirrell and Schuman laboratories allowing the incorporation of noncanonical amino acids (ncAA) into newly-synthesized proteins. We review established strategies for proteomics, especially cell-selective proteomics. We introduce the concept and mechanism of BONCAT and address the advantages of BONCAT in the investigation of phenotypic heterogeneity and bacterial persistence.
\r\n\r\nIn Chapter 3, we describe our work using BONCAT for understanding bacterial persistence. In particular, we investigated the process of persister resuscitation, as it is closely related to the reoccurrence of P. aeruginosa infections. The characteristics of the heterogeneity of persister cells during persister awakening were examined by survival assays and by ScanLag, an automated colony-based system allowing high-throughput acquisition of time-lapse images, quantification, and analysis of growth of bacterial colonies. Two BONCAT methods were developed in the P. aeruginosa strain PA14 by treating cells either with L-azidohomoalanine (Aha), which avoids extensive usage of antibiotic markers and allows direct integration with PA14 transposon insertion library, or with L-azidonorleucine (Anl), which has the advantage of specificity, as well as direct application in nutrition-rich medium. Through BONCAT enrichment experiments, we found proteins involved in the biosynthesis of pyochelin, a secondary siderophore involved in bacterial iron acquisition, were up-regulated in the regrowth phase. We further explored whether the up-regulation was a result of the modulation of HigB-HigA toxin-antitoxin system.
\r\n\r\nIn Chapter 4, we describe our work for understanding molecular redundancy. The chapter follows up on our observation of up-regulation of pyochelin-related proteins during persister regrowth. We discuss the hypothesis that pyochelin confers a growth advantage in persister cells subject to carbon-limited conditions. In addition, we discuss the potential role of Fur, a ferric uptake regulator, in bacterial persistence.
" }, { "name": "Maggiolo, Ailiena Okumura", "degree": "PhD", "year": "2023", "title": "Crystallographic Studies of Nitrogenase", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062023-051752771", "creators": [ { "name": { "family": "Maggiolo", "given": "Ailiena Okumura" }, "id": "Maggiolo-Ailiena-Okumura", "orcid": "0000-0003-1707-5060", "display_name": "Maggiolo, Ailiena Okumura" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p232-4w49", "abstract": "Nitrogenase is the only enzyme known to reduce atmospheric dinitrogen to ammonia, producing a biologically available form of nitrogen. The primary component of nitrogenase, the molybdenum-iron (MoFe) protein, binds and turns over substrate after reduction by multiple electron equivalents, which are supplied by the obligate reductase, the iron (Fe) protein. Previous high-resolution X-ray crystal structures have provided pictures of the nitrogenase proteins and revealed the geometry of their metalloclusters. In this thesis, we study MoFe protein crystal isoforms and their crystal pathologies to classify isomorphous candidates suitable for crystallographic merging. We then leverage this classification to determine a high-resolution structure of the MoFe protein with improved geometric accuracy and lower coordinate error than currently available models. The reduced states of the MoFe protein are challenging to capture and therefore have been minimally characterized. We explore the structural consequences of introducing reductants and oxidants into MoFe protein crystals and study the effects of X-ray induced photoreduction on the metalloclusters. Further, we determine the radiation damage-free X-ray crystal structure of MoFe protein. The Fe protein adopts various conformational states as it functions in ATP-coupled electron transfer to the MoFe protein. We examine a set of proteins that are evolutionarily related to the Fe protein and have diverse functionalities, but retain similarity in their ATP-dependent function and allostery as a result of their conserved structural features. Finally, we characterize the structural and functional aspects of the Fe protein lacking an iron-sulfur cluster. These studies expand our understanding of the structural properties of nitrogenase and shed light on previously uncharacterized states of these proteins.
" }, { "name": "McFadden, Molly Elizabeth", "degree": "PhD", "year": "2023", "title": "The Emerging Mechanochemistry of Naphthopyran", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182023-034742629", "creators": [ { "name": { "family": "McFadden", "given": "Molly Elizabeth" }, "id": "McFadden-Molly-Elizabeth", "orcid": "0000-0003-3174-6385", "display_name": "McFadden, Molly Elizabeth" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/r4gk-rn51", "abstract": "Asserting remote control over reactivity is a pervasive goal in modern chemistry. Several external stimuli can supply energy to facilitate productive chemical transformations. In recent years, that list has grown to include mechanical force. In the growing field of polymer mechanochemistry, privileged, mechanically sensitive molecules called mechanophores undergo desirable chemical reactions under force. Force is transduced to mechanophores through covalently attached polymer chains. Among many applications, mechanophores that react to produce colored species can be used for visual stress and damage detection in plastics. Naphthopyran is a highly modular molecular switch that can undergo ring-opening reaction to generates intensely colored merocyanine dyes. The studies described in this dissertation have thoroughly established the versatility and complexity of naphthopyran-based mechanochromic mechanophores.
\r\n\r\nIn Chapter 1, the history of naphthopyran molecular switches is summarized with particular emphasis on the exhaustive and generalizable merocyanine structure-property relationships established for photochromic naphthopyrans. Naphthopyran mechanochemistry is reviewed and contextualized among other mechanochromic mechanophores. Mechanochromic structure-function relationships are highlighted, as well as a series of studies using the naphthopyran platform for illustration of the unusual reaction pathways accessible under force, and studies demonstrating that multimodal naphthopyrans are an ideal platform for multicolor mechanochromism.
\r\n\r\nAs discussed extensively in Chapter 1, merocyanines are typically susceptible to thermal recyclization. However, Chapter 2 describes a scissile naphthopyran mechanophore that undergoes an unusual secondary mechanochemical ester cleavage after the ring-opening reaction. By revealing a \u03b2-hydroxy ketone group with a stable intramolecular hydrogen bonding interaction, mechanical force uniquely generates persistent merocyanine species.
\r\n\r\nThe irreversible reaction sequence described in Chapter 2 enables determination of mechanochemical reaction kinetics under solution-phase ultrasound-mediated mechanical force. However, common methods for determining reaction rate constants under these conditions are time-intensive and convoluted by the competitive side reaction of nonspecific polymer backbone scission. In Chapter 3, through model studies on the highly efficient scissile naphthopyran and a comparatively inefficient coumarin dimer mechanophore, we validate a time-efficient and accurate initial rates method for determination of selective mechanophore reaction kinetics under ultrasonication.
\r\n\r\nThe ability to colorimetrically report on the magnitude of applied stress is a grand challenge in the field of mechanochromism. Chapter 4 describes the first single mechanophore capable of such behavior. Mechanical force induces unexpectedly simultaneous ring-opening reactions from a bis-naphthopyran mechanophore, biasing a dynamic equilibrium between two distinct merocyanine states to effect gradient force-dependent multicolor mechanochromism.
\r\n\r\nIn further studies seeking multicolor mechanochromic systems, it was discovered that mechanical force facilitates the first reported dual-ring-opening reaction of naphthodipyran. Chapter 5 describes the mechanochemical generation of an unusual dimerocyanine species with near-IR absorption that is not formed photochemically.
" }, { "name": "Meier, Madeline Claire", "degree": "PhD", "year": "2023", "title": "Inorganic Phototropism: Emergent Properties Directing Growth of Mesostructured Semiconductors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012023-020314168", "creators": [ { "name": { "family": "Meier", "given": "Madeline Claire" }, "id": "Meier-Madeline-Claire", "orcid": "0000-0003-1608-0810", "display_name": "Meier, Madeline Claire" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "member", "display_name": "Faber, Katherine T." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rqwq-tv81", "abstract": "Nature exhibits emergent growth phenomena where in neighboring features result in ensemble effects that direct the overall growth morphologies. Plants, such as palm trees, display phototropism where-in the crown grows toward the time weighted average position of the sun to optimize solar collection. A methodology, known as inorganic phototropic growth, utilizes a similar mechanism with the incident illumination during electrochemical deposition directing the growth of mesostructured semiconductors. This photoelectrochemical deposition process, generates highly anisotropic, periodic lamellar features resulting in the capability to fabricate nanostructured features over macroscopic areas. The process is lithography-free and uses no templates or directing agents of any kind and relies solely on the incident illumination to direct semiconductor growth. In this thesis, the nanophotonic phenomena and emergent synergistic absorption that drives the inorganic phototropic growth process was investigated using unconstrained and confined susbtrates. Additionally, the impact of inclined, off-normal incident illumination on the evolution of structure morphology was investigated for patterned and isotropic substrates revealing the mechanism behind the non-monotonic relationship between incident angle and observed out-of-plane orientation for unconstrained substrates.
" }, { "name": "Meyerowitz, Joseph Toshiro", "degree": "PhD", "year": "2023", "title": "Engineering and Rapid Prototyping for Biology in Extreme Conditions", "advisor": "Murray, Richard M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022022-073109279", "creators": [ { "name": { "family": "Meyerowitz", "given": "Joseph Toshiro" }, "id": "Meyerowitz-Joseph-Toshiro", "orcid": "0000-0002-3426-0885", "display_name": "Meyerowitz, Joseph Toshiro" } ], "advisors": [ { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "orcid": "0000-0002-3426-0885", "role": "advisor", "display_name": "Murray, Richard M." } ], "committee": [ { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "chair", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "orcid": "0000-0002-5785-7481", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "biochem" ], "doi": "10.7907/9gbb-n831", "abstract": "In this thesis we show three projects in which biological systems are engineered for increased robustness to environmental stressors such as toxic small molecules. Several lignocellulose-derived growth inhibitors commonly found in industrial feedstocks for fermentation were used to grow a panel of yeast knockouts for several efflux pumps and detoxifying enzymes. Some specific knockout strains showed slowed growth on specific growth inhibitors, while other knockout strains showed the same growth rate as the wild-type. One efflux pump was identified for vanillin, YHK8, and was overexpressed in yeast. The overexpression strain did not show an improved tolerance to vanillin, and grew more slowly than the wild-type. To regulate the expression of the vanillin pump, a sensor for vanillin was created. The starting enzyme was the wild-type qacR transcription factor, and several variants were generated using computational protein design. The designs were synthesized and tested using in vitro transcription-translation (TX-TL) as part of a rapid prototyping process. This rapid prototyping considerably sped up the design-build-test process. Finally, four bacteria, Pseudomonas synxantha 2-79, Pseudomonas chlororaphis PCL1391, Pseudomonas aureofaciens 30-84, and E. coli are tested against the same lignocellulose growth inhibitors. The Pseudomonas spp. show an improved tolerance to the growth inhibitors. We then develop some ability to engineer and prototype in all three species. A panel of promoter parts were integrated into the P. synxantha genome to produce a collection of test strains. These same promoter parts were also used as DNA templates for TX-TL reactions. The in vivo measurements of promoter strength and in vitro measurements show similar relative strengths between the parts, showing the Pseudomonas-based TX-TL systems can be used for design-build-test activities in these non-model organisms. This alternate approach to developing tolerance, starting with a species that already has a working tolerance to the stressor in question, changes the problem to one of building engineering capabilities in the new chassis." }, { "name": "Morla, Maureen Baradi", "degree": "PhD", "year": "2023", "title": "Redox-Activated Covalent Functionalization of Semiconductor Surfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:04252023-051729803", "creators": [ { "name": { "family": "Morla", "given": "Maureen Baradi" }, "id": "Morla-Maureen-Baradi", "orcid": "0000-0002-2520-9543", "display_name": "Morla, Maureen Baradi" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1exn-0t72", "abstract": "Semiconducting materials are those with a band gap across which electrons can be excited when the material absorbs photons with sufficient energy. Surface functionalization of semiconductors involves manipulation of the properties of the material by attaching organic small molecules through a surficial covalent bond. By controlling the surface properties of the material, functionalization has enabled the application of semiconductors in a myriad of fields, prompting a highly active field of research. To aid in this effort, we explore a new reaction methodology based on redox-mediated surface functionalization, where an outer-sphere, one-electron metallocene reductant or oxidant is added to the solution medium containing the semiconductor and the small molecule to be added to its surface. Using density functional theory, we elucidated the thermodynamic and kinetic factors that limit the experimentally observed upper coverage bound of reductant-activated methylation of 1T\u2032-molybdenum disulfide by determining two governing factors: 1) sulfur sites with longer Mo\u2013S bonds are more thermodynamically favorable for methyl addition, and 2) sulfur sites with fewer adjacent methylated sulfur sites are preferentially functionalized due to steric hindrance. We then expanded this reductant-activated reaction methodology to silicon(111) surfaces and demonstrated that the reductant solution potential must lie near or above the silicon(111) conduction band edge to observe reactivity. By extending this study to silicon nanocrystals of different sized diameters and different conduction band edges, we found that the extent of surface reactivity relied heavily on reductant strength, but the energy difference between the conduction band edges was too small to observe a distinct dependency on nanocrystal size. The work encompassed in this thesis expanded our understanding of redox-mediated reactions on semiconductor surfaces, providing a new avenue for attaining atomic-level control of the surficial properties of the material using mild reaction conditions and no specialized equipment. Furthermore, redox-activated addition enables the use of new functional groups that would otherwise be reactive in other functionalization methods, promoting an abundance of opportunities to explore new applications of semiconductor materials." }, { "name": "Nistanaki, Sepand K.", "degree": "PhD", "year": "2023", "title": "Application of Dewar Heterocycles and Vinyl Carbocations in Organic Synthesis", "advisor": "Nelson, Hosea M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072023-204031343", "creators": [ { "name": { "family": "Nistanaki", "given": "Sepand K." }, "id": "Nistanaki-Sepand-K", "orcid": "0000-0002-5252-803X", "display_name": "Nistanaki, Sepand K." } ], "advisors": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "advisor", "display_name": "Nelson, Hosea M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/m1t7-tm48", "abstract": "High-energy molecules are frequently employed in the construction of organic molecules and materials in both academic and industrial settings. This thesis describes the application of two distinct classes of reactive molecules in organic synthesis: (1) Dewar heterocycles, which contain a highly strained bicyclic structure; (2) vinyl cations, a class of dicoordinated carbocations containing an electron-deficient carbon center bound to only two atoms. A description of our experimental work relevant to this thesis commences with the exploration of Dewar pyrone in the total synthesis of (\u00b1)-vibralactone. Next, the application of Dewar heterocycles to the synthesis of new strained-ring polymers will be discussed, including examples of post-polymerization strategies to access soluble poly(acetylene) derivatives and \u03b2-amino acid type polymers. Finally, the development of a catalytic asymmetric C\u2013H insertion reaction of vinyl carbocations will be described, with an emphasis on reaction development, scope, and mechanism.
" }, { "name": "O'Rourke, Matthew John", "degree": "PhD", "year": "2023", "title": "Towards High-Accuracy Simulations of Strongly Correlated Materials Using Tensor Networks", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312023-221353362", "creators": [ { "name": { "family": "O'Rourke", "given": "Matthew John" }, "id": "Orourke-Matthew-John", "orcid": "0000-0002-5779-2577", "display_name": "O'Rourke, Matthew John" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Chen", "given": "Xie" }, "id": "Chen-Xie", "orcid": "0000-0003-2215-2497", "role": "member", "display_name": "Chen, Xie" }, { "name": { "family": "Hutzler", "given": "Nicholas R." }, "id": "Hutzler-N-R", "orcid": "0000-0002-5203-3635", "role": "member", "display_name": "Hutzler, Nicholas R." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wwka-as73", "abstract": "Accurate and verifiable computation of the properties of real materials with strong electron correlation has been a long-standing challenge in the fields of chemistry, physics, and material science. Most existing algorithms suffer from either approximations that are too inaccurate, or fundamental computational complexity that is too high. In studies of simplified models of strongly-correlated materials, tensor network algorithms have demonstrated the potential to overcome these limitations. This thesis describes our research efforts to develop new algorithms for two-dimensional (2D) tensor networks that extend their range of applicability beyond simple models and toward simulations of realistic materials.
\r\n\r\nWe begin by describing three algorithms for projected entangled-pair states (PEPS, a type of 2D tensor network) that address three of their major limitations: numerical stability, long-range interactions, and computational efficiency of operators. We first describe (Ch. 2) a technique for converting a PEPS into a canonical form. By generalizing the QR matrix factorization to entire columns of a PEPS, we approximately generate a PEPS with analogous properties to the well-studied canonical 1D tensor network. This connection enables enhanced numerical stability and ground state optimization protocols. Next, we describe (Ch. 3) a technique to efficiently represent physically realistic long-range interactions between particles in a 2D tensor network operator, a projected entangled-pair operator (PEPO). We express the long-range interaction as a linear combination of correlation functions of an auxiliary system with only nearest-neighbor interactions. This allows us to represent long-range pairwise interactions with linear scaling in the system size. The third algorithm we present (Ch. 4) is a method to rewrite the 2D PEPO in terms of a set of quasi-1D tensor network operators, by exploiting intrinsic redundancies in the PEPO representation. We also report an on-the-fly contraction algorithm using these operators that allows for a significant reduction in computational complexity, enabling larger scale simulations of more complex problems.
\r\n\r\nWe then move on to describe (Ch. 5) an extensive study of a \"synthetic 2D material\"---a two-dimensional square array of ultracold Rydberg atoms---enabled by some of the new algorithms. We investigate the ground state quantum phases of this system in the bulk and on large finite arrays directly comparable to recent quantum simulation experiments. We find a greatly altered phase diagram compared to earlier numerical and experimental studies, and in particular, we uncover an unexpected entangled nematic phase that appears in the absence of geometric frustration.
\r\n \r\nFinally, we finish by describing (Ch. 6) a somewhat unrelated, but topically similar project in which we investigate the feasibility of laser cooling small molecules with two metal atoms to ultracold temperatures. We study in detail the properties of the molecules YbCCCa and YbCCAl for application in precision measurement experiments.
" }, { "name": "Ober, Douglas Clifford", "degree": "PhD", "year": "2023", "title": "Laser Spectroscopy of Hydrocarbons for Applications in Atmospheric and Space Science", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312023-235401985", "creators": [ { "name": { "family": "Ober", "given": "Douglas Clifford" }, "id": "Ober-Douglas-Clifford", "orcid": "0009-0005-2257-5029", "display_name": "Ober, Douglas Clifford" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Hodyss", "given": "Robert P." }, "id": "Hodyss-Robert-P", "orcid": "0000-0002-6523-3660", "role": "member", "display_name": "Hodyss, Robert P." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x42v-ry39", "abstract": "This thesis describes applications of spectroscopy and mass spectrometry towards applications of in situ sensing, chemical kinetics, and photodissociation processes of hydrocarbon species. Both mass spectrometry and cavity ring-down spectroscopy are used in this work. Irradiation of protonated coronene was used to study photodissociation process of polycyclic aromatic hydrocarbons (PAHs), with the power, irradiation time, and fragmentation studied to elucidate a photofragmentation mechanism. Biomolecules were ionized via Direct Analysis in Real Time (DART) to explore the feasibility and sensitivity of the ionization technique for different chemical species for in situ measurement in simulated extraterrestrial conditions. Photofragmentation and DART ionization were combined to quantify mixtures of isobaric PAHs, providing a tunable and complimentary technique for in situ analysis of mixtures. Finally, frequency-stabilized cavity ring-down spectroscopy was used to analyze precise \u00b9\u00b3CH\u2084, CH\u2083D, and CH\u2082D\u2082 to CH\u2084 isotologue ratios using optically-switched dual-wavelengths, allowing for sensitive measurement of the kinetic isotope effect of methane oxidation with O(\u00b9D).
" }, { "name": "Ousey, James Anthony", "degree": "PhD", "year": "2023", "title": "Gut Microbiota Modulation of Host Feeding Behavior", "advisor": "Mazmanian, Sarkis K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112022-203906821", "creators": [ { "name": { "family": "Ousey", "given": "James Anthony" }, "id": "Ousey-James-Anthony", "orcid": "0000-0003-4886-0053", "display_name": "Ousey, James Anthony" } ], "advisors": [ { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "advisor", "display_name": "Mazmanian, Sarkis K." } ], "committee": [ { "name": { "family": "Prober", "given": "David A." }, "id": "Prober-D-A", "orcid": "0000-0002-7371-4675", "role": "chair", "display_name": "Prober, David A." }, { "name": { "family": "Lois", "given": "Carlos" }, "id": "Lois-Carlos", "orcid": "0000-0002-7305-2317", "role": "member", "display_name": "Lois, Carlos" }, { "name": { "family": "Oka", "given": "Yuki" }, "id": "Oka-Yuki", "orcid": "0000-0003-2686-0677", "role": "member", "display_name": "Oka, Yuki" }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "member", "display_name": "Mazmanian, Sarkis K." } ], "option_major": [ "biochem" ], "doi": "10.7907/8ghx-2b24", "abstract": "The rich, diverse community of microorganisms in the gastrointestinal tract of animals, or gut microbiota, regulates aspects of host metabolism, immunity, and neural function, with resulting effects on the expression of complex behaviors, including feeding.
\r\n\r\nIn this thesis, we sought to characterize gut microbiota influences on the behavioral response to palatable foods in mice. We discover that binge-like consumption of palatable foods, including high-sucrose pellets and a high-fat diet, is exacerbated in mice in the absence of a gut microbiota. Furthermore, using automated feeding dispensers and video analysis, we find that microbiota depletion with oral antibiotics results in elongated feeding bouts and conserved changes in the dynamics of palatable food intake. We show the hyperphagic phenotype of antibiotic-treated mice is reversible upon microbiota reconstitution via fecal microbiota transplant. Operant conditioning tests reveal that the motivation to pursue high-sucrose rewards is augmented in microbiota-depleted mice. The mesolimbic brain region activity induced upon high-sucrose pellet consumption is elevated in antibiotic-treated mice. Gut bacteria from the family S24-7 and genus Lactobacillus were identified by differential antibiotic treatment and fecal microbiota transplants as correlating with reduction of high-sucrose pellet consumption. Indeed, colonization of vancomycin-treated mice with a mixture of S24-7 and Lactobacillus johnsonii reduces overconsumption of high-sucrose pellets in a limited-access binge-eating model. The work in this thesis comprehensively demonstrates that the gut microbiota regulates feeding induced in response to palatable foods in mice.
" }, { "name": "Overholts, Anna Camille", "degree": "PhD", "year": "2023", "title": "A Novel Platform for Mechanochemical Multicolor Lithography and Models for Solution-Phase Mechanophore Activation", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182023-163804024", "creators": [ { "name": { "family": "Overholts", "given": "Anna Camille" }, "id": "Overholts-Anna-Camille", "orcid": "0000-0002-0593-6903", "display_name": "Overholts, Anna Camille" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/px5z-aj53", "abstract": "The use of mechanical force to trigger chemical reactions has generated many exciting applications in stimuli-responsive materials. Advancement of this area of study requires the development of fundamental models for mechanical activation as well as the design of new force-responsive units, termed mechanophores. This thesis investigates models for solution-phase activation kinetics and activation efficiency and details the development of a novel mechanophore platform for multicolor mechanochemical lithography." }, { "name": "Pennington, Elyse Ann", "degree": "PhD", "year": "2023", "title": "Development of Numerical Models to Advance the Understanding of Air Quality in Los Angeles", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292022-204343735", "creators": [ { "name": { "family": "Pennington", "given": "Elyse Ann" }, "id": "Pennington-Elyse-Ann", "orcid": "0000-0003-1736-2342", "display_name": "Pennington, Elyse Ann" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Wang", "given": "Yuan" }, "id": "Wang-Yuan", "orcid": "0000-0001-6657-8401", "role": "member", "display_name": "Wang, Yuan" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/cvzw-kt61", "abstract": "Atmospheric pollutants such as particulate matter (PM) and ozone (O\u2083) are harmful to human health and intensify climate change. Secondary organic aerosol (SOA) is a main component of PM and is formed via atmospheric oxidation reactions of thousands of gas- and aerosol-phase precursors. Regional-scale chemical transport models predict the formation of these pollutants by representing natural and human emissions of hundreds of species and their subsequent chemical and physical processing in the atmosphere. These models are useful in the absence of detailed measurements and allow researchers to investigate the impact of changing emissions and weather. Los Angeles has unique meteorology and anthropogenic emissions which lead to dangerous pollution events and make this region an important area to study SOA, PM, and O\u2083 formation. As vehicles have become cleaner and their emissions have declined, other sources of emissions have become increasingly important. One important category of emissions is volatile chemical products (VCPs), which are consumer and industrial products that have high volatile organic compound (VOC) emissions that have not been well-constrained or studied in relation to their SOA and O\u2083 formation potential. In this dissertation, I use the Community Multiscale Air Quality (CMAQ) model to represent the air quality of the Los Angeles Basin. First, a new chemical mechanism is developed to represent the formation of SOA from VCPs, implemented in the CMAQ model to simulate 2010 California, and the impact of VCPs on atmospheric pollutants is quantified. Next, we created contemporary inputs to CMAQ by simulating the meteorology, emissions, and land surface of the Los Angeles Basin in 2020. Lastly, the new inputs and chemistry are applied to CMAQ to understand current air quality issues in Los Angeles. We quantify the impact of VCPs on SOA, PM, O\u2083, and other pollutants in both 2010 and 2020. The apportionment of other emission sources and the impact of the COVID-19 pandemic are investigated, and pollutant concentrations are compared to measurements made throughout the Basin and specifically in Pasadena. This works demonstrates the importance of intentional policies to mitigate harmful air pollution events. Limiting NO\u2093 emissions is not sufficient to limit the formation of ozone and PM, and there must be a simultaneous reduction of VOC emissions." }, { "name": "Pinton Tomaleri, Giovani", "degree": "PhD", "year": "2023", "title": "Structure and Mechanism of the Human ER Membrane Protein Complex", "advisor": "Voorhees, Rebecca M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012023-220838845", "creators": [ { "name": { "family": "Pinton Tomaleri", "given": "Giovani" }, "id": "Pinton-Tomaleri-Giovani", "orcid": "0000-0001-9661-6480", "display_name": "Pinton Tomaleri, Giovani" } ], "advisors": [ { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "advisor", "display_name": "Voorhees, Rebecca M." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." } ], "option_major": [ "biochem" ], "doi": "10.7907/e85y-re86", "abstract": "The successful synthesis, targeting, insertion, folding, and assembly of membrane proteins into designated membranes is a crucial process in cell biology. Recent research has shed valuable light on this process through the discovery of the endoplasmic reticulum (ER) membrane protein complex (EMC) and its role in membrane protein biogenesis and quality control. As part of my Ph.D. research in the Voorhees lab, I collaborated with esteemed scientists to investigate the EMC in atomic detail. Described in this thesis is the mechanistic basis of EMC function in membrane protein biogenesis, including recent insights into its broader role beyond its well-defined insertase function. First, we determined the structure of the human EMC using single-particle cryo-electron microscopy (cryo-EM). The structure revealed that it utilizes a mechanism similar to other protein-conducting channels, which involves membrane thinning and polar intramembrane residues to transport substrate transmembrane domains from the cytosol into the membrane. The EMC structure provided the foundation for the subsequent rigorous analysis of its role in membrane protein biogenesis. Through this work, we demonstrate the molecular mechanisms involved in the EMC-dependent path a membrane protein takes, from its initial cytosolic capture by methionine-rich loops of the EMC to its eventual membrane insertion via a hydrophilic vestibule. We further show that specific polar intramembrane residues on the EMC serve as an ER \u201cselectivity filter\u201d which uses charge-repulsion properties to reject mis-targeted mitochondrial membrane proteins and maintain organelle integrity. We also demonstrate that the EMC ensures that transmembrane-spanning substrates adopt the correct topology by promoting the \u201cpositive-inside\u201d rule, which states that positively and negatively charged amino acids localize to the interior (cytoplasmic) and exterior (non-cytoplasmic) sides of membranes, respectively. Finally, our studies suggest that the EMC has a broader role beyond its well-defined insertase function. Specifically, we found that the EMC physically binds to other factors involved in membrane protein biogenesis, providing a shared interaction surface that acts as a hub to integrate signals from other pathways. Using a combination of structural and functional approaches, we identified the EMC\u2019s interaction with Nodal modulator (NOMO) complex, which is part of the multipass translocon complex and facilitate membrane protein biogenesis. Together, these results define and expand the model for membrane protein biogenesis at the ER membrane by the EMC and highlight the complex interplay between different factors in this important process. Together, these results define and expand the model for membrane protein biogenesis at the ER membrane by the EMC and highlight the complex interplay between different factors in this important process." }, { "name": "Qiao, Zhuoran", "degree": "PhD", "year": "2023", "title": "Physics-Informed Neural Approaches for Multiscale Molecular Modeling and Design", "advisor": "Anandkumar, Anima", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102022-055022458", "creators": [ { "name": { "family": "Qiao", "given": "Zhuoran" }, "id": "Qiao-Zhuoran", "orcid": "0000-0002-5704-7331", "display_name": "Qiao, Zhuoran" } ], "advisors": [ { "name": { "family": "Anandkumar", "given": "Anima" }, "id": "Anandkumar-A", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Anandkumar, Anima" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Anandkumar", "given": "Anima" }, "id": "Anandkumar-A", "orcid": "0000-0002-6974-6797", "role": "member", "display_name": "Anandkumar, Anima" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/48d1-ja21", "abstract": "Chemical processes in nature span multiple characteristic length and time scales, and the computational simulation for systems at the intersection of different scales is highly challenging with far-reaching implications for numerous scientific and industrial problems. To facilitate the computational modeling and design for large molecular systems and address the cost-resolution tradeoffs in conventional strategies, in this dissertation we introduce a series of physics-informed machine learning methods for the efficient computational modeling of chemical systems and the accurate prediction of their properties such as energetics, structures, and dynamics. In Chapters 2-3, we introduce a family of orbital-based geometric deep learning methods for the prediction of quantum chemical properties while adhering to the scaling and symmetry constraints of electronic structure theory. The presented methods achieve a chemical accuracy on community-wide benchmarks for molecular property prediction, and are shown to be transferable among diverse main-group molecular systems. In Chapter 4, we introduce a method for the prediction of protein-ligand complex structures based on a finite-time stochastic process parameterized by deep equivariant neural networks. The presented method achieves improved structure prediction accuracy against existing approaches, and is able to rapidly sample protein structures for folding landscapes that are modulated by inter-molecular interactions.
" }, { "name": "Sarai, Nicholas Singh", "degree": "PhD", "year": "2023", "title": "Engineering Cytochrome P450BM3 for Oxidation and Silicon\u2013Carbon Bond Cleavage of Volatile Methylsiloxanes", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152023-034200704", "creators": [ { "name": { "family": "Sarai", "given": "Nicholas Singh" }, "id": "Sarai-Nicholas-Singh", "orcid": "0000-0002-4655-0038", "display_name": "Sarai, Nicholas Singh" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "chair", "display_name": "Newman, Dianne K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "biochem" ], "doi": "10.7907/gn1j-fz77", "abstract": "Directed evolution of enzymes can reveal activities that do not occur in the natural world. While most examples of directed evolution of new-to-nature chemistry have been applied in a synthetic direction, enzymatic biodegradation typically relies on wild-type enzymes. This thesis posits that directed evolution can generate enzymes capable of degrading non-biodegradable anthropogenic compounds, focusing on efforts to break silicon\u2013carbon bonds, which are not known to be cleaved by enzymes in Nature. Chapter I establishes background on how enzymes evolve to catalyze degradation of compounds over long timescales in Nature, highlighting the enzymatic depolymerization of lignocellulosic biomass. This sets the stage for a case study of rapid enzyme evolution in response to anthropogenic molecules such as plastics and agrochemicals. With this background, directed evolution of new-to-nature synthetic activities is presented to demonstrate how new enzymatic activities can be evolved in the laboratory. In Chapter II, the state of the art for biocatalytic reactions involving organosilicon compounds is reviewed, starting with a description of how biology uses silicon and concluding with a perspective on future opportunities in this nascent field. Finally, Chapter III describes the engineering of a novel siloxane oxidase based on a cytochrome P450, which conducts two reaction steps in tandem to cleave silicon\u2013carbon bonds. First, it hydroxylates the C\u2013H bonds of siloxanes\u2014the anthropogenic building blocks of silicone polymers\u2014to yield a carbinol species, an activity reminiscent of the parent enzyme\u2019s native hydroxylation of fatty acids. Via a function entirely different than its native activity, the enzyme converts this carbinol to a silanol species. In performing both of these steps, this is the first known enzyme that can cleave Si\u2013C bonds, an activity which is the first step toward enzymatic degradation of these persistent, man-made compounds. In sum, this thesis demonstrates that directed evolution can reveal enzymatic degradation chemistries that are not known in Nature by establishing new-to-nature Si\u2013C cleavage of siloxanes." }, { "name": "Scott, Anna Gustavus", "degree": "PhD", "year": "2023", "title": "MFeS Clusters as Models for Complex Multimetallic Systems", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112023-231330051", "creators": [ { "name": { "family": "Scott", "given": "Anna Gustavus" }, "id": "Scott-Anna-Gustavus", "display_name": "Scott, Anna Gustavus" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v161-td03", "abstract": "The impressive chemistry of the FeMco-factor of nitrogenase is still under intense study with many remaining mechanistic questions about the important transformation of N2 to NH3, including the role of the synthetically interesting carbide ligand and the complex structure of the octanuclear active site cluster. This thesis describes efforts to incorporate bridging carbon based ligands into synthetic MFeS clusters, which remains a significant synthetic challenge in inorganic chemistry. The subsequent characterization and reactivity studies of such clusters provide insight into how cluster structural properties, including ligand identity, metal identity, and cluster composition and geometry affect cluster electronic properties and reactivity.
\r\n\r\nChapter II describes the synthesis of an unprecedented WFe3S3(\u00b53-carbyne) cluster and comparisons with a WFe3S3(\u00b53-S) cluster provide insight into the role of the bridging carbide in FeMco. The generality of the developed method for synthesis of MFe3S3(\u00b53-carbyne) clusters is also demonstrated. Characterization of the various carbyne clusters are discussed. Cleavage of the C-Si bond of MFe3S3(\u00b53-CSiMe3) clusters towards bridging methylidyne clusters is also demonstrated.
\r\n\r\nChapter III discusses the synthesis of novel octanuclear (CHn) bridged Mo2Fe6S6 clusters and describes the reactivity of these bridges in the context of organometallic and nitrogenase chemistry.
\r\n\r\nChapter IV describes spectroscopic data of an extensive family of MFeS cubane clusters that is currently lacking in the literature and provides important structure property benchmarking information for synthetic and biological FeS clusters.
Chapter V describes the synthesis of well-defined high nuclearity Fe13 clusters resulting from studies of WFeS clusters. These clusters exhibit high spin states and undergo well-defined reactivity with small molecules and thus provide an unprecedented atomically resolved study of reactivities of high-nuclearity transition metal clusters.
" }, { "name": "Sercel, Zachary Patrick", "degree": "PhD", "year": "2023", "title": "Synthesis of Organic Building Blocks and Synthetic Strategies Toward Aleutianamine", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312023-053933898", "creators": [ { "name": { "family": "Sercel", "given": "Zachary Patrick" }, "id": "Sercel-Zachary-Patrick", "orcid": "0000-0001-7977-8509", "display_name": "Sercel, Zachary Patrick" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3ezw-2h57", "abstract": "Described herein are the development of the palladium-catalyzed decarboxylative asymmetric allylic alkylation of medicinally relevant 5- and 7-membered diazaheterocycles and efforts toward the total synthesis of the cytotoxic pyrroloiminoquinone marine alkaloid aleutianamine. The former methodology provides a new tactic to incorporate Csp3 structural complexity into future lead compounds containing diazepane and imidazolidine moieties. The latter project is ongoing.
\r\n\r\nAdditionally, Chapter 3 discusses preliminary attempts to improve the synthetic accessibility of minimally substituted corroles, which were conducted during a research internship in the laboratory of Prof. Zeev Gross at the Technion. During the course of this research, the first example of a \u03b2-unsubstituted free base monoazaporphyrin was isolated, and its cobalt complex was characterized by x-ray crystallography.
\r\n\r\nFinally, Appendix 8 presents a series of cationic and radical-mediated fragmentations of a derivative of (+)-3-Carene, a chiral pool material. These experiments led to the observation and mechanistic study of an unexpected rearrangement.
" }, { "name": "Shiau, Angela Ann", "degree": "PhD", "year": "2023", "title": "Tetranuclear CaMn\u2083O\u2084 and Mn\u2084O\u2084 Complexes as Spectroscopic Models of the Oxygen Evolving Complex of Photosystem II", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012023-232619718", "creators": [ { "name": { "family": "Shiau", "given": "Angela Ann" }, "id": "Shiau-Angela-Ann", "orcid": "0000-0003-4395-9847", "display_name": "Shiau, Angela Ann" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hdx3-fe49", "abstract": "This thesis describes a series of studies focused on tetranuclear model complexes of the Oxygen Evolving Complex (OEC) of Photosystem II (PSII). The OEC is a unique CaMn4O4 metallocofactor responsible for biological water oxidation, producing the dioxygen in the atmosphere required for aerobic life. Advances in spectroscopic and structural studies have deepened our understanding of the mechanism and S-state intermediates of the OEC, but details regarding the (1) role of Ca2+, (2) location of substrate waters, (3) (electronic) structures of the S-states, and (4) precise mechanism of the O\u2212O bond formation remain debated. It is proposed that synthetic model complexes, due to tunability in aspects such as metal composition, oxidation state, geometry, and ligand environment, can provide important structure-function and structure-property relationships applicable to the OEC. However, due to synthetic challenges, series of complexes suitable for such comparisons remain rare in the literature.
\r\n\r\nIn Chapter 1, a brief introduction to the OEC and recent advances in the characterization of the S-state intermediates is discussed. Relationships between synthetic model complexes and how they influence mechanistic proposals for the biological system are highlighted. While it is clear spin state and cluster geometry are strongly correlated, it is important to also consider the effects of smaller, systematic changes in structure and ligand environment on the spectroscopic properties of multimetallic model complexes.
\r\n\r\nChapter 2 presents a magnetometry and spectroscopic study of a series of related CaMnIV3O4 complexes varying in the symmetry of the cluster core, ligand environment, and protonation state of the bridging oxo groups. These complexes serve as models of the CaMnIV3 cuboidal subsite, where cluster spin state has been previously proposed to be indicative of cluster geometry. Results from our study show that intact CaMnIV3O4 cubane structures can possess spin states of S = 3/2, 5/2, and 9/2, with spin state changes attributed to minor distortions within the cluster core and, importantly, from protonation state of bridging oxo moieties. Thus, interpretation of and structural assignments based on the assumption of a S = 9/2 CaMnIV3O4 subsite must be done cautiously.
\r\n\r\nChapter 3 presents a series of MnIIIMnIV3 cuboidal complexes as spectroscopic models of the S2 state of the OEC. Though not in the same geometric arrangement of Mn ions as in the OEC, these model complexes bear remarkably similar EPR spectroscopic features to the low-spin multiline signal of the S2 state. Importantly, differences within this series of essentially isostructural complexes emphasize how the electronic structures of tetranuclear Mn complexes are highly sensitive to changes in ligand environment. Specifically, the energy gap between the ground S = 1/2 spin state and higher spin excited states can be tuned based on ligand electronics, resulting in complexes where both high-spin and low-spin features can be observed by EPR spectroscopy.
\r\n\r\nIn Chapter 4, we expand upon our previous series of MnIIIMnIV3 model complexes utilizing a new synthetic approach to access complexes varying in Mn coordination numbers of five and six. Importantly, both proposed structures of the S2 state contain a five-coordinate MnIII poised for binding an additional aquo or hydroxide ligand in the S2 to S3 transition. Results from this study demonstrate that Mn coordination number can significantly affect the spin state and observed spectroscopy of tetramanganese-oxo clusters. The complex featuring a five coordinate MnIII possesses a ground spin state of SG = 5/2 and reactivity with water generates a MnIIIMnIV3O4 complex with all pseudo-octahedral Mn centers displaying a S = 1/2 ground state.
\r\n\r\nChapter 5 details ligand design strategies in accessing higher oxidation state clusters beyond MnIIIMnIV3. The S3-state is the last observable intermediate prior to O\u2212O bond formation and assigned as S = 3. Previous studies from our group demonstrated the first synthetic example corroborating this spin state, concurrent with a change from antiferromagnetic coupling within the cluster core to overall ferromagnetic coupling upon oxidation to the MnIV4 oxidation state. Synthetic challenges remain in accessing related, isolable clusters. Utilizing aspects of ligand charge and basicity of a disiloxide ligand, a room temperature stable MnIV4O4 cluster was isolated and studied via magnetometry and EPR spectroscopy. Results provide a second example of a MnIV4 cluster assigned as S = 3.
\r\n\r\nWhile unfinished, Appendix 1 presents spectroscopic studies of model MnIIIMnIV3 complexes putatively bound to biologically relevant substrates such as water, hydroxide, methanol, and ammonia. Such chemical alterations and the spectroscopic effects arising from them have been widely studied in the biological system, providing information on the electronic structure of the OEC as well as, importantly, ruling out potential substrate water binding sites. As reactivity with small molecules typically requires an open-coordination site, such studies have been rare in the literature due to the difficulty in accessing lower-coordinate Mn sites within multimetallic Mn clusters. Thus, the ongoing characterization of these reaction products are proposed to be invaluable as benchmarking tools for future mechanistic work.
" }, { "name": "Shimozono, Alexander Mitsuo", "degree": "PhD", "year": "2023", "title": "The Development of Ni-Catalyzed Methods for Application in Total Synthesis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11032022-004822338", "creators": [ { "name": { "family": "Shimozono", "given": "Alexander Mitsuo" }, "id": "Shimozono-Alexander-Mitsuo", "orcid": "0000-0001-7164-4741", "display_name": "Shimozono, Alexander Mitsuo" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h0w0-1d25", "abstract": "The total synthesis of complex natural products often requires the development of mild, selective transformations. Once developed, these methods can serve as starting points for related methodologies, fundamental mechanistic studies, or applied in other total syntheses. Herein, a series of projects that embody this relationship are described. Inspired by unexpected challenges in the synthesis of complex diterpenoid alkaloid talatisamine, a Ni-catalyzed enol-triflate-halogen exchange reaction was developed. In addition to finding application toward the synthesis of talatisamine, this reaction found further use in an attempted route toward enmein-type ent-kauranoid natural products. En route to the synthesis of these natural products, a need for meso-anhydride functionalization was identified which inspired a research program dedicated to Ni-catalyzed reductive functionalization of anhydrides.
" }, { "name": "Tao, Yujia", "degree": "PhD", "year": "2023", "title": "Synthetic Studies Toward the Total Synthesis of Enterocin", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182023-054024067", "creators": [ { "name": { "family": "Tao", "given": "Yujia" }, "id": "Tao-Yujia", "orcid": "0000-0003-4615-6409", "display_name": "Tao, Yujia" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jdhq-sb66", "abstract": "As part of a broader program aimed at the synthesis of complex and highly oxygenated natural products, we initiated a chemical synthesis of the natural polyketide enterocin. This dissertation will disclose our efforts to bridge that gap through the development of synthetic strategies for the total synthesis of the enterocin. The studies herein will address three unique strategies to access the tactical difficulties in the rich oxygenation patterns and caged core structure of enterocin. The program was first inspired by a SeO2 multioxidation reaction, and the methodology has been successfully applied to install bridgehead oxygenation patterns in enterocin. A strategy featuring a radical-polar crossover reaction as an annulation step to quickly construct the [3.2.1] bicyclic core of enterocin is detailed. Initial studies have successfully achieved the radical-polar crossover annulation reaction to forge [3.2.1]bicycles with bridgehead hydroxyl groups, and will guide the future development toward the total synthesis of enterocin. An intermolecular aldol approach will be discussed to address the challenge on pyrone installation and core structure synthesis. In summary, the development of an efficient and general approach will allow the development of novel reactions and a comprehensive evaluation of the potential of caged polyketides to serve as medicinally interesting molecules." }, { "name": "Tribby, Ariana Linnae", "degree": "PhD", "year": "2023", "title": "Inference of Global Methane Emissions from Oil and Gas Production", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-045855497", "creators": [ { "name": { "family": "Tribby", "given": "Ariana Linnae" }, "id": "Tribby-Ariana-Linnae", "orcid": "0000-0002-6435-4575", "display_name": "Tribby, Ariana Linnae" } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pjn3-az83", "abstract": "Atmospheric methane plays a significant role in warming the climate. Characterizing its sources and sinks is important for future climate and air quality impacts. Global methane background trends suggest a sustained increase in emissions since 2007. There is no debate that reducing anthropogenic (human-driven) emissions can lead to short-term decreases in atmospheric methane, posing an attractive avenue towards mitigating climate change. Yet, effective policy to limit emissions from energy-related activities relies on accurate emission estimates, and historically, it has been challenging to diagnose both the magnitude and origin of methane leaks from a wide range of facilities and components across production, transmission, storage, and distribution systems. We present a novel Bayesian hierarchical model to improve methane emission estimates on global and regional scales from oil and gas processes. We also present methods to optimize time and cost of model simulations of certain trace gases, including several of which have important climate implications. Finally, we present our efforts in characterizing fossil methane from burgeoning oil production in Oklahoma and Texas using long term ground-based remote-sensing observations combined with Stochastic Time-Inverted Larangian Transport modeling.
" }, { "name": "Turro, Raymond Farnon", "degree": "PhD", "year": "2023", "title": "Mechanistic Investigations and Development of Ni-Catalyzed Cross- Electrophile Coupling Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312023-172947562", "creators": [ { "name": { "family": "Turro", "given": "Raymond Farnon" }, "id": "Turro-Raymond-Farnon", "orcid": "0000-0001-9774-4556", "display_name": "Turro, Raymond Farnon" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/na61-ed84", "abstract": "Transition metal-catalyzed cross-coupling reactions have proven to be a powerful technology for the modular construction of carbon-carbon and carbon-heteroatom bonds over the last half century. More recently, reductive cross-coupling catalyzed by nickel has emerged as a complementary synthetic approach that couples electrophilic fragments and is rendered catalytic by the inclusion of a terminal reductant. These reactions are advantageous because the use electrophiles as coupling partners which display greater stability, functional group tolerance, and commercial availability over the corresponding nucleophilic coupling partners. Additionally, Ni catalysts are less prone to \u03b2-hydride elimination compared to later transition metals which enables C(sp\u00b3)\u2013C(sp\u207f) couplings. The challenge with using coupling partners of the same polarity is developing a catalyst that can activate each electrophile in a mechanistically distinct way in order to get high levels off cross-selectivity, over statistical mixtures of cross- and homocoupled products.
\r\n\r\nHerein, we describe a mechanistic investigation on Ni-catalyzed cross-electrophile couplings developed in our lab; specifically, the asymmetric reductive alkenylation of N-hydroxyphthalimide (NHP) esters and benzylic chlorides. Investigations of the redox properties of the Ni-bis(oxazoline) catalyst, the reaction kinetics, and mode of electrophile activation show divergent mechanisms for these two related transformations. Notably, the mechanism of C(sp\u00b3) activation changes from a Ni-mediated process when benzyl chlorides and Mn\u2070 are used to a reductant-mediated process that is gated by a Lewis acid when NHP esters and tetrakis(dimethylamino)ethylene is used. Kinetic experiments show that changing the identity of the Lewis acid can be used to tune the rate of NHP ester reduction. Spectroscopic studies support a Ni^(\u026a\u026a)\u2013alkenyl oxidative addition complex as the catalyst resting state. DFT calculations suggest an enantiodetermining radical capture step and elucidate the origin of enantioinduction for this Ni-BOX catalyst.
\r\n\r\nEfforts to expand the scope of coupling partners in XEC reactions to include novel classes of electrophiles, such as N-alkyl imines, are also described. The preparation of heterobenzylic amines by a Ni-catalyzed reductive cross-coupling between heteroaryl imines and C(sp\u00b3) electrophiles is reported. This umpolung-type alkylation proceeds under mild conditions, avoids the pre-generation of organometallic reagents, and exhibits good functional group tolerance. Mechanistic studies are consistent with the imine substrate acting as a redox-active ligand upon coordination to a low-valent Ni center. The resulting bis(2-imino)heterocycle\u00b7Ni complexes can engage in alkylation reactions with a variety of C(sp\u00b3) electrophiles, giving heterobenzylic amine products in good yields.
" }, { "name": "Versaw, Brooke Ann", "degree": "PhD", "year": "2023", "title": "Thermally and Mechanically Responsive Platforms for Functional Polymeric Materials", "advisor": "Robb, Maxwell J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272023-220317123", "creators": [ { "name": { "family": "Versaw", "given": "Brooke Ann" }, "id": "Versaw-Brooke-Ann", "orcid": "0000-0002-6200-7203", "display_name": "Versaw, Brooke Ann" } ], "advisors": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "advisor", "display_name": "Robb, Maxwell J." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2hwm-af78", "abstract": "Connecting a polymer\u2019s reactivity or properties to its working environment is a grand challenge in polymer chemistry. Research towards this goal is driven both by a fundamental interest in mimicking nature\u2019s ability to create surfaces that adapt to their surroundings and a practical desire to tailor the properties of materials to the wide-ranging contexts where they find use. This thesis investigates the development of polymers that exhibit productive changes in physical properties or chemical reactivity under an applied environmental stimulus." }, { "name": "Williams, Chloe Gabrielle", "degree": "PhD", "year": "2023", "title": "Development of Selective Carbon\u2013Carbon Bond-Forming Reactions of Vinyl Carbocations", "advisor": "Nelson, Hosea M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052023-155701672", "creators": [ { "name": { "family": "Williams", "given": "Chloe Gabrielle" }, "id": "Williams-Chloe-Gabrielle", "orcid": "0000-0001-5090-8146", "display_name": "Williams, Chloe Gabrielle" } ], "advisors": [ { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "advisor", "display_name": "Nelson, Hosea M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rkge-pz74", "abstract": "Carbocationic intermediates play an important role in the construction of complex molecules, from biosynthetic pathways in nature to the synthesis of natural products by organic chemists. Herein, a brief introduction that surveys C\u2013C bond forming reactions of vinyl carbocations is highlighted. The discussion of experimental work commences with the development of a main group-catalyzed approach towards accessing vinylated esters through the trapping of vinyl carbocations with silyl ketene acetals. Next, a Claisen-type rearrangement is discussed, which is a result of trapping vinyl carbocations with allyl ethers to form an allyl vinyl oxonium intermediate in situ that can subsequently rearrange. Finally, the last method that is highlighted includes the development of an asymmetric C\u2013H insertion reaction of vinyl carbocations to forge bicyclic products in a highly enantioselective fashion." }, { "name": "Xiong, Shuoyan", "degree": "PhD", "year": "2023", "title": "Insertion of Olefins into Nickel Alkyl Complexes: Mechanistic Studies and Polymerization Catalysis", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:03282023-190134907", "creators": [ { "name": { "family": "Xiong", "given": "Shuoyan" }, "id": "Xiong-Shuoyan", "orcid": "0000-0002-2579-4260", "display_name": "Xiong, Shuoyan" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n59w-qg36", "abstract": "Polyolefins account for over half of global plastic production. The incorporation of polar functionalities can provide value-added polyolefins with desirable material properties and potential degradability. To achieve this, coordination copolymerization of ethylene and fundamental polar comonomers by transition-metal catalysts is the most direct, economical, and environmentally friendly method. Though it has been pursued for decades, the catalyst performance (e.g. activity, thermal stability) is still far below practical thresholds. The major issue is the \"polar monomer problem\": coordination of the polar group in the comonomer to the metal center competes with vinyl coordination, a prerequisite for the monomer enchainment (chain propagation).
\r\n\r\nThis thesis describes mechanism-driven developments of industrially applicable molecular catalysts toward addressing the \"polar monomer problem\", with a focus on nickel catalysts for ethylene/acrylate copolymerization.
" }, { "name": "Yang, Chien-I", "degree": "PhD", "year": "2023", "title": "Mechanism and Function of Nascent Protein Modification in Bacteria", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:07032022-182356199", "creators": [ { "name": { "family": "Yang", "given": "Chien-I" }, "id": "Yang-Chien-I", "orcid": "0000-0001-8606-5013", "display_name": "Yang, Chien-I" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "orcid": "0000-0002-4011-258X", "role": "member", "display_name": "Varshavsky, Alexander J." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qhz7-a383", "abstract": "Newly synthesized proteins undergo multiple modifications to ensure proper biogenesis and acquire their functions. N-terminal methionine excision (NME), mediated by the sequential actions of peptide deformylase (PDF) and methionine aminopeptidase (MAP), is an essential and the most prevalent N-terminal protein modification in the bacterial proteome. Despite the extensive studies on enzymatic catalysis, how NME impacts various cellular functions and how the enzymes achieve timing and selectivity under complex cellular conditions have been long-standing puzzles.
\r\n\r\nIn this work, we use a combination of biochemical analyses, computational modeling, and in vivo measurements to investigate the molecular mechanisms and physiological functions of cotranslational NME reactions. We show that the interactions between the ribosome, the nascent chain, the NME enzymes, and other ribosome-associated protein biogenesis factors dramatically remodel the kinetics and specificity of NME reactions under physiological conditions. In addition, we apply time-resolved, system-wide analyses on the translatome and steady-state proteome to study how the inhibition of PDF influences diverse cellular pathways in bacteria. The results unveil the impact of NME on the biogenesis of nascent proteins and highlight the role of the membrane in coupling the biochemical activities of NME enzymes to cellular physiology.
" }, { "name": "Zak, Joshua Joseph", "degree": "PhD", "year": "2023", "title": "Complex Charge Compensation Mechanisms in Lithium-Rich Chalcogenide Cathodes", "advisor": "See, Kimberly", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022023-055053747", "creators": [ { "name": { "family": "Zak", "given": "Joshua Joseph" }, "id": "Zak-Joshua-Joseph", "orcid": "0000-0003-3793-7254", "display_name": "Zak, Joshua Joseph" } ], "advisors": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "advisor", "display_name": "See, Kimberly" } ], "committee": [ { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "chair", "display_name": "Cushing, Scott K." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "member", "display_name": "Faber, Katherine T." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1k50-3811", "abstract": "Lithium-ion batteries have revolutionized the world by enabling long-lasting portable electronics, electrified transportation, and grid storage solutions for renewable energy implementation. However, current commercialized technologies are limited by the one electron transfer per transition metal paradigm utilized by cathode materials that operate with an intercalation-based charge storage mechanism. Finding ways to increase the charge storage capabilities of the cathode into the multielectron regime has long been a focus of research efforts, and involvement of structural anions in the redox has been demonstrated as a promising way to accomplish multielectron storage. Layered lithium-rich oxide materials have been shown to afford dramatic improvements to overall storage capacity but are plagued by complex mechanisms and unwanted side reactions that lead to poor cycling stability and characterization difficulties. This thesis expands upon previous understanding of oxide-based anion redox materials and extends the exploration into sulfide and selenide systems, which allow the study of anion redox without the side processes that affect oxides. First, a dynamic charge compensation mechanism of late group metal-poor, lithium-rich oxide, Li2Ru0.3Mn0.7O3, is uncovered and found to involve an irreversible anion oxidation that leads to involvement of redox states on transition metals previously thought to be unavailable. Second, active electrolyte additives are explored as a method of stabilizing the cathode-electrolyte interface of anion redox material, Li2RuO3. Third, reversible anion redox is demonstrated in alkali-rich sulfides, Li2FeS2 and LiNaFeS2, and proven to occur through oxidation of sulfides (S2-) to persulfides ([S2]2-). Understanding of the structural ramifications of anion oxidation in Li2FeS2 is further expanded through computational and experimental methods. Fourth, the role of metal-anion covalency is systematically investigated through anion substitution of Li2FeS2 with S2-, highlighting the importance of a holistic understanding of changes to the electronic and physical structure of anion redox materials to predict long-term performance. Finally, detailed perspectives and future outlooks on sulfur redox in lithium battery systems are offered with an exhaustive survey of thermodynamically stable binary and ternary persulfide materials.
" }, { "name": "Zott, Michael David", "degree": "PhD", "year": "2023", "title": "Strategic Applications of Electrochemistry in Ammonia Oxidation and Alkyl Halide Reduction", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282023-205948012", "creators": [ { "name": { "family": "Zott", "given": "Michael David" }, "id": "Zott-Michael-David", "orcid": "0000-0003-0535-0512", "display_name": "Zott, Michael David" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "chair", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4fr8-7r78", "abstract": "This thesis describes the strategic application of electrochemistry in the development of catalytic systems for two challenging processes: alkyl halide reduction and ammonia oxidation. In the case of alkyl halide reduction, the ability to precisely tune electrochemical potential favored the use of electrochemistry as compared to chemical reagents. By contrast, for ammonia oxidation, electrochemistry was specifically targeted due to motivations in the eventual development of ammonia fuel cell technology. The first chapter introduces these and other advantages of electrochemistry, as well as details regarding the thermodynamic potentials and kinetic barriers associated with alkyl halide reduction or ammonia oxidation. The second chapter details our development of photoelectrochemical methodology to employ a strongly luminescent dicopper system for outer-sphere, single-electron transfer reduction of benzyl chlorides. The third chapter marks the beginning of our work in molecular iron-mediated ammonia oxidation catalysis, in which we develop our hypothesis that catalyst structures featuring cis-labile coordination sites should mediate ammonia oxidation. We disclose the first iron electrocatalyst ([(TPA)Fe(MeCN)\u2082]\u00b2\u207a) as well as a framework for the analysis of metrics such as overpotential, catalytic rate, and catalyst stability. The fourth chapter introduces a hypothesis for catalyst improvement\u2014favoring low-spin electronic structures\u2014and a model system for testing: ([(BPM)Fe(MeCN)\u2082]\u00b2\u207a). Using this second-generation catalyst, improved stability, enhanced activity, and lowered overpotential were observed. The fifth chapter explores the validity of the cis-labile and low-spin hypotheses via Hammett-type substituent studies on both the [(TPA)Fe(MeCN)\u2082]\u00b2\u207a and the [(BPM)Fe(MeCN)\u2082]\u00b2\u207a platforms. This study resulted in the development of a further enhanced molecular electrocatalyst for ammonia oxidation and revealed mechanistic information pertinent to the development of future catalytic systems." }, { "name": "Zou, Fangyu Nathan", "degree": "Senior Thesis", "year": "2023", "title": "Manufacturing 3-D Lithium-Ion Batteries with Interpenetrating Lattice Electrodes", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06202023-173615207", "creators": [ { "name": { "family": "Zou", "given": "Fangyu Nathan" }, "id": "Zou-Fangyu-Nathan", "display_name": "Zou, Fangyu Nathan" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/t8n9-wj51", "abstract": "3-D lithium-ion batteries have been proven to exhibit a higher energy density while minimizing power loss compared to the standard, layer-by-layer constructed 2-D lithium-ion batteries. This thesis explores the implementation of additive manufacturing in the process of constructing the proposed 3-D battery due to its capability of architecting materials with high accuracy and tunability. A 3-D lithium-ion battery backbone was created using a 2-step process, in which the first step 3-D printed the overall structure as a polymer, and the second step sputtered gold onto the polymer for conductive properties. The 3-D printed battery backbone consisted of two interpenetrating lattices made of post-cured PR48 resin that would serve as the anode and cathode, while the electrolyte would fill the space between the two electrodes. During the sputtering process, the polymer structure was rotated 6 times to guarantee that the sputtering will be conformal throughout the lattice. Electrodeposition was used to generate a LiCoO2 anode and a Li cathode. The electrodeposition of the lithium cobalt oxide cathode onto the lattice structure was proven to be unsuccessful due to the low thermal stability and high reactivity of the 3-D printed polymer when submerged into the electrolyte, consisting of KOH at 260 \u00b0C. Results indicate that the uniform electrodeposition of the lithium anode onto the lattice structure was successful using a 1s on, 1s off pulse current for a 60-minute duration. Using a titanium and gold layer proved to increase the uniformity of the coating. However, due to the failure of the lithium cobalt oxide electrodeposition, a different backbone structure may need to be considered. Having two separate structures serving as the anode and cathode (and later combining them into one structure) as opposed to both electrodes being on one structure may be beneficial. This allows for the cathode to be altered without altering both electrodes, allowing more flexibility to coat the structure with lithium cobalt oxide." }, { "name": "Abernathy, Morgan Elizabeth", "degree": "PhD", "year": "2022", "title": "Antibody Targeting of HIV-1 Env: a Structural Perspective", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012022-191225421", "creators": [ { "name": { "family": "Abernathy", "given": "Morgan Elizabeth" }, "id": "Abernathy-Morgan-Elizabeth", "orcid": "0000-0001-9959-7713", "display_name": "Abernathy, Morgan Elizabeth" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0p2b-aa45", "abstract": "A key component of contemporary efforts toward a human immunodeficiency virus 1 (HIV-1) vaccine is the use of structural biology to understand the structural characteristics of antibodies elicited both from human patients and animals immunized with engineered 'immunogens,' or early vaccine candidates. This thesis will report on projects characterizing both types of antibodies against HIV-1. Chapter 1 will introduce relevant topics, including the reasons HIV-1 is particularly capable of evading the immune system in natural infection and after vaccination, the 20+ year history of unsuccessful HIV-1 vaccine large-scale efficacy trials, an introduction to broadly neutralizing antibodies (bNAbs), and a review of common strategies utilized in HIV-1 immunogen design today. Chapter 2 describes the isolation, high-resolution structural characterization, and in vitro resistance profile of a new bNAb, 1-18, that is both very broad and potent, as well as able to restrict HIV-1 escape in vivo. Chapter 3 reports the results of an epitope-focusing immunogen design and immunization experiment carried out in wild type mice, rabbits, and non-human primates where it was shown that B cells targeting the desired epitope were expanded after a single prime immunization with immunogen RC1 or a variant, RC1-4fill. Chapter 4 describes Ab1245, an off-target non-neutralizing monoclonal antibody isolated in a macaque that had been immunized with a series of sequential immunogens after the prime immunization reported in Chapter 3. The antibody structure describes a specific type of distracting response as it binds in a way that causes a large structural change in Env, resulting in the destruction of the neutralizing fusion peptide epitope. Chapter 5 is adapted from a review about how antibodies differentially recognize the viruses HIV-1, SARS-CoV-2, and Zika virus. This review serves as an introduction to the virus SARS-CoV-2, which is the topic of the final chapter, Chapter 6. In this chapter, structures of many neutralizing antibodies isolated from SARS-CoV-2 patients were used to define potentially therapeutic classes of neutralizing receptor-binding domain (RBD) antibodies based on their epitopes and binding profiles." }, { "name": "Arrastia, Mary Villanueva", "degree": "PhD", "year": "2022", "title": "Development of Single-Cell SPRITE: a Tool for Measuring Heterogeneity of 3D DNA Organization", "advisor": "Ismagilov, Rustem F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10012021-223453672", "creators": [ { "name": { "family": "Arrastia", "given": "Mary Villanueva" }, "id": "Arrastia-Mary-Villanueva", "orcid": "0000-0002-0723-3574", "display_name": "Arrastia, Mary Villanueva" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "advisor", "display_name": "Ismagilov, Rustem F." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w70x-2294", "abstract": "Across eukaryotic cells, DNA from each nucleus is organized in three dimensions in order to help regulate transcriptional activity. Decades of chromosome capture technologies have revealed fundamental chromatin structures, providing information about how DNA is assembled genome-wide. The majority of these methods utilize direct physical ligation of DNA molecules to generate pairwise interactions, which have provided information about short-range interactions and intra-chromosomal structures. Recent technologies have moved toward identifying multiple DNA interactions simultaneously without physical ligation of DNA molecules, revealing information about long-range interactions and inter-chromosomal structures. One of the biggest limitations of these methods is that they only study DNA organization in bulk, which misses the heterogeneity of chromosomal structures at the single-cell level. As a result, single-cell chromosome capture methods have been developed to begin probing into the cell-to-cell variability of DNA organization and answer long-standing questions regarding single-cell structure. However, single-cell methods are currently limited to identifying low-resolution, intra-chromosomal DNA interactions with few numbers of cells. This creates a need for an improved, high-throughput single-cell method that can capture high-resolution structures and simultaneous mapping of both intra- and inter-chromosomal interactions to better elucidate single-cell DNA organization. In this thesis, we describe the development of 'single-cell split-pool recognition of interactions by tag extension' (scSPRITE), a single-cell chromosome capture method that allows for mapping of high-resolution, intra- and inter-chromosomal structures across thousands of cells. Through scSPRITE, we were not only able to reveal fundamental information about single-cell DNA organizations, but we can also quantitatively measure the variability of DNA interactions from cell to cell.
" }, { "name": "Banks, Rachel A.", "degree": "PhD", "year": "2022", "title": "Experimental and Theoretical Studies of Non-Equilibrium Systems: Motor-Microtubule Assemblies and the Human-Earth System", "advisor": "Phillips, Robert B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11282021-042001335", "creators": [ { "name": { "family": "Banks", "given": "Rachel A." }, "id": "Banks-Rachel-A", "orcid": "0000-0003-2028-2925", "display_name": "Banks, Rachel A." } ], "advisors": [ { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "advisor", "display_name": "Phillips, Robert B." } ], "committee": [ { "name": { "family": "Van Valen", "given": "David A." }, "id": "Van-Valen-D", "orcid": "0000-0001-7534-7621", "role": "chair", "display_name": "Van Valen, David A." }, { "name": { "family": "Bois", "given": "Justin S." }, "id": "Bois-J-S", "orcid": "0000-0001-7137-8746", "role": "member", "display_name": "Bois, Justin S." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "biochem" ], "doi": "10.7907/5ee6-j454", "abstract": "Systems out of equilibrium are pervasive around us. In fact, being out of equilibrium is a key property of life, as described by Erwin Schrodinger in his series of essays \"What is life?\". Through the consumption of energy, i.e. food, living organisms achieve ordered states that would be very unlikely to occur at equilibrium, such as the mitotic spindle during cell division, swarms of bacteria, or flocks of starlings. The Earth system is another example of a non-equilibrium system. The state of the Earth has been evolving for billions of years, often under the influence of life. Today, humanity is a dominant influence forcing the Earth system to new states. Understanding these non-equilibrium systems has posed many challenges; in this thesis, we work towards quantitatively dissecting and gaining an intuition for the functioning of both a molecular scale and planetary scale non-equilibrium system.
\r\n\r\nUnderlying many cellular functions such as cell division and transportation of organelles is the cytoskeleton composed of motor proteins and their constituent filaments. One of the key components are kinesin motors, which consume chemical energy to walk along and reorganize microtubules. Collections of these motors and microtubules are able to form organized structures. Understanding how these structures are formed has remained an open question. In Chapter 2, we develop a system of kinesin motors and microtubules wherein motor activity is controlled by light, thereby gaining spatiotemporal control over the formation of motor-microtubule assemblies. We demonstrate the creation of a variety of structures of different sizes and geometry, and measure how length and time scales of these assemblies depend on the activated region.
\r\n\r\nA remaining question was how the microscopic details of the interaction between motors and microtubule affect the dynamics and steady-state structure formed. With our scheme for light-control in hand, we extended the system to a variety of motor proteins that have different speeds, processivities (how many steps they take before unbinding from the microtubule), directionalities (which end of the microtubule they walk towards), and forces they are able to exert in Chapter 3. We found that the size of steady-state structures, distribution of motors within assemblies, and rate of contraction of networks depend on motor properties. Further, we demonstrate that various structures can be formed by combining different motors. This work begins to build a connection between the detailed microscopic interactions of cytoskeletal components to the larger scale structures they form.
\r\n\r\nChapter 4 begins our work on understanding the state of the human-Earth system. A major hurdle to quantitatively understanding this system is the difficulty of finding and parsing the relevant data, which is often within long, complicated reports. In order to facilitate access to this data, we created the Human Impacts Database, which houses a collection of $>$ 300 carefully curated values related to human impacts on the Earth, introduced in Chapter 4. In this chapter, we describe the format of the database as well as demonstrate how it can be harnessed to gain a more holistic perspective on humanity's influence on the Earth.
\r\n\r\nHaving this data is only a starting point towards deciphering the ways that humans are altering the state of the Earth, though. In Chapter 5, we combine these quantitative measurements with simple order-of-magnitude estimates to gain an intuition for the magnitude of several of the values. In this way, we show that many of the ways humanity is affecting the Earth can be tied back to how much land, water, and power we use. We further contextualize the magnitude of human influence by comparing human activities to natural analogs, finding that humans currently rival natural processes in influencing the state of the Earth system.
" }, { "name": "Bateman, Orland Christopher Lycurgue", "degree": "PhD", "year": "2022", "title": "Design and Application of Novel Membrane Materials", "advisor": "Kornfield, Julia A.; Diallo, Mamadou S.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222021-065913893", "creators": [ { "name": { "family": "Bateman", "given": "Orland Christopher Lycurgue" }, "id": "Bateman-Orland-Christopher-Lycurgue", "orcid": "0000-0002-6985-494X", "display_name": "Bateman, Orland Christopher Lycurgue" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Diallo", "given": "Mamadou S." }, "id": "Diallo-Mamadou-S", "role": "co-advisor", "display_name": "Diallo, Mamadou S." } ], "committee": [ { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "orcid": "0000-0001-6585-2536", "role": "chair", "display_name": "Faber, Katherine T." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Diallo", "given": "Mamadou S." }, "id": "Diallo-Mamadou-S", "role": "member", "display_name": "Diallo, Mamadou S." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9w23-ax66", "abstract": "Membrane technology is uniquely suited to meet the growing need for more sustainable processes due to membranes\u2019 tailorable selectivity and energy efficiency. Efforts to further improve membrane performance and modify them for new applications have found success in academic studies with a versatile class of membranes known as mixed-matrix membranes (MMM). Mixed-matrix membranes combine the strength and controlled morphology of semicrystalline polymeric membranes with superior functionality of a separate material dispersed in the polymer matrix. The strength and toughness of the resulting membranes depends on polymer morphology, including degree of crystallinity and pore structure. Control of the membrane morphology is achieved by kinetically trapping a partially phase separated state, for example, using Nonsolvent Induced Phase Separation (NIPS) to drive liquid-liquid and solid-liquid demixing. However, the processes used to control the polymer morphology are influenced by the functional particles and can result in novel morphologies. In Chapter 2, we used a promising strategy for stably incorporating functional polymeric particles in a structural polymer matrix to investigate the role of the particles during NIPS. The interplay of functional polymeric particle loading and nonsolvent induced phase separation are examined using x-ray diffraction (to deduce the crystal morph adopted by polyvinylidene difluoride, PVDF) and scanning electron microscopy (to observe membrane morphology and the size and distribution of functional particles). We found that the interaction between nonsolvent and functional particles enables a shift in crystal phase usually not attainable with our solvent.
\r\n\r\nIn addition to studying the fundamentals underlying MMM formation, we investigated two applications for novel membrane materials: purification of therapeutic antibodies and size-selective particle capture. Purification of proteins for medical use requires several chromatographic steps in order to produce solutions of sufficient purity. For many years, the gold standard in the field was resin-based packed bed chromatography; however, more recently membrane chromatography has gained prevalence due to its faster processing time, lower cost, and low operating pressure. With these advantages come the drawbacks of low binding capacity and a sensitivity to the concentration of salt ions in the solution. To address these two drawbacks, we investigated the chromatographic abilities of a modified MMM, in Chapter 3, and a novel membrane material comprising an MMM-ceramic composite, in Chapter 4. We discovered that the performance of the modified MMM is dependent on crosslinker chemistry and crosslink density. Upon optimization, the modified membrane demonstrated a binding capacity consistent with the upper range of available literature values as well as reduced sensitivity to salt. In addition, the development of the novel MMM-ceramic composite enables the use of a broader range of polymer matrix compositions for membrane chromatography.
\r\n\r\nCapture of pathogens from complex fluids, such as blood, has received substantial attention due to rising rates of sepsis and antibiotic resistance. \tIn Chapter 5, we pursued the capture of pathogens from model fluids using the size-based separation capabilities of dendritic ceramic membranes. We found that interactions between the ceramic surface and the suspended particles played a significant role in membrane performance.
" }, { "name": "Buzard, Camillus Francis", "degree": "PhD", "year": "2022", "title": "Detecting Small Signals: Near-Infrared Studies of Substellar Companions", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192022-142030043", "creators": [ { "name": { "family": "Buzard", "given": "Camillus Francis" }, "id": "Buzard-Camillus-Francis", "orcid": "0000-0002-9943-6124", "display_name": "Buzard, Camillus Francis" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Knutson", "given": "Heather A." }, "id": "Knutson-H-A", "orcid": "0000-0002-5375-4725", "role": "member", "display_name": "Knutson, Heather A." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/kwkz-t588", "abstract": "As the number of known exoplanets, or planets in other solar systems, grows, we have become empowered to ask deeper and more specific questions about the possibilities presented by our universe. A group of giant gaseous planets called \"hot Jupiters\" spurred us to think in new ways about giant planet formation. The diversity of solar system architectures, exoplanet sizes, atmospheric composition and dynamics expands our perspective on the many possible outcomes resulting from the same primordial ingredients in different amounts and in different environments. To fully answer these questions, we need to look directly into exoplanet atmospheres. Infrared spectra can reveal atmospheres' molecular content and certain physical processes, such as winds and rotation effects. From spectoscopic measurements, we can test theories of planet formation, evolution, and habitability. Unfortunately, most current direct exoplanet characterization techniques are limited to certain populations, whether planets with specific orbital geometries or planets either very far from or very near their host stars. These well-established methods miss a key population of exoplanets, specifically those that are non-transiting and with orbital separations between roughly 0.15 and 5 AU. This group contains around 19% of the exoplanets known today (a percentage which will only increase in the coming extreme precision radial velocity era) and will almost certainly include the nearest potentially habitable world. This dissertation presents two projects. In the first, we work to further a direct exoplanet characterization approach that will be sensitive to these elusive planets by identifying and reducing an insidious source of structured noise - in the process, making it easier to directly detect planetary emission. With advancements promised by the simulation framework presented in this dissertation, our multi-epoch direct detection approach, in combination with planet-to-star contrast gains enabled by high-contrast imaging technology, will be uniquely capable of characterizing ever smaller, cooler, and more complex planetary atmospheres. In the second project, we apply the direct detection method to a particularly interesting substellar object, a brown dwarf in a very close (<2 hour) orbit around a white dwarf, in order to understand how gaseous atmospheres behave in exotic irradiation environments. Together, these projects demonstrate the capacity of multi-epoch spectroscopic observations to serve as a window into gaseous atmospheres and a pathway to potentially habitable worlds." }, { "name": "Chang, Daniel Kwon", "degree": "Masters", "year": "2022", "title": "Nickel-Catalyzed Electroreductive Cross-Coupling Reactions of Anhydrides and Alkyl Halides", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122022-031448609", "creators": [ { "name": { "family": "Chang", "given": "Daniel Kwon" }, "id": "Chang-Daniel-Kwon", "orcid": "0000-0003-4314-5886", "display_name": "Chang, Daniel Kwon" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w0pr-fs28", "abstract": "The formation of new carbon\u2013carbon bonds is one of the most important transformations in organic chemistry due to its ability to build the backbone of organic molecules. Nickel-catalyzed reductive cross-coupling reactions have recently emerged as an efficient and powerful strategy for the creation of new carbon\u2013carbon bonds. Furthermore, electrochemistry can be harnessed to overcome some of the challenges encountered in many of the reductive cross-coupling reactions in the literature. Herein, we discuss the development of a new electroreductive nickel-catalyzed cross-coupling of anhydrides with unactivated alkyl bromides in collaboration with Amgen to produce large amounts of substituted cyclobutane products." }, { "name": "Chea, Peter Hing-Yin", "degree": "Senior Thesis", "year": "2022", "title": "Evaluation of Flow Rate and Leakage on Mask Effectiveness and Investigation of Double Masks", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252024-034444812", "creators": [ { "name": { "family": "Chea", "given": "Peter Hing-Yin" }, "id": "Chea-Peter-Hing-Yin", "orcid": "0009-0005-0774-6715", "display_name": "Chea, Peter Hing-Yin" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jrw9-h427", "abstract": "Mask-wearing emerged as the primary safety measure to prevent spreading COVID-19. During the COVID-19 pandemic, there was growing evidence that SARS-CoV-2 could spread by aerosol transmission. Thus, increased understanding of mask performance was important to help reduce viral transmission. In addition, the CDC recommended wearing double masks to provide better fit and additional protection when people could not access respirators. This thesis aims to investigate the performance of single mask and double mask combinations, and using a parallel resistance model to quantify leakage.
\r\n \r\nMultiple copies of different mask types were tested: N95 respirators, KN95 respirators, procedure masks, and cloth masks. For all of the single masks, the penetration increased with flow rate, while the most penetrating particle size (MPPS) generally decreased. The peak penetration is lowest for N95 respirators, and the peak penetration is highest for cloth masks at all flow rates. For double masking, we observe that wearing a combination of cloth and procedure masks has a higher amount of decreased penetration and a lower amount of increased pressure drop than a combination involving N95 and KN95 respirators. For quantifying leakage, a parallel resistance model was used to calculate the resistance for leaks. The procedure and cloth masks had lower resistance for leaks and leakage flow rates than N95 and KN95 respirators. The procedure and cloth masks are more susceptible to leaks than respirators and thus reducing the effectiveness of these masks.
" }, { "name": "Cheng, Lixue", "degree": "PhD", "year": "2022", "title": "Accurate and Transferable Molecular-Orbital-Based Machine Learning for Molecular Modeling", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechThesis:04012022-153013173", "creators": [ { "name": { "family": "Cheng", "given": "Lixue" }, "id": "Cheng-Lixue", "orcid": "0000-0002-7329-0585", "display_name": "Cheng, Lixue" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Anandkumar", "given": "Anima" }, "id": "Anandkumar-A", "orcid": "0000-0002-6974-6797", "role": "member", "display_name": "Anandkumar, Anima" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/cjak-4x38", "abstract": "Quantum simulation is a powerful tool for chemists to understand the chemical processes and discover their nature accurately by expensive wavefunction theory or approximately by cheap density function theory (DFT)\\nomenclature{DFT}{Density Functional Theory}. However, the cost-accuracy trade-offs in electronic structure methods limit the application of quantum simulation to large chemical and biological systems. In this thesis, an accurate, transferable, and physical-driven molecular modelling framework, i.e., molecular-orbital-based machine learning (MOB-ML), is introduced to provide accurate wavefunction-quality molecular descriptions with at most mean-field level computational cost. Instead of directly predicting the total molecular energies, MOB-ML describes the post-Hartree-Fock correlation energy from molecular orbital information at the cost of Hartree-Fock computations. \r\nPreserving all the physical constraints, molecular orbital based (MOB) features represent the chemical space faithfully in both supervised clustering and unsupervised learning for chemical space explorations. The development of local regressions with scalable exact Gaussian processes within clusters further allows MOB-ML to provide the most accurate approach in both low and big data regimes. As exciting and general new tool to tackle various problems in chemistry, MOB-ML offers great accuracies of predicting total energies and serves as a universal density functional for organic molecules and non-covalent interactions in various chemical systems. With the availability of analytical nuclear gradients, MOB-ML is also capable of generating accurate PESs with few reference high-level electronic structure computations in the diffusion Monte Carlo accurately and efficiently for computational spectroscopy.
" }, { "name": "DeLano, Travis Jon", "degree": "PhD", "year": "2022", "title": "Development of Nickel-Catalyzed Asymmetric Cross-Coupling Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272022-163740814", "creators": [ { "name": { "family": "DeLano", "given": "Travis Jon" }, "id": "DeLano-Travis-Jon", "orcid": "0000-0002-2052-611X", "display_name": "DeLano, Travis Jon" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "chair", "display_name": "Robb, Maxwell J." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pzfp-ad90", "abstract": "Asymmetric cross-coupling reactions have emerged in recent decades as powerful tools for the formation of valuable carbon\u2013carbon bonds in the synthesis of enantioenriched small molecules. Nickel catalysis in particular has proven to be an especially powerful tool for the formation of C(sp\u00b2)\u2013C(sp\u00b3) bonds in part due to the propensity of nickel catalysts to access odd oxidation states and interact with radical intermediates. Application of asymmetric nickel catalysis to a variety of radical precursors has resulted in the development of a broad range of stereoconvergent reductive and redox-neutral cross coupling reactions, allowing for the highly enantioselective formation of many synthetically useful and biologically relevant molecules.
\r\n\r\nHerein we describe our recent efforts in the development of new nickel-catalyzed enantioselective cross-coupling reactions. First, an enantioselective reductive cross- coupling of alkenyl and benzyl halides was rendered electroreductive. Careful electrochemical cell design proved critical for this reaction, which represents the first report of an enantioselective nickel-catalyzed electroreductive cross coupling reaction. We next discuss our development of an enantioselective reductive cross coupling of \u237a-chloroesters with aryl iodides. This reaction proceeds with especially high ee when \u03b2-branched substrates are employed, prompting the development of a multivariate linear regression model to probe the origin of the observed enantioselectivity trends. Finally, a redox-neutral nickel/photoredox co-catalyzed coupling of \u237a-N-heterocyclic potassium alkyl trifluoroborates and aryl bromides is reported. This reaction, developed in collaboration with researchers at Merck, provides rapid enantioselective access to motifs commonly found in bioactive molecules.
" }, { "name": "Du, Yun Emily", "degree": "Senior Thesis", "year": "2022", "title": "Surveying Notions of Queer Asian American Community Through Literature: 1972\u20131998", "advisor": "Dykstra, Maura", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082022-220335559", "creators": [ { "name": { "family": "Du", "given": "Yun Emily" }, "id": "Du-Yun-Emily", "orcid": "0000-0003-0634-910X", "display_name": "Du, Yun Emily" } ], "advisors": [ { "name": { "family": "Dykstra", "given": "Maura" }, "id": "Dykstra-M", "orcid": "0000-0001-6036-6440", "role": "advisor", "display_name": "Dykstra, Maura" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry", "history" ], "doi": "10.7907/43ya-7t94", "abstract": "The history of queer Asian America has, to date, largely been studied as a history of organizations. This has lent a particular tilt to both the preservation and the study of queer Asian America: the activism of the late 20th century has been archivally and academically preserved, while records of everyday queer Asian American experiences -- of the ways individuals discovered their identities, formed communities, found loves, and filled their days -- have been more rarely preserved and written of. This thesis seeks to fill that gap by analyzing the history of queer Asian American literature. Specifically, the thesis offers a broad survey of queer Asian American writing from the 1970s through the 90s. It then uses methods of literary and historical analysis to shed light on how individuals have grappled with the question of what it means to be queer and Asian American. Ultimately, the thesis turns to the queer Asian American community and asks, \"Who are 'we'?\"
" }, { "name": "Esswein, Shannon Rose", "degree": "PhD", "year": "2022", "title": "Structural Basis of Antibody Recognition of Viruses", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202022-005152490", "creators": [ { "name": { "family": "Esswein", "given": "Shannon Rose" }, "id": "Esswein-Shannon-Rose", "orcid": "0000-0002-5142-0190", "display_name": "Esswein, Shannon Rose" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Orphan", "given": "Victoria J." }, "id": "Orphan-V-J", "orcid": "0000-0002-5374-6178", "role": "member", "display_name": "Orphan, Victoria J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "biochem" ], "doi": "10.7907/krjp-se81", "abstract": "The Zika epidemic in 2015-2016 and COVID-19 pandemic in 2019-2021 are the latest reminders of the enormous impact of viruses on the world. Zika, a flavivirus transmitted by mosquitos, can cause severe neurodevelopmental abnormalities including microcephaly in the newborns of the infected mothers. Vaccine design is complicated by concern that elicited antibodies may also recognize other epidemic-causing flaviviruses that share a similar envelope protein, such as dengue virus, West Nile Virus, and yellow fever virus. This cross-reactivity, if non-neutralizing, may worsen symptoms of a subsequent infection through antibody-dependent enhancement (ADE). To better understand the neutralizing antibody response and risk of ADE, we compared germline and mature antibody binding to Zika and other flaviviruses. We showed that affinity maturation of the light chain variable domain is important for strong binding of VH3-23/VK1-5 neutralizing antibodies to Zika virus envelope domain III (EDIII) and identified interactions that contribute to weak, cross-reactive binding to West Nile Virus EDIII. These findings informed our design of EDIII-conjugated mosaic nanoparticles as a pan-flavivirus vaccine candidate. Sera from immunization trials with nanoparticles displaying EDIIIs of Zika and dengue serotypes 1-4 showed cross-reactive binding to Zika, dengue 1-4, and West Nile Virus, a promising step towards the development of safe and effective flavivirus vaccines.
\r\n\r\nCoronaviruses are another group of viruses responsible for widespread morbidity and mortality, including the severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East Respiratory Syndrome coronavirus (MERS-CoV) epidemics and current SARS-CoV-2 pandemic. Given concerns regarding new SARS-CoV-2 variants and the possibility for additional zoonotic betacoronaviruses to cause future outbreaks, we investigated how the epitopes on the SARS-CoV-2 receptor binding domain (RBD) targeted by VH3-30-derived antibodies correlate with their neutralization potency and breadth of betacoronavirus recognition. Analyses showed how variations in antibody light chains and CDRH3 lengths facilitate the diverse RBD epitopes, cross-reactivity, and neutralization profiles of VH3-30 Abs, illustrating their importance for vaccine design and therapeutic antibody development.
" }, { "name": "Fastuca, Nicholas James", "degree": "PhD", "year": "2022", "title": "Fragment Coupling Approach To C\u2081\u2089- AND C\u2082\u2080-Diterpenoid Alkaloids: Total Synthesis of (\u2013)-Talatisamine, (\u2013)-Liljestrandisine, and (\u2013)-Liljestrandinine", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292022-214045444", "creators": [ { "name": { "family": "Fastuca", "given": "Nicholas James" }, "id": "Fastuca-Nicholas-James", "orcid": "0000-0003-4081-6031", "display_name": "Fastuca, Nicholas James" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vf11-jy04", "abstract": "A unified, convergent fragment coupling approach to the C\u2081\u2089- and C\u2082\u2080-diterpenoid alkaloid natural products is presented. The highly-caged aconitine, denudatine, and napelline cores are disconnected through the central B-ring cyclohexane to an A/E/F-ring fragment common to the structures all three subfamilies. 1,2-addition of an appropriate organometallic C/D-bicycle to an A/F-ring hydrindane epoxy ketone fragment followed by a Lewis acid-catalyzed semipinacol reaction couples the two fragments together and sets a key all-carbon quaternary center at C11. This strategy is realized in the synthesis of the C\u2081\u2089-aconitine core by using a [3.2.1]-bicyclooctene C/D-fragment as the nucleophile in the 1,2-addition. This C/D-fragment is prepared using a meta-photocycloaddition; this represents an alternative approach to the commonly employed biomimetic Wagner-Meerwein rearrangement of a [2.2.2]-bicyclooctane.
\r\n\r\nTo complete the aconitine core, a radical cyclization cascade to form the E-ring piperidine and B-ring cyclohexane in a single step is investigated. N-centered radicals were evaluated to initiate the cascade via a 6-exo-trig cyclization. A neutral aminyl radical gave rise to an unexpected Hoffman-L\u00f6ffler-Freytag type product resulting from 1,5-hydrogen atom transfer. Employing Lewis-acidic single electron reducing metal catalyst led to formation of the E-ring cyclized product, however the second cyclization to close the B-ring did not occur.
\r\n\r\nAs an alternative approach, the E-ring was closed via an intramolecular aziridination. Treatment of this aziridine with acetyl bromide results in an aziridine-opened alkyl bromide product. This alkyl bromide is used as a functional group handle to form the final ring of the aconitine core. From there, the total synteheses of the C\u2081\u2089-diterpenoid alkaloids (\u2013)-talatisamine, (\u2013)-liljestrandisine, and (\u2013)-liljestrandinine were completed in short order. These synthetic efforts led to revision of the proposed structure of (\u2013)-liljestrandisine.
" }, { "name": "Fornace, Mark Evan", "degree": "PhD", "year": "2022", "title": "Computational Methods for Simulating and Parameterizing Nucleic Acid Secondary Structure Thermodynamics and Kinetics", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12212021-202554260", "creators": [ { "name": { "family": "Fornace", "given": "Mark Evan" }, "id": "Fornace-Mark-Evan", "orcid": "0000-0002-5829-5839", "display_name": "Fornace, Mark Evan" } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "advisor", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "orcid": "0000-0002-5899-7523", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ayeg-at42", "abstract": "Nucleic acid secondary structure models offer a simplified but powerful lens through which to view, analyze, and design nucleic acid chemistry. Computational approaches based on such models are central to current research directions across molecular programming, synthetic biology, and the life sciences more broadly. Our framework combines three ingredients. First, we develop new recursions to include contributions from coaxial and dangle stacking in an efficient and principled way. Second, we formulate the concept of an evaluation algebra, which defines the mathematical form of each subproblem in the dynamic program. Whereas previous modeling efforts have relied on case-by-case handling of different thermodynamic quantities, we use evaluation algebras to elegantly and efficiently compute a variety of physical quantities using the same recursions. Third, we develop efficient operation orders for a variety of physical quantities of experimental interest. Combining our advances, we are able to achieve speedups of 20-120x and scalable calculations of complexes of up to 30,000 nucleotides. Our achievements promise to dramatically expand the scope and utility of computational analysis and design of nucleic acid thermodynamics.
\r\n\r\nWhile current dynamic programming algorithms achieve efficient computation of thermodynamic quantities for a given nucleic acid sequence, they do not provide kinetic information. Therefore, investigations of secondary structure kinetics rely on stochastic simulations of trajectories in secondary structure space. We improve upon these simulation methodologies to achieve lower computational complexities and large empirical speedups. We extend our algorithms to an ensemble which fully includes coaxial and dangle stacking states, expanding the scope of the kinetic analysis that is currently possible.
\r\n\r\nCurrent secondary structure models are parametrized using thermodynamic information gleaned from decades of melt experiments of RNA and DNA in specific experimental conditions. Only rough kinetic information is currently available from past experiments, and information on solvent and material dependence is lacking. We develop a fully computational approach based on Gaussian processes and molecular dynamics in order to provide a generic method for estimating thermodynamic and kinetic parameters, applicable conceptually to any nucleic acid material and experimental setting of interest. Our methodology offers an atomistic view of nucleic acid base pairing and faithfully reproduces most experimental data. It thus provides a powerful black-box approach for extensibly calculating the kinetic and thermodynamic parameters that secondary structure models require.
" }, { "name": "Freas, Dylan Joshua", "degree": "PhD", "year": "2022", "title": "The Synthesis of Diverse Families of Organic Compounds via Nickel-Catalyzed Nucleophilic Substitution Reactions", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182021-220809412", "creators": [ { "name": { "family": "Freas", "given": "Dylan Joshua" }, "id": "Freas-Dylan-Joshua", "orcid": "0000-0003-0611-7907", "display_name": "Freas, Dylan Joshua" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e76h-vh27", "abstract": "Transition metal-catalyzed cross-coupling has provided an exceptionally powerful approach to carbon\u2013carbon bond formation, allowing chemists to solve a number of important problems in organic synthesis. However, by the early 2000s, its application to the formation of alkyl\u2013alkyl bonds had been limited by the slow oxidative addition of palladium catalysts toward alkyl halides and the tendency of transition-metal-alkyls to undergo \u03b2-hydride elimination. Since then, complexes based on nickel, an earth-abundant metal, have emerged as efficient catalysts for the nucleophilic substitution of alkyl electrophiles. The propensity for nickel to access a range of oxidation states allows it to react via one-electron pathways to generate radical intermediates, opening the door to couplings of sterically-hindered electrophiles and offering a ready mechanism for enantioconvergence.
\r\n\r\nOur group has applied nickel catalysts to substitution reactions of activated and unactivated 2o and 3o alkyl electrophiles by carbon\u2013 as well as by heteroatom-based nucleophiles, including a number of enantioconvergent processes. However, given the enormous range of conceivable coupling partners, many interesting challenges have yet to be addressed. The application of nickel-catalyzed substitution reactions to the synthesis of diverse families of compounds, particularly those with frequent uses in organic synthesis and pharmaceutical science, is described in this thesis. While reaction development is the primary focus of this work, a variety of synthetic applications and mechanistic investigations are also detailed within.
\r\n\r\nChapter 2 describes two methods for the catalytic enantioconvergent synthesis of amines, which involve the coupling of an alkylzinc reagent with a racemic electrophile (specifically, an \u03b1-phthalimido alkyl chloride and an N-hydroxyphthalimide ester of a protected \u03b1-amino acid). A one-pot variant of this transformation is possible, enabling the efficient enantioselective synthesis of a range of interesting target molecules. Several mechanistic insights are also detailed.
\r\n\r\nChapter 3 outlines the nickel-catalyzed alkylation of racemic \u03b1-haloglycine derivatives, a class of electrophile previously unemployed in metal-catalyzed asymmetric cross-coupling reactions, with alkylzinc reagents to generate protected unnatural \u03b1-amino acids. This method is applied to the generation of several enantioenriched unnatural \u03b1-amino acids that have previously been shown to serve as useful intermediates in the synthesis of bioactive compounds.
\r\n\r\nChapter 4 details the development of a nickel-catalyzed cross-coupling for the asymmetric synthesis of protected thiols. The synthesis of an N-hydroxyphthalimide ester containing a geminal thioester (a previously unreported class of molecule with no applications to cross-coupling) is described, along with its reactivity toward alkylzinc reagents and other classes of organometallic nucleophiles.
\r\n\r\nChapter 5 examines the ability of nickel to catalyze the nucleophilic fluorination of unactivated alkyl halides, a transformation whose application to the synthesis of alkyl fluorides has been impeded by the low nucleophilicity and high basicity of fluoride. The reactivities of unactivated 1o, 2o, and 3o alkyl bromides, as well as several preliminary mechanistic investigations, are presented.
" }, { "name": "Fry, Michelle Yen", "degree": "PhD", "year": "2022", "title": "Mechanistic Studies of Tail-Anchored Membrane Protein Targeting to the ER", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232021-203647268", "creators": [ { "name": { "family": "Fry", "given": "Michelle Yen" }, "id": "Fry-Michelle-Yen", "orcid": "0000-0002-3209-5492", "display_name": "Fry, Michelle Yen" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/b3yj-c572", "abstract": "The successful biogenesis \u2013 synthesis, delivery, and insertion into designated membranes \u2013 of membrane proteins is a crucial cellular process. One particular class of membrane proteins, tail-anchored (TA) proteins have a single transmembrane domain (TMD) that this located at their C-termini and are targeted to membranes post-translationally. Multiple pathways have been identified to target TA proteins to the ER membranes, but designated pathways for targeting TA proteins to the mitochondria remain elusive. The most well understood ER TA protein pathway is the Guided Entry of Tail-anchored proteins (GET) pathway, consisting of six (fungal) or seven (metazoans) proteins, SGTA, Get1-5, and Bag6 (metazoans only), has nearly been studied exclusively in Opisthokants (fungi and metazoans). Here we employed a combination of x-ray crystallography, cryo-electron microscopy, computational modeling, cellular biology, fluorescent imaging, and bioinformatics in order to understand the underlying factors that regulate the targeting of these TA proteins to their correct membranes. Our work reveals that ER-bound TA proteins tend to have a hydrophobic face whereas mitochondria-bound TA proteins contain a charge following their TMD. This finding corroborates our observation that the first component of the GET pathway to interact with TA proteins, SGTA, falls in a category of other hydrophobic segment binding domains, dubbed STI1-domains. Structures presented here demonstrate that the overall structure of Get3 is conserved in organisms as distant as Excavats and Opistokonts, and slight conformational changes in the ATPase allows the described chaperone cascade of the GET pathway to progress. Together these results refine the model for TA protein targeting to the ER membrane.
" }, { "name": "Fu, Harold Jin", "degree": "PhD", "year": "2022", "title": "Open-Circuit Stability and Integration of Silicon Electrodes for Solar Fuels Devices", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:10092021-015926914", "creators": [ { "name": { "family": "Fu", "given": "Harold Jin" }, "id": "Fu-Harold-Jin", "orcid": "0000-0001-9738-209X", "display_name": "Fu, Harold Jin" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pgx5-fj77", "abstract": "Two significant challenges that impede the realization of inexpensive, solar-driven water electrolysis involve the corrosion and integration of component materials. For instance, Si is a prominent light absorbing material that readily corrodes in alkaline electrolyte unless subjected to an oxidative potential. Although a protective coating can be applied to mitigate corrosion, the underlying semiconductor remains exposed to electrolyte at pinholes on the protective coating. Illumination slows the dissolution of Si photoanodes further by 2-3 orders of magnitude via oxidation to SiOx. However, Si is still susceptible to corrosion under nighttime conditions and device stability must be maintained regardless of diurnal patterns of sunlight. This thesis explores two approaches to drive Si passivation in the dark at open circuit. First, a protective electrolyte can be introduced to solution that acts as an oxidizing agent to Si. Secondly, a catalytic thin film like NiOx on Si can drive the electrode potential positive by catalyzing O2 in electrolyte. Applying either passivation strategy yielded extended stability of Si photoanodes subjected to simulated day/night cycling. In addition to corrosion, device performance is critically dependent on the integration of component materials. Efficient water splitting requires that at least two semiconductors be connected in series to drive the reaction, while lateral resistance losses in electrolyte preclude large (> cm2) planar photoelectrode areas. Si can be vertically arranged as high aspect ratio microwires that can be embedded in an ion exchange membrane. This assembly can be laminated to a tandem partner arranged in a similar configuration using an electrically conductive interlayer. This thesis additionally investigates the bulk and interfacial properties of Nafion-PEDOT:PSS composite films as a candidate material for this interlayer. After solvent treatment, the composite film exhibited percolation of electrically conductive PEDOT domains even at dilute PEDOT concentrations (~ 0.2 wt%). Despite the presence of an insulating Nafion-rich layer on the surface, the composite forms a low resistance contact to CH3-terminated p-Si, thereby making the composite a viable interlayer for use in a fully integrated, tandem water splitting device.
" }, { "name": "Fulton, Tyler James", "degree": "PhD", "year": "2022", "title": "Asymmetric Total Synthesis of (\u2013)-Myrifabral A and B, Havellockate, and New Strategies for Acyclic Stereocontrol", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062022-012944875", "creators": [ { "name": { "family": "Fulton", "given": "Tyler James" }, "id": "Fulton-Tyler-James", "orcid": "0000-0002-9343-2456", "display_name": "Fulton, Tyler James" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qb9s-xj38", "abstract": "Research in the Stoltz group aims, generally, to develop novel technologies for the preparation of stereochemically rich molecules and, further, to apply these technologies in the context of complex natural product total synthesis. Chapter 1 of this thesis describes the strategic utilization of a Pd-catalyzed asymmetric allylic allylation and N-acyl iminium ion cyclization to accomplish short, enantioselective total syntheses of (\u2013)-myrifabral A and (\u2013)-myrifabral B. Chapter 2 describes the development of a Pd-catalyzed asymmetric allylic alkylation to generate acyclic \u03b1-quaternary carboxylic acid derivatives from geometrically defined fully substituted N-acyl indole-derived allyl enol carbonates. While ester-derived enol carbonates could be prepared with a high degree of enolate geometry control, they were ineffective in the asymmetric allylic alkylation reaction. Thus, N-acyl indole substrates served as excellent carboxylic ester equivalents. Chapter 3 discusses an unusual Pd-catalyzed decarboxylative \u03b1,\u03b2-dehydrogenation reaction of N-acyl indole-derived enol carbonates enabled by a novel, highly electron-deficient phosphinooxazoline ligand. Research presented in Chapter 4 delineates a globally diastereoconvergent approach to the Ireland\u2013Claisen rearrangement for the synthesis of \u03b1-tetrasubstituted amino acids bearing vicinal tertiary stereogenic centers. Computational investigation of the diastereoconvergence in Ireland\u2013Claisen rearrangement revealed key intramolecular interactions which enable the reaction to proceed in exceptional diastereoselectivity without the need for a selective enolization protocol. Additionally, a diastereodivergent approach for the Ireland\u2013Claisen rearrangement in acyclic systems to generate vicinal quaternary/tertiary and quaternary/quaternary stereogenic centers in good to high diastereoselectivity is discussed. Enolate geometry control and substrate design are critical for achieving high diastereoselectivity in these transformations.
" }, { "name": "Galstyan, Vahe", "degree": "PhD", "year": "2022", "title": "Studies in Physical Biology: Exploring Allosteric Regulation, Enzymatic Error Correction, and Cytoskeletal Self-Organization Using Theory and Modeling", "advisor": "Phillips, Robert B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08242021-212959886", "creators": [ { "name": { "family": "Galstyan", "given": "Vahe" }, "id": "Galstyan-Vahe", "orcid": "0000-0001-7073-9175", "display_name": "Galstyan, Vahe" } ], "advisors": [ { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "advisor", "display_name": "Phillips, Robert B." } ], "committee": [ { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "chair", "display_name": "Thomson, Matthew" }, { "name": { "family": "Van Valen", "given": "David A." }, "id": "Van-Valen-D", "orcid": "0000-0001-7534-7621", "role": "member", "display_name": "Van Valen, David A." }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "orcid": "0000-0002-5899-7523", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "biochem" ], "doi": "10.7907/1fzr-1240", "abstract": "Physical biology offers powerful tools for quantitatively dissecting the various aspects of cellular life that one cannot attribute to inanimate matter. Signature examples of living matter include adaptation, self-organization, and division. In this thesis, we explore different interconnected facets of these processes using statistical mechanics, nonequilibrium thermodynamics, and biophysical modeling.
\r\n\r\nOne of the key mechanisms underlying physiological and evolutionary adaptation is allosteric regulation. It allows cells to dynamically respond to changes in the state of the environment often expressed through altered levels of different environmental cues. The first thread of our work is dedicated to exploring the combinatorial diversity of responses available to allosteric proteins that are subject to multi-ligand regulation. We demonstrate that proteins characterized through the Monod-Wyman-Changeux model of allostery and operating at thermodynamic equilibrium are capable of eliciting a wide range of response behaviors which include the kinds known from the field of digital circuits (e.g., NAND logic response), as well as more sophisticated computations such as ratiometric sensing.
\r\n\r\nDespite the fact that biomolecules at thermodynamic equilibrium are able to orchestrate a variety of fascinating behaviors, the cell is ultimately 'alive' because it constantly metabolizes nutrients and generates energy to drive functions that cannot be sustained in the absence of energy consumption. One prominent example of such a function is nonequilibrium error correction present in high-fidelity processes such as protein synthesis, DNA replication, or pathogen recognition. We begin the second thread of our work by providing a conceptual understanding of the prevailing mechanism used in explaining this high-fidelity behavior, namely that of kinetic proofreading. Specifically, we develop an allostery-based mechanochemical model of a kinetic proofreader where chemical driving is replaced with a mechanical engine with tunable knobs which allow modulating the amount of dissipation in a transparent way. We demonstrate how varying levels of error correction can be attained at different regimes of dissipation and offer intuitive interpretations for the conditions required for efficient biological proofreading.
\r\n\r\nWe then extend the notion of error correction to equilibrium enzymes not endowed with structural features typically required for proofreading. We show that, under physiological conditions, purely diffusing enzymes can take advantage of the existing nonequilibrium organization of their substrates in space and enhance the fidelity of catalysis. Our proposed mechanism called spatial proofreading offers a novel perspective on spatial structures and compartmentalization in cells as a route to specificity.
\r\n\r\nIn the last thread of the thesis, we make a transition from molecular-scale studies to the mesoscopic scale, and explore the principles of self-organization in nonequilibrium structures formed in reconstituted microtubule-motor mixtures. In particular, we develop a theoretical framework that predicts the spatial distribution of kinesin motors in radially symmetric microtubule asters formed under various conditions using optogenetic control. The model manages to accurately recapitulate the experimentally measured motor profiles through effective parameters that are specific for each kind of kinesin motor used. Our theoretical work of rigorously assessing the motor distribution therefore offers an avenue for understanding the link between the microscopic motor properties (e.g., processivity or binding affinity) and the large-scale structures they create.
\r\n\r\nIn all, the thesis encompasses a series of case studies with shared themes of allostery and nonequilibrium, highlighting the capacity of living matter to perform remarkable tasks inaccessible to nonliving materials.
" }, { "name": "Glisman, Alec Gregory", "degree": "Masters", "year": "2022", "title": "Swimming in Potential Flow", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12052021-002539806", "creators": [ { "name": { "family": "Glisman", "given": "Alec Gregory" }, "id": "Glisman-Alec-Gregory", "orcid": "0000-0001-9677-1958", "display_name": "Glisman, Alec Gregory" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Colonius", "given": "Tim" }, "id": "Colonius-T", "orcid": "0000-0003-0326-3909", "role": "member", "display_name": "Colonius, Tim" }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6xkb-rs66", "abstract": "Active bodies undergo self-propulsive motion in a fluid medium and span a broad range of length and time scales. This report focuses specifically on the motion at high Reynolds number, where inertial forces dominate the fluid dynamics. Many active systems spontaneously self-organize into visually striking structures: fish schooling, birds flocking, and bacterial colonies growing. Current models of emergent behavior in the inertial regime are mainly phenomenological and do not account for the fluid-mediated interactions between bodies. We seek to advance physical models of swimmers in high inertia environments. To this end, we explicitly model the hydrodynamics to discern what role the fluid medium plays in active group dynamics and whether it can reproduce the observed emergent phenomenon without the imposition of phenomenologically based interaction rules.
\r\n\r\nA minimal swimmer model consisting of three linked spheres is constructed, and we find self-propulsion without external forces or momentum transfer via vortex shedding. The inertial swimmer is also compared to an identical swimmer in the Stokes regime---where fluid inertia is neglected. The Stokes hydrodynamics are longer-ranged at leading order, and we demonstrate that the stronger hydrodynamic interactions lead to a greater center of mass translation after a period of articulation.
" }, { "name": "Goldberg, Nathaniel Wood", "degree": "PhD", "year": "2022", "title": "Non-Native Chemistry of Metalloenzymes", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:02232022-224045858", "creators": [ { "name": { "family": "Goldberg", "given": "Nathaniel Wood" }, "id": "Goldberg-Nathaniel-Wood", "orcid": "0000-0003-0201-8856", "display_name": "Goldberg, Nathaniel Wood" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6sec-zx89", "abstract": "Metalloenzymes are important catalysts in biochemistry, but the scope of their naturally occurring activities is dwarfed by the range of chemistry achieved by synthetic transition-metal catalysts. To date, efforts to expand the catalytic repertoire of metalloproteins beyond their native activities have focused almost exclusively on heme-binding proteins, which have been engineered to catalyze a wide variety of carbene- and nitrene-transfer chemistry. Heme-binding proteins represent only a limited subset of the vast diversity of metalloproteins that exists in Nature, and the non-native chemistry of the rest of the metalloproteome remains largely unexplored. This thesis details the discovery and engineering of non-native catalytic abilities of non-heme metalloproteins. Chapter 1 introduces metalloproteins as biocatalysts in synthetic chemistry, and various approaches to expand their catalytic activities. Chapter 2 describes efforts towards enzyme-catalyzed hydrosilylation, including the curation and development of a diverse library of non-heme metalloproteins. In Chapter 3, a non-heme iron-dependent dioxygenase (Pseudomonas savastanoi ethylene-forming enzyme, PsEFE) is found to catalyze nitrene-transfer chemistry, and is engineered by directed evolution to improve this non-native activity. The nitrene transfer activity and selectivity of PsEFE can be modulated by small-molecule metal-coordinating ligands. Chapter 4 describes the discovery and development of a PsEFE-catalyzed olefin aminoarylation reaction, a previously unknown reaction of sulfonyl azides and olefins. This reaction is unprecedented in the existing chemical literature, and displays a number of unusual mechanistic features. Together, the work described here represents the expansion of non-native chemistry to a new class of metalloenzymes, enabling the discovery of previously unknown catalytic activities.
" }, { "name": "Grant, Stephen Nicholas", "degree": "PhD", "year": "2022", "title": "Investigation of Some Small Molecule-Protein and Protein-Protein Interactions in Nicotine Addiction, Opioid Use Disorder, and COVID-19", "advisor": "Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07142021-175425546", "creators": [ { "name": { "family": "Grant", "given": "Stephen Nicholas" }, "id": "Grant-Stephen-Nicholas", "orcid": "0000-0003-0923-8886", "display_name": "Grant, Stephen Nicholas" } ], "advisors": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pdtj-8238", "abstract": "Nicotine addiction, opioid use disorder, and COVID-19 have made lasting impacts on every aspect of society. These are complicated conditions, and studies in these fields will likely continue for decades, if not centuries. Here, we make contributions to each of these issues using electrophysiology and microscopy. The first chapter goes into the motivation behind this thesis and the major experiments I used in my graduate career. In the second chapter, we introduce a new amino acid into the mouse muscle nicotinic acetylcholine receptor in an attempt to understand the dynamics of receptor activation. In the third chapter, we continue the Lester lab\u2019s work on the neuroscientific effects of menthol and how it plays a role in nicotine addiction. We found the binding site for menthol on the \u03b14\u03b22 nicotinic acetylcholine receptor, which continues our hypothesis that the neuroscientific effects of menthol are detrimental to cigarette smokers. Fortunately, partly because of our studies, mentholated nicotine products are being phased out of the United States. The fourth and fifth chapters investigate \u03bc-opioid receptor trafficking, both the trafficking from the endoplasmic reticulum and endocytosis from the plasma membrane. Both of these events play a role in inducing opioid use disorder and increasing the danger of using opioids. We hope that these studies will help other researchers understand opioid use disorder and fight the opioid epidemic. Finally, we studied the effects of SARS-COV-2 proteins on epithelial sodium channels. These channels are important for regulating lung fluid levels where their improper function may cause pulmonary edema. Pulmonary edema has been observed in COVID-19 patients. Altogether, we believe that we have made meaningful impacts on these important health concerns in this thesis. We look forward to how the scientific communities continue to build on our results.
" }, { "name": "Gu, Alan Yalun", "degree": "PhD", "year": "2022", "title": "Aqueous Aerosols in Atmospheric Chemistry and Airborne Diseases", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142022-025410011", "creators": [ { "name": { "family": "Gu", "given": "Alan Yalun" }, "id": "Gu-Alan-Yalun", "orcid": "0000-0001-8095-3634", "display_name": "Gu, Alan Yalun" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "chair", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/4spy-az88", "abstract": "Aqueous atmospheric aerosols are small droplets (typically smaller than 5 \u03bcm) suspended in the air that are comprised of water and water-soluble components. These aerosols provide an air-water interfacial reaction environment on their surfaces, and act as a medium for airborne disease transmission. In this thesis, Chapters II and V explore atmospherically relevant reactions on the aqueous aerosol surface using an online mass spectrometry, while Chapter III investigates the SARS-CoV-2 airborne transmission considering suspended virus-laden aerosols as the transmission media. Spinning off this SARS-CoV-2 work, Chapter IV describes a newly developed quantitative RNA amplification test kit for COVID-19, with an emphasis on the amplification result photo recognition component." }, { "name": "Hafeman, Nicholas Joseph", "degree": "PhD", "year": "2022", "title": "Synthesis and Applications of Terpenoid Natural Products: Total Synthesis of Scabrolide A and Havellockate, and Synthesis of Pinene Oxidation Products for Atmospheric Investigations", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032022-194915019", "creators": [ { "name": { "family": "Hafeman", "given": "Nicholas Joseph" }, "id": "Hafeman-Nicholas-Joseph", "orcid": "0000-0001-7525-7597", "display_name": "Hafeman, Nicholas Joseph" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Nelson", "given": "Hosea M." }, "id": "Nelson-H-M", "orcid": "0000-0002-4666-2793", "role": "member", "display_name": "Nelson, Hosea M." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3st9-6a73", "abstract": "The total synthesis of complex natural products remains one of the enduring challenges in organic chemistry. Whether motivated by the biological activity of the target, or its structural complexity, total synthesis continues to serve as a proving ground for synthetic methodology as well as strategic planning. Herein is described the first total synthesis of the polycyclic furanobutenolide-derived (nor)cembranoid diterpenoids scabrolide A and havellockate. Our total synthesis of scabrolide A involves an intramolecular [4+2] cycloaddition, which forges a fused [5\u20135\u20136] tricycle possessing two of the three carbocycles that characterize the natural product. Next, a photocycloaddition/fragementation sequence is employed to forge the final seven-membered ring and complete the total synthesis. Using a similar strategy, we could forge the [5\u20135\u20136] tricyclic core of the related diterpenoid havellockate with an intramolecular [4+2] cycloaddition. This is followed by a challenging enone allylation which installs the final carbon atoms of the target. Finally, elaboration of the allyl group, followed by a Cu/TEMPO-catalyzed oxidative lactonization furnishes havellockate. The final chapter of this thesis describes the synthesis and characterization of several pinene oxidation products and their dimers, which have been observed in pinene-derived secondary organic aerosol samples, as standards for atmospheric studies. This research uses the power of chemical synthesis to confirm (and in some cases reassign) the structures of naturally occurring, yet difficult to characterize chemical species found in the atmosphere.
" }, { "name": "Hamann, Kathryn Rose", "degree": "PhD", "year": "2022", "title": "Exploration of Materials and Mesostructures Accessible via Inorganic Phototropic Growth", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05212022-202251527", "creators": [ { "name": { "family": "Hamann", "given": "Kathryn Rose" }, "id": "Hamann-Kathryn-Rose", "orcid": "0000-0003-1163-7173", "display_name": "Hamann, Kathryn Rose" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "member", "display_name": "Greer, Julia R." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/z725-v841", "abstract": "Biological systems have evolved complex methods to interact with and adapt to a given environment to optimize fitness, and replication of these natural mechanisms in artificial systems has been a long-standing area of research interest with significant potential utility. Phototropic growth is a natural phenomenon wherein an organism spatially orients biomass addition to optimize light collection. An artificial analog, inorganic phototropic growth, has been demonstrated and relies on a similar process: semiconductor mass is selectively added near regions of high light absorption, thus optimizing light collection and instructing further localized material addition. Inorganic phototropic growth effected via light-mediated electrodeposition has been used to generate anisotropic Se-Te mesostructures with optically-defined morphologies by capitalizing on inherent asymmetries in light absorption at structured, semiconducting interfaces to direct anisotropic growth. This thesis broadens the previous understanding of inorganic phototropic growth via a series of investigations that expand both the material library and complex morphologies accessible and includes detailed analyses of associated structural evolutions and the underlying optical phenomena. First, inorganic phototropic growth of highly ordered and periodic PbSe and CdSe mesostructures with optically-defined morphologies is demonstrated. Second, deposition using temporally varying illumination inputs to generate Se-Te mesostructures with tunable morphological complexity in both the in-plane and out-of-plane directions is examined. Third, the use of single, static, short wavelength (green to ultraviolet) inputs to simultaneously define two orthogonal sets of periodic features in Se-Te deposits is explored. A suite of optically-based simulations is used throughout to model the growth processes and elucidate the fundamental light-matter interactions which defined the empirically observed morphologies.
" }, { "name": "Holman, Elizabeth Anne", "degree": "PhD", "year": "2022", "title": "Developing Technologies for Real-Time Whole-Organism Imaging via FTIR Spectromicroscopy", "advisor": "Sternberg, Paul W.; Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312021-211824138", "creators": [ { "name": { "family": "Holman", "given": "Elizabeth Anne" }, "id": "Holman-Elizabeth-Anne", "orcid": "0000-0002-5158-4689", "display_name": "Holman, Elizabeth Anne" } ], "advisors": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "advisor", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "co-advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/es4r-kq84", "abstract": "FTIR spectromicroscopy heavily resides in the domain of cell-based and tissue-based studies when focusing on its direct application to biological systems. The goal of the reported graduate research is to extend FTIR spectromicroscopy to multicellular whole-organism imaging, ideally for non-invasive, non-destructive, and label-free spatiochemical imaging of biological model Caenorhabditis elegans (C. elegans). With modern optics, detector, and light source technologies implemented at synchrotron facilities, this thesis focuses on exploring the feasibility of multicellular whole-organism imaging while identifying challenges and presenting working solutions for them.
" }, { "name": "Holman, Karli Rose", "degree": "PhD", "year": "2022", "title": "Palladium-Catalyzed Cascade Cyclizations in Natural Product Synthesis: Synthetic Studies of Noraugustamine and Falcatin A", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292022-203100439", "creators": [ { "name": { "family": "Holman", "given": "Karli Rose" }, "id": "Holman-Karli-Rose", "orcid": "0000-0001-6424-9479", "display_name": "Holman, Karli Rose" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9r6z-tw08", "abstract": "Palladium-catalyzed cascade cyclizations present a powerful strategy for the rapid assembly of polycyclic skeletal frameworks, enabling the efficient synthesis of bioactive and structurally complex natural products. Herein, we review the field of palladium-catalyzed cascade cyclizations in natural product synthesis and describe our application of these transformations toward the total syntheses of noraugustamine and falcatin A.
\r\n\r\nOur approach to the Amaryllidaceae alkaloid noraugustamine was driven by the simultaneous disconnection of a C\u2013C and a C\u2013N bond, with the aim of forming both bonds and two of the target\u2019s six rings in a single step. A radical cascade cyclization delivered noraugustamine but displayed poor regioselectivity for 6-exo-trig versus 7-endo-trig cyclization. Improved regioselectivity was achieved using a palladium-catalyzed Heck cyclization, leading to the development of a novel oxidative Heck/aza-Wacker cascade forming both of the desired bonds with good yield and selectivity. This transformation and the general lessons taken from this work should find broad utility in the design of cascade cyclizations toward alkaloids of similar complexity.
\r\n\r\nWe also investigated a palladium-catalyzed carboetherification cascade toward the synthesis of the central five- and seven-membered rings of the myrsinane diterpene falcatin A. In this case, competitive C\u2013O coupling, olefin insertion, and cyclopropanation hindered our efforts to develop the proposed transformation in a simplified model system. A stereoselective bromoetherification and a nickel-catalyzed Nozaki\u2013Hiyama\u2013Kishi reaction were ultimately successful, forming the targeted rings. Efforts to synthesize a fully elaborated cyclization substrate, translate the key steps from the model system, and complete the synthesis of falcatin A are ongoing.
" }, { "name": "Jacobson, Daniel Rance", "degree": "PhD", "year": "2022", "title": "Computational Studies of Dendritic Deposition and Trajectory Phase Coexistence", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272022-201237457", "creators": [ { "name": { "family": "Jacobson", "given": "Daniel Rance" }, "id": "Jacobson-Daniel-Rance", "orcid": "0000-0001-7990-4093", "display_name": "Jacobson, Daniel Rance" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/dje7-ey77", "abstract": "Many out-of-equilibrium systems display collective transitions in the behavior of particles akin to phase transitions. The field of nonequilibrium statistical mechanics seeks to develop new theories and methods to characterize these phenomena. In this thesis, we advance this aim by presenting computational studies of two different kinds of nonequilibrium transitions: the compact-to-dendritic (CTD) transition in the deposition of Brownian particles and trajectory phase coexistence (TPC) in stochastic dynamical systems.
\r\n\r\nThe CTD transition occurs when Brownian particles (like ions, colloids, or misfolded proteins) deposit from all sides onto a reactive cluster. While the cluster initially maintains a compact morphology, upon reaching a critical radius, it spontaneously develops dendritic branches. Although the size of the critical radius depends on the deposition conditions, this relationship is not well understood at a mechanistic level. Here, we show that contrary to previous evidence, the critical radius in Brownian dynamics simulations follows the behavior predicted by a continuum analysis. That is, dendrites emerge when the cluster circumference exceeds the length that particles can diffuse in the characteristic reaction timescale. Consequently, our results provide microscopic validation for continuum methods that are widely applied to study dendrite formation in electrodeposition and lithium metal batteries.
\r\n\r\nTrajectory phase coexistence (TPC) arises when qualitatively different trajectory behaviors interconvert in a stochastic dynamical system. This type of coexistence plays a central role in theories of glassy dynamics. In this work, we focus on two different research areas related to TPC. First, we introduce an importance sampling method, Variational Ansatz for Rare Dynamics (VARD), for characterizing a system's rate function. VARD is technically and conceptually straightforward yet can still sample the large deviations of many-body models found in the literature. We then examine the meaning of kinks in the scaled cumulant generating function (SCGF). Although these singularities are often taken to be proof that TPC occurs, a more precise understanding of the connection between kinks and coexistence remains lacking. By characterizing the dynamics of two kinds of random walkers, we show that kinks actually result from diverging timescales in the dynamics and do not always indicate the presence of TPC.
" }, { "name": "Jette, Claudia Angela", "degree": "PhD", "year": "2022", "title": "Targeting Fusion Proteins of HIV-1 and SARS-CoV-2", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechThesis:04282022-192922044", "creators": [ { "name": { "family": "Jette", "given": "Claudia Angela" }, "id": "Jette-Claudia-Angela", "orcid": "0000-0002-5085-8027", "display_name": "Jette, Claudia Angela" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "orcid": "0000-0001-8723-8190", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "biochem" ], "doi": "10.7907/pxa2-dy41", "abstract": "Viruses are disease-causing pathogenic agents that require host cells to replicate. Fusion of host and viral membranes is critical for the lifecycle of enveloped viruses. Studying viral fusion proteins can allow us to better understand how they shape immune responses and inform the design of therapeutics such as drugs, monoclonal antibodies, and vaccines. This thesis discusses two approaches to targeting two fusion proteins: Env from HIV-1 and S from SARS-CoV-2. The first chapter of this thesis is an introduction to viruses with a specific focus on HIV-1 CD4 mimetic drugs and antibodies against SARS-CoV-2. It discusses the architecture of these viruses and fusion proteins and how small molecules, peptides, and antibodies can target these proteins successfully to treat and prevent disease. In addition, a brief overview is included of the techniques involved in structural biology and how it has informed the study of viruses. For the interested reader, chapter 2 contains a review article that serves as a more in-depth introduction for both viruses as well as how the use of structural biology has informed the study of viral surface proteins and neutralizing antibody responses to them. The subsequent chapters provide a body of work divided into two parts. The first part in chapter 3 involves a study on conformational changes induced in the HIV-1 Env protein by CD4-mimemtic drugs using single particle cryo-EM. The second part encompassing chapters 4 and 5 includes two studies on antibodies isolated from convalescent COVID-19 donors. The former involves classification of antibody responses to the SARS-CoV-2 S receptor-binding domain (RBD). The latter discusses an anti-RBD antibody class that binds to a conserved epitope on the RBD and shows cross-binding and cross-neutralization to other coronaviruses in the sarbecovirus subgenus.
" }, { "name": "Kenseth, Christopher M.", "degree": "PhD", "year": "2022", "title": "Formation, Abundance, and Evolution of Molecular Products in \u03b1-Pinene and \u03b2-Pinene Secondary Organic Aerosol", "advisor": "Seinfeld, John H.; Stoltz, Brian M.; Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03242022-211905773", "creators": [ { "name": { "family": "Kenseth", "given": "Christopher M." }, "id": "Kenseth-Christopher-M", "orcid": "0000-0003-3188-2336", "display_name": "Kenseth, Christopher M." } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "co-advisor", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "co-advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "chair", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bj1b-1441", "abstract": "The atmospheric oxidation of \u03b1-pinene and \u03b2-pinene (C10H16), emitted in appreciable quantities from forested regions (~85 Tg y\u20131), contributes significantly to the global burden of secondary organic aerosol (SOA), a substantial component (15\u201380% by mass) of atmospheric fine particulate matter (PM2.5), which exerts large but uncertain effects on climate as well as adverse impacts on air quality and human health. Deciphering the molecular composition, and in turn formation and aging mechanisms, of \u03b1-pinene and \u03b2-pinene SOA is essential to reducing uncertainty in assessment of their environmental and health impacts. However, molecular characterization of \u03b1-pinene and \u03b2-pinene SOA is significantly hindered by their chemical complexity. In this work, we constrain the formation, abundance, and evolution of molecular products in SOA derived from ozonolysis and photooxidation of \u03b1-pinene and \u03b2-pinene using a combination of laboratory experiments, liquid chromatography/electrospray ionization mass spectrometry (LC/ESI-MS), and organic synthesis. Through detailed MS/MS analysis, coupled with 13C isotopic labeling and OH scavenging, we identify a suite of dimeric compounds (C15\u201319H24\u201332O5\u201311) formed from synergistic O3 + OH oxidation of \u03b2-pinene (i.e., accretion of O3- and OH-derived products/intermediates). Informed by these structural analyses, together with 18O isotopic labeling and H/D exchange, we synthesize the first authentic standards of several major dimer esters identified in SOA from ozonolysis of \u03b1-pinene and \u03b2-pinene and elucidate their formation mechanism from targeted environmental chamber experiments. Additionally, we synthesize a series of pinene-derived carboxylic acid and dimer ester homologues and find that the ESI efficiencies of the dimer esters are 19\u201336 times higher than that of commercial cis-pinonic acid, a common quantification surrogate. Finally, we investigate the aqueous (photo)chemistry (kinetics, products, and mechanisms) of the carboxylic acid and dimer ester homologues at cloudwater-relevant concentrations as a function of pH.
" }, { "name": "Kim, Jeongmin", "degree": "PhD", "year": "2022", "title": "Molecular Simulations of Charge Transport for Energy Storage and Conversion Applications", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08202021-200738765", "creators": [ { "name": { "family": "Kim", "given": "Jeongmin" }, "id": "Jeongmin-Kim", "orcid": "0000-0002-7405-8200", "display_name": "Kim, Jeongmin" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Jones", "given": "Simon C." }, "id": "Jones-Simon-C", "orcid": "0000-0002-1952-3720", "role": "member", "display_name": "Jones, Simon C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5haz-ch54", "abstract": "Molecular simulation plays a variety of roles in accelerating the development of energy materials, from providing a fundamental understanding of molecular processes to predicting their performance spanning a wide range of chemical space. In this thesis, we present molecular simulation studies of charge transport both in bulk energy materials and at their interfaces to provide molecular principles for advanced rechargeable batteries in part I and electricity generation using a metal nanofilm from water motion in part II.
\r\n\r\nIn part I, we discuss ion transport and interfacial electron transfer in polymeric battery materials, both of which are closely associated with battery operation. As a bulk electrolyte and a solid electrolyte interphase (SEI), polymeric materials often benefit rechargeable batteries, allowing for enhanced safety and increased energy density. Firstly, we propose a unique mechanism of lithium-ion transport in polymer-based electrolytes, including conjugated polymers with an imidazolium sidechain and polyborane-based single-ion conductors, which utilizes the formation of a percolating ion network to facilitate lithium ion transport. Secondly, we discuss interfacial ion solvation structure and dynamics that are closely related to interfacial electron-transfer kinetics. Simulations provide molecular insights into how a functional SEI passivates a metal electrode, thereby accelerating materials discovery such as an artificial SEI of self-assembled monolayers.
\r\n\r\nIn part II, we present molecular principles of energy conversion from a flow of ionic solution to electricity using metal nanolayers. The energy conversion emerges at a water-solid interface and requires a boundary of an electrical double layer at which ion adsorption and desorption occur along with the flow. We discuss charge induction mechanisms related to a heterolayered structure of a metal nanolayer and investigate factors that affect energy conversion efficiency in two different modes of operation, namely a flow cell and a wavetank.
" }, { "name": "Kim, Seungkyeum", "degree": "PhD", "year": "2022", "title": "Development of Electrochemical Processes for More Practical and Effective Onsite Wastewater Treatment", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252022-162959411", "creators": [ { "name": { "family": "Kim", "given": "Seungkyeum" }, "id": "Kim-Seungkyeum", "orcid": "0000-0002-0948-6452", "display_name": "Kim, Seungkyeum" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ab1v-he77", "abstract": "In spite of the lack of safely managed sanitation and water supply systems, developing countries with rapid urbanization cannot afford to implement advanced treatment technologies that are highly centralized, calling for the development of practical onsite wastewater treatment. As effective yet practical solutions to the water crisis, I have developed high-performance earth-abundant electrocatalysts and an uncoupled electro-peroxone (E-peroxone) prototype reactor that can be applied in and as decentralized wastewater treatment systems. A series of conductive TiO\u2082 nanotube array electrodes are known to be effective for chlorine evolution reaction (CER) for wastewater treatment and oxygen evolution reaction (OER) for water splitting. In order to further enhance their electrocatalytic activities, an ultrathin layer of Al\u2082O\u2083 was deposited onto TiO\u2082 nanotube arrays via atomic layer deposition (ALD). Due to the facilitated formation of Ti\u00b3\u207a and oxygen vacancies by Al\u2082O\u2083 ALD, black TiO\u2082 nanotube arrays with 8 ALD cycles achieved up to 30% enhancement in CER and OER overpotentials in comparison to those without Al\u2082O\u2083 coating. Moreover, the ultrathin Al\u2082O\u2083 overlayer (~2 nm) reduced the charge transfer resistance and increased the electrochemical chemical surface area (ECSA) 3-fold for both reactions. Black TiO\u2082 nanotube arrays with 8 cycles were applied for toilet wastewater treatment and outperformed a dimensionally stable anode (DSA) in terms of chemical oxygen demand (COD) and ammonia reductions. The simplicity of the synthetic procedures and the use of inexpensive metal oxides suggest that Al\u2082O\u2083-deposited TiO\u2082 nanotube arrays can provide a promising approach to wastewater treatment and water splitting as practical alternatives for costly DSAs.
\r\n\r\nThe uncoupled E-peroxone reactor system integrates ozonation with in situ hydrogen peroxide (H\u2082O\u2082) production to generate hydroxyl radicals for wastewater treatment. The E-peroxone process variables such as H2O2 concentration and ozone dose were optimized to maximize the treatment efficiency. Consequently, the system succeeded in reducing COD by 89%, total organic carbon (TOC) by 91%, biochemical oxygen demand (BOD) by 86%, and turbidity by 95% after 90-minute treatment of synthetic graywater. Moreover, the system reclaimed treated wastewater as an electrolyte for H\u2082O\u2082 production for subsequent treatment and maintained over 80% and 70% reductions in COD and TOC, respectively, over four consecutive treatment cycles. This system does not need any chemical additive, utilizes the energy-efficient E-peroxone process, and comprises inexpensive, accessible components. As a result, these advantages significantly reduce the system\u2019s capital and operational costs. The promising results and cost-effectiveness show that it can provide a viable solution for the treatment of graywater and human wastewater in low-resource settings.
" }, { "name": "Kjeldbjerg, Camilla Maria", "degree": "PhD", "year": "2022", "title": "The Effects of Confinement in Active Matter: the Casimir Effect, Partitioning, and Hindered Diffusion", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102021-231944176", "creators": [ { "name": { "family": "Kjeldbjerg", "given": "Camilla Maria" }, "id": "Kjeldbjerg-Camilla-Maria", "orcid": "0000-0003-2224-0534", "display_name": "Kjeldbjerg, Camilla Maria" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/avfw-fh81", "abstract": "Active matter describes a class of materials for which constituent \"particles\" convert chemical energy into mechanical motion leading to self-propulsion (swimming). The origins of this swimming motion for both biological and synthetic constituents is a thriving area of research. However, here we focus on the physical properties and mechanics of the active matter systems. We model active particles using the active Brownian particle (ABP) model that is the simplest model that captures the essential physics, where a particle translates with a swim speed U0 in a direction q for a characteristic reorientation time \tτR; the average length they move between each reorientation is called the run, or persistence, length ℓ = U0τR. Owing to this persistent swimming, the ABPs distribute non-homogenously near surfaces, accumulating at no-flux boundaries leading to a concentration boundary layer near solid surfaces. Active particles often have an effective size—their run length—which can be much larger than their geometric size such that they experience confinement in geometries whose size is on the order of the run length. Active systems are inherently far from equilibrium, and we cannot appeal to properties of equilibrium thermodynamic such as the chemical potential to predict the partitioning. Fortunately, active particles are still subject to the laws of mechanics, and in this work, we present a simple macroscopic balance that allows one to predict behavior without detailed calculations. We predict the attractive force between two parallel plates in a reservoir (also called the Casimir effect) and find that the average concentration between the plates equals that in the bulk reservoir independent of the degree of confinement (ratio of run length to the spacing between the plates). We then examine the confinement effects in a channel geometry, where the behavior is fundamentally different, and the average concentration grows linearly with the degree of confinement. The understanding of these fundamental geometries motivated us to look into more complex geometries such as porous media. Based on dimensional analysis and our predictive model, we explain the transient behavior and steady-state partitioning of active particles between a fluid reservoir and a porous medium. Lastly, we discuss the hindered diffusion in periodic porous media and how the diffusion depends not only on the porosity of the medium but also on the degree of confinement. We believe that utilizing the insights in effects of confinement for these fundamental geometries and the porous media will be valuable in designing optimal structures for enhancing or isolating active particles.
" }, { "name": "Lacker, Caitlin Rebecca", "degree": "PhD", "year": "2022", "title": "The Modular Synthesis and Functionalization of Cyclic Compounds Using Modern Methods", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09072021-162545226", "creators": [ { "name": { "family": "Lacker", "given": "Caitlin Rebecca" }, "id": "Lacker-Caitlin-Rebecca", "orcid": "0000-0003-2531-2636", "display_name": "Lacker, Caitlin Rebecca" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/61ky-5w83", "abstract": "Accessing libraries of similar compounds quickly is important in the pharmaceutical industry, as it allows for the expedient investigation of a wide variety of parameters. An efficient strategy to access compounds of interest is to start from a single intermediate containing an interesting or pharmaceutically active structure and decorating it with varying functionality to generate a library of related compounds. Cross-coupling is a powerful tool for this type of divergent, modular approach.
\r\n\r\nHerein, we discuss several strategies geared towards the synthesis of small libraries of compounds of interest. First, a modular approach towards a library of enantioenriched trans cyclobutanes is discussed. This strategy allows for the synthesis of diverse substrates from a single enantioenriched intermediate, and this approach was applied to the synthesis of the small molecule (+)-rumphellaone A. Finally, the development of an enantioselective nickel-catalyzed photoredox cross-coupling to form N-(hetero)benzylic azoles in collaboration with researchers at Merck is discussed.
" }, { "name": "Lhota, Red C.", "degree": "PhD", "year": "2022", "title": "Rheological Characterization of Polymer Additives for Mist Control and Drag Reduction", "advisor": "Kornfield, Julia", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262022-231652129", "creators": [ { "name": { "family": "Lhota", "given": "Red C." }, "id": "Lhota-Red-C", "orcid": "0000-0002-8481-3716", "display_name": "Lhota, Red C." } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia" }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "McKeon", "given": "Beverley J." }, "id": "McKeon-B-J", "orcid": "0000-0003-4220-1583", "role": "member", "display_name": "McKeon, Beverley J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/wav1-4t47", "abstract": "Long flexible polymers in solution at low concentrations strongly change the extensional properties of fluids due to chain stretching that resists flow, while their compact conformation in shear has weak effects. This dramatic difference between their effects on extension and shear is desirable in a variety of applications--controlling drop size in sprayed mists, reducing drag in turbulent flow, and preventing rebound in drop impact. Traditional long covalent polymers, however, are not practical in many applications because they undergo mechanical degradation, i.e. chain scission, under strong flow conditions. Megasupramolecular polymer systems, consisting of long end-associative telechelic polymers that assemble in solutions into multi-million molecular weight supramolecules, meet this practical need. Through association, they act like traditional covalently-bonded polymers in extension, while reversibly dissociating under the strong flows that cause scission for those long polymers.
\r\nThis thesis examines the interplay of flow and degradation that imposes an upper-bound on useful lengths of invididual end-associative chains (how long is too long) (Chapters 2 and 3); the quiescent coil size that affects the onset of stretching in fluids of interest (water and polyalphaolefin lubricant) (Chapters 2 and 4);\r\nrheological approachs to detect variations in the degree of end-functionalization that affect formation of ultra-long supramolecules (Chapter 5); and the changes to turbulent flow when long polymers are present at low concentration (Chapter 2). Ultimately, the audience who might enjoy this thesis is limited by barriers of rheological jargon. In the pursuit of broader rheological and overall scientific understanding, I describe evidence-based pedagogical techniques and my approach to implementing them in chemical engineering and polymer physics classrooms (Chapter 6).
" }, { "name": "MacArdle, Siobh\u00e1n Gaustad", "degree": "PhD", "year": "2022", "title": "Analytical Chemistry Investigations Toward Understanding the Mechanism of Nitrogenase from Azotobacter vinelandii and the Role of the 4Fe-4S Cluster of Dna2 from Saccharomyces cerevisiae", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252022-173757484", "creators": [ { "name": { "family": "MacArdle", "given": "Siobh\u00e1n Gaustad" }, "id": "MacArdle-Siobh\u00e1n-Gaustad", "orcid": "0000-0001-7843-5977", "display_name": "MacArdle, Siobh\u00e1n Gaustad" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/afrw-sx78", "abstract": "Iron sulfur clusters are ubiquitous metal cofactors that play a variety of roles in many enzymes important for health and the climate. The bacterial nitrogenase enzyme, which supports the growth of all organisms by converting atmospheric dinitrogen into ammonia, contains three different redox-active iron sulfur clusters that are central to its function. Dna2, found in all eukaryotes, is integral to genome maintenance and coordinates an iron sulfur cluster of unknown function. Many details of the nitrogenase mechanism are yet to be revealed and pursuits toward this goal will support human efforts to develop more sustainable solutions to nitrogen fixation, which is required for maintaining our food supply. Thorough characterization of the DNA-maintenance enzyme Dna2 will allow us to develop better technologies for cancer prevention and treatment. Development and optimization, as well as technical critique, of a variety of analytical chemistry techniques were performed toward the goal of increasing our understanding of these two important enzymes. Yeast Dna2 was successfully overexpressed and purified from E. coli and spectroscopic features of the 4Fe-4S cluster were characterized. Toward measuring the redox potential of the 4Fe-4S cluster of Dna2, the DNA-modified electrochemistry technique was evaluated leading to the discovery that the source of electrochemical signals proposed to be due to redox activity of 4Fe-4S clusters in DNA-binding proteins are actually due to the redox activity of Fe-EDTA complexes that form in the buffers of these proteins. These results will support future scientists in accurately interpreting the electrochemical signals from DNA-modified electrochemistry. The solvent isotope effect of nitrogenase reduction was investigated by measuring deuterium incorporation into nitrogenase products by GC-MS, FTIR and NMR, revealing that the enzyme exhibits modest preference for H vs. D in acetylene reduction to ethylene, but significant preference for H in the reduction of protons to dihydrogen. These results indicate that there are distinct mechanisms of H atom transfer in the reduction of these two substrates and the experimental design that we developed opens the door for a new avenue of nitrogenase research to reveal the solvent isotope effects of reduction of a variety of different substrates under different experimental conditions. Finally, a new ATPase assay using ion chromatography was developed to measure ATPase activity of the Fe protein, which provides a tool for future pursuits toward quantifying inorganic phosphate release by ATPases and led to our surprising result that the apo-form of the Fe protein is active in ATP hydrolysis.
" }, { "name": "Maser, Michael Robert", "degree": "PhD", "year": "2022", "title": "Machine Learning Methods Inspired by Challenges in Total Synthesis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022022-183557614", "creators": [ { "name": { "family": "Maser", "given": "Michael Robert" }, "id": "Maser-Michael-Robert", "orcid": "0000-0001-7895-7804", "display_name": "Maser, Michael Robert" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Yue", "given": "Yisong" }, "id": "Yue-Yisong", "orcid": "0000-0001-9127-1989", "role": "member", "display_name": "Yue, Yisong" }, { "name": { "family": "Listgarten", "given": "Jennifer" }, "id": "Listgarten-Jennifer", "orcid": "0000-0002-6600-1431", "role": "member", "display_name": "Listgarten, Jennifer" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ffjk-g059", "abstract": "Synthetic organic chemists face a dearth of challenges in the efficient construction of functional molecules, particularly bioactive compounds. Predictive approaches offer reductions to research timelines and resource costs and allow chemists to devote their expertise where it is most valuable. Promising machine learning (ML) methods have evolved for uncovering patterns in chemical data that are beyond the grasp of expert humans, but a number of grand challenges in molecular ML remain. First, the learning of chemical structure representations rooted in physical first principles has yet to be robustly demonstrated. Second, the practical task of predicting successful \"over-the-arrow\" reaction conditions remains elusive. Finally, the demonstration of such solutions in the context of complex synthesis has yet to be realized.
\r\n\r\nHerein, approaches to these grand challenges are developed and described. Inspiration is derived from the successful synthesis of the anticancer marine natural product ritterazine B. Reaction condition prediction is approached first, where a novel graph neural network architecture is developed under a multilabel classification framework. The resulting model is successfully demonstrated on datasets of four high-value reaction types in modern synthesis. Next, 3D-to-1D representation learning is approached by development of a volumetric neural architecture based on inception networks. Such voxel models are demonstrated for the prediction of expensive quantum mechanical properties from space-filled data alone.
\r\n\r\nThe merging of these approaches for reaction condition optimization and utility in complex settings is discussed and forecasted for future works, which are currently underway.
" }, { "name": "Mazza, Michael Francis", "degree": "PhD", "year": "2022", "title": "Defect-Driven Reactivity of Layered Materials Examined through Atomic Layer Deposition", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042022-032834418", "creators": [ { "name": { "family": "Mazza", "given": "Michael Francis" }, "id": "Mazza-Michael-Francis", "orcid": "0000-0003-3995-3100", "display_name": "Mazza, Michael Francis" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "orcid": "0000-0002-6135-6727", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nnwh-5355", "abstract": "Layered materials are a unique class of materials that are characterized by strong covalent bonds in single layers in the two-dimensional plane, but much weaker van der Waals interactions between layers. This unique bonding environment gives rise to remarkable chemical and physical properties. These materials can be easily exfoliated into single atomic layers, true two-dimensional materials, or few-layer stacks. As the number of layers changes, the physical and chemical properties can be modified. Similarly, as the relative position of one or more layers is changed, this change in the bonding environment has substantial impacts on the properties. Due to their unique bonding environment, layered materials are unusually inert to atomic layer deposition. Atomic layer deposition (ALD) is a surface-sensitive deposition technique that relies on a sequence of chemical reactions on the surface of a substrate to deposit the target material. Using this surface-sensitive deposition technique, the crystal structure and chemical bonding environment of the layered material can be interrogated.
\r\n\r\nChapter 1 investigates the spontaneous formation of highly ordered triangular and linear pattern depositions on layered material substrates. These patterns form with two different layered material substrates and with two separate ALD reactions. The pattern depositions do not change with increasing deposition time or with different concentrations of reactants. These networks, while highly unusual to observe chemically, are discussed through a well-established dislocation theory, where defects in the crystal structure of layered materials can impact the surface reactivity.
\r\n\r\nChapter 2 explores the stacking order characteristics of few-layer materials and discusses how changing the stacking order can change the crystal structure and the electronic properties of the materials. The chapter describes the field of few-layer materials and the process of modifying or transferring nanoflakes to new substrates. The chapter introduces a new transfer system that allows for patterned nanoflakes with stacking fault networks to be transferred to new substrates with micron-scale precision. The crystal structure of both the deposited triangular networks and the layered material beneath is discussed.
\r\n\r\nChapter 3 describes a new approach to selectively targeting defect sites in monolayer graphene. A new, water-free atomic layer deposition chemistry is introduced to precisely react metal oxides with high-energy defect sites on graphene. The quality of the film is interrogated and the selectivity of the film is determined by measuring the thickness of the film deposited on the defect-rich regions. The results confirm that this ALD process creates a robust passivating film while keeping the unperturbed regions clean of any metal oxide.
" }, { "name": "Mendoza, Skyler Dakota", "degree": "PhD", "year": "2022", "title": "Development of a Synthetic Strategy Toward Falcatin A. Development of an Asymmetric Diels\u2013Alder Reaction of \u03b1-Acyloxy Enones", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062021-003540914", "creators": [ { "name": { "family": "Mendoza", "given": "Skyler Dakota" }, "id": "Mendoza-Skyler-Dakota", "orcid": "0000-0003-1939-1884", "display_name": "Mendoza, Skyler Dakota" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/v3ys-kj69", "abstract": "Accessing natural products via de novo synthetic methods is important for the discovery of new medicines, antibiotics, agrochemicals, and more. Design and investigation of efficient strategies is of interest to many pharmaceutical industries.
\r\n\r\nHerein, we discuss several strategies geared towards the synthesis of the natural product falcatin A. First, a general discussion of the class of natural products is discussed. Secondly, we discuss our first generation photoredox cascade cyclization approach toward the synthesis of falcatin A. This strategy allows for the efficient and convergent synthesis of two halves of falcatin. Next, a transition metal-catalyzed cascade cyclization approach is discussed in which we were able to successfully synthesize the core of the natural product on a model system. Efforts are ongoing to elaborate to more advanced fragments for the synthesis of falcatin A. Lasty, we discuss our work on the yttrium-catalyzed asymmetric Diels\u2013Alder reaction of \u03b1-acyloxy enone dienophiles, performed in collaboration with BASF. We demonstrate that this methodology can be utilized to access enantioenriched natural product T-4-ol.
" }, { "name": "Peng, Zhiwei", "degree": "PhD", "year": "2022", "title": "Transport and Microrheology of Active Colloids", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292022-213605156", "creators": [ { "name": { "family": "Peng", "given": "Zhiwei" }, "id": "Peng-Zhiwei", "orcid": "0000-0002-9486-2837", "display_name": "Peng, Zhiwei" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Colonius", "given": "Tim" }, "id": "Colonius-T", "orcid": "0000-0003-0326-3909", "role": "member", "display_name": "Colonius, Tim" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/wa00-y892", "abstract": "Active colloids are micron-sized particles that self-propel through viscous fluids by converting energy extracted from their environment into mechanical motion. The origin or mechanism of their locomotion can be either biological or synthetic ranging from motile bacteria to artificial phoretic particles. Owing to their ability to self-propel, active colloids are out of thermodynamic equilibrium and exhibit interesting macroscopic or collective dynamics. In particular, active colloids exhibit accumulation at confining boundaries, upstream swimming in Poiseuille flow, and a reduced or negative apparent shear viscosity. My work has been focused on a theoretical and computational understanding of the dynamics of active colloids under the influence of confinement and external fluid flows, which are ubiquitous in biological processes. I consider the transport of active colloids in channel flows, the microrheology of active colloids, and lastly I propose and study a vesicle propulsion system based on the learned principles.
\r\n\r\nA generalized Taylor dispersion theory is developed to study the transport of active colloids in channel flows. I show that the often-observed upstream swimming can be explained by the biased upstream reorientation due to the flow vorticity. The longitudinal dispersion of active colloids includes the classical shear-enhanced dispersion and an active swim diffusivity. Their coupling results in a non-monotonic variation of the dispersivity as a function of the flow speed. To understand the effect of particle shape on the transport of active colloids, a simulation algorithm is developed that is able to faithfully resolve the inelastic collision between an ellipsoidal particle and the channel walls. I show that the collision-induced rotation for active ellipsoids can suppress upstream swimming. I then investigate the particle-tracking microrheology of active colloids. I show that active colloids exhibit a swim-thinning microrheology and a negative microviscosity can be observed when certain hydrodynamic effects are considered. I show that the traditional constant-velocity probe model is not suitable for the quantification of fluctuations in the suspension. To resolve this difficulty, a generalized microrheology model that closely mimics the experimental setup is developed. I conclude by proposing a microscale propulsion system in which active colloids are encapsulated in a vesicle with a semi-permeable membrane that allows water to pass through. By maintaining an asymmetric number density distribution, I show that the vesicle can self-propel through the surrounding viscous fluid.
" }, { "name": "Petrovic, Stefan", "degree": "PhD", "year": "2022", "title": "Structure and Function of the Human Nuclear Pore Complex", "advisor": "Hoelz, Andre", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262022-064823923", "creators": [ { "name": { "family": "Petrovic", "given": "Stefan" }, "id": "Petrovic-Stefan", "orcid": "0000-0002-4979-8696", "display_name": "Petrovic, Stefan" } ], "advisors": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-1726-0127", "role": "advisor", "display_name": "Hoelz, Andre" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Martin", "given": "Andreas" }, "id": "Martin-Andreas", "orcid": "0000-0003-0923-3284", "role": "member", "display_name": "Martin, Andreas" }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-0923-3284", "role": "member", "display_name": "Hoelz, Andre" } ], "option_major": [ "biochem" ], "doi": "10.7907/g77e-h329", "abstract": "The nuclear pore complex (NPC) mediates the selective transport of macromolecules between the nucleus and the cytoplasm of the eukaryotic cell. In humans, the NPC is a ~110 MDa assembly of ~1,000 proteins, termed nucleoporins, which establishes a ~50 nm wide central transport channel that traverses both membranes of the nuclear envelope. In the central transport channel, natively unfolded nucleoporin regions rich in repeated phenylalanine-glycine (FG) motifs form a size-selective barrier that limits the diffusion of macromolecules. Active cargo transport is facilitated by dedicated mobile transport factors that exchange through the FG barrier and couple binding and unbinding of cargo to GTP hydrolysis by the small GTPase Ran. By contrast, nuclear export of mature mRNA is driven by ATP-dependent remodeling of messenger ribonucleoprotein (mRNP) at the NPC's cytoplasmic face. Whereas the mechanisms of the mobile Ran dependent transport machinery have been conceptually rationalized, the NPC's role in facilitating and modulating nucleocytoplasmic transport, including mRNA export, remains poorly understood. Addressing gaps in the understanding of the NPC's structure and function, this thesis presents comprehensive interdisciplinary analyses of the NPC's inner ring, linker scaffold, and cytoplasmic face architectures. First, we determined the structure, stoichiometry, and location of the channel nucleoporin heterotrimer that provides the bulk of the FG repeats in the central transport channel. Second, we elucidated the molecular details and topology of the network of linker nucleoporins previously shown to assemble folded scaffold nucleoporins into protomeric subcomplexes of the inner ring. Third, we characterized the composition, stoichiometry, and attachment mechanism of cytoplasmic filament nucleoporins, which present manifold Ran- and RNA-binding domains on the cytoplasmic face of the NPC. The resulting near atomic structure of the human NPC provides a rich foundation for rationalizing the dilation and constriction of the central transport channel, the nucleocytoplasmic transport of integral membrane proteins, and the spatial arrangement of cytoplasmic filament nucleoporins that are involved in mRNA export and etiologies of several human diseases.
" }, { "name": "Razo-Mejia, Manuel", "degree": "PhD", "year": "2022", "title": "Physical Biology of Cellular Information Processing", "advisor": "Phillips, Robert B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08242021-212609828", "creators": [ { "name": { "family": "Razo-Mejia", "given": "Manuel" }, "id": "Razo-Mejia-Manuel", "orcid": "0000-0002-9510-0527", "display_name": "Razo-Mejia, Manuel" } ], "advisors": [ { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "advisor", "display_name": "Phillips, Robert B." } ], "committee": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "chair", "display_name": "Newman, Dianne K." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Goentoro", "given": "Lea A." }, "id": "Goentoro-L-A", "orcid": "0000-0002-3904-0195", "role": "member", "display_name": "Goentoro, Lea A." }, { "name": { "family": "Pachter", "given": "Lior S." }, "id": "Pachter-L", "orcid": "0000-0002-9164-6231", "role": "member", "display_name": "Pachter, Lior S." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "biochem" ], "doi": "10.7907/kpc2-b345", "abstract": "The state of matter that we define as life is different from anything else we have encountered so far in the universe. Living systems not only perpetuate their existence out of equilibrium against the will of the second law of thermodynamics, but they do so while keeping up with an ever-changing environment. A key part of this capacity to adapt to environmental changes is the ability of organisms to gather information from their surroundings to put together an adequate response to the challenges presented to them. This thesis presents an effort to understand, from first principles, this fundamental feature of information gathering that all life on earth shares. We dig into the physics behind one of the most pervasive mechanisms through which living systems sense and respond to the environment\u2013the ability to turn on and off genes. In doing so, we hope to uncover general principles of how organisms deal with the problem of collecting information about the world that surrounds them.
\r\n\r\nIn Chapter 1, we develop the theoretical and conceptual tools to navigate the rest of the thesis. I introduce the idea of gene regulation, as well as different theoretical models of this pervasive biological phenomenon. We also delve into the realm of information theory and learn how the plastic concept of information can be mathematically defined and quantified.
\r\n\r\nThe second stop in our exploration (Chapter 2) asks the following question: can we understand, from first principles, how it is that proteins allow cells to regulate their genes on-demand upon sensing environmental cues? For this, we explore the physics behind transcriptional control due to allosteric transcription factors. Using simple quasi-equilibrium models of the two processes involved in this type of regulation\u2014the regulation of the gene by the binding and unbinding of the transcription factor, and the regulation of the activity of the transcription factor itself by the binding and unbinding of an effector molecule\u2014we are able to predict the input-output function of a simple genetic circuit, and compare such predictions with experimental determinations of the mean response of a population of bacterial cells.
\r\n\r\nWe then expand on these insights to ask questions about the inescapable cell-to-cell variability that isogenic cells encounter. For this, we have to leave behind the pure thermodynamic framework and work in the language of chemical kinetics. This allows us to make predictions beyond the mean input-output gene expression response of cells by reconstructing full gene expression distributions. With these probabilistic input-output functions, in Chapter 3 we formalize the question of the amount of information that cells can gather from the environment. For this, we turn to information-theoretic concepts of maximal mutual information (otherwise known as channel capacity) between the state of the environment and the gene expression response from bacterial cells. Finally, we compare our predictions of the maximum amount of information\u2014measured in bits\u2014that cells can gather with single-cell inferences of this quantity.
" }, { "name": "Ribson, Ryan Dillon", "degree": "PhD", "year": "2022", "title": "Spectroscopic Characterization of Electronic and Magnetic Relaxation Phenomena in Molecular Systems", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192022-171213261", "creators": [ { "name": { "family": "Ribson", "given": "Ryan Dillon" }, "id": "Ribson-Ryan-Dillon", "orcid": "0000-0002-3755-5777", "display_name": "Ribson, Ryan Dillon" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e2mj-qs04", "abstract": "The thesis herein describes the application of time-resolved spectroscopic techniques to the understanding of a variety of electronic and magnetic relaxation phenomena in molecular systems. Chapter I presents the techniques and theory behind transient absorption spectroscopy and electron paramagnetic resonance spectroscopy, which are two tools that are used throughout the thesis. Chapter II recounts the study of singlet fission in a series of bipentacene dipyridyl pyrrolides, including HDPP-Pent, Li\u2082(DPP-Pent)\u2082, and KDPP-Pent. Using transient absorption and kinetic modeling, we found that deprotonation and metal coordination induced a change in the rate of singlet fission (~7 fold increase going from HDPP-Pent to Li\u2082(DPP-Pent)\u2082) and ultimate triplet yield. Chapter III details the study of the temperature-dependent magnetic relaxation studies of S = \u00bd spin systems copper (II) phthalocyanine (CuPc) and vanadyl phthalocyanine (VOPc). Although the spin-lattice relaxation time (T\u2081) of CuPc is greater than that of VOPc at low temperatures (<30 K), the CuPc T\u2081\u2019s decline more substantially with temperature than those of VOPc, which we attribute to the increased spin-orbit coupling constant of Cu over V. Ultimately, the phase memory times (T\u2082) are T\u2081-limited in CuPc by 150 K, whereas room temperature coherence is observed in VOPc. In Chapter IV, 2,9-dialkyl substituted 1,10-phenanthroline complexes of Cu(I) are studied computationally to assign entatic energies to the steric contributions attributed to the ligand that dictate the electrochemical and photophysical properties of the complexes. We performed experimental validation of reduction potential, low-temperature emission bandwidth and excited state relaxation energies, and \u00b3MLCT lifetimes to support the computational work. In Chapter V, we present ongoing work toward the characterization of triplet and triplet pair states generated via singlet fission in HDPP-Pent, Li\u2082(DPP-Pent)\u2082, and KDPP-Pent by time-resolved electron paramagnetic resonance spectroscopy in collaboration with Drs. Jens Niklas and Oleg Poluektov. Finally, in Chapter VI, we present data collected toward the photophysical characterization of a series of Ni(II) 2,2\u2019-bipyridine aryl halide complexes synthesized by David Cagan, which are relevant for photochemical transformations. We provide supporting materials for Chapters II, III, and V in Appendices A, B, and C, respectively." }, { "name": "Rinaldi, Katherine Zoe", "degree": "PhD", "year": "2022", "title": "A Technical and Systems Analysis of Hydrogen Fuel in Renewable Energy Systems", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06222021-223726087", "creators": [ { "name": { "family": "Rinaldi", "given": "Katherine Zoe" }, "id": "Rinaldi-Katherine-Zoe", "orcid": "0000-0002-0746-2852", "display_name": "Rinaldi, Katherine Zoe" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h8x1-xb98", "abstract": "Within the next century, we must tackle the dual challenges of continuing to meet the increasing global demand for energy services while stabilizing global temperatures to mitigate the effects of anthropogenic climate change. Doing so will require a major restructuring of all energy services on a global scale. Here, we contribute to the understanding of the role of hydrogen fuel in net-zero emissions systems from both a technical and systems perspective.
\r\n\r\nFrom the technical perspective, we evaluate the activation mechanism of an electrodeposited cobalt selenide hydrogen evolution reaction (HER) catalyst using operando Raman spectroscopy. During this activation process these films, which originally show no catalytic activity toward HER, undergo a compositional change in which selenium in the form of loose, polymeric chains is electrochemically reduced from the material. This work provides a facile method towards investigating catalytic materials under operando conditions, elucidates the changes that occur in this cobalt selenide material during the activation step, and offers potential paths toward the improvement of the cobalt selenide catalyst.
\r\n\r\nAt the systems level, we use hourly weather data over multiple decades and historical electricity demand data to analyze the gaps between wind and solar supply and electricity demand for California (CA) and the Western Interconnect (WECC). We quantify the occurrence of resource droughts when the daily power from each resource was less than half of the 39-year daily mean for that day of the year. Using a macro-scale electricity model, we then evaluate the potential for both long-term storage (in the form of power-to-gas-to-power) and more geographically diverse generation resources to minimize system costs. For wind-solar-battery electricity systems, meeting California demand with WECC generation resources reduces the cost by 9% compared to constraining resources entirely to California. Adding long-duration storage lowers system costs by 21% when treating California as an island. This data-driven analysis quantifies rare weather-related events and provides an understanding that can be used to inform stakeholders in future electricity systems.
" }, { "name": "Rosa-Ra\u00edces, Jorge Luis", "degree": "PhD", "year": "2022", "title": "Path Space Markov Chain Monte Carlo Methods for Molecular Simulation", "advisor": "Miller, Thomas F.; Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292022-234015177", "creators": [ { "name": { "family": "Rosa-Ra\u00edces", "given": "Jorge Luis" }, "id": "Rosa-Ra\u00edces-Jorge-Luis", "orcid": "0000-0003-2311-2948", "display_name": "Rosa-Ra\u00edces, Jorge Luis" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "co-advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Stuart", "given": "Andrew M." }, "id": "Stuart-A-M", "orcid": "0000-0001-9091-7266", "role": "member", "display_name": "Stuart, Andrew M." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/10jr-hg67", "abstract": "Path space Markov-chain Monte Carlo (McMC) provides a versatile framework for simulating the structure and dynamics of condensed-phase systems aptly described by classical and quantum Boltzmann statistics. This thesis comprises our efforts to design, analyze and improve path space McMC algorithms to achieve numerically advantageous, and physically accurate, simulation of molecular processes across a range of scales. To improve molecular dynamics (MD) simulations of atomically resolved systems exhibiting pronounced nuclear quantum effects, we introduce a family of integrators for non-preconditioned path-integral MD exhibiting dimension-free statistical accuracy and efficiency, and enabling a many-fold increase in time-step stability relative to conventional approaches at no additional computational cost or implementation complexity. The integrators come with robust performance guarantees that are borne out in thermostatted ring-polymer MD simulations of realistic condensed-phase models. Concurrently, toward extending the range of accessible timescales in stochastic MD simulations of mesoscale coarse-grained molecular systems, we introduce a parallel-in-time integrator for the overdamped Langevin equation based on McMC evaluation of a path-integral representation of the many time-step stochastic MD transition kernel. The parallel-in-time integrator achieves simultaneous integration of multiple stochastic MD time-steps at no greater wall-time cost and with no lesser accuracy than a standard Euler--Maruyama integrator does in serial, and thus instantiates new opportunities to accelerate stochastic dynamics simulations on massively parallel computer architectures. Our work along these two methodological avenues extends the utility of path space McMC across applications in molecular simulation and has broader implications in other disciplines that require accurate and efficient simulations of Markov diffusion processes in state spaces or path spaces.
" }, { "name": "Row, Hyeongjoo", "degree": "PhD", "year": "2022", "title": "Mechanical Approach to Active Matter: Reverse Osmotic Effect and Motility-Induced Phase Separation", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252022-172145394", "creators": [ { "name": { "family": "Row", "given": "Hyeongjoo" }, "id": "Row-Hyeongjoo", "orcid": "0000-0003-3623-512X", "display_name": "Row, Hyeongjoo" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" } ], "option_major": [ "chemeng" ], "doi": "10.7907/qef0-e420", "abstract": "The defining feature of active matter, self-propulsion requires constant consumption of energy to be maintained. As a result, active matter systems are inherently out of equilibrium and some principles that are accepted as common knowledge, particularly from thermodynamics, do not apply to the active matter systems. Arguably the most popular example is the motility-induced phase separation (MIPS) -- active matter can spontaneously phase separate into liquid-like dense phase and gas-like sparse phase even without any attractive interactions between the self-propelling constituents. In this thesis, I demonstrate the utility of a mechanical perspective in revealing and understanding the underlying physics of seemingly confounding behaviors of active matter systems. In Chapters 2 and 3, I consider the mechanics of a suspension of active colloidal particles when the transport properties (self-propelling speed and diffusivities) vary spatially. The mechanical analysis reveals the reverse-osmotic nature of active matter systems with a spatial variation in activity. I provide an explanation for why physical processes governed by the osmotic pressure of particles can appear in a reversed manner in active matter systems, e.g. a fluid can flow from regions of high concentration to low in a suspension of active colloids. In Chapter 4, I develop a mechanical theory of phase coexistence that applies to both equilibrium and nonequilibrium systems. By applying the mechanical theory to MIPS, I find phase coexistence conditions of the MIPS that allow a construction of a phase diagram, which excellently agrees with the results from computer simulations. The mechanical theory also allows access to the microscopic structure of phase interfaces. By investigating the interfacial structure, I discover interesting nonequilibrium interfacial behavior of the MIPS. I find that the width of the MIPS interface varies nonmonotically with the activity of particles and provide a mechanical explanation for the phenomena." }, { "name": "Saccone, Max Anthony", "degree": "PhD", "year": "2022", "title": "Vat Photopolymerization Additive Manufacturing of Functional Materials: from Batteries to Metals and Alloys", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062022-211326081", "creators": [ { "name": { "family": "Saccone", "given": "Max Anthony" }, "id": "Saccone-Max-Anthony", "orcid": "0000-0003-3846-2908", "display_name": "Saccone, Max Anthony" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "Manthiram", "given": "Karthish" }, "id": "Manthiram-Karthish", "orcid": "0000-0001-9260-3391", "role": "chair", "display_name": "Manthiram, Karthish" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "member", "display_name": "Greer, Julia R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/v3cn-8h28", "abstract": "In recent years, additive manufacturing (AM), also known as 3D printing, has emerged as a uniquely powerful tool for rapid prototyping and for creating complex, high value structures. Vat polymerization (VP) is an AM technique which forms parts through light-initiated polymerization, capable of achieving both high resolution and high throughput. While VP has been utilized to fabricate a wide variety of polymeric materials, fabricating functional materials such as ceramics, metals, and inorganic composites has remained a challenge. This thesis focuses on developing fabrication methods for a range of functional materials, from battery active materials to metals and ceramics, via vat polymerization additive manufacturing, taking advantage of chemical reactions within an AM part after fabrication to form target materials in situ.
\r\n\r\nWe demonstrate the use of emulsions to introduce aqueous active material precursors into organic photopolymer resins to create architected lithium sulfide/carbon composites for use as lithium-sulfur battery cathodes. Such architected cathode materials are promising for mitigating mechanical degradation in high volume-change battery materials such as the sulfur cathode. We additionally performed nanome- chanical experiments on lithium sulfide powders to determine how lithium sulfide yields, deforms, and fails in the context of volume-change-induced stress during battery cycling. Because lithium sulfide is present as a discharge product in all lithium sulfur batteries, these nanomechanical particle compressions have bearing on the entire field, beyond the realm of 3D architected cathodes.
\r\n\r\nWe additionally demonstrate the use of organogel templates to streamline the AM process by enabling the fabrication of many materials starting with a single resin composition, followed by infiltration of appropriate metal precursors and post-processing heat treatment to convert the polymer/precursor matrix to the target metal via calcination and reduction reactions. We fabricate and characterize copper, nickel, silver, cobalt, cupronickel alloys, tungsten, and more to highlight the wide-ranging versatility of achievable materials and microstructures.
" }, { "name": "Schild, Dirk Jacob", "degree": "PhD", "year": "2022", "title": "Synthesis, Characterization, and Reactivity of Iron Hydrides in Nitrogen Fixation and Proton Coupled Electron Transfer from C-H bonds", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192021-161648176", "creators": [ { "name": { "family": "Schild", "given": "Dirk Jacob" }, "id": "Schild-Dirk-Jacob", "orcid": "0000-0003-0179-6023", "display_name": "Schild, Dirk Jacob" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1ytm-7s85", "abstract": "Mitigating the hydrogen evolution (HER) is an outstanding challenge in small molecule reduction catalysis using protons and electrons. Nitrogen fixation is a fundamental reaction where this selectivity is of great importance. This thesis details mechanistic studies into the nitrogen fixation reaction and factors that contribute to hydrogen evolution. In addition to the mechanistic studies, the development of reagents with weak X-H bonds, with applications in N-H bond formation is presented. Chapter 1 presents a brief overview of catalytic nitrogen fixation, the role of hydride ligands, and the importance of reagents required for the formation of weak N-H bonds. Chapter 2 details the mechanism of photo-enhanced iron mediated N2 fixation. It is shown that off-path iron complexes bearing hydride ligands play an active role in hydrogen evolution by N2 fixation catalysts. The data presented lends further insight into the selectivity, activity, and required driving force relevant to iron (and other) N2RR catalysts. The third chapter describes the synthesis and characterization of a highly reactive iron(III) nitrido complex, a proposed key intermediate in nitrogen fixation mediated by [(P3B)Fe]+. The ability to synthesize and characterize such an intermediate provides additional support for a distal catalytic cycle for this catalyst. In Chapters 4 and 5, the reactivity of iron hydrides and their role as precursors towards weak C-H bonds is discussed. These chapters outline a valuable approach for the differentiation of a ring- versus a metal bound H-atom. Chapter 4 provides a structural, thermochemical, and mechanistic foundation for the characterization of ring protonated indene-based ligands with remarkably weak C-H bonds. Chapter 5 extends the characterization of such reactive species and presents ligand induced migration of the hydride to a Cp* ring.
" }, { "name": "Tao, Xuecheng", "degree": "PhD", "year": "2022", "title": "Capturing Nuclear Quantum Effects at Classical Efficiency: a Path-Integral Approach", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03282022-213805038", "creators": [ { "name": { "family": "Tao", "given": "Xuecheng" }, "id": "Tao-Xuecheng", "orcid": "0000-0003-2907-3839", "display_name": "Tao, Xuecheng" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s929-5x12", "abstract": "Quantum mechanical effects of nuclei are ubiquitous in chemistry. For a typical example, zero-point energies and tunneling effects of the nuclei shift the chemical equilibrium and manipulate the reaction rate. However, theoretical investigation of such nuclear quantum effects in chemical reactions remains a challenge due to the heavy computation cost. To this end, imaginary-time path-integral based approximate methods have been previously introduced, which allows the inclusion of nuclear quantization in real-time chemical dynamics simulations at the efficiency of classical Newtonian dynamics. In the dissertation, we further extend the applicability of those path-integral methods and exploit the methods for practical chemical investigations. Specifically, we introduce novel dynamics approaches based on ring-polymer molecular dynamics methodology to incorporate nuclear quantum effects in the simulations of excited state dynamics and microcanonical scattering processes, and to examine the nuclear quantum effects in Hydrogen/Deuterium sticking to the graphene surface.
" }, { "name": "Tookmanian, Elise M.", "degree": "PhD", "year": "2022", "title": "Investigation of the Roles of Hopanoids in the Lifecycle of Bradyrhizobium diazoefficiens in the Context of Climate Change", "advisor": "Newman, Dianne K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09072021-015258902", "creators": [ { "name": { "family": "Tookmanian", "given": "Elise M." }, "id": "Tookmanian-Elise-M", "display_name": "Tookmanian, Elise M." } ], "advisors": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "advisor", "display_name": "Newman, Dianne K." } ], "committee": [ { "name": { "family": "Ondrus", "given": "Alison E." }, "id": "Ondrus-A-E", "orcid": "0000-0002-6023-3290", "role": "chair", "display_name": "Ondrus, Alison E." }, { "name": { "family": "Sessions", "given": "Alex L." }, "id": "Sessions-A-L", "orcid": "0000-0001-6120-2763", "role": "member", "display_name": "Sessions, Alex L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h0xe-jb65", "abstract": "Rhizobia are a group of bacteria that participate in plant-growth promoting symbioses with legumes, where the bacteria supply the plant with a source of useable nitrogen. In agriculture, crop rotation capitalizes on this symbiosis by planting legumes to restore the nitrogen content of depleted soils. The effects of climate change, such as increased temperature and changing precipitation patterns, threaten the future viability of agriculture. Rhizobia exemplify the role bacteria can play to improve agriculture\u2019s resilience to climate change and prevent land degradation and food insecurity. However, in order for bacteria to realize this potential, they need to survive the challenges of climate change. In my thesis, I detail the environments that rhizobia experience throughout their lifecycle and how the soil environment will likely change as the climate changes. Then, I connect these environmental parameters, especially hypo and hyperosmolarity, to the outer membrane. The outer membrane is the first line of defense for bacteria against external assaults. Rhizobia make many changes to their outer membrane compared to commonly studied enteric bacteria. For example, the ability to synthesize hopanoids, steroid-like lipids, is overrepresented in rhizobia.
\r\n\r\nHopanoids are known to help protect bacteria against a wide range of stresses \u2013 but, surprisingly, we found that the extended hopanoid class is not required for a moderately successful symbiosis between rhizobia strain Bradyrhizobium diazoefficiens and the tropical legume Aeschynomene afraspera. The main defect was in the initiation of the symbiosis, perhaps due to motility defects in the extended hopanoid\u2014deficient mutant. As we investigated this paradox, we discovered that hopanoids are conditionally essential in B. diazoefficiens depending on the medium in which the organism is grown. Specifically, we investigated the role of hypoosmolarity and divalent cation concentration, discovering that extended hopanoids confer robustness to the physicochemical environment. This property indicates that extended hopanoids may be important in the soil environment, which is prone to osmotic variability, especially as the climate changes. This work increases our understanding of the role of the outer membrane and hopanoids in bacterial resilience which may help with engineering or selection of better crop additives in the future.
" }, { "name": "Vasquez, Krystal TonyBeth", "degree": "PhD", "year": "2022", "title": "Isomer Separation of Multifunctional Atmospheric Compounds Using Gas Chromatography and Chemical Ionization Mass Spectrometry", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112022-233628713", "creators": [ { "name": { "family": "Vasquez", "given": "Krystal TonyBeth" }, "id": "Vasquez-Krystal-TonyBeth", "orcid": "000-0003-4540-4212", "display_name": "Vasquez, Krystal TonyBeth" } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemistry" ], "doi": "10.7907/yaz8-qr39", "abstract": "Oxygenated volatile organic compounds are a group of carbon-containing species that include one or more functional groups. They are formed during oxidation of hydrocarbons in the atmosphere. Afterwards, they readily undergo atmospheric processing, which\u2014depending on their chemical properties\u2014can lead to the formation of harmful pollutants, such as ozone or secondary organic aerosols (SOA). Prolonged exposure to either compound can negatively impact human health.
\r\n\r\nUnfortunately, most existing analytical techniques struggle to quantify the concentrations of the majority of OVOCs due to their characteristic low abundances and high reactivities. In addition, most of these compounds are also made up of a complex mixture of isomers that few instruments are able to resolve. Since even slight changes in structure can impact an OVOC\u2019s atmospheric fate, this can lead to uncertainties when elucidating their chemical mechanisms. As a result, despite decades of research, there are still many outstanding questions pertaining to atmospheric processing of OVOCs and, by extension, their impact on air quality.
\r\n\r\nTo combat this issue, novel instrumentation was developed that can provide accurate, isomer-resolved measurements of a wide variety of OVOCs, which it achieves by combining the sensitive, specific nature of gas chromatography (GC) with the equally sensitive, yet non-invasive aspects of chemical ionization mass spectrometry (CIMS). To showcase its capabilities, these new instrumental methods are applied to the study of isoprene oxidation. More specifically, we report new insights into the isomer-specific loss processes of isoprene-derived hydroxy nitrates. Inclusion of our findings into atmospheric models can greatly improve our simulations of NO\u2093, ozone, and nitric acid.
" }, { "name": "Wilkins, Olivia Harper", "degree": "PhD", "year": "2022", "title": "High-Resolution Imaging of Chemistry in Extreme Interstellar Environments", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032022-154242981", "creators": [ { "name": { "family": "Wilkins", "given": "Olivia Harper" }, "id": "Wilkins-Olivia-Harper", "orcid": "0000-0001-7794-7639", "display_name": "Wilkins, Olivia Harper" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "de Kleer", "given": "Katherine R." }, "id": "de-Kleer-K-R", "orcid": "0000-0002-9068-3428", "role": "member", "display_name": "de Kleer, Katherine R." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rwj8-8683", "abstract": "Advancements in imaging technologies have changed the ways in which we see and understand our chemical universe. Given the extreme distances between Earth, from which we observe the wider chemical universe, and the molecular clouds where stars are born, we cannot resolve the chemical structure of these interstellar laboratories on the same scales as we can with samples on Earth. Nevertheless, with the advent of larger and more sophisticated telescopes, such as the Atacama Large Millimeter/submillimeter Array (ALMA) in Chile, we can now look at interstellar chemistry on scales much smaller than the solar system. The research presented here uses ALMA to investigate the chemistry in (massive) star-forming regions in different parts of the Milky Way with high spatial resolution.
\r\n\r\nThis thesis first focuses on the nearby Orion Kleinmann-Low nebula (Orion KL), the closest (at about 400 parsecs away) massive star-forming region to us, at spatial scales smaller than those of typical planetary systems. Using methanol and methyl cyanide as molecular probes, we provide new insight into the physical structure\u2014especially the thermal structure\u2014of the nebula by mapping physical parameters derived from observed spectra. We also use different isotopologues of methanol to understand its chemistry, specifically after it forms on the surfaces of icy dust grains. This work provides a new view of Orion KL by providing high-angular-resolution maps of parameters such as abundance and temperature, whereas much of the existing literature provides a single set of parameters for a region.
\r\n\r\nHowever, Orion KL is only one interstellar laboratory, and it is part of a cohort of star-forming regions that are the targets of repeated astrochemical observations. The second part of this thesis ventures into the so-called molecular ring, a region 4-8 kiloparsecs from the galactic center that has remained relatively unexplored in the context of astrochemistry. Using the Atacama Compact Array (ACA) component of ALMA, we observed a slew of millimeter-emitting objects across 11 giant molecular clouds at higher angular resolutions than most previous observations of our sample, and we characterize their chemistry for the first time. This pilot survey establishes a catalogue of interstellar laboratories for future higher-angular-resolution observations. Over time, this catalogue will drive a better understanding of the chemistry in molecular-ring young stellar objects, allowing us to see whether (and if so, how) chemistry varies across distance from the galactic center and significantly increasing the number of targets for astrochemical observations.
" }, { "name": "Ylitalo, Andrew Samuel", "degree": "PhD", "year": "2022", "title": "A Bubble Is Born: Nucleation and Early Growth of CO\u2082 Bubbles in Polymer Foams", "advisor": "Kornfield, Julia A.; Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:03222022-221436705", "creators": [ { "name": { "family": "Ylitalo", "given": "Andrew Samuel" }, "id": "Ylitalo-Andrew-Samuel", "orcid": "0000-0003-4086-3508", "display_name": "Ylitalo, Andrew Samuel" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "co-advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/cdgw-7c18", "abstract": "Gas bubble nucleation is a fundamental phenomenon both throughout the natural sciences and in the production of foams for lightweight, functional materials; it is also the basis for many a bubbly beverage. Enhancing bubble nucleation in polyurethane insulating foams used for refrigeration can further reduce their low thermal conductivity without resorting to hazardous blowing agents used in the past. Experimental challenges of measuring the kinetics of the rapid, multiscale process of bubble nucleation pose a roadblock to investigation of suitable processing conditions, as well as the development of theoretical models of bubbles and foams.
\r\n \r\nHere, using a microfluidic flow-focusing technique developed for measurement of protein and chemical kinetics, we built a microfluidic cell to probe gas bubble nucleation of CO\u2082 in polyol, a model system for polyurethane insulating foams, at controlled pressure with millisecond resolution over acquisition times sufficient for optical, IR, and X-ray measurements. This technique allows for repeated measurements of bubble nucleation at any degree of supersaturation without the interference of heterogeneous nucleation from surfaces. By extrapolating a model fit to high-speed optical microscopy measurements of bubble growth backward in time, we estimated the degree of supersaturation at nucleation for thousands of bubbles. Estimates of the nucleation rate based on Poisson statistics were consistent with predictions by a string method model based on density functional theory and G-ADSA measurements. This model predicted that the addition of cyclopentane (a common physical blowing agent in polyurethane foams) can dramatically reduce the nucleation energy barrier due to the formation of a liquid-like layer of cyclopentane and CO\u2082 along the surface of the bubble that reduces the interfacial tension, which previous models have only predicted at significantly higher saturation pressures. This prediction was supported by thermodynamic measurement of a three-phase coexistence under similar conditions, which is a known fingerprint for such nucleation pathways, and measurement of significantly higher bubble nucleation rates upon the addition of cyclopentane. These findings shed light on the possibility of a previously unappreciated role of physical blowing agents like cyclopentane in enhancing bubble nucleation by opening up a qualitatively distinct and more favorable nucleation pathway.
" }, { "name": "Zhang, Juner", "degree": "PhD", "year": "2022", "title": "New-to-Nature Selective C-H Alkylation Using Engineered Carbene Transferases", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:04252022-204451583", "creators": [ { "name": { "family": "Zhang", "given": "Juner" }, "id": "Zhang-Juner", "orcid": "0000-0001-8181-1187", "display_name": "Zhang, Juner" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "orcid": "0000-0001-9170-2283", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4kv8-f830", "abstract": "Synthetic methods to selectively convert C\u2013H bonds, a prevalent motif in organic molecules, into functionalities can significantly accelerate the syntheses and derivatization of molecules. In the past decade, many enzymatic catalysts have emerged as greener, more selective, and more versatile alternatives to small-molecule catalysts for selective C\u2013H functionalization reactions. In nature, enzymes only catalyze a limited set of C\u2013H functionalization reactions that are useful for chemical synthesis, as the overwhelming majority of known C\u2013H functionalization enzymes in nature are hydroxylases. The diversity of the enzymatic reaction scope needs to be substantially expanded to make them broadly useful to synthetic chemists. This thesis will describe new enzymes, which we repurposed from one of the most prevalent C\u2013H hydroxylases in nature, cytochromes P450, which are now able to catalyze new-to-nature C\u2013H alkylation reactions via selective carbene transfer. Given the central role of C\u2013C bond forming reactions in building and elaborating the carbon skeleton of organic molecules, these transformations are of high interest in many fields of research, such as medicinal chemistry and material chemistry. In Chapter 1, I review a recent surge in newly identified enzymes, repurposed enzymes, and artificial metalloenzymes which can catalyze selective C\u2013H functionalization reactions. Chapter 2 details the development of a panel of enantiodivergent \u03b1-amino C(sp\u00b3)\u2212H fluoroalkylases. Using directed evolution, the carbene transferases can install fluoroalkyl groups onto these C\u2013H bonds with high activity (4,070 total turnovers, TTN) and selectivity (>99% ee). Notably, complementary regioselectivity can be achieved using an alternative enzyme, P411-PFA-(S). In Chapter 3, I report the first carbene transferase, P411-ACHF, which can transfer an \u03b1-cyanocarbene to arene C\u2013H bonds of N-substituted benzenes. Chemodivergent C(sp\u00b2)\u2013H and C(sp\u00b3)\u2013H functionalization can be achieved using P411-ACHF and P411-PFA. Additionally, structural studies revealed an unprecedented backbone carbonyl flip within the long I-helix of P411-PFA, which may suggest how these enzymes have evolved to bind and activate diazo compounds for carbene transfer reactions. In Chapter 4, I discuss the efforts I took toward stabilizing an interesting but unstable P450, CYP3A4. This enzyme exhibits large active site volume and high substrate promiscuity and therefore can be a great candidate to develop late-stage carbene and nitrene transferases. I adopted consensus sequence mutagenesis and predicted five mutations which have the potential to have the strongest beneficial effects on improving CYP3A4's thermostability. In summary, this thesis work addresses the urgent need for expansion of the current enzymatic C\u2013H functionalization reaction scope and the development of more sustainable and selective C\u2013H functionalization catalysts which can be synthetically useful.
" }, { "name": "Zimmer, Matthew Holden", "degree": "PhD", "year": "2022", "title": "Cotranslational Pulling Forces Alter Outcomes of Protein Synthesis", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232021-171251780", "creators": [ { "name": { "family": "Zimmer", "given": "Matthew Holden" }, "id": "Zimmer-Matthew-Holden", "orcid": "0000-0002-1437-2636", "display_name": "Zimmer, Matthew Holden" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Voorhees", "given": "Rebecca M." }, "id": "Voorhees-R-M", "orcid": "0000-0003-1640-2293", "role": "member", "display_name": "Voorhees, Rebecca M." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "biochem" ], "doi": "10.7907/p7vk-cf03", "abstract": "As nascent proteins are synthesized by the ribosome, interactions between the nascent protein and its environment can create pulling forces that are transmitted to the ribosome's catalytic center. These forces can affect the rate and outcomes of translation. We use atomistic and coarse-grained simulation to characterize the origins of pulling forces, the propagation of force to catalytic center of the ribosome, and the effects of force on synthetic outcomes. We uncover a novel form of pulling force-mediated regulation in which the forces generated by the integration of a transmembrane helix induce frameshifting in a viral polyprotein. Computational force measurements of hundreds of mutant viral sequences in combination with deep mutational scanning experiments reveal the structural and sequence-level features that enable this powerful regulatory mechanism. Force measurements are also used to provide a molecular picture for complex pulling force experiments on multispanning membrane proteins. In particular, we identify signatures of cotranslational helix packing interactions and the translocation of surface helices. To understand how forces are propagated through the nascent protein in the ribosomal exit tunnel, we ran and analyzed hundreds of microseconds of atomistic molecular dynamics with an applied pulling force on the nascent protein. The simulations reveal how the secondary structure of nascent proteins and their interactions with the ribosome control force propagation. The inhibition of force transduction by nascent protein-ribosome interactions explains how amino acids tens of angstroms away from the catalytic center of the ribosome can still influence the force-induced restart of stalled ribosomes.
" }, { "name": "Allen, Hannah Marie", "degree": "PhD", "year": "2021", "title": "Constraining the Formation and Fate of Hydroperoxides in the Remote Atmosphere", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012021-172201123", "creators": [ { "name": { "family": "Allen", "given": "Hannah Marie" }, "id": "Allen-Hannah-Marie", "orcid": "0000-0002-4218-5133", "display_name": "Allen, Hannah Marie" } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1108-c936", "abstract": "Atmospheric hydroperoxides form as second generation products in the atmospheric oxidation of many volatile organic compounds (VOCs) during reactions of these VOCs with OH and HO2 (i.e. HOx), where HOx are among the atmosphere's main oxidants and thus drivers of the majority of atmospheric chemistry. Once formed, the lifetime and ultimate fate of hydroperoxides are set by a variety of potential chemical and physical pathways that have different impacts on the atmosphere's oxidizing capacity, including either recycling HOx or removing HOx. This dissertation explores the role of hydroperoxides with several different structures through field and laboratory studies using CF3O- chemical ionization mass spectrometry (CIMS) to understand the role of these hydroperoxides in the oxidation chemistry of the remote atmosphere.
\r\n\r\nHydrogen peroxide (H2O2) and methyl hydroperoxide (MHP, CH3OOH) are two of the most abundant hydroperoxides found in oceanic environments. Both hydroperoxides were measured using time of flight and tandem quadrupole CIMS aboard the NASA DC-8 aircraft during the Atmospheric Tomography Mission, enabling a seasonal investigation into their global distribution with near pole-to-pole coverage across the Pacific and Atlantic Oceans and ranging in altitude from the marine boundary layer to the upper troposphere and lower stratosphere. Hydroxymethyl hydroperoxide (HMHP, HOCH2OOH) and isoprene hydroxy hydroperoxides (ISOPOOH, HOC5H8OOH) are organic hydroperoxides derived from the oxidation of isoprene, one of the dominant biogenic VOCs in forested environments. The loss of HMHP from the atmosphere via reaction with OH is investigated in the laboratory using time of flight CIMS and laser induced fluorescence along with theoretical chemical modeling methods. To better distinguish the varying roles of structurally complex hydroperoxides, a novel field-deployable gas chromatograph integrated with a high resolution time of flight CIMS is developed that sensitively detects hydroperoxides along with a number of other oxidation products. This instrument is deployed at a rural forested site in northern Michigan during the PROPHET field campaign to probe the relative contribution of different ISOPOOH isomers to the oxidation pathways of isoprene.
" }, { "name": "Arnett, Charles Haden", "degree": "PhD", "year": "2021", "title": "Multimetallic Models of the Nitrogenase Active Site", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:09042020-064530373", "creators": [ { "name": { "family": "Arnett", "given": "Charles Haden" }, "id": "Arnett-Charles-Haden", "orcid": "0000-0002-1272-3797", "display_name": "Arnett, Charles Haden" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fgje-ns05", "abstract": "Motivated by the lack of an atomic-level understanding of the reduction of small molecule substrates by nitrogenase, this dissertation describes the synthesis, characterization and reactivity of well-defined model clusters of the enzyme active site.
\r\n\r\nChapter 2 describes a series of site-differentiated, high spin iron clusters which reversibly bind carbon monoxide in redox states FeII\u2084 through FeIIFeIII\u2083. Detailed spectroscopic and thermochemical studies reveal that this remarkable reactivity can be attributed to the ability of remote metal centers to shuttle reducing equivalents to the small molecule binding site.
\r\n\r\nChapter 3 further explores the consequences of internal electron transfer events on the thermodynamics of small molecule binding by site-differentiated, tetranuclear iron clusters. To systematically tune the electronic properties of the cluster, a Hammett series was prepared. Counterintuitively, introduction of electron-donating substituents suppresses the first CO binding event but enhances the second. Detailed spectroscopic studies revealed that the origin of this behavior can be traced to the effect of the substituents on the redox reorganization energy associated with internal electron transfer.
\r\n\r\nChapter 4 presents the synthesis and characterization of the first open-shell diiron \u00b5-carbyne complex, which also features a biologically relevant Fe(\u00b5-C)(\u00b5-H)Fe core. This electronically unusual species could be activated toward binding of N\u2082 upon addition of H\u207a/e, which initially involves an iron-carbene intermediate.
\r\n\r\nChapter 5 describes the synthesis and spectroscopic investigation of the first carbonbridged, bimetallic complexes featuring odd numbers of valence electrons as spectroscopic models of the critical E\u2084(4H) intermediate of nitrogenase. Detailed pulse EPR studies revealed the effects of electronic localization on the spectroscopic signatures of the \u00b5-hydride motif and provide insight into the electronic distribution in a reduced state of FeMoco.
\r\n\r\nChapter 6 describes the synthesis and characterization of terminal iron-carbene complexes, including EPR characterization of open-shell variants.
\r\n\r\nAppendix A describes unpublished efforts to prepared site-differentiated models of FeMoco featuring carbon- or sulfur-based donors.
\r\n\r\nAppendix B presents unpublished work towards modelling the cooperative activation and reduction of N\u2082 by diiron complexes featuring carbon-based bridging ligands.
" }, { "name": "Bagley, Jacob David", "degree": "PhD", "year": "2021", "title": "Fabrication of Pristine and Doped Graphene Nanostripes and their Application in Energy Storage", "advisor": "Yeh, Nai-Chang", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012021-171503477", "creators": [ { "name": { "family": "Bagley", "given": "Jacob David" }, "id": "Bagley-Jacob-David", "orcid": "0000-0001-9490-1341", "display_name": "Bagley, Jacob David" } ], "advisors": [ { "name": { "family": "Yeh", "given": "Nai-Chang" }, "id": "Yeh-Nai-Chang", "orcid": "0000-0002-1826-419X", "role": "advisor", "display_name": "Yeh, Nai-Chang" } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Yeh", "given": "Nai-Chang" }, "id": "Yeh-Nai-Chang", "orcid": "0000-0002-1826-419X", "role": "member", "display_name": "Yeh, Nai-Chang" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hfdw-fs13", "abstract": "Fossil fuel usage causing rising CO2 levels and leading to climate change is, perhaps, the most pressing issue of our time. However, our economic dependence on energy necessitates its usage such that reducing energy usage is not possible leaving transitioning to renewable energy technologies as the only sustainable option. Currently, the largest barrier to large scale incorporation of renewable energy sources (e.g., solar, wind) is the high cost of energy storage technologies. Electrochemical energy storage technologies (e.g., lithium-ion batteries and supercapacitors) have been identified as a key approach for enabling the transition to renewable energy technologies.
\r\n\r\nGraphene is a material with exceptional properties that is receiving much attention for application in various energy storage technologies and could help reduce the cost of energy storage technologies. This thesis describes a novel fabrication procedure for low-cost and efficient synthesis of high-quality graphene nanostripes (GNSPs) and their application in lithium-ion battery and supercapacitor electrodes.
\r\n\r\nThis thesis is structured as follows. Chapter 1 outlines the motivation and technical background of this research. Chapter 2 describes the instrumentation and procedures for fabricating GNSPs. Chapter 3 describes in situ exfoliation of GNSPs as electrodes in supercapacitors to increase the capacitance. Chapter 4 describes synthesis and application of pyridinic-type nitrogen-doped GNSPs as a lithium-ion battery anode. Chapter 5 describes the synthesis and application of silicon-, germanium-, and tin-doped GNSPs and their application in lithium-ion battery anodes. Chapter 6 concludes and synthesizes the findings of the thesis holistically. Additionally, future outlook and potential research objectives are presented.
" }, { "name": "Carim, Azhar Iqbal", "degree": "PhD", "year": "2021", "title": "Growth Towards Light: Translation of Optical Inputs into Mesostructured Outputs via Inorganic Phototropism", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202021-164652779", "creators": [ { "name": { "family": "Carim", "given": "Azhar Iqbal" }, "id": "Carim-Azhar-Iqbal", "orcid": "0000-0003-36306872", "display_name": "Carim, Azhar Iqbal" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "orcid": "0000-0002-4571-6884", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mn62-wc26", "abstract": "Palm trees exhibit phototropic growth wherein physical extension of the plant guides the crown towards the time-averaged position of the sun to maximize solar harvesting. In analogous fashion, the directed growth and resultant nanoscale morphology of an evolving inorganic semiconductor deposit can be precisely defined in three-dimensional space using incoherent, uncorrelated light with spatially-invariant intensity. Maskless, photo-driven electrochemical deposition of semiconductor films generates highly ordered, periodic mesostructures with anisotropic, nanoscale features conformally over macroscale areas. This inorganic phototropic growth process does not utilize any physical nor chemical templating agents. Rather, as with natural phototropism, wherein the morphological phenotype expressed by an organism is a function of the light available in the habitat during growth, the precise mesostructures are set by the deposition illumination. Structural complexity and anisotropy result as consequences of inherent asymmetry in the light-material interactions during growth. Here, the morphological outcomes defined by specific illumination inputs are explored and the microscopic optical phenomena underpinning this physical recording of light information is interrogated via both experimental and computational methodologies." }, { "name": "Charan, Sophia Mohini", "degree": "PhD", "year": "2021", "title": "Secondary Organic Aerosol Formation from Volatile Chemical Products: Understanding Aerosol Yields and Dynamics", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312021-044610797", "creators": [ { "name": { "family": "Charan", "given": "Sophia Mohini" }, "id": "Charan-Sophia-Mohini", "orcid": "0000-0002-2023-6403", "display_name": "Charan, Sophia Mohini" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/yvj9-fv16", "abstract": "Particulate matter impacts public health and climate. A major component of small particulate matter, called secondary organic aerosol (SOA), is formed from the condensation of the oxidation products of organic compounds emitted into the atmosphere in the gas phase. Recent analysis suggests that volatile chemical products are responsible for a large fraction of the particulate matter formed from petroleum sources: perhaps more than motor vehicles. This is especially the case in urban areas, which have significant air pollution burdens.
\r\n \r\nUnderstanding exactly which precursors are responsible for this large SOA formation and under which conditions is difficult: for each compound, different chemical pathways dominate and even similar molecules can form vastly varied amounts of aerosol. Even if one could study every compound, extrapolating data to the atmosphere is non-trivial. SOA formation is principally understood through laboratory chamber studies, but these studies require a rigorous, quantitative grasp of chamber phenomena to meaningfully interpret the results.
\r\n \r\nIn this dissertation, computational simulations of environmental chambers illuminate the physico-chemical processes that occur within a chamber and the manner in which these processes interact, in order to help extrapolate data to real-world conditions. In particular, the contribution of particle charge to the rate of particle-wall deposition within environmental chambers is investigated.
\r\n\r\nWith this understanding, the amount of aerosol formed per precursor emitted, called the secondary organic aerosol yield, is investigated for benzyl alcohol and decamethylcylopentasiloxane (D5). At atmospherically relevant concentrations, benzyl alcohol and D5 have disparate SOA mass yields: as much as 100% for benzyl alcohol and ~1% for D5. Both of these findings differ from what was previously modeled and measured, indicating the importance of performing experiments on the compounds of interest and evaluating the oxidation products under atmospherically relevant conditions.
" }, { "name": "Dulaney, Austin Ryan", "degree": "PhD", "year": "2021", "title": "Density Fluctuations and Machine Learning in Active Matter", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12282020-233314685", "creators": [ { "name": { "family": "Dulaney", "given": "Austin Ryan" }, "id": "Dulaney-Austin-Ryan", "orcid": "0000-0002-2428-8913", "display_name": "Dulaney, Austin Ryan" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ne1a-je31", "abstract": "Active matter is a class of materials that has constituents capable of self-propulsion through the conversion of energy into mechanical motion. The origin or specific details of their method of locomotion is a rich area of research, but is not important for understanding some aspects of their dynamics. Our interest is in the single-particle dynamics and the large-scale collective motion observed in these systems. Thus, we use the minimal active Brownian particle (ABP) model to model self-propulsion. The ABP model consists of particles of radius a that swim with an intrinsic speed U\u2080 in some direction q and reorients on a timescale \u03c4R. Active motion is persistent in that a particle will continue to swim in a direction until it reorients itself, giving rise to a swim or persistence length \u2113 = U\u2080\u03c4R. This persistence leads to directed motion at short times but has been shown to become diffusive at long times with a diffusivity that originates from the random swim steps. I show that while these particles do become diffusive at steady state, they display wavelike dynamics while relaxing from an initial point source, which is shown by fluctuations in the number density. The strength of these fluctuations is determined by the ratio of the swim diffusivity to thermal diffusivity. Our resulting theory predicts these dynamics in other instances where spatial gradients in number density are present. This motivated me to look into fluctuations in interacting suspensions of ABPs by studying the \"isothermal\" compressibility. Our theoretical perspective and simulation results show that the compressibility behaves just like a thermodynamic response function, even though these suspensions are driven far from equilibrium. As such, the compressibility is capable of predicting the critical point for the motility induced phase separation (MIPS). We then developed a machine learning (ML) model to predict particle phase identity near the MIPS critical point in the coexistence region -- where fluctuations are large -- to recreate the binodal. Our successful recreation of the binodal and understanding of compressibility resulted in our attempt to define a Widom line (an extension of the coexistence line) for ABPs. The Widom line is the collection of points where density fluctuations are maximized and marks where supercritical behavior goes from being more gas-like to more liquid-like. I conclude by discussing current works in progress to further our understanding of the MIPS transition by using ML to identify particles in the interface of the coexisting phases. From the work on compressibility, we believe the interface plays a crucial role in describing active phase behavior.
" }, { "name": "Eng, Chee Huat (Linus)", "degree": "PhD", "year": "2021", "title": "Plus Ultra: Genome-Wide Spatial Transcriptomics with RNA seqFISH+", "advisor": "Cai, Long", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302021-051953086", "creators": [ { "name": { "family": "Eng", "given": "Chee Huat (Linus)" }, "id": "Eng-Chee-Huat-Linus", "orcid": "0000-0002-2521-9696", "display_name": "Eng, Chee Huat (Linus)" } ], "advisors": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "advisor", "display_name": "Cai, Long" } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Thomson", "given": "Matthew" }, "id": "Thomson-M-W", "orcid": "0000-0003-1021-1234", "role": "member", "display_name": "Thomson, Matthew" }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "orcid": "0000-0003-4748-9352", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nvfe-5j74", "abstract": "Visualizing single cells and their organization in intact tissue is crucial to understanding their governing biological function. Even though single cell RNA sequencing has provided many insights into the heterogeneity and gene expression profiles across many tissue types, the dissociation process which loses the spatial information is hindering our deeper understanding of how these transcriptional distinct cell types are organized and interacting in their native tissue environment.
\r\n\r\nThe thesis begins by giving a background on how single cell RNA sequencing has transformed biology and the emergence of spatial technology such as sequential fluorescence in situ hybridization (seqFISH). While spatial methods are useful for mapping the cell types identified from single cell RNA sequencing, the need for turning spatial technology such as seqFISH, which has high detection efficiency of the transcriptome with spatial information, into an in situ discovery tool is discussed as the scientific community\u2019s goal heads towards building spatial atlases for every human tissues and organs such as the brain.
\r\n \r\nWhile seqFISH has high detection efficiency, it is still limited in the number of genes capable of profiling at once. The major obstacle is the optical crowding problems when more RNA species are targeted and imaged using a fluorescence microscope. In Chapter 2, we first investigated, if the RNA molecules are instead captured on a coverslip and profiled with sequential barcoding strategy, the FISH-based method will reliably characterize the transcriptome when molecular crowding is not an issue.
\r\n \r\nFinally, in Chapter 3, we demonstrate the barcoding strategy to break through the molecular crowding limit of multiplexed FISH. From being able to profile hundreds to a thousand genes by various multiplexed FISH methods at that time in the field, we succeeded in profiling 10,000 genes by RNA seqFISH+, an evolved version of seqFISH, in various intact tissue sections, turning seqFISH+ into a spatial discovery technology with its genome-wide coverage and high detection efficiency. The work described in this part of the thesis is highlighted in Nature Method\u2019s Method of The Year 2020- Spatially-resolved Transcriptomic article.
" }, { "name": "Ford, Rachel Rae", "degree": "PhD", "year": "2021", "title": "Controlling the Dynamics of Microstructure Formation in Mixed-Matrix Polymeric-Particle Membranes", "advisor": "Kornfield, Julia A.; Diallo, Mamadou S.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192021-200916929", "creators": [ { "name": { "family": "Ford", "given": "Rachel Rae" }, "id": "Ford-Rachel-Rae", "orcid": "0000-0001-9844-1557", "display_name": "Ford, Rachel Rae" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Diallo", "given": "Mamadou S." }, "id": "Diallo-Mamadou-S", "role": "co-advisor", "display_name": "Diallo, Mamadou S." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wei", "given": "Lu" }, "id": "Wei-Lu", "role": "member", "display_name": "Wei, Lu" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Diallo", "given": "Mamadou S." }, "id": "Diallo-Mamadou-S", "role": "member", "display_name": "Diallo, Mamadou S." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fqgq-vd04", "abstract": "Polymer membranes are increasingly important in energy generation, water purification, and resource recovery. Control over chemistry, morphology, and mechanical properties gives organic polymers unparalleled advantages for membrane technology\u2014but only if these complementary functions can be married into a cohesive material. Herein I have sought to expand upon the chemical tools for integrating diverse polymers into multifunctional membrane materials, making them easily tunable to various applications. To overcome a fundamental challenge in polymer science\u2014namely, that polymers with different functions often do not mix\u2014the functional polymer is grown in situ in a solution containing a preformed scaffold polymer, a method pioneered by co-advisor Mamadou Diallo. The hierarchical structure of the resulting mixed matrix polymeric-particle (M2P2) membrane is governed by the kinetic competition between polymerization and phase separation of the functional polymer from the scaffold polymer. This competition is quenched by immersion in a nonsolvent, which rapidly solidifies the material to trap the metastable structure formed during synthesis.
\r\n\r\nIn my quest to understand how these competing processes interact to inform multifunctional membrane design, I developed a general method for studying transient structure using ultra-small angle neutron scattering (Chapter II), working closely with Kornfield Group alumnus Dr. Joey Kim. I then investigated the synergistic effects of incorporating different functional polymer architectures in M2P2 membranes (Chapter III), working with fellow graduate student Orland Bateman. By combining low-generation dendrimers with randomly hyperbranched oligomers bearing similar chemical functionality, we can systematically tune the characteristic length of domains formed during synthesis. In the final chapter I discuss the main conclusions and describe future directions for understanding structure during processing in M2P2 membranes. My thesis ultimately provides a broadly relevant platform for membrane design and synthesis, one in which the favorable properties of different polymers may be combined to strike a balance between function, stability, and ease of fabrication.
" }, { "name": "Helms, Phillip Laurence", "degree": "PhD", "year": "2021", "title": "Tensor Network Methods for Nonequilibrium Statistical Mechanics", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072021-223407413", "creators": [ { "name": { "family": "Helms", "given": "Phillip Laurence" }, "id": "Helms-Phillip-Laurence", "orcid": "0000-0002-6064-3193", "display_name": "Helms, Phillip Laurence" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/kram-8g47", "abstract": "Large deviation theory has emerged as a powerful mathematical scaffolding for studying nonequilibrium statistical mechanics, particularly for characterizing the macroscopic effects of microscopic fluctuations. While the large deviation approach is firmly established, it relates the effects of fluctuations to the likelihood of exponentially rare events, which naively requires exponentially large simulation costs. This, in turn, necessitates the development of appropriate numerical simulation techniques. While the standard Monte Carlo toolkit has expanded to incorporate methods towards making rare events typical, in this thesis I propose and evaluate a powerful unorthodox approach adopted from quantum simulation, namely tensor network algorithms, which can work in concert with standard methods to deepen our understanding of nonequilibrium phenomena.
\r\n\r\nAs a testbed for this novel approach, I consider the dynamical phase behavior of several versions of the simple exclusion process, a paradigmatic model of classical driven diffusion. Using a matrix product state, a one-dimensional tensor network ansatz, and the density matrix renormalization group algorithm, a corresponding optimization routine, I characterize the dynamical phase transition between a jammed and maximal current phase in both the one-dimensional and multi-lane simple exclusion processes. The matrix product state is found to be an efficient representation of the nonequilibrium steady-state biased to arbitrarily rare currents via large deviation theory. Because the one-dimensional ansatz is limited to finite-width systems, I extend this success to study the fully two-dimensional simple exclusion process. There, the projected entangled pair state, a two-dimensional tensor network ansatz, is used with the time evolution via block decimation algorithm to demonstrate that the phase transition observed in one-dimension persists in the fully two-dimensional system.
\r\n\r\nTowards the goal of making tensor network methods adaptable for a broad range of physically important systems, both classical and quantum, I also present progress towards studying systems in the continuum limit with interacting particles in two dimensions. This builds upon previous work proposing tensor network representations of quantum operators with long-range interactions in two dimensions by evaluating three operator representations in practice and finding two competitive and viable approaches.
" }, { "name": "Jette, Carina Ivonne", "degree": "PhD", "year": "2021", "title": "Transition Metal-Catalyzed Enantioselective Alpha Functionalization of Nitrogen and Oxygen-Containing Heterocycles", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192020-190811434", "creators": [ { "name": { "family": "Jette", "given": "Carina Ivonne" }, "id": "Jette-Carina-Ivonne", "orcid": "0000-0002-8476-6032", "display_name": "Jette, Carina Ivonne" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qs4z-3803", "abstract": "Research in the Stoltz group is focused on the development of synthetic methods for the preparation of stereochemically rich molecules and the total synthesis of complex natural products. One major theme of our group\u2019s methods development is transition-metal catalyzed \u03b1-functionalization of carbonyl derivatives, with a particular focus on the development of allylic alkylation protocols. Although the \u03b1-functionalization of carbonyl derivatives such as enolates, has been extensively studied, the use of nitrogen and oxygen- containing heterocycles, such as lactams and lactones, remains under- developed. These types of nucleophiles are significantly more reactive, and in the case of the \u03b3-butyrolactones and \u03b3-lactams, may be smaller in size. Because of these differences, the conditions that have been developed for the functionalization of carbonyl derivatives such as ketones does not translate well to these nucleophiles. Furthermore, within the context of enantioselective functionalization, the unique characteristics of these nucleophiles necessitates the development of large, bulky ligands that enable the formation of a very well-defined chiral environment around the transition metal catalyst. This thesis mainly describes strategies that have been developed for the enantioselective \u03b1-functionalization of nitrogen and oxygen-containing heterocycles, with a particular focus on the \u03b3-lactams and \u03b3-butyrolactones.
" }, { "name": "Kempler, Paul Andrew", "degree": "PhD", "year": "2021", "title": "High-Aspect Ratio Structures in Light-Absorbers and Electrocatalysts for Solar Fuels Devices", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:09232020-234052730", "creators": [ { "name": { "family": "Kempler", "given": "Paul Andrew" }, "id": "Kempler-Paul-Andrew", "orcid": "0000-0003-3909-1790", "display_name": "Kempler, Paul Andrew" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xpty-9891", "abstract": "Solar fuels devices produce hydrogen fuel from water and sunlight and address a critical societal need for inexpensive, long-duration energy storage. Such devices are prepared from combinations of light-absorbing semiconductors and catalysts to sunlight to drive thermodynamically uphill reactions. This dissertation puts forth strategies for controlling the three-dimensional structure of semiconductors, electrocatalysts, and the film of gas bubbles evolved on the top and bottom of a solar fuels device. High-aspect ratio features led to unexpected effects in semiconductor/electrocatalyst assemblies. Optical losses were decoupled from the mass-loading of cobalt phosphide and copper electrocatalysts integrated onto silicon microwire photocathodes for the photoelectrochemical generation of hydrogen and hydrocarbons, respectively. Anti-reflective silicon microcone arrays were patterned with continuous films of Pt or CoP particles with minimal reflection losses due to the catalyst films. Transparent metal films were prepared from nanostructured metal phosphides, a class of earth-abundant hydrogen evolution catalysts. Silicon microwire array (photo)electrode surfaces were used to force bubbles away from electrocatalyst surfaces, even when oriented against gravity, leading to sustained operation in the absence of external convection.
" }, { "name": "Klumpe, Heidi Elizabeth", "degree": "PhD", "year": "2021", "title": "Context-Dependent, Combinatorial Logic of BMP Signaling", "advisor": "Elowitz, Michael B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312021-221223611", "creators": [ { "name": { "family": "Klumpe", "given": "Heidi Elizabeth" }, "id": "klumpe-Heidi-Elizabeth", "orcid": "0000-0001-8938-2006", "display_name": "Klumpe, Heidi Elizabeth" } ], "advisors": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "display_name": "Elowitz, Michael B." } ], "committee": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Goentoro", "given": "Lea A." }, "id": "Goentoro-L-A", "orcid": "0000-0002-3904-0195", "display_name": "Goentoro, Lea A." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "display_name": "Phillips, Robert B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3vv4-bk06", "abstract": "Evolution generated diverse signaling proteins for the control of multicellular patterns and organ- isms. These include the proteins of the Bone Morphogenetic Protein (BMP) pathway. Nearly a dozen BMPs activate the BMP pathway to promote the formation of tissues as diverse as bone, cartilage, blood vessels, and the kidney, making them attractive therapeutics for regenerating those tissues in adults. During development, the response to a given BMP depends heavily on context, such as which other BMPs are present and which BMP receptors are expressed on the cell being ac- tivated. However, despite knowing that context matters, the overall logic of this context-dependent signal processing, including the roles of specific ligands and receptors in shaping context and how this logic arises from biochemical features of specific pathway components, remains unclear. Inspired by maps of gene epistasis and drug interactions that functionally classify members of complex biological systems, we comprehensively measured responses to all pairs of ten BMP homodimers (BMP2, BMP4, BMP5, BMP6, BMP7, BMP9, BMP10, GDF5, GDF6, and GDF7), combining robotic liquid handling with a high-throughput fluorescent reporter of pathway activa- tion. These data functionally classify ligands into \"equivalence groups,\" or ligands that combine in the same way with all other ligands across combinations. Surprisingly, the functional groupings do not correlate with similarity of ligand sequence and can change with cell context. Together, the context-dependent equivalence groups summarize the diverse responses to combinations of BMP ligands and their dependence on specific BMP receptors. The experimentally observed pairwise responses are also consistent with a mathematical model where BMP ligands compete for limited BMP receptors with different affinities and then produce outputs with different ligand-specific activ- ities. Ultimately, these results provide a useful reference for explaining the unique effects of BMP combinations in different tissues or time points in development, as well as highlighting counter- intuitive mechanisms for this complex signal processing. Chapter 1 provides an introduction to how and why we study cell-cell signaling. Chapter 2 provides a summary of the determination of equivalence groups, their dependence on receptor context, and fitting the mathematical model of receptor competition. Chapter 3 provides suggestions for future work, including recommendations for improved model fitting as well as crucial extensions to the definitions of BMP \"combinations\" and \"context\" to deepen our understanding and control of this critical pathway." }, { "name": "Kong, Weimeng (Stephanie)", "degree": "PhD", "year": "2021", "title": "Nanometer-sized Aerosol Particles in the Atmosphere: Measurement, Analysis, and Impact", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272020-215437294", "creators": [ { "name": { "family": "Kong", "given": "Weimeng (Stephanie)" }, "id": "Kong-Weimeng-Stephanie", "orcid": "0000-0002-9432-2857", "display_name": "Kong, Weimeng (Stephanie)" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "co-advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/893j-7x60", "abstract": "New particle formation (NPF) from gaseous precursor vapors is frequently observed in the ambient environment and contributes to a major source of global cloud condensation nuclei (CCN). The survival and CCN activation of newly formed particles are highly dependent on particle growth below 10 nm. Characterizing and understanding nanoparticle early growth will therefore help to quantify the impact of NPF on cloud reflectivity and global energy budget. In this work, I first present a recently developed instrument, the Caltech nano-Scanning Electrical Mobility Spectrometer (nSEMS), which consists of a charge conditioner, a novel differential mobility analyzer (DMA), and a two-stage condensation particle counter (CPC). This new design, coupled with a data inversion method that combines empirical calibration and COMSOL simulation, can help to measure nanoparticle size distributions from 1.5 nm to 25 nm more accurately. This instrument was employed in the experiments conducted in the Cosmics Leaving OUtdoor Droplets (CLOUD) chamber at the European Organization for Nuclear Research (CERN) to better understand NPF, particle growth and survival. Multiple experimental parameters were varied to study the influence of different highly oxygenated molecules (HOMs) and inorganic trace gases, such as ammonia and nitrogen oxides on particle early growth. Experiment results have suggested a novel mechanism that may help to explain nanoparticle formation and growth in highly polluted urban environments or in the cold free troposphere. In as little as a few minutes, freshly nucleated particles as small as 2 nanometers in diameter can grow very rapidly due to simultaneous condensation of nitric acid and ammonia. This can help them to survive through the so-called \"valley of death\" where they would otherwise be lost to larger particles, and instead allow them to grow to sizes where they are less vulnerable to loss and can continue on to sizes where they influence local air quality or climate. Further, the laboratory results of nanoparticle growth were incorporated into the Global Model of Aerosol Processes (GLOMAP) model to study the impact of this extremely rapid growth on the global CCN budget. Having realized the importance of conducting well-controlled chamber experiments and of using chamber experimental data, we established an online data infrastructure, the Index of Chamber Atmospheric Research in the United States (ICARUS), for storing, sharing, and using chamber data. A combined effort of the described works contributes to better measuring the size distribution of nanoparticles and to understanding their impact on global climate.
" }, { "name": "Laccetti, Benjamin Joseph", "degree": "PhD", "year": "2021", "title": "Therapeutic Microparticles and Biolistic Drug-Delivery to the Cornea", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10182020-133113205", "creators": [ { "name": { "family": "Laccetti", "given": "Benjamin Joseph" }, "id": "Laccetti-Benjamin-Joseph", "orcid": "0000-0002-0399-1204", "display_name": "Laccetti, Benjamin Joseph" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "orcid": "0000-0002-2912-0001", "role": "member", "display_name": "Ravichandran, Guruswami" }, { "name": { "family": "Gao", "given": "Wei" }, "id": "Gao-Wei", "orcid": "0000-0002-8503-4562", "role": "member", "display_name": "Gao, Wei" } ], "option_major": [ "chemeng" ], "doi": "10.7907/nf29-gy82", "abstract": "The ability to deliver therapeutic compounds to the cornea using high-velocity microparticles is assessed and a method to synthesize therapeutic particles suitable for the cornea is demonstrated. Using a commercial gene gun (BioRad; PDS1000), a pneumatic capillary gun, and custom biolistic technology, microparticles were accelerated and made to embed in target materials: either homogeneous gels or corneal tissue. In homogeneous gels, penetration was shown to be directly proportional to particle size and density. In contrast, penetration of microparticles into the cornea is insensitive to particle size and density: varying the sectional density by 680% failed to penetrate beyond the epithelium (ca. 50 microns). The corneal epithelium exhibits two distinct kinetic energy thresholds that must be exceeded to first embed particles in the epithelium (rather than stopping on its anterior surface) and second to embed particles in the stroma (rather than stopping at the posterior surface of the epithelium). Penetration profiles show that the stroma is a highly effective stopping medium for high velocity microparticles. Despite the high water content of corneal tissue (76 w%) compared to the stratum corneum of skin (40 w%), the resistance to penetration of the cornea is comparable to literature values for skin. Ideal particles for drug delivery to the cornea would dissolve away completely, leaving no residue that might scatter light. With a vibrating orifice aerosol generator and a temperature-controlled column, 30-50 \u00b5m particles were composed of 1% Eosin Y with poly(ethylene glycol). Using low density polymer particles with a therapeutic agent payload, it was demonstrated that bulk material can be ballistically delivered to the central 1 cm\u00b2 of the corneal epithelium rapidly, in an even, quantifiable layer." }, { "name": "Lee, Kyra SoHyun", "degree": "PhD", "year": "2021", "title": "2-D Material Sensors on the Electronic Nose for the Sensitive Detection of VOCs", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:09202020-194859590", "creators": [ { "name": { "family": "Lee", "given": "Kyra SoHyun" }, "id": "Lee-Kyra-SoHyun", "orcid": "0000-0002-2100-1534", "display_name": "Lee, Kyra SoHyun" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/j5e1-k535", "abstract": "Chapter 1
\r\n\r\nWhen coated with a polymer surface layer and suspended on 3-D textured glass electrodes, the hybrid combination of polymer and graphene yields sensitive chemiresistive vapor sensors. The expansion and contraction of the polymer layer when it absorbs/reacts with the VOCs, is proposed to produce tremendous train on the suspended graphene. Hence, when VOCs permeates into the polymer layer, sizable electrical resistive changes as folds and creases is induced in the graphene due to its high gauge factor. The hybrid suspended polymer/Gr sensor exhibits substantial responses to polar organic vapors, especially pyridine, while also exhibiting reversibility and the potential future tunability in the types of polymers used as the reactive surface layer.
\r\n\r\nChapter 2
\r\n\r\nVarious polar and non-polar functional groups were covalently bonded onto MoS2 yielding incredibly sensitive chemiresistive vapor sensors. The VOCs' interaction to the functional end groups produced tremendous signal, while also exhibiting reproducibility and reversibility. Future work will further standardize the sensors while also exploring tunability in the types of groups used.
\r\n\r\nChapter 3
\r\n\r\nThis chapter reflects the very start of my PhD research, and one of the important lessons to learn about the electronic nose. It is an example that I wish my predecessors taught me (all had graduated by the time I began my research) that I hope to pass onto future nose users. It is just one example of many projects that had similar end result. Many key lessons can be learned for future nose users. Readers can choose to skip reading this.
" }, { "name": "Lee, Sebastian James Rice", "degree": "PhD", "year": "2021", "title": "Combining High- and Low-Level Electronic Structure Theories for the Efficient Exploration of Potential Energy Surfaces", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292020-175326058", "creators": [ { "name": { "family": "Lee", "given": "Sebastian James Rice" }, "id": "Lee-Sebastian-James-Rice", "orcid": "0000-0001-7006-9378", "display_name": "Lee, Sebastian James Rice" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "chair", "display_name": "Chan, Garnet K." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/saf3-j798", "abstract": "The efficient exploration and characterization of potential energy surfaces paves the way for the theoretical elucidation of complex chemical processes. A potential energy surface arises from the application of the Born-Oppenheimer approximation when solving the Schr\u00f6dinger equation for a molecular system. The extraction of energies and nuclear gradients from the Schr\u00f6dinger equation is typically cost-prohibitive, which has inspired a plethora of approximations. In this thesis, we present the development of embedding and machine learning methodologies that provide fast and accurate energies and nuclear gradients for different chemical classes by combining high- and low-level electronic structure theories. If a chemical change occurs in a spatially localized region, embedding strategies offer an effective approach for balancing accuracy and computational cost. We first consider embedded mean-field theory (EMFT), which seamlessly combines different mean-field theories for different subsystems to describe the whole molecular system. We analyze the errors in EMFT calculations that occur when subsystems employ different atomic-orbital basis sets. These errors can be alleviated by a Fock-matrix correction scheme or by following general basis set recommendations. Systems exhibiting a more complicated electronic structure require a systematically improvable level of theory for the subsystems, which can be realized by projection-based embedding. Projection-based embedding enables the description of a small part of a molecular system at the level of a correlated wavefunction method while the remainder of the system is described at the mean-field level. We go on to derive and numerically demonstrate the analytical nuclear gradients for projection-based embedding. If description of the entire system at the high level of theory is deemed necessary, molecular-orbital-based machine learning (MOB-ML) calculations offers a framework to predict accurate correlation energies at the cost of obtaining molecular orbitals. We go on to present the derivation, implementation, and numerical demonstration of MOB-ML analytical nuclear gradients. We demonstrate the developed methodologies by exploring potential energy surfaces of organic and transition-metal containing molecules.
" }, { "name": "Mead, Griffin John", "degree": "PhD", "year": "2021", "title": "Chirped Pulse Microwave and Single-Shot Terahertz Spectroscopy Studies of Intermolecular Interactions", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12072020-235133438", "creators": [ { "name": { "family": "Mead", "given": "Griffin John" }, "id": "Mead-Griffin-John", "orcid": "0000-0003-0067-4219", "display_name": "Mead, Griffin John" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Lewis", "given": "Nathan S." }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan S." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7wzt-ak58", "abstract": "While the glow of a sodium vapor lamp or the crisp reds in autumn leaves are eye-catching examples of transitions between atomic and molecular energy levels (hv ~2-3 eV), it is arguably the much lower energy, thermally populated intermolecular \"bath\" states (hv ~10\u207b\u2075-10\u207b\u00b2 eV) that contribute most directly to the physical properties of matter. Although invisible to the human eye, in this thesis we study fundamentals of these low-energy interactions with two complementary techniques: chirped pulse microwave spectroscopy and nonlinear single-shot terahertz (THz) Kerr effect spectroscopy.
\r\n \r\nIn the first section, we apply chirped pulse-Fourier transform microwave (CP-FTMW) spectroscopy from 8-16 GHz to study fundamental hydrogen bonding motifs in gas phase alcohol water dimers. Hydrogen bonding is ubiquitous in nature and directly contributes to a range of phenomena from phase transitions in water to solvation of ions to enzymatic activity. Our focus on gas phase dimers reduces the spectral ambiguity arising in condensed phase samples, where inhomogeneous and homogeneous broadening can hamper observation of conserved intermolecular interaction motifs. The hydrogen bonding conformation of two alcohol-water dimers, n-propanol-water and isopropanol-water, were characterized. Both were found to adopt a shared water donor-alcohol acceptor conformation.
\r\n \r\nThe following sections use nonlinear THz spectroscopy from 0.1-10 THz to investigate molecular dynamics in the condensed phase. We focus on halogenated methane liquids, whose intense intramolecular vibrational modes are commensurate in energy to the intermolecular bath states. One central goal of this section was developing a technique to more rapidly collect nonlinear, multi-dimensional data from liquid systems. To that end, we developed a single-shot measurement approach using a reflective nickel echelon mirror and a high frame rate camera. With this new device we achieved an order of magnitude reduction in experimental integration times. High resolution, nonlinear multi-dimensional THz studies of several halogenated methane liquids and materials were produced as a result. From these data, we identified important spectral contributions from the experimental instrument response function.
" }, { "name": "Messinger, Joseph Peter Herman", "degree": "PhD", "year": "2021", "title": "Spectroscopy and Kinetics of Atmospheric and Astrochemical Reactions", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022020-190300132", "creators": [ { "name": { "family": "Messinger", "given": "Joseph Peter Herman" }, "id": "Messinger-Joseph-Peter-Herman", "orcid": "0000-0001-7305-3945", "display_name": "Messinger, Joseph Peter Herman" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ak7w-w439", "abstract": "The reactions between reactive radicals and other neutral compounds have long been known to be important in atmospheric chemistry and astrochemistry. This work uses pulsed-laser photolysis cavity ringdown spectroscopy and laser-induced fluorescence to measure the rate constants and branching ratios of chemical reactions over a wide range of temperatures and pressures relevant to both polluted atmospheres, and the interstellar medium. This includes studying the OH + NO\u2082 reaction in the 253 \u2013 333 K range, the reaction of CN with benzene (C\u2086H\u2086) and toluene (C\u2087H\u2088) down to 16 K, and the OH + CO reaction down to 30 K.
" }, { "name": "Ngamnithiporn, Aurapat Fa", "degree": "PhD", "year": "2021", "title": "I. Development of Nickel- and Palladium-Catalyzed Asymmetric Allylic Alkylation Reactions. II. Enantioselective Syntheses of Tetrahydroisoquinoline\u2013Based Natural Products and Unnatural Analogs", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122021-181842560", "creators": [ { "name": { "family": "Ngamnithiporn", "given": "Aurapat Fa" }, "id": "Ngamnithiporn-Aurapat-Fa", "orcid": "0000-0002-5389-8171", "display_name": "Ngamnithiporn, Aurapat Fa" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/999q-qm11", "abstract": "Described in this thesis are four projects related to the development of synthetic methodologies for the preparation of enantioenriched building blocks, and the total syntheses of complex tetrahydroisoquinoline natural products. In Chapter 1, the development of nickel-catalyzed asymmetric allylic alkylation of lactones and lactams with allylic alcohols is presented. In Chapter 2, the development of palladium-catalyzed enantioselective decarboxylative allylic alkylation of silicon-containing heterocycles is detailed. In these chapters, the utilization of prochiral enolates as nucleophiles has enabled access to enantioenriched all-carbon quaternary stereocenters.
\r\n\r\nChapter 3 describes the total syntheses of bis-tetrahydroisoquinoline alkaloids, \r\n(\u2013)-jorumycin and (\u2013)-jorunnamycin A. A general synthetic strategy, which exploits the tandem cross-coupling/hydrogenation approach, represents the first non-biomimetic synthetic route and allows for an efficient construction of the pentacyclic core in a highly modular fashion. Additional bis-tetrahydroisoquinoline analogs were prepared, and preliminary studies to probe their cytotoxicity against cancer cell lines were conducted. Finally, an extension of the enantioselective and diastereoselective hydrogenation technology to include simple 1,3-disubstituted isoquinolines is described in Chapter 4.
" }, { "name": "Nu\u00f1ez, Paul Daniel", "degree": "PhD", "year": "2021", "title": "Investigating Unexpected but Advantageous Integrated Systems for Solar Water Splitting", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:01162020-234409466", "creators": [ { "name": { "family": "Nu\u00f1ez", "given": "Paul Daniel" }, "id": "Nu\u00f1ez-Paul-Daniel", "orcid": "0000-0001-7039-0516", "display_name": "Nu\u00f1ez, Paul Daniel" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "orcid": "0000-0002-6135-6727", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8q5x-9d27", "abstract": "Advantageous systems are frequently utilized for solar water splitting sometimes are not the most well-understood. Based on fundamental understandings of semiconductor physics, certain combinations of materials should never be advantageous for applications in solar water splitting. (Un)fortunately, these expectations are unrealized. Specifically, we address herein how photogenerated current is able to pass through a-TiO\u2082 from n-Si as well as the formation of a barrier height from electroless-deposited Pt on p-Si.
\r\n\r\nChapter 2 addresses how charge is able to pass through thick layers of atomic layer deposited a-TiO\u2082 even though the deep valence band of the a-TiO\u2082 should make the a-TiO\u2082 act as a blocking layer. It was found that the presence of mid-gap defect states, observable by x-ray photospectroscopy (XPS) valence band spectrum and electron paramagnetic resonance (EPR), in the a-TiO\u2082 act as a channel for current to pass. The implications of the current traversing through the mid-gap defect states are that global and local changes to the mid-gap defect concentration will strongly affect the amount of current able to pass at all potentials. Thus, the choice of top contacts is limited to metals that have a work-function less than ~5.2 eV else the resistivity would increase.
\r\n\r\nChapter 3 focuses on explaining the origin of the barrier height for electroless Pt on p-Si during hydrogen evolution. The work function of Pt should create an ohmic contact which is observed when Pt is e-beam deposited to p-Si. The origin of the barrier height was found to be dependent on the route for charge transfer. Facile redox couples showed that the solution potential of the redox couple controlled the barrier height as charge transferred occurred favorably at the h-terminated surface. While performing hydrogen evolution reaction, the barrier height is formed through the formation of a hydrogen dipole layer that occurs at the interface of the SiO\u2093|Pt interface.
" }, { "name": "Obana, Maiko", "degree": "PhD", "year": "2021", "title": "Genetically Encoded 3,4-Ethylenedioxythiophene (EDOT) Functionality for Fabrication of Protein-Based Conductive Polymers", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11032020-013753331", "creators": [ { "name": { "family": "Obana", "given": "Maiko" }, "id": "Obana-Maiko", "orcid": "0000-0003-4150-0055", "display_name": "Obana, Maiko" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/a9qc-cp16", "abstract": "Genetic code expansion provides powerful strategies to improve the properties of protein-based materials. One novel application of this technique is to genetically incorporate an electroactive functional group into proteins, which can be subsequently polymerized into conductive polymers, enabling fabrication of various protein\u2013conductive polymer hybrids that are widely applicable in bioelectronics. To this end, we developed a technique to incorporate an amino acid bearing 3,4-ethylenedioxythiophene (EDOT), the monomer precursor of a well-known conductive polymer PEDOT.
\r\n\r\nIn Chapter 1, we review the basics of protein-based materials and genetic code expansion technology. We also highlight some examples where genetic code expansion was used for the development of protein-based materials. Finally, we discuss applications of protein and peptide-based materials in bioelectronics.
\r\n\r\nIn Chapter 2, we describe our effort to incorporate an amino acid bearing EDOT group (EDOT-Ala) designed as an analogue of aromatic canonical amino acids. We synthesized EDOT-Ala in three steps of organic reaction, and evaluated the activity of known aminoacyl-tRNA synthetase (aaRS) variants for EDOT-Ala. In addition, we performed evolution of aaRS for EDOT-Ala using two different evolution techniques: cell viability- based approach and phage-assisted approach. Although the evolution experiment did not yield an aaRS variant that can incorporate EDOT-Ala, the results presented in this chapter provide valuable information for engineering of aaRS and incorporation of non-canonical amino acids (ncAA) with bulky functional groups.
\r\n\r\nIn Chapter 3, we describe the incorporation of another EDOT-functionalized amino acid (EDOT-Lys) designed as an analogue of a canonical amino acid pyrrolysine (Pyl). When we co-expressed a GFP reporter and a mutant pyrrolysyl-tRNA synthetase (PylRS) in E. coli in the presence of EDOT-Lys, the cells exhibited strong fluorescence as an indication of successful incorporation of EDOT-Lys into GFP. We further confirmed the incorporation using MALDI-TOF mass spectrometry.
\r\n\r\nIn Chapter 4, we describe the electropolymerization of a model protein XTEN that carries genetically incorporated EDOT-Lys (XTEN-E49am). We performed electropolymerization of XTEN-E49am in the presence of a self-doping EDOT monomer (EDOT-S) by cyclic voltammetry. The solution formed dark blue solids immediately after the potential cycles. The composition of the product was determined by FT-IR spectroscopy, suggesting that one protein is found per 12.5 monomer units of PEDOT. In addition, we investigated the effect of amino acids located adjacent to EDOT-Lys. Although the presence of cysteine (Cys), lysine (Lys), methionine (Met), arginine (Arg), and tryptophan (Trp) located adjacent to EDOT-Lys had an impact on the electropolymerization of model peptides, XTEN proteins carrying these adjacent residues (XTEN-E49am-G50Z; Z = Cys, Lys, Met, Arg, Trp) were electropolymerized with EDOT-S without noticeable effect from these adjacent residues, indicating that the EDOT-Lys residues in proteins undergo electropolymerization with EDOT-S in different chemical environments.
\r\n\r\nIn Chapter 5, we describe the oxidative chemical polymerization of XTEN proteins and model peptides. When XTEN-E49am was polymerized with EDOT-S by addition of ammonium persulfate (APS) and iron(III) chloride (FeCl3), the solution yielded dark blue solids. To evaluate the reactivity of the EDOT-Lys residue in the protein, we reacted the protein with an end-capped EDOT derivative (EDOT-cap). MALDI-TOF mass spectrometry revealed the appearance of new peaks corresponding to the addition of one or two EDOT-caps to the protein, suggesting that EDOT-Lys residue in the protein can react with EDOT derivatives. We also investigated the effect of adjacent amino acids using a series of model peptides. In polymerization using APS without FeCl3 catalyst, peptides carrying basic amino acids (His, Lys, Arg) adjacent to EDOT-Lys showed enhanced polymerization compared to the ones carrying neutral and acidic adjacent residues. All the tested peptides polymerized well when FeCl3 was added as a catalyst. The results presented in this chapter provide valuable insights into synthesis of protein\u2013PEDOT conjugates via oxidative chemical polymerization.
" }, { "name": "Poceviciute, Roberta", "degree": "PhD", "year": "2021", "title": "Mucosal Landscape of the Gut: Development and Application of 3D Imaging Tools for Interrogation of Host-Microbe Mucosal Interface in Mice and Humans", "advisor": "Ismagilov, Rustem F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09012020-121925511", "creators": [ { "name": { "family": "Poceviciute", "given": "Roberta" }, "id": "Poceviciute-Roberta", "orcid": "0000-0002-6649-2170", "display_name": "Poceviciute, Roberta" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "advisor", "display_name": "Ismagilov, Rustem F." } ], "committee": [ { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "chair", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/83t8-mv42", "abstract": "Mammalian gastrointestinal tract is inhabited by trillions of microbes that, in number, amount to the total number of cells in the human body. These microbes, collectively known as microbiota, are found on the skin and in body cavities, and come in close contact with the host on mucosal surfaces. Here, pivotal host-microbe interactions likely take place because close proximity to the host enhances the uptake of microbial metabolites by the host and enables direct contact. To aid the investigation of these interactions, we developed an imaging technology that preserves fragile mucosal structure, enables to explore large areas of mucosal surface, and image the structurally and biochemically complex host-microbe interface in 3D in a mouse. However, 3D imaging presents challenges, such as slow transport of large molecular weight reagents and low signal/background ratio at depth, and these challenges are further exacerbated in particularly thick samples, such as small intestinal samples with long finger-like villus protrusions and thick human gut samples. Therefore, we further advanced our technology to improve sensitivity and specificity at depth, and we have taken steps to translate our technology to precious resected human gut samples from inflammatory bowel disease patients. Finally, we applied these tools to interrogate Enterobacteriaceae \u2013 Bacteroidaceae interactions in the small intestine of a mouse weakened by malnutrition. Using complementary tools, we have first determined that Bacteroidaceae required malnutrition to increase in number in the jejunum digesta, whereas Enterobacteriaceae required both malnutrition and Bacteroidaceae. With imaging, we visualized that in malnourished mice not exposed to Enterobacteriaceae and Bacteroidaceae, bacteria were effectively cleared after digesta passage, whereas in exposed mice bacterial retention was detected, suggestive of bacterial adherence to and colonization of mucosa. Finally, we detected a rare event of abundant bacterial colonization of small intestinal mucosa and captured in 3D.
" }, { "name": "Reimann, Christopher Elias", "degree": "PhD", "year": "2021", "title": "Convergent Synthetic Strategies toward Heterodimeric Bisindole Alkaloids and Polyoxygenated Diterpenoids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08052020-191152340", "creators": [ { "name": { "family": "Reimann", "given": "Christopher Elias" }, "id": "Reimann-Christopher-Elias", "orcid": "0000-0003-3274-7590", "display_name": "Reimann, Christopher Elias" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Ondrus", "given": "Alison E." }, "id": "Ondrus-A-E", "orcid": "0000-0002-6023-3290", "role": "member", "display_name": "Ondrus, Alison E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j1y9-g269", "abstract": "Described herein are two projects in the field of natural product synthesis unified by their use of convergent strategies. An introduction into a relevant subclass of natural products, the bis(monoterpenoid) indole alkaloids, precedes our synthetic efforts. The molecules in this class are comprised of two monoterpenoid indole alkaloids conjoined by at least one carbon\u2013carbon bond, and we review efforts to construct these dimers using semi-, partial, and total synthesis.
\r\n\r\nThe account of our synthetic work begins with a detailed approach to the bis(monoterpenoid) indole alkaloid leucophyllidine. An enantioselective Pd-catalyzed decarboxylative allylic alkylation generates an \u03b1-quaternary-substituted lactam, which serves as a building block for both monomeric subunits. The northern fragment, eburnamonine, is constructed through a five-step sequence comprised of Fischer indole synthesis, Bischler\u2013Napieralski cyclization, and diastereoselective hydrogenation. The southern fragment, eucophylline, is constructed through a ten-step formal synthesis comprised of a Friedla\u0308nder quinoline synthesis, followed by two orthogonal C\u2013H functionalizations that each displayed unexpected reactivity.
\r\n\r\nWe then describe the evolution of a convergent coupling strategy to unify the two polycyclic fragments. While the \"biomimetic\" Friedel\u2013Crafts and \"bio-inspired\" organometallic addition approaches failed, a Pd-catalyzed cross-coupling was ultimately successful in forging the key C\u2013C bond. Extensive efforts to install the final stereogenic center with a variety of reducing agents were unsuccessful, and DFT modeling was utilized to probe the recalcitrant nature of the trisubstituted alkene. Preliminary investigations of a directed hydrogenation are then discussed.
\r\n\r\nFinally, we report an approach to the first total synthesis of the polyoxygenated diterpenoid (\u2013)-scabrolide A. The route begins with the synthesis of an enantioenriched cyclopentendiol building block and an acyclic diyne from (R)-linalool and (R)-carvone, respectively. A Stieglich esterification and thermal [4+2] cycloaddition affords a tricylic intermediate bearing all 19 carbons observed in the natural product. The cycloheptenoid motif is installed through a photochemical [2+2]/fragmentation sequence, exploiting an unusual alkene protecting group strategy to counteract unexpected reactivity.
" }, { "name": "Shin, Jieun", "degree": "PhD", "year": "2021", "title": "Investigating the Catalytic Mechanisms of Bio-degrading Copper Proteins: Multi-copper Oxidases (MCOs) and Lytic Polysaccharide Monooxygenases (LPMOs)", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072021-073626662", "creators": [ { "name": { "family": "Shin", "given": "Jieun" }, "id": "Shin-Jieun", "orcid": "0000-0003-3817-6282", "display_name": "Shin, Jieun" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Fischer", "given": "Woodward W." }, "id": "Fischer-W-W", "orcid": "0000-0002-8836-3054", "role": "member", "display_name": "Fischer, Woodward W." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/m5n0-ck53", "abstract": "Lignin and cellulose comprise a large portion of the renewable biomass on Earth. However, substantially due to laborious course of processing, the conversion efficiency of these biomaterials to accessible biofuel is very low. Therefore, effective depolymerization and utilization of these biopolymers are requirements for environmentally friendly and sustainable energy development. In the hope of finding solutions to these biomass utilization challenges, there have been growing interests in using biodegrading metalloenzymes as active biocatalysts. However, there still remain many questions regarding mechanistic details of enzyme catalysis and effective application of these enzymes. This thesis focuses on investigating the redox chemistry involved in the catalytic mechanisms of two main lignin- and cellulose- degrading copper enzymes: multicopper oxidases (MCOs) and lytic polysaccharide monooxygenases (LPMOs).
\r\n\r\nMCOs are capable of aerobic oxidation of lignin as their primary function, but the nature of their substrate variability also allows the oxidation of not only diverse high potential organic and inorganic complexes, but also earth abundant divalent metal ions such as manganese. LPMOs, on the other hand, enable the cleavage of glycosidic bonds in recalcitrant insoluble cellulosic substances, which are not degradable by other hydrolytic enzymes such as endoglucanases and cellulobiohydrolases.
\r\n\r\nIt is remarkable that nature has created such versatile enzymes with specific active site metals and redox-active amino acids involved in electron transfer, which contribute to substrate oxidation as well as enzyme survival against oxidative damage during catalysis. By gaining a deeper understanding of how these enzymes work, we could greatly enhance current usage efficiencies and develop more energy-efficient biocatalysts.
\r\n\r\nChapter I gives an introduction to biological coppers, two groups of bio-degrading copper enzymes: multicopper oxidases (MCOs) and lytic polysaccharide monooxygenases (LPMOs), and the role of redox-active amino acids in electron transfer and enzyme catalysis. For the MCO work, a thermophilic laccase (Tth-lac) from Thermus thermophilus HB27 and a CotA laccase (CotA-lac) from Bacillus Subtilis were studied. For the LPMO work, two cellulose active LPMOs (ScLPMO10B and ScLPMO10C) and a chitin active LPMO (BlLPMO10A) were studied.
\r\n\r\nChapter II describes thermodynamic aspects of Tth-lac catalysis. The temperature dependence of the formal potential of type I copper (CuT1) in Tth-lac is reported, and the interplay between many competing dynamic and thermodynamic factors which results in thermostability and activity of Tth-lac is discussed.
\r\n\r\nChapter III reports the electron transfer (ET) kinetics data obtained with Tth-lac using the transient absorption spectroscopy. The results of photochemical electron/hole transfer studies indicate that the chains of Trp and Tyr can participate in electron transfer through Tth-lac, which could potentially have a role in enzyme catalysis as well.
\r\n\r\nChapter IV discusses the protective role of a Trp/Tyr pair positioned close to the trinuclear copper cluster (TNC) in Tth-lac. It is indeed remarkable that laccases are capable of utilizing the power of oxygen to catalyze the oxidation of diverse high-potential substrates. But, as a tradeoff, the utilization of dioxygen can make the enzyme highly susceptible to oxidative damage. Chapter IV provides supporting evidence that led us to conclude that the TNC-proximal Trp/Tyr pair functions as an internal antioxidant for prolonging the enzyme lifetime.
\r\n\r\nChapter V describes investigations on the factors that affect MCO catalysis, which include the potentials of the active site coppers, possible reactive intermediates, and common structural motifs. Based on the structural homology between Tth-lac and CotA-lac, some preliminary work done on CotA-lac is also reported.
\r\n\r\nChapter VI outlines the work on LPMOs. After the successful expression and purification of ScLPMO10B, ScLPMO10B and BlLPMO10A, standard activity assays were done with insoluble cellulose and chitin substrates to confirm the enzyme activity. The results are compared with that from the photo-degradation experiments to investigate if the photochemically generated Cu(III) species are active intermediates in LPMO catalysis.
\r\n\r\nChapter VII reports the results on bioinformatics analysis on the distribution of vicinal amino acids in different enzyme classes. This study was to examine the biological significance of amino acid pairs and clusters existing in many different enzyme classes, with vicinal surface tyrosines in CotA-lac as an underlying motivation behind the work.
\r\n\r\nThis thesis demonstrates that MCOs and LPMOs are truly versatile enzymes which can oxidize such diverse refractory substrates, and there could be multiple pathways that the enzymes achieve this task. As shown so far, not only the active site metals but also the chain of redox-active amino acids as well as metal coordinating residues can contribute to enzyme catalysis.
" }, { "name": "Simonoff, Ethan", "degree": "PhD", "year": "2021", "title": "Understanding Pattern Formation and Improving Fidelity in Phototropic Growth", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:12312020-053502722", "creators": [ { "name": { "family": "Simonoff", "given": "Ethan" }, "id": "Simonoff-Ethan", "orcid": "0000-0002-2156-8602", "display_name": "Simonoff, Ethan" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "orcid": "0000-0002-6135-6727", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v869-s074", "abstract": "Phototropic growth of Se-Te yields highly anisotropic lamellar nanostructures and is achieved photoelectrochemically from an isotropic solution of oxidized Se and Te precursors deposited onto isotropic conductive substrates under conformal illumination. In contrast to other spontaneous patterning processes, phototropic growth has no requirement for illumination source coherency and can be performed under mild conditions using low illumination power. Furthermore, as a bottom-up, solution-based synthesis, phototropic growth is scalable and demonstrates high tunability via optical input (i.e. control of wavelength and polarization). However, relative to more traditional lithographic patterning methods, phototropically grown films exhibit defective patterns which may impede their application in devices requiring high pattern fidelities.
\r\n\r\nChapter I investigates the role of the growth substrate and its effect on pattern fidelity in phototropically grown Se-Te films, quantified by peak-fitting and analysis of frequency modes in 2D Fourier transform spectra. The work function or Fermi level of the substrate was determined to be the major factor in determining pattern fidelity. Substrates that had work functions closely aligned with Se-Te (p\u207a-Si and Au) demonstrated higher fidelity patterns than those that had misaligned work functions (n\u207a-Si and Ti). In cases of both nominally identical illumination conditions and nominally identical growth rates, phototropically grown Se-Te films on p\u207a-Si exhibited a higher degree of anisotropy and higher pattern fidelity than phototropically grown Se-Te films on n\u207a-Si, attributed to energetics and charge conduction at the junction formed by the substrate and growing Se-Te film.
\r\n\r\nChapter II follows up on the analysis performed in Chapter I by investigating the role of nucleation and the earliest levels of mass addition to growth substrates in the phototropic growth of Se-Te films. In particular, the relationship between the inter-nucleate spacing of the initial dark electrodeposited material and the pattern formation pathways during the phototropic growth process is described. Conditions that produced small nucleate spacings resulted in phototropically grown films with a higher pattern fidelity and a pattern period that more strongly agreed with the theoretical trend (\u03bb/2n). Furthermore, on substrates that generally produced low pattern fidelity films, use of an applied striking potential during the initial nucleation stage demonstrated both smaller nucleate spacings and improved pattern fidelity of resulting phototropically grown films.
\r\n\r\nFinally, Chapter III investigates the effect of extrinsic (i.e. lithographically patterned) optical scattering elements on the phototropic growth process. Relative to non-templated substrates, substrates with templated ridges demonstrated higher pattern fidelities, confined pattern periods, and enforced pattern orientation. Full-wave electromagnetic modeling and Monte Carlo growth simulations of Se-Te onto simulated templated substrates resulted in simulated films demonstrating good agreement with the patterns observed experimentally. In simulation, for a given set of illumination conditions that produced a single pattern period on non-templated substrates, films grown on templated substrates were able to attain a much wider range of periods (~80% to ~160% vs. the non-templated pattern period). Additionally, the orientation of phototropically grown patterns (usually dependent on the axis polarization) were enforced to the orientation of the templates to an angular offset tolerance of up to ~40\u00b0.
" }, { "name": "Stroscio, Gautam Dutta", "degree": "PhD", "year": "2021", "title": "Understanding the Electronic Structures of First-Row Transition Metal Complexes for Solar Energy Conversion and Catalysis", "advisor": "Hadt, Ryan G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02062021-054659966", "creators": [ { "name": { "family": "Stroscio", "given": "Gautam Dutta" }, "id": "Stroscio-Gautam-Dutta", "orcid": "0000-0002-0827-1062", "display_name": "Stroscio, Gautam Dutta" } ], "advisors": [ { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "advisor", "display_name": "Hadt, Ryan G." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Hadt", "given": "Ryan G." }, "id": "Hadt-Ryan-G", "orcid": "0000-0001-6026-1358", "role": "member", "display_name": "Hadt, Ryan G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4627-9w77", "abstract": "Chapter 1 discusses the major findings and themes of the studies presented in this thesis. Chapter 2 presents a DFT-based methodology for quantifying entatic states. Here it is applied to Cu-based photosensitizers used for solar electricity generation, solar fuels synthesis, organic light emitting diodes (OLEDs), and photoredox catalysis. The methodology can be used to decouple the steric and electronic contributions to excited state dynamics and, in turn, can be used to guide the design of future photosensitizers. The computed entatic energies in some of the photosensitizers were the largest quantified to date: ~20 kcal mol-1 relative to the conformationally flexible [Cu(phen)2]+. Of course, considering typical chemical barriers and driving forces, these values are significant.
\r\n\r\nChapter 3 is an investigation of the ground and excited spin state energetics of a free carbene and several of its iron porphyrin carbene (IPC) analogs. Here it is shown that for the IPC models, multireference ab initio wave function methods give results most consistent with experiment. Specifically, the predicted, mixed singlet ground state is mostly dominated by the closed-shell singlet (Fe(II)\u2190{:C(X)Y}0) configuration, with a small contribution from an Fe(III)\u2013{C(X)Y}\u2013\u2022 open-shell singlet configuration (hole in d(xz)). This description differs from that obtained by using DFT. Also, using the multireference ab initio wave methods, elongation of the IPC Fe\u2013C(carbene) bond increases the weighting of this particular open-shell configuration within the ground state singlet.
\r\n\r\nChapter 4 also deals with a system where DFT and multireference ab initio results diverge: the light-induced Ni(II)\u2013C homolytic bond dissociation in Ni 2,2'-bipyridine photoredox catalysts. DFT calculations give a barrier of ~30 kcal mol-1 while multireference ab initio calculations giving a barrier of ~70 kcal mol-1. Thus, within the latter description, a previously proposed mechanism of thermally assisted dissociation from the lowest energy triplet ligand field excited state is unfavorable. Instead, the mechanism given by the multireference description is initial population of a singlet Ni(II)-to-bpy metal-to-ligand charge transfer (1MLCT) excited state followed by intersystem crossing and aryl-to-Ni(III) charge transfer. From accessible repulsive triplet excited states, homolytic bond dissociation can occur.
" }, { "name": "Sun, Chong", "degree": "PhD", "year": "2021", "title": "Finite Temperature Simulations of Strongly Correlated Systems", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102020-032212115", "creators": [ { "name": { "family": "Sun", "given": "Chong" }, "id": "Sun-Chong", "orcid": "0000-0002-8299-9094", "display_name": "Sun, Chong" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "orcid": "0000-0002-9671-9540", "role": "member", "display_name": "Minnich, Austin J." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/dchn-p020", "abstract": "This thesis describes several topics related to finite temperature studies of strongly correlated systems: finite temperature density matrix embedding theory (FT-DMET), finite temperature metal-insulator transition, and quantum algorithms including quantum imaginary time evolution (QITE), quantum Lanczos (QLanczos), and quantum minimally entangled typical thermal states (QMETTS) algorithms.
\r\n\r\nWhile the absolute zero temperature is not reachable, studies of physical and chemical problems at finite temperatures, especially at low temperature, is essential for understanding the quantum behaviors of materials in realistic conditions. Here we define low temperature as the temperature regime where the quantum effect is not largely dissipated due to thermal fluctuation. Treatment of systems at low temperature is specially difficult compared to both high temperature - where classical approximation can be applied - and zero temperature where only the ground state is required to describe the system of interest. FT-DMET is a wavefunction-based embedding scheme which can handle finite temperature simulations of a variety of strongly correlated problems. The \"high-level in low-level\" framework enables FT-DMET to tackle large bulk sizes and capture the majority of the entanglement at the same time. FT-DMET formulations and implementation details for both model systems and ab initio problems are provided in Chapter 2 and Chapter 3.
\r\n\r\nMetal-insulator transition is a common but important phase transition in many strongly correlated materials. The widely accepted scheme to distinguish an insulator from a metal is band structure theory based on a single-particle picture. However, insulating phases caused by disorder or strong correlation cannot be explained merely with the band structure. In Chapter 4, we demonstrate that electron locality/mobility is a more general criteria to detect metal-insulator transition. We further introduce complex polarization as the order parameter to reflect the electron locality/mobility and provide a formalism based on thermofield theory to evaluate the complex polarization at finite temperature.
\r\n\r\nQuantum algorithms are designed to perform simulations on a quantum device. The infrastructure of a quantum processing unit (QPU) utilizes the superposition property of quantum bits (qubits), and thus can potentially outplay the classical simulations in computational scaling for certain problems. In Chapter 5, we introduce the QITE algorithm, which can be applied to quantum simulations of both ground state and finite temperature problems. We further introduce a subspace method, QLanczos algorithm, and a a finite temperature quantum algorithm, QMETTS, where QITE is used as a building block for the two algorithms. We demonstrate above quantum algorithms with simulations on both classical computers and quantum computers.
" }, { "name": "Threatt, Stephanie Denise", "degree": "PhD", "year": "2021", "title": "In Vivo Activity of Rhodium Metalloinsertors and Exploration of Drug Delivery Systems", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09082020-225341960", "creators": [ { "name": { "family": "Threatt", "given": "Stephanie Denise" }, "id": "Threatt-Stephanie-Denise", "orcid": "0000-0002-2303-2166", "display_name": "Threatt, Stephanie Denise" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Synold", "given": "Timothy" }, "id": "Synold-Timothy", "orcid": "0000-0002-4075-2544", "role": "member", "display_name": "Synold, Timothy" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "biochem" ], "doi": "10.7907/dmqv-ed54", "abstract": "Rhodium metalloinsertors are octahedral complexes developed to selectively target the mismatches and insertions/deletions (indels) that result from mismatch repair (MMR) deficient cancers. By incorporating particularly wide, aromatic, inserting ligands, these complexes are able to detect thermodynamically destabilized mismatch sites via a binding mode known as metalloinsertion, in which the inserting ligand binds DNA via the minor groove and results in ejection of the destabilized mismatched base pair. In vitro analyses of metalloinsertors have found that these complexes are selectively cytotoxic towards MMR-deficient cancer cells compared to MMR-proficient cells. Furthermore, the newest family of Rh-O metalloinsertors, which includes [Rh(phen)(chrysi)(PPO)]\u00b2\u207a (Rh-PPO), displays preferential cytotoxicities in the nanomolar range, which is significantly more potent than first generation metalloinsertors and many standard of care chemotherapeutics. Given the high level of potency and selectivity of Rh-O metalloinsertors, further clinical development of these complexes has been pursued.
\r\n\r\nHere, we present the first preclinical mouse evaluation of a rhodium metalloinsertor as an anticancer agent. The Rh-O metalloinsertor Rh-PPO was evaluated in the HCT116 colorectal cancer xenograft tumor model alongside saline and oxaliplatin controls. Intraperitoneal studies with Rh-PPO showed significant decreases in tumor volumes over time and final tumor weights, indicating Rh-PPO has notable anticancer activity. Additionally, Rh-PPO treatment resulted in a noteworthy increase in the length of mouse survival that was on par with the FDA approved chemotherapeutic oxaliplatin. Pharmacokinetic analyses revealed rapid absorption of Rh-PPO in plasma with notable accumulation in the liver compared to tumors. Importantly, intratumoral metalloinsertor administration resulted in enhanced anticancer effects, which points to a need for more selective delivery methods in order to further metalloinsertor development.
\r\n\r\nIn order to target cancerous cells with still higher selectivity, routes to metalloinsertor antibody drug conjugate (ADC) designs were explored. By attaching Rh-O metalloinsertors to an antibody specific to cancer-associated antigens, our complexes may become even more specifically directed to induce selective cytotoxicity in diseased cells. Three ADC drug linkers that incorporate maleimide groups into the N^O coordinating ligand of a Rh-O metalloinsertor were designed, synthesized, and characterized. These complexes were evaluated for their cellular potency and selectivity toward MMR-deficient cancer cells. Studies revealed that functionalization of the hydroxyl-containing ancillary ligand resulted in decreased potency and abolished preferential cytotoxicity, contrary to previous studies that assessed modifications of this ligand.
\r\n\r\nLiposomal formulations of Rh-PPO were also explored to further target metalloinsertors to malignant cells. Liposomal drug encapsulations have a demonstrated ability to decrease systemic toxicity and increase tumor drug uptake; therefore, the biological activity of Rh-PPO liposomal formulations was explored. Four distinct Rh-PPO liposome formation methods were developed and the resulting liposomes were assessed for their encapsulation efficiency, cellular toxicity, and stability. Remote loaded Rh-PPO liposomes were found to display the most promising chemical and biological characteristics, although additional optimization of encapsulation procedures is necessary for further preclinical evaluation of this metalloinsertor drug delivery approach.
\r\n\r\nAs metalloinsertors continue preclinical assessment and development, a greater understanding of their mechanism of action is imperative. Biological studies with Rh-PPO and the fluorescent analogue RhPPO-Cy3 have shown that DNA damage from metalloinsertor treatment involves the formation of DNA double strand breaks near metalloinsertor-mismatch binding sites. Furthermore, the DNA damage response, including recruitment of pH2AX and Rad51 proteins, becomes activated in response to Rh-PPO treatment. In order to further elucidate the unique mechanism of action of Rh-O metalloinsertors, which involves both metalloinsertor enantiomers binding to DNA mismatches and displaying biological activity, structural studies are ongoing. X-ray crystallography and microelectron diffraction (microED) techniques have been used in attempts to obtain a high resolution structure of Rh-O metalloinsertors bound to DNA mismatch sites. Gaining these structural insights will be critical to understanding the increased cytotoxic selectivity and uniquely high potency of these second generation metalloinsertor complexes.
\r\n\r\nThe experiments detailed in this thesis have advanced the preclinical development of rhodium metalloinsertors. The ability of Rh-O metalloinsertors to decrease tumor growth in vivo has been established. Additionally, liposomal and ADC metalloinsertor drug formulations have been pursued as drug delivery systems, and the biological mechanisms relevant to metalloinsertor activity have been analyzed. Additional efforts to study rhodium metalloinsertors will continue to advance these promising chemotherapeutics as novel, targeted treatments for MMR-deficient cancers.
" }, { "name": "Wang, Jingzhou", "degree": "PhD", "year": "2021", "title": "CDRxAb: Antibody Small-Molecule Conjugates with Computationally Designed Target-Binding Synergy", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282021-080632319", "creators": [ { "name": { "family": "Wang", "given": "Jingzhou" }, "id": "Wang-Jingzhou", "orcid": "0000-0002-2850-330X", "display_name": "Wang, Jingzhou" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/p0kj-9d56", "abstract": "Antibody-drug conjugates (ADCs), or chimeric modalities in general, combine the advantages and offset the flaws of their constituent parts to achieve a broader target space than traditional approaches of pharmaceutical development. My project combines the concept of ADCs with the full atomic simulation capability of computational protein design to define a new class of molecular recognition agents: CDR-extended antibodies, abbreviated as CDRxAbs. A CDRxAb incorporates a small-molecule binding event into de novo designed antibody/target interactions, creating antibody small-molecule conjugates that bind tighter against the target of the small molecule than the small molecule itself. In a proof-of-concept study using monomeric streptavidin/biotin pairs at either a nanomolar or micromolar-level affinity, nanobody-biotin conjugates were efficiently designed to exhibit >20-fold affinity improvement against the model protein targets, with stepwise optimization of binding kinetics and the overall stability. A yeast display-based workflow was subsequently developed to further improve the off rate of the best designed conjugate by another 6 folds. By fully incorporating the chemical space of immunoglobulins into the optimization of small molecule binding events, the workflow explored in this work could be potentially used as a generalizable new method to optimize small molecule-based therapeutics, by exploring a previously uncharted chemical space and the related target space. Chapter 1 reviews background information to justify the proposed CDRxAb molecular construct. Chapter 2 documents the detailed computational design process that generated the 10 conjugates, of which the characterization and discussion are elaborated in Chapter 3. Appendix I documents a slightly related ongoing work that uses computational design to improve existing antibody therapeutics.
" }, { "name": "Wu, Zachary", "degree": "PhD", "year": "2021", "title": "Data-Driven Protein Engineering", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042021-220032574", "creators": [ { "name": { "family": "Wu", "given": "Zachary" }, "id": "Wu-Zachary", "orcid": "0000-0003-2429-9812", "display_name": "Wu, Zachary" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Yue", "given": "Yisong" }, "id": "Yue-Yisong", "orcid": "0000-0001-9127-1989", "role": "member", "display_name": "Yue, Yisong" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/nx3c-qb44", "abstract": "Directed evolution has enabled the adaptation of natural protein sequences for an endless variety of human applications. Given a starting point - a sequence with measurable activity - directed evolution is able to improve protein sequences by iteratively accumulating beneficial mutations. However, directed evolution requires investing large experimental effort, which continues to be the major bottleneck in efficient protein optimization. To this end, we describe a framework for incorporating machine learning in the directed evolution process to maximize the utility of generated experimental data in Chapter 2. In Chapter 3, we then show that this framework outperforms traditional directed evolution methods on an empirical fitness landscape. However, directed evolution is fundamentally limited by its need for a starting point, or a sequence with measurable activity. To tackle this issue, we test the ability of nascent deep learning techniques for generating short, functional amino acid sequences in Chapter 4. Encouraged by this success, we attempted to generate full length enzymatic sequences for desired substrates without success. However, we were able to apply this deep learning approach to model other aspects of enzymatic protein sequences in Chapter 5. Finally, the field of data-driven protein sequence generation is enjoying a recent surge in interest, and we provide an updated review of protein engineering with machine learning, focusing on recent work in deep generative modeling in Chapter 1.
" }, { "name": "Yan, Ellen", "degree": "PhD", "year": "2021", "title": "Experimental and Theoretical Investigation of a Reductant-Activated Methodology for Covalent Functionalization of 1T' Transition Metal Dichalcogenides MoS\u2082 and WS\u2082", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242021-164534392", "creators": [ { "name": { "family": "Yan", "given": "Ellen" }, "id": "Yan-Ellen", "orcid": "0000-0003-3252-790X", "display_name": "Yan, Ellen" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gcjw-bb78", "abstract": "Chemically exfoliated MoS\u2082 (ceMoS\u2082) is a two-dimensional layered transition metal dichalcogenide in the 1T' phase that can be synthesized by intercalating and exfoliating MoS\u2082 of the thermodynamically stable and relatively inert 2H phase. Several functionalization techniques have emerged in the past decade to functionalize both the 2H and 1T' phases, with growing interest given the array of applications for MoS\u2082 in optoelectronics, catalysis, sensing, bioimaging, drug delivery, and photothermal treatment. To aid in this effort, we expanded upon a recently reported covalent functionalization method by developing a reduction-activated methodology to functionalize ceMoS\u2082 using one-electron metallocenes and showed that the coverage of a functional group increases as the reduction potential increases, allowing for greater control of the coverage. Using density functional theory (DFT), we found that the coverage of the smallest functional group, a methyl, is expected to be limited to ~64% per MoS\u2082 due to the steric hinderance associated with the methylation of sulfur sites that are adjacent to more than one methyl group. We also found that a similar coverage trend can be observed when applying reduction-activated functionalization to ceWS\u2082, albeit with a lower coverage at every potential that can be explained using DFT calculations as a difference in the thermodynamic favorability of the reaction. Reductant-activated functionalization provides a driving force that enables ceMoS\u2082 and 2H-MoS\u2082 to be functionalized when it is otherwise unreactive with electrophiles. Conceptualizing the work herein as part of a redox-activated functionalization method, there is an abundance of opportunity to explore oxidant- and reductant-activated functionalization on other chalcogenides, pnictides, and materials in the carbon and boron groups using both solution oxidants and reductants, as well as electrode-based electrochemical methods. Further exploration of redox-activated techniques expands the functionalization toolbox and enables researchers to develop application-specific functional materials.
" }, { "name": "Yu, Weilai", "degree": "PhD", "year": "2021", "title": "Stability of Photo-Electrochemical Interface for Solar Fuels", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172021-221106133", "creators": [ { "name": { "family": "Yu", "given": "Weilai" }, "id": "Yu-Weilai", "orcid": "0000-0002-9420-0702", "display_name": "Yu, Weilai" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2z16-d005", "abstract": "Photoelectrochemical (PEC) water splitting is a promising approach to convert renewable solar energy to clean hydrogen (H2) fuels in one simple step. Although \u2162-\u2164 semiconductors are attractive candidates as light-absorbers in tandem solar-fuel devices, their long-term stability for the hydrogen-evolution reaction (HER) in either acidic or alkaline aqueous electrolytes needs to be established. Chapter 2-5 of this thesis first aims at revealing the underlying corrosion chemistry for a variety of \u2162-\u2164 semiconductors specifically under the HER conditions, offering a rational understanding towards the stability of semiconductor photoelectrode.
\r\n \r\nIn Chapter 2, we start from p-InP and reveal its susceptibility to cathodic photocorrosion forming metallic In0, which however can be completely mitigated by the presence of Pt catalyst due to kinetic stabilization. We also show that the resulting PEC performance of p-InP/Pt electrodes is sensitive to the changes in surface stoichiometry, whereas an InOx-rich surface developed in KOH caused a substantial degradation in the current density-potential (J-E) behavior. In Chapter 3, we discovered that a non-stoichiometric and As0-rich surface of p-GaAs, resulting from a galvanic corrosion by Pt, led to mid-gap surface states as well as a complete loss in photoactivity. In Chapter 4-5, we demonstrate similar kinetic stabilization applied to both p-InGaP2/Pt and pn+-InGaP2/Pt photocathodes for the HER at both pH 0 and pH 14. Additionally, we found that the corrosion of underlying GaAs substrates for the pn+-InGaP2/Pt photocathodes at positive potentials caused damage of structural integrity as well as instability in electrode performance. Altogether these works underscore the mutual dependence of the physical and electrochemical stability of semiconductor photoelectrodes during the HER, which also need to be considered separately. Moreover, both catalytic kinetics and surface stoichiometry are crucial factors for defining long-term corrosion chemistry for semiconductor photoelectrode.
\r\n \r\nIn Chapter 6-7, we further explore solar fuels beyond H2, namely electrochemical N2-to-NH3 conversion. We first establish a new analytical method to isotopically quantify the concentrations of 15NH3 in aqueous solutions with a high sensitivity and a low limit-of-detection of <1 \u03bcM. Further we applied this advanced method to rigorously verify the electrocatalytic activity of a CoMo electrode for reducing N2(g) to NH3. We show that the additional ammonia detected in electrolyte was instead attributed to the corrosion of N impurities present in the CoMo electrode under cathodic bias, thus giving false positive results. These works emphasize the importance of both rigorous product analysis and experiment design in further catalyst development.
" }, { "name": "Zhou, Andrew Z.", "degree": "Senior Thesis", "year": "2021", "title": "Biocatalytic Lactone Carbene C\u2013H, B\u2013H, and N\u2013H Insertion Reactions Enabled by Directed Evolution", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechThesis:06232021-201833496", "creators": [ { "name": { "family": "Zhou", "given": "Andrew Z." }, "id": "Zhou-Andrew-Z", "orcid": "0000-0002-1763-7353", "display_name": "Zhou, Andrew Z." } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zqcp-jt95", "abstract": "Enzymes are biological catalysts, and they accelerate reactions by lowering the activation barrier. In nature, enzymes have been optimized by natural selection and possess precise three-dimensional active sites. With these active sites, they can typically catalyze reactions with high efficiency and specificity. Compared to traditional catalysts, enzymes are generally more environmentally friendly, and they can catalyze reactions in water and at ambient temperature and pressure. However, native enzymes are usually only well suited for a restricted range of substrates and are limited in the types of reactions they perform. The Arnold lab has recently focused on endowing enzymes with the ability to catalyze new-to-nature reactions through directed evolution. Here, we present a set of enzymes engineered for the ability to insert a lactone carbene into B\u2013H, C\u2013H, and N\u2013H bonds with high yield and enantioselectivity. B\u2013H insertion is achieved by engineered cytochrome c enzymes, while N\u2013H and C\u2013H insertions are achieved by engineered cytochrome P450 enzymes. With this work, we expand nature\u2019s toolbox for lactone insertion chemistry. Since lactones are highly bioactive, these engineered enzymes could be powerful tools in the synthesis of a range of pharmaceuticals and natural product targets." }, { "name": "Zhou, Dan", "degree": "PhD", "year": "2021", "title": "Mechanism of Action of a Therapeutic Peptide, Risuteganib, Suggests that Supporting Mitochondrial Function Underlies its Clinical Efficacy in Treating Leading Causes of Blindness", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282021-020006678", "creators": [ { "name": { "family": "Zhou", "given": "Dan" }, "id": "Zhou-Dan", "orcid": "0000-0003-2367-2822", "display_name": "Zhou, Dan" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "chair", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9kqf-yr35", "abstract": "Age-related macular degeneration (AMD) and diabetic retinopathy (DR) are the leading causes of blindness in the developed world and on the rise globally due to the growth of an aging population and an increasing number of diabetics. Antibodies of vascular endothelial growth factor (VEGF), which target neovascularization in the advanced stages of both diseases, have been the main treatment for the past decade. However, anti-VEGF therapies suffer from short half-life and high cost inherent to antibodies, limiting the medical availability to a broader population.
\r\n\r\nTo fill the unmet medical need for treating retinal diseases, a novel therapeutic oligopeptide, risuteganib, is currently in Phase II clinical trials. Results from completed trials suggest that risuteganib has comparable drug efficacy to anti-VEGF therapies, long half-life, low cost, and absence of drug-related adverse events in several hundred patients enrolled in clinical trials for diabetic macular edema (DME) and dry AMD. Risuteganib was originally designed to target neovascularization, intending to inhibit integrin cell-surface receptors and thereby block adhesion and migration of abnormal blood vessel cells. Early in our study, we found experimental evidence contrary to this mechanism of action (MOA).
\r\n\r\nOur journey began with an unbiased search for the binding loci in retinal tissue, using peptide-directed fluorescent labeling. We found out that risuteganib specifically binds to a monolayer of cells, the retinal pigment epithelium (RPE), which has essential functions in maintaining the homeostasis of the retina, and its dysfunction is the hallmark for both blinding retinal diseases. In vitro study in an RPE cell model, ARPE19, showed that risuteganib protects cells against elevated oxidative stress that is associated with AMD and DR. This protective effect correlates with maintaining mitochondrial function. Further study of mitochondrial bioenergetics, in collaboration with Dr. Cris Kenney at UCI, revealed that risuteganib supports oxidative phosphorylation metabolism in the mitochondria.
\r\n\r\nBased on the chemical similarity of risuteganib with a natural product, we hypothesized that risuteganib may act through a mitochondrial enzyme, pyruvate dehydrogenase kinase (PDK), specifically PDK1 that is responsive to disease-related hypoxia-inducible factor 1 alpha (HIF-1\u03b1). Protein phosphorylation assay and enzymatic assay confirmed that risuteganib inhibits PDK1, as a result, reducing phosphorylation of an essential enzyme, pyruvate dehydrogenase (PDH). Leaving PDH in its unphosphorylated form allows its continued activity in oxidative phosphorylation metabolism, which offers a molecular explanation of the ability to support mitochondrial activity. This leads to our current hypothesis that risuteganib\u2019s mechanism of action (MOA) is through inhibition of PDK and protection of mitochondrial functions in RPE cells for treating retinal diseases.
\r\n\r\nProtecting mitochondrial functions may be beneficial to other cell types and in other diseases that subject cells to oxidative stress. As the mitochondria targeting is a potential therapy for diverse life-threatening diseases, including inflammatory disease, cardiovascular disease, and cancer, the present hypothesis invites us to expand our scope of view for this study to broader applications.
" }, { "name": "Zhou, Wen", "degree": "PhD", "year": "2021", "title": "Single-Cell Analysis of Normal and Perturbed Early T-Cell Developmental Processes", "advisor": "Rothenberg, Ellen V.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01292021-130102777", "creators": [ { "name": { "family": "Zhou", "given": "Wen" }, "id": "Zhou-Wen", "orcid": "0000-0003-0357-2744", "display_name": "Zhou, Wen" } ], "advisors": [ { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "advisor", "display_name": "Rothenberg, Ellen V." } ], "committee": [ { "name": { "family": "Wold", "given": "Barbara J." }, "id": "Wold-B-J", "orcid": "0000-0003-3235-8130", "role": "chair", "display_name": "Wold, Barbara J." }, { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "orcid": "0000-0003-4274-1862", "role": "member", "display_name": "Bronner, Marianne E." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "orcid": "0000-0002-7154-5361", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." } ], "option_major": [ "biochem" ], "doi": "10.7907/733t-mg82", "abstract": "Early T-cell development converts multipotent precursors to committed pro-T cells, silencing progenitor genes while inducing T-cell genes. However, both the underlying steps of developmental progression and the regulations involved have remained obscure. Although some of the expressions of important regulators in early T-cell development have been studied in bulk populations, the nature of heterogeneity in this constantly refreshed developmental continuum makes it difficult to understand the developmental trajectories that the cells have undergone using bulk analysis, both in natural conditions and under gene perturbations.
\r\n\r\nCombining droplet-based single cell RNA sequencing (scRNA-seq), deep-sequenced whole-transcript scRNA-seq, and seqFISH for key regulatory genes, we established regulatory phenotypes of sequential ETP subsets; confirmed initial co-expression of progenitor- with T-cell specification genes; defined stage-specific relationships between cell-cycle and differentiation; and generated a pseudotime model from ETP to T-lineage commitment, supported by RNA velocity and transcription factor perturbations. This model was validated by developmental kinetics of ETP subsets at population and clonal levels. The results imply that multilineage priming is integral to T-cell specification in natural developing pro-T cells in the thymus.
\r\n\r\nMoreover, we examined the functional implications of some of the transcription factors (TFs) through bone marrow (BM) derived ex-vivo differentiation systems. Using scRNA-seq, Cell Hashing, and a pool-based CRISPR/Cas9 perturbation system, we established the normal and perturbed developmental trajectories before and after the T-lineage commitment stages. Our analysis revealed that, without the essential lineage commitment TF, Bcl11b, the developing early T cells immediately realized the lack of the essential regulator around the proliferating late DN2a stage. But instead of pushing the developmental path backwards to resemble the earlier stage of uncommitted cells, cells lacking Bcl11b underwent a diverging route of accumulation of 'non-T' genes that are not naturally expressed in earlier stages, potentially leading to the eventual loss of Notch responses. Our results also revealed the complex regulations by TFs that set up the earliest T-lineage progression and commitment conditions. The SCENIC analysis suggested that Gata3 and Tcf7, despite both being important regulatory factors for T-lineage progression, have very different regulatory roles in controlling proliferation and suppressing myeloid lineages. Furthermore, pseudotime analysis also showed that some of the stem and progenitor genes and 'multilineage' associated genes expressed by early pro-T cells potentially hold back the T-lineage differentiation speed. In summary, our study leveraged both in vivo thymic pro-T cells' developmental trajectory obtained through single-cell analysis and ex-vivo derived T cells for internal-controlled perturbations, and revealed some profound roles of TFs in regulating early T-cell differentiation processes.
" }, { "name": "Aksenfeld, Rita Beth", "degree": "Senior Thesis", "year": "2020", "title": "Investigating the Functional Significance of O-GlcNAc Substrate/Interactor Networks", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06092020-142540694", "creators": [ { "name": { "family": "Aksenfeld", "given": "Rita Beth" }, "id": "Aksenfeld-Rita-Beth", "orcid": "0000-0002-2911-9211", "display_name": "Aksenfeld, Rita Beth" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gvhh-xf87", "abstract": "O-linked \u03b2-N-acetylglucosamine glycosylation (O-GlcNAcylation) is a dynamic, inducible post-translational modification (PTM) of thousands of intracellular proteins. There are only two enzymes responsible for O-GlcNAc cycling in higher eukaryotes, O-GlcNAc transferase (OGT) and O-GlcNAcase (OGA), which catalyze addition and removal, respectively. We hypothesized that constructing OGT substrate/interactor networks could serve as a useful foundation for understanding the functions of O-GlcNAcylation. Moreover, this approach might reveal novel insights into how OGT is able to coordinate the specific modification of thousands of proteins in response to individual stimuli.
\r\n\r\nHere, we first sought to validate interactor-substrate relationships suggested by these networks. Specifically, we found that knockdown (KD) of OGT interacting proteins was sufficient to disrupt O-GlcNAcylation of non-interacting OGT substrates. KD of the OGT interacting protein BAP1 changed the O-GlcNAcylation of several of its interactor proteins, many of which do not themselves interact with OGT. This KD strategy was attempted with other potential adaptor proteins such as WDR5 and CDK9, but KD was unsuccessful. KD of the OGT interacting protein GIT1 lead to intriguing changes in the O-GlcNAcylation of liprin-\u03b11. Both of these proteins are vital for synaptic function in excitatory neurons. This result appears significant to the latter protein\u2019s function as it changes with neuronal activity. The aforementioned two findings suggest that association between OGT and its interactors may allow OGT to engage different sets of substrates in different contexts.
\r\n\r\nFurther, we investigated whether modulating global O-GlcNAcylation can affect peroxisome and lipid droplet biogenesis and function, a potentially novel role for O-GlcNAcylation revealed by our network. Together, these studies demonstrate that our networking approach highlights functional connections between OGT interactors and substrates.
" }, { "name": "Al-Saihati, Zainab Ahmed", "degree": "PhD", "year": "2020", "title": "C(sp\u00b3)\u2013H Activation via Dehydrogenation of Cyclic and Heterocyclic Alkanes by Single-Site Iridium Pincer Ligated Complexes", "advisor": "Grubbs, Robert H.; Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012020-135910044", "creators": [ { "name": { "family": "Al-Saihati", "given": "Zainab Ahmed" }, "id": "Al-Saihati-Zainab-Ahmed", "orcid": "0000-0002-3837-9736", "display_name": "Al-Saihati, Zainab Ahmed" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "co-advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "co-advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/tsge-5m91", "abstract": "The direct dehydroaromatization of C(sp\u00b3)\u2013H alkanes may seem conceptually simple but in fact is a challenging transformation. Industrially practiced methods utilize energy intensive processes operating at high pressures and temperatures due to the requirement of such conditions to overcome the endergonic and unreactive nature of alkanes. Chapter 1 briefly discusses early and recent achievements in the field of alkanes dehydrogenation by Ir pincer ligated complexes. While there has been great advancement in the dehydrogenation transformation recently, the direct dehydroaromatization of heterocyclic substrates generating functionalized aromatics is significantly underdeveloped. In Chapter 2, we successfully extended the applicability of Ir catalyzed dehydrogenation systems using pincer ligated complexes on a diverse collection of heterocyclic alkanes with functionalities known to be strongly coordinating and poorly compatible with (PCP)\u2013Ir type catalysts. Carbo- and heteroarenes containing oxygen and nitrogen can be synthesized in moderate to excellent yields up to 99%, and the reaction tolerates functional groups such as bromides and fluorides. In Chapter 3, we demonstrate the efficient disproportionation of cycloalkenes to the corresponding arenes and cycloalkanes with up to 100% conversion, which has been a long-standing challenge in the field of pincer-ligated Ir-catalyzed dehydrogenation studies. For example, 1-cyclohexene was disproportionated to benzene and cyclohexane and 1-4-vinyl-1-cyclohexene was disproportionated to ethylbenzene and ethylcyclohexane. We also demonstrate that a key mechanistic feature of our system is a lack of catalyst inhibition by arenes. In addition, our method is advantageous to previous reports as no sacrificial olefin is used, thereby circumventing the requirement for exogeneous hydrogen acceptors. Our studies presented in Chapter 2 and Chapter 3 provides a novel and a complementary pathway to access important aromatic building blocks and may help create alternative routes to complex molecules via late stage dehydrogenation without the need of stoichiometric oxidants." }, { "name": "Alexy, Eric John", "degree": "PhD", "year": "2020", "title": "Development of Enantioselective Transition-Metal Catalyzed Allylic Alkylation Methodologies", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222020-215559562", "creators": [ { "name": { "family": "Alexy", "given": "Eric John" }, "id": "Alexy-Eric-John", "orcid": "0000-0002-2971-9698", "display_name": "Alexy, Eric John" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/41nh-wb31", "abstract": "Research in the Stoltz group is directed, generally, at the development of synthetic methods for the preparation of stereochemically rich molecules, and the total synthesis of complex natural products. One major theme of our group\u2019s methods development is transition-metal catalyzed allylic alkylation, of which we have reported Pd, Ir, Cu, and Ni catalyzed strategies. Described in this thesis are projects related to these interests, primarily focused on new approaches toward acyclic stereocenters via palladium catalysis; however also include an iridium-catalyzed formal \u03b3-alkylation of malonates and \u03b2-ketoesters, as well as an Overman rearrangement strategy for synthesizing \u03b1-amino ketones. A majority of asymmetric enolate functionalization methods, developed by our group and others, pertain to cyclic systems in which only one enolate geometry isomer is possible due to the constrained ring. In acyclic systems, however, this issue of enolate geometry becomes a major challenge that must be addressed. When one seeks to prepare a tetrasubstituted acyclic enolate, which would lead to a fully-substituted stereocenter following functionalization, one must contend with the issue of non-selective formation of a mixture of enolates which generally leads toward less selective transformations. Strategies toward overcoming this issue, as well as new insights gained regarding the palladium-catalyzed alkylation of acyclic enolates, are described in the subsequent chapters.
" }, { "name": "Brugman, Katherine Irene", "degree": "PhD", "year": "2020", "title": "Pezo-1 Function in Caenorhabditis elegans", "advisor": "Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312020-153151158", "creators": [ { "name": { "family": "Brugman", "given": "Katherine Irene" }, "id": "Brugman-Katherine-Irene", "orcid": "0000-0003-2625-2903", "display_name": "Brugman, Katherine Irene" } ], "advisors": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "chair", "display_name": "Lester, Henry A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Goentoro", "given": "Lea A." }, "id": "Goentoro-L-A", "role": "member", "display_name": "Goentoro, Lea A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "biochem" ], "doi": "10.7907/fz4z-c850", "abstract": "The piezo class of mechanosensative ion channels is a recently discovered class of cation channels with orthologs found in every phylogenetic clade aside from yeast and bacteria. THey are large channels, both in gene length and in overall diameter, with the diameter of the human PIEZO2 protein measuring in at 280 \u00c5 in its full homotrimeric form. In addition, like many similar mechanosensitive channels, such as the DEG/ENaC channels, TRP channels, and TREK/TRAAK channels, they have been linked to a number of different functions within drosophila, zebrafish, and mice, including light touch, nociception, blood cell volume regulation, vascular development, and neuropathic pain. Structurally, this channel is intriguing as it possesses no previously categorized structural motifs and is organized into a central pore with a cap, surrounded by three \"propeller blade\" regions that are theorized to anchor the channel to the membrane and control gating through hydrophobic mismatch based on membrane curvature.
\r\n\r\nThe C. elegans piezo, pezo-1, has not yet been fully characterized, even though a crystal structure of part of this particular piezo was used to assist in the resolution of the first set of cryo-EM images. Here, I generated a number of GFP transcriptional fusions of non-coding potential promoter regions to track the expression of the pezo-1 gene in C. elegans, using these expression patterns to design further experiments. From these expression patterns, I identified expression in a number of neurons of the C. elegans male tail, the primary mating apparatus of the male, and identified these neurons as key neurons as relating to mating. In particular, I identified neurons HOB, PCB, PCC and various ray neurons as potential candidates, which are ciliated neurons theorized to have mechanosensitive properties. In addition, I also identified expression in the vulva muscle and spermatheca of the hermaphrodite, both theorized to be involved in ovulation and egg-laying processes.
\r\n\r\nFrom there, I designed CRISPR/Cas9 mutants with defects in pezo-1 in order to investigate the potential link between the pezo-1 expression in those neurons and mating behavior via a mating assay. Similarly, I devised a fecundity assay to investigate the link between pezo-1 expression in ovulation organs and progeny survival. I have discovered that pezo-1 has function in both of these areas, with pezo-1 mutant males demonstrating discrete mating defects that correlate with the expression pattern seen from the GFP transcriptional fusion mutants and with pezo-1 mutant hermaphrodites having much smaller brood sizes than wildtype hermaphrodites. However, I have also discovered that the processes this mechanotransducer is involved in are also more complex than I originally believed, as I discovered that pezo-1 appears to interact with another mechanotransducer, trp-4, illuminating some potentially novel pathway considerations for how these channels overlap in function.
" }, { "name": "Chalkley, Matthew J.", "degree": "PhD", "year": "2020", "title": "Proton-Coupled Electron Transfer in Nitrogen Fixation", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052020-203503014", "creators": [ { "name": { "family": "Chalkley", "given": "Matthew J." }, "id": "Chalkley-Matthew-J", "orcid": "0000-0002-0484-7335", "display_name": "Chalkley, Matthew J." } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FE9D-9K14", "abstract": "This thesis focuses on the management of protons and electrons in the formation of X\u2212H bonds. In our pursuit of better understanding this process, we have been particularly interested in the nitrogen fixation reaction (N2-to-NH3) because of the high number of protons and electrons involved in this conversion (6) and the significant difficulty of functionalizing N2. The first chapter introduces the important themes of this thesis: (i) multiple bonding, (ii) proton-coupled electron transfer, (iii) overpotential in N2 fixation, and (iv) selectivity in N2 fixation. The second chapter discusses the bonding of an iron complex with a small molecule (NO) and how this bonding is key to activating the small molecule for reactivity. The third chapter looks at how employing a new proton and electron source allows an Fe catalyst to achieve improved selectivity and turnover number for the reduction of N2 to NH3 despite a lowered overpotential relative to previous reactions. It also raises the hypothesis that this is possible due to proton-coupled electron transfer mediated by a metallocene. The fourth chapter studies the effect of acid strength on N2 fixation selectivity and demonstrates circumstantial evidence for the involvement of a decamethylcobaltocene (Cp*2Co) in the formation of N\u2212H bonds via proton-coupled electron transfer. It also highlights how the addition of co-catalytic [Cp*2Co]+ to electrochemical experiments with our Fe catalyst enabled truly electrocatalytic N2 fixation for the first time. The fifth chapter provides both atomistic detail on the protonation reactivity of Cp*2Co and experimentally verifies the prediction that this species would be an extremely strong hydrogen-atom donor. It also develops a conceptual framework to explain the uniquely weak C\u2212H bonds both homolytic and heterolytic that result from metallocene protonation and discusses their potential to play a role in not only the hydrogen evolution reaction (HER), but also the N2 fixation reaction. In the final chapter, we develop a synthetic route to a base appended cobaltocene. We demonstrate that this second-generation cobaltocene can, unlike the first generation, serve as a net hydrogen-atom donor under electrocatalytic conditions. As a demonstration of the utility of this, we use the base-appended cobaltocene for the selective, proton-coupled reduction of ketones to pinacols via a rate-determing concerted proton-electron transfer.
" }, { "name": "Chen, Kai", "degree": "PhD", "year": "2020", "title": "Expanding the Catalytic Repertoire of Hemeproteins as Carbene Transferases to Access Diverse Molecular Structures", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192020-111207482", "creators": [ { "name": { "family": "Chen", "given": "Kai" }, "id": "Chen-Kai", "orcid": "0000-0002-3325-3536", "display_name": "Chen, Kai" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9b3c-nr61", "abstract": "The efficiency, selectivity, and sustainability benefits offered by enzymes are enticing chemists to consider biocatalytic transformations to complement or even supplant more traditional synthetic routes. Increasing demands for efficient and versatile synthetic methods combined with powerful new discovery and engineering tools have prompted innovations in biocatalysis, especially the development of new enzymes for precise transformations. The past decade has witnessed impressive expansion of the catalytic repertoire of enzymes to include new and useful transformations not known (or relevant) in the biological world. The continuing discovery and improvement of these new enzyme activities is opening a floodgate that connects the chemistry of the biological world to that invented by humans over the last 100 years.
\r\n\r\nThis thesis describes a new set of enzymes, derived from a cytochrome P450 monooxygenase and a cytochrome c electron-transfer protein, which are able to function as carbene transferases to construct diverse molecular structures, including strained carbocycles and lactone derivatives. Chapter 1 illustrates different approaches researchers have utilized to explore and develop new catalytic machineries of diverse enzymes. These efforts have identified new genetically-encoded biocatalysts that can be tuned and diversified through directed evolution. Chapter 2 presents the discovery of P450 variants that catalyze the formation of highly strained carbocycles, bicyclobutanes and cyclopropenes, via carbene addition to carbon\u2012carbon triple bonds. The intrinsic strain energies of these small rigid carbocycles allow them to have broad applications in different fields, but also create challenges for their construction. Using a diazo substrate as the carbene precursor, the enzyme variants optimized by directed evolution could act on structurally diverse alkynes (aromatic or aliphatic, terminal or internal) with high efficiency and selectivity, providing an effective route to an array of chiral strained structures. The carbene transferase activity is then extended to the assembly of various lactone structures, a fundamental class of organic moieties with applications in fields varying from synthetic chemistry, to materials science, to medicinal chemistry. Chapter 3 details a strategy using lactone-based carbenes, for the transfer to different functionalities, enabling rapid access to a broad range of \u03b1-substituted and spiro-lactones with unprecedented efficiencies and selectivities. A different approach based on intramolecular carbene C\u2013H insertion is outlined in Chapter 4, which allows for the synthesis of lactones in a higher order of structural diversity. Directed evolution of a P450 variant identified a lineage of potent variants, capable of assembling lactones in different sizes (5- to 7-membered) and also with sophisticated three-dimensional structures based on fused, spiro and bridged rings. Computational tools were employed to understand the reaction mechanisms and to explain some mutational effect. In sum, the thesis work lays out how protein engineering integrated with chemical rationalization enables the expansion of the chemical space accessible to native hemeproteins, especially in building diverse molecular structures.
" }, { "name": "Davis, Hunter Cole Davis", "degree": "PhD", "year": "2020", "title": "Mechanistic Insights for Magnetic Imaging and Control of Cellular Function", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072019-141728052", "creators": [ { "name": { "family": "Davis", "given": "Hunter Cole Davis" }, "id": "Davis-Hunter-Cole-Davis", "orcid": "0000-0003-1655-692X", "display_name": "Davis, Hunter Cole Davis" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Meister", "given": "Markus" }, "id": "Meister-M", "orcid": "0000-0003-2136-6506", "role": "member", "display_name": "Meister, Markus" }, { "name": { "family": "Cushing", "given": "Scott K." }, "id": "Cushing-Scott-K", "orcid": "0000-0003-3538-2259", "role": "member", "display_name": "Cushing, Scott K." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9QEJ-6H55", "abstract": "The vast biomolecular toolkit for optical imaging and control of cellular function has revolutionized the study of in vitro samples and superficial tissues in living organisms but leaves deep tissue unexplored. To look deeper in tissue and observe system-level biological function in large organisms requires a modality that exploits a more penetrant form of energy than visible light. Magnetic imaging with MRI reveals the previously unseen, with endogenous tissue contrast and practically infinite penetration depth. While these clear advantages have made MRI a cornerstone of modern medical imaging, the sparse library of molecular agents for MRI have severely limited its utility for studies of cellular function in vivo. The development of new molecular agents for MRI has suffered from a lack of tools to study the connection between changes in the microscale cellular environment and the corresponding millimeter-scale MRI contrast. Bridging this gap requires revisiting the mechanistic underpinnings of MRI contrast, casting aside some of the simplifications that smooth over sub-voxel heterogeneity that is rich with information pertinent to the underlying cell state.
\r\n\r\nHere, we will demonstrate theoretical, computational, and experimental connections between subtle changes in microscale cellular environment and resultant MRI contrast. After reviewing some foundational principles of MRI physics in the first chapter, the second chapter of the thesis will explore computational models that have significantly enhanced the development of genetically encoded agents for MRI, including the first genetically encoded contrast agent for diffusion weighted imaging. By improving the efficacy of these genetically encoded agents, we unlock MRI reporter genes for in vivo studies of cellular dynamics much in the same way that the engineering of Green Fluorescent Protein has dramatically improved in vitro studies of cellular function.
\r\n\r\nIn the third chapter, we introduce our study that maps microscale magnetic fields in cells and tissues and connects those magnetic fields to MRI contrast. Such a connection has previously been experimentally intractable due to the lack of methods to resolve small magnetic perturbations with microscale resolution. To overcome this challenge, we leverage nitrogen vacancy diamond magnetometry to optically probe magnetic fields in cells with sub-micron resolution and nanotesla sensitivity, together with iterative localization of field sources and Monte Carlo simulation of nuclear spins to predict the corresponding MRI contrast. We demonstrate the utility of this technology in an in vitro model of macrophage iron uptake and histological samples from a mouse model of hepatic iron overload. In addition, we show that this technique can follow dynamic changes in the magnetic field occurring during contrast agent endocytosis by living cells. This approach bridges a fundamental gap between an MRI voxel and its microscopic constituents and provides a new capability for noninvasive imaging of opaque tissues.
\r\n\r\nIn the fourth chapter, we focus on the use of magnetic fields to perturb, rather than image, biological function. Recent suggestions of nanoscale heat confinement on the surface of synthetic and biogenic magnetic nanoparticles during heating by radiofrequency alternating magnetic fields have generated intense interest due to the potential utility of this phenomenon in non-invasive control of biomolecular and cellular function. However, such confinement would represent a significant departure from classical heat transfer theory. We present an experimental investigation of nanoscale heat confinement on the surface of several types of iron oxide nanoparticles commonly used in biological research, using an all-optical method devoid of potential artifacts present in previous studies. By simultaneously measuring the fluorescence of distinct thermochromic dyes attached to the particle surface or dissolved in the surrounding fluid during radiofrequency magnetic stimulation, we found no measurable difference between the nanoparticle surface temperature and that of the surrounding fluid for three distinct nanoparticle types. Furthermore, the metalloprotein ferritin produced no temperature increase on the protein surface, nor in the surrounding fluid. Experiments mimicking the designs of previous studies revealed potential sources of artifacts. These findings inform the use of magnetic nanoparticle hyperthermia in engineered cellular and molecular systems and can help direct future resources towards tractable avenues of magnetic control of cellular function.
" }, { "name": "Deegan, Meaghan Marie", "degree": "PhD", "year": "2020", "title": "Small Molecule Reactivity of Trisphosphine-Supported Iron and Cobalt Complexes", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09252019-210323106", "creators": [ { "name": { "family": "Deegan", "given": "Meaghan Marie" }, "id": "Deegan-Meaghan-Marie", "orcid": "0000-0002-7633-2074", "display_name": "Deegan, Meaghan Marie" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QDAW-M003", "abstract": "The work described in this thesis emphasizes accessing novel reactivity patterns in the activation of carbon monoxide, dinitrogen, and dihydrogen by leveraging phosphine-supported iron and cobalt complexes. In Chapters 2 and 3, systems that access CO and N2 reductive functionalization from highly reduced Fe-hydride precursors are described. These systems access productive C-H and N-H bond forming steps from hydride precursors that ultimately allows for the liberation of four-electron reduced products through novel chemical pathways. Chapter 4 describes an unusual example of a terminal cobalt carbyne through the O-functionalization of a carbonyl complex. Next, in Chapter 5, we consider electronically unusual examples of dihydrogen complexes and explore their propensity for accessing H-atom and hydride transfer. Finally, to conclude, Chapter 6 details our synthetic efforts targeting the synthesis of a terminal Fe-carbide complex through the cleavage of a thiocarbonyl precursor.
" }, { "name": "Del Ciello, Sarah Anne", "degree": "PhD", "year": "2020", "title": "Kinetic Studies of Hydrogen Oxidation by Cobaloximes and Synthesis, Spectroscopy and Boronation of a New Heteroleptic Ruthenium Cyanide Complex", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11152019-095230239", "creators": [ { "name": { "family": "Del Ciello", "given": "Sarah Anne" }, "id": "Del-Ciello-Sarah-Anne", "orcid": "0000-0002-7571-8944", "display_name": "Del Ciello, Sarah Anne" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6QTC-G360", "abstract": "Cobaloximes are macrocyclic complexes well-studied as homogeneous catalysts for hydrogen evolution, but they are also competent at the microscopic reverse reaction, hydrogen oxidation. Kinetic studies of Co(dmgBF2)2L2 reacting with hydrogen and base reveal a rate law that is second-order in cobalt and first-order in H2, indicating that the mechanism of H-H bond breaking is homolytic.
\r\n\r\nThe reduction potentials of metal cyanide complexes can be tuned by appending boranes to the N-terminus. By boronating ruthenium cyanide complexes containing diimine ligands, the RuII/III couple can be tuned without drastic modification of the diimine0/- couple. A new member of the [Ru(dimmine)(CN)4]2- family is synthesized with the ligand 4,4\u2019-bis(trifluoromethyl)-2,2\u2019-bipyridine (CF3bpy) and boronated, resulting in a molecule with two reversible redox events separated by 3.2 V.
" }, { "name": "Fajardo, Javier, Jr.", "degree": "PhD", "year": "2020", "title": "Transition Metal Complexes for Challenging Reductive Transformations: From Nitrogen Fixation Catalysts to Photoreductants", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082020-141438135", "creators": [ { "name": { "family": "Fajardo", "given": "Javier, Jr." }, "id": "Fajardo-Javier-Jr", "orcid": "0000-0003-0612-7953", "display_name": "Fajardo, Javier, Jr." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0fgd-j835", "abstract": "Transition metal complexes are routinely employed as catalysts for the reductive cleavage of a diverse array of strong chemical bonds. Two notable research areas that exemplify such utility are nitrogen fixation, involving cleavage of the notoriously unreactive triple bond of dinitrogen (N\u2082) to form ammonia (NH\u2083), and photoredox catalysis, wherein powerful photoreductants generated by visible light excitation facilitate challenging reduction steps in a host of synthetic organic transformations. This thesis focuses on a number of structure-function studies conducted on group 8 transition metal complexes that catalyze N\u2082-to-NH\u2083 conversion, commonly referred to as the nitrogen reduction reaction (N\u2082RR), and on homoleptic tungsten(0) arylisocyanides that, among their many attractive qualities, possess highly reducing electronically excited states. These comparative studies provide fundamental insight into critical design features which can guide efforts to improve existing N\u2082RR or photocatalysts or rationally tailor them for specific applications.
\r\n\r\nChapter 2 details the effect apical Lewis acidic atom substitution in P\u2083XFe platforms (X = B, Al, Ga) has on structure, bonding, and N\u2082RR activity. Structural, spectroscopic, electrochemical, and computational studies reveal that all three P\u2083XFe systems possess similar electronic structures, degrees of N\u2082 activation, and geometric flexibility, but P\u2083AlFe and P\u2083GaFe display significantly lower N\u2082RR efficiencies than P\u2083BFe when treated with HBArF\u2084/KC\u2088 or [H\u2082NPh\u2082][OTf]/Cp*\u2082Co at \u201378 \u00b0C in Et\u2082O.
\r\n\r\nChapter 3 reports on isostructural tris(phosphino)silyl Ru and Os complexes that mediate catalytic N\u2082RR. The study of the homologous, isostructural series of complexes P\u2083SiM (M = Fe, Ru, Os) helps delineate important factors for N\u2082RR catalyst design. Low-temperature protonation of P\u2083SiOs\u2013N\u2082\u207b yields P\u2083SiOs=NNH\u2082\u207a, representing the first instance of an Os\u2013N\u2082 species being converted to a protonated Os\u2013NxHy product.
\r\n\r\nChapter 4 communicates a novel series of homoleptic tungsten(0) photoactive complexes supported by fused-ring (CN-1-(2-iPr)-Naph) or alkynyl-bridged (CNDippCCAr) arylisocyanide ligands. Systematic studies establish facile electronic variation of the CNDippCCAr platform as a straightforward method by which to rationally modulate the ground- and excited-state properties of W(CNDippCCAr)\u2086 complexes. The photophysical properties of W(CN-1-(2-iPr)-Naph)\u2086 reveal potential benefits of utilizing fused-ring arylisocyanide ligands in the design of this class of photosensitizers.
" }, { "name": "Fan, Chengcheng", "degree": "PhD", "year": "2020", "title": "Structure, Function, and Application of Bacterial ABC Transporters", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012020-160106726", "creators": [ { "name": { "family": "Fan", "given": "Chengcheng" }, "id": "Fan-Chengcheng", "orcid": "0000-0003-4213-5758", "display_name": "Fan, Chengcheng" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/5t65-0047", "abstract": "The ATP-binding cassette (ABC) transporter of mitochondria (Atm1) mediates iron homeostasis in eukaryotes, while the prokaryotic homolog from Novosphingobium aromaticivorans (NaAtm1) can export glutathione derivatives and confer protection against heavy metal toxicity. To establish the structural framework underlying the NaAtm1 transport mechanism, we determined eight structures by X-ray crystallography and single particle cryo-EM in distinct conformational states, stabilized by individual disulfide crosslinks and nucleotides. As NaAtm1 progresses through the transport cycle, conformational changes in transmembrane helix 6 (TM6) alter the glutathione binding site and the associated substrate binding cavity. Significantly, kinking of TM6 in the post-ATP hydrolysis state stabilized by MgADPVO4 eliminates this cavity, precluding uptake of glutathione derivatives. The presence of this cavity during the transition from the inward-facing to outward-facing conformational states, and its absence in the reverse direction, thereby provides an elegant and conceptually simple mechanism for enforcing the export directionality of transport by NaAtm1. One of the disulfide crosslinked NaAtm1 variants characterized in this work retains significant glutathione transport activity, suggesting ATP hydrolysis and substrate transport by Atm1 may involve a limited set of conformational states with minimal separation of the nucleotide binding domains in the inward-facing conformation.
\r\n\r\nThe ATPase kinetic data was fit to a non-essential activator model with expansion to two substrate binding sites. While the structural data suggests that MgATP and GSSG bind to distinct states, outward- and inward-facing conformations, respectively, and hence might be expected to exhibit negative cooperativity, the kinetic data support a more complex interplay and also the importance of lipid molecule presence. How GSSG binding stimulates ATPase activity remains an open question and highlights the importance of the still elusive ternary complex with both MgATP and GSSG bound to NaAtm1.
\r\n\r\nBesides the structural and functional characterizations of the ABC exporter, NaAtm1, we additionally determined crystal structures of the repurposed periplasmic binding protein (PBP) from the ABC importer system. These PBPs are designed with circularly permutated GFP to act as biosensors to sense the concentrations of smoking cessation drugs and neurotransmitters under cellular conditions. The crystal structures determined for the nicotine and acetylcholine biosensors not only revealed the key residues in ligand binding, but also demonstrated similar ligand induced conformational changes as seen in other PBPs by following the Venus-flytrap mechanism.
" }, { "name": "Feng, Sean S. L.", "degree": "PhD", "year": "2020", "title": "Development of a Modular Strategy Towards the Total Synthesis of (+)-Pleuromutilin and Progress Towards the Synthesis of (\u2013)-Merrilactone A", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052020-172131873", "creators": [ { "name": { "family": "Feng", "given": "Sean S. L." }, "id": "Feng-Sean-S-L", "orcid": "0000-0002-8095-6402", "display_name": "Feng, Sean S. L." } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/chfe-0q83", "abstract": "Natural products have long stood as a rich source of biologically relevant molecules bearing highly functionalized and complex architectures. On one hand, they are a focal point for the development of new therapeutic agents owing to their inherent biological activities. On the other, they serve as an exciting testing ground for existing synthetic methodologies and provide opportunities for the development of new reactions.
\r\n\r\nHerein, we describe a modular strategy that was employed for the total synthesis of the antibiotic (+)-pleuromutilin. Key features of our synthesis include (1) the development of a highly stereoselective SmI\u2082-mediated ketyl radical cyclization to establish the central eight-membered ring and (2) a modular crotylation reaction to install the eight-membered ring\u2019s backbone that permits full control over the stereochemistry at C12 as desired. During our synthetic studies, a transannular [1,5]-hydrogen atom transfer reaction that affects a stereospecific redox relay to set the C10 stereocenter was serendipitously uncovered. This strategy enabled the completion of a concise total synthesis of (+)-pleuromutilin, proceeding in 18 steps. To demonstrate the modularity of our synthetic approach, the same strategy was readily applied to the synthesis of (+)-12-epi-pleuromutilin with no reoptimization, providing a new platform for the preparation of fully synthetic derivatives that may hold promise as broad-spectrum antibiotics.
\r\n\r\nThis report also highlights the work we have conducted in the development of a synthetic strategy towards (\u2013)-merrilactone A. We detail our investigation of a Pd-catalyzed asymmetric allylic alkylation reaction that rapidly constructs the D-ring bearing the C5 and C6 vicinal quaternary centers. Potential paths forward to complete the synthesis of this neurotropic natural product leveraging this advanced intermediate will also be discussed.
" }, { "name": "Goldstein, Elizabeth Lee", "degree": "PhD", "year": "2020", "title": "Synthesis of Enantioenriched (Poly)Fluorinated Building Blocks, 2,2-Disubstituted Pyrrolidines and [7,7]Paracyclophanes", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042020-213305750", "creators": [ { "name": { "family": "Goldstein", "given": "Elizabeth Lee" }, "id": "Goldstein-Elizabeth-Lee", "orcid": "0000-0002-2208-6090", "display_name": "Goldstein, Elizabeth Lee" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hks0-tg22", "abstract": "The Stoltz group, and moreover the synthetic community at large, has long been interested in the synthesis of enantioenriched compounds with interesting biological activities. This thesis presents three projects unified in an attempt to access compounds with relevance to the medicinal chemistry and natural products communities, encompassing reaction development, synthetic strategy and natural product synthesis.
\r\n\r\nA general method for the enantioselective synthesis of carbo- and heterocyclic carbonyl compounds bearing fluorinated \u03b1-tetrasubstituted stereocenters using palladium-catalyzed allylic alkylation is described. These fluorinated, stereochemically rich building blocks hold potential value in medicinal chemistry and are prepared using an orthogonal and enantioselective approach into such chiral moieties compared to traditional approaches, often without the use of electrophilic fluorinating reagents.
\r\n\r\nThe synthesis of a variety of enantioenriched 2,2-disubstituted pyrrolidines is described. A stereogenic quaternary center is first formed utilizing an asymmetric allylic alkylation reaction of a benzyloxy imide, which can then be reduced to a chiral hydroxamic acid. This compound can then undergo a thermal \"Spino\" ring contraction to afford a carbamate protected 2,2-disubstituted pyrrolidine stereospecifically, allowing access to new molecules that could be useful in the medicinal chemistry community.
\r\n\r\nFinally, we have developed a synthesis of an enaptioenriched [7,7]paracyclophane compound using sequential C-H functionalization reactions, including selective Rh-catalyzed C-H insertion reactions developed by the Davies group at Emory University. Investigations are currently ongoing into potential antimicrobial activity of different [7,7]paracyclophanes and the total synthesis of naturally occurring [7,7]paracyclophanes.
" }, { "name": "Gu, Nina Xiao", "degree": "PhD", "year": "2020", "title": "Synthesis, Characterization, and Reactivity of Thiolate-Supported Metalloradicals", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04102020-135244808", "creators": [ { "name": { "family": "Gu", "given": "Nina Xiao" }, "id": "Gu-Nina-Xiao", "orcid": "0000-0002-4637-8418", "display_name": "Gu, Nina Xiao" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8zwz-gh20", "abstract": "Reactive metalloradical intermediates have been implicated in both biological and synthetic catalyst systems for small molecule activation processes, including proton reduction and ammonia oxidation. Towards a greater mechanistic understanding of such transformations on well-defined model complexes, this thesis explores relevant H\u2013H and N\u2013N bond-forming reactions mediated by trivalent Fe and Ni species, as well as catalytic N\u2013N bond cleavage mediated by an open-shell VFe bimetallic complex. First, a pair of thiolate-supported, S = \u00bd iron and nickel hydrides are synthesized and spectroscopically characterized at low temperatures (Chapters 2, 3). Paramagnetic iron and nickel hydrides have been proposed as catalytic intermediates of [NiFe] hydrogenase and nitrogenase, but characterization of such molecular species are limited. For both the FeIII and NiIII hydride complexes described herein, spin delocalization onto the thiolate ligand is proposed to stabilize the formal 3+ metal oxidation state. Furthermore, both the FeIII\u2013H and NiIII\u2013H species are demonstrated to undergo the bimolecular reductive elimination of dihydrogen upon warming, albeit with distinct activation parameters consistent with different proposed pathways for H\u2013H bond formation. Chapter 4 expands upon the H\u2013H bond forming chemistry demonstrated on the Ni system to demonstrate related N\u2013N bond formation from an analogous NiIII\u2013NH2 species, resulting in the formation of a NiII2(N2H4) complex. Given the diverse mechanistic possibilities for the overall 6e-/6H+ transformation to oxidize ammonia to dinitrogen, identification of the active M(NHx) intermediate and pathway for N\u2013N bond formation is a central mechanistic question. While the homocoupling of M\u2013NH2 species to form hydrazine has been hypothesized as the key N\u2013N bond forming step in ammonia oxidation systems, stoichiometric examples of this transformation from M\u2013NH2 complexes are rare. Lastly, Chapter 5 details the synthesis of a heterobimetallic VFe complex featuring a bridging thiolate, inspired by the structure of the VFe nitrogenase cofactor. This VFe species is demonstrated to be an active catalyst for the disproportionation of hydrazine to dinitrogen and ammonia. Notably, the heterobimetallic complex is appreciably more active than monometallic analogues of the individual V and Fe sites, suggesting that bimetallic cooperativity may facilitate the observed catalysis.
" }, { "name": "Hirscher, Nathanael Allen", "degree": "PhD", "year": "2020", "title": "Investigation of Ethylene Tetramerization Catalysis from Structurally-Defined Organochromium Compounds", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012019-192629717", "creators": [ { "name": { "family": "Hirscher", "given": "Nathanael Allen" }, "id": "Hirscher-Nathanael-Allen", "display_name": "Hirscher, Nathanael Allen" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GVYR-MV95", "abstract": "Chapter 1 is a general introduction to the topic of ethylene tetramerization catalysis.
\r\n\r\nChapter 2 presents the synthesis and catalytic utility of chromium multi-aryl complexes that were the first examples of ethylene tetramerization catalysts that could be produced without excess alkyl aluminum reagents.
\r\n\r\nChapter 3 describes the mechanistic analysis of the ethylene tetramerization reaction using isotopically labelled ethylene. Co-production of 1-hexene along with 1-octene was determined to be intrinsic to the reaction mechanism. This is due to the intermediacy of a chromacyclic species that can either eliminate 1-hexene or insert a fourth ethylene.
\r\n\r\nChapter 4 presents the synthesis of additional Cr tris(aryl) complexes, which are coordinatively saturated, and were used to generate a crystallographically-characterized Cr(III) cationic species. This was the first reported single-component precatalyst for ethylene tetramerization.
\r\n\r\nChapter 5 describes the isotopic labelling of a well-defined ethylene tetramerization precatalyst with a deuteriomethyl group. This label was tracked following protonation of the neutral Cr complex via pulse EPR. Successful detection of deuterium on Cr-alkyl ligands led to in situ analysis of the catalytic mixture. A low-spin species derived from deuterated ethylene was observed.
\r\n\r\nAppendix 1 describes the synthesis of various Cr aryl amine complexes. Appendix 2 provides the results of additional catalytic experiments for ethylene tetramerization, including those with a more soluble precatalyst, and those at higher ethylene pressure. Appendix 3 details the synthesis of a molecular Re catalyst for CO2 electroreduction which was used to modify electrodes. Appendix 4 lists various X-ray crystal structures that were obtained, but not related elsewhere in the thesis.
" }, { "name": "Jung, Yonil", "degree": "PhD", "year": "2020", "title": "Neurons that Control Social States in Drosophila melanogaster", "advisor": "Anderson, David J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122020-231054692", "creators": [ { "name": { "family": "Jung", "given": "Yonil" }, "id": "Jung-Yonil", "orcid": "0000-0002-1673-4450", "display_name": "Jung, Yonil" } ], "advisors": [ { "name": { "family": "Anderson", "given": "David J." }, "id": "Anderson-D-J", "role": "advisor", "display_name": "Anderson, David J." } ], "committee": [ { "name": { "family": "Meister", "given": "Markus" }, "id": "Meister-M", "role": "chair", "display_name": "Meister, Markus" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Anderson", "given": "David J." }, "id": "Anderson-D-J", "role": "member", "display_name": "Anderson, David J." } ], "option_major": [ "biochem" ], "doi": "10.7907/pard-ed88", "abstract": "Animal behaviors are influences not only by the immediate stimuli they are receiving but also by internal states. Internal states such as fear, hunger, and arousal can change subjective \"feeling\", and result in complex behavioral outcome even if animals receive the same stimuli. In most cases, these state-dependent behavioral changes persist long after the sensory input that caused internal state change is removed, and affect future behavior, reflexing previous experience. This feature of state-control allows animals to adapt their behavior to be more suitable for their internal demands.
\r\n\r\nThe influence of the internal state on animal behavior has been emphasized for decades. There are multiple studies and attempts to identify persistent neuronal mechanisms which are the important feature of the internal state. However, how persistency makes the behavioral state interact with behavioral process to induce input/output relationship has been largely unknown. In addition, it is not clear what the behavioral functions of the persistence are, and what the circuit implementation of persistent activity is. Are there neurons that are persistently activated by external stimulus? Here we approached these questions by investigating social state of fruit flies, Drosophila melanogaster.
\r\n\r\nFruit flies exhibit complex social behaviors that are appropriate for given social cues. For example, male flies show courtship behavior toward female flies, and show aggressive behavior such as wing threat and fighting when they encounter opponent male files. Previous studies have been focused on what sensory cues induce these behaviors: detection of female specific pheromones, 7,11-HD, causes male files to court, and male specific pheromone, cVA, induces inter-male aggression. In this study, we have focused more on how these cues might affect internal state changes rather than immediate behavioral response.
\r\n\r\nStudying persistent social state change has been challenging due to the difficulty of precise, time-resolved presentation of the social cues. For instance, courtship behaviors require constant presence of female object toward which male flies show oriented behavior. The male-male aggressive behaviors such as lunging and tussling require constant interaction between two animals, and removal of opponent male fly is technically impossible. Therefore, we first developed an optogenetic tool in fly systems to study persistent feature of the social state change to mimic transient presentation of the social cue. In Chapter II, we describe an optogenetic tool that allows the manipulation of neural activity in a freely moving fly. We used Red activatable Channelrhodopsin (ReachR), which enabled us to manipulate activation of neurons in freely behaving adult flies in millisecond precision without interfering normal visual function. Using such an activation tool, we show that activation of female sensing neurons, P1 neurons, induces persistent courtship behaviors in male flies that last several minutes after the stimulation of P1 neurons.
\r\n\r\nAlthough we show that persistent internal state change can be induced by transient stimulation of the sensory cues in Chapter II, the circuit implementation of such a persistency is not clear. In Chapter III, we show that activation of P1 neurons triggers persistent activity in its downstream neurons, pCd neurons, that is necessary for the persistent social behavior induced by transient social behaviors. Interestingly, manipulation of the pCd neurons do not affect immediate behavioral response that are shown during the presentation of social cues (P1 stimulation), implying that there are parallel and dissociable pathways for the immediate response and enduring response derived from persistent internal state change, although these responses are caused by common cue. Although the neural mechanism to encode persistent activity is still unclear, this finding shows how internal state and command pathway interact with each other to affect behavioral outcome.
\r\n\r\nAltogether, these findings described in this dissertation offer new insights for future researchers to understand behavioral state control.
\r\n" }, { "name": "Krueger, Rachel Ann", "degree": "PhD", "year": "2020", "title": "Theoretical Characterization of Aromatic Exciplex Fluorescence", "advisor": "Blanquart, Guillaume", "url": "https://resolver.caltech.edu/CaltechTHESIS:07242019-140324087", "creators": [ { "name": { "family": "Krueger", "given": "Rachel Ann" }, "id": "Krueger-Rachel-Ann", "orcid": "0000-0002-5457-2931", "display_name": "Krueger, Rachel Ann" } ], "advisors": [ { "name": { "family": "Blanquart", "given": "Guillaume" }, "id": "Blanquart-G", "orcid": "0000-0002-5074-9728", "role": "advisor", "display_name": "Blanquart, Guillaume" } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Blanquart", "given": "Guillaume" }, "id": "Blanquart-G", "orcid": "0000-0002-5074-9728", "role": "member", "display_name": "Blanquart, Guillaume" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FW2R-BF41", "abstract": "The negative effects of soot on the environment and human health are well known, but efforts to decrease soot production in combustion processes are hampered by the absence of accurate, transferable models for soot formation. Uncertainties about the soot nucleation mechanism, including the size and properties of the molecules involved and the relative importance of chemical and physical stabilization, have made model development difficult. Electronic spectroscopy methods such as laser-induced fluorescence (LIF) have the potential to characterize transient soot nuclei, but interpreting spectra requires a comprehensive understanding of the photoresponse of likely soot precursors, namely polycyclic aromatic hydrocarbon (PAH) dimers and clusters. To build up a picture of this photoresponse using theory, it is necessary to evaluate which methods are capable of treating the relevant molecules at reasonable cost while capturing the excited-state and noncovalent interactions involved in excimer and exciplex formation, a key excited-state process for aromatic clusters. In this work, we describe extensive benchmarking of basis set error in highly-accurate perturbatively-corrected multireference calculations of exciplex interaction strength and use the best possible multireference approach to evaluate the performance of less-expensive time-dependent density functional theory (TDDFT) results. Using the most accurate TDDFT methods, we explore how the geometric and electronic properties of the monomers influence excited-state interactions in complexes, considering a large database of complexes. A predictive model for exciplex fluorescence emissions of complexes containing six-membered ring PAHs based on monomer HOMO-LUMO gaps is proposed. We describe the contrasting photoresponse of PAHs containing five-membered rings, where nonaromatic groups produce conformational flexibility that has a strong impact on absorption and emission behavior.
" }, { "name": "Lee, Kyu Hyun", "degree": "PhD", "year": "2020", "title": "Visual Computations in the Superior Colliculus", "advisor": "Meister, Markus", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012020-165101402", "creators": [ { "name": { "family": "Lee", "given": "Kyu Hyun" }, "id": "Lee-Kyu-Hyun", "orcid": "0000-0001-6483-9444", "display_name": "Lee, Kyu Hyun" } ], "advisors": [ { "name": { "family": "Meister", "given": "Markus" }, "id": "Meister-M", "role": "advisor", "display_name": "Meister, Markus" } ], "committee": [ { "name": { "family": "Tsao", "given": "Doris Y." }, "id": "Tsao-D-Y", "role": "chair", "display_name": "Tsao, Doris Y." }, { "name": { "family": "Anderson", "given": "David J." }, "id": "Anderson-D-J", "role": "member", "display_name": "Anderson, David J." }, { "name": { "family": "Rutishauser", "given": "Ueli" }, "id": "Rutishauser-U", "role": "member", "display_name": "Rutishauser, Ueli" }, { "name": { "family": "Meister", "given": "Markus" }, "id": "Meister-M", "role": "member", "display_name": "Meister, Markus" } ], "option_major": [ "biochem" ], "doi": "10.7907/zn2j-m319", "abstract": "This thesis presents two projects related to large-scale extracellular recordings of neural signals. The first project asks how the brain sifts the onslaught of sensory information to identify the few bits that are relevant for guiding behavior. This question is studied in the context of the looming reaction, an innate defensive behavior against an approaching aerial predator. Interestingly, the mouse responds very selectively to the looming stimulus regardless of changes in orthogonal features, such as its position. The neural basis of this phenomenon is investigated with extracellular recordings in the superior colliculus, a midbrain visual area known to mediate the looming reaction. A detailed analysis of the difference between the superficial and deeper layers of the superior colliculus highlights a core function of visual processing: to discard information intelligently.
\r\n\r\nThe second project presents electrode pooling, a novel method to increase the yield of extracellular recordings with the modern silicon electrode array. The fundamental constraint of wire volume in these devices is identified, and a solution that makes use of the switching circuitry and the sparseness of the neural signal in the time axis is described. Specifically, the method proposes to intelligently choose many recording sites that carry signal and connect them to a single wire via manipulating the switches. This pooled recording is subsequently un-mixed by a spike-sorting algorithm. The method is implemented in a state-of-the-art silicon neural probe, and its effect on signal and noise is analyzed by theory and experiment. Recommendations on the design of silicon devices are made to facilitate the incorporation of this method in the future.
" }, { "name": "Li, Jiaming", "degree": "PhD", "year": "2020", "title": "Concise Total Syntheses of \u2206\u00b9\u00b2-Prostaglandin J Natural Products Using Stereoretentive Metathesis", "advisor": "Grubbs, Robert H.; Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202019-023320724", "creators": [ { "name": { "family": "Li", "given": "Jiaming" }, "id": "Li-Jiaming", "orcid": "0000-0001-6646-5693", "display_name": "Li, Jiaming" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "co-advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q78K-7R18", "abstract": "\u2206\u00b9\u00b2-Prostaglandin J family is a type of secondary metabolite isolated in cell culture, and is recently discovered to have potent anticancer activity. Concise syntheses of four \u2206\u00b9\u00b2-prostaglandin J natural products (7\u20138 steps in the longest linear sequences) are developed, enabled by convergent stereoretentive cross-metathesis by Ru-based metathesis catalyst. Exceptional control of alkene geometry was achieved through stereoretention.
" }, { "name": "Liu, Xinran", "degree": "PhD", "year": "2020", "title": "Cell-Selective Proteomic Profiling in Complex Biological Systems", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282020-112303076", "creators": [ { "name": { "family": "Liu", "given": "Xinran" }, "id": "Liu-Xinran", "orcid": "0000-0003-0045-8823", "display_name": "Liu, Xinran" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." } ], "option_major": [ "chemeng" ], "doi": "10.7907/p18t-5j69", "abstract": "Cells within biological systems are constantly adjusting their protein synthesis in response to various environmental changes. To study the rapid cellular regulations in complex biological systems, global proteomic profiling provides important information on system-level regulations, yet physiological properties characteristic of individual cellular subpopulations could be hidden under the characterization. Instead, cell-selective proteomic profiling allows researchers to reveal the heterogeneities in biological systems with phenotypically and even genetically distinct subpopulations under different microenvironments.
\r\n\r\nChapter 1 describes the development of bioorthogonal noncanonical amino acid tagging (BONCAT) for proteomic profiling with resolution in both space and time: its initial role is protein labeling with temporal resolution via pulse-addition of noncanonical amino acid, which could be recognized by endogenous aminoacyl tRNA-synthetase (aaRS), into systems of interest; later on, mutant aaRSs are identified through mutant synthetase library screening, which allows for efficient incorporation of various types of noncanonical amino acids that could hardly be activated by endogenous machineries. The identification and exploitation of mutant aaRSs allow sensitive cellular selectivity during protein labeling. With unprecedented spatiotemporal resolution of BONCAT, and the advancement in high-resolution mass spectrometry and computational algorithms, BONCAT is a powerful technique for selective proteomic profiling to study physiological regulations in a wide range of complex biological systems.\r\nChapter 2 describes the application of the BONCAT method in cell-selective proteomic profiling in Pseudomonas aeruginosa biofilms. In this work, we targeted an iron-starved subpopulation in biofilms and compared its proteomic profile with that of the entire system. Key gene and pathway regulations in the subpopulation are found through the analysis of the proteomic data, which suggest that iron-starved cells shift their priority towards housing keeping pathways, adapt an energy- and resources-saving mode to cope with their harsh local environmental conditions, and get prepared to disperse for better survival. Analysis of poorly studied proteins highly upregulated in the subpopulation led to the discovery of a previously uncharacterized protein (PA14_52000) that is potentially related to iron acquisition. The transposon insertion mutant PA14_52000::tn showed significantly enhanced pyoverdine production in rich medium and reduced biofilm formation.
\r\n\r\nChapter 3 describes the study of physiological regulations in Bacillus subtilis K-state subpopulation via BONCAT. A subset of B. subtilis cells, typically 10% - 20% of the entire population, enter K-state in a stochastic manner. With the low level of K-state entry rate and high randomness, we challenged BONCAT to specifically capture gene and pathway regulations in K-state cells and compared the proteomic profiling with that of the entire population. Regardless of the difficulties of selective protein labeling inherent in the system, our results indicate that BONCAT has high specificity and resolution in proteomic profiling for minor subpopulations and proteins with low overall absolute abundance. We found multiple pathways and genes characteristic of K-state regulated differentially from the entire population, either significantly up- or down-regulated. Proteins that are uncharacterized or previously known for functions irrelevant of K-state are highly abundant in the subpopulation, providing new insight toward their alternative functions critical for K-state cells and future investigation directions of K-state study.
" }, { "name": "Lunny, Elizabeth Margaret", "degree": "PhD", "year": "2020", "title": "High-Resolution Photoacoustic Spectroscopy of the Oxygen A-Band", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082020-132244698", "creators": [ { "name": { "family": "Lunny", "given": "Elizabeth Margaret" }, "id": "Lunny-Elizabeth-Margaret", "orcid": "0000-0002-1464-8233", "display_name": "Lunny, Elizabeth Margaret" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "orcid": "0000-0002-6126-3854", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Drouin", "given": "Brian J." }, "id": "Drouin-Brian-J", "orcid": "0000-0002-9125-2822", "role": "member", "display_name": "Drouin, Brian J." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qxcm-4909", "abstract": "There have been many advances in recent years in remote sensing and ground-based measurement technologies utilizing optical detection to identify and quantify species in the atmosphere. Many of these instruments record high signal-to-noise spectra requiring sophisticated spectral modeling beyond the Voigt profile. In order to properly quantify the higher order spectral effects, high-resolution laboratory data measuring samples of known composition under carefully controlled conditions are required.
\r\n\r\nThe oxygen A-band is used in a number of atmospheric composition measurements due to the uniform, well-known concentration of oxygen throughout the atmosphere. Previous laboratory A-band measurements using cavity ring-down spectroscopy and Fourier transform spectroscopy have greatly improved the understanding of spectral parameters. However, current spectral models are insufficient to fit some high quality remote sensing data, such as the OCO missions. The largest spectroscopic uncertainties in modeling result from characterization of line mixing and collision-induced absorption. These collisional effects, resulting in small absorption changes in the baseline and wings, which become more prominent at elevated pressures can be accurately measured with photoacoustic spectroscopy, a background free measurement with a large dynamic range producing high signal-to-noise spectra.
\r\n\r\nA novel high-resolution photoacoustic spectrometer was designed and constructed to improve the understanding of A-band spectral parameters to meet the OCO mission goals. The spectrometer is capable of measuring both the P and R-branches of the A-band up to J'=28 with a signal-to-noise ratio of 30,000 for pressures of 50-4,000 Torr. A temperature control system was also implemented to allow for measurements over the range of atmospherically relevant temperatures.
\r\n\r\nResults from spectral fitting of data from the newly developed spectrometer provide the most accurate A-band pressure shift coefficients for both oxygen and air measured to date. The data also indicates the importance of lineshape profile choice for resonant absorption in order to accurately characterize line mixing and collision-induced absorption; the speed-dependent Nelkin-Ghatak profile is required for the current data set. Finally, preliminary fitting of line mixing and collision-induced absorption suggests the photoacoustic data achieves the required sensitivity to provide improved understanding of line mixing and collision-induced absorption based on fundamental physical principles.
" }, { "name": "McNicholas, Brendon James", "degree": "PhD", "year": "2020", "title": "New Electrolytic Media and Methods for Energy Storage and Conversion", "advisor": "Gray, Harry B.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082020-143301441", "creators": [ { "name": { "family": "McNicholas", "given": "Brendon James" }, "id": "McNicholas-Brendon-James", "orcid": "0000-0002-3654-681X", "display_name": "McNicholas, Brendon James" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "chair", "display_name": "See, Kimberly" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1sew-r360", "abstract": "New electrolytic media and methods for energy storage and conversion are needed to fully realize the sustained use of renewable energy and complete removal of dependence on fossil fuels. Motivated by this urgency, researchers today are heavily invested in developing new electrocatalytic systems for carbon dioxide sequestration to reduce greenhouse gas emissions and new battery architectures, such as non-aqueous redox flow batteries, to keep solar energy at our disposal during peak times of energy consumption. Chapter 1 provides an overview of the conceptual frameworks for these two alternative energy technologies and a literature review of relevant work and inspiration in these fields. Chapter 2 demonstrates one of the first examples of ionic liquid voltammetry of a molecular species, namely (tpfc)Mn, and its electron transfer reactivity in ionic liquids with varying solvent viscosity, effective electrolyte concentration, and donor strength. As well as showing the non-unity diffusional properties of molecular species in ionic liquids and the capability of ionic liquid anions to coordinate to molecular species, these studies suggest the viability of ionic liquids as conductive media for energy storage and conversion. Chapter 3 introduces methods for immobilization of molecular catalysts in polymeric ion gels, a general strategy that bridges the divide between homogeneous solution-state catalysis and heterogeneous solid-state catalysis. These results provide insight into how environment, catalyst concentration, catalyst mobility, substrate availability, and dielectric properties of a medium all affect the catalytic response and overpotential for CO2 reduction. Further implementation of these ion gel composites in solid-state devices, in aqueous environments, and in gas diffusion electrodes is also discussed. In Chapter 4, a brief overview of the use of boranes as capping ligands for cyanide is provided. The synthesis, electronic properties, and theoretical calculations of homoleptic, boronated Fe(II) hexacyanoferrates are reported. Addition of borane to cyanometallates dramatically alters electronic structures and is a novel method for permanent modification of formal potentials while simultaneously maintaining or improving electrochemical reversibility and ambient stability. These complexes are characterized and studied by cyclic and differential pulse voltammetry, UV-vis, IR, and Raman spectroscopy, and flash-quench photolysis. Chapter 5 extends the unique reactivity of borane adducts to the characterization of a full series of hexaisocyanoboratometallates (Cr, Mn, Fe, Ru, Os), compounds which demonstrate the concept of cyanide as a \u201cvariable-field\u201d ligand, including magnetic circular dichroism spectroscopy, electron paramagnetic resonance spectroscopy, luminescence studies, excited-state lifetime studies, and electrochemistry. As electrolytes for non-aqueous redox flow batteries, these species exhibit excellent Coulombic and voltage efficiencies and fast electron transfer rates. The highly oxidizing species will also find use as reversible oxidants for chemical oxidations. Chapter 6 extends the concept of modifying formal potentials to heteroleptic cyanometallates (M = Fe, Ru) with diimine ligands (L = bipyridine, phenanthroline, 4,4\u2019-trifluoromethylbipyridine). These species are shown to be potent excited-state reductants and oxidants, strong and long-lived phosphors, and promising electrolytes for symmetric, non-aqueous redox flow batteries. These data also demonstrate improved excited-state lifetimes for borane-appended species, likely due to inhibition of non-radiative decay pathways. Chapter 7 focuses on the generation of a solution stable, square pyramidal Co(II) species, which is studied by electrochemistry, UV-vis-NIR spectroscopy, X-band and Q-band CW EPR, and pulsed EPR techniques (HYSCORE, ENDOR). These studies demonstrate that boronation of cyanide differentially affects the energies of ligand field transitions based on \u03c0 backbonding ability." }, { "name": "Ng, Ryan Cecil", "degree": "PhD", "year": "2020", "title": "Nanophotonic Phenomena in Dielectric Photonic Crystals", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02122020-151048251", "creators": [ { "name": { "family": "Ng", "given": "Ryan Cecil" }, "id": "Ng-Ryan-Cecil", "orcid": "0000-0002-0527-9130", "display_name": "Ng, Ryan Cecil" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "Faraon", "given": "Andrei" }, "id": "Faraon-A", "role": "chair", "display_name": "Faraon, Andrei" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "member", "display_name": "Greer, Julia R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZP30-F550", "abstract": "Photonic crystals are periodic optical nanostructures with varying dielectric constant that allow light flow to be controlled and manipulated much in a similar way to electrons within a semiconductor crystal. These nanostructures tend to have a spatially varying refractive index on the order of the wavelength of light to be manipulated. 1D and 2D photonic crystals have already garnered significant attention in the realm of thin-film optics, while 3D photonic crystals have been thus far limited in application, due to difficulties in fabrication and a lack of available materials for fabrication.
\r\n\r\nIn this work, we first explore 1D and 2D photonic crystals based on the concept of a guided mode resonance, which manifests as a narrow near-unity resonance in reflection or transmission that arise from the coupling of an incident wave into a leaky waveguide mode via a grating vector that is subsequently re-radiated. Such a resonance is well-suited for multi- and hyper- spectral filtering applications in the infrared. We designed a platform consisting of amorphous Si arrays embedded in SiO2 in simulation and experiment for application as narrow stopband filters. We present the tunability of the spectral characteristics of the resonance in these arrays through variation of array geometric parameters in simulation and experiment. Guided mode resonance designs often consider only the case of an infinite array, where the leaky waveguide mode can propagate laterally for hundreds of periods, allowing for this mode to eventually scatter out of the array giving rise to the characteristic narrow near-unity rapid spectral variations of a GMR. With an insufficient number of periods, the quality factor and thus the optical filtering performance is greatly diminished. Thus, we further extend our analysis to compact periodic arrays of finite size, which are required for high spatial resolution snapshot imaging, and introduce array designs that operate under finite size limitations in the near-infrared.
\r\n\r\nWe then transition to 3D photonic crystals, exploring the use of an additive manufacturing process to directly fabricate nanocrystalline rutile TiO2 with ~100 nm resolution. Though TiO2 was chosen as the model material, the key to this work is that a similar process can be used to print many different materials, enabling future applications of 3D photonic crystals. The focus here is the additive manufacturing of high index materials such as TiO2, and its potential for photonic applications is demonstrated by characterizing the optical band gap of 3D PhC TiO2 structures printed with this method. We present a system where the ability to print high refractive index 3D photonic crystals would be useful, by studying 3D polymer-germanium core-shell structures that should exhibit all-angle negative refraction in the mid-infrared regime.
" }, { "name": "Porubsky, Nicholas James", "degree": "PhD", "year": "2020", "title": "Enhanced Algorithms for Analysis and Design of Nucleic Acid Reaction Pathways", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062019-213347699", "creators": [ { "name": { "family": "Porubsky", "given": "Nicholas James" }, "id": "Porubsky-Nicholas-James", "orcid": "0000-0001-6330-2645", "display_name": "Porubsky, Nicholas James" } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "advisor", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "role": "chair", "display_name": "Winfree, Erik" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/M8CZ-MW98", "abstract": "Nucleic acids provide a powerful platform for programming at the molecular level. This is possible because the free energy of nucleic acid structures is dominated by the local interactions of base pairing and base pair stacking. The nearest neighbor secondary structure model implied by these energetics has enabled development of a set of algorithms for calculating thermodynamic quantities of nucleic acid sequences. Molecular programmers and synthetic biologists continue to extend their reach to larger, more complicated nucleic acid complexes, reaction pathways, and systems. This necessitates a focus on new algorithm development and efficient implementations to enable analysis and design of such systems.
\r\n\r\nConcerning analysis of nucleic acids, we collect seemingly diverse algorithms under a unified three-component dynamic programming framework consisting of: 1) recursions that specify the dependencies between subproblems and incorporate the details of the structural ensemble and the free energy model, 2) evaluation algebras that define the mathematical form of each subproblem, 3) operation orders that specify the computational trajectory through the dependency graph of subproblems. Changes to the set of recursions allows operation over the complex ensemble including coaxial and dangle stacking states, affecting all thermodynamic quantities. An updated operation order for structure sampling allows simultaneous generation of a set of structures sampled from the Boltzmann distribution in time that scales empirically sublinearly in the number of samples and leads to an order of magnitude or more speedup over repeated single-structure sampling.
\r\n\r\nFor the problem of sequence design for reaction pathway engineering, we introduce an optimization algorithm to minimize the multitstate test tube ensemble defect, which simultaneously designs for reactant, intermediate, and product states along the reaction pathway (positive design) and against crosstalk interactions (negative design). Each of these on-pathway or crosstalk states is represented as a target test tube ensemble containing arbitrary numbers of on-target complexes, each with a target secondary structure and target concentration, and arbitrary numbers of off-target complexes, each with vanishing target concentration. Our test tube specification formalism enables conversion of a reaction pathway specification into a set of target test tubes. Sequences are designed subject to a set of hard constraints allowing specification of properties such as sequence composition, sequence complementarity, prevention of unwanted sequence patterns, and inclusion of biological sequences. We then extend this algorithm with soft constraints, enhancing flexibility through new constraint types and reducing design cost by up to two orders of magnitude in the most highly constrained cases. These soft constraints enable multiobjective design of the multitstate test tube ensemble defect simultaneously with heuristics for avoiding kinetic traps and equalizing reaction rates to further aid reaction pathway engineering.
\r\n" }, { "name": "Schuman, David Phillip", "degree": "PhD", "year": "2020", "title": "Development and Mechanistic Investigation of Potassium Tert-Butoxide Catalyzed C\u2013H Silylation", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132020-174738338", "creators": [ { "name": { "family": "Schuman", "given": "David Phillip" }, "id": "Schuman-David-Phillip", "display_name": "Schuman, David Phillip" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/248y-cp18", "abstract": "The synthetic organic community has a long history of concurrent development of new methods, total syntheses, and mechanistic investigations. For example, new methods may allow the synthesis of previously inaccessible synthetic targets or a challenging transformation in a total synthesis may lead to the development of new reaction methods. Understanding the mechanism of a reaction may lead to the development of new methods or application in total synthesis. Historically, the Stoltz group has found great success focusing on the synergistic development of reaction methods, total synthesis, and mechanistic investigation. This thesis focuses on the mechanistic investigation of a novel method developed by our group and a number of new methods inspired by this better understanding of the reaction mechanism.
\r\n\r\nInitially, an overview of transition-metal-free, catalytic C\u2013H silylation reactions is presented. Next, a detailed mechanistic investigation into the KOt-Bu-catalyzed C\u2013H silylation reaction of aromatic heterocycles is presented. This investigation covers a series of experimental, computational, and analytic techniques to probe possible radical or ionic reaction mechanisms. The development of a number of new methods is presented including the catalytic trimethylsilylation of aromatic heterocycles and catalytic silylation of terminal alkynes.
\r\n\r\nFinally, the current progress of our efforts toward the total synthesis of the natural product illisimonin A are presented.
" }, { "name": "Schwan, Lars Josef", "degree": "PhD", "year": "2020", "title": "Electronic Structures of Perfunctionalized Dodecaborate Clusters", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04062020-155127311", "creators": [ { "name": { "family": "Schwan", "given": "Lars Josef" }, "id": "Schwan-Lars-Josef", "orcid": "0000-0002-1086-6698", "display_name": "Schwan, Lars Josef" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jf75-8k37", "abstract": "Dodecahydro-closo-dodecaborate is only stable as a dianionic closed-shell species, however, some alkyloxy- and aryloxy-perfunctionalized dodecaborate clusters ([B12(OR)12], R = alkyl or aryl) can be isolated in hypoelectronic hypocloso-dodecaborate(1-) and hypercloso-dodecaborate(0) states. These hypoelectronic clusters display strong visible absorption bands and highly reversible redox behavior, which have inspired applications in photochemistry, charge-storage and as dopants in conducting polymers. Chapter 1 provides a historic overview of dodecaborate research with particular focus on the development and applications of hypoelectronic clusters. Chapter 2 summarizes our spectroscopic investigtion of the photochemistry and photophysical properties of aryloxy-perfunctionalized hypercloso-dodecaborate(0) clusters. Obtaining reliable photophysical data proved exceedingly difficult due to formation of reduced hypocloso-dodecaborate(1-) species through solvent photooxidation, disproportionation and solvent-cluster interactions. A detailed discussion on these issues is presented, along with the final luminescence data collected for hypercloso-dodecaborate(0) and hypocloso-dodecaborate(1-) clusters. In Chapter 3, we present evidence indicating that certain alkyloxy-perfunctionalized dodecaborate clusters can be further oxidized to a cationic state. Electrochemical and spectroelectrochemical characterization indicate reversible conversion between the dodecaborate(0) and dodecaborate(1+) state. The results are further corroborated by EPR studies on dodecaborate(1+) clusters in-situ generated using the strong oxidant tris(2,4-dibromophenyl)ammoniumyl hexachloroantimonate. In chapter 4, we present Q-band pulsed EPR results that give a quantitative measure of the spin distribution of both hypercloso-dodecaborate(1-) and super-oxidized dodecaborate(1+) clusters. This is to our knowledge the first time pulsed EPR techniques have been applied to hypoelectronic dodecaborate clusters. The EPR data indicate that the frontier orbitals of hypoelectronic dodecaborate clusters are confined to the cluster core and delocalized evenly across the B12 pseudo-icosahedron. Furthermore, we provide UV\u2013vis\u2013NIR evidence indicating that the visible and NIR electronic transitions of these clusters occur between orbitals that are largely confined to the cluster core. Chapter 5 summarizes our results and discusses future directions." }, { "name": "Silva, Rebekah Miriam Brawer", "degree": "PhD", "year": "2020", "title": "Attributes of the [4Fe4S] Cofactor Coordinated by UvrC, a DNA Repair Enzyme", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082020-163907557", "creators": [ { "name": { "family": "Silva", "given": "Rebekah Miriam Brawer" }, "id": "Silva-Rebekah-Miriam-Brawer", "orcid": "0000-0002-9144-4939", "display_name": "Silva, Rebekah Miriam Brawer" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/r0j6-jk09", "abstract": "Protein-bound iron sulfur clusters are critical in cells and allow proteins to carry out many essential functions as electron carriers, catalysts for challenging organic reactions, and sensors of cellular environments. A wide range of protein families are known to coordinate iron sulfur clusters, and a growing category includes proteins involved in maintenance of the genome. Within the last three decades, iron sulfur clusters have been demonstrated to be important for enzymes that function in DNA repair, DNA replication, and transcription pathways. To date, iron sulfur clusters in the cubane [4Fe4S] geometry with all cysteine ligands have been exclusively reported for DNA repair and replication enzymes. In contrast to enzymes where the cofactor is necessary for active site chemistry or directly-linked to protein function, the [4Fe4S] cluster in the overwhelming majority of repair and replication enzymes is not involved in the catalytic modification of DNA substrates. Rather, the role of the cofactor appears to vary in function from protein to protein, and has been demonstrated to be important for protein stability, in the assembly of multisubunit proteins, and for substrate recognition, among other roles. Through investigations of the redox chemistry of the cofactor, our group has found that these enzymes participate in DNA-mediated charge transport chemistry, the process through which electrons rapidly migrate through well-stacked, duplex DNA. Long-range, DNA-mediated redox signaling provides a means of rapid communication among DNA-processing proteins for organizing repair and replication activities across the nucleus.
\r\n\r\nNotably, the first observations of the [4Fe4S] cofactor associated with repair and replications enzymes has consistently occurred well after the first biochemical studies of these enzymes. In some cases, the demonstration of a [4Fe4S] center has taken place decades later after initial work. Some proteins have required use of anaerobic methods in order to detect the cofactor, perhaps explaining why in some cases the metal center had eluded observation. Analysis of protein sequences might be expected to help accelerate identification of new iron sulfur centers in repair and replication enzymes. However, even with the abundance of sequencing data available in the post-genomic era, prediction of a metal center based on sequences alone has been challenging. This is in large part because the spacing of the coordinating cysteine residues can be quite irregular, leading to a weak bioinformatic signature.
\r\n\r\nIdentifying proteins with overlooked [4Fe4S] cofactors poses an exciting challenge, and there are some elegant examples in the literature where data from genetics assays has been used in combination with careful sequence analysis to predict and discover iron sulfur centers in repair and replication enzymes. Described here is the evolution of our studies on one well-known repair enzyme from Escherichia coli, UvrC. UvrC is part of the nucleotide excision repair pathway in the Bacteria domain which is responsible for addressing the wide class of bulky, helix-distorting lesions that can form after exposure to sources such as ultraviolet light, cigarette smoke, chemotherapeutics, and protein-DNA crosslinks. UvrC, an excision nuclease with two distinct active sites that incise the phosphodiester backbone on either side of the site of damage, has been historically challenging to study. Given how essential UvrC is in repairing damaged substrates, new insight has been greatly needed.
\r\n\r\nThrough integration of several key reports from the literature regarding the sequence of UvrC and evidence that pointed to a cofactor from genetics assays, our group predicted that UvrC is a [4Fe4S] protein. Development of a new overexpression system and an anaerobic purification method allowed for isolation of UvrC in holo form. We used spectroscopic techniques to confirm that the cluster type was [4Fe4S], and a combination of spectroscopy and chromatography to demonstrate that the UvrC-bound cofactor is susceptible to oxidative degradation. We also found that loss of the cofactor, either through aerobic degradation or mutation of coordinating cysteines, is associated with aggregation of apoprotein. Importantly, in its holo form with the cofactor bound, UvrC forms high affinity complexes with duplexed DNA substrates; the apparent dissociation constants to well-matched and damaged duplex substrates are 100 \u00b1 20 nM and 80 \u00b1 30 nM, respectively. This high affinity DNA binding contrasts reports made for isolated protein lacking the cofactor. Moreover, using DNA electrochemistry, we find that the cluster coordinated by UvrC is redox-active and participates in DNA-mediated charge transport chemistry with DNA-bound midpoint potential of 90 mV vs. NHE.
\r\n\r\nThe work detailed in this dissertation has highlighted how critical the [4Fe4S] center is for UvrC, where the cofactor has been implicated in protein stabilization, substrate binding, and redox signaling on DNA. Handling an apo form of UvrC may have led to the previous challenges catalogued by researchers. Through the development of entirely new methods to study UvrC under anaerobic conditions, many opportunities are now available to study UvrC and the NER pathway anew in vitro and in vivo. Such work will contribute additional insight on how iron sulfur clusters are essential for enzymes that maintain genomic integrity.
\r\n\r\n" }, { "name": "Silverman, Bradley Ross", "degree": "PhD", "year": "2020", "title": "Protein-Mediated Colloidal Assembly", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302020-111741817", "creators": [ { "name": { "family": "Silverman", "given": "Bradley Ross" }, "id": "Silverman-Bradley-Ross", "orcid": "0000-0002-9256-8941", "display_name": "Silverman, Bradley Ross" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "member", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/x3ya-fq67", "abstract": "The assembly of colloidal-sized particles into larger structures by the manipulation of inter-particle forces has been a subject of significant research towards applications in materials science, soft matter physics, and synthetic biology. To date, much of this work has utilized manipulation of electrostatic or depletion interactions to drive the aggregation of the particles. More recently, specific (bio)-chemical interactions have been harnessed, particularly the use of deoxyribonucleic acid (DNA) linkers to program particle interactions by Watson-Crick base-pairing. In this thesis, we will demonstrate the use of an alternative set of biochemical interactions, protein-protein interactions, which have useful properties (in particular, their ability to be completely genetically-programmable).
\r\n\r\nIn Chapter 2, we discuss the development of a model system for the protein-mediated assembly of colloidal micro-particles. Associative proteins are grafted onto the surface of polystyrene micro-particles, enabling their assembly into aggregates either through reversible coiled-coil interactions or by irreversible isopeptide linkages. The sizes of the resulting aggregates are tunable and can be controlled by the concentration of the immobilized associative proteins on their surface. Further, we show that particles grafted with different protein pairs show excellent self-sorting into separate aggregates. Finally, we demonstrate that these protein-protein interactions can be used to assemble complex core-shell aggregates. The principles of protein-mediated colloidal assembly learned in this chapter will be instructive as we attempt the more complex assembly of living microbial cells.
\r\n\r\nIn Chapter 3, we discuss the implementation of a protein-driven aggregation system in living bacterial cells. Similarly to Chapter 2, we demonstrate that we can drive the aggregation of bacteria by the surface display of proteins enabling reversible coiled-coil interactions or irreversible isopeptide bonds. The sizes of these aggregates are tunable by titration of surface expression levels by standard synthetic biology techniques. Finally, we show that this programmable aggregation of bacteria may have physiological consequences for the cells, in particular, the activation of a quorum sensing circuit due to a higher local concentration of bacteria.
\r\n\r\nIn Chapter 4, we further investigate how the properties of the aggregates described in Chapter 3 can be controlled and how these relate to the underlying properties of the associative proteins and shear field. we demonstrate control of the assembly kinetics and equilibrium sizes of the resulting flocs over several orders of magnitude using different associating proteins and expression levels. Finally, we show that a single point mutation in the associative protein leads to an unexpected ultra-sensitive pH-responsive coil, demonstrating the importance of molecular-scale interactions on the macro-scale properties of the aggregates.
\r\n\r\nIn Chapter 5, we discuss the ability of the bacterial aggregates described in Chapters 3 and 4 to enable substrate channeling between bacterial strains, leading to enhancement of titers in multi-step biosynthetic pathways. When biosynthetic pathways are split into separate bacterial strains, dilution of the intermediate compound into the bulk media may decrease reaction flux. By aggregating the bacteria, the intermediate compound is able to rapidly diffuse into the downstream cell without being diluted, enabling higher reaction fluxes. we demonstrate through the model flavonoid synthesis pathway that aggregation can lead to substantially higher titers of the desired compound without pathway re-engineering, and develop a mathematical model by which this result can be understood.
" }, { "name": "Su, Yapeng", "degree": "PhD", "year": "2020", "title": "Resistance is Futile: Physical Science, Systems Biology and Single-Cell Analysis to Understanding the Plastic and Heterogeneous Nature of Melanoma and Their Role in Non-Genetic Drug Resistance", "advisor": "Heath, James R.; Baltimore, David L.; Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102020-003449091", "creators": [ { "name": { "family": "Su", "given": "Yapeng" }, "id": "Su-Yapeng", "orcid": "0000-0002-6305-8467", "display_name": "Su, Yapeng" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "role": "advisor", "display_name": "Baltimore, David L." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "co-advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/78ZP-Y270", "abstract": "Melanoma is the most deadly form of skin cancer due to its great metastatic potential. Targeted therapy that inhibits the BRAF-V600E driver mutation has shown impressive initial responses in melanoma patients. However, drug resistance, as the universal phenomenon for any cancer therapy, always limits treatment efficacy and compromises outcomes. As the early-step of resistance development, non-genetic mechanisms enable cancer cells to transition into a drug-resistant state in as early as a few days after drug treatment without alteration of the genome. This early mechanism is, to a large extent, due to the heterogeneous and highly plastic nature of tumor cells. Therefore, it imperative to understand the plastic and heterogeneous nature of the melanoma cells in order to identify combination therapies that can overcome resistance.
\r\n\r\nIn this thesis, we investigate these two fundamental natures of non-genetic drug resistance using BRAF inhibition of BRAF-mutant melanomas as the model system. These melanoma cells undergo multi-step, reversible drug-induced cell-state transitions from the original sensitive phenotype to a drug-resistant one.
\r\n\r\nWe first conducted bulk analysis to characterize the detailed kinetics of the entire transition from drug-sensitive state towards drug-resistant state, revealing expression changes of thousands of genes and extensive chromatin remodeling. A 3-step computational biology approach greatly simplified the complexity and revealed that the whole cell-state transition was controlled by a gene module activated within just the first three days of drug treatment, with the RelA transcription factor driving chromatin remodeling to establish an epigenetic program encoding long-term phenotype changes towards resistance. From there, a detailed mechanism connecting tumor epigenetic plasticity with non-genetic drug resistance was resolved through in-depth molecular biology experiments. The mechanism was validated in clinical patient samples.
\r\n\r\nWe further investigated heterogeneity by moving from bulk cellular studies to single-cell analysis. The single-cell view further revealed that two driving forces from both cell-state interconversions and phenotype-specific drug selection control the cell-state transition dynamics. The single-cell studies also pinpointed the signaling network hub, RelA, as the driver molecule of the initiation of the adaptive transition. These two competing driving forces were further quantitatively modeled via a thermodynamic-inspired surprisal analysis and a modified Fokker-Planck-type kinetic model.
\r\n\r\nFinally, using integrated single-cell proteomic and metabolic technology I developed to characterize the early-stage signaling and metabolic changes upon initial drug responses, we further identified two distinct paths connecting drug-sensitive and drug-tolerant states. Melanoma cells exclusively traverse one of the two paths depending on the level of MITF in the drug-na\u00efve cells. The two trajectories are associated with distinct signaling and metabolic susceptibilities and are independently druggable.
\r\n\r\nIn total, this thesis combines and synergizes various physical science and systems biology approaches together with several unique single-cell technologies and analysis to obtain a deep and comprehensive understanding of non-genetic drug resistance in cancer. The findings from this thesis provide several novel insights into the rational design of effective combination therapy for overcoming the development of resistance in response to cancer treatments.
" }, { "name": "Wang, Shuai", "degree": "PhD", "year": "2020", "title": "Co-Translational Protein Targeting and Insertion by SecA", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:10022019-105854314", "creators": [ { "name": { "family": "Wang", "given": "Shuai" }, "id": "Wang-Shuai", "orcid": "0000-0002-8920-969X", "display_name": "Wang, Shuai" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "role": "member", "display_name": "Varshavsky, Alexander J." } ], "option_major": [ "biochem" ], "doi": "10.7907/YAQY-3460", "abstract": "Co-translational protein targeting is a conserved process for the biogenesis of membrane proteins. This pathway was generally thought to depend on signal-recognition particle (SRP) for recognition of nascent protein and delivery to the membrane. Recently, SecA was found to also bind ribosomes near the nascent polypeptide exit tunnel, but the function of SecA\u2019s ribosome interaction remains unclear.
\r\n\r\nA combination of in vitro reconstitution and in vivo targeting assays show that SecA is necessary and sufficient to direct the targeting and translocation of RodZ to the bacterial plasma membrane in an obligatorily co-translational mechanism. The N-terminal extension preceding the transmembrane domain and periplasmic domain sequences immediately downstream of the transmembrane domain of RodZ provide distinguishing features that allow RodZ to engage SecA instead of the SRP machinery. Biochemical and cryoEM analyses further show that the N- terminal amphipathic helix on SecA and the ribosomal protein uL23 together form a composite binding site for the transmembrane domain (TMD) on the nascent chain. This interaction positions additional sites on the ribosome and SecA for recognition of the charged residues on both sides of the TMD, explaining the substrate specificity of SecA recognition. Quantitative kinetic analyses demonstrate that membrane-embedded SecYEG can associate with and remodel the SecA-bound ribosome-nascent chain complex, which together with elongation of the nascent polypeptide facilitates handover of the translating ribosome to the translocase.
" }, { "name": "Weaver, Sara Jean", "degree": "PhD", "year": "2020", "title": "Visualizing Small Proteins with the cryoEM Platform and The Structure of the Vibrio cholerae Type IV Competence Pilus Secretin PilQ", "advisor": "Jensen, Grant J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12092019-141850032", "creators": [ { "name": { "family": "Weaver", "given": "Sara Jean" }, "id": "Weaver-Sara-Jean", "orcid": "0000-0001-7753-6215", "display_name": "Weaver, Sara Jean" } ], "advisors": [ { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "role": "advisor", "display_name": "Jensen, Grant J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Voorhees", "given": "Rebecca M" }, "id": "Voorhees-R-M", "role": "member", "display_name": "Voorhees, Rebecca M" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9B9V-PK08", "abstract": "Solving protein structures by single-particle cryoelectron microscopy (cryo-EM) has become a crucial tool in structural biology. While exciting progress is being made toward the visualization of small macromolecules, the median protein size in both eukaryotes and bacteria is still beyond the reach of cryo-EM. To overcome this problem, we implemented a platform strategy in which a small protein target was rigidly attached to a large, symmetric base via a selectable adapter. Of our seven designs, the best construct used a designed ankyrin repeat protein (DARPin) rigidly fused to tetrameric rabbit muscle aldolase through a helical linker. The DARPin retained its ability to bind its target: GFP. We solved the structure of this complex to 3.0 \u00c5 resolution overall, with 5-8 \u00c5 resolution in the GFP region. As flexibility in the DARPin position limited the overall resolution of the target, we describe strategies to rigidify this element.
\r\n\r\nNatural competence is the process by which bacteria take up genetic material from their environment and integrate it into their genome using homologous recombination. In Vibrio cholerae, the Type IV competence pilus is thought to mediate DNA uptake by binding DNA and retracting back toward the cell. How the DNA enters the periplasm is unclear. One hypothesis suggests that the DNA-bound Type IV competence pilus retracts completely so that the DNA would pass through the outer membrane secretin pore (PilQ). PilQ is a 870 kDa outer membrane pore with C14 symmetry. Here, we purify the V. cholerae PilQ secretin from V. cholerae cells in amphipols for single particle cryogenic electron microscopy (cryoEM). We solve the structure to 3.0 \u00c5 and provide insight on the channel DNA may traverse through during uptake.
" }, { "name": "Wright, Austin Cameron", "degree": "PhD", "year": "2020", "title": "Evolving Strategies Toward the Synthesis of Curcusone C", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272020-105741489", "creators": [ { "name": { "family": "Wright", "given": "Austin Cameron" }, "id": "Wright-Austin-Cameron", "display_name": "Wright, Austin Cameron" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Ondrus", "given": "Alison E." }, "id": "Ondrus-A-E", "role": "member", "display_name": "Ondrus, Alison E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6FET-N212", "abstract": "Curcusone C is a tricyclic diterpenoid natural product possessing potent anti-cancer activities as well as a structurally unusual 2,3,7,8-tetrahydroazulene-1,4-dione skeleton. Herein, we report our evolving synthetic efforts toward the divergent total syntheses of ent-curcusone C and several structural congeners, which commenced with a Suzuki coupling of the peripheral carbon-based rings. Whereas the boronate partner was constructed from cyclopentenone, the halide partner could be elaborated from (S)-perillaldehyde. The alcohol coupling product was next esterified, then subjected to diazo transfer and cyclopropanation to produce a lactone. The resulting vinyl cyclopropane moiety was exposed to Kauffmann olefination conditions in order to form a divinylcyclopropane, which upon reductive lactone opening smoothly underwent a Cope rearrangement to establish the essential tricyclic core embedded in the curcusones.
\r\n\r\nDue to ongoing issues of scalability as well as unsatisfactory yields for the key cyclopropanation step, this route was ultimately abandoned, and an alternative strategy was devised which instead relied on a cross-electrophile coupling to join the peripheral rings. We further found that a central ring could be constructed via either Stetter annulation or ring-closing metathesis (RCM), accessing the tricyclic core of the curcusones in only 9 steps. Potential end-game strategies are further described.
\r\n\r\nWe additionally report our experimental research into the acyl-amination of in situ-generated arynes using symmetrical imides. The difunctionalized aryl products could be further derivatized to synthetically useful indoles and quinolones via McMurray coupling and Camps cyclization, respectively.
\r\n" }, { "name": "Zhukov, Dmitriy Vladimirovich", "degree": "PhD", "year": "2020", "title": "Facilitating Miniaturized Bioanalytical Assays in Microfluidic Devices", "advisor": "Ismagilov, Rustem F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02062020-145031701", "creators": [ { "name": { "family": "Zhukov", "given": "Dmitriy Vladimirovich" }, "id": "Zhukov-Dmitriy-Vladimirovich", "orcid": "0000-0002-4834-3147", "display_name": "Zhukov, Dmitriy Vladimirovich" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem F." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Gao", "given": "Wei" }, "id": "Gao-Wei", "role": "member", "display_name": "Gao, Wei" } ], "option_major": [ "chemeng" ], "doi": "10.7907/x9wq-h920", "abstract": "This work describes several efforts in making microfluidic lab-on-a-chip technology more convenient to use for bioanalysis in limited-resource settings (Chapters 2-3), and describes a device for miniaturized multistep process execution (Chapter 4). One underlying theme of these projects is the streamlining of the 'chip-to-world' interfacing to help bring this technology from specialized labs of its developers into more widespread utilization by potential users in other disciplines. Chapter 2 outlines a portable method for achieving stable fluid pumping for sample loading and flow control in microfluidic devices. Chapter 3 details a method for digital nucleic acid test readout with unmodified smartphone cameras. Chapter 4 demonstrates a lab-on-a-chip platform capable of carrying out complex multiplexed biochemical reactions requiring multiple sequential additions of reagents by performing RNA barcoding for multiplexed cDNA library generation.
" }, { "name": "Beck, Jordan Casey", "degree": "PhD", "year": "2019", "title": "Reaction Development for the Total Syntheses of the Terpenoid Natural Products (+)-Psiguadial B, (+)-Rumphellaone A, and (\u2013)-Isodocarpin", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142019-181954795", "creators": [ { "name": { "family": "Beck", "given": "Jordan Casey" }, "id": "Beck-Jordan-Casey", "orcid": "0000-0003-0898-5644", "display_name": "Beck, Jordan Casey" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/78A5-K715", "abstract": "The de novo synthesis of bioactive natural products provides an opportunity to learn more about the mechanism of bioactivity and to develop novel chemistry that is of interest to the synthetic community. Herein, we describe our strategy for the total synthesis of the trans-fused cyclobutane containing meroterpenoid (+)-psiguadial B. Key to this strategy was the development of a photochemical Wolff Rearrangement with asymmetric ketene aminolysis. A palladium-catalyzed C\u2013H alkenylation is used to build structural complexity, and we use two different epimerization strategies to perform an enantiodivergent synthesis of (+)-psiguadial B.
\r\n \r\nThis strategy was explored further and applied to the synthesis of chiral cyclobutanes through a 1,2-difunctionalization strategy, wherein a C\u2013H arylation forges one carbon-carbon bond and a subsequent decarboxylative cross-coupling enables functionalization at the adjacent carbon. This strategy enabled the asymmetric total synthesis of (+)-rumphellaone A in 9 steps.
\r\n \r\nThis report also highlights the work we have conducted in the development of a unified strategy for the enmein-type ent-kauranoid natural product, (\u2013)-isodocarpin. We detail our investigation of a convergent cross-electrophile coupling as a means to build the core of (\u2013)-isodocarpin. We also discuss our development of a 1,2-addition/semi-Pinacol rearrangement strategy for the preparation of all-carbon quaternary centers, which can be elaborated to enmein-type ent-kauranoid natural product scaffolds.
\r\n" }, { "name": "Blom, Antoinette Elisabeth Maria", "degree": "PhD", "year": "2019", "title": "Functional Evaluation and Development of Novel Agonists and Modulators of Neuronal Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-145818414", "creators": [ { "name": { "family": "Blom", "given": "Antoinette Elisabeth Maria" }, "id": "Blom-Antoinette-Elisabeth-Maria", "orcid": "0000-0002-7441-4893", "display_name": "Blom, Antoinette Elisabeth Maria" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RG56-G044", "abstract": "This dissertation describes studies of activation of neuronal ion channels and evaluating new ligands to modulate this process. In chapter two, we expanded the binding model of cytisine to the \u03b14\u03b22 nicotinic acetylcholine receptor. We also determined how C(10)-modification of cytisine impacts the key binding interactions between cytisine and its binding site. To achieve this, we used non-canonical amino acid mutagenesis to probe the electrostatic binding interactions of a novel series of C(10)-cytisine derivatives. In order to perform similar studies in the \u03b13\u03b24 nAChR subtype, we describe the heterologous expression of mouse and human \u03b13\u03b24 nAChRs in Xenopus Laevis oocytes in appendix one. Chapter three describes the development and functional evaluation of a novel series of pyrrolidinoindolines for agonism and modulation of the GABAA receptor. Additionally, we performed mutagenesis studies to identify the binding site of these novel ligands. Appendix two describes a different screen for activation or modulation of GABAA receptors using a set of phenolic compounds implicated in Autism Spectrum Disorder. Chapter four shifts focus to voltage-gated ion channels: in this chapter, the ultimate goal was to photochemically control the activation of VGSCs and make progress towards developing a RubpyC17-based photoswitch that could be used in an artificial retina. To this end, we determined the functional effects of several ruthenium bipyridine analogs on voltage-gated sodium and potassium channels.
" }, { "name": "Blunt, Catriona Emily Wilson", "degree": "PhD", "year": "2019", "title": "Noncovalent Interactions of Silent Agonists Binding to the Nicotinic Acetylcholine Receptor -and- Investigation into Expanding the Substrate Scope and Improving the Efficiency of Organic Photochemical Protecting Groups", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232019-143649929", "creators": [ { "name": { "family": "Blunt", "given": "Catriona Emily Wilson" }, "id": "Blunt-Catriona-Emily-Wilson", "orcid": "0000-0002-4663-4602", "display_name": "Blunt, Catriona Emily Wilson" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JYY6-GY46", "abstract": "This dissertation describes two very different projects. The first project focuses on the binding of a silent agonist to a ligand gated ion channel. The second project focuses on the study of development of new longer wavelength photolabile protecting groups for use in a biological setting to enable the spatially and temporally controlled release of biologically active small molecules.
\r\n\r\nChapter I introduces ligand gated ion channels and in particular a model of agonist binding at the nicotinic acetylcholine receptor. In addition, the nonsense suppression methodology used to incorporate the non-canonical amino acids required to probe non-covalent binding interactions is detailed. The second chapter details the use of non-canonical amino acids to study the binding of silent agonist NS6740 at the nicotinic acetylcholine receptor \u03b17 subunit and the discovery of a novel hydrogen bond that modulates silent agonist activity.
\r\n\r\nChapters III, IV and V focus on efforts to expand the scope of photolabile protecting groups towards designing longer wavelength derivatives. Chapter III introduces the topic of photoremovable protecting groups and details the mechanist background of a quinone methide based photochemical protecting group.
\r\n\r\nThe fourth chapter investigates the use of quinoline and quinolinium derivatives as photochemical quinone methide precursors. Two quinoline derivatives were found to form a quinone methide transient when irradiated. Quinolinium derivatives proved photostable, most likely due to the electron withdrawing nature of the quinolinium.
\r\n\r\nThe final chapter details efforts to improve the photochemical reaction efficiency of quinone photoreduction by using a radical decarboxylation strategy to trap the charge transfer state. Synthesis of two glycine containing quinone compounds is detailed and their photochemistry is evaluated. Both proved to be photostable.
\r\n" }, { "name": "Blythe, Emily Elizabeth", "degree": "PhD", "year": "2019", "title": "Characterization of Adaptor Binding and Substrate Processing by VCP/p97", "advisor": "Deshaies, Raymond Joseph", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222019-125958370", "creators": [ { "name": { "family": "Blythe", "given": "Emily Elizabeth" }, "id": "Blythe-Emily-Elizabeth", "orcid": "0000-0001-6363-2644", "display_name": "Blythe, Emily Elizabeth" } ], "advisors": [ { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "advisor", "display_name": "Deshaies, Raymond Joseph" } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "role": "member", "display_name": "Varshavsky, Alexander J." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" } ], "option_major": [ "biochem" ], "doi": "10.7907/9K4M-0C48", "abstract": "Valosin-containing protein (VCP/p97) is an essential AAA+ ATPase that is critical to numerous important cellular pathways, such as ER-associated degradation. p97 works in concert with a repertoire of adaptor proteins to extract ubiquitylated proteins from membranes or complexes and, often, target them for degradation by the protesome. The nature of the p97 system\u2014dependent upon a complex network of accessory proteins and targeted to substrates that are unstable and heterogeneous\u2014makes the mechanism of substrate processing challenging to study. Here, we developed in vitro biochemical assays to reconstitute two important steps in the p97 pathway for mechanistic study: adaptor binding and substrate processing. We showed that p97-adaptor complexes are highly dynamic, recapitulating observations made in cell lysate. Using a model p97 substrate, we demonstrated for the first time that p97 processes its substrates through unfolding, a fact long presumed but never explicitly proven. Finally, with these model systems in hand, we explored the effects of p97 mutations that cause the neurodegenerative disease multisystem proteinopathy (MSP) on p97-adaptor-substrate complexes. MSP mutations cause faster substrate unfolding, and we hypothesize that this increase is due to a higher affinity for the requisite adaptors Ufd1-Npl4. Our biochemical data presents evidence for a gain of function model for MSP pathology and suggests new avenues for treating MSP." }, { "name": "Boyle, Kelsey Melinda", "degree": "PhD", "year": "2019", "title": "Exploring the Biological Activity of Rhodium Metalloinsertors", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12212018-140003184", "creators": [ { "name": { "family": "Boyle", "given": "Kelsey Melinda" }, "id": "Boyle-Kelsey-Melinda", "orcid": "0000-0002-6728-8403", "display_name": "Boyle, Kelsey Melinda" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1KNM-Y111", "abstract": "Rhodium metalloinsertors are a unique family of potential anticancer agents that have been show to bind selectively to thermodynamically destabilized DNA base pair mismatches, abasic sites, and insertions/deletions (indels) in vitro. These metalloinsertors are also able to target mismatches in cells: metalloinsertors preferentially kill mismatch repair (MMR)-deficient cancer cells, which have a relative abundance of uncorrected DNA mismatches and indels, over MMR-proficient cells, which can repair these lesions. As such, these complexes have shown great promise as a potential treatment strategy for MMR-deficient cancers, which are often resistant to classic chemotherapies.
\r\n\r\nRecently, a new class of metalloinsertors that bear a rhodium-oxygen bond was synthesized and shown to have remarkable potency and selectivity towards MMR-deficient cells. We have discovered many key differences between first generation metalloinsertors and these new Rh-O metalloinsertors: (1) the MMR-selectivity of first generation metalloinsertors is heavily influenced by ancillary ligand bulk and lipophilicity, whereas the MMR-selectivity of Rh-O metalloinsertors is strong regardless of ancillary ligand properties, (2) first generation metalloinsertors have toxicities in the micromolar range while Rh-O metalloinsertors have toxicities in the nanomolar range, and (3) first generation metalloinsertors can only bind DNA via the \u0394-enantiomer while Rh-O metalloinsertors can bind DNA via both the \u0394- and \u039b-enantiomers. Excitingly, the improved potency and selectivity of these \"Rh-O\" metalloinsertors brings them into a realm of clinical relevance.
\r\n\r\nHere we examine the basis for the improved potency and selectivity of these new Rh-O metalloinsertors. A family of six Rh-O metalloinsertors that vary in the steric bulk and lipophilicity of an ancillary ligand was synthesized and characterized. Regardless of ancillary ligand identity, these Rh-O metalloinsertors exhibit nanomolar or low-micromolar toxicities and all preferentially target MMR-deficient cancer cells over MMR-proficient cells. Notably, the off-target accumulation of these metalloinsertors in mitochondria is very low. This cellular distribution is in stark contrast with first generation metalloinsertors in which increased ligand lipophilicity led to increased mitochondrial uptake and ultimately non-selective mitochondrial-mediated cell death. We believe robust selectivity of these complexes is retained in part due to their low off-target accumulation in the mitochondria, which is further complemented by the low dosing requirements of these potent therapeutic agents.
\r\n\r\nOur studies also suggest the high potency of these complexes may be due to a difference in DNA-binding abilities, which is supported by observed differences in which enantiomers can bind to DNA mismatches, differences in ligand buckling at physiological pH, and lipophilicity of the therapeutics, with Rh-O metalloinsertors being dramatically more lipophilic than their first generation counterparts. To better understand the structural basis for this increased potency, crystallographic experiments are underway. A first generation metalloinsertor was previously crystallized with mismatched DNA, and the structure was pivotal in identifying the DNA binding mode of metalloinsertion. Using similar methods, we are working to produce a high-resolution crystal structure of an Rh-O metalloinsertor with mismatched DNA in order to gain structural insights into the increased potency of these new complexes. A significant difference in DNA binding could result in different biological activation of proteins and overall higher potency of these Rh-O metalloinsertors.
\r\n\r\nFinally, as metalloinsertors are moved towards pre-clinical study, understanding their biological activity in diverse cell culture experiments is essential. We examined a metalloinsertor and the FDA approved chemotherapeutic agent cisplatin in 27 diverse colorectal cancer cell lines. The comparison of these drugs revealed the metalloinsertor to be on average five times more potent than cisplatin in this panel. The potency of the metalloinsertor in different cell lines spanned nearly three orders of magnitude and correlated with whole-cell uptake of rhodium. Additionally, a fluorescent metalloinsertor conjugate was used to quantify the number of lesions in DNA that could be targeted by metalloinsertion, a result that correlated well with the potency of a metalloinsertor across several cell lines, consistent with DNA mismatches as the effective biological target of the metalloinsertor.
\r\n\r\nThe experiments described within this thesis have allowed us to gain a better understanding of the biological activity of rhodium metalloinsertors. We have established that Rh-O metalloinsertors are distinct from first generation metalloinsertors, and that these new metalloinsertors can serve as highly tunable, potent, and mismatch-selective anticancer agents. Furthermore, this potency is observed across diverse cell lines and has been shown to correlate with the number of genomic DNA lesions that can be bound by metalloinsertion. The unique biological activity of these complexes makes them ideal candidates for the treatment of MMR-deficient cancers, and the potency and tunability of Rh-O metalloinsertors will allow for the development of previously unattainable diagnostic and therapeutic tools for MMR-deficiencies.
" }, { "name": "Burkholder, Eric William", "degree": "PhD", "year": "2019", "title": "Single Particle Motion in Active Matter", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232018-084606596", "creators": [ { "name": { "family": "Burkholder", "given": "Eric William" }, "id": "Burkholder-Eric-William", "orcid": "0000-0001-7420-4290", "display_name": "Burkholder, Eric William" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/SGHS-CH87", "abstract": "\"Active matter\" refers to a broad class of materials in which the constituent particles or organisms are able to self-propel (swim) by some internal physicochemical mechanism. Though the origin of this self-propulsive motion is a rich area of study, we are primarily interested in the collective effects of this motion on the physical properties — and in particular, the rheology — of the active material as a whole. As such we model self-propulsive motion using the minimal active Brownian particle (ABP) model: a particle of size a , swims in a direction q with a speed U0, and the direction of its motion changes randomly over some time scale \u03c4R.
\r\n\r\nOn a macroscopic scale, active motion leads to unique hydrodynamic and mechanical stresses exerted by the particles on their embedding medium. These stresses arise from the microscopic force associated with particle locomotion — the swim force F swim. Though the idea of the swim force is widely recognized in the abstract, little attention has been given to the characterization and mechanical consequences of this force. In this work we are particularly interested the role of the swim force in the effective motion of passive constituents in active environments, and how the swim force affects long-ranged hydrodynamic interactions (HI) in active suspensions. We examine these issues through the lens of microrheology: tracking the motion of a colloidal probe particle through an active medium, and using its motions to infer the effective viscoelastic properties of the suspension.
\r\n\r\nUsing generalized Taylor dispersion theory, we find an activity-driven enhancement to the diffusion of the probe in an active medium. This first-principles theory unites many experimental observations of tracer diffusion, and provides simple physical descriptions of the problem that do not rely on the specific self-propulsion mechanism of the swimmer. This same framework is then used to compute the suspension microviscosity (as measured by the drag on the probe particle), and the fluctuation-dissipation relation in an active system. We find that activity reduces the drag on the probe, but the drag is still larger than it would be in a Newtonian fluid; this stands in contrast to experimental measurements of reduced shear viscosities. We show that the microviscosity of a suspension is reduced — and may even become negative! — due to HI, and that this effect is not due to the fluid velocity disturbance associated with the swimmers' self-propulsion.
" }, { "name": "Chen, Wen", "degree": "PhD", "year": "2019", "title": "Proteomics Profiling and Functional Characterization of Caenorhabditis elegans Excreted/Secreted Proteins", "advisor": "Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-035956740", "creators": [ { "name": { "family": "Chen", "given": "Wen" }, "id": "Chen-Wen-Biochemistry-Molecular-Biophysics", "orcid": "0000-0001-8056-5711", "display_name": "Chen, Wen" } ], "advisors": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." } ], "option_major": [ "biochem" ], "doi": "10.7907/WTMK-7M75", "abstract": "Excretory-secretory products (ESPs) are first characterized and defined in parasitic nematode proteomics studies as the combination of various biomolecules that are continuously excreted or secreted into the environment throughout the whole life cycle. ESPs are particularly interesting to many scientists as anti-parasitic vaccine candidates and\r\nas promising drug targets since large portions of ESPs are active enzymes that potentially function directly at the parasite-host or worm-environment interfaces. However, majority of the parasites lack whole genome sequence knowledge and genome-editing tools. Thus, the number of ESPs identified is limited and many functions of ES proteins cannot be elucidated. Therefore, we use the most studied nematode, Caenorhabditis elegans, as the model to characterize the composition of excreted/secreted proteins with the help of nanoliquid chromatography coupled with tandem mass spectrometry (nanoLC-MS/MS). We characterized more than 509 excreted/secreted proteins with mix-staged worms, including many metalloproteases, cysteine proteases, and lysozymes. Proteases and proteases inhibitors are a major group in C. elegans ESPs. We performed stable isotope dimethylvlabeling quantitative proteomics and compared C. elegans ESPs on different bacteria diets. Lysozymes are not only enriched in C. elegans ESPs but are also up-regulated in response to pathogen and bacteria.
\r\n\r\nComparative studies of expression profiles of developmental life stages and pathogen infections elucidate the dynamics in regulating ESP components. We successfully identified stage-specific ESP groups associated with L1, L3, adult, L2 dauer, and postdauer. We demonstrated that proteases activities are down regulated by increased protease inhibitor expressions, while during dauer exit proteases expressions are increased. The comparison between dauer excretome/secretome and RNA-seq dauer expression profiles revealed 91 ESP encoding genes that are highly expressed in dauers. We performed dauer formation assay to these dauer-associated gene mutants. The great prediction rate confirmed that our comparative method is the simplest way to quickly pick out candidates for functional assays. Similarly, we employed this comparative method to pathogeninduced transcriptomes. We reported a group of genes that are associated with Serratia marcescens infection and a group of bacterial pathogens responding genes. We confirmed the roles of C. elegans ESPs in immuoregulation by infection assays with various pathogens. Lysosomes and cysteine protease inhibitor are among the most important genes in innate immune response pathway of C. elegans defending pathogen infection.
\r\n\r\nThe recent discovery of a C. elegans sibling species, Caenorhabditis inopinata, allows the deeply comparative study for evolutional interpretation. The excretome/secretome of C. inopinata has not been characterized. We took advantage of the sensitive and highthroughput technique of nanoscale liquid chromatography coupled to tandem mass spectrometry (nano LC-MS/MS) to directly characterize the protein components of C. inopinata excretome/secretome. Functional annotations reveal several protein families, including C-type lectins, Cathepsin Z, Cathepsin B family, transthyretin, and saposin-like families, suggesting ESPs play critical roles in regulating innate immune response. We compared C. inopinata excretome/secretome with C. elegans. The structures are highly conserved across species, suggesting the sibling species share common mechanism to respond to environmental stimuli.
" }, { "name": "Chio, Un Seng", "degree": "PhD", "year": "2019", "title": "Mechanistic Bases for Privileged Capture and Unidirectional Targeting of Tail-Anchored Proteins by the Get3 ATPase", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:01112019-160835213", "creators": [ { "name": { "family": "Chio", "given": "Un Seng" }, "id": "Chio-Un-Seng", "orcid": "0000-0002-5295-2690", "display_name": "Chio, Un Seng" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "member", "display_name": "Hoelz, Andre" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S1CD-5Z42", "abstract": "C-terminal tail-anchored membrane proteins (TAs) are targeted post-translationally to the endoplasmic reticulum (ER) in eukaryotic cells mainly through the Guided entry of tail-anchored protein (GET) pathway. Here we use biochemical and biophysical approaches to shed further mechanistic insight into how the central chaperone, the Get3 ATPase, is able to capture TA substrates in a privileged manner and provide unidirectional targeting to the ER.
\r\n\r\nSpecifically, we first show in Chapter 2 that Get3 dynamically samples open and closed conformations as a \"protean clamp\". Binding of TA substrates induces Get3 to sample more open conformations that causes Get3 to dissociate from the cytosolic regulatory Get4/5 complex, hydrolyze ATP, and become primed to interact with the Get1/2 membrane receptors. Therefore, a TA substrate acts as the switch for unidirectional targeting, transitioning Get3 from a \"TA-loading mode\" to a \"membrane targeting mode\". Next, in Chapter 3, we show that a small, conserved alpha-helical lid motif, known as \u03b18, lining the substrate binding groove is necessary for Get3 to efficiently capture TA substrates in a privileged manner over competing off-pathway chaperones.
" }, { "name": "Cowper, Nicholas Glenn William", "degree": "PhD", "year": "2019", "title": "The Development of a Synthetic Strategy Toward Oxazine-Containing Natural Products Enabled by Novel Copper Catalysis", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022019-233820328", "creators": [ { "name": { "family": "Cowper", "given": "Nicholas Glenn William" }, "id": "Cowper-Nicholas-Glenn-William", "display_name": "Cowper, Nicholas Glenn William" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y9WZ-TZ31", "abstract": "1,2-oxazine natural products are a small closely related family of highly oxidized compounds. Herein, the development of a synthetic strategy toward gliovirin and the trichodermamides is described which enabled the synthesis of the western fragments of gliovirin and trichodermamide B. To that end, we developed two novel copper-catalyzed transformations:the asymmetric propargylation of an oxime and the diasteroeselective oxidative cyclization of hydroxamic acid with a diene.
\r\n\r\nThe challenge of working with tetrahydro-1,2-oxazines is their sensitivity to a variety of reaction conditions and purification methods. Extensive optimization of each transformation was accomplished, bringing to bear the state-of-the-art in oxidative modifications, including a palladium-catalyzed direct desaturation of an epoxy ketone. As well as this work led to the rare observation of a vinylogous Payne rearrangement.
\r\n\r\nThe successful synthesis of the fully functionalized western and eastern fragments of gliovirin are described toward a late-stage diketopiperazine formation and thiolation. Interrogation of our late-stage strategy with these fragments demonstrates that the coupling of the fully functionalized western and eastern fragments is not an effective strategy toward gliovirin proof-of-concept experiments suggest this chemistry could be used toward the synthesis of the trichodermamides.
" }, { "name": "Grantz Pansing, Amanda", "degree": "PhD", "year": "2019", "title": "Aerosol Particle Measurements: Strategies for Health-Relevant Data Collection and Analysis", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-161940566", "creators": [ { "name": { "family": "Grantz Pansing", "given": "Amanda" }, "id": "Grantz-Pansing-Amanda", "display_name": "Grantz Pansing, Amanda" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Y730-W245", "abstract": "Particulate matter (PM) is an important component of outdoor and indoor air pollution that can cause significant harm to human health. The present work, organized into two parts, introduces strategies for optimizing the collection and analysis of airborne particle measurements to inform PM health-effect research.
\r\n\r\nPart I focuses on the fundamental aerosol data analysis task of interpreting indirect measurements of particle size to reveal the distribution of sizes of particles in a sampled aerosol. An approach to this aerosol data inversion problem is developed that shows improved particle size distribution recovery compared to other common approaches described in the literature. This inverse solution method incorporates cubic spline interpolation to represent the particle size distribution within a discrete linear model of the inverse problem while placing no constraints on the number or spacing of solution points. The inverse problem setup can then interface with three established numerical methods for solution computation. The accuracy of this procedure is demonstrated through analysis of test-case data for differential mobility analyzer systems. Source code and supporting documentation are also provided to encourage researchers to use and adapt this inversion algorithm for analyzing data collected from existing as well as potential future measurement systems.
\r\n\r\nPart II of this work focuses on the retrieval of health-relevant information from aerosol particle measurement data. The inversion analysis introduced in Part I is incorporated into an extended analysis procedure for evaluating the metrics of PM exposure and respiratory dose that can be obtained from different measurement systems. Applying this evaluation procedure to a range of existing and potential future measurement techniques reveals that full characterization of particle size distributions need not be time and resource intensive and should be pursued for the great benefits this information would provide to health studies. Not only can size distribution information permit lung tissue dose estimates through a set of relatively simple calculations, but a single set of size distribution data can be analyzed and reanalyzed to provide dose estimates for human populations of interest by applying the appropriate respiratory tract deposition profiles. The measurement evaluation procedure developed here reveals target criteria for the particle characterization necessary to provide sufficient exposure and dose information for health studies. The intent is not to eliminate the current measurements and standards, but to help direct future developments in health-related aerosol particle measurement design.
" }, { "name": "Gr\u00fcnenfelder, Denise Christine", "degree": "PhD", "year": "2019", "title": "Synthetic Strategies for the Total Synthesis of Acutumine Alkaloids and the Development of Radical Deoxychlorination Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01152019-115519988", "creators": [ { "name": { "family": "Gr\u00fcnenfelder", "given": "Denise Christine" }, "id": "Gr\u00fcnenfelder-Denise-Christine", "orcid": "0000-0002-0334-2167", "display_name": "Gr\u00fcnenfelder, Denise Christine" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FS86-HB55", "abstract": "The acutumine alkaloids are a family of architecturally complex propellane natural products with promising medicinal properties. Herein, we disclose the continued development of a synthetic strategy toward the asymmetric total synthesis of acutumine alkaloids. The spirocyclic scaffold was synthesized in two new series, which follow our successful access to the dechloroacutumine core in 2013. Central to the synthetic design is the retro-aldol/Dieckmann cyclization of a cyclobutyl lactone to install the spirocycle. The key cyclobutane intermediate is obtained via a photo-mediated [2+2]-cycloaddition of a furanyl dihydroindolone, which is accessible via a stereoselective 1,2-addition/reductive cyclization sequence of a benzoquinone-derived imine. Installation of the dimethoxyenone motif is accomplished via a late-stage elimination of a dimethoxyketal, which furnished the requisite vinylogous ester after methylation. Overall, these efforts have culminated in the synthesis of the complete carbocyclic core and oxidation pattern of the natural product (\u2013)-acutuminine, with a C10 neopentyl alcohol in place of the neopentyl chloride.
\r\n\r\nTen of the known acutumine alkaloids contain a neopentyl chloride; this motif provided underlying motivation for the development of novel radical deoxychlorination reactions, including the chlorination of cesium oxalates. This reaction allows access to hindered 2\u00b0 and 3\u00b0 alkyl chlorides, provides complementary reactivity to standard heterolytic conditions, and is performed under mild conditions using visible light and ethyl trichloroacetate as a Cl\u2022 source. Application to deoxybromination and deoxyfluorination is also demonstrated, showcasing the versatility of the discovered halogenation. This method should find broad utility in the deoxyhalogenation of hindered alcohols, particularly in the pharmaceutical industry where selective installation of fluorides is a common challenge.
" }, { "name": "Han, Arthur", "degree": "PhD", "year": "2019", "title": "Synthetic Strategies for the Total Synthesis of the Ryanoid and Isoryanoid Diterpenes", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292018-211645714", "creators": [ { "name": { "family": "Han", "given": "Arthur" }, "id": "Han-Arthur", "orcid": "0000-0001-8691-699X", "display_name": "Han, Arthur" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JDZV-P010", "abstract": "Highly oxygenated, polycyclic terpenoids provide a rich source of biologically active natural products, yet the translation of their activity to lead candidate analogs and useful biological probes requires concise solutions to address, at once, accessibility and diversification. This dissertation will disclose our efforts to bridge that gap through the development of synthetic strategies for the total synthesis of the ryanoid and isoryanoid diterpenes. The studies herein will address the strategy and logic that rendered the success of a challenging C3 acylation to directly incorporate a pyrrole-2-carboxylate ester, ultimately resulting in an 18-step total synthesis of (+)-ryanodine. The versatility of the route was demonstrated by the preparation of the related ryanoid diterpene (+)-20-deoxyspiganthine. Enabling the success of both syntheses was the development of robust conditions to induce late-stage reductive ring closure and forge the C1\u2013C15 bond.
\r\n\r\nThe lessons learned from these synthetic efforts drew us thereafter to the complex, polycyclic structure of the isoryanoid diterpene (+)-perseanol. The evaluation of several different approaches culminated in the discovery of a successful fragment coupling approach, hinging on a 2-step sequence involving (1) 1,2-addition to induce convergent union of two fragments of equal complexity and (2) Heck-Stille cyclization/cross-coupling cascade to complete the preparation of the ABC tricyclic core. Emphasis will be placed on the strategic use of our fragment coupling approach to overcome the inherent stereochemical bias presented by late-stage intermediates, thereby enabling an 18-step total synthesis. The oxidation tactics developed herein should find broad utility in the preparation of other ryanoid, isoryanoid, and highly oxidized diterpenoids.
" }, { "name": "Hannoun, Kareem Imad", "degree": "PhD", "year": "2019", "title": "Mechanistic Study of Cu-Mediated, Photoinduced C\u2013S Bond Formation and Demonstration of Electrochemical Ammonia Production by a Surface-Attached Iron Complex", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302019-070503222", "creators": [ { "name": { "family": "Hannoun", "given": "Kareem Imad" }, "id": "Hannoun-Kareem-Imad", "orcid": "0000-0003-3176-1104", "display_name": "Hannoun, Kareem Imad" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R9EJ-KX83", "abstract": "The worldwide reliance on fossil fuels for energy and petrochemicals poses a massive environmental hazard. Furthermore, many chemical processes rely on precious metals that have low abundance on Earth and are threatened. As the world population grows rapidly, these factors pose an increasing threat to our planet and new chemical processes are needed that employ earth-abundant catalysts and alternative chemical currencies such as light and electricity derived from renewable sources.
\r\n\r\nChapter 2 discusses an in-depth mechanistic study of the photoinduced, copper-mediated cross-coupling of aryl thiols with aryl halides. This reaction employs light energy and an earth-abundant metal to achieve bond formation through a pathway distinct from that of thermal reactions. In particular, I focus on the stoichiometric photochemistry and subsequent reactivity of a [CuI(SAr)2]\u2013 complex (Ar = 2,6-dimethylphenyl). A broad array of experimental techniques furnish data consistent with a pathway in which a photoexcited [CuI(SAr)2]-* complex undergoes SET to generate a CuII species and an aryl radical, which then couple through an in-cage radical recombination.
\r\n\r\nChapter 3 discusses the surface attachment of a P3BFe complex to a carbon electrode, and the electrochemical generation of ammonia from N2 by the surface-appended species (P3BFe = tris-phosphinoborane). Ammonia production is achieved industrially by the combination of N2 and H2, the latter of which is derived from methane with concomitant production of CO2. Alternative chemical processes, such as the use of energy derived from electricity, are vital for the decreasing the carbon footprint of ammonia production. Synthetic modification of a previously-reported P3BFe complex by addition of three pyrene substituents onto the catalyst backbone allows non-covalent attachment onto a graphite surface. The resulting functionalized electrode shows good stability towards iron desorption under highly reducing conditions, and produces 1.4 equiv NH3 per iron site. The data presented provide the first demonstration of electrochemical nitrogen fixation by a molecular complex appended to an electrode.
" }, { "name": "Ho, Samuel Hin-Yuen", "degree": "PhD", "year": "2019", "title": "Chemical Tools for Protein Imaging in Live Bacterial Cells", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312019-211114775", "creators": [ { "name": { "family": "Ho", "given": "Samuel Hin-Yuen" }, "id": "Ho-Samuel-Hin-Yuen", "orcid": "0000-0001-7647-0752", "display_name": "Ho, Samuel Hin-Yuen" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KNWF-CZ96", "abstract": "Bacteria spatially and temporally localize their proteins to carry out fundamental cellular processes. Methods for visualizing protein subcellular localization have been critical to our understanding of prokaryotic cell biology. Fluorescent reporters have been instrumental for imaging bacterial proteins in live cells. Small-molecule fluorescent dyes, which have favorable spectral properties, including high brightness and photostability, are attractive in labeling proteins of interest. Here we present a method to site-specifically label the N-termini of bacterial protein targets in situ for fluorescence imaging in bacterial cells. The method uses the eukaryotic enzyme N-myristoyltransferase to ligate target proteins, bearing a nonapeptide recognition sequence, with an azide-bearing fatty acid. Subsequent strain-promoted azide\u2013alkyne cycloaddition with fluorophores enable tagging of chemotaxis and cell division proteins in live cells. We describe using a reactive BODIPY fluorophore for visualization of the chemotaxis proteins Tar and CheA and the division proteins FtsZ and FtsA. Next we integrate a single copy of the gene encoding the protein target into the chromosome via Tn7 transposon mutagenesis and use the method to fluorescently label a bacterial chemoreceptor. Finally, we describe the preparation of photoswitchable rhodamine spirolactam dyes for super-resolution imaging in live bacterial cells. Our work highlights the utility of using photoswitchable molecules to label intracellular protein targets. The ability to tag proteins, perform super-resolution imaging, and visualize proteins in space and time will prove broadly useful." }, { "name": "Hofstra, Julie Lyn", "degree": "PhD", "year": "2019", "title": "Development and Mechanistic Studies of Ni-Catalyzed Asymmetric Reductive Cross-Coupling Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012019-034543690", "creators": [ { "name": { "family": "Hofstra", "given": "Julie Lyn" }, "id": "Hofstra-Julie-Lyn", "orcid": "0000-0001-9558-4317", "display_name": "Hofstra, Julie Lyn" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/G8M3-CQ05", "abstract": "Cross-coupling reactions have emerged as powerful methods to form carbon-carbon and carbon-heteroatom bonds in a vast array of synthetic contexts. Nickel-catalyzed reductive cross-coupling reactions have opened up a new mode of reactivity, allowing for the cross-coupling of bench-stable electrophiles as both coupling partners. Asymmetric variants, which use a chiral ligand, increase molecular complexity by introducing stereocenters with high levels of enantioselectivity. Application of this methodology to an array of electrophiles has led to the development of a number of transformations incorporating both C(sp2)-hybridized electrophiles (aryl iodides, alkenyl bromides, and acyl chlorides) and C(sp3)-hybridized electrophiles (benzyl chlorides and \u03b1-chloronitriles).
\r\n\r\nHerein we discuss our most recent efforts in the development and application of Ni-catalyzed asymmetric cross-coupling reactions with alkenyl electrophiles. First, the expansion of our previously developed methodology has allowed for bulky trimethylsilyl groups on the benzyl chloride electrophile, providing chiral allylic silane products in good yield and enantioselectivity. The utility of these products with both traditional and newly developed methodology is highlighted. Following this, we describe the development of reaction conditions that proceed with benzyl N-hydroxyphthalimide esters. This approach proceeds through a decarboxylative strategy, generates previously accessible radical intermediates, and proceeds with the use of a homogenous reductant. Our investigations into the mechanism on the cross-coupling of alkenyl bromides and benzyl chlorides is also disclosed, where we first identified the formation of alkenyl chloride and alkenyl iodide intermediates under the reaction conditions. This inspired us to develop a Ni-catalyzed alkenyl triflate halogenation in order to prepare alkenyl halide synthetic intermediates.
" }, { "name": "Huang, Yufeng", "degree": "PhD", "year": "2019", "title": "Computational Heterogeneous Electrochemistry \u2013 From Quantum Mechanics to Machine Learning", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:12232018-185711169", "creators": [ { "name": { "family": "Huang", "given": "Yufeng" }, "id": "Huang-Yufeng", "orcid": "0000-0002-0373-2210", "display_name": "Huang, Yufeng" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemeng" ], "doi": "10.7907/MCGV-Y790", "abstract": "Because of coulomb interactions and complex surface morphologies, rigorous methods for heterogeneous electrochemical catalysis were not well-established. Thus, for different types of electrochemical systems, a specific strategy must be adapted. In this thesis, we first used the cluster model to study the chemistry on a 1D chain of MoS2 edges. Then, a rigorous grand canonical potential kinetics (GCP-K) method was developed for general crystalline systems. Starting from quantum mechanical calculations, the method gave rise to a different picture from the traditional description given by the Butler-Volmer kinetics. Next, we studied the chemical selectivity of CO2 reduction on polycrystalline copper nanoparticles. Because of the complexity of the reaction sites, we combined the reactive force field, density functional theory, and machine learning method to predict the reactive sites on 20,000 sites on a roughly 200,000-atom nanoparticle. Such a strategy opens up new way to understand chemistries on a much wider range of complex structures that were impossible to study theoretically. Lastly, we formulated a machine learning force field strategy using atomic energies for amorphous systems. We have shown that such a method can be used to reproduce quantum mechanical accuracies for molecular dynamics. This method will enable the accurate study of the dynamics of heterogeneous systems during electrochemical reactions. In summary, we have developed quantum chemical methods and machine learning strategies to reformulate rigorous ways to study a wide range of heterogeneous electrochemical catalysts.
" }, { "name": "Huber, Ferdinand Michael", "degree": "PhD", "year": "2019", "title": "Molecular Basis for Ribosomal Protein Protection from Cellular Degradation", "advisor": "Hoelz, Andre", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242019-115311540", "creators": [ { "name": { "family": "Huber", "given": "Ferdinand Michael" }, "id": "Huber-Ferdinand-Michael", "display_name": "Huber, Ferdinand Michael" } ], "advisors": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-0923-3284", "role": "advisor", "display_name": "Hoelz, Andre" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-0923-3284", "role": "member", "display_name": "Hoelz, Andre" } ], "option_major": [ "biochem" ], "doi": "10.7907/4S7C-V170", "abstract": "Ribosomes are large macromolecular machineries composed of both protein and RNA constituents with a species-dependent molecular mass of at least ~3.3\u00a0MDa for the fully assembled eukaryotic 80S ribosome. Their catalytic activity is dependent on ribosomal RNA; therefore, ribosomes are bona fide ribozymes, and as such they mediate the final step of gene expression from DNA to RNA to protein by peptide bond formation between amino acids. Importantly, spatial separation of ribosome function and biogenesis into distinct cellular compartments allows for intricate regulatory mechanisms and rigorous quality control. Ribosome biogenesis occurs predominantly in the nucleolus and nucleus of the cell with final cytoplasmic maturation and quality control steps. Briefly, nucleolar ribosomal RNA together with ~200 trans-acting assembly factors co-transcriptionally forms the 40S and 60S pre-ribosomal subunits into which ~80 ribosomal proteins are incorporated in a hierarchical fashion.
\r\n\t\r\nRecent studies, including this thesis, have identified a novel class of dedicated ribosome assembly chaperones, in addition to the ~200 trans-acting ribosome assembly factors, which facilitate ribosomal protein shuttling. Ribosomal proteins are generated in the cytoplasm, and with only few exceptions they all have to enter the nucleus for incorporation into the pre-ribosomal subunits. Assembly chaperones can bind and protect unassembled ribosomal proteins either co-translationally or following nuclear import and shuttle them in a timely fashion to their destination sites at the maturing pre-ribosomal subunits. The first chapter of this thesis describes the identification and characterization of a dedicated assembly chaperone for the large ribosomal subunit protein RpL4, termed Acl4. Interestingly, Acl4 and likely also other dedicated assembly chaperones not only interact with ribosomal proteins to avoid aggregation and to shield them from unfavorable interactions, but also protect their client proteins from cellular degradation by the ubiquitin-proteasome machinery.
\r\n\t\r\nRibosomes are built by assembling equimolar amounts of ribosomal proteins, which generates a challenge for the cell to ensure stoichiometric quantities of ribosomal proteins. Recent studies have demonstrated that stoichiometric levels of ribosomal proteins are established by cellular degradation of excess protein via ubiquitination of unassembled components. The second chapter of this thesis describes a conserved degradation pathway, which is dependent on the E3 ubiquitin ligase Tom1 to mark unprotected and unassembled ribosomal proteins and target them for degradation. Moreover, it is demonstrated in the third chapter for the first time how an assembly chaperone protects its client ribosomal protein from ubiquitination and proteasome-mediated degradation. High resolution structures of the Acl4\u2022RpL4 complex as well as RpL4 in complex with the nuclear transport factor Kap104 visualize the molecular interactions of those proteins and uncover the molecular mechanism of protecting conserved Tom1-target sites within RpL4. Together, the reported results identify and characterize both a novel degradation pathway as well as a protection mechanism for ribosomal proteins and advance the understanding of the intricate regulation of ribosome biogenesis.
" }, { "name": "Hui, Aileen Oyama Ah Yee", "degree": "PhD", "year": "2019", "title": "Atmospheric Peroxy Radical Chemistry Studied by Infrared Kinetic Spectroscopy", "advisor": "Okumura, Mitchio; Sander, Stanley P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01172019-135430092", "creators": [ { "name": { "family": "Hui", "given": "Aileen Oyama Ah Yee" }, "id": "Hui-Aileen-Oyama-Ah-Yee", "orcid": "0000-0003-4217-2698", "display_name": "Hui, Aileen Oyama Ah Yee" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "co-advisor", "display_name": "Sander, Stanley P." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "member", "display_name": "Sander, Stanley P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9H0-1H20", "abstract": "Peroxy radical (RO2) chemistry plays a central role in atmospheric science. RO2 radicals control the oxidative capacity of the atmosphere and are key intermediates in the cycling of ozone in the troposphere in regions where levels of nitrogen oxides (NOx ≡ NO + NO2) are high. In more remote regions of the Earth where NOx concentrations are low, RO2 loss is dominated by reaction with hydroperoxy (HO2) and other peroxy radicals, leading to removal of reactive radicals from the troposphere. However, for certain species of RO2, reaction with HO2 can also propagate radical chemistry by recycling hydroxyl (OH) radicals, a primary oxidant in the atmosphere. Both HO2 and OH radicals play important roles in atmospheric oxidation reactions. Accurate characterization of various RO2 reactions that contribute to consuming and recycling HOx (HOx ≡ HO2 + OH) are instrumental for understanding the effects of atmospheric composition on climate forcing, air quality, and the global ozone budget.
\r\n\r\nMy thesis work used laboratory studies to characterize gas phase organic peroxy radical (RO2) reactions that are relevant to atmospheric chemistry. The main body of my work focused on studying the self reactions of HO2 and RO2 as well as their cross reactions (HO2 + RO2) using a time-resolved experimental technique called Infrared Kinetic Spectroscopy (IRKS), which combines infrared (IR) and ultraviolet (UV) absorption spectroscopy. Perfect isolation of one specific reaction is generally difficult or impossible due to radical recycling and secondary chemistry, which leads to numerous reactions occurring simultaneously. Thus, although laboratory studies provide controlled environments to study these reactions, the accuracy of the results are highly dependent on the experiment's selectivity and sensitivity to specific transient species. In this work, a new mid-IR (MIR) laser was implemented into the existing apparatus for measuring OH radicals. In addition to UV absorption spectroscopy, the IRKS apparatus was equipped for selective detection of HO2 and OH radicals in the near-IR (NIR) and MIR, respectively.
\r\n\r\nThe kinetics and product yields of a reaction are two important factors for assessing the impact of these reactions on the atmosphere. IRKS was used to study the kinetics of the self reactions of acetylperoxy (CH3C(O)O2) and acetonylperoxy (CH3C(O)CH2O2), as well as their reactions with HO2. The OH and O3 yields from the reaction of HO2 + CH3C(O)O2 were also measured, providing the first parametrization of the temperature dependence of the OH product channel. The temperature dependence of the HO2 self reaction kinetics was re-investigated to resolve discrepancies in the results previously reported in the literature. Furthermore, this work identified and characterized rate enhancement effects on the HO2 self reaction by the adducts of HO2 formed from the reaction of HO2 with methanol (CH3OH), acetaldehyde (CH3CHO), and acetone (CH3C(O)CH3), which were used as radical precursors for HO2, CH3C(O)O2, and CH3C(O)CH2O2, respectively.
\r\n\r\nFinally, the improved sensitivity of the IRKS apparatus enabled the investigation of fast reaction kinetics. The rate constants of Cl atoms with CH3OH and CH3CHO were measured over a wide range of temperatures. The results were consistent with previously reported values in the literature and additionally validated assumptions that had been made regarding the temperature independence of these reactions. The temperature and pressure dependences of the OH yield from the reaction of CH3CO with O2 were also studied to resolve current discrepancies in the literature. The yield of HO2 from this reaction was also directly measured for the first time.
" }, { "name": "Hwang-Fu, Yu-Hsien", "degree": "PhD", "year": "2019", "title": "Dynamic Regulations of Co-Translational Protein Targeting by the Signal Recognition Particle Receptor in E. coli and Human", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122018-102847326", "creators": [ { "name": { "family": "Hwang-Fu", "given": "Yu-Hsien" }, "id": "Hwang-Fu-Yu-Hsien", "orcid": "0000-0002-2861-4843", "display_name": "Hwang-Fu, Yu-Hsien" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/STGW-8V12", "abstract": "The Signal Recognition Particle (SRP) and its receptor (SR) co-translationally deliver the majority of secretory and membrane proteins to their membrane destinations. SRP recognizes and binds to the cargo, and SR recruits the transit complex to the target membrane. Precise timing and coordination are encoded into the interactions between SRP and SR in response to the cargo and environment to enable efficient and accurate targeting. This dissertation explores the regulation mechanisms of SRP membrane recruitment by SR in both bacteria and eukaryotes.
\r\n\r\nThe bacterial SR is a peripheral membrane protein and recruits SRP by adjusting its membrane-binding modes. A complete kinetic model of SRP membrane recruitment by the SR was established based on direct observations and quantitative analyses of protein-membrane binding events at single-molecule resolution. Biochemical and cell biological examinations validated the physiological significance of the newly discovered dynamic membrane-binding mode of the SR. The two-stage SR membrane binding mechanism ensures both speed and specificity in bacterial co-translational protein targeting.
\r\n\r\nIn eukaryotes, a proper initial recognition of SRP sets the right course for membrane delivery of the transit complex, as eukaryotic SR is anchored on the endoplasmic reticulum. A Molecular Recognition Feature (MoRF) in the disordered linker domain of eukaryotic SR was identified and characterized. The SR MoRF element enables rapid SRP-SR assembly in response to the ribosomal content of the cargo. The stimulation by SR MoRF is only present in eukaryotes and is likely a functional replacement of the tetraloop in bacterial SRP RNA whose stimulatory role was abolished during evolution.
" }, { "name": "Jarman, John Bryce", "degree": "PhD", "year": "2019", "title": "Chemical Tools for the Control of Biological Systems", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032019-100329207", "creators": [ { "name": { "family": "Jarman", "given": "John Bryce" }, "id": "Jarman-John-Bryce", "orcid": "0000-0002-7581-686X", "display_name": "Jarman, John Bryce" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MV3V-2R09", "abstract": "Described within is an exploration of noncanonical amino acids and photochemistry in the context of chemical biology. The thesis first covers attempts to expand the use of chemically acylated tRNA into new systems, before describing explorations into singlet oxygen as a powerful photochemical tool." }, { "name": "Johnstone, Christopher Patrick", "degree": "Senior Thesis", "year": "2019", "title": "Control of Aggregated Bacterial Communities through Engineered Surface Displayed Proteins", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102019-011804885", "creators": [ { "name": { "family": "Johnstone", "given": "Christopher Patrick" }, "id": "Johnstone-Christopher-Patrick", "orcid": "0000-0002-7255-0218", "display_name": "Johnstone, Christopher Patrick" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/827E-J857", "abstract": "Bacterial aggregation through surface display of cross-associating proteins has previously been demonstrated, but the formation of these aggregates is only controllable and reversible through the addition of chemical inducers or soluble proteins. Here, we present a design for a photoswitchable surface-display system that causes bacterial aggregation. This system should reversibly disaggregate under exposure to blue light. We created our mutant by modifying Photoactive Yellow Protein (PYP), a fluorescent protein that undergoes a large reversible conformational change when exposed to blue light. We computationally designed this mutant to drive photoswitchable sequestration of a cap domain that is designed to selectively aggregate with SynZip18. Characterization of this designed protein's photoactivity was inconclusive due to its limited solubility though the synthesized chormophore, a p-coumaric acid derivative, was capable of reconstituting native photoactive PYP. While we did not show that the designed mutant could cause disaggregation under exposure to blue light, it was capable of selectively aggregating with surface displayed SynZip18 as desired.
" }, { "name": "Kang, Jong Hun", "degree": "PhD", "year": "2019", "title": "I. Shape Selectivity of Small-pore Molecular Sieves for the Methanol-to-Olefins Reaction and II. Synthesis and Topotactic Transformation of Germanosilicate CIT-13", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-032220561", "creators": [ { "name": { "family": "Kang", "given": "Jong Hun" }, "id": "Kang-Jong-Hun", "orcid": "0000-0002-4197-9070", "display_name": "Kang, Jong Hun" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/PG34-B728", "abstract": "This thesis presents research results from two projects involving molecular sieves. These investigations concern their synthesis, characterization and use as heterogeneous catalysis.
\r\n\r\nIn part I, the shape selectivity in the methanol-to-olefins (MTO) reaction is studied, and a new molecular sieve structure \u2013 MTO reaction selectivity relationship is developed. 17 zeolites and 13 phosphate-based molecular sieves having 14 selected cage-type/small-pore topologies (CHA, AFX, SFW, LEV, ERI, DDR, AEI, RTH, ITE, SAV, LTA, RHO, KFI, and UFI) are synthesized. The MTO reaction is performed using these catalysts at the same reaction conditions.
\r\n\r\nThe reaction results lead to the conclusion that the molecular sieve cage topology is the most important structural factor that primarily determines the olefin product distribution. For example, AEI and CHA are synthesized with four different elemental compositions (zeolite, SAPO, CoAPO, MgAPO). Regardless of differences in elemental compositions, very similar product distribution patterns are observed in each of the isostructural groups of molecular sieves. Additionally, other isostructural pairs of SAPOs and zeolites show similar product distributions.
\r\n\r\nThe reaction results from 14 topologies are grouped into four categories. Category I consists of CHA, AFX, SFW, and other GME-related topologies. Catalysts having these topologies show ethylene-to-propylene ratios close to one. Category II is a group of ERI and LEV which generate more ethylene than propylene. Category III is a group of DDR, AEI, RTH, ITE, and SAV which shows propylene selectivities higher than those of ethylene. Category IV is a group of LTA, RHO, KFI, and UFI which possess LTA-cages. These types of catalysts give high butylene selectivities.
\r\n\r\nThe concept of cage-defining ring and its size is introduced as a reliable geometric indicator on the basis of a hypothetical ellipsoid cage model. The cage-defining ring size can be easily calculated from crystallographic information which is available online. A strong correlation is found between the cage-defining ring sizes and the four categories of reaction behavior.
\r\n\r\nIn part II, an extra-large-pore germanosilicate molecular sieve CIT-13 with 14- and 10-ring pores is synthesized using monoquaternary, methylbenzylimidazolium-derivative OSDAs, and the synthesis conditions are optimized. Fluoride-free synthetic pathways for pure germanosilicate CIT-13 and isomorphous aluminum substitution in synthesis of aluminogermanosilicate CIT-13 are also described. The nature of disorder in the arrangement within CIT-13 framework is discussed, and its physicochemical properties compared to a UTL-type germanosilicate IM-12.
\r\n\r\nA comprehensive network of topotactic transformation and postsynthetic modification pathways starting from germanosilicate CIT-13 (Ge-CIT-13) is described. The moisture-mediated transformation of Ge-CIT-13 into another extra-large-pore CFI-type germanosilicate (Ge-CIT-5) is discovered, and the role of sorbed water in the transformation kinetics studied. The resultant Ge-CIT-5 is the first germanosilicate molecular sieve having a CFI topology, and the corresponding transformation is also the first inter-germanosilicate transformation occurring at room temperature. The microporosity of Ge-CIT-5 matched well with the reference pure-silica CIT-5 synthesized using the sparteine-type OSDA.
\r\n\r\nThe acid-delamination processes of Ge-CIT-13 and Ge-CIT-5 are investigated. Ge-CIT-13 can be transformed into two new frameworks, CIT-14 with 12- and 8-ring pores and CIT-15 with 10-ring pores, on the basis of an ADOR-type topotactic transformation. The inverse sigma transformation of Ge-CIT-13 directly into CIT-14 is also firstly described. The conventional acid-delamination of Ge-CIT-13 does not yield Ge-CIT-5. However, the CIT-15-type material is obtained via the base-delamination pathway from Ge-CIT-5. The postsynthetic alumination of Ge-CIT-13 and Ge-CIT-5 is also achievable.
\r\n" }, { "name": "Kim, Joey Dongjin", "degree": "PhD", "year": "2019", "title": "Effects of Branching on Conformation, Crystallization, and Self-Assembly of Polymers", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302019-112215583", "creators": [ { "name": { "family": "Kim", "given": "Joey Dongjin" }, "id": "Kim-Joey-Dongjin", "orcid": "0000-0002-3359-4875", "display_name": "Kim, Joey Dongjin" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/8AFE-YC54", "abstract": "The central feature of bottlebrush polymers is the stiffening of the main-chain (MC) due to side-chain side-chain (SC-SC) repulsion, amplified by densely grafting long SCs, particularly in good solvent conditions. The expectation of stiffening has led most prior studies to refer to bottlebrush polymers as \"worm-like,\" \"cylindrical\" or a \"self-avoiding walk (SAW) of superblobs\". However, there is no direct evidence of stiffening of the main-chain and measurements of the overall segment distribution of the whole molecule have failed to discriminate between competing models. Here, we provide a set of measurements of the main-chain conformation (neutron scattering in a solvent that is contrast matched to the side chains) together with the overall conformation of the bottlebrush as a whole (light, X-ray, and neutron scattering) under conditions that highlight SC-SC repulsion: the side-chains are relatively long compared to prior literature, the concentration of bottlebrushes is low, and the solvent quality is good. Surprisingly, the main-chain has a conformation that does not conform to any prior models: all three main-chain lengths examined showed a window of length scales in which the scattering power increased less than linearly with length scale. In particular, the MC conformation is not worm-like. Direct observation of the main-chain conformation and the overall conformation discriminates among models more powerfully than the overall conformation alone. Inspired by the Paturej-Rubinstein tension blob model, we examined a conceptual model in which tension of the MC accumulates with distance from the ends of the MC and found that it can capture the salient features of both the MC- and whole bottlebrush scattering more gradually than previous theoretical models predicted. The conceptual model also explains our observation of a substantial increase in anisometry with increasing MC length, opposite to a worm-like chain. The results indicate that synthetically accessible bottlebrushes are not fractals; they cannot have self-similar (fractal) conformation because each increase in main-chain length accesses greater side-chain crowding than any of its shorter siblings. We expanded the work to understand the behavior in \u03b8 conditions and shorter side-chains expected to have reduced tension as well as the behavior at different concentrations.
\r\n\r\nIn addition, we characterized the interplay of self-assembly and polymer crystallization through analysis of three representative bottlebrush copolymer systems. Our results revealed a surprising number of unexpected behaviors ranging from unexpected morphologies, control of thermal properties even to complete suppression of phase transitions, and control of the orientation of crystal stem with respect to the morphological interface, which highlights the potential of the bottlebrush architecture.
" }, { "name": "Kozlowski, Mark Tybalt", "degree": "PhD", "year": "2019", "title": "Use of Recombinant Self-Associating Proteins for Altering Cellular Fate and Behavior", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-133006433", "creators": [ { "name": { "family": "Kozlowski", "given": "Mark Tybalt" }, "id": "Kozlowski-Mark-Tybalt", "orcid": "0000-0003-4714-8697", "display_name": "Kozlowski, Mark Tybalt" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3Z3B-V584", "abstract": "The behavior of mammalian and bacterial cells is governed by their surroundings, and the interactions of cells with their nearest neighbors. In this work, I will demonstrate how self-associating proteins such as leucine zippers or SpyTag and SpyCatcher can be used either in hydrogels for cell culture, or to drive the aggregation of cells into artificial, engineered communities. I further demonstrate how these self-associating protein-based materials can either alter the fate of cultured cells, or directly change cellular behavior through the activation of a quorum sensing circuit.
\r\n\r\nIn the first chapter, I discuss protein-based methods for making different types of organoids. Organoids are groups of cells derived from stem or progenitor cells that form a multicellular structure consisting of different cell types. These organoids are currently of interest as disease model systems, pharmaceutical test platforms, and replacement tissues. However, most studies of organoids to date have derived them from Matrigel-based cultures. While versatile and inexpensive, Matrigel is undefined, suffers from batch-to-batch variability, and its xenogeneic nature means that organoids derived from Matrigel are unlikely to be approved for clinical use. In Chapter 1, I review current state-of-the-art materials developed as alternatives to Matrigel, such as naturally-derived extracellular matrices, synthetic hydrogels, and recombinant proteins serving as artificial extracellular matrices. I consider the advantages and disadvantages of each method, as well as speculate on possible future directions for the field.
\r\n\r\nOf these alternatives to Matrigel, recombinant protein-based artificial extracellular matrices have the advantage of being easy to engineer, as genetic encoding of the material allows precise control over molecular weight and functionality. Development of these types of materials has long been a focus of work in our laboratory, and in Chapter 2, I discuss the development of two protein-based hydrogels expressed in Escherichia coli, which are based on a previously-reported PEP hydrogel. These new \u201cPEXEP-type\u201d hydrogels are physically cross-linked by leucine zippers derived from rat cartilage oligomeric matrix protein (COMPcc), incorporate chemical cues from fibronectin and collagen IV, and were used for pancreatic cell culture in defined medium. When comparing this defined, protein-based medium to methylcellulose-Matrigel, we find that the growth of endocrine cells is promoted, as opposed to the ductal cells found in methylcellulose-Matrigel culture. We further find a difference in colony types observed based on whether the fibronectin or collagen IV cue is present. More interestingly, the protein-based culture material promotes the growth of endocrine progenitor cells, which may be useful for further studying the formation of the Islets of Langerhans. Finally, we observe that sorted populations of murine cells cultured in our protein hydrogels have a lower rate of colony formation, and this reduction in the number of colonies is not observed in methylcellulose-Matrigel culture. We believe that this might be evidence for a paracrine effect that promotes cell growth, particularly the growth of putative endocrine colonies, though further experiments are required to confirm this effect.
\r\n\r\nIn Chapter 2, I demonstrate how a self-associating protein can be used to change the fate of a cell culture, and give rise to multicellular colonies. However, for the purpose of constructing bioreactors, microbial fuel cells, or systems for environmental remediation, it may be advantageous to design tissue-like systems de novo, making multifunctional communities of bacteria that function as artificial tissues. In Chapter 3, I will discuss the construction of a synthetic microbial community of E. coli cells, whose quorum sensing response is governed by aggregation of the cells. This aggregation in turn is driven by the expression of surface-displayed self-associating proteins, and I will discuss methods developed to control the size, reversibility, and morphology of these aggregates. As the behavior of these aggregates is dependent on cell-cell communication facilitated by proximity, these consortia represent early examples of synthetically-designed artificial tissues that can be governed by engineered cell-cell signaling.
" }, { "name": "Kurmis, Alexis Anna", "degree": "PhD", "year": "2019", "title": "Activity of Py-Im Polyamides in Anti-Androgen Resistant Prostate Cancer Models", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182019-112436661", "creators": [ { "name": { "family": "Kurmis", "given": "Alexis Anna" }, "id": "Kurmis-Alexis-Anna", "orcid": "0000-0002-8427-2198", "display_name": "Kurmis, Alexis Anna" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Ondrus", "given": "Alison E." }, "id": "Ondrus-A-E", "role": "member", "display_name": "Ondrus, Alison E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HC6V-FV39", "abstract": "The antiproliferative effects of Py-Im polyamides have been evaluated in several cancer models. The work presented here focuses on prostate cancer and the application of Py-Im polyamides targeted to the sequence 5\u2032-WGWWCW-3\u2032, which is found in a subset of androgen response elements. We begin by exploring the effect of a Py-Im polyamide in the VCaP model, which overexpresses wildtype AR and is genomically unstable due to ERG overexpression caused by the TMPRSS2-ERG translocation. In this model, Py-Im polyamide treatment reduces ERG protein level and DNA fragmentation, and reduces VCaP xenograft growth. Transcriptomic analysis of Py-Im polyamide treated VCaP cells provides a novel potential mechanism of blockage of topoisomerase I and II activity by polyamides. We next evaluate the activity of a second generation Py-Im polyamide in two models of anti-androgen resistant prostate cancers, and demonstrate growth inhibition in both cell culture and tumor models. Transcriptomic analysis of the model cell lines revealed suppression of androgen receptor signaling. Further, expression profiles are consistent with transcription inhibition in both cell samples and tumor samples. Finally, we examine the effect of a Py-Im polyamide on the AR cistrome in prostate cancer cells. We find through ChIP-Seq analysis that loci differentially affected by Py-Im polyamide treatment are enriched for potential ARE half-sites consistent with the polyamide target site. In summary, we find that Py-Im polyamides interfere with several DNA dependent processes, similar to other DNA minor groove binders, and we show through AR cistromic analysis that Py-Im polyamides reduce AR occupancy in a pattern that is predicted by Py-Im polyamide pairing rules.
" }, { "name": "Lee, Heui Beom", "degree": "PhD", "year": "2019", "title": "Electronic Structure and Spectroscopy of Tetranuclear Mn4O4 and CaMn3O4 Complexes as Models of the Oxygen Evolving Complex in Photosystem II", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112019-204258320", "creators": [ { "name": { "family": "Lee", "given": "Heui Beom" }, "id": "Lee-Heui-Beom", "orcid": "0000-0002-9550-2649", "display_name": "Lee, Heui Beom" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S6NR-3N42", "abstract": "This thesis describes a series of studies devoted toward the synthesis of model complexes that mimic aspects of structure, redox state, and spectroscopy of the oxygen evolving complex (OEC) of Photosystem II. The OEC is a unique metallocofactor featuring a heteronuclear CaMn4 core that catalyzes water oxidation. While advances in spectroscopic and structural techniques offer an ever more detailed view of the structure of the S-state catalytic intermediates, the precise mechanism of O\u2212O bond formation remains debated. Aspects such as (1) role of Ca2+, (2) the location of the substrate waters, and (3) the (electronic) structure of the S-state intermediates remain unclear. To obtain a better understanding of the OEC, systematic structure\u2212function(property) studies on relevant model complexes may be necessary. Despite significant efforts to prepare tetra- and pentanuclear complexes as models of the OEC, relevant complexes in terms of structure, redox state, spectroscopy, and reactivity are rare, likely due to the synthetic challenges of accessing a series of isolable clusters that are suitable for comparisons.
\r\n\r\nChapter 1 presents a survey of tetramanganese model compounds with an emphasis on redox state and electronic structure, as probed by magnetometry and EPR spectroscopy. Structurally characterized model complexes are grouped according to Mn oxidation states and the S-state that they are mirroring. In contrast to the vast number of spectroscopic studies on the OEC, studies that probe the effect of systematic changes in structure on the spectroscopy of model complexes are rare in the literature.
\r\n\r\nChapter 2 presents ongoing synthetic efforts to prepare accurate structural models of the OEC. The synthesis of accurate structural models is hampered by the low structural symmetry of the cluster, the presence of two types of metals, and the propensity of oxo moieties to form extended oligomeric structures. Desymmetrization of the previously reported trinucleating ligand leads to the formation of tetranuclear Mn4II precursors. Oxidation in the presence of Ca2+ leads to a CaMn4O2 model of the OEC, underscoring the utility of low-symmetry multinucleating ligands in the synthesis of hitherto unobserved oxo-bridged multimetallic core geometries related to the OEC.
\r\n\r\nChapter 3 presents a series of [MnIIIMn3IVO4] cuboidal complexes as spectroscopic models of the S2 state of the OEC. Such complexes resemble the oxidation state and EPR spectra of the S2 state, and the effect of systematic changes in the nature of the bridging ligands on spectroscopy was studied. Results show that the electronic structure of tetranuclear Mn complexes is highly sensitive to even small geometric changes and the nature of the bridging ligands. Model studies suggest that the spectroscopic properties of the OEC may also react very sensitively to small changes in structure; the effect of protonation state and other reorganization processes needs to be carefully assessed.
\r\n\r\nChapter 4 presents a series of [YMn3O4] complexes as models of the [CaMn3O4] subsite of the OEC. The effect of systematic changes in the basicity and chelating properties of the bridging ligands on redox potential was studied. Results show that in the absence of ligand-induced geometric distortions that enforce a contraction of metal-oxo distances, increasing the basicity of the ligands results in a decrease of cluster reduction potential. A small contraction of metal-oxo/metal-metal distances by ~0.1 \u00c5 enforced by a chelating ligand results in an increase of cluster reduction potential even in the presence of strong basic donors. Such small, protein-induced changes in Ca-oxo/Ca-Mn distances may have a similar effect in tuning the redox potential of the OEC through entatic states, and may explain the cation size dependence on the progression of the S-state cycle.
\r\n\r\nChapter 5 presents a series of [CaMn3O4] and [YMn3O4] complexes as models of the [CaMn3O4] subsite of the OEC. The effect of systematic changes in cluster geometry, heterometal identity, and bridging oxo protonation on cluster spin state structure was studied. Results show that the electronic structure of the Mn3IV core is highly sensitive to small geometric changes, the nature of the bridging ligands, and the protonation state of the bridging oxos: the spin ground states of essentially isostructural compounds can be S = 3/2, 5/2, or 9/2. Interpretation of EPR signals and subsequent structural assignments based on an S = 9/2 spin state of the CaMn3O4 subsite of the OEC must be done very cautiously.
\r\n\r\nWhile unfinished, appendices 1 and 2 present other important aspect in OEC model chemistry. Appendix 1 presents the synthesis of 17O-labeled [MnIIIMn3IVO4] and [CaMn3IVO4] complexes as models of the OEC. Ongoing characterization of \u03bc3-oxos in such complexes provide valuable benchmarking parameters for future mechanistic studies. Appendix 2 presents the synthesis and characterization of [Mn4IVO4] cuboidal complexes as spectroscopic models of the S3 state of the OEC, the last observable intermediate prior to O\u2212O bond formation at the OEC.
" }, { "name": "Lee, Jae Ho", "degree": "PhD", "year": "2019", "title": "Mechanisms of Co-Translational Protein Targeting by Mammalian SRP", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-142906583", "creators": [ { "name": { "family": "Lee", "given": "Jae Ho" }, "id": "Lee-Jae-Ho", "orcid": "0000-0002-8663-3209", "display_name": "Lee, Jae Ho" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "chair", "display_name": "Hoelz, Andre" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RF8Y-DK59", "abstract": "Proper biogenesis of nascent protein is essential for cell survival. Signal recognition particle (SRP) is an essential and universally conserved factor involved in biogenesis of ~30% of the proteome through co-translational targeting of nascent proteins to Endoplasmic Reticulum (ER). Despite its importance, the mechanisms by which eukaryotic SRP ensure selective and efficient delivery of substrates to ER is poorly understood. Here, we reconstituted human SRP and SRP receptor (SR) to study the interaction between human SRP and SR, and conformational dynamics of SRP and SRP-SR targeting complex through biochemical and biophysical methods. We find that signal sequence and ribosomal components of the substrate sequentially activate human SRP. Especially, presence of signal sequence pre-organizes SRP conformation for efficient recruitment of SR, allowing specific and efficient targeting. In addition, we discover two essential roles of a conformational change in SR, where it is required not only for brining targeting complex near the ER membrane, but also for inducing subsequent conformational changes of SRP-SR complex that ensures proper delivery of substrates to Sec61 translocon on ER membrane.
" }, { "name": "Loskot, Steven Anthony", "degree": "PhD", "year": "2019", "title": "Applications of the Enantioselective Allylic Alkylation Toward the Synthesis of Complex Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132019-092701701", "creators": [ { "name": { "family": "Loskot", "given": "Steven Anthony" }, "id": "Loskot-Steven-Anthony", "display_name": "Loskot, Steven Anthony" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TZHG-9B35", "abstract": "The Stoltz group, and moreover the synthetic community at large, has long been interested in the development of methods for the synthesis of enantioenriched all-carbon quaternary stereocenters. This thesis present three projects all unified by the development and use of the palladium-catalyzed decarboxylative allylic alkylation to synthesize enantioenriched all-carbon quaternary stereocenter containing cyclopentanones as well as the natural product total synthesis.
" }, { "name": "Low, Choon Heng (Marcus)", "degree": "PhD", "year": "2019", "title": "Hemilabile, Non-Innocent (Poly)arylene Donors for Accessing Novel Reactivity at Transition Metal Centers", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222019-121353860", "creators": [ { "name": { "family": "Low", "given": "Choon Heng (Marcus)" }, "id": "Low-Choon-Heng-Marcus", "orcid": "0000-0002-9219-3377", "display_name": "Low, Choon Heng (Marcus)" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BQJM-BN49", "abstract": "Understanding the effects that ligands have on the coordination environment and reactivity of metal complexes is an endeavor that drives much of the field of inorganic chemistry. The use of ligands capable of flexible binding modes and redox states further enriches the chemistry of these complexes. This dissertation describes studies on metal complexes bearing pendant (poly)arylene donors that demonstrate hemilability and redox non-innocence. Within this context, conditions that result in coordination mode change and the multi-electron bond transformation that is made possible by the hemilability and/or non-innocence of the ligand are discussed.
\r\n\r\nChapter 2 investigates the meta-terphenyl diphosphine framework bearing a central phenolate donor as an anionic POP pincer on a variety of first-row transition metals. The circumstances under which coordination mode change from the phenolate donor to the arene face are investigated. Reduction of the cobalt and nickel complexes induced a coordination mode change from phenolate oxygen to metal-arene binding, while Lewis acid additives induced a coordination mode change in some iron POP complexes. Additionally, it was found that iron chloride POP complex initially not amendable to two-electron reduction was cleanly reduced in the presence of Lewis acids, suggesting a role the Lewis acid plays in quenching the negatively charged phenolate and stabilizing the overall transformation.
\r\n\r\nChapter 3 discusses reactivity on 1,4-naphthalenediyl diphosphine molybdenum complexes in the context of carbon monoxide (CO) coupling. Similar to the previously studied phenylene system, the reductive coupling of CO can be carried out. However, the naphthalene system showed a distinct and exclusive selectivity for the two-electron reductive CO coupling to a bis(siloxy)acetylene motif, without C\u2013O bond cleavage. This difference in selectivity is proposed to be a result of accessible \u03b74-arene binding modes previously not observed in the phenylene variant. Additionally, the bis(siloxy)acetylene complex also displays \u03b74-binding to the central arene. Further CO catenation can be effected from this species, providing a metallacyclobutenone complex that bears a C3 fragment derived completely from CO.
\r\n\r\nIn Chapter 4, the reactivity of 9,10-anthracenediyl bis(phenoxide) zirconium complexes is presented. The more expanded polyaromatic system with a milder reduction potential allowed the anthracene motif to function as a non-innocent ligand. This enabled facile reductive elimination of ancillary benzyl ligands on the metal center without the use of harsh reductants. This reduced complex was then able to oxidatively couple alkynes, and alkynes with nitriles. Furthermore, further insertion of an additional nitrile followed by reductive elimination, likely facilitated by the non-innocent anthracene motif, allowed for the catalytic synthesis of pyridines and pyrimidines with high yields and selectivities. This reactivity was further leveraged in the final Chapter of this dissertation. Chapter 5 presents the development of a new methodology towards the synthesis of pyridine or pyrimidine-containing polycyclic aromatic hydrocarbons (PAHs) using polyaromatic alkyne and nitrile building blocks. Because conventional methods of oxidative cyclodehydrogenation towards N-doped nanographenes proved ineffective with these PAHs, a new reductive cyclization route was developed offering a complementary method towards the challenging synthesis of these N-doped nanographenes.
\r\n\r\nAppendix A briefly explores additional reactivity on the 1,4-naphthalenediyl diphosphine complexes with regard to nitrile activation. Appendix B explores the synthesis of iron complexes supported by a benzene tris(thiophenolate) ligand towards potential model compounds for the iron molybdenum cofactor in nitrogenase. Appendix C presents preliminary studies on the 9,10-anthracenediyl bis(phenoxide) zirconium complex towards oxidative coupling of alkynes with CO2.
" }, { "name": "Matier, Carson Douglas", "degree": "PhD", "year": "2019", "title": "Copper and Nickel Catalysis for the Construction of Novel C\u2212N and C\u2212C Bonds", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142019-145414091", "creators": [ { "name": { "family": "Matier", "given": "Carson Douglas" }, "id": "Matier-Carson-Douglas", "orcid": "0000-0002-1618-7944", "display_name": "Matier, Carson Douglas" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/G3Q9-8F81", "abstract": "First-row transition-metals such as nickel and copper have revolutionized cross-coupling chemistry. Their propensity to form radical intermediates from alkyl electrophiles has greatly expanded the scope of traditional cross-coupling reactions. Alkyl radicals can be recaptured by a chiral transition-metal catalyst allowing for enantioselective bond formation. In general, alkyl radicals rapidly epimerize, and thus both enantiomers of a racemic mixture of an alkyl electrophile can be processed into the same enantiomer of product, rendering the overall process enantioconvergent. Herein, the development of basic bond constructions and the development of asymmetric reactions leveraging alkyl radical intermediates for carbon-nitrogen and carbon-carbon bond formations are discussed. Reaction development is the primary focus of this work, though mechanistic insights discovered along the way are also detailed within.
\r\n\r\nChapter 2 describes the development of an enantioconvergent alkylation of amine nucleophiles with alkyl electrophiles. Carbazole and indole derivatives are employed as nucleophiles to undergo copper-catalyzed cross-coupling with tertiary \u03b1-chloroamide electrophiles under visible light irradiation. Reaction optimization, scope of reactivity, inorganic synthesis, and mechanistic insights are described within.
\r\n\r\nChapter 3 details the development of a non-asymmetric copper-catalyzed alkylation of aliphatic amines with unactivated alkyl electrophiles under visible light irradiation. The development of a novel catalytic system to circumvent the issues with the photophysical properties of aliphatic amine-copper complexes is discussed. Scope of reactivity and mechanistic investigations are detailed within. Additionally, our efforts to develop an asymmetric variant of this reaction are enclosed.
\r\n\r\nChapter 4 discusses the development of a copper-catalyzed alkylation of N-heterocycles with \u03b1-halolactams in the absence of light. The scope of the reactivity is detailed within. Mechanistic studies contained in this section suggest a unique and interesting reaction pathway\u2014one that does not proceed through a radical intermediate.
\r\n\r\nChapter 5 presents a novel class of organosilane electrophiles employed in an enantioconvergent nickel-catalyzed cross-coupling reaction. Here, the development of the reaction, scope of reactivity, and initial mechanistic insights are discussed.
\r\n\r\n" }, { "name": "Moreno-Hernandez, Ivan A.", "degree": "PhD", "year": "2019", "title": "Earth-Abundant Metal Oxides for Anodic Reactions in Acidic Electrolytes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042019-235050436", "creators": [ { "name": { "family": "Moreno-Hernandez", "given": "Ivan A." }, "id": "Moreno-Hernandez-Ivan-A", "orcid": "0000-0001-6461-9214", "display_name": "Moreno-Hernandez, Ivan A." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XRN5-FV98", "abstract": "The development of electrochemical systems such as electrolyzers and photoelectrochemical devices in corrosive electrolytes has been limited by the lack of earth-abundant materials that are both stable in acidic electrolytes and efficiently utilize energy for electrochemical reactions. Chapter 1 introduces several of the challenges in developing earth-abundant materials for electrochemical systems in acidic electrolytes, such as electrocatalysts for the oxygen and the chlorine evolution reactions, and protective layers for photoanodes. Chapter 2 reports the electrochemical behavior of crystalline transition metal antimonates consisting of solid solutions of MnSb2O6 with NiSb2O6 for the oxygen evolution reaction in strongly acidic electrolytes. In Chapter 3, the crystalline transition metal antimonates NiSb2O6, CoSb2O6, and MnSb2O6 are investigated for the chlorine evolution reaction, and CoSb2O6 is found to exhibit activity and stability comparable to noble metal oxide electrocatalysts. Chapter 4 describes the development of earth-abundant SnOx coatings as protective heterojunctions for planar Si photoanodes in corrosive electrolytes. Chapter 5 focuses on the development of conformal SnOx coatings that form protective heterojunctions on Si microcone photoanodes. The work presented herein demonstrates several strategies towards the development of stable earth-abundant materials for efficient electrochemical and photoelectrochemical energy conversion in acidic electrolytes.
" }, { "name": "Mosesso, Richard Albert", "degree": "PhD", "year": "2019", "title": "Mechanistic Investigations of Receptor Signaling via Canonical and Non-Canonical Amino Acid Mutagenesis", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-131615199", "creators": [ { "name": { "family": "Mosesso", "given": "Richard Albert" }, "id": "Mosesso-Richard-Albert", "orcid": "0000-0003-0927-0843", "display_name": "Mosesso, Richard Albert" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/X18Z-XE16", "abstract": "This dissertation primarily describes investigations of the mechanisms by which pentameric ligand-gated ion channels (pLGICs) activate (\"gating\") using canonical and non-canonical amino acid mutagenesis. Chapter 1 provides an introduction to the systems being studied, their physiological roles, and the techniques that we have used to study them. Chapter 2 describes a series of experiments comparing the roles of amino acid residues proximal to the neurotransmitter binding site in the type 3 serotonin receptor (5-HT3R) to the aligning residues of the muscle-type nicotinic acetylcholine receptor (nAChR). The findings presented in Chapter 3 assess the functional roles of proline residues in the prokaryotic pLGIC, Erwinia ligand-gated ion channel (ELIC). Chapter 4 describes an extensive investigation of salient details of 5-HT3R gating using canonical and non-canonical amino acid mutagenesis of amino acid residues at the interface of the extracellular domain and transmembrane domain of this receptor. Chapter 5 applies a photocrosslinking strategy employing the non-canonical amino acid p-azidophenylalanine to study dimerization and cofactor interactions of the estrogen receptor \u03b1.
" }, { "name": "Omar, Ahmad Khalid", "degree": "PhD", "year": "2019", "title": "Dynamics, Mechanics and Stability of Physical Gels", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062019-082100687", "creators": [ { "name": { "family": "Omar", "given": "Ahmad Khalid" }, "id": "Omar-Ahmad-Khalid", "orcid": "0000-0002-6404-7612", "display_name": "Omar, Ahmad Khalid" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3F0A-4S95", "abstract": "From the commercial products that we encounter in our daily lives to the mucous that lines our gut, gels assembled by the reversible association of polymers or colloids are a ubiquitous, important and fascinating class of soft materials. The dual solid and fluid-like (viscoelastic) properties of associative polymer gels render them useful in a number of applications including as tissue-regeneration scaffolds, drug delivery vectors and organic electronics and batter technologies. However, there remains a number of open questions regarding the microscopic origins of many of the dynamical and mechanical properties that make these materials so appealing. The wide range of length and timescales in physical gels present a formidable challenge towards the formulation of a complete microscopic dynamical and rheological portrait. My work has focused on the development of microscopically-informed and experimentally verifiable explanations for some of the fundamental dynamical and mechanical properties of associative gels. I first present our viewpoint, informed by computer simulation and experiment, on the origin of the long-time self-diffusivity of telechelic polymer gels. Our perspective and resulting theory compare favorably with experiments. Shearing an associative polymer gel is found to result in the emergence of new diffusive modes with applied shear that are can destabilize homogeneous flow for gels sufficiently close to the two phase boundary. This finding motivates the idea that nonequilibrium forcing may promote the relaxation of arrested colloidal materials, such as a colloidal gel, closer to their thermodynamic ground state. The driving force need not be externally applied. The induced collective motion in colloidal gels subject to internal driving forces (such as the presence of a small fraction of self-propelling colloids) can drive the system from a state of arrested metastablity to a state of lower free energy. I conclude by showing that the internal stress generated by the self-propelling particles -- the active stress -- is not a \"true\" stress, but rather an equivalent stress analogous to the dynamic pressure of fluids in a gravitational field. The importance of this finding is demonstrated in resolving the perplexing finding of a negative surface tension in phase separated active materials.
" }, { "name": "Piraner, Dan Ilya", "degree": "PhD", "year": "2019", "title": "Tunable Thermal Bioswitches as a Control Modality for Next Generation Therapeutics", "advisor": "Shapiro, Mikhail G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312019-045041264", "creators": [ { "name": { "family": "Piraner", "given": "Dan Ilya" }, "id": "Piraner-Dan-Ilya", "orcid": "0000-0003-3857-9487", "display_name": "Piraner, Dan Ilya" } ], "advisors": [ { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "advisor", "display_name": "Shapiro, Mikhail G." } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "biochem" ], "doi": "10.7907/DH10-6N61", "abstract": "Synthetic biology is rapidly contributing to the field of therapeutic development to create increasingly potent agents for the treatment of a variety of diseases. These living \"designer therapeutics\" are capable of integrating multiple sensory inputs into decision making processes to unleash an array of powerful signaling and effector responses. Included in the great therapeutic potential of these agents, however, is a cognate risk of severe toxicity resulting from runaway on-target or erroneously induced off-target activity. The ability to remotely control engineered therapeutic cells after deployment into patient tissue would drastically reduce the potential dangers of such interventions. However, among existing biological control methods, systemic chemical administration typically lacks the spatial precision needed to modulate activity at specific anatomical locations, while optical approaches suffer from poor light penetration into biological tissue. On the other hand, temperature can be controlled both globally and locally \u2014 at depth \u2014 using technologies such as focused ultrasound, infrared light and magnetic particle hyperthermia. In addition, body temperature can serve as an indicator of the patient's condition. Overall, temperature is a versatile signal which can provide a handle to actuate a biological response for the control of therapeutic agents.
\r\n\r\nIn this thesis, a tunable and modular system is developed to respond to thermal perturbations in cellular environments and affect a biological response. At the core of this system is a pair of single-component thermosensing proteins whose dimerization is strongly and sharply coupled to their thermal environment. These domains are first utilized in their native context as negative regulators of transcription in prokaryotes, wherein they are integrated into genetic circuits to control expression of reporter genes. These gene circuits show strong and sharp thermal activation and can be utilized in multiplex to affect higher order logical operations. Cells imbued with these circuits demonstrate transcriptional activation upon global thermal elevation within the host animal within which they reside (fever) or upon a spatiotemporally localized temperature shift imparted by focused ultrasound hyperthermia. In subsequent work, one of these bioswitches is introduced into mammalian cells where it functions as a modular Protein-Protein Interaction (PPI) domain, conferring temperature-dependent protein localization.
\r\n\r\nThe work conducted in this thesis demonstrates the feasibility of utilizing temperature as a stimulus for biological activity. This technology can be harnessed to regulate therapeutically relevant processes in bacterial and mammalian cells such as transcriptional regulation and protein localization, and potentially broader protein function. The thermal bioswitches described herein could be utilized to engineer an array of research tools and biological therapies with actuation driven by spatiotemporally precise noninvasively applied stimuli or by real-time sensing of host conditions.
" }, { "name": "Poremba, Kelsey Elizabeth", "degree": "PhD", "year": "2019", "title": "Development of Nickel-Catalyzed Asymmetric Reductive Cross-Coupling Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222019-135022700", "creators": [ { "name": { "family": "Poremba", "given": "Kelsey Elizabeth" }, "id": "Poremba-Kelsey-Elizabeth", "orcid": "0000-0002-7446-257X", "display_name": "Poremba, Kelsey Elizabeth" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZW64-GJ97", "abstract": "Asymmetric reductive cross-electrophile coupling is a powerful method to forge C\u2013C bonds and access enantioenriched small molecules, which can be further functionalized to access scaffolds present in natural products and bioactive pharmaceutical agents. However, an innate challenge of this methodology is identifying a chiral catalyst that achieves optimal cross-selectivity and stereocontrol. Herein, we report studies on the asymmetric cross-coupling of C(sp3) electrophiles, such as benzyl chlorides, \u03b1-chloroesters, and N-hydroxyphthalimide esters, with several classes of C(sp2) electrophiles.
\r\n\r\nWe describe the asymmetric Ni-catalyzed reductive cross-coupling of (hetero)aryl iodides and benzyl chlorides to prepare enantioenriched 1,1-diarylalkanes. As part of these studies, a new chiral bi(oxazoline) ligand, 4-HeptylBiOX, was developed to obtain products in synthetically useful yield and enantioselectivity. This novel ligand is demonstrated to expand the substrate scope of these stereoconvergent reductive cross- couplings to include the asymmetric cross-coupling of \u03b1-chloroesters with aryl iodides, and sterically hindered N-hydroxyphthalimide esters with alkenyl bromides. Model studies have been initiated to study the application of these reactions toward the total synthesis of cylindrocyclophane natural products.
" }, { "name": "Praske, Eric", "degree": "PhD", "year": "2019", "title": "Intramolecular Hydrogen-shift Reactions of Peroxy Radicals", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122018-171618053", "creators": [ { "name": { "family": "Praske", "given": "Eric" }, "id": "Praske-Eric", "orcid": "0000-0001-7169-4423", "display_name": "Praske, Eric" } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KBX8-H010", "abstract": "Straight chain alkanes with more than five carbons, emitted in cities due to incomplete combustion and fuel evaporation, undergo atmospheric gas-phase oxidation with the hydroxyl radical to produce alkyl radicals. These alkyl radicals subsequently add O2, leading to the formation of peroxy radicals. Following further reaction of these radicals in urban areas, hydroxy-substituted peroxy radicals are formed. Previously, the fate of these peroxy radicals was assumed to be dominated by reaction with nitric oxide, a common air pollutant. Computational and experimental investigations of the oxidation mechanism of 2-hexanol, however, demonstrate that hydrogens \u03b1 to the hydroxy group exhibit a significantly reduced energetic barrier toward intramolecular hydrogen shifts to the peroxy radical. The barrier reduction for these hydrogen shift reactions results in rate constants that are orders of magnitude larger than for alkyl hydrogens that lack \u03b1 substitution. Due to significant reductions of nitric oxide emissions in North America, these rate constants are sufficiently large to suggest that this chemistry is competitive even in large cities, particularly during warm summer days. Gas-phase alkyl hydroperoxides, a class of compounds previously expected to exist in negligible quantities in cities, are major products of this chemistry.
\r\n\r\nFurther oxidation of alkyl hydroperoxides leads to the formation of hydroperoxy-substituted peroxy radicals. The chemistry of such peroxy radicals is evaluated through the oxidation of 2-hydroperoxy-2-methylpentane. Experimental observations confirm the previously reported computational result that these peroxy radicals rapidly isomerize by intramolecular hydrogen shift of the hydroperoxide hydrogen. This isomerization occurs on timescales that are much faster than those of bimolecular reaction in essentially all regions of the troposphere. As a consequence of the isomerization, one peroxy radical isomer produced in the oxidation of 2-hydroperoxy-2-methylpentane exhibits an \u03b1 hydroperoxide hydrogen shift. This reaction rate constant is similar to that reported for the \u03b1 hydroxy hydrogen shift in the 2-hexanol system.
\r\n\r\nAlkoxy radicals produced in the oxidation of 2-hydroperoxy-2-methylpentane are similarly shown to undergo a very rapid hydrogen shift of the hydroperoxide hydrogen. One of these shifts results in a peroxy radical that exhibits an \u03b1 hydroxy hydrogen shift. Thus, the rapid scrambling of hydroperoxy-subsituted alkoxy and peroxy radicals is a key process that can enable additional unimolecular pathways that are otherwise inaccessible. This chemistry has the potential to introduce significant mechanistic complexity and, due to the rapid nature of the reactions, cannot be neglected even under typical \"high NO\" conditions employed in chamber studies.
" }, { "name": "Preska Steinberg, Asher Raphael", "degree": "PhD", "year": "2019", "title": "How Polymers Shape the Physicochemical Environment of the Gut", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162019-155405091", "creators": [ { "name": { "family": "Preska Steinberg", "given": "Asher Raphael" }, "id": "Preska-Steinberg-Asher-Raphael", "orcid": "0000-0002-8694-7224", "display_name": "Preska Steinberg, Asher Raphael" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XPEZ-G864", "abstract": "The gut is where food is digested and nutrients are absorbed, therapeutics are often delivered, and many infections take hold. The gut microbiota is in symbiosis with its host, and can influence host health and behavior. Though the gut holds these central roles, little is understood about the physics of how soft materials interact with and shape the physicochemical environment of the gut. Soft materials abound in the gut in the form of particulates (e.g., microbes, viruses, therapeutic particles, food granules) and polymers (e.g., dietary fibers, therapeutics, food additives). This thesis explores the soft matter physics of the gut and how physicochemical interactions can influence gut structure and function. This is studied through a combination of mouse experiments and numerical calculations. In the first part of this thesis, we investigate how particulates interact with polymers in the small intestine. We find that polymers from dietary fiber can aggregate particulates by a mechanism that is qualitatively consistent with depletion interactions. This mechanism is distinct from agglutination via specific chemical interactions. In the second part of this thesis, we investigate how polymers interact with the colonic mucus hydrogel. Colonic mucus is the nexus of host-microbe interactions. It is a barrier which protects against microbial infiltration, and alterations to its physical structure have been linked to changes in host health. Here, we find that polymers compress the colonic mucus hydrogel. For uncharged polymers, this mechanism can be described by a simple, mean-field model based on Flory-Huggins solution theory. Further, we find that microbes can modulate the extent of mucus compression by degrading polymers in the gut. In the last part of this thesis, we find that charged polymers (polyelectrolytes) compress mucus by a Donnan mechanism.
" }, { "name": "Ramachandran, Karthik", "degree": "PhD", "year": "2019", "title": "Bioresorbable Vascular Scaffolds Gain Ductility, Resistance to Hydrolysis, and Radial Strength via a Unique Poly L-lactide Microstructure", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11162018-140640407", "creators": [ { "name": { "family": "Ramachandran", "given": "Karthik" }, "id": "Ramachandran-Karthik", "orcid": "0000-0003-1820-7555", "display_name": "Ramachandran, Karthik" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9146-5159", "abstract": "Advances in tissue engineering over the past few decades are poised to revolutionize drug delivery and biomedical implants. Bioresorbable vascular scaffolds (BVS), which are made from the semicrystalline polymer poly (L-lactide), are an example of polymers saving and improving the quality of human life. BVSs are emerging as a promising alternative to metal stents for the treatment of coronary heart disease (CHD), one of the leading causes of death in the world. In contrast to permanent stents, BVSs are designed to have a limited lifespan in the body; they restore blood flow through the occluded artery by lending it support for 3-6 months, but are completely resorbed in 2-3 years, leaving behind a healthy artery. This transient character of BVS restores vasomotion in the treated artery and can eliminate the risk of thrombosis, a dreaded complication regarded as the bane of stenting.
\r\n\r\nThe promising success of the first and currently only clinically-approved BVS (FDA-approval in 2016) provides an impetus to continue its development. The struts of the BVS (~ 150\u03bcm) are nearly two times thicker than in metal stents (~ 80\u03bcm). A thicker device is challenging to implant and is unable to treat smaller and tortuous arteries. Furthermore, clinicians speculate that irregular blow flow over thicker struts may contribute towards thrombosis. An added complication of working with BVSs is that they are difficult to visualize with X-rays owing to the low atomic mass of polymers. The need for a BVS that is thinner, stronger, and radio-opaque is the motivation for this thesis, which aims to extend the benefits of transient implants to a broader patient population. Chapter I provides a brief chronological overview of the evolution of cardiovascular therapeutics to combat CHD. Chapters II and III elucidate micron-scale gradients in the PLLA microstructure of the clinically-approved BVS that overcome PLLA\u2019s inherent brittleness and provide lasting radial support to the artery. Chapter IV discusses the fabrication of novel instrumentation to establish structure-property relationships for scaffolds, and Chapter V explores polylactide nanocomposites that not only increase radial strength in a thinner profile but also provide radio-opacity.
" }, { "name": "Reed, Christopher John", "degree": "PhD", "year": "2019", "title": "Activation of Nitric Oxide and Water by Transition Metal Clusters Relevant to Active Sites in Biology", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-140931627", "creators": [ { "name": { "family": "Reed", "given": "Christopher John" }, "id": "Reed-Christopher-John", "orcid": "0000-0002-8774-5106", "display_name": "Reed, Christopher John" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QWMZ-HA45", "abstract": "This dissertation discusses the synthesis, characterization, and reactivity of site-differentiated tetranuclear clusters containing Fe and Mn with NO and H2O-derived ligands. The motivation of this work was to conduct a detailed examination of structure-property relationships in well-defined molecular systems focused on unique features of multinuclear systems, such as bridging ligands, neighboring metal identity, and cluster oxidation state. Reactivity towards NO and H2O-derived ligands was targeted due to their relevance to biological multinuclear transition metal active sites that promote multi-electron small molecule transformations.
\r\n\r\nChapter 2 discusses the synthesis of Fe-nitrosyl clusters bearing an interstitial \u03bc4-F atom. These clusters were prepared to compare their reactivity to previously synthesized [Fe33OFeNO] clusters with an analogous structure. A redox series of the [Fe3FFe] and [Fe3FFeNO] clusters were accessed, with the nitrosyl clusters displaying five cluster oxidation states, from FeII3{FeNO}8 to FeIII3{FeNO}7. Overall, the weaker bonding of the F- ligand resulted in attenuation of the activation and reactivity of the {FeNO}7, relative to the corresponding \u03bc4-O clusters. Furthermore, the ability of distal Fe oxidation state changes to influence the activation of NO was decreased, demonstrating lower cooperativity between metals in clusters linked by a weaker \u03bc4-atom This represents a rare case where the effects of bridging atom ligands could be compared in isostructural multinuclear complexes and decoupled from changes in metal ion coordination number, oxidation states, or geometry.
\r\n\r\nChapter 3 describes the synthesis of site-differentiated heterometallic clusters of [Fe3OMn], displaying facile ligand substitution at the five-coordinate Mn. This system was able to coordinate H2O and thermodynamic parameters of the proton and electron transfer processes from the MnII\u2013OH2 to form a MnIII\u2013OH moiety were studied. The oxidation state distribution of the neighboring Fe centers had a significant influence on these thermodynamic parameters, which was similar to the analogous parameters for mononuclear Mn systems, demonstrating that oxidation state changes in neighboring metals of a cluster can perturb the reactivity of a Mn\u2013OHx unit nearly as much as an oxidation state change at the Mn\u2013OHx. Subsequent experiments attempted to find spectroscopic or electrochemical evidence for formation of a terminal Mn-oxo in this system; however, that was not obtained, even in relatively extreme conditions. This established a lower limit for the bond dissociation enthalpy of the MnIII\u2013OH of ca. 93 kcal/mol, which makes formation of a terminal Mn-oxo cluster unfavorable in most organic solvents, due to expected facile hydrogen atom abstraction of a solvent C\u2013H bond.
\r\n\r\nThe insights obtained on the reactivity of these tetranuclear metal-hydroxide clusters was applied towards stabilizing a terminal metal-oxo in a multinuclear complex, as outlined in Chapter 4. Through the use of pendant hydrogen bond donors with tert-butyl-aminopyrazolate ligands, tetranuclear Fe clusters bearing terminal-hydroxide and -oxo ligands could be stabilized and structurally characterized. A similar thermodynamic analysis of the FeIII\u2013OH bond dissociation enthalpy was conducted, which demonstrated FeIII-oxo clusters could be accessed with a range of reactivity at the terminal-oxo ligand, based on the redox distribution of the neighboring Fe centers. The kinetics of C\u2013H activation for the [FeII2FeIII2]-oxo cluster redox state were analyzed, demonstrating a strong dependence of the C\u2013H bond pKa on the rate of proton coupled electron transfer.
\r\n\r\nLastly, Chapter 5 describes the synthesis and reactivity of tetranuclear Fe clusters bearing unsubstituted pyrazolate ligands, focusing on attempts to observe evidence for a terminal Fe-oxo or Fe-imido motif. Clusters bearing a labile trifluoromethanesulfonate ligand at the five-coordinate Fe center could be prepared, and would react with oxygen atom transfer reagents to produce a terminal Fe-hydroxide cluster, which, upon dehydration, led to isolation of an octanuclear \u03bc2-O cluster. The pathway for Fe-hydroxide formation was investigated, but could not conclusively determine whether reactivity occurred from a transient terminal Fe-oxo. Similarly, the reduced tetra-iron cluster, in the [FeII3FeIII], redox state was prepared, and demonstrated reactivity towards electron deficient aryl azides. Isolation of aryl amide clusters (Fe-NHAr) was observed, suggesting, again, formation of a reactive Fe-imido which decomposes through formal hydrogen atom abstraction. Efforts to stabilize either of these Fe=O/NR multiply-bonded species through a more acidic Fe were investigated by synthesizing the corresponding pyrazolate bridged \u03bc4-F clusters. The [FeII4] cluster also displayed reactivity towards oxygen atom transfer reagents, and produced a similar octanuclear \u03bc2-O cluster, but the observation of \u03bc4-F substitution with oxygen to produce \u03bc4-O clusters with a terminal F ligand likely precluded formation of a reactive terminal-oxo cluster. Instead, thermodynamically favorable cluster rearrangement to the [Fe3OFe] structure dominates.
" }, { "name": "Rolando, Justin Charles", "degree": "PhD", "year": "2019", "title": "Bioanalytical Tools to Develop Rapid Diagnostics and Study Physiology", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-112017023", "creators": [ { "name": { "family": "Rolando", "given": "Justin Charles" }, "id": "Rolando-Justin-Charles", "orcid": "0000-0001-8948-319X", "display_name": "Rolando, Justin Charles" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/99NT-WP75", "abstract": "This work details the development of bioanalytical tools for use in rapid diagnostics (Chapters 2-4) and in the study of physiology (Chapters 5-6). This research harness the power of real-time, singlemolecule microfluidics to study loop-mediated isothermal amplification in urinary tract infections (Chapter 2), chlamydia (Chapter 3), and gonorrhea (Chapter 4). In Chapter 5, non-reactive beads are designed and optimized to study the impact of polymers on murine gastrointestinal mucosa. Chapter 6 details the implementation of a mass spectrometry method to quantify bile acids and investigate their interaction with the microbiota in the murine gastro-intestinal tract.
" }, { "name": "Sampson, Jessica", "degree": "PhD", "year": "2019", "title": "Nuclearity and \u03c0-\u03c0 Interaction Effects on Olefin Polymerization and Coordination Chemistry", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072019-122030433", "creators": [ { "name": { "family": "Sampson", "given": "Jessica" }, "id": "Sampson-Jessica", "orcid": "0000-0001-5273-6843", "display_name": "Sampson, Jessica" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1BT2-BR52", "abstract": "This thesis details work performed on the use of secondary coordination sphere effects to impact olefin polymerization activity and tacticity control and the coordination chemistry of Y, Fe, and Cu. Chapter One provides a general introduction and summary of each chapter. Chapter Two describes work in collaboration with KFUPM on nuclearity effects in Zr bisamine bisphenolate complexes. Chapter Three describes the coordination chemistry of arene-appended Y di(pyridyl) pyrrolide complexes and the olefin polymerization activity of tris(dimethylamido) Ti, Zr, and Hf di(pyridyl) pyrrolide complexes. Appendix A describes the effects of bulky trialkylsilyl, triphenylsilyl, and diphenyl(alkyl)silyl substituents on the tacticity control of monozirconium amine bis(phenolate) complexes in 1-hexene polymerization. Appendix B describes the synthesis and structures of miscellaneous dizirconium amine bis(phenolate) complexes which could not be isolated in sufficient purity for olefin polymerization tests. Appendix C describes the synthesis, electrochemistry, and reduction of mesityl-substituted di(pyridyl) NHC supported Fe complexes. Appendix D describes the preparation, solid-state structures, and electrochemistry of di(pyridyl) pyrrolide and di(pyridyl) NHC Cu(I) and Cu(II) complexes displaying \u03c0-\u03c0 interactions in the solid state. Appendix E describes work towards the synthesis of di(pyridyl) guanidinate proligands and metal complexes supported by di(pyridyl) urea, monopyridyl and di(pyridyl) N-heterocyclic olefin and N-heterocyclic vinylidene ligands for use in Lewis acid assisted olefin polymerization. Appendix F includes relevant spectra.
" }, { "name": "Schoepp, Nathan Garrett", "degree": "PhD", "year": "2019", "title": "Phenotypic Antimicrobial Susceptibility Testing Based on Nucleic Acid Analysis", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302019-162535966", "creators": [ { "name": { "family": "Schoepp", "given": "Nathan Garrett" }, "id": "Schoepp-Nathan-Garrett", "orcid": "0000-0002-2406-3693", "display_name": "Schoepp, Nathan Garrett" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5F6B-F452", "abstract": "Antimicrobial resistance (AMR) is one of the most widely recognized threats to global health, and one that continues to grow as new mechanisms of resistance evolve and resistant pathogens spread. Antibiotics are a cornerstone of modern medicine, but their misuse and overuse has constantly and consistently reduced their efficacy to the critically low levels we observe today. As a result, the rate of mortality as a direct result of AMR is approaching over a million deaths annually, with 20-year projections in the ten-millions. Rapid, phenotypic antimicrobial susceptibility testing (AST) that could be performed at the point of care (most notably in \u2264 30 min) would decrease the overuse of antimicrobials, allow physicians to make informed choices about which antimicrobials to prescribe, and improve patient outcomes. Today no such method exists. The ultimate goal of the below work is to allow physicians to choose, instead of guess, which antibiotics to use. We envision that development of these tests into distributable diagnostics will drastically improve patient outcomes, curb the spread of resistance, strengthen global antibiotic stewardship, and forestall the post-antibiotic era.
" }, { "name": "Shen, Kevin", "degree": "PhD", "year": "2019", "title": "Conformations and Charge Fluctuations in Polyelectrolyte Solutions", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:08142018-105206326", "creators": [ { "name": { "family": "Shen", "given": "Kevin" }, "id": "Shen-Kevin", "orcid": "0000-0001-9715-7474", "display_name": "Shen, Kevin" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Y6VG-0297", "abstract": "From DNA and RNA encoding life to flocculation agents used in water remediation, charged polymers (polyelectrolytes) are prevalent in nearly all facets of our lives. The charged nature of polyelectrolytes has rendered them useful in many applications, from the stabilization of colloids to the formation of nanoparticles for drug or gene delivery. There are open questions regarding the factors that dictate polyelectrolyte stability, and electrostatic fluctuations, first elucidated by Debye and H\u00fcckel for simple electrolytes, are key to the thermodynamic description of such charged systems. Electrostatic fluctuations lead to ionic clouds around charges, leading to favorable energy decreases. While charge-fluctuations are well-described for simple electrolytes, the impact of polyelectrolyte (PE) charge connectivity on charge fluctuations is much less well understood: a huge number of degrees of freedom must be considered in order to describe the multicomponent nature of polyelectrolyte solutions and the large number of conformations the polyelectrolytes themselves can assume. Past theories have both under- and over-estimated the connectivity effects on electrostatic fluctuations, and do not give a clear picture of the transition from weak to strong electrostatic fluctuations.
\r\n\r\nMy work has focused on coming up with a theory that self-consistently accounts for the coupling of chain connectivity and electrostatic fluctuations, thus spanning electrostatic fluctuations from weak to intermediate fluctuation strengths. In particular, I present a novel renormalized Gaussian fluctuation (RGF) theory that identifies the renormalization of chain structure as a key physical consequence of intermediate-strength electrostatic fluctuations. The theory self-consistently couples chain structure with the thermodynamics, and mediates the transition from weak, linearized fluctuations to the onset of stronger fluctuation effects like ion pairing. While the onset of these different fluctuation effects has a clear sequence, they are all coupled and must be determined self-consistently. A key concept introduced by the theory is the notion of the polyelectrolyte self energy, which describes the electrostatic work required to charge the molecule in solution, and provides a useful perspective from which to understand and rationalize the effects of chain conformation on thermodynamic behavior. We use the theory to study the phase behavior of polyelectrolyte solutions and connect theory to experimental results.
" }, { "name": "Smarte, Matthew David", "degree": "PhD", "year": "2019", "title": "Kinetic and Spectroscopic Studies of Atmospheric Intermediates", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102019-013016109", "creators": [ { "name": { "family": "Smarte", "given": "Matthew David" }, "id": "Smarte-Matthew-David", "orcid": "0000-0002-4835-7880", "display_name": "Smarte, Matthew David" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E3W5-QR05", "abstract": "Atmospheric chemistry investigates the chemical transformations of atmospheric trace constituents through three complementary approaches: field observations, laboratory experiments, and computational modeling. This thesis used the laboratory experiment approach to explore persistent unknowns associated with free radical chemistry in the troposphere and stratosphere. Studies were conducted using two powerful techniques for the study of chemical kinetics: multiplexed synchrotron photoionization mass spectrometry and cavity ringdown spectroscopy.
\r\n\r\nIn the first part of this thesis, we describe experiments measuring of the absolute photoionization cross sections of chlorine monoxide (ClO) and chlorine dioxide (ClOOCl). The cross sections of ClO were found to be at least a factor of three greater than a prior determination and those of ClOOCl were measured for the first time. ClO and ClOOCl play important roles in the catalytic destruction of polar stratospheric ozone and yet values of the parameters controlling the rate of atmospheric ClOOCl photolysis are uncertain. Our results show that photoionization spectroscopy is highly sensitive to the ClO radical and may be ideally suited for future experiments constraining the quantum yields of ClOOCl photolysis at wavelengths of relevance to the polar stratosphere.
\r\n\r\nWe next discuss experiments investigating the kinetics of chlorine-substituted peroxy radicals (ClRO2). These species are formed in the troposphere upon oxidation of alkenes by chlorine atoms. We present rate constants for the formation and loss pathways of the simplest intermediate in this class: the \u03b2\u2013chloroethyl peroxy radical. We also discuss measurements of the rate constants between NO and the ClRO2 formed upon oxidation of ethene, propene, 1-butene, 2-butene, 1,3-butadiene, and isoprene.
\r\n\r\nFinally, we present results exploring the impact of temperature and humidity on the chemistry of hydroxyl-substituted peroxy radicals (HORO2). In particular, the self reaction of the \u03b2\u2013hydroxyethyl peroxy radical was investigated and found to be significantly enhanced by water vapor at cold temperatures. The product branching ratio was also studied and found to shift in favor of radical suppression. Given the prevalence of water vapor throughout the troposphere, altered reactivity of HORO2\u2013H2O complexes likely plays an important role in atmospheric oxidation mechanisms.
" }, { "name": "Sun, Alexander Wang", "degree": "PhD", "year": "2019", "title": "Stereoselective Synthesis of Diazaheterocycles by Decarboxylative Asymmetric Allylic Alkylation", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132019-140157302", "creators": [ { "name": { "family": "Sun", "given": "Alexander Wang" }, "id": "Sun-Alexander-Wang", "orcid": "0000-0001-6639-4469", "display_name": "Sun, Alexander Wang" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E2YS-GJ06", "abstract": "The Stoltz group has developed transition-metal catalyzed methods to synthesize quaternary and tetrasubstituted stereocenters over the past fourteen years. Using iridium, palladium, copper, and nickel, the group has synthesized a myriad cyclic and acylic quaternary motifs of incredible synthetic and medicinal utility. This thesis presents several projects that further expand the scope of Pd-catalyzed decarboxylative allylic alkylation and examine its applications to the synthesis of medicinally important small molecules. The synthesis of chiral gem-disubstituted five-, six-, and seven-membered diazaheterocycles is presented. Their utility as building blocks for complex medicinal compounds is highlighted. Then, we explore the utility of gem-disubstituted heterocycles in the context of medicinal chemistry.
" }, { "name": "Swisher, Nicholas Adam", "degree": "PhD", "year": "2019", "title": "Synthesis, Characterization, and Reactivity of \"Reverse Pyridine\" Bis(phosphinite) Pincer Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202019-132250450", "creators": [ { "name": { "family": "Swisher", "given": "Nicholas Adam" }, "id": "Swisher-Nicholas-Adam", "orcid": "0000-0002-5320-407X", "display_name": "Swisher, Nicholas Adam" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/S8YH-QR85", "abstract": "In chapter 1 the synthesis of several pincer complexes based on a \"reverse pyridine\" bis(phosphinite) ligand motif is described. Coordination of a borane Lewis acid to the parent ligand is described, as well as factors influencing the subsequent metalation of both the \"free base\" ligand and borane-adduct ligand. The effect of Lewis acid coordination on the spectroscopic and electrochemical properties of the resulting metal complexes is discussed. The reversibility of Lewis acid binding for some complexes is also described.
\r\n\r\nIn chapter 2, an unusual method for carbon-oxygen and carbon-sulfur bond cleavage mediated by alkoxide salts and using silanes as reductants is described.
" }, { "name": "Thompson, Annelise C.", "degree": "PhD", "year": "2019", "title": "Interfacial Behavior of 2D Materials in Devices for Solar Fuels and Sensing Applications", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032019-105139564", "creators": [ { "name": { "family": "Thompson", "given": "Annelise C." }, "id": "Thompson-Annelise-C", "orcid": "0000-0003-2414-7050", "display_name": "Thompson, Annelise C." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "See", "given": "Kimberly" }, "id": "See-Kimberly", "orcid": "0000-0002-0133-9693", "role": "member", "display_name": "See, Kimberly" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DQF7-JD96", "abstract": "The field of 2D materials has expanded widely in the past 15 years to include many materials beyond graphene. However, the applications of graphene and its derivatives are still limited by the lack of thorough knowledge on how to successfully integrate a 2D material into a device while maintaining its unique properties. The work in this thesis investigates the application of 2D materials, such as graphene, fluorinated graphene, and hexagonal boron nitride, in solar fuels and sensing devices to reveal patterns that can inform device design with these and other materials in the future. In the second chapter, lightly fluorinated graphene is investigated as a protective layer on silicon photoanodes. This material is shown to possess superior abilities as a protective layer against oxidizing conditions as well as other deleterious surface reactions. The introduction of fluorine atoms to the lattice at postulated to terminate defects found along grain boundaries, leading to enhanced stability over 24h. The third chapter addresses the energetics of silicon/2D material/liquid junctions to elucidate how the density of states in these materials affect the formation of efficient charge-separation junctions. Hexagonal boron nitride on p-type silicon is shown to form a superior junction to graphene, as measured by changes in the open-circuit potential against a range of one-electron redox couples. Finally, chapter four shows the integration of a monolayer of graphene into a polymer-based chemiresistive vapor sensor to substantially enhance the signal of the sensor over the graphene or polymer alone. The response is dependent on strain at the graphene interface as demonstrated by Raman spectroscopy.
" }, { "name": "Walton, David Paul", "degree": "PhD", "year": "2019", "title": "General Strategies for Visible-Light Decaging Based on Quinone Photochemistry", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012019-134839099", "creators": [ { "name": { "family": "Walton", "given": "David Paul" }, "id": "Walton-David-Paul", "orcid": "0000-0002-9557-6461", "display_name": "Walton, David Paul" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0793-KJ34", "abstract": "The design, synthesis, and photochemistry of several quinone based photoremovable protecting groups is reported. A visible light (400-600 nm) intramolecular photoreduction of 1,4-benzoquinones and 1,4-naphthoquinones mediated by amine and sulfide substituents was employed to launch a fast thermal lactonization step. Both the trimethyl lock and o-coumarinic acid lactonizations were incorporated into these designs. Quantum yields in air equilibrated solvents are moderate (\u03a6 = 0.01-0.10), and chemical yields are generally quantitative. Detailed mechanistic studies reveal a mechanism distinct from typical n,\u03c0* quinone photochemistry. Biological applications and longer wavelength derivatives were further explored.
" }, { "name": "Wenke, Belinda B.", "degree": "PhD", "year": "2019", "title": "The Many Roles of the Nitrogenase Iron Protein", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222019-175445561", "creators": [ { "name": { "family": "Wenke", "given": "Belinda B." }, "id": "Wenke-Belinda-B", "orcid": "0000-0003-3214-6197", "display_name": "Wenke, Belinda B." } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "role": "chair", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/8RB1-HC30", "abstract": "Nitrogenase is the only known enzyme capable of reducing atmospheric nitrogen (N2) into ammonia (NH3) for incorporation into cellular material. N2 reduction by nitrogenase is accomplished by sequential electron transfer between two component proteins: the substrate reductase (the MoFe-protein), and a specialized low-potential electron donor (the Fe-protein). The MoFe-protein contains the active site for nitrogen reduction, the FeMocofactor (FeMo-co). During nitrogen reduction, each Fe-protein dimer docks onto the MoFe-protein, transferring electrons to an intermediate cluster (P-cluster), and ultimately to the FeMo-co.
\r\n\r\nStrikingly, the Fe-protein has another critical role in nitrogen fixation. The Fe-protein is required for the biosynthesis of the two unique metalloclusters of the MoFe-protein: the Pcluster [8Fe:7S] and the active site FeMo-co ([Mo:7Fe:9S:C]-R-homocitrate) cluster. During FeMo-co-cluster maturation, the Fe-protein forms a complex with NifEN, a scaffolding protein homologous to the MoFe-protein, catalyzing the final step in the FeMoco biosynthesis. Studies indicate that the Fe-protein catalyzes insertion of molybdenum and R-homocitrate into an all-iron FeMo-co precursor in a reductant and nucleotide dependent manner. The remaining questions about the cellular functions of the Fe-protein include how the Fe-protein interacts with other maturation proteins in distinct (or similar) ways compared to the MoFe-protein, and how the Fe-protein contributes to the activation and insertion of molybdenum into the FeMo-co.
" }, { "name": "Wong, Alice Rose", "degree": "PhD", "year": "2019", "title": "Total Syntheses of the C19 Diterpenoid Alkaloids (\u2013)-Liljestrandisine and (\u2013)-Liljestrandinine", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082019-154532666", "creators": [ { "name": { "family": "Wong", "given": "Alice Rose" }, "id": "Wong-Alice-Rose", "display_name": "Wong, Alice Rose" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Robb", "given": "Maxwell J." }, "id": "Robb-M-J", "orcid": "0000-0002-0528-9857", "role": "member", "display_name": "Robb, Maxwell J." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "orcid": "0000-0001-8244-9300", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0KR7-PP68", "abstract": "A unified synthetic strategy to access diterpenoid alkaloid natural products is presented. The highly bridged hexacyclic natural products are characterized as having a hydrindane bridged piperidyl motif that is common to the C19 aconitine type diterpenoid alkaloids and the C20 napelline and denudatine type diterpenoid alkaloids. A unified strategy to the C19 and C20 diterpenoid alkaloids is developed. An asymmetric synthesis of an epoxy-hydrindane fragment enables the development of the key unified strategy, involving a 1,2-addition followed by a semipinacol rearrangement in a key fragment coupling process. The fragment coupling is demonstrated generally with a variety of substrates, including an aromatic substrate that is advanced to a key bicyclo[2.2.1]heptane intermediate towards the C20 diterpenoid alkaloids.
\r\n\r\nThe developed 1,2-addition/semipinacol-rearrangement strategy is ultimately leveraged in the total synthesis of two different C19 aconitine type diterpenoid alkaloids. An asymmetric synthesis of a bridged bicyclo[3.2.1]octane fragment is presented. The bridged bicyclo[3.2.1]octane fragment is advanced through the developed 1,2-addition/semipinacol rearrangement fragment coupling strategy affording a key tetracyclic intermediate. This work ultimately culminates in the total syntheses of two natural products (\u2013)-liljestrandisine and (\u2013)-liljestrandinine. Key steps for the completion of the total syntheses include advancement of the key tetracyclic intermediate from the fragment coupling through a series of C\u2013N and C\u2013C bond forming reactions, including an intramolecular aziridination reaction and a radical cyclization.
" }, { "name": "Yang, Kevin Kaichuang", "degree": "PhD", "year": "2019", "title": "Probabilistic Protein Engineering", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222018-173706714", "creators": [ { "name": { "family": "Yang", "given": "Kevin Kaichuang" }, "id": "Yang-Kevin-Kaichuang", "orcid": "0000-0001-9045-6826", "display_name": "Yang, Kevin Kaichuang" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Yue", "given": "Yisong" }, "id": "Yue-Yisong", "orcid": "0000-0001-9127-1989", "role": "member", "display_name": "Yue, Yisong" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZR4M-K630", "abstract": "Machine learning-guided protein engineering is a new paradigm that enables the optimization of complex protein functions. Machine-learning methods use data to predict protein function without requiring a detailed model of the underlying physics or biological pathways. They accelerate protein engineering by learning from information contained in all measured variants and using it to select variants that are likely to be improved. We begin with a review of the basics of machine learning with a focus on applications to protein engineering and protein sequence-function datasets (Chapter 1). We used the entire machine-learning guided engineering paradigm to engineer the algal-derived light-gated channel channelrhodopsin (ChR), which can be used to modulate neuronal activity with light. We build models that discover ChRs with strong plasma membrane localization in mammalian cells (Chapter 2) and unprecedented light sensitivity and photocurrents for optogenetic applications (Chapter 3). Machine learning-guided evolution requires a machine-learning model that learns the relationship between sequence and function. For machine-learning models to learn about protein sequences, protein sequences must be represented as vectors or matrices of numbers. How each protein sequence is represented determines what can be learned. We learn continuous vector encodings of sequences from patterns in unlabeled sequences (Chapter 4). Learned encodings are low-dimensional, do not require alignments, and may improve performance by transferring information in unlabeled sequences to specific prediction tasks. Alternately, we demonstrate an interpretable Gaussian process kernel tailored to biological sequences (Chapter 6). In addition to a model to predict function from sequence, engineering requires a method to use the model to choose sequences for the next round of evolution. Most machine-learning guided engineering strategies assume that selected sequences can be queried directly. However, in directed evolution it is common to design a library of sequences and then sample stochastic batches from that library. We propose a batched stochastic Bayesian optimization algorithm for iteratively designing and screening site-saturation mutagenesis libraries (Chapter 5).
" }, { "name": "Yu, Helen", "degree": "PhD", "year": "2019", "title": "Subunit Selective Degradation of WIZ, a Lenalidomide- and Pomalidomide-Dependent Substrate of E3 Ubiquitin Ligase CRL4CRBN", "advisor": "Deshaies, Raymond Joseph", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232019-210733826", "creators": [ { "name": { "family": "Yu", "given": "Helen" }, "id": "Yu-Helen", "orcid": "0000-0001-9881-8414", "display_name": "Yu, Helen" } ], "advisors": [ { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "advisor", "display_name": "Deshaies, Raymond Joseph" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z7PK-NH81", "abstract": "This dissertation is focused on identifying novel targets of immunomodulatory(IMiD) drugs. IMiDs are a class of drugs that are used to treat multiple myeloma.The first chapter is an introduction to the clinical use of IMiDs, as well as the proteincereblon (CRBN), the primary target of IMiDs. The second chapter describes worktowards the identification of a novel IMiD target, WIZ, that is regulated by CRBNin an IMiD dependent manner. Mass spectrometry was performed to identify novelbinding partners, and IMiD dependent regulation by CRBN was validated usingchemical and genetic methods. Understanding how these drugs work will informthe production of more potent and more selective drugs.
" }, { "name": "Yu, Jason Miao", "degree": "Masters", "year": "2019", "title": "Coupled Cluster Green's Functions for Periodic Systems: Ab-Inito Computation and Applications", "advisor": "Chan, Garnet K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07202019-210018604", "creators": [ { "name": { "family": "Yu", "given": "Jason Miao" }, "id": "Yu-Jason-Miao", "orcid": "0000-0002-2270-6798", "display_name": "Yu, Jason Miao" } ], "advisors": [ { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "advisor", "display_name": "Chan, Garnet K." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-Garnet-K-L", "orcid": "0000-0001-8009-6038", "role": "member", "display_name": "Chan, Garnet K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0P9H-ZQ15", "abstract": "The Coupled Cluster Green\u2019s function method is expanded to periodic systems and preliminary results of the spectral function for diamond and graphene are shown. Future improvements and potential applications are discussed.
" }, { "name": "Yun, Hyun Gi", "degree": "PhD", "year": "2019", "title": "Structural and Biochemical Studies of Enzymes in Bacterial Glycobiology", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292019-144516804", "creators": [ { "name": { "family": "Yun", "given": "Hyun Gi" }, "id": "Yun-Hyun-Gi", "orcid": "0000-0002-3508-5791", "display_name": "Yun, Hyun Gi" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VKH3-XX98", "abstract": "The speed that bacterial pathogens gain resistance to antibiotics is alarming. Designing new antibacterial agents is urgent, but it requires understanding their bacterial targets at the molecular level to achieve high specificity and potency. In this thesis, I discuss the structural and biochemical investigations of three potential protein targets for antibiotics. The first is a UDP-Glc/GlcNAc 4-epimerase, called Gne, from the human pathogen Campylobacter jejuni. This enzyme is the sole source of N-acetylgalactosamine (GalNAc) in C. jejuni, which is a common component in three major glycoconjugates decorating the cell surface and is critical for pathogenesis. The second target protein is an integral membrane protein, called MraY, which catalyzes the transfer of phospho-N-acetylmuramyl (MurNAc) pentapeptide to a lipid carrier, undecaprenyl phosphate (C55-P), producing Lipid I in the peptidoglycan biosynthesis pathway. In the following step, a peripheral protein called MurG catalyzes transferring N-acetylglucosamine (GlcNAc) to Lipid I and produces Lipid II, which provides the first building block of the peptidoglycan layer. Peptidoglycan is uniquely bacterial, with MraY and MurG both being essential for cell viability; therefore, they are attractive targets for the development of antibacterial agents and work toward their structures is presented. Finally, MraY from Escherichia coli is the target for the lysis protein E from phage \u03a6X174.Efforts toward elucidating the EcMraY-E complexstructure are demonstrated here. In total, this thesis provides important data toward a full mechanistic understanding of these important antibacterial targets." }, { "name": "Zhang, Ruijie", "degree": "PhD", "year": "2019", "title": "Engineering Heme Proteins for Olefin and Carbon\u2212Hydrogen Bond Functionalization Reactions", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:03102019-234035587", "creators": [ { "name": { "family": "Zhang", "given": "Ruijie" }, "id": "Zhang-Ruijie", "orcid": "0000-0002-7251-5527", "display_name": "Zhang, Ruijie" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "orcid": "0000-0002-0927-680X", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2076-CX23", "abstract": "One of the most important challenges in chemistry is the creation of new catalysts. Nature excels at this: constructed from biologically available elements, enzymes are versatile catalysts which adapt quickly to changing environments in order to sustain life. The combination of adaptable proteins with abiological reagents from synthetic chemistry affords a new direction for catalyst development. This thesis describes new enzymes, derived from a cytochrome P450 monooxygenase, which catalyze nitrogen and carbon atom transfer reactions to olefins and carbon\u2212hydrogen bonds. Chapter 1 introduces directed evolution, a strategy for the laboratory optimization of proteins, in the context of improving metalloproteins for their native catalysis or for new reactions. Chapter 2 details the development of an enzyme-catalyzed transformation of olefins to aziridines, a valuable motif which is both present in bioactive molecules and used as a versatile building block for synthesis. This study establishes that when provided the appropriate reagents (e.g. styrenes and tosyl azide), heme proteins can adopt a nitrene transfer catalytic cycle to form aziridine products and that the turnover and selectivity of the catalyst can be optimized through mutation of its amino acid sequence. The activity of heme protein catalysts is extended to the functionalization of sp3 hybridized C\u2212H bonds for carbon\u2013nitrogen and carbon\u2013carbon bond formation through nitrene and carbene insertion respectively (Chapters 3 and 4). With the exception of C\u2212H oxygenation chemistry, iron complexes are under-utilized for sp3 C\u2212H functionalization reactions, despite iron being readily available and non-toxic. Combining previously engineered heme proteins with suitable substrates led to initial reaction discovery. Directed evolution of these enzymes significantly improved their C\u2212H functionalization activity (by 140-fold in Chapter 4). Characterization of evolved enzymes, including the attainment of an X-ray crystal structure (Chapter 3) and substrate scope studies (Chapters 3 and 4), were pursued. In sum, the thesis work addresses both the biological question of expanding the catalytic capabilities of existing enzymes through mutation and expands the chemistry of iron-porphyrin catalysts." }, { "name": "Zhang, Yandong", "degree": "PhD", "year": "2019", "title": "Highly Multiplexed Imaging of E. Coli Chromosome and Sensitive Detection of Single-Cell Protein", "advisor": "Cai, Long", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072019-153337463", "creators": [ { "name": { "family": "Zhang", "given": "Yandong" }, "id": "Zhang-Yandong", "orcid": "0000-0003-3291-9209", "display_name": "Zhang, Yandong" } ], "advisors": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "advisor", "display_name": "Cai, Long" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CDSX-MR28", "abstract": "The driving force for biology research is the development of new techniques which allow high-sensitivity, high-throughput measurement in various contexts. Over the past decade, the emerging of a variety of single-cell techniques have greatly transformed our understanding of biological system. My thesis work was therefore focused on development of new single- cell techniques and use the techniques to generate new insights into biological system. Specifically, in the first part of my thesis work, we developed DNA seqFISH, a technique that allows us to image more than 100 different loci on the chromosome in single cells. We applied this technique to image E. coli chromosome with 50kb genomic resolution and 50nm spatial precision. Our data allows us to parse the E. coli chromosome structure according to their different spatial conformations and different cell-cycle stages. We identified two chromosome conformations with distinct domain structures, which is obscured from previous population-average research. We further characterized the domain structure dynamics during daughter chromosome segregation. Therefore, our data provides a high- resolution, dynamic view of E. coli chromosome structure.
\r\n\r\nIn the second part, we developed a novel method for sensitive detection of targeted protein and its post-translational modification (PTM) isoform in single cells. Instead of depending on antibodies to distinguish targeted protein and its PTM isoform, we developed an efficient covalent barcoding strategy to barcode targeted protein inside the cells. Thereafter, targeted protein and its PTM isoform are separated by conventional gel electrophoresis, while their single-cell identity is preserved in the covalently attached oligo. By counting the attached DNA oligos using next-generation sequencing, targeted protein, and its PTM isoform can be accurately measured. We demonstrated the utility of the technology by quantification of histone protein, H2B and its mono-ubiquitination isoform, H2Bub at single-cell level. Our method revealed the single-cell heterogeneities of H2Bub/H2B ratio and its cell-cycle dynamics. Our method therefore provides an antibody-free method for sensitive detection of proteins and its isoforms in single cells.
" }, { "name": "Zhou, Andy", "degree": "PhD", "year": "2019", "title": "Investigations of DNA-Mediated Redox Signaling Between E.coli DNA Repair Pathways", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11262018-103442842", "creators": [ { "name": { "family": "Zhou", "given": "Andy" }, "id": "Zhou-Andy", "orcid": "0000-0003-3383-0855", "display_name": "Zhou, Andy" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "biochem" ], "doi": "10.7907/G7NF-S349", "abstract": "The 4Fe4S cluster has been identified in various DNA-processing proteins spanning a variety of biological functions and all domains of life. Recently, a novel functional role for the cluster has been identified for proteins in DNA repair and replication as a redox switch for DNA binding. Human DNA primase utilizes this redox switch to coordinate primer handoff in replication. The enzymatic activity of DNA polymerase \u03b4 is tuned by the redox-switch, allowing for a fast and reversible regulation of replication in response to oxidative stress. In all cases, the redox of the 4Fe4S cluster is achieved through DNA-mediated charge transport (CT), the ability for DNA to carry charge through its \u03c0-stack. Due to the reliance of this phenomena on the \u03c0-stacking of the nitrogenous bases, DNA CT is sensitive to DNA lesions and mismatches and can proceed over long molecular distances if the DNA is well-stacked. Given this powerful biological phenomena, new inter-protein signaling interactions have been identified with important downstream consequences for genome fidelity. Here, we investigate the ways DNA-mediated charge transport between DNA processing enzymes results in efficient DNA repair or prevention of DNA-damage.
\r\n\r\nFirst, we investigated Dps, a bacterial ferritin that protects DNA from oxidative stress and implicated in bacterial survival and virulence. Dps iron sites can scavenge diffusing oxidants directly but additionally electrons and electron holes can be rapidly transported through the base-pair \u03c0-stack though DNA CT, thus providing an additional mechanism of genome protection by Dps. Using X-band EPR, we monitored formation of mononuclear high-spin Fe(III) sites of low symmetry as a gauge of effective Dps protection via oxidation of its iron sites. Using poly(dGdC)2 or poly(dAdT)2 DNA, we uncovered the dependence of DNA protection by Dps to the formation of guanine radical intermediates. Oxidation of Dps iron sites depended on the presence of the W52 residue. Point mutations of W52 revealed its involvement in an electron transfer (ET) pathway for the oxidation of the Dps iron sites. Finally, we investigated the in vivo consequences of the Dps W52 residue by complementing knockout Dps E.coli with plasmids expressing WT, W52A, or W52Y Dps and applying oxidative stress to the cells through hydrogen peroxide treatment. These assays further demonstrated the ability of Dps to protect the E.coli genome from harmful oxidants DNA-mediated electron transfer processes.
\r\n\r\nSecond, we assessed the redox properties of EndoIII and MutY, two base excision repair glycosylases containing 4Fe4S clusters, in the presence and absence of DNA. Previous work has shown these proteins to have a midpoint redox potential around 80mV vs. NHE when bound to DNA with a positive shift in potential in the absence of DNA. However, electrochemical details that define this midpoint potential have not been uncovered. Using a pyrolytic graphite edge electrode, we measured the midopoint potential of point mutations of EndoIII where point charges are flipped near the cluster (K208E, Y205H, and E200K) in the absence of DNA. Our measurements suggest that a change in a single point charge is not enough to shift the 4Fe4S cluster midpoint potential dramatically. Addition of a poly-L-glutamate polyanion introduced a slight negative shift (~20mV), but with the introduction of DNA a large negative shift was observed (70mV). Overall, binding to the DNA polyanion is the dominant effect in tuning the redox potential of the 4Fe4S cluster, helping to explain why all DNA binding proteins with 4Fe4S clusters studied to date have similar DNA-bound potentials.
\r\n\r\nWith these similar DNA-bound potentials, inter-protein redox signaling should occur. Previous works have demonstrated DNA-mediated redox signaling such as EndoIII signaling to DinG helicase, involved in R-loop maturation, increasing cellular survival by resolving deleterious R-loops. Additionally, different cluster- containing repair proteins of different functions and domains of life have been shown using atomic force microscopy (AFM) to localize to DNA mismatches through a redox switch for DNA-binding affinity. Given a DNA-mediated redox signaling system to scan the genome for lesions, the expression levels of these proteins may play a role in defining the scanning efficiency. We identified that the EndoIII E.coli knockout strain was sensitive to UV irradiation. This implies that EndoIII assists the nucleotide excision repair (NER) pathway via DNA-mediated redox signaling. However, knockout of MutY, another 4Fe4S glycosylase, does not impart the same UV sensitivity, and thus suggests key differences between MutY and EndoIII that define effective DNA-mediated redox signaling. Thus, the effect of protein expression level on the efficiency of DNA-mediated redox signaling was investigated using inducible protein expression of EndoIII to rescue UV-sensitivity. Using both plasmid-based and genome integrated constructs, we uncovered that low amounts of EndoIII expression were enough to rescue the growth defect, and overexpression of WT EndoIII leads to a greater defect caused by excess non-specific enzyme activity. These findings further informed investigation of this unique protein signaling interaction between EndoIII and NER protein UvrC.
\r\n\r\nWith proper EndoIII rescue plasmids, we further characterized the DNA- mediated redox signaling interaction between EndoIII and UvrC. Using UV-irradiation of genetic knockout strains and growth curve analysis, we demonstrate that EndoIII expression is essential for efficient repair of UV-induced DNA lesions, as measured through quantitative changes in growth lag-time when wild-type or mutant EndoIII is present in the cell. Electrochemical analysis of EndoIII point mutants quantify the DNA-CT inefficiencies that lead to the observed phenotypes. EndoIII, a BER repair protein, assists the NER pathway in the repair of UV-induced DNA lesions via DNA-mediated redox signaling. These results give evidence of a new signaling crosstalk between two distinct DNA repair pathways.
" }, { "name": "Ahmed, Tonia Sarah", "degree": "PhD", "year": "2018", "title": "Achieving High Stereoselectivity in Ruthenium-Catalyzed Olefin Metathesis Reactions for Organic and Polymer Synthesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312018-145533563", "creators": [ { "name": { "family": "Ahmed", "given": "Tonia Sarah" }, "id": "Ahmed-Tonia-Sarah", "orcid": "0000-0001-9407-0250", "display_name": "Ahmed, Tonia Sarah" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KCM2-6W92", "abstract": "Transition metal-catalyzed olefin metathesis has emerged as a powerful tool for constructing C\u2212C double bonds. This thesis delineates the development of Ru-based catalysts for the stereoselective formation of olefins and mechanistic studies used to examine how catalyst structure influences selectivity and activity.
\r\n\r\nChapter 2 details the synthesis of Z-selective, cyclometalated catalysts bearing nitrite X-ligands. The activity and selectivity of these catalysts were examined in an array of ring-opening metathesis polymerization and cross metathesis reactions. Comparison of these catalysts with their nitrate-bound analogues is described.
\r\n\r\nChapter 3 describes the examination of several Z-selective, cyclometalated catalysts in ring-opening metathesis polymerizations. The polymerizations of a variety of norbornene and norbornene derivatives were examined to determine the tacticity and microstructure of the resulting polymer. Computational studies were used to examine the mechanism of the polymerization reactions.
\r\n\r\nChapter 4 examines the decomposition of Fischer carbene complexes derived from cyclometalated catalysts. In-depth NMR studies are used to determine the identity of the decomposition product, and the decomposition pathway is examined through computational studies.
\r\n\r\nChapter 5 describes the first example of highly E-selective cross metathesis through kinetic control using stereoretentive, Ru-based catalysts bearing dithiolate catalysts. The preparation of additional stereoretentive catalysts is described for increasing catalyst activity while maintaining or increasing selectivity. A model for the observed stereoselectivity is proposed.
\r\n\r\nChapter 6 delineates the preparation of a series of fast initiating, stereoretentive catalysts. These catalysts are assessed in an array of cross metathesis reactions, and significantly enhanced activity is observed in E-selective reactions. The examination of the relationships between the structure of a catalyst and its selectivity and activity is described.
\r\n\r\nChapter 7 examines the use of stereoretentive catalysts in the synthesis of Z-macrocycles from diene starting materials bearing a Z-olefin and a terminal olefin. Initiation rate studies are conducted to examine the activity of these catalysts compared to previously reported cyclometallated catalysts used in this ring-closing metathesis reaction. The synthesis of twelve- to seventeen-membered rings with high Z-selectivity is described.
\r\n\r\nChapter 8 explores the use of fast-initiating, stereoretentive catalysts for synthesizing E-macrocycles. The preparation of diene starting materials containing two E-olefins is described. Using these catalysts, twelve- to eighteen-membered rings are constructed with high E-selectivity.
\r\n" }, { "name": "Ahn, Jun Myun", "degree": "PhD", "year": "2018", "title": "Copper Carbazolides in Photoinduced C\u2013N Couplings", "advisor": "Fu, Gregory C.; Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282018-184138570", "creators": [ { "name": { "family": "Ahn", "given": "Jun Myun" }, "id": "Ahn-Jun-Myun", "orcid": "0000-0002-8181-908X", "display_name": "Ahn, Jun Myun" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "co-advisor", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "co-advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/H8AP-G249", "abstract": "Photoinduced, copper-catalyzed reactions of organohalides have emerged in recent years as a powerful tool to construct a wide array of C\u2013N bonds, which are prevalent in organic materials and polymers, pharmaceuticals, natural products, and ligands in transition metal catalysts. Described herein is the study and applications of copper complexes ligated by carbazole and its derivatives in photoinduced, copper-catalyzed C\u2013N bond-constructing transformations. Various areas of synthetic inorganic and organic chemistry are explored, including in-depth mechanistic elucidation, ligand and catalyst design, reaction development, as well as spectroscopic and structural characterization of reactive copper complexes.\r\nChapter 2 describes the mechanistic investigation on photoinduced, copper-catalyzed couplings of carbazoles with unactivated alkyl halides. A wide array of mechanistic tools suggests the viability of an out-of-cage C(sp\u00b3)\u2013N coupling pathway. Spectroscopic and structural characterization data of the key intermediates are detailed.\r\nChapter 3 outlines the design and preparation of a new copper-based photoredox catalyst supported by a tridentate bis(phosphino)carbazole ligands. The ground- and excited-state properties of the new photocatalyst are examined.\r\nChapter 4 details the development of photoinduced, copper-catalyzed C(sp\u00b3)\u2013N couplings of carbamates with unactivated alkyl bromides using the new copper photoredox system. The scope with respect to the nucleophile and the electrophile and mechanistic investigations are communicated.\r\nChapter 5 illustrates the chemistry of copper complexes supported by bidentate (phosphino)carbazole ligands. A diverse array of copper complexes in both the S = 0 and S = 1/2 states are reported, including a rare, paramagnetic copper\u2013phosphine complex that may serve as a structural model for key copper intermediates of the enantioselective C(sp\u00b3)\u2013N couplings of carbazoles." }, { "name": "Akagi, Allison Emi", "degree": "PhD", "year": "2018", "title": "The Biosynthesis of Ascarosides in Caenorhabditis elegans", "advisor": "Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282017-132944334", "creators": [ { "name": { "family": "Akagi", "given": "Allison Emi" }, "id": "Akagi-Allison-Emi", "orcid": "0000-0002-7233-6190", "display_name": "Akagi, Allison Emi" } ], "advisors": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ZK5DVT", "abstract": "Ascarosides comprise a family of small signaling molecules that have been shown to regulate important events and behaviors in the life history of the nematode Caenorhabditis elegans. Although the different roles of individual ascarosides appear to be determined by the variances in chemical structure, the mechanisms by which ascarosides are synthesized as well as the locations in which ascarosides are produced within the worm are largely unknown. In this thesis, we examined ascaroside production in the intestine, hypodermis, and body wall muscle of the worm by driving the expression of the protein DAF-22 under different tissue-specific gene promoters. While the body wall muscle and hypodermis are capable of synthesizing ascarosides, the intestine appears to be the major site of pheromone production. Additionally, we found through transgenic rescue and HPLC-MS analysis, that the acyl-CoA synthetase ACS-7 plays a significant role in the addition of moieties derived from primary metabolic pathways to the 4\u2019-position of the ascarylose sugar core of ascr#9.
" }, { "name": "Arias, Renee Justine", "degree": "PhD", "year": "2018", "title": "Examination of Selenium Incorporation and Product Formation in the Nitrogenase FeMo-Cofactor", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252018-140505343", "creators": [ { "name": { "family": "Arias", "given": "Renee Justine" }, "id": "Arias-Renee-Justine", "orcid": "0000-0002-6505-7513", "display_name": "Arias, Renee Justine" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "biochem" ], "doi": "10.7907/5WZV-R440", "abstract": "Nitrogenase is the only known enzyme to convert the triply bonded atmospheric dinitrogen (N2) to bioavailable ammonia (NH3) in an ambient environment, breaking one of the strongest chemical bond in nature in the process. Industrially, the Haber-Bosch process is also capable of reducing dinitrogen to ammonia, and is essential for worldwide food production 1,2. Due to the high temperatures and pressures required for the Haber-Bosch process (between 300-550\u00baC and 15-25 MPa) and its requirement for molecular hydrogen, it has become paramount to scientifically investigate the biological processes of nitrogen fixation to ultimately develop more efficient methods to produce bioavailable ammonia. Nitrogenase utilizes two component proteins, the Fe-protein and the MoFe-protein, to reduce ammonia in an ATP-hydrolysis dependent and electron-intensive reaction. Besides the canonical dinitrogen reduction reaction, nitrogenase can reduce a variety of other substrates including: acetylene (C2H2), carbon dioxide (CO2), carbon monoxide (CO), carbonyl sulfide (COS), nitrous oxide (N2O), diazene (N2H2), and more 3-11. CO has long been of interest to the study of the mechanism of nitrogenase, owing to its isoelectronic identity to N2, and its potent inhibitor properties at well as its ability to serve as a weak substrate 12,13. Like CO, cyanide compounds (X-CN) are also of interest to the study of nitrogenase due to the isoelectronic nature of CN- to N2. However, cyanide compounds serve as particularly interesting spectroscopic and crystallographic tools, because X in X-CN can be substituted for more significant sulfur or selenium (Se). In this study, we investigate the substrate properties of SeCN-, with Se-incorporation into the active site FeMo-cofactor and concurrent reduction of SeCN- to methane (CH4). This study serves as yet another link between substrate reduction in nitrogenase. Part of this work describes the incorporation of Se into the cofactor as a vehicle for high-resolution study of nitrogenase under turnover using spectroscopy and crystallography, while another part describes a proposal for future work on the trapping of enzyme intermediates by fast-growing crystallography.
" }, { "name": "Barraza, Kevin Mitchell", "degree": "PhD", "year": "2018", "title": "The Study of the Stepwise Hydroxyl Radical-Mediated Oxidation of Alkyl Surfactants at the Air-Water Interface", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09252017-114900745", "creators": [ { "name": { "family": "Barraza", "given": "Kevin Mitchell" }, "id": "Barraza-Kevin-Mitchell", "orcid": "0000-0003-1849-5219", "display_name": "Barraza, Kevin Mitchell" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9BG2M5K", "abstract": "This thesis presents work on the heterogeneous chemistry of surfactant monolayers adsorbed at the air-water interface with gas phase hydroxyl radicals (OH). A novel hydroxyl radical source utilizing a low-temperature plasma known as the dielectric barrier discharge source (DBDS) is designed, characterized, and implemented as a high concentration OH generator (approximately 1000 fold higher than ambient conditions) in these experiments. Millimeter-sized water droplets containing a monolayer of surface-adsorbed species are exposed to this OH source until a designated level of oxidation. Field-induced droplet ionization mass spectrometry (FIDI-MS), which has been previously proven to be a surface-selective ionization technique, is used as an analytical method to determine the identity and relative quantity of oxidation products at the interface by sampling progeny droplets expelled upon the application of a pulsed electric field. Chapter 2 establishes the utility of the DBDS and FIDI-MS setup by oxidizing the 12-carbon n-alkyl surfactant dodecyltrimethylammonium (DTA+). Mechanistic details can be determined through the evolution of high mass oxidation products through a nearly complete conversion of the parent monolayer. Carbonyl, hydroxyl, peroxyl, and small amounts of fragmentation products can be discerned from the collision-induced dissociation mass spectra and through hydrogen-deuterium exchange experiments. Psuedo-first order kinetics can also be observed in this system, suggesting a Langmuir-Hinshelwood mechanism of OH-initiated oxidation. Chapter 3 extends the study of oxidation of hydrocarbon surfactants by looking at neighbor chain competition among a bis-quaternary ammonium gemini surfactants, a species that contains two long alkyl chains. Specifically, the experiment assesses the ability of two non-identical alkyl chains to compete with each other for the impinging gas phase hydroxyl radical. The increased reactivity of singly oxidized chains is evaluated by the oxidation of a gemini surfactant parent with identical alkyl chains. Chapter 4 investigates the oxidation of \u03b1,\u03c9-surfactants, those that contain polar functional group separated by methylene spacers, discussing deviations of this class of surfactants with those that contain only one head group (i.e. DTA+). Chapter 5 demonstrates the DBDS and FIDI-MS system for use as a peptide footprinting technique for the amphiphilic species substance P. Localization of the site of oxidation can be done through FIDI-MS/MS analysis.
" }, { "name": "Bartels, Phillip Leon", "degree": "PhD", "year": "2018", "title": "Elucidating the Role of [4Fe4S] Clusters in DNA Replication and Repair Proteins", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012018-094939210", "creators": [ { "name": { "family": "Bartels", "given": "Phillip Leon" }, "id": "Bartels-Phillip-Leon", "orcid": "0000-0002-9688-6592", "display_name": "Bartels, Phillip Leon" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9H1307G", "abstract": "[4Fe4S] clusters, redox cofactors, have been discovered in DNA processing enzymes ranging from bacterial base excision repair glycosylases to eukaryotic DNA polymerases. Bacterial repair proteins are activated toward redox activity when bound to DNA and can take advantage of DNA-mediated charge transport (DNA CT) to search the genome for lesions. DNA CT involves the rapid transport of charges through the \u03c0-stacked base pairs and is sharply attenuated in the presence of lesions, mismatches, or other stacking perturbations. Thus, [4Fe4S] repair proteins use this chemistry to rapidly redistribute to target lesions and communicate with one another over long distances.
\r\n\r\nThe general function of [4Fe4S] clusters in bacterial DNA repair has received much attention, but previous efforts have left several critical questions unanswered. First, while the redox potential of these proteins is affected by DNA binding, the relative importance of the negatively-charged DNA, the protein environment surrounding the cluster, and solvent has remained unclear. Second, the importance of [4Fe4S] clusters and DNA CT to human disease has never been directly addressed. The biological consequences of this chemistry are certainly a pressing issue, as numerous disease-relevant mutations in the human homologues of well-studied repair proteins have been recorded. Finally, the existence of [4Fe4S] clusters in eukaryotic DNA replication proteins in general, and in the B-family DNA polymerases in particular, was entirely unexpected. The function of the [4Fe4S] cluster in replication proteins was far from obvious, and the functional differences from repair proteins made them difficult to explain even in the context of CT signaling. Herein, these questions have been addressed using a combination of electrochemical, spectroscopic, and biochemical approaches.
\r\n\r\nFirst, we describe the use of pyrolytic graphite edge electrodes (PGE) and S K-edge X-ray absorption spectroscopy (XAS) to address the influence of protein environment, DNA, and solvation on the [4Fe4S] cluster redox potential in the bacterial base excision repair glycosylases endonuclease III (EndoIII) and MutY. The PGE surface is rough and favorable for protein binding; electron transfer can be further enhanced in the presence of carbon nanotubes. Electrochemical signals for EndoIII and MutY in the absence of DNA are large and reproducible, and a potential shift upon DNA binding is observed. With respect to studying proteins in the absence of DNA, the PGE electrode represents a significant advance over previously used highly-oriented pyrolytic graphite (HOPG), which is hydrophobic and difficult to prepare. To test the effect of protein environment on redox potential, a series of EndoIII point mutants were prepared in which the charge within 5 \u00c5 of the cluster was reversed or added in. None of these mutations induced a significant shift in redox potential relative to wild type, arguing that DNA electrostatics are the dominant factor in potential modulation. In parallel, XAS studies were performed on EndoIII and MutY in the presence and absence of DNA, and in the presence and absence of solvent. Ligating cysteinyl thiols and inorganic S atoms in the [4Fe4S] cluster absorb at different intensities in XAS depending on solvent environment and local electrostatics; these changes, in turn, directly correlate to redox potential. By XAS, DNA was found to induce a significant shift in absorbance, and thus potential; the removal of solvent had a smaller effect. Together, these studies provide new approaches for the study of DNA-binding [4Fe4S] proteins and reveal the critical role of DNA in tuning the redox potential.
\r\n\r\nSecond, we report on a novel mutation in human MUTYH identified from a colorectal cancer patient and confirmed to be pathological. MUTYH is responsible for repairing certain lesions induced by oxidative stress and is thus frequently implicated in cancer. This new variant, C306W, contains a mutation in one of the cysteines that ligates the [4Fe4S] cluster. Electrochemistry, activity and DNA binding assays, and spectroscopic analyses were performed for C306W alongside wild type MUTYH and two other disease-relevant mutants, Y179C and G396D, with an unaltered cluster environment. From this work, it is now clear that C306W can still bind a cluster, but it is susceptible to oxidative degradation to the [3Fe4S]+ state upon redox signaling in an aerobic environment. Consequently, enzymatic activity is very low, and DNA binding is poor. Overall, this represents the first complete characterization of the [4Fe4S] cluster in a human homologue of MutY, and the first demonstration of pathology resulting from a mutation that primarily affects the [4Fe4S] cluster.
\r\n\r\nMoving into DNA replication proteins, we report on the characterization of the [4Fe4S] cluster in yeast DNA polymerase (Pol) \u03b4, the eukaryotic lagging strand polymerase. Pol \u03b4 shows reversible electrochemical signals at a midpoint potential indistinguishable from EndoIII under the same conditions, and EPR spectroscopy confirms use of the [4Fe4S]3+/2+ couple. The electrochemical signal is attenuated on DNA containing an abasic site or a CA mismatch, confirming that Pol \u03b4 is capable of DNA-mediated signaling. Bulk electrolysis and photooxidation were used to oxidize Pol \u03b4 under anaerobic conditions, and activity assays were carried out using oxidized or untreated protein. Oxidation stalls replication activity, while electrochemical reduction of oxidized samples restores activity to untreated levels. These results thus reveal that cluster oxidation serves as a reversible switch regulating Pol \u03b4 activity, suggesting an in vivo role in responding to replication stress, especially oxidative stress. In an effort to address these possibilities, we have carried out preliminary efforts in the characterization of two potentially CT-deficient mutants, W1053A and Y1078A. Both mutants were found to be too structurally unstable to proceed with in vivo experiments, but they can serve to guide future efforts in this direction.
\r\n\r\nFinally, a strategy to examine charge transport through RPA-bound single-stranded DNA is reported. RPA is the eukaryotic single-stranded binding protein and forms a protective coat around vulnerable unwound DNA at replication forks. Given the importance of redox signaling in replication proteins, we aimed to use photooxidation experiments to determine if CT through RPA is a viable pathway; if so, this would open up a large set of long-range transfer pathways to [4Fe4S] proteins in replication. These efforts are ongoing, but the experimental strategy and initial efforts are discussed.
" }, { "name": "Burke, Kelly Suzanne", "degree": "PhD", "year": "2018", "title": "Visualizing mRNA Translation in situ in Single Cells", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292017-201142545", "creators": [ { "name": { "family": "Burke", "given": "Kelly Suzanne" }, "id": "Burke-Kelly-Suzanne", "orcid": "0000-0002-3615-9828", "display_name": "Burke, Kelly Suzanne" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92B8W6R", "abstract": "Translation of mRNA is tightly regulated in cells to ensure that proteins are synthesized at the right time, in the right location, and at appropriate levels. Single-molecule fluorescence in situ hybridization (smFISH) is a simple and widely used method to measure mRNA transcription through determining the abundance and localization of mRNAs in single cells. A comparable single-molecule in situ method to measure mRNA translation would enable a more complete understanding of gene regulation. In this thesis, we describe the development and characterization of a fluorescence assay to detect ribosome interactions with mRNA (FLARIM). The method adapts smFISH to visualize and characterize translation of single molecules of mRNA in fixed cells. To visualize ribosome-mRNA interactions, we use pairs of oligonucleotide probes that bind separately to ribosomes (via ribosomal RNA) and to the mRNA of interest, and that produce strong fluorescence signals via the hybridization chain reaction (HCR) when the probes are in close proximity. FLARIM does not require genetic manipulation, is applicable to practically any endogenous mRNA transcript, and provides both spatial and temporal information.
\r\n\r\nWe first characterize FLARIM in mouse fibroblast cells. We show that FLARIM is sensitive to changes in ribosome association with mRNA upon inhibition of global translation with puromycin. We also show that FLARIM detects changes in ribosome association with an mRNA whose translation is upregulated in response to increased concentrations of iron. Finally, we demonstrate FLARIM in mouse hippocampal neurons, in which local translation of mRNA in the neuronal processes is essential to cell growth and development. We first demonstrate FLARIM in neurons using probes for \u03b2-actin mRNA. We then show that FLARIM detects increased transcription and translation of activity regulated cytoskeletal protein (Arc) mRNA in response to neuronal activation with brain-derived neurotrophic factor (BDNF). We also compare the cellular distribution between the major microtubule-associated protein 2 (MAP2) mRNA isoforms, whose translation will be characterized in future FLARIM experiments. Overall, this work expands the capability of smFISH to study mRNA translation in addition to transcription, and it shows the utility of in situ translation analysis in characterizing single-cell gene expression.
\r\n" }, { "name": "Buscagan, Trixia Marie", "degree": "PhD", "year": "2018", "title": "Transition Metals as Catalysts for Cross-Coupling and Dinitrogen Fixation", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09202017-130540216", "creators": [ { "name": { "family": "Buscagan", "given": "Trixia Marie" }, "id": "Buscagan-Trixia-Marie", "orcid": "0000-0001-8242-9203", "display_name": "Buscagan, Trixia Marie" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z98P5XPM", "abstract": "Transition metals are used as catalysts in the laboratory and by nature to facilitate difficult chemical transformations. Herein, three different metal containing catalysts are discussed: Pd and Ni catalysts towards the formation of carbon-carbon (C-C) bonds and Fe catalysts towards the reduction of N2 to NH3.
\r\n\r\nIn Chapter 2, mechanistic studies of Pd- and Ni-catalyzed cross-coupling reactions are discussed. The mechanism of transmetalation of a Pd-catalyzed Suzuki cross-coupling reaction is studied using a stereochemical probe, revealing that transmetalation occurs with retention of configuration, consistent with transmetalation occurring through a frontside-attack mechanism. Next, to explore the viability of a transmetalation first pathway in an asymmetric Negishi cross-coupling reaction, S = 1/2 NiIBr and NiI\u2013alkyl complexes were synthesized, crystallographically characterized, and their reactivities explored. Based on these reactivity studies, evidence against a transmetalation first pathway is provided using a variety of spectroscopic methods.
\r\n\r\nIn Chapter 3, new Fe(N2)(H)x complexes are synthesized. These complexes catalyze the reduction of N2 to NH3 and the yields for NH3 are improved if the reactions are performed in the presence of Hg lamp photolysis. Preliminary mechanistic studies exploring the role of light are discussed. In the final chapter, new ligand scaffolds are developed that can bind a Lewis acidic and Lewis basic metal center. These ligand frameworks support one- and two-atom bridges between the two metal sites. Finally, we discovered that some of the new complexes are catalysts for N2 to NH3 reduction and olefin hydrogenation.
" }, { "name": "Buss, Joshua Alan", "degree": "PhD", "year": "2018", "title": "Molybdenum Para-Terphenyl Diphosphine Complexes", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162018-150106151", "creators": [ { "name": { "family": "Buss", "given": "Joshua Alan" }, "id": "Buss-Joshua-Alan", "orcid": "0000-0002-3347-8583", "display_name": "Buss, Joshua Alan" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/SJTG-3388", "abstract": "This dissertation describes studies exploring the coordination chemistry and reactivity of molybdenum complexes bearing a flexible and redox non-innocent para-terphenyl diphosphine ligand. Within this context, transformations relevant to energy storage and conversion, fundamental structure function studies, and unusual group transfer reactivity are presented.
\r\n \r\nChapter 2 accounts the ability of Mo para-terphenyl diphosphine complexes to catalyze extensive ammonia borane dehydrogenation, releasing greater than two equiv. of hydrogen (H2). Initially believed to be a frontrunner as a high energy density H2 storage medium, AB is a Lewis acid/base adduct that features both hydridic B\u2013H bond and protic N\u2013H bonds. As a highly reactive molecule, the controlled dehydrogenation of AB, accessing \u2265 2 of the 3 stored equiv. of H2, is uncommon. We disclose a catalytic system, utilizing an earth-abundant metal, that is capable of such reactivity. The mechanism by which the catalysis proceeds is dependent on the oxidation state of the precatalyst, with MoII proceeding through a II/IV cycle and Mo0 proceeding through a 0/II cycle. Several Mo hydride complexes were characterized in conjunction with this work. Importantly, the ability of the para-terphenyl diphosphine ancillary ligand to support a range of Mo oxidation states and coordination numbers was established, a feature that provides a foundation for the work presented in subsequent chapters.
\r\n \r\nIn Chapter 3, new features of the para-terphenyl diphosphine ligand were discovered, namely facilitation of electron loading that subsequently leads to small molecule functionalization and cleavage. From the Mo dicarbonyl complex described in Chapter 2, stepwise reduction affords Mo0, Mo-II, and Mo-III compounds, all of which were characterized both structurally and by a variety of spectroscopies. The latter two complexes were demonstrated to react with silyl electrophiles, instigating deoxygenative reductive coupling of the bound CO ligands to a metal-free C2O1 fragment. This remarkable four-electron process was studied in detail, characterizing twelve different reaction intermediates, including rare examples of bis(siloxy)carbyne, terminal carbide, and mixed dicarbyne motifs. The cleavage of a bound carbon monoxide (CO), subsequent coupling, and spontaneous product release was an unprecendented sequence of chemical transformations, the detailed mechanistic study of which provides valuable precedent for catalyses for the conversion of C1 oxygenates to multicarbon products.
\r\n \r\nChapter 4 discusses continuations of this work in an attempt to model Fischer-Tropsch catalysis with higher fidelity. To this end, the silyl electrophiles used in the fundamental studies in Chapter 3 needed to be replaced with protons. Addition of protons to the super-reduced Mo complexes resulted in formal arene hydrogenation; no evidence for C\u2013O functionalization was obtained. These diene-linked complexes; however, provided an opportunity to explore how the nature of the basal \u03c0-system effects CO catenation chemistry and ultimately led to the preparation of a Mo-bound C3O3 unit derived entirely from CO. Reactivity with protons was likewise explored for downstream intermediates. Carbide protonation yields a stable methylidyne carbonyl complex, that, upon treatment with hydride, forms a methylidene. Comparison to a silyl-bearing model system suggests that subsequent carbene carbonylation affords enthenone.
\r\n \r\nChapter 5 and 6 focus on the synthesis and reactivity of Mo(IV) terminal pnictogen complexes isoelectronic to the carbyne and carbide complexes prepared in Chapters 3 and 4. Chapter 5 describes successful N\u2013C bond formation through N\u2013 transfer to CO from a MoII anionic nitride precursor. In Chapter 6, the first example of a terminal transition metal phosphide with d-electrons was prepared via a 4 e\u2013 oxidative group transfer. This species can undergo a single-electron oxidation, providing, at low temperatures, an unstable Mo(V) phosphide cation that studied extensively by CW and pulse EPR techniques. Upon warming, P\u2013P bond formation is evidenced by chemical trapping and characterization of coupling byproducts. Related phosphinidene (Mo=PR), phosphide (Mo-PR2), and dinuclear \u03bc-phosphido compounds are also reported. In a collaboration with Mr. Yohei Ueda and Dr. Masa Hirahara these complexes were explored for proton reduction reactivity. Isotopic labeling suggests formation of a dinuclear \u03bc-phosphinidene upon treatment with acid, and a bimetallic hydride \u03bc-phosphide was accessed from reaction with hydride.
\r\n \r\nThe final chapters of this dissertation are focused on the reduction of carbon dioxide (CO2). Chapter 7 presents a fundamental study involving Lewis acid (LA) aditives, that demonstrates the importance of kinetic stabilization, and not just thermodynamic activation, in productive small molecule functionalization chemistry. Upon addition of LAs, well-defined adducts are formed with Mo-bound CO2. Protonation results in C\u2013O bond cleavage, utilizing two electrons from the metal center to reduce CO2 to CO and H2O. Though the degree of CO2 activation trends well as a function of Lewis acidity, the residence time of the bound CO2, reported via the rate of CO2 self-exchange, is shown to correlate to the degree of C\u2013O scission. Chapter 8 looks at CO2 reactivity with E\u2013H bonds, describing first stoichiometric reactivity with silanes. In this system, CO2 is reduced to CO and silanol; mechanistic studies suggest a pathway that involves oxygen atom transfer to silane from a transient Mo oxo. In a collaboration with Dr. Naoki Shida, CO2 hydrogenation was explored, with demonstration of bidirectional catalysis in addition to detailed studies investigating the elementary steps of both formate formation and formic acid dehydrogenation.
" }, { "name": "Cai, Sarah Wang", "degree": "Senior Thesis", "year": "2018", "title": "Elucidating the Mechanism of mRNA Export Regulation by the Nuclear Pore Complex", "advisor": "Hoelz, Andre", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042018-212155038", "creators": [ { "name": { "family": "Cai", "given": "Sarah Wang" }, "id": "Cai-Sarah-Wang", "display_name": "Cai, Sarah Wang" } ], "advisors": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "advisor", "display_name": "Hoelz, Andre" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dca1-n844", "abstract": "The nuclear pore complex (NPC) is one of the largest and most complex protein assemblies in eukaryotic cells, and it facilitates and regulates the bidirectional transfer of molecules between the nucleus and cytoplasm. One of the essential functions of the NPC is to directly regulate the export of mature mRNAs, but the mechanism is not well understood, especially in humans. Export of mRNA is completed at the cytoplasmic side of the NPC, where ATPase activity of the DEAD-box helicase DDX19 is specifically activated by the NPC components Gle1, Nup42, and Nup214. The mRNA export factor Gle1 is an essential nucleoporin, and Gle1 dysfunction has been linked to human diseases. We show that the Gle1-Nup42 interaction is highly conserved with X-ray crystal structures and that the thermostability of Gle1 is highly dependent on Nup42. We also find that disease-linked mutants of Gle1 show strongly altered thermostability. Analysis of DDX19 steady-state ATPase activity reveals a novel mode of activation by Gle1 in humans. Structural studies of DDX19 complement the biochemical characterization of DDX19, and we have proposed a working model for the DDX19 catalytic cycle. An outstanding question remains in this model, as the details of DDX19-mediated removal of the export factor NXF1-NXT1 from mRNA are unknown. We describe a method for large-scale purification of retroviral constitutive transport element (CTE) RNA, which hijacks NXF1-NXT1 to be exported through the NPC, for X-ray crystallographic studies of a NXF1-NXT1-CTE complex. Together, these results provide a detailed structural and functional description of mRNA export regulation by the NPC and a framework for understanding the molecular basis of human disease linked to Gle1 and viral proliferation. " }, { "name": "Carroll, Paul Brandon", "degree": "PhD", "year": "2018", "title": "Laboratory and Astronomical Rotational Spectroscopy", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062018-120951718", "creators": [ { "name": { "family": "Carroll", "given": "Paul Brandon" }, "id": "Carroll-Paul-Brandon", "orcid": "0000-0002-3191-5401", "display_name": "Carroll, Paul Brandon" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8Y1M-6C76", "abstract": "Rotational spectroscopy is a capable technique with a rich history in a variety of chemical physics applications that is undergoing a renaissance thanks to new approaches and powerful new experimental capabilities. This thesis demonstrates that flexibility by examining multiple uses of rotational spectroscopy from instrument development, analytical chemistry, fundamental chemical physics, and astrochemistry.
\r\n\r\nIn chapter 2 we discuss the development of two novel coherent microwave spectrometers. These low cost instruments have only recently become feasible thanks to the burgeoning development of highly flexible digital electronics. The first instrument is designed for undergraduate teaching labs and can be used to demonstrate many new concepts of coherent spectroscopy that are used in modern spectroscopy. It is a rotational spectrometer and can, therefore, also be used for a variety of basic spectroscopy experiments. The second instrument uses the stability and consistency of waveguides and broadband microwave instruments to measure the rotational spectrum and abundance of isotopologues to high accuracy.
\r\n\r\nChapter 3 describes the measurement of the rotational spectrum of the cyclopentanol--water dimer. Using microwave spectroscopy, the spectrum is measured and assigned, and the structure of the dimer is determined. The cyclopentanol--water dimer shows a structure dominated by both strong hydrogen bonding and multiple weaker hydrogen bonds from the hydrocarbon ring. The monomer spectrum is measured, though unassigned due to the strong perturbation from the motion of the ring. Dimerization with water is shown to suppress this motion. This system is shown to be an excellent example of the effect of weak hydrogen bonding on the secondary structure and dynamics of molecular systems.
\r\n\r\nChapter 4 moves to astronomical observations of rotational transitions with the detection of a new species: propylene oxide. Measuring the inventory, abundance, and distribution of molecular species provides tests of our understanding of interstellar chemistry. Propylene oxide is an important addition to this inventory because it is the first chiral species detected beyond our solar system. Chiral species play an enormously important role in biology on Earth, and it is believed that interstellar chemistry may contribute to the early inventory of prebiotic species on newly formed planets. The detection of propylene oxide is discussed in the context of the origin and distribution of chiral molecules in the universe.
\r\n\r\nChapter 5 discusses recent data from the Atacama Large Millimeter/Submillimeter Array. The data maps the distribution of CH3CN isotopologues at incredibly high spatial resolution toward the Orion KL region. The measurement of isotopic ratios in CH3CN is used to inform our understanding the formation mechanisms of cyanides in star forming regions. More broadly, the maps are used to show the extreme spatial heterogeneity of the region, with numerous dense clumps roughly the size of a solar system, each with their own unique chemical and physical structure that reflects their distinct evolutionary histories.
\r\n\r\nFinally, chapter 6 discusses the non-detection of trans ethylmethyl ether. Ethylmethyl ether is one of the largest molecules claimed to be detected in the interstellar medium. Due to its size, it is believed to be produced on grain surfaces as a secondary or tertiary product from dissociation of ice constituents. Given its complexity, its abundance may be an important metric of the accuracy of chemical models of ice chemistry. The study claiming its detection reported an unusually high abundance of the species toward W51 e1/e2. Follow up observations and analysis showed that the original detection was mistaken, likely caused by interference from other features.
" }, { "name": "Chan, Katie Marie", "degree": "Masters", "year": "2018", "title": "Development of a Method for the Copper-Catalyzed Asymmetric Propargylation of Oxime Esters", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12272017-150231015", "creators": [ { "name": { "family": "Chan", "given": "Katie Marie" }, "id": "Chan-Katie-Marie", "orcid": "0000-0002-8220-9013", "display_name": "Chan, Katie Marie" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9CR5RJC", "abstract": "Alkynes represent a significant motif in natural products and pharmaceutical drugs, and the wide variety of reactions they can undergo makes them a handy tool in total synthesis. They can be introduced readily in various manners, including via propargylations of ketones and aldehydes. However, one reaction that remains to be examined is the propargylation of oximes to give a propargyl hydroxylamine. Current enantioselective propargylations of oximes typically require a chiral auxiliary and/or rare metals such as palladium or indium. Having an enantioselective propargylation of oximes which could use an external ligand and more commonly available metals would facilitate use of the product in total synthesis, as well as potentially as an unnatural amino acid. Unusual amino acids including alkynes are desirable for their use in copper(I)-catalyzed azide-alkyne [3+2] dipolar cycloadditions, a common bioorthogonal reaction.
\r\n\r\nHerein, the development of a copper-catalyzed propargylation of oxime esters is described. Initial efforts to induce enantioselectivity using a zinc nucleophile-based system proved fruitless. Although some Lewis acids could raise the yield, the enantioselectivity remained very low. Therefore, new reaction conditions using a boronate nucleophile were investigated. The use of a copper catalyst with a diphosphine ligand gave the desired product in high enantioselectivity, albeit low yield.
" }, { "name": "Chang, Alice B.", "degree": "PhD", "year": "2018", "title": "Synthesis and Self-Assembly of Bottlebrush Block Polymers: Molecular Architecture and Materials Design", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302018-104109274", "creators": [ { "name": { "family": "Chang", "given": "Alice B." }, "id": "Chang-Alice-B", "orcid": "0000-0001-5036-2681", "display_name": "Chang, Alice B." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4xdv-9302", "abstract": "Bottlebrush polymers represent a unique molecular architecture and a modular platform for materials design. However, the properties and self-assembly of bottlebrush polymers remain relatively unexplored, in large part due to the synthetic challenges imposed by the sterically demanding architecture. This thesis describes our work to close this gap, connecting (1) the synthesis of polymers with precisely tailored molecular architectures, (2) the study of fundamental structure-property relationships, and (3) the design of functional materials.
\r\n\r\nChapter 1 introduces key concepts related to polymer architecture and block polymer phase behavior. Recent developments in the synthesis and self-assembly of bottlebrush block polymers are highlighted in order to frame the work presented in Chapters 2\u20136.
\r\n\r\nChapter 2 introduces a versatile strategy to design polymer architectures with arbitrary side chain chemistry and connectivity. Simultaneous control over the molecular weight, grafting density, and graft distribution can be achieved via living ring-opening metathesis polymerization (ROMP). Copolymerizing a macromonomer and a small-molecule co-monomer provides access to well-defined polymers spanning the linear, comb, and bottlebrush regimes. This design strategy creates new opportunities for molecular and materials design.
\r\n\r\nChapter 3 explores the physical consequences of varying the grafting density and graft distribution in two contexts: block polymer self-assembly and linear rheological properties. The molecular architecture strongly influences packing demands and therefore the conformations of the backbone and side chains. Collectively, these studies represent progress toward a universal model connecting the chemistry and conformations of graft polymers.
\r\n\r\nChapter 4 discusses the phase behavior of ABA' and ABC bottlebrush triblock terpolymers. Low-χ interactions between the end blocks promote organization into a unique mixed-domain lamellar morphology, LAMP. X-ray scattering experiments reveal an unusual trend: the domain spacing strongly decreases with increasing total molecular weight. Insights into this behavior provide new opportunities for block polymer design with potential consequences spanning all self-assembling soft materials.
\r\n\r\nChapter 5 describes other physical consequences of low-χ block polymer design. The ternary phase diagrams for ABC, ACB, and BAC bottlebrush triblock terpolymers reveal the influences of low-χ A/C interactions, frustration, and the molecular architecture. Potential non-equilibrium effects and crystallization in these bottlebrush polymers will also be discussed.
\r\n\r\nChapter 6 describes applications of bottlebrush polymers as functional materials. Self-assembly enables mesoscale structural control over many materials properties, such as reflectivity, conductivity, and modulus. The synthetic methods (Chapter 2) and physical insights (Chapters 3\u22125) provided in previous chapters illustrate opportunities for materials design. We will discuss AB brush diblock polymers that self-assemble to photonic crystals and ABA brush triblock copolymers in solid polymer electrolytes.
\r\n" }, { "name": "Davis, Matthew Robert", "degree": "PhD", "year": "2018", "title": "Computational Studies of Noncovalent Interactions in Ligand-Gated Ion Channels \u2013 and - Synthesis and Characterization of Red and Near Infrared Cyanine Dyes", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08182017-161833257", "creators": [ { "name": { "family": "Davis", "given": "Matthew Robert" }, "id": "Davis-Matthew-Robert", "orcid": "0000-0002-6374-4555", "display_name": "Davis, Matthew Robert" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9XK8CQF", "abstract": "This thesis is presented in two parts. The first part, Chapter 2, 3, and 4, offers a series of studies on noncovalent interactions in Ligand Gation Ion Channels (LGICs). The second part describes a series of studies involving the synthesis and characterization of cyanine dyes. The common thread in this work is the use of Density Functional Theory (DFT) to study chemical-scale phenomenon. Chapter 1 offers a brief introduction to DFT and a comparison with other traditional computational chemistry methodology; Hartree-Fock (HF). Summaries of the use of DFT to study both noncovalent interations and electronically excited states are also presented. In addition, the author comments on the correct application of DFT.
\r\n\r\nChapter 2 details a computational study of the cation-\u03c0 interaction of complex cations to substituted benzenes and indoles. The cation-\u03c0 interaction is the electrostatic interaction between a cation and the negative electrostatic potential on an aromatic ring originating from its large permanent quadrupole moment. This chapter, in addition to establishing the correct computational parameters, establishes a large set of substituent effects with which to study cation-\u03c0 interactions in vivo. These binding energy values are compared to previous applications of cation-\u03c0 binding energies from our lab, and it was found that the derived binding energies are sufficiently accurate.
\r\n\r\nChapter 3 applies the foundational knowledge from the previous chapter to study cation-\u03c0 interactions of cationic ligands to multiple aromatics. This is a common motif in vivo known as the aromatic box. Using this methodology, it is established that cation binding in this form is cooperative. Further, many aromatic boxes from crystal structures were evaluated energetically.
\r\n\r\nChapter 4 describes work to develop a new amino acid to study hydrogen bonds in Xenopus laevis oocytes. These fluorinated aliphatic amino acids inductively attenuate the hydrogen bond accepting ability of the carbonyl. This new strategy was used to probe for a hydrogen bond between the indole NH \u03b14 TrpB and a backbone carbonyl associated with L119 on the \u03b22 subunit of the \u03b14\u03b22 nicotinic acetylcholine receptor (nAChR). The fluorinated amino acids were validated computationally and with NMR studies. This new strategy showed that the \u03b14-\u03b22 interfacial hydrogen prediction was false.
\r\n\r\nChapter 5 describes the synthesis and characterization of a series of meso-aromatic-acetylene cyanine dyes which feature a very large Stokes shift. Synthesis of the dyes features a key Sonagashira reaction. These dyes are investigated photophysically and computationally using time dependent DFT (TDDFT). The mechanism for this Stokes shift is an excitation to the S2 state, relaxation to the S1 state, and normal cyanine fluorescence.
\r\n\r\nChapter 6 describes three separate strategies to construct a cyanine-based photocage to release drugs in vivo using an ortho-quinone methide strategy. One strategy utilized an acetylene-aromatic cyanine dye much like those described in Chapter 5, the second utilized an ethynyl-trimethylphenyl cation dye, and the third a photoinduced electron transfer cyanine dye. None of these strategies produced a usable photocage. The failure of these strategies are ascribed to both the short excited state lifetime of cyanine dyes and the direction of the transition dipole moment.
\r\n\r\nFinally, three appendices are presented. Appendix A describes early work to synthesize and characterize a meso-hydroxy substituted Cy5 dye. Appendix B offers many of the same computations as Chapters 2 and 3 using HF instead of DFT. Appendix C describes orbital mixing of cyanine dyes from Chapter 5 using HF instead of DFT.
" }, { "name": "Del Castillo, Trevor James", "degree": "PhD", "year": "2018", "title": "The Quest for Electrocatalytic Nitrogen Fixation with a Molecular Catalyst and What We Learned Along the Way", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152018-150143251", "creators": [ { "name": { "family": "Del Castillo", "given": "Trevor James" }, "id": "Del-Castillo-Trevor-James", "orcid": "0000-0001-5120-1935", "display_name": "Del Castillo, Trevor James" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CM5B-RG20", "abstract": "This report details research into the mechanism and operating principles underlying the nitrogen fixation efficacy of a tris(phosphine)borane iron complex (P3BFe). The data presented provide what is to our knowledge the first unambiguous demonstration of electrocatalytic nitrogen fixation by a molecular catalyst and contribute to a growing body of evidence that metallocenes may play multiple roles during reductive catalysis.
" }, { "name": "Edwards, Julian Peter", "degree": "PhD", "year": "2018", "title": "Cyclic Polyolefins via Ring-Expansion Metathesis Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252018-104854693", "creators": [ { "name": { "family": "Edwards", "given": "Julian Peter" }, "id": "Edwards-Julian-Peter", "orcid": "0000-0001-9243-8197", "display_name": "Edwards, Julian Peter" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/kmh1-y153", "abstract": "The synthesis of cyclic polyolefins prepared using a supported, molecular ring-expansion metathesis polymerization catalyst is described. The synthesis of the catalysts, themselves, is described in detail. Additionally, thorough physical characterization of cyclic polymers with comparison to linear polymer analogues is reported.
" }, { "name": "Kim, Jungwoo", "degree": "PhD", "year": "2018", "title": "Microfluidic Analysis in Patient Biopsies: toward Precision Medicine for Glioblastoma Multiforme", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09042017-140704721", "creators": [ { "name": { "family": "Kim", "given": "Jungwoo" }, "id": "Kim-Jungwoo", "orcid": "0000-0002-5215-2044", "display_name": "Kim, Jungwoo" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9639MX2", "abstract": "Although every individual has a unique biology, most medicine still relies on the one-size-fits-all approach, which often fails in the treatment of heterogeneous diseases like cancer. An emerging approach to disease treatment is precision medicine, in which a specific treatment is tailored for individual patients using their biological information, including their genome, phenome, and proteome. Two clinical actions are important for implementing precision medicine in cancer therapies: choosing the correct drugs via patient stratification and choosing a suitable drug dosage and duration via drug response monitoring.
\r\n\r\nAfter selecting the potential drug candidate, it is crucial to monitor tumor response to drug therapy because cancer is a dynamic disease that can develop drug resistance. Although non-invasive tumor imaging techniques such as magnetic resonance imaging, computed tomography, and positron emission tomography can assess physical size and metabolic activity of tumors, these techniques have poor time resolution and cannot capture the dynamic changes of bio-molecules implicated with drug resistance. Thus, to effectively monitor drug response, supplemental diagnostic or prognostic markers must be routinely measured from patient biopsies. Unfortunately, routine monitoring of multiple biomarkers from patient biopsies is impractical, as conventional analytical assays require large sample amounts (up to 100-1,000 mg of tissue or 10 mL of blood).
\r\n\r\nIn response to this challenge, this thesis describes the development of various microfluidic technologies that can perform multiplexed measurements (up to 20-plex) using minute amounts of sample (10,000-100,000 cells or 30\u00b5L of blood) in a miniaturized analytical platform (maximum 75 \u00d7 26 \u00d7 1 mm footprint). We applied these technologies for drug screening and drug response monitoring in glioblastoma multiforme, a highly lethal brain tumor, assaying two different types of patient biopsies: cancer cells and blood.
\r\n\r\nFirst, we developed an integrated microfluidics-chip/beta particle imaging system that can screen for effective therapies using small amounts of patient-derived cell lines. Since glioblastoma cells have abnormally high glycolytic activity, this was used as a read-out for drug response. Single cells were isolated in micro-traps, and their glycolytic activity was quantitated using a radioactive probe. This platform can assess potential drug targets directly from patient biopsies without administering drugs to the patient.
\r\n\r\nSecond, we developed an in vitro diagnostic test that can monitor tumor drug resistance by measuring up to 14 proteins in finger-prick volumes of blood. This test relies on microfluidics and microarray patterning of antibodies to carry out multiplexed sandwich-type immunofluorescence assays. Using this technology and conventional tumor imaging techniques, we linked proteomic signatures to tumor growth, establishing diagnostic and prognostic models in two clinical treatment cases of bevacizumab and buparlisib. Moreover, we adopted the multiplexed proteomic measurement platform to rapidly screen out small peptide binding agents that target an oncogenic protein in glioblastoma.
\r\n\r\nThe microfluidic tools developed here are sample-efficient and highly informative, and we propose that these techniques could enable routine evaluation of drug response in a precision medicine workflow.
\r\n" }, { "name": "Letsou, William Peter", "degree": "PhD", "year": "2018", "title": "Noncommutative Biology: Sequential Regulation of Complex Networks and Connected Matter", "advisor": "Cai, Long", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-192944407", "creators": [ { "name": { "family": "Letsou", "given": "William Peter" }, "id": "Letsou-William-Peter", "orcid": "0000-0002-4969-2330", "display_name": "Letsou, William Peter" } ], "advisors": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "advisor", "display_name": "Cai, Long" } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9B5E-F105", "abstract": "During animal development from zygote to adult, a limited set of regulatory molecules are autonomously deployed in the service of tissue-specific gene expression (reviewed in chapter 1). Inherent in the process is the tension that single cells sample heterogeneous expression states while robustly maintaining a collective final outcome. This thesis addresses theoretical issues that help resolve the paradox that one cell simultaneously contains the fate information of many.
\r\n\r\nPrevious models of development have likened cell fate to minima on a smooth potential energy surface. Such static pictures can be misleading because they suggest the egg knows the path it will take to the adult before it divides even once. Recognition that the potential analogy is an oversimplification has led others to propose that the surface is actually nonsmooth. Chapter 2 reviews the theoretical basis for smooth potentials and resolves these problems by appealing to the tangent space of gene expression. It is then shown that if the potential difference is sufficient to characterize the difference between egg and adult, then the tangent space controls on gene expression are one-dimensional. Furthermore, a shortcoming of models ignoring the connectivity and common origin of dividing cells is that they erect artificial barriers between alternative fates. A fundamentally different picture is sketched wherein the difference between egg and adult is schematized as the shape of the locus of equipotential fates accessible at the same point in time. The conjugacy of space and time is invoked to explain how the requirement that each fate be on a line of equipotential is the same as requiring that each alternative fate move the same distance down the surface at each step. The developmental trajectory is deterministic but not known in advance because it needs to be ascertained at each step which way cells \"turn\" in order to maintain their equipotential relationship. Chapters 3 and 4 refine this sequential model of collective development with specific examples.
\r\n\r\nA simple solution to the problem of cell-type specific gene expression is combinatorial binding of transcription factors at promoters. It is shown in chapter 3 that such models result in substantial information bottlenecks, because all cell fate information is concentrated at the start. We explore a novel, noncommutative model of gene regulation—known as sequential logic—that spreads the information out over time. It is shown using time sequences of noncommutative controllers that targets which otherwise would have been activated together can be regulated independently. We derive scaling laws for two noncommutative models of regulation, motivated by phosphorylation/neural networks and chromosome folding, respectively, and show that they scale super-exponentially in the number of regulators. It is also shown that specificity in control is robust to loss of a regulator. Consequently, sequential logic overcomes the information bottleneck in complex problems and enables novel solutions through roundabout strategies. The theoretical results are connected to real biological networks demonstrating specificity in the context of promiscuity.
\r\n\r\nNoncommutative sequential logic has improved storage capacity, but it does not specify who or what supplies the sequences of input that determine cell fate. Chapter 4 offers a solution by way of the seemingly unrelated problem of looping in twisted strings. Cells and strings obey a set of common space-time constraints, ultimately due to the conservation of energy. It is argued that the most parsimonious allocation of energy from the straight to strained string is the one in which each segment sees the same share of the total. Planar looping is shown to be a consequence of the parsimony principle and the Euler-Poincaré equations for rotational motion in the presence an applied torque. We then solve the problem for the looping of a twisted string; with two strains, the Euler-Poincaré predict a different answer than the classical Frenet-Serret equations. Using the results of chapter 2, it is concluded that the Frenet-Serret curvatures assigned ahead of time are not guaranteed to generate space curves that conserve energy: the predicted string has localized strains the Euler-Poincaré solution lacks. Rotational dynamics of strings are connected to developing organisms by postulating conserved RNA polymerase as an analog of angular momentum, and transcriptional activity as energy. Alternative fates along a one-dimensional \"string\" of dividing cells are possible by finding the RNAP distribution that conserves transcriptional activity along a curve of constant developmental potential. Consequently, each alternative fate samples a different sequence of changes to the distribution as it follows a local gradient downhill from high to low developmental potential over time.
\r\n\r\nIn conclusion, regulation in the tangent space of gene expression resolves the paradox that development has a unique solution specified in the DNA of the egg which cannot be determined with certainty until completion of the adult. Noncommutative sequential logic generates complexity that cannot be realized at the start, while interdependent cells (and strings) require time to ensure that each fate is at the same potential difference from a common ancestor. This fundamental reimagining of the Waddington framework can be tested using new multiplexed mRNA imaging technologies that preserve the spatial context of cells in developing tissue.
" }, { "name": "Liang, JingXin", "degree": "PhD", "year": "2018", "title": "Interrogating the Structural Landscape of Malaria Biomarkers with Epitope Targeted Peptide Capture Agents", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-181603942", "creators": [ { "name": { "family": "Liang", "given": "JingXin" }, "id": "Liang-JingXin", "orcid": "0000-0001-6600-8409", "display_name": "Liang, JingXin" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rxtr-6152", "abstract": "Antibodies have conventionally been used as molecular recognition agents against epitopes, or antigenic regions, for protein capture and detection. The ability of monoclonal and polyclonal antibodies to selectively bind their targets with high affinities makes them excellent agents for specific protein recognition. However, as large proteins themselves (~150 kDa), antibodies are susceptible to changes in pH, temperature, and biochemical environment, particularly proteolytic cleavage. Additionally, epitope binding on antibodies is reliant on their rigid tertiary structure to position key functional groups that facilitation antigen recognition. Retaining the integrity of the protein structure creates rigid limitations against chemical modifications of antibodies to suit unique needs.
\r\n\r\nProtein-catalyzed capture agents (PCCs) developed within the Heath group at Caltech address the limitation of antibodies as affinity agents. Using epitope-targeted in situ click screening methodology, the Heath group has developed peptidomimetic molecules that offer an alternative solution to antibodies. These PCCs exhibit high affinity and selectivity for their protein targets. As peptide-based molecules, PCCs can be engineered to be biochemically stable and resistant to changes in their chemical environment. Their peptide-based structures are readily amenable to chemical modifications and allow for adaptation to a range of applications.
\r\n\r\nThis thesis describes the development of PCCs against unique protein biomarkers for the detection of the most lethal species of malaria infection, Plasmodium falciparum. Malaria is a global health epidemic and its eradication is reliant on rapid and accurate diagnostics for prompt treatment. We targeted the P. falciparum specific biomarkers lactate dehydrogenase (LDH) and Histidine-rich protein 2 (HRP2), both of which present unique challenges for protein capture. The LDH biomarker is homologous across malaria species, whereas HRP2 is highly polymorphic and lacks distinct secondary structure. The variation in sensitivity of HRP2 detection by antibody-based tests has been attributed to the genetic polymorphism of the biomarker.
\r\n\r\nIn Chapter 1, we describe the development of high affinity PCCs that bind selectively to the LDH biomarker. We targeted an epitope that was highly homologous across LDH species. This chapter also details the expansion of mono-valent PCC agents into bivalent ligands using the protein architecture to select secondary ligands for binding improvement. For the HRP2 biomarker, we developed a multiple epitope targeting strategy to address protein polymorphism. We targeted for epitopes in HRP2 and developed PCCs that bind in the range of monoclonal antibodies.
\r\n\r\nChapter 2 details the expansion of PCC agents developed against HRP2 into multivalent molecules for improved binding. The development of bivalent ligands from combinatorial screening of linker libraries is presented. The optimal linker lengths determined by the screens are described.
\r\n\r\nIn Chapter 3, a general strategy for targeting the protein landscape to inhibit formation of a protein and biomolecule complex with PCCs against HRP2 is demonstrated. Specifically, the inhibition of heme sequestration by HRP2 is shown. A bivalent ligand that targets two epitopes on HRP2 is shown to have enhanced inhibitory potency over any single or cocktail combination of PCCs.
\r\n\r\nAltogether, the studies herein demonstrate the utility of peptidomimetic molecules as agents for protein capture and detection as well as a generalizable strategy of functional inhibition through epitope-targeting.
" }, { "name": "Lichterman, Michael Yang", "degree": "PhD", "year": "2018", "title": "Analysis of Metal-Oxide Protected Photoelectrochemical Systems for Water Splitting", "advisor": "Lewis, Nathan Saul; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06122018-090745040", "creators": [ { "name": { "family": "Lichterman", "given": "Michael Yang" }, "id": "Lichterman-Michael-Frankston-Yang", "orcid": "0000-0002-0710-7068", "display_name": "Lichterman, Michael Yang" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-advisor", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/aq89-jv13", "abstract": "The photoelectrochemical splitting of water into oxygen and hydrogen gas is one pathway toward the renewable and economic generation of a fuel which is sufficiently scalable to power a large fraction, or even a majority, of the power requirements of\r\nmodern society. In order to make such a device economically promising, it must be sufficiently cheap, have sufficiently high efficiency, or some combination thereof. In this work, two primary routes toward such a device are discussed; the first is the use of a cheaply prepared photoanode material, BiVO4, the interactions of this material with cobalt oxide based catalysts, and the use of such structures in more extreme pH ranges than have previous been reported. The second route details the application of a protective layer, TiO2, on otherwise unstable materials such as GaP and CdTe when operated as\r\nphotoanodes in alkaline media. The further work herein applies operando ambientpressure x-ray photoelectron spectroscopy (AP-XPS) to understand the nature of the energetics which allow conduction in the aforementioned TiO2, as well as other\r\nenergetics in the electrochemical double layer in the adjacent electrolyte. Further experiments using Raman spectroscopy on associated III-V photoanode devices are also described." }, { "name": "Mak, Victor Wei-Dek", "degree": "PhD", "year": "2018", "title": "Development of Synthetic Strategies for the Total Synthesis of Ent-Kauranoid and Diterpenoid Alkaloid Natural Products", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08042017-162439257", "creators": [ { "name": { "family": "Mak", "given": "Victor Wei-Dek" }, "id": "Mak-Victor-Wei-Dek", "display_name": "Mak, Victor Wei-Dek" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ST7N04", "abstract": "As part of an ongoing synthetic effort directed towards biologically active ent-kauranoid natural products, the preparation of two structurally unique natural products, (\u2013)-trichorabdal A and (\u2013)-longikaurin E, is presented. The syntheses intercept an early intermediate from the synthetic route towards the rearranged natural product (\u2013)-maoecrystal Z, and thus, represents a unified synthetic strategy to access structurally unique ent-kauranoids. Specifically, the syntheses are enabled by a palladium-mediated oxidative cyclization of a silyl ketene acetal to install a key quaternary center within the bicyclo[3.2.1]octane unit, as well as a reductive cyclization of an aldehyde-lactone to construct the oxabicyclo[2.2.2]octane motif of (\u2013)-longikaurin E.
\r\n\r\nA synthetic strategy to access C19-diterpenoid alkaloids, specifically of the aconitine type, is presented. These highly bridged polycyclic natural products are generally characterized by a substituted piperidyl ring bridging a hydrindane framework that is further attached to a bicyclo[3.2.1]octane. The synthetic strategy relies on the enantioselective synthesis of two bicyclic fragments, which are coupled in a convergent fashion through a 1,2-addition/semipinacol rearrangement sequence to forge a sterically hindered quaternary center. Efficient access to late stage intermediates has enabled the synthesis of the aconitine carbocyclic core, with appropriate functionality for advancement to a selective voltage-gated K+ channel blocker, talatisamine. Additionally, the synthetic strategy described herein is well applicable to the synthesis of related denudatine and napelline type C20-diterpenoid alkaloids.
" }, { "name": "Marshall, Kevin James", "degree": "PhD", "year": "2018", "title": "The Hydrodynamics of Active Particles Inside of a Porous Container and the Galerkin Boundary Element Discretization of Stokes Flow", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10252017-021526235", "creators": [ { "name": { "family": "Marshall", "given": "Kevin James" }, "id": "Marshall-Kevin-James", "orcid": "0000-0001-6025-7674", "display_name": "Marshall, Kevin James" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Barr", "given": "Alan H." }, "id": "Barr-A-H", "role": "member", "display_name": "Barr, Alan H." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9MP51G8", "abstract": "In this thesis I formulate and present a novel and new framework for simulating the dynamics of arbitrarily shaped active or passive particles immersed in a Stokesian fluid and evolving under confinement by a porous container or in free space. I use a completed double layer boundary integral equation to model the particle's dynamics and combine this with a new formulation that uses a second kind integral equation for describing the motion of the porous container. This newly formulated porous container model permits fluid to pass through the container's surface at a velocity in proportion to a discontinuous jump in stress across the container's surface. This jump in stress is induced by the active particle's motion. The proposed porous container model is general in the sense that it allows fluid to pass through the membrane with finite tangential and normal velocity components. I obtain the exact analytical solution to this model when the active particle and porous container are perfectly concentric. In addition, I numerically solve this system of boundary integral equations for arbitrary particle positions, and fully characterize the particle and container dynamics by performing a vast number of trajectory studies. Both the container and particle are seen to move in complicated ways owing to their self and pairwise hydrodynamic interactions. This system is studied over a vast parameter space, for multiple container to particle size ratios, multiple types of active particles, and various permeability parameterizations. This coupled set of particle and container boundary integral equations is discretized using a novel interpretation and new extension of the Galerkin Boundary Element discretization to multi-body particle systems in Stokes flow. I also implement and extend an h-adaptive conformal mesh refinement algorithm to accurately resolve near-contact particle and container interactions. In addition, I perform all Galerkin BEM calculations on CUDA enabled GPUs, allowing for these simulations to be run on modern desktop computers in seconds. I combine all of these techniques in a modern C++ Galerkin Boundary Element Method computational framework called GPUGBEM.
" }, { "name": "Marshall, Stephen Sandell", "degree": "PhD", "year": "2018", "title": "Improvement of Integral Membrane Protein Expression via Optimization of Simulated Integration Efficiency", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292017-151537318", "creators": [ { "name": { "family": "Marshall", "given": "Stephen Sandell" }, "id": "Marshall-Stephen-Sandell", "orcid": "0000-0003-2263-6854", "display_name": "Marshall, Stephen Sandell" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9Q23XD3", "abstract": "Integral membrane protein characterization is limited by the low levels of protein obtainable from heterologous overexpression in hosts such as Escherichia coli. Differences in the efficiencies of subdomains of the co-translational integration processes of membrane proteins into the membrane could explain the observed variation in the experimental expression of closely related homologs in E. coli. We have developed a method to predict and increase the expression of individual membrane proteins by optimizing the efficiency of their translocon-mediated integration into the membrane. The integration efficiency of each component of a membrane protein is calculated using a coarse-grained co-translational simulated integration model. The results of model simulations, experimental expression levels quantified by integral membrane protein-GFP fusion fluorescence, and a novel antibiotic survival test that reports on misintegration in vivo are applied to test the relationship between the integration efficiency of specific domains and experimental expression. Changes in simulated integration efficiencies due to sequence modifications agree with the effects on experimental expression in vivo. In the case of the TatC protein family, misintegration of the C-tail is found to be a major contributor to expression failure in E. coli. Beneficial sequence modifications that improve both simulated integration efficiency and experimental expression levels can be identified using the model. Preliminary evidence shows that simulated integration efficiency could potentially predict the effects of mutations on Haemophilus influenzae GlpG experimental expression in E. coli. The process described herein allows for the rational overexpression of integral membrane proteins through the identification and mitigation of inefficiencies in the underlying co-translational membrane integration process.
" }, { "name": "Matson, Benjamin David", "degree": "PhD", "year": "2018", "title": "Interplay of Proton Transfer, Electron Transfer and Proton-Coupled Electron Transfer in Transition Metal Mediated Nitrogen Fixation", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02232018-152758526", "creators": [ { "name": { "family": "Matson", "given": "Benjamin David" }, "id": "Matson-Benjamin-David", "orcid": "0000-0001-5733-0893", "display_name": "Matson, Benjamin David" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9MS3R0Z", "abstract": "Mitigation of the hydrogen evolution reaction (HER) is a key challenge in selective small molecule reduction catalysis, including the nitrogen (N2) reduction reactions (N2RR) using H+/e- currency. Here we explore, via DFT calculations, three iron model systems, P3EFe (E = B, Si, C), known to mediate both N2RR and HER, but with different selectivity depending on the identity of the auxiliary ligand. It is shown that the respective efficiencies of these systems for N2RR trend with the predicted N\u2013H bonds strengths of two putative hydrazido intermediates of the proposed catalytic cycle, P3EFe(NNH2)+ and P3EFe(NNH2). Bimolecular proton-coupled electron transfer (PCET) from intermediates with weak N\u2013H bonds is posited as a major source of H2 instead of more traditional scenarios that proceed via metal hydride intermediates and proton transfer/electron transfer (PT/ET) pathways.
\r\n\r\nStudies on our most efficient molecular iron catalyst, [P3BFe]+, reveal that the interaction of acid and reductant, Cp*2Co, is critical to achieve high efficiency for NH3, leading to the demonstration of electrocatalytic N2RR. Stoichiometric reactivity shows that Cp*2Co is required to observe productive N\u2013H bond formation with anilinium triflate acids under catalytic conditions. A study of substituted anilinium triflate acids demonstrates a strong correlation between pKa and the efficiency for NH3, which DFT studies attribute to the kinetics and thermodynamics of Cp*2Co protonation. These results contribute to the growing body of evidence suggesting that metallocenes should be considered as more than single electron transfer reagents in the proton-coupled reduction of small molecule substrates and that ring-functionalized metallocenes, believed to be intermediates on the background HER pathway, can play a critical role in productive bond-forming steps.
" }, { "name": "McAvoy, Camille Zandra", "degree": "PhD", "year": "2018", "title": "Harnessing Biological Tools of Protein Transport and Catalysis", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152018-143529378", "creators": [ { "name": { "family": "McAvoy", "given": "Camille Zandra" }, "id": "McAvoy-Camille-Zandra", "orcid": "0000-0002-9828-1538", "display_name": "McAvoy, Camille Zandra" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EXJK-C379", "abstract": "This work covers two projects related to protein structure and function. The first focuses on studies of chloroplast signal recognition particle 43 (cpSRP43), its interaction with substrate (the light-harvesting, chlorophyll-binding proteins, or LHCP), the role of conformational change in its activity, and the use of cpSRP43 as a tool for handling nonnative proteins. This work utilizes a variety of biochemical and biophysical approaches including light scattering and electron paramagnetic resonance to probe the structure-function relationship of cpSRP43. The second project entails the study of the C-C bond formation mechanism of nitrogenase, a biological nitrogen fixer found in soil microorganisms. Together these projects make for an interesting story of the medicinal and agricultural applications of basic biochemistry.
" }, { "name": "McCarthy, Amy Michelle", "degree": "PhD", "year": "2018", "title": "Advancing the Protein-Catalyzed Capture Agent Technology to New Frontiers", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012018-005336099", "creators": [ { "name": { "family": "McCarthy", "given": "Amy Michelle" }, "id": "McCarthy-Amy-Michelle", "orcid": "0000-0003-3456-0383", "display_name": "McCarthy, Amy Michelle" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HHP5-1Z83", "abstract": "Protein-catalyzed capture (PCC) agents are a nascent synthetic aptamer technology that was first disclosed in 2009. In addition to reviewing the different classes of peptide-based aptamers in chapter 1, this thesis records efforts to advance the PCC technology in two ways. First, in chapter 2 the development of a barcoded-rapid assay platform (B-RAP) technology enables the parallel analysis of up to fifteen PCC agents at once as well as dramatically shortening the time required to characterize the binding affinity for a pool of ligands from weeks to a couple of days. Secondly, the capture agent technology was utilized to target difficult proteins. Kirsten rat sarcoma (KRas) protein is a GTPase that acts as a light switch for several important cellular signaling pathways. Oncogenic variants of KRas are responsible for driving roughly 20-25% of all cancers, but KRas is considered \u201cundruggable\u201d from a small molecule targeting point of view. We report the identification of PCC ligands that bind to conserved allosteric switches on KRas and inhibit the protein\u2019s GTPase enzymatic activity. The biomarker Plasmodium falciparum Histidine Rich Protein II (HRP2) presents an unusual challenge as it is a highly variable, unstructured and sticky protein. In chapter 3 we report on efforts to develop low nM binding capture agents against highly prevalent epitopes of HRP2, and the use of medicinal chemistry optimization to prepare structurally related variants of the lead capture agent for probing the structure-activity relationship and how it affects binding to HRP2." }, { "name": "Miller, Gregory Martin", "degree": "PhD", "year": "2018", "title": "Eph Receptor Clustering by Chondroitin Sulfate Inhibits Axon Regeneration", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02132018-133402404", "creators": [ { "name": { "family": "Miller", "given": "Gregory Martin" }, "id": "Miller-Gregory-Martin", "display_name": "Miller, Gregory Martin" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "chair", "display_name": "Hoelz, Andre" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9RJ4GPT", "abstract": "Chondroitin sulfate proteoglycans (CSPGs) play important roles in the developing and mature nervous system, where they guide axons, maintain stable connections, restrict synaptic plasticity, and prevent axon regeneration following CNS injury. The chondroitin sulfate glycosaminoglycan (CS GAG) chains that decorate CSPGs are essential for their functions. Through these sugar chains, CSPGs are able to bind and regulate the activity of a diverse range of proteins and through these interactions can regulate neuronal growth. These CS-protein interactions depend on specific sulfation patterns within the CS GAG chains, and accordingly, particular CS sulfation motifs are upregulated during development, in the mature nervous system, and in response to CNS injury. Thus, spatiotemporal regulation of CS GAG biosynthesis may provide an important mechanism to control the functions of CSPGs and modulate intracellular signaling pathways. Here, we will discuss these sulfation-dependent processes and highlight how the CS sugars on CSPGs contribute to neuronal growth, axon guidance, and plasticity in the nervous system.
\r\n\r\nChondroitin sulfate proteoglycans (CSPGs) are a major barrier to regenerating axons in the central nervous system (CNS), exerting their inhibitory effect through their polysaccharide side chains. Chondroitin sulfate (CS) potently inhibits axon regeneration through modulation of inhibitory signaling pathways induced by carbohydrate binding to protein ligands and receptors. Here, we identify a novel carbohydrate-protein interaction between CS and EphA4 that inhibits axon regrowth. We characterize the mechanism of activation and demonstrate how carbohydrate binding induces phosphorylation of the intracellular kinase domain through clustering of cell surface EphA4. Collectively, our studies present a novel mechanism of EphA4 activation by CS independent of the canonical ephrin ligands and uncover the role of this interaction in inhibition of neurite regrowth after injury. Our results underscore a mechanism of action by which carbohydrates can function as direct, activating ligands for protein receptors and provide mechanistic insights into the inhibition of axon growth by CS following injury to the CNS.
\r\n\r\nChondroitin sulfate proteoglycans (CSPGs) regulate neuronal plasticity, as well as axon regeneration and guidance through their ability to bind protein ligands and cell surface receptors. In this way, extracellular CSPGs can modulate the activity of intracellular signaling pathways. Here, a computational analysis of EphA4-CS interactions is performed to characterize the importance of key arginine and lysine residues towards CS binding, and to identify structural differences in CS-A, CS-C, CS-D, and CS-E docking to EphA4. Carbohydrate-induced Eph receptor clustering could be a general mechanism of Eph receptor activation. To identify additional Eph receptors that interact with CS, CS-E was docked to all EphA and EphB family members to predict relative binding affinities. The relative strengths of the predicted binding energies are: EphB4 > EphA8 > EphA1 > EphA3 > EphB1 > EphB3 > EphA7 > EphA5 > EphA4 > EphA6 > EphB2 > EphB6 > EphA2. In addition, the arginine and lysine residues that mediate CS binding are identified for each Eph receptor. These computational predictions provide mechanistic insights into Eph receptor activation by chondroitin sulfate and have implications for inhibition of axon regeneration following injury to the nervous system and axon guidance during development.
" }, { "name": "Nesbit, Mark Allen", "degree": "PhD", "year": "2018", "title": "Iron, Cobalt, and Nickel Metalloboranes: Reactivity, Catalysis, N2 Activation and Stabilization of Reactive N2Hx Ligands", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02232018-173939270", "creators": [ { "name": { "family": "Nesbit", "given": "Mark Allen" }, "id": "Nesbit-Mark-Allen", "orcid": "0000-0002-5642-9303", "display_name": "Nesbit, Mark Allen" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9G15Z28", "abstract": "The reactivity of Fe and Co compounds supported by a bisphosphinoborane (DPB) ligand ([(DPB)Fe]2(N2) and (DPB)Co(N2)) towards E-H bonds (E = C, N, S, O, Si) is reported along with the catalytic hydrosilylation of ketones and aldehydes. The Fe and Co compounds displayed a mix of 1-electron and 2-electron chemistry. In some cases [(DPB)Fe]2(N2) and (DPB)Co(N2) facilitated oxidative addition of the E-H bond across the M-B interaction, and in others evolution of H2 giving a 1-electron oxidized complex of the general form (DPB)M(E) was observed. The reaction of Ph2SiH2 with (DPB)Co(N2) was found to be reversible, similar to the previously reported related nickel complex (PhDPBMes)Ni. The reactivity of these Fe and Co compounds is compared to previously reported Ni compounds supported by a similar ligand which catalyze olefin hydrogenation and hydrosilylation of substituted benzaldehydes.
\r\n\r\nThe synthesis and metalation with nickel of two new variants of the DPB ligand (DP*BPh and DP*BMes) is described. The primary modification introduced in DP*BPh and DP*BMes is the incorporation of a tertiary amine moiety into the secondary coordination sphere. This was done with the hypothesis that the amine moiety might act as a proton shuttle and facilitate proton reduction or hydrogen oxidation electrocatalysis. The process of screening these compounds for activity as proton reduction and hydrogen oxidation catalysts is also discussed. Additionally, the stoichiometric reactivity of [(DP*BPh)Ni]2(N2) and (DP*BMes)Ni(N2) with H2 was studied. We observed that [(DP*BPh)Ni]2(N2) slowly decomposed to an unidentified mixture of products while (DP*BMes)Ni(N2) dimerized to form a phosphine bridged Ni-borohydride dimer [(DP*BMesH)Ni]2. [(DP*BPh)Ni]2(N2) and (DP*BMes)Ni(N2) were also tested as precatalysts for olefin hydrogenation and found to be less active that their previously reported counterpart (PhDPBMes)Ni. [(DP*BPh)Ni]2(N2) and (DP*BMes)Ni(N2) correspondingly showed no activity for hydrogenation of polar substrates such as ketones, aldehydes, or CO2.
\r\n\r\nLastly, the synthesis of a new trisphosphinoborane ligand (ArP3B) with bulky aryl substituents on the phosphines and its metalation with Fe is described. The anionic-N2 adduct [(ArP3B)Fe(N2)][Na(12-C-4)2] was observed to react with H+ sources to generate the first observed parent iron-diazenido (ArP3B)Fe(NNH) and an iron-hydrazido(2-) [(ArP3B)Fe(NNH2)]+. [(ArP3B)Fe(NNH2)]+ was found to have similar spectroscopic properties to the previously reported [(TPB)Fe(NNH2)]+. A thorough characterization of [(ArP3B)Fe(N2)][Na(12-C-4)2], (ArP3B)Fe(NNH), and [(ArP3B)Fe(NNH2)]+ by a variety of continuous wave and pulsed ERP techniques is presented along with 57Fe M\u00f6ssbauer data. The new (ArP3B)Fe system was also canvassed for activity as a catalyst for conversion of N2 to NH3 and found to yield substoichiometric amounts of NH3 in the presence of KC8 and HBArF24\u20222Et2O while no NH3 was observed using CoCp*2 and [H2NPh2][OTf].
" }, { "name": "Nguyen, Phong Thanh", "degree": "PhD", "year": "2018", "title": "Structural and Functional Characterization of the Escherichia coli MetNI Methionine Transporter\r ", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302018-143201092", "creators": [ { "name": { "family": "Nguyen", "given": "Phong Thanh" }, "id": "Nguyen-Phong-Thanh", "orcid": "0000-0002-6390-7350", "display_name": "Nguyen, Phong Thanh" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/x9ed-9n64", "abstract": "Despite the ubiquitous role of ATP Binding Cassette (ABC) importers in nutrient uptake, only the E. coli maltose and vitamin B12 ABC transporters have been structurally characterized in multiple conformations relevant to the alternating access transport mechanism. To complement our previous structure determination of the E. coli MetNI methionine importer partner in the inward facing conformation (Kadaba et al. Science 321, 250-253, 2008), we have explored conditions stabilizing the outward facing conformation. Using two variants, the Walker B E166Q mutation with ATP and EDTA to stabilize MetNI in the ATP-bound conformation, and the N229A variant of the binding protein MetQ to disrupt methionine binding as shown in this work, a high affinity MetNIQ complex was formed with a dissociation constant measured to be 27 nM. We then solved a 2.95 \u00c5 resolution crystal structure of the outward-facing conformation of the MetNI transporter, in complex with its binding protein, MetQ. The structure sheds light on how the C-regulatory domains regulate transport activity by rearrangement of a hydrogen bonding network between their interfaces in two different conformations. Structure of the substrate-free homologous MetQ from N. meningitides was also resolved using the N-to-A mutation (N238A). Superimposition of the substrate-bound, substrate-free (homologous model) MetQ and the binding protein MetQ in complex with its MetNI transporter (complexed MetQ) reveals unexpected structural features of the complexed MetQ, indicates a different substrate delivery mechanism for the MetNI transporter. These structural insights, coupled with thermodynamic binding constant and in vivo transport studies, support an unconventional transport mechanism for the Type-I methionine ABC importer.\r\n" }, { "name": "Niesen, Michiel Jacobus Maria", "degree": "PhD", "year": "2018", "title": "Coarse-Grained Simulation Approaches for Protein Integration and Translocation via the Sec Translocon", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052018-112428695", "creators": [ { "name": { "family": "Niesen", "given": "Michiel Jacobus Maria" }, "id": "Niesen-Michiel-Jacobus-Maria", "orcid": "0000-0002-9255-6203", "display_name": "Niesen, Michiel Jacobus Maria" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z91N7ZBS", "abstract": "This thesis describes coarse-grained approaches for simulating the co-translational integration and translocation of proteins via the Sec translocon, which is a key step in the biogenesis of membrane and secretory proteins. We present a coarse-grained simulation approach that is capable of simulating minute-timescale dynamics while retaining sufficient chemical and structural detail to capture sequence-specific interactions. The model is validated through comparison to existing experimental data and applied to characterize the forces that act on nascent proteins and drive successful integration and translocation. We also apply coarse-grained simulations of the integration of multi-spanning membrane proteins to understand the effect of sequence modifications on expression levels. We uncover the link between integration efficiency and observed expression levels for membrane proteins, and utilize coarse-grained simulations to predict sequence modifications that improve heterologous overexpression.
" }, { "name": "O'Brien, Elizabeth", "degree": "PhD", "year": "2018", "title": "Redox Signaling in Eukaryotic DNA Replication and Repair", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-200314076", "creators": [ { "name": { "family": "O'Brien", "given": "Elizabeth" }, "id": "O'Brien-Elizabeth", "orcid": "0000-0003-2889-1688", "display_name": "O'Brien, Elizabeth" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KGCP-SD98", "abstract": "DNA-mediated charge transport chemistry (DNA CT) offers an intriguing regulatory mechanism in biology, as it is long-range, rapid, and sensitive to mismatches and perturbations to base stacking. DNA-processing enzymes in all three domains of life moreover have been shown to contain [4Fe4S] clusters, commonly redox cofactors. Bacterial [4Fe4S] repair proteins have been shown to signal one another using long-range DNA-mediated charge transport (DNA CT), facilitating the redistribution to damaged genomic DNA in cells. The role of metabolically expensive, [4Fe4S] cluster cofactors in eukaryotic systems, however, was less clear than in prokaryotes.
\r\n\r\nHere we examine the chemical role of the [4Fe4S] cluster in eukaryotic DNA primase and the human base excision repair glycosylase, MUTYH. The primase cluster functions as a redox switch regulating DNA binding and redox signaling activity in humans and yeast. Yeast moreover require the primase redox switch for viability. Human MUTYH, a bifunctional glycosylase which repairs oxidative DNA lesions, performs DNA-mediated redox signaling, similarly to the bacterial homologue MutY. The MUTYH mutation which destabilizes the [4Fe4S] cluster during redox signaling, C306W, promotes degradation and loss of activity, associated with hereditary colorectal cancer.
\r\n\r\nTo assess the redox role of the human primase [4Fe4S] cluster, we perform anaerobic DNA electrochemistry on the [4Fe4S] domain of human primase (p58C), which independently binds DNA. On DNA-modified Au electrodes, we compare the redox activity of electrochemically oxidized and electrochemically reduced p58C. Oxidized [4Fe4S]3+ p58C is electrochemically active, and reduced [4Fe4S]2+ p58C state is redox-inert. This redox-driven switch is electrochemically reversible, and is mediated by a triad of conserved tyrosines between the DNA binding interface and [4Fe4S] cluster. Mutation of residues Y309, Y345, and Y347 to phenylalanine causes attenuation of redox switching on DNA. Single-atom mutations in the redox pathway moreover compromise initiation and truncation of primer synthesis but do not affect RNA polymerase activity. We find that primase truncation is gated by DNA CT in vitro; a single mismatch in the nascent primer abrogates truncation of primase products. As\r\nprimase is tethered to DNA polymerase \u03b1, a putative [4Fe4S] enzyme to which primase hands off the RNA-primed template, we propose that DNA-mediated signaling between primase and polymerase \u03b1 chemically regulates this handoff during the first steps of replication.
\r\n\r\nEukaryotic primase must bind both DNA and nucleotide triphosphates (NTPs) in order to convert to active form. Using DNA electrochemistry we show that p58C, and full-length DNA primase, display a robust, semi-reversible NTP-dependent signal on DNA, centered near 150mV vs. NHE. This signal is dependent on the tyrosine redox pathway. The presence of reversible redox activity at a physiological potential when primase is bound to DNA and NTPs suggests that reversible redox switching from the [4Fe4S]2+ to the [4Fe4S]3+ state is important for the activity of primase during replication.
\r\n\r\nThe cluster serves as a redox switch governing DNA binding in yeast primase, just as in human primase. Mutation of tyrosines 395 and 397 in yeast primase moreover, alters the same electron transfer chemistry as the mutation of their orthologues, Y345 and Y347, respectively, alters in human primase. Although these tyrosines are arranged differently in the yeast and human proteins, they perform the same reaction to affect the switch. The single-atom Y395F mutation causes some sensitivity to chemically induced oxidative stress in yeast, and single-residue mutation Y397L confers lethality in yeast cells. A constellation of tyrosines for protein-DNA electron transfer mediates the redox switch in eukaryotic primases, regulates the affinity for RNA-primed DNA template, and is required for primase function in vivo.
\r\n\r\nWe finally characterize a novel mutation in the [4Fe4S] human base excision repair protein, MUTYH, which destabilizes the cluster environment and has pathogenic consequences. The MUTYH C306W mutation alters one of the cysteines coordinating the cluster to tryptophan. This mutation moreover is associated with hereditary colorectal cancer and causes defective DNA binding and enzymatic activity. We perform DNA electrochemistry on WT MUTYH, as well as C306W and two cancer-associated mutants, Y197C and G396D, which have an unaltered cluster environment. MUTYH variants participate in redox signaling, but C306W is destabilized upon oxidation from the [4Fe4S]2+ to the [4Fe4S]3+ state during signaling on DNA, leading to degradation to a [3Fe4S]+ cluster and loss of DNA binding and activity. A [4Fe4S] human DNA repair enzyme performs redox signaling on DNA; dysregulation of this signaling activity is linked to tumorigenesis.
\r\n" }, { "name": "Ordner, Ciara Mary", "degree": "Senior Thesis", "year": "2018", "title": "Synthesis of Enantioenriched Heterocycles by Tandem Sakurai Allylation/Intramolecular Cyclization Processes", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192018-145939043", "creators": [ { "name": { "family": "Ordner", "given": "Ciara Mary" }, "id": "Ordner-Ciara-Mary", "orcid": "0000-0002-6644-7863", "display_name": "Ordner, Ciara Mary" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FHRD-3724", "abstract": "Organosilanes are advantageous in organic synthesis due to their ability to act as both stable products and reactive intermediates. A stereospecific one-pot cascade reaction that converts chiral allylic silanes into chiral heterocycles was developed using Lewis acid catalysis. We report on the development of this cascade reaction, optimization to benchtop- scale chemistry, and preliminary investigation into the synthetic scope. In our studies, we were successful in varying the cyclization ring size, investigating cyclization preference in the presence of multiple electrophilic leaving groups, and altering the functional groups present on the aldehyde starting material. Ultimately, we envision this method will be useful in the synthesis of a variety of enantioenriched heterocycles found in bioactive natural products, many of which have may find use as potential drug targets." }, { "name": "Ratani, Tanvi Siraj", "degree": "PhD", "year": "2018", "title": "Photoinduced, Copper-Catalyzed C-N and C-C Bond Formation and Photocatalytic Co-Mediated Nitrite Reduction to N\u2082O: Reactivity and Mechanism", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312017-153922571", "creators": [ { "name": { "family": "Ratani", "given": "Tanvi Siraj" }, "id": "Ratani-Tanvi-Siraj", "display_name": "Ratani, Tanvi Siraj" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ZP44BF", "abstract": "Photocatalytic reactions with first-row transition metals are presented as a method for sustainable chemistry with great potential for new forms of reactivity and mechanistic pathways. Chapters 2 and 3 of this thesis discuss mechanism and reactivity of photoinduced, copper-catalyzed bond constructions. The Peters and Fu groups have reported that a variety of couplings of nitrogen, sulfur, oxygen, and carbon nucleophiles with organic halides can be achieved under mild conditions (\u221240 to 30 \u00b0C) through the use of light and a copper catalyst. Insight into the various mechanisms by which these reactions proceed may enhance our understanding of chemical reactivity and facilitate the development of new methods. We apply an array of tools (EPR, NMR, transient absorption, and UV\u2212vis spectroscopy; ESI\u2212MS; X-ray crystallography; DFT calculations; reactivity, stereochemical, and product studies) to investigate the photoinduced, copper-catalyzed coupling of carbazole with alkyl bromides. Our observations are consistent with pathways wherein both an excited state of the copper(I) carbazolide complex ([CuI(carb)2]\u2212) and an excited state of the nucleophile (Li(carb)) can serve as photoreductants of the alkyl bromide. The catalytically dominant pathway proceeds from the excited state of Li(carb), generating a carbazyl radical and an alkyl radical. The cross-coupling of these radicals is catalyzed by copper via an out-of-cage mechanism in which [CuI(carb)2]\u2212 and [CuII(carb)3]\u2212 (carb = carbazolide), both of which have been identified under coupling conditions, are key intermediates, and [CuII(carb)3]\u2212 serves as the persistent radical that is responsible for predominant cross-coupling. This study underscores the versatility of copper(II) complexes in engaging with radical intermediates that are generated by disparate pathways, en route to targeted bond constructions.
\r\n\r\nIn Chapter 3, we establish that photoinduced, copper-catalyzed alkylation can also be applied to C\u2212C bond formation, specifically, that the cyanation of unactivated secondary alkyl chlorides can be achieved at room temperature to afford nitriles, an important class of target molecules. In the presence of an inexpensive copper catalyst (CuI; no ligand coadditive) and a readily available light source (UVC compact fluorescent light bulb), a wide array of alkyl halides undergo cyanation in good yield. Our initial mechanistic studies are consistent with the hypothesis that an excited state of [Cu(CN)2]\u2212 may play a role, via single electron transfer, in this process. This investigation provides a rare example of a transition metal-catalyzed cyanation of an alkyl halide, as well as the first illustrations of photoinduced, copper-catalyzed alkylation with either a carbon nucleophile or a secondary alkyl chloride.
\r\n\r\nChapter 4 presents a mechanistic study of the photocatalytic reduction of nitrite to nitrous oxide with the use of an Ir photocatalyst ([Ir(ppy)2(phen)][PF6]) and a bimetallic CoMg co-catalyst with a diimine-dioxime ligand platform. Insights into the mechanism of this reaction may enhance our current understanding of N\u2013N coupling processes relative to other pathways of reactivity for nitrosyl ligands, such as nitroxyl (HNO) dimerization. We propose a mechanism in which a coordinated and an uncoordinated \u2022NO are coupled at a single Co center. One electron reduction of [(Cl)(NO)Co(Medoen)Mg(Me3TACN)(H2O)][BPh4] ({CoNO}8), a species we show to be catalytically relevant, forms a {CoNO}9 species that is characterized by UV-Vis, EPR, and FT-IR spectroscopy and whose electronic structure is supported by density functional theory (DFT). We formulate the {CoNO}9 as a 5-coordinate, S = 3/2 Co(II) antiferromagnetically coupled with an anionic S = 1 3NO\u2013 ligand. Experimental data suggest a mechanism in which this {CoNO}9 intermediate can release \u2022NO, thereby reducing the Co(II) center to Co(I). This free \u2022NO can react with another {CoNO}9 complex to generate a Co(NONO) intermediate which was observed by step-scan time-resolved IR spectroscopy and whose assignment was supported with DFT calculations. This Co(NONO) species, which can generate N2O and H2O, is formulated as a neutral hyponitrite intermediate with significant neutral radical character on both nitrosyl nitrogen atoms and a weak N\u2013N bond.
" }, { "name": "Schlappi, Travis Stratton", "degree": "PhD", "year": "2018", "title": "Improving the Speed and Performance of Point-of-Care Diagnostics with Microfluidics", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292017-182342238", "creators": [ { "name": { "family": "Schlappi", "given": "Travis Stratton" }, "id": "Schlappi-Travis-Stratton", "orcid": "0000-0001-6132-6459", "display_name": "Schlappi, Travis Stratton" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "chair", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9K935Q6", "abstract": "Microfluidic devices play an important role in improving global health because they reduce the study of biological phenomena into physiological scales and lay the foundation for point-of-care (POC) diagnostics. Health is improved and lives are saved because POC diagnostics can enable earlier diagnosis of diseases and therefore more effective treatment. Accurate and available diagnostics also prevent accelerated drug resistance that stems from overtreatment or mistreatment with antibiotics, which is projected to cause up to $100 trillion in lost economic output and 10 million deaths by 2050. This work details new diagnostic assays and theoretical analysis of microfluidic devices that can be implemented at the point-of-care to improve global health." }, { "name": "Shen, Linhan", "degree": "PhD", "year": "2018", "title": "Cavity Ring-Down and Multi-Pass Spectroscopies for Methane Source Attribution and Chemical Kinetics Studies", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:04122018-141241438", "creators": [ { "name": { "family": "Shen", "given": "Linhan" }, "id": "Shen-Linhan", "orcid": "0000-0003-3871-655X", "display_name": "Shen, Linhan" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "role": "member", "display_name": "Eiler, John M." }, { "name": { "family": "Christensen", "given": "Lance E." }, "id": "Christensen-Lance-E", "role": "member", "display_name": "Christensen, Lance E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WE40-5W54", "abstract": "Methane is the most abundant hydrocarbon in the Earth atmosphere, is also an important greenhouse gas, energy source, and microbial metabolic energy source and product. With the rapid increase of atmospheric methane concentration, it has become very important to quantify methane emissions from different sources. This thesis describes the applications of cavity ring-down applications on atmospheric ethane measurements and measurements of doubly substituted methane for methane source attributions. We also present our work on chemical kinetics studies of an alkene ozonolysis intermediate, Criegee intermediate, using a multi-pass absorption technique.
\r\n\r\nIn Chapter 2, we demonstrated the performance of a continuous-wave (cw) interband cascade laser (ICL) based mid-infrared cavity ring-down spectroscopy (CRDS) sensor for atmospheric ethane (C2H6) detection. A 3.36 \u00b5m cw ICL with an was used to target two ethane absorption bands at 2976.788 cm-1 and 2983.383 cm-1. This technique utilizes the long effective pathlength (~ 4.5 km) of CRDS to increase sensitivity of atmospheric ethane detection. Our spectrometer can measure atmospheric ethane concentration as low as 200 pptv at standard temperature and pressure. We have used this instrument to measure the atmospheric ethane composition in ambient air collected in Pasadena, California. We have utilized this instrument to aid in the study of soil microbial response post the Porter Ranch gas leak. Results were shown in Chapter 3.
\r\n\r\nIn Chapter 4, we demonstrate high sensitivity measurements of both 13CH3D and 12CH2D2 isotopologues using a high precision and high resolution spectroscopy technique, frequency stabilized cavity ring-down spectroscopy (FS-CRDS). Measurements of the abundances of doubly-substituted methane isotopologues (13CH3D and 12CH2D2) are important in methane source attributions. Currently, methods developed for 13CH3D and 12CH2D2 measurements have been mostly focused on the use of isotope ratio mass spectrometry (IRMS), which faces the challenges of mass resolutions. In this work, we focus on measuring these low abundant methane isotopologues optically, taking advantage of the distinct absorption features of them. This technique can be used as a potential complement to IRMS measurements for its ability to measure abundances of rare methane isotopologues with a short time average (~1 hour average per isotope ratio measurement).
\r\n\r\nIn Chapter 5, we utilized our IR kinetic spectroscopy (IRKS) apparatus to study the formation of HCO radicals from the smallest Criegee Intermediate (CH2OO), which is an important intermediate from oznolysis of the smallest alkene.
\r\n" }, { "name": "Shockley, Samantha Elizabeth", "degree": "PhD", "year": "2018", "title": "Development of Stereoselective Iridium-Catalyzed Allylic Alkylation Methods", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302018-124410879", "creators": [ { "name": { "family": "Shockley", "given": "Samantha Elizabeth" }, "id": "Shockley-Samantha-Elizabeth", "orcid": "0000-0001-5682-8569", "display_name": "Shockley, Samantha Elizabeth" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/S93J-6P85", "abstract": "The Stoltz group, and moreover the synthetic community at large, has long been interested in the development of methods for the synthesis of enantioenriched all-carbon quaternary stereocenters. Historically, our group\u2019s interest has centered on palladium-catalyzed allylic alkylation, though recently effort has moved to include the study of iridium catalysts. This thesis presents four related projects, all unified by the use of enantioselective iridium-catalyzed allylic alkylation to construct highly-congested C\u2013C bonds.
\r\n\r\nFirst, the development of the first diastereo-, enantio-, and regioselective iridium-catalyzed allylic alkylation reaction of prochiral enolates to form vicinal tertiary and all-carbon quaternary stereodyads with alkyl-substituted allylic electrophiles is described. Next, the first enantioselective iridium-catalyzed allylic alkylation reaction of a masked acyl cyanide (MAC) nucleophile is presented, representing a rare example of umpolung strategy in iridium-catalyzed allylic alkylation. Additionally, the application of a MAC reagent in the first highly enantioselective iridium-catalyzed allylic alkylation to provide access to products bearing an allylic all-carbon quaternary stereocenter is detailed. The use of the MAC nucleophile enables the one-pot preparation of \u03b1-quaternary carboxylic acids, esters, and amides with a high degree of enantioselectivity. Finally, the first enantioselective transition metal-catalyzed allylic alkylation providing access to acyclic products bearing vicinal all-carbon quaternary centers is presented.
\r\n" }, { "name": "Stone, Shannon Elizabeth", "degree": "PhD", "year": "2018", "title": "Cell-Selective Chemoproteomics for Biological Discovery", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07222017-155020423", "creators": [ { "name": { "family": "Stone", "given": "Shannon Elizabeth" }, "id": "Stone-Shannon-Elizabeth", "orcid": "0000-0002-6617-3874", "display_name": "Stone, Shannon Elizabeth" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9V122ZF", "abstract": "Cellular protein synthesis changes rapidly in response to internal and external cues in ways that vary from cell to cell. Global proteomic analyses of microbial communities, tissues, and organisms have provided important insights into the behavior of such systems, but can obscure the diversity of responses characteristic of different cellular subpopulations. Recent advances in cell-specific proteomics\u2014fueled in part by the development of bioorthogonal chemistries, more sensitive mass spectrometers and more advanced mining algorithms\u2014have yielded unprecedented glimpses into how proteins are expressed in space and time. Whereas previous cell-specific proteomic analyses were confined to abundant cells in relatively simple systems, recent advances in chemoproteomics allow researchers to map the protein expression patterns of even rare cells in complex tissues and whole organisms.
\r\n\r\nChapter 1 highlights recently developed strategies for cell-selective proteomics, including metabolic labeling strategies such as bioorthogonal noncanonical amino acid tagging (BONCAT). Bioorthogonal noncanonical amino acid tagging (BONCAT) is a chemoproteomic technique that enables temporal labeling of proteins. In cell-selective BONCAT, expressing a mutant aminoacyl-tRNA synthetase under the control of cell-specific genetic elements affords cellular resolution; only cells of interest can selectively incorporate a noncanonical amino acid into proteins for subsequent detection and identification. Chapter 2 details protocols to set up a cell-selective BONCAT system.
\r\n\r\nWhile BONCAT had previously been applied to studies of microbial pathogenesis in tissue culture-based models of infection, we sought to further develop the method to identify the proteome of methicillin-resistant Staphylococcus aureus (MRSA) within a mouse model of infection, as detailed in Chapter 3. We used this technique to enrich for staphylococcal proteins made within the host and in addition to finding many factors known to be important for infection, we also found many that had not previously been associated with infection. Screening several of these previously unknown factors in vivo led to the discovery of a novel protein important for MRSA infection. This unbiased approach to cell-selectively label pathogenic proteins during infection could be used as a global discovery tool for novel anti-infective strategies.
\r\n\r\nIn Chapter 4, we combine this cell-selective BONCAT strategy with microbial identification after passive clarity technique (MiPACT) to visualize both staphylococcal protein synthesis and ribosomal RNA within whole skin abscesses during infection. In Chapter 5, we continue developing cell-selective BONCAT to study microbial protein synthesis in the context of a living mouse by extending the system to Bacteroides fragilis, a common human gut commensal.
\r\n\r\nFinally, cell-selective BONCAT is wholly dependent on the bioorthogonal nature of the azide and its detection reagents. Fishing out an azide-tagged molecule from the rest of the cellular milieu requires optimization of enrichment-based strategies. In Chapter 6, we describe the development of a peptide to quantitate the gain of our enrichments.
\r\n\r\nWhile innovations in mass spectrometry and computational algorithms have facilitated the identification and quantification of thousands of proteins simultaneously from complex samples, this abundance of data does not necessarily lead to biological insight. Cell-specific proteomic techniques will play a key role in the identification of the mechanisms that govern cell specialization and that allow organisms to respond to changing environments. Overall, this work demonstrates the power of cell-selective chemoproteomics to ascertain biological insights in complex systems.
" }, { "name": "Thompson, Niklas Bjarne", "degree": "PhD", "year": "2018", "title": "A Synthetic Nitrogenase: Insights into the Mechanism of Nitrogen Fixation by a Single-Site Fe Catalyst", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-165300346", "creators": [ { "name": { "family": "Thompson", "given": "Niklas Bjarne" }, "id": "Thompson-Niklas-Bjarne", "orcid": "0000-0003-2745-4945", "display_name": "Thompson, Niklas Bjarne" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Chan", "given": "Garnet K." }, "id": "Chan-G-K", "role": "member", "display_name": "Chan, Garnet K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/T4WQ-TM68", "abstract": "Nitrogen fixation, specifically the conversion of molecular nitrogen into ammonia, is a fundamental reaction necessary to support life. Our group has recently discovered the first family of well-defined iron complexes that catalyze the conversion of dinitrogen to ammonia. This thesis details mechanistic study of the nitrogen fixation chemistry these complexes. Chapter 1 presents an abbreviated overview of catalytic nitrogen fixation, which places our work in a larger context. Chapter 2 details the synthesis and nitrogen fixation activity of a series of cobalt complexes that are homologous to the known iron-based catalysts. The central goal of this work was to provide a structure-function study of the isostructural cobalt and iron complexes, in which the nature of the transition metal ion was changed in a fashion that predictably modulated the electronics of the system. Chapter 3 details in situ mechanistic studies of nitrogen fixation catalyzed by the iron complexes under the originally-reported reaction conditions. In this study, we were able to achieve a nearly order-of-magnitude improvement of catalyst turnover. Study of the reaction dynamics evidence a single-site mechanism for dinitrogen reduction, which is corroborated by in situ monitoring of catalytic reaction mixtures using freeze-quench M\u00f6ssbauer spectroscopy. In Chapter 4, we study the key N-N bond cleavage step in the catalytic cycle for nitrogen fixation. In this chapter, we demonstrate that sequential reduction and low-temperature protonation of an iron catalyst results in the formation of ammonia and a terminal Fe(IV) nitrido complex. This result provides a compelling proposal for the mechanism of the catalytic nitrogen fixation reaction. Finally, in Chapter 5 we present spectroscopic and computational studies detailing the electronic structures of a redox series of Fe(NNR2) complexes that model key catalytic intermediates occurring prior to the N-N bond cleavage step. We evidence one-electron redox non-innocence of the \u201cNNR2\u201d ligand, which resembles that of the classically non-innocent ligand, NO, and may have mechanistic implications for the divergent nitrogen fixation activity of the some of the iron complexes studied by our group.
" }, { "name": "Torelli, Daniel Anthony", "degree": "PhD", "year": "2018", "title": "The Discovery of Novel Materials for the Electrocatalytic Reduction of Carbon Dioxide", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-142628914", "creators": [ { "name": { "family": "Torelli", "given": "Daniel Anthony" }, "id": "Torelli-Daniel-Anthony", "orcid": "0000-0002-6222-817X", "display_name": "Torelli, Daniel Anthony" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RBD5-B141", "abstract": "The removal of atmospheric carbon dioxide is likely the only route to mitigating the effects of decades of increased fossil fuel combustion. Artificial photosynthesis presents one method for removal and conversion of problematic carbon dioxide into chemically useful products. By coupling electrochemical CO2 reduction (CO2R) to a renewable energy source atmospheric CO2 could be converted back into a fuel such as ethanol, or a commodity chemical such as ethylene. These products could then be consumed for energy or used to generate plastics effectively removing CO2 from the atmosphere. Significant advances in current electrocatalysts are needed in order for large scale CO2R to become a reality. Most known catalysts are only capable of transferring 2 electrons with needed protons to CO2 producing either carbon monoxide or formic acid. Copper is the only known metal capable of reducing CO2 to hydrocarbons at appreciable rates and low overpotentials. This work aims to find new materials that produce similar hydrocarbons, but at lower overpotentials with higher rates and greater selectivity than current copper catalysts. By implementing a cyclic process referred to as the Catalyst Discovery Cycle (CDC) iterations between predications, catalyst testing, and active site characterization allow for the rational design and discovery of new and improved catalysts. This methodology led to the discovery of nickel-gallium bimetallics as low overpotential catalysts for CO2R to methane, ethylene, and ethane. In addition, theoretical and experimental observations have determined a proposed active site and side reactions detrimental to their activity. " }, { "name": "Upton, Kathleen Tiffany", "degree": "PhD", "year": "2018", "title": "Analysis and Characterization of Titan Aerosol Simulants by Mass Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09252017-082932563", "creators": [ { "name": { "family": "Upton", "given": "Kathleen Tiffany" }, "id": "Upton-Kathleen-Tiffany", "orcid": "0000-0003-4292-7616", "display_name": "Upton, Kathleen Tiffany" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9XG9PBK", "abstract": "Saturn\u2019s large moon of Titan is unique as the only solid body in the outer solar system to possess a dense atmosphere, which is comprised of mostly nitrogen and methane. Atmospheric chemistry on this moon creates aerosols comprised of carbon, hydrogen, and nitrogen. Laboratory based synthesis of simulated Titan aerosols, also called tholins, led to molecules with rich chemical diversity, functionalities, and molecular weights. While this diversity has intriguing implications for Titan, it complicates the analysis and characterization of these simulants. This thesis discusses three different mass spectrometry methodologies, prioritizing a combination of mission applicability, broad spectrum characterization, and specific functional group identification. Chapters 2 and 3 utilize a home-built Direct Analysis in Real Time (DART) ionization source, termed EZ-DART, to test its suitability for the analysis of these simulants and the source\u2019s mission applicability. Chapter 2 focuses on the development and characterization of the EZ-DART source. Chapter 3 presents the analysis of Titan aerosol simulants, produced in a new and unique way, by EZ-DART, allowing for the identification of various compounds of astrobiological significance. Solid phase microextraction gas chromatography mass spectrometry (SPME-GC-MS) is utilized in Chapter 4 with different Titan aerosol simulants, identifying multiple compounds of significance to Titan and astrobiology. The versatility allowed by SPME increases the applicability of GC for future lander missions. While not mission applicable, Chapter 5 shows the breadth of primary amines in Titan aerosol simulants through the use of supramolecular complexation to 18-crown-6 ether. This technique not only enabled the unambiguous identification of primary amines, but also allowed for the structural characterization of some components. The range of methods and identified compounds discussed within this thesis demonstrates not only the rich chemistry of these Titan aerosol simulants, but also introduces intriguing possibilities for Titan\u2019s atmospheric chemistry and presents potential significance to astrobiology." }, { "name": "Wu, Yong Yi", "degree": "PhD", "year": "2018", "title": "Engineering Biosynthetic Pathways in Cell-Free Systems for Sustainability and Chemical Innovation\r ", "advisor": "Murray, Richard M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08302017-121452132", "creators": [ { "name": { "family": "Wu", "given": "Yong Yi" }, "id": "Wu-Yong-Yi", "orcid": "0000-0002-5401-3662", "display_name": "Wu, Yong Yi" } ], "advisors": [ { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "advisor", "display_name": "Murray, Richard M." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Culler", "given": "Stephanie J." }, "id": "Culler-S-J", "role": "member", "display_name": "Culler, Stephanie J." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z99W0CN1", "abstract": "This work presents the cell-free transcription-translation (TX-TL) system as a research and development platform for renewable synthesis and molecular discovery. TX-TL is easy to use and provides a biomolecular breadboard for the rapid prototyping and engineering of biosynthetic pathways. This work has validated the capabilities of the cell-free TX-TL system for simultaneous protein expression and chemical synthesis. Specifically, this work shows that TX-TL supports the conversion of intermediates from carbohydrate metabolism and amino acids into valuable compounds. Metabolic flux through cofactor dependent pathways confirms that active cofactor metabolism is occurring in TX-TL. This work has also demonstrated the industrial relevance of TX-TL through exploring design space of a biosynthetic pathway for improved product yield and expanding substrate scope of another biosynthetic pathway.
\r\n\r\nCurrent methods for assembling biosynthetic pathways in microorganisms require a process of repeated trial and error and have long design-build-test cycles. We describe the use of a cell-free transcription-translation (TX-TL) system as a biomolecular breadboard for the rapid engineering of the 1,4-butanediol (BDO) pathway. In this work, we have verified enzyme expression and enzyme activity and identified the conversion of 4-hydroxybutyrate to downstream metabolites as the pathway bottleneck. We demonstrate the reliability of using linear DNA in TX-TL as a tool for engineering biological systems by undertaking a careful characterization of its transcription and translation capabilities and provide a detailed analysis of its metabolic output. Pathway constructs of varying pathway enzyme expression levels are tested in TX-TL and in vivo to identify correlations between the two systems, and we find that the production of BDO is correlated to the expression of enzyme ald in both systems. The use of TX-TL to survey the design space of the BDO pathway enables rapid tuning of pathway enzyme expression levels for improved product yield. Different pathway combinations are also tested in TX-TL for its application in pathway ranking. Leveraging TX-TL to screen enzyme variants for improved catalytic activity accelerates design iterations that can be directly applied to in vivo strain development.
\r\n\r\nTX-TL simulates a customizable cellular environment that can be controlled by manipulating pH, changing cellular components, or adding exogenous substrates. By adding linear DNA encoding individual enzymes of the violacein pathway and tryptophan analogs in TX-TL reactions, we have discovered new violacein analogs. TX-TL enables rapid production of natural product analogs with diverse substitution, which allows small-scale biosynthesis of potential drug candidates and offers a new platform for drug discovery. This work also presents TX-TL as a platform for protein engineering. Residues targeted for site-saturated mutagenesis were identified with protein-ligand docking. Linear DNAs of individual enzyme mutants were added into TX-TL reactions to screen for improved enzyme variant. Screening result indicates vioE mutant Y17H reduces byproduct formation and redirects metabolic flux towards target metabolites. Protein engineering for improved enzyme activity can further expand the substrate scope of a natural product pathway and result with more natural product analogs that can be applied for medical applications.
\r\n\r\nThis work demonstrates that the cell-free TX-TL system can become a valuable tool that complements the process of engineering biosynthesis in the whole cell in vivo system or the purified protein in vitro system. Future engineering and development of the TX-TL system can further expand the chemical space for biosynthesis.
\r\n" }, { "name": "Wyatt, Emily Ann", "degree": "PhD", "year": "2018", "title": "Targeted Nanoparticle Delivery of Therapeutics Across the Blood-Brain and Blood-Tumor Barriers to Breast Cancer Brain Metastases", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062018-180959061", "creators": [ { "name": { "family": "Wyatt", "given": "Emily Ann" }, "id": "Wyatt-Emily-Ann", "orcid": "0000-0002-7534-0582", "display_name": "Wyatt, Emily Ann" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "role": "member", "display_name": "Mazmanian, Sarkis K." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5qpd-0736", "abstract": "Brain metastases of human epidermal growth factor receptor 2 (HER2)-positive breast cancer are presenting an increasing problem in the clinic. While HER2-targeted therapies effectively control systemic disease, their efficacy against brain metastases is hindered by their inability to penetrate the blood-brain and blood-tumor barriers (BBB and BTB). One promising strategy to increase brain penetration of systemic therapeutics is to exploit endogenous transport systems at the BBB to shuttle drugs into the brain. Previous studies showed that gold nanoparticles designed to shed transferrin receptor (TfR)-targeting ligands under acidic conditions encountered during transcytosis of the BBB demonstrated increased accumulation in the brain. The focus of this work was to determine whether therapeutic, TfR-targeted nanoparticles using an improved acid-cleavable chemistry could be used to deliver therapeutically useful amounts of drug to the brain.
\r\n\r\nTo accomplish this goal, a new animal model of HER2-positive breast cancer brain metastasis was developed in an attempt to create a clinically representative, impermeable barrier to standard therapeutics. This new model establishes brain metastases by methods that more closely resemble the human disease, forming whole-body tumors that eventually metastasize to the brain. Brain metastases formed by this new methodology show no response to standard HER2-targeted agents, mimicking the clinical situation.
\r\n\r\nNext, efficacy and brain uptake of TfR-targeted, single-agent therapeutic nanoparticles were investigated in the newly developed model, as well as two common models from the literature. These nanoparticles show significant tumor growth delay and increased accumulation in both brain metastases and healthy brain tissue in all three models, highlighting their therapeutic potential. Additionally, non-BBB-penetrant small molecule and non-targeted nanoparticle therapeutics elicit a substantial antitumor response as well as brain tumor accumulation in the most commonly used literature model. In contrast, the new model and one gaining popularity in the literature provide for a more clinically relevant, impermeable barrier to non-BBB-penetrant agents, indicating that the method used to establish brain metastases can affect efficacy and brain uptake of therapeutics.
" }, { "name": "Yang, Kuang-Wei", "degree": "PhD", "year": "2018", "title": "Synthesis, NMR Solution Structure, and Neuritogenic Activity of Chondroitin Sulfate D and E", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292018-232454800", "creators": [ { "name": { "family": "Yang", "given": "Kuang-Wei" }, "id": "Yang-Kuang-Wei", "display_name": "Yang, Kuang-Wei" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/TPD7-FB87", "abstract": "Chondroitin sulfate are ubiquitously expressed linear, sulfated polysaccharides that play critical roles in neuronal development and regeneration growth factor signaling, morphogenesis, and virus invasion. The diverse sulfation patterns presented by chondroitin sulfate has been suggested to regulate its activity, but the structural complexity and heterogeneity have hampered the understanding of structure-activity relationship. Therefore, we envisioned that chemically synthesized chondroitin sulfate oligosaccharide may provide a unique opportunity to specifically study the functions of sulfation patterns.
\r\n\r\nHere, we report the synthesis of a CS-D and CS-E tetrasaccharide in a step-efficient manner. By generating a disaccharide precursor from hydrolysis of polysaccharides, we were able to streamline the synthesis and reduce the number of steps by one-third comparing to the traditional synthesis without losing versatility of the synthetic route and functionality of the final product. With the structurally defined molecules, we were able to determine the NMR solution structure of CS-D and CS-E. In this work, we accomplished the first structural study of CS-D tetrasaccharide and the most thorough study of CS-E to date. Furthermore, we also discovered the existence of a second conformer in CS-D, which is the first time for such behavior to be observed experimentally in chondroitin sulfate. The electrostatic potential surface constructed based on the NMR structure presented unique structural features that may allow proteins to interact specifically.
\r\n\r\nThe CS-D and CS-E tetrasaccharide, along with a CS-D disaccharide, was\r\ninvestigated for their neuritogenic activity. We discovered that the CS-D tetrasaccharide specifically stimulates dendritic growth whereas the CS-E tetrasaccharide preferentially promoted axonal growth, revealing the potential critical role chondroitin sulfate with specific sulfation patterns may play in the nervous system. The lack of activity of the CS-D disaccharide suggested that the minimum motif required for activity of CS-D is a tetrasaccharide.
\r\n" }, { "name": "Zwang, Theodore Joseph", "degree": "PhD", "year": "2018", "title": "Magnetic Field Effects and Biophysical Studies on DNA Charge Transport and Repair", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282017-141924517", "creators": [ { "name": { "family": "Zwang", "given": "Theodore Joseph" }, "id": "Zwang-Theodore-Joseph", "display_name": "Zwang, Theodore Joseph" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9TT4P4H", "abstract": "DNA-mediated charge transport (DNA CT) is well established in both ground and excited state systems. Although theoretical models are still being developed, it is clear that the integrity of the extended \u03c0-stack of the aromatic heterocycles, the nucleic acid bases, plays a critical role. Electron donors and acceptors must be electronically well coupled into the \u03c0-stack, typically via intercalation. Perturbations that distort the \u03c0-stack, such as single-base mismatches, abasic sites, base lesions, and protein binding that kinks the double helix, attenuate DNA CT dramatically.
\r\n\r\nThis thesis encompasses work that first aims to understand how DNA duplex structure informs characteristics of DNA CT and then continues to develop an understanding of the role these structural features play in biological systems. To contextualize these advancements, this first chapter outlines foundational work that has shown ways that DNA structure influences its ability to conduct charge.
\r\n\r\nNext, experiments were conducted on magnetized DNA-modified electrodes to explore spin-selective electron transport through hydrated duplex DNA. These results show that the two spins migrate through duplex DNA with a different yield and that spin selectivity requires charge transport through the DNA duplex. Significantly, shifting the same duplex DNA between right-handed B- and left-handed Z-forms leads to a diode-like switch in spin selectivity; which spin moves more efficiently through the duplex depends upon the DNA helicity. With DNA, the supramolecular organization of chiral moieties, rather than the chirality of the individual monomers, determines the selectivity in spin, and thus a conformational change can switch the spin selectivity.
\r\n\r\nThis exquisite spin selectivity begged the question: how might biology take advantage of such a spin filter? Photolyase and cryptochromes both have been shown to exhibit magnetosensitive chemistry nearby a DNA binding pocket, and photolyase had previously been shown capable of DNA CT. Thus, electrochemical studies were conducted to monitor the repair of cyclobutane pyrimidine dimer lesions by E coli photolyase and truncated A Thaliana Cryptochrome 1 with an applied magnetic field. We find that the yield of dimer repair is dependent on the strength and angle of the applied magnetic field even when using magnetic fields weaker than 1 Gauss, though spin selective DNA CT is not involved. These data illustrate how cyclobutane dimer repair could be used in a biological compass that is informed by the angles of Earth\u2019s magnetic field.
\r\n\r\nNext DNA-mediated electrochemistry and atomic force microscopy studies were used to describe a role for redox active [4Fe4S] clusters in DNA-mediated charge transport signaling. DNA-modified electrochemistry shows that the [4Fe4S] cluster of DNA-bound DinG, an ATP-dependent helicase that repairs R-loops, is redox-active at cellular potentials and ATP hydrolysis increases DNA-mediated redox signaling. Atomic force microscopy experiments demonstrate that DinG and Endonuclease III, a base excision repair enzyme, cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. These data are then described using an equilibrium model which elucidates fundamental characteristics of this redox chemistry that allow DNA CT to coordinate the activities of DNA repair enzymes across the genome.
\r\n\r\nThe importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process is then further explored. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process.
" }, { "name": "Bachman, Shoshana", "degree": "PhD", "year": "2017", "title": "Development of Cu- and Ni-Catalyzed C\u2013C and C\u2013N Bond Forming Reactions", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042017-233801526", "creators": [ { "name": { "family": "Bachman", "given": "Shoshana" }, "id": "Bachman-Shoshana", "display_name": "Bachman, Shoshana" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z99S1P2G", "abstract": "Chapters 1 and 2 describe the development of photoinduced, Cu-catalyzed coupling reactions of unactivated secondary alkyl halides with amide and cyanide nucleophiles. These reactions may be conducted at room temperature under operationally simple conditions. Mechanistic studies are consistent with the intermediacy of alkyl radicals in these processes.
\r\n\r\nChapter 3 describes progress toward the development of the first enantioselective Ni-catalyzed cross coupling of racemic alkyl halides and heteroatom nucleophiles. Borylation of secondary benzylic chlorides with B2(pin)2 may be achieved in good yield and promising levels of enantioselectivity.
\r\n\r\nChapter 4 describes enantioselective Ni-catalyzed couplings of \u03b1-substituted lactam enolates with benzonitrile derivatives resulting in formal intermolecular C- acylation via in situ hydrolysis of an imine intermediate.
" }, { "name": "Bates, Kelvin Hamilton", "degree": "PhD", "year": "2017", "title": "Isoprene Oxidation Mechanisms and Secondary Organic Aerosol Formation Under HO2-Dominated Conditions", "advisor": "Seinfeld, John H.; Wennberg, Paul O.; Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312017-144547085", "creators": [ { "name": { "family": "Bates", "given": "Kelvin Hamilton" }, "id": "Bates-Kelvin-Hamilton", "orcid": "0000-0001-7544-9580", "display_name": "Bates, Kelvin Hamilton" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "co-advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "co-advisor", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "co-advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9930R6T", "abstract": "Isoprene, a volatile hydrocarbon emitted by plants, represents the single most abundant source of non-methane organic carbon to the atmosphere. After its rapid oxidation by OH radicals in the troposphere, isoprene may follow any of a number of complex reaction mechanisms to form more highly functionalized products, depending in large part on the relative abundance of reactive radicals such as HO2 and NO; some of these products can be sufficiently water-soluble, non-volatile, and/or reactive to partition into atmospheric particles and contribute to the creation of secondary organic aerosol (SOA). In this work, I explore the gas-phase oxidation mechanisms and SOA formation potential of second- and later-generation products formed in the HO2-dominated reaction cascade, which predominates in remote regions and is estimated to account for over >40% of isoprene oxidation. Pure standards of significant isoprene products, such as isoprene epoxydiols (IEPOX) and C4 dihydroxycarbonyl compounds, are synthesized, and the rates and product yields of their gas-phase reactions with OH are measured by CF3O- chemical ionization mass spectrometry in environmental chamber experiments. Results are compared to field observations from the Southern Oxidant and Aerosol Study in the Southeastern United States, where significant concentrations of these compounds were detected, and are integrated into a global chemical transport model to investigate their effects throughout the atmosphere. Further, the results from these and other gas-phase kinetic and product studies are incorporated into an explicit isoprene oxidation mechanism, designed to simulate the effects of isoprene chemistry on oxidant concentrations and to produce accurate representations of products known to be involved in condensed phase processes, including IEPOX. Finally, additional chamber experiments with synthetic IEPOX and inorganic seed aerosol are performed to derive particle uptake coefficients and examine the effects of particle pH, liquid water content, and chemical composition on IEPOX-SOA formation, using aerosol mass spectrometry and differential mobility analysis. The gas- and particle-phase reaction rates and product yields reported herein, along with the explicit model, provide important constraints on the fate of isoprene-derived carbon in the atmosphere and on the influence the HO2-dominated isoprene oxidation pathway exerts on SOA and oxidant budgets.
" }, { "name": "Blumenfeld, Carl Michael", "degree": "PhD", "year": "2017", "title": "Covalent Functionalization of Metal-Oxide Surfaces with Non-Traditional Ligands", "advisor": "Grubbs, Robert H.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-104255604", "creators": [ { "name": { "family": "Blumenfeld", "given": "Carl Michael" }, "id": "Blumenfeld-Carl-Michael", "display_name": "Blumenfeld, Carl Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "orcid": "0000-0002-4571-6884", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9FJ2DT7", "abstract": "Herein detailed are the syntheses, properties, and applications of metal-oxide nanosubstrates\r\ncovalently functionalized with two classes of materials, inorganic macrocycles called\r\ncorroles, and genomic deoxyribonucleic acid (DNA). These products have found biomedical\r\napplications in tumor imaging and chemotherapeutic sequestration, respectively. Both\r\nclasses of prepared materials are the first of their kind.
\r\n\r\nCorroles are tetrapyrrolic macrocycles, which have found applications in tumor imaging and\r\ntreatment, catalysis, solar fuels, and energy conversion. The direct functionalization of\r\nmetal-oxides with inorganic macrocycles, including corroles, has largely revolved around\r\nthe formation of hydrogen bonding type interactions between the substrate and the ligand.\r\nHydrogen bonding motifs result in materials with only moderate stability due to solvent\r\ndissolution. In the first three chapters of this thesis, the scalable preparation of 5,10,15-\r\n(trispentafluorophenyl) corrole and its subsequent covalent functionalization of metal-oxide\r\nsurfaces are discussed.
\r\n\r\nChapter 1 details mechanistic elements of the oligomerization and oxidative cyclization of\r\n5,10,15-(trispentafluorophenyl) corrole from pentafluorobenzaldehyde and pyrrole. Prior to\r\nthis work the synthesis of triperfluoroaryl corroles was dangerously exothermic and could\r\nonly be carried out on milligram scale. Mechanistic insights led to a safe and scalable\r\nsynthesis of the desired corrole species, achieving a 17.0 % yield (4.58 g). A detailed\r\ndiscussion of the covalent functionalization of the surface of TiO2 with chlorosulfonated\r\nderivatives of 5,10,15-tris(pentafluorophenyl) corrole is presented in Chapter 2. The\r\nchlorosulfonated species investigated include the freebase, gallium, and aluminum corroles.\r\nHydroxyl groups on the metal-oxide react with the chlorosulfonyl groups of the corrole ring\r\nvia nucleophilic attack, resulting in the formation of sulfonic ester linkages. The aluminum\r\nspecies was further investigated as a potential near-infrared optical contrast agent. The\r\ndetails of this study, described in Chapter 3, include imaging experiments with immortalized\r\nhuman cancer lines and harvested mouse hepatocytes. This nanoconjugate exhibited low\r\ntoxicity and efficient cellular uptake.
\r\n\r\nConventional chemotherapy agents that target DNA are notorious for producing severe\r\nside-effects. Sequestering chemotherapeutics that enters systemic circulation, in a process\r\ndeemed \u201cChemoFiltration,\u201d is a strategy for reducing off-target toxicity. Materials capable\r\nof such activity have yet to be fully realized. Reported in Chapter 4 are the first methods\r\ncovalent attachments of genomic DNA to surfaces, namely magnetite (Fe3O4) nanoparticles,\r\nvia two separate strategies. These materials show efficacy in removing doxorubicin,\r\ncisplatin, and epirubicin from biologically relevant solutions. A device coated with this\r\nmaterial demonstrated in vivo activity in a porcine model.
" }, { "name": "Boynton, Adam Nathaniel", "degree": "PhD", "year": "2017", "title": "Targeting DNA Mismatches with Luminescent Ruthenium Complexes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06092017-062335915", "creators": [ { "name": { "family": "Boynton", "given": "Adam Nathaniel" }, "id": "Boynton-Adam-Nathaniel", "display_name": "Boynton, Adam Nathaniel" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9CF9N5M", "abstract": "DNA base pair mismatches occur naturally in cells, typically as a result of errors during replication. Cells have evolved a DNA damage response pathway called mismatch repair (MMR) that identifies and corrects base pair mismatches in newly synthesized DNA. However, proteins involved in MMR can undergo mutations, rendering them incapable of correcting mismatches. Such deficiencies in MMR leads to an increase in genetic mutations and are associated with several forms of cancer. Because a higher mismatch frequency serves as an early indicator of cancer progression, DNA mismatches are a promising target in the design of small molecule therapeutics and diagnostics. In this context, transition metal complexes are prime candidates, owing to their\u00a0valuable spectroscopic and photophysical properties and versatile coordination sphere geometries. Our laboratory focuses on generating octahedral rhodium and ruthenium complexes that selectively target DNA mismatches. A class of rhodium complexes bearing sterically expansive planar ligands bind DNA mismatches with high selectivity and exhibit preferential cytotoxicity towards MMR-deficient cancer cells. These compounds bind to DNA through metalloinsertion, in which the bulky ligand inserts into the duplex at the thermodynamically destabilized mismatch site, displacing the mismatched bases into the DNA groove.
\r\n\r\nHerein we describe recent advances in the development of luminescent ruthenium complexes that selectively probe DNA mismatches. We demonstrate that [Ru(Me4phen)2(dppz)]2+ (Me4phen = 3,4,7,8-tetramethyl-1,10-phenanthroline; dppz = dipyrido[3,2-a:2\u2019,3\u2019-c]phenazine) is a DNA \u201clight switch\u201d that exhibits a significantly brighter steady-state emission in the presence of a DNA duplex containing a mismatch relative to completely well-matched DNA. Importantly, the bulky Me4phen ancillary ligands discourage deep intercalation of dppz between well-matched base pairs, and instead, [Ru(Me4phen)2(dppz)]2+ favors metalloinsertion at thermodynamically destabilized mismatches. [Ru(Me4phen)2(dppz)]2+ possesses a higher binding affinity towards a DNA mismatch relative to well-matched base pairs, and furthermore exhibits a longer excited-state emission lifetime when bound to a mismatch compared to that when intercalated at well-matched sites; both of these observations contribute to the dramatic steady-state emission enhancement detected with the mismatched DNA duplex. Additionally, we reveal that the right-handed delta (\u2206) isomer of [Ru(Me4phen)2(dppz)]2+ is the enantiomer which imparts all mismatch selectivity, consistent with the handedness of B-form DNA.
\r\n\r\nAnother mismatch-specific luminescent probe presented in this work is [Ru(bpy)2(BNIQ)]2+ (bpy = 2,2\u2019-bipyridine; BNIQ = benzo[c][1,7]naphthyridine-1-isoquinoline). In contrast to [Ru(Me4phen)2(dppz)]2+, the BNIQ complex exploits a bulky inserting ligand that selectively undergoes metalloinsertion at a DNA mismatch. This compound too exhibits a brighter steady-state emission in the presence of a mismatched duplex compared to entirely well-matched DNA, which we attribute to the fact that [Ru(bpy)2(BNIQ)]2+ possesses nearly a 500-fold higher binding affinity for the mismatch site compared to well-matched base pairs. Taken together, [Ru(Me4phen)2(dppz)]2+ and [Ru(bpy)2(BNIQ)]2+ represent two different yet valid approaches in the rational design of mismatch-specific small molecules, one based on ancillary ligand functionalization and the other on incorporating a sterically expansive inserting ligand.
\r\n\r\nA third approach towards the design of mismatch-specific luminescent ruthenium probes that is briefly explored here is the modification of the intercalating dppz ligand of [Ru(bpy)2(dppz)]2+. Bearing a dppz ligand substituted with four methyl groups, [Ru(bpy)2(tmdppz)]2+ (tmdppz = 3,4,7,8-tetramethyl dipyridophenazine) shows no luminescence discrimination between mismatched and well-matched duplexes. This observation ostensibly arises from the fact that the appended methyl groups shield the dppz phenazine nitrogen atoms from interactions with water when intercalated within the DNA.
\r\n\r\nWith mismatch-specific luminescent metalloinsertors such as [Ru(Me4phen)2(dppz)]2+ in hand, we have commenced biological investigations to see whether these compounds can serve as luminescent proxies for rhodium metalloinsertors in MMR-deficient cancer cells. Confocal microscopy of HCT116N and HCT116O cells reveals that [Ru(Me4phen)2(dppz)]2+ does preferentially localize to mitochondria, unlike potent cell-selective rhodium complexes such as [Rh(chrysi)(phen)(PPO)]2+ (PPO = 2-(pyridine-2-yl)propan-2-ol; chrysi = 5,6-chrysenequinone diimine); however, [Ru(Me4phen)2(dppz)]2+ shows some degree of nuclear entry. Here our goal is the application of the mismatch-specific luminescent probe in co-localization experiments to investigate what proteins are involved in the DNA damage response that is activated upon metalloinsertor binding in cellulo.
\r\n\r\nThe work presented here expands beyond the study of luminescent ruthenium complexes. Amino acid conjugates of the earlier-generation rhodium metalloinsertor [Rh(HDPA)2(chrysi)]3+ (HDPA = 2,2\u2019-dipyridylamine) were synthesized. While these conjugates exhibit mismatch binding affinities comparable to other rhodium metalloinsertors, they lose cell-selective biological activity, which may arise from altered uptake and/or sub-cellular localization. Finally, preliminary investigations were conducted on [Re(CO)3(pyOEt)(dppn)]+ (pyOEt = ethyl 3-(pyridin-4-yl)propanoate; dppn = benzodipyridophenazine) and [Ru(CN)(tpy)(dppz)]+ (tpy = terpyridine; CN = cyano), which were designed as IR-active probes to study the kinetics of DNA-mediated charge transport (CT) by time-resolved infrared (TRIR) spectroscopy. While these complexes do not possess the desired spectral TRIR properties as originally intended, steady-state luminescence experiments do suggest that this donor-acceptor pair is capable of undergoing DNA-mediated electron transfer.
\r\n\r\nAltogether, this work demonstrates the versatility of transition metal complexes as non-covalent probes for DNA. Importantly, through the rational modification of their three-dimensional ligand scaffold, one can achieve site-specific recognition of clinically relevant biomarkers such as DNA mismatches.
" }, { "name": "Brand, Stephen Kramer", "degree": "PhD", "year": "2017", "title": "I. Tin Silsesquioxanes as Analogs for the Open and Closed Sites in Tin-Containing Zeotype Beta and II. Enantiomerically Enriched, Polycrystalline Molecular Sieves", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182017-134255198", "creators": [ { "name": { "family": "Brand", "given": "Stephen Kramer" }, "id": "Brand-Stephen-Kramer", "orcid": "0000-0002-0894-401X", "display_name": "Brand, Stephen Kramer" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z96T0JPX", "abstract": "The use of biomass as a resource to produce value-added products has garnered significant interest as a means of reducing reliance on fossil fuels. This task is complicated by the complex, highly functionalized nature of abundant biomass derivatives, such as glucose. Tin-containing zeolite Beta (Sn-Beta) has been investigated as a catalyst for isomerizing aldohexoses into ketohexoses through a Lewis acid mediated hydride shift (1,2-intramolecular hydride shift, 1,2-HS). Recent studies on the reactivities of Lewis base-doped and alkali-exchanged Sn-Beta samples have conclusively demonstrated that the open tin site performs the glucose isomerization reaction. With Lewis base doped Sn-Beta, glucose conversion is almost completely eliminated and product selectivity is shifted predominantly to mannose, formed through a 1,2-intramolecular carbon shift (1,2-CS). To understand the structure-activity relationships between the conditions of the active sites in the zeolite, three molecular models (tin silsesquioxanes) of the tin sites in the zeolite are synthesized. Two tin silsesquioxanes that contain an octahedral tin site with and without an adjacent silanol group are prepared and used as catalysts for the reaction of glucose. The catalyst that contains the adjacent silanol group selectively forms fructose through a 1,2-HS while the catalyst without the silanol group yields mannose through a 1,2-CS. These results provide further evidence for the nature of the active sites in Sn-Beta. A methyl-ligated tin silsesquioxane is experimentally and theoretically examined to examine possible reactivities at the closed site. This compound is an active glucose conversion catalyst that selectively produces mannose, although the rates of reaction are far below those obtained from Sn-Beta. Additionally, a hybrid quantum mechanical/molecular mechanics model is constructed, and the complete catalytic cycle is computationally examined via considering ring-opening, three distinct pathways for each hydride- and carbon-shift reaction, and ring-closing. The combined experimental and computational results suggest that there could be reaction pathways that involve Si-O-Sn cleavage that give much slower reaction rates than the open tin site in Sn-Beta.
\r\n\r\nZeolite and zeolite-like molecular sieves are being used in a large number of applications such as adsorption and catalysis. Achievement of the long-standing goal of creating a chiral, polycrystalline molecular sieve with bulk enantioenrichment would enable these materials to perform enantioselective functions. In part II of this thesis, the synthesis of enantiomerically enriched samples of a molecular sieve is reported. Enantiopure organic structure directing agents (OSDAs) are designed with the assistance of computational methods, and used to synthesize enantioenriched, polycrystalline molecular sieve samples of either enantiomer. Computational results correctly predicted which enantiomer is obtained, and enantiomeric enrichment is proven by high-resolution transmission electron microscopy. The enantioenriched and racemic samples of the molecular sieves are tested as adsorbents and heterogeneous catalysts. The enantioenriched molecular sieves show enantioselectivity for the ring opening reaction of epoxides and enantioselective adsorption of 2-butanol (R enantiomer of the molecular sieve shows opposite and approximately equal enantioselectivity from the S enantiomer of the molecular sieve, while the racemic sample of the molecular sieve shows no enantioselectivity).
\r\n" }, { "name": "Chapman, Lauren Marie", "degree": "PhD", "year": "2017", "title": "Development of a Synthetic Strategy Toward Trans-Cyclobutane-Containing Natural Products: Enantioselective Total Synthesis of (+)-Psiguadial B", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-010024254", "creators": [ { "name": { "family": "Chapman", "given": "Lauren Marie" }, "id": "Chapman-Lauren-Marie", "display_name": "Chapman, Lauren Marie" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z90G3H5M", "abstract": "Trans-cyclobutane-containing meroterpenoids are a structurally intriguing class of natural products with a diverse array of pharmacologically interesting properties. Herein, the development of a synthetic strategy for de novo construction of the trans-cyclobutane motif is described, which has enabled the first enantioselective total synthesis of the cytotoxic natural product, (+)-psiguadial B. Specifically, we have developed a photochemical Wolff rearrangement with tandem catalytic, asymmetric addition to a ketene generated in situ. To our knowledge, this work represents the first example of this methodology used to prepare enantioenriched amides. A palladium-catalyzed, directed C(sp3)\u2013H alkenylation reaction is used to quickly build molecular complexity, and two distinct epimerization strategies permit access to either enantiomer of the natural product from a single enantiomer of organocatalyst.
\r\n\r\nIn the course of this work, three different synthetic routes toward (+)-psiguadial B were investigated and each is discussed. These studies have led to the execution of several challenging key transformations, including an ortho-quinone methide hetero\u2013Diels\u2013Alder cycloaddition with a cyclohexanone-derived enol ether, a vinyl sulfide-mediated Prins cyclization, and a modified Norrish\u2013Yang cyclization. Ultimately, the successful synthetic strategy was realized by employing a ring-closing metathesis to form the strained, 7-membered terpene framework, and a late-stage benzylic oxidation/arylation strategy to complete the core of the natural product. Finally, in an effort to apply these key strategy concepts in the context of other bioactive trans-cyclobutane-containing natural products, initial results toward a concise total synthesis of (+)-rumphellaone A are presented.
\r\n" }, { "name": "Cheung, Sheldon Ting Fong", "degree": "PhD", "year": "2017", "title": "Discovery and Development of Small-Molecule Modulators for the Sulfation of Glycosaminoglycans and Studying the Role of O-GlcNAc on CREB through Semisynthesis", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032016-103410952", "creators": [ { "name": { "family": "Cheung", "given": "Sheldon Ting Fong" }, "id": "Cheung-Sheldon-Ting-Fong", "display_name": "Cheung, Sheldon Ting Fong" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9PR7T0K", "abstract": "Glycosaminoglycans (GAGs) are sulfated polysaccharides that play key roles in many cellular processes, ranging from viral invasion and cancer metastasis to neuronal development. Their diverse biological activities stem from their complex sulfation patterns, which are tightly regulated in vivo. For instance, the GAG chondroitin sulfate (CS) has been shown to undergo regiochemical sulfation during development and after spinal cord injury. However, few tools exist to modulate specific GAG sulfation patterns and study their importance in different biological contexts. Here, we identified the first cell-permeable small molecule that can selectively inhibit GAG sulfotransferases and modify the fine structure of GAGs. We demonstrate that the inhibitor reduces GAG sulfation in vitro and in cells and reverses CS-E-mediated inhibition of neuronal outgrowth. This small molecule may serve as a useful lead compound or chemical tool for studying the importance of CS and other GAGs in normal biology and disease.
\r\n\r\nThe \u03b2-N-acetyl-D-glucosamine (O-GlcNAc) post-translational modification plays a major role in many diseases such as cancer, diabetes, and neurodegenerative disorders, but much is still unknown about its molecular-level influence on protein structure and function. Although post-translational modifications have been known to induce important structural changes in proteins, notably, no structures of O-GlcNAcylated proteins exist. The challenge of obtaining homogeneous glycoproteins bearing the GlcNAc sugar at defined sites has hindered the structural and biochemical studies of this modification. Here we have utilized a semisynthetic approach to generate a homogeneously O-GlcNAcylated form of cyclic-AMP response element binding protein (CREB) for structural and functional studies.
" }, { "name": "Chu, Crystal Kitying", "degree": "PhD", "year": "2017", "title": "Advances in Selectivity and Reactivity in Transition Metal Catalysis: Carbon\u2013Silicon Bond Formation, Wacker Oxidation, and Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-155930157", "creators": [ { "name": { "family": "Chu", "given": "Crystal Kitying" }, "id": "Chu-Crystal-Kitying", "display_name": "Chu, Crystal Kitying" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z90C4SV7", "abstract": "The development of reaction methodology and catalysts that promote challenging transformations with high yields and selectivities is presented in Chapters 2\u20134 of this thesis. The three projects discussed address challenges in cross-coupling, olefin oxidation, and olefin metathesis.
\r\n\r\nChapter 2 describes a nickel-catalyzed cross-coupling strategy for the formation of C\u2013Si bonds using unactivated alkyl halides as substrates. Reaction optimization, exploration of the substrate scope, and mechanistic studies are described. This method is unique in its compatibility with not only secondary alkyl bromides, but tertiary alkyl bromides as well. Low loadings of the nickel catalyst, the absence of an added ligand, and relative tolerance of air and moisture contribute to the efficiency and robustness of this reaction. Mechanistic studies suggest that oxidative addition proceeds through a radical intermediate, consistent with previous studies of C\u2013C bond formation.
\r\n\r\nChapter 3 describes the application of an aldehyde-selective Wacker oxidation to allylic fluoride substrates to produce beta-fluorinated aldehydes with remarkably high regioselectivities. Efficient anti-Markovnikov oxidation of allylic fluorides bearing a variety of functional groups was possible with reduced loadings of palladium, copper, and nitrite catalysts. In order to highlight the utility of this methodology, further derivatization of the aldehyde products to diverse fluorinated products is described. Mechanistic studies demonstrate the role of inductive effects in enhancing the regioselectivity of oxidation.
\r\n\r\nChapter 4 investigates the synthesis, characterization, and reactivity studies of a new class of second-generation ruthenium olefin metathesis catalysts bearing aminophosphine ligands. The incorporation of P\u2013N bonds into the dissociating phosphine ligand results in trends in catalyst initiation rates and catalyst activity that reveal important considerations for ligand design. The results from kinetics experiments correlate well with computational studies, which indicate that there are significant effects derived from sterics, electronic induction, orbital overlap from the nitrogen (aminophosphine) lone pair, and ligand distortion energies that contribute to trends in phosphine dissociation.
" }, { "name": "Darnton, Tania Victoria", "degree": "PhD", "year": "2017", "title": "Structures and Reactions of Diplatinum Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04172017-185314743", "creators": [ { "name": { "family": "Darnton", "given": "Tania Victoria" }, "id": "Darnton-Tania-Victoria", "display_name": "Darnton, Tania Victoria" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NK3C2J", "abstract": "A d8\u2212d8 complex [Pt2(\u03bc-P2O5(BF2)4]4\u2212 (abbreviated Pt(pop-BF2)4\u2212) undergoes two 1e\u2212 reductions at E1/2 = \u22121.68 and Ep = \u22122.46 V (vs Fc+/Fc) producing reduced Pt(pop-B2)5\u2212 and superreduced Pt(pop-BF2)6\u2212 species, respectively. The EPR spectrum of Pt(pop-BF2)5\u2212 and UV\u2212vis spectra of both the reduced and the superreduced complexes, together with TD-DFT calculations, reveal successive filling of the 6p\u03c3 orbital accompanied by gradual strengthening of Pt\u2212Pt bonding interactions and, because of 6p\u03c3 delocalization, of Pt\u2212P bonds in the course of the two reductions. Both reduction steps proceed without changing either d8 Pt electronic configuration, making the superreduced Pt(pop-BF2)6\u2212 a very rare 6p2 \u03c3-bonded binuclear complex. However, the Pt\u2212Pt \u03c3 bonding interaction is limited by the relatively long bridging-ligand-imposed Pt\u2212Pt distance accompanied by repulsive electronic congestion. Pt(pop-BF2)4\u2212 is predicted to be a very strong photooxidant (potentials of +1.57 and +0.86 V are estimated for the singlet and triplet d\u03c3*p\u03c3 excited states, respectively).
\r\n\r\nFurther study of the electronic excited states of Pt(pop-BF2)4- in the presence of luminescence quenchers revealed Stern-Volmer type dynamic quenching of the triplet state by trialkyl and triaryl amines. Quenching of the singlet as well as the triplet was observed in the presence of CoII trisbipyridine complexes, but sample decomposition and the observed presence of simultaneous static and dynamic quenching behaviors hampered quantitative analysis.
\r\n" }, { "name": "Dong, Sijia S.", "degree": "PhD", "year": "2017", "title": "First-Principles-Based Simulations for G Protein-Coupled Receptor Activation and for Large-Scale Nonadiabatic Electron Dynamics", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032017-003321706", "creators": [ { "name": { "family": "Dong", "given": "Sijia S." }, "id": "Dong-Sijia-S", "orcid": "0000-0001-8182-6522", "display_name": "Dong, Sijia S." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z98C9T8D", "abstract": "This thesis focuses on simulating large molecular systems within and beyond the Born-Oppenheimer framework from first principles. Two approaches have been developed for very different but important applications.
\r\n\r\nThe first one is a hybrid method based on classical force fields that predicts the high-energy ensemble of three-dimensional structures of a class of proteins critical in human physiology: the G protein-coupled receptors (GPCRs). GPCRs' functions rely on their activation marked by a series of conformational changes related to binding of certain ligands, but the short of experimental structures has hampered the study of their activation mechanism and drug discovery. Our method, combining homology modeling, hierarchical sampling, and nanosecond-scale molecular dynamics, is one of the very few computational methods that can predict their active-state conformations and is one of the most computationally inexpensive. It enables the conformational landscape and the first quantitative energy landscape of GPCR activation to be efficiently mapped out.
\r\n\r\nThis method, named ActiveGEnSeMBLE, allows the inactive- and active-state conformations of GPCRs without an experimental structure to be systematically predicted. We have validated the method with one of the most well-studied GPCRs, human β2 adrenergic receptor (hβ2AR), and applied the method on a GPCR without an experimental structure, human somatostatin receptor 5 (hSSTR5). Insights on GPCR activation as well as structure prediction methods are discussed.
\r\n\r\nThe second one is a semiclassical approach for large-scale nonadiabatic dynamics of condensed systems in extreme conditions, termed Gaussian Hartree Approximated Quantum Mechanics (GHA-QM). Many nonadiabatic processes related to important applications (e.g. renewable energy) happen in large systems, but existing excited state dynamics methods are too computationally demanding for their long timescale simulations. GHA-QM is based on the electron force field (eFF) framework where we model electrons as Gaussian wavepackets and nuclei as classical point charges, and obtain a simplified solution to the time-dependent Schr\u00f6dinger equation as the equation of motion. We employ a force field philosophy approximating the total energy as a sum of electronic kinetic energies, electrostatic energies and a Pauli correction, which corrects for the lack of explicit antisymmetry in the wavefunctions. New designs of the Pauli potential and preliminary results on hydrogen systems are discussed. With the new development, we hope to improve the accuracy and range of applications of eFF to simulate the nonadiabatic dynamics of hundreds of thousands of electrons on nanosecond timescale.
" }, { "name": "Duquette, Douglas Charles", "degree": "PhD", "year": "2017", "title": "Highly Enantioselective Palladium-Catalyzed Allylic Alkylation Reactions of Carbocyclic Enaminones and Acyclic Substrates", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042017-104254217", "creators": [ { "name": { "family": "Duquette", "given": "Douglas Charles" }, "id": "Duquette-Douglas-Charles", "display_name": "Duquette, Douglas Charles" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9S46Q0P", "abstract": "This report details the studies of the palladium-catalyzed asymmetric allylic alkylation reactions of carbocyclic substrates, specifically of vinylogous amides and enaminones, resulting in the discovery of a new substrate class (enaminones) with the highest enantioselectivies observed for this catalytic system to date. Moreover, conditions were discovered and developed for the asymmetric allylic alkylation of acyclic substrates by the selective formation of fully substituted enolates and application of a novel C2-symmetric Pd ligand.
" }, { "name": "Fang, Katharine Yan", "degree": "PhD", "year": "2017", "title": "Modulating Biophysical Properties of Insulin with Non-Canonical Mutagenesis at Position B28", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03092017-164905231", "creators": [ { "name": { "family": "Fang", "given": "Katharine Yan" }, "id": "Fang-Katharine-Yan", "display_name": "Fang, Katharine Yan" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Ku", "given": "H. Teresa" }, "id": "Ku-H-T", "role": "member", "display_name": "Ku, H. Teresa" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9V40S6J", "abstract": "Non-canonical amino acids are tools for altering the chemical and physical properties of proteins, providing a facile strategy to engineer proteins with novel properties, especially where canonical amino acid mutagenesis has exhausted nearly all avenues for further optimization. Insulin, for example, is one of the most widely studied therapeutic proteins; however, non-canonical insulin engineering is a subfield that has been largely unexplored. To this end, my thesis research has focused on the use of non-canonical amino acids to understand and engineer the biophysical properties of insulin.
\r\n\r\nProtein structure and function are sensitive to the smallest of changes; even small differences such as a single atom substitution or change in stereo-orientation can cause large, unsuspected, and unpredictable global changes. Chapters 2 to 4 describe substitutions at the 4th position of proline at position 28 of insulin\u2019s B chain (ProB28) in a manner analogous to the structure-activity-relationships that are widely used in medicinal chemistry. Canonical mutagenesis at ProB28 has led to the discovery of rapid-acting insulins (RAIs): a class of therapeutic insulins with enhanced pharmacokinetic properties. Therefore, we chose to incorporate proline analogs with substitutions such as hydroxyl and fluoro groups, and different ring compositions to assess their effects on the biophysical properties (i.e. stability, dissociation rates and oligomerizations states) of insulin. Chapter 2 describes the discovery of a hydroxyinsulin variant with faster hexamer dissociation rates and enhanced stability compared to wild-type insulin in vitro. We find crystallographic evidence of a novel hydrogen bond in the insulin dimer interface which we hypothesize stabilizes the insulin dimer state. To complement the findings in chapter 2, chapters 3 and 4 detail an investigation of the importance of hydrophobic and nonpolar interactions for modulating the biophysical properties of insulin.
\r\n\r\nEstablishing structure-activity-relationships for insulin will create new opportunities for further engineering using non-canonical amino acids. In chapter 5, we describe progress towards a general, simple screening method to discover new aminoacyl-tRNA synthetases for the incorporation of non-canonical amino acids in E. coli. Implementing such a high-throughput screening system will allow scientists to perform medicinal chemistry on proteins and discover new or improved therapeutics to help manage human diseases.
" }, { "name": "Finneran, Ian Alan", "degree": "PhD", "year": "2017", "title": "Terahertz and Microwave Spectroscopy of Liquids and Hydrogen-Bonded Clusters", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03082017-151032634", "creators": [ { "name": { "family": "Finneran", "given": "Ian Alan" }, "id": "Finneran-Ian-Alan", "orcid": "0000-0003-2506-4652", "display_name": "Finneran, Ian Alan" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9348HD4", "abstract": "The microwave (MW, 0.3-100 GHz) and terahertz (THz, 0.1-10 THz) regions of the electromagnetic spectrum are replete with a rich set of molecular motions, including soft inter- and intramolecular vibrations, torsions, and rotations. At room temperature these motions are well populated, and play an active role in condensed-phase chemistry on Earth. This work details the development of one MW and two THz spectrometers along with their application to the study of liquids and hydrogen-bonded clusters.
\r\n\r\nIn the first section, we cover the design and construction of a chirped pulse Fourier transform microwave (CP-FTMW) spectrometer. The instrument relies on a compact, inexpensive direct digital synthesis board to generate 2 GHz, 1 microsecond chirped pulses that, after amplification, polarize the rotational states of gas-phase molecules in a pulsed supersonic jet. In an initial demonstration, the CP-FTMW instrument is used to collect the 8-18 GHz rotational spectra of the ethanol-water and ethanol-methanol dimers. These data reveal evidence of quantum tunneling, and a complicated interplay between weak and strong hydrogen-bonds in both dimers.
\r\n\r\nNext, we describe the ongoing development of a decade spanning high precision THz frequency comb, using THz time-domain spectroscopy. The instrument is capable of generating ~28000 comb teeth from 0.15-2.4 THz with a fractional precision of 1.8x10-9 and a Doppler-limited accuracy of 6.1x10-8. Further prospects for studies of intermolecular interactions in jet-cooled molecular clusters are also discussed.
\r\n\r\nIn the last section, we move to condensed-phase studies of THz orientational and vibrational motions of liquids. The liquids are excited with one or two intense time-delayed ultrafast THz pulses and probed with a non-resonant 40 fs Raman pulse. Initially, we use this approach to measure the picosecond molecular orientational alignment and decay timescales in several aromatic liquids. By adding a second THz pulse to the experiment and adjusting the delays between the three pulses, we control the orientational alignment of the molecules, and acquire phase-coherent 2D-THz-THz-Raman spectra in the time domain. The 2D responses of liquid CHBr3, CCl4, and CCl2Br2 show off-diagonal peaks from coupling between thermally-populated vibrational modes. In an extended bandwidth measurement, we observe photon-echo signals from liquid CHBr3 and a complicated pattern of dipole forbidden transitions. The molecular origins of the forbidden transitions are still under investigation, but are likely due to nonlinearities in the condensed-phase dipole moment surface. Coherence transfer, vibrational anharmonicity, and intermolecular coupling are also considered in this analysis.
" }, { "name": "Flowers, Cristofer Addison", "degree": "PhD", "year": "2017", "title": "Full Spectrum Ultrahigh Efficiency Photovoltaics: System Design, Integration, and Characterization", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082017-225442178", "creators": [ { "name": { "family": "Flowers", "given": "Cristofer Addison" }, "id": "Flowers-Cristofer-Addison", "orcid": "0000-0001-7864-3629", "display_name": "Flowers, Cristofer Addison" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9DF6P90", "abstract": "The sun is an immense source of power, radiating more energy than all known non-renewable reserves onto the Earth every year in the form of sunlight. In spite of this abundant availability, photovoltaic electricity conversion provides less than 1% of the of the global energy consumption. This lack of deployment is largely a consequence of the cost of photovoltaics relative to other technologies, but increased efficiency is a strong driver for cost reduction due to its ability to impact both photovoltaic module and balance of systems costs. In this thesis, we present enabling technologies for achieving increased efficiency and energy yield for photovoltaic conversion of sunlight. First, we develop finite element cell modeling and electrical contact optimization tools. These models are used to deploy unconstrained optimization techniques that expand the design space of solar cell contacts. Additionally, constrained optimization techniques are used to design solar cell electrical contacts for lateral spectrum-splitting photovoltaic submodules. The lateral spectrum-splitting submodule uses a series of filters to divide broadband sunlight into seven wavelength bands, sending each onto a solar cell with bandgap chosen to minimize thermalization and sub-bandgap transmission losses. By employing a wholistic design model covering limiting efficiency, material constraints, optical ray tracing, and electrical modeling, we generate designs capable of ultrahigh (>50%) efficiency. We then design, integrate, and prototype the first photovoltaic converter with seven unique bandgaps. Characterization of this prototype and its constituent components shows an integrated 84.5% optical efficiency and 30.2% submodule efficiency. The exemplary optical performance highlights the promise of the design with further development of the cells. Finally, we develop module circuit and power combination topologies that enable independent electrical connection to two or more subcells in a multijunction photovoltaic converter. This circuit architecture enables independent power production from each device, which reduces the module sensitivity to diurnal and seasonal spectral changes and increases panel annual energy yield. The photovoltaic technologies developed herein often break with convention and demonstrate a feasible pathway to very high (>40%) and ultrahigh (>50%) efficiency modules." }, { "name": "Glasser, Nathaniel Robert", "degree": "PhD", "year": "2017", "title": "Physiological and Biochemical Mechanisms of Phenazine-Mediated Survival in Pseudomonas aeruginosa", "advisor": "Newman, Dianne K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312017-133325449", "creators": [ { "name": { "family": "Glasser", "given": "Nathaniel Robert" }, "id": "Glasser-Nathaniel-Robert", "orcid": "0000-0002-2833-5166", "display_name": "Glasser, Nathaniel Robert" } ], "advisors": [ { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "advisor", "display_name": "Newman, Dianne K." } ], "committee": [ { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "chair", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9SN070S", "abstract": "The opportunistic pathogen Pseudomonas aeruginosa secretes a class of colorful redox-active small molecules known as phenazines. Numerous functions have been proposed for phenazines, including antibiotic activity, virulence, cell-to-cell signaling, iron acquisition, and survival. This thesis delves into mechanisms of the latter role, that of long-term survival under oxidant-limiting conditions. Using a diverse array of methods, I investigated how phenazines support survival and how cells transfer electrons to phenazines, as well as the downstream effects that phenazines have on P. aeruginosa.
\r\n\r\nDirect measurements of NAD(H), ATP, the membrane potential, and fermentation products revealed that phenazines promote redox homeostasis and subsequently ATP synthesis. The ATP is used to maintain a membrane potential through the reverse action of the ATP synthase complex. Even though P. aeruginosa does not ferment on sugars, phenazines enable the anaerobic oxidation of glucose to acetate, suggesting P. aeruginosa may have previously under-appreciated metabolic flexibility in the absence of terminal electron acceptors. Activity assays with proteins purified natively from P. aeruginosa showed that glucose oxidation might be enabled in vivo by the pyruvate dehydrogenase complex, which can directly reduce phenazines using pyruvate as an electron donor. Liquid chromatography and mass spectrometry of culture supernatants showed that phenazines alter the chain length distribution of secreted quinolones, which may have indirect downstream signaling effects. Based on this result, combined with data from survival experiments, I hypothesize that phenazine-mediated redox homeostasis promotes \u03b2-oxidation and that fatty acid metabolism contributes to long-term survival. Further analysis also showed that P. aeruginosa cultures contain several previously-unreported sulfonated phenazines. In its natural environment, P. aeruginosa undoubtedly encounters other microbial species that consume or modify its phenazines. At least one of these, a Mycobacterium, contains a pyocyanin demethylating enzyme. The X-ray crystal structure of this protein revealed a novel reaction mechanism wherein the substrate is its own electron acceptor. Together, this work illuminates some of the many ways phenazines shape microbial communities in both clinical and environmental contexts.
\r\n" }, { "name": "Griffin, Matthew Everett", "degree": "PhD", "year": "2017", "title": "Discovering Biological Roles of Glycosaminoglycans and Protein O-GlcNAcylation Using Chemical Tools", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042017-183300784", "creators": [ { "name": { "family": "Griffin", "given": "Matthew Everett" }, "id": "Griffin-Matthew-Everett", "orcid": "0000-0001-9549-4418", "display_name": "Griffin, Matthew Everett" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9610XCH", "abstract": "Carbohydrates surround nearly every cell in the human body. Glycosaminoglycans like chondroitin sulfate and heparan sulfate on the cell surface regulate protein ligand engagement and receptor activation to control a variety of biological processes including development, angiogenesis, and neuronal growth. These polysaccharides exert activity through protein binding to their diverse chemical structures. Therefore, the development of methods to tailor glycosaminoglycan populations at the cell surface with defined structures could provide novel approaches to control biological activity. Herein, two new methods to engineer the cell surface glycocalyx with known glycosaminoglycans are reported. Together, these methods provide complementary short- and long-term approaches to change carbohydrate structures at the cell surface and guide neuronal growth and stem cell differentiation. It is also critical to identify unknown protein-carbohydrate interactions that underlie biological phenomena. Studies delineating novel GAG interactions with an orphan receptor and related soluble ligands are reported herein as well as work towards understanding the biological functions of these newly discovered interactions. These results showcase the utility of chemical biology and biochemical tools to discover and modulate various GAG-protein interactions in diverse biological systems.
\r\n\r\nWithin the cell, thousands of proteins are modified by O-GlcNAc glycosylation, a process that is uniquely catalyzed by a single transferase and hydrolase pair unlike many other post-translational modifications. O-GlcNAcylation functions in many biological contexts including transcription, translation, proteostasis, and metabolism. Key to understanding its effects on these physiological phenomena is the discovery of O-GlcNAc modification sites. However, due to a number of technical challenges, O-GlcNAc proteomics has not progressed nearly as quickly as phosphoproteomics. Thus, developing new methods to enrich O-GlcNAcylated substrates and map modification sites is critical to unravel the myriad functions of O-GlcNAc. Herein, a labeling approach using a chemically cleavable tag is reported as an improved method to capture and release O-GlcNAcylated substrates. Unlike other methods, the cleavable Dde tag is quantitatively removed under mild, neutral conditions and leaves a minimal residual tag on the O-GlcNAcylated peptide to be analyzed. Moreover, the Dde linker outcompetes a previously used UV-cleavable tag both at the protein and peptide enrichment levels. Together, these results highlight the potential usefulness of this method to illuminate novel roles of O-GlcNAcylation in diverse systems.
\r\n" }, { "name": "Griffith, Adam Reid", "degree": "PhD", "year": "2017", "title": "DarwinDock and GAG-Dock: Methods and Applications for Small Molecule Docking", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:06122017-230026717", "creators": [ { "name": { "family": "Griffith", "given": "Adam Reid" }, "id": "Griffith-Adam-Reid", "display_name": "Griffith, Adam Reid" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z91Z42GS", "abstract": "Computational modeling is an effective tool in studying complex biological systems. Docking of small molecule ligands in particular is useful both in understanding the functioning of proteins as well as in the development of pharmaceuticals. Together with experiment, modeling can often provide a thorough picture of a given system. Computation can often provide details that are difficult or impossible to determine experimentally, while experiments provide guidance on what calculations are useful or interesting. Our goal is to extend computational modeling, specifically ligand docking, to systems not previously possible, such as the challenging glycosaminoglycan (GAG) systems. In order to do this it was first necessary to develop an automatic way of performing docking without extensive user input and experimental knowledge to narrow the list of candidate poses. DarwinDock represents our efforts in this respect. It is a method for small-molecule docking that separates pose generation and scoring into separate stages, which allows for complete binding site sampling followed by efficient, hierarchical sampling. Our convergence criteria for complete sampling allows for diverse systems to be studied without prior knowledge of how large a set of poses needs to be to span a given binding site, making the procedure more automatic. We also replace bulky, nonpolar residues with alanine, which we refer to as \"alanization\". This allows the ligand to interact more closely with polar sidechains, which help to orient the ligand. Additionally, alanization reduces the impact of incorrect sidechain placement on ligand placement, a concern that sometimes requires user intervention. With DarwinDock working for standard small molecules, it was then necessary to modify the procedure to work on challenging GAG ligands, which are large and have strong negative charges. A modification to DarwinDock \u2013 GAG-Dock \u2013 allows the method to be applied to GAGs and protein surface interactions. GAGs are large, linear polysaccharides with strong negative charge. They typically interact with the surfaces of proteins, rather than the cavities favored by most small-molecule drugs. GAG-Dock systematically samples the protein surface for unknown binding sites and modifies the pose generation to allow for large, surface-interacting ligands. GAG-Dock allowed us to study several systems important for neuronal development and answer interesting questions posed by experiment. Finally, we needed a way to validate our predictions for GAG binding sites. We used a systematic approach to identify sets of beneficial mutations to the GAG binding sites by building up from individual in silico mutations. Standard mutation experiments typically employ large mutations, such as arginine to alanine, which decrease or destroy binding. However, such information is not always definitive, as large mutations can have wide-ranging effects beyond direct protein-ligand interactions. Mutations that increase binding, however, are less ambiguous because they must form new interactions with the ligand in order to affect binding energies or affinity. Therefore, we have identified and proposed sets of mutations for our GAG predictions for PTPs, NgR1, NgR3, and EphB3. We encourage our experimentalist colleagues to try these mutations and validate our predictions.
" }, { "name": "Guo, Shaobin", "degree": "PhD", "year": "2017", "title": "Prototyping Diverse Synthetic Biological Circuits in a Cell-Free Transcription-Translation System", "advisor": "Murray, Richard M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03082017-163613964", "creators": [ { "name": { "family": "Guo", "given": "Shaobin" }, "id": "Guo-Shaobin", "orcid": "0000-0001-9736-4078", "display_name": "Guo, Shaobin" } ], "advisors": [ { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "advisor", "display_name": "Murray, Richard M." } ], "committee": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "chair", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Goentoro", "given": "Lea A." }, "id": "Goentoro-L-A", "role": "member", "display_name": "Goentoro, Lea A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9CR5RDK", "abstract": "Synthetic biological circuits are the foundation for the ultimate goals of controlling cells and building artificial cells from the ground up. To get closer to these goals in a more efficient way, we utilize a cell-free transcription-translation system to help perfect biological circuits for the simplicity, freedom, and convenience that the system offers. In this thesis, we demonstrate three distinct aspects of biological circuits in a cell-free transcription-translation system: circuit dynamics, phosphorylation, and membrane proteins. We start with a simple feedforward circuit, which shows dynamic responses to the input. We first prototype the feedforward circuit in the cell-free system with the aid of mathematical modeling. Then, based on the knowledge learned from prototyping, we successfully implement the circuit in cells. Not only do we show that a circuit with dynamics can be prototyped in the cell- free system, but we also test a more complicated circuit involving a phosphorylation cycle. The phosphorylation-based insulator circuit is prototyped and then a model created for the circuit is shown to be identifiable in the cell-free system. To further expand the capability of the cell-free system, we demonstrate that biologically active membrane proteins can be generated in the cell-free system with engineering, suggesting that even biological circuits requiring membrane proteins can be prototyped in the system. These results help advance our knowledge of both biological circuits and the cell-free transcription-translation system, and bring us one step closer to our ultimate goals of implementing control theory in synthetic biology." }, { "name": "Hedelius, Jacob K.", "degree": "PhD", "year": "2017", "title": "What Can We Infer About the Atmospheric Composition Within the South Coast Air Basin from Remote Sensing?", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142017-135033314", "creators": [ { "name": { "family": "Hedelius", "given": "Jacob K." }, "id": "Hedelius-Jacob-K", "orcid": "0000-0003-2025-7519", "display_name": "Hedelius, Jacob K." } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9862DGR", "abstract": "To observe a change in a gas (e.g., CO2) flux from an area, the change must exceed the error of the flux estimate. Changing bias could be misinterpreted as a change in flux, and should be avoided. Errors can arise in column CO2 (XCO2) retrievals, in mis-interpreting XCO2 variations, or in the models to estimate fluxes. My thesis work has focused on recognizing and quantifying these errors and biases.
\r\n\r\nThe most widely-used ground-based observations of XCO2 are from the Total Carbon Column Observing Network (TCCON), which uses observations from similar spectrometers at high (0.02 cm-1) resolution. Within the past 5 years there has been increased use of portable, lower resolution (0.5 cm-1) spectrometers for focused, short-term campaigns. This thesis discusses sources of errors and biases in retrievals from these lower resolution spectrometers.
\r\n\r\nPrevious error estimates for the TCCON were made by propagating various perturbations through the retrieval. These uncertainty estimates were about 0.2 % for CO2 and 0.4 % for CH4. A pair of portable 0.5 cm-1 resolution spectrometers were used to empirically diagnose the magnitude of bias among TCCON sites. Median estimates were about 0.1 %.
\r\n\r\nColumn measurements have increased in popularity within the last 15 years because of their reduced sensitivity to the dry mole fractions (DMF) of gases near the surface. However, in the presence of a sharp gradient between the atmospheric mixed layer (ML) and free troposphere rapid changes in terrain may cause the ML height above ground level and XCO2 to vary significantly over a small area. This explains ~20-36 % of the difference in XCO2 between 2 sites (Caltech and JPL) within 10 km of each other in the South Coast Air Basin (SoCAB).
\r\n\r\nDynamical models may have biases (e.g., in wind speed) compared to true atmospheric behavior. This may cause biases in flux estimates. An estimate of the SoCAB CO2 flux using readily available model data is higher than those reported by bottom-up methods, perhaps due to a high wind speed bias. The flux is also sensitive to sub-sampling, which highlights the need to filter out biased data and the benefits additional observations could provide.
\r\n\r\nCarbon dioxide is not the only radiative forcer---aerosols are the largest source of uncertainty on the global radiative forcing budget, and additional measurements may better constrain their impacts. Estimate of changes in aerosol optical depth (AOD) can be made using portable spectrometers. While these estimates are not highly accurate, they are a value-added product and may increase the understanding of atmospheric behavior.
" }, { "name": "Henning, Ryan Kenneth", "degree": "PhD", "year": "2017", "title": "Targeting Undruggable Oncoprotein Epitopes with Protein Catalyzed Capture Agents", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022017-070813473", "creators": [ { "name": { "family": "Henning", "given": "Ryan Kenneth" }, "id": "Henning-Ryan-Kenneth", "orcid": "0000-0002-3783-2455", "display_name": "Henning, Ryan Kenneth" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "orcid": "0000-0003-0923-3284", "role": "member", "display_name": "Hoelz, Andre" }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "orcid": "0000-0002-3671-9354", "role": "member", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9CJ8BJG", "abstract": "The protein catalyzed capture (PCC) agent platform provides a new strategy to develop peptide-based ligands for difficult protein targets. This approach utilizes the target-guided in situ click reaction to allow the protein of interest to assemble its own binder. Developing a PCC agent begins with an epitope targeting strategy to develop anchor candidates against a specific region of interest on the target protein. This approach has been used to target diverse epitopes including unstructured hydrophobic regions, allosteric enzyme sites, and single amino acid point mutations. The process can then be iterated to expand a monoligand into a multiligand binder with affinity and selectivity that rivals monoclonal antibodies.
\r\n\r\nOne disease-associated protein of particular importance is the serine/threonine kinase Akt. Akt is a key regulator of signal transduction pathways and is implicated in many disease such as cancer, diabetes, and neurodegeneration. Several ligands for Akt have been developed recently with the PCC agent screening approach. PCC agents now exist that can alter Akt enzymatic activity, detect its position in the cell, identify mutations within the protein, and even cause its destruction within the cell. The first part of this thesis summarizes the prior efforts to develop PCC agents against Akt and then describes new applications for these reagents while the latter part describes efforts to develop new PCC agents against another interesting target.
\r\n\r\nChapter 1 provides a summary of the technology and describes how it has be utilized thus far. Chapter 2 describes how a PCC agent was used as an imaging probe capable of detecting Akt membrane localization. Chapter 3 provides several examples of the modularity of PCC agents and demonstrates how they can be used to influence a target protein in cells. A pair of allosteric Akt modulators were functionalized with a cell penetrating peptide for cellular delivery and were subsequently used to activate or inhibit Akt enzymatic activity. PCC agents can also be used as a targeting moiety to deliver a specific signal to a protein. When functionalized with a degradation tag the Akt-binding capture agents caused the protein to be degraded. This provides another demonstration of the usefulness of Proteolysis Targeting Chimeric Molecules, or PROTACs, in destroying disease-associated proteins. Finally, Chapter 4 describes the development of PCC agents against the oncoprotein K-RasG12D and how these molecules can be used to target this protein in new ways.
" }, { "name": "Herrera, Nadia", "degree": "PhD", "year": "2017", "title": "Structure and Function of the Mycobacterial Mechanosensitive Channel of Large Conductance, MscL\r ", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162017-130844945", "creators": [ { "name": { "family": "Herrera", "given": "Nadia" }, "id": "Herrera-Nadia", "orcid": "0000-0003-4157-9429", "display_name": "Herrera, Nadia" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9JH3J77", "abstract": "MscL is a ubiquitous channel found in bacterial membranes. It provides a protective response to osmotic downshock by opening and closing in response to tension in the membrane. A number of studies have aimed to develop a mechanism for the gating of MscL in E. coli, but structural details describing the process have remained elusive. A few structures of non-conducting states of MscL have been solved using X-ray crystallography, Mycobacterium tuberculosis (Mt) MscL and Staphylococcus aureus (Sa) MscL with a C-terminal domain truncation. In addition, the structure of the E. coli (Ec) MscL C-terminal cytoplasmic domain has been solved.
\r\n \r\nThe goals of the studies presented in this thesis are as follows: (i) capturing a C-terminal domain truncation of MtMscL using X-ray crystallography, and (ii) analyzing the functional regulation of MscL channels in mycobacteria. To achieve the latter goal, we generated a knockout of the mscL gene in a fast-growing mycobacteria species, Mycobacterium smegmatis. This strain was used to analyze the role of MscL in the cell during antibiotic entry. Structural studies of MtMscL are focused on identifying the role of the C-terminal domain by studying a channel with a truncation at the C-terminal domain. The motivation for this goal comes from the structure of SaMscL, which showed that truncation of the C-terminal domain resulted in crystallizing the protein as a tetramer, an alternative oligomeric state to the pentameric state observed for the MtMscL structure. Studies on an MtMscL C-terminal domain truncation aimed to further establish that correlation. This protein was overexpressed in E. coli BL21 DE3 mscL-, purified, and crystallized by sitting drop vapor diffusion. Native crystals diffracted to 6.5 \u00c5, and heavy atom derivative crystals diffracted to 5.8 \u00c5. The structure of the MtMscL C-terminal truncation has been solved, and is presented in this thesis. Our studies on the structure show that the pentameric state of the channel remains intact upon truncation of the C-terminal domain. To analyze the function of our mutant, we utilized patch clamp electrophysiology studies using our expression strain as the giant spheroplast platform. The findings from the electrophysiology studies indicate that MtMscL C-terminal domain truncation results in a channel that has gating tension requirements similar to EcMscL, whereas full-length MtMscL has much higher gating tension requirements than our construct. In addition, the role of MscL in mycobacterial antibiotic susceptibility is being tested in Mycobacterium smegmatis. We have created a strain of M. smegmatis with the mscL gene knocked out, MC2155 mscL- and we have observed that upon deletion of mscL an increase in tolerance to spectinomycin is observed in our knockout strain.
" }, { "name": "Hong, Yun-Hua", "degree": "PhD", "year": "2017", "title": "Theory of Dynamical Processes in Semiconductor Quantum Dots", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08102016-154641607", "creators": [ { "name": { "family": "Hong", "given": "Yun-Hua" }, "id": "Hong-Yun-Hua", "orcid": "0000-0002-5868-8827", "display_name": "Hong, Yun-Hua" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z99G5JT3", "abstract": "The focus of this dissertation is on the theory of the electronic dynamical processes in semiconductor quantum dots (QDs). The first part of the dissertation introduces the calculation method of electronic eigenstates used through the dissertation, the sp3s* tight-binding (TB) method, and the application of the symmetry-adapted linear combination (SALC) of atomic orbitals to the TB method. The combination of the SALC and TB method reduces the computational load, and generates reliable electronic eigenstates and eigenvalues of Wurtzite CdSe QDs. The second part of the dissertation uses the calculated eigenstates and eigenvalues of CdSe QDs, whose band gap states are removed by a passivation layer, to calculate various kinds of physical properties, such as the structure, the permanent dipole moment, the band gap, the molecular orbitals, the density of states (DOS), and the absorption spectrum. These calculated results are compared with the respective experimental measurements in further discussions. The last part of the dissertation focuses on the studies of the size-dependent trend of the Auger electron-hole recombination process that causes the semiconductor QDs to remain in the dark state, including the cases of a negative trion, a positive trion, and a biexciton, in semiconductor QDs. The rates of these Auger processes are expressed in the form of Fermi\u2019s golden rule, where the Coulombic interaction between the two electrons is the operator. Although the calculated results shows larger size dependence than that of the experimental findings, the literature of recent experiments and theories points out potential remedies to the discrepancy by modifying the current computational setting and theory in the dissertation." }, { "name": "Hunter, Bryan Michael", "degree": "PhD", "year": "2017", "title": "Fuels and Materials from Sunlight and Water", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022017-112043547", "creators": [ { "name": { "family": "Hunter", "given": "Bryan Michael" }, "id": "Hunter-Bryan-Michael", "orcid": "0000-0001-8559-9304", "display_name": "Hunter, Bryan Michael" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9FQ9TNB", "abstract": "The urgency to develop new technologies that harness energy and natural feedstocks in a sustainable fashion has never been more apparent. With global power consumption growing at an exponential rate, only one resource is truly capable of powering the planet: the sun. Sunlight is reliable, clean, and free.
\r\n\r\nSignificant resources have been pledged to develop and refine solar energy devices that convert photons into electricity (i.e. photovoltaics), but the sun\u2019s intermittency and the poor overlap of solar irradiance with global power demand a different strategy. In light of these limitations, we have proposed a device which converts solar energy into reduced chemical fuels (e.g. dihydrogen or methane) that can be indefinitely stored and easily transported. In principle, the only required inputs are sunlight, an earth-abundant feedstock such as carbon dioxide, protons (H+), and reducing equivalents (e-). The source of these protons and electrons must be abundant and ubiquitous\u2014we chose water.
\r\n\r\nDespite the 2-billion-year history of plants performing water oxidation to produce molecular oxygen, protons, and electrons (Photosystem II), our understanding of this complex 4H+/4e- process has been severely limited. Only recently have high-performing, earth-abundant heterogeneous electrocatalysts been reported that can be scaled up to make functioning devices.
\r\n\r\nThis dissertation describes progress on both the synthetic and mechanistic fronts in developing earth-abundant heterogeneous water oxidation catalysts for solar-driven water splitting. We have synthesized nanoparticulate Ni-Fe catalysts with the highest measured activity on flat electrodes to date. We carefully characterized these materials spectroscopically to determine that edge-site iron was active in catalysis. We then undertook novel in-situ spectroelectrochemical techniques in non-aqueous media to identify the active iron species, which is surprisingly a cis-dioxo-iron(VI) corner site. The data also indicate that geminal iron-oxo coupling may be the operative mechanism of O-O bond formation, a new scheme with potential biological relevance.
\r\n\r\nFinally, we have expanded our goal to include sustainably reducing other feedstocks, such as carbon dioxide and hydrocarbons. In doing so, we aim to make pharmaceuticals, polymers, and other high-value products from sunlight and water.
" }, { "name": "Ignatowich, Michael Joseph", "degree": "PhD", "year": "2017", "title": "An Investigation of Nonstoichiometric Oxides for Solar-Driven Thermochemical Fuel Production", "advisor": "Haile, Sossina M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-162306037", "creators": [ { "name": { "family": "Ignatowich", "given": "Michael Joseph" }, "id": "Ignatowich-Michael-Joseph", "orcid": "0000-0002-0097-664X", "display_name": "Ignatowich, Michael Joseph" } ], "advisors": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "advisor", "display_name": "Haile, Sossina M." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Faber", "given": "Katherine T." }, "id": "Faber-K-T", "role": "member", "display_name": "Faber, Katherine T." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "role": "member", "display_name": "Ravichandran, Guruswami" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z92805PM", "abstract": "In order to realize energy independence and substantially combat global climate change, renewable and sustainable energy technologies must be developed. Solar energy is the most readily abundant, and if converted into a chemical fuel, could be stored and transported easily. Solar-driven thermochemical cycling is a method of chemical fuel production that shows great promise, but current state-of-the-art systems have very low efficiencies. This work discusses new reactor designs and cycling techniques using nonstoichiometric oxides that will enable more efficient solar to fuel energy conversion. Practical aspects of the reactor design are explored \u2013 specifically, thermochemical expansion of the reactive oxide, and morphologies aimed at enhancing the reaction kinetics. Additionally, doped fluorite- and perovskite-structured materials are evaluated for thermodynamic behavior and in-situ thermochemical cycling performance. Oxide morphology and new doped compounds show little improvement over previously established neat ceria due to thermodynamic limitations. The thermodynamic limit is explored in new reactor geometries and is shown to demonstrate significantly more efficient fuel production. Finally, different nonstoichiometry thermodynamics are explored to provide guidance for further material exploration, as well as applicable methodologies.
" }, { "name": "Ji, Yuewei Lucy", "degree": "PhD", "year": "2017", "title": "Organic Structure Directing Agent Free Synthesis of Small Pore Zeolite Catalysts for the Methanol-to-Olefins Reaction\r ", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192016-131948034", "creators": [ { "name": { "family": "Ji", "given": "Yuewei Lucy" }, "id": "Ji-Yuewei-Lucy", "orcid": "0000-0002-6625-4252", "display_name": "Ji, Yuewei Lucy" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9MG7MG0", "abstract": "Light olefins, ethylene and propylene, are two of the highest produced petrochemicals globally. The methanol-to-olefins (MTO) reaction is a promising route for making these chemicals from non-petroleum feedstocks such as natural gas and coal that has been successfully commercialized. The catalysts employed for this reaction are typically microporous molecular sieves with Br\u00f8nsted acidity, e.g., zeolites and silicoaluminophosphates, that generally require costly organic structure directing agents (OSDAs) to synthesize.
\r\n\r\nThis thesis explores an alternative, low cost method for synthesizing small pore zeolite catalysts for the MTO reaction without the use of OSDAs. Small pore zeolites are first synthesized in the absence of OSDAs. The resulting high-aluminum materials are then converted into useful catalysts via high temperature (500-800\u00b0C) steam treatments that extract a portion of the framework aluminum, thereby modifying the acid site concentration, pore structure and catalytic behavior of the materials. This synthesis method is demonstrated on three small pore zeolite structures that are prepared without using OSDAs: CHA, RHO and KFI. In the as-synthesized forms, these materials deactivate rapidly when evaluated as catalysts for the MTO reaction due to their high aluminum contents. Upon steam treatment, however, improved catalyst lifetimes and olefin selectivities are observed that are attributed to a decrease in the total Br\u00f8nsted acid site concentration and the creation of mesopores that facilitate transport of reactants and products.
\r\n\r\nImprovements in the activity were observed for all three of the zeolites chosen for investigation with CHA-type zeolites performing best, though differences in olefin selectivities were observed. Poisoning of acid sites located in the mesopores and on external surface of the steamed zeolites did not change the observed product distribution, suggesting that these differences do not arise from secondary reactions of olefins and instead may be attributed to differences in the pore structures.
\r\n\r\nOverall, the successful demonstration of this catalyst preparation method on three different zeolite structures suggests that it may be a useful route for converting any small pore zeolite that can be synthesized without using OSDAs into catalysts that may be useful for reactions like MTO.
\r\n" }, { "name": "Kamajaya, Aron", "degree": "PhD", "year": "2017", "title": "Structural Study of Piezo Channel, a Unique Family of Eukaryotic Mechanosensitive Channel", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07182016-144756449", "creators": [ { "name": { "family": "Kamajaya", "given": "Aron" }, "id": "Kamajaya-Aron", "display_name": "Kamajaya, Aron" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "chair", "display_name": "Lester, Henry A." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9JQ0Z00", "abstract": "Piezo is a unique family of eukaryotic mechanosensitive (MS) channel. With over 2500 amino acids per subunit, intact Piezo channel is one of the largest ion channels known to date. Two versions of Piezo can be found in vertebrates, namely PIEZO1 and PIEZO2. PIEZO1 appears to play roles in processes which control physiological homeostasis, whereas PIEZO2 assumes roles in mechanical somatosensation. A number of mutations mapped onto PIEZO1 or PIEZO2 are found in several hereditary human diseases, such as Dehydrated Hereditary Stomatocytosis, Gordon syndrome, and Distal Arthrogryposis. Although biochemical and functional studies provided many insightful findings, structural study of Piezo was very minimal. Herein, I described the structural investigation of Piezo channel. In the first study, we isolated a conserved soluble domain of Piezo (C-terminal loop 2, CTL2) from the C. elegans homolog, and provided the first molecular glimpse into this enigmatic MS channel. Subsequently, I described challenges that are associated with the expression and protein preparation of the full length Piezo channel. Recently, the full length mouse PIEZO1 structure solved by single particle cryo-EM revealed trimeric arrangement of the intact channel. CTL2 domain forms an extracellular cap which makes up the central core in this Piezo model. Lastly, we isolated a stable C-terminal fragment of Piezo. This fragment corresponds to the entire central core of Piezo channel and a few upstream transmembrane helices. This fragment can be localized to the plasma membrane. Further investigation is needed to look at the functionality of this fragment." }, { "name": "Kim, Kelly Eun-Jung", "degree": "PhD", "year": "2017", "title": "The Synthesis and Late-Stage Diversification of the Cyanthiwigin Natural Product Core and Synthetic Insights Derived Therein", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202017-173233936", "creators": [ { "name": { "family": "Kim", "given": "Kelly Eun-Jung" }, "id": "Kim-Kelly-Eun-Jung", "orcid": "0000-0002-4132-2474", "display_name": "Kim, Kelly Eun-Jung" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9KP8046", "abstract": "Inspired by the therapeutic properties of many natural products and the ever-growing need for novel medicines, research programs for the late-stage diversification of complex molecular scaffolds have risen in popularity over the past few decades. In addition to generating a wide range of non-natural compounds for biological evaluation, these research efforts provide valuable synthetic insights into the preapration and reactivity of structurally intricate molecules. After a brief summary of the various strategies for late-stage diversification, examples of previous studies toward the derivatization of natural product-inspired scaffolds are highlighted.
\r\n\r\nA second-generation synthesis of the cyanthiwigin natural product core employing recently developed technologies is described. Re-optimization of the key double asymmetric catalytic alkylation transformation facilitates large-scale operations, and application of the aldehyde-selective Tsuji\u2013Wacker oxidation enables productive recycling of an advanced intermediate. Together, these modifications expedite the preparation of the tricyclic cyanthiwigin framework on multi-gram scale.
\r\n\r\nThe aldehyde-selective Tsuji\u2013Wacker reaction is demonstrated to be effective for the oxidation of terminal alkenes bearing quaternary carbons at the allylic or homoallylic position. The synthetic utility of this method is extended through further transformation of the crude aldehyde products, permitting catalytic conversion of hindered terminal olefins to a variety of other synthetically useful functional groups.
\r\n\r\nWith access to large quantities of the cyanthiwigin natural product core, a comparative study of various methods for intermolecular C\u2013H oxidation was conducted. Examination of the reactivity of the cyanthiwigin framework under established conditions for allylic C\u2013H acetoxylation, C\u2013H hydroxylation, C\u2013H amination, C\u2013H azidation, and C\u2013H chlorination reveals significant steric and electronic influences and suggests that functionalization is guided by innate reactivity within the substrate.
\r\n\r\nFinally, the preparation of several non-natural cyanthiwigin\u2013gagunin hybrid molecules from the cyanthiwigin core is described. Preliminary studies toward the biological activities of synthetic intermediates are presented, and future directions for the synthesis of novel cyanthiwigin\u2013gagunin hybrids are outlined.
" }, { "name": "Li, Qi Wen", "degree": "PhD", "year": "2017", "title": "Biophysical Characterization of an ABC L-methionine Transporter", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022017-212739773", "creators": [ { "name": { "family": "Li", "given": "Qi Wen" }, "id": "Li-Qi-Wen", "orcid": "0000-0001-9493-2316", "display_name": "Li, Qi Wen" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goentoro", "given": "Lea A." }, "id": "Goentoro-L-A", "role": "member", "display_name": "Goentoro, Lea A." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9125QN9", "abstract": "The ATP-binding cassette (ABC) superfamily is pivotal to a number of important biochemical processes and ubiquitous in all kingdoms of life. Previous studies of ABC transporters have been heavily focused on the structural determination of the different intermediates of the transport cycle. In order to characterize the mechanism of an E. coli L-methionine transporter, which is an ABC importer, we first collated previously reported structural information on the conformational states of several well characterized ABC importers and associated binding proteins, and identified four major conformations (i.e., pre-T, outward, post-T, and inward state). We stabilized these intermediates using appropriate mutations, substrates, and nucleotides. We then studied the kinetics and thermodynamics of the formation of these states using surface plasmon resonance (BiaCore, GE Healthcare) and MicroScale Thermophoresis (NanoTemper). We developed a quantitative model that details the kinetic and molecular mechanism of E. coli MetNI. Towards this goal, we extended the Two-State, alternating access model to include other intermediates that are crucial to transport and are using this to provide a temporal understanding of transport. While this model is developed to describe the behavior of the Lmethionine MetNI importer, it may also have predictive power for other ABC Type I importers, since the NBD\u2019s response for coupling transport to ATP-binding and hydrolysis are highly conserved in this family.
" }, { "name": "Lieblich, Seth Aharon", "degree": "PhD", "year": "2017", "title": "Non-Canonical Amino Acid Mutagenesis of Position B28 In Insulin with Proline Analogs", "advisor": "Tirrell, David A.; Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112017-233327193", "creators": [ { "name": { "family": "Lieblich", "given": "Seth Aharon" }, "id": "Lieblich-Seth-Aharon", "display_name": "Lieblich, Seth Aharon" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "co-advisor", "display_name": "Tirrell, David A." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "co-advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z90Z71BD", "abstract": "Insulin is a protein hormone that is crucial for maintaining the concentration of blood glucose in vivo and is used clinically as a drug for the treatment of diabetes.
\r\n\r\nChapter I provides for an overview and background on the state of the art in insulin treatment of diabetes and the many attempts, over 95 years, to improve the pharmaceutically relevant properties of insulin and improve our understanding of the model globular protein.
\r\n\r\nChapter II demonstrates the incorporation of hydroxyproline analogs into insulin and shares the discovery of insulin with enhanced stability and an accelerated kinetic rate of dissociation. We also provide the highest resolution structure deposited in the PDB of insulin in the T2 state and the 3rd highest of any insulin to date.
\r\n \r\nChapter III extends the incorporation of proline analogs in insulin to include fluorinated insulins. We also provide, for the first time, high-resolution structures of a single globular protein systematically mutated with all possible stereoisomers of fluorination at the 4-position on a single proline residue (4S, 4R, di-substituted).
\r\n\r\nChapter IV extends the incorporation of proline analogs in insulin to include ring variant analogs. We also provide, for the first time, high-resolution structures of globular proteins containing pipecolic acid, azetidine-2-carboxylic acid and 3,4 dehydroproline in the polypeptide chain.
\r\n\r\nChapter V discusses the significance of the findings described herein and discusses future directions to undertake in further engineering insulin for improved characteristics.
\r\n\r\nThis thesis describes a systematic approach, akin to medicinal chemistry, of altering a particular protein side chain by atomistic changes. I hope that the breadth of different amino acids incorporated into a single globular protein combined with the structural, functional, thermodynamic and kinetic information contained within this set of mutants will provide future protein engineers, computational protein designers and proline enthusiasts with a wealth of new information to be used to improve our understanding of proteins and predictive power.
\r\n" }, { "name": "Lin, Daniel Hanyang", "degree": "PhD", "year": "2017", "title": "The Architecture of the Nuclear Pore Complex", "advisor": "Hoelz, Andre", "url": "https://resolver.caltech.edu/CaltechTHESIS:06092017-125142341", "creators": [ { "name": { "family": "Lin", "given": "Daniel Hanyang" }, "id": "Lin-Daniel-Hanyang", "display_name": "Lin, Daniel Hanyang" } ], "advisors": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "advisor", "display_name": "Hoelz, Andre" } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "member", "display_name": "Hoelz, Andre" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z98P5XK8", "abstract": "Nucleocytoplasmic transport, the regulated trafficking of macromolecules in and out of the nucleus, occurs primarily through nuclear pore complexes (NPCs). NPCs are massive macromolecular machines embedded in the nuclear envelope which generate ~40 nanometer transport channels to facilitate transport. Because of its size and complexity (~1000 subunits, ~120 MDa), the structure of the NPC has remained poorly understood. This thesis presents a bottom-up approach to understanding the structure and function of the NPC through reconstitution of the proteins and structural and biochemical studies. The first three chapters present work towards determining the composite structure of the symmetric core of the NPC. X-ray crystal structures are described for many of the components of the symmetric core. This includes a heterohexameric coat nucleoporin complex containing Nup120, Nup85, Nup145C, Sec13, Seh1, and Nup84, revealing how these proteins assemble into one of the main subcomplexes in the NPC. Reconstitution of the symmetric core components and analysis of the protein-protein interaction between the components provides a detailed biochemical map for the protein interaction network in the NPC. X-ray crystal structures of overlapping fragments facilitate the generation of accurate atomic model for full-length proteins. An iterative, sequential docking approach is developed to dock these models into a cryoelectron tomographic reconstruction of the human NPC, yielding a composite model for the structure of the symmetric core of the NPC. In the next two chapters, this analysis is extended to the cytoplasmic-specific decorations of the NPC. The structure of the C-terminal domain of Nup358 is reported and its catalytic activity is described. Lastly, reconstitution of human DDX19 activation by the NPC reveals mechanistic insight into how the NPC directly regulates the last step of mRNA export." }, { "name": "Liontas, Rachel", "degree": "PhD", "year": "2017", "title": "Controlling Deformability in Metallic Glass Nanopillars and Nanolattices", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132016-104159178", "creators": [ { "name": { "family": "Liontas", "given": "Rachel" }, "id": "Liontas-Rachel", "orcid": "0000-0001-9925-9466", "display_name": "Liontas, Rachel" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Johnson", "given": "William Lewis" }, "id": "Johnson-W-L", "role": "member", "display_name": "Johnson, William Lewis" }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "member", "display_name": "Greer, Julia R." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9028PHX", "abstract": "Metallic glasses offer desirable mechanical properties, including high strength, hardness, and elasticity. In bulk, they suffer from catastrophic failure upon mechanical loads. However, ductility may emerge upon (1) reducing the characteristic dimension of the metallic glass to the nanoscale or (2) irradiating the metallic glass. These two methods of controlling metallic glass deformability are investigated through a host of mechanical experiments on metallic glass nanopillars and nanolattices before and after irradiation. The mechanical experiments are conducted inside a scanning electron microscope to allow simultaneous mechanical loading and visualization of nanoscale deformation behavior.
\r\n\r\nSuch experiments reveal that helium irradiation of electrodeposited Ni73P27 metallic glass tensile nanopillars increases plasticity by a factor of two with no sacrifice in strength. Other tensile experiments on Zr-Ni-Al metallic glass nanopillars in as-sputtered and annealed states reveal substantial ductility, highly dependent upon both the nanopillar size and processing conditions. Molecular dynamics simulations, transmission electron microscopy, and synchrotron x-ray diffraction are used to explain the observed mechanical behavior through changes in free volume and short-range order.
\r\n\r\nLarger nanolattice structures are fabricated to contain hollow beams of metallic glass, with beam wall thicknesses in the nanoscale size range that may allow proliferation of the beneficial \u201csmaller is more ductile\u201d size effect observed in metallic glass nanopillars. Compression experiments on Zr-Ni-Al metallic glass nanolattices reveal enhanced deformability as the nanolattice wall thickness is reduced and upon irradiation. This work points to metallic glass nanolattices as promising candidates for radiation-intensive applications and demonstrates that by fabricating the metallic glass in a nanolattice architecture the beneficial nanoscale size effect in deformability can be preserved.
\r\n" }, { "name": "Mertens, Laura Anna", "degree": "PhD", "year": "2017", "title": "Experiments on Gas Phase Chemistry with High Sensitivity Laser Spectroscopy", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172016-103350209", "creators": [ { "name": { "family": "Mertens", "given": "Laura Anna" }, "id": "Mertens-Laura-Anna", "display_name": "Mertens, Laura Anna" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z95X26XD", "abstract": "Gas phase chemistry is important to many environments on Earth and beyond. The Earth\u2019s atmosphere is dominated by free radical reactions that, when perturbed by pollution, can lead to serious environmental problems like stratospheric ozone depletion and urban smog. Outside Earth, many other planetary atmospheres are affected by gas phase, radical chemistry, including the atmosphere of Saturn\u2019s Moon Titan. Gas phase chemistry in interstellar clouds can synthesize the molecular building blocks of our universe. Studying gas phase chemistry has also led to basic chemical knowledge of how chemical reactions proceed and how intermolecular forces work.
\r\n\r\nThis work is dedicated to studying gas phase chemical reactions with high-sensitivity laser spectroscopy. Laser spectroscopy can be a sensitive and selective way to detect gas phase species. Since laser pulses can both create reactants and detect the products, laser techniques allow the study of chemical kinetics in real time. Consequently, many different laser techniques have been developed to study gas phase chemistry. This thesis is divided into two sections: a longer first section on my work at the California Institute of Technology in Pasadena, CA and a smaller second section based on my work at the Universit\u00e9 de Rennes 1 in Rennes, France. These two sections, while on different topics \u2013 atmospheric chemical reactions and collisional rotational energy transfer at ultra-low temperatures \u2013 are united by their study of gas phase with laser spectroscopy, which shows the breadth of this experimental approach. This thesis will both look at kinetics (the rate of chemical reactions) and product yield of chemical reactions, both key pieces of information to modeling gas phase reactions.
\r\n\r\nThe first part of this work outlines my work at the California Institute of Technology, studying atmospheric radical chemistry with cavity-ringdown spectroscopy (CRDS). Chapter 1 put this work in a broader picture of current scientific work on Earth\u2019s atmosphere. Chapter 2 provides a detailed description of our cavity-ringdown spectrometer and temperature-controlled flow cell. Next, I discuss work on three important atmospheric reactions: the isomerization of simple alkoxy radicals (Chapter 3), the reaction of HO\u2082 with NO (Chapter 4), and the reaction of OH with NO2 (Chapter 5).
\r\n\r\nThe second, and smaller, part of this work, contains one chapter \u2013 chapter 6 \u2013 on work done at the Universit\u00e9 de Rennes 1, which describes work on the rotational energy transfer in collisions between CO and Ar at temperatures from 293 to 30 K with infrared-vacuum ultraviolet double resonance CRESU experiments.
" }, { "name": "Mock, Jee Young", "degree": "PhD", "year": "2017", "title": "The Bag6 Complex: Biological Complexity through Modularity", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052017-184553539", "creators": [ { "name": { "family": "Mock", "given": "Jee Young" }, "id": "Mock-Jee-Young", "orcid": "0000-0002-4656-3357", "display_name": "Mock, Jee Young" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z91C1TXQ", "abstract": "Proper synthesis and targeting of membrane proteins that contain hydrophobic transmembrane domains are mediated by chaperones and targeting factors. Tail-anchored (TA) proteins are a special class of membrane proteins that are characterized by a single carboxy (C) terminal helix that anchors them to biological membranes. Fungal Guided Entry of Tail-anchored protein (GET) pathway components, which include four soluble proteins\u2014Sgt2, Get3, Get4, Get5\u2014and two membrane bound receptors\u2014Get1 and Get2\u2014mediate TA biogenesis. These proteins maintain TA protein solubility in the aqueous cytosol and target TA to the endoplasmic reticulum. While most of the components are conserved in metazoans, one additional protein, Bag6, reorganizes the sorting complex from the heterotetrameric Get4-5 to the heterotrimeric Bag6-TRC35-Ubl4A. To understand the molecular architecture and mechanism of the Bag6 complex, we took a multidisciplinary approach that combines x-ray crystallography, biochemical reconstitution, and cell biology. Our studies demonstrate that the BAG domain of Bag6 is not a canonical BAG domain. Instead, main role of the Bag6 'mock' BAG domain is to dimerize with Ubl4A. Furthermore, the truncated Bag6 complex defined in this study is sufficient to facilitate substrate transfer from SGTA to TRC40. Lastly, our results unequivocally establish TRC35 as a cytoplasmic retention factor for Bag6. These results provide structural, biochemical and cell biological bases for modular Bag6 function and regulation of nucleocytoplasmic distribution of Bag6 by TRC35." }, { "name": "Morrison, Christine Nichole", "degree": "PhD", "year": "2017", "title": "Insights into the Mechanism of Biological Nitrogen Fixation through Characterization of the Nitrogenase Molybdenum-Iron Protein", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112017-113214704", "creators": [ { "name": { "family": "Morrison", "given": "Christine Nichole" }, "id": "Morrison-Christine-Nichole", "orcid": "0000-0002-4180-8407", "display_name": "Morrison, Christine Nichole" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z95B00HX", "abstract": "Nitrogen fixation, the process of converting dinitrogen to ammonia, is performed industrially and biologically by the Haber-Bosch process and nitrogenase, respectively. The resulting ammonia is largely used as fertilizer. Since there is a finite amount of ammonia produced by nitrogenase, we are heavily dependent on the Haber-Bosch process \u2013 only two-fifths of the world\u2019s population could be fed without it. Although the importance of the Haber-Bosch process cannot be overstated, our dependence on it has several drawbacks, including significant energy costs (~5% of the annual natural gas consumption), greenhouse gas emissions, and nitrate runoffs. By understanding the biological mechanism of nitrogen fixation, we may be able to (1) develop more efficient nitrogen fixing catalysts to replace those in the Haber-Bosch process or (2) express de novo nitrogen fixing proteins in plants so crops can essentially fertilize themselves. The projects described in this thesis aim to contribute to our understanding of the mechanism of biological nitrogen fixation through structural studies of nitrogenase. Nitrogenase consists of the iron and molybdenum-iron (MoFe) proteins, the latter of which contains the active site, the FeMo-cofactor. Throughout my work, I compare the MoFe proteins from Azotobacter vinelandii (Av1) and Clostridium pasteurianum (Cp1), the two most structurally divergent molybdenum nitrogenases known. Determining the similarities and differences between these proteins may aid our understanding of biological nitrogen fixation. My first project (Chapter III) compares a 1.08 \u00c5 Cp1 X-ray structure to a previously published 1.0 \u00c5 Av1 structure. I determined that the center atom of the Cp1 FeMo-cofactor is carbon, showing conservation of cofactor structure among molybdenum nitrogenases. Next, I compared substrate pathways in Av1 and Cp1 via Xe pressurization and identification of small molecule binding sites (Chapter IV). My most significant results include the structural and electronic characterization of a reversible protonated resting state of Av1 and Cp1 (Chapter VII).
" }, { "name": "O'Connor, Nicholas R.", "degree": "PhD", "year": "2017", "title": "Methodological Developments and Synthetic Applications of Strained Rings and Allylic C-H Functionalization of Hindered Substrates", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03072017-164212272", "creators": [ { "name": { "family": "O'Connor", "given": "Nicholas R." }, "id": "O'Connor-Nicholas-R", "display_name": "O'Connor, Nicholas R." } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9JS9NF6", "abstract": "Formal dipolar cycloadditions of cyclopropanes and aziridines are useful methods for the formation of carbo- and heterocycles. Given our group\u2019s previous interest in this area, we sought to expand the scope of strained ring cycloadditions by employing heterocumulenes as dipolarophiles. This thesis describes our development of Lewis acid catalyzed formal (3 + 2) cycloadditions between donor\u2013acceptor cyclopropanes and isocyanates, isothiocyanates, and carbodiimides to furnish various five-membered heterocycles. Enantioenriched cycloadducts can be accessed through a stereospecific reaction if enantiopure substrates are employed. We also present a method to access more highly nitrogenated heterocycles by replacing donor\u2013acceptor cyclopropanes with activated aziridines. These aziridines react smoothly with isothiocyanates and carbodiimides in the presence of zinc Lewis acids to afford iminothiazolidine and iminoimidazolidine products in good yields. Our efforts to apply a cyclopropane cycloaddition toward the total synthesis of the indole alkaloid calophyline A are also described.
\r\n\r\nIn addition, a method for the activation of sterically hindered allylic C\u2013H bonds is presented. Despite numerous recent advances in the functionalization of allylic C\u2013H bonds and the general utility of these transformations, reactions of sterically hindered substrates remain challenging. In this thesis we describe the development of a novel system for the palladium(II)-catalyzed allylic C\u2013H acetoxylation of \u03b1-allyl lactams. We believe the lactam moiety may act as a directing group to aid in the palladation of these generally unreactive substrates. During optimization, we also discovered enal products were formed if water was added. These conditions represent the first example of a transition metal catalyzed C\u2013H oxidation system with tunable selectivity over the extent of oxidation.
\r\n" }, { "name": "Orazov, Marat", "degree": "PhD", "year": "2017", "title": "Development and Characterization of Catalytic Systems for Biomass-Derived Chemical Feedstocks", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07202016-150438490", "creators": [ { "name": { "family": "Orazov", "given": "Marat" }, "id": "Orazov-Marat", "orcid": "0000-0003-1621-1331", "display_name": "Orazov, Marat" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9X63JZZ", "abstract": "Heterogeneous catalysis by Br\u00f8nsted and/or Lewis acid sites isolated within microporous environments is a topic that is perpetually growing in scope and importance. While Br\u00f8nsted acid sites in zeolites have been studied and applied extensively in the petrochemical industry, new opportunities for green processes based on renewable chemical feedstocks call for applications of new microporous materials that possess Lewis acid sites (e.g., zeotypes with framework Sn, Ti, Zr, or Hf). Characterization of such materials and the specific structures of the Lewis acid sites provides insights for rational catalyst design and application.
\r\n\r\nThis work provides experimental evidence for the identities of the active sites in Sn-Beta zeotype for the 1,2-intramolecular hydride shift (1,2-HS) reaction that results in D-glucose isomerization to D-fructose, and for the 1,2-intramolecular carbon shift (1,2-CS) reaction that results in D-glucose isomerization to D-mannose. Specifically, by selective poisoning experiments, the partially-hydrolyzed, \"open\" Sn site is shown to be the active site for the 1,2-HS reaction. The participation of the proximal silanol of such an open Sn site in the 1,2-HS reaction is demonstrated thorough alkali-exchange experiments. Such experiments also reveal that the active site for the 1,2-CS reaction is an open Sn site with a cation-exchanged proximal silanol.
\r\n\r\n1,2-CS catalysts, in general, are shown to also catalyze retro-aldol reactions of hexoses at moderate temperatures (ca. 100 \u00b0C), and to be compatible with microporous 1,2-HS catalysts in tandem catalytic schemes that enable production of alkyl lactates.
\r\n\r\nFinally, the Lewis acidity of framework Zn in zincosilicate microporous materials is demonstrated through probe-molecule infrared spectroscopy. One such material is then shown to catalyze Diels-Alder cycloaddition-dehydration reactions of oxygenated furans and ethylene. To the best of our knowledge, these materials are the first heterogeneous catalysts reported to catalyze the direct formation of terephthalate esters from ethylene and dimethyl 2,5-furandicarboxylate with appreciable selectivity.
\r\n" }, { "name": "Plymale, Noah Thomas", "degree": "PhD", "year": "2017", "title": "Spectroscopic, Electronic, and Mechanistic Studies of Silicon Surfaces Chemically Modified with Short Alkyl Chains", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062016-204445939", "creators": [ { "name": { "family": "Plymale", "given": "Noah Thomas" }, "id": "Plymale-Noah-Thomas", "orcid": "0000-0003-2564-8009", "display_name": "Plymale, Noah Thomas" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9FF3QB1", "abstract": "The chemical, structural, and electronic properties of semiconductor surfaces are known to strongly influence the energetics at semiconductor interfaces. Inexpensive and scalable wet chemical modification of semiconductor surfaces provides a means to impart a desired functionality at semiconductor interfaces for the development of new devices based on precise and cost-effective chemistry. This thesis is composed of three studies that focused on identifying the spectroscopic, electronic, and mechanistic properties of reactions at Si surfaces. First, ethynyl- and propynyl-terminated Si(111) surfaces were prepared and characterized by vibrational and photoelectron spectroscopy as well as electrochemical scanning-tunneling microscopy. Ethynyl-terminated Si(111) exhibited \u2261C\u2212H, C\u2261C, Si\u2212C stretching signals and a fractional monolayer (ML) coverage (\u03a6) of \u03a6Si\u2212CCH = 0.63 \u00b1 0.08 ML and \u03a6Si\u2212OH = 0.35 \u00b1 0.03 ML. Propynyl-terminated Si(111) showed (C\u2212H)CH3 bending, Si\u2212C stretching, and C\u2261C stretching with \u03a6Si\u2212CCCH3 = 1.05 \u00b1 0.06 ML. Deprotonation of ethynyl-terminated Si(111) surfaces formed a unique surface-bound lithium acetylide that acted as nucleophile. This work provides definitive spectroscopic and microscopic evidence for the covalent attachment of ethynyl and propynyl groups to the Si(111) surface. \r\n
\r\n\r\nSecond, Si(111) surfaces were modified with 3,4,5-trifluorophenylacetylene (TFPA) groups to impart a positive dipole at the Si(111) surface. This negative surface dipole provides the necessary band-edge shift at the Si surface to maximize the interface between p-type Si and the proton reduction half reaction. Vibrational and photoelectron spectroscopy provided evidence for the attachment of TFPA groups to the Si(111) surface. Mixed methyl/TFPA monolayers were prepared and characterized using electrochemical and photoelectrochemical methods to show that the band-edge positions and open-circuit voltages were shifted positive with increasing fractional TFPA coverage on the surface. This work demonstrates that monolayer chemistry can be used to manipulate the band-edge positions of Si surfaces as a function of surface composition.\r\n
\r\n\r\nFinally, mechanistic studies of the reaction of liquid methanol with hydride-terminated Si(111) surfaces in the presence of an oxidant were carried out. Vibrational and photoelectron spectroscopy showed that acetylferrocenium, ferrocenium, and dimethyl-ferrocenium could serve as oxidants to promote an increased rate of methoxylation of the H\u2013Si(111) surface in the dark. Illumination of intrinsic and n-type surfaces resulted in an increased rate of methoxylation, resulting from a positive shift in energy of the electron quasi-Fermi level in the presence of light. The results are described in the context of a kinetic charge transfer formalism that is consistent with the experimentally observed results. This work provides a general framework to describe the kinetics of charge transfer reactions that occur on semiconductor surfaces.
" }, { "name": "Pritchett, Beau Patrick", "degree": "PhD", "year": "2017", "title": "Studies in Palladium-Catalyzed Allylic Alkylation: Enantioselective Total Syntheses of Structurally Diverse Alkaloids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232017-150306598", "creators": [ { "name": { "family": "Pritchett", "given": "Beau Patrick" }, "id": "Pritchett-Beau-Patrick", "orcid": "0000-0001-9922-9160", "display_name": "Pritchett, Beau Patrick" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ZG6Q9Q", "abstract": "Presented herein are three projects, all unified by the use of palladium-catalyzed, enantioconvergent, decarboxylative allylic alkylations to synthesize stereochemically rich, nitrogen-containing small molecules. The ubiquity of nitrogen in biologically active natural products and pharmaceutical ingredients necessitates perpetual exploration and development of relevant small molecules. Highly robust palladium-catalyzed allylic alkylation reactions of non-stabilized enolates enable the construction of sterically encumbered all-carbon quaternary and tetrasubstituted tertiary stereocenters present within such targets.
\r\n\r\nThe successful development of a novel substrate class for palladium-catalyzed allylic alkylation, namely dihydropyrido[1,2-a]indolones (DHPIs), has enabled divergent syntheses of multiple monoterpene indole alkaloids. By setting the C20 quaternary stereocenter present within these alkaloids at an early stage in the synthesis, the remaining stereocenters can be forged with exquisite levels of control. Critical to the success of this work was the identification of highly tunable and predictable cyclizations between an indole and a C2-tethered iminium moiety. Regiodivergent cyclizations were used to complete the first catalytic enantioselective total synthesis of (\u2013)-goniomitine, along with efficient formal syntheses of (+)-aspidospermidine and (\u2013)-quebrachamine. Stereodivergent cyclization strategies were then employed in total syntheses of (+)-limaspermidine and (+)-kopsihainanine A. Synthetic efforts toward the highly caged Kopsia alkaloids (\u2013)-kopsinine, (\u2013)-kopsinilam, and (\u2013)-kopsifoline G are also discussed.
\r\n\r\nLastly, the synthesis of challenging alpha-quaternary Mannich-type products was accomplished through a simple, elegant inversion of strategy. The chiral building blocks made available by this technology bear significant potential in the realm of medicinal chemistry. Furthermore, this work enabled rapid total syntheses of (\u2013)-isonitramine and (+)-sibirinine.
" }, { "name": "Rapp, Peter Butterweck", "degree": "PhD", "year": "2017", "title": "Diffusion and Molecular Association in Artificial Protein Hydrogels", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012017-074605131", "creators": [ { "name": { "family": "Rapp", "given": "Peter Butterweck" }, "id": "Rapp-Peter-Butterweck", "orcid": "0000-0002-9586-2126", "display_name": "Rapp, Peter Butterweck" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9CV4FSF", "abstract": "Artificial proteins may be programmed to reversibly self-assemble into water-soluble networks, or \u201chydrogels\u201d, by encoding them with terminal coiled-coil forming domains. Such networks are model viscoelastic materials. The well-defined molecular structures adopted by proteins, combined with their facile preparation by recombinant synthesis, invite a careful exploration of the relationship between protein sequence and the resulting network properties.
\r\n\r\nThis work explores the relationship between network reorganization and diffusion from the perspective of single chains, using artificial elastin-like proteins as a model system. We make use of fluorescence recovery after photobleaching (FRAP), a classic biophysical technique, to measure chain mobilities as a function of network structure and probe architecture. Reversible network association is demonstrated to control the effective diffusivity of network-bound chains, and a novel mechanism of chain transport is proposed: the chains naturally partition into various bound states, and move by \u201chopping\u201d from site to site in between binding events.
\r\n\r\nA careful analysis of the equilibrium constants that control this partioning leads to the conclusion that the sequential binding of identical chain ends to the network is inherently asymmetric: the first association is always stronger than the second. This binding asymmetry is shown to arise from a strong entropic penalty for chain entry into the fully bound state due to local network structure. We derive a simple equation predicting the degree of binding asymmetry as a function of network geometry from equilibrium statistical mechanics. A large set of self-diffusivity measurements on a series of model telechelic proteins finds good agreement with this new theory. Generalized binding asymmetry for chains with many associative domains also holds.
\r\n\r\nFinally, the inherent viscoelasticity of the elastin-like network is found to couple with an entropically driven phase separation above a critical temperature set point. Relaxation of the viscoelastic stress throughout the process of phase domain segregation is found to induce highly dynamic phase patterns. The time evolution of these patterns illustrates that a delicate balance of surface tension and viscoelastic stress controls pattern formation in viscoelastic materials.
" }, { "name": "Rienzo, Matthew", "degree": "PhD", "year": "2017", "title": "Non-Canonical Amino Acids As Biochemical Probes of Ligand-Gated Ion Channel Structure and Function", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09022016-105040371", "creators": [ { "name": { "family": "Rienzo", "given": "Matthew" }, "id": "Rienzo-Matthew", "orcid": "0000-0002-9389-1310", "display_name": "Rienzo, Matthew" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9G44N8W", "abstract": "This dissertation describes several different chemical-scale studies of proteins involved in cellular signaling. The primary focus of this work is on ligand-gated ion channels, an important family of membrane receptors. In each study, the incorporation of structurally diverse non-canonical amino acids have been used to attain a high level of precision in probing the mechanisms of molecular processes. The first chapter provides an introduction to the nonsense suppression methodology used to genetically encode these probes, and surveys the classes of proteins studied herein.
\r\n\r\nThe second and third chapters are concerned with the mechanism of \r\nactivation of a prokaryotic receptor, Gloeobacter violaceus ligand-gated ion channel. In these experiments, novel histidine derivatives were designed, synthesized, and incorporated to test the functional importance of acid-base titration at several positions in the receptor. Then, a battery of proline analogs were used to identify necessary structural features of several critical proline residues, providing clues to conformational changes that occur during receptor activation.
\r\n\r\nThe fourth chapter discusses studies of a different class of receptors, the Acid-Sensing Ion Channels. Several fluorinated aspartic acid and glutamic acid derivatives were targeted to modulate the acidity of putative proton binding sites. Attempts at preparation of these compounds for incorporation into proteins are detailed. Additional sections describe, efforts to elucidate factors in the binding selectivity of the tarantula venom psalmotoxin and selectivity of cation permeability.
\r\n\r\nIn the final chapter, early efforts at developing crosslinking assays for protein-protein interactions in mammalian cells are outlined. These assays involve the introduction of orthogonal tRNA/synthetase pairs for genetically encoding photoreactive phenylalanine analogs. The most successful studies involve the ligand-dependent dimerization of the soluble nuclear receptor, estrogen receptor \u03b1. However, the ultimate goal of this work is to to probe protein-protein interactions among membrane receptors and other proteins. Progress toward extension of the photocrosslinking assay into membrane receptors is described.
" }, { "name": "Rosebrugh, Lauren Estelle", "degree": "PhD", "year": "2017", "title": "Stereoselective Olefin Metathesis Processes Using Cyclometalated Ruthenium Alkylidene Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062017-172749049", "creators": [ { "name": { "family": "Rosebrugh", "given": "Lauren Estelle" }, "id": "Rosebrugh-Lauren-Estelle", "display_name": "Rosebrugh, Lauren Estelle" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9C53HVW", "abstract": "The recent development of a class of Z-selective ruthenium metathesis catalysts containing a crucial cyclometalated N-heterocyclic carbene (NHC) ligand has extended the applicability of ruthenium-mediated olefin metathesis to the production of a variety of useful Z-olefin-containing small molecules, polymers, and natural products. This thesis explores the synthesis and application of a number of novel Z-selective cyclometalated ruthenium alkylidene complexes displaying enhanced activity and selectivity across a range of metathesis transformations. Mechanistic investigations aimed at understanding and controlling stereoselectivity specifically in ring-opening metathesis polymerization (ROMP) are also detailed.
\r\n\r\nChapter 2 describes the preparation of new Z-selective cyclometalated ruthenium metathesis catalysts via an improved method employing sodium carboxylates. Effects of the cyclometalated NHC ligand on catalyst activity and selectivity in several cross metathesis assays, as well as macrocyclic ring-closing metathesis and other industrially relevant transformations, are investigated.
\r\n\r\nChapter 3 relates a story in two parts: the first details the synthesis and activity of a series of novel cyclometalated ruthenium alkylidenes displaying unprecedented cis,syndio-selectivity in the ROMP of norbornene- and norbornadiene-derived monomers. The second comprises an extensive study into the origins of stereoselectivity in ROMP in these and related cyclometalated ruthenium initiators. Experimental results are used in conjunction with a computational analysis of propagation transition states to develop a complete stereochemical model for cis,syndio-selctivity in these systems.
" }, { "name": "Roske, Christopher William", "degree": "PhD", "year": "2017", "title": "Towards a Hydrobromic Acid Splitting Device Using Earth-Abundant Materials", "advisor": "Gray, Harry B.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062016-162323180", "creators": [ { "name": { "family": "Roske", "given": "Christopher William" }, "id": "Roske-Christopher-William", "display_name": "Roske, Christopher William" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NS0RWS", "abstract": "This thesis disembarks from the traditional approach of tailoring a system to the water splitting reaction. As detailed in Chapter 2, this thesis predicts that two silicon photoelectrons connected in parallel are ideally suited to electricity storage in an integrated light collector and chemical storage device driving the splitting of hydrobromic acid (2HBr -> H2 + Br2). The predicted dual photoelectrode system could potentially obtain high solar-to-hydrogen conversion efficiencies of up to an \u03b7STH, HBr of 12 %, whereas an equivalent water splitting system is not possible due to the small band gap of silicon. Unfortunately, silicon possesses low catalytic activity for both the hydrogen evolution half-reaction and the bromide oxidation half-reaction. In the past, the electrocatalysis of silicon has been aided by using Pt/Ir alloys to act as both a protective and electrocatalytic layer. Herein, efforts are detailed to replace these precious metals, where possible, by using only earth-abundant materials to decrease the cost of a module. Our hope is that efforts along this path will aid the field of artificial photosynthesis as a whole.
\r\n\r\nWe begin by further testing a chemical insight previously noted within our group and discover a surprisingly high activity electrocatalyst for the hydrogen evolution reaction by cobalt phosphide (CoP) nanoparticles, detailed in Chapter 3. Falling on a traditional technique of increasing the surface area of particular facets, we nanostructured our crystalline CoP to increase its surface area of exposed (111) facets and hoped it would increase our catalytic activity; however, we found that simple structuring resulted in poor adhesion of nanostructures and poorer activity than our multi-faceted CoP nanocrystals (see the appendix to find out more). Our original catalysis efforts spurred a flurry of activity in the literature, and consequently, alternative devices that are more scalable arose. We detail the developments occurring since our work in the last appendix.
\r\n\r\nNow, with a potential catalyst in hand, comes the difficulty of balancing the delicate interplay between light absorption and catalysis, as detailed in Chapter 4. While CoP is active for HER, our particles possess a relatively low turnover frequency compared to hydrogenase or platinum, and thus require high mass loadings of material (2 mg/cm2) to obtain competitive extrinsic performance. Planar electrodes are incompatible with our particles because of substantial light absorption by the thick catalyst overlayer. By structuring our photoelectrode, we abnegate our catalyst limitations by exploiting the properties of microwires. High-aspect ratio microwires have shown promise as potentially low-cost materials for future photovoltaic applications as well as photocathodes functioning as part of an energy storage device. We discuss how to integrate our materials with silicon microwires (the wires were grown by an unscalable process to serve in place of functional CVD wires with radial emitters) to prototype a candidate photocathode. While a parasitic resistance limited the overall efficiency of the photocathode candidate, it still had promising stability. The parasitic resistance was addressed by electrodepositing the cobalt phosphide, thereby giving us a promising efficiency limited by the quality of the p-n junction.
\r\n\r\nWhile high-catalytic activity for the HER in acidic solutions using earth-abundant materials represents a significant advance, the photocathode is just one component of what is necessary for a complex system of splitting hydrobromic acid. Silicon, by its virtue of being a small band gap material, is easily passivated in aqueous solutions by the formation of a silicon oxide. In the past, our colleagues had shown that a monolayer of graphene could occasionally provide protection in a test solution, but batch-to-batch variability provided a considerable challenge. The putative hypothesis offered for the degradation argued defects in the crystalline graphene at grain-boundaries were the culprit. In Chapter 5 we present a method to passivate defects in the graphene crystal by light fluorination and observe a considerable enhancement in stability relative to typical graphene-protected silicon photoanodes. We had hoped that catalysis for bromide oxidation would be aided by the near-perfect graphene liquid junction, but electrodeposited Pt was required to effect photoxidation. A cursory stability test shows promising stability for one-half of an hour, but we would like to avoid using Pt. Finally, we also turned our attention to protecting silicon surfaces from oxidation by exploiting covalent silicon surface chemistry, accessible via a two-step chlorination/alkylation procedure, and explored the deposition of potentially protective thin-film metal oxides (see the appendix).
" }, { "name": "Selck, David Anthony", "degree": "PhD", "year": "2017", "title": "Microfluidics for Molecular Measurements and Quantitative Distributable Diagnostics", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292016-195927111", "creators": [ { "name": { "family": "Selck", "given": "David Anthony" }, "id": "Selck-David-Anthony", "orcid": "0000-0002-0591-4165", "display_name": "Selck, David Anthony" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "chair", "display_name": "Cai, Long" }, { "name": { "family": "Guttman", "given": "Mitchell" }, "id": "Guttman-M", "role": "member", "display_name": "Guttman, Mitchell" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ZC80XT", "abstract": "A major challenge in global health care is a lack of portable and affordable quantitative diagnostic devices. This is because classic quantification of biomolecules is typically performed using kinetic assays that require strict control only found in controlled laboratory environments. By using the power of microfluidics, quantitative assays can be performed robustly in a \"digital\" format that is decoupled from precise kinetics through highly parallelized qualitative reactions. The benefits of performing quantitative assays in a digital format extend beyond just assay robustness to reduction of instrumental complexity, increase in quantitative precision, and an increase in the amount of information that can be gained from a single experiment. These microfluidic architectures, however, are not limited to usage in scenarios of quantification of biomolecules. These architectures can also potentially be extended to answering complex biological questions in single cells, such as determining the 3-dimensional organization of nuclear DNA and RNA." }, { "name": "Takatori, Sho C.", "degree": "PhD", "year": "2017", "title": "Forces, Stresses, and the (Thermo?) Dynamics of Active Matter: The Swim Pressure", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142017-141527247", "creators": [ { "name": { "family": "Takatori", "given": "Sho C." }, "id": "Takatori-Sho-C", "orcid": "0000-0002-7839-3399", "display_name": "Takatori, Sho C." } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "orcid": "0000-0002-0291-4215", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9RN35WF", "abstract": "A core feature of many living systems is their ability to move, self-propel, and be active. From bird flocks to bacteria swarms, to even cytoskeletal networks, active matter systems exhibit collective and emergent dynamics owing to their constituents' ability to convert chemical fuel into mechanical activity. Active matter systems generate their own internal stress, which drives them far from equilibrium and thus frees them from conventional thermodynamic constraints, and by so doing they can control and direct their own behavior and that of their surrounding environment. This gives rise to fascinating behaviors such as spontaneous self-assembly and pattern formation, but also makes the theoretical understanding of their complex dynamical behaviors a challenging problem in the statistical physics of soft matter.
\r\n\r\nIn this thesis, I present a new principle that all active matter systems display---namely, through their self-motion they generate an intrinsic `swim pressure' that impacts their dynamic and collective behavior. I combine experimental and computational methods to demonstrate how intrinsic activity imparts new behaviors to soft materials that explain a variety of complex phenomena, including the collective motion of self-propelled particles and the complete loss of shear viscosity in fluid suspensions. These nonequilibrium phenomena are driven fundamentally by the active constituent's tendency to diffuse, undergo a random walk, and exert a mechanical force or a pressure on a confining wall. The swim pressure theory is conceptually similar to the kinetic theory of gases, where molecular collisions with the container walls exert a pressure, or to the Brownian osmotic pressure exerted by molecular or colloidal solutes in solution. In contrast to thermodynamic quantities such as the chemical potential and free energy, the mechanical pressure (or stress) is valid out of equilibrium because it comes directly from the micromechanical equations of motion. I apply this swim pressure framework in a broad context to interpret living matter as a material and understand its complex behavior using tools of hydrodynamics, kinetic theory, and nonequilibrium statistical mechanics. The present theory is applied to active systems that are driven by self-propulsion and motility, but there are other types of nonequilibrium driving work that may fit into this general theoretical framework, like driven autocatalytic reactions in electrochemical and biochemical systems.
" }, { "name": "Toutov, Anton Alexandrovich", "degree": "PhD", "year": "2017", "title": "Alkaline Salts of Sodium and Potassium: from C\u2013X Reduction to C\u2013H Functionalization and Beyond", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172016-133616811", "creators": [ { "name": { "family": "Toutov", "given": "Anton Alexandrovich" }, "id": "Toutov-Anton-Alexandrovich", "orcid": "0000-0002-6561-0462", "display_name": "Toutov, Anton Alexandrovich" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9VM499F", "abstract": "The discovery and contemplations of Gilbert N. Lewis (1875\u20131946) regarding the concept of electron pair acceptors has led to an improved fundamental understanding of molecular interactions. Lewis\u2019s recognition that acidic character can exist in substances not containing hydrogen (i.e.,\r\nBr\u00f8nsted acids) led to the classification of a new group of reagents and catalysts for organic synthesis: Lewis acids. Over the last half-century, the application of these reagents and catalysts has in turn led to the discovery of a plethora of new chemical reactions, enabling previously unknown\r\ntransformations. It has also been appreciated that electron pair donors (i.e., Lewis bases) are characterized by analogous and opposite behavior. Perhaps most intriguing is that in certain cases Lewis bases are capable of modifying simultaneously the electrophilic and nucleophilic character of\r\nthe substance to which they are coordinated. It is also known that neutral tetravalent silicon can act as a Lewis acid for a variety of nucleophiles (i.e., Lewis bases) generating pentavalent Si species; these adducts are observed to have enhanced electrophilicity at Si and enhanced electron density at the ligands bound to silicon. In the case of organosilanes wherein at least one of the groups on silicon is a hydrogen (i.e., a hydrosilane), the reaction with Lewis bases can lead to pentavalent adducts with weakened Si\u2013H bonds wherein the H has enhanced hydridic character. This property has been exploited by researchers in a number of ways, perhaps most prevalently in the development of hydrosilanes as mild reducing agents for the reduction of carbonyl compounds or for the mechanistically-related carbonyl hydrosilylation reaction.
\r\n\r\nThis thesis details the discovery and development of fundamentally new chemical reactivity of silanes enabled by their interaction with basic salts of certain alkali metals (and includes some, but certainly not all of the work that I have performed in this area). First, it was found that specific combinations of hydrosilanes with basic alkali metal salts \u2013 in particular KOt-Bu \u2013 under certain conditions form exceptionally powerful reductive couples capable of selectively cleaving strong aromatic C\u2013O and C\u2013S bonds with exceptional effectiveness and novel selectivity. Second, I found that certain modifications and elaborations of this chemical system lead to dramatic changes in the operative reaction manifold: from C\u2013X bond cleavage to E\u2013Si bond formation. I determined that this concept of activating hydrosilanes with alkaline salts of the alkali metals can be harnessed for the mild and efficient construction of a wide array of E\u2013Si bond classes by catalytic crossdehydrogenative coupling. Surprisingly, these challenging chemistries all occur in the absence of transition metal species, providing new horizons and opportunities for investigating Earth-abundant elements as catalysts and reagents for a host of applications.
" }, { "name": "Vu, Tran Minh Tri", "degree": "PhD", "year": "2017", "title": "Studies of the N-end Rule Pathway in Bacteria and Mammals", "advisor": "Varshavsky, Alexander J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07022016-190718870", "creators": [ { "name": { "family": "Vu", "given": "Tran Minh Tri" }, "id": "Vu-Tran-Minh-Tri", "display_name": "Vu, Tran Minh Tri" } ], "advisors": [ { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "role": "advisor", "display_name": "Varshavsky, Alexander J." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "role": "member", "display_name": "Varshavsky, Alexander J." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9668B5J", "abstract": "Many intracellular proteins are either conditionally or constitutively short-lived, with in vivo half-lives that can be as brief as a minute or so. The regulated and processive degradation of intracellular proteins is carried out largely by the ubiquitin (Ub)-proteasome system (UPS), in conjunction with molecular chaperones, autophagy, and lysosomal proteolysis. The N-end rule pathway, the first specific pathway of UPS to be discovered, relates the in vivo half-life of a protein to the identity of its N-terminal residue. Physiological functions of the N-end rule pathway are strikingly broad and continue to be discovered. In bacteria and in eukaryotic organelles mitochondria and chloroplasts all nascent proteins bear the pretranslationally formed N-terminal formyl-methionine (fMet) residue. What is the main biological function of this metabolically costly, transient, and not strictly essential modification of N-terminal Met, and why has Met formylation not been eliminated during bacterial evolution? One possibility is that the formyl groups of N-terminal Met in Nt formylated bacterial proteins may signify a proteolytic role of Nt-formylation. My colleagues and I addressed this hypothesis experimentally, as described in Chapter 3 of this thesis.
\r\n\r\nAmong the multitude of biological functions of the mammalian Arg/N-end rule pathway are its roles in the brain, including the regulation of synaptic transmission and the regulation of brain\u2019s G-protein circuits. This regulation is mediated, in part, by the its Ate1-mediated arginylation branch of the Arg/N-end rule pathway. One role of the Ate1 arginyltransferase (R-transferase) is to mediate the conditional degradation of three G-protein down-regulators, Rgs4, Rgs5, and Rgs16. Ate1-/- mice, which lack the Ate1 R-transferase, exhibit a variety of abnormal phenotypes. Chapter 4 describes our studies of neurological abnormalities in Ate1-/- mice (and also in mice that express Ate1 conditionally, upon the addition of doxycycline), with an emphasis on the propensity of these mice to epileptic seizures.
\r\n" }, { "name": "Wang, Mu", "degree": "PhD", "year": "2017", "title": "Constant Stress and Pressure Rheology of Dense Colloidal Suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182016-183910155", "creators": [ { "name": { "family": "Wang", "given": "Mu" }, "id": "Wang-Mu", "orcid": "0000-0001-6090-6187", "display_name": "Wang, Mu" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Johnson", "given": "William Lewis" }, "id": "Johnson-W-L", "role": "member", "display_name": "Johnson, William Lewis" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9BC3WHQ", "abstract": "This thesis is a computational investigation on several aspects of the constant stress and pressure rheology of dense polydisperse colloidal suspensions. Using bidisperse suspensions as a model, we first study the influences of size polydispersity on short-time transport properties. The hydrodynamic interactions are calculated using a polydisperse implementation of Stokesian Dynamics (SD) via a Monte-Carlo approach. We carefully compare the SD computations with existing theoretical and numerical results, and critically assess the strengths and weaknesses of the SD algorithm. For suspensions, we find that the Pairwise Additive (PA) approximations with the Percus-Yevick structural input is valid up to volume fraction φ=0.1. We also develop an semi-analytical approximation scheme to predict the wavenumber-dependent partial hydrodynamic functions based on the δγ-scheme of Beenakker & Mazur [Physica 120A (1983) 388 & 126A (1984) 349], which is shown to be valid up to φ=0.4.
\r\n\r\nTo meet the computation requirements of dynamic simulations, we then developed the Spectral Ewald Accelerated Stokesian Dynamics (SEASD) based on the framework of SD with extension to compressible solvents. The SEASD uses the Spectral Ewald (SE) method [Lindbo & Tornberg, J. Comput. Phys. 229 (2010) 8994] for mobility computation with flexible error control, a novel block-diagonal preconditioner for the iterative solver, and the Graphic Processing Units (GPU) acceleration. For further speedup, we developed the SEASD-nf, a polydisperse extension of the mean-field Brownian approximation of Banchio & Brady [J. Chem. Phys. 118 (2003) 10323]. The SEASD and SEASD-nf are extensively validated with static and dynamic computations, and are found to scale as O(NlogN) with N the system size. The SEASD and SEASD-nf agree satisfactorily over a wide range of parameters for dynamic simulations.
\r\n\r\nNext, we investigate the colloidal film drying processes to understand the structural and mechanical implications when the constant pressure constraint is imposed by confining boundaries. The suspension is sandwiched between a stationary substrate and an interface moving either at a constant velocity or with constant imposed stress. Using Brownian Dynamics (BD) simulations without hydrodynamic interactions, we find that both fast and slow interface movement promote crystallization via distinct mechanisms. The most amorphous suspension structures occur when the interface moves at a rate comparable to particle Brownian motion. Imposing constant normal stresses leads to similar suspension behaviors, except that the interface stops moving when the suspension osmotic pressure matches the imposed stress. We also compare the simulation results with a continuum model. This work reveals the critical role of interface movement on the stress and structure of the suspension.
\r\n\r\nFinally, we study the constant shear stress and pressure rheology of dense colloidal suspensions using both BD and SEASD-nf to identify the role of hydrodynamic interactions. The constant pressure constraint is imposed by introducing a compressible solvent. We focus on the rheological, structural, and dynamical characteristics of flowing suspensions. Although hydrodynamic interactions profoundly affect the suspension structure and dynamics, they only quantitatively influence the behaviors of amorphous suspensions. The suspension becomes glassy, i.e., exhibits flow-arrest transitions, when the imposed pressure is high, and reveals the Shear Arrest Point (SAP) in the non-Brownian limit. From a granular perspective, we find that the suspensions move away from the arrested state in a universal fashion regardless of the imposed pressure, suggesting the critical role of the jamming physics. The hydrodynamic simulations quantitatively agree with the experiments of Boyer et al. [Phys. Rev. Lett. 107 (2011) 188301] with a volume fraction shift. The results at all imposed stresses and pressures reveal a generalized Stokes-Einstein-Sutherland relation with an effective temperature proportional to the pressure. We develop a model that accurately describes the rheology and diffusion of glassy suspensions. Our results show the critical role of pressure on the behaviors of dense colloidal suspensions.
" }, { "name": "Wiensch, Joshua David", "degree": "PhD", "year": "2017", "title": "Differential Reactivity at Edge and Terrace Sites of Transition Metal Dichalcogenides", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232017-102424232", "creators": [ { "name": { "family": "Wiensch", "given": "Joshua David" }, "id": "Wiensch-Joshua-David", "orcid": "0000-0002-8235-6937", "display_name": "Wiensch, Joshua David" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9GB223X", "abstract": "This dissertation describes efforts towards understanding the surface reactivity and catalytic properties of a promising class of materials, which have the potential to be integrated as part of a solar-fuels device and help usher-in the solar age. Because of their multifunctional behavior, layered transition metal dichalcogenides are potential candidates for not only light absorption in a solar fuels device, but also as catalysts for the hydrogen evolution reaction.
\r\n\r\nWe begin in chapter one with an introduction related to global energy sources and trends, highlighting the motivation for the work performed in this dissertation. The second chapter describes a discovery into the interplay of pH and morphology for the hydrogen evolution reaction on MoSe2. This discovery suggested a possibility for a different mechanism for the hydrogen evolution reaction being active in acidic and alkaline media. The third chapter describes an exploration into selective small molecule binding to macroscopic edge sites of MoSe2 and WSe2. The fourth chapter is a study of the protective effects of ALD-TiO2 when grown on a variety of MX2\u2019s. The inert nature of terrace sites in MoSe2 and other MX2\u2019s prevented the growth of a conformal thin film of TiO2 but yielded nanoparticles on the surface instead. Finally, in appendix A, I describe the work performed prior to joining the Lewis group relating to the design and synthesis of a binuclear titanium complex that was explored for its ability to copolymerize olefins and enable the incorporation of polar monomers.
" }, { "name": "Wong, Betty Ko", "degree": "PhD", "year": "2017", "title": "Biophysical Studies of Ligand-gated Ion Channels", "advisor": "Dougherty, Dennis A.; Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302017-225018783", "creators": [ { "name": { "family": "Wong", "given": "Betty Ko" }, "id": "Wong-Betty-Ko", "display_name": "Wong, Betty Ko" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "co-advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9TT4P0Q", "abstract": "This dissertation describes building a methodology for and the biophysical studies of ligand-gated ion channels (LGICs).
\r\n\r\nThe primary focus of the first half of this dissertation is on developing a fluorescence-based assay to broadly study LGICs. Chapter 2 describes the site-selective incorporation of a turn-on fluorophore via unnatural amino acid mutagenesis on the mouse muscle-type nicotinic acetylcholine receptor (nAChR) in Xenopus oocytes as a proof-of-principle study. This method has proven to yield very low levels of undesired fluorescent background, which was a problem for previous incorporation techniques. Chapter 3 describes efforts towards imaging this in vivo system using lifetime imaging with efforts hampered by the inability to detect a clear signal. Chapter 4 describes efforts to apply the lifetime imaging approach towards a different system involving 5-HT3 proteins fused to fluorescent proteins in COS-7 cells.
\r\n\r\nThe second half of this dissertation focuses on studies of menthol, a flavorant added to cigarettes that contributes to smoking addiction, as a negative allosteric modulator of the \u03b1\u03b242 nAChR. Chapter 5 reveals the stereochemical effects, or rather lack of, of menthol on the two stoichiometries of the \u03b1\u03b242 receptor. Chapter 6 seeks to identify the residue interactions with menthol of the \u03b1\u03b242 receptor using a combination of computational and experimental studies.
\r\n" }, { "name": "Zhuang, Bilin", "degree": "PhD", "year": "2017", "title": "Dipolar Liquids and Their Mixtures: Equilibrium and Nonequilibrium Properties with Field-Theoretic Approaches", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042017-233656614", "creators": [ { "name": { "family": "Zhuang", "given": "Bilin" }, "id": "Bilin-Zhuang", "orcid": "0000-0003-2934-4264", "display_name": "Zhuang, Bilin" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9VQ30QR", "abstract": "Liquid is a state of matter that is intermediate between the gas state and the solid state. Though it is an ordinary state of matter, the application of statistical mechanics for understanding its properties is far from complete. Compared to the solid state, the liquid state has molecules that can move around freely, and yet, unlike that in the gas state, the intermolecular correlations are significant in the liquid state. Therefore, the distance dependent correlations in a liquid need to be taken into account to properly describe a liquid. In particular, all molecules are polarizable. The polarizable nature allows the molecules to induce polarization in surrounding molecules, giving rise to van der Waals interactions that have important consequences on the properties of a liquid. In addition to polarizability, many molecules are intrinsically polar. The long-ranged dipole-dipole correlations contribute to the complexity of interactions and lead to a myriad of interesting properties special to a liquid.
\r\n\r\nIn recent years, field-theoretic technique has emerged as a convenient and systematic tool for deriving coarse-grained theories for a wide range of complex-fluid and soft-matter systems while preserving the essential physics. In this thesis, we present the application of field-theoretic approaches to two problems of liquids and their mixtures. The first problem is to describe the dielectric properties of an ordinary liquid or liquid mixture under equilibrium condition, where current field-theoretic methods are inadequate. In this problem, we apply a variational field-theoretic approach to develop a statistical field theory of the liquid, and predict the dielectric constant and the miscibility of liquids using the variational free energies derived. The second problem involves the nonequilibrium solvent composition and orientational polarization surrounding some charged solute in the context of electron transfer reactions. Using a self-consistent-field theory with constrained coarse-grained fields, we derive expressions for the nonequilibrium solvation energy, and apply it to compute the reorganization energy of electron transfer reactions. The theories presented in this thesis lead to simple analytical expressions for the equilibrium and the nonequilibrium free energies, making it possible to theoretically survey a wide range of liquids. In addition, our models involve only a few readily-available molecular parameters and avoid the use of any adjustable parameters, allowing one to make a priori predictions on the properties of liquids and their mixtures.
" }, { "name": "Babin, Brett Michael", "degree": "PhD", "year": "2016", "title": "Bioorthogonal Noncanonical Amino Acid Tagging for Selective Analysis of the Pseudomonas aeruginosa Proteome", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062016-131543245", "creators": [ { "name": { "family": "Babin", "given": "Brett Michael" }, "id": "Babin-Brett-Michael", "orcid": "0000-0002-4133-6665", "display_name": "Babin, Brett Michael" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z94X55S1", "abstract": "In natural environments, bacterial physiology is frequently characterized by slow metabolic rates and complex cellular heterogeneities. The opportunistic pathogen Pseudomonas aeruginosa provides one such example; P. aeruginosa forms untreatable chronic biofilm infections of the cystic fibrosis lung, where oxygen limitation can lead to states of metabolic dormancy. To better understand the biology of these states, in vitro experiments must be adapted to better recapitulate natural settings. However, low rates of protein turnover and cellular or phenotypic complexity make these systems difficult to study using established methods. Here we adapt the bioorthogonal noncanonical amino acid tagging (BONCAT) method for time- and cell-selective proteomic analysis to the study of P. aeruginosa. Analysis of proteins synthesized in an anoxic dormancy state led to the discovery of a new type of transcriptional regulator which we designated SutA. We performed detailed analyses of SutA\u2019s role in transcription under slow growth states and we elucidated the structural basis for its regulatory behavior. Additionally, we used cell-selective targeting of BONCAT labeling to measure the dynamic proteomic response of an antibiotic-tolerant biofilm subpopulation. Overall this work shows the utility of selective proteomics as applied to bacterial physiology and describes the broad biological insight obtained from that application." }, { "name": "Cahn, Jackson Kenai Blender", "degree": "PhD", "year": "2016", "title": "Engineering, Predicting, and Understanding Nicotinamide Cofactor Specificity", "advisor": "Arnold, Frances Hamilton; Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212016-225223309", "creators": [ { "name": { "family": "Cahn", "given": "Jackson Kenai Blender" }, "id": "Cahn-Jackson-Kenai-Blender", "display_name": "Cahn, Jackson Kenai Blender" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "co-advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9QV3JJ8", "abstract": "Oxidoreductases, the enzymes that catalyze the transfer of electrons between molecules, represent the largest group of enzymes in metabolism, and the vast majority of these enzymes use the functionally-equivalent cofactors nicotinamide adenine dinucleotide (NAD) or nicotinamide adenine dinucleotide phosphate (NADP) for the storage and transport of the electrons. Understanding the interactions of these proteins with their cofactors is therefore crucial to the engineering of biological pathways and systems that involve these enzymes. In particular, because cells tightly regulate the levels of oxidized and reduced NAD and NADP, it is often valuable to engineer the specificity of enzymes to better integrate them into particular metabolic contexts.
\r\n\r\nThe first section of this thesis focuses on this specificity, taking as a model system the ketol-acid reductoisomerase (KARI) enzyme family. Prior to the work described here, all known members of the KARI enzyme family displayed a strict specificity for NADP over NAD. However, the use of these enzymes in a constructed pathway for the production of medium-chain alcohols created a clear need for NAD-specific KARIs to improve yields. Chapter 1 briefly summarizes the prior state of the art in nicotinamide cofactor specificity engineering before describing how a previous switching of the KARI from E. coli was extended to create a simple recipe for the specificity reversal of any KARI enzyme. Chapter 2 then uses the insights into cofactor specificity in KARIs afforded by the engineering in Chapter 1 to search databases of KARI sequences and predict naturally NAD-specific KARIs, resulting in the discovery of extremophilic NAD-utilizing KARIs with properties that outstrip those of the best engineered enzymes. Chapter 3 extends this prediction approach into another enzyme family, xylose reductases, and discusses its strengths and limitations across diverse enzyme folds and families.
\r\n\r\nThe next section of the thesis diverges from the topic of cofactor specificity engineering to briefly explore three structural questions which arise from the study of KARIs. Chapter 4 covers an analysis of several new KARI crystal structures, including those obtained during the efforts described in Chapters 1 and 2. From a comprehensive comparison of these structures, two topics are addressed: (1) the effect of insertions and deletions in the cofactor specificity loop on the binding geometry of NAD and NADP, and (2) the conformational motions involved in the binding of cofactor, substrate, and metal ions. Based on a pair of structures from Chapter 4, Chapter 5 experimentally explores the structural evolution of the KARI enzyme family\u2019s two distinct structural classes, replicating in a class I KARI the structural duplication that produced the class II KARI fold, and demonstrating a remarkable retention of enzymatic activity. Chapter 6 explores a curious sensitivity to mutations observed around the adenine moiety of several KARIs, and extends this observation to a range of other NADP- and NAD-dependent enzymes, with implications both for engineering these proteins and for understanding protein evolution more generally.
\r\n\r\nThe third and final section discusses the development of a general method for the cofactor specificity reversal of any NAD(P)-utilizing enzyme. Chapter 7 explains the approach used and how it represents a new paradigm in protein engineering, as well as covering the thorough experimental validation to which the method was subjected. This method was developed into a web applet (CSR-SALAD) for public use, and Chapter 8 discusses the development and use of this tool. This third section represents the culmination of the preceeding work, drawing from an understanding of the sequence and structural determinants of cofactor binding as explored in the preceeding six chapters to create the heuristic picture of specificity which informed the comprehensive engineering approach.
" }, { "name": "Carsch, Kurtis Mickel", "degree": "Masters", "year": "2016", "title": "Bio-Inspired Homometallic and Heterometallic Clusters Relevant to the Oxygen-Evolving Complex of Photosystem II", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022016-225404694", "creators": [ { "name": { "family": "Carsch", "given": "Kurtis Mickel" }, "id": "Carsch-Kurtis-Mickel", "display_name": "Carsch, Kurtis Mickel" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9HH6H3V", "abstract": "The following two chapters delineate several endeavors to isolate and characterize functional models of the oxygen-evolving complex (OEC) of photosystem II. Understanding the electronic structure and the precise mechanism of the O\u2013O bond coupling step in the Kok cycle affords insight into this fundamental process and will guide the design of new earth-abundant catalysts to perform water oxidation under environmentally benign conditions. Nature performs this transformation by a heterometallic CaMn4O5 cluster arranged a tetra-metallic cubane bridged to a dangling manganese ion. Although a myriad of synthetic inorganic complexes are capable of water oxidation, these structures significantly underperform the OEC in terms of turnover number and turnover frequency. The objectives of this thesis are (i) to construct multimetallic clusters using the OEC as inspiration, (ii) to explore the reactivity of these clusters with oxygen-atom transfer reagents, and (iii) to identify intermediates responsible for oxygen-based chemistry.
\r\n\r\nIn Chapter 1, a series of pseudo-C3 symmetric tetra-manganese clusters with an interstitial \u00b54-oxygen was synthesized and characterized in several oxidation states. These clusters (of the general formula [LMn3(PhPz)3OMn][OTx]x; x = 1, 2) are supported by pyridine and alkoxide donors connected by a 1,3,5-triarylbenzene spacer. A \u00b54-oxygen coordinates all four metal centers that are also bridged by phenyl pyrazolate (PhPz) ligands. This arrangement furnishes a vacant coordination site at a site-differentiated (apical) metal center. Exposure of these clusters to oxygen-atom transfer reagents (OAT\u2019s) results in the intramolecular oxygenation of a C(sp2)\u2013H bond of the bridging phenyl pyrazolate. Similarly, using 2,6-difluorophenyl pyrazolate (F2ArPz) as the bridging ligand results in the oxygenation of the C\u2013F bond with concurrent F-atom transfer. This reactivity represents an unprecedented C\u2013F activation for molecular manganese complexes. All hydroxylated and fluorinated clusters were independently prepared to confirm the observed reactivity upon exposure to OAT\u2019s. The pathways responsible for arene activation \u2013 postulated to proceed through an iodosobenzene adduct and subsequent formation of a transient high-valent manganese-oxo motif \u2013 are discussed.
\r\n\r\nIn Chapter 2, a series of pseudo-C3 symmetric heterometallic Fe3Mn clusters of the general formula [LMn3(PhPz)3OMn][OTf]x (x = 1\u20133) was synthesized and characterized. Similar to their homometallic tetra-manganese and tetra-iron analogs (Chapter 1), these clusters contain four metal centers with a central bridging interstitial \u00b54-oxygen atom and bridging phenyl pyrazolate ligands. These clusters are further supported by pyridine and alkoxide donors, linked through a 1,3,5-triarylbenzene spacer. All complexes were characterized by zero-field 57Fe M\u00f6ssbauer spectroscopy to confirm the presence of a manganese metal center in the apical position, illustrating that these clusters are stable with respect to metal scrambling and/or decomposition. Treatment of these clusters with 1-(tert-butylsulfonyl)-2-iodosylbenzene (sPhIO) resulted in the oxygenation of the C(sp2)\u2013H bond of the proximal phenyl pyrazolate motif to afford [LMn3(PhPz)2(OArPz)OMn][OTf]x (x = 2, 3). During these studies, an unusual iodosobenzene adduct of [FeIII3MnII]3+ was isolated prior to C\u2013H activation. This adduct has been characterized both by single-crystal XRD and 1H-NMR spectroscopy. In order to gain insight into the C\u2013H bond oxygenation by this iodosobenzene adduct, preliminary computational studies are presented to discuss the viability of a transient manganese-oxo species responsible for arene hydroxylation.
\r\n" }, { "name": "Chaubard, Jean-Luc", "degree": "PhD", "year": "2016", "title": "Development of Chemoenzymatic Labeling Approaches for the Detection of Fucosylated Biomarkers", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052016-123724002", "creators": [ { "name": { "family": "Chaubard", "given": "Jean-Luc" }, "id": "Chaubard-Jean-Luc", "display_name": "Chaubard, Jean-Luc" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9K35RN1", "abstract": "Protein fucosylation regulates a diverse set of physiological functions such as memory and learning, development, and disease pathogenesis. However, our current understanding of these processes is far behind that of other post-translational modifications, such as phosphorylation. This is, in part, due to the lack of tools available for the study of this important protein modification. To address this need, I have developed novel chemoenzymatic methods that enable the labeling and detection of unique forms of fucosylation, specifically fucose-\u03b1(1-2)-galactose (Fuc\u03b1(1-2)Gal) and core fucose. Additionally, novel glycosyltransferase assays were developed in-house to aid in the future development of both new and existing chemoenzymatic approaches.
\r\n\r\nI have demonstrated that the approach to detect Fuc\u03b1(1-2)Gal is highly selective for this disaccharide motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of this motif on live cells, discriminating malignant from normal cells. I have also shown that the chemoenzymatic detection of core fucose exhibits superior specificity towards this glycan on a variety of complex N-glycans and when compared to current fucose-specific lectins. Further, the approach is amenable to detection of core fucosylated glycans from multiple biological settings, can be exploited as an antibody-conjugation method, and can be integrated into a diagnostic platform for the profiling of protein specific core fucosylation levels. These approaches represent new potential strategies for biomarker identification and expand the technologies available for understanding the role of these important fucosylated glycans in physiology and disease.
\r\n" }, { "name": "Chuang, Kangway V.", "degree": "PhD", "year": "2016", "title": "A Total Synthesis of (+)-Ryanodol", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082016-142725994", "creators": [ { "name": { "family": "Chuang", "given": "Kangway V." }, "id": "Chuang-Kangway-V", "orcid": "0000-0002-0652-8071", "display_name": "Chuang, Kangway V." } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z95X26ZV", "abstract": "Highly oxygenated, architecturally complex terpenoids constitute a biologically important class of natural products, yet their development into medicinally relevant analogs and effective biological probes are obstructed by their synthetic accessibility. Ryanodine is a unique diterpenoid that exhibits high affinity to a class of intracellular calcium ion channels bearing its name: ryanodine receptors. Structure-activity relationship studies have demonstrated how peripheral structural modifications affect binding affinity and selectivity among receptor isoforms, but to date have been limited to analogs prepared via chemical derivatization of natural material due to the intractability of total chemical synthesis.
\r\n\r\nThis thesis details synthetic efforts culminating in a total synthesis of ryanodol that proceeds in only 15-steps from commercially available (\u2013)-pulegone. Early stage oxygen atom incorporation is strategically implemented to facilitate key, stereoselective carbon-carbon bond formation. In particular, a rhodium-catalyzed, intramolecular Pauson\u2013Khand reaction is utilized to rapidly assemble the tetracyclic ABCD-ring system that constitutes the anhydroryanodol core. A novel, selenium-dioxide mediated oxidation to install three oxidation states and three oxygen atoms was discovered, enabling the rapid oxidative functionalization of the ryanodol A-ring. The modular route described herein allows for the preparation of synthetic structural analogs not readily accessible via chemical degradation, and is anticipated to enable rapid construction and evaluation of biologically active ryanodine analogs.
\r\n" }, { "name": "Clark, Andrew James", "degree": "PhD", "year": "2016", "title": "Delivery of Targeted Nanoparticles Across the Blood-Brain Barrier Using a Detachable Targeting Ligand", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282016-162609209", "creators": [ { "name": { "family": "Clark", "given": "Andrew James" }, "id": "Clark-Andrew-James", "orcid": "0000-0003-4240-7119", "display_name": "Clark, Andrew James" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9WH2MZ6", "abstract": "Chronic diseases of the central nervous system are poorly treated due to the inability of most therapeutics to cross the blood-brain barrier. The blood-brain barrier is an anatomical and physiological barrier that severely restricts solute influx, including most drugs, from the blood to the brain. One promising method to overcome this obstacle is to use endogenous solute influx systems at the blood-brain barrier to transport drugs. Therapeutics designed to enter the brain through transcytosis by binding the transferrin receptor, however, are restricted within endothelial cells. The focus of this work was to develop a method to increase uptake of transferrin-containing nanoparticles into the brain by overcoming these restrictive processes.
\r\n\r\nTo accomplish this goal, nanoparticles were prepared with surface transferrin molecules bound through various liable chemical bonds. These nanoparticles were designed to shed the targeting molecule during transcytosis to allow increased accumulation of nanoparticles within the brain.
\r\n\r\nTransferrin was added to the surface of nanoparticles through either redox or pH sensitive chemistry. First, nanoparticles with transferrin bound through disulfide bonds were prepared. These nanoparticles showed decreased avidity for the transferrin receptor after exposure to reducing agents and increased ability to enter the brain in vivo compared to those lacking the disulfide link.
\r\n \r\nNext, transferrin was attached through a chemical bond that cleaves at mildly acidic pH. Nanoparticles containing a cleavable link between transferrin and gold nanoparticle cores were found to both cross an in vitro model of the blood-brain barrier and accumulate within the brain in significantly higher numbers than similar nanoparticles lacking the cleavable bond. Also, this increased accumulation was not seen when using this same strategy with an antibody to transferrin receptor, indicating that behavior of nanoparticles at the blood-brain barrier varies depending on what type of targeting ligand is used.
\r\n\r\nFinally, polymeric nanoparticles loaded with dopamine and utilizing a superior acid-cleavable targeting chemistry were investigated as a potential treatment for Parkinson\u2019s disease. These nanoparticles were capable of increasing dopamine quantities in the brains of healthy mice, highlighting the therapeutic potential of this design. Overall, this work describes a novel method to increase targeted nanoparticle accumulation in the brain.
\r\n" }, { "name": "Coggon, Matthew Mitchell", "degree": "PhD", "year": "2016", "title": "Field and Laboratory Studies of Atmospheric Organic Aerosol", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09222015-114148959", "creators": [ { "name": { "family": "Coggon", "given": "Matthew Mitchell" }, "id": "Coggon-Matthew-Mitchell", "display_name": "Coggon, Matthew Mitchell" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Sorooshian", "given": "Armin" }, "id": "Sorooshian-A", "role": "member", "display_name": "Sorooshian, Armin" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9959FH7", "abstract": "This thesis is the culmination of field and laboratory studies aimed at assessing processes that affect the composition and distribution of atmospheric organic aerosol. An emphasis is placed on measurements conducted using compact and high-resolution Aerodyne Aerosol Mass Spectrometers (AMS). The first three chapters summarize results from aircraft campaigns designed to evaluate anthropogenic and biogenic impacts on marine aerosol and clouds off the coast of California. Subsequent chapters describe laboratory studies intended to evaluate gas and particle-phase mechanisms of organic aerosol oxidation.
\r\n\r\nThe 2013 Nucleation in California Experiment (NiCE) was a campaign designed to study environments impacted by nucleated and/or freshly formed aerosol particles. Terrestrial biogenic aerosol with > 85% organic mass was observed to reside in the free troposphere above marine stratocumulus. This biogenic organic aerosol (BOA) originated from the Northwestern United States and was transported to the marine atmosphere during periodic cloud-clearing events. Spectra recorded by a cloud condensation nuclei counter demonstrated that BOA is CCN active. BOA enhancements at latitudes north of San Francisco, CA coincided with enhanced cloud water concentrations of organic species such as acetate and formate.
\r\n\r\nAirborne measurements conducted during the 2011 Eastern Pacific Emitted Aerosol Cloud Experiment (E-PEACE) were aimed at evaluating the contribution of ship emissions to the properties of marine aerosol and clouds off the coast of central California. In one study, analysis of organic aerosol mass spectra during periods of enhanced shipping activity yielded unique tracers indicative of cloud-processed ship emissions (m/z 42 and 99). The variation of their organic fraction (f42 and f99) was found to coincide with periods of heavy (f42 > 0.15; f99 > 0.04), moderate (0.05 < f42 < 0.15; 0.01 < f99 < 0.04), and negligible (f42 < 0.05; f99 < 0.01) ship influence. Application of these conditions to all measurements conducted during E-PEACE demonstrated that a large fraction of cloud droplet (72%) and dry aerosol mass (12%) sampled in the California coastal study region was heavily or moderately influenced by ship emissions. Another study investigated the chemical and physical evolution of a controlled organic plume emitted from the R/V Point Sur. Under sunny conditions, nucleated particles composed of oxidized organic compounds contributed nearly an order of magnitude more cloud condensation nuclei (CCN) than less oxidized particles formed under cloudy conditions. The processing time necessary for particles to become CCN active was short ( < 1 hr) compared to the time needed for particles to become hygroscopic at sub-saturated humidity ( > 4 hr).
\r\n\r\nLaboratory chamber experiments were also conducted to evaluate particle-phase processes influencing aerosol phase and composition. In one study, ammonium sulfate seed was coated with a layer of secondary organic aerosol (SOA) from toluene oxidation followed by a layer of SOA from α-pinene oxidation. The system exhibited different evaporative properties than ammonium sulfate seed initially coated with \u03b1-pinene SOA followed by a layer of toluene SOA. This behavior is consistent with a shell-and-core model and suggests limited mixing among different SOA types. Another study investigated the reactive uptake of isoprene epoxy diols (IEPOX) onto non-acidified aerosol. It was demonstrated that particle acidity has limited influence on organic aerosol formation onto ammonium sulfate seed, and that the chemical system is limited by the availability of nucleophiles such as sulfate.
\r\n\r\n\r\nFlow tube experiments were conducted to examine the role of iron in the reactive uptake and chemical oxidation of glycolaldehyde. Aerosol particles doped with iron and hydrogen peroxide were mixed with gas-phase glycolaldehyde and photochemically aged in a custom-built flow reactor. Compared to particles free of iron, iron-doped aerosols significantly enhanced the oxygen to carbon (O/C) ratio of accumulated organic mass. The primary oxidation mechanism is suggested to be a combination of Fenton and photo-Fenton reactions which enhance particle-phase OH radical concentrations.
" }, { "name": "Creutz, Sidney E.", "degree": "PhD", "year": "2016", "title": "Design, Synthesis, and Study of Novel Platforms for Iron-N2 Chemistry and Photoinduced, Copper-mediated C-N Bond Formation", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02242016-013157998", "creators": [ { "name": { "family": "Creutz", "given": "Sidney E." }, "id": "Creutz-Sidney-E", "display_name": "Creutz, Sidney E." } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92V2D1M ", "abstract": "Several new ligand platforms designed to support iron dinitrogen chemistry have been developed. First, we report Fe complexes of a tris(phosphino)alkyl (CPiPr3) ligand featuring an axial carbon donor intended to conceptually model the interstitial carbide atom of the nitrogenase iron-molybdenum cofactor (FeMoco). It is established that in this scaffold, the iron center binds dinitrogen trans to the Calkyl anchor in three structurally characterized oxidation states. Fe-Calkyl lengthening is observed upon reduction, reflective of significant ionic character in the Fe-Calkyl interaction. The anionic (CPiPr3)FeN2- species can be functionalized by a silyl electrophile to generate (CPiPr3)Fe-N2SiR3. This species also functions as a modest catalyst for the reduction of N2 to NH3. Next, we introduce a new binucleating ligand scaffold that supports an Fe(\u03bc-SAr)Fe diiron subunit that coordinates dinitrogen (N2-Fe(\u03bc-SAr)Fe-N2) across at least three oxidation states (FeIIFeII, FeIIFeI, and FeIFeI). Despite the sulfur-rich coordination environment of iron in FeMoco, synthetic examples of transition metal model complexes that bind N2 and also feature sulfur donor ligands remain scarce; these complexes thus represent an unusual series of low-valent diiron complexes featuring thiolate and dinitrogen ligands. The (N2-Fe(\u03bc-SAr)Fe-N2) system undergoes reduction of the bound N2 to produce NH3 (~50% yield) and can efficiently catalyze the disproportionation of N2H4 to NH3 and N2. The present scaffold also supports dinitrogen binding concomitant with hydride as a co-ligand. Next, inspired by the importance of secondary-sphere interactions in many metalloenzymes, we present complexes of iron in two new ligand scaffolds ([SiPNMe3] and [SiPiPr2PNMe]) that incorporate hydrogen-bond acceptors (tertiary amines) which engage in interactions with nitrogenous substrates bound to the iron center (NH3 and N2H4). Cation binding is also facilitated in anionic Fe(0)-N2 complexes. While Fe-N2 complexes of a related ligand ([SiPiPr3]) lacking hydrogen-bond acceptors produce a substantial amount of ammonia when treated with acid and reductant, the presence of the pendant amines instead facilitates the formation of metal hydride species.
\r\n\r\nAdditionally, we present the development and mechanistic study of copper-mediated and copper-catalyzed photoinduced C-N bond forming reactions. Irradiation of a copper-amido complex, ((m-tol)3P)2Cu(carbazolide), in the presence of aryl halides furnishes N-phenylcarbazole under mild conditions. The mechanism likely proceeds via single-electron transfer from an excited state of the copper complex to the aryl halide, generating an aryl radical. An array of experimental data are consistent with a radical intermediate, including a cyclization/stereochemical investigation and a reactivity study, providing the first substantial experimental support for the viability of a radical pathway for Ullmann C-N bond formation. The copper complex can also be used as a precatalyst for Ullmann C-N couplings. We also disclose further study of catalytic Calkyl-N couplings using a CuI precatalyst, and discuss the likely role of [Cu(carbazolide)2]- and [Cu(carbazolide)3]- species as intermediates in these reactions.
\r\n \r\nFinally, we report a series of four-coordinate, pseudotetrahedral P3FeII-X complexes supported by tris(phosphine)borate ([PhBP3FeR]-) and phosphiniminato X-type ligands (-N=PR'3) that in combination tune the spin-crossover behavior of the system. Low-coordinate transition metal complexes such as these that undergo reversible spin-crossover remain rare, and the spin equilibria of these systems have been studied in detail by a suite of spectroscopic techniques.
\r\n" }, { "name": "Crowley, Jason Michael", "degree": "PhD", "year": "2016", "title": "Resolution of the Band Gap Prediction Problem for Materials Design", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312016-081457742", "creators": [ { "name": { "family": "Crowley", "given": "Jason Michael" }, "id": "Crowley-Jason-Michael", "display_name": "Crowley, Jason Michael" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9D21VKZ", "abstract": "An important property with any new material is the band gap. In order to design new materials in silico, it is critical to have an accurate and computationally inexpensive tool for predicting band gaps. Standard density functional theory (DFT) methods are computationally efficient, but grossly underestimate band gaps. Hybrid density functionals are known to improve band gap predictions, but the computational cost in the overwhelmingly popular plane-wave basis set codes used for solids is a serious drawback. Exact exchange can be evaluated much more efficiently using localized Gaussian basis functions; however, the most readily available Gaussian basis periodic quantum chemistry code lacked spin-orbit coupling. This seriously limited the range of compounds that can be studies. In this thesis, spin-orbit coupling was implemented in the periodic, Gaussian basis set code CRYSTAL. Using the modified code, band gaps were computed using the B3PW91 hybrid density functional for 70 compounds spanning the entire periodic table and a factor of 500 in band gap (0.014 - 15 eV). To benchmark the quality of the hybrid method, we compared to the rigorous GW many-body perturbation theory method. Surprisingly, the MAD for B3PW91 is about 1.5 times smaller than the MAD for GW. Furthermore, B3PW91 is three to four orders of magnitude faster computationally. We also show that increasing (decreasing) the amount of exact exchange compared to B3PW91 leads to systematic overestimates (underestimates) of band gaps. Finally, we show that the pathological vanishing of the density of states at the Fermi level of a metal cannot be observed in practical calculations of real metals. Thus, we believe that B3PW91 is a practical tool for predicting the band gaps of materials before they are synthesized while being computationally efficient enough for high-throughput applications and represents a solution to the band gap prediction problem for materials design." }, { "name": "Davenport, Andrew M.", "degree": "PhD", "year": "2016", "title": "The Molecular Basis of Lysine Acetylation: Addition, Removal, and Recognition", "advisor": "Hoelz, Andre", "url": "https://resolver.caltech.edu/CaltechTHESIS:09012015-173735253", "creators": [ { "name": { "family": "Davenport", "given": "Andrew M." }, "id": "Davenport-Andrew-M", "display_name": "Davenport, Andrew M." } ], "advisors": [ { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "advisor", "display_name": "Hoelz, Andre" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Hoelz", "given": "Andre" }, "id": "Hoelz-A", "role": "member", "display_name": "Hoelz, Andre" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9BG2KWK", "abstract": "Acetyltransferases and deacetylases catalyze the addition and removal, respectively, of acetyl groups to the epsilon-amino group of protein lysine residues. This modification can affect the function of a protein through several means, including the recruitment of specific binding partners called acetyl-lysine readers. Acetyltransferases, deacetylases, and acetyl-lysine readers have emerged as crucial regulators of biological processes and prominent targets for the treatment of human disease. This work describes a combination of structural, biochemical, biophysical, cell-biological, and organismal studies undertaken on a set of proteins that cumulatively include all steps of the acetylation process: the acetyltransferase MEC-17, the deacetylase SIRT1, and the acetyl-lysine reader DPF2. Tubulin acetylation by MEC-17 is associated with stable, long-lived microtubule structures. We determined the crystal structure of the catalytic domain of human MEC-17 in complex with the cofactor acetyl-CoA. The structure in combination with an extensive enzymatic analysis of MEC-17 mutants identified residues for cofactor and substrate recognition and activity. A large, evolutionarily conserved hydrophobic surface patch distal to the active site was shown to be necessary for catalysis, suggesting that specificity is achieved by interactions with the alpha-tubulin substrate that extend outside of the modified surface loop. Experiments in C. elegans showed that while MEC-17 is required for touch sensitivity, MEC-17 enzymatic activity is dispensible for this behavior. SIRT1 deacetylates a wide range of substrates, including p53, NF-kappaB, FOXO transcription factors, and PGC-1-alpha, with roles in cellular processes ranging from energy metabolism to cell survival. SIRT1 activity is uniquely controlled by a C-terminal regulatory segment (CTR). Here we present crystal structures of the catalytic domain of human SIRT1 in complex with the CTR in an apo form and in complex with a cofactor and a pseudo-substrate peptide. The catalytic domain adopts the canonical sirtuin fold. The CTR forms a beta-hairpin structure that complements the beta-sheet of the NAD^+-binding domain, covering an essentially invariant, hydrophobic surface. A comparison of the apo and cofactor bound structures revealed conformational changes throughout catalysis, including a rotation of a smaller subdomain with respect to the larger NAD^+-binding subdomain. A biochemical analysis identified key residues in the active site, an inhibitory role for the CTR, and distinct structural features of the CTR that mediate binding and inhibition of the SIRT1 catalytic domain. DPF2 represses myeloid differentiation in acute myelogenous leukemia. Finally, we solved the crystal structure of the tandem PHD domain of human DPF2. We showed that DPF2 preferentially binds H3 tail peptides acetylated at Lys14, and binds H4 tail peptides with no preference for acetylation state. Through a structural and mutational analysis we identify the molecular basis of histone recognition. We propose a model for the role of DPF2 in AML and identify the DPF2 tandem PHD finger domain as a promising novel target for anti-leukemia therapeutics." }, { "name": "Dodson, Leah G.", "degree": "PhD", "year": "2016", "title": "Gas Phase Spectroscopy and Kinetics of Atmospheric Radicals", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122016-112417957", "creators": [ { "name": { "family": "Dodson", "given": "Leah G." }, "id": "Dodson-Leah-G", "orcid": "0000-0001-5960-056X", "display_name": "Dodson, Leah G." } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9XD0ZP8", "abstract": "An important goal for atmospheric and combustion chemists is continued improvement in our understanding of the gas phase reactivity of free radical intermediates formed during hydrocarbon oxidation. The primary focus of this thesis was to measure gas phase kinetics of prototypical free radicals relevant to atmospheric and combustion chemistry, a goal that requires spectroscopy, quantitative product detection, and computational chemistry in order to address these complex chemical systems.
\r\n\r\nNear-infrared cavity ringdown spectroscopy was used to study the peroxy radicals (RO2) formed from chlorine-initiated oxidation of isoprene and other unsaturated hydrocarbons. Isoprene is one of the most important hydrocarbons in the atmosphere; detection of RO2 formed directly from isoprene oxidation will aid in understanding the initial steps of its fate in the atmosphere. As expected, the near-infrared chloro-isoprenyl peroxy radical spectrum has many features; each spectral feature corresponds to a different isomer and conformer, indicating that several RO2 structures are formed. In small RO2, it was possible to identify the molecular structure of the absorber by comparing the experimental spectrum with the vibrationally-resolved electronic spectrum generated by computational chemistry. Identification of each feature then enabled preliminary isomer-specific kinetics measurements.
\r\n\r\nPhotoionization mass spectrometry is another useful method for selective detection of radicals, with the added bonus of detecting many of the other species of interest, leading to a comprehensive understanding of the reaction mechanism. The yields of radical chain-propagating product channels of prototypical RO2 reactions (self- and cross-reactions) are important in understanding radical chemistry in gas phase hydrocarbon oxidation. We obtained branching ratio information for reactions of acetyl peroxy radicals with HO2, with particular focus on OH-regenerating reactions. Along the way, we observed unexpected product formation from low-pressure reactions of acetyl radicals and oxygen. Using the same techniques, we also looked at the self-reaction of ethyl peroxy radicals, confirming past measurements of the radical-propagating channel for this reaction, and investigated interesting product formation, like what may be the dialkyl peroxide. These studies were supported by measurements of VUV photoionization cross sections for several radical species. The utility of this instrumentation was also extended by the development of a low-temperature (200\u2013300 K) flow reactor.
\r\n\r\nFinally, using time-resolved broadband cavity-enhanced absorption spectroscopy, we measured the rate coefficient of reactions of the smallest Criegee intermediate, CH2OO with ozone. We observed that this reaction is rather fast, which could have significant implications for experimental ozonolysis studies that are carried out under high initial reactant concentrations.
" }, { "name": "Dooling, Lawrence Joseph", "degree": "PhD", "year": "2016", "title": "Programming Molecular Association and Viscoelastic Behavior in Protein Hydrogels", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022016-152749956", "creators": [ { "name": { "family": "Dooling", "given": "Lawrence Joseph" }, "id": "Dooling-Lawrence-Joseph", "orcid": "0000-0002-1688-2066", "display_name": "Dooling, Lawrence Joseph" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "role": "member", "display_name": "Ravichandran, Guruswami" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9PK0D41", "abstract": "Recombinant artificial proteins contain genetically encoded information that specifies their assembly into higher order structures by physical or chemical cross-linking as well as elastic behavior and biological or chemical function. This thesis describes the use of artificial proteins to construct molecular networks containing covalent cross-links involving the thiol side chain of cysteine residues and physical cross-links involving the association of helical domains as coiled coils. The goal of this work was to demonstrate how the viscoelastic properties of protein hydrogels could be encoded within an artificial protein sequence.
\r\n\r\nUsing genetic engineering methods, a telechelic protein denoted ERE was designed from elastin- and fibronectin-derived repeating units and expressed in Escherichia coli. ERE was end-linked by the reaction of terminal cysteine residues with tetrakis-vinyl sulfone-functionalized 4-arm star PEG to form hydrogel networks. The effects of varying the precursor concentration and cross-linker stoichiometry on the swelling ratio and mechanical properties of the hydrogels were studied in detail in Chapter 2. The capacity for ERE hydrogels to serve as an artificial extracellular matrix was also assessed by the encapsulation of mouse fibroblasts, which survived the cross-linking reaction and exhibited a spread morphology within the gel.
\r\n\r\nChapter 3 describes a set of recombinant artificial proteins that can be cross-linked by covalent bonds, by association of helical domains, or by both mechanisms. These proteins were used to construct chemical, physical, and chemical-physical hydrogel networks in which the mechanism of cross-linking determines whether the material response to mechanical deformation is elastic or viscoelastic. In viscoelastic networks, stress relaxation and energy dissipation could be tuned by controlling the ratio of physical cross-linking to chemical cross-linking, and the physical cross-links could be disrupted either by protein denaturation or by mutation of the primary sequence.
\r\n\r\nNetwork dynamics control the viscoelasticity and erosion rate of materials and influence biological processes at multiple length scales.In Chapter 4, variation of the protein sequence was explored as a strategy to tune the characteristic relaxation timescale of protein networks. Single point mutations to coiled-coil physical cross-linking domains in chemical-physical hydrogels altered the characteristic relaxation time over five orders of magnitude. Using a pair of orthogonal coiled-coil physical cross-linking domains, networks with two distinct relaxation timescales were also engineered.
\r\n\r\nThe dynamic properties of protein hydrogels can also be controlled by interactions between protein domains and small molecule ligands. In Chapter 5, the viscoelastic behavior of chemical-physical protein gels was tuned by swelling the gels with small hydrophobic molecules including vitamin D3 and fatty acids. The proposed mechanism for this effect involves binding of the ligands within the hydrophobic pore or channel created by a coiled-coil physical cross-link. Exploiting natural and designed protein-ligand interactions represents a new approach to developing hydrogel \u201cformulations\u201d in which the viscoelastic properties of the material can be engineered to meet specific design criteria.
\r\n\r\nIn addition to exhibiting interesting dynamic properties, polymeric hydrogels containing permanent covalent cross-links and reversible physical cross-links often display enhanced toughness and extensibility. Protein hydrogels cross-linked by covalent thioether bonds and physical coiled coils could be extended further than control covalent hydrogels and exhibited a greater work of extension, which is considered a measure of material toughness. These results demonstrate progress toward engineering tougher, more extensible protein-based materials by the incorporation of coiled-coil physical cross-links within a covalent hydrogel network.
" }, { "name": "Edouard, Guy Anthony", "degree": "PhD", "year": "2016", "title": "Late Transition Metals Supported by Aryl Ethers and Phenoxides Bearing Pendant Phosphines: Mechanistic Insights Relevant to Ether C-O Bond Cleavage", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032016-141952494", "creators": [ { "name": { "family": "Edouard", "given": "Guy Anthony" }, "id": "Edouard-Guy-Anthony", "display_name": "Edouard, Guy Anthony" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9Z60KZJ", "abstract": "Terphenyl diphosphines bearing pendant ethers were prepared to provide mechanistic insight into the mechanism of activation of aryl C\u2013O bonds with Group 9 and Group 10 transition metals. Chapters 2 and 3 of this dissertation describe the reactivity of compounds supported by the model phosphine and extension of this chemistry to heterogenous C\u2013O bond activation.
\r\n\r\nChapter 2 describes the synthesis and reactivity of aryl-methyl and aryl-aryl model systems. The metallation of these compounds with Ni, Pd, Pt, Co, Rh, and Ir is described. Intramolecular bond activation pathways are described. In the case of the aryl-methyl ether, aryl C\u2013O bond activation was observed only for Ni, Rh, and Ir.
\r\n\r\nChapter 3 outlines the reactivity of heterogenous Rh and Ir catalysts for aryl ether C\u2013O bond cleavage. Using Rh/C and an organometallic Ir precursor, aryl ethers were treated with H2 and heat to afford products of hydrogenolysis and hydrogenation. Conditions were modified to optimize the yield of hydrogenolysis product. Hydrogenation could not be fully suppressed in these systems.
\r\n\r\nAppendix A describes initial investigations of bisphenoxyiminoquinoline dichromium compounds for selective C2H4 oligomerization to afford \u03b1-olefins. The synthesis of monometallic and bimetallic Cr complexes is described. These compounds are compared to literature examples and found to be less active and non-selective for production of \u03b1-olefins.
\r\n\r\nAppendix B describes the coordination chemistry of terphenyl diphosphines, terphenyl bisphosphinophenols, and biphenyl phosphinophenols proligands with molybdenum, cobalt, and nickel. Since their synthesis, terphenyl diphosphine molybdenum compounds have been reported to be good catalysts for the dehydrogenation of ammonia borane. Biphenyl phosphinophenols are demonstrated provide both phosphine and arene donors to transition metals while maintaining a sterically accessible coordination sphere. Such ligands may be promising in the context of the activation of other small molecules.
\r\n\r\nAppendix C contains relevant NMR spectra for the compounds presented in the preceding sections.
\r\n" }, { "name": "Eisler, Carissa Nicole", "degree": "PhD", "year": "2016", "title": "Photonic and Device Design Principles for Ultrahigh-Efficiency (>50%), Spectrum-Splitting Photovoltaics", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242015-234332347", "creators": [ { "name": { "family": "Eisler", "given": "Carissa Nicole" }, "id": "Eisler-Carissa-Nicole", "orcid": "0000-0002-5755-5280", "display_name": "Eisler, Carissa Nicole" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Faraon", "given": "Andrei" }, "id": "Faraon-A", "role": "member", "display_name": "Faraon, Andrei" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "appliedphys" ], "doi": "10.7907/Z9PN93HB", "abstract": "The sun has the potential to power the Earth's total energy needs, but electricity from solar power still constitutes an extremely small fraction of our power generation because of its high cost relative to traditional energy sources. Therefore, the cost of solar must be reduced to realize a more sustainable future. This can be achieved by significantly increasing the efficiency of modules that convert solar radiation to electricity. In this thesis, we consider several strategies to improve the device and photonic design of solar modules to achieve record, ultrahigh (> 50%) solar module efficiencies. First, we investigate the potential of a new passivation treatment, trioctylphosphine sulfide, to increase the performance of small GaAs solar cells for cheaper and more durable modules. We show that small cells (mm2), which currently have a significant efficiency decrease (~ 5%) compared to larger cells (cm2) because small cells have a higher fraction of recombination-active surface from the sidewalls, can achieve significantly higher efficiencies with effective passivation of the sidewalls. We experimentally validate the passivation qualities of treatment by trioctylphosphine sulfide (TOP:S) through four independent studies and show that this facile treatment can enable efficient small devices. Then, we discuss our efforts toward the design and prototyping of a spectrum-splitting module that employs optical elements to divide the incident spectrum into different color bands, which allows for higher efficiencies than traditional methods. We present a design, the polyhedral specular reflector, that has the potential for > 50% module efficiencies even with realistic losses from combined optics, cell, and electrical models. Prototyping efforts of one of these designs using glass concentrators yields an optical module whose combined spectrum-splitting and concentration should correspond to a record module efficiency of 42%. Finally, we consider how the manipulation of radiatively emitted photons from subcells in multijunction architectures can be used to achieve even higher efficiencies than previously thought, inspiring both optimization of incident and radiatively emitted photons for future high efficiency designs. In this thesis work, we explore novel device and photonic designs that represent a significant departure from current solar cell manufacturing techniques and ultimately show the potential for much higher solar cell efficiencies. " }, { "name": "Evoen, Vanessa", "degree": "PhD", "year": "2016", "title": "Electrocatalysis in Solid Acid Fuel Cell Electrodes", "advisor": "Haile, Sossina M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032016-203656058", "creators": [ { "name": { "family": "Evoen", "given": "Vanessa" }, "id": "Evoen-Vanessa", "orcid": "0000-0003-2824-1896", "display_name": "Evoen, Vanessa" } ], "advisors": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "advisor", "display_name": "Haile, Sossina M." } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "chair", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9NV9G72", "abstract": "Fuel cells are appealing alternatives to combustion engines for efficient conversion of chemical energy to electrical energy, with the potential to meet substantial energy demands with a small carbon footprint. Intermediate temperature fuel cells (200-300 \u00b0C) combine the kinetic benefits and fuel flexibility of higher operating temperatures along with the flexibility in material choices that lower operating temperatures allow. Solid acid fuel cells (SAFCs) offer the unique benefit amongst intermediate temperature fuel cells of a truly solid electrolyte, specifically, CsH2PO4, which in turn, provides significant system simplifications relative to phosphoric acid or alkaline fuel cells. However, the power output of even the most advanced SAFCs has not yet reached levels typical of conventional polymer electrolyte or solid oxide fuel cells. This is largely due to poor activity of the cathodes. That is, while it has been possible to limit electrolyte voltage losses in SAFCs through fabrication of thin-membrane fuel cells (with electrolyte thicknesses of 25\u201350 \u03bcm), it has not been possible to attain high activity cathodes or to limit Pt loadings to competitive levels. In this thesis, the efficacy of non-precious metal catalysts in the solid acid electrochemical system is evaluated. In addition, an attractive synthesis route (specifically, the electrospray method) to fabricating high surface area electrodes with high catalyst utilization is presented.
\r\n\r\nElimination of Pt was pursued by the evaluation of carbon nanostructures as potential oxygen reduction reaction (ORR) catalysts in the solid acid electrochemical system. Multi-walled carbon nanotubes were the most consistently catalytically active in comparison with nano-graphite. It is demonstrated that the a) precursor partial pressure, b) seed catalyst size, c) growth temperature and d) chemical functionalization can be used to control the defect density and atomic composition of multi-walled carbon nanotubes (MWCNTs), all of which play a significant role on the measured ORR activity. Increasing the precursor partial pressure, decreasing the seed catalyst size, and decreasing the growth temperature increases the density of ORR active defects. In addition, the oxygen reduction reaction (ORR) electrochemical activity evaluated by symmetric cell AC impedance spectroscopy and fuel cell measurements, were significantly enhanced by chemical functionalization with oxygen containing functional groups. Area normalized impedance responses as low as 7 \u03a9 cm2 were measured on symmetric MWCNT/ CsH2PO4 cells. However, it was discovered that these reactive MWCNTs also catalyze and are slightly consumed by steam reforming. Moreover, the orders of magnitude improvement with functionalization measured in impedance measurements is not replicated in fuel cell power output as a result of a decrease in open circuit voltage relative to standard cells. It is proposed that the loss in voltage results from hydrogen production at the cathode via the steam reforming reaction, although formation of hydrogen peroxide rather than water as the oxygen reduction product cannot be ruled out. This work has a significant contribution to catalysis, it demonstrates how carbon nanostructures can be designed by synthesis routes and chemical functionalization processes, to create active precious-metal-free ORR catalysts. It is also important that we have demonstrated potential ORR catalysts in acidic media. These catalysts have potential applications in phosphoric acid fuel cells and PEMFCs.
\r\n\r\nIn addition to the study of carbon nanostructures, oxides were evaluated as potential ORR catalysts. Specifically, TiOx nanoparticles were studied. Analysis shows that the activity is controlled by the oxidation state of Ti. The active site seems to be on or near slightly reduced Ti sites. In this study we have outlined synthesis routes to tune the oxidation state of Ti and enhance ORR activity in the solid acid fuel cell.
\r\n\r\nFinally, the fundamentals of the electrospray process are explored to understand how the particle size ultimately resulting from electrospray synthesis depends on both solution properties and process parameters. This analysis presents a systematic way to control the fabrication of high surface area SAFC electrodes with increased throughput, catalyst utilization and consequently power density.
" }, { "name": "Forte, Lila", "degree": "Masters", "year": "2016", "title": "Statistical Mechanical Framework for Predicting Cellular Response", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272016-101847646", "creators": [ { "name": { "family": "Forte", "given": "Lila" }, "id": "Forte-Lila", "display_name": "Forte, Lila" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9K07273", "abstract": "Developments in singe-cell analysis techniques allow simultaneous high-resolution measurements of cellular component copy number and variation within a cell population. These data provide a probability distribution for all possible states of the cell, as determined by the measured component copy number per cell. We have developed a highly-flexible, theoretical statistical mechanical framework that uses single-cell cellular component data to model the evolution of the probability distribution of those components in a cell in response to an external, physical or molecular, perturbation. This framework uses Bayesian inference to compare potential functional descriptions of how the perturbation couples to the system, and to determine the uncertainty in the parameter estimations given the data. We have applied this methodology to study the impact of changes in oxygen partial pressure on the behavior of glioblastoma multiform cancer cells. We find that oxygen concentration couples not only to individual proteins, but effects the underlying effective interactions between the studied proteins as well. The underlying effective interactions were found to couple linearly to the system, indicating a simple proportional change in the protein network across oxygen concentrations. This description of the system provides improved predictive capabilities for describing the probability distribution of the measured cellular components across a wider range of perturbation conditions than previous methods. Additionally, we apply this methodology to show how it could be used to predict effects in difficult experimental perturbation regimes, identifying undruggable regimes, as well as the result of knocking our individual or combinations of proteins or protein interactions." }, { "name": "Good, Jacob Thomas", "degree": "PhD", "year": "2016", "title": "Design and Applications of a Decade-Spanning Terahertz Frequency Comb Spectrometer: Doppler-limited Rotational Spectroscopy of Methanol and Methanol-OD", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-124438217", "creators": [ { "name": { "family": "Good", "given": "Jacob Thomas" }, "id": "Good-Jacob-Thomas", "display_name": "Good, Jacob Thomas" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9MW2F37", "abstract": "This thesis details the design and applications of a terahertz (THz) frequency comb spectrometer. The spectrometer employs two offset locked Ti:Sapphire femtosecond oscillators with repetition rates of approximately 80 MHz, offset locked at 100 Hz to continuously sample a time delay of 12.5 ns at a maximum time delay resolution of 15.6 fs. These oscillators emit continuous pulse trains, allowing the generation of a THz pulse train by the master, or pump, oscillator and the sampling of this THz pulse train by the slave, or probe, oscillator via the electro-optic effect. Collecting a train of 16 consecutive THz pulses and taking the Fourier transform of this pulse train produces a decade-spanning frequency comb, from 0.25 to 2.5 THz, with a comb tooth width of 5 MHz and a comb tooth spacing of ~80 MHz. This frequency comb is suitable for Doppler-limited rotational spectroscopy of small molecules. Here, the data from 68 individual scans at slightly different pump oscillator repetition rates were combined, producing an interleaved THz frequency comb spectrum, with a maximum interval between comb teeth of 1.4 MHz, enabling THz frequency comb spectroscopy.
\r\n\r\nThe accuracy of the THz frequency comb spectrometer was tested, achieving a root mean square error of 92 kHz measuring selected absorption center frequencies of water vapor at 10 mTorr, and a root mean square error of 150 kHz in measurements of a K-stack of acetonitrile. This accuracy is sufficient for fitting of measured transitions to a model Hamiltonian to generate a predicted spectrum for molecules of interest in the fields of astronomy and physical chemistry. As such, the rotational spectra of methanol and methanol-OD were acquired by the spectrometer. Absorptions from 1.3 THz to 2.0 THz were compared to JPL catalog data for methanol and the spectrometer achieved an RMS error of 402 kHz, improving to 303 kHz when excluding low signal-to-noise absorptions. This level of accuracy compares favorably with the ~100 kHz accuracy achieved by JPL frequency multiplier submillimeter spectrometers. Additionally, the relative intensity performance of the THz frequency comb spectrometer is linear across the entire decade-spanning bandwidth, making it the preferred instrument for recovering lineshapes and taking absolute intensity measurements in the THz region. The data acquired by the Terahertz Frequency Comb Spectrometer for methanol-OD is of comparable accuracy to the methanol data and may be used to refine the fit parameters for the predicted spectrum of methanol-OD.
" }, { "name": "Grodick, Michael Andrew", "degree": "PhD", "year": "2016", "title": "DNA-Mediated Charge Transport Signaling Within the Cell", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07192015-214603085", "creators": [ { "name": { "family": "Grodick", "given": "Michael Andrew" }, "id": "Grodick-Michael-Andrew", "display_name": "Grodick, Michael Andrew" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9F769GX", "abstract": "DNA possesses the curious ability to conduct charge longitudinally through the \u03c0-stacked base pairs that reside within the interior of the double helix. The rate of charge transport (CT) through DNA has a shallow distance dependence. DNA CT can occur over at least 34 nm, a very long molecular distance. Lastly, DNA CT is exquisitely sensitive to disruptions, such as DNA damage, that affect the dynamics of base-pair stacking. Many DNA repair and DNA-processing enzymes are being found to contain 4Fe-4S clusters. These co-factors have been found in glycosylases, helicases, helicase-nucleases, and even enzymes such as DNA polymerase, RNA polymerase, and primase across the phylogeny. The role of these clusters in these enzymes has remained elusive. Generally, iron-sulfur clusters serve redox roles in nature since, formally, the cluster can exist in multiple oxidation states that can be accessed within a biological context. Taken together, these facts were used as a foundation for the hypothesis that DNA-binding proteins with 4Fe-4S clusters utilize DNA-mediated CT as a means to signal one another to scan the genome as a first step in locating the subtle damage that occurs within a sea of undamaged bases within cells.
\r\n\r\nHerein we describe a role for 4Fe-4S clusters in DNA-mediated charge transport signaling among EndoIII, MutY, and DinG, which are from distinct repair pathways in E. coli. The DinG helicase is an ATP-dependent helicase that contains a 4Fe-4S cluster. To study the DNA-bound redox properties of DinG, DNA-modified electrochemistry was used to show that the 4Fe-4S cluster of DNA-bound DinG is redox-active at cellular potentials, and shares the 80 mV vs. NHE redox potential of EndoIII and MutY. ATP hydrolysis by DinG increases the DNA-mediated redox signal observed electrochemically, likely reflecting better coupling of the 4Fe-4S cluster to DNA while DinG unwinds DNA, which could have interesting biological implications. Atomic force microscopy experiments demonstrate that DinG and EndoIII cooperate at long range using DNA charge transport to redistribute to regions of DNA damage. Genetics experiments, moreover, reveal that this DNA-mediated signaling among proteins also occurs within the cell and, remarkably, is required for cellular viability under conditions of stress. Knocking out DinG in CC104 cells leads to a decrease in MutY activity that is rescued by EndoIII D138A, but not EndoIII Y82A. DinG, thus, appears to help MutY find its substrate using DNA-mediated CT, but do MutY or EndoIII aid DinG in a similar way? The InvA strain of bacteria was used to observe DinG activity, since DinG activity is required within InvA to maintain normal growth. Silencing the gene encoding EndoIII in InvA results in a significant growth defect that is rescued by the overexpression of RNAseH, a protein that dismantles the substrate of DinG, R-loops. This establishes signaling between DinG and EndoIII. Furthermore, rescue of this growth defect by the expression of EndoIII D138A, the catalytically inactive but CT-proficient mutant of EndoIII, is also observed, but expression of EndoIII Y82A, which is CT-deficient but enzymatically active, does not rescue growth. These results provide strong evidence that DinG and EndoIII utilize DNA-mediated signaling to process DNA damage. This work thus expands the scope of DNA-mediated signaling within the cell, as it indicates that DNA-mediated signaling facilitates the activities of DNA repair enzymes across the genome, even for proteins from distinct repair pathways.
\r\n\r\nIn separate work presented here, it is shown that the UvrC protein from E. coli contains a hitherto undiscovered 4Fe-4S cluster. A broad shoulder at 410 nm, characteristic of 4Fe-4S clusters, is observed in the UV-visible absorbance spectrum of UvrC. Electron paramagnetic resonance spectroscopy of UvrC incubated with sodium dithionite, reveals a spectrum with the signature features of a reduced, [4Fe-4S]+1, cluster. DNA-modified electrodes were used to show that UvrC has the same DNA-bound redox potential, of ~80 mV vs. NHE, as EndoIII, DinG, and MutY. Again, this means that these proteins are capable of performing inter-protein electron transfer reactions. Does UvrC use DNA-mediated signaling to facilitate the repair of its substrates?
\r\n\r\nUvrC is part of the nucleotide excision repair (NER) pathway in E. coli and is the protein within the pathway that performs the chemistry required to repair bulky DNA lesions, such as cyclopyrimidine dimers, that form as a product of UV irradiation. We tested if UvrC utilizes DNA-mediated signaling to facilitate the efficient repair of UV-induced DNA damage products by helping UvrC locate DNA damage. The UV sensitivity of E. coli cells lacking DinG, a putative signaling partner of UvrC, was examined. Knocking out DinG in E. coli leads to a sensitivity of the cells to UV irradiation. A 5-10 fold reduction in the amount of cells that survive after irradiation with 90 J/m2 of UV light is observed. This is consistent with the hypothesis that UvrC and DinG are signaling partners, but is this signaling due to DNA-mediated CT? Complementing the knockout cells with EndoIII D138A, which can also serve as a DNA CT signaling partner, rescues cells lacking DinG from UV irradiation, while complementing the cells with EndoIII Y82A shows no rescue of viability. These results indicate that there is cross-talk between the NER pathway and DinG via DNA-mediated signaling. Perhaps more importantly, this work also establishes that DinG, EndoIII, MutY, and UvrC comprise a signaling network that seems to be unified by the ability of these proteins to perform long range DNA-mediated CT signaling via their 4Fe-4S clusters.
\r\n\r\n\r\n" }, { "name": "Gupta, Ayush", "degree": "Senior Thesis", "year": "2016", "title": "Noncovalent Immobilization of Electrocatalysts on Carbon Electrodes via a Pyrenyl Ligand", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032016-120223836", "creators": [ { "name": { "family": "Gupta", "given": "Ayush" }, "id": "Gupta-Ayush", "display_name": "Gupta, Ayush" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9G15XTQ", "abstract": "There are many problems that need to be overcome if solar energy is to be viable on a global scale. Photons must be harvested and stored in a usable to allow efficient use of energy throughout the day. The functionalization of electrode surfaces with molecular catalysts is an attractive route for assembling (photo)electrochemical devices that convert renewable energy into chemical fuels. This work focuses on one method of noncovalently attaching molecular catalysts to graphitic surfaces.\r\nThe first part describes the synthesis of a pyrene-appended bipyridine ligand that serves as the linker between the catalysts and the surface. Using this ligand, a rhodium proton-reduction catalyst and a rhenium CO2-reduction catalyst were synthesized in order to study the electrochemistry of the surface-attached species. Electrochemical and spectroscopic analysis confirm catalyst immobilization and electrocatalytically active assemblies. Bulk electrolysis of the surface-attached complexes confirm catalytic turnover formation of H2 for the rhodium complex and CO for the rhenium complex.\r\nThe second part describes three new complexes utilizing the same pyrene-appended bipyridine ligand. These are [Ru(P)(4,4\u2019-dimethyl-2,2\u2019-bipyridine)2]Cl2, [Cp*Ir(P)Cl]Cl, and [Mn(P)(CO)3Br]. Once again, spectroscopic and electrochemical analyses confirmed successful immobilization of these complexes on high surface area carbon electrodes. The iridium complex was found to be unstable with respect to redox cycling due to ligand exchange. The ruthenium complex exhibited very high stability over long periods of redox cycling. The manganese complex was found to catalytically produce CO during bulk electrolysis.\r\n" }, { "name": "Haley, Christopher Keating", "degree": "PhD", "year": "2016", "title": "Aryne Reactions in the Synthesis of Heterocyclic Molecules", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-185612554", "creators": [ { "name": { "family": "Haley", "given": "Christopher Keating" }, "id": "Haley-Christopher-Keating", "display_name": "Haley, Christopher Keating" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9QN64P5", "abstract": "Reactive intermediates play an important the within the realm of chemical synthesis. Their high energy and transient nature make them difficult to observe and characterize, but it is these same properties that empower them to form bonds traditionally seen as difficult to prepare and unusual architectures quickly and efficiently. Herein, two reactive intermediates, arynes and transitient (2azaaryl)-cuprates, are exploited for their abilities to prepare important chemical motifs. Both serve as an avenue into the functionalization of arenes to provide products which hold value in a variety of fields including natural product total syntethis, pharmaseuticals and ligand design. " }, { "name": "Han, Seojung", "degree": "PhD", "year": "2016", "title": "I. Synthetic Studies Toward the Total Synthesis of Polycyclic Natural Products \u2013 Communesin F, Perophoramidine and Ineleganolide. II. Nickel Catalyzed Intramolecular C\u2013O Bond Formation", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172016-222905476", "creators": [ { "name": { "family": "Han", "given": "Seojung" }, "id": "Han-Seojung", "display_name": "Han, Seojung" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NV9G6M", "abstract": "Expedient synthetic approaches to the highly functionalized polycyclic alkaloids communesin F and perophoramidine are described using a unified approach featuring a key decarboxylative allylic alkylation to access a crucial and highly congested 3,3-disubstituted oxindole. Described are two distinct, stereoselective alkylations that produce structures in divergent diastereomeric series possessing the critical vicinal all-carbon quaternary centers needed for each synthesis. Synthetic studies toward these challenging core structures have revealed a number of unanticipated modes of reactivity inherent to these complex alkaloid scaffolds. Finally, a previously unknown mild and efficient deprotection protocol for the o-nitrobenzyl group is disclosed \u2013 this serendipitous discovery permitted a concise endgame for the formal syntheses of both communesin F and perophoramidine.
\r\n\r\nIn addition, the atroposelective synthesis of PINAP ligands has been accomplished via a palladium-catalyzed C\u2013P coupling process through dynamic kinetic resolution. These catalytic conditions allow access to a wide variety of alkoxy- and benzyloxy-substituted PINAP ligands in high enantiomeric excess.
\r\n\r\nAn efficient and exceptionally mild intramolecular nickel-catalyzed carbon\u2013oxygen bond-forming reaction between vinyl halides and primary, secondary, and tertiary alcohols has been achieved. This operationally simple method allows direct access to cyclic vinyl ethers in high yields in a single step.
\r\n\r\nFinally, synthetic studies toward polycyclic ineleganolide are described. The entire fragmented carbon framework has been constructed from this work. Highly (Z)-selective olefination was achieved by the method by the Ando group.
" }, { "name": "Henthorn, Justin Travis", "degree": "PhD", "year": "2016", "title": "Molybdenum Quinonoid Complexes: Synthesis, Characterization, and Reactivity", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechThesis:06082016-214138510", "creators": [ { "name": { "family": "Henthorn", "given": "Justin Travis" }, "id": "Henthorn-Justin-Travis", "orcid": "0000-0003-4876-2680", "display_name": "Henthorn, Justin Travis" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9V40S53", "abstract": "Pi-bound Molybdenum-quinonoid complexes supported by pendant phosphines were prepared and investigated for metal-ligand cooperative reactivity and access to multiple equivalents of protons and electrons within a single transition metal complex. Chapters 3, 4, and 5 of this dissertation describe the synthesis, characterization, and reactivity of these complexes in the context of multiproton, multielectron chemistry and small molecule activation.
\r\n\r\nChapter 2 presents the synthesis of an unprecedented bis-borane supported peroxide dianion, prepared from a mixture of ferrocenes, borane, and dioxygen. The peculiarity of such a structure is emphasized, and reactivity explored. While ferrocenes of varying reduction potential were found to lead to the peroxide, only tris(pentafluorophenyl)borane was found to yield isolable peroxide, with other boranes leading to oxygenation or borate formation.
\r\n\r\nChapter 3 describes the synthesis of a series of \u03c0-bound Molybdenum-quinonoid complexes and explores their reactivity with dioxygen. The Mo-quinonoid interaction is probed and elucidated through a number of reactions and experiments, highlighting the importance of the electronic coupling of the metal center with the organic fragment on overall reactivity with O2.
\r\n\r\nChapter 4 further explores the \u03c0-bound Molybdenum-quinonoid complexes in various protonation and oxidation states, totaling four electrons and two protons accessible to the system. Proton-coupled electron transfer was demonstrated in two different oxidation states, and the effects of the metal-quinonoid interaction on the transfer of protons and electrons investigated thermochemically.
\r\n\r\nChapter 5 explores the potential for \u03c0-bound Molybdenum-quinonoid complexes to access inner-sphere reactivity. The activation of E\u2013X bonds, including H2 and PhSiH3, is demonstrated, as well as catalytic hydrosilylation of aldehydes.
\r\n\r\nAppendix A describes initial investigations into the preparation of heterobimetallic complexes supported by the catechol-diphosphine ligand framework. The synthesis of heterobimetallic MoCu complexes is presented and their structural parameters discussed.
\r\n\r\nAppendix B outlines the synthesis of multinucleating ligand platforms based off bipyridine frameworks, for the preparation of biologically inspired multimetallic complexes. Dioxygen reactivity of a dicopper system is also briefly presented.
\r\n\r\nAppendix C contains relevant NMR spectra for the compounds presented in the preceding sections.
" }, { "name": "Horak, Kyle Tadashi", "degree": "PhD", "year": "2016", "title": "The Design and Synthesis of Transition Metal Complexes Supported by Non-innocent Ligand Scaffolds for Small Molecule Activation", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:02162016-101008749", "creators": [ { "name": { "family": "Horak", "given": "Kyle Tadashi" }, "id": "Horak-Kyle-Tadashi", "display_name": "Horak, Kyle Tadashi" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9TB14VB", "abstract": "This dissertation focuses on the incorporation of non-innocent or multifunctional moieties into different ligand scaffolds to support one or multiple metal centers in close proximity. Chapter 2 focuses on the initial efforts to synthesize hetero- or homometallic tri- or dinuclear metal carbonyl complexes supported by para-terphenyl diphosphine ligands. A series of [M2M\u2019(CO)4]-type clusters (M = Ni, Pd; M\u2019 = Fe, Co) could be accessed and used to relate the metal composition to the properties of the complexes. During these studies it was also found that non-innocent behavior was observed in dinuclear Fe complexes that result from changes in oxidation state of the cluster. These studies led to efforts to rationally incorporate central arene moieties capable managing both protons and electrons during small molecule activation.
\r\n\r\nChapter 3 discusses the synthesis of metal complexes supported by a novel para-terphenyl diphosphine ligand containing a non-innocent 1,4-hydroquinone moiety as the central arene. A Pd0-hydroquinone complex was found to mediate the activation of a variety of small molecules to form the corresponding Pd0-quinone complexes in a formal two proton ⁄ two electron transformation. Mechanistic investigations of dioxygen activation revealed a metal-first activation process followed by subsequent proton and electron transfer from the ligand. These studies revealed the capacity of the central arene substituent to serve as a reservoir for a formal equivalent of dihydrogen, although the stability of the M-quinone compounds prevented access to the PdII-quinone oxidation state, thus hindering of small molecule transformations requiring more than two electrons per equivalent of metal complex.
\r\n\r\nChapter 4 discusses the synthesis of metal complexes supported by a ligand containing a 3,5-substituted pyridine moiety as the linker separating the phenylene phosphine donors. Nickel and palladium complexes supported by this ligand were found to tolerate a wide variety of pyridine nitrogen-coordinated electrophiles which were found to alter central pyridine electronics, and therefore metal-pyridine \u03c0-system interactions, substantially. Furthermore, nickel complexes supported by this ligand were found to activate H-B and H-Si bonds and formally hydroborate and hydrosilylate the central pyridine ring. These systems highlight the potential use of pyridine \u03c0-system-coordinated metal complexes to reversibly store reducing equivalents within the ligand framework in a manner akin to the previously discussed 1,4-hydroquinone diphosphine ligand scaffold.
\r\n\r\nChapter 5 departs from the phosphine-based chemistry and instead focuses on the incorporation of hydrogen bonding networks into the secondary coordination sphere of [Fe4(\u03bc4-O)]-type clusters supported by various pyrazolate ligands. The aim of this project is to stabilize reactive oxygenic species, such as oxos, to study their spectroscopy and reactivity in the context of complicated multimetallic clusters. Herein is reported this synthesis and electrochemical and M\u00f6ssbauer characterization of a series of chloride clusters have been synthesized using parent pyrazolate and a 3-aminophenyl substituted pyrazolate ligand. Efforts to rationally access hydroxo and oxo clusters from these chloride precursors represents ongoing work that will continue in the group.
\r\n\r\nAppendix A discusses attempts to access [Fe3Ni]-type clusters as models of the enzymatic active site of [NiFe] carbon monoxide dehydrogenase. Efforts to construct tetranuclear clusters with an interstitial sulfide proved unsuccessful, although a (\u03bc3-S) ligand could be installed through non-oxidative routes into triiron clusters. While [Fe3Ni(\u03bc4-O)]-type clusters could be assembled, accessing an open heterobimetallic edge site proved challenging, thus prohibiting efforts to study chemical transformations, such as hydroxide attack onto carbon monoxide or carbon dioxide coordination, relevant to the native enzyme. Appendix B discusses the attempts to synthesize models of the full H-cluster of [FeFe]-hydrogenase using a bioinorganic approach. A synthetic peptide containing three cysteine donors was successfully synthesized and found to chelate a preformed synthetic [Fe4S4] cluster. However, efforts to incorporate the diiron subsite model complex proved challenging as the planned thioester exchange reaction was found to non-selectively acetylate the peptide backbone, thus preventing the construction of the full six-iron cluster.
" }, { "name": "Husain, Naeem Shahab", "degree": "PhD", "year": "2016", "title": "Mapping mRNA and Protein Expression with High Signal-to-Background in Diverse Organisms", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02252016-123239637", "creators": [ { "name": { "family": "Husain", "given": "Naeem Shahab" }, "id": "Husain-Naeem-Shahab", "display_name": "Husain, Naeem Shahab" } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "advisor", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "chair", "display_name": "Cai, Long" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Prober", "given": "David A." }, "id": "Prober-D-A", "role": "member", "display_name": "Prober, David A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9DF6P73", "abstract": "In situ hybridization (ISH) techniques allow for the study of the nucleic acid expression within whole biological samples. The quality of probes for ISH dictates how accurate and bright the signal is for the experiment; however, there is currently not a systematic way to determine what the best probe set would be. In response to this, we have developed a framework to optimize an ISH probe set to achieve the greatest signal-to-background ratio. As methods like ISH help obtain more information about biological processes, there is a growing desire to simultaneously analyze various targets within the same sample to examine these complex genetic interactions. To facilitate this, a novel amplification technique called hybridization chain reaction (HCR) has allowed for the in situ detection of multiple target mRNAs concurrently in zebrafish embryos. We have now expanded this technology further by adapting HCR amplification for ISH to other model organisms, particularly, whole mount Drosophila melanogaster embryos and formalin-fixed parafin-embedded human tissue sections. Beyond looking at mRNA, immunohistochemistry (IHC) provides another tool to understand biological systems by analyzing protein expression patterns. The ability to easily look at both mRNAs and proteins in the same sample offers significant advantages as each provides unique information, but current methods are technically difficult and labor intensive. In response, we have engineered a scheme to use HCR to amplify signal for IHC. We then used this advancement to develop a straightforward protocol using HCR amplification for simultaneous detection of multiple proteins and mRNAs with a high signal-to-background ratio." }, { "name": "Kadunce, Nathaniel Thomas", "degree": "PhD", "year": "2016", "title": "Development of Ni-Catalyzed Asymmetric Reductive Cross-Coupling Reactions", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032016-162550993", "creators": [ { "name": { "family": "Kadunce", "given": "Nathaniel Thomas" }, "id": "Kadunce-Nathaniel-Thomas", "display_name": "Kadunce, Nathaniel Thomas" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "chair", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9JS9NDR", "abstract": "Over the last half century, the development of metal-catalyzed cross-coupling reactions has transformed the toolkit of transformations available to synthetic chemists. From the very beginning of this effort, researchers have studied the application of these reactions to afford enantioenriched products via asymmetric catalysis. A great deal of success has been achieved in this arena, giving rise to an ever-growing number of chiral catalysts for a wide range of transformations. Despite these efforts, inherent difficulties in the reactivity of C(sp3) electrophiles with the most common noble metal catalysts have limited the development of these substrates until more recently. A resurgence of interest in Ni-catalysis has enabled the stereoconvergent cross-coupling of C(sp3) electrophiles with many partners, opening doors to access these challenging chiral products.
\r\n\r\nReductive cross-coupling, involving the union of two different electrophiles, has emerged still more recently, and had previously not been employed asymmetrically. Herein we describe our efforts to develop the first Ni-catalyzed asymmetric reductive cross-couplings of C(sp3) halides to afford highly enantioenriched products. In the first such reaction, the coupling of acyl chlorides with benzylic chlorides affords acyclic \u03b1-tertiary ketone products. Following this, we describe the coupling of new C(sp3) partners, \u03b1-chloronitriles, with challenging Lewis-basic heteroaryl iodides, enabled by the development of a novel PHOX ligand scaffold. Finally, we report the extension of a more general dioxane/TMSCl solvent condition to new asymmetric reductive couplings, including that of heteroaryl iodides with benzylic chlorides, as well as additional preliminary results with new substrate classes.
\r\n" }, { "name": "Li, Boyu", "degree": "PhD", "year": "2016", "title": "Ring/Chain versus Network: Architecture Induced by Self- versus Pairwise-Association of Telechelic Polymers", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272016-171126982", "creators": [ { "name": { "family": "Li", "given": "Boyu" }, "id": "Li-Boyu", "orcid": "0000-0002-7648-3745", "display_name": "Li, Boyu" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NS0RTW", "abstract": "Non-covalent associations, including hydrophobic interaction or ionic interaction for self-association, and metal coordination or hydrogen-bonding for complementary-association, have been widely used as key interactions in supramolecules formation with telechelic associative polymers. And a specific application of long associative telechelic polymers has been developed by our group for the mist-control and drag-reduction of liquid fuels. During the research on this project, self- and pairwise-associative telechelic polymers are able to be compared for the first time, and are shown to display distinct associative patterns. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer chemical structure and their topology and dynamics.
\r\n\r\nIn this thesis, self-associative telechelic polymer refers to \u03b1,\u03c9-di(isophthalic acid) polycyclooctadiene (DA-PCOD), which can associate with itself through its acid ends. When tertiary amine-ended polymer is added into the mixture, isophthalic acid preferably associates pairwisely with tertiary amine due to the higher binding strength of charge-assisted hydrogen bond. And the 1:1 molar ratio mixture of \u03b1,\u03c9-di(isophthalic acid) and \u03b1,\u03c9-di(di(tertiary amine)) PCOD (DA/DB-PCOD) is named as pairwise-associative telechelic polymers. DA-PCOD is capable of multimeric association via directional hydrogen bonding due to the specific chemical structure of the isophthalic acid end, while DA/DB-PCOD exhibits dynamics that strikingly resembles that for linear covalent polymers. Temperature determines the binding strength of self- and pairwise- end association, and furthermore, the fraction of unbound ends and the distribution and topology of formed supramolecules/aggregates. Polymer length affects the dynamics of DA-PCOD mainly through determining the concentration of the end groups. And the net effect of chain length on the dynamics of DA/DB-PCOD is non-monotonic and varies with the specific temperature and concentration. The knowledge of structure-property relationships obtained from this work will enable future design of end group entities and other properties of these associative telechelic polymers for their specific applications.
\r\n" }, { "name": "Liang, Yufan", "degree": "PhD", "year": "2016", "title": "Applications of Nickel-Catalyzed Cross-Coupling Methods in the Synthesis of Organofluorine Compounds", "advisor": "Fu, Gregory C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012016-104838419", "creators": [ { "name": { "family": "Liang", "given": "Yufan" }, "id": "Liang-Yufan", "orcid": "0000-0002-0533-2982", "display_name": "Liang, Yufan" } ], "advisors": [ { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "advisor", "display_name": "Fu, Gregory C." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9CF9N45", "abstract": "The applications of nickel-catalyzed cross-coupling strategy to the synthesis of organofluorine compounds are explored in this thesis.
\r\n\r\nChapter 2 describes the development of the first enantioselective cross-coupling method using secondary geminal dihalides as electrophiles. This method provides a unique approach for the generation of enantioenriched tertiary alkyl fluorides. These cross-coupling products can be further transformed into a variety of potentially valuable chiral building blocks.
\r\n\r\nChapter 3 describes the development of a practical and versatile Negishi alkylation method employing \u03b1-halo-\u03b1-perfluoroalkyl secondary electrophiles. Target molecules bearing perfluoroalkyl-substituted (including trifluoromethyl-substituted) tertiary carbons can be easily generated from fluorinated electrophiles. Competition experiments and mechanistic studies have been performed to reveal the unique properties of these electrophiles and also prove the existence of alkyl radicals.
\r\n\r\nChapter 4 describes the development of an asymmetric Negishi arylation protocol with \u03b1-halo-\u03b1-trifluoromethyl secondary electrophiles. This study provides a unique approach to construct trifluoromethyl-substituted tertiary stereocenters. The optimized condition can also be directly applied to substrates bearing an array of fluoroalkyl groups.
\r\n\r\nChapter 5 details the progress towards the development of an asymmetric alkynylation method employing \u03b1-halo-\u03b1-trifluoromethyl secondary electrophiles. Preliminary studies also demonstrate that the protocol we developed has the potential to be used for other non-fluorinated secondary electrophiles.
\r\n" }, { "name": "Lionetti, Davide", "degree": "PhD", "year": "2016", "title": "Heterometallic Complexes as Models of Enzymatic Active Sites", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:09282015-080838463", "creators": [ { "name": { "family": "Lionetti", "given": "Davide" }, "id": "Lionetti-Davide", "display_name": "Lionetti, Davide" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z98G8HMT", "abstract": "This dissertation describes studies on two multinucleating ligand architectures: the first scaffold was designed to support tricopper complexes, while the second platform was developed to support tri- and tetrametallic clusters.
\r\n\r\nIn Chapter 2, the synthesis of yttrium (and lanthanide) complexes supported by a tripodal ligand framework designed to bind three copper centers in close proximity is described. Tricopper complexes were shown to react with dioxygen in a 1:1 [Cu3]/O2 stoichiometry to form intermediates in which the O\u2013O bond was fully cleaved, as characterized via UV-Vis spectroscopy and determination of the reaction stoichiometry. Pre-arrangement of the three Cu centers was pivotal to cooperative O2 activation, as mono-copper complexes reacted differently with dioxgyen. The reactivity of the observed intermediates was studied with various substrates (reductants, O-atom acceptors, H-atom donors, Br\u00f8nsted acids) to determine their properties. In Chapter 3, the reactivity of the same yttrium-tricopper complex with nitric oxide was explored. Reductive coupling to form a trans-hyponitrite complex (characterized by X-ray crystallography) was observed via cooperative reactivity by an yttrium and a copper center on two distinct tetrametallic units. The hyponitrite complex was observed to release nitrous oxide upon treatment with a Br\u00f8nsted acid, supporting its viability as an intermediate in nitric oxide reduction to nitrous oxide.
\r\n\r\nIn Chapter 4, a different multinucleating ligand scaffold was employed to synthesize heterometallic triiron clusters containing one oxide and one hydroxide bridges. The effects of the redox-inactive, Lewis acidic heterometals on redox potential was studied by cyclic voltammetry, unveiling a linear correlation between redox potential and heterometal Lewis acidity. Further studies on these complexes showed that the Lewis acidity of the redox-inactive metals also affected the oxygen-atom transfer reactivity of these clusters. Comparisons of this reactivity with manganese systems, collaborative efforts to reassign the structures of related manganese oxo-hydroxo clusters, and synthetic attempts to access related dioxo clusters are also described.
\r\n\r\nIn Appendix A, ongoing efforts to synthesize new clusters supported by the same multinucleating ligand platform are described. Studies of novel approaches towards ligand exchange in tetrametallic clusters and incorporation of new supporting and bridging ligand motifs in trinuclear complexes are presented.
" }, { "name": "Liu, Fan", "degree": "PhD", "year": "2016", "title": "Classical Force Field Simulations of Biological Processes and Quantum Chemical Computations of Homogeneous Catalysts", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062016-153802648", "creators": [ { "name": { "family": "Liu", "given": "Fan" }, "id": "Liu-Fan", "orcid": "0000-0001-5650-2809", "display_name": "Liu, Fan" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94M92J2", "abstract": "Computational chemistry methods and tools have enabled studies of biological processes and chemical reactions to get insights from detailed atomic structures and reaction mechanisms. In this thesis, two biological problems are attacked by the classical force fields simulations and two homogeneous catalysis problems are studied by quantum chemical calculations. In all four problems, new insights have been revealed by the computational results.
\r\n\r\nChapter 1 briefly reviews the computational chemistry theories and methods developed and popularized in the past few decades. Chapter 2 addresses the protein-protein interaction problem in the onset of meningitis where E. coli OmpA interacts with Fc\u03b3RI \u03b1-chain (Fc\u03b3RIa) to invade macrophages. Computationally predicted three-dimensional structure of the OmpA-Fc\u03b3RIa complex showed the role of three N-glycans in Fc\u03b3RIa in the interaction. Chapter 3 studies the molecular origin of the bitter aftertaste of a kind of natural sweetener called steviol glycosides. By examining the predicted binding complexes between the human bitter taste receptors 2R4 and 2R14 which could be activated by steviol glycosides, a general activation model is proposed to explain the structure-function relationship and to predict new natural sweeteners with less bitterness. Chapter 4 investigated the reaction mechanisms of methane to methanol conversion by a biomimetic tricopper cluster compound. An unusual exchange-stabilized multiradical state is found to be responsible for the hydrogen abstraction reactivity and a methyl radical rebound mechanism is proposed for methane oxidation. Calculations also show interesting spin crossing during the reaction cycle with high spin state forbidden for methyl rebound. Chapter 5 examines the reaction mechanisms in olefin hydrosilylation by the Pt-based Karstedt\u2019s catalyst. An unexpected rate-determining step of agostic bond dissociation is found in between the elementary reaction steps proposed previously. The regioselectivity of the products are studied. An alternative reaction cycle which is kinetically unflavored is proposed. Oxygen stability is studied.
" }, { "name": "Lubeck, Eric", "degree": "PhD", "year": "2016", "title": "Towards in situ Single Cell Systems Biology", "advisor": "Cai, Long", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262016-115004310", "creators": [ { "name": { "family": "Lubeck", "given": "Eric" }, "id": "Lubeck-Eric", "orcid": "0000-0002-5457-0258", "display_name": "Lubeck, Eric" } ], "advisors": [ { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "advisor", "display_name": "Cai, Long" } ], "committee": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "chair", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "member", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Gradinaru", "given": "Viviana" }, "id": "Gradinaru-V", "role": "member", "display_name": "Gradinaru, Viviana" }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9BK1999", "abstract": "Systems-level studies of biological systems rely on observations taken at a resolution lower than\r\nthe essential unit of biology, the cell. Recent technical advances in DNA sequencing have enabled\r\nmeasurements of the transcriptomes in single cells excised from their environment, but it remains a\r\ndaunting technical problem to reconstruct in situ gene expression patterns from sequencing data. In\r\nthis thesis I develop methods for the routine, quantitative in situ measurement of gene expression\r\nusing fluorescence microscopy.
\r\n\r\nThe number of molecular species that can be measured simultaneously by fluorescence microscopy\r\nis limited by the pallet of spectrally distinct fluorophores. Thus, fluorescence microscopy is traditionally\r\nlimited to the simultaneous measurement of only five labeled biomolecules at a time. The\r\ntwo methods described in this thesis, super-resolution barcoding and temporal barcoding, represent\r\nstrategies for overcoming this limitation to monitor expression of many genes in a single cell.\r\nSuper-resolution barcoding employs optical super-resolution microscopy (SRM) and combinatorial\r\nlabeling via-smFISH (single molecule fluorescence in situ hybridization) to uniquely label individual\r\nmRNA species with distinct barcodes resolvable at nanometer resolution. This method dramatically\r\nincreases the optical space in a cell, allowing a large numbers of barcodes to be visualized\r\nsimultaneously. As a proof of principle this technology was used to study the S. cerevisiae calcium\r\nstress response. The second method, sequential barcoding, reads out a temporal barcode through\r\nmultiple rounds of oligonucleotide hybridization to the same mRNA. The multiplexing capacity of\r\nsequential barcoding increases exponentially with the number of rounds of hybridization, allowing\r\nover a hundred genes to be profiled in only a few rounds of hybridization.
\r\n\r\nThe utility of sequential barcoding was further demonstrated by adapting this method to study\r\ngene expression in mammalian tissues. Mammalian tissues suffer both from a large amount of\r\nauto-fluorescence and light scattering, making detection of smFISH probes on mRNA difficult. An\r\namplified single molecule detection technology, smHCR (single molecule hairpin chain reaction),\r\nwas developed to allow for the quantification of mRNA in tissue. This technology is demonstrated\r\nin combination with light sheet microscopy and background reducing tissue clearing technology,\r\nenabling whole-organ sequential barcoding to monitor in situ gene expression directly in intact\r\nmammalian tissue.
\r\n\r\nThe methods presented in this thesis, specifically sequential barcoding and smHCR, enable multiplexed\r\ntranscriptional observations in any tissue of interest. These technologies will serve as a\r\ngeneral platform for future transcriptomic studies of complex tissues.
" }, { "name": "Martinez, Thomas Farid", "degree": "PhD", "year": "2016", "title": "Investigations of Pyrrole-Imidazole Polyamide Effects on DNA Replication", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06292015-212932175", "creators": [ { "name": { "family": "Martinez", "given": "Thomas Farid" }, "id": "Martinez-Thomas-Farid", "orcid": "0000-0002-4011-8164", "display_name": "Martinez, Thomas Farid" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9RF5RZ2", "abstract": "Pyrrole\u2013Imidazole polyamides are programmable, cell-permeable small molecules that bind in the minor groove of double-stranded DNA sequence-specifically. Polyamide binding has been shown to alter the local helical structure of DNA, disrupt protein-DNA interactions, and modulate endogenous gene expression. Py\u2013Im polyamides targeted to the androgen receptor-DNA interface have been observed to decrease expression of androgen-regulated genes, upregulate p53, and induce apoptosis in a hormone-sensitive prostate cancer cell line. Here we report that androgen response element (ARE)-targeted polyamides induced DNA replication stress in a hormone-insensitive prostate cancer cell line. The ATR checkpoint kinase was activated in response to this stress, causing phosphorylation of MCM2, and FANCD2 was monoubiquitinated. Surprisingly, little single-stranded DNA was exhibited, and the ATR targets RPA2 and Chk1 were not phosphorylated. We conclude that polyamide induces relatively low level replication stress, and suggest inhibition of the replicative helicase as a putative mechanism based on in vitro assays. We also demonstrate polyamide-induced inhibition of DNA replication in cell free extracts from X. laevis oocytes. In this system, inhibition of chromatin decondensation is observed, preventing DNA replication initiation. Finally, we show that Py-Im polyamides targeted to the ARE and ETS binding sequence downregulate AR- and ERG-driven signaling in a prostate cancer cell line harboring the TMPRSS2-ERG fusion. In a mouse xenograft model, ARE-targeted polyamide treatment reduced growth of the tumor.
" }, { "name": "McVay, Renee Catherine", "degree": "PhD", "year": "2016", "title": "Modeling the Effect of Vapor Wall Deposition on the Formation of Secondary Organic Aerosol in Chamber Studies", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172016-133615016", "creators": [ { "name": { "family": "McVay", "given": "Renee Catherine" }, "id": "McVay-Renee-Catherine", "orcid": "0000-0001-7766-5009", "display_name": "McVay, Renee Catherine" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9FX77DG", "abstract": "Laboratory chamber experiments are used to investigate formation of secondary organic aerosol (SOA) from biogenic and anthropogenic precursors under a variety of environmental conditions. Simulations of these experiments test our understanding of the prevailing chemistry of SOA formation as well as the dynamic processes occurring in the chamber itself. One dynamic process occurring in the chamber that was only recently recognized is the deposition of vapor species to the Teflon walls of the chamber. Low-volatility products formed from the oxidation of volatile organic compounds (VOCs) deposit on the walls rather than forming SOA, decreasing the amount of SOA formed (quantified as the SOA yield: mass of SOA formed per mass of VOC reacted). In this work, several modeling studies are presented that address the effect of vapor wall deposition on SOA formation in chambers.\r\n\r\nA coupled vapor-particle dynamics model is used to examine the competition among the rates of gas-phase oxidation to low volatility products, wall deposition of these products, and mass transfer to the particle phase. The relative time scales of these rates control the amount of SOA formed by affecting the influence of vapor wall deposition. Simulations show that an effect on SOA yield of changing the vapor-particle mass transfer rate is only observed when SOA formation is kinetically limited. For systems with kinetically limited SOA formation, increasing the rate of vapor-particle mass transfer by increasing the concentration of seed particles is an effective way to minimize the effect of vapor wall deposition.
\r\n\r\nThis coupled vapor-particle dynamics model is then applied to α-pinene ozonolysis SOA experiments. Experiments show that the SOA yield is affected when changing the oxidation rate but not when changing the rate of gas-particle mass transfer by changing the concentration of seed particles. Model simulations show that the absence of an effect of changing the seed particle concentration is consistent with SOA formation being governed by quasi-equilibrium growth, in which gas-particle equilibrium is established much faster than the rate of change of the gas-phase concentration. The observed effect of oxidation rate on SOA yield arises due to the presence of vapor wall deposition: gas-phase oxidation products are produced more quickly and condense preferentially onto seed particles before being lost to the walls. Therefore, for α-pinene ozonolysis, increasing the oxidation rate is the most effective way to mitigate the influence of vapor wall deposition.
\r\n\r\nFinally, the detailed model GECKO-A (Generator for Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to simulate α-pinene photooxidation SOA experiments. Unexpectedly, α-pinene OH oxidation experiments show no effect when changing either the oxidation rate or the vapor-particle mass transfer rate, whereas GECKO-A predicts that changing the oxidation rate should drastically affect the SOA yield. Sensitivity studies show that the assumed magnitude of the vapor wall deposition rate can greatly affect conclusions drawn from comparisons between simulations and experiments. If vapor wall loss in the Caltech chamber is of order 10-5 s-1, GECKO-A greatly overpredicts SOA during high UV experiments, likely due to an overprediction of second-generation products. However, if instead vapor wall loss in the Caltech chamber is of order 10-3 s-1, GECKO-A greatly underpredicts SOA during low UV experiments, possibly due to missing autoxidation pathways in the α-pinene mechanism.
" }, { "name": "Nielander, Adam Christopher", "degree": "PhD", "year": "2016", "title": "Chemical and Electrochemical Behavior of Graphene-Covered Silicon Photoanodes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:03042016-133215131", "creators": [ { "name": { "family": "Nielander", "given": "Adam Christopher" }, "id": "Nielander-Adam-Christopher", "orcid": "0000-0002-3639-2427", "display_name": "Nielander, Adam Christopher" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92R3PNB", "abstract": "This dissertation describes efforts over the last five years to develop protective layers for semiconductor photoelectrodes based on monolayer or few-layer graphene sheets. Graphene is an attractive candidate for a protective layer because of its known chemical inertness, transparency, ease of deposition, and limited number of electronic states. Monolayer graphene was found to effectively inhibit loss of photocurrent over 1000 seconds at n-Si/aqueous electrolyte interfaces that exhibit total loss over photocurrent over 100 seconds. Further, the presence of graphene was found to effect only partial Fermi level pinning at the Si/graphene interface with respect to a range of nonaqueous electrolytes. Fluorination of graphene was found to extend the stability imparted on n-Si by the monolayer sheet in aqueous Fe(CN)63-/4- electrolyte to over 100,000 seconds. It was demonstrated that the stability of the photocurrent of n-Si/fluorinated graphene/aqueous electrolyte interfaces relative to n-Si/aqueous electrolyte interfaces is likely attributable to the inhibition of oxidation of the silicon surface.
\r\n\r\nThis dissertation also relates efforts to describe and define terminology relevant to the field of photoelectrochemistry and solar fuels production. Terminology describing varying interfaces employed in electrochemical solar fuels devices are defined, and the research challenges associated with each are discussed. Methods for determining the efficiency of varying photoelectrochemical and solar-fuel-producing cells from the current-voltage behavior of the individual components of such a device without requiring the device be constructed are described, and a range of commonly employed performance metrics are explored.\t
\r\n" }, { "name": "Owens, Gwen Ellen", "degree": "PhD", "year": "2016", "title": "Biochemical and Biophysical Characterization of Huntingtin", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042015-142900908", "creators": [ { "name": { "family": "Owens", "given": "Gwen Ellen" }, "id": "Owens-Gwen-Ellen", "orcid": "0000-0003-0793-1994", "display_name": "Owens, Gwen Ellen" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Zinn", "given": "Kai George" }, "id": "Zinn-K-G", "orcid": "0000-0002-6706-5605", "role": "member", "display_name": "Zinn, Kai George" }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9TM7835", "abstract": "Huntington\u2019s disease (HD) is a fatal autosomal dominant neurodegenerative disease. HD has no cure, and patients pass away 10-20 years after the onset of symptoms. The causal mutation for HD is a trinucleotide repeat expansion in exon 1 of the huntingtin gene that leads to a polyglutamine (polyQ) repeat expansion in the N-terminal region of the huntingtin protein. Interestingly, there is a threshold of 37 polyQ repeats under which little or no disease exists; and above which, patients invariably show symptoms of HD. The huntingtin protein is a 350 kDa protein with unclear function. As the polyQ stretch expands, its propensity to aggregate increases with polyQ length. Models for polyQ toxicity include formation of aggregates that recruit and sequester essential cellular proteins, or altered function producing improper interactions between mutant huntingtin and other proteins. In both models, soluble expanded polyQ may be an intermediate state that can be targeted by potential therapeutics.
\r\n\r\nIn the first study described herein, the conformation of soluble, expanded polyQ was determined to be linear and extended using equilibrium gel filtration and small-angle X-ray scattering. While attempts to purify and crystallize domains of the huntingtin protein were unsuccessful, the aggregation of huntingtin exon 1 was investigated using other biochemical techniques including dynamic light scattering, turbidity analysis, Congo red staining, and thioflavin T fluorescence. Chapter 4 describes crystallization experiments sent to the International Space Station and determination of the X-ray crystal structure of the anti-polyQ Fab MW1. In the final study, multimeric fibronectin type III (FN3) domain proteins were engineered to bind with high avidity to expanded polyQ tracts in mutant huntingtin exon 1. Surface plasmon resonance was used to observe binding of monomeric and multimeric FN3 proteins with huntingtin.
" }, { "name": "Pan, Dorothy Weichi", "degree": "PhD", "year": "2016", "title": "Development of a Cationic Mucic Acid Polymer-Based Nanoparticle siRNA Delivery System", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092016-155820873", "creators": [ { "name": { "family": "Pan", "given": "Dorothy Weichi" }, "id": "Pan-Dorothy-Weichi", "orcid": "0000-0003-4066-7750", "display_name": "Pan, Dorothy Weichi" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9VM497J ", "abstract": "Cancer chemotherapy has advanced from highly toxic drugs to more targeted treatments in the last 70 years. Chapter 1 opens with an introduction to targeted therapy for cancer. The benefits of using a nanoparticle to deliver therapeutics are discussed. We move on to siRNA in particular, and why it would be advantageous as a therapy. Specific to siRNA delivery are some challenges, such as nuclease degradation, quick clearance from circulation, needing to enter cells, and getting to the cytosol. We propose the development of a nanoparticle delivery system to tackle these challenges so that siRNA can be effective.
\r\n\r\nChapter 2 of this thesis discusses the synthesis and analysis of a cationic mucic acid polymer (cMAP) which condenses siRNA to form a nanoparticle. Various methods to add polyethylene glycol (PEG) for stabilizing the nanoparticle in physiologic solutions, including using a boronic acid binding to diols on mucic acid, forming a copolymer of cMAP with PEG, and creating a triblock with mPEG on both ends of cMAP. The goal of these various pegylation strategies was to increase the circulation time of the siRNA nanoparticle in the bloodstream to allow more of the nanoparticle to reach tumor tissue by the enhanced permeation and retention effect. We found that the triblock mPEG-cMAP-PEGm polymer condensed siRNA to form very stable 30-40 nm particles that circulated for the longest time \u2013 almost 10% of the formulation remained in the bloodstream of mice 1 h after intravenous injection.
\r\n\r\nChapter 3 explores the use of an antibody as a targeting agent for nanoparticles. Some antibodies of the IgG1 subtype are able to recruit natural killer cells that effect antibody dependent cellular cytotoxicity (ADCC) to kill the targeted cell to which the antibody is bound. There is evidence that the ADCC effect remains in antibody-drug conjugates, so we wanted to know whether the ADCC effect is preserved when the antibody is bound to a nanoparticle, which is a much larger and complex entity. We utilized antibodies against epidermal growth factor receptor with similar binding and pharmacokinetics, cetuximab and panitumumab, which differ in that cetuximab is an IgG1 and panitumumab is an IgG2 (which does not cause ADCC). Although a natural killer cell culture model showed that gold nanoparticles with a full antibody targeting agent can elicit target cell lysis, we found that this effect was not preserved in vivo. Whether this is due to the antibody not being accessible to immune cells or whether the natural killer cells are inactivated in a tumor xenograft remains unknown. It is possible that using a full antibody still has value if there are immune functions which are altered in a complex in vivo environment that are intact in an in vitro system, so the value of using a full antibody as a targeting agent versus using an antibody fragment or a protein such as transferrin is still open to further exploration.
\r\n\r\nIn chapter 4, nanoparticle targeting and endosomal escape are further discussed with respect to the cMAP nanoparticle system. A diboronic acid entity, which gives an order of magnitude greater binding (than boronic acid) to cMAP due to the vicinal diols in mucic acid, was synthesized, attached to 5kD or 10kD PEG, and conjugated to either transferrin or cetuximab. A histidine was incorporated into the triblock polymer between cMAP and the PEG blocks to allow for siRNA endosomal escape. Nanoparticle size remained 30-40 nm with a slightly negative ca. -3 mV zeta potential with the triblock polymer containing histidine and when targeting agents were added. Greater mRNA knockdown was seen with the endosomal escape mechanism than without. The nanoparticle formulations were able to knock down the targeted mRNA in vitro. Mixed effects suggesting function were seen in vivo.
\r\n\r\nChapter 5 summarizes the project and provides an outlook on siRNA delivery as well as targeted combination therapies for the future of personalized medicine in cancer treatment.
\r\n" }, { "name": "Perez, Kathryn A.", "degree": "PhD", "year": "2016", "title": "Structural and Biochemical Characterization of Ligand Bound States of the FeMo-Cofactor of Nitrogenase", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262016-050606547", "creators": [ { "name": { "family": "Perez", "given": "Kathryn A." }, "id": "Perez-Kathryn-A", "display_name": "Perez, Kathryn A." } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9M043DX", "abstract": "Nitrogenase is the only known enzyme capable of nitrogen fixation, the reduction of dinitrogen to ammonia, a metabolically available form of nitrogen. Developing an understanding of the complex mechanism required for biological nitrogen fixation requires that the enzyme be characterized in catalytically relevant states, such as those involving ligand binding and reduction. Nitrogenase catalyzes this reaction through the cyclic interaction of two metalloproteins, the Fe-protein and the MoFe-protein which contain three distinct metalloclusters, in an ATP-hydrolysis dependent electron transfer reaction. The binding and subsequent reduction of substrates requires multiple electrons donated from the Fe-protein to the MoFe-protein, in which the active site is located. In this study, we have structurally characterized the binding of two inhibitors to the FeMo-cofactor, CO and the Se of SeCN-. Both interactions involve the displacement of a single S, and the Se was used as a label to follow the interchange of three S sites within the FeMo-cofactor during catalysis. These finding change any future approaches to characterize the mechanism of biological nitrogen fixation, requiring that structural changes be considered for substrate binding and reduction." }, { "name": "Post, Michael Robert", "degree": "PhD", "year": "2016", "title": "Agonist Binding Studies at Two Subtypes of the Nicotinic Acetylcholine Receptor Involved in Parkinson\u2019s Disease and Addiction", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072016-160630609", "creators": [ { "name": { "family": "Post", "given": "Michael Robert" }, "id": "Post-Michael-Robert", "orcid": "0000-0002-3214-7619", "display_name": "Post, Michael Robert" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "co-chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9GT5K50", "abstract": "Neuronal nicotinic acetylcholine receptors (nAChR) consist of pentameric ligand gated ion channels that typically regulate the release of neurotransmitter. This group of receptors is made of many subunits that combine into pentamers to form different subtypes, with each subtype having a unique pharmacology, function, and localization in the nervous system. The \u03b16\u03b22 subtype is found predominantly in the dopaminergic pathways in the brain, and is therefore a promising target for addiction and Parkinson\u2019s disease. A major goal in treating these disorders is to develop subtype-selective agonists, and advanced knowledge of the binding site which sits at the \u03b16-\u03b22 subunit interface is critical. This thesis dissertation describes high precision, chemical scale structure-function studies designed to probe specific interactions between a variety of agonists and the amino acids which make up the \u03b16\u03b22 binding site.
\r\n\r\nBefore these studies, which utilize nonsense suppression-based non-canonical amino acid mutagenesis, could be conducted, a heterologous expression system for \u03b16\u03b22 had to be developed.
\r\n\r\nChapter 2 details four reporter mutations that allow high expression levels of \u03b16\u03b22 in Xenopus oocytes. Further work presented in this chapter characterizes a variety of compounds at this subtype including acetylcholine, the endogenous agonist, nicotine, and TC299423, a promising drug candidate designed to be \u03b16-selective.
\r\n\r\nChapters 3 and 4 discuss the structure-function studies used to probe for binding interactions of acetylcholine, nicotine, and TC299423 with the \u03b16-\u03b22 interface. Fluorination series were executed to probe for cation-\u03c0 interactions with TrpB, TyrA, and TyrC2, all sites of the \u03b16 face. Of the nine possible agonist-side chain interactions, the only functionally important cation-\u03c0 interaction was found between acetylcholine and TrpB, suggesting the subtype has a unique pharmacology. Studies utilizing \u03b1-hydroxy acids were then performed to determine whether these agonists make a functional hydrogen bond between their amine NH and the backbone carbonyl associated with TrpB. Here, nicotine was found to make a strong hydrogen bond, whose energy was quantified via double-mutant cycle analysis, but TC299423 was not.
\r\n\r\nChapter 5 further explores TC299423 at the \u03b14\u03b22 subtype. Experiments here showed that TC299423 makes a dual cation-\u03c0 interaction with both TrpB and TyrC2. Further studies revealed this dual cation-\u03c0 effect to be true for several secondary amines, and a structure-function study with nornicotine established this as a general feature for secondary amines.
\r\n\r\nChapter 6 describes work done to probe for a hydrogen bond between the indole NH of \u03b14 TrpB and a backbone carbonyl associated with L119 on the \u03b22 subunit. This study required development of a new strategy to probe for hydrogen bonds as the amino acid sequence does not allow for \u03b1-hydroxy substitution. Instead, a fluorinated side chain strategy was used to inductively attenuate the hydrogen bond accepting ability of the carbonyl, and it proved the \u03b14-\u03b22 interfacial hydrogen prediction false.
\r\n\r\nFinally two appendices suggest possible avenues to explore with the new \u03b16\u03b22 expression system. Appendix A describes work done to determine whether there is cross-talk between \u03b16\u03b22 and P2X receptors. Appendix B details initial investigations on the effects of ethanol and other alcohols on the function of \u03b16\u03b22.
" }, { "name": "Quigley, Brendan Liam", "degree": "PhD", "year": "2016", "title": "Understanding Selectivity and Activity in Z-selective Metathesis with Cyclometallated Ru-based Catalysts ", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052016-231830980", "creators": [ { "name": { "family": "Quigley", "given": "Brendan Liam" }, "id": "Quigley-Brendan-Liam", "display_name": "Quigley, Brendan Liam" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z96W984J", "abstract": "With the advent of well-defined highly active catalysts, olefin metathesis has become a powerful tool for the formation of carbon\u2013carbon double bonds in a variety of settings. However, these traditional catalysts preferentially form the E-alkene product. Recent efforts have yielded several families of Z-selective metathesis catalysts, including a family of Ru complexes with cyclometallated NHC ligands developed in our group. The work in this thesis describes efforts to develop an improved understanding of the catalyst features that govern activity and selectivity in the cyclometallated Ru-based catalysts, as well as to expand the scope of reactivity in these systems.
\r\n\r\nChapter 1 provides an outline of the key features that govern selectivity in cross metathesis applications.
\r\n\r\nChapter 2 describes the application of cyclometallated Ru-based catalysts in Z-selective cross metathesis (CM) of allylic-substituted olefins. Efficient CM is demonstrated in the case of acrolein acetals providing a new route to access Z-\u03b1,\u03b2-unsaturated acetals and aldehydes. For a variety of other allylic-substituted olefins, reactivity was lower but could be correlated with the structure of the catalyst and substrate. The implications of the observed reactivity are discussed and contextualized with regard to reactivity of previous metathesis catalysts.
\r\n\r\nChapter 3 describes the development of a series of cyclometallated Z-selective metathesis with varying N-aryl groups that allow elucidation of the key catalyst features that govern activity and selectivity in these systems. The synthesis of the catalyst series is described, including several strategies employed to circumvent unexpected side-reactions. The second part of the chapter focuses on the dynamic behavior of the catalysts in solution and studies of an unusual C\u2013H\u00b7\u00b7\u00b7\u00b7F\u2013C intramolecular interaction observed in some of these catalysts. Finally, the reactivity of these catalysts in a variety of CM applications are discussed, which allows for development of a refined model of how the N-aryl group affects Z-selectivity and activity in these catalysts systems and how this varies across different classes of substrate.
" }, { "name": "Rao, Meera", "degree": "PhD", "year": "2016", "title": "Mechanisms of Regulation and Fidelity in Tail-Anchored Membrane Protein Targeting", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232016-135949451", "creators": [ { "name": { "family": "Rao", "given": "Meera" }, "id": "Rao-Meera", "orcid": "0000-0001-8650-6253", "display_name": "Rao, Meera" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9G73BQN", "abstract": "Accurate protein localization is crucial to generate and to maintain cellular organization. Achieving accuracy is challenging, as the molecular signals that dictate a protein\u2019s destination are often promiscuous. The localization of tail-anchored (TA) proteins, whose transmembrane domain resides at its extreme C-terminus, presents major challenges to protein targeting machineries. This dissertation explores how TA capture and release are spatially and temporally regulated in the Guided Entry of Tail Anchored proteins (GET) pathway and how endoplasmic reticulum (ER) destined TAs are targeted with high fidelity.
\r\n\r\nA quantitative framework of the Get3 ATPase cycle reveals that ATP and GET pathway effector proteins specifically induce multiple conformational changes in Get3, which culminate in the ATPase activation that drives unidirectional targeting in the pathway. The Get4/5 TA loading complex locks Get3 in the ATP-bound state that is primed for TA protein capture, whereas the TA substrate induces tetramerization of Get3 and activates its ATPase reaction.
\r\n\r\nAdditional analyses define multiple physicochemical features that distinguish TA proteins destined to different organelles. The GET pathway selects for these features at distinct stages using mechanisms such as differential binding, induced fit, and kinetic proofreading after ATP hydrolysis by Get3. These results reveal new roles for the cochaperone Sgt2 in providing key selection filters, and provide a biological logic for the complex cascade of substrate relay events during post-translational membrane protein targeting.
" }, { "name": "Regan, Clinton Joseph", "degree": "PhD", "year": "2016", "title": "Photochemical Strategies to Decage Organic Compounds", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082016-025813806", "creators": [ { "name": { "family": "Regan", "given": "Clinton Joseph" }, "id": "Regan-Clinton-Joseph", "display_name": "Regan, Clinton Joseph" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9C53HTF", "abstract": "This dissertation primarily describes new photochemical decaging systems that are activated by visible light. Such systems are expected to be useful as chemical biology tools or as drug delivery systems in a therapeutic context. A primary motivation for the development of these systems is for the treatment of traumatic brain injury, where a decaging strategy would require activation by low energy near-infrared light. Since most photochemical reactions are initiated using ultraviolet light, a primary challenge in developing these systems is overcoming the low energy efficiency of typical photochemical processes. Initial model systems are designed to address this challenge through use of the photoacidic effect. While many hydroxyaromatic compounds are known to become much more acidic in their excited state, the effect has never been utilized to accelerate an acid-catalyzed chemical reaction. Investigations are carried out in Chapter 2 to probe for the possibility of this unprecedented photochemistry. Ultimately, the results suggest that the acid-catalyzed decaging processes are too slow to be useful in a photochemical context. This finding led to the development of decaging strategies that utilize a phototriggered approach. In Chapter 2, a system is described where decaging occurs through rapid lactonization of a photogenerated hydroquinone. Formation of the hydroquinone results from an intramolecular photoreduction of the benzoquinone due to activation by violet light. Detailed mechanistic studies carried out on this system ultimately establish the importance of the triplet state in the overall reaction. While most benzoquinones form the triplet with unit efficiency, the system studied here forms the triplet in less than 10% yield. However, when the triplet is formed, it proceeds cleanly to products with high efficiency. Although the benzoquinone system has been useful for mechanistic studies, its application as a therapeutic decaging strategy has been challenging. Efforts to extend the wavelength toward the near-infrared have led to loss in photochemical reactivity. Ultimately, this challenge was overcome through the use of methylene blue. Methylene blue is a common organic dye that is activated by red light and undergoes photoreduction to a colorless form, similar to the benzoquinone systems. In Chapter 4, derivatives of methylene blue that are capable of undergoing photoreductive cyclization are designed and synthesized. Ultimately, these systems are found to be capable of rapidly decaging alcohols using red light." }, { "name": "Rittle, Jonathan Daniel", "degree": "PhD", "year": "2016", "title": "Proton-Coupled Reduction of N\u2082 Facilitated by Molecular Fe Complexes", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12012015-124453213", "creators": [ { "name": { "family": "Rittle", "given": "Jonathan Daniel" }, "id": "Rittle-Jonathan-Daniel", "display_name": "Rittle, Jonathan Daniel" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9QJ7F7D", "abstract": "The activation of Fe-coordinated N2 via the formal addition of hydrogen atom equivalents is explored in this thesis. These reactions may occur in nitrogenase enzymes during the biological conversion of N2 to NH3. To understand these reactions, the N2 reactivity of a series of molecular Fe(N2) platforms is investigated. A trigonal pyramidal, carbon-ligated FeI complex was prepared that displays a similar geometry to that of the resting state 'belt' Fe atoms of nitrogenase. Upon reduction, this species was shown to coordinate N2, concomitant with significant weakening of the C-Fe interaction. This hemilability of the axial ligand may play a critical role in mediating the interconversion of Fe(NxHy) species during N2 conversion to NH3. In fact, a trigonal pyramidal borane-ligated Fe complex was shown to catalyze this transformation, generating up to 8.49 equivalents of NH3. To shed light on the mechanistic details of this reaction, protonation of a borane-ligated Fe(N2) complex was investigated and found to give rise to a mixture of species that contains an iron hydrazido(2-) [Fe(NNH2)] complex. The identification of this species is suggestive of an early N-N bond cleavage event en route to NH3 production, but the highly-reactive nature of this complex frustrated direct attempts to probe this possibility. A structurally-analogous silyl-ligated Fe(N2) complex was found to react productively with hydrogen atom equivalents, giving rise to an isolable Fe(NNH2) species. Spectroscopic and crystallographic studies benefited from the enhanced stability of this complex relative to the borane analogue. One-electron reduction of this species initiates a spontaneous disproportionation reaction with an iron hydrazine [Fe(NH2NH2)] complex as the predominant reaction product. This transformation provides support for an Fe-mediated N2 activation mechanism that proceeds via a late N-N bond cleavage. In hopes of gaining more fundamental insight into these reactions, a series of Fe(CN) complexes were prepared and reacted with hydrogen-atom equivalents. Significant quantities of CH4 and NH3 are generated in these reactions as a result of complete C-N bond activation. A series of Fe(CNHx) were found to be exceptionally stable and may be intermediates in these reactions. The stability of these compounds permitted collection of thermodynamic parameters pertinent to the unique N-H bonds. This data is comparatively discussed with the theoretically-predicted data of the N2-derived Fe(NNHx) species. Exceptionally-weak N-H bond enthalpies are found for many of these compounds, and sheds light on their short-lived nature and tendency to evolve H2. As a whole, these works both establish and provide a means to understand Fe-mediated N2 activation via the addition of hydrogen atom equivalents." }, { "name": "Schmidt, Joel Edward", "degree": "PhD", "year": "2016", "title": "Imidazolium-Based Organic Structure Directing Agents for the Synthesis of Microporous Materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062015-163035886", "creators": [ { "name": { "family": "Schmidt", "given": "Joel Edward" }, "id": "Schmidt-Joel-Edward", "orcid": "0000-0002-0039-2863", "display_name": "Schmidt, Joel Edward" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z96H4FBM", "abstract": "The central theme of this thesis is the use of imidazolium-based organic structure directing agents (OSDAs) in microporous materials synthesis. Imidazoliums are advantageous OSDAs as they are relatively inexpensive and simple to prepare, show robust stability under microporous material synthesis conditions, have led to a wide range of products, and have many permutations in structure that can be explored. The work I present involves the use of mono-, di-, and triquaternary imidazolium-based OSDAs in a wide variety of microporous material syntheses. Much of this work was motivated by successful computational predictions (Chapter 2) that led me to continue to explore these types of OSDAs. Some of the important discoveries with these OSDAs include the following: 1) Experimental evaluation and confirmation of a computational method that predicted a new OSDA for pure-silica STW, a desired framework containing helical pores that was previously very difficult to synthesize. 2) Discovery of a number of new imidazolium OSDAs to synthesize zeolite RTH, a zeolite desired for both the methanol-to-olefins reaction as well as NOX reduction in exhaust gases. This discovery enables the use of RTH for many additional investigations as the previous OSDA used to make this framework was difficult to synthesize, such that no large scale preparations would be practical. 3) The synthesis of pure-silica RTH by topotactic condensation from a layered precursor (denoted CIT-10), that can also be pillared to make a new framework material with an expanded pore system, denoted CIT-11, that can be calcined to form a new microporous material, denoted CIT-12. CIT-10 is also interesting since it is the first layered material to contain 8 membered rings through the layers, making it potentially useful in separations if delamination methods can be developed. 4) The synthesis of a new microporous material, denoted CIT-7 (framework code CSV) that contains a 2-dimensional system of 8 and 10 membered rings with a large cage at channel intersections. This material is especially important since it can be synthesized as a pure-silica framework under low-water, fluoride-mediated synthesis conditions, and as an aluminosilicate material under hydroxide mediated conditions. 5) The synthesis of high-silica heulandite (HEU) by topotactic condensation as well as direct synthesis, demonstrating new, more hydrothermally stable compositions of a previously known framework. 6) The synthesis of germanosilicate and aluminophosphate LTA using a triquaternary OSDA. All of these materials show the diverse range of products that can be formed from OSDAs that can be prepared by straightforward syntheses and have made many of these materials accessible for the first time under facile zeolite synthesis conditions. " }, { "name": "Segal, Helen Muriel", "degree": "PhD", "year": "2016", "title": "Electrochemical Methods to Study Iron-Sulfur Cluster Proteins", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-131059745", "creators": [ { "name": { "family": "Segal", "given": "Helen Muriel" }, "id": "Segal-Helen-Muriel", "display_name": "Segal, Helen Muriel" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92Z13HT", "abstract": "Electron transfer between proteins is an important mechanism in multiple biological processes. In this thesis, methods were developed to study electron transfer in two biological contexts: 1) DNA-mediated signaling between DNA binding proteins with 4Fe-4S clusters and 2) nitrogenase.
\r\n\r\nThe first portion of this thesis focuses on the spectroscopic and electrochemical characterization of the iron-sulfur cluster in Dna2. Dna2 is a helicase-nuclease that is involved in Okazaki fragment maturation, double strand break repair, mitochondrial genome maintenance, and telomere maintenance. Dna2 is one of multiple DNA repair and replication proteins that contain a 4Fe-4S cluster, a cofactor that generally participates in electron transfer processes. It has been proposed that these enzymes may use their 4Fe-4S clusters to signal one another over large molecular distances to coordinate their activity on biological time scales through DNA-mediated redox chemistry. A combination of EPR and UV-visible absorption spectroscopy along with electrochemistry studies on DNA-modified gold electrodes was performed to provide insight into the chemical characteristics of the 4Fe-4S cluster in Dna2. These studies also provide a foundation for how DNA charge transport might coordinate the action of eukaryotic DNA repair and replication proteins with 4Fe-4S clusters.
\r\n\r\nThe second portion of this thesis describes the development of electrochemical methods to study nitrogenase, the enzyme that catalyzes the reduction of atmospheric dinitrogen to bioavailable ammonia. First, flavodoxin II, the biological reductant of the Fe-protein of nitrogenase, was characterized using a combination of electrochemical and structural methods to determine the molecular interactions that facilitate reduction of the nitrogenase iron protein. Second, two electrochemical methods, edge-plane pyrolytic graphite electrodes and single crystal gold electrodes modified with \u03c9-functionalized alkane-thiols, were adapted to study the redox chemistry at the iron-sulfur cluster of the Fe-protein. These studies provided insight into both the fundamental characteristics of electron transfer reactions involving nitrogenase, as well as insight into how to better study this enzyme using electrochemical methods.
\r\n\r\n" }, { "name": "Shafaat, Oliver Syed", "degree": "PhD", "year": "2016", "title": "Temporal Control of Ion Channel Activation", "advisor": "Gray, Harry B.; Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122016-095434020", "creators": [ { "name": { "family": "Shafaat", "given": "Oliver Syed" }, "id": "Shafaat-Oliver-Syed", "orcid": "0000-0002-3170-2553", "display_name": "Shafaat, Oliver Syed" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "co-advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z98P5XGX", "abstract": "Ion channels are a large class of integral membrane proteins that allow for the diffusion of ions across a cellular membrane and are found in all forms of life. Pentameric ligand-gated ion channels (pLGICs) comprise a large family of proteins that include the nicotinic acetylcholine receptor (nAChR) and the \u03b3-aminobutyric acid (GABA) receptor. These ion channels are responsible for the fast synaptic transmission that occurs in humans and as a result are of fundamental biological importance. pLGICs bind ligands (neurotransmitters), and upon ligand-binding undergo activation. The activation event causes an ion channel to enter a new physical state that is able to conduct ions. Ion channels allow for the flux of ions across the membrane through a pore that is formed upon ion channel activation. For pLGICs to function properly both ligand-binding and ion channel activation must occur. The ligand-binding event has been studied extensively over the past few decades, and a detailed mechanism of binding has emerged. During activation the ion channel must undergo structural rearrangements that allow the protein to enter a conformation in which ions can flow through. Despite this great and ubiquitous importance, a fundamental understanding of the ion channel activation mechanism and kinetics, as well as concomitant structural arrangements, remains elusive.
\r\n\r\nThis dissertation describes efforts that have been made to temporally control the activation of ligand-gated ion channels. Temporal control of ion channel activation provides a means by which to activate ion channels when desired. The majority of this work examines the use of light to activate ion channels. Several photocages were examined in this thesis; photocages are molecules that release a ligand under irradiation, and, for the work described here, the released ligand then activates the ion channel. First, a new water-soluble photoacid was developed for the activation\r\nof proton-sensitive ion channels. Activation of acid-sensing ion channels, ASIC2a and GLIC, was observed only upon irradiation. Next, a variety of Ru2+ photocages were also developed for the release of amine ligands. The Ru2+ systems interacted in a deleterious manner with a representative subset of biologically essential ion channels. The rapid mixing of ion channels with agonist was also examined. A detection system was built to monitor ion channels activation in the rapid mixing experiments. I have shown that liposomes, and functionally-reconstituted ELIC, are not destroyed during the mixing process. The work presented here provides the means to deliver agonist to ligand-gated ion channels in a controlled fashion.
\r\n\r\n" }, { "name": "Shaner, Matthew Reed", "degree": "PhD", "year": "2016", "title": "An Experimental and Technoeconomic Study of Silicon Microwire Arrays for Fuel Production Using Solar Energy", "advisor": "Lewis, Nathan Saul; Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312016-151045544", "creators": [ { "name": { "family": "Shaner", "given": "Matthew Reed" }, "id": "Shaner-Matthew-Reed", "orcid": "0000-0003-4682-9757", "display_name": "Shaner, Matthew Reed" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-advisor", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "co-advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z98C9T7Z", "abstract": "Direct solar energy conversion is one of few sustainable energy resources able to wholly satisfy global energy demand; however, utility scale adoption and reliance are currently limited by the lack of a cost effective energy storage technology. The production of fuel from sunlight (solar fuels) enables solar energy storage in chemical bonds, a volumetrically and gravimetrically dense form compatible with current infrastructure worldwide. Hydrogen production via water splitting is a first generation solar fuel targeted herein that is currently used for hydrocarbon up-grading and fertilizer production and could further be utilized in combustion cycles and/or fuel cells for electricity and heat production and transportation.
\r\n\r\nThis thesis presents achievements that form the foundation for Si microwire array based solar water splitting devices beginning with a tandem junction device design using Si microwire arrays as the architectural motif and one of many active components. Si microwire arrays have potential advantages over two dimensional planar device architectures such as minimized resistance losses, lower semiconductor material usage, and embedment in a polymeric membrane enabling a flexible device.
\r\n\r\nExperimental fabrication and characterization of this tandem junction device design was realized in the form of a np+-Si microwire array coated by either tungsten oxide (WO3) or titanium dioxide (TiO2) as the second tandem semiconductor. The Si/TiO2 device demonstrated the highest performance with an expected solar-to-hydrogen efficiency of 0.39%. To achieve these demonstrations new processing methods were needed and developed for formation of the np+-Si microwire array homojunction and formation of a low resistance contact between the p+-Si and second semiconductor using sputtered tin- doped indium oxide (ITO) and spray pyrolyzed fluorine-doped tin oxide (FTO).
\r\n\r\nAnother achievement includes demonstration of the longest known (>2200 hours) photoanode stability for water oxidation using a np+-Si microwire array coated with an in-house developed amorphous TiO2 protection layer and NiCrOx electrocatalyst. Additionally, the Si microwire array architecture was used to enable decoupling of semiconductor light absorption and catalytic activity, two performance metrics that ideally are maximized simultaneously. However, all previous demonstrations have shown anti-correlation between these performance metrics because planar architectures are subject to a trade-off where adding electrocatalyst increases catalytic activity, but decreases semiconductor light absorption and vice versa.
\r\n\r\nFinally, a techno-economic analysis of solar water splitting production facilities was performed to assess economic competitiveness because this is the ultimate metric by which all energy production technologies are currently evaluated. This analysis suggests that a hydrogen production facility that is cosmetically similar to current solar panel installations with hydrogen collection from distributed tilted panels is unlikely to achieve cost competitiveness with fossil fuel derived hydrogen due to the balance of systems costs alone. A cost of CO2 greater than ~$800 (ton CO2)-1 was estimated to be necessary for the least expensive base-case solar-to-hydrogen system to reach price parity with hydrogen derived from steam reforming of methane priced at $3 (MM BTU)-1 ($1.39 (kg H2)-1). Direct CO2 reduction systems were also explored and resulted in even larger challenges than hydrogen production. Accordingly, major facility wide breakthroughs are required to obtain viable economic costs for solar hydrogen production, but the barriers to achieve cost-competitiveness with existing large-scale thermochemical processes for CO2 reduction are even greater.
" }, { "name": "Sutherland, Alexander Muir", "degree": "PhD", "year": "2016", "title": "Technology for Single Cell Protein Analysis in Immunology and Cancer Prognostics", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10012015-132559997", "creators": [ { "name": { "family": "Sutherland", "given": "Alexander Muir" }, "id": "Sutherland-Alexander-Muir", "display_name": "Sutherland, Alexander Muir" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9PK0D3K", "abstract": "The first chapter of this thesis deals with automating data gathering for single cell microfluidic tests. The programs developed saved significant amounts of time with no loss in accuracy. The technology from this chapter was applied to experiments in both Chapters 4 and 5.
\r\n\r\nThe second chapter describes the use of statistical learning to prognose if an anti-angiogenic drug (Bevacizumab) would successfully treat a glioblastoma multiforme tumor. This was conducted by first measuring protein levels from 92 blood samples using the DNA-encoded antibody library platform. This allowed the measure of 35 different proteins per sample, with comparable sensitivity to ELISA. Two statistical learning models were developed in order to predict whether the treatment would succeed. The first, logistic regression, predicted with 85% accuracy and an AUC of 0.901 using a five protein panel. These five proteins were statistically significant predictors and gave insight into the mechanism behind anti-angiogenic success/failure. The second model, an ensemble model of logistic regression, kNN, and random forest, predicted with a slightly higher accuracy of 87%.
\r\n\r\nThe third chapter details the development of a photocleavable conjugate that multiplexed cell surface detection in microfluidic devices. The method successfully detected streptavidin on coated beads with 92% positive predictive rate. Furthermore, chambers with 0, 1, 2, and 3+ beads were statistically distinguishable. The method was then used to detect CD3 on Jurkat T cells, yielding a positive predictive rate of 49% and false positive rate of 0%.
\r\n\r\nThe fourth chapter talks about the use of measuring T cell polyfunctionality in order to predict whether a patient will succeed an adoptive T cells transfer therapy. In 15 patients, we measured 10 proteins from individual T cells (~300 cells per patient). The polyfunctional strength index was calculated, which was then correlated with the patient's progress free survival (PFS) time. 52 other parameters measured in the single cell test were correlated with the PFS. No statistical correlator has been determined, however, and more data is necessary to reach a conclusion.
\r\n\r\nFinally, the fifth chapter talks about the interactions between T cells and how that affects their protein secretion. It was observed that T cells in direct contact selectively enhance their protein secretion, in some cases by over 5 fold. This occurred for Granzyme B, Perforin, CCL4, TNFa, and IFNg. IL- 10 was shown to decrease slightly upon contact. This phenomenon held true for T cells from all patients tested (n=8). Using single cell data, the theoretical protein secretion frequency was calculated for two cells and then compared to the observed rate of secretion for both two cells not in contact, and two cells in contact. In over 90% of cases, the theoretical protein secretion rate matched that of two cells not in contact.
" }, { "name": "Thomas, Daniel Aaron", "degree": "PhD", "year": "2016", "title": "Chemical Reaction Dynamics of the Liquid/Vapor Interface Studied by Mass Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182016-140524270", "creators": [ { "name": { "family": "Thomas", "given": "Daniel Aaron" }, "id": "Thomas-Daniel-Aaron", "orcid": "0000-0001-9415-5991", "display_name": "Thomas, Daniel Aaron" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9SN06XG", "abstract": "This thesis presents investigations of chemical reactions occurring at the liquid/vapor interface studied using novel sampling methodologies coupled with detection by mass spectrometry. Chapters 2 and 3 utilize the recently developed technique of field-induced droplet ionization mass spectrometry (FIDI-MS), in which the application of a strong electric field to a pendant microliter droplet results in the ejection of highly charged progeny droplets from the liquid surface. In Chapter 2, this method is employed to study the base-catalyzed dissociation of a surfactant molecule at the liquid/vapor interface upon uptake of ammonia from the gas phase. This process is observed to occur without significant modulation of the bulk solution pH, suggesting a transient increase in surface pH following the uptake of gaseous ammonia. Chapter 3 presents real-time studies of the oxidation of the model tropospheric organic compound glycolaldehyde by photodissociation of iron (III) oxalate complexes. The oxidation products of glycolaldehyde formed in this process are identified, and experiments in a deoxygenated environment identify the role of oxygen in the oxidation pathway and in the regeneration of iron (III) following photo-initiated reduction. Chapter 4 explores alternative methods for the study of heterogeneous reaction processes by mass spectrometric sampling from liquid surfaces. Bursting bubble ionization (BBI) and interfacial sampling with an acoustic transducer (ISAT) generate nanoliter droplets from a liquid surface that can be sampled via the atmospheric pressure interface of a mass spectrometer. Experiments on the oxidation of oleic acid by ozone using ISAT are also presented. Chapters 5 and 6 detail mechanistic studies and applications of free-radical-initiated peptide sequencing (FRIPS), a technique employing gas-phase free radical chemistry to the sequencing of peptides and proteins by mass spectrometry. Chapter 5 presents experimental and theoretical studies on the anomalous mechanism of dissociation observed in the presence of serine and threonine residues in peptides. Chapter 6 demonstrates the combination of FRIPS with ion mobility-mass spectrometry (IM-MS) for the separation of isomeric peptides." }, { "name": "Wang, Connie Yuan-Ying", "degree": "PhD", "year": "2016", "title": "Understanding Co-Translational Protein Targeting and Lithium Dendrite Formation through Free Energy Simulations and Coarse-Grained Models", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232016-092808469", "creators": [ { "name": { "family": "Wang", "given": "Connie Yuan-Ying" }, "id": "Wang-Connie-Yuan-Ying", "orcid": "0000-0003-2971-3971", "display_name": "Wang, Connie Yuan-Ying" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z97H1GHF", "abstract": "We describe the application of alchemical free energy methods and coarse-grained models to study two key problems: (i) co-translational protein targeting and insertion to direct membrane proteins to the endoplasmic reticulum for proper localization and folding, (ii) lithium dendrite formation during recharging of lithium metal batteries. We show that conformational changes in the signal recognition particle, a central component of the protein targeting machinery, confer additional specificity during the the recognition of signal sequences. We then develop a three-dimensional coarse-grained model to study the long-timescale dynamics of membrane protein integration at the translocon and a framework for the calculation of binding free energies between the ribosome and translocon. Finally, we develop a coarse-grained model to capture the dynamics of lithium deposition and dissolution at the electrode interface with time-dependent voltages to show that pulse plating and reverse pulse plating methods can mitigate dendrite growth." }, { "name": "Webb, Michael Anthony", "degree": "PhD", "year": "2016", "title": "Path-Integral and Coarse-Graining Strategies for Complex Molecular Phenomena", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-213050706", "creators": [ { "name": { "family": "Webb", "given": "Michael Anthony" }, "id": "Webb-Michael-Anthony", "orcid": "0000-0002-7420-4474", "display_name": "Webb, Michael Anthony" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "role": "member", "display_name": "Eiler, John M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z90Z7172", "abstract": "Molecular simulation provides a powerful tool for connecting molecular-level processes to physical observables. However, the facility to make those connections relies upon the application and development of theoretical methods that permit appropriate descriptions of the systems or processes to be studied. In this thesis, we utilize molecular simulation to study and predict two phenomena with very different theoretical challenges, beginning with (1) lithium-ion transport behavior in polymers and following with (2) equilibrium isotope effects with relevance to position-specific and clumped isotope studies. In the case of ion transport in polymers, there is motivation to use molecular simulation to provide guidance in polymer electrolyte design, but the length and timescales relevant for ion diffusion in polymers preclude the use of direct molecular dynamics simulation to compute ion diffusivities in more than a handful of candidate systems. In the case of equilibrium isotope effects, the thermodynamic driving forces for isotopic fractionation are often fundamentally quantum mechanical in nature, and the high precision of experimental instruments demands correspondingly accurate theoretical approaches. Herein, we describe respectively coarse-graining and path-integral strategies to address outstanding questions in these two subject areas." }, { "name": "Yuet, Kai P.", "degree": "PhD", "year": "2016", "title": "Tools For Spatiotemporally Specific Proteomic Analysis In Multicellular Organisms", "advisor": "Tirrell, David A.; Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252016-151033826", "creators": [ { "name": { "family": "Yuet", "given": "Kai P." }, "id": "Yuet-Kai-P", "orcid": "0000-0002-1381-8923", "display_name": "Yuet, Kai P." } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "co-advisor", "display_name": "Tirrell, David A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "co-advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "co-chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "co-chair", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9VD6WDH", "abstract": "The emergence of mass spectrometry-based proteomics has revolutionized the study of proteins and their abundances, functions, interactions, and modifications. However, in a multicellular organism, it is difficult to monitor dynamic changes in protein synthesis in a specific cell type within its native environment. In this thesis, we describe methods that enable the metabolic labeling, purification, and analysis of proteins in specific cell types and during defined periods in live animals. We first engineered a eukaryotic phenylalanyl-tRNA synthetase (PheRS) to selectively recognize the unnatural L-phenylalanine analog p-azido-L-phenylalanine (Azf). Using Caenorhabditis elegans, we expressed the engineered PheRS in a cell type of choice (i.e. body wall muscles, intestinal epithelial cells, neurons, pharyngeal muscles), permitting proteins in those cells -- and only those cells -- to be labeled with azides. Labeled proteins are therefore subject to \"click\" conjugation to cyclooctyne-functionalized affnity probes, separation from the rest of the protein pool and identification by mass spectrometry. By coupling our methodology with heavy isotopic labeling, we successfully identified proteins -- including proteins with previously unknown expression patterns -- expressed in targeted subsets of cells. While cell types like body wall or pharyngeal muscles can be targeted with a single promoter, many cells cannot; spatiotemporal selectivity typically results from the combinatorial action of multiple regulators. To enhance spatiotemporal selectivity, we next developed a two-component system to drive overlapping -- but not identical -- patterns of expression of engineered PheRS, restricting labeling to cells that express both elements. Specifically, we developed a split-intein-based split-PheRS system for highly efficient PheRS-reconstitution through protein splicing. Together, these tools represent a powerful approach for unbiased discovery of proteins uniquely expressed in a subset of cells at specific developmental stages." }, { "name": "Agbo, Peter Chukwudi Ifeanychukwu", "degree": "PhD", "year": "2015", "title": "Development of Metalloenzyme Dioxygen Reduction Cathodes", "advisor": "Gray, Harry B.; Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09192014-121956600", "creators": [ { "name": { "family": "Agbo", "given": "Peter Chukwudi Ifeanychukwu" }, "id": "Agbo-Peter-Chukwudi-Ifeanychukwu", "display_name": "Agbo, Peter Chukwudi Ifeanychukwu" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "co-advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9MK69TD", "abstract": "The prime thrust of this dissertation is to advance the development of fuel cell dioxygen reduction cathodes that employ some variant of multicopper oxidase enzymes as the catalyst. The low earth-abundance of platinum metal and its correspondingly high market cost has prompted a general search amongst chemists and materials scientists for reasonable alternatives to this metal for facilitating catalytic dioxygen reduction chemistry. The multicopper oxidases (MCOs), which constitute a class of enzyme that naturally catalyze the reaction O2 + 4H+ + 4e- \u2192 2H2O, provide a promising set of biochemical contenders for fuel cell cathode catalysts. In MCOs, a substrate reduces a copper atom at the type 1 site, where charge is then transferred to a trinuclear copper cluster consisting of a mononuclear type 2 or \u201cnormal copper\u201d site and a binuclear type 3 copper site. Following the reduction of all four copper atoms in the enzyme, dioxygen is then reduced to water in two two-electron steps, upon binding to the trinuclear copper cluster. We identified an MCO, a laccase from the hyperthermophilic bacterium Thermus thermophilus strain HB27, as a promising candidate for cathodic fuel cell catalysis. This protein demonstrates resilience at high temperatures, exhibiting no denaturing transition at temperatures high as 95\u00b0C, conditions relevant to typical polymer electrolyte fuel cell operation.
\r\n\r\nIn Chapter I of this thesis, we discuss initial efforts to physically characterize the enzyme when operating as a heterogeneous cathode catalyst. Following this, in Chapter II we then outline the development of a model capable of describing the observed electrochemical behavior of this enzyme when operating on porous carbon electrodes. Developing a rigorous mathematical framework with which to describe this system had the potential to improve our understanding of MCO electrokinetics, while also providing a level of predictive power that might guide any future efforts to fabricate MCO cathodes with optimized electrochemical performance. In Chapter III we detail efforts to reduce electrode overpotentials through site-directed mutagenesis of the inner and outer-sphere ligands of the Cu sites in laccase, using electrochemical methods and electronic spectroscopy to try and understand the resultant behavior of our mutant constructs. Finally, in Chapter IV, we examine future work concerning the fabrication of enhanced MCO cathodes, exploring the possibility of new cathode materials and advanced enzyme deposition techniques.
" }, { "name": "Allodi, Marco Alberto", "degree": "PhD", "year": "2015", "title": "On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312015-221615628", "creators": [ { "name": { "family": "Allodi", "given": "Marco Alberto" }, "id": "Allodi-Marco-Alberto", "orcid": "0000-0002-3289-1659", "display_name": "Allodi, Marco Alberto" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z97D2S2P", "abstract": "Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz\r\n(THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz,\r\n3 cm-1 to 300 cm-1, or 3000 \u03bcm to 30 \u03bcm) has been shown to provide unique possibilities in the\r\nstudy of condensed-phase processes. The goal of this work is to expand the possibilities available in\r\nthe THz region and undertake new investigations of fundamental interest to chemistry. Since we are\r\nfundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz\r\nspectroscopy can provide new understanding: astrochemistry and solvation science.\r\nTo advance these fields, we had to develop new instrumentation that would enable the experiments\r\nnecessary to answer new questions in either astrochemistry or solvation science. We first\r\ndeveloped a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz\r\n(THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm-1) and the mid-IR (400 -\r\n4000 cm-1). The importance of astrochemical ices lies in their key role in the formation of complex\r\norganic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of\r\nperforming variety of spectroscopic studies that can provide especially relevant laboratory data to\r\nsupport astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric\r\nObservatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array\r\n(ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm\r\nplasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz\r\n(~0.3 cm-1) resolution.
\r\n\r\nUsing the above instrumentation, experimental spectra of astrochemical ice analogs of water and\r\ncarbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high\r\nvacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a\r\nnew feature in both amorphous solid water and crystalline water at 33 cm-1 (1 THz). In addition,\r\nour studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide\r\nas it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz\r\nspectra of mixed and layered ices are further analyzed by fitting their spectra features to those of\r\npure amorphous solid water and crystalline water ice to quantify the effects of temperature changes\r\non structure. From the results of this work, it appears that THz spectroscopy is potentially well\r\nsuited to study thermal transformations within the ice.
\r\n\r\nTo advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear\r\nTHz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy.\r\nWe implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased\r\nTHz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate\r\n(DSTMS), and high numerical aperture optics which generates THz electric field in excess of\r\n300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz\r\n(THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar\r\ninteraction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument\r\nimproves on both the frequency coverage, and sensitivity previously reported; it also ensures\r\na backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we\r\nobserve a quantum beat at 3.66 THz (122 cm-1), in exact agreement with the fundamental transition\r\nfrequency of the \u03c54 vibration of the molecule. This result provides new insight into dipolar\r\nvs. Raman selection rules at terahertz frequencies.
\r\n\r\nTo conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab.\r\nWe report the first results from an experiment using a plasma-based THz source for nonlinear\r\nspectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal\r\nresolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping.\r\nFinally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz\r\ndata and how such a scheme could be implemented in the Blake lab. The instruments developed\r\nherein will hopefully remain a part of the groups core competencies and serve as building blocks\r\nfor the next generation of THz instrumentation that pushes the frontiers of both chemistry and the\r\nscientific enterprise as a whole.
" }, { "name": "Arnold, Anna Ruth", "degree": "PhD", "year": "2015", "title": "Investigations of DNA-Mediated Protein Oxidation", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062015-192618908", "creators": [ { "name": { "family": "Arnold", "given": "Anna Ruth" }, "id": "Arnold-Anna-Ruth", "display_name": "Arnold, Anna Ruth" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9ZW1HVN", "abstract": "DNA charge transport (CT) involves the efficient transfer of electrons or electron holes through the DNA π-stack over long molecular distances of at least 100 base-pairs. Despite this shallow distance dependence, DNA CT is sensitive to mismatches or lesions that disrupt π-stacking and is critically dependent on proper electronic coupling of the donor and acceptor moieties into the base stack. Favorable DNA CT is very rapid, occurring on the picosecond timescale. Because of this speed, electron holes equilibrate along the DNA π-stack, forming a characteristic pattern of DNA damage at low oxidation potential guanine multiplets. Furthermore, DNA CT may be used in a biological context. DNA processing enzymes with 4Fe4S clusters can perform DNA-mediated electron transfer (ET) self-exchange reactions with other 4Fe4S cluster proteins, even if the proteins are quite dissimilar, as long as the DNA-bound [4Fe4S]3+/2+ redox potentials are conserved. This mechanism would allow low copy number DNA repair proteins to find their lesions efficiently within the cell. DNA CT may also be used biologically for the long-range, selective activation of redox-active transcription factors. Within this work, we pursue other proteins that may utilize DNA CT within the cell and further elucidate aspects of the DNA-mediated ET self-exchange reaction of 4Fe4S cluster proteins.
\r\n\r\nDps proteins, bacterial mini-ferritins that protect DNA from oxidative stress, are implicated in the survival and virulence of pathogenic bacteria. One aspect of their protection involves ferroxidase activity, whereby ferrous iron is bound and oxidized selectively by hydrogen peroxide, thereby preventing formation of damaging hydroxyl radicals via Fenton chemistry. Understanding the specific mechanism by which Dps proteins protect the bacterial genome could inform the development of new antibiotics. We investigate whether DNA-binding E. coli Dps can utilize DNA CT to protect the genome from a distance. An intercalating ruthenium photooxidant was employed to generate oxidative DNA damage via the flash-quench technique, which localizes to a low potential guanine triplet. We find that Dps loaded with ferrous iron, in contrast to Apo-Dps and ferric iron-loaded Dps which lack available reducing equivalents, significantly attenuates the yield of oxidative DNA damage at the guanine triplet. These data demonstrate that ferrous iron-loaded Dps is selectively oxidized to fill guanine radical holes, thereby restoring the integrity of the DNA. Luminescence studies indicate no direct interaction between the ruthenium photooxidant and Dps, supporting the DNA-mediated oxidation of ferrous iron-loaded Dps. Thus DNA CT may be a mechanism by which Dps efficiently protects the genome of pathogenic bacteria from a distance.
\r\n\r\nFurther work focused on spectroscopic characterization of the DNA-mediated oxidation of ferrous iron-loaded Dps. X-band EPR was used to monitor the oxidation of DNA-bound Dps after DNA photooxidation via the flash-quench technique. Upon irradiation with poly(dGdC)2, a signal arises with g = 4.3, consistent with the formation of mononuclear high-spin Fe(III) sites of low symmetry, the expected oxidation product of Dps with one iron bound at each ferroxidase site. When poly(dGdC)2 is substituted with poly(dAdT)2, the yield of Dps oxidation is decreased significantly, indicating that guanine radicals facilitate Dps oxidation. The more favorable oxidation of Dps by guanine radicals supports the feasibility of a long-distance protection mechanism via DNA CT where Dps is oxidized to fill guanine radical holes in the bacterial genome produced by reactive oxygen species.
\r\n\r\nWe have also explored possible electron transfer intermediates in the DNA-mediated oxidation of ferrous iron-loaded Dps. Dps proteins contain a conserved tryptophan residue in close proximity to the ferroxidase site (W52 in E. coli Dps). In comparison to WT Dps, in EPR studies of the oxidation of ferrous iron-loaded Dps following DNA photooxidation, W52Y and W52A mutants were deficient in forming the characteristic EPR signal at g = 4.3, with a larger deficiency for W52A compared to W52Y. In addition to EPR, we also probed the role of W52 Dps in cells using a hydrogen peroxide survival assay. Bacteria containing W52Y Dps survived the hydrogen peroxide challenge more similarly to those containing WT Dps, whereas cells with W52A Dps died off as quickly as cells without Dps. Overall, these results suggest the possibility of W52 as a CT hopping intermediate.
\r\n\r\nDNA-modified electrodes have become an essential tool for the study of the redox chemistry of DNA processing enzymes with 4Fe4S clusters. In many cases, it is necessary to investigate different complex samples and substrates in parallel in order to elucidate this chemistry. Therefore, we optimized and characterized a multiplexed electrochemical platform with the 4Fe4S cluster base excision repair glycosylase Endonuclease III (EndoIII). Closely packed DNA films, where the protein has limited surface accessibility, produce EndoIII electrochemical signals sensitive to an intervening mismatch, indicating a DNA-mediated process. Multiplexed analysis allowed more robust characterization of the CT-deficient Y82A EndoIII mutant, as well as comparison of a new family of mutations altering the electrostatics surrounding the 4Fe4S cluster in an effort to shift the reduction potential of the cluster. While little change in the DNA-bound midpoint potential was found for this family of mutants, likely indicating the dominant effect of DNA-binding on establishing the protein redox potential, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we proposed that the electron transfer pathway in EndoIII can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster.
\r\n\r\nWhile the 4Fe4S cluster of EndoIII is relatively insensitive to oxidation and reduction in solution, we have found that upon DNA binding, the reduction potential of the [4Fe4S]3+/2+ couple shifts negatively by approximately 200 mV, bringing this couple into a physiologically relevant range. Demonstrated using electrochemistry experiments in the presence and absence of DNA, these studies do not provide direct molecular evidence for the species being observed. Sulfur K-edge X-ray absorbance spectroscopy (XAS) can be used to probe directly the covalency of iron-sulfur clusters, which is correlated to their reduction potential. We have shown that the Fe-S covalency of the 4Fe4S cluster of EndoIII increases upon DNA binding, stabilizing the oxidized [4Fe4S]3+ cluster, consistent with a negative shift in reduction potential. The 7% increase in Fe-S covalency corresponds to an approximately 150 mV shift, remarkably similar to DNA electrochemistry results. Therefore we have obtained direct molecular evidence for the shift in 4Fe4S reduction potential of EndoIII upon DNA binding, supporting the feasibility of our model whereby these proteins can utilize DNA CT to cooperate in order to efficiently find DNA lesions inside cells.
\r\n\r\nIn conclusion, in this work we have explored the biological applications of DNA CT. We discovered that the DNA-binding bacterial ferritin Dps can protect the bacterial genome from a distance via DNA CT, perhaps contributing to pathogen survival and virulence. Furthermore, we optimized a multiplexed electrochemical platform for the study of the redox chemistry of DNA-bound 4Fe4S cluster proteins. Finally, we have used sulfur K-edge XAS to obtain direct molecular evidence for the negative shift in 4Fe4S cluster reduction potential of EndoIII upon DNA binding. These studies contribute to the understanding of DNA-mediated protein oxidation within cells.
" }, { "name": "Barnes, Taylor Arnold", "degree": "PhD", "year": "2015", "title": "Development and Application of Embedding Methods for the Simulation of Large Chemical Systems", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212015-084744168", "creators": [ { "name": { "family": "Barnes", "given": "Taylor Arnold" }, "id": "Barnes-Taylor-Arnold", "display_name": "Barnes, Taylor Arnold" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Fultz", "given": "Brent T." }, "id": "Fultz-B-T", "role": "member", "display_name": "Fultz, Brent T." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9KK98P1", "abstract": "The high computational cost of correlated wavefunction theory (WFT) calculations has motivated the development of numerous methods to partition the description of large chemical systems into smaller subsystem calculations. For example, WFT-in-DFT embedding methods facilitate the partitioning of a system into two subsystems: a subsystem A that is treated using an accurate WFT method, and a subsystem B that is treated using a more efficient Kohn-Sham density functional theory (KS-DFT) method. Representation of the interactions between subsystems is non-trivial, and often requires the use of approximate kinetic energy functionals or computationally challenging optimized effective potential calculations; however, it has recently been shown that these challenges can be eliminated through the use of a projection operator. This dissertation describes the development and application of embedding methods that enable accurate and efficient calculation of the properties of large chemical systems.
\r\n\r\nChapter 1 introduces a method for efficiently performing projection-based WFT-in-DFT embedding calculations on large systems. This is accomplished by using a truncated basis set representation of the subsystem A wavefunction. We show that naive truncation of the basis set associated with subsystem A can lead to large numerical artifacts, and present an approach for systematically controlling these artifacts.
\r\n\r\nChapter 2 describes the application of the projection-based embedding method to investigate the oxidative stability of lithium-ion batteries. We study the oxidation potentials of mixtures of ethylene carbonate (EC) and dimethyl carbonate (DMC) by using the projection-based embedding method to calculate the vertical ionization energy (IE) of individual molecules at the CCSD(T) level of theory, while explicitly accounting for the solvent using DFT. Interestingly, we reveal that large contributions to the solvation properties of DMC originate from quadrupolar interactions, resulting in a much larger solvent reorganization energy than that predicted using simple dielectric continuum models. Demonstration that the solvation properties of EC and DMC are governed by fundamentally different intermolecular interactions provides insight into key aspects of lithium-ion batteries, with relevance to electrolyte decomposition processes, solid-electrolyte interphase formation, and the local solvation environment of lithium cations.
\r\n" }, { "name": "Betz, Kerry Nicole", "degree": "Senior Thesis", "year": "2015", "title": "A Novel, General Method for the Construction of C-Si Bonds by an Earth-Abundant Metal Catalyst", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12162015-163246183", "creators": [ { "name": { "family": "Betz", "given": "Kerry Nicole" }, "id": "Betz-Kerry-Nicole", "orcid": "0000-0001-9118-5909", "display_name": "Betz, Kerry Nicole" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9FT8HZ9", "abstract": "Compounds containing carbon-silicon (C-Si) bonds are of great interest in numerous fields, including but not limited to synthetic chemistry, organic electronics, pharmaceutical chemistry, nuclear medicine, and complex molecule synthesis. Compounds that contain C-Si bonds display useful physicochemical properties, and the C-Si bond can readily be converted into other desirable functional groups. Current methods for the creation of C-Si bonds are somewhat limited, requiring either stoichiometric pyrophoric organometallic species or highly expensive, fine-tuned precious-metal catalysts; both methods have significant limitations in terms of applicability and scope. A novel and general catalytic approach to C-Si bond construction avoiding such limitations has been developed. Herein is disclosed a new method of cross-dehydrogenative heteroaromatic C-H functionalization catalyzed by certain Earth-abundant alkali metal species that is able to access all hybridizations of carbon: sp3, sp2, and sp -hybridized carbons are all silylated in good yield under different conditions; prior to the discovery of this method, no known chemistry for C-Si bond construction was capable of accessing all hybridizations of carbon. Aromatic compounds, including heterocycles and oxygen-substituted arenes; benzylic sp3-hybridized carbons; and terminal alkynes, are directly silylated by potassium and sodium bases using hydrosilanes as the Si source, furnishing the silylated product in a single step. The overall catalysis is highly efficient: it proceeds under mild conditions, in the absence of hydrogen acceptors or other additives, and liberates dihydrogen as the sole byproduct; no competing hydrosilylation is observed. The scope of the method is broad, enabling the direct silylation of aromatic and aliphatic substrates in the presence of a wide array of valuable functional groups. Substrate classes such as nitrogen heterocycles that are challenging to activate with known transition metal catalysis strategies are functionalized in good yields by this Earth-abundant metal catalysis. Facile scalability, low cost, and excellent scope make this an attractive method for either large scale synthesis of versatile building blocks or late-stage functionalization of advanced intermediates and lead compounds. Turn-over numbers (TONs) of nearly 100 are achieved, demonstrating the remarkably high, albeit unanticipated efficiency and activity of the catalysis. The derived products readily engage in versatile transformations enabling new synthetic strategies for molecular diversification, and are useful in their own right in pharmaceutical and materials science applications." }, { "name": "Bui, Thinh Quoc", "degree": "PhD", "year": "2015", "title": "Cavity Enhanced Spectroscopies for Applications of Remote Sensing, Chemical Kinetics and Detection of Radical Species", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032015-151007228", "creators": [ { "name": { "family": "Bui", "given": "Thinh Quoc" }, "id": "Bui-Thinh-Quoc", "display_name": "Bui, Thinh Quoc" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Libbrecht", "given": "Kenneth George" }, "id": "Libbrecht-K-G", "role": "member", "display_name": "Libbrecht, Kenneth George" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z96D5QXW", "abstract": "This thesis describes applications of cavity enhanced spectroscopy towards applications of remote sensing, chemical kinetics and detection of transient radical molecular species. Both direct absorption spectroscopy and cavity ring-down spectroscopy are used in this work. Frequency-stabilized cavity ring-down spectroscopy (FS-CRDS) was utilized for measurements of spectral lineshapes of O2 and CO2 for obtaining laboratory reference data in support of NASA\u2019s OCO-2 mission. FS-CRDS is highly sensitive (> 10 km absorption path length) and precise (> 10000:1 SNR), making it ideal to study subtle non-Voigt lineshape effects. In addition, these advantages of FS-CRDS were further extended for measuring kinetic isotope effects: A dual-wavelength variation of FS-CRDS was used for measuring precise D/H and 13C/12C methane isotope ratios (sigma>0.026%) for the purpose of measuring the temperature dependent kinetic isotope effects of methane oxidation with O(1D) and OH radicals. Finally, direct absorption spectroscopic detection of the trans-DOCO radical via a frequency combs spectrometer was conducted in collaboration with professor Jun Ye at JILA/University of Colorado. " }, { "name": "Cherney, Alan Hayden", "degree": "PhD", "year": "2015", "title": "Development of Nickel-Catalyzed Asymmetric Reductive Cross-Coupling of Benzylic Electrophiles", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012015-102412340", "creators": [ { "name": { "family": "Cherney", "given": "Alan Hayden" }, "id": "Cherney-Alan-Hayden", "orcid": "0000-0001-7440-6634", "display_name": "Cherney, Alan Hayden" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z99W0CDW", "abstract": "Over the last forty years, the advent of transition metal-catalyzed cross-coupling has revolutionized the synthetic chemist\u2019s ability to generate C\u2013C bonds. Since the 1970s, a parallel effort to control the stereochemical outcome of such transformations has yielded a variety of chiral catalyst complexes that deliver enantioenriched cross-coupled products. Nonetheless, challenges in the use of C(sp3)-hybridized coupling partners have limited asymmetric variants to a narrow fraction of the total number of cross-coupling methodologies published each year.
\r\n\r\nHerein, we report studies on the asymmetric cross-coupling of benzylic groups under either Pd or Ni catalysis. We have developed a Pd-catalyzed Fukuyama cross-coupling of thioesters and secondary benzylzinc halides to deliver racemic ketones under mild conditions. Investigations with chiral catalysts revealed that a promising asymmetric transformation could be achieved to give modestly enantioenriched ketones.
\r\n\r\nReductive cross-coupling, involving the union of two different electrophiles, has the added advantage of avoiding harsh or expensive organometallic reagents. We have discovered the first highly enantioselective Ni-catalyzed reductive cross-couplings of two organohalide electrophiles. Treatment of an acid chloride and a secondary benzyl chloride with a chiral nickel/bis(oxazoline) complex and Mn(0) as the stoichiometric reductant furnishes ketone products in good yield and high enantioselectivity. Expanding on this result, we have demonstrated that vinyl bromides and secondary benzyl chlorides can be cross-coupled using a different chiral nickel/bis(oxazoline) complex, illustrating the generality of an asymmetric reductive coupling platform. Preliminary studies directed toward other coupling partners are also disclosed.
" }, { "name": "Craig, Robert Allen, II", "degree": "PhD", "year": "2015", "title": "Progress Toward the Enantioselective Total Synthesis of Ineleganolide and the Polycyclic Norcembranoid Diterpenes and Construction of the Ineleganoloids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242015-134810426", "creators": [ { "name": { "family": "Craig", "given": "Robert Allen, II" }, "id": "Craig-Robert-Allen-II", "display_name": "Craig, Robert Allen, II" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92B8VZ6", "abstract": "Ineleganolide, horiolide, kavaranolide, sinulochmodin C, scabrolide A, scabrolide B, and yonarolide are related polycyclic furanobutenolide norcembranoid natural products that exhibit potent biological activity, and feature highly oxygenate carbocyclic scaffolds with complex stereochemical frameworks. Herein, we describe a unified synthetic approach toward ineleganolide and the related furanobutenolide norcembranoids. Assembly of the tetracyclic scaffold of ineleganolide is accomplished in a convergent manner from (R)-carvone and an enantioenriched cis-1,3-cyclopentenediol fragment, which is constructed by a key enantioselective allylic alkylation. From the combined product of the two major fragments, we employ a tandem intramolecular cyclopropanation/Cope rearrangement to furnish the cycloheptene carbocyclic core characteristic of ineleganolide.
\r\n \r\nSynthetic manipulations of this carbocyclic core are extensively investigated; several constitutional isomers of ineleganolide are synthesized through these studies. Many approaches are explored to assist in the completion of the synthesis. Computational studies inform our understanding of the conformational bias of late-stage intermediates. The retroaldol-aldol carbocyclic isomerization from the core of ineleganolide to the core of sinulochmodin C is also investigated.
\r\n\r\nAdditionally, our work on the (3 + 2) cycloadditions of heterocumulenes with donor\u2013acceptor cyclopropanes and with N\u2013H- and N\u2013sulfonyl aziridines is disclosed. The exploration of substrate scope, reaction mechanism, and the enantiospecific formation of heterocyclic products in investigated.
" }, { "name": "Da Silva Tavares, Ximena", "degree": "PhD", "year": "2015", "title": "Binding Studies of Neuronal Nicotinic Acetylcholine Receptors Expressing Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04242015-121623394", "creators": [ { "name": { "family": "Da Silva Tavares", "given": "Ximena" }, "id": "Da-Silva-Tavares-Ximena", "display_name": "Da Silva Tavares, Ximena" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NC5Z45", "abstract": "Nicotinic acetylcholine receptors are pentameric ligand-gated ion channels mediating fast synaptic transmission throughout the peripheral and central nervous systems. They have been implicated in various processes related to cognitive functions, learning and memory, arousal, reward, motor control and analgesia. Therefore, these receptors present alluring potential therapeutic targets for the treatment of pain, epilepsy, Alzheimer\u2019s disease, Parkinson\u2019s disease, Tourette\u2019s syndrome, schizophrenia, anxiety, depression and nicotine addiction. The work detailed in this thesis focuses on binding studies of neuronal nicotinic receptors and aims to further our knowledge of subtype specific functional and structural information.
\r\n\r\nChapter 1 is an introductory chapter describing the structure and function of nicotinic acetylcholine receptors as well as the methodologies used for the dissertation work described herein. There are several different subtypes of nicotinic acetylcholine receptors known to date and the subtle variations in their structure and function present a challenging area of study. The work presented in this thesis deals specifically with the \u03b14\u03b22 subtype of nicotinic acetylcholine receptor. This subtype assembles into 2 closely related stoichiometries, termed throughout this thesis as A3B2 and A2B3 after their respective subunit composition. Chapter 2 describes binding studies of select nicotinic agonists on A3B2 and A2B3 receptors determined by whole-cell recording. Three key binding interactions, a cation-\u03c0 and two hydrogen bonds, were probed for four nicotinic agonists, acetylcholine, nicotine, smoking cessation drug varenicline (Chantix\u00ae) and the related natural product cytisine.
\r\n\r\nResults from the binding studies presented in Chapter 2 show that the major difference in binding of these four agonists to A3B2 and A2B3 receptors lies in one of the two hydrogen bond interactions where the agonist acts as the hydrogen bond acceptor and the backbone NH of a conserved leucine residue in the receptor acts as the hydrogen bond donor. Chapter 3 focuses on studying the effect of modulating the hydrogen bond acceptor ability of nicotine and epibatidine on A3B2 receptor function determined by whole-cell recording. Finally, Chapter 4 describes single-channel recording studies of varenicline binding to A2B3 and A3B2 receptors.
" }, { "name": "Day, Tristan William", "degree": "PhD", "year": "2015", "title": "Superionic Noble Metal Chalcogenide Thermoelectrics", "advisor": "Snyder, G. Jeffrey", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302015-170849147", "creators": [ { "name": { "family": "Day", "given": "Tristan William" }, "id": "Day-Tristan-William", "display_name": "Day, Tristan William" } ], "advisors": [ { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "advisor", "display_name": "Snyder, G. Jeffrey" } ], "committee": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "chair", "display_name": "Haile, Sossina M." }, { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "member", "display_name": "Snyder, G. Jeffrey" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9862DCD", "abstract": "Measurements and modeling of Cu2Se, Ag2Se, and Cu2S show that superionic conductors have great potential as thermoelectric materials. Cu2Se and Ag2Se are predicted to reach a zT of 1.2 at room temperature if their carrier concentrations can be reduced, and Cu-vacancy doped Cu2S reaches a maximum zT of 1.7 at 1000 K. Te-doped Ag2Se achieves a zT of 1.2 at 520 K, and could reach\r\na zT of 1.7 if its carrier concentration could be reduced. However, superionic conductors tend to have high carrier concentrations due to the presence of metal defects. The carrier concentration has been found to be difficult to reduce by altering the defect concentration, therefore materials that are underdoped relative to the optimum carrier concentration are easier to optimize. The results of Te-doping of Ag2Se show that reducing the carrier concentration is possible by reducing the maximum Fermi level in the material.
\r\n\r\nTwo new methods for analyzing thermoelectric transport data were developed. The first involves scaling the temperature-dependent transport data according to the temperature dependences expected of a single parabolic band model and using all of the scaled data to perform a single parabolic band analysis, instead of being restricted to using one data point per sample at a fixed temperature. This allows for a more efficient use of the transport data. The second involves scaling only the Seebeck coefficient and electrical conductivity. This allows for an estimate of the quality factor (and therefore the maximum zT in the material) without using Hall effect data, which are\r\nnot always available due to time and budget constraints and are difficult to obtain in high-resistivity materials.\r\n\r\nMethods for solving the coherent potential approximation effective medium equations were developed in conjunction with measurements of the resistivity tensor elements of composite materials. This allows the electrical conductivity and mobility of each phase in the composite to be determined from measurements of the bulk. This points out a new method for measuring the pure-phase electrical\r\nproperties in impure materials, for measuring the electrical properties of unknown phases in\r\ncomposites, and for quantifying the effects of quantum interactions in composites.
" }, { "name": "Deimund, Mark Austin", "degree": "PhD", "year": "2015", "title": "I. Nickel-Exchanged Zincosilicate Catalysts for the Oligomerization of Propylene and II. Organic SDA-Free Catalysts for the Methanol-to-Olefins Reaction", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112015-143241169", "creators": [ { "name": { "family": "Deimund", "given": "Mark Austin" }, "id": "Deimund-Mark-Austin", "display_name": "Deimund, Mark Austin" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9XK8CG9", "abstract": "Nickel-containing catalysts are developed to oligomerize light olefins. Two nickel-containing zincosilicates (Ni-CIT-6 and Ni-Zn-MCM-41) and two nickel-containing aluminosilicates (Ni-HiAl-BEA and Ni-USY) are synthesized as catalysts to oligomerize propylene into C3n (C6 and C9) products. All catalysts oligomerize propylene, with the zincosilicates demonstrating higher average selectivities to C3n products, likely due to the reduced acidity of the Zn heteroatom.
\r\n\r\nTo test whether light alkanes can be incorporated into this oligomerization reaction, a supported homogeneous catalyst is combined with Ni-containing zincosilicates. The homogeneous catalyst is included to provide dehydrogenation/hydrogenation functions. When this tandem catalyst system is evaluated using a propylene/n-butane feed, no significant integration of alkanes are observed.
\r\n\r\nNi-containing zincosilicates are reacted with 1-butene and an equimolar propylene/1-butene mixture to study other olefinic feeds. Further, other divalent metal cations such as Mn2+, Co2+, Cu2+, and Zn2+ are exchanged onto CIT-6 samples to investigate stability and potential use for other reactions. Co-CIT-6 oligomerizes propylene, albeit less effectively than Ni-CIT-6. The other M-CIT-6 samples, while not able to oligomerize light olefins, may be useful for other reactions, such as deNOx.
\r\n\r\nMolecular sieves are synthesized, characterized, and used to catalyze the methanol-to-olefins (MTO) reaction. The Al concentration in SSZ-13 samples is varied to investigate the effect of Al number on MTO reactivity when compared to a SAPO-34 sample with only isolated Si Br\u00f8nsted acid sites. These SSZ-13 samples display reduced transient selectivity behavior and extended reaction lifetimes as Si/Al increases; attributable to fewer paired Al sites. MTO reactivity for the higher Si/Al SSZ-13s resembles the SAPO-34 sample, suggesting that both catalysts owe their stable reaction behavior to isolated Br\u00f8nsted acid sites.
\r\n\r\nZeolites CHA and RHO are prepared without the use of organic structure-directing agents (OSDAs), dealuminated by steam treatments (500\u00b0C-800\u00b0C), and evaluated as catalysts for the MTO reaction. The effects of temperature and steam partial pressure during steaming are investigated. X-ray diffraction (XRD) and Ar physisorption show that steaming causes partial structural collapse of the zeolite, with degradation increasing with steaming temperature. 27Al MAS NMR spectra of steamed materials reveal the presence of tetrahedral, pentacoordinate, and hexacoordinate aluminum.
\r\n\r\nProton forms of as-synthesized CHA (Si/Al=2.4) and RHO (Si/Al=2.8) rapidly deactivate under MTO testing conditions (400\u00b0C, atmospheric pressure). CHA samples steamed at 600\u00b0C performed best among samples tested, showing increased olefin selectivities and catalyst lifetime. Acid washing these steamed samples further improved activity. Reaction results for RHO were similar to CHA, with the RHO sample steamed at 800\u00b0C producing the highest light olefin selectivities. Catalyst lifetime and C2-C3 olefin selectivities increase with increasing reaction temperature for both CHA-type and RHO-type steamed samples.
" }, { "name": "Farwell, Christopher C.", "degree": "PhD", "year": "2015", "title": "Engineering and Characterization of Cytochrome P450 Enzymes for Nitrogen-Atom Transfer Reactions", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302015-155404718", "creators": [ { "name": { "family": "Farwell", "given": "Christopher C." }, "id": "Farwell-Christopher-C", "display_name": "Farwell, Christopher C." } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9765C71", "abstract": "The creation of novel enzyme activity is a great challenge to protein engineers, but nature has done so repeatedly throughout the process of natural selection. I begin by outlining the multitude of distinct reactions catalyzed by a single enzyme class, cytochrome P450 monooxygenases. I discuss the ability of cytochrome P450 to generate reactive intermediates capable of diverse reactivity, suggesting this enzyme can also be used to generate novel reactive intermediates in the form of metal-carbenoid and nitrenoid species. I then show that cytochrome P450 from Bacillus megaterium (P450BM3) and its isolated cofactor can catalyze metal-nitrenoid transfer in the form of intramolecular C\u2013H bond amination. Mutations to the protein sequence can enhance the reactivity and selectivity of this transformation significantly beyond that of the free cofactor. Next, I demonstrate an intermolecular nitrene transfer reaction catalyzed by P450BM3 in the form of sulfide imidation. Understanding that sulfur heteroatoms are strong nucleophiles, I show that increasing the sulfide nucleophilicity through substituents on the aryl sulfide ring can dramatically increase reaction productivity. To explore engineering nitrenoid transfer in P450BM3, active site mutagenesis is employed to tune the regioselectivity intramolecular C\u2013H amination catalysts. The solution of the crystal structure of a highly selective variant demonstrates that hydrophobic residues in the active site strongly modulate reactivity and regioselectivity. Finally, I use a similar strategy to develop P450-based catalysts for intermolecular olefin aziridination, demonstrating that active site mutagenesis can greatly enhance this nitrene transfer reaction. The resulting variant can catalyze intermolecular aziridination with more than 1000 total turnovers and enantioselectivity of up to 99% ee. " }, { "name": "Fong, Henry", "degree": "PhD", "year": "2015", "title": "Metallaboratrane Facilitated E\u2012H Bond Activation and Hydrogenation Catalysis", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152014-181907516", "creators": [ { "name": { "family": "Fong", "given": "Henry" }, "id": "Fong-Henry", "display_name": "Fong, Henry" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9TX3C9P", "abstract": "The E\u2012H bond activation chemistry of tris-phosophino-iron and -cobalt metallaboratranes is discussed. The ferraboratrane complex (TPB)Fe(N2) heterolytically activates H\u2012H and the C\u2012H bonds of formaldehyde and arylacetylenes across an Fe\u2012B bond. In particular, H\u2012H bond cleavage at (TPB)Fe(N2) is reversible and affords the iron-hydride-borohydride complex (TPB)(\u03bc\u2012H)Fe(L)(H) (L = H2, N2). (TPB)(\u03bc\u2012H)Fe(L)(H) and (TPB)Fe(N2) are competent olefin and arylacetylene hydrogenation catalysts. Stoichiometric studies indicate that the B\u2012H unit is capable of acting as a hydride shuttle in the hydrogenation of olefin and arylacetylene substrates. The heterolytic cleavage of H2 by the (TPB)Fe system is distinct from the previously reported (TPB)Co(H2) complex, where H2 coordinates as a non-classical H2 adduct based on X-ray, spectroscopic, and reactivity data. The non-classical H2 ligand in (TPB)Co(H2) is confirmed in this work by single crystal neutron diffraction, which unequivocally shows an intact H\u2012H bond of 0.83 \u00c5 in the solid state. The neutron structure also shows that the H2 ligand is localized at two orientations on cobalt trans to the boron. This localization in the solid state contrasts with the results from ENDOR spectroscopy that show that the H2 ligand freely rotates about the Co\u2012H2 axis in frozen solution. Finally, the (TPB)Fe system, as well as related tris-phosphino-iron complexes that contain a different apical ligand unit (Si, PhB, C, and N) in place of the boron in (TPB)Fe, were studied for CO2 hydrogenation chemistry. The (TPB)Fe system is not catalytically competent, while the silicon, borate, carbon variants, (SiPR3)Fe, (PhBPiPr3)Fe, and (CPiPr3)Fe, respectively, are catalysts for the hydrogenation of CO2 to formate and methylformate. The hydricity of the CO2 reactive species in the silatrane system (SiPiPr3)Fe(N2)(H) has been experimentally estimated. " }, { "name": "Fountaine, Katherine Theresa", "degree": "PhD", "year": "2015", "title": "Mesoscale Optoelectronic Design of Wire-Based Photovoltaic and Photoelectrochemical Devices", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-151831184", "creators": [ { "name": { "family": "Fountaine", "given": "Katherine Theresa" }, "id": "Fountaine-Katherine-Theresa", "orcid": "0000-0002-0414-8227", "display_name": "Fountaine, Katherine Theresa" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Lewerenz", "given": "Hans Joachim" }, "id": "Lewerenz-H-J", "role": "member", "display_name": "Lewerenz, Hans Joachim" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9P26W1K", "abstract": "The overarching theme of this thesis is mesoscale optical and optoelectronic design of photovoltaic and photoelectrochemical devices. In a photovoltaic device, light absorption and charge carrier transport are coupled together on the mesoscale, and in a photoelectrochemical device, light absorption, charge carrier transport, catalysis, and solution species transport are all coupled together on the mesoscale. The work discussed herein demonstrates that simulation-based mesoscale optical and optoelectronic modeling can lead to detailed understanding of the operation and performance of these complex mesostructured devices, serve as a powerful tool for device optimization, and efficiently guide device design and experimental fabrication efforts. In-depth studies of two mesoscale wire-based device designs illustrate these principles\u2014(i) an optoelectronic study of a tandem Si|WO3 microwire photoelectrochemical device, and (ii) an optical study of III-V nanowire arrays.
\r\n\r\nThe study of the monolithic, tandem, Si|WO3 microwire photoelectrochemical device begins with development and validation of an optoelectronic model with experiment. This study capitalizes on synergy between experiment and simulation to demonstrate the model\u2019s predictive power for extractable device voltage and light-limited current density. The developed model is then used to understand the limiting factors of the device and optimize its optoelectronic performance. The results of this work reveal that high fidelity modeling can facilitate unequivocal identification of limiting phenomena, such as parasitic absorption via excitation of a surface plasmon-polariton mode, and quick design optimization, achieving over a 300% enhancement in optoelectronic performance over a nominal design for this device architecture, which would be time-consuming and challenging to do via experiment.
\r\n\r\nThe work on III-V nanowire arrays also starts as a collaboration of experiment and simulation aimed at gaining understanding of unprecedented, experimentally observed absorption enhancements in sparse arrays of vertically-oriented GaAs nanowires. To explain this resonant absorption in periodic arrays of high index semiconductor nanowires, a unified framework that combines a leaky waveguide theory perspective and that of photonic crystals supporting Bloch modes is developed in the context of silicon, using both analytic theory and electromagnetic simulations. This detailed theoretical understanding is then applied to a simulation-based optimization of light absorption in sparse arrays of GaAs nanowires. Near-unity absorption in sparse, 5% fill fraction arrays is demonstrated via tapering of nanowires and multiple wire radii in a single array. Finally, experimental efforts are presented towards fabrication of the optimized array geometries. A hybrid self-catalyzed and selective area MOCVD growth method is used to establish morphology control of GaP nanowire arrays. Similarly, morphology and pattern control of nanowires is demonstrated with ICP-RIE of InP. Optical characterization of the InP nanowire arrays gives proof of principle that tapering and multiple wire radii can lead to near-unity absorption in sparse arrays of InP nanowires.
" }, { "name": "Fu, Amy Hau Yu", "degree": "PhD", "year": "2015", "title": "Mitigating Scarring and Inflammation during Corneal Wound Healing using Nanofiber-Hydrogel Scaffolds", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272015-172038281", "creators": [ { "name": { "family": "Fu", "given": "Amy Hau Yu" }, "id": "Fu-Amy-Hau-Yu", "display_name": "Fu, Amy Hau Yu" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9Q81B00", "abstract": "Due to the universal lack of donor tissue, there has been emerging interest in engineering materials to stimulate living cells to restore the features and functions of injured organs. We are particularly interested in developing materials for corneal use, where the necessity to maintain the tissue\u2019s transparency presents an additional challenge. Every year, there are 1.5 \u2013 2 million new cases of monocular blindness due to irregular healing of corneal injuries, dwarfing the approximately 150,000 corneal transplants performed. The large gap between the need and availability of cornea transplantation motivates us to develop a wound-healing scaffold that can prevent corneal blindness.
\r\n\r\nTo develop such a scaffold, it is necessary to regulate the cells responsible for repairing the damaged cornea, namely myofibroblasts, which are responsible for the disordered and non-refractive index matched scar that leads to corneal blindness. Using in vitro assays, we identified that protein nanofibers of certain orientation can promote cell migration and modulate the myofibroblast phenotype. The nanofibers are also transparent, easy to handle and non-cytotoxic. To adhere the nanofibers to a wound bed, we examined the use of two different in situ forming hydrogels: an artificial extracellular matrix protein (aECM)-based gel and a photo-crosslinkable heparin-based gel. Both hydrogels can be formed within minutes, are transparent upon gelation and are easily tunable.
\r\n\r\nUsing an in vivo mouse model for epithelial defects, we show that our corneal scaffolds (nanofibers together with hydrogel) are well-tolerated (no inflammatory response or turbidity) and support epithelium regrowth. We developed an ex vivo corneal tissue culture model where corneas that are wounded and treated with our scaffold can be cultured while retaining their ability to repair wounds for up to 21 days. Using this technique, we found that the aECM-based treatment induced a more favorable wound response than the heparin-based treatment, prompting us to further examine the efficacy of the aECM-based treatment in vivo using a rabbit model for stromal wounds. Results show that treated corneas have fewer myofibroblasts and immune cells than untreated ones, indicating that our corneal scaffold shows promise in promoting a calmer wound response and preventing corneal haze formation.
\r\n" }, { "name": "Furst, Ariel Lesa", "degree": "PhD", "year": "2015", "title": "DNA-Mediated Charge Transport Devices for Protein Detection", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022015-103853129", "creators": [ { "name": { "family": "Furst", "given": "Ariel Lesa" }, "id": "Furst-Ariel-Lesa", "orcid": "0000-0001-9583-9703", "display_name": "Furst, Ariel Lesa" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9KH0K88", "abstract": "Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the \u03c0-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.
\r\n\r\nFirst, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.
\r\n\r\nUsing low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.
\r\n\r\nFor effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 \u03bcL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.
\r\n\r\nWith the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.
\r\n\r\nAs differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.
\r\n" }, { "name": "Gibbs, Zachary Michael", "degree": "PhD", "year": "2015", "title": "Band Engineering in Thermoelectric Materials Using Optical, Electronic, and Ab-Initio Computed Properties", "advisor": "Snyder, G. Jeffrey", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142015-004120562", "creators": [ { "name": { "family": "Gibbs", "given": "Zachary Michael" }, "id": "Gibbs-Zachary-Michael", "display_name": "Gibbs, Zachary Michael" } ], "advisors": [ { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "advisor", "display_name": "Snyder, G. Jeffrey" } ], "committee": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "chair", "display_name": "Haile, Sossina M." }, { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "member", "display_name": "Snyder, G. Jeffrey" }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Minnich", "given": "Austin J." }, "id": "Minnich-A-J", "role": "member", "display_name": "Minnich, Austin J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9XS5S9Z", "abstract": "Thermoelectric materials have demanded a significant amount of attention for their ability to convert waste heat directly to electricity with no moving parts. A resurgence in thermoelectrics research has led to significant enhancements in the thermoelectric figure of merit, zT, even for materials that were already well studied. This thesis approaches thermoelectric zT optimization by developing a detailed understanding of the electronic structure using a combination of electronic/thermoelectric properties, optical properties, and ab-initio computed electronic band structures. This is accomplished by applying these techniques to three important classes of thermoelectric materials: IV-VI materials (the lead chalcogenides), Half-Heusler\u2019s (XNiSn where X=Zr, Ti, Hf), and CoSb3 skutterudites.
\r\nIn the IV-VI materials (PbTe, PbSe, PbS) I present a shifting temperature-dependent optical absorption edge which correlates well to the computed ab-initio molecular dynamics result. Contrary to prior literature that suggests convergence of the primary and secondary bands at 400 K, I suggest a higher convergence temperature of 700, 900, and 1000 K for PbTe, PbSe, and PbS, respectively. This finding can help guide electronic properties modelling by providing a concrete value for the band gap and valence band offset as a function of temperature.
\r\nAnother important thermoelectric material, ZrNiSn (half-Heusler), is analyzed for both its optical and electronic properties; transport properties indicate a largely different band gap depending on whether the material is doped n-type or p-type. By measuring and reporting the optical band gap value of 0.13 eV, I resolve the discrepancy in the gap calculated from electronic properties (maximum Seebeck and resistivity) by correlating these estimates to the electron-to-hole weighted mobility ratio, A, in narrow gap materials (A is found to be approximately 5.0 in ZrNiSn).
\r\nI also show that CoSb3 contains multiple conduction bands that contribute to the thermoelectric properties. These bands are also observed to shift towards each other with temperature, eventually reaching effective convergence for T>500 K. This implies that the electronic structure in CoSb3 is critically important (and possibly engineerable) with regards to its high thermoelectric figure of merit.
" }, { "name": "Gordon, Jonny Robert", "degree": "PhD", "year": "2015", "title": "Applications of a Concise and General Strategy for the Syntheses of Transtaganolide and Basiliolide Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082015-185228801", "creators": [ { "name": { "family": "Gordon", "given": "Jonny Robert" }, "id": "Gordon-Jonny-Robert", "display_name": "Gordon, Jonny Robert" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z99021P4", "abstract": "Herein are described the total syntheses of all members of the transtaganolide and basiliolide natural product family. Utilitzation of an Ireland\u2013Claisen rearrangement/Diels\u2013Alder cycloaddition cascade (ICR/DA) allowed for rapid assembly of the transtaganolide and basiliolide oxabicyclo[2.2.2]octane core. This methodology is general and was applicable to all members of the natural product family.
\r\n\r\nA brief introduction outlines all the synthetic progress previously disclosed by Lee, Dudley, and Johansson. This also includes the initial syntheses of transtaganolides C and D, as well as basiliolide B and epi-basiliolide B accomplished by Stoltz in 2011. Lastly, we discuss our racemic synthesis of basililide C and epi-basiliolide C, which utilized an ICR/DA cascade to constuct the oxabicyclo[2.2.2]octane core and formal [5+2] annulation to form the ketene-acetal containing 7-membered C-ring.
\r\n\r\nNext, we describe a strategy for an asymmetric ICR/DA cascade, by incorporation of a chiral silane directing group. This allowed for enantioselective construction of the C8 all-carbon quaternary center formed in the Ireland\u2013Claisen rearrangement. Furthermore, a single hydride reduction and subsequent translactonization of a C4 methylester bearing oxabicyclo[2.2.2]octane core demonstrated a viable strategy for the desired skeletal rearrangement to obtain pentacyclic transtaganolides A and B. Application of the asymmetric strategy culminated in the total syntheses of (\u2013)-transtaganolide A, (+)-transtaganolide B, (+)-transtaganolide C, and (\u2013)-transtaganolide D. Comparison of the optical rotation data of the synthetically derived transtaganolides to that from the isolated counterparts has overarching biosynthetic implications which are discussed.
\r\n\r\nLastly, improvement to the formal [5+2] annulation strategy is described. Negishi cross-coupling of methoxyethynyl zinc chloride using a palladium Xantphos catalyst is optimized for iodo-cyclohexene. Application of this technology to an iodo-pyrone geranyl ester allowed for formation and isolation of the eneyne product. Hydration of the enenye product forms natural metabolite basiliopyrone. Furthermore, the eneyne product can undergo an ICR/DA cascade and form transtaganolides C and D in a single step from an achiral monocyclic precursor.
\r\n" }, { "name": "Gristick, Harry Benjamin", "degree": "PhD", "year": "2015", "title": "Investigating the Role of the GET3-GET4/GET5 Interaction During Tail-Anchor Protein Targeting", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052015-162319516", "creators": [ { "name": { "family": "Gristick", "given": "Harry Benjamin" }, "id": "Gristick-Harry-Benjamin", "display_name": "Gristick, Harry Benjamin" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z95718ZD", "abstract": "The proper targeting of membrane proteins is essential to the viability of all cells. Tail-anchored (TA) proteins, defined as having a single transmembrane helix at their C-terminus, are post-translationally targeted to the endoplasmic reticulum (ER) membrane by the GET pathway (Guided Entry of TA proteins). In the yeast pathway, the handover of TA substrates is mediated by the heterotetrameric Get4/Get5 (Get4/5) complex, which tethers the co-chaperone Sgt2 to the central targeting factor, the Get3 ATPase. Although binding of Get4/5 to Get3 is critical for efficient TA targeting, the mechanisms by which Get4 regulates Get3 are unknown. To understand the molecular basis of Get4 function, we used a combination of structural biology, biochemistry, and cell biology. Get4/5 binds across the Get3 dimer interface, in an orientation only compatible with a closed Get3, providing insight into the role of nucleotide in complex formation. Additionally, this structure reveals two functionally distinct binding interfaces for anchoring and ATPase regulation, and loss of the regulatory interface leads to strong defects in vitro and in vivo. Additional crystal structures of the Get3-Get4/5 complex give rise to an alternate conformation, which represents an initial binding interaction mediated by electrostatics that facilitates the rate of subsequent inhibited complex formation. This interface is supported by an in-depth kinetic analysis of the Get3-Get4/5 interaction confirming the two-step complex formation. These results allow us to generate a refined model for Get4/5 function in TA targeting." }, { "name": "Gu, Xun Wendy", "degree": "PhD", "year": "2015", "title": "Strength, Deformation and Fracture in Metallic Nanostructures", "advisor": "Greer, Julia R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02242015-173330087", "creators": [ { "name": { "family": "Gu", "given": "Xun Wendy" }, "id": "Gu-Xun-Wendy", "display_name": "Gu, Xun Wendy" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "advisor", "display_name": "Greer, Julia R." } ], "committee": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "chair", "display_name": "Greer, Julia R." }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Kochmann", "given": "Dennis M." }, "id": "Kochmann-D-M", "role": "member", "display_name": "Kochmann, Dennis M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z91J97NV", "abstract": "An understanding of the mechanics of nanoscale metals and semiconductors is necessary for the safe and prolonged operation of nanostructured devices from transistors to nanowire- based solar cells to miniaturized electrodes. This is a fascinating but challenging pursuit because mechanical properties that are size-invariant in conventional materials, such as strength, ductility and fracture behavior, can depend critically on sample size when materials are reduced to sub- micron dimensions. In this thesis, the effect of nanoscale sample size, microstructure and structural geometry on mechanical strength, deformation and fracture are explored for several classes of solid materials. Nanocrystalline platinum nano-cylinders with diameters of 60 nm to 1 \u03bcm and 12 nm sized grains are fabricated and tested in compression. We find that nano-sized metals containing few grains weaken as sample diameter is reduced relative to grain size due to a change from deformation governed by internal grains to surface grain governed deformation. Fracture at the nanoscale is explored by performing in-situ SEM tension tests on nanocrystalline platinum and amorphous, metallic glass nano-cylinders containing purposely introduced structural flaws. It is found that failure location, mechanism and strength are determined by the stress concentration with the highest local stress whether this is at the structural flaw or a microstructural feature. Principles of nano-mechanics are used to design and test mechanically robust hierarchical nanostructures with structural and electrochemical applications. 2-photon lithography and electroplating are used to fabricate 3D solid Cu octet meso-lattices with micron- scale features that exhibit strength higher than that of bulk Cu. An in-situ SEM lithiation stage is developed and used to simultaneously examine morphological and electrochemical changes in Si-coated Cu meso-lattices that are of interest as high energy capacity electrodes for Li-ion batteries." }, { "name": "Hong, Qi-Jun", "degree": "PhD", "year": "2015", "title": "Methods for Melting Temperature Calculation", "advisor": "van de Walle, Axel", "url": "https://resolver.caltech.edu/CaltechTHESIS:11092014-074023936", "creators": [ { "name": { "family": "Hong", "given": "Qi-Jun" }, "id": "Hong-Qi-Jun", "display_name": "Hong, Qi-Jun" } ], "advisors": [ { "name": { "family": "van de Walle", "given": "Axel" }, "id": "van-de-Walle-A", "role": "advisor", "display_name": "van de Walle, Axel" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "van de Walle", "given": "Axel" }, "id": "van-de-Walle-A", "role": "member", "display_name": "van de Walle, Axel" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z98C9T6H", "abstract": "Melting temperature calculation has important applications in the theoretical study of phase diagrams and computational materials screenings. In this thesis, we present two new methods, i.e., the improved Widom's particle insertion method and the small-cell coexistence method, which we developed in order to capture melting temperatures both accurately and quickly.
\r\n\r\nWe propose a scheme that drastically improves the efficiency of Widom's particle insertion method by efficiently sampling cavities while calculating the integrals providing the chemical potentials of a physical system. This idea enables us to calculate chemical potentials of liquids directly from first-principles without the help of any reference system, which is necessary in the commonly used thermodynamic integration method. As an example, we apply our scheme, combined with the density functional formalism, to the calculation of the chemical potential of liquid copper. The calculated chemical potential is further used to locate the melting temperature. The calculated results closely agree with experiments.
\r\n\r\nWe propose the small-cell coexistence method based on the statistical analysis of small-size coexistence MD simulations. It eliminates the risk of a metastable superheated solid in the fast-heating method, while also significantly reducing the computer cost relative to the traditional large-scale coexistence method. Using empirical potentials, we validate the method and systematically study the finite-size effect on the calculated melting points. The method converges to the exact result in the limit of a large system size. An accuracy within 100 K in melting temperature is usually achieved when the simulation contains more than 100 atoms. DFT examples of Tantalum, high-pressure Sodium, and ionic material NaCl are shown to demonstrate the accuracy and flexibility of the method in its practical applications. The method serves as a promising approach for large-scale automated material screening in which the melting temperature is a design criterion.
\r\n\r\nWe present in detail two examples of refractory materials. First, we demonstrate how key material properties that provide guidance in the design of refractory materials can be accurately determined via ab initio thermodynamic calculations in conjunction with experimental techniques based on synchrotron X-ray diffraction and thermal analysis under laser-heated aerodynamic levitation. The properties considered include melting point, heat of fusion, heat capacity, thermal expansion coefficients, thermal stability, and sublattice disordering, as illustrated in a motivating example of lanthanum zirconate (La2Zr2O7). The close agreement with experiment in the known but structurally complex compound La2Zr2O7 provides good indication that the computation methods described can be used within a computational screening framework to identify novel refractory materials. Second, we report an extensive investigation into the melting temperatures of the Hf-C and Hf-Ta-C systems using ab initio calculations. With melting points above 4000 K, hafnium carbide (HfC) and tantalum carbide (TaC) are among the most refractory binary compounds known to date. Their mixture, with a general formula TaxHf1-xCy, is known to have a melting point of 4215 K at the composition Ta4HfC5, which has long been considered as the highest melting temperature for any solid. Very few measurements of melting point in tantalum and hafnium carbides have been documented, because of the obvious experimental difficulties at extreme temperatures. The investigation lets us identify three major chemical factors that contribute to the high melting temperatures. Based on these three factors, we propose and explore a new class of materials, which, according to our ab initio calculations, may possess even higher melting temperatures than Ta-Hf-C. This example also demonstrates the feasibility of materials screening and discovery via ab initio calculations for the optimization of \"higher-level\" properties whose determination requires extensive sampling of atomic configuration space.
\r\n" }, { "name": "Idigo, Chinenye Abiodun", "degree": "PhD", "year": "2015", "title": "Structural and Biophysical Characterization of Variants of the Mechanosensitive Channel of Large Conductance (MsCL)", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152014-153232034", "creators": [ { "name": { "family": "Idigo", "given": "Chinenye Abiodun" }, "id": "Idigo-Chinenye-Abiodun", "display_name": "Idigo, Chinenye Abiodun" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "chair", "display_name": "Lester, Henry A." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9542KJ3", "abstract": "The ability to sense mechanical force is vital to all organisms to interact with and respond to stimuli in their environment. Mechanosensation is critical to many physiological functions such as the senses of hearing and touch in animals, gravitropism in plants and osmoregulation in bacteria. Of these processes, the best understood at the molecular level involve bacterial mechanosensitive channels. Under hypo-osmotic stress, bacteria are able to alleviate turgor pressure through mechanosensitive channels that gate directly in response to tension in the membrane lipid bilayer. A key participant in this response is the mechanosensitive channel of large conductance (MscL), a non-selective channel with a high conductance of ~3 nS that gates at tensions close to the membrane lytic tension.
\r\n\r\nIt has been appreciated since the original discovery by C. Kung that the small subunit size (~130 to 160 residues) and the high conductance necessitate that MscL forms a homo-oligomeric channel. Over the past 20 years of study, the proposed oligomeric state of MscL has ranged from monomer to hexamer. Oligomeric state has been shown to vary between MscL homologues and is influenced by lipid/detergent environment. In this thesis, we report the creation of a chimera library to systematically survey the correlation between MscL sequence and oligomeric state to identify the sequence determinants of oligomeric state. Our results demonstrate that although there is no combination of sequences uniquely associated with a given oligomeric state (or mixture of oligomeric states), there are significant correlations. In the quest to characterize the oligomeric state of MscL, an exciting discovery was made about the dynamic nature of the MscL complex. We found that in detergent solution, under mild heating conditions (37 \u00b0C \u2013 60 \u00b0C), subunits of MscL can exchange between complexes, and the dynamics of this process are sensitive to the protein sequence.
\r\n\r\nExtensive efforts were made to produce high diffraction quality crystals of MscL for the determination of a high resolution X-ray crystal structure of a full length channel. The surface entropy reduction strategy was applied to the design of S. aureus MscL variants and while the strategy appears to have improved the crystallizability of S. aureus MscL, unfortunately the diffraction qualities of these crystals were not significantly improved. MscL chimeras were also screened for crystallization in various solubilization detergents, but also failed to yield high quality crystals.
\r\n\r\nMscL is a fascinating protein and continues to serve as a model system for the study of the structural and functional properties of mechanosensitive channels. Further characterization of the MscL chimera library will offer more insight into the characteristics of the channel. Of particular interest are the functional characterization of the chimeras and the exploration of the physiological relevance of intercomplex subunit exchange.
" }, { "name": "Kanady, Jacob Steven", "degree": "PhD", "year": "2015", "title": "Models of the Oxygen-Evolving Complex of Photosystem II", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272014-031912941", "creators": [ { "name": { "family": "Kanady", "given": "Jacob Steven" }, "id": "Kanady-Jacob-Steven", "display_name": "Kanady, Jacob Steven" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9C53HS0", "abstract": "In the five chapters that follow, I delineate my efforts over the last five years to synthesize structurally and chemically relevant models of the Oxygen Evolving Complex (OEC) of Photosystem II. The OEC is nature\u2019s only water oxidation catalyst, in that it forms the dioxygen in our atmosphere necessary for oxygenic life. Therefore understanding its structure and function is of deep fundamental interest and could provide design elements for artificial photosynthesis and manmade water oxidation catalysts. Synthetic endeavors towards OEC mimics have been an active area of research since the mid 1970s and have mutually evolved alongside biochemical and spectroscopic studies, affording ever-refined proposals for the structure of the OEC and the mechanism of water oxidation. This research has culminated in the most recent proposal: a low symmetry Mn4CaO5 cluster with a distorted Mn3CaO4 cubane bridged to a fourth, dangling Mn. To give context for how my graduate work fits into this rich history of OEC research, Chapter 1 provides a historical timeline of proposals for OEC structure, emphasizing the role that synthetic Mn and MnCa clusters have played, and ending with our Mn3CaO4 heterometallic cubane complexes.
\r\n\r\nIn Chapter 2, the triarylbenzene ligand framework used throughout my work is introduced, and trinuclear clusters of Mn, Co, and Ni are discussed. The ligand scaffold consistently coordinates three metals in close proximity while leaving coordination sites open for further modification through ancillary ligand binding. The ligands coordinated could be varied, with a range of carboxylates and some less coordinating anions studied. These complexes\u2019 structures, magnetic behavior, and redox properties are discussed.
\r\n\r\nChapter 3 explores the redox chemistry of the trimanganese system more thoroughly in the presence of a fourth Mn equivalent, finding a range of oxidation states and oxide incorporation dependent on oxidant, solvent, and Mn salt. Oxidation states from MnII4 to MnIIIMnIV3 were observed, with 1-4 O2\u2013 ligands incorporated, modeling the photoactivation of the OEC. These complexes were studied by X-ray diffraction, EPR, XAS, magnetometry, and CV.
\r\n\r\nAs Ca2+ is a necessary component of the OEC, Chapter 4 discusses synthetic strategies for making highly structurally accurate models of the OEC containing both Mn and Ca in the Mn3CaO4 cubane + dangling Mn geometry. Structural and electrochemical characterization of the first Mn3CaO4 heterometallic cubane complex\u2014 and comparison to an all-Mn Mn4O4 analog\u2014suggests a role for Ca2+ in the OEC. Modification of the Mn3CaO4 system by ligand substitution affords low symmetry Mn3CaO4 complexes that are the most accurate models of the OEC to date.
\r\n\r\nFinally, in Chapter 5 the reactivity of the Mn3CaO4 cubane complexes toward O- atom transfer is discussed. The metal M strongly affects the reactivity. The mechanisms of O-atom transfer and water incorporation from and into Mn4O4 and Mn4O3 clusters, respectively, are studied through computation and 18O-labeling studies. The \u03bc3-oxos of the Mn4O4 system prove fluxional, lending support for proposals of O2\u2013 fluxionality within the OEC.
" }, { "name": "Kang, JeenJoo Sophia", "degree": "PhD", "year": "2015", "title": "Targeting DNA Repeat Sequences with Py-Im Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052015-200117829", "creators": [ { "name": { "family": "Kang", "given": "JeenJoo Sophia" }, "id": "Kang-JeenJoo-Sophia", "display_name": "Kang, JeenJoo Sophia" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z93R0QSQ", "abstract": "Hairpin pyrrole-imdazole polyamides are cell-permeable, sequence-programmable oligomers that bind in the minor groove of DNA. This thesis describes studies of Py-Im polyamides targeted to biologically important DNA repeat sequences for the purpose of modulating disease states. Design of a hairpin polyamide that binds the CG dyad, a site of DNA methylation that can become dysregulated in cancer, is described. We report the synthesis of a DNA methylation antagonist, its sequence specificity and affinity informed by Bind-n-Seq and iteratively designed, which improves inhibitory activity in a cell-free assay by 1000-fold to low nanomolar IC50. Additionally, a hairpin polyamide targeted to the telomeric sequence is found to trigger a slow necrotic-type cell death with the release of inflammatory molecules in a model of B cell lymphoma. The effects of the polyamide are unique in this class of oligomers; its effects are characterized and a functional assay of phagocytosis by macrophages is described. Additionally, hairpin polyamides targeted to pathologically expanded CTG\u2022CAG triplet repeat DNA sequences, the molecular cause of myotonic dystrophy type 1, are synthesized and assessed for toxicity. Lastly, ChIP-seq of Hypoxia-Inducible Factor is performed under hypoxia-induced conditions. The study results show that ChIP-seq can be employed to understand the genome-wide perturbation of Hypoxia-Inducible Factor occupancy by a Py-Im polyamide." }, { "name": "Kieffer, Madeleine Eileen", "degree": "PhD", "year": "2015", "title": "New Catalytic Methods for the Preparation of Tryptophans and Pyrroloindolines: Total Synthesis of (+)-Naseseazines A and B and (\u2013)-Aspergilazine A\r ", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052015-132556787", "creators": [ { "name": { "family": "Kieffer", "given": "Madeleine Eileen" }, "id": "Kieffer-Madeleine-Eileen", "display_name": "Kieffer, Madeleine Eileen" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9X0650X", "abstract": "Tryptophan and unnatural tryptophan derivatives are important building blocks for the total synthesis of natural products, as well as the development of new drugs, biological probes, and chiral small molecule catalysts. This thesis describes various catalytic methods for the preparation of tryptophan derivatives as well as their functionalization and use in natural product total synthesis.
\r\n\r\nHerein, the tandem Friedel\u2013Crafts conjugate addition/asymmetric protonation reaction between 2-substituted indoles and methyl 2-acetamidoacrylate to provide enantioenriched trytophans is reported. This method inspired further work in the area of transition metal catalyzed arylation reactions. We report the development of the coppercatalyzed arylation of tryptamine and tryptophan derivatives. The utility of these transformations is highlighted in the five-step syntheses of the natural products (+)-naseseazine A and B. Further work on the development of a mild and general Larock indolization protocol to access unnatural tryptophans is also discussed.
" }, { "name": "Kirkpatrick, Andrea", "degree": "PhD", "year": "2015", "title": "Computational Predictions of G Protein-Coupled Receptor Structures and Binding Sites", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132015-220841374", "creators": [ { "name": { "family": "Kirkpatrick", "given": "Andrea" }, "id": "Kirkpatrick-Andrea", "orcid": "0000-0002-7212-7946", "display_name": "Kirkpatrick, Andrea" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NG4NJG", "abstract": "G protein-coupled receptors (GPCRs) are the largest family of proteins within the human genome. They consist of seven transmembrane (TM) helices, with a N-terminal region of varying length and structure on the extracellular side, and a C-terminus on the intracellular side. GPCRs are involved in transmitting extracellular signals to cells, and as such are crucial drug targets. Designing pharmaceuticals to target GPCRs is greatly aided by full-atom structural information of the proteins. In particular, the TM region of GPCRs is where small molecule ligands (much more bioavailable than peptide ligands) typically bind to the receptors. In recent years nearly thirty distinct GPCR TM regions have been crystallized. However, there are more than 1,000 GPCRs, leaving the vast majority of GPCRs with limited structural information. Additionally, GPCRs are known to exist in a myriad of conformational states in the body, rendering the static x-ray crystal structures an incomplete reflection of GPCR structures. In order to obtain an ensemble of GPCR structures, we have developed the GEnSeMBLE procedure to rapidly sample a large number of variations of GPCR helix rotations and tilts. The lowest energy GEnSeMBLE structures are then docked to small molecule ligands and optimized. The GPCR family consists of five subfamilies with little to no sequence homology between them: class A, B1, B2, C, and Frizzled/Taste2. Almost all of the GPCR crystal structures have been of class A GPCRs, and much is known about their conserved interactions and binding sites. In this work we particularly focus on class B1 GPCRs, and aim to understand that family\u2019s interactions and binding sites both to small molecules and their native peptide ligands. Specifically, we predict the full atom structure and peptide binding site of the glucagon-like peptide receptor and the TM region and small molecule binding sites for eight other class B1 GPCRs: CALRL, CRFR1, GIPR, GLR, PACR, PTH1R, VIPR1, and VIPR2. Our class B1 work reveals multiple conserved interactions across the B1 subfamily as well as a consistent small molecule binding site centrally located in the TM bundle. Both the interactions and the binding sites are distinct from those seen in the more well-characterized class A GPCRs, and as such our work provides a strong starting point for drug design targeting class B1 proteins. We also predict the full structure of CXCR4 bound to a small molecule, a class A GPCR that was not closely related to any of the class A GPCRs at the time of the work." }, { "name": "Kretchmer, Joshua S.", "degree": "PhD", "year": "2015", "title": "Direct Simulation of Proton-Coupled Electron Transfer Reaction Dynamics and Mechanisms", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202015-085910230", "creators": [ { "name": { "family": "Kretchmer", "given": "Joshua S." }, "id": "Kretchmer-Joshua-S", "display_name": "Kretchmer, Joshua S." } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z98913T5", "abstract": "Proton-coupled electron transfer (PCET) reactions are ubiquitous throughout chemistry and biology. However, challenges arise in both the the experimental and theoretical investigation of PCET reactions; the rare-event nature of the reactions and the coupling between quantum mechanical electron- and proton-transfer with the slower classical dynamics of the surrounding environment necessitates the development of robust simulation methodology. In the following dissertation, novel path-integral based methods are developed and employed for the direct simulation of the reaction dynamics and mechanisms of condensed-phase PCET." }, { "name": "Lam, Yan Choi", "degree": "PhD", "year": "2015", "title": "Synthesis, Oxidation and Photophysics of Perfluoroborated Tetrakis(pyrophosphito)diplatinate (II) and Density Functional Theory (DFT) Study of Electrochemical CO2 Reduction by Mn Catalysts", "advisor": "Gray, Harry B.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05212015-155730829", "creators": [ { "name": { "family": "Lam", "given": "Yan Choi" }, "id": "Lam-Yan-Choi", "orcid": "0000-0001-7809-4471", "display_name": "Lam, Yan Choi" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94J0C2D", "abstract": "In the first part of this thesis (Chapters I and II), the synthesis, characterization, reactivity and photophysics of per(difluoroborated) tetrakis(pyrophosphito)diplatinate(II) (Pt(POPBF2)) are discussed. Pt(POP-BF2) was obtained by reaction of [Pt2(POP)4]4- with neat boron trifluoride diethyl etherate (BF3\u00b7Et2O). While Pt(POP-BF2) and [Pt2(POP)4]4- have similar structures and absorption spectra, they differ in significant ways. Firstly, as discussed in Chapter I, the former is less susceptible to oxidation, as evidenced by the reversibility of its oxidation by I2. Secondly, while the first excited triplet states (T1) of both Pt(POP-BF2) and [Pt2(POP)4]4- exhibit long lifetimes (ca. 0.01 ms at room temperature) and substantial zero-field splitting (40 cm-1), Pt(POP-BF2) also has a remarkably long-lived (1.6 ns at room temperature) singlet excited state (S1), indicating slow intersystem crossing (ISC). Fluorescence lifetime and quantum yield (QY) of Pt(POP-BF2) were measured over a range of temperatures, providing insight into the slow ISC process. The remarkable spectroscopic and photophysical properties of Pt(POP-BF2), both in solution and as a microcrystalline powder, form the theme of Chapter II.
\r\n\r\nIn the second part of the thesis (Chapters III and IV), the electrochemical reduction of CO2 to CO by [(L)Mn(CO)3]- catalysts is investigated using density functional theory (DFT). As discussed in Chapter III, the turnover frequency (TOF)-limiting step is the dehydroxylation of [(bpy)Mn(CO)3(CO2H)]0/- (bpy = bipyridine) by trifluoroethanol (TFEH) to form [(bpy)Mn(CO)4]+/0. Because the dehydroxylation of [(bpy)Mn(CO)3(CO2H)]- is faster, maximum TOF (TOFmax) is achieved at potentials sufficient to completely reduce [(bpy)Mn(CO)3(CO2H)]0 to [(bpy)Mn(CO)3(CO2H)]-. Substitution of bipyridine with bipyrimidine reduces the overpotential needed, but at the expense of TOFmax. In Chapter IV, the decoration of the bipyrimidine ligand with a pendant alcohol is discussed as a strategy to increase CO2 reduction activity. Our calculations predict that the pendant alcohol acts in concert with an external TFEH molecule, the latter acidifying the former, resulting in a ~ 80,000-fold improvement in the rate of TOF-limiting dehydroxylation of [(L)Mn(CO)3(CO2H)]-.
\r\n\r\nAn interesting strategy for the co-upgrading of light olefins and alkanes into heavier alkanes is the subject of Appendix B. The proposed scheme involves dimerization of the light olefin, operating in tandem with transfer hydrogenation between the olefin dimer and the light alkane. The work presented therein involved a Ta olefin dimerization catalyst and a silica-supported Ir transfer hydrogenation catalyst. Olefin dimer was formed under reaction conditions; however, this did not undergo transfer hydrogenation with the light alkane. A significant challenge is that the Ta catalyst selectively produces highly branched dimers, which are unable to undergo transfer hydrogenation.
" }, { "name": "Lee, Chung Whan", "degree": "PhD", "year": "2015", "title": "Progress Toward the Total Synthesis of Curcusone C and Mechanistic Elucidation of an Unexpected Rearrangement", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-143832701", "creators": [ { "name": { "family": "Lee", "given": "Chung Whan" }, "id": "Lee-Chung-Whan", "display_name": "Lee, Chung Whan" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9J964C4", "abstract": "Curcusone C is tricyclic diterpenoid natural product isolated from Jatropha curcas that exhibits potent biological activity and features a 2,3,7,8- tetrahydroazulene-1,4-dione moiety. Herein, we describe a synthetic approach toward ent-curcusone C. Construction of the tricyclic scaffold of ent-curcusone C is achieved from a cyclopentenol boronate and a vinyl bromide, which was synthesized from (S)-perillaldehyde. Suzuki coupling of the two precursors furnished a dieneol, which was converted to a diazoester via transesterification followed by diazo transfer reaction. A divinylcyclopropane was synthesized from the diazoester by intramolecular cyclopropanation and subsequent Kauffmann olefination. The tricyclic core of ent-curcusone C was accomplished by divinylcyclopropane rearrangement, which was initiated by reduction of the lactone moiety.
\r\n\r\nWe discovered an unexpected rearrangement during the course of our investigation toward the synthesis of curcusone C. Surprisingly, a silyl enol ether was converted to a complex tetracyclic compound under mild heating conditions. The transformation was elucidated as a unique reaction cascade of [3,3] Cope rearrangement, [1,5] silyl migration, Ireland\u2013Claisen rearrangement, retro Claisen rearrangement, and [1,5] silyl migration by computational and experimental efforts.
\r\n\r\nAdditionally, our work on the development of a bis(phosphine) copper catalyst for the asymmetric alkylation of 3-Bromooxindoles with \u03b1-arylated malonate esters is described. Versatile copper sources and chiral bis(phosphine) ligands were investigated.
" }, { "name": "Liu, Yiyang", "degree": "PhD", "year": "2015", "title": "Palladium-Catalyzed Decarboxylative and Decarbonylative Transformations in the Synthesis of Fine and Commodity Chemicals", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-170352881", "creators": [ { "name": { "family": "Liu", "given": "Yiyang" }, "id": "Liu-Yiyang", "display_name": "Liu, Yiyang" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9NZ85NC", "abstract": "Decarboxylation and decarbonylation are important reactions in synthetic organic chemistry, transforming readily available carboxylic acids and their derivatives into various products through loss of carbon dioxide or carbon monoxide. In the past few decades, palladium-catalyzed decarboxylative and decarbonylative reactions experienced tremendous growth due to the excellent catalytic activity of palladium. Development of new reactions in this category for fine and commodity chemical synthesis continues to draw attention from the chemistry community.
\r\n\r\nThe Stoltz laboratory has established a palladium-catalyzed enantioselective decarboxylative allylic alkylation of \u03b2-keto esters for the synthesis of \u03b1-quaternary ketones since 2005. Recently, we extended this chemistry to lactams due to the ubiquity and importance of nitrogen-containing heterocycles. A wide variety of \u03b1-quaternary and tetrasubstituted \u03b1-tertiary lactams were obtained in excellent yields and exceptional enantioselectivities using our palladium-catalyzed decarboxylative allylic alkylation chemistry. Enantioenriched \u03b1-quaternary carbonyl compounds are versatile building blocks that can be further elaborated to intercept synthetic intermediates en route to many classical natural products. Thus our chemistry enables catalytic asymmetric formal synthesis of these complex molecules.
\r\n\r\nIn addition to fine chemicals, we became interested in commodity chemical synthesis using renewable feedstocks. In collaboration with the Grubbs group, we developed a palladium-catalyzed decarbonylative dehydration reaction that converts abundant and inexpensive fatty acids into value-added linear alpha olefins. The chemistry proceeds under relatively mild conditions, requires very low catalyst loading, tolerates a variety of functional groups, and is easily performed on a large scale. An additional advantage of this chemistry is that it provides access to expensive odd-numbered alpha olefins.
\r\n\r\nFinally, combining features of both projects, we applied a small-scale decarbonylative dehydration reaction to the synthesis of \u03b1-vinyl carbonyl compounds. Direct \u03b1-vinylation is challenging, and asymmetric vinylations are rare. Taking advantage of our decarbonylative dehydration chemistry, we were able to transform enantioenriched \u03b4-oxocarboxylic acids into quaternary \u03b1-vinyl carbonyl compounds in good yields with complete retention of stereochemistry. Our explorations culminated in the catalytic enantioselective total synthesis of (\u2013)-aspewentin B, a terpenoid natural product featuring a quaternary \u03b1-vinyl ketone. Both decarboxylative and decarbonylative chemistries found application in the late stage of the total synthesis.
" }, { "name": "Marotta, Christopher Bruno", "degree": "PhD", "year": "2015", "title": "Structure-Function Studies of Nicotinic Acetylcholine Receptors Using Selective Agonists and Positive Allosteric Modulators", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292015-144036736", "creators": [ { "name": { "family": "Marotta", "given": "Christopher Bruno" }, "id": "Marotta-Christopher-Bruno", "orcid": "0000-0002-3110-0819", "display_name": "Marotta, Christopher Bruno" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9V122Q9", "abstract": "This dissertation primarily describes chemical-scale studies of nicotinic acetylcholine receptors (nAChRs) in order to better understand ligand-receptor selectivity and allosteric modulation influences during receptor activation. Electrophysiology coupled with canonical and non-canonical amino acids mutagenesis is used to probe subtle changes in receptor function.
\r\n\t\r\nThe first half of this dissertation focuses on differential agonist selectivity of \u03b14\u03b22-containing nAChRs. The \u03b14\u03b22 nAChR can assemble in alternative stoichiometries as well as assemble with other accessory subunits. Chapter 2 identifies key structural residues that dictate binding and activation of three stoichiometry-dependent \u03b14\u03b22 receptor ligands: sazetidine-A, cytisine, and NS9283. These do not follow previously suggested hydrogen-bonding patterns of selectivity. Instead, three residues on the complementary subunit strongly influence binding ability of a ligand and receptor activation. Chapter 3 involves isolation of a \u03b15\u03b14\u03b22 receptor-enriched population to test for a potential alternative agonist binding location at the \u03b15 \u03b14 interface. Results strongly suggest that agonist occupation of this site is not necessary for receptor activation and that the \u03b15 subunit only incorporates at the accessory subunit location.
\r\n\t\r\nThe second half of this dissertation seeks to identify residue interactions with positive allosteric modulators (PAMs) of the \u03b17 nAChR. Chapter 4 focuses on methods development to study loss of potentiation of Type I PAMs, which indicate residues vital to propagation of PAM effects and/or binding. Chapter 5 investigates \u03b17 receptor modulation by a Type II PAM (PNU 120596). These results show that PNU 120596 does not alter the agonist binding site, thus is relegated to influencing only the gating component of activation. From this, we were able to map a potential network of residues from the agonist binding site to the proposed PNU 120596 binding site that are essential for receptor potentiation.
" }, { "name": "McGuire, Brett Andrew", "degree": "PhD", "year": "2015", "title": "Time-Domain TeraHertz Spectroscopy and Observational Probes of Prebiotic Interstellar Gas and Ice Chemistry", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232014-152145064", "creators": [ { "name": { "family": "McGuire", "given": "Brett Andrew" }, "id": "McGuire-Brett-Andrew", "orcid": "0000-0003-1254-4817", "display_name": "McGuire, Brett Andrew" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Remijan", "given": "Anthony J." }, "id": "Remijan-A-J", "role": "member", "display_name": "Remijan, Anthony J." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9B27S79", "abstract": "Understanding the origin of life on Earth has long fascinated the minds of the global community, and has been a driving factor in interdisciplinary research for centuries. Beyond the pioneering work of Darwin, perhaps the most widely known study in the last century is that of Miller and Urey, who examined the possibility of the formation of prebiotic chemical precursors on the primordial Earth [1]. More recent studies have shown that amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth, are present in meteoritic samples, and that the molecules extracted from the meteorites display isotopic signatures indicative of an extraterrestrial origin [2]. The most recent major discovery in this area has been the detection of glycine (NH2CH2COOH), the simplest amino acid, in pristine cometary samples returned by the NASA STARDUST mission [3]. Indeed, the open questions left by these discoveries, both in the public and scientific communities, hold such fascination that NASA has designated the understanding of our \"Cosmic Origins\" as a key mission priority.
\r\n\r\nDespite these exciting discoveries, our understanding of the chemical and physical pathways to the formation of prebiotic molecules is woefully incomplete. This is largely because we do not yet fully understand how the interplay between grain-surface and sub-surface ice reactions and the gas-phase affects astrophysical chemical evolution, and our knowledge of chemical inventories in these regions is incomplete. The research presented here aims to directly address both these issues, so that future work to understand the formation of prebiotic molecules has a solid foundation from which to work.
\r\n\r\nFrom an observational standpoint, a dedicated campaign to identify hydroxylamine (NH2OH), potentially a direct precursor to glycine, in the gas-phase was undertaken. No trace of NH2OH was found. These observations motivated a refinement of the chemical models of glycine formation, and have largely ruled out a gas-phase route to the synthesis of the simplest amino acid in the ISM. A molecular mystery in the case of the carrier of a series of transitions was resolved using observational data toward a large number of sources, confirming the identity of this important carbon-chemistry intermediate B11244 as l-C3H+ and identifying it in at least two new environments. Finally, the doubly-nitrogenated molecule carbodiimide HNCNH was identified in the ISM for the first time through maser emission features in the centimeter-wavelength regime.
\r\n\r\nIn the laboratory, a TeraHertz Time-Domain Spectrometer was constructed to obtain the experimental spectra necessary to search for solid-phase species in the ISM in the THz region of the spectrum. These investigations have shown a striking dependence on large-scale, long-range (i.e. lattice) structure of the ices on the spectra they present in the THz. A database of molecular spectra has been started, and both the simplest and most abundant ice species, which have already been identified, as well as a number of more complex species, have been studied. The exquisite sensitivity of the THz spectra to both the structure and thermal history of these ices may lead to better probes of complex chemical and dynamical evolution in interstellar environments.
" }, { "name": "Ni, Jane", "degree": "PhD", "year": "2015", "title": "Development of Asymmetric Protonation Reactions for the Synthesis of Indoline Alkaloids", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152014-112952177", "creators": [ { "name": { "family": "Ni", "given": "Jane" }, "id": "Ni-Jane", "display_name": "Ni, Jane" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z95B00C4", "abstract": "Nitrogen-containing heterocycles, such as indolines and pyrroloindolines, are prevalent in a variety of diverse natural products, many of which exhibit remarkable biological activities. These frameworks have inspired innovative research aimed at discovering novel methods for their stereoselective preparation.
\r\n\r\nWe have developed an enantioselective synthesis of pyrroloindolines based on a formal (3 + 2) cycloaddition of indoles and 2-amidoacrylates. This reaction is promoted by (R)-BINOL\u2022SnCl4; this complex is a Lewis acid-assisted Br\u00f8nsted acid that effects a highly face-selective catalyst-controlled protonation of an enolate. Mechanistic studies also determined that the initial product of this reaction is an indolinium ion, which upon aqueous workup undergoes cyclization to the pyrroloindoline.
\r\n\r\nBased on this result, we investigated alternative nucleophiles to trap the indolinium ion. First, addition of sodium borohydride to the optimized reaction conditions yields indoline-containing amino acid derivatives.
\r\n\r\nNext, carbon nucleophiles were explored. Indole substrates incorporating a tethered alkene were exposed to the conditions for the formal (3 + 2) cycloaddition, resulting in a conjugate addition/asymmetric protonation/Prins cyclization cascade. In this transformation, the indolinium ion is attacked by the olefin, and the resulting carbocation is quenched by a chloride ion. Zirconium tetrachloride was found to be the optimal Lewis acid. Stoichiometric proton and chloride sources were also found to be crucial for reactivity.
\r\n" }, { "name": "Pacheco, Joshua Joseph", "degree": "PhD", "year": "2015", "title": "New Catalysts for the Renewable Production of Monomers for Bioplastics", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182015-163742452", "creators": [ { "name": { "family": "Pacheco", "given": "Joshua Joseph" }, "id": "Pacheco-Joshua-Joseph", "display_name": "Pacheco, Joshua Joseph" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9N58JBZ", "abstract": "Terephthalic acid (PTA) is one of the monomers used for the synthesis of the polyester, polyethylene terephthalate (PET), that is used for the large-scale manufacture of synthetic fibers and plastic bottles. PTA is largely produced from the liquid-phase oxidation of petroleum-derived p-xylene (PX). However, there are now ongoing worldwide efforts exploring alternative routes for producing PTA from renewable, biomass resources.
\r\n\r\nIn this thesis, I present a new route to PTA starting from the biomass-derived platform chemical, 5-hydroxymethylfurfural (HMF). This route utilizes new, selective Diels-Alder-dehydration reactions involving ethylene and is advantageous over the previously proposed Diels-Alder-dehydration route to PTA from HMF via 2,5-dimethylfuran (DMF) since the H2 reduction of HMF to DMF is avoided. Specifically, oxidized derivatives of HMF are reacted as is, or after etherification-esterification with methanol, with ethylene over solid Lewis acid catalysts that do not contain strong Br\u00f8nsted acids in order to synthesize intermediates of PTA and its equally important diester, dimethyl terephthalate (DMT). The partially oxidized HMF, 5-(hydroxymethyl)furoic acid (HMFA) is reacted with high pressure ethylene over a pure-silica molecular sieve catalyst containing framework tin (Sn-Beta) to produce the Diels-Alder-dehydration product, 4-(hydroxymethyl)benzoic acid (HMBA), with ~30% selectivity at ~20% yield. If HMFA is protected with methanol to form methyl 5-(methoxymethyl)furan-2-carboxylate (MMFC), MMFC can react with ethylene in the presence of a pure-silica molecular sieve containing framework zirconium (Zr-Beta) to produce methyl 4-(methoxymethyl)benzenecarboxylate (MMBC) with >70% selectivity at >20% yield. HMBA and MMBC can then be oxidized to produce PTA and DMT, respectively. When Lewis acid containing mesoporous silica (MCM-41) and amorphous silica, or Br\u00f8nsted acid containing zeolites (Al-Beta), are used as catalysts, a significant decrease in selectivity/yield of the Diels-Alder-dehydration product is observed.
\r\n\r\nAn investigation to elucidate the reaction network and side products in the conversion of MMFC to MMBC was performed, and the main side products are found to be methyl 4-formylcyclohexa-1,3-diene-1-carboxylate and the ethylene Diels-Alder adduct of this cyclohexadiene. These products presumably form by a different dehydration pathway of the MMFC/ethylene Diels-Alder adduct and should be included when determining the overall selectivity to PTA or DMT since, like MMBC, these compounds are precursors to PTA or DMT.
\r\n\r\nFundamental physical and chemical information on the ethylene Diels-Alder-dehydration reactions catalyzed by the Lewis acid-containing molecular sieves was obtained. Madon-Boudart experiments using Zr-Beta as catalyst show that the reaction rates are limited by chemical kinetics only (physical transport limitations are not present), all the Zr4+ centers are incorporated into the framework of the molecular sieve, and the whole molecular sieve crystal is accessible for catalysis. Apparent activation energies using Zr-Beta are low, suggesting that the overall activation energy of the system may be determined by a collection of terms and is not the true activation energy of a single chemical step.
\r\n" }, { "name": "Reeves, Corey Michael", "degree": "PhD", "year": "2015", "title": "Strategies for the Stereoselective Synthesis of Carbon Quaternary Centers via Transition Metal-Catalyzed Alkylation of Enolate Compounds", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192015-131629900", "creators": [ { "name": { "family": "Reeves", "given": "Corey Michael" }, "id": "Reeves-Corey-Michael", "display_name": "Reeves, Corey Michael" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9VX0DGH", "abstract": "Notwithstanding advances in modern chemical methods, the selective installation of sterically encumbered carbon stereocenters, in particular all-carbon quaternary centers, remains an unsolved problem in organic chemistry. The prevalence of all-carbon quaternary centers in biologically active natural products and pharmaceutical compounds provides a strong impetus to address current limitations in the state of the art of their generation. This thesis presents four related projects, all of which share in the goal of constructing highly-congested carbon centers in a stereoselective manner, and in the use of transition-metal catalyzed alkylation as a means to address that goal.
\r\n\r\nThe first research described is an extension of allylic alkylation methodology previously developed in the Stoltz group to small, strained rings. This research constitutes the first transition metal-catalyzed enantioselective \u03b1-alkylation of cyclobutanones. Under Pd-catalysis, this chemistry affords all\u2013carbon \u03b1-quaternary cyclobutanones in good to excellent yields and enantioselectivities.
\r\n\r\nNext is described our development of a (trimethylsilyl)ethyl \u03b2-ketoester class of enolate precursors, and their application in palladium\u2013catalyzed asymmetric allylic alkylation to yield a variety of \u03b1-quaternary ketones and lactams. Independent coupling partner synthesis engenders enhanced allyl substrate scope relative to allyl \u03b2-ketoester substrates; highly functionalized \u03b1-quaternary ketones generated by the union of our fluoride-triggered \u03b2-ketoesters and sensitive allylic alkylation coupling partners serve to demonstrate the utility of this method for complex fragment coupling.
\r\n\r\nLastly, our development of an Ir-catalyzed asymmetric allylic alkylation of cyclic \u03b2-ketoesters to afford highly congested, vicinal stereocenters comprised of tertiary and all-carbon quaternary centers with outstanding regio-, diastereo-, and enantiocontrol is detailed. Implementation of a subsequent Pd-catalyzed alkylation affords dialkylated products with pinpoint stereochemical control of both chiral centers. The chemistry is then extended to include acyclic \u03b2-ketoesters and similar levels of selective and functional group tolerance are observed. Critical to the successful development of this method was the employment of iridium catalysis in concert with N-aryl-phosphoramidite ligands.
\r\n" }, { "name": "Schaefer, Kathryn Nicole", "degree": "PhD", "year": "2015", "title": "DNA-Mediated Oxidation of Transcription Factor p53", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02122015-130640999", "creators": [ { "name": { "family": "Schaefer", "given": "Kathryn Nicole" }, "id": "Schaefer-Kathryn-Nicole", "orcid": "0000-0003-0908-3191", "display_name": "Schaefer, Kathryn Nicole" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9BV7DJQ", "abstract": "Transcription factor p53 is the most commonly altered gene in human cancer. As a redox-active protein in direct contact with DNA, p53 can directly sense oxidative stress through DNA-mediated charge transport. Electron hole transport occurs with a shallow distance dependence over long distances through the \u03c0-stacked DNA bases, leading to the oxidation and dissociation of DNA-bound p53. The extent of p53 dissociation depends upon the redox potential of the response element DNA in direct contact with each p53 monomer. The DNA sequence dependence of p53 oxidative dissociation was examined by electrophoretic mobility shift assays using radiolabeled oligonucleotides containing both synthetic and human p53 response elements with an appended anthraquinone photooxidant. Greater p53 dissociation is observed from DNA sequences containing low redox potential purine regions, particularly guanine triplets, within the p53 response element. Using denaturing polyacrylamide gel electrophoresis of irradiated anthraquinone-modified DNA, the DNA damage sites, which correspond to locations of preferred electron hole localization, were determined. The resulting DNA damage preferentially localizes to guanine doublets and triplets within the response element. Oxidative DNA damage is inhibited in the presence of p53, however, only at DNA sites within the response element, and therefore in direct contact with p53. From these data, predictions about the sensitivity of human p53-binding sites to oxidative stress, as well as possible biological implications, have been made. On the basis of our data, the guanine pattern within the purine region of each p53-binding site determines the response of p53 to DNA-mediated oxidation, yielding for some sequences the oxidative dissociation of p53 from a distance and thereby providing another potential role for DNA charge transport chemistry within the cell.
\r\n\r\nTo determine whether the change in p53 response element occupancy observed in vitro also correlates in cellulo, chromatin immunoprecipition (ChIP) and quantitative PCR (qPCR) were used to directly quantify p53 binding to certain response elements in HCT116N cells. The HCT116N cells containing a wild type p53 were treated with the photooxidant [Rh(phi)2bpy]3+, Nutlin-3 to upregulate p53, and subsequently irradiated to induce oxidative genomic stress. To covalently tether p53 interacting with DNA, the cells were fixed with disuccinimidyl glutarate and formaldehyde. The nuclei of the harvested cells were isolated, sonicated, and immunoprecipitated using magnetic beads conjugated with a monoclonal p53 antibody. The purified immounoprecipiated DNA was then quantified via qPCR and genomic sequencing. Overall, the ChIP results were significantly varied over ten experimental trials, but one trend is observed overall: greater variation of p53 occupancy is observed in response elements from which oxidative dissociation would be expected, while significantly less change in p53 occupancy occurs for response elements from which oxidative dissociation would not be anticipated.
\r\n\r\nThe chemical oxidation of transcription factor p53 via DNA CT was also investigated with respect to the protein at the amino acid level. Transcription factor p53 plays a critical role in the cellular response to stress stimuli, which may be modulated through the redox modulation of conserved cysteine residues within the DNA-binding domain. Residues within p53 that enable oxidative dissociation are herein investigated. Of the 8 mutants studied by electrophoretic mobility shift assay (EMSA), only the C275S mutation significantly decreased the protein affinity (KD) for the Gadd45 response element. EMSA assays of p53 oxidative dissociation promoted by photoexcitation of anthraquinone-tethered Gadd45 oligonucleotides were used to determine the influence of p53 mutations on oxidative dissociation; mutation to C275S severely attenuates oxidative dissociation while C277S substantially attenuates dissociation. Differential thiol labeling was used to determine the oxidation states of cysteine residues within p53 after DNA-mediated oxidation. Reduced cysteines were iodoacetamide labeled, while oxidized cysteines participating in disulfide bonds were 13C2D2-iodoacetamide labeled. Intensities of respective iodoacetamide-modified peptide fragments were analyzed using a QTRAP 6500 LC-MS/MS system, quantified with Skyline, and directly compared. A distinct shift in peptide labeling toward 13C2D2-iodoacetamide labeled cysteines is observed in oxidized samples as compared to the respective controls. All of the observable cysteine residues trend toward the heavy label under conditions of DNA CT, indicating the formation of multiple disulfide bonds potentially among the C124, C135, C141, C182, C275, and C277. Based on these data it is proposed that disulfide formation involving C275 is critical for inducing oxidative dissociation of p53 from DNA.
\r\n" }, { "name": "Schilling, Katherine Ann", "degree": "PhD", "year": "2015", "title": "Secondary Organic Aerosol Composition Studies Using Mass Spectrometry", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222015-145550415", "creators": [ { "name": { "family": "Schilling", "given": "Katherine Ann" }, "id": "Schilling-Katherine-Ann", "display_name": "Schilling, Katherine Ann" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z93F4MJR", "abstract": "Trace volatile organic compounds emitted by biogenic and anthropogenic sources into the atmosphere can undergo extensive photooxidation to form species with lower volatility. By equilibrium partitioning or reactive uptake, these compounds can nucleate into new aerosol particles or deposit onto already-existing particles to form secondary organic aerosol (SOA). SOA and other atmospheric particulate matter have measurable effects on global climate and public health, making understanding SOA formation a needed field of scientific inquiry. SOA formation can be done in a laboratory setting, using an environmental chamber; under these controlled conditions it is possible to generate SOA from a single parent compound and study the chemical composition of the gas and particle phases. By studying the SOA composition, it is possible to gain understanding of the chemical reactions that occur in the gas phase and particle phase, and identify potential heterogeneous processes that occur at the surface of SOA particles. In this thesis, mass spectrometric methods are used to identify qualitatively and qualitatively the chemical components of SOA derived from the photooxidation of important anthropogenic volatile organic compounds that are associated with gasoline and diesel fuels and industrial activity (C12 alkanes, toluene, and o-, m-, and p-cresols). The conditions under which SOA was generated in each system were varied to explore the effect of NOx and inorganic seed composition on SOA chemical composition. The structure of the parent alkane was varied to investigate the effect on the functionalization and fragmentation of the resulting oxidation products. Relative humidity was varied in the alkane system as well to measure the effect of increased particle-phase water on condensed-phase reactions. In all systems, oligomeric species, resulting potentially from particle-phase and heterogeneous processes, were identified. Imines produced by reactions between (NH4)2SO4 seed and carbonyl compounds were identified in all systems. Multigenerational photochemistry producing low- and extremely low-volatility organic compounds (LVOC and ELVOC) was reflected strongly in the particle-phase composition as well." }, { "name": "Suseno, Sandy", "degree": "PhD", "year": "2015", "title": "Homo- and Heteronuclear Transition Metal Complexes Supported by Multinucleating Ligands", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202014-184045649", "creators": [ { "name": { "family": "Suseno", "given": "Sandy" }, "id": "Suseno-Sandy", "display_name": "Suseno, Sandy" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9668B43", "abstract": "This dissertation is mainly divided into two sub-parts: organometallic and bioinorganic/materials projects. The approach for the projects involves the use of two different multinucleating ligands to synthesize mono- and multinuclear complexes. Chapter 2 describes the synthesis of a multinucleating tris(phosphinoaryl)benzene ligand used to support mono-nickel and palladium complexes. The isolated mononuclear complexes were observed to undergo intramolecular arene C\u00ac\u2013H to C\u2013P functionalization. The transformation was studied by nuclear magnetic resonance spectroscopy and X-ray crystallography, and represents a rare type of C\u2013H functionalization mechanism, facilitated by the interactions of the group 10 metal with the arene \u03c0\u2013system.
\r\n\r\nChapter 3 describes the construction of multinickel complexes supported by the same triphosphine ligand from Chapter 2. This chapter shows how the central arene in the ligand\u2019s triarylbenzene framework can interact with dinickel and trinickel moieties in various binding modes. X-ray diffraction studies indicated that all compounds display strong metal\u2013arene interactions. A cofacial triangulo nickel(0) complex supported by this ligand scaffold was also isolated and characterized. This chapter demonstrates the use of an arene as versatile ligand design element for small molecular clusters.
\r\n\r\nChapter 4 presents the syntheses of a series of discrete mixed transition metal Mn oxido clusters and their characterization. The synthesis of these oxide clusters displaying two types of transition metals were targeted for systematic metal composition-property studies relevant to mixed transition metal oxides employed in electrocatalysis. A series of heterometallic trimanganese tetraoxido cubanes capped with a redox-active metal [MMn3O4] (M = Fe, Co, Ni, Cu) was synthesized starting from a [CaMn3O4] precursor and structurally characterized by X-ray crystallography and anomalous diffraction to conclusively determine that M is incorporated at a single position in the cluster. The electrochemical properties of these complexes were studied via cyclic voltammetry. The redox chemistry of the series of complexes was investigated by the addition of a reductant and oxidant. X-ray absorption and electron paramagnetic resonance spectroscopies were also employed to evaluate the product of the oxidation/reduction reaction to determine the site of electron transfer given the presence of two types of redox-active metals. Additional studies on oxygen atom transfer reactivities of [MMn3O4] and [MMn3O2] series were performed to investigate the effect of the heterometal M in the reaction rates.
\r\n\r\nChapter 5 focuses on the use of [CoMn3O4] and [NiMn3O4] cubane complexes discussed in Chapter 4 as precursors to heterogeneous oxygen evolution reaction (OER) electrocatalysts. These well-defined complexes were dropcasted on electrodes with/without heat treatment, and the OER activities of the resulting films were evaluated. Multiple spectroscopic techniques were performed on the surface of the electrocatalysts to gain insight into the structure-function relationships based on the heterometallic composition. Depending on film preparation, the Co-Mn-oxide was found to change metal composition during catalysis, while the Ni-Mn oxide maintained the NiMn3 ratio. These studies represent the use of discrete heterometallic-oxide clusters as precursors for heterogeneous water oxidation catalysts.
\r\n\r\nAppendix A describes the ongoing effort to synthesize a series of heteromultimetallic [MMn3X] clusters (X = O, S, F). Complexes such as [ZnMn3O], [CoMn3O], [Mn3S], and [Mn4F] have been synthesized and structurally characterized. An amino-bis-oxime ligand (PRABO) has been installed on the [ZnMn3O] cluster. Upon the addition of O2, the desymmetrized [ZnMn3O] cluster only underwent an outer-sphere, one-electron oxidation. Efforts to build and manipulate other heterometallic [MMn3X] clusters are still ongoing, targeting O2 binding and reduction. Appendix B summarizes the multiple synthetic approaches to build a [Co4O4]-cubane complex relevant to heterogeneous OER electrocatalysis. Starting with the tricobalt cluster [LCo3(O2CR)3] and treatment various strong oxidants that can serve as oxygen atom source in the presence Co2+ salt only yielded tricobalt mono\u2013oxo complexes. Appendix C presents the efforts to model the H-cluster framework of [FeFe]-hydrogenase by incorporating a synthetic diiron complex onto a protein-supported or a synthetic ligand-supported [Fe4S4]-cluster. The mutant ferredoxin with a [Fe4S4]-cluster and triscarbene ligand have been characterized by multiple spectroscopic techniques. The reconstruction of an H-cluster mimic has not yet been achieved, due to the difficulty of obtaining crystallographic evidence and the ambiguity of the EPR results.
\r\n" }, { "name": "Wang, Andrew Chih-Kae", "degree": "PhD", "year": "2015", "title": "Investigating the Role of O-GlcNAc Glycosylation in Neurodegeneration", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032015-135024245", "creators": [ { "name": { "family": "Wang", "given": "Andrew Chih-Kae" }, "id": "Wang-Andrew-Chih-Kae", "display_name": "Wang, Andrew Chih-Kae" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z97W695K", "abstract": "O-GlcNAc glycosylation of nuclear and cytosolic proteins is an essential post-translational modification implicated in many diseases, from cancer to diabetes. Importantly, many important neuronal proteins are also O-GlcNAc modified, and aberrant O-GlcNAcylation of these proteins may contribute to the pathology of neurodegenerative diseases although these mechanisms have not been well defined. Here we investigated the role of O-GlcNAc glycosylation in the brain, utilizing both chemistry and molecular biology to study O-GlcNAc transferase (OGT), the enzyme that adds the sugar modification. To evaluate the role of OGT in adult neurons, we generated a forebrain-specific conditional knockout of OGT (OGT cKO) in mice. Although indistinguishable from wild-type littermates at birth, after three weeks we observe progressive neurodegeneration in OGT cKO mice. Hallmarks of Alzheimer\u2019s disease, including neuronal loss, neuroinflammation, behavioral deficits, hyperphosphorylated tau, and amyloid beta peptide accumulation, are observed. Furthermore, decreases in OGT protein levels were found in human AD brain tissue, suggesting that altered O-GlcNAcylation likely contributes to neurodegenerative diseases in humans. This model is one of a few mouse models that recapitulate AD phenotypes without mutating and overexpressing human tau, amyloid precursor protein, or presenilin, highlighting the essential role of OGT in neurodegenerative pathways.
\r\n\r\nGiven the importance of OGT in the brain, we further investigated the regulation of the OGT enzyme by phosphorylation. We found that phosphorylation of OGT near its C-terminus reduces its activity in cancer cells, and have developed phosphorylation-specific antibodies to aid mechanistic studies. Furthermore, mutation of this phosphorylation site on OGT, followed by overexpression in neurons was shown to enhance neurite outgrowth, demonstrating a functional consequence for this site. Thus phosphorylation of OGT inhibits its activity and enhances neurite outgrowth, and current studies aim to characterize the signaling pathway that regulates OGT phosphorylation in neurons.
" }, { "name": "Wang, Haoxuan", "degree": "PhD", "year": "2015", "title": "Enantioselective Total Synthesis of Diketopiperazinecontaining Natural Products: (\u2013)-Lansai B, (+)-Nocardioazines A and B, and (\u2013)-Acetylapoaranotin", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052015-143010623", "creators": [ { "name": { "family": "Wang", "given": "Haoxuan" }, "id": "Wang-Haoxuan", "orcid": "0000-0002-8663-3073", "display_name": "Wang, Haoxuan" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z92V2D3H", "abstract": "Diketopiperazine (DKP) motif is found in a wide range of biologically active natural products. This work details our efforts toward two classes of DKP-containing natural products.
\r\n\r\nClass one features the pyrroloindoline structure, derived from tryptophans. Our group developed a highly enantioselective (3 + 2) formal cycloaddition between indoles and acrylates to provide pyrroloindoline products possessing three stereocenters. Utilizing this methodology, we accomplished asymmetric total synthesis of three natural products: (\u2013)-lansai B, (+)-nocardioazines A and B. Total synthesis of (\u2013)-lansai B was realized in six steps, and featured an amino acid dimerization strategy. The total synthesis of (+)-nocardioazine B was also successfully completed in ten steps. Challenges were met in approaching (+)-nocardioazine A, where a seemingly easy last-step epoxidization did not prove successful. After re-examining our synthetic strategy, an early-stage epoxidation strategy was pursued, which eventually yielded a nine-step total synthesis of (+)-nocardioazine A.
\r\n\r\nClass two is the epidithiodiketopiperazine (ETP) natural products, which possesses an additional episulfide bridge in the DKP core. With the goal of accessing ETPs with different peripheral structures for structure-activity relationship studies, a highly divergent route was successfully developed, which was showcased in the formal synthesis of (\u2013)-emethallicin E and (\u2013)-haematocin, and the first asymmetric synthesis of (\u2013)-acetylapoaranotin.
" }, { "name": "Wang, Rui", "degree": "PhD", "year": "2015", "title": "Effects of Self Energy of the Ions on the Double Layer Structure and Properties at the Dielectric Interface", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102014-125310289", "creators": [ { "name": { "family": "Wang", "given": "Rui" }, "id": "Wang-Rui", "display_name": "Wang, Rui" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9DN431P", "abstract": "Although numerous theoretical efforts have been put forth, a systematic, unified and predictive theoretical framework that is able to capture all the essential physics of the interfacial behaviors of ions, such as the Hofmeister series effect, Jones-Ray effect and the salt effect on the bubble coalescence remain an outstanding challenge. The most common approach to treating electrostatic interactions in the presence of salt ions is the Poisson-Boltzmann (PB) theory. However, there are many systems for which the PB theory fails to offer even a qualitative explanation of the behavior, especially for ions distributed in the vicinity of an interface with dielectric contrast between the two media (like the water-vapor/oil interface). A key factor missing in the PB theory is the self energy of the ion.
\r\n\r\nIn this thesis, we develop a self-consistent theory that treats the electrostatic self energy (including both the short-range Born solvation energy and the long-range image charge interactions), the nonelectrostatic contribution of the self energy, the ion-ion correlation and the screening effect systematically in a single framework. By assuming a finite charge spread of the ion instead of using the point-charge model, the self energy obtained by our theory is free of the divergence problems and gives a continuous self energy across the interface. This continuous feature allows ions on the water side and the vapor/oil side of the interface to be treated in a unified framework. The theory involves a minimum set of parameters of the ion, such as the valency, radius, polarizability of the ions, and the dielectric constants of the medium, that are both intrinsic and readily available. The general theory is first applied to study the thermodynamic property of the bulk electrolyte solution, which shows good agreement with the experiment result for predicting the activity coefficient and osmotic coefficient.
\r\n\r\nNext, we address the effect of local Born solvation energy on the bulk thermodynamics and interfacial properties of electrolyte solution mixtures. We show that difference in the solvation energy between the cations and anions naturally gives rise to local charge separation near the interface, and a finite Galvani potential between two coexisting solutions. The miscibility of the mixture can either increases or decreases depending on the competition between the solvation energy and translation entropy of the ions. The interfacial tension shows a non-monotonic dependence on the salt concentration: it increases linearly with the salt concentration at higher concentrations, and decreases approximately as the square root of the salt concentration for dilute solutions, which is in agreement with the Jones-Ray effect observed in experiment.
\r\n\r\nNext, we investigate the image effects on the double layer structure and interfacial properties near a single charged plate. We show that the image charge repulsion creates a depletion boundary layer that cannot be captured by a regular perturbation approach. The correct weak-coupling theory must include the self-energy of the ion due to the image charge interaction. The image force qualitatively alters the double layer structure and properties, and gives rise to many non-PB effects, such as nonmonotonic dependence of the surface energy on concentration and charge inversion. The image charge effect is then studied for electrolyte solutions between two plates. For two neutral plates, we show that depletion of the salt ions by the image charge repulsion results in short-range attractive and long-range repulsive forces. If cations and anions are of different valency, the asymmetric depletion leads to the formation of an induced electrical double layer. For two charged plates, the competition between the surface charge and the image charge effect can give rise to like- charge attraction.
\r\n\r\nThen, we study the inhomogeneous screening effect near the dielectric interface due to the anisotropic and nonuniform ion distribution. We show that the double layer structure and interfacial properties is drastically affected by the inhomogeneous screening if the bulk Debye screening length is comparable or smaller than the Bjerrum length. The width of the depletion layer is characterized by the Bjerrum length, independent of the salt concentration. We predict that the negative adsorption of ions at the interface increases linearly with the salt concentration, which cannot be captured by either the bulk screening approximation or the WKB approximation. For asymmetric salt, the inhomogeneous screening enhances the charge separation in the induced double layer and significantly increases the value of the surface potential.
\r\n\r\nFinally, to account for the ion specificity, we study the self energy of a single ion across the dielectric interface. The ion is considered to be polarizable: its charge distribution can be self-adjusted to the local dielectric environment to minimize the self energy. Using intrinsic parameters of the ions, such as the valency, radius, and polarizability, we predict the specific ion effect on the interfacial affinity of halogen anions at the water/air interface, and the strong adsorption of hydrophobic ions at the water/oil interface, in agreement with experiments and atomistic simulations.
\r\n\r\nThe theory developed in this work represents the most systematic theoretical technique for weak-coupling electrolytes. We expect the theory to be more useful for studying a wide range of structural and dynamic properties in physicochemical, colloidal, soft-matter and biophysical systems.
" }, { "name": "Weidmann, Alyson Gloria", "degree": "PhD", "year": "2015", "title": "Biological Activity of Rhodium Metalloinsertors and the Design of Bifunctional Conjugates", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022015-104348919", "creators": [ { "name": { "family": "Weidmann", "given": "Alyson Gloria" }, "id": "Weidmann-Alyson-Gloria", "orcid": "0000-0003-3876-2847", "display_name": "Weidmann, Alyson Gloria" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9RX991X", "abstract": "The Barton laboratory has established that octahedral rhodium complexes bearing the sterically expansive 5,6-chrysene diimine ligand can target thermodynamically destabilized sites, such as base pair mismatches, in DNA with high affinity and selectivity. These complexes approach DNA from the minor groove, ejecting the mismatched base pairs from the duplex in a binding mode termed metalloinsertion. In recent years, we have shown that these metalloinsertor complexes also exhibit cytotoxicity preferentially in cancer cells that are deficient in the mismatch repair (MMR) machinery.
\r\n\r\nHere, we establish that a sensitive structure-activity relationship exists for rhodium metalloinsertors. We studied the relationship between the chemical structures of metalloinsertors and their effect on biological activity for ten complexes with similar DNA binding affinities, but wide variation in their lipophilicity. Drastic differences were observed in the selectivities of the complexes for MMR-deficient cells. Compounds with hydrophilic ligands were highly selective, exhibiting preferential cytotoxicity in MMR-deficient cells at low concentrations and short incubation periods, whereas complexes with lipophilic ligands displayed poor cell-selectivity. It was discovered that all of the complexes localized to the nucleus in concentrations sufficient for mismatch binding; however, highly lipophilic complexes also exhibited high mitochondrial uptake. Significantly, these results support the notion that mitochondrial DNA is not the desired target for our metalloinsertor complexes; instead, selectivity stems from targeting mismatches in genomic DNA.
\r\n\r\nWe have also explored the potential for metalloinsertors to be developed into more complex structures with multiple functionalities that could either enhance their overall potency or impart mismatch selectivity onto other therapeutic cargo. We have constructed a family of bifunctional metalloinsertor conjugates incorporating cis-platinum, each unique in its chemical structure, DNA binding interactions, and biological activity. The study of these complexes in MMR-deficient cells has established that the cell-selective biological activity of rhodium metalloinsertors proceeds through a critical cellular pathway leading to necrosis.
\r\n\r\nWe further explored the underlying mechanisms surrounding the biological response to mismatch recognition by metalloinsertors in the genome. Immunofluorescence assays of MMR-deficient and MMR-proficient cells revealed that a critical biomarker for DNA damage, phosphorylation of histone H2AX (\u03b3H2AX) rapidly accumulates in response to metalloinsertor treatment, signifying the induction of double strand breaks in the genome. Significantly, we have discovered that our metalloinsertor complexes selectively inhibit transcription in MMR-deficient cells, which may be a crucial checkpoint in the eventual breakdown of the cell via necrosis. Additionally, preliminary in vivo studies have revealed the capability of these compounds to traverse the complex environments of multicellular organisms and accumulate in MMR-deficient tumors. Our ever-increasing understanding of metalloinsertors, as well as the development of new generations of complexes both monofunctional and bifunctional, enables their continued progress into the clinic as promising new chemotherapeutic agents.
" }, { "name": "Weitekamp, Raymond Andrew", "degree": "PhD", "year": "2015", "title": "Multifunctional Materials: Bottom-Up and Top-Down", "advisor": "Grubbs, Robert H.; Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042015-140901217", "creators": [ { "name": { "family": "Weitekamp", "given": "Raymond Andrew" }, "id": "Weitekamp-Raymond-Andrew", "display_name": "Weitekamp, Raymond Andrew" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "co-advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "co-advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z90C4SSB", "abstract": "This thesis is thematically separated into two complimentary approaches to advanced materials synthesis: bottom-up and top-down. Part I will discuss the self-assembly of photonic crystals, a unique class of periodic nanostructured materials featuring resonant optical response. Chapter 1 will introduce the concepts of self-assembly, specifically in the context of colloidal crystals and block copolymer nanostructures. Chapter 2 summarizes many years of work towards the goal of utilizing brush block copolymers as paintable photonic crystals. We employed 2D colloidal crystals as resonant light-trapping elements to improve the performance of thin-film solar cells; this work is described in Chapter 3. Part II of the thesis is centered around the concept of functional lithography: the ability to directly pattern materials with tailored physical properties and chemically active interfaces. We will briefly provide a history of photolithography in Chapter 4, and outline some of the limitations of the incumbent lithographic methods. The discovery of latent reactivity in ruthenium vinyl ether complexes, and the subsequent development of PhotoLithographic Olefin Metathesis Polymerization (PLOMP), are discussed in Chapter 5. This discovery has since blossomed into a true platform technology. We will discuss improvements to the functional group tolerance of PLOMP, as well as a few of our efforts to use PLOMP towards specific applications in Chapter 6. In the final Chapter 7 we document our attempts to activate PLOMP resists via multiphoton absorption, towards 3D printing of chemically functional microstructures." }, { "name": "Wickens, Zachary Kimble", "degree": "PhD", "year": "2015", "title": "Manipulating Selectivity and Reactivity in Palladium-Catalyzed Oxidation Reactions", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082015-101231805", "creators": [ { "name": { "family": "Wickens", "given": "Zachary Kimble" }, "id": "Wickens-Zachary-Kimble", "display_name": "Wickens, Zachary Kimble" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z97S7KS9", "abstract": "Since the initial discovery of the Wacker process over half a century ago, the Wacker oxidation has become a premier reaction for the oxidation of terminal alkenes to methyl ketones. This thesis describes strategies for manipulating selectivity and reactivity in Wacker-type oxidations to provide synthetically useful transformations.
\r\n\r\nChapter 2 describes how nitrite co-catalysts can be exploited in Wacker oxidations to reverse their typically high Markovnikov selectivity. Using these aerobic oxidation conditions, alkenes can be oxidized to aldehydes in high yield and selectivity. Preliminary mechanistic experiments are presented that are consistent with oxygen atom transfer from the nitrite catalyst to the substrate. The influence of proximal functionality on the new reaction is explored, yielding both synthetically useful transformations and further mechanistic insight.
\r\n\r\nChapter 3 investigates how minor modifications to the nitrite-modified Wacker can interrupt the Wacker oxidation pathway, providing dioxygenated products using molecular oxygen as the terminal oxidant. A variety of functional groups are tolerated and high yields of 1,2-diacetoxylated products are obtained with a range of substrates. Mechanistic experiments are presented that demonstrate the kinetic competency of nitrogen dioxide to mediate the reaction and probe the nature of the reductive elimination event.
\r\n\r\nChapter 4 details the development of a highly active Wacker-type oxidation capable of efficiently oxidizing internal alkenes, which are unreactive under\r\nclassical conditions. Under these simple and mild reaction conditions, a wide range of functional groups are tolerated and molecular oxygen can be employed as the terminal oxidant. Furthermore, the regioselectivity in unsymmetrical internal alkenes is investigated.
\r\n\r\nChapter 5 explores the origins of innate regioselectivity in Wacker oxidations. Systematic investigations of both internal and terminal alkenes illustrate that inductive effects are sufficient to dramatically influence Wacker regioselectivity. These observations lead to the development of a simple set of reactions conditions that strongly enforces Markovnikov's rule, even with substrates that provide mixtures of aldehydes and ketones under classical conditions.
" }, { "name": "Xiao, Hai", "degree": "PhD", "year": "2015", "title": "First Principles Based Multiparadigm Modeling of Electronic Structures and Dynamics", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202015-113328412", "creators": [ { "name": { "family": "Xiao", "given": "Hai" }, "id": "Xiao-Hai", "orcid": "0000-0001-9399-1584", "display_name": "Xiao, Hai" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94747T1", "abstract": "Electronic structures and dynamics are the key to linking the material composition and structure to functionality and performance.
\r\n\r\nAn essential issue in developing semiconductor devices for photovoltaics is to design materials with optimal band gaps and relative positioning of band levels. Approximate DFT methods have been justified to predict band gaps from KS/GKS eigenvalues, but the accuracy is decisively dependent on the choice of XC functionals. We show here for CuInSe2 and CuGaSe2, the parent compounds of the promising CIGS solar cells, conventional LDA and GGA obtain gaps of 0.0-0.01 and 0.02-0.24 eV (versus experimental values of 1.04 and 1.67 eV), while the historically first global hybrid functional, B3PW91, is surprisingly the best, with band gaps of 1.07 and 1.58 eV. Furthermore, we show that for 27 related binary and ternary semiconductors, B3PW91 predicts gaps with a MAD of only 0.09 eV, which is substantially better than all modern hybrid functionals, including B3LYP (MAD of 0.19 eV) and screened hybrid functional HSE06 (MAD of 0.18 eV).
\r\n\r\nThe laboratory performance of CIGS solar cells (> 20% efficiency) makes them promising candidate photovoltaic devices. However, there remains little understanding of how defects at the CIGS/CdS interface affect the band offsets and interfacial energies, and hence the performance of manufactured devices. To determine these relationships, we use the B3PW91 hybrid functional of DFT with the AEP method that we validate to provide very accurate descriptions of both band gaps and band offsets. This confirms the weak dependence of band offsets on surface orientation observed experimentally. We predict that the CBO of perfect CuInSe2/CdS interface is large, 0.79 eV, which would dramatically degrade performance. Moreover we show that band gap widening induced by Ga adjusts only the VBO, and we find that Cd impurities do not significantly affect the CBO. Thus we show that Cu vacancies at the interface play the key role in enabling the tunability of CBO. We predict that Na further improves the CBO through electrostatically elevating the valence levels to decrease the CBO, explaining the observed essential role of Na for high performance. Moreover we find that K leads to a dramatic decrease in the CBO to 0.05 eV, much better than Na. We suggest that the efficiency of CIGS devices might be improved substantially by tuning the ratio of Na to K, with the improved phase stability of Na balancing phase instability from K. All these defects reduce interfacial stability slightly, but not significantly.
\r\n\r\nA number of exotic structures have been formed through high pressure chemistry, but applications have been hindered by difficulties in recovering the high pressure phase to ambient conditions (i.e., one atmosphere and room temperature). Here we use dispersion-corrected DFT (PBE-ulg flavor) to predict that above 60 GPa the most stable form of N2O (the laughing gas in its molecular form) is a 1D polymer with an all-nitrogen backbone analogous to cis-polyacetylene in which alternate N are bonded (ionic covalent) to O. The analogous trans-polymer is only 0.03-0.10 eV/molecular unit less stable. Upon relaxation to ambient conditions both polymers relax below 14 GPa to the same stable non-planar trans-polymer, accompanied by possible electronic structure transitions. The predicted phonon spectrum and dissociation kinetics validate the stability of this trans-poly-NNO at ambient conditions, which has potential applications as a new type of conducting polymer with all-nitrogen chains and as a high-energy oxidizer for rocket propulsion. This work illustrates in silico materials discovery particularly in the realm of extreme conditions.
\r\n\r\nModeling non-adiabatic electron dynamics has been a long-standing challenge for computational chemistry and materials science, and the eFF method presents a cost-efficient alternative. However, due to the deficiency of FSG representation, eFF is limited to low-Z elements with electrons of predominant s-character. To overcome this, we introduce a formal set of ECP extensions that enable accurate description of p-block elements. The extensions consist of a model representing the core electrons with the nucleus as a single pseudo particle represented by FSG, interacting with valence electrons through ECPs. We demonstrate and validate the ECP extensions for complex bonding structures, geometries, and energetics of systems with p-block character (C, O, Al, Si) and apply them to study materials under extreme mechanical loading conditions.
\r\n\r\nDespite its success, the eFF framework has some limitations, originated from both the design of Pauli potentials and the FSG representation. To overcome these, we develop a new framework of two-level hierarchy that is a more rigorous and accurate successor to the eFF method. The fundamental level, GHA-QM, is based on a new set of Pauli potentials that renders exact QM level of accuracy for any FSG represented electron systems. To achieve this, we start with using exactly derived energy expressions for the same spin electron pair, and fitting a simple functional form, inspired by DFT, against open singlet electron pair curves (H2 systems). Symmetric and asymmetric scaling factors are then introduced at this level to recover the QM total energies of multiple electron pair systems from the sum of local interactions. To complement the imperfect FSG representation, the AMPERE extension is implemented, and aims at embedding the interactions associated with both the cusp condition and explicit nodal structures. The whole GHA-QM+AMPERE framework is tested on H element, and the preliminary results are promising.
" }, { "name": "Ailianou, Artemis", "degree": "PhD", "year": "2014", "title": "Development of Semicrystalline Morphology of Poly(L-lactic Acid) during Processing of a Vascular Scaffold", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-173923900", "creators": [ { "name": { "family": "Ailianou", "given": "Artemis" }, "id": "Ailianou-Artemis", "display_name": "Ailianou, Artemis" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Shapiro", "given": "Mikhail G." }, "id": "Shapiro-M-G", "role": "member", "display_name": "Shapiro, Mikhail G." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9VT1Q26", "abstract": "New and promising treatments for coronary heart disease are enabled by vascular scaffolds made of poly(L-lactic acid) (PLLA), as demonstrated by Abbott Vascular\u2019s bioresorbable vascular scaffold. PLLA is a semicrystalline polymer whose degree of crystallinity and crystalline microstructure depend on the thermal and deformation history during processing. In turn, the semicrystalline morphology determines scaffold strength and biodegradation time. However, spatially-resolved information about the resulting material structure (crystallinity and crystal orientation) is needed to interpret in vivo observations.
\r\n \r\nThe first manufacturing step of the scaffold is tube expansion in a process similar to injection blow molding. Spatial uniformity of the tube microstructure is essential for the consistent production and performance of the final scaffold. For implantation into the artery, solid-state deformation below the glass transition temperature is imposed on a laser-cut subassembly to crimp it into a small diameter. Regions of localized strain during crimping are implicated in deployment behavior.
\r\n\r\nTo examine the semicrystalline microstructure development of the scaffold, we employed complementary techniques of scanning electron and polarized light microscopy, wide-angle X-ray scattering, and X-ray microdiffraction. These techniques enabled us to assess the microstructure at the micro and nano length scale. The results show that the expanded tube is very uniform in the azimuthal and axial directions and that radial variations are more pronounced. The crimping step dramatically changes the microstructure of the subassembly by imposing extreme elongation and compression. Spatial information on the degree and direction of chain orientation from X-ray microdiffraction data gives insight into the mechanism by which the PLLA dissipates the stresses during crimping, without fracture. Finally, analysis of the microstructure after deployment shows that it is inherited from the crimping step and contributes to the scaffold\u2019s successful implantation in vivo.
\r\n" }, { "name": "Akopian, David", "degree": "PhD", "year": "2014", "title": "Phospholipids and a Protein-Conducting Channel Regulate Cotranslational Protein Targeting", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202014-104709210", "creators": [ { "name": { "family": "Akopian", "given": "David" }, "id": "Akopian-David", "display_name": "Akopian, David" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "biochem" ], "doi": "10.7907/PMBG-Y424", "abstract": "Signal recognition particle (SRP) and signal recognition particle receptor (SR) are evolutionarily conserved GTPases that deliver secretory and membrane proteins to the protein-conducting channel Sec61 complex in the lipid bilayer of the endoplasmic reticulum in eukaryotes or the SecYEG complex in the inner membrane of bacteria. Unlike the canonical Ras-type GTPases, SRP and SR are activated via nucleotide-dependent heterodimerization. Upon formation of the SR\u2022SRP targeting complex, SRP and SR undergo a series of discrete conformational changes that culminate in their reciprocal activation and hydrolysis of GTP. How the SR\u2022SRP GTPase cycle is regulated and coupled to the delivery of the cargo protein to the protein-conducting channel at the target membrane is not well-understood. Here we examine the role of the lipid bilayer and SecYEG in regulation of the SRP-mediated protein targeting pathway and show that they serve as important biological cues that spatially control the targeting reaction.
\r\n\r\nIn the first chapter, we show that anionic phospholipids of the inner membrane activate the bacterial SR, FtsY, and favor the late conformational states of the targeting complex conducive to efficient unloading of the cargo. The results of our studies suggest that the lipid bilayer acts as a spatial cue that weakens the interaction of the cargo protein with SRP and primes the complex for unloading its cargo onto SecYEG.
\r\n\r\nIn the second chapter, we focus on the effect of SecYEG on the conformational states and activity of the targeting complex. While phospholipids prime the complex for unloading its cargo, they are insufficient to trigger hydrolysis of GTP and the release of the cargo from the complex. SecYEG modulates the conformation of the targeting complex and triggers the GTP hydrolysis from the complex, thus driving the targeting reaction to completion. The results of this study suggest that SecYEG is not a passive recipient of the cargo protein; rather, it actively releases the cargo from the targeting complex. Together, anionic phospholipids and SecYEG serve distinct yet complementary roles. They spatially control the targeting reaction in a sequential manner, ensuring efficient delivery and unloading of the cargo protein.
\r\n\r\nIn the third chapter, we reconstitute the transfer reaction in vitro and visualize it in real time. We show that the ribosome-nascent chain complex is transferred to SecYEG via a stepwise mechanism with gradual dissolution and formation of the contacts with SRP and SecYEG, respectively, explaining how the cargo is kept tethered to the membrane during the transfer and how its loss to the cytosol is avoided.
\r\n\r\nIn the fourth chapter, we examine interaction of SecYEG with secretory and membrane proteins and attempt to address the role of a novel insertase YidC in this interaction. We show that detergent-solubilized SecYEG is capable of discriminating between the nascent chains of various lengths and engages a signal sequence in a well-defined conformation in the absence of accessory factors. Further, YidC alters the conformation of the signal peptide bound to SecYEG. The results described in this chapter show that YidC affects the SecYEG-nascent chain interaction at early stages of translocation/insertion and suggest a YidC-facilitated mechanism for lateral exit of transmembrane domains from SecYEG into the lipid bilayer.
\r\n\r\n\r\n\r\n\r\n\r\n" }, { "name": "Anderson, John Stuart", "degree": "PhD", "year": "2014", "title": "Catalytic Conversion of Nitrogen to Ammonia by an Iron Model Complex", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09182013-164526961", "creators": [ { "name": { "family": "Anderson", "given": "John Stuart" }, "id": "Anderson-John-Stuart", "display_name": "Anderson, John Stuart" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/NS23-B474", "abstract": "Threefold symmetric Fe phosphine complexes have been used to model the structural and functional aspects of biological N2 fixation by nitrogenases. Low-valent bridging Fe-S-Fe complexes in the formal oxidation states Fe(II)Fe(II), Fe(II)/Fe(I), and Fe(I)/Fe(I) have been synthesized which display rich spectroscopic and magnetic behavior. A series of cationic tris-phosphine borane (TPB) ligated Fe complexes have been synthesized and been shown to bind a variety of nitrogenous ligands including N2H4, NH3, and NH2
Treatment of an anionic FeN2 complex with excess acid also results in the formation of some NH3, suggesting the possibility of a catalytic cycle for the conversion of N2 to NH3 mediated by Fe. Indeed, use of excess acid and reductant results in the formation of seven equivalents of NH3 per Fe center, demonstrating Fe mediated catalytic N2 fixation with acids and protons for the first time. Numerous control experiments indicate that this catalysis is likely being mediated by a molecular species.
\r\n\r\nA number of other phosphine ligated Fe complexes have also been tested for catalysis and suggest that a hemi-labile Fe-B interaction may be critical for catalysis. Additionally, various conditions for the catalysis have been investigated. These studies further support the assignment of a molecular species and delineate some of the conditions required for catalysis.
\r\n\r\nFinally, combined spectroscopic studies have been performed on a putative intermediate for catalysis. These studies converge on an assignment of this new species as a hydrazido(2-) complex. Such species have been known on group 6 metals for some time, but this represents the first characterization of this ligand on Fe. Further spectroscopic studies suggest that this species is present in catalytic mixtures, which suggests that the first steps of a distal mechanism for N2 fixation are feasible in this system.
" }, { "name": "Ariosa, Aileen Renia", "degree": "PhD", "year": "2014", "title": "Mechanisms of Substrate Selection by the Signal Recognition Particle", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-103528106", "creators": [ { "name": { "family": "Ariosa", "given": "Aileen Renia" }, "id": "Ariosa-Aileen-Renia", "display_name": "Ariosa, Aileen Renia" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "biochem" ], "doi": "10.7907/AEDK-0925", "abstract": "The signal recognition particle (SRP) targets membrane and secretory proteins to their correct cellular destination with remarkably high fidelity. Previous studies have shown that multiple checkpoints exist within this targeting pathway that allows \u2018correct cargo\u2019 to be quickly and efficiently targeted and for \u2018incorrect cargo\u2019 to be promptly rejected. In this work, we delved further into understanding the mechanisms of how substrates are selected or discarded by the SRP. First, we discovered the role of the SRP fingerloop and how it activates the SRP and SRP receptor (SR) GTPases to target and unload cargo in response to signal sequence binding. Second, we learned how an \u2018avoidance signal\u2019 found in the bacterial autotransporter, EspP, allows this protein to escape the SRP pathway by causing the SRP and SR to form a \u2018distorted\u2019 complex that is inefficient in delivering the cargo to the membrane. Lastly, we determined how Trigger Factor, a co-translational chaperone, helps SRP discriminate against \u2018incorrect cargo\u2019 at three distinct stages: SRP binding to RNC; targeting of RNC to the membrane via SRP-FtsY assembly; and stronger antagonism of SRP targeting of ribosomes bearing nascent polypeptides that exceed a critical length. Overall, results delineate the rich underlying mechanisms by which SRP recognizes its substrates, which in turn activates the targeting pathway and provides a conceptual foundation to understand how timely and accurate selection of substrates is achieved by this protein targeting machinery. " }, { "name": "Beardslee, Joseph Allen", "degree": "PhD", "year": "2014", "title": "Magnetic Alignment of High-Aspect Ratio Microwires into Vertical Arrays", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292014-124316181", "creators": [ { "name": { "family": "Beardslee", "given": "Joseph Allen" }, "id": "Beardslee-Joseph-Allen", "display_name": "Beardslee, Joseph Allen" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KNHK-AK52", "abstract": "Fundamental studies of magnetic alignment of highly anisotropic mesostructures can enable the clean-room-free fabrication of flexible, array-based solar and electronic devices, in which preferential orientation of nano- or microwire-type objects is desired. In this study, ensembles of 100 micron long Si microwires with ferromagnetic Ni and Co coatings are oriented vertically in the presence of magnetic fields. The degree of vertical alignment and threshold field strength depend on geometric factors, such as microwire length and ferromagnetic coating thickness, as well as interfacial interactions, which are modulated by varying solvent and substrate surface chemistry. Microwire ensembles with vertical alignment over 97% within 10 degrees of normal, as measured by X-ray diffraction, are achieved over square cm scale areas and set into flexible polymer films. A force balance model has been developed as a predictive tool for magnetic alignment, incorporating magnetic torque and empirically derived surface adhesion parameters. As supported by these calculations, microwires are shown to detach from the surface and align vertically in the presence of magnetic fields on the order of 100 gauss. Microwires aligned in this manner are set into a polydimethylsiloxane film where they retain their vertical alignment after the field has been removed and can subsequently be used as a flexible solar absorber layer. Finally, these microwires arrays can be protected for use in electrochemical cells by the conformal deposition of a graphene layer." }, { "name": "Bermejo-Deval, Ricardo", "degree": "PhD", "year": "2014", "title": "Reaction of Glucose Catalyzed by Framework and Extraframework Tin Sites in Zeolite Beta", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192014-100254158", "creators": [ { "name": { "family": "Bermejo-Deval", "given": "Ricardo" }, "id": "Bermejo-Deval-Ricardo", "display_name": "Bermejo-Deval, Ricardo" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6AYX-9086", "abstract": "The isomerization of glucose into fructose is a large-scale reaction for the production of high-fructose corn syrup, and is now being considered as an intermediate step in the possible route of biomass conversion into fuels and chemicals. Recently, it has been shown that a hydrophobic, large pore, silica molecular sieve having the zeolite beta structure and containing framework Sn4+ (Sn-Beta) is able to isomerize glucose into fructose in aqueous media. Here, I have investigated how this catalyst converts glucose to fructose and show that it is analogous to that achieved with metalloenzymes. Specifically, glucose partitions into the molecular sieve in the pyranose form, ring opens to the acyclic form in the presence of the Lewis acid center (framework Sn4+), isomerizes into the acyclic form of fructose and finally ring closes to yield the furanose product. Akin to the metalloenzyme, the isomerization step proceeds by intramolecular hydride transfer from C2 to C1. Extraframework tin oxides located within hydrophobic channels of the molecular sieve that exclude liquid water can also isomerize glucose to fructose in aqueous media, but do so through a base-catalyzed proton abstraction mechanism. Extraframework tin oxide particles located at the external surface of the molecular sieve crystals or on amorphous silica supports are not active in aqueous media but are able to perform the isomerization in methanol by a base-catalyzed proton abstraction mechanism. Post-synthetic exchange of Na+ with Sn-Beta alters the glucose reaction pathway from the 1,2 intramolecular hydrogen shift (isomerization) to produce fructose towards the 1,2 intramolecular carbon shift (epimerization) that forms mannose. Na+ remains exchanged onto silanol groups during reaction in methanol solvent, leading to a near complete shift in selectivity towards glucose epimerization to mannose. In contrast, decationation occurs during reaction in aqueous solutions and gradually increases the reaction selectivity to isomerization at the expense of epimerization. Decationation and concomitant changes in selectivity can be eliminated by addition of NaCl to the aqueous reaction solution. Thus, framework tin sites with a proximal silanol group are the active sites for the 1, 2 intramolecular hydride shift in the isomerization of glucose to fructose, while these sites with Na-exchanged silanol group are the active sites for the 1, 2 intramolecular carbon shift in epimerization of glucose to mannose. " }, { "name": "Berry, Alexandria Helen T.", "degree": "PhD", "year": "2014", "title": "Designing Conformational Control of Human Tissue Transglutaminase", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282014-131036761", "creators": [ { "name": { "family": "Berry", "given": "Alexandria Helen T." }, "id": "Berry-Alexandria-Helen-T", "display_name": "Berry, Alexandria Helen T." } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/WW1E-VT19", "abstract": "Understanding the mechanisms of enzymes is crucial for our understanding of their role in biology and for designing methods to perturb or harness their activities for medical treatments, industrial processes, or biological engineering. One aspect of enzymes that makes them difficult to fully understand is that they are in constant motion, and these motions and the conformations adopted throughout these transitions often play a role in their function.
\r\n\r\nTraditionally, it has been difficult to isolate a protein in a particular conformation to determine what role each form plays in the reaction or biology of that enzyme. A new technology, computational protein design, makes the isolation of various conformations possible, and therefore is an extremely powerful tool in enabling a fuller understanding of the role a protein conformation plays in various biological processes.
\r\n\r\nOne such protein that undergoes large structural shifts during different activities is human type II transglutaminase (TG2). TG2 is an enzyme that exists in two dramatically different conformational states: (1) an open, extended form, which is adopted upon the binding of calcium, and (2) a closed, compact form, which is adopted upon the binding of GTP or GDP. TG2 possess two separate active sites, each with a radically different activity. This open, calcium-bound form of TG2 is believed to act as a transglutaminse, where it catalyzes the formation of an isopeptide bond between the sidechain of a peptide-bound glutamine and a primary amine. The closed, GTP-bound conformation is believed to act as a GTPase. TG2 is also implicated in a variety of biological and pathological processes.
\r\n\r\nTo better understand the effects of TG2\u2019s conformations on its activities and pathological processes, we set out to design variants of TG2 isolated in either the closed or open conformations. We were able to design open-locked and closed-biased TG2 variants, and use these designs to unseat the current understanding of the activities and their concurrent conformations of TG2 and explore each conformation\u2019s role in celiac disease models. This work also enabled us to help explain older confusing results in regards to this enzyme and its activities. The new model for TG2 activity has immense implications for our understanding of its functional capabilities in various environments, and for our ability to understand which conformations need to be inhibited in the design of new drugs for diseases in which TG2\u2019s activities are believed to elicit pathological effects.
\r\n" }, { "name": "Boney, Evans T. D.", "degree": "PhD", "year": "2014", "title": "Vibrational Pooling and Constrained Equilibration on Surfaces", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09302013-141151012", "creators": [ { "name": { "family": "Boney", "given": "Evans T. D." }, "id": "Boney-Evans-T-D", "display_name": "Boney, Evans T. D." } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JM2J-XX84", "abstract": "In this thesis, we provide a statistical theory for the vibrational pooling and fluorescence time dependence observed in infrared laser excitation of CO on an NaCl surface. The pooling is seen in experiment and in computer simulations. In the theory, we assume a rapid equilibration of the quanta in the substrate and minimize the free energy subject to the constraint at any time t of a fixed number of vibrational quanta N(t). At low incident intensity, the distribution is limited to one- quantum exchanges with the solid and so the Debye frequency of the solid plays a key role in limiting the range of this one-quantum domain. The resulting inverted vibrational equilibrium population depends only on fundamental parameters of the oscillator (\u03c9e and \u03c9e\u03c7e) and the surface (\u03c9D and T). Possible applications and relation to the Treanor gas phase treatment are discussed. Unlike the solid phase system, the gas phase system has no Debye-constraining maximum. We discuss the possible distributions for arbitrary N-conserving diatom-surface pairs, and include application to H:Si(111) as an example.
\r\n\r\nComputations are presented to describe and analyze the high levels of infrared laser-induced vibrational excitation of a monolayer of absorbed 13CO on a NaCl(100) surface. The calculations confirm that, for situations where the Debye frequency limited n domain restriction approximately holds, the vibrational state population deviates from a Boltzmann population linearly in n. Nonetheless, the full kinetic calculation is necessary to capture the result in detail.
\r\n\r\nWe discuss the one-to-one relationship between N and \u03b3 and the examine the state space of the new distribution function for varied \u03b3. We derive the Free Energy, F = N\u03b3kT \u2212 kTln(∑Pn), and effective chemical potential, \u03bcn \u2248 \u03b3kT, for the vibrational pool. We also find the anti correlation of neighbor vibrations leads to an emergent correlation that appears to extend further than nearest neighbor.
\r\n\r\n" }, { "name": "Bosco, Jeffrey Paul", "degree": "PhD", "year": "2014", "title": "Rational Design of Zinc Phosphide Heterojunction Photovoltaics", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052014-153503097", "creators": [ { "name": { "family": "Bosco", "given": "Jeffrey Paul" }, "id": "Bosco-Jeffrey-Paul", "orcid": "0000-0002-4570-6934", "display_name": "Bosco, Jeffrey Paul" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "chair", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "chemeng" ], "doi": "10.7907/09NG-5E90", "abstract": "The prospect of terawatt-scale electricity generation using a photovoltaic (PV) device places strict requirements on the active semiconductor optoelectronic properties and elemental abundance. After reviewing the constraints placed on an \"earth-abundant\" solar absorber, we find zinc phosphide (\u03b1-Zn3P2) to be an ideal candidate. In addition to its near-optimal direct band gap of 1.5 eV, high visible-light absorption coefficient (>104 cm-1), and long minority-carrier diffusion length (>5 \u03bcm), Zn3P2 is composed of abundant Zn and P elements and has excellent physical properties for scalable thin-film deposition. However, to date, a Zn3P2 device of sufficient efficiency for commercial applications has not been demonstrated. Record efficiencies of 6.0% for multicrystalline and 4.3% for thin-film cells have been reported, respectively. Performance has been limited by the intrinsic p-type conductivity of Zn3P2 which restricts us to Schottky and heterojunction device designs. Due to our poor understanding of Zn3P2 interfaces, an ideal heterojunction partner has not yet been found.
\r\n\r\nThe goal of this thesis is to explore the upper limit of solar conversion efficiency achievable with a Zn3P2 absorber through the design of an optimal heterojunction PV device. To do so, we investigate three key aspects of material growth, interface energetics, and device design. First, the growth of Zn3P2 on GaAs(001) is studied using compound-source molecular-beam epitaxy (MBE). We successfully demonstrate the pseudomorphic growth of Zn3P2 epilayers of controlled orientation and optoelectronic properties. Next, the energy-band alignments of epitaxial Zn3P2 and II-VI and III-V semiconductor interfaces are measured via high-resolution x-ray photoelectron spectroscopy in order to determine the most appropriate heterojunction partner. From this work, we identify ZnSe as a nearly ideal n-type emitter for a Zn3P2 PV device. Finally, various II-VI/Zn3P2 heterojunction solar cells designs are fabricated, including substrate and superstrate architectures, and evaluated based on their solar conversion efficiency.
" }, { "name": "Brown, Joshua Micah", "degree": "PhD", "year": "2014", "title": "Investigation of Receptors for the Modulation of Neuronal Growth by Chondroitin Sulfate", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09162013-140043647", "creators": [ { "name": { "family": "Brown", "given": "Joshua Micah" }, "id": "Brown-Joshua-Micah", "display_name": "Brown, Joshua Micah" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "chair", "display_name": "Chan, David C." }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z90G3H45", "abstract": "A major obstacle to neural regeneration after injury in the central nervous system (CNS) is the environment encountered by injured axons. This environment is inhibitory due to proteins expressed by the CNS myelin as well as molecules present in the glial scar. Experimental results have implicated chondroitin sulfate proteoglycans (CSPGs) as major inhibitors of axonal regeneration after CNS injury, but until recently, the mechanisms of this inhibition were not well understood. Furthermore, the complex nature of the chondroitin sulfate (CS) chains made it difficult to study their contribution to CSPG function. This thesis describes a specific carbohydrate epitope, CS-E, that is primarily responsible for the inhibition of CNS axonal regrowth in the presence of CSPGs. We show that removal or blocking of the CS-E motif via genetic elimination of the enzyme responsible for generating CS-E or a monoclonal antibody that binds specifically to the CS-E motif significantly reduces the inhibitory activity of CSPGs on axon growth. Furthermore, we show that CS-E functions as a protein recognition element to engage receptors, including the transmembrane protein tyrosine phosphatase PTP\u03c3, which had been previously established to be a receptor for CSPGs. Finally, we show that the protein tyrosine kinase receptor EphA4 is a novel receptor for the CS-E motif, and as with PTP\u03c3, neurons deficient in EphA4 exhibit reduced inhibition by CS-E. Our results demonstrate that a specific sugar epitope within chondroitin sulfate polysaccharides directs important physiological processes, and establish the importance of the chemical structure of CS chains in modulating the activity of CSPGs in vivo. The identification of receptors that mediate the inhibitory effect of CS-E advances our understanding of the mechanisms of axon regeneration following injury to the CNS when CS-E expression is upregulated. These findings provide us with the opportunity to develop therapies for the recovery of axonal outgrowth after damage to the nervous system, which in conjunction with blocking approaches targeting the CS motif, can provide a powerful strategy for allowing recovery after injury to the CNS." }, { "name": "Campbell, Taryn Langley", "degree": "Masters", "year": "2014", "title": "Studies Toward the Total Synthesis of Ritterazine B: The Investigation of Alkynylation Reactions for Use in the Synthesis of the Western Fragment", "advisor": "Reisman, Sarah", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282014-120132545", "creators": [ { "name": { "family": "Campbell", "given": "Taryn Langley" }, "id": "Campbell-Taryn-Langley", "display_name": "Campbell, Taryn Langley" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah" }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9P848WN", "abstract": "The ritterazine and cephalostatin natural products have biological activities and structures that are interesting to synthetic organic chemists. These products have been found to exhibit significant cytotoxicity against P388 murine leukemia cells, and therefore have the potential to be used as anticancer drugs. The ritterazines and cephalostatins are steroidal dimers joined by a central pyrazine ring. Given that the steroid halves are unsymmetrical and highly oxygenated, there are several challenges in synthesizing these compounds in an organic laboratory.
\r\n\r\nRitterazine B is the most potent derivative in the ritterazine family. Its biological activity is comparable to drugs that are being used to treat cancer today. For this reason, and the fact that there are no reported syntheses of ritterazine B to date, our lab set out to synthesize this natural product.
\r\n\r\nHerein, efforts toward the synthesis of the western fragment of ritterazine B are described. Two different routes are explored to access a common intermediate. An alkyne conjugate addition reaction was initially investigated due to the success of this key reaction in the synthesis of the eastern fragment. However, it has been found that a propargylation reaction has greater reactivity and yields, and has the potential to reduce the step count of the synthesis of the western fragment of ritterazine B.
\r\n" }, { "name": "Codelli, Julian Andrew", "degree": "PhD", "year": "2014", "title": "The Development of a Synthetic Strategy Toward Dihydrooxepine-Containing Epipolythiodiketopiperazines: Enantioselective Total Synthesis of (-)-Acetylaranotin and Related Investigations", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172013-192454898", "creators": [ { "name": { "family": "Codelli", "given": "Julian Andrew" }, "id": "Codelli-Julian-Andrew", "display_name": "Codelli, Julian Andrew" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9CR5RC4", "abstract": "To the chemist, the epipolythiodiketopiperazine (ETP) fungal metabolites represent a fascinating family of natural products, not only for their unique structural elements, but also for the unusual modes by which they are hypothesized to exert their biological activities. Though efforts at the total synthesis of these molecules have led to an evolution of innovative synthetic methodologies and strategies, challenges remain\u2014particularly with respect to acid-sensitive and highly oxygenated ETP structures, such as those containing one or more dihydrooxepine ring. As part of a broad research program targeting ETP natural products, we have developed a synthetic strategy towards dihydrooxepine-containing ETPs.
\r\n\t\r\nHerein, the enantioselective total synthesis of (\u2013)-acetylaranotin is described. This represents the first total synthesis of any dihydrooxepine-containing ETP natural product. The key steps of the synthesis include an enantioselective azomethine ylide (1,3)-dipolar cycloaddition reaction to set the absolute and relative stereochemistry, a rhodium-catalyzed cycloisomerization/chloride elimination sequence to generate the dihydrooxepine moiety, and a stereoretentive diketopiperazine sulfenylation to install the epidisulfide.
\r\n\t\r\nOur strategy was extended to the synthesis of a small panel of epitetrathiodiketopiperazines, including the natural products SCH64877 and emethallicin C as well as analogs, which are currently being evaluated for biological activity. Furthermore, preliminary investigations into the synthesis of dihydrooxepine-containing macrocycles have been conducted, with a particular focus on the preparation of bis(ortho-methoxyaryl) ethers.
\r\n\t\r\nFinally, as part of our efforts to further explore interesting side reactions observed during synthetic studies toward acetylaranotin, a catalytic asymmetric double (1,3)-dipolar cycloaddition reaction was developed. This reaction provides access to highly substituted, enantioenriched pyrrolidizines from inexpensive, commercially available starting materials. Furthermore, the reactivity of diketopiperazine intermediates prepared en route to acetylaranotin toward aerobic oxidation was briefly explored.
" }, { "name": "Daeffler, Kristina Nicole-McCleary", "degree": "PhD", "year": "2014", "title": "Functional Evaluation of Noncovalent Interactions in Neuroreceptors and Progress Toward the Expansion of Unnatural Amino Acid Methodology", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042014-135648744", "creators": [ { "name": { "family": "Daeffler", "given": "Kristina Nicole-McCleary" }, "id": "Daeffler-Kristina-Nicole-McCleary", "display_name": "Daeffler, Kristina Nicole-McCleary" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ST7S-DB65", "abstract": "This dissertation primarily describes chemical-scale studies of G protein-coupled receptors and Cys-loop ligand-gated ion channels to better understand ligand binding interactions and the mechanism of channel activation using recently published crystal structures as a guide. These studies employ the use of unnatural amino acid mutagenesis and electrophysiology to measure subtle changes in receptor function.
\r\n\r\nIn chapter 2, the role of a conserved aromatic microdomain predicted in the D3 dopamine receptor is probed in the closely related D2 and D4 dopamine receptors. This domain was found to act as a structural unit near the ligand binding site that is important for receptor function. The domain consists of several functionally important noncovalent interactions including hydrogen bond, aromatic-aromatic, and sulfur-\u03c0 interactions that show strong couplings by mutant cycle analysis. We also assign an alternate interpretation for the linear fluorination plot observed at W6.48, a residue previously thought to participate in a cation-\u03c0 interaction with dopamine.
\r\n\r\nChapter 3 outlines attempts to incorporate chemically synthesized and in vitro acylated unnatural amino acids into mammalian cells. While our attempts were not successful, method optimizations and data for nonsense suppression with an in vivo acylated tRNA are included. This chapter is aimed to aid future researchers attempting unnatural amino acid mutagenesis in mammalian cells.
\r\n\r\nChapter 4 identifies a cation-\u03c0 interaction between glutamate and a tyrosine residue on loop C in the GluCl\u03b2 receptor. Using the recently published crystal structure of the homologous GluCl\u03b1 receptor, other ligand-binding and protein-protein interactions are probed to determine the similarity between this invertebrate receptor and other more distantly related vertebrate Cys-loop receptors. We find that many of the interactions previously observed are conserved in the GluCl receptors, however care must be taken when extrapolating structural data.
\r\n\r\nChapter 5 examines inherent properties of the GluCl\u03b1 receptor that are responsible for the observed glutamate insensitivity of the receptor. Chimera synthesis and mutagenesis reveal the C-terminal portion of the M4 helix and the C-terminus as contributing to formation of the decoupled state, where ligand binding is incapable of triggering channel gating. Receptor mutagenesis was unable to identify single residue mismatches or impaired protein-protein interactions within this domain. We conclude that M4 helix structure and/or membrane dynamics are likely the cause of ligand insensitivity in this receptor and that the M4 helix has an role important in the activation process.
" }, { "name": "Deyle, Kaycie Marie", "degree": "PhD", "year": "2014", "title": "Development of Protein-Catalyzed Capture (PCC) Agents with Application to the Specific Targeting of the E17K Point Mutation of AKt1", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272014-114201666", "creators": [ { "name": { "family": "Deyle", "given": "Kaycie Marie" }, "id": "Deyle-Kaycie-Marie", "display_name": "Deyle, Kaycie Marie" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/F8HW-TX51", "abstract": "This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.
\r\n\r\nThese technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.
" }, { "name": "Dilworth, Crystal Noelle", "degree": "PhD", "year": "2014", "title": "Fluorescence Microscopy of Nicotinic Acetylcholine Receptors", "advisor": "Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282014-200718606", "creators": [ { "name": { "family": "Dilworth", "given": "Crystal Noelle" }, "id": "Dilworth-Crystal-Noelle", "display_name": "Dilworth, Crystal Noelle" } ], "advisors": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z96D5QZB", "abstract": "Neuronal nicotinic acetylcholine receptors (nAChRs) are pentameric ligand gated ion channels abundantly expressed in the central nervous system. Changes in the assembly and trafficking of nAChRs are pertinent to disease states including nicotine dependence, autosomal dominant nocturnal frontal lobe epilepsy (ADNFLE), and Parkinson\u2019s disease (PD). Here we investigate the application of high resolution fluorescence techniques for the study of nAChR assembly and trafficking. We also describe the construction and validation of a fluorescent \u03b15 subunit and subsequent experiments to elucidate the cellular mechanisms through which \u03b15 subunits are expressed, assembled into mature receptors, and trafficked to the cell surface. The effects of a known single nucleotide polymorphism (D398N) in the intracellular loop of \u03b15 are also examined.
\r\n\r\nAdditionally, this report describes the development of a combined total internal reflection fluorescence (TIRF) and lifetime imaging (FLIM) technique and the first application of this methodology for elucidation of stochiometric composition of nAChRs. Many distinct subunit combinations can form functional receptors. Receptor composition and stoichiometry confers unique biophysical and pharmacological properties to each receptor sub-type. Understanding the nature of assembly and expression of each receptor subtype yields important information about the molecular processes that may underlie the mechanisms through which nAChR contribute to disease and addiction states.
" }, { "name": "Duffy, Noah Hanville", "degree": "PhD", "year": "2014", "title": "Studies of the Serotonin Type 3A Receptor and the Chemical Preparation of tRNA", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062014-151417635", "creators": [ { "name": { "family": "Duffy", "given": "Noah Hanville" }, "id": "Duffy-Noah-Hanville", "display_name": "Duffy, Noah Hanville" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/X1YA-DM13", "abstract": "This thesis describes studies surrounding a ligand-gated ion channel (LGIC): the serotonin type 3A receptor (5-HT3AR). Structure-function experiments using unnatural amino acid mutagenesis are described, as well as experiments on the methodology of unnatural amino acid mutagenesis. Chapter 1 introduces LGICs, experimental methods, and an overview of the unnatural amino acid mutagenesis.
\r\n\r\nIn Chapter 2, the binding orientation of the clinically available drugs ondansetron and granisetron within 5-HT3A is determined through a combination of unnatural amino acid mutagenesis and an inhibition based assay. A cation-\u03c0 interaction is found for both ondansetron and granisetron with a specific tryptophan residue (Trp183, TrpB) of the mouse 5-HT3AR, which establishes a binding orientation for these drugs.
\r\n\r\nIn Chapter 3, further studies were performed with ondansetron and granisetron with 5-HT3A. The primary determinant of binding for these drugs was determined to not include interactions with a specific tyrosine residue (Tyr234, TyrC2). In completing these studies, evidence supporting a cation-\u03c0 interaction of a synthetic agonist, meta-chlorophenylbiguanide, was found with TyrC2.
\r\n\r\nIn Chapter 4, a direct chemical acylation strategy was implemented to prepare full-length suppressor tRNA mediated by lanthanum(III) and amino acid phosphate esters. The derived aminoacyl-tRNA is shown to be translationally competent in Xenopus oocytes.
\r\n\r\nAppendix A.1 gives details of a pharmacological method for determining the equilibrium dissociation constant, KB, of a competitive antagonist with a receptor, known as Schild analysis. Appendix A.2 describes an examination of the inhibitory activity of new chemical analogs of the 5-HT3A antagonist ondansetron. Appendix A.3 reports an organic synthesis of an intermediate for a new unnatural amino acid. Appendix A.4 covers an additional methodological examination for the preparation of amino-acyl tRNA.
" }, { "name": "Ener, Maraia Emily", "degree": "PhD", "year": "2014", "title": "Electron Flow Through Cytochrome P450", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272014-175135389", "creators": [ { "name": { "family": "Ener", "given": "Maraia Emily" }, "id": "Ener-Maraia-Emily", "display_name": "Ener, Maraia Emily" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CFD7-DK06", "abstract": "The cytochromes P450 (P450s) are a remarkable class of heme enzymes that catalyze the metabolism of xenobiotics and the biosynthesis of signaling molecules. Controlled electron flow into the thiolate-ligated heme active site allows P450s to activate molecular oxygen and hydroxylate aliphatic C\u2013H bonds via the formation of high-valent metal-oxo intermediates (compounds I and II). Due to the reactive nature and short lifetimes of these intermediates, many of the fundamental steps in catalysis have not been observed directly. The Gray group and others have developed photochemical methods, known as \u201cflash-quench,\u201d for triggering electron transfer (ET) and generating redox intermediates in proteins in the absence of native ET partners. Photo-triggering affords a high degree of temporal precision for the gating of an ET event; the initial ET and subsequent reactions can be monitored on the nanosecond-to-second timescale using transient absorption (TA) spectroscopies. Chapter 1 catalogues critical aspects of P450 structure and mechanism, including the native pathway for formation of compound I, and outlines the development of photochemical processes that can be used to artificially trigger ET in proteins. Chapters 2 and 3 describe the development of these photochemical methods to establish electronic communication between a photosensitizer and the buried P450 heme. Chapter 2 describes the design and characterization of a Ru-P450-BM3 conjugate containing a ruthenium photosensitizer covalently tethered to the P450 surface, and nanosecond-to-second kinetics of the photo-triggered ET event are presented. By analyzing data at multiple wavelengths, we have identified the formation of multiple ET intermediates, including the catalytically relevant compound II; this intermediate is generated by oxidation of a bound water molecule in the ferric resting state enzyme. The work in Chapter 3 probes the role of a tryptophan residue situated between the photosensitizer and heme in the aforementioned Ru-P450 BM3 conjugate. Replacement of this tryptophan with histidine does not perturb the P450 structure, yet it completely eliminates the ET reactivity described in Chapter 2. The presence of an analogous tryptophan in Ru-P450 CYP119 conjugates also is necessary for observing oxidative ET, but the yield of heme oxidation is lower. Chapter 4 offers a basic description of the theoretical underpinnings required to analyze ET. Single-step ET theory is first presented, followed by extensions to multistep ET: electron \u201chopping.\u201d The generation of \u201chopping maps\u201d and use of a hopping map program to analyze the rate advantage of hopping over single-step ET is described, beginning with an established rhenium-tryptophan-azurin hopping system. This ET analysis is then applied to the Ru-tryptophan-P450 systems described in Chapter 2; this strongly supports the presence of hopping in Ru-P450 conjugates. Chapter 5 explores the implementation of flash-quench and other phototriggered methods to examine the native reductive ET and gas binding events that activate molecular oxygen. In particular, TA kinetics that demonstrate heme reduction on the microsecond timescale for four Ru-P450 conjugates are presented. In addition, we implement laser flash-photolysis of P450 ferrous\u2013CO to study the rates of CO rebinding in the thermophilic P450 CYP119 at variable temperature. Chapter 6 describes the development and implementation of air-sensitive potentiometric redox titrations to determine the solution reduction potentials of a series of P450 BM3 mutants, which were designed for non-native cyclopropanation of styrene in vivo. An important conclusion from this work is that substitution of the axial cysteine for serine shifts the wild type reduction potential positive by 130 mV, facilitating reduction by biological redox cofactors in the presence of poorly-bound substrates. While this mutation abolishes oxygenation activity, these mutants are capable of catalyzing the cyclopropanation of styrene, even within the confines of an E. coli cell. Four appendices are also provided, including photochemical heme oxidation in ruthenium-modified nitric oxide synthase (Appendix A), general protocols (Appendix B), Chapter-specific notes (Appendix C) and Matlab scripts used for data analysis (Appendix D)." }, { "name": "Ensberg, Joseph James", "degree": "PhD", "year": "2014", "title": "Studies of Ambient Organic and Inorganic Aerosol in Southern California", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192014-130444619", "creators": [ { "name": { "family": "Ensberg", "given": "Joseph James" }, "id": "Ensberg-Joseph-James", "display_name": "Ensberg, Joseph James" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Dabdub", "given": "Donald" }, "id": "Dabdub-D", "role": "member", "display_name": "Dabdub, Donald" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4J4Q-HP22", "abstract": "The negative impacts of ambient aerosol particles, or particulate matter (PM), on human health and climate are well recognized. However, owing to the complexity of aerosol particle formation and chemical evolution, emissions control strategies remain difficult to develop in a cost effective manner. In this work, three studies are presented to address several key issues currently stymieing California's efforts to continue improving its air quality.
\r\n\r\nGas-phase organic mass (GPOM) and CO emission factors are used in conjunction with measured enhancements in oxygenated organic aerosol (OOA) relative to CO to quantify the significant lack of closure between expected and observed organic aerosol concentrations attributable to fossil-fuel emissions. Two possible conclusions emerge from the analysis to yield consistency with the ambient organic data: (1) vehicular emissions are not a dominant source of anthropogenic fossil SOA in the Los Angeles Basin, or (2) the ambient SOA mass yields used to determine the SOA formation potential of vehicular emissions are substantially higher than those derived from laboratory chamber studies. Additional laboratory chamber studies confirm that, owing to vapor-phase wall loss, the SOA mass yields currently used in virtually all 3D chemical transport models are biased low by as much as a factor of 4. Furthermore, predictions from the Statistical Oxidation Model suggest that this bias could be as high as a factor of 8 if the influence of the chamber walls could be removed entirely.
\r\n\r\nOnce vapor-phase wall loss has been accounted for in a new suite of laboratory chamber experiments, the SOA parameterizations within atmospheric chemical transport models should also be updated. To address the numerical challenges of implementing the next generation of SOA models in atmospheric chemical transport models, a novel mathematical framework, termed the Moment Method, is designed and presented. Assessment of the Moment Method strengths and weaknesses provide valuable insight that can guide future development of SOA modules for atmospheric CTMs.
\r\n\r\nFinally, regional inorganic aerosol formation and evolution is investigated via detailed comparison of predictions from the Community Multiscale Air Quality (CMAQ version 4.7.1) model against a suite of airborne and ground-based meteorological measurements, gas- and aerosol-phase inorganic measurements, and black carbon (BC) measurements over Southern California during the CalNex field campaign in May/June 2010. Results suggests that continuing to target sulfur emissions with the hopes of reducing ambient PM concentrations may not the most effective strategy for Southern California. Instead, targeting dairy emissions is likely to be an effective strategy for substantially reducing ammonium nitrate concentrations in the eastern part of the Los Angeles Basin.
\r\n" }, { "name": "Fu, Ross", "degree": "PhD", "year": "2014", "title": "Iridium and Rhodium Analogues of the Shilov Cycle Catalyst; and The Investigation and Applications of the Reduction-Coupled Oxo Activation (ROA) Mechanistic Motif towards Alkane Upgrading", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05212014-155104252", "creators": [ { "name": { "family": "Fu", "given": "Ross" }, "id": "Fu-Ross", "display_name": "Fu, Ross" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WY3F-DZ94", "abstract": "This dissertation will cover several disparate topics, with the overarching theme centering on the investigation of organometallic C-H activation and hydrocarbon transformation and upgrading. Chapters 2 and 3 discuss iridium and rhodium analogues of the Shilov cycle catalyst for methane to methanol oxidation, and Chapter 4 on the recently discovered ROA mechanistic motif in catalysts for various alkane partial oxidation reactions. In addition, Chapter 5 discusses the mechanism of nickel pyridine bisoxazoline Negishi catalysts for asymmetric and stereoconvergent C-C coupling, and the appendices discuss smaller projects on rhodium H/D exchange catalysts and DFT method benchmarking." }, { "name": "Gleason-Rohrer, David Charles", "degree": "PhD", "year": "2014", "title": "Measurement of the Band Bending and Surface Dipole at Chemically Functionalized Si(111)/Vacuum Interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202013-144350295", "creators": [ { "name": { "family": "Gleason-Rohrer", "given": "David Charles" }, "id": "Gleason-Rohrer-David-Charles", "display_name": "Gleason-Rohrer, David Charles" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PD7F-P488", "abstract": "The core-level energy shifts observed using X-ray photoelectron spectroscopy (XPS) have been used to determine the band bending at Si(111) surfaces terminated with Si-Br, Si-H, and Si-CH3 groups, respectively. The surface termination influenced the band bending, with the Si 2p3/2 binding energy affected more by the surface chemistry than by the dopant type. The highest binding energies were measured on Si(111)-Br (whose Fermi level was positioned near the conduction band at the surface), followed by Si(111)-H, followed by Si(111)-CH3 (whose Fermi level was positioned near mid-gap at the surface). Si(111)-CH3 surfaces exposed to Br2(g) yielded the lowest binding energies, with the Fermi level positioned between mid-gap and the valence band. The Fermi level position of Br2(g)-exposed Si(111)-CH3 was consistent with the presence of negatively charged bromine-containing ions on such surfaces. The binding energies of all of the species detected on the surface (C, O, Br) shifted with the band bending, illustrating the importance of isolating the effects of band bending when measuring chemical shifts on semiconductor surfaces. The influence of band bending was confirmed by surface photovoltage (SPV) measurements, which showed that the core levels shifted toward their flat-band values upon illumination. Where applicable, the contribution from the X-ray source to the SPV was isolated and quantified. Work functions were measured by ultraviolet photoelectron spectroscopy (UPS), allowing for calculation of the sign and magnitude of the surface dipole in such systems. The values of the surface dipoles were in good agreement with previous measurements as well as with electronegativity considerations. The binding energies of the adventitious carbon signals were affected by band bending as well as by the surface dipole. A model of band bending in which charged surface states are located exterior to the surface dipole is consistent with the XPS and UPS behavior of the chemically functionalized Si(111) surfaces investigated herein.
" }, { "name": "Goodpaster, Jason Daniel", "degree": "PhD", "year": "2014", "title": "Density Functional Theory Embedding for Correlated Wavefunctions", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-220000101", "creators": [ { "name": { "family": "Goodpaster", "given": "Jason Daniel" }, "id": "Goodpaster-Jason-Daniel", "display_name": "Goodpaster, Jason Daniel" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "chair", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RX3S-GH65", "abstract": "Methods that exploit the intrinsic locality of molecular interactions show significant promise in making tractable the electronic structure calculation of large-scale systems. In particular, embedded density functional theory (e-DFT) offers a formally exact approach to electronic structure calculations in which the interactions between subsystems are evaluated in terms of their electronic density. In the following dissertation, methodological advances of embedded density functional theory are described, numerically tested, and applied to real chemical systems.
\r\n\r\nFirst, we describe an e-DFT protocol in which the non-additive kinetic energy component of the embedding potential is treated exactly. Then, we present a general implementation of the exact calculation of the non-additive kinetic potential (NAKP) and apply it to molecular systems. We demonstrate that the implementation using the exact NAKP is in excellent agreement with reference Kohn-Sham calculations, whereas the approximate functionals lead to qualitative failures in the calculated energies and equilibrium structures.
\r\n\r\nNext, we introduce density-embedding techniques to enable the accurate and stable calculation of correlated wavefunction (CW) in complex environments. Embedding potentials calculated using e-DFT introduce the effect of the environment on a subsystem for CW calculations (WFT-in-DFT). We demonstrate that WFT-in-DFT calculations are in good agreement with CW calculations performed on the full complex.
\r\n\r\nWe significantly improve the numerics of the algorithm by enforcing orthogonality between subsystems by introduction of a projection operator. Utilizing the projection-based embedding scheme, we rigorously analyze the sources of error in quantum embedding calculations in which an active subsystem is treated using CWs, and the remainder using density functional theory. We show that the embedding potential felt by the electrons in the active subsystem makes only a small contribution to the error of the method, whereas the error in the nonadditive exchange-correlation energy dominates. We develop an algorithm which corrects this term and demonstrate the accuracy of this corrected embedding scheme.
" }, { "name": "Herbert, Myles Benton", "degree": "PhD", "year": "2014", "title": "Z-Selectivc Olefin Metathesis using Chelating Ruthenium Alkylidene Catalysts", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122014-144957040", "creators": [ { "name": { "family": "Herbert", "given": "Myles Benton" }, "id": "Herbert-Myles-Benton", "display_name": "Herbert, Myles Benton" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/M04T-PP58", "abstract": "Publications about olefin metathesis will generally discuss how the discovery and development of well-defined catalysts to carry out this unique transformation have revolutionized many fields, from natural product and materials chemistry, to green chemistry and biology. However, until recently, an entire manifestation of this methodology had been inaccessible. Except for a few select examples, metathesis catalysts favor the thermodynamic trans- or E-olefin products in cross metathesis (CM), macrocyclic ring closing metathesis (mRCM), ring opening metathesis polymerization (ROMP), and many other types of reactions. Judicious choice of substrates had allowed for the direct synthesis of cis- or Z-olefins or species that could be converted upon further reaction, however the catalyst controlled synthesis of Z-olefins was not possible until very recently.
\r\n\t\r\nResearch into the structure and stability of metallacyclobutane intermediates has led to the proposal of models to impart Z-selectivity in metathesis reactions. Having the ability to influence the orientation of metallacyclobutane substituents to cause productive formation of Z- double bonds using steric and electronic effects was highly desired. The first successful realization of this concept was by Schrock and Hoveyda et al. who synthesized monoaryloxide pyrolidine (MAP) complexes of tungsten and molybdenum that promoted Z-selective CM. The Z-selectivity of these catalysts was attributed to the difference in the size of the two axial ligands. This size difference influences the orientation of the substituents on the forming/incipient metallacyclobutane intermediate to a cis-geometry and leads to productive formation of Z-olefins. These catalysts have shown great utility in the synthesis of complicated natural product precursors and stereoregular polymers. More recently, ruthenium catalysts capable of promoting Z-selective metathesis have been reported by our group and others. This thesis will discuss the development of ruthenium-based NHC chelated Z-selective catalysts, studies probing their unique metathesis mechanism, and synthetic applications that have been investigated thus far.
\r\n \r\nChapter 1 will focus on studies into the stability of NHC chelated complexes and the synthesis of new and improved stable chelating architectures. Chapter 2 will discuss applications of the highly active and Z-selective developed in Chapter 1, including the formation of lepidopteran female sex pheromones using olefin cross metathesis and highly Z- and highly E-macrocycles using macrocyclic ring closing metathesis and Z-selective ethenolysis. Chapter 3 will explore studies into the unique mechanism of olefin metathesis reactions catalyzed by these NHC chelated, highly Z-selective catalysts, explaining observed trends by investigating the stability of relevant, substituted metallacyclobutane intermediates.
\r\n" }, { "name": "Holder, Jeffrey Clinton", "degree": "PhD", "year": "2014", "title": "The Development of an Asymmetric Palladium-Catalyzed Conjugate Addition and Its Application Toward the Total Syntheses of Taiwaniaquinoid Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132014-111254056", "creators": [ { "name": { "family": "Holder", "given": "Jeffrey Clinton" }, "id": "Holder-J-C", "display_name": "Holder, Jeffrey Clinton" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EW6K-2D88", "abstract": "The asymmetric synthesis of quaternary stereocenters remains a challenging problem in organic synthesis. Past work from the Stoltz laboratory has resulted in methodology to install quaternary stereocenters \u03b1- or \u03b3- to carbonyl compounds. Thus, the asymmetric synthesis of \u03b2-quaternary stereocenters was a desirable objective, and was accomplished by engineering the palladium-catalyzed addition of arylmetal organometallic reagents to \u03b1,\u03b2-unsaturated conjugate acceptors.
\r\n\r\nHerein, we described the rational design of a palladium-catalyzed conjugate addition reactions utilizing a catalyst derived from palladium(II) trifluoroacetate and pyridinooxazole ligands. This reaction is highly tolerant of protic solvents and oxygen atmosphere, making it a practical and operationally simple reaction. The mild conditions facilitate a remarkably high functional group tolerance, including carbonyls, halogens, and fluorinated functional groups. Furthermore, the reaction catalyzed conjugate additions with high enantioselectivity with conjugate acceptors of 5-, 6-, and 7-membered ring sizes. Extension of the methodology toward the asymmetric synthesis of flavanone products is presented, as well.
\r\n \r\nA computational and experimental investigation into the reaction mechanism provided a stereochemical model for enantioinduction, whereby the \u03b1-methylene protons adjacent the enone carbonyl clashes with the tert-butyl groups of the chiral ligand. Additionally, it was found that the addition of water and ammonium hexafluorophosphate significantly increases the reaction rate without sacrificing enantioselectivity. The synergistic effects of these additives allowed for the reaction to proceed at a lower temperature, and thus facilitated expansion of the substrate scope to sensitive functional groups such as protic amides and aryl bromides. Investigations into a scale-up synthesis of the chiral ligand (S)-tert-butylPyOx are also presented. This three-step synthetic route allowed for synthesis of the target compound of greater than 10 g scale.
\r\n\r\nFinally, the application of the newly developed conjugate addition reaction toward the synthesis of the taiwaniaquinoid class of terpenoid natural products is discussed. The conjugate addition reaction formed the key benzylic quaternary stereocenter in high enantioselectivity, joining together the majority of the carbons in the taiwaniaquinoid scaffold. Efforts toward the synthesis of the B-ring are presented.
\r\n" }, { "name": "Holland, Daniel Brian", "degree": "PhD", "year": "2014", "title": "Design, Construction, and Applications of a High-Resolution Terahertz Time-Domain Spectrometer", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222014-120506633", "creators": [ { "name": { "family": "Holland", "given": "Daniel Brian" }, "id": "Holland-Daniel-Brian", "display_name": "Holland, Daniel Brian" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z91J97QR", "abstract": "This thesis reports on the design, construction, and initial applications of a high-resolution terahertz time-domain ASOPS spectrometer. The instrument employs asynchronous optical sampling (ASOPS) between two Ti:sapphire ultrafast lasers operating at a repetition rate of approximately 80 MHz, and we thus demonstrate a THz frequency resolution approaching the limit of that repetition rate. This is an order of magnitude improvement in resolution over typical THz time-domain spectrometers. The improved resolution is important for our primary effort of collecting THz spectra for far-infrared astronomy. We report on various spectroscopic applications including the THz rotational spectrum of water, where we achieve a mean frequency error, relative to established line centers, of 27.0 MHz. We also demonstrate application of the THz system to the long-duration observation of a coherent magnon mode in a anti-ferromagnetic yttrium iron oxide (YFeO3) crystal. Furthermore, we apply the all-optical virtual delay line of ASOPS to a transient thermoreflectance experiment for quickly measuring the thermal conductivity of semiconductors." }, { "name": "Jeon, Seokmin", "degree": "PhD", "year": "2014", "title": "Structure, Chemistry, and Energetics of Organic and Inorganic Adsorbates on Ga-rich GaAs and GaP(00l) Surfaces", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:10082013-111509695", "creators": [ { "name": { "family": "Jeon", "given": "Seokmin" }, "id": "Jeon-Seokmin", "display_name": "Jeon, Seokmin" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1T2B-J793", "abstract": "The work described in this dissertation includes fundamental investigations into three surface processes, namely inorganic film growth, water-induced oxidation, and organic functionalization/passivation, on the GaP and GaAs(001) surfaces. The techniques used to carry out this work include scanning tunneling microscopy (STM), X-ray photoelectron spectroscopy (XPS), and density functional theory (DFT) calculations. Atomic structure, electronic structure, reaction mechanisms, and energetics related to these surface processes are discussed at atomic or molecular levels.
\r\n\r\nFirst, we investigate epitaxial Zn3P2 films grown on the Ga-rich GaAs(001)(6\u00d76) surface. The film growth mechanism, electronic properties, and atomic structure of the Zn3P2/GaAs(001) system are discussed based on experimental and theoretical observations. We discover that a P-rich amorphous layer covers the crystalline Zn3P2 film during and after growth. We also propose more accurate picture of the GaP interfacial layer between Zn3P2 and GaAs, based on the atomic structure, chemical bonding, band diagram, and P-replacement energetics, than was previously anticipated.
\r\n\r\nSecond, DFT calculations are carried out in order to understand water-induced oxidation mechanisms on the Ga-rich GaP(001)(2\u00d74) surface. Structural and energetic information of every step in the gaseous water-induced GaP oxidation reactions are elucidated at the atomic level in great detail. We explore all reasonable ground states involved in most of the possible adsorption and decomposition pathways. We also investigate structures and energies of the transition states in the first hydrogen dissociation of a water molecule on the (2\u00d74) surface.
\r\n\r\nFinally, adsorption structures and thermal decomposition reactions of 1-propanethiol on the Ga-rich GaP(001)(2\u00d74) surface are investigated using high resolution STM, XPS, and DFT simulations. We elucidate adsorption locations and their associated atomic structures of a single 1-propanethiol molecule on the (2\u00d74) surface as a function of annealing temperature. DFT calculations are carried out to optimize ground state structures and search transition states. XPS is used to investigate variations of the chemical bonding nature and coverage of the adsorbate species.
\r\n" }, { "name": "Jiang, Siduo (Stone)", "degree": "Senior Thesis", "year": "2014", "title": "Structure-Guided Design and Biophysical Characterization of Novel Anti-HIV Reagents", "advisor": "Bjorkman, Pamela J.; Galimidi, Rachel P.; West, Anthony P.; Sievers, Stuart A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06172014-114402762", "creators": [ { "name": { "family": "Jiang", "given": "Siduo (Stone)" }, "id": "Jiang-Siduo-Stone", "orcid": "0000-0002-2143-4030", "display_name": "Jiang, Siduo (Stone)" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Galimidi", "given": "Rachel P." }, "id": "Galimidi-R-P", "role": "co-advisor", "display_name": "Galimidi, Rachel P." }, { "name": { "family": "West", "given": "Anthony P." }, "id": "West-A-P", "role": "co-advisor", "display_name": "West, Anthony P." }, { "name": { "family": "Sievers", "given": "Stuart A." }, "id": "Sievers-S-A", "role": "co-advisor", "display_name": "Sievers, Stuart A." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "biology", "chemistry" ], "doi": "10.7907/SP19-9R34", "abstract": "Despite over 30 years of effort, an HIV-1 vaccine that elicits protective antibodies still does not exist. Recent clinical studies have identified that during natural infection about 20% of the population is capable of mounting a potent and protective antibody response. Closer inspection of these individuals reveal that a subset of these antibodies, recently termed potent VRC01-like (PVL), derive exclusively from a single human germline heavy chain gene. Induced clonal expansion of the B cell encoding this gene is the first step through which PVL antibodies may be elicited. Unfortunately, naturally occurring HIV gp120s fail to bind to this germline, and as a result cannot be used as the initial prime for a vaccine regimen. We have determined the crystal structure of an important germline antibody that is a promising target for vaccine design efforts, and have set out to engineer a more likely candidate using computationally-guided rational design.
\r\n\r\nIn addition to prevention efforts on the side of vaccine design, recently characterized broadly neutralizing anti-HIV antibodies have excellent potential for use in gene therapy and passive immunotherapy. The separation distance between functional Fabs on an antibody is important due to the sparse distribution of envelop spikes on HIV compared to other viruses. We set out to build and characterize novel antibody architectures by incorporating structured linkers into the hinge region of an anti-HIV antibody b12. The goal was to observe whether these linkers increased the arm-span of the IgG dimer. When incorporated, flexible Gly4Ser repeats did not result in detectable extensions of the IgG antigen binding domains, by contrast to linkers including more rigid domains such as \u03b22-microglobulin, Zn-\u03b12-glycoprotein, and tetratricopeptide repeats (TPRs). This study adds an additional set of linkers with varying lengths and rigidities to the available linker repertoire, which may be useful for the modification and construction of antibodies and other fusion proteins.
\r\n" }, { "name": "Kelley, Paul", "degree": "PhD", "year": "2014", "title": "Fundamental Studies of Carbon Oxygen Bond Activation in Nickel Diphosphine Ether Complexes. And, Metallomacrocycles as Ligands: Synthesis and Characterization of Aluminum-Bridged Bisglyoximato Complexes of Iron and Cobalt", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082014-155448927", "creators": [ { "name": { "family": "Kelley", "given": "Paul" }, "id": "Kelley-Paul", "display_name": "Kelley, Paul" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZKZ0-TP24", "abstract": "In order to develop better catalysts for the cleavage of aryl-X bonds fundamental studies of the mechanism and individual steps of the mechanism have been investigated in detail. As the described studies are difficult at best in catalytic systems, model systems are frequently used. To study aryl-oxygen bond activation, a terphenyl diphosphine scaffold containing an ether moiety in the central arene was designed. The first three chapters of this dissertation focus on the studies of the nickel complexes supported by this diphosphine backbone and the research efforts in regards to aryl-oxygen bond activation.
\r\n\r\nChapter 2 outlines the synthesis of a variety of diphosphine terphenyl ether ligand scaffolds. The metallation of these scaffolds with nickel is described. The reactivity of these nickel(0) systems is also outlined. The systems were found to typically undergo a reductive cleavage of the aryl oxygen bond. The mechanism was found to be a subsequent oxidative addition, \u03b2-H elimination, reductive elimination and (or) decarbonylation.
\r\n\r\nChapter 3 presents kinetic studies of the aryl oxygen bond in the systems outlined in Chapter 2. Using a series of nickel(0) diphosphine terphenyl ether complexes the kinetics of aryl oxygen bond activation was studied. The activation parameters of oxidative addition for the model systems were determined. Little variation was observed in the rate and activation parameters of oxidative addition with varying electronics in the model system. The cause of the lack of variation is due to the ground state and oxidative addition transition state being affected similarly. Attempts were made to extend this study to catalytic systems.
\r\n\r\nChapter 4 investigates aryl oxygen bond activation in the presence of additives. It was found that the addition of certain metal alkyls to the nickel(0) model system lead to an increase in the rate of aryl oxygen bond activation. The addition of excess Grignard reagent led to an order of magnitude increase in the rate of aryl oxygen bond activation. Similarly the addition of AlMe3 led to a three order of magnitude rate increase. Addition of AlMe3 at -80 \u00b0C led to the formation of an intermediate which was identified by NOESY correlations as a system in which the AlMe3 is coordinated to the ether moiety of the backbone. The rates and activation parameters of aryl oxygen bond activation in the presence of AlMe3 were investigated.
\r\n\r\nThe last two chapters involve the study of metalla-macrocycles as ligands. Chapter 5 details the synthesis of a variety of glyoxime backbones and diphenol precursors and their metallation with aluminum. The coordination chemistry of iron on the aluminum scaffolds was investigated. Varying the electronics of the aluminum macrocycle was found to affect the observed electrochemistry of the iron center.
\r\n\r\nChapter 6 extends the studies of chapter 5 to cobalt complexes. The synthesis of cobalt dialuminum glyoxime metal complexes is described. The electrochemistry of the cobalt complexes was investigated. The electrochemistry was compared to the observed electrochemistry of a zinc analog to identify the redox activity of the ligand. In the presence of acid the cobalt complexes were found to electrochemically reduce protons to dihydrogen. The electronics of the ancillary aluminum ligands were found to affect the potential of proton reduction in the cobalt complexes. These potentials were compared to other diglyoximate complexes.
\r\n" }, { "name": "Klet, Rachel Christine", "degree": "PhD", "year": "2014", "title": "Carbon-Carbon Bond Forming Reactions from Bis(carbene)-Platinum(II) Complexes and Olefin Polymerization and Oligomerization using Group 4 Post-Metallocene Complexes ", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262013-092439684", "creators": [ { "name": { "family": "Klet", "given": "Rachel Christine" }, "id": "Klet-Rachel-Christine", "display_name": "Klet, Rachel Christine" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WRTW-6Z10", "abstract": "A long-standing challenge in transition metal catalysis is selective C\u2013C bond coupling of simple feedstocks, such as carbon monoxide, ethylene or propylene, to yield value-added products. This work describes efforts toward selective C\u2013C bond formation using early- and late-transition metals, which may have important implications for the production of fuels and plastics, as well as many other commodity chemicals.
\r\n\r\nThe industrial Fischer-Tropsch (F-T) process converts synthesis gas (syngas, a mixture of CO + H2) into a complex mixture of hydrocarbons and oxygenates. Well-defined homogeneous catalysts for F-T may provide greater product selectivity for fuel-range liquid hydrocarbons compared to traditional heterogeneous catalysts. The first part of this work involved the preparation of late-transition metal complexes for use in syngas conversion. We investigated C\u2013C bond forming reactions via carbene coupling using bis(carbene)platinum(II) compounds, which are models for putative metal\u2013carbene intermediates in F-T chemistry. It was found that C\u2013C bond formation could be induced by either (1) chemical reduction of or (2) exogenous phosphine coordination to the platinum(II) starting complexes. These two mild methods afforded different products, constitutional isomers, suggesting that at least two different mechanisms are possible for C\u2013C bond formation from carbene intermediates. These results are encouraging for the development of a multicomponent homogeneous catalysis system for the generation of higher hydrocarbons.
\r\n\r\nA second avenue of research focused on the design and synthesis of post-metallocene catalysts for olefin polymerization. The polymerization chemistry of a new class of group 4 complexes supported by asymmetric anilide(pyridine)phenolate (NNO) pincer ligands was explored. Unlike typical early transition metal polymerization catalysts, NNO-ligated catalysts produce nearly regiorandom polypropylene, with as many as 30-40 mol % of insertions being 2,1-inserted (versus 1,2-inserted), compared to <1 mol % in most metallocene systems. A survey of model Ti polymerization catalysts suggests that catalyst modification pathways that could affect regioselectivity, such as C\u2013H activation of the anilide ring, cleavage of the amine R-group, or monomer insertion into metal\u2013ligand bonds are unlikely. A parallel investigation of a Ti\u2013amido(pyridine)phenolate polymerization catalyst, which features a five- rather than a six-membered Ti\u2013N chelate ring, but maintained a dianionic NNO motif, revealed that simply maintaining this motif was not enough to produce regioirregular polypropylene; in fact, these experiments seem to indicate that only an intact anilide(pyridine)phenolate ligated-complex will lead to regioirregular polypropylene. As yet, the underlying causes for the unique regioselectivity of anilide(pyridine)phenolate polymerization catalysts remains unknown. Further exploration of NNO-ligated polymerization catalysts could lead to the controlled synthesis of new types of polymer architectures.
\r\n\r\nFinally, we investigated the reactivity of a known Ti\u2013phenoxy(imine) (Ti-FI) catalyst that has been shown to be very active for ethylene homotrimerization in an effort to upgrade simple feedstocks to liquid hydrocarbon fuels through co-oligomerization of heavy and light olefins. We demonstrated that the Ti-FI catalyst can homo-oligomerize 1-hexene to C12 and C18 alkenes through olefin dimerization and trimerization, respectively. Future work will include kinetic studies to determine monomer selectivity by investigating the relative rates of insertion of light olefins (e.g., ethylene) vs. higher \u03b1-olefins, as well as a more detailed mechanistic study of olefin trimerization. Our ultimate goal is to exploit this catalyst in a multi-catalyst system for conversion of simple alkenes into hydrocarbon fuels.
\r\n" }, { "name": "Komor, Alexis Christine", "degree": "PhD", "year": "2014", "title": "Design, Synthesis, and Biological Activity of Rhodium Metalloinsertors", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282014-143107089", "creators": [ { "name": { "family": "Komor", "given": "Alexis Christine" }, "id": "Komor-Alexis-Christine", "display_name": "Komor, Alexis Christine" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KPCY-JS09", "abstract": "Deficiencies in the mismatch repair (MMR) pathway are associated with several types of cancers, as well as resistance to commonly used chemotherapeutics. Rhodium metalloinsertors have been found to bind DNA mismatches with high affinity and specificity in vitro, and also exhibit cell-selective cytotoxicity, targeting MMR-deficient cells over MMR-proficient cells.
\r\n \r\nHere we examine the biological fate of rhodium metalloinsertors bearing dipyridylamine ancillary ligands. These complexes are shown to exhibit accelerated cellular uptake which permits the observation of various cellular responses, including disruption of the cell cycle and induction of necrosis, which occur preferentially in the MMR-deficient cell line. These cellular responses provide insight into the mechanisms underlying the selective activity of this novel class of targeted anti-cancer agents.
\r\n\r\nIn addition, ten distinct metalloinsertors with varying lipophilicities are synthesized and their mismatch binding affinities and biological activities studied. While they are found to have similar binding affinities, their cell-selective antiproliferative and cytotoxic activities vary significantly. Inductively coupled plasma mass spectrometry (ICP-MS) experiments show that all of these metalloinsertors localize in the nucleus at sufficient concentrations for binding to DNA mismatches. Furthermore, metalloinsertors with high rhodium localization in the mitochondria show toxicity that is not selective for MMR-deficient cells. This work supports the notion that specific targeting of the metalloinsertors to nuclear DNA gives rise to their cytotoxic and antiproliferative activities that are selective for cells deficient in MMR.
\r\n\r\nTo explore further the basis of the unique selectivity of the metlloinsertors in targeting MMR-deficient cells, experiments were conducted using engineered NCI-H23 lung adenocarcinoma cells that contain a doxycycline-inducible shRNA which suppresses the expression of the MMR gene MLH1. Here we use this new cell line to further validate rhodium metalloinsertors as compounds capable of differentially inhibiting the proliferation of MMR-deficient cancer cells over isogenic MMR-proficient cells. General DNA damaging agents, such as cisplatin and etoposide, in contrast, are less effective in the induced cell line defective in MMR.
\r\n\r\nFinally, we describe a new subclass of metalloinsertors with enhanced potency and selectivity, in which the complexes show Rh-O coordination. In particular, it has been found that both \u0394 and \u039b enantiomers of [Rh(chrysi)(phen)(DPE)]2+ bind to DNA with similar affinities, suggesting a possible different binding conformation than previous metalloinsertors. Remarkably, all members of this new family of compounds have significantly increased potency in a range of cellular assays; indeed, all are more potent than the FDA-approved anticancer drugs cisplatin and MNNG. Moreover, these activities are coupled with high levels of selectivity for MMR-deficient cells.
\r\n" }, { "name": "Laga, Stephanie Midori", "degree": "Senior Thesis", "year": "2014", "title": "A Tale of Two Cobalts", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192014-150810287", "creators": [ { "name": { "family": "Laga", "given": "Stephanie Midori" }, "id": "Laga-Stephanie-Midori", "display_name": "Laga, Stephanie Midori" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1B9V-AW18", "abstract": "There are important problems to overcome if solar energy or other renewable energy sources are to be used effectively on a global scale. Solar photons must not only be harvested and converted into a usable form, but they must also be efficiently stored so that energy is available for use on cloudy days and at night. In this work, both the energy conversion and energy storage problems are addressed. Specifically, two cobalt complexes were designed and their reactivity probed for applications in energy conversion and storage. The first chapter describes a cobalt complex that is the first example of a dimeric cobalt compound with two singly proton-bridged cobaloxime units linked by a central BO4--bridge. Using electrochemical methods, the redox properties of the dimer were evaluated and it was found to be an electrocatalyst for proton reduction in acetonitrile.
\r\n\r\nBecause hydrogen gas is difficult to handle and store, the hydrogenation of CO2 and later dehydrogenation of the liquid product, formic acid, has been proposed as a hydrogen storage system. Thus, a second complex, described in chapter two, supported by a triphosphine ligand framework was used as a catalyst precursor for this key dehydrogenation step. The studies here demonstrate the efficacy of the complex as a precatalyst for the desired reaction, with good conversion of starting formic acid to CO2 and H2. In order to better understand the properties of the triphosphine cobalt complex, a synthetic procedure for substituting electron donating groups (e.g., methoxy groups) onto the ligand was investigated, yielding a novel diphosphine cobalt(II) complex.
" }, { "name": "Lattimer, Judith Rebecca Cabelli", "degree": "PhD", "year": "2014", "title": "Functionalization of Si(111) Surfaces and the Formation of Mixed Monolayers for the Covalent Attachment of Molecular Catalysts in Photoelectrochemical Devices", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022014-101347718", "creators": [ { "name": { "family": "Lattimer", "given": "Judith Rebecca Cabelli" }, "id": "Lattimer-Judith-Rebecca-Cabelli", "display_name": "Lattimer, Judith Rebecca Cabelli" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5EJQ-5134", "abstract": "The functionalization of silicon surfaces with molecular catalysts for proton reduction is an important part of the development of a solar-powered, water-splitting device for solar fuel formation. The covalent attachment of these catalysts to silicon without damaging the underlying electronic properties of silicon that make it a good photocathode has proven difficult. We report the formation of mixed monolayer-functionalized surfaces that incor- porate both methyl and vinylferrocenyl or vinylbipyridyl (vbpy) moieties. The silicon was functionalized using reaction conditions analogous to those of hydrosilylation, but instead of a H-terminated Si surface, a chlorine-terminated Si precursor surface was used to produce the linked vinyl-modified functional group. The functionalized surfaces were characterized by time-resolved photoconductivity decay, X-ray photoelectron spectroscopy (XPS), electro- chemical, and photoelectrochemical measurements. The functionalized Si surfaces were well passivated, exhibited high surface coverage and few remaining reactive Si atop sites, had a very low surface recombination velocity, and displayed little initial surface oxidation. The surfaces were stable toward atmospheric and electrochemical oxidation. The surface coverage of ferrocene or bipyridine was controllably varied from 0 up to 30% of a monolayer without loss of the underlying electronic properties of the silicon. Interfacial charge transfer to the attached ferrocene group was relatively rapid, and a photovoltage of 0.4 V was generated upon illumination of functionalized n-type silicon surfaces in CH3CN. The immobilized bipyridine ligands bound transition metal ions, and thus enabled the assembly of metal complexes on the silicon surface. XPS studies demonstrated that [Cp\u2217Rh(vbpy)Cl]Cl, [Cp\u2217Ir(vbpy)Cl]Cl, and Ru(acac)2vbpy were assembled on the surface. For the surface prepared with iridium, x-ray absorption spectroscopy at the Ir LIII edge showed an edge energy and post-edge features virtually identical to a powder sample of [Cp\u2217Ir(bipy)Cl]Cl (bipy is 2,2 \u0301-bipyridyl). Electrochemical studies on these surfaces confirmed that the assembled complexes were electrochemically active." }, { "name": "Lenton, Taylor Nichole Baker", "degree": "PhD", "year": "2014", "title": "Bis(thiophenolate)pyridine Pincer Ligands and Trivalent Zirconocene Complexes Relevant to Earlv Transition Metal Polymerization Catalysts", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09242013-191401866", "creators": [ { "name": { "family": "Lenton", "given": "Taylor Nichole Baker" }, "id": "Lenton-Taylor-Nichole-Baker", "display_name": "Lenton, Taylor Nichole Baker" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FPP5-0461", "abstract": "Two major topics are covered: the first chapter is focused on the development of post-metallocene complexes for propylene polymerization. The second and third chapters investigate the consequences of diisobutylaluminum hydride (HAliBu2) additives in zirconocene based polymerization systems.
\r\n\r\nThe synthesis, structure, and solution behavior of early metal complexes with a new tridentate LX2 type ligand, bis(thiophenolate)pyridine ((SNS) = (2-C6H4S)2-2,6-C5H3N) are investigated. SNS complexes of Ti, Zr, and Ta having dialkylamido coligands were synthesized and structurally characterized. The zirconium complex, (SNS)Zr(NMe2)2, displays C2 symmetry in the solid state. Solid-state structures of tantalum complexes (SNS)Ta(NMe2)3 and (SNS)TaCl(NEt2)2 also display pronounced C2 twisting of the SNS ligand. 1D and 2D NMR experiments show that (SNS)Ta(NMe2)3 is fluxional with rotation about the Ta N(amide) bonds occurring on the NMR timescale. The fluxional behavior of (SNS)TaCl(NEt2)2 in solution was also studied by variable temperature 1H NMR. Observation of separate signals for the diastereotopic protons of the methylene unit of the diethylamide indicates that the complex remains locked on the NMR timescale in one diastereomeric conformation at temperatures below -50 \u00b0C.
\r\n\r\nReduction of Zr(IV) metallocenium cations with sodium amalgam (NaHg) produces EPR signals assignable to Zr(III) metallocene complexes. Thus, chloro-bridged heterobinuclear ansa-zirconocenium cation [((SBI))Zr(μ-Cl)2AlMe2]+B(C6F5)4¯ (SBI = rac-dimethylsilylbis(1-indenyl)), gives rise to an EPR signal assignable to the complex (SBI)ZrIII(μ-Cl)2AlMe2, while (SBI)ZrIII-Me and (SBI)ZrIII(-H)2AliBu2 are formed by reduction of [(SBI)Zr(μ-Me)2AlMe2]+B(C6F5)4¯ and [(SBI)Zr(μ-H)3(AliBu2)2]+B(C6F5)4¯, respectively. These products are also formed, along with (SBI)ZrIII-iBu and [(SBI)ZrIII]+ AlR4¯ when (SBI)ZrMe2 reacts with HAliBu2, eliminating isobutane en route to the Zr(III) complex. Studies concerning the interconversion reactions between these and other (SBI)Zr(III) complexes and reaction mechanisms involved in their formation are also reported.
\r\n\r\nThe addition of HAliBu2 to precatalyst [(SBI)Zr(\u00b5-H)3(AliBu2)2]+ significantly slows the polymerization of propylene and changes the kinetics of polymerization from 1st to 2nd order with respect to propylene. This is likely due to competitive inhibition by HAliBu2. When the same reaction is investigated using [(nBuCp)2Zr(μ-H)3(AliBu2)2]+, hydroalumination between propylene and HAliBu2 is observed instead of propylene polymerization.
\r\n" }, { "name": "Lin, Sibo", "degree": "PhD", "year": "2014", "title": "Chelation-Enforced Metal-Arene Interactions: Insights into Substrate Binding and Catalvsis by Late Transition Metal Complexes", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282014-232356909", "creators": [ { "name": { "family": "Lin", "given": "Sibo" }, "id": "Lin-Sibo", "display_name": "Lin, Sibo" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94T6G9T", "abstract": "Understanding and catalyzing chemical reactions requiring multiple electron transfers is an endeavor relevant to many outstanding challenges in the field of chemistry. To study multi-electron reactions, a terphenyl diphosphine framework was designed to support one or more metals in multiple redox states via stabilizing interactions with the central arene of the terphenyl backbone. A variety of unusual compounds and reactions and their relevance toward prominent research efforts in chemistry are the subject of this dissertation.
\r\n\r\nChapter 2 introduces the para-terphenyl diphosphine framework and its coordination chemistry with group 10 transition metal centers. Both mononuclear and dinuclear compounds are characterized. In many cases, the metal center(s) are stabilized by the terphenyl central arene. These metal\u2013arene interactions are characterized both statically, in the solid state, and fluxionally, in solution. As a proof-of-principle, a dinickel framework is shown to span multiple redox states, showing that multielectron chemistry can be supported by the coordinatively flexible terphenyl diphosphine.
\r\n\r\nChapter 3 presents reactivity of the terphenyl diphosphine when bound to a metal center. Because of the dearomatizing effect of the metal center, the central arene of the ligand is susceptible to reactions that do not normally affect arenes. In particular, Ni-to-arene H-transfer and arene dihydrogenation reactions are presented. Additionally, evidence for reversibility of the Ni-to-arene H-transfer is discussed.
\r\n\r\nChapter 4 expands beyond the chelated metal-arene interactions of the previous chapters. A dipalladium(I) terphenyl diphosphine framework is used to bind a variety of exogenous organic ligands including arenes, dienes, heteroarenes, thioethers, and anionic ligands. The compounds are structurally characterized, and many ligands exhibit unprecedented bindng modes across two metal centers. The relative binding affinities are evaluated spectroscopically, and equilibrium binding constants for the examined ligands are determined to span over 13 orders of magnitude. As an application of this framework, mild hydrogenation conditions of bound thiophene are presented.
\r\n\r\nChapter 5 studies nickel-mediated C\u2013O bond cleavage of aryl alkyl ethers, a transformation with emerging applications in fields such as lignin biofuels and organic methodology. Other group members have shown the mechanism of C\u2013O bond cleavage of an aryl methyl ether incorporated into a meta-terphenyl diphosphine framework to proceed through \u03b2-H elimination of an alkoxide. First, the electronic selectivity of the model system is examined computationally and compared with catalytic systems. The lessons learned from the model system are then applied to isotopic labeling studies for catalytic aryl alkyl ether cleavage under dihydrogen. Results from selective deuteration experiments and mass spectrometry draw a clear analogy between the mechanisms of the model and catalytic systems that does not require dihydrogen for C\u2013O bond cleavage, although dihydrogen is proposed to play a role in catalyst activation and catalytic turnover.
\r\n\r\nAppendix A presents initial efforts toward heterodinuclear complexes as models for CO dehydrogenase and Fischer Tropsch chemistry. A catechol-incorporating terphenyl diphosphine is reported, and metal complexes thereof are discussed.
\r\n\r\nAppendix B highlights some structurally characterized terphenyl diphosphine complexes that either do not thematically belong in the research chapters or proved to be difficult to reproduce. These compounds show unusual coordination modes of the terphenyl diphosphine from which other researchers may glean insights.
" }, { "name": "Liu, Wei-Guang", "degree": "PhD", "year": "2014", "title": "First-Principle Studies of the Initiation Mechanism of Energetic Materials", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232014-150103448", "creators": [ { "name": { "family": "Liu", "given": "Wei-Guang" }, "id": "Liu-Wei-Guang", "orcid": "0000-0002-6633-7795", "display_name": "Liu, Wei-Guang" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9445JGM", "abstract": "It is important to understand the initiation mechanism of energetic materials to improve and engineer them. In this thesis first-principle calculation is used to study the initiation of several explosives and propellants.
\r\n\r\nThe second chapter is focused on a new energetic material, silicon pentaerythritol tetranitrate (Si-PETN), DFT calculations have identified the novel rearrangement that explains the very dramatic increase in sensitivity observed experimentally. The critical difference is that Si-PETN allows a favorable five-coordinate transition state in which the new Si\u2212O and C\u2212O bonds form simultaneously, leading to a transition state barrier of 33 kcal/mol (it is 80 kcal/mol for PETN) and much lower than the normal O\u2212NO2 bond fission observed in other energetic materials (40 kcal/mol). In addition this new mechanism is very exothermic (45 kcal/mol) leading to a large net energy release at the very early stages of Si-PETN decomposition.
\r\n\r\nThe third chapter is about nitrogen-rich compounds, which has high heat of formation and releases the energy by decomposing into stable N2 molecules. Two families of compounds, azobistetrazoles and azobistriazoles, were studied. Based on the calculated mechanisms, for azobistetrazoles with four N atoms in the five-member ring, a clearly-defined N=N fragment can always be found in the ring, and its decomposition starts with ring-opening to free one end of N=N followed by N2 dissociation and heat generation. This barrier is around 28-35 kcal/mol, which is low enough to dominate the sensitivity of material. For azobistriazoles, only 1,1\u2019-azobis-1,2,3-triazole has a N=N fragment in the original 5-member ring and similar ring-opening - N2 dissociation pathway is favored. For the remaining compounds, an additional isomerization is necessary to release N2, which gives the barrier around 55~60 kcal/mol, making these compound less sensitive.
\r\n\r\nThe fourth chapter shifts focus to hypergolic propellants. DFT calculations with B3LYP functional was applied to study the hypergolic reaction between N,N,N',N'-tetramethylethylenediamine (TMEDA), N,N,N',N'-Tetramethylmethylenediamine (TMMDA) and HNO3. Bond energies in TMEDA and TMMDA were calculated and compared with their alkane analogues to demonstrate that the lone-pair electrons on N atoms plays the role of activating adjacent chemical bonds. Two key factors relating to the ignition delay were calculated at atomistic level. The first factor is the exothermicity of the formation of the dinitrate salt of TMEDA and TMMDA. Because of the shorter distance between basic amines in TMMDA, it is more difficult to protonate both amines for the stronger electrostatic repulsion, resulting in the smaller heat of dinitrate salt formation by 6.3kcal/mol. The second factor is the reaction rate of TMEDA and TMMDA reacting with NO2 to the step that releases enough heat and more reactive species to propagate reaction. In TMEDA, the formation of the intermediate with C-C double bond and the low bond energy of C-C single bond provide a route with low barrier to oxidize C. Both factors can contribute to the shorter ignition delay of TMEDA.
\r\n\r\nThe fifth chapter is about the other pair of hypergolic propellant, monomethylhydrazine (MMH) with oxidizers NO2/N2O4. Experimentally several IR-active species were identified in the early reactions, including HONO, monomethylhydrazinium nitrite (MMH\u2022HONO), methyl diazene (CH3N=NH), methyl nitrate (CH3ONO2), methyl nitrite (CH3ONO), nitromethane (CH3NO2), methyl azide (CH3N3), H2O, N2O and NO. In order to elucidate the mechanisms by which these observed products are formed, we carried out quantum mechanics calculations (CCSD(T)/6-31G**//M06-2X/6-311G**++) for the possible reaction pathways. Based on these studies, we proposed that the oxidation of MMH in an atmosphere of NO2 occurs via two mechanisms: (1) sequential H-abstraction and HONO formation, and (2) reaction of MMH with asymmetric ONONO2, leading to formation of methyl nitrate. These mechanisms successfully explain all intermediates observed experimentally. We concluded that the formation of asymmetric ONONO2 is assisted by an aerosol formed by HONO and MMH that provides a large surface area for ONONO2 to condense, leading to the generation of methyl nitrate. Thus we proposed that the overall pre-ignition process involves both gas-phase and aerosol-phase reactions.
\r\n\r\nThe sixth chapter is about another pair of hypergolic propellant, unsymmetrical dimethylhydrazine (UDMH) with oxidizers NO2/N2O4. We carried out the same level of quantum mechanics calculations as MMH to study this pair. We proposed that the oxidation of UDMH in an atmosphere of NO2 occurs via two mechanisms, similar with MMH: (1) sequential H-abstraction and HONO formation in gas phase, which has no more than 20 kcal/mol barrier and leads to the production of (CH3)2NNO and HONO. (2)UDMH reacts with asymmetric ONONO2 in aerosol phase, leading to formation of CH3N3 and then CH3ONO2, with a 26.8 kcal/mol enthalpic barrier, which is 10 kcal/mol higher than the corresponding reaction barrier for MMH. Thus we predicted the low production rate of CH3ONO2 for UDMH/NO2 pair. Experimental evidences support our mechanisms for both MMH and UDMH reacting with NO2.
\r\n" }, { "name": "Lu, Ying Ying", "degree": "PhD", "year": "2014", "title": "Revealing, Illuminating, and Modifying Proteins in Human Diseases using Noncanonical Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232013-210427528", "creators": [ { "name": { "family": "Lu", "given": "Ying Ying" }, "id": "Lu-Ying-Ying", "display_name": "Lu, Ying Ying" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/NPBC-3N67", "abstract": "To better understand human diseases, much recent work has focused on proteins to either identify disease targets through proteomics or produce therapeutics via protein engineering. Noncanonical amino acids (ncAAs) are tools for altering the chemical and physical properties of proteins, providing a facile strategy not only to label proteins but also to engineer proteins with novel properties. My thesis research has focused on the development and applications of noncanonical amino acids in identifying, imaging, and engineering proteins for studying human diseases. Chapter 1 introduces the concept of ncAAs and reveals insights to how I chose my thesis projects.
\r\n\r\nncAAs have been incorporated to tag and enrich newly synthesized proteins for mass spectrometry through a method termed BONCAT, or bioorthogonal noncanonical amino acid tagging. Chapter 2 describes the investigation of the proteomic response of human breast cancer cells to induced expression of tumor suppressor microRNA miR-126 by combining BONCAT with another proteomic method, SILAC or stable isotope labeling by amino acids in cell culture. This proteomic analysis led to the discovery of a direct target of miR-126, shedding new light on its role in suppressing cancer metastasis.
\r\n\r\nIn addition to mass spectrometry, ncAAs can also be utilized to fluorescently label proteins. Chapter 3 details the synthesis of a set of cell-permeant cyclooctyne probes and demonstration of selective labeling of newly synthesized proteins in live mammalian cells using azidohomoalanine. Similar to live cell imaging, the ability to selectively label a particular cell type within a mixed cell population is important to interrogating many biological systems, such as tumor microenvironments. By taking advantage of the metabolic differences between cancer and normal cells, Chapter 5 discusses efforts to develop selective labeling of cancer cells using a glutamine analogue.
\r\n\r\nFurthermore, Chapter 4 describes the first demonstration of global replacement at polar amino acid positions and its application in developing an alternative PEGylation strategy for therapeutic proteins. Polar amino acids typically occupy solvent-exposed positions on the protein surface, and incorporation of noncanonical amino acids at these positions should allow easier modification and cause less perturbation compared to replacements at the interior positions of proteins.
" }, { "name": "Menzeleev, Artur R.", "degree": "PhD", "year": "2014", "title": "Direct Simulation of Quantum Dynamics in Complex Systems", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302014-112920946", "creators": [ { "name": { "family": "Menzeleev", "given": "Artur R." }, "id": "Menzeleev-Artur-R", "display_name": "Menzeleev, Artur R." } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PZ32-ZN60", "abstract": "Accurate simulation of quantum dynamics in complex systems poses a fundamental theoretical challenge with immediate application to problems in biological catalysis, charge transfer, and solar energy conversion. The varied length- and timescales that characterize these kinds of processes necessitate development of novel simulation methodology that can both accurately evolve the coupled quantum and classical degrees of freedom and also be easily applicable to large, complex systems. In the following dissertation, the problems of quantum dynamics in complex systems are explored through direct simulation using path-integral methods as well as application of state-of-the-art analytical rate theories." }, { "name": "Minor, Paul Joseph", "degree": "PhD", "year": "2014", "title": "Wnt and FGF Signaling in C. elegans Vulval Cell Lineage Polarity", "advisor": "Sternberg, Paul W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08142013-092554646", "creators": [ { "name": { "family": "Minor", "given": "Paul Joseph" }, "id": "Minor-Paul-Joseph", "display_name": "Minor, Paul Joseph" } ], "advisors": [ { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "advisor", "display_name": "Sternberg, Paul W." } ], "committee": [ { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "role": "chair", "display_name": "Bronner, Marianne E." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Hay", "given": "Bruce A." }, "id": "Hay-B-A", "role": "member", "display_name": "Hay, Bruce A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "bioch" ], "doi": "10.7907/99ZE-5Y87", "abstract": "The interpretation of extracellular cues leading to the polarization of intracellular components and asymmetric cell divisions is a fundamental part of metazoan organogenesis. The C. elegans vulva, with its invariant cell lineage and interaction of multiple cell signaling pathways, provides an excellent model for the study of cell polarity within an organized epithelial tissue. Herein I discuss the interaction of Wnt and FGF signaling in controlling vulval cell lineage polarity with emphasis on the posterior-most cell that forms the vulva, P7.p.
\r\n\r\nThe mirror symmetry of the C. elegans vulva is achieved by the opposite division orientation of the vulval precursor cells (VPCs) flanking the axis of symmetry. Opposing Wnt signals control the division patterns of the VPCs by controlling the localization of SYS-1/ \u03b2-catenin toward the direction of the Wnt gradient. Multiple Wnt signals, expressed at the axis of symmetry, promote the wild-type, anterior-facing, P7.p orientation, whereas Wnts EGL-20 and CWN-1 from the tail and posterior body wall muscle, respectively, promote the daughter cells of P7.p to face the posterior. EGL-20 acts through a member of the LDL receptor superfamily, LRP-2, along with Ror/CAM-1 and Van Gogh/VANG-1. All three transmembrane proteins control orientation through the localization of the SYS-1.
\r\n\r\nThe Fibroblast Growth Factor (FGF) pathway acts in concert with LIN-17/Frizzled to regulate the localization of SYS-1. The source of the FGF ligand is the 1\u00b0 VPC, P6.p, which controls the polarity of the neighboring 2\u00b0 VPC, P7.p, by signaling through the sex myoblasts (SMs), activating the FGF pathway. The Wnt, cwn-1, is expressed in the posterior body wall muscle of the worm as well as the SMs, making it the only Wnt expressed on the posterior and anterior sides of P7.p at the time of the polarity decision. Both sources of cwn-1 act instructively to influence P7.p polarity in the direction of the Wnt gradient. The FGF pathway leads to the regulation of cwn-1 transcripts in the SMs. These results illustrate the first evidence of the interaction between FGF and Wnt in C. elegans development and vulval cell lineage polarity as well as highlight the promiscuous nature of Wnt signaling within C. elegans.
" }, { "name": "Mou, Yun", "degree": "PhD", "year": "2014", "title": "Computational Design of Self-Assembling Proteins and Protein-DNA Nanowires", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232014-201621983", "creators": [ { "name": { "family": "Mou", "given": "Yun" }, "id": "Mou-Yun", "display_name": "Mou, Yun" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9PG1PPV", "abstract": "Computational protein design (CPD) is a burgeoning field that uses a physical-chemical or knowledge-based scoring function to create protein variants with new or improved properties. This exciting approach has recently been used to generate proteins with entirely new functions, ones that are not observed in naturally occurring proteins. For example, several enzymes were designed to catalyze reactions that are not in the repertoire of any known natural enzyme. In these designs, novel catalytic activity was built de novo (from scratch) into a previously inert protein scaffold. In addition to de novo enzyme design, the computational design of protein-protein interactions can also be used to create novel functionality, such as neutralization of influenza. Our goal here was to design a protein that can self-assemble with DNA into nanowires. We used computational tools to homodimerize a transcription factor that binds a specific sequence of double-stranded DNA. We arranged the protein-protein and protein-DNA binding sites so that the self-assembly could occur in a linear fashion to generate nanowires. Upon mixing our designed protein homodimer with the double-stranded DNA, the molecules immediately self-assembled into nanowires. This nanowire topology was confirmed using atomic force microscopy. Co-crystal structure showed that the nanowire is assembled via the desired interactions. To the best of our knowledge, this is the first example of a protein-DNA self-assembly that does not rely on covalent interactions. We anticipate that this new material will stimulate further interest in the development of advanced biomaterials." }, { "name": "Mui, Timothy Paul", "degree": "PhD", "year": "2014", "title": "Expanding the Repertoire of DNA-Mediated Signaling in DNA Repair", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09102013-094001578", "creators": [ { "name": { "family": "Mui", "given": "Timothy Paul" }, "id": "Mui-Timothy-Paul", "display_name": "Mui, Timothy Paul" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WXQM-CJ32", "abstract": "DNA damage is extremely detrimental to the cell and must be repaired to protect the genome. DNA is capable of conducting charge through the overlapping \u03c0-orbitals of stacked bases; this phenomenon is extremely sensitive to the integrity of the \u03c0-stack, as perturbations attenuate DNA charge transport (CT). Based on the E. coli base excision repair (BER) proteins EndoIII and MutY, it has recently been proposed that redox-active proteins containing metal clusters can utilize DNA CT to signal one another to locate sites of DNA damage.
\r\n\t\r\nTo expand our repertoire of proteins that utilize DNA-mediated signaling, we measured the DNA-bound redox potential of the nucleotide excision repair (NER) helicase XPD from Sulfolobus acidocaldarius. A midpoint potential of 82 mV versus NHE was observed, resembling that of the previously reported BER proteins. The redox signal increases in intensity with ATP hydrolysis in only the WT protein and mutants that maintain ATPase activity and not for ATPase-deficient mutants. The signal increase correlates directly with ATP activity, suggesting that DNA-mediated signaling may play a general role in protein signaling. Several mutations in human XPD that lead to XP-related diseases have been identified; using SaXPD, we explored how these mutations, which are conserved in the thermophile, affect protein electrochemistry.
\r\n\r\nTo further understand the electrochemical signaling of XPD, we studied the yeast S. cerevisiae Rad3 protein. ScRad3 mutants were incubated on a DNA-modified electrode and exhibited a similar redox potential to SaXPD. We developed a haploid strain of S. cerevisiae that allowed for easy manipulation of Rad3. In a survival assay, the ATPase- and helicase-deficient mutants show little survival, while the two disease-related mutants exhibit survival similar to WT. When both a WT and G47R (ATPase/helicase deficient) strain were challenged with different DNA damaging agents, both exhibited comparable survival in the presence of hydroxyurea, while with methyl methanesulfonate and camptothecin, the G47R strain exhibits a significant change in growth, suggesting that Rad3 is involved in repairing damage beyond traditional NER substrates. Together, these data expand our understanding of redox-active proteins at the interface of DNA repair.
\r\n" }, { "name": "Navarro, Raul", "degree": "PhD", "year": "2014", "title": "New Strategies for the Total Synthesis of Aza-Propellane Natural Products", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022013-141841545", "creators": [ { "name": { "family": "Navarro", "given": "Raul" }, "id": "Navarro-Raul", "display_name": "Navarro, Raul" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XQ0M-NT53", "abstract": "The propellane alkaloids comprise a large class of natural products that possess varying degrees of structural complexity and biological activity. The earliest of these to be isolated was acutumine, a chlorinated alkaloid that has been shown to exhibit selective T-cell cytotoxicity and antiamnesic properties. Alternatively, the hasubanan family of natural products has garnered considerable attention from the synthetic community in part due to its structural similarities to morphine. While these alkaloids have been the subject of numerous synthetic studies over the last forty years, very few enantioselective total syntheses have been reported to date.
\r\n\r\nAs part of a research program directed towards the synthesis of various alkaloid natural products, we have developed a unified strategy for the preparation of the hasubanan and acutumine alkaloids. Specifically, a highly diastereoselective 1,2-addition of organometallic reagents to benzoquinone-derived tert-butanesulfinimines was established, which provides access to enantioenriched 4-aminocyclohexadienone products. This methodology enabled the enantioselective construction of functionalized dihydroindolones, which were found to undergo intramolecular Friedel-Crafts conjugate additions to furnish the propellane cores of several hasubanan alkaloids. As a result of these studies, the first enantioselective total syntheses of 8-demethoxyrunanine and cepharatines A, C, and D were accomplished in 9-11 steps from commercially available starting materials.
\r\n\r\nMore recent efforts have focused on applying the sulfinimine methodology to the synthesis of a more structurally complex propellane alkaloid, acutumine. Extensive studies have determined that a properly functionalized dihydroindolone undergoes a photochemical [2+2] cycloaddition followed by a lactone fragmentation/Dieckmann cyclization to establish the carbocyclic framework of the natural product. The preparation of more appropriately oxidized propellane intermediates is currently under investigation, and is anticipated to facilitate our synthetic endeavors toward acutumine.
\r\n\r\n" }, { "name": "Pfeilsticker, Jessica A.", "degree": "PhD", "year": "2014", "title": "A Cocktail of Thermally Stable, Chemically Synthesized Capture Agents for the Efficient Detection of Anti-gp41 Antibodies from Human Sera and Techniques", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262014-170142267", "creators": [ { "name": { "family": "Pfeilsticker", "given": "Jessica A." }, "id": "Pfeilsticker-Jessica-A", "display_name": "Pfeilsticker, Jessica A." } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0FT2-EF04", "abstract": "This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60\u00b0C. " }, { "name": "Pheeney, Catrina Gale", "degree": "PhD", "year": "2014", "title": "Multiplexed DNA-Mediated Electrochemistry", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09192013-114842407", "creators": [ { "name": { "family": "Pheeney", "given": "Catrina Gale" }, "id": "Pheeney-Catrina-Gale", "display_name": "Pheeney, Catrina Gale" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PCF7-9669", "abstract": "The aromatic core of double helical DNA possesses the unique and remarkable ability to form a conduit for electrons to travel over exceptionally long molecular distances. This core of \u03c0-stacked nucleobases creates an efficient pathway for charge transfer to proceed that is exquisitely sensitive to even subtle perturbations. Ground state electrochemistry of DNA-modified electrodes has been one of the major techniques used both to investigate and to harness the property of DNA-mediated charge transfer. DNA-modified electrodes have been an essential tool for both gaining insights into the fundamental properties of DNA and, due to the exquisite specificity of DNA-mediated charge transfer for the integrity of the \u03c0-stack, for use in next generation diagnostic sensing. Here, multiplexed DNA-modified electrodes are used to (i) gain new insights on the electrochemical coupling of metalloproteins to the DNA \u03c0-stack with relevance to the fundaments of in vivo DNA-mediated charge transfer and (ii) enhance the overall sensitivity of DNA-mediated reduction for use in the detection of low abundance diagnostic targets.
\r\n\r\nFirst, Methylene Blue (MB\u2032) was covalently attached to DNA through a flexible C12 alkyl linker to yield a new redox reporter for DNA electrochemistry measurements with enhanced sensitivity. Tethered, intercalated MB\u2032 was reduced through DNA-mediated charge transport. The redox signal intensity for MB\u2032-dT-C12-DNA was found to be at least 3 fold larger than that of previously used Nile Blue (NB)-dT-DNA, which is coupled to the base stack via direct conjugation. The signal attenuation, due to an intervening mismatch, and therefore the degree of DNA-mediated reduction, does, however, depend on the DNA film morphology and the backfilling agent used to passivate the surface. These results highlight two possible mechanisms for the reduction of MB\u2032 on the DNA-modified electrode that are distinguishable by their kinetics: reduction mediated by the DNA base pair stack and direct surface reduction of MB\u2032 at the electrode. The extent of direct reduction at the surface can be minimized by overall DNA assembly conditions.
\r\n\r\nNext, a series of intercalation-based DNA-mediated electrochemical reporters were developed, using a flexible alkane linkage to validate and explore their DNA-mediated reduction. The general mechanism for the reduction of distally bound redox active species, covalently tethered to DNA through flexible alkyl linkages, was established to be an intraduplex DNA-mediated pathway. MB, NB, and anthraquinone were covalently tethered to DNA with three different covalent linkages. The extent of electronic coupling of the reporter was shown to correlate with the DNA binding affinity of the redox active species, supporting an intercalative mechanism. These electrochemical signals were shown to be exceptionally sensitive to a single intervening \u03c0-stack perturbation, an AC mismatch, in a densely packed DNA monolayer, which further supports that the reduction is DNA-mediated. Finally, this DNA-mediated reduction of MB occurs primarily via intra- rather than inter duplex intercalation, as probed through varying the proximity and integrity of the neighboring duplex DNA.\r\nFurther gains to electrochemical sensitivity of our DNA-modified devices were then achieved through the application of electrocatalytic signal amplification using these solvent accessible intercalative reporters, MB-dT-C8, and hemoglobin as a novel electron sink. Electrocatalysis offers an excellent means of electrochemical signal amplification, yet in DNA based sensors, its application has been limited due to strict assembly conditions. We describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low density DNA films. Electrocatalysis of MB that is covalently tethered to the DNA by a flexible alkyl linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of single CA mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: it is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling.
\r\n\r\nFinally, we expanded the application of our multiplexed DNA-modified electrodes to the electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins that contain redox cofactors. Multiplexed analysis of EndonucleaseIII (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, elucidated subtle differences in the electrochemical behavior as a function of DNA morphology. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction. Closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. The electrochemical comparison of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster, was able to be quantitatively performed. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. Based on the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues, but also through changes in solvation near the cluster.
\r\n" }, { "name": "Pirogovsky, Paul Peter", "degree": "PhD", "year": "2014", "title": "Intramolecular Conflict: Conformation and Self-Assembly of Architecturally Complex Macromolecules in Solution", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182013-104133647", "creators": [ { "name": { "family": "Pirogovsky", "given": "Paul Peter" }, "id": "Pirogovsky-Paul-Peter", "display_name": "Pirogovsky, Paul Peter" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0DXJ-3H18", "abstract": "The solution behavior of linear polymer chains is well understood, having been the subject of intense study throughout the previous century. As plastics have become ubiquitous in everyday life, polymer science has grown into a major field of study. The conformation of a polymer in solution depends on the molecular architecture and its interactions with the surroundings. Developments in synthetic techniques have led to the creation of precision-tailored polymeric materials with varied topologies and functionalities. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer architecture and their conformation and behavior. To meet that need, this thesis investigates the conformation and self-assembly of three architecturally complex macromolecular systems with rich and varied behaviors driven by the resolution of intramolecular conflicts. First we describe the development of a robust and facile synthetic approach to reproducible bottlebrush polymers (Chapter 2). The method was used to produce homologous series of bottlebrush polymers with polynorbornene backbones, which revealed the effect of side-chain and backbone length on the overall conformation in both good and theta solvent conditions (Chapter 3). The side-chain conformation was obtained from a series of SANS experiments and determined to be indistinguishable from the behavior of free linear polymer chains. Using deuterium-labeled bottlebrushes, we were able for the first time to directly observe the backbone conformation of a bottlebrush polymer which showed self-avoiding walk behavior. Secondly, a series of SANS experiments was conducted on a homologous series of Side Group Liquid Crystalline Polymers (SGLCPs) in a perdeuterated small molecule liquid crystal (5CB). Monodomain, aligned, dilute samples of SGLCP-b-PS block copolymers were seen to self-assemble into complex micellar structures with mutually orthogonally oriented anisotropies at different length scales (Chapter 4). Finally, we present the results from the first scattering experiments on a set of fuel-soluble, associating telechelic polymers. We observed the formation of supramolecular aggregates in dilute (\u22640.5wt%) solutions of telechelic polymers and determined that the choice of solvent has a significant effect on the strength of association and the size of the supramolecules (Chapter 5). A method was developed for the direct estimation of supramolecular aggregation number from SANS data. The insight into structure-property relationships obtained from this work will enable the more targeted development of these molecular architectures for their respective applications. " }, { "name": "Radlauer, Madalyn Rachel", "degree": "PhD", "year": "2014", "title": "Bimetallic Olefin Polymerization Catalysis: Mechanisms and Applications of Proximal Effects", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:01232014-115518399", "creators": [ { "name": { "family": "Radlauer", "given": "Madalyn Rachel" }, "id": "Radlauer-Madalyn-Rachel", "display_name": "Radlauer, Madalyn Rachel" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9MQM-7R57", "abstract": "This dissertation covers progress with bimetallic polymerization catalysts. The complexes we have designed were aimed at expanding the capabilities of homogeneous polymerization catalysts by taking advantage of multimetallic effects. Such effects were examined in group 4 and group 10 bimetallic complexes; proximity and steric repulsion were determined to be major factors in the effects observed.
\r\n\r\nChapters 2 and 3 introduce the rigid p-terphenyl dinucleating framework utilized in most of this thesis. The permethylation of the central arene allows for the separation of syn and anti atropisomers of the terphenyl compounds. Kinetic studies were carried out to examine the isomerization of the dinucleating bis(salicylaldimine) ligand precursors. Metallation of the syn and anti bis(salicylaldimine)s using Ni(Me)2(tmeda) and excess pyridine afforded dinickel bisphenoxyiminato complexes with a methyl and a pyridyl ligand on each nickel. The syn and anti atropisomers of the dinickel complexes were structurally characterized and utilized in ethylene and ethylene/\u03b1-olefin polymerizations. Monometallic analogues were also synthesized and tested for polymerization activity. Ethylene polymerizations were performed in the presence of primary, secondary, and tertiary amines \u2013 additives that generally deactivate nickel polymerization catalysts. Inhibition of this deactivation was observed with the syn atropisomer of the bimetallic species, but not with the anti or monometallic analogues. A mechanism was proposed wherein steric repulsion of the substituents on proximal nickel centers disfavors simultaneous ligation of base to both of the metal centers. The bimetallic effect has been explored with respect to size and binding ability of the added base.
\r\n\r\nChapter 4 presents the optimization of the bisphenoxyimine ligand synthesis and synthesis of syn and anti m-terphenyl analogues. Metallation with NiClMe(PMe3)2 yielded phosphine-ligated dinickel complexes, which have been structurally characterized. Ethylene/1-hexene copolymerizations in the presence of amines using Ni(COD)2 as a phosphine scavenger showed significantly improved activity relative to the pyridine-ligated analogues. Incorporation of amino olefins in copolymerizations with ethylene was accomplished, and a mechanism was proposed based on proximal effects. Copolymerization trials with a variety of amino olefins and ethylene/1-hexene/amino olefin terpolymerizations were completed.
\r\n\r\nEarly transition metal complexes based on the rigid p-terphenyl framework were designed with a variety of donor sets (Chapter 5 and Appendix B). Chapter 5 details the use of syn dizirconium di[amine bis(phenolate)] complexes for isoselective 1-hexene and propylene homopolymerizations. Ligand variation and monometallic complexes were studied to determine the origin of tacticity control. A mechanistic proposal was presented based on the symmetry at zirconium and the steric effects of the proximal metal center. Appendix B covers additional studies of bimetallic early transition metal complexes based on the p-terphenyl. Dititanium, dizirconium, and asymmetric complexes with bisphenoxyiminato ligands and derivatives thereof were targeted. Progress toward the synthesis of these complexes is described along with preliminary polymerization data. 1-hexene/diene copolymerizations and attempted polymerizations in the presence of ethers and esters with the syn dizirconium di[amine bis(phenolate)] complexes demonstrate the potential for further applications of this system in catalysis.
\r\n\r\nAppendix A includes work toward palladium catalysts for insertion polymerization of polar monomers. These complexes were based on dioxime and diimine frameworks with the intent of binding Lewis acidic metals at the oxime oxygens, at pendant phenolic donors, or at pendant aminediol moieties. The synthesis and structural characterization of a number of palladium and Lewis acid complexes is presented. Due to the instability of the desired species, efforts toward isolation of the desired complexes proved unsuccessful, though preliminary ethylene/methyl acrylate copolymerizations using in situ activation of the palladium species were attempted.
\r\n\u2003" }, { "name": "Repka, Lindsay Michelle", "degree": "PhD", "year": "2014", "title": "Enantiosclective Synthesis of Pyrroloindolines and Tryptophan Derivatives by an Asvmmetric Protonation Reaction", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192013-205304543", "creators": [ { "name": { "family": "Repka", "given": "Lindsay Michelle" }, "id": "Repka-Lindsay-Michelle", "display_name": "Repka, Lindsay Michelle" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y8MS-J286", "abstract": "Pyrroloindoline and unnatural tryptophan motifs are important targets for synthesis based on their incorporation into a diverse array of biologically active natural products. Both types of alkaloids have also found applications as chiral catalysts and tryptophan derivatives are commonly employed as biological probes. On account of their applications, these frameworks have inspired the development of numerous enantioselective, catalytic reactions. In particular, the past few years have witnessed an impressive number of novel approaches for pyrroloindoline formation.
\r\n\r\nThe first project described herein involves our contribution to pyrroloindoline research. We have developed an (R)-BINOL\u2022SnCl4-catalyzed formal (3 + 2) cycloaddition reaction between 3-substituted indoles and 2-amidoacrylates that affords pyrroloindoline-2-carboxylates bearing an all-carbon quaternary center. Mechanistic studies have elucidated that the enantiodetermining step is a highly face-selective catalyst-controlled protonation reaction.
\r\n\r\nSecond, application of this asymmetric protonation strategy to the synthesis of a variety of enantioenriched tryptophan derivatives is discussed. Finally, we found that these derivatives could undergo selective functionalization. More specifically, we were able to prepare novel hydroxypyrroloindolines that are currently the subject of a collaboration project with the Dougherty lab aimed at identifying novel positive allosteric modulators of ligand-gated ion channels.
\r\n" }, { "name": "Rreza, Iva", "degree": "Senior Thesis", "year": "2014", "title": "Development of Tantalum Phenoxy-Imine Compounds for Selective Ethylene Oligomerization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052014-141223337", "creators": [ { "name": { "family": "Rreza", "given": "Iva" }, "id": "Rreza-Iva", "display_name": "Rreza, Iva" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YDBK-V594", "abstract": "The development of catalysts that selectively oligomerize light olefins for uses in polymers and fuels remains of interest to the petrochemical and materials industry. For this purpose, two tantalum compounds, (FI)TaMe2Cl2 and (FI)TaMe4, implementing a previously reported phenoxy-imine (FI) ligand framework, have been synthesized and characterized with NMR spectroscopy and X-ray crystallography. When tested for ethylene oligomerization catalysis, (FI)TaMe2Cl2 was found to dimerize ethylene when activated with Et2Zn or EtMgCl, and (FI)TaMe4 dimerized ethylene when activated with B(C6F5)3, both at room temperature." }, { "name": "Scott, Caitlin Eileen", "degree": "PhD", "year": "2014", "title": "Role of Conformational Changes in G Protein-Coupled Receptor Activation", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312014-002701930", "creators": [ { "name": { "family": "Scott", "given": "Caitlin Eileen" }, "id": "Scott-Caitlin-Eileen", "display_name": "Scott, Caitlin Eileen" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Abrol", "given": "Ravinder" }, "id": "Abrol-R", "role": "member", "display_name": "Abrol, Ravinder" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94747VG", "abstract": "Transmembrane signal transduction is achieved by activation of G protein-coupled receptors (GPCRs) like the human cannabinoid type 1 (CB1) receptor, the human cannabinoid type 2 (CB2) receptor, and the human mu-opioid receptor. These receptors exist in the membrane in an ensemble of conformations each of which might bind to different signaling molecules and cause different physiological effects. Understanding the structural basis of their activation will eventually help us in designing drugs that target these receptors with potentially minimal undesirable side effects. CB1 is of particular interest because it is located in the central nervous system and modulates hunger, making it an attractive anti-obesity drug target. In this receptor, mutating a single residue, threonine 210, to isoleucine in the third transmembrane (TM3) domain makes it far more active than the wild-type (WT) receptor, whereas mutating it to alanine makes it fully inactive. CB1 is difficult to model because it has a small sequence identity with the receptors that have been crystallized. We used the first principles-based GEnSeMBLE method to predict 3D structures of these receptors representing the fully inactive to highly constitutively active states. With this software, we quickly found a set of low energy receptor conformations by sampling trillions of helix orientations. Differences in the intracellular surface explain experimental differences in activation for the CB1 receptor and its mutants. These predictions were validated by designing double mutants that were expected to switch the inactive T210A to WT levels of activation and expected to switch the very active L207A to T210A levels of activation. These predictions were first verified computationally then experimentally with GTPgammaS assays. The accuracy of our predictions indicate that the GEnSeMBLE method is a useful procedure for predicting GPCR structures at various activation states. Known inverse agonists were docked to these predicted CB1 receptor structures, and the resulting complexes were inserted into a solvated lipid bilayer for 50 ns of NPT molecular dynamics with NAMD software. The inverse agonist preferentially binds to a pre-activated CB1 state, but during MD, traits of the inactive structure start to form suggesting that the ligand induces conformational changes." }, { "name": "Sheng, Gloria J.", "degree": "PhD", "year": "2014", "title": "Tunable Heparan Sulfate Glycomimetics for Modulating Chemokine Activity", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272014-224131184", "creators": [ { "name": { "family": "Sheng", "given": "Gloria J." }, "id": "Sheng-Gloria-J", "display_name": "Sheng, Gloria J." } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JQ2Z-EN67", "abstract": "Heparan sulfate (HS) glycosaminoglycans participate in critical biological processes by modulating the activity of a diverse set of protein binding partners. Such proteins include all known members of the chemokine superfamily, which are thought to guide the migration of distinct subsets of immune cells through their interactions with HS proteoglycans on endothelial cell surfaces. Animal-derived heparin polysaccharides have been shown to reduce inflammation levels through the inhibition of HS-chemokine interactions; however, the clinical usage of heparin as an anti-inflammatory drug is hampered by its anticoagulant activity and potential risk for side effects, such as heparin-induced thrombocytopenia (HIT).
\r\n\r\nHere, we describe an expedient, divergent synthesis to prepare defined glycomimetics of HS that recapitulate the macromolecular structure and biological activity of natural HS glycosaminoglycans. Our synthetic approach uses a core disaccharide precursor to generate a library of four differentially sulfated polymers. We show that a trisulfated glycopolymer antagonizes the chemotactic activities of pro-inflammatory chemokine RANTES with similar potency as heparin polysaccharide, without potentiating the anticoagulant activities of antithrombin III. The same glycopolymer also inhibited the homeostatic chemokine SDF-1 with significantly more efficacy than heparin. Our work offers a general strategy for modulating chemokines and dissecting the pleiotropic functions of HS/heparin through the presentation of defined sulfation motifs within multivalent polymeric scaffolds.
" }, { "name": "Sun, Bing", "degree": "PhD", "year": "2014", "title": "Mechanistic Studies of Reactions at the Single-Molecule Level using Microfluidics with Applications in Molecular Diagnostics", "advisor": "Ismagilov, Rustem", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052014-142031176", "creators": [ { "name": { "family": "Sun", "given": "Bing" }, "id": "Sun-Bing", "display_name": "Sun, Bing" } ], "advisors": [ { "name": { "family": "Ismagilov", "given": "Rustem" }, "id": "Ismagilov-R-F", "role": "advisor", "display_name": "Ismagilov, Rustem" } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BT81-YX06", "abstract": "Motivated by needs in molecular diagnostics and advances in microfabrication, researchers started to seek help from microfluidic technology, as it provides approaches to achieve high throughput, high sensitivity, and high resolution. One strategy applied in microfluidics to fulfill such requirements is to convert continuous analog signal into digitalized signal. One most commonly used example for this conversion is digital PCR, where by counting the number of reacted compartments (triggered by the presence of the target entity) out of the total number of compartments, one could use Poisson statistics to calculate the amount of input target.
\r\n\r\nHowever, there are still problems to be solved and assumptions to be validated before the technology is widely employed. In this dissertation, the digital quantification strategy has been examined from two angles: efficiency and robustness. The former is a critical factor for ensuring the accuracy of absolute quantification methods, and the latter is the premise for such technology to be practically implemented in diagnosis beyond the laboratory. The two angles are further framed into a \u201cfate\u201d and \u201crate\u201d determination scheme, where the influence of different parameters is attributed to fate determination step or rate determination step. In this discussion, microfluidic platforms have been used to understand reaction mechanism at single molecule level. Although the discussion raises more challenges for digital assay development, it brings the problem to the attention of the scientific community for the first time.
\r\n\r\nThis dissertation also contributes towards developing POC test in limited resource settings. On one hand, it adds ease of access to the tests by incorporating massively producible, low cost plastic material and by integrating new features that allow instant result acquisition and result feedback. On the other hand, it explores new isothermal chemistry and new strategies to address important global health concerns such as cyctatin C quantification, HIV/HCV detection and treatment monitoring as well as HCV genotyping.
\r\n" }, { "name": "Sveinbj\u00f6rnsson, Benjam\u00edn Ragnar", "degree": "PhD", "year": "2014", "title": "Self-Assembly of Brush Polymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202014-173643723", "creators": [ { "name": { "family": "Sveinbj\u00f6rnsson", "given": "Benjam\u00edn Ragnar" }, "id": "Sveinbjornsson-Benjam\u00edn-Ragnar", "display_name": "Sveinbj\u00f6rnsson, Benjam\u00edn Ragnar" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9RR1W7W", "abstract": "The unique structure and properties of brush polymers have led to increased interest in them within the scientific community. This thesis describes studies on the self-assembly of these brush polymers.
\r\n\r\nChapter 2 describes a study on the rapid self-assembly of brush block copolymers into nanostructures with photonic bandgaps spanning the entire visible spectrum, from ultraviolet to near infrared. Linear relationships are observed between the peak wavelengths of reflection and polymer molecular weights. This work enables \"bottom-up\" fabrication of photonic crystals with application-tailored bandgaps, through synthetic control of the polymer molecular weight and the method of self-assembly.
\r\n\r\nChapter 3 details the analysis of the self-assembly of symmetrical brush block copolymers in bulk and thin films. Highly ordered lamellae with domain spacing ranging from 20 to 240 nm are obtained by varying molecular weight of the backbone. The relationship between degree of polymerization and the domain spacing is reported, and evidence is provided for how rapidly the brush block copolymers self-assemble and achieve thermodynamic equilibrium.
\r\n\r\nChapter 4 describes investigations into where morphology transitions take place as the volume fraction of each block is varied in asymmetrical brush block copolymers. Imaging techniques are used to observe a transition from lamellar to a cylindrical morphology as the volume fraction of one of the blocks exceeds 70%. It is also shown that the asymmetric brush block copolymers can be kinetically trapped into undulating lamellar structures by drop casting the samples.
\r\n\r\nChapter 5 explores the capability of macromolecules to interdigitate into densely grafted molecular brush copolymers using stereocomplex formation as a driving force. The stereocomplex formation between complementary linear polymers and brush copolymers is demonstrated, while the stereocomplex formation between complementary brush copolymers is shown to be restricted.
" }, { "name": "Tan, Frederick Eng How", "degree": "PhD", "year": "2014", "title": "Brfl Post-Transcriptionally Regulates Pluripotency and Differentiation Responses Downstream of Erk MAP Kinase", "advisor": "Elowitz, Michael B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292014-234047875", "creators": [ { "name": { "family": "Tan", "given": "Frederick Eng How" }, "id": "Tan-Frederick-Eng-How", "display_name": "Tan, Frederick Eng How" } ], "advisors": [ { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "advisor", "display_name": "Elowitz, Michael B." } ], "committee": [ { "name": { "family": "Stathopoulos", "given": "Angelike" }, "id": "Stathopoulos-A", "role": "chair", "display_name": "Stathopoulos, Angelike" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Plath", "given": "Kathrin" }, "id": "Plath-K", "role": "member", "display_name": "Plath, Kathrin" }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "member", "display_name": "Elowitz, Michael B." } ], "option_major": [ "biochem" ], "doi": "10.7907/MM53-XC23", "abstract": "FGF/Erk MAP Kinase Signaling is a central regulator of mouse embryonic stem cell (mESC) self-renewal, pluripotency and differentiation. However, the mechanistic connection between this signaling pathway activity and the gene circuits stabilizing mESCs in vitro remain unclear. Here we show that FGF signaling post-transcriptionally regulates the mESC transcription factor network by controlling the expression of Brf1 (zfp36l1), an AU-rich element mRNA binding protein. Changes in Brf1 level disrupts the expression of core pluripotency-associated genes and attenuates mESC self-renewal without inducing differentiation. These regulatory effects are mediated by rapid and direct destabilization of Brf1 targets, such as Nanog mRNA. Interestingly, enhancing Brf1 expression does not compromise mESC pluripotency, but does preferentially regulate differentiation to mesendoderm by accelerating the expression of primitive streak markers. Together, these studies demonstrate that FGF signals utilize targeted mRNA degradation by Brf1 to enable rapid post-transcriptional control of gene expression." }, { "name": "Tsui, Emily Yuan", "degree": "PhD", "year": "2014", "title": "Transition Metal Clusters Supported by Multinucleating Ligand Frameworks as Models of Biological Active Sites", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302014-134133118", "creators": [ { "name": { "family": "Tsui", "given": "Emily Yuan" }, "id": "Tsui-Emily-Yuan", "orcid": "0000-0001-6419-3954", "display_name": "Tsui, Emily Yuan" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CWJ4-QQ41", "abstract": "This dissertation describes efforts to model biological active sites with small molecule clusters. The approach used took advantage of a multinucleating ligand to control the structure and nuclearity of the product complexes, allowing the study of many different homo- and heterometallic clusters. Chapter 2 describes the synthesis of the multinucleating hexapyridyl trialkoxy ligand used throughout this thesis and the synthesis of trinuclear first row transition metal complexes supported by this framework, with an emphasis on tricopper systems as models of biological multicopper oxidases. The magnetic susceptibility of these complexes were studied, and a linear relation was found between the Cu-O(alkoxide)-Cu angles and the antiferromagnetic coupling between copper centers. The triiron(II) and trizinc(II) complexes of the ligand were also isolated and structurally characterized.
\r\n\r\nChapter 3 describes the synthesis of a series of heterometallic tetranuclear manganese dioxido complexes with various incorporated apical redox-inactive metal cations (M = Na+, Ca2+, Sr2+, Zn2+, Y3+). Chapter 4 presents the synthesis of heterometallic trimanganese(IV) tetraoxido complexes structurally related to the CaMn3 subsite of the oxygen-evolving complex (OEC) of Photosystem II. The reduction potentials of these complexes were studied, and it was found that each isostructural series displays a linear correlation between the reduction potentials and the Lewis acidities of the incorporated redox-inactive metals. The slopes of the plotted lines for both the dioxido and tetraoxido clusters are the same, suggesting a more general relationship between the electrochemical potentials of heterometallic manganese oxido clusters and their \"spectator\" cations. Additionally, these studies suggest that Ca2+ plays a role in modulating the redox potential of the OEC for water oxidation.
\r\n\r\nChapter 5 presents studies of the effects of the redox-inactive metals on the reactivities of the heterometallic manganese complexes discussed in Chapters 3 and 4. Oxygen atom transfer from the clusters to phosphines is studied; although the reactivity is kinetically controlled in the tetraoxido clusters, the dioxido clusters with more Lewis acidic metal ions (Y3+ vs. Ca2+) appear to be more reactive. Investigations of hydrogen atom transfer and electron transfer rates are also discussed.
\r\n\r\nAppendix A describes the synthesis, and metallation reactions of a new dinucleating bis(N-heterocyclic carbene)ligand framework. Dicopper(I) and dicobalt(II) complexes of this ligand were prepared and structurally characterized. A dinickel(I) dichloride complex was synthesized, reduced, and found to activate carbon dioxide. Appendix B describes preliminary efforts to desymmetrize the manganese oxido clusters via functionalization of the basal multinucleating ligand used in the preceding sections of this dissertation. Finally, Appendix C presents some partially characterized side products and unexpected structures that were isolated throughout the course of these studies.
\r\n" }, { "name": "Van Arnam, Ethan Buggie", "degree": "PhD", "year": "2014", "title": "Chemical-Scale Studies of G Protein-Coupled Receptors and Ligand-Gated Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182014-130629055", "creators": [ { "name": { "family": "Van Arnam", "given": "Ethan Buggie" }, "id": "Van-Arnam-Ethan-Buggie", "display_name": "Van Arnam, Ethan Buggie" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0XEB-8013", "abstract": "This dissertation describes studies of G protein-coupled receptors (GPCRs) and ligand-gated ion channels (LGICs) using unnatural amino acid mutagenesis to gain high precision insights into the function of these important membrane proteins.
\r\n \r\nChapter 2 considers the functional role of highly conserved proline residues within the transmembrane helices of the D2 dopamine GPCR. Through mutagenesis employing unnatural \u03b1-hydroxy acids, proline analogs, and N-methyl amino acids, we find that lack of backbone hydrogen bond donor ability is important to proline function. At one proline site we additionally find that a substituent on the proline backbone N is important to receptor function.
\r\n \r\nIn Chapter 3, side chain conformation is probed by mutagenesis of GPCRs and the muscle-type nAChR. Specific side chain rearrangements of highly conserved residues have been proposed to accompany activation of these receptors. These rearrangements were probed using conformationally-biased \u03b2-substituted analogs of Trp and Phe and unnatural stereoisomers of Thr and Ile. We also modeled the conformational bias of the unnatural Trp and Phe analogs employed.
\r\n \r\nChapters 4 and 5 examine details of ligand binding to nAChRs. Chapter 4 describes a study investigating the importance of hydrogen bonds between ligands and the complementary face of muscle-type and \u03b14\u03b24 nAChRs. A hydrogen bond involving the agonist appears to be important for ligand binding in the muscle-type receptor but not the \u03b14\u03b24 receptor.
\r\n \r\nChapter 5 describes a study characterizing the binding of varenicline, an actively prescribed smoking cessation therapeutic, to the \u03b17 nAChR. Additionally, binding interactions to the complementary face of the \u03b17 binding site were examined for a small panel of agonists. We identified side chains important for binding large agonists such as varenicline, but dispensable for binding the small agonist ACh.
\r\n \r\nChapter 6 describes efforts to image nAChRs site-specifically modified with a fluorophore by unnatural amino acid mutagenesis. While progress was hampered by high levels of fluorescent background, improvements to sample preparation and alternative strategies for fluorophore incorporation are described.
\r\n \r\nChapter 7 describes efforts toward a fluorescence assay for G protein association with a GPCR, with the ultimate goal of probing key protein-protein interactions along the G protein/receptor interface. A wide range of fluorescent protein fusions were generated, expressed in Xenopus oocytes, and evaluated for their ability to associate with each other.
\r\n" }, { "name": "Varghese, Joseph O.", "degree": "PhD", "year": "2014", "title": "Scanning Probe Studies of Thin Films", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202014-111613067", "creators": [ { "name": { "family": "Varghese", "given": "Joseph O." }, "id": "Varghese-Joseph-O", "display_name": "Varghese, Joseph O." } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z95B00DK", "abstract": "The first part of this thesis deals with the phenomenon of thermoelectricity. It involves the improvement of the thermoelectric properties of silicon using innovative nanostructures. My contribution was to help fabricate these thermoelectric devices, and is the focus of this part of the thesis.
\r\n\r\nThe second part and primary focus of this thesis is the analysis of thin films using scanning probe techniques. These surface techniques include atomic force microscopy, electric force microscopy, Kelvin probe force microscopy, and scanning tunneling microscopy. The thin films studied are graphene and molybdenum disulfide, two remarkable materials that display unique two-dimensional qualities. These materials are shown to be useful in studying the properties of adsorbates trapped between them and the substrate on which they rest. Moreover, these adsorbed species are seen to affect the structural and electronic properties of the thin films themselves. Scanning probe analyses are particularly useful in elucidating the properties of these materials, as surface effects play a significant role in determining their characteristics.
\r\n\r\nThe final part of this thesis is concerned with the study of Akt in live cells using protein capture agents previously developed by my colleagues. The activation and degradation of Akt is investigated using various biological assays, including Western blots, in vitro kinase assays, and cell viability assays. Finally, the usefulness of synthetic capture agents in perturbing protein pathways and as delivery agents is assessed and analyzed.
\r\n" }, { "name": "Vowles, James Vincent", "degree": "PhD", "year": "2014", "title": "Cell-Targeted Regulation of Gene Expression through Synthetic RNA Devices", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152014-153300531", "creators": [ { "name": { "family": "Vowles", "given": "James Vincent" }, "id": "Vowles-James-Vincent", "display_name": "Vowles, James Vincent" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XE3K-QA07", "abstract": "The ability to interface with and program cellular function remains a challenging research frontier in biotechnology. Although the emerging field of synthetic biology has recently generated a variety of gene-regulatory strategies based on synthetic RNA molecules, few strategies exist through which to control such regulatory effects in response to specific exogenous or endogenous molecular signals. Here, we present the development of an engineered RNA-based device platform to detect and act on endogenous protein signals, linking these signals to the regulation of genes and thus cellular function.
\r\n\r\nWe describe efforts to develop an RNA-based device framework for regulating endogenous genes in human cells. Previously developed RNA control devices have demonstrated programmable ligand-responsive genetic regulation in diverse cell types, and we attempted to adapt this class of cis-acting control elements to function in trans. We divided the device into two strands that reconstitute activity upon hybridization. Device function was optimized using an in vivo model system, and we found that device sequence is not as flexible as previously reported. After verifying the in vitro activity of our optimized design, we attempted to establish gene regulation in a human cell line using additional elements to direct device stability, structure, and localization. The significant limitations of our platform prevented endogenous gene regulation.
\r\n\r\nWe next describe the development of a protein-responsive RNA-based regulatory platform. Employing various design strategies, we demonstrated functional devices that both up- and downregulate gene expression in response to a heterologous protein in a human cell line. The activity of our platform exceeded that of a similar, small-molecule-responsive platform. We demonstrated the ability of our devices to respond to both cytoplasmic- and nuclear-localized protein, providing insight into the mechanism of action and distinguishing our platform from previously described devices with more restrictive ligand localization requirements. Finally, we demonstrated the versatility of our device platform by developing a regulatory device that responds to an endogenous signaling protein.
\r\n\r\nThe foundational tool we present here possesses unique advantages over previously described RNA-based gene-regulatory platforms. This genetically encoded technology may find future applications in the development of more effective diagnostic tools and targeted molecular therapy strategies.
" }, { "name": "Wei, Ming-Hsin", "degree": "PhD", "year": "2014", "title": "Synthesis and Potency of Long End-Associative Polymers for Mist Control", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192013-181502465", "creators": [ { "name": { "family": "Wei", "given": "Ming-Hsin" }, "id": "Wei-Ming-Hsin", "display_name": "Wei, Ming-Hsin" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Sarohia", "given": "Virendra" }, "id": "Sarohia-V", "role": "member", "display_name": "Sarohia, Virendra" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z91834FW", "abstract": "Long linear polymers that are end-functionalized with associative groups were studied as additives to hydrocarbon fluids to mitigate the fire hazard associated with the presence of mist in a crash scenario. These polymers were molecularly designed to overcome both the shear-degradation of long polymer chains in turbulent flows, and the chain collapse induced by the random placement of associative groups along polymer backbones. Architectures of associative groups on the polymer chain ends that were tested included clusters of self-associative carboxyl groups and pairs of hetero-complementary associative units.
\r\n\r\nLinear polymers with clusters of discrete numbers of carboxyl groups on their chain ends were investigated first: an innovative synthetic strategy was devised to achieve unprecedented backbone lengths and precise control of the number of carboxyl groups on chain ends (N). We found that a very narrow range of N allows the co-existence of sufficient end-association strength and polymer solubility in apolar media. Subsequent steady-flow rheological study on solution behavior of such soluble polymers in apolar media revealed that the end-association of very long chains in apolar media leads to the formation of flower-like micelles interconnected by bridging chains, which trap significant fraction of polymer chains into looped structures with low contribution to mist-control. The efficacy of very long 1,4-polybutadiene chains end-functionalized with clusters of four carboxyl groups as mist-control additives for jet fuel was further tested. In addition to being shear-resistant, the polymer was found capable of providing fire-protection to jet fuel at concentrations as low as 0.3wt%. We also found that this polymer has excellent solubility in jet fuel over a wide range of temperature (-30 to +70\u00b0C) and negligible interference with dewatering of jet fuel. It does not cause an adverse increase in viscosity at concentrations where mist-control efficacy exists.
\r\n\r\nFour pairs of hetero-complementary associative end-groups of varying strengths were subsequently investigated, in the hopes of achieving supramolecular aggregates with both mist-control ability and better utilization of polymer building blocks. Rheological study of solutions of the corresponding complementary associative polymer pairs in apolar media revealed the strength of complementary end-association required to achieve supramolecular aggregates capable of modulating rheological properties of the solution.
\r\n\r\nBoth self-associating and complementary associating polymers have therefore been found to resist shear degradation. The successful strategy of building soluble, end-associative polymers with either self-associative or complementary associative groups will guide the next generation of mist-control technology.
" }, { "name": "Wiggenhorn, David Craig", "degree": "PhD", "year": "2014", "title": "Nanostructured Tungsten Trioxide Photoanodes for Solar Energy Conversion", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102014-204136086", "creators": [ { "name": { "family": "Wiggenhorn", "given": "David Craig" }, "id": "Wiggenhorn-David-Craig", "display_name": "Wiggenhorn, David Craig" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0CKV-SM88", "abstract": "Nanostructured tungsten trioxide (WO3) photoelectrodes are potential candidates for the anodic portion of an integrated solar water-splitting device that generates hydrogen fuel and oxygen from water. These nanostructured materials can potentially offer improved performance in photooxidation reactions compared to unstructured materials because of enhancements in light scattering, increases in surface area, and their decoupling of the directions of light absorption and carrier collection. To evaluate the presence of these effects and their contributions toward energy conversion efficiency, a variety of nanostructured WO3 photoanodes were synthesized by electrodeposition within nanoporous templates and by anodization of tungsten foils. A robust fabrication process was developed for the creation of oriented WO3 nanorod arrays, which allows for control nanorod diameter and length. Films of nanostructured WO3 platelets were grown via anodization, the morphology of the films was controlled by the anodization conditions, and the current-voltage performance and spectral response properties of these films were studied. The observed photocurrents were consistent with the apparent morphologies of the nanostructured arrays. Measurements of electrochemically active surface area and other physical characteristics were correlated with observed differences in absorbance, external quantum yield, and photocurrent density for the anodized arrays. The capability to quantify these characteristics and relate them to photoanode performance metrics can allow for selection of appropriate structural parameters when designing photoanodes for solar energy conversion." }, { "name": "Yang, Fei", "degree": "PhD", "year": "2014", "title": "Antitumor Activity of Py-lm Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302013-124522822", "creators": [ { "name": { "family": "Yang", "given": "Fei" }, "id": "Yang-Fei", "display_name": "Yang, Fei" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VCN2-H580", "abstract": "Molecules that inhibit DNA dependent processes are the most commonly used agents for the treatment of cancer. The genotoxicity associated with their mechanisms of action, unfortunately, make them extremely toxic to the patient and cancer cells alike. The work presented in this thesis outlines the development of Py-Im polyamides as non-genotoxic DNA-targeted antitumor molecules that interfere with RNA polymerase II elongation. We initially characterized the pharmacokinetic profiles of two hairpin polyamides to establish their bioavailability in the serum and tissues after a single administration. We next determined the molecular mechanism that contributes to toxicity of a hairpin polyamide in human prostate cancer cells in cell culture and we demonstrated antitumor effects of the compound against LNCaP xenografts in mice. Finally, we conducted animal toxicity experiments on 4 polyamides that vary on the gamma-turn with respect to the substitution of amino and acetamide groups at the alpha and beta positions. From this study we identified a second generation compound that retains antitumor activity with significantly reduce animal toxicity. This work sets the foundation for the development of Py-Im polyamides as DNA targeted therapeutics for the treatment of advanced prostate cancer." }, { "name": "Yeoman, John Thomas Schafer", "degree": "PhD", "year": "2014", "title": "A Unified Strategy to Ent-Kauranoid Natural Products: Total Syntheses of (-)-Maoecrystal Z, (-)-Trichorabdal A, and (-)-Longikaurin E", "advisor": "Reisman, Sarah E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252014-222127174", "creators": [ { "name": { "family": "Yeoman", "given": "John Thomas Schafer" }, "id": "Yeoman-John-Thomas-Schafer", "display_name": "Yeoman, John Thomas Schafer" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5TDN-7M11", "abstract": "The diterpenoid constituents of the Isodon plants have attracted reasearchers interested in both their chemical structures and biological properties for more than a half-century. In recent years, the isolations of new members displaying previously unprecedented ring systems and highly selective biological properties have piqued interest from the synthetic community in this class of natural products.
\r\n\r\nReported herein is the first total synthesis of such a recently isolated diterpenoid, (\u2013)-maoecrystal Z. The principal transformations implemented in this synthesis include two highly diastereoselective radical cyclization reactions: a Sm(II)-mediated reductive cascade cyclization, which forms two rings and establishes four new stereocenters in a single step, and a Ti(III)-mediated reductive epoxide-acrylate coupling that yields a functionalized spirolactone product, which forms a core bicycle of maoecrystal Z.
\r\n\r\nThe preparation of two additional ent-kauranoid natural products, (\u2013)-trichorabdal A and (\u2013)-longikaurin E, is also described from a derivative of this key spirolactone. These syntheses are additionally enabled by the palladium-mediated oxidative cyclization reaction of a silyl ketene acetal precursor that is used to install the bridgehead all-carbon quaternary stereocenter and bicyclo[3.2.1]octane present in each natural product. These studies have established a synthetic relationship among three architecturally distinct ent-kaurane diterpenoids and have forged a path for the preparation of interesting unnatural ent-kauranoid structural analogs for more thorough biological study.
" }, { "name": "Abrecht, David Gregory", "degree": "PhD", "year": "2013", "title": "Thermodynamic Properties of Organometallic Dihydrogen Complexes for Hydrogen Storage Applications", "advisor": "Fultz, Brent T.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102012-132511810", "creators": [ { "name": { "family": "Abrecht", "given": "David Gregory" }, "id": "Abrecht-David-Gregory", "display_name": "Abrecht, David Gregory" } ], "advisors": [ { "name": { "family": "Fultz", "given": "Brent T." }, "id": "Fultz-B-T", "role": "advisor", "display_name": "Fultz, Brent T." } ], "committee": [ { "name": { "family": "Fultz", "given": "Brent T." }, "id": "Fultz-B-T", "role": "chair", "display_name": "Fultz, Brent T." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/z9057cvb", "abstract": "The mechanism and thermodynamic properties of hydrogen binding to the solid-state complexes [M(CO)dppe2][BArF24] (M = Mn, Re, Tc) and [M'Hdppe2][NTf2] (M' = Fe, Ru, Os) were investigated experimentally and computationally over the temperature range 298K-373K and pressure range 0-2800 torr, based on the Sieverts method. The bulk absorption behavior was found to be accurately described by Langmuir isotherms. Enthalpy and entropy values of ΔH° = -52.2 kJ/mol and ΔS° = -99.6 J/mol-K were obtained experimentally for hydrogen absorption onto [Mn(CO)dppe2][BArF24] from the Langmuir equilibrium constant, and values obtained from electronic structure calculations using the LANL2DZ-ECP basis set were found to successfully reproduce both the pressure-temperature-composition behavior and the thermodynamic values to within 5% of those obtained through experiment. Results from simulations for all complexes yielded large enthalpy values similar to metal hydride formation enthalpies for all complexes studied, and the substitution of the metal center reproduced qualitative binding strength trends of 5d>3d>4d consistent with those previously reported for the group 6 metals.
\r\n\r\nX-ray diffraction patterns and Mössbauer spectra were taken to determine the thermal decomposition pathway for [FeH(η2-H2)dppe2][NTf2]. Simulations at the B3LYP/TZVP level of theory and experimental Mössbauer spectra confirmed the direct thermal decomposition from singlet-state [FeH(η2-H2)dppe2][NTf2] to triplet-state [FeHdppe2][NTf2] under vacuum conditions at 398K. Evaluation of the partial quadrupole splitting values of Q(H2) = -0.245 mm/s from Mössbauer spectroscopy significantly differ from typical values obtained for hydrides, indicating an underutilized mechanism for identification of dihydrogen ligands. Singlet-state thermodynamic values from simulation were consistent with experimental observations for Ru and Os, and ruthenium complexes were found to have thermodynamic properties within appropriate ranges for hydrogen storage applications. Simulated thermodynamic values for Fe complexes were found to significantly underestimate experimental behavior, demonstrating the importance of the magnetic spin state of the molecule to hydrogen binding properties.
" }, { "name": "Bennett, Nathan Bruce", "degree": "PhD", "year": "2013", "title": "Palladium-Catalyzed Asymmetric Allylic Alkylation: Insights, Application Toward Cyclopentanoid and Cycloheptanoid Molecules, and the Total Synthesis of Several Daucane Sesquiterpenes ", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102013-121027424", "creators": [ { "name": { "family": "Bennett", "given": "Nathan Bruce" }, "id": "Bennett-Nathan-Bruce", "display_name": "Bennett, Nathan Bruce" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Fu", "given": "Gregory C." }, "id": "Fu-G-C", "role": "member", "display_name": "Fu, Gregory C." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZP3K-A474", "abstract": "The asymmetric construction of quaternary stereocenters is a topic of great interest in the organic chemistry community given their prevalence in natural products and biologically active molecules. Over the last decade, the Stoltz group has pursued the synthesis of this challenging motif via a palladium-catalyzed allylic alkylation using chiral phosphinooxazoline (PHOX) ligands. Recent results indicate that the alkylation of lactams and imides consistently proceeds with enantioselectivities substantially higher than any other substrate class previously examined in this system. This observation prompted exploration of the characteristics that distinguish these molecules as superior alkylation substrates, resulting in newfound insights and marked improvements in the allylic alkylation of carbocyclic compounds.
\r\n\r\nGeneral routes to cyclopentanoid and cycloheptanoid core structures have been developed that incorporate the palladium-catalyzed allylic alkylation as a key transformation. The unique reactivity of \u03b1-quaternary vinylogous esters upon addition of hydride or organometallic reagents enables divergent access to \u03b3-quaternary acylcyclopentenes or cycloheptenones through respective ring contraction or carbonyl transposition pathways. Derivatization of the resulting molecules provides a series of mono-, bi-, and tricyclic systems that can serve as valuable intermediates for the total synthesis of complex natural products.
\r\n\r\nThe allylic alkylation and ring contraction methodology has been employed to prepare variably functionalized bicyclo[5.3.0]decane molecules and enables the enantioselective total syntheses of daucene, daucenal, epoxydaucenal B, and 14-p-anisoyloxydauc-4,8-diene. This route overcomes the challenge of accessing \u03b2-substituted acylcyclopentenes by employing a siloxyenone to effect the Grignard addition and ring opening in a single step. Subsequent ring-closing metathesis and aldol reactions form the hydroazulene core of these targets. Derivatization of a key enone intermediate allows access to either the daucane sesquiterpene or sphenobolane diterpene carbon skeletons, as well as other oxygenated scaffolds.
\r\n" }, { "name": "Bhawe, Yashodhan", "degree": "PhD", "year": "2013", "title": "I: Solid Materials for Low Temperature Thermochemical Water Splitting. II: Structure-Property Relationships on the Zeolite Catalyzed Conversion of Methanol to Light Olefins", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11282012-141927745", "creators": [ { "name": { "family": "Bhawe", "given": "Yashodhan" }, "id": "Bhawe-Yashodhan", "display_name": "Bhawe, Yashodhan" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/05FG-JG39", "abstract": "This thesis describes two separate projects. The first part of the thesis involves the synthesis of materials for enabling thermochemical water splitting at temperatures below 1000\u00baC, while the second part focuses on the structure-property relationships for the catalytic conversion of methanol-to-olefins.
\r\n\r\nIn the first project, metal oxide clusters are impregnated in a silica support and tested as catalysts for the thermochemical splitting of water at temperatures below 1000\u00baC. These supported catalysts are able to do either the oxidation or reduction half cycle, but not both. Thermodynamic analyses reveal that for most common metal / metal oxide pairs, a thermochemical water splitting cycle can not occur in two steps below 1000\u00baC. Thus, a multi-step thermochemical cycle is developed using Mn3O4 and Na2CO3. This new cycle can be closed at temperatures that do not exceed 850\u00baC. Additionally, three metal spinels (Mn, Fe and Co based) are investigated with three alkali metal carbonates (Li, Na and K) for both thermochemical water splitting and thermochemical CO2 reduction. The manganese, sodium system is found to be the optimal combination for water splitting.
\r\n\r\nThe second project explores the effects that zeolite structure has on the product selectivity in the methanol-to-olefins (MTO) reaction. After first ensuring that literature results on the more common MTO catalysts could be reproduced, the effects of several zeolite structure features on product selectivity are elucidated. Structural features such as channel width and channel eccentricity, cage size (tested on the LEV, CHA and AFX frameworks) and framework composition (tested on the LEV, AEI, CHA and AFX frameworks) are explored. It is found that the product selectivity does not have a strong correlation with channel width and eccentricity. Ethylene selectivity did increase with a reduction in cage size, while propylene selectivity is a maximum with the CHA cage. The most consistent theme noted is that between the aluminosilicates (zeolites) and the silicoaluminophosphates (SAPOs), the effect of temperature on the C3=/C2= is the same (if the aluminosilicate shows an increase in C3=/C2= with an increase in temperature, so does the silicoaluminophosphate, etc.).
" }, { "name": "Boekelheide, Nicholas", "degree": "PhD", "year": "2013", "title": "Quantum Simulation of Enzyme Catalysis", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102013-024419372", "creators": [ { "name": { "family": "Boekelheide", "given": "Nicholas" }, "id": "Boekelheide-Nicholas", "display_name": "Boekelheide, Nicholas" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/A27J-Q614", "abstract": "Separating the dynamics of variables that evolve on different timescales is a common assumption in exploring complex systems, and a great deal of progress has been made in understanding chemical systems by treating independently the fast processes of an activated chemical species from the slower processes that proceed activation. Protein motion underlies all biocatalytic reactions, and understanding the nature of this motion is central to understanding how enzymes catalyze reactions with such specificity and such rate enhancement. This understanding is challenged by evidence of breakdowns in the separability of timescales of dynamics in the active site form motions of the solvating protein. Quantum simulation methods that bridge these timescales by simultaneously evolving quantum and classical degrees of freedom provide an important method on which to explore this breakdown. In the following dissertation, three problems of enzyme catalysis are explored through quantum simulation. " }, { "name": "Chartron, Justin William", "degree": "PhD", "year": "2013", "title": "The Structure of a Transmembrane Protein Sorting Complex", "advisor": "Clemons, William M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10012012-155636249", "creators": [ { "name": { "family": "Chartron", "given": "Justin William" }, "id": "Chartron-Justin-William", "display_name": "Chartron, Justin William" } ], "advisors": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "advisor", "display_name": "Clemons, William M." } ], "committee": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "chair", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "biochem" ], "doi": "10.7907/QVCV-8A76", "abstract": "The biogenesis of membrane proteins is an essential process in biology. It requires the protection of hydrophobic transmembrane domains from aggregation in the cytosol as well as targeting to the proper membrane. Tail-anchored (TA) proteins have a single transmembrane helix near their carboxyl termini and require a post-translational mechanism for targeting and insertion. In yeast, the Guided Entry of Tail-anchored proteins (GET) pathway delivers TA proteins to the endoplasmic reticulum (ER). A sorting complex comprising Get4, Get5, and Sgt2 load ER destined TA proteins onto the targeting factor Get3. X-ray crystallography, solution NMR, and small angle X-ray scattering were used to characterize this assembly. Get4 and Get5 form an extended adapter complex. Get4 maintains Get3 in a state competent to receive TA proteins. The N-terminus of Get5 tightly binds Get4, while the C-terminus of Get5 is a homodimerization domain, resulting in a heterotetrameric assembly. A ubiquitin-like domain within Get5 binds the heat-shock protein (HSP) co-chaperone Sgt2, providing a physical link between ER destined TA protein targeting and protein folding pathways. Sgt2 is also an extended homodimeric complex, and can directly bind four major classes of HSPs. The Get4/Get5/Sgt2 sorting complex is multivalent, flexible and the binding of individual components is transient. These results build a model for post-translational protein targeting in eukaryotes that is distinct from other pathways." }, { "name": "Coelho, Pedro de Souza Le\u00e3o", "degree": "PhD", "year": "2013", "title": "Olefin Cyclopropanation and Carbon-Hydrogen Amination via Carbene and Nitrene Transfers Catalyzed by Engineered Cytochrome P450 Enzymes", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072013-230318757", "creators": [ { "name": { "family": "Coelho", "given": "Pedro de Souza Le\u00e3o" }, "id": "Coelho-Pedro-de-Souza-Le\u00e3o", "display_name": "Coelho, Pedro de Souza Le\u00e3o" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HSPH-AF89", "abstract": "Synthetic biology promises to transform organic synthesis by enabling artificial catalysis in living cells. I start by reviewing the state of the art in this young field and recognizing that new approaches are required for designing enzymes that catalyze nonnatural reactions, in order to expand the scope of biocatalytic transformations. Carbene and nitrene transfers to C=C and C-H bonds are reactions of tremendous synthetic utility that lack biological counterparts. I show that various heme proteins, including cytochrome P450BM3, will catalyze promiscuous levels of olefin cyclopropanation when provided with the appropriate synthetic reagents (e.g., diazoesters and styrene). Only a few amino acid substitutions are required to install synthetically useful levels of stereoselective cyclopropanation activity in P450BM3. Understanding that the ferrous-heme is the active species for catalysis and that the artificial reagents are unable to induce a spin-shift-dependent increase in the redox potential of the ferric P450, I design a high-potential serine-heme ligated P450 (P411) that can efficiently catalyze cyclopropanation using NAD(P)H. Intact E. coli whole-cells expressing P411 are highly efficient asymmetric catalysts for olefin cyclopropanation. I also show that engineered P450s can catalyze intramolecular amination of benzylic C-H bonds from arylsulfonyl azides. Finally, I review other examples of where synthetic reagents have been used to drive the evolution of novel enzymatic activity in the environment and in the laboratory. I invoke preadaptation to explain these observations and propose that other man-invented reactions may also be transferrable to natural enzymes by using a mechanism-based approach for choosing the enzymes and the reagents. Overall, this work shows that existing enzymes can be readily adapted for catalysis of synthetically important reactions not previously observed in nature." }, { "name": "Craven, Jill Suzanne", "degree": "PhD", "year": "2013", "title": "Studies of Ambient and Chamber Aerosol Composition Using the Aerosol Mass Spectrometer", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112013-190107672", "creators": [ { "name": { "family": "Craven", "given": "Jill Suzanne" }, "id": "Craven-Jill-Suzanne", "display_name": "Craven, Jill Suzanne" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/J69H-EK18", "abstract": "This thesis presents composition measurements for atmospherically relevant inorganic and organic aerosol from laboratory and ambient measurements using the Aerodyne aerosol mass spectrometer. Studies include the oxidation of dodecane in the Caltech environmental chambers, and several aircraft- and ground-based field studies, which include the quantification of wildfire emissions off the coast of California, and Los Angeles urban emissions.
\r\n\r\nThe oxidation of dodecane by OH under low NO conditions and the formation of secondary organic aerosol (SOA) was explored using a gas-phase chemical model, gas-phase CIMS measurements, and high molecular weight ion traces from particle- phase HR-TOF-AMS mass spectra. The combination of these measurements support the hypothesis that particle-phase chemistry leading to peroxyhemiacetal formation is important. Positive matrix factorization (PMF) was applied to the AMS mass spectra which revealed three factors representing a combination of gas-particle partitioning, chemical conversion in the aerosol, and wall deposition.
\r\n\r\nAirborne measurements of biomass burning emissions from a chaparral fire on the central Californian coast were carried out in November 2009. Physical and chemical changes were reported for smoke ages 0 \u2013 4 h old. CO2 normalized ammonium, nitrate, and sulfate increased, whereas the normalized OA decreased sharply in the first 1.5 - 2 h, and then slowly increased for the remaining 2 h (net decrease in normalized OA). Comparison to wildfire samples from the Yucatan revealed that factors such as relative humidity, incident UV radiation, age of smoke, and concentration of emissions are important for wildfire evolution.
\r\n\r\nGround-based aerosol composition is reported for Pasadena, CA during the summer of 2009. The OA component, which dominated the submicron aerosol mass, was deconvolved into hydrocarbon-like organic aerosol (HOA), semi-volatile oxidized organic aerosol (SVOOA), and low-volatility oxidized organic aerosol (LVOOA). The HOA/OA was only 0.08\u20130.23, indicating that most of Pasadena OA in the summer months is dominated by oxidized OA resulting from transported emissions that have undergone photochemistry and/or moisture-influenced processing, as apposed to only primary organic aerosol emissions. Airborne measurements and model predictions of aerosol composition are reported for the 2010 CalNex field campaign.
" }, { "name": "D'Espaux, Leopold Daniel", "degree": "PhD", "year": "2013", "title": "Synthetic Regulation of Eukaryotic Gene Expression by Noncoding RNA", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-121826969", "creators": [ { "name": { "family": "D'Espaux", "given": "Leopold Daniel" }, "id": "D'Espaux-Leopold-Daniel", "display_name": "D'Espaux, Leopold Daniel" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Hay", "given": "Bruce A." }, "id": "Hay-B-A", "role": "member", "display_name": "Hay, Bruce A." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9CR5RBP", "abstract": "Synthetic biological systems promise to combine the spectacular diversity of biological functionality with engineering principles to design new life to address many pressing needs. As these engineered systems advance in sophistication, there is ever-greater need for customizable, situation-specific expression of desired genes. However, existing gene control platforms are generally not modular, or do not display performance requirements required for robust phenotypic responses to input signals. This work expands the capabilities of eukaryotic gene control in two important directions.
\r\n\r\nFor development of greater modularity, we extend the use of synthetic self-cleaving ribozyme switches to detect changes in input protein levels and convey that information into programmed gene expression in eukaryotic cells. We demonstrate both up- and down-regulation of levels of an output transgene by more than 4-fold in response to rising input protein levels, with maximal output gene expression approaching the highest levels observed in yeast. In vitro experiments demonstrate protein-dependent ribozyme activity modulation. We further demonstrate the platform in mammalian cells. Our switch devices do not depend on special input protein activity, and can be tailored to respond to any input protein to which a suitable RNA aptamer can be developed. This platform can potentially be employed to regulate the expression of any transgene or any endogenous gene by 3\u2019 UTR replacement, allowing for more complex cell state-specific reprogramming.
\r\n\r\nWe also address an important concern with ribozyme switches, and riboswitch performance in general, their dynamic range. While riboswitches have generally allowed for versatile and modular regulation, so far their dynamic ranges of output gene modulation have been modest, generally at most 10-fold. We address this shortcoming by developing a modular genetic amplifier for near-digital control of eukaryotic gene expression. We combine ribozyme switch-mediated regulation of a synthetic TF with TF-mediated regulation of an output gene. The amplifier platform allows for as much as 20-fold regulation of output gene expression in response to input signal, with maximal expression approaching the highest levels observed in yeast, yet being tunable to intermediate and lower expression levels. EC50 values are more than 4 times lower than in previously best-performing non-amplifier ribozyme switches. The system design retains the modular-input architecture of the ribozyme switch platform, and the near-digital dynamic ranges of TF-based gene control.
\r\n\r\nTogether, these developments suggest great potential for the wide applicability of these platforms for better-performing eukaryotic gene regulation, and more sophisticated, customizable reprogramming of cellular activity.
\r\n" }, { "name": "Daeffler, Christopher Scot", "degree": "PhD", "year": "2013", "title": "Ring-Opening Metathesis of Bulky Norbornene Monomers and the Radical-Mediated Hydrophosphonation of Olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03312013-175520336", "creators": [ { "name": { "family": "Daeffler", "given": "Christopher Scot" }, "id": "Daeffler-Christopher-Scot", "display_name": "Daeffler, Christopher Scot" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E7VW-EX09", "abstract": "This thesis discusses two major topics: the ring-opening metathesis polymerization (ROMP) of bulky monomers and the radical-mediated hydrophosphonation of olefins. The research into the ROMP of bulky monomers is further divided into three chapters: wedge-shaped monomers, the alternating copolymerization of 1-methyloxanorbornene derivatives with cyclooctene, and the kinetic resolution polymerization of 1-methyloxanorbornene derivatives. The wedge-shaped monomers can be polymerized into diblock copolymers that possess photonic crystal properties. The alternating copolymerization of 1-methyloxanorbornene derivatives with cyclooctene is performed with > 90% alternation via two different routes: typical alternating copolymerization and a sequence editing approach. The kinetic resolution polymerization of these same 1-methyloxanorbornene monomers achieves only modest selectivity (S=4), but there is evidence that the growing polymer chain forms a helix that influences the selectivity of the resolution. The last topic is the radical-mediated hydrophosphonation of olefins. This synthetic method provides access to Wittig reagents that are capable of highly cis-selective olefinations of aldehydes." }, { "name": "Ford, Nicole Danielle Bouley", "degree": "PhD", "year": "2013", "title": "Capturing Protein Dynamics with Time-Resolved Luminescence Spectroscopy", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302013-155904165", "creators": [ { "name": { "family": "Ford", "given": "Nicole Danielle Bouley" }, "id": "Ford-Nicole-Danielle-Bouley", "display_name": "Ford, Nicole Danielle Bouley" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/N8B5-4644", "abstract": "The presented doctoral research utilizes time-resolved spectroscopy to characterize protein dynamics and folding mechanisms. We resolve millisecond-timescale folding by coupling time-resolved fluorescence energy transfer (trFRET) to a continuous flow microfluidic mixer to obtain intramolecular distance distributions throughout the folding process. We have elucidated the folding mechanisms of two cytochromes---one that exhibits two-state folding (cytochrome
We have also investigated intrachain contact dynamics in unfolded cytochrome
In addition, we have explored the pathway dependence of electron tunneling rates between metal sites in proteins. Our research group has converted cytochrome
Donor\u2013acceptor cyclopropanes are a versatile class of synthetic intermediates, compatible in a broad range of ring-opening reactions and formal cycloadditions, and employed in numerous natural product syntheses. We have developed new Lewis acid mediated cycloadditions for the synthesis of five-membered heterocycles, and applied existing a transition metal catalyzed cyclopropane cycloaddition method toward the synthesis of complex alkaloids.
\r\n\r\nFirst, described is the development of a Lewis acid mediated (3 + 2) cycloaddition of donor\u2013acceptor cyclopropanes with isocyanates, isothiocyanates and carbodiimides. This reaction was found in certain cases to proceed with excellent stereochemical fidelity, providing access to an array of enantioenriched thioimidates and amidines.
\r\n\r\nSecond, we targeted the Melodinus alkaloids for total synthesis due to their unique structural features. Synthetic efforts toward scandine, the parent of the natural product family, are detailed herein. Our approach features a palladium catalyzed formal (3 + 2) cycloaddition of a vinyl cyclopropane and a \u03b2-nitrostyrene to rapidly assemble the central cyclopentane core of the natural product. Initial efforts focused on the synthesis and application of a 1,1-divinylcyclopropane to the formal (3 + 2) cycloaddition reaction, whereas later work entailed the use of a mono-vinylcyclopropane with the goal of installing the second requisite vinyl group at a later stage using modern C\u2013H functionalization technologies.
\r\n" }, { "name": "Han, Han", "degree": "PhD", "year": "2013", "title": "Development of Targeted, Polymeric Delivery Vehicles for Camptothesin and siRNA Via Boronic Acid-Diol Complexation", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01262013-020116009", "creators": [ { "name": { "family": "Han", "given": "Han" }, "id": "Han-Han", "display_name": "Han, Han" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NWSP-0Y35", "abstract": "Our research lab has developed polymer-based nanoparticle delivery systems for the anticancer drug, camptothecin (CPT), CRLX101; and for the small interfering RNA (siRNA), CALAA-01. CRLX101 has shown great success in both animal studies and clinical trials. However, it is incapable of achieving targeted delivery. CALAA-01 has demonstrated effectiveness in a phase I clinical trial. However, it suffers from its rapid in vivo clearance. To address the issues of targeting in the anticancer drug delivery system and the short circulation time in the siRNA delivery system, we have created a new delivery platform involving the use of boronic acid-diol complexation. This thesis is divided into two parts to discuss CPT delivery and siRNA delivery separately.
\r\n\r\nIn Part I, the targeted delivery of CPT via boronic acid-diol complexation is described. CPT was conjugated to a copolymer of mucic acid and PEG (MAP) and self-assembled into MAP-CPT nanoparticles. The targeting agent, Herceptin antibody was attached to boronic acid (BA), this was then complexed with the diol-containing MAP to form a targeted nanoparticle carrying ca. 60 CPT, with a 40 nm diameter and a slightly negative surface charge. The attachment of a single Herceptin per nanoparticle was sufficient to enhance cellular uptake of nanoparticles into BT-474, a HER2 overexpressing cell line by 70% compared to the non-targeted version. Nude mice bearing BT-474 xenograft tumors treated with targeted MAP-CPT nanoparticles resulted in all mice revealing complete tumor regression.
\r\n\r\nIn Part II, the boronic acid-diol complexation delivery platform is applied for the delivery of siRNA. First, the CALAA-01 delivery system for siRNA was further characterized and optimized. Then, a copolymer of mucic acid and dimethylsuberimidate (MAD) was synthesized and used in condensing the anionic siRNA into nanoparticles. Nanoparticles were stabilized by placing a surface PEG layer through boronic acid-diol complexation. Targeting was achieved by conjugating the distal end of the BA-PEG with a targeting agent, Herceptin antibody. MAD/siRNA nanoparticles effectively entered cells and demonstrated low cellular toxicity. MAD/siRNA nanoparticles stabilized with nitroPBA-PEG resulted in a diameter of 130 nm with a slightly negative surface charge. Pharmacokinetic studies in mice demonstrated improved circulation compared to CALAA-01.
\r\n\r\n" }, { "name": "Hochrein, Lisa Marie", "degree": "PhD", "year": "2013", "title": "Towards Conditional RNAi : Shape and Sequence Transduction with Small Conditional RNAs", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-160243112", "creators": [ { "name": { "family": "Hochrein", "given": "Lisa Marie" }, "id": "Hochrein-Lisa-Marie", "display_name": "Hochrein, Lisa Marie" } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "advisor", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Rossi", "given": "John J." }, "id": "Rossi-J-J", "role": "member", "display_name": "Rossi, John J." }, { "name": { "family": "Burnett", "given": "John" }, "id": "Burnett-J", "role": "member", "display_name": "Burnett, John" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NTZT-8Q67", "abstract": "RNA interference (RNAi) is a powerful biological pathway allowing for sequence-specific knockdown of any gene of interest. While RNAi is a proven tool for probing gene function in biological circuits, it is limited by being constitutively ON and executes the logical operation: silence gene Y. To provide greater control over post-transcriptional gene silencing, we propose engineering a biological logic gate to implement \u201cconditional RNAi.\u201d Such a logic gate would silence gene Y only upon the expression of gene X, a completely unrelated gene, executing the logic: if gene X is transcribed, silence independent gene Y. Silencing of gene Y could be confined to a specific time and/or tissue by appropriately selecting gene X.
\r\n\r\nTo implement the logic of conditional RNAi, we present the design and experimental validation of three nucleic acid self-assembly mechanisms which detect a sub-sequence of mRNA X and produce a Dicer substrate specific to gene Y. We introduce small conditional RNAs (scRNAs) to execute the signal transduction under isothermal conditions. scRNAs are small RNAs which change conformation, leading to both shape and sequence signal transduction, in response to hybridization to an input nucleic acid target. While all three conditional RNAi mechanisms execute the same logical operation, they explore various design alternatives for nucleic acid self-assembly pathways, including the use of duplex and monomer scRNAs, stable versus metastable reactants, multiple methods of nucleation, and 3-way and 4-way branch migration.
\r\n\r\nWe demonstrate the isothermal execution of the conditional RNAi mechanisms in a test tube with recombinant Dicer. These mechanisms execute the logic: if mRNA X is detected, produce a Dicer substrate targeting independent mRNA Y. Only the final Dicer substrate, not the scRNA reactants or intermediates, is efficiently processed by Dicer. Additional work in human whole-cell extracts and a model tissue-culture system delves into both the promise and challenge of implementing conditional RNAi in vivo.
" }, { "name": "Hoh, Nicholas Jeffrey", "degree": "PhD", "year": "2013", "title": "Effects of Particle Size Ratio on Single Particle Motion in Colloidal Dispersions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-154128559", "creators": [ { "name": { "family": "Hoh", "given": "Nicholas Jeffrey" }, "id": "Hoh-Nicholas-Jeffrey", "display_name": "Hoh, Nicholas Jeffrey" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Andrade", "given": "Jose E." }, "id": "Andrade-J-E", "role": "member", "display_name": "Andrade, Jose E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/XN4G-TB33", "abstract": "The motion of a single Brownian particle of arbitrary size through a dilute colloidal dispersion of neutrally buoyant bath spheres of another characteristic size in a Newtonian solvent is examined in two contexts. First, the particle in question, the probe particle, is subject to a constant applied external force drawing it through the suspension as a simple model for active and nonlinear microrheology. The strength of the applied external force, normalized by the restoring forces of Brownian motion, is the P\u00e9clet number, Pe. This dimensionless quantity describes how strongly the probe is upsetting the equilibrium distribution of the bath particles. The mean motion and fluctuations in the probe position are related to interpreted quantities of an effective viscosity of the suspension. These interpreted quantities are calculated to first order in the volume fraction of bath particles and are intimately tied to the spatial distribution, or microstructure, of bath particles relative to the probe. For weak Pe, the disturbance to the equilibrium microstructure is dipolar in nature, with accumulation and depletion regions on the front and rear faces of the probe, respectively. With increasing applied force, the accumulation region compresses to form a thin boundary layer whose thickness scales with the inverse of Pe. The depletion region lengthens to form a trailing wake. The magnitude of the microstructural disturbance is found to grow with increasing bath particle size -- small bath particles in the solvent resemble a continuum with effective microviscosity given by Einstein's viscosity correction for a dilute dispersion of spheres. Large bath particles readily advect toward the minimum approach distance possible between the probe and bath particle, and the probe and bath particle pair rotating as a doublet is the primary mechanism by which the probe particle is able to move past; this is a process that slows the motion of the probe by a factor of the size ratio. The intrinsic microviscosity is found to force thin at low P\u00e9clet number due to decreasing contributions from Brownian motion, and force thicken at high P\u00e9clet number due to the increasing influence of the configuration-averaged reduction in the probe's hydrodynamic self mobility. Nonmonotonicity at finite sizes is evident in the limiting high-Pe intrinsic microviscosity plateau as a function of bath-to-probe particle size ratio. The intrinsic microviscosity is found to grow with the size ratio for very small probes even at large-but-finite P\u00e9clet numbers. However, even a small repulsive interparticle potential, that excludes lubrication interactions, can reduce this intrinsic microviscosity back to an order one quantity. The results of this active microrheology study are compared to previous theoretical studies of falling-ball and towed-ball rheometry and sedimentation and diffusion in polydisperse suspensions, and the singular limit of full hydrodynamic interactions is noted.
\r\n\r\nSecond, the probe particle in question is no longer subject to a constant applied external force. Rather, the particle is considered to be a catalytically-active motor, consuming the bath reactant particles on its reactive face while passively colliding with reactant particles on its inert face. By creating an asymmetric distribution of reactant about its surface, the motor is able to diffusiophoretically propel itself with some mean velocity. The effects of finite size of the solute are examined on the leading order diffusive microstructure of reactant about the motor. Brownian and interparticle contributions to the motor velocity are computed for several interparticle interaction potential lengths and finite reactant-to-motor particle size ratios, with the dimensionless motor velocity increasing with decreasing motor size. A discussion on Brownian rotation frames the context in which these results could be applicable, and future directions are proposed which properly incorporate reactant advection at high motor velocities.
" }, { "name": "Hong, Allen Yu", "degree": "PhD", "year": "2013", "title": "Development of a Novel Ring Contraction Strategy and Application to the Total Synthesis of Presilphiperfolanol Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12192012-071010744", "creators": [ { "name": { "family": "Hong", "given": "Allen Yu" }, "id": "Hong-Allen-Yu", "orcid": "0000-0002-4691-548X", "display_name": "Hong, Allen Yu" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9WW7FMB", "abstract": "Biologically active and structurally complex natural products provide a powerful driving force for the development of novel reaction methodology. Major advances can reshape the way chemists approach the construction of challenging chemical bonds.
\r\n\r\nIn this work, we begin by describing the development of a catalytic asymmetric synthesis of five and seven-membered rings containing all-carbon quaternary stereocenters. Enantioselective Pd-catalyzed decarboxylative allylic alkylation reactions of \u03b2-ketoester substrates afforded a variety of chiral seven-membered \u03b1-quaternary vinylogous esters. Initial attempts to convert these compounds to \u03b3-quaternary cycloheptenones led to the discovery of a two-carbon ring contraction reaction, which provided isomeric \u03b3-quaternary acylcyclopentenes. Subsequent adjustment of reaction parameters provided divergent access to the originally targeted cycloheptenones. Numerous synthetic applications of the two versatile product types are demonstrated. The methodology expands on our previous investigations of six-membered ring scaffolds and provides additional chiral building blocks for asymmetric total synthesis.
\r\n \r\nThe ring contraction approach to acylcyclopentenes was further developed in the total synthesis of the presilphiperfolanols, which are important intermediates in sesquiterpene biosynthesis. Key to our synthetic route to the tricyclic core was the application of intramolecular Diels\u2013Alder and Ni-catalyzed 1,4-hydroboration reactions. From these efforts, the enantioselective total synthesis of presilphiperfolan-1\u03b2-ol was achieved. Future research efforts seek to extend the synthetic route to presilphiperfolan-9\u03b1-ol and study the synthetic compounds in biomimetic carbocation rearrangement processes.
" }, { "name": "Hwang, Kiwook", "degree": "PhD", "year": "2013", "title": "Biotechnologies for Cancer Diagnostics: Cell Sorting, Protein Analysis and Imaging of Cellular Metabolism", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072013-111912342", "creators": [ { "name": { "family": "Hwang", "given": "Kiwook" }, "id": "Hwang-Kiwook", "display_name": "Hwang, Kiwook" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z6DN-0483", "abstract": "This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called \u201cNucleic Acid Cell Sorting (NACS)\u201d, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.
\r\n \r\nSecondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called \u201cRadiopharmaceutical Imaging Chip\u201d (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.
\r\n \r\nThe last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.
\r\n" }, { "name": "Kalbarczyk, Karolina Zbigniew", "degree": "Senior Thesis", "year": "2013", "title": "Directed Evolution of Terpene Synthases for Non-Natural Substrates", "advisor": "Arnold, Frances Hamilton; Lauchli, Ryan", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302013-204117395", "creators": [ { "name": { "family": "Kalbarczyk", "given": "Karolina Zbigniew" }, "id": "Kalbarczyk-Karolina-Zbigniew", "display_name": "Kalbarczyk, Karolina Zbigniew" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Lauchli", "given": "Ryan" }, "id": "Lauchli-R", "role": "co-advisor", "display_name": "Lauchli, Ryan" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/N4T5-FP16", "abstract": "Terpenes represent about half of known natural products, with terpene synthases catalyzing reactions to increase the complexity of substrates and generate cyclizations of the linear diphosphate substrates, therefore forming rings and stereocenters. With their diverse functionality, terpene synthases may be highly evolvable, with the ability to accept a wide range of non-natural compounds and with high product selectivity. Our hypothesis is that directed evolution of terpene synthases can be used to increase selectivity of the synthase on a specific substrate. In the first part of the work presented herein, three natural terpene synthases, Cop2, BcBOT2, and SSCG_02150, were tested for activity against the natural substrate and a non-natural substrate, called Surrogate 1, and the relative activities on both the natural and non-natural substrates were compared. In the second part of this work, a terpene synthase variant of BcBOT2 that has been evolved for thermostability, was used for directed evolution for increased activity and selectivity on the non-natural substrate referred to as Surrogate 2. Mutations for this evolution were introduced using random mutagenesis, with error prone polymerase chain reactions, and using site-specific saturation mutagenesis, in which an NNK library is designed with a specific active site amino acid targeted for mutation. The mutant enzymes were then screened and selected for enhancement of the desired functionality. Two neutral mutants, 19B7 W367F and 19B7 W118Q, were found to maintain activity on Surrogate 2, as measured by the screen." }, { "name": "Keitz, Benjamin Keith", "degree": "PhD", "year": "2013", "title": "Selectivity in Ruthenium Catalyzed Olefin Metathesis: Applications and Origins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07312012-134600191", "creators": [ { "name": { "family": "Keitz", "given": "Benjamin Keith" }, "id": "Keitz-Benjamin-Keith", "display_name": "Keitz, Benjamin Keith" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/01TJ-QC10", "abstract": "Ruthenium-based catalysts for olefin metathesis display high activity in the presence of common functional groups and have been utilized in a variety of chemical disciplines. This thesis describes the development of new catalysts with superior properties and mechanistic studies directed at understanding the factors governing catalyst activity and selectivity.
\r\n\tChapter 2 describes the preparation of acid-activated olefin metathesis catalysts containing acetylacetonate (acac)-type ligands. The effect of ligand structure and the exogenous acid on catalytic activity was examined. The acid-activated catalysts were also combined with a photoacid generator (PAG), which resulted in a highly active system for photo-activated olefin metathesis.
\r\n\tChapter 3 details the incorporation of mesoionic carbenes (MICs) into ruthenium metathesis catalysts. The activity of these catalysts in several metathesis assays was measured and correlated to their initiation rates. The protonolysis of a Ru-MIC bond and the incorporation of this reaction into an acid-activated catalyst are also described. \t
\r\n\tChapter 4 explores the relationship between catalyst structure and degenerate metathesis. A ring-closing metathesis assay was used to measure the preference of different catalysts for productive or degenerate metathesis. The relationship between degenerate metathesis and reactions such as ethenolysis is also discussed.
\r\n\tChapter 5 describes the study of ruthenacyclobutanes formed from the degenerate metathesis selective catalysts presented in Chapter 4. The rates of various chemical exchange processes were measured and correlated to catalyst structure. Kinetic parameters for the rate-limiting step in ring-closing metathesis were also measured and used to rationalize the differences in productive/degenerate selectivity for various catalysts.
\t\r\n\tChapter 6 details the preparation and study of C-H-activated ruthenium catalysts for Z-selective olefin metathesis. Ligand effects on catalyst activity and selectivity are explored along with the application of these catalysts in Z-selective cross-metathesis and ring-opening metathesis polymerization.
" }, { "name": "Keller, Gretchen Eva", "degree": "PhD", "year": "2013", "title": "Phototriggering Nitric Oxide Synthase from Geobacillus stearothermophilus", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052013-133909189", "creators": [ { "name": { "family": "Keller", "given": "Gretchen Eva" }, "id": "Keller-Gretchen-Eva", "display_name": "Keller, Gretchen Eva" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HBFQ-8V20", "abstract": "Nitric oxide synthases (NOS) produce L-citrulline and nitric oxide (NO) in two turnovers from L-arginine via the bound intermediate, N-hydroxy-L-arginine. NO is an important biological signaling molecule, and NOS-like enzymes have been identified in all kingdoms of life. NOS enzymes utilize electrons from a reductase domain as well as a unique redox-active cofactor, tetrahydrobiopterin, in the activation of dioxygen. The NOS catalytic mechanism is only partially known, with proposed hihg-valent oxygenating intermediates similar to those of other monooxygenases. In the continued effort to understand the mechanism by which NOS catalytically produces NO, we have chosen to study NOS from the thermostable, nonpathogenic bacterium Geobacillus stearothermophilus (gsNOS).
\r\n\r\nIn this work, covalently modified gsNOS with a ruthenium(II) diimine photosensitizer has been prepared to circumvent the need for an external reductase domain, while maintaining access to the substrate-binding channel. In this way, we hoped to produce the NOS ferrous state by rapid electron injection and to be able to access intermediates that form downstream. Chapter two describes the engineered gsNOS for selective cysteine labeling with [Ru(bpy)2(IA-phen)]2+ (IA-phen = 5-iodoacetamido-1,10-phenanthroline) to form the conjugate Ru(II)K115C-gsNOS. The labeled protein was characterized by mass spectrometry, UV-visible absorbance, and circular dichroism spectroscopy. Ru(II)K115C-gsNOS was crystallized and its structure solved to 2.6 \u00c5 resolution. Chapter three details phototriggered reduction by laser flash-quench methodology using the reversible, reductive quencher p-methoxy-N,N-dimethylanaline. Transient absorption studies have shown that rapid phototriggered heme reduction occurs on the order of 625 ns. Binding of substrates and/or cofactor is known to alter the heme reduction potential in NOS. However, these observed reduction rates are independent of substrate/cofactor, suggesting that the system is driving force optimized. Studies performed in the presence of oxygen were complicated by side-reactions with the ruthenium label and small molecule quencher. Excitingly, enzymatic turnover was achieved by steady-state LED illumination at 470 nm using the irreversible reductive quencher diethyldithiocarbamate, and is described in chapter four. NO produced from light-driven Ru(II)K115C-gsNOS catalysis was measured by the Griess Assay and L-citrulline production confirmed by liquid chromatography-mass spectrometry. In chapter five, we show how phototriggered heme reduction can be used to monitor CO binding and potential studies of gas diffusion pathways, and substrate/cofactor effects are discussed. In all, the development of this ruthenium-modified gsNOS system has enabled preliminary studies of reduction kinetics, diatomic ligand binding, and light-driven catalysis and may provide a useful platform for further investigation into the catalytic cycle of NOS.
" }, { "name": "Kelley, Matthew James", "degree": "PhD", "year": "2013", "title": "Terahertz Time Domain Spectroscopy of Amino Acids and Sugars", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232013-183107863", "creators": [ { "name": { "family": "Kelley", "given": "Matthew James" }, "id": "Kelley-Matthew-James", "display_name": "Kelley, Matthew James" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FQ9S-JF63", "abstract": "A time-domain spectrometer for use in the terahertz (THz) spectral range was designed and constructed. Due to there being few existing methods of generating and detecting THz radiation, the spectrometer is expected to have vast applications to solid, liquid, and gas phase samples. In particular, knowledge of complex organic chemistry and chemical abundances in the interstellar medium (ISM) can be obtained when compared to astronomical data. The THz spectral region is of particular interest due to reduced line density when compared to the millimeter wave spectrum, the existence of high resolution observatories, and potentially strong transitions resulting from the lowest-lying vibrational modes of large molecules.
\r\n\r\nThe heart of the THz time-domain spectrometer (THz-TDS) is the ultrafast laser. Due to the femtosecond duration of ultrafast laser pulses and an energy-time uncertainty relationship, the pulses typically have a several-THz bandwidth. By various means of optical rectification, the optical pulse carrier envelope shape, i.e. intensity-time profile, can be transferred to the phase of the resulting THz pulse. As a consequence, optical pump-THz probe spectroscopy\r\nis readily achieved, as was demonstrated in studies of dye-sensitized TiO2, as discussed in chapter 4. Detection of the terahertz radiation is commonly based on electro-optic sampling and provides full phase information. This allows for accurate determination of both the real and imaginary index of refraction, the so-called optical constants, without additional analysis. A suite of amino acids and sugars, all of which have been found in meteorites, were studied in crystalline form embedded in a polyethylene matrix. As the temperature was varied between 10 and 310 K, various strong vibrational modes were found to shift in spectral intensity and frequency. Such modes can be attributed to intramolecular, intermolecular, or phonon modes, or to some combination of the three.
" }, { "name": "Krishnamurthy, Chithra", "degree": "PhD", "year": "2013", "title": "Chemical Probes to Study Fucosylated Glycans", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052013-123658997", "creators": [ { "name": { "family": "Krishnamurthy", "given": "Chithra" }, "id": "Krishnamurthy-Chithra", "display_name": "Krishnamurthy, Chithra" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z99021SG", "abstract": "Fucosylated glycans have many critical biological roles, from leukocyte adhesion to host-microbe interactions. However, a molecular level understanding of these sugars has been lacking, in part due to the chemical and structural diversity of glycans that make them challenging to study. In order to gain a deeper understanding of fucosylated glycans, we have explored the use of chemical probes to study these structures. In Chapters 1 and 2, we apply a metabolic labeling technique for the investigation of fucosylated glycans in neurons, where they have been implicated in learning and memory processes. However, the molecular mechanisms by which these sugars influence neuronal processes are not well understood, and only a handful of fucosylated glycoproteins have been identified. In order to facilitate our understanding of these processes, we exploit non-natural fucose analogs to identify the fucose proteome in rat cortical neurons, identifying proteins involved in cell adhesion, neuronal signaling, and synaptic transmission. Moreover, we track fucosylated glycoproteins in hippocampal neurons, and show that fucosylated glycoproteins localize to the Golgi, axons, and dendrites, and are enriched in synapses. In Chapter 4, we report a new chemoenzymatic strategy for the sensitive detection of the Fuc\u03b1(1-2)Gal epitope, which has been implicated in tumorigenesis as a potential biomarker of cancer progression. We demonstrate that the approach is highly selective for the Fuc\u03b1(1-2)Gal motif, detects a variety of complex glycans and glycoproteins, and can be used to profile the relative abundance of the motif on live cells, discriminating malignant from normal cells. These approaches represent new potential applications and strategies for the investigation of fucosylated glycans, and expand the technologies available for understanding the roles of this important class of carbohydrates in physiology and disease." }, { "name": "Kulkarni, Chethana", "degree": "PhD", "year": "2013", "title": "Selective Functionalization of the Protein N-Terminus with N-Myristoyl Transferase in Bacteria\r ", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07042012-153011199", "creators": [ { "name": { "family": "Kulkarni", "given": "Chethana" }, "id": "Kulkarni-Chethana", "display_name": "Kulkarni, Chethana" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MR6A-R648", "abstract": "Proteins are involved in myriad processes in all organisms. They provide structural support in the membrane and scaffolding of each cell; they aid in the transmission of biochemical signals within and between cells; and they play central roles in combating various disease states. The development of techniques enabling selective and site-specific functionalization of proteins is an active area of investigation, as such modifications are critical to many studies and uses of proteins. For instance, with the addition of a unique reactive handle, a protein may be conjugated to a polymer for the production of protein-based therapeutics exhibiting improved bioavailability. Alternatively, proteins may be attached to slides to prepare diagnostic microarrays, reacted with hydrogels to create functional biomaterials, or decorated with fluorophores for in vivo imaging. Site-specific protein tagging techniques have already contributed greatly to biomedical research and will continue to advance the state of the field.
\r\n\r\nThe focus of my thesis research has been the development of a novel site-specific protein labeling method centered on the eukaryotic enzyme N-myristoyl transferase (NMT). In a process called myristoylation, NMT appends a fatty acid to the N-terminus of numerous substrate proteins. Previous work demonstrated that NMT tolerates a wide range of chemically functionalized analogs of its natural fatty acid substrate. Here, we describe efforts that exploit various features of NMT: its ability to bind and utilize reactive fatty acid analogs, its exquisite selectivity toward its protein substrates, and its orthogonality toward those proteins naturally present in bacteria.
\r\n\r\nFirst, in Chapter II, we discuss the development of a model system for NMT-mediated protein labeling in the bacterium Escherichia coli. We synthesized an azide fatty acid analog that can participate in bioorthogonal chemistries, and we prepared two GFP-based substrate proteins, each displaying a recognition sequence derived from a known substrate of NMT. Our experiments indicate that labeling by NMT is site-specific, quantitative, and highly selective for each engineered substrate within the bacterial milieu.
\r\n\r\nAs summarized in Chapter III, the model system was extended to the N-terminal labeling of two neuronal proteins, calcineurin (CaN) and calmodulin (CaM). While CaN is naturally myristoylated, CaM was engineered to achieve labeling by NMT. Experiments with CaN and CaM confirmed that our NMT-based system is quantitative and selective in its labeling of both natural and engineered substrate proteins. Extensive characterization of each protein allowed us to identify constructs that retain wild-type levels of activity even after labeling with the azide fatty acid.
\r\n\r\nThree of the protein constructs reported in Chapters II and III were utilized for microarray studies, as described in Chapter IV. We achieved rapid surface immobilization of each azide-labeled protein directly from lysate, a significant advantage when considering the time and resources normally required to purify proteins for downstream applications. The experiments and methods summarized in this chapter will be adapted for high-throughput biochemical research with protein microarrays.
\r\n\r\nFinally, the orthogonality of NMT toward bacterial systems was probed further for the purpose of selective labeling of individual bacterial proteins for live-cell imaging. In addition to identifying an azide fatty acid suitable for such studies, we also selected two bacterial proteins that exhibit interesting functions and localization patterns, and we developed corresponding protein constructs for NMT-mediated labeling. Progress toward the use of NMT for in vivo imaging applications in bacteria is described in Chapter V.
\r\n\r\nUltimately, our objective throughout the design and execution of these projects was to create and validate a new technique to achieve site-specific protein labeling. The particular advantages of NMT include its tolerance of reactive fatty acid analogs and engineered substrate proteins, and its lack of interaction with proteins present in the widely used E. coli expression host. We believe that the ideas and results presented in this thesis establish NMT-mediated protein labeling as a valuable tool for addition to the existing set of site-specific protein labeling methods. Development of such methods represents an important and exciting area within the field of modern chemical biology.
\r\n" }, { "name": "Kurji, Zuleikha", "degree": "PhD", "year": "2013", "title": "Molecular Design of Side-Group Liquid Crystalline Polymers: Understanding Their Interactions with Small Molecule Liquid Crystal Solvent", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06102013-114658448", "creators": [ { "name": { "family": "Kurji", "given": "Zuleikha" }, "id": "Kurji-Zuleikha", "display_name": "Kurji, Zuleikha" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9WH2N6R", "abstract": "Liquid crystal (LC) gels \u2013 the combination of macromolecules with small molecule LCs \u2013 couple the\r\nelasticity and mechanical strength of polymers to the order inherent to LCs and are attractive to many\r\nresearchers hoping to marry liquid crystals' optical and electro-optical responsiveness with polymers'\r\nmechanical strength and ease of processing. In particular, side-group liquid crystal polymers (SGLCPs)\r\nare flexible-chain polymers that are functionalized with LC side-groups. Here we introduce the concept\r\nof polymer dopants: homogenously dissolved LC-containing SGLCP homopolymers that are molecularly\r\ndesigned for solubility in and coupling to small molecule LC solvents. Using polymer analogous\r\nchemistry (changing the molecular makeup of the side groups and their linkers, while keeping backbone\r\nmolecular weight, polydispersity index, and degree of polymerization constant), we\u2019ve targeted the effect\r\nof side-group orientation, dipole position and strength, spacer length and linking-group type on\r\npolymer solubility and bulk material properties. We've shown that, at low concentration, these dopants\r\ncan have significant effects on the bulk material properties of two types of LCs: ferroelectric and vertically\r\naligned nematic LCs." }, { "name": "Li, Benjamin Chun Yeung", "degree": "PhD", "year": "2013", "title": "Synthesis and Biological Studies of DNA-binding Cyclic Py-Im Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282013-171348639", "creators": [ { "name": { "family": "Li", "given": "Benjamin Chun Yeung" }, "id": "Li-Benjamin-Chun-Yeung", "display_name": "Li, Benjamin Chun Yeung" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/82YX-QB29", "abstract": "Pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind to the minor groove of DNA in a sequence-specific manner at affinities comparable to natural DNA-binding proteins. Hairpin polyamides have been shown to localize within the nucleus of live cells, disrupt protein-DNA interactions, and modulate endogenous gene expression. Cyclic polyamides display further enhanced DNA binding affinities and exhibit similar gene regulatory effects, but investigations into their biological activity have been limited by the lack of effective synthetic methods. Herein, we demonstrate the efficient synthesis of a focused library of cyclic polyamide utilizing a novel microwave-assisted solid-phase technique. The orthogonal protection strategy allowed for selective turn modifications, and the mild cleavage conditions gave access to polyamide cores beginning with a C-terminal imidazole. In addition to expanding our synthetic repertoire, we further examined the cytotoxicity and cell uptake profiles of the cyclic polyamide variants, which highlighted the significant changes in biological activity resulting from minor structural modifications. Molecular recognition of the polyamide turn unit was also explored by installing heteroatom substituents at the \u03b1-position. Interestingly, while none of the fluoro, hydroxyl, or amino derivatives increased turn specificity, the (S)-fluoro turn exhibited better tolerance for binding a C\u2022G pair. Finally, we optimized the synthesis of several biologically active hairpin polyamides on a 50-mg scale and examined their antitumor activity in mice xenograft models." }, { "name": "Limapichat, Walrati", "degree": "PhD", "year": "2013", "title": "Probing the Roles of Receptor Structure, Drug-Receptor Interactions, and Receptor Crosstalk in Ligand-Gated Ion Channel Function", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052012-192506907", "creators": [ { "name": { "family": "Limapichat", "given": "Walrati" }, "id": "Limapichat-Walrati", "display_name": "Limapichat, Walrati" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YPMW-9E79", "abstract": "Ligand-gated ion channels are multi-subunit transmembrane proteins that play crucial roles in synaptic transmission in the nervous system. These include the Cys-loop receptor superfamily, the ionotropic glutamate receptor (iGluR) family, and the purinergic P2X receptor family. Binding of specific neurotransmitters at the ligand-binding site triggers a series of conformational changes that ultimately leads to ion channel opening. This dissertation describes three molecular-scale functional studies on these receptors.
\r\n\r\nThe first project (Chapter 2) describes structure-function studies of the conserved Phe-Pro motif in the Cys loop of the nicotinic acetylcholine receptor (nAChR) of the Cys-loop superfamily. Both residues were substituted with natural and unnatural amino acids. A strong interaction between the Phe and Pro residues is evident, as is a preference for aromaticity at the Phe site. Hydrophobicity is preferred at both sites. A correlation between receptor function and the cis bias at the proline backbone suggests a significant role for the cis proline conformer in receptor function.
\r\n\r\nThe second project (Chapter 3) concerns the key binding interaction of memantine, a prescribed drug for Alzheimer\u2019s disease, on the N-methyl-D-aspartate (NMDA) receptor of the iGluR family. The data suggest that the special property of memantine as an NMDA receptor blocker stems from the presence of the two methyl groups and a proper shape-matching to the binding site. Comparing affinities of memantine and amantadine, a structurally related drug, in response to pore mutations allows an identification of the methyl group binding pockets on the NMDA channel pore.
\r\n\r\nThe final project (Chapter 4) involves a study of inhibitory crosstalk between two families of ion channels: \u03b16\u03b24-containing nAChRs and P2X receptors. When these two distinct receptors are co-expressed, their properties are modulated from their normal behavior when expressed alone. The effect is constitutive and does not require channel activation. When they are co-activated by their respective agonists, the observed current is smaller than the sum of the currents evoked by individual application of their agonists. This functional interaction between these nicotinic and purinergic receptors in dorsal root ganglion neurons is proposed to be involved in pain sensation.
\r\n" }, { "name": "Loza, Christine Lauren", "degree": "PhD", "year": "2013", "title": "Investigations of Secondary Organic Aerosol Formation in Laboratory Chambers", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312013-115629933", "creators": [ { "name": { "family": "Loza", "given": "Christine Lauren" }, "id": "Loza-Christine-Lauren", "display_name": "Loza, Christine Lauren" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "member", "display_name": "Sander, Stanley P." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WZXD-KX70", "abstract": "Secondary organic aerosol (SOA) is produced in the atmosphere by oxidation of volatile organic compounds. Laboratory chambers are used understand the formation mechanisms and evolution of SOA formed under controlled conditions. This thesis presents studies of SOA formed from anthropogenic and biogenic precursors and discusses the effects of chamber walls on suspended vapors and particles.
\r\n\r\nDuring a chamber experiment, suspended vapors and particles can interact with the chamber walls. Particle wall loss is relatively well-understood, but vapor wall losses have received little study. Vapor wall loss of 2,3-epoxy-1,4-butanediol (BEPOX) and glyoxal was identified, quantified, and found to depend on chamber age and relative humidity.
\r\n\r\nParticles reside in the atmosphere for a week or more and can evolve chemically during that time period, a process termed aging. Simulating aging in laboratory chambers has proven to be challenging. A protocol was developed to extend the duration of a chamber experiment to 36 h of oxidation and was used to evaluate aging of SOA produced from m-xylene. Total SOA mass concentration increased and then decreased with increasing photooxidation suggesting a transition from functionalization to fragmentation chemistry driven by photochemical processes. SOA oxidation, measured as the bulk particle elemental oxygen-to-carbon ratio and fraction of organic mass at m/z 44, increased continuously starting after 5 h of photooxidation.
\r\n\r\nThe physical state and chemical composition of an organic aerosol affect the mixing of aerosol components and its interactions with condensing species. A laboratory chamber protocol was developed to evaluate the mixing of SOA produced sequentially from two different sources by heating the chamber to induce particle evaporation. Using this protocol, SOA produced from toluene was found to be less volatile than that produced from a-pinene. When the two types of SOA were formed sequentially, the evaporation behavior most closely represented that of SOA from the second parent hydrocarbon, suggesting that the structure of the mixed SOA particles resembles a core of SOA from the first precursor coated by a layer of SOA from the second precursor, indicative of limiting mixing.
" }, { "name": "McCaig, Heather Catherine", "degree": "PhD", "year": "2013", "title": "Resonant Nanocantilever Chemical Vapor Sensors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102013-152319367", "creators": [ { "name": { "family": "McCaig", "given": "Heather Catherine" }, "id": "McCaig-Heather-Catherine", "display_name": "McCaig, Heather Catherine" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Roukes", "given": "Michael Lee" }, "id": "Roukes-M-L", "role": "member", "display_name": "Roukes, Michael Lee" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z957191Q", "abstract": "Chemical vapor sensors are used in a wide variety of fields such as security, environmental monitoring, the food and beverage industry, and healthcare to detect disease biomarkers on exhaled breath. An electronic nose is composed of an array of cross-responsive chemical vapor sensors, in which every sensor responds to a varying degree to each chemical vapor, creating a \"fingerprint\" for that vapor. Incorporating an electronic nose into a highly-miniaturized vapor detection system, capable of bringing near laboratory-quality analysis into the field, requires the use of extremely small, fast, and sensitive sensors. One option is resonant nanocantilevers, which respond to changes in mass and stiffness by shifts in resonant frequency, and are capable of detecting mass-loading at the attogram (10-18 g) level in ambient conditions.
\r\n\r\nTo determine whether nanocantilevers can be used in an electronic nose, an array of five nanocantilevers, wherein each sensor was coated with a different dropcast polymer film (2-10 nm thick), were exposed to seven chemical vapors with a range of functional groups. The array successfully discriminated between all vapors, indicating that sensor responses were dominated by vapor absorption into polymer films, and not by non-specific physisorption. The thinness of the polymer film, combined with the small vapor capture area of the nanocantilevers, resulted in lower sensitivity than desired, limiting their effectiveness. To overcome this challenge, surface initiated atom transfer radical polymerization (SI-ATRP) was used to grow a 100 nm thick, uniform films of poly(methylmethacrylate) (PMMA), poly(methyl acrylate) (PMA), and poly(n-butyl methacrylate) (PBMA) on nanocantilevers. The thick polymer films absorbed more vapor, significantly increasing nanocantilever sensitivity. To determine the relative roles of mass loading and stiffness change on nanocantilever sensor response, SI-ATRP was combined with chromium masking, enabling polymer film growth to be localized to either the clamped end (sensitive to stiffness) or the free end (sensitive to mass-loading) of the nanocantilevers. These experiments revealed that changes in stiffness, induced by vapor absorption into the polymer films, dominated the sensor responses, and not mass-loading as was initially assumed. This work demonstrated that an array resonant nanocantilevers can be successfully used a sensitive, nanoscale electronic nose.
" }, { "name": "McKone, James Robert", "degree": "PhD", "year": "2013", "title": "Earth-Abundant Materials for Solar Hydrogen Generation", "advisor": "Gray, Harry B.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052013-140402659", "creators": [ { "name": { "family": "McKone", "given": "James Robert" }, "id": "McKone-James-Robert", "orcid": "0000-0001-6445-7884", "display_name": "McKone, James Robert" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NDDJ-P611", "abstract": "A critical challenge for the 21st century is shifting from the predominant use of fossil fuels to renewables for energy. Among many options, sunlight is the only single renewable resource with sufficient abundance to replace most or all of our current fossil energy use. However, existing photovoltaic and solar thermal technologies cannot be scaled infinitely due to the temporal and geographic intermittency of sunlight. Therefore efficient and inexpensive methods for storage of solar energy in a dense medium are needed in order to greatly increase utilization of the sun as a primary resource. For this purpose we have proposed an artificial photosynthetic system consisting of semiconductors, electrocatalysts, and polymer membranes to carry out photoelectrochemical water splitting as a method for solar fuel generation.
\r\n\r\nThis dissertation describes efforts over the last five years to develop critical semiconductor and catalyst components for efficient and scalable photoelectrochemical hydrogen evolution, one of the half reactions for water splitting. We identified and developed Ni\u2013Mo alloy and Ni2P nanoparticles as promising earth-abundant electrocatalysts for hydrogen evolution. We thoroughly characterized Ni\u2013Mo alloys alongside Ni and Pt catalysts deposited onto planar and structured Si light absorbers for solar hydrogen generation. We sought to address several key challenges that emerged in the use of non-noble catalysts for solar fuels generation, resulting in the synthesis and characterization of Ni\u2013Mo nanopowder for use in a new photocathode device architecture. To address the mismatch in stability between non-noble metal alloys and Si absorbers, we also synthesized and characterized p-type WSe2 as a candidate light absorber alternative to Si that is stable under acidic and alkaline conditions.
" }, { "name": "Montgomery, David Church", "degree": "PhD", "year": "2013", "title": "Improving the Biological Activity of Pyrrole-Imidazole Polyamides ", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182013-113509606", "creators": [ { "name": { "family": "Montgomery", "given": "David Church" }, "id": "Montgomery-David-Church", "display_name": "Montgomery, David Church" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/28SH-6Z27", "abstract": "DNA is nature\u2019s blueprint, holding within it the genetic code that defines the structure and function of an organism. A complex network of DNA-binding proteins called transcription factors can largely control the flow of information from DNA, so modulating the function of transcription factors is a promising approach for treating many diseases. Pyrrole-imidazole (Py-Im) polyamides are a class of DNA-binding oligomers, which can be synthetically programmed to bind a target sequence of DNA. Due to their unique shape complementarity and a series of favorable hydrogen bonding interactions that occur upon DNA-binding, Py-Im polyamides can bind to the minor groove of DNA with affinities comparable to transcription factors. Previous studies have demonstrated that these cell-permeable small molecules can enter cell nuclei and disrupt the transcription factor-DNA interface, thereby repressing transcription. As the use of Py-Im polyamides has significant potential as a type of modular therapeutic platform, the need for polyamides with extremely favorable biological properties and high potency will be essential. Described herein, a variety of studies have been performed aimed at improving the biological activity of Py-Im polyamides. To improve the biological potency and cellular uptake of these compounds, we have developed a next-generation class of polyamides bearing aryl-turn moieties, a simple structural modification that allows significant improvements in cellular uptake. This strategy was also applied to a panel of high-affinity cyclic Py-Im polyamides, again demonstrating the remarkable effect minor structural changes can have on biological activity. The solubility properties of Py-Im polyamides and use of formulating reagents with their treatment have also been examined. Finally, we describe the study of Py-Im polyamides as a potential artificial transcription factor." }, { "name": "Moore, Matthew Michaels", "degree": "PhD", "year": "2013", "title": "Applications of Computational Protein Design to Red Fluorescent Proteins", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132012-234333515", "creators": [ { "name": { "family": "Moore", "given": "Matthew Michaels" }, "id": "Moore-Matthew-Michaels", "display_name": "Moore, Matthew Michaels" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/6876-A570", "abstract": "The research comprising this thesis is presented in three chapters divided into two parts. Part One, Chapters 2 and 3, of the thesis focuses on the application of rational design and CPD to the core residues of FPs. Chapter 2 applies CPD to the well known red fluorescent protein mCherry. Design hypotheses in this work were driven by a desire to red-shift the fluorescence emission of the parent protein. Chapter 3 takes the most successful results from the mCherry system and attempts to applies these results to the far-red FP mPlum. These two proteins, mCherry and mPlum, share a directed evolution parent, mRFP1. Part Two, consisting of Chapter 4, presents the beginnings of a comprehensive study into the applications CPD for designing FP surfaces. The system used is based on DsRed, the oligomeric parent of monomer mCherry. Professional and personal acknowledgments conclude the thesis." }, { "name": "Morris, Melody Ann", "degree": "Senior Thesis", "year": "2013", "title": "Three-Dimensional Self-Assembly of Brush Block Copolymers to Photonic Crystals", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06182013-115805695", "creators": [ { "name": { "family": "Morris", "given": "Melody Ann" }, "id": "Morris-Melody-Ann", "display_name": "Morris, Melody Ann" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/D77G-4K14", "abstract": "The development of Ring Opening Metathesis Polymerization has allowed the world of block copolymers to expand into brush block copolymers. Brush block copolymers consist of a polymer backbone with polymeric side chains, forcing the backbone to hold a stretched conformation and giving it a worm-like shape. These brush block copolymers have a number of advantages over tradition block copolymers, including faster self-assembly behavior, larger domain sizes, and much less entanglement. This makes them an ideal candidate in the development of a bottom-up approach to forming photonic crystals. Photonic crystals are periodic nanostructures that transmit and reflect only certain wavelengths of light, forming a band gap. These are used in a number of coatings and other optical uses. One and two dimensional photonic crystals are commercially available, though are often expensive and difficult to manufacture. Previous work has focused on the creation of one dimensional photonic crystals from brush block copolymers. In this thesis, I will focus on the synthesis and characterization of asymmetric brush block copolymers for self-assembly into two and three dimensional photonic crystals. Three series of brush block copolymers were made and characterized by Gel Permeation Chromatography and Nuclear Magnetic Resonance spectroscopy. They were then made into films through compressive thermal annealing and characterized by UV-Vis Spectroscopy and Scanning Electron Microscopy. Evidence of non-lamellar structures were seen, indicating the first reported creation of two or three dimensional photonic crystals from brush block copolymers." }, { "name": "Muren, Natalie Bloom", "degree": "PhD", "year": "2013", "title": "DNA-Mediated Charge Transport for Long-Range Sensing and Protein Detection", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01282013-083506263", "creators": [ { "name": { "family": "Muren", "given": "Natalie Bloom" }, "id": "Muren-Natalie-Bloom", "display_name": "Muren, Natalie Bloom" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6KG5-KQ87", "abstract": "The structural core of DNA, a continuous stack of aromatic heterocycles\u2014the base pairs\u2014that extends down the helical axis, gives rise to the fascinating electronic properties of this molecule that is so critical for life. This \u03c0-stacked structure facilitates a unique form of charge conduction, termed DNA-mediated charge transport (DNA CT). Experiments with diverse platforms, in solution, on surfaces, and with single molecules, collectively provide a broad and consistent perspective on the essential characteristics of this chemistry. Notably, DNA CT can proceed over long molecular distances, but is remarkably sensitive to perturbations in base pair stacking. These characteristics suggest that DNA CT may be used for long-range sensing both in nature and in nanoelectronic applications. Here, measurements of DNA CT with surface and single molecule platforms are used to (i) determine how ground state DNA CT varies over regimes of increasing distance and (ii) apply this chemistry to the electrical detection of DNA-binding proteins.
\r\n\r\nFirst, the design and fabrication of multiplexed, DNA-modified electrodes on silicon chips is reported. These lithographically patterned chips with 16 individually addressable gold electrodes allow for the measurement of DNA CT with four different types of DNA, side by side on the same surface, with four-fold redundancy. Discrimination of DNA with a single base mismatch and detection of sequence-specific restriction enzyme activity are both achieved with these chips. Scaling of these devices to microelectrode dimensions is also demonstrated. Importantly, these chips show greater reproducibility and consistency than commercially available rod electrodes. This greater signal quality, combined with the capacity to examine different samples side by side, opens the door for more complex applications of this platform.
\r\n\r\nThe fully developed, multiplexed chips are first used to compare DNA CT over short and long distance regimes. DNA is evaluated in this context because the efficacy of a long-range sensor, in either nature or nanoelectronics, is determined largely by its capacity to facilitate CT in a manner that is minimally affected by the CT distance. DNA CT over 34 nm in 100-mer monolayers is found to yield electrochemical signals that are comparable in size to shorter 17-mer DNA. Signal attenuation from a single base-pair mismatch in the 100-mer is also comparable to that for 17-mers, and confirms that CT in these 100-mer films is DNA-mediated. Efficient cleavage by a restriction enzyme indicates that the 100-mer DNA adopts a native, upright conformation. The alkanethiol linker used to anchor the DNA to the electrode is found to limit the electron-transfer rate for both DNA lengths. Thus the impact of increasing the CT distance on DNA CT is too small to be resolved by this platform, even over 34 nm. These measurements put DNA among the longest and most conductive molecular wires reported to date.
\r\n\r\nNext, DNA CT with multiplexed chips is extended to the electrochemical detection of methyltransferases, proteins that are attractive targets because of their prominent role in the initial stages of many types of cancer. Electrochemical detection of binding and activity by these proteins is achieved by two different methods. First, DNA-binding and base-flipping by these proteins disrupts the DNA \u03c0-stack and may be used for direct \u201csignal OFF\u201d detection. Using this method, the concentration- and cofactor- dependence of SssI methyltransferase, the bacterial analog of human methyltransferases, are examined. Second, methylation-conferred protection of DNA against cutting by a restriction enzyme may be used for \u201csignal ON\u201d detection of methyltransferase activity. With this approach, the use of both unmethylated and hemimethylated DNA substrates is demonstrated for the sensitive detection of both bacterial (SssI) and human (Dnmt1) methyltransferase activity. Importantly, the electrochemical format of these assays requires minimal equipment, is low cost, and may be easily applied to high throughput studies, making it an accessible option for a variety of research and clinical settings.
\r\n\r\nAlongside work with this surface, electrochemical platform, a single molecule, carbon nanotube-DNA (CNT-DNA) platform is also used to evaluate DNA CT over increasing distances and to detect protein binding. CNT-DNA devices consist of a single molecule of DNA that is made to bridge a gap cut in a CNT covalently, such that current flow through the device is DNA-mediated. Upon introduction of DNA bridges of varying length (15-mer, 60-mer, and 100-mer), the device resistance is minimally affected, echoing the result of long distance electrochemistry experiments. These devices are also used to detect SssI methyltransferase binding by the direct \u201csignal OFF\u201d method used with multiplexed chips; DNA-binding and base-flipping disrupts DNA CT and shuts off current flow through the device. CNT-DNA devices are used to electronically measure the sequence-specific, cofactor-dependent, and reversible binding of SssI. DNA methylation catalyzed by SssI is also detected based on its alteration of the protein-binding affinity of the device. This detection approach, which relies on DNA as both a recognition element and electrical transducer, represents a unique strategy for the specific, single molecule detection of protein binding and activity.
\r\n" }, { "name": "Nag, Arundhati", "degree": "PhD", "year": "2013", "title": "Developing Peptide Based Capture Agents for Diagnostics and Therapeutics ", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-235430660", "creators": [ { "name": { "family": "Nag", "given": "Arundhati" }, "id": "Nag-Arundhati", "display_name": "Nag, Arundhati" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Cai", "given": "Long" }, "id": "Cai-Long", "role": "member", "display_name": "Cai, Long" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y064-VD39", "abstract": "Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions." }, { "name": "Nani, Roger Rauhauser", "degree": "PhD", "year": "2013", "title": "The Intramolecular Buchner Reaction of \u03b1-Diazo-\u03b2-Ketonitriles: Development and Application to the Total Synthesis of (+)-Salvileucalin B", "advisor": "Reisman, Sarah", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-031825238", "creators": [ { "name": { "family": "Nani", "given": "Roger Rauhauser" }, "id": "Nani-Roger-Rauhauser", "display_name": "Nani, Roger Rauhauser" } ], "advisors": [ { "name": { "family": "Reisman", "given": "Sarah" }, "id": "Reisman-S-E", "role": "advisor", "display_name": "Reisman, Sarah" } ], "committee": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "chair", "display_name": "Peters, Jonas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2KGP-7X92", "abstract": "Since its discovery in 1896, the Buchner reaction has fascinated chemists for more than a century. The highly reactive nature of the carbene intermediates allows for facile dearomatization of stable aromatic rings, and provides access to a diverse array of cyclopropane and seven-membered ring architectures. The power inherent in this transformation has been exploited in the context of a natural product total synthesis and methodology studies.
\r\n\r\nThe total synthesis work details efforts employed in the enantioselective total synthesis of (+)-salvileucalin B. The fully-substituted cyclopropane within the core of the molecule arises from an unprecedented intramolecular Buchner reaction involving a highly functionalized arene and an \u03b1-diazo-\u03b2-ketonitrile. An unusual retro-Claisen rearrangement of a complex late-stage intermediate was discovered on route to the natural product.
\r\n\r\nThe unique reactivity of \u03b1-diazo-\u03b2-ketonitriles toward arene cyclopropanation was then investigated in a broader methodological study. This specific di-substituted diazo moiety possesses hitherto unreported selectivity in intramolecular Buchner reactions. This technology was enables the preparation of highly functionalized norcaradienes and cyclopropanes, which themselves undergo various ring opening transformations to afford complex polycyclic structures.
\r\n\r\nFinally, an enantioselective variant of the intramolecular Buchner reaction is described. Various chiral copper and dirhodium catalysts afforded moderate stereoinduction in the cyclization event.
\r\n" }, { "name": "Nelson, Hosea Martin", "degree": "PhD", "year": "2013", "title": "A Unified Synthetic Approach to the Transtaganolide and Basiliolide Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09282012-144447840", "creators": [ { "name": { "family": "Nelson", "given": "Hosea Martin" }, "id": "Nelson-Hosea-Martin", "display_name": "Nelson, Hosea Martin" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/09DW-P586", "abstract": "Herein are described the first total syntheses of several members of the transtaganolide and basiliolide natural product family. A general strategy, hinging upon the use of a biomimetic Ireland\u2013Claisen rearrangement/Diels\u2013Alder cycloaddition cascade, was developed. It allowed for the rapid assembly of the most structurally complex, and biologically active members of the family.
\r\n\r\nA brief introduction that surveys the use of the pyrone Diels\u2013Alder cycloaddition in total synthesis precedes details of our synthetic efforts. The diversity of structural motifs accessible through this reaction manifold is described through literature examples.
\r\n\r\nThe account of our experimental work begins with details of extensive model studies. First, a simple system was prepared which probed the ability to construct basiliolide B via an intramolecular pyrone Diels\u2013Alder reaction. It was demonstrated that the sterically congested core could be constructed in a highly diastereoselective fashion using this technology. Second, a simple prenylated pyrone was constructed, and shown to undergo a facile Ireland\u2013Claisen rearrangement under a variety of conditions. Subsequently, the utilization of these two methods within a cascade allowed for the rapid construction of racemic transtaganolide C, transtaganolide D, basiliolide B, and epi-8-basiliolide B. Furthermore, a novel Pd-catalyzed [5+2] annulation technology is utilized to construct the venerable, carboxy-ketene-acetal containing C-ring present in most of the metabolites.
\r\n\r\nIntegration of asymmetry into our general strategy is also described. Utilization of a chiral silane directing group allowed for the successful and rare application of an enantioselective Ireland\u2013Claisen rearrangement, culminating in the total syntheses of (+)- transtaganolide C, (\u2013)-transtaganolide D, (+)-transtaganolide B, and (\u2013)-transtaganolide A. Furthermore, the impact of this work on existing biosynthetic hypotheses is discussed.
\r\n" }, { "name": "Nguyen, Thang Xuan", "degree": "PhD", "year": "2013", "title": "A Study of Protein Targeting Reveals Insights into Mitigating Protein Aggregation", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:06052013-151748060", "creators": [ { "name": { "family": "Nguyen", "given": "Thang Xuan" }, "id": "Nguyen-Thang-Xuan", "display_name": "Nguyen, Thang Xuan" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JA4R-TE24", "abstract": "A unique chloroplast Signal Recognition Particle (SRP) in green plants is primarily dedicated to the post-translational targeting of light harvesting chlorophyll-a/b binding (LHC) proteins. Our study of the thermodynamics and kinetics of the GTPases of the system demonstrates that GTPase complex assembly and activation are highly coupled in the chloroplast GTPases, suggesting they may forego the GTPase activation step as a key regulatory point. This reflects adaptations of the chloroplast SRP to the delivery of their unique substrate protein. Devotion to one highly hydrophobic family of proteins also may have allowed the chloroplast SRP system to evolve an efficient chaperone in the cpSRP43 subunit. To understand the mechanism of disaggregation, we showed that LHC proteins form micellar, disc-shaped aggregates that present a recognition motif (L18) on the aggregate surface. Further molecular genetic and structure-activity analyses reveal that the action of cpSRP43 can be dissected into two steps: (i) initial recognition of L18 on the aggregate surface; and (ii) aggregate remodeling, during which highly adaptable binding interactions of cpSRP43 with hydrophobic transmembrane domains of the substrate protein compete with the packing interactions within the aggregate. We also tested the adaptability of cpSRP43 for alternative substrates, specifically in attempts to improve membrane protein expression and inhibition of amyloid beta fibrillization. These preliminary results attest to cpSRP43\u2019s potential as a molecular chaperone and provides the impetus for further engineering endeavors to address problems that stem from protein aggregation." }, { "name": "Oh, Young In", "degree": "PhD", "year": "2013", "title": "Synthesis and Biological Activity of Anticoagulant Heparan Sulfate Glycopolymers ", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022013-204012683", "creators": [ { "name": { "family": "Oh", "given": "Young In" }, "id": "Oh-Young-In", "display_name": "Oh, Young In" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E16S-6T52", "abstract": "Heparin has been used as an anticoagulant drug for more than 70 years. The global distribution of contaminated heparin in 2007, which resulted in adverse clinical effects and over 100 deaths, emphasizes the necessity for safer alternatives to animal-sourced heparin. The structural complexity and heterogeneity of animal-sourced heparin not only impedes safe access to these biologically active molecules, but also hinders investigations on the significance of structural constituents at a molecular level. Efficient methods for preparing new synthetic heparins with targeted biological activity are necessary not only to ensure clinical safety, but to optimize derivative design to minimize potential side effects. Low molecular weight heparins have become a reliable alternative to heparin, due to their predictable dosages, long half-lives, and reduced side effects. However, heparin oligosaccharide synthesis is a challenging endeavor due to the necessity for complex protecting group manipulation and stereoselective glycosidic linkage chemistry, which often result in lengthy synthetic routes and low yields. Recently, chemoenzymatic syntheses have produced targeted ultralow molecular weight heparins with high-efficiency, but continue to be restricted by the substrate specificities of enzymes.
\r\n\r\nTo address the need for access to homogeneous, complex glycosaminoglycan structures, we have synthesized novel heparan sulfate glycopolymers with well-defined carbohydrate structures and tunable chain length through ring-opening metathesis polymerization chemistry. These polymers recapitulate the key features of anticoagulant heparan sulfate by displaying the sulfation pattern responsible for heparin\u2019s anticoagulant activity. The use of polymerization chemistry greatly simplifies the synthesis of complex glycosaminoglycan structures, providing a facile method to generate homogeneous macromolecules with tunable biological and chemical properties. Through the use of in vitro chromogenic substrate assays and ex vivo clotting assays, we found that the HS glycopolymers exhibited anticoagulant activity in a sulfation pattern and length-dependent manner. Compared to heparin standards, our short polymers did not display any activity. However, our longer polymers were able to incorporate in vitro and ex vivo characteristics of both low-molecular-weight heparin derivatives and heparin, displaying hybrid anticoagulant properties. These studies emphasize the significance of sulfation pattern specificity in specific carbohydrate-protein interactions, and demonstrate the effectiveness of multivalent molecules in recapitulating the activity of natural polysaccharides.
" }, { "name": "Rogers, Claude Joseph", "degree": "PhD", "year": "2013", "title": "Discovery of New Roles for Chondroitin Sulfate in Neurotrophin Signaling and Retinotopic Development", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01272013-150337805", "creators": [ { "name": { "family": "Rogers", "given": "Claude Joseph" }, "id": "Rogers-Claude-Joseph", "display_name": "Rogers, Claude Joseph" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Zinn", "given": "Kai George" }, "id": "Zinn-K-G", "role": "member", "display_name": "Zinn, Kai George" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9N58JCD", "abstract": "Chondroitin sulfate (CS), a member of the glycosaminoglycan family of linear polysaccharides, is involved in the formation and maintenance of neuronal networks. CS has dual roles in regulating neuronal morphology: promoting or inhibiting neuronal outgrowth, depending on the context. A single sulfated epitope, CS-E, is capable of inducing both types of activity.
\r\n\r\nMembers of the neurotrophin (NT) family of growth factors are required for CS- E-induced neurite outgrowth in hippocampal neurons. Here, we demonstrate that CS is capable of forming ternary complexes with NTs and their receptors. These complexes were discovered using a novel, carbohydrate microarray-based approach that allows for the rapid screening of such interactions. To support these findings, we computationally determined the CS-E-binding site of the complexes, suggesting a structural basis for the interaction. In addition, we showed that CS-E is capable of attenuating NT signaling in cells, consistent with our computational and microarray data. This is the first demonstration that CS-E is involved in NT signaling and that CS is capable of supporting multimeric signaling complexes.
\r\n\r\nIn addition to stimulating growth factor signaling, CS has been known to repulsively guide retinal ganglion cell (RGC) axons for over twenty years. However, its function in vivo is unknown. RGCs are the only neuron type that transmits visual information to the brain, and their guidance, which maps a topographic projection of the retina to the superior colliculus (SC), is tightly regulated. Here, we show that CS-E is required for the proper formation of this topographic order. CS-E, but not the other major sulfation patterns, is a repellent guidance cue for RGC axons, with a graded activity profile from low to high along the dorsal-ventral axis of the retina, congruent with EphB3 expression. EphB3 binds specifically to CS-E with physiologically relevant affinity, and is required for CS-E-mediated guidance. CS-E-null mice have defects in topographic mapping in which ventral axons form ectopic termina- tions medial to their correct location in the SC. These results indicate that CS is a repulsive guidance cue required to map the dorsal-ventral axis of the retina along the lateral-medial axis of the SC. This is the first report of a non-protein topographical\r\nguidance cue.
" }, { "name": "Santori, Elizabeth Anne", "degree": "PhD", "year": "2013", "title": "Si Microwire Array Photoanodes for Artificial Photosynthetic Devices", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:11172012-135639556", "creators": [ { "name": { "family": "Santori", "given": "Elizabeth Anne" }, "id": "Santori-Elizabeth-Anne", "display_name": "Santori, Elizabeth Anne" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5YDX-5Y66", "abstract": "To realize the large-scale deployment of solar power, new materials and strategies must be developed for the fabrication of economical and sustainable artificial photosynthetic devices. These systems have multiple constraints, which are typically met by employing expensive, multi-junction solar cells coupled to noble metal catalysts. However, to supply and store power on a global, terawatt scale, these technologies must shift towards utilizing abundant elements and low-cost deposition techniques, while maintaining device efficiency. Driven by these challenges, this thesis presents achievements in Si microwire arrays to realize cost competitive and sustainable artificial photosynthetic devices.
\r\n\r\nThe device performance of Si microwire arrays, a thin-film photovoltaic technology, was investigated using photoelectrochemical methods. Both n-type and lightly doped Si microwire arrays demonstrated improved performance as photoanodes, and may be used in an artificial photosynthetic device to perform oxidative reactions. In addition, lightly doped Si microwire arrays operating under high-level injection conditions achieved performance comparable to that of optimally doped p-type Si microwire array photocathodes, with Voc values exceeding 450 mV and carrier collection efficiencies of ~ 0.85. A model of these devices operating under high-level injection conditions was developed, using finite-element device physics simulations. These simulations predicted that the carrier collection efficiencies of the devices should deviate from unity, even for minority-carrier diffusion lengths greater than the radius. Such behavior was confirmed by experimental internal quantum yield measurements, reaffirming that these devices are limited by axial transport of carriers along the length of the wire. However, optimized arrays have the potential to generate voltages that exceed those generated by arrays operating under low-level injection conditions. Such studies offer increased understanding of the performance of structured, concentrator photovoltaics and considerations for structuring lightly doped materials on the nano- and microscale.
\r\n" }, { "name": "Shen, Kuang", "degree": "PhD", "year": "2013", "title": "Novel Roles of the SRP RNA in Co-Translational Protein Targeting", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05292013-215935625", "creators": [ { "name": { "family": "Shen", "given": "Kuang" }, "id": "Shen-Kuang", "display_name": "Shen, Kuang" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NWWW-0867", "abstract": "The signal recognition particle (SRP) and its receptor (SR) are universally conserved protein machineries that deliver nascent peptides to their proper destination. The SRP RNA is a universally conserved and essential component of SRP, which serves as the \u201ccatalyst\u201d of the protein targeting cycle. The SRP RNA accelerates SRP-SR complex formation at the beginning of the protein targeting reaction, and triggers GTP hydrolysis and SRP-SR complex disassembly at the end. Here we combined biochemical and biophysical approaches to investigate the molecular mechanism of the functions of the SRP RNA. We found that two functional ends in the SRP RNA mediate distinct functions. The tetraloop end facilitates initial assembly of SRP and SR by mediating an electrostatic interaction with the Lys399 receptor, which ensures efficient and accurate substrate targeting. At the later stage of the SRP cycle, the SRP-SR complex relocalizes ~ 100 Angstrom to the 5\u2019,3\u2019-distal end of the RNA, a conformation crucial for GTPase activation and cargo handover. These results, combined with recent structural work, elucidate the functions of the SRP RNA during the protein targeting reaction. " }, { "name": "Suess, Daniel Leif Migdow", "degree": "PhD", "year": "2013", "title": "Reactions of Small Molecules Facilitated by Metal-Acceptor Interactions", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302013-182601874", "creators": [ { "name": { "family": "Suess", "given": "Daniel Leif Migdow" }, "id": "Suess-Daniel-Leif-Migdow", "display_name": "Suess, Daniel Leif Migdow" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q4B0-AG41", "abstract": "The role of metal-acceptor interactions arising from M\u2013BR3 and M\u2013PR3 bonding is discussed with respect to reactions between first-row transition metals and N2, H2, and CO. Thermally robust, S = 1/2 (TPB)Co(H2) and (TPB)Co(N2) complexes (TPB = tris(2- (diisopropylphosphino)phenyl)borane) are described and the energetics of N2 and H2 binding are measured. The H2 and N2 ligands are bound more weakly in the (TPB)Co complexes than in related (SiP3)M(L) complexes (SiP3 = tris(2- (diisopropylphosphino)phenyl)silyl). Comparisons within and between these two ligand platforms allow for the factors that affect N2 (and H2) binding and activation to be delineated. The characterization and reactivity of (DPB)Fe complexes (DPB = bis(2- (diisopropylphosphino)phenyl)phenylborane) in the context of N2 functionalization and E\u2013H bond addition (E = H, C, N, Si) are described. This platform allows for the one-pot transformation of free N2 to an Fe hydrazido(-) complex via an Fe aminoimide intermediate. The principles learned from the N2 chemistry using (DPB)Fe are applied to CO reduction on the same system. The preparation of (DPB)Fe(CO)2 is described as well as its reductive functionalization to generate an unprecedented Fe dicarbyne. The bonding in this highly covalent complex is discussed in detail. Initial studies of the reactivity of the Fe dicarbyne reveal that a CO-derived olefin is released upon hydrogenation. Alternative approaches to uncovering unusual reactivity using metal- acceptor interactions are described in Chapters 5 and 6, including initial studies on a new \u03c0-accepting tridentate diphosphinosulfinyl ligand and strategies for designing ligands that undergo site-selective metallation to generate heterobimetallic complexes." }, { "name": "Ting, Christina Lei", "degree": "PhD", "year": "2013", "title": "A Novel Method for Studying Nucleated Pathways in Membranes: Development and Applications for Gene Delivery", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:08282012-110955629", "creators": [ { "name": { "family": "Ting", "given": "Christina Lei" }, "id": "Ting-Christina-Lei", "display_name": "Ting, Christina Lei" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "biochem" ], "doi": "10.7907/8FTH-8H35", "abstract": "The development of a safe, selective, and efficient gene delivery system is key to the success of human gene therapy. In polymer-based gene delivery systems, biocompatible polymers electrostatically bind and condense the genetic material into protective nanoparticles. These nanoparticles must subsequently overcome several challenges, which remain poorly understood. In particular, once internalized by the cell, the nanoparticles are trapped inside a membrane-bound compartment called the endosome. In the proton sponge hypothesis, the buffering capacity of the polymers leads to an increase in osmotic pressure that eventually ruptures the endosomal membrane and releases the trapped nanoparticles.
\r\n\r\nTo obtain a mechanistic understanding of the endosomal escape, we first develop a coarse-grained model to study the equilibrium interaction between a positively charged nanoparticle and a lipid membrane. Results indicate the existence of a pore with an inserted particle, whose metastability depends on the membrane tension and particle properties (size and charge). These pores are subsequently shown to lower the critical tension necessary for membrane rupture, thus possibly enhancing the release of the trapped genetic material from the endosome.
\r\n\r\nNext, we address the actual escape pathway, which is likely a thermally nucleated process and cannot be simulated directly or studied by equilibrium methods. Hence, we develop a novel method for studying minimum free energy paths in membranes. Our results indicate that thermally nucleated rupture may be an important factor for the low rupture strains observed in lipid membranes. Under the moderate tensions found in this regime, there are multiple pathways for crossing the membrane: (1) particle-assisted membrane rupture, (2) particle insertion into a metastable pore followed by translocation and membrane resealing, and (3) particle insertion into a metastable pore followed by membrane rupture. This suggests a direct role of the nanoparticle in the endosomal escape not previously envisioned in the proton sponge hypothesis, and illustrates the importance of having an induced tension on the membrane.
\r\n\r\nFinally, the methodology developed in this work represents the most advanced theoretical technique for describing nucleation pathways in soft condensed matter systems that also include hard-particle degrees of freedom. We expect the method to be useful for studying a wide range of nucleation phenomena beyond membrane systems, for example, in nanoparticle polymer composites.
\r\n" }, { "name": "Truong, Frank", "degree": "PhD", "year": "2013", "title": "Expanding Protein Sequence Space through Incorporation of Non-Canonical Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02182013-221231959", "creators": [ { "name": { "family": "Truong", "given": "Frank" }, "id": "Truong-Frank", "display_name": "Truong, Frank" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Ismagilov", "given": "Rustem F." }, "id": "Ismagilov-R-F", "orcid": "0000-0002-3680-4399", "role": "member", "display_name": "Ismagilov, Rustem F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6CXB-2092", "abstract": "Protein sequence space has been augmented by researchers wanting to expand the diversity of chemical functionalities that can exist within proteins. Artificial amino acids can range from simple atom substitutions such as fluorination, to installation of reactive handles like azides and alkynes. Researchers build upon the framework of natural proteins and have developed methods of installing a wide variety of artificial amino acids into proteins. Chapter 1 discusses in detail the two methods for metabolic incorporation of unnatural amino acids: site-specific incorporation and residue-specific incorporation. Advantages and disadvantages to each method are detailed as well as applications of these methods to the examination of problems in chemical biology.
\r\n\r\nNon-canonical amino acids analogues that are structurally similar to their canonical counterparts can be recognized by the endogenous translational machinery for residue-specific incorporation. Chapter 2 describes the directed evolution of the methionyl-tRNA synthetase (MetRS) to incorporate propargylglycine, an alkyne analogue that is not recognized by the wild-type MetRS. A new MetRS variant active towards propargylglycine was identified after screening libraries of both active site mutations and error-prone PCR mutations. PraRS is capable of producing proteins where methionine is quantitatively replaced by propargylglycine. PraRS also does not recognize azidonorleucine, an azide methionine analogue for which the NLL-MetRS was evolved in order to enable cell-specific protein labeling. A method to identify cellular origins of proteins from two different bacterial strains in co-culture was developed using the NLL-MetRS and PraRS.
\r\n\r\nhapter 3 illustrates the effects of global incorporation of non-canonical amino acids into globular proteins. Although trifluoroleucine and homoisoleucine have shown to increase the thermostability of model proteins, incorporation into more chloramphenicol acetyltransferase (CAT) does not yield the same benefits. We find that mutations that stabilize CAT for fluorinated amino acid incorporation do not protect against homoisoleucine incorporation.
\r\n\r\nLastly, access to new chemical reactions for protein modification requires synthesis and incorporation of new non-canonical amino acid analogues. Chapter 4 describes the design of two new artificial amino acids, S-allyl-homocysteine and 3-furanylalanine, for residue specific incorporation without expression of mutant synthetases. Also, a third amino acid, azidomethylphenylalanine, was designed for activation by a previously discovered phenylalanine-tRNA synthetase mutant. Incorporation of these three analogues provides chemical handles that are potential reagents for cross metathesis, Diels-Alder cycloaddition, and generation of a molecular epitope for binding to synthetic receptors.
\r\n" }, { "name": "Van Wingerden, Matthew Martin", "degree": "PhD", "year": "2013", "title": "Improving the Efficiency of Ruthenium-Catalyzed Olefin Metathesis with Solid-Supported Catalysts, Microfluidic Reactors, and Novel X-Type Ligands ", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062013-162840550", "creators": [ { "name": { "family": "Van Wingerden", "given": "Matthew Martin" }, "id": "Van-Wingerden-Matthew-Martin", "display_name": "Van Wingerden, Matthew Martin" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2A9B-HY16", "abstract": "Olefin metathesis has become an important tool in modern organic chemistry. Key to the development of olefin metathesis as a methodology has been the discovery of the highly active, selective, and tolerant ruthenium-based Grubbs catalysts. The overall efficiency and utility of these catalysts are determined by a complex set of parameters including catalyst design, reaction conditions, reactor design, and purification strategy. These parameters can be varied to achieve higher catalyst turnovers, better product selectivity and reduced product contamination. This research seeks to improve the efficiency and utility of olefin metathesis using three strategies; the covalent attachment of catalysts to silica supports, the development of biphasic microfluidic reactors, and the synthesis of novel catalyst architectures.
\r\n\r\nSolid-supported catalysts present an effective strategy to eliminate metal contamination in metathesis products. These catalysts, however, are generally ill defined and their active species and decomposition pathways are poorly understood. In order to further study both the activity and decomposition of silica-supported catalysts, both a brominated alkylidene ligand and a cleavable linker were prepared. The brominated ligand was designed to bind only active catalyst, but was found to indiscriminately bind all ruthenium species. The cleavable linker was synthesized with an ortho-benzyl nitro ether moiety, rendering it cleavable by UV light. Future studies will use this UV-triggered lability to study the solid-supported catalysts with solution phase techniques.
\r\n\r\nBiphasic microfluidic reactors were developed to address the generation or consumption of ethylene gas in metathesis. By using either alternating flow or parallel flow gas-liquid reactors, the mass transfer of ethylene was facilitated. The enhanced mass transfer gave higher yields and catalyst turnovers in ethenolysis and ring-closing metathesis reactions.
\r\n\r\nNovel catalyst architectures were designed and synthesized to increase catalyst activity. While chloride-based catalysts have generally been used because of their higher activity, the activity of fluoride and hydroxide catalysts remains under explored, due mainly to practical challenges associated with their synthesis. A set of fluoride catalysts based on the Piers-type catalyst and a hydroxide catalyst based on the recently developed Z-selective catalysts were synthesized and characterized. The hydroxide catalyst showed promising activity while the fluoride catalyst was found to be inactive under all but the most forcing of conditions.
\r\n\r\nIn general, the utility of ruthenium-based catalysts has caused rapid growth in the field of olefin metathesis. The work presented herein covers a variety of strategies to improve the overall utility and efficiency of these catalysts, including insights into decomposition pathways, controlling phase interactions, and synthesizing novel catalysts. Further pursuits of these strategies will prove valuable to the advancement of olefin metathesis.
" }, { "name": "Warren, Emily Lowell", "degree": "PhD", "year": "2013", "title": "Silicon Microwire Arrays for Photoelectrochemical and Photovoltaic Applications", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212013-111210437", "creators": [ { "name": { "family": "Warren", "given": "Emily Lowell" }, "id": "Warren-Emily-Lowell", "orcid": "0000-0001-8568-7881", "display_name": "Warren, Emily Lowell" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/8Q2S-DX81", "abstract": "Si microwire (Si MW) arrays grown by the vapor-liquid-solid (VLS) process are promising materials for next-generation solar energy devices. High-aspect-ratio semiconductor structures have attracted recent interest as solar absorber materials because their radial geometry decouples the direction of light absorption and carrier collection, enabling the use of materials with shorter minority-carrier diffusion lengths than would be acceptable in a planar geometry. The VLS growth process is a low-cost deposition technique, which can be used to fabricate flexible, high-performance semiconductor materials. Si MW arrays have been investigated as an inexpensive alternative to wafer-based solar photovoltaics for low- cost electricity generation. Another potential application is to use these vertically oriented wire arrays as photocathodes of a solar fuel conversion devices, where instead of producing electricity, sunlight is used to directly drive a fuel-forming reaction (e.g., splitting water to form O2 and H2). The high aspect ratio of the Si MW arrays provides a large surface area for the integration of fuel-forming catalysts, allowing for the development of a low-cost, scalable, energy storage technology.
\r\n\r\nThis thesis discusses the fabrication and photoelectrochemical characterization of Si MWs grown by the VLS process, focusing on the use of these wire arrays as hydrogen- evolving photocathodes for solar water-splitting. To optimize such a device it is important to balance all of the factors that will affect performance: light absorption, band energetics, attainable open circuit voltage, and catalysis. First, we characterize the electrical performance of the wire arrays using regenerative photoelectrochemistry to understand the material quality and band energetics at the Si/water interface. We demonstrate the fabrication of H2-evolving photocathodes using p-n junction Si MW arrays and earth-abundant Ni\u2013Mo alloy hydrogen evolution catalysts. We then investigate modifying the fabrication techniques for wire growth to lower the cost and processing time required to grow arrays of Si MWs. Finally, we study the band energetics of Si decorated with Pt to build a preliminary model of the heterogeneous catalyst/semiconductor/liquid interface.
" }, { "name": "Wibowo, Arif", "degree": "PhD", "year": "2013", "title": "Identification of Fucose-\u03b1(1-2)-Galactose Binding Proteins in the Mammalian Brain", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012013-114632816", "creators": [ { "name": { "family": "Wibowo", "given": "Arif" }, "id": "Wibowo-Arif", "display_name": "Wibowo, Arif" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ETC4-N802", "abstract": "Fucose-\u03b1(1-2)-galactose (Fuc\u03b1(1-2)Gal) carbohydrates have been implicated in cognitive functions. However, the underlying molecular mechanisms that govern these processes are not well understood. While significant progress has been made toward identifying glycoconjugates bearing this carbohydrate epitope, a major challenge remains the discovery of interactions mediated by these sugars. Here, we employ the use of multivalent glycopolymers to enable the proteomic identification of weak affinity, low abundant Fuc\u03b1(1-2)Gal-binding proteins (i.e. lectins) from the brain. End-biotinylated glycopolymers containing photoactivatable crosslinkers were used to capture and enrich potential Fuc\u03b1(1-2)Gal-specific lectins from rat brain lysates. Candidate lectins were tested for their ability to bind Fuc\u03b1(1-2)Gal, and the functional significance of the interaction was investigated for one such candidate, SV2a, using a knock-out mouse system. Our results suggest an important role for this glycan-lectin interaction in facilitating synaptic changes necessary for neuronal communication. This study highlights the use of glycopolymer mimetics to discover novel lectins and identify functional interactions between fucosyl carbohydrates and lectins in the brain." }, { "name": "Wiley, Devin Thomas", "degree": "PhD", "year": "2013", "title": "Design of Nanoparticles that Cross the Blood-Brain Barrier by Receptor Mediated Transcytosis", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062013-145838327", "creators": [ { "name": { "family": "Wiley", "given": "Devin Thomas" }, "id": "Wiley-Devin-Thomas", "display_name": "Wiley, Devin Thomas" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Webster", "given": "Paul" }, "id": "Webster-P", "role": "member", "display_name": "Webster, Paul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DKRM-S631", "abstract": "The primary objective of my thesis work is to establish a set of design criteria for nanoparticles whose purpose is to safely and efficiently access the brain after systemic injection. Nanoparticles that can access the brain may be able to deliver therapeutic molecules to the brain that otherwise would be excluded by the blood-brain barrier.
\r\n\r\nE. coli glycoprotein 96 (Ecgp96) is explored as a candidate receptor on the blood-brain barrier that could potentially facilitate nanoparticle-receptor mediated transcytosis into the brain. Results from studies utilizing PET/CT, SPECT/CT, MRI, Xenogen fluorescence imaging, and confocal microscopy conclude that Ecgp96 is observed in the blood-brain barrier endothelial cells, but is not accessible from the blood of adult or neonatal mice under normal, non-pathological conditions.
\r\n\r\nTransferrin receptor is a well-characterized receptor on the blood-brain barrier that is accessible from the blood and known to transcytose transferrin. I focused on this receptor and on synthesizing and characterizing a well-defined set of transferrin containing gold nanoparticles of various sizes and transferrin compositions that would be investigated during in-vivo studies. Nanoparticle sizes were measured by DLS and nanoparticle tracking analysis. Zeta potentials were also measured. Nanoparticle transferrin content was directly measured by labeling transferrin with 64Cu and measuring the nanoparticle associated gamma activity. The nanoparticle binding avidities to mouse transferrin receptors were ranked by a silver enhancement fluorescence-based method using the mouse Neruo2A cell line.
\r\n\r\nEach nanoparticle formulation was systemically injected into mice, and localization in the mouse brain was observed by silver enhancement light microscopy, and TEM. The quantitation of the gold was determined by ICP-MS. Nanoparticles with large amounts of transferrin remain strongly attached to brain endothelial cells, while nanoparticles with less transferrin are capable of both interacting with transferrin receptor on the luminal side of the blood-brain barrier and detaching from transferrin receptor on the brain side of the blood-brain barrier. These results highlight the fact that the nanoparticle avidity must be tuned to maximize the number of nanoparticles exiting the endothelial cells and entering the brain tissue. Lanthanum nitrate perfusion-fixation studies demonstrate that the nanoparticle formulations investigated do not degrade the blood-brain barrier integrity and enter the brain by transferrin receptor-mediated transcytosis. The results from these studies provide initial design criteria for creating nanoparticle therapeutics for delivery to the brain from systemic administrations.
\r\n" }, { "name": "Williamson, Heather R.", "degree": "PhD", "year": "2013", "title": "Engineering Multi Step Electron Tunneling Systems in Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112013-202017350", "creators": [ { "name": { "family": "Williamson", "given": "Heather R." }, "id": "Williamson-Heather-R", "display_name": "Williamson, Heather R." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BRZJ-YZ76", "abstract": "Multi-step electron tunneling, or \u201chopping,\u201d has become a fast-developing research field with studies ranging from theoretical modeling systems, inorganic complexes, to biological systems. In particular, the field is exploring hopping mechanisms in new proteins and protein complexes, as well as further understanding the classical biological hopping systems such as ribonuclease reductase, DNA photolyases, and photosystem II. Despite the plethora of natural systems, only a few biologically engineered systems exist. Engineered hopping systems can provide valuable information on key structural and electronic features, just like other kinds of biological model systems. Also, engineered systems can harness common biologic processes and utilize them for alternative reactions. In this thesis, two new hopping systems are engineered and characterized.
\r\n\r\nThe protein Pseudomonas aeruginosa azurin is used as a building block to create the two new hopping systems. Besides being well studied and amenable to mutation, azurin already has been used to successfully engineer a hopping system. The two hopping systems presented in this thesis have a histidine-attached high potential rhenium 4,7-dimethyl-1,10-phenanthroline tricarbonyl [Re(dmp)(CO)3] + label which, when excited, acts as the initial electron acceptor. The metal donor is the type I copper of the azurin protein. The hopping intermediates are all tryptophan, an amino acid mutated into the azurin at select sites between the photoactive metal label and the protein metal site. One system exhibits an inter-molecular hopping through a protein dimer interface; the other system undergoes intra-molecular multi-hopping utilizing a tryptophan \u201cwire.\u201d The electron transfer reactions are triggered by excitation of the rhenium label and monitored by UV-Visible transient absorption, luminescence decays measurements, and time-resolved Infrared spectroscopy (TRIR). Both systems were structurally characterized by protein X-ray crystallography.
" }, { "name": "Winston, Matthew Steven", "degree": "PhD", "year": "2013", "title": "Chemistry of PNP Bis(phosphide) Pincer Ligands and Palladium(II) Dimers as Robust, Versatile Precatalysts for Olefin Isomerization, Oligomerization, and Oxidation", "advisor": "Bercaw, John E.; Labinger, Jay A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10052012-153447918", "creators": [ { "name": { "family": "Winston", "given": "Matthew Steven" }, "id": "Winston-Matthew-Steven", "display_name": "Winston, Matthew Steven" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "co-advisor", "display_name": "Labinger, Jay A." } ], "committee": [ { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "chair", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/GES9-N146", "abstract": "The first half of this thesis details the synthesis and coordination chemistry of a very unusual pyridine-linked bis(secondary phosphine) pincer ligand system. Despite the highly nucleophilic phosphide donors, this dianionic system is an unexpectedly poor pincer ligand. Crystallographic and DFT studies reveal that both phosphide-metal \u03c3- and \u03c0-bonding is compromised by long metal-phosphorus bonds, which result in significant distortions to the chelate ring. The neutral ligand coordinates readily \u03ba2 (via phosphines) to late metals, such as palladium(II), affording P-chirogenic diastereomers. Crystallographic and spectroscopic analysis of a series of palladium(II) dihalides stabilized by this bis(phosphine) indicate that one diastereomer is enthalpically favored, while the other more structurally versatile diastereomer is favored entropically. There is also evidence of an interesting phosphine epimerization pathway assisted by the non-coordinated pyridine ring.
\r\n\r\nEthylene polymerization and ethylene/1-hexene copolymerization activities of several zirconium(IV) and vanadium(III) polymerization precatalysts supported by heterocycle-linked bis(phenolate) ligands are also discussed. Activities as high as 106 g PE/(mol x h) were observed, but only the vanadium catalyst incorporates comonomer, albeit with low efficiency (<1 mol%).
\r\n\r\nFinally, catalytic applications of air- and water-tolerant bis(\u03bc-hydroxy) palladium(II) dimers have been investigated. Mechanistic studies show that this precatalyst can oxygenate olefins via a Wacker-type mechanism upon dimer dissociation. In the absence of stoichiometric oxidant, the resulting palladium(II) hydride intermediate can then isomerize and oligomerize olefins with turnover numbers at room temperature as high as 2100/h and 600/h, respectively. We also show that the catalyst is insensitive to water and air, so that olefin isomerization and oligomerization can be carried out on the benchtop in the absence of activators. In the presence of excess tert-butylhydroperoxide, Wacker-type behavior is favored, and neither isomerization nor oligomerization is observed. These dimers can also catalyze the aerobic dehydrogenation of cyclohexene to benzene with relatively low turnover numbers (1/h). Nevertheless, mechanistic studies indicate a C-H activation/\u03b2-hydride elimination sequence that does not involve an allylic-activated species.
\r\n" }, { "name": "Zhang, Bin", "degree": "PhD", "year": "2013", "title": "Sec-facilitated Protein Translocation and Membrane Integration", "advisor": "Miller, Thomas F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172012-174905364", "creators": [ { "name": { "family": "Zhang", "given": "Bin" }, "id": "Zhang-Bin", "display_name": "Zhang, Bin" } ], "advisors": [ { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "advisor", "display_name": "Miller, Thomas F." } ], "committee": [ { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "chair", "display_name": "Clemons, William M." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6WWV-V190", "abstract": "The Sec translocon is a central component of the cellular machinery for targeting and delivering nascent proteins. Ubiquitous across all kingdoms of life, it is a protein-conducting channel that facilitates recognition of integral membrane protein domains and the establishment of integral membrane protein topology. Structural, biochemical, and biophysical studies have illuminated the role of the Sec translocon in both cotranslational and posttranslational protein targeting. In particular, quantitative assays have established the dependence of transmembrane domain (TM) stop-transfer efficiency and integral membrane protein topogenesis on the physicochemical properties of the translocon and protein nascent chain. These studies provide a valuable starting point for understanding the molecular regulation of the translocon and its sensitivity to mutations in protein sequence and external driving forces; however, complexities associated with the Sec machinery, including the role of collaborating molecular motors, the importance of large-scale conformational changes in the translocon, and the crowded molecular environment of the channel interior, obscure the mechanistic basis for many experimentally observed trends. My PhD research has focused on the development of a unified, mechanistic understanding of Sec-facilitated protein targeting.
\r\n\r\nUsing both atomistic and coarse-grained molecular simulations, we have investigated the conformational landscape for the Sec translocon. We found that inclusion of a hydrophobic peptide substrate in the translocon stabilizes an open conformation of the lateral gate (LG) that is necessary for membrane integration, whereas inclusion of a hydrophilic peptide substrate favors only the closed LG conformation. We demonstrated that the translocon plug moiety adopts markedly different conformations in the channel, depending on whether the substrate peptide is hydrophobic or hydrophilic in character. Finally, we showed that the energetics of the translocon LG opening in the presence of the substrate peptides can be modeled in terms of the energetics of the peptide interface with the membrane. The manuscript associated with this study is published in PNAS, 107, 5399 (2010).
\r\n\r\nWe further developed a novel computational protocol that combines nonequilibrium growth of the nascent protein with microsecond-timescale molecular dynamics trajectories. Analysis of multiple, long-timescale simulations elucidated molecular features of protein insertion into the translocon, including signal-peptide docking at the translocon LG, large-lengthscale conformational rearrangement of the translocon LG helices, and partial membrane integration of hydrophobic nascent-protein sequences. Furthermore, the simulations demonstrated the role of specific molecular interactions in the regulation of protein secretion, membrane integration, and integral membrane protein topology. Salt-bridge contacts between the nascent-protein N-terminus, cytosolic translocon residues, and phospholipid head groups were shown to favor conformations of the nascent protein upon early-stage insertion that are consistent with the Type II (Ncyt/Cexo) integral membrane protein topology; and extended hydrophobic contacts between the nascent protein and the membrane lipid bilayer were shown to stabilize configurations that are consistent with the Type III (Nexo/Ccyt) topology. These results provide a detailed, mechanistic basis for understanding experimentally observed correlations between integral membrane protein topology, translocon mutagenesis, and nascent-protein sequence. The manuscript associated with this study is published in J. Am. Chem. Soc., 134, 13700 (2012).
\r\n\r\nFinally, we introduced a coarse-grained modeling approach that spans the nanosecond to minute-timescale dynamics of cotranslational protein translocation. The method enabled direct simulation of both integral membrane protein topogenesis and TM stop-transfer efficiency. Simulations revealed multiple kinetic pathways for protein integration, including a mechanism in which the nascent protein undergoes slow-timescale reorientation, or flipping, in the confined environment of the translocon channel. Competition among these pathways gives rise to the experimentally observed dependence of protein topology on ribosomal translation rate and protein length. We further demonstrated that sigmoidal dependence of stop-transfer efficiency on TM hydrophobicity arises from local equilibration of the TM across the translocon LG, and it was predicted that slowing ribosomal translation yields decreased stop-transfer efficiency in long proteins. This work reveals the balance between equilibrium and nonequilibrium processes in protein targeting, and it provides new insight into the molecular regulation of the Sec translocon. The manuscript associated with this study is published in Cell Reports, in press.
\r\n\r\nThis research has significantly enriched the mechanistic understanding of Sec-facilitated protein translocation and membrane integration with ample molecular details. The unifying picture that we propose establishes fundamental connections between previously disparate experimental studies, and it lays down the foundation for future verification and refinement.
" }, { "name": "Blum, Angela Patricia", "degree": "PhD", "year": "2012", "title": "Structure-Function Studies of Nicotinic Acetylcholine Receptors Using Unnatural Amino Acids and Synthetic Agonist Analogs ", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042011-173102026", "creators": [ { "name": { "family": "Blum", "given": "Angela Patricia" }, "id": "Blum-Angela-Patricia", "display_name": "Blum, Angela Patricia" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KFPV-JN09", "abstract": "This dissertation primarily describes structure-function studies of the prototypical Cys-loop ligand-gated ion channel, the nicotinic acetylcholine receptors (nAChRs).
\r\n\r\nAgonists that bind nAChRs, including acetylcholine, nicotine, and the smoking cessation drug varenicline, share one of the longest-known, best-studied pharmacophores, consisting of a cationic N and a hydrogen bond acceptor. A major theme of this thesis is concerned with defining the nAChR residues that bind the nicotinic pharmacophore. Chapters 2 and 3 establish that a hydrogen bond links the pharmacophore\u2019s hydrogen bond acceptor to a backbone NH in the protein. The establishment of this interaction, and the disproval of other predicted interactions, represents the completion of the nicotinic pharmacophore binding model. Chapter 4 uses this model to characterize how the nAChR differentiates between stereoisomers of an agonist.
\r\n\r\nChapter 5 describes functional studies of a vicinal disulfide that has played a pivotal role in a number of pioneering studies of nAChRs. Despite its historical importance, the functional role of this disulfide has not been defined. We identify a speculative role for the vicinal disulfide that involves the formation of a functionally important network of hydrogen bonds.
\r\n\r\nChapter 6 outlines three strategies for the photochemical cleavage of protein and peptide backbones using unnatural amino acids. One of these strategies is based on a selenide-mediated cleavage of a backbone ester moiety. Model studies establish the viability of this chemistry and suggest that it could be a useful tool for protein structure-function studies.
\r\n\r\nChapter 7 concerns preliminary work from a collaboration with laboratories from USC and Caltech that is aimed at developing small-molecule treatments for vision loss associated with photoreceptor degeneration. The initial goal of this project is to develop a photosensitive small molecule that can activate a voltage-gated potassium channel.
\r\n\r\nThe final chapter discusses work that was done in the Grubbs lab at Caltech in which a strategy for preparing N-heterocyclic carbene-containing metal complexes was developed.
\r\n \t\r\n\r\n" }, { "name": "Cheng, Mu-Jeng", "degree": "PhD", "year": "2012", "title": "Mechanistic Insights into Alkane C-H Activation and Functionalization by Metal Oxide Surfaces and Organometallic Complexes", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222012-224148199", "creators": [ { "name": { "family": "Cheng", "given": "Mu-Jeng" }, "id": "Cheng-Mu-Jeng", "display_name": "Cheng, Mu-Jeng" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K4XH-V434", "abstract": "Alkanes are the major components of natural gas and petroleum; however, there are only few practical processes that can functionalize them into more valuable products such as alkene or alcohols. The reason for this difficulty is because alkanes possess strong and inert C-H bonds. The development of such a process that can convert alkanes to other more valuable functionalized hydrocarbons in a catalytic fashion would produce enormous economic benefits. The key to achieve this goal is to develop a proper catalyst. The catalysts can be organometallic complexes or metal oxide surfaces that catalyze alkane C-H activation and functionalization in homogeneous or heterogeneous conditions.
\r\n\r\nIn this thesis, we apply quantum mechanics to study the known alkane functionalization reactions to provide more insight into those catalytic processes, and we further utilize our computational results to design new reaction pathways for alkane functionalization. Each chapter presented herein constitutes an independent publication focusing on different aspects of the problem.
\r\n\r\nChapter 1: Single-Site Vanadyl Activation, Functionalization, and Reoxidation Reaction Mechanism for Propane Oxidative Dehydrogenation on the Cubic V4O10 Cluster: Vanadium oxide is a powerful heterogeneous catalyst that can convert oxidative dehydrogenation (ODH) of propane. Despite numerous studies, either computational or experimental, on this topic, no complete catalytic cycle is provided. In this paper, we examined the detailed mechanism for propane reacting with a V4O10 cluster to model the catalytic oxidative dehydrogenation (ODH) of propane on the V2O5(001) surface. We reported the mechanism of the complete catalytic cycle, including the regeneration of the reduced catalyst using gaseous O2, in which only a single vanadyl site is involved. This mechanism is applicable to propane ODH on the supported vanadium oxide catalysts where only monovanadate (O=V-(O)4-) species is present.
\r\n \r\nChapter 2: The Magnetic and Electronic Structure of Vanadyl Pyrophosphate from Density Functional Theory: We have studied the magnetic structure of the high-symmetry vanadyl pyrophosphate, focusing on the spin exchange couplings, applying density functional theory with exact exchange and the full three-dimensional periodicity to this system for the first time. Based on the local density of states and the response of spin couplings to varying the cell parameter a, we found that two major types of spin exchange couplings originate from different mechanisms: one from a super-exchange interaction and the other from a direct exchange interaction. Based on the variations in V\u2013O bond length as a function of strain along a, we found that the V\u2013O bonds of V\u2013(OPO)2\u2013V are covalent and rigid, whereas the bonds of V\u2013(O)2\u2013V are fragile and dative.
\r\n\r\nChapter 3: The Para-Substituent Effect and pH-Dependence of the Organometallic Baeyer-Villiger Oxidation of Rhenium-Carbon Bonds: Organometallic Baeyer-Villiger represents another means of oxidizing M-R to M-OR. In this work, we conducted a series of calculations with the goal of providing more insights into the reaction. We find that during this organometallic BV oxidation, the migrating phenyl plays the role of a nucleophile and the leaving group OH is nucleophile. Moreover, we also find that for R = Ph the reaction rate is much faster than that for R = Me, which is later confirmed by experiments.
\r\n\r\nChapter 4: Carbon-Oxygen Bond-Forming Mechanisms in Rhenium Oxo-Alkyl Complexes: Intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds is one of the few means of oxy-functionalizing M-R to M-OR bonds. This strategy works for R = Ph, but fails for R = Me and Et. In this work, we study these systems with the goal of understanding the reason. We find that when R = Me and Et the \u03b1-hydrogen is very acidic and easy to abstract even with weak base, such as the counter ion of the complex, leading to unwanted by-products. We find that these side reactions can be avoided by two means: (1) use counter ions with weaker basicity to increase proton abstraction barriers, and (2) use R = iPr, which has a higher migratory aptitude, to accelerate the 1,2-migration rate.
\r\n \r\nChapter 5: A Homolytic Oxy-Functionalization Mechanism: Intermolecular Hydrocarbyl Migration from M-R to Vanadyl Oxo: Oxy-functionalization M\u03b4+-R\u03b4- to M-OR bonds is one of the key challenges in the development of hydrocarbon hydroxylation catalysts. This can be achieved by limited means: (1) organometallic Baeyer-Villiger oxidation, and (2) intramolecular 1,2-migration of hydrocarbyl across metal-oxo bonds. In this work, we have examined C-O bond formation in the reaction of OVCl3 with Ph2Hg to generate phenol using quantum mechanics. Surprisingly, we find this reaction is through an unprecedented bimolecular, one-electron oxidation of the V-Ph bond by a second V=O moiety, not through the experimentally proposed intramolecular phenyl 1,2-migration across V=O bonds. Our calculations on the oxidation of Rh-CH3 and Ir-CH3 complexes by OVCl3 further suggest that the possibility of integrating this new oxidation mechanism into alkane oxidation catalytic cycles. We also give guidelines to choose the systems in which this oxidation mechanism may play an important role.
" }, { "name": "Culic-Viskota, Jelena", "degree": "PhD", "year": "2012", "title": "Synthesis and Functionalization of Second Harmonic Generation Nanocrystals and Their Application in Biological Imaging", "advisor": "Fraser, Scott E.; Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282012-134754737", "creators": [ { "name": { "family": "Culic-Viskota", "given": "Jelena" }, "id": "Culic-Viskota-Jelena", "display_name": "Culic-Viskota, Jelena" } ], "advisors": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "advisor", "display_name": "Fraser, Scott E." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "co-advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "chair", "display_name": "Fraser, Scott E." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Pantazis", "given": "Periklis" }, "id": "Pantazis-P", "role": "member", "display_name": "Pantazis, Periklis" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XFXJ-7987", "abstract": "The discovery and use of fluorescent proteins has been of extreme importance in biological imaging of cells, tissues, and organs. In order to address some of the limitations of fluorescent tags, second harmonic generation can be used. Second harmonic generating nanoprobes allow nontoxic, long-term imaging that, with proper functionalization, can be utilized for biological imaging applications. As a proof of principle, commercial tetragonal barium titanate nanoparticles were functionalized to expose surface amine groups, which could be further modified for a plethora of biological applications. Barium titanate nanoparticles were functionalized for selective targeting of tissue sections, biorthogonal linkages and for nonspecific long-term imaging using biocompatible polymers enabling the study of cells as they differentiate during zebrafish development. Since the commercial barium titanate nanoparticles do not have a narrow size distribution, which limits the application of such nanoprobes, synthesis of monodisperse nanocrystals was attempted.
\r\n\r\nZinc oxide nanocrystals were synthesized by solvothermal methods involving the base hydrolysis of zinc salts in the presence of capping ligands. Different synthesis procedures were investigated based on the properties of the prepared nanoparticles. To prevent nanoparticle aggregation and to achieve good dispersion, a capping agent was chosen that provides a tightly bound shell around the nanoparticles. It was observed that the polymerization of PEG molecules with the organic ligands bound to the surface of zinc oxide provided the most adequate coating for the desired size control and dispersion of the nanocrystals. Exploration of the experimental conditions enabled production of variable size hexagonal zinc oxide nanocrystals, which can be used both as SHG probes and as quantum dots.
" }, { "name": "Downard, Andrew Joseph", "degree": "PhD", "year": "2012", "title": "Classification of Sub-10 nm Aerosol: Theory, Instrument Development, and Experiment", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302012-163207555", "creators": [ { "name": { "family": "Downard", "given": "Andrew Joseph" }, "id": "Downard-Andrew-Joseph", "display_name": "Downard, Andrew Joseph" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemeng" ], "doi": "10.7907/KP0F-8T32", "abstract": "The large diffusion coefficients of sub-10 nm aerosol have posed a long-standing challenge to the aerosol community; to understand nucleation and early growth, there is a need for methods such as those presented here that transmit a strong, high resolution signal of classified charged aerosol to the detector. I introduce a framework for comparison of the Flagan Laboratory classifiers to other instruments, and I show why our instruments perform favorably relative to these alternatives. Reducing the size of the classification region reduces the effect of diffusion on performance and will ultimately enable the development of personal health monitors. The deployment of our instruments to the Cosmics Leaving OUtdoor Droplets experiment at CERN motivated a deeper look into detector performance and design for extreme operating conditions. I caution about the possible interference of ion nucleation with measurements and introduce a process for optimizing detector performance at arbitrary temperature. My experience with aerosol classifications has inspired the invention of separation methods for related fields; I conclude by describing methods for the high resolution separation of gas ions and of aqueous particles such as proteins and antibodies." }, { "name": "Durrell, Alec Charles", "degree": "PhD", "year": "2012", "title": "Electronic Structures and Reactivity Patterns of Dipalladium(11,11) and Diplatinum(11,11) Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172012-112437443", "creators": [ { "name": { "family": "Durrell", "given": "Alec Charles" }, "id": "Durrell-Alec-Charles", "display_name": "Durrell, Alec Charles" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/91HV-2R03", "abstract": "This work explores the electronic structures and reactivity patterns of diplatinum(II, II) and dipalladium(II, II) complexes. Complexes containing metal-metal bonds play important roles in both inorganic and organometallic chemistry. Among the many examples of these complexes, dimers of square planar RhI, IrI, and PtII centers comprise a special class that feature attractive d8\u2013d8 interactions. The unique electronic structure characteristic of these complexes gives rise to chemical, photochemical, and photophysical properties that have engaged researchers for the past 35 years.
\r\n\r\nOne of the best-known examples of these compounds is tetrakis(\u00b5-pyrophosphito)platinum(II), Pt(pop). Herein, the photophysical properties of Pt(pop) are compared with its fluoroborated analogue, Pt(pop-BF2). This complex possesses eight BF2 groups that replace the hydrogen atoms located between each \u201cpop\u201d ligand. When compared with Pt(pop), Pt(pop-BF2) has a much greater singlet lifetime (1.56 ns) and singlet quantum yield (0.27). The enhancement is the result of a drastically slower 1A2u \u2192 3A2u intersystem crossing rate. In particular, the thermal barrier to intersystem crossing is significantly higher in Pt(pop-BF2) (2230 cm-1 vs. 1190 cm-1). We believe this is primarily the result of the increased rigidity of the complex afforded by the BF2 groups. The rigidity increases the energy of symmetry-lowering vibrational modes, which are necessary to promote spin-orbit mixing of the 1d\u03c3*p\u03c3 and 3d\u03c3*p\u03c3 states.
\r\n\r\nDespite the many examples of M-M bonded d8\u2013d8 complexes of RhI, IrI, and PtII in the literature, until recently there were no PdII complexes fitting this description. Our investigations of clamshell-shaped PdII dimers [(2-phenylpyridine)Pd(\u00b5-X)]2 and [(2-p-tolylpyridine)Pd(\u00b5-X)]2 (X = OAc or TFA) revealed short Pd\u2013Pd distances (~ 2.85 \u00c5). The molecules adopt this unusual geometry in part because of a d8\u2013d8 bonding interaction between the two Pd centers. Density functional theory (DFT) and ab initio (AI) analyses confirm the presence of a Pd\u2013Pd bonding interaction in [(2-phenylpyridine)Pd(\u00b5-X)]2 and show that the HOMO is a dz2 \u03c3*Pd\u2013Pd antibonding orbital, while the LUMO and proximal unoccupied orbitals are mainly located on the 2-phenylpyridine rings. Computational analyses of other PdII\u2013PdII dimers that have short Pd\u2013Pd distances yield an orbital ordering similar to that of [(2-phenylpyridine)Pd(\u00b5-X)]2, but quite different from that found for d8\u2013d8 dimers of Rh, Ir, and Pt. This difference in orbital ordering arises because of the unusually large energy gap between the 4d and 5p orbitals in Pd, and may explain why Pd d8\u2013d8 dimers do not exhibit the distinctive photophysical properties of related Rh, Ir, and Pt species.
\r\n\r\nOur work on PdII\u2013PdII electronic structures led us to employ these complexes as electrocatalysts in the regioselective chlorination of C\u2013H bonds. Previous work on d8\u2013d8 complexes has established that when treated with halogens (Cl2, Br2, or I2), the complex undergoes two-center oxidative addition to form an axially coordinated X\u2013d7\u2013d7\u2013X species. Similar products are observed following electrochemical oxidation in the presence of a halide (Cl\u2013, Br\u2013, or I\u2013). Recently, related PdII\u2013PdII complexes were found to selectively chlorinate benzo[h]quinoline through reductive elimination from a Cl\u2013PdIII\u2013PdIII\u2013Cl species. This led us to probe the viability of the analogous electrochemical route. Cyclic voltammetry, spectroelectrochemistry, and bulk electrolysis measurements confirm that electrochemical oxidation of PdII\u2013PdII yields the identical Cl\u2013PdIII\u2013PdIII\u2013Cl intermediate, which is capable of reductive chlorination of C\u2013H bonds. Additional evidence for formation of axially coordinated bromide and acetate species is also presented. Over 10 turnovers of 10-chlorobenzo[h]quinoline were achieved at 80% isolated yield. Further research into the area may lead to a potentially versatile, useful, and green route for C\u2013H bond functionalization reactions.
\r\n\r\n" }, { "name": "Galloway, Kate Elizabeth", "degree": "PhD", "year": "2012", "title": "The Development of RNA-based Control Systems to Regulate Signaling and Dictate Cell Fate in a Model MAPK Pathway", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072012-150636005", "creators": [ { "name": { "family": "Galloway", "given": "Kate Elizabeth" }, "id": "Galloway-Kate-Elizabeth", "display_name": "Galloway, Kate Elizabeth" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "role": "member", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/CBBN-GX03", "abstract": "Cells integrate extracellular information via native signaling pathways to spatially and temporally coordinate complex tasks such as development and the immune response. Cellular programming holds the potential of harnessing the sophisticated and complex biological processes of living cells for diverse applications. In the last decade, cellular reprogramming has emerged as a viable therapeutic strategy. In large, reprogramming strategies have relied on statically programmed levels of gene expression to alter cellular behaviors. To construct more sophisticated programs requires dynamic control of expression and strategies for the facile construction of complex control architectures. Additionally, the application of synthetic programs to the control of native regulatory pathways requires the development of tools for interfacing with these pathways, as well as the construction of stringent controllers. Further, control systems composed of modular and tunable elements will facilitate the expansion of synthetic circuitry to a wide array of natural networks with varying system properties.
\r\n \r\nHere we describe the development of RNA-based control systems to regulate signaling and dictate cell fate in a model mitogen-activated protein kinase (MAPK) pathway. We construct networks of RNA-based control systems that interface with the Saccharomyces cerevisiae mating pathway to dictate entry into one of three programmed alternative fates dependent on environmental stimuli. We present a readily translatable method for identifying control points within natural networks that enable the construction of a modular interface between synthetic circuitry and native networks. In building these networks, we demonstrate the rational tuning of circuit performance via the exchange of well-defined parts to compose networks capable of actuating changes in cellular behavior in response to environmental cues. Further, we construct network architectures which facilitate reduced interference from simultaneously integrated opposing programs and identified sensitive parameters for engineering robust circuit performance. Finally, we present the development of a novel RNA-based control element for the regulation of both synthetic and endogenous transcripts. This work provides a model for engineering systems that regulate signaling and direct cell fate which may be applied to additional decision-making pathways to advance tissue engineering strategies, treat diseases, and study the behavior of natural regulatory networks.
\r\n" }, { "name": "Gamba, Jason M.", "degree": "PhD", "year": "2012", "title": "The Role of Transport Phenomena in Whispering Gallery Mode Optical Biosensor Performance", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202012-131523365", "creators": [ { "name": { "family": "Gamba", "given": "Jason M." }, "id": "Gamba-Jason-M", "display_name": "Gamba, Jason M." } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Armani", "given": "Andrea" }, "id": "Armani-A-M", "role": "member", "display_name": "Armani, Andrea" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/DQP0-RY11", "abstract": "Whispering gallery mode (WGM) optical resonator sensors have emerged as promising tools for label-free detection of biomolecules in solution. These devices have even demonstrated single-molecule limits of detection in complex biological uids. This extraordinary sensitivity makes them ideal for low-concentration analytical and diagnostic measurements, but a great deal of work must be done toward understanding and optimizing their performance before they are capable of reliable quantitative measurents. The present work explores the physical processes behind this extreme sensitivity and how to best take advantage of them for practical applications of this technology.
\r\n\r\nI begin by examining the nature of the interaction between the intense electromagnetic elds that build up in the optical biosensor and the biomolecules that bind to its surface. This work addresses the need for a coherent and thorough physical model that can be used to predict sensor behavior for a range of experimental parameters. While this knowledge will prove critical for the development of this technology, it has also shone a light on nonlinear thermo-optical and optical phenomena that these devices are uniquely suited to probing. The surprisingly rapid transient response of toroidal WGM biosensors despite sub-femtomolar analyte concentrations is also addressed. The development of asymmetric boundary layers around these devices under ow is revealed to enhance the capture rate of proteins from solution compared to the spherical sensors used previously. These lessons will guide the design of ow systems to minimize measurement time and consumption of precious sample, a key factor in any medically relevant assay.
\r\n\r\nFinally, experimental results suggesting that WGM biosensors could be used to improve the quantitative detection of small-molecule biomarkers in exhaled breath condensate demonstrate how their exceptional sensitivity and transient response can enable the use of this noninvasive method to probe respiratory distress. WGM bioensors are unlike any other analytical tool, and the work presented here focuses on answering engineering questions surrounding their performance and potential.
" }, { "name": "Geil, Wendy Mercer", "degree": "PhD", "year": "2012", "title": "Regulation of Wild-Type and Mutant p53 through DNA-mediated Charge Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062011-140224145", "creators": [ { "name": { "family": "Geil", "given": "Wendy Mercer" }, "id": "Geil-Wendy-Mercer", "display_name": "Geil, Wendy Mercer" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0NVZ-QC23", "abstract": "The global transcription factor p53 controls many cellular processes, including the cellular response to oxidative stress. It had been determined that that dissociation of wild type p53 from its promoter site can occur upon DNA-mediated oxidation. In this work, we use site-directed mutagenesis to construct charge-deficient mutants of p53; the chemistry of DNA-mediated oxidation of p53 was examined using these mutants.
\r\n\r\nThe control point for p53 oxidation through DNA-mediated charge transport (DNA CT) is cysteine 275. Using differential thiol labeling and detection of modified peptides with mass spectrometry, we demonstrated that cysteines 124 and 141 in superstable p53 form a terminal disulfide bond upon DNA-mediated oxidation. This leads to a conformational change that inhibits DNA from binding by p53. The disulfide formed between cysteines 124 and 141 is a result of a series of disulfide bond exchange across the protein from the DNA base stack.
\r\n\r\nWe also investigated the dependence of p53 oxidation on DNA sequences. ESMA analysis of biologically derived p53 recognition sequences with varying quantities of guanine doublets and triplets showed efficient p53 oxidation to depend on the presence of low energy GG or GGG sites. Moreover, consistent results were found with biologically derived promoter sequences. Sequence S100A2, with guanine triplets on the same strand, showed the most oxidation of p53, followed by ODC1 and caspase-1. We confirmed these sequence-specific effects by measuring the change in expression level of the genes after induction of DNA CT in vivo. S100A2 mRNA levels decreased after photooxidant and light treatment, reflecting the oxidation and dissociation of p53 from the S100A2 site. However, caspase-1 and ODC1 mRNA levels remained the same, indicating less DNA-mediated p53 oxidation.
\r\n\r\nThe results from this study illustrate how protein oxidation at a distance through DNA CT contributes to cellular signaling. This oxidative signaling can control how p53 regulates gene expression under oxidative stress, and this signaling may be disrupted in cancerous cells.
\r\n" }, { "name": "Gilmore, Christopher Dennis", "degree": "PhD", "year": "2012", "title": "Aryne Annulation Reactions Toward the Synthesis of Heterocyclic Molecules", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212012-034245395", "creators": [ { "name": { "family": "Gilmore", "given": "Christopher Dennis" }, "id": "Gilmore-Christopher-Dennis", "display_name": "Gilmore, Christopher Dennis" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/C8F7-DQ34", "abstract": "The last decade has seen an outgrowth in the development of synthetic methodologies exploiting benzyne. The unique ability of this reactive intermediate to directly furnish ortho-difuntionalized aromatic systems first stoked interest in this research group as a possible partner in asymmetric arylation reactions. Since our initial forays, we have expanded our synthetic strategies to include bond insertions, cycloadditions, condensations, and multicomponent reactions. The first project discussed in this volume is the development of an aryne annulation strategy for constructing common, synthetically useful heterocyclic structures in a convergent manner. We have developed a convergent approach to indoles and indolines. Likewise, through an orthogonal functional group intallation upon an enamine substrate, isoquinolines, quinolines, and isoquinolones can all be accessed as well. In this manner, we have been able to generate an array of functionalized heterocycles, including some that are prohibited by traditional means of synthesis. We have also begun to understand some of the reactivity trends in this context for the elusive aryne reaction partner. The development of the aryne annulation strategy for the synthesis of isoquinolines directly led to the shortest reported total synthesis of the opiate alkaloid papaverine, and the tetrahydroisoquinoline anticancer antibiotic quinocarcin. Our more recent, ongoing efforts toward the synthesis of the bis-tetrahydroisoquinoline antitumor molecule jorumycin and its many structural relatives are detailed herein. Jorumycin has been targeted through a combination of aryne annulation and acyl-alkylation/condensation methodologies aimed at the synthesis of a functionalized bis-isoquinoline intermediate. Reduction of this key bis-isoquinoline to a bis-tetrahydroisoquinoline and subsequent lactamization will provide the pentacyclic core of jorumycin and related natural products in only three steps from simple isoquinoline building blocks. The final project described is the development of several different aryne multicomponent reactions to form novel carbo- and heterocyclic scaffolds, including iminoisobenzfurans, iminoindenones, dibenzoketocaprolactams, and 2-quinolones.\r\n" }, { "name": "Kedrowski, Sean M. A.", "degree": "PhD", "year": "2012", "title": "I. Chemical-Scale Studies of Ligand-Gated Ion Channels, and II. Novel Methods for Phosphonate Synthesis", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10112011-135016656", "creators": [ { "name": { "family": "Kedrowski", "given": "Sean M. A." }, "id": "Kedrowski-Sean-M-A", "display_name": "Kedrowski, Sean M. A." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RQ16-6C44", "abstract": "Section 1: Chemical-Scale Studies of Ligand-Gated Ion Channels : Ligand-gated ion channels are amazing molecular machines that respond to specific small-molecule agonists by opening a central pore to enable ions to flow through them. In the aggregate, they transduce chemical signals into electrical currents, and they have numerous critical physiological functions. The tools of pharmacology and unnatural amino acid (and hydroxy acid) mutagenesis enable us to study these receptors on an atomic level. Two such projects are presented here. First, the synthesis of a new 5-HT3 receptor agonist helps to map the receptor\u2019s binding site. Second, mutant cycle analysis in the nicotinic acetylcholine receptor with the novel unnatural residue \u03b1-hydroxyserine (Sah) enables the identification of a crucial hydrogen bond whose formation is part of the pathway leading from acetylcholine binding to pore opening.
\r\nSection 2: Novel Methods for Phosphonate Synthesis : Phosphonates are a key functional group in both organic synthesis and biological chemistry. The Arbuzov reaction stands as dominant method available for synthesizing this important class of compounds. Two new methods for phosphonate synthesis are presented here. The first method enables room-temperature phosphonate synthesis from carboxylic acids, taking advantage of a novel Wolff-Kishner-type reductive deoxygenation of an intermediate acyl phosphonate. The second method enables phosphonate synthesis through the reductive coupling of ketones/aldehydes with dialkyl phosphites, mediated by a tosylhydrazone derivative. The latter method requires only mild heating (60 \u00b0C) and enables access to phosphonates containing azides, benzyl halides, and other functional groups poorly tolerated by the Arbuzov onditions.
" }, { "name": "Kimball, Gregory Michael", "degree": "PhD", "year": "2012", "title": "Zn\u2083P\u2082 and Cu\u2082O Substrates for Solar Energy Conversion\r ", "advisor": "Atwater, Harry Albert; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302011-182613259", "creators": [ { "name": { "family": "Kimball", "given": "Gregory Michael" }, "id": "Kimball-Gregory-Michael", "display_name": "Kimball, Gregory Michael" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q4F1-H538", "abstract": "Zinc phosphide (Zn3P2) and cuprous oxide (Cu2O) are promising and earth-abundant alternatives to traditional thin film photovoltaics materials such as CIGS, CdTe, and a-Si. We have prepared high purity substrates of Zn3P2 from elemental zinc and phosphorus, and Cu2O by the thermal oxidation of copper foils, to investigate their fundamental material properties and potential for solar energy conversion. Photoluminescence-based measurements of Zn3P2 substrates have revealed a fundamental indirect band gap at 1.38 eV and a direct band gap at 1.50 eV, with time-resolved data indicating minority carrier diusion lengths of \u22657 \u03bcm. Solar cells based on Mg/Zn3P2 junctions with solar energy conversion efficiency reaching 4.5% were examined by composition profiling to elucidate the passivation reaction between Mg metal and Zn3P2 surfaces. Semiconductor/liquid junctions incorporating Cu2O substrates exhibited open-circuit voltage, Voc, values in excess of 800 mV and internal quantum yields approaching 100% in the 400\u2013500 nm spectral range." }, { "name": "Komor, Russell Scott", "degree": "PhD", "year": "2012", "title": "Recombinatorial and Predictive Methods to Increase Cellulase Thermostability and Structural Analysis of a Thermostable P450", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:12212011-144253704", "creators": [ { "name": { "family": "Komor", "given": "Russell Scott" }, "id": "Komor-Russell-Scott", "display_name": "Komor, Russell Scott" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemeng" ], "doi": "10.7907/A1ZX-3W42", "abstract": "To address the world\u2019s need for improved biomass breakdown for the production of renewable fuel, we sought to improve cellulase thermostability and thereby enzyme lifetime, operating temperature, and specific activity. We created an eight block SCHEMA recombination library based on five fungal cellobiohydrolase class I (CBHI) enzymes. By characterizing this library, we identified several stabilizing sequence blocks and combined these to produce a set of well-expressed, thermostable CBHI chimeras. To further increase the stability of these chimeras, we used a combination of the chimera thermostability screening data, a consensus analysis of 40 naturally occurring CBHI sequences, and FoldX \u0394\u0394G predictions to identify individual mutations for testing. Our final enzyme has a T50 9.3 \u00b0C greater than that of the most stable parental CBHI, resulting in a 10 \u00b0C increase in optimal temperature and a 50% increase in total sugar production at the optimal temperature.
\r\n\r\nTo produce an ideal parent for directed evolution for improved activity on varied compounds, we increased the thermostability of a P450BM3 enzyme with broad substrate specificity to produce enzyme 9-10ATS. Directed evolution libraries based on 9-10ATS produced variants with improved activity on a number of structurally diverse compounds. We determined the structure of 9-10ATS using x-ray crystallography and compared it to other P450BM3 structures. Examination of the stucture shows clear structural basis for the thermostabilizing mutations and broad substrate specificity.
\r\n" }, { "name": "Li, Jean", "degree": "PhD", "year": "2012", "title": "Improving Selectivity in Olefin Metathesis for Small Molecule Synthesis and Materials Applications", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10162011-170949582", "creators": [ { "name": { "family": "Li", "given": "Jean" }, "id": "Li-Jean", "display_name": "Li, Jean" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JVC6-7A52", "abstract": "The olefin metathesis reaction has been studied extensively from the perspective of catalyst design and synthesis, as well as from that of reaction control and application in a variety of fields. Beginning with the design of enantioselective catalysts based on the \u201cgeared\u201d C2-symmetric N-heterocyclic carbene (NHC) containing ruthenium catalysts, architectural modifications were envisioned and implemented in order to control the N-bound arene tilt angle (Chapter 2). From there, the asymmetric class of olefin metathesis reactions were explored and trends in enantioselectivities were obtained and reapplied in the further design of novel, chiral catalysts. These asymmetric catalysts were developed not only for their useful application in a range of asymmetric metathesis reactions, but also to provide insight into the spatial arrangement of the NHC ligand during the catalytic cycle.
\r\n\r\nAmidst this overall cyclical process, mechanistic understandings of the ruthenium-based olefin metathesis catalysts were garnered and integrated; and the concept of a covalentlylinked NHC ligand was born. In Chapter 3, both the cis-fused and trans-fused versions of this linked NHC were constructed, with each independent synthesis hinging on a key ringclosing metathesis reaction mediated by ruthenium catalysts. These novel NHCs were then translated into rhodium-bound complexes and their unique structural conformations were studied with X-Ray crystallography.
\r\n\r\nChapter 4 explores the forefront of control and selectivity in olefin metathesis, specifically, in the selective reactivity of dienes in cross-metathesis reactions. The desire to synthesize conjugated dienes, thus limiting reactivity to one of two potentially reactive olefins, is both mechanistically intriguing and contains practical applications for the synthesis of linear pheromone natural products. These pheromones show great utility as a green, biorational pesticide with few ecological and biological side-effects. Thus, exploration of the general diene cross-metathesis reaction was focused on the actual synthesis of codlemone, one of the world\u2019s most sought-after insecticides.
\r\n\r\nThe potential of the olefin metathesis reaction for biomedical applications was further explored in the application of peptide-containing polynorbornenes formed from ringopening metathesis polymerization (ROMP). In order to apply synthetic materials made from ROMP in biological applications, a route towards ruthenium removal to the FDAapproved levels of 10 parts per million (ppm) was developed. Once low ppm remnant ruthenium content was obtained, the synthesis of varying monomers for crosslinking to bulk materials was explored.
" }, { "name": "Liang, Joe Chih Yao", "degree": "PhD", "year": "2012", "title": "High-Throughput Strategies for the Scalable Generation of RNA Component Functions", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312012-154032563", "creators": [ { "name": { "family": "Liang", "given": "Joe Chih Yao" }, "id": "Liang-Joe-Chih-Yao", "display_name": "Liang, Joe Chih Yao" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/FQHC-EW36", "abstract": "Engineered biological systems hold great promise in providing solutions to many global challenges, including environmental remediation, sustainability, scalable manufacturing, and health and medicine. Synthetic biology is an emerging research field with a primary goal of making the engineering of biology more streamlined and reliable. Recent advances in synthetic RNA biology have led to design of RNA-based gene-regulatory devices from assembly of functional RNA components that encode more basic functions, including sensing, information transmission, and actuation functions. These synthetic RNA control devices allow access and control information on cellular state, thereby advancing our ability to interact with and program biology.
\r\n\r\nA modular ribozyme device platform was recently described to link an aptamer (sensor) to a hammerhead ribozyme (actuator) through a distinct sequence (information transmitter) capable of a strand-displacement event. The utilization of ribozyme as the actuator in the platform, whose mechanism of action is independent of cell-specific machinery, allows transport of the resultant devices to in vitro or different cellular environments. The broad implementation of these devices requires enabling technologies to support efficient generation of new functional RNA components and quantitative tailoring of device regulatory performance for specific cellular applications. Current component generation and device tailoring strategies are limited in their throughputs and efficiencies, and thus have hampered our ability to generate new ribozyme devices for cellular engineering applications.
\r\n\r\nTo support scalable generation and tailoring of ribozyme devices, we have described high-throughput in vitro selection and in vivo screening strategies based on the modular ribozyme device platform. We proposed a high-throughput solution-based in vitro selection strategy to generate new sensing functions within the device platform. A high-throughput and quantitative two-color FACS-based screening strategy was developed to complement the in vitro selection strategy by allowing efficient tailoring of device regulatory activities in the cellular environments. We further developed quantitative assays based on the surface plasmon resonance (SPR) technology to allow rapid measurements of the device and component activities. Together, these enabling strategies will offer a scalable and integrated process for the construction and programming of RNA control devices for broad cellular engineering applications, thus laying an important foundation for engineering more complex biological systems.
" }, { "name": "Long, David Alexander", "degree": "PhD", "year": "2012", "title": "Frequency-Stabilized Cavity Ring-Down Spectroscopy of O\u2082 and CO\u2082 to Support Atmospheric Remote Sensing", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06282011-172416252", "creators": [ { "name": { "family": "Long", "given": "David Alexander" }, "id": "Long-David-Alexander", "display_name": "Long, David Alexander" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Miller", "given": "Charles E." }, "id": "Miller-C-E", "role": "member", "display_name": "Miller, Charles E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CTFH-GZ09", "abstract": "Recent remote-sensing satellite missions have aimed to measure global greenhouse gas concentrations with precisions as demanding as 0.25%. These high-resolution measurements should allow for the quantification of carbon sources and sinks, thus, allowing for a considerable reduction in present carbon cycle uncertainties. To achieve these unprecedented measurement goals will require the most precise body of spectroscopic reference data \t(i.e., laboratory measurements) ever assembled. In order to aid these missions, we have measured ultraprecise spectroscopic parameters for the (30012)\t←(00001) CO2 band at 1.57 µm and the O2 A-band at 0.76 µm. These near-infrared transitions are utilized in recent greenhouse gas monitoring missions, with the A-band being employed to derive pressure and temperature profiles. In these investigations we have employed frequency-stabilized cavity ring-down spectroscopy (FS-CRDS), a novel ultrasensitive spectroscopic technique. In the O2 A-band we have measured magnetic dipole line parameters for 16O2 as well as each of the rare isotopologues and have produced calculated, HITRAN-style line lists. Due to the clear presence of collisional narrowing in the spectra, we have utilized the Galatry line profile in these studies and have reported narrowing parameters under self- and air-broadened conditions. We anticipate that the use of these spectral parameters will greatly reduce the uncertainties of atmospheric remote-sensing retrievals. In addition, the spectral fidelity of FS-CRDS allowed us to observe and quantify unresolved hyperfine structure for the 17O-containing isotopologues. Furthermore, the high sensitivity of FS-CRDS enabled measurements of ultraweak (S~10\u221230 cm molec.\u22121) electric quadrupole transitions in the A-band, many of which had not previously been observed. Recently we have begun a series of studies of the near-infrared CO2 transitions. Measurements at low pressures (<40 kPa) have revealed the simultaneous presence of Dicke narrowing and speed dependence of collisional broadening and shifting. In addition, we have demonstrated that the use of the simple Voigt profile (which neglects these effects) in the pressure range will lead to several percent biases in the retrieved Lorentzian width and spectral area. " }, { "name": "Metcalf, Andrew Richard", "degree": "PhD", "year": "2012", "title": "Atmospheric Black Carbon: Measurements in the Los Angeles Atmosphere and Aging by Condensation of Organic Aerosol", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242012-112013951", "creators": [ { "name": { "family": "Metcalf", "given": "Andrew Richard" }, "id": "Metcalf-Andrew-Richard", "orcid": "0000-0003-0385-1356", "display_name": "Metcalf, Andrew Richard" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "chair", "display_name": "Yung, Yuk L." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." } ], "option_major": [ "envreng" ], "doi": "10.7907/YZY9-EW06", "abstract": "Aerosol particles in the atmosphere scatter and absorb solar radiation; an interaction that yields the largest uncertainty in models of future climate change. While most aerosols scatter light and, therefore, cool the environment, absorbing aerosol warms the environment. In particular, black carbon (BC) aerosol, the largest component of absorbing aerosol, may exhibit the second-largest forcing on climate behind greenhouse gases. In addition, the mixing state of BC aerosol, or the degree to which a BC core is coated with a scattering substance, may significantly increase the absorbing potential of BC. This thesis presents results from field and laboratory studies of BC aerosol, its mixing state in the atmosphere, and how it ages in the presence of condensing secondary organic aerosol.
\r\n\r\nA major field study, CalNex 2010, was conducted in Southern California to study air quality and climate change issues. Measurements of BC aerosol in and around the Los Angeles (LA) Basin reveal the evolution of BC aerosol from a thinly coated state near sources in the eastern LA Basin to a more thickly coated state in the outflow regions of the Basin. While the majority of BC aerosol emitted in the LA Basin remains near the surface, some BC aerosol is transported to the free troposphere through sea-breeze and mountain-flow coupling. BC aerosol above the inversion layer tends to be thickly coated, indicating that it is more aged than the BC measured near the surface.
\r\n\r\nTo understand how the mixing state of BC evolves with secondary formation of species in the atmosphere, carefully controlled environmental chamber experiments were conducted. Two types of secondary organic aerosol (SOA) precursors, alpha-pinene and naphthalene, were reacted in the chamber to condense secondary products onto BC seed aerosol. The rate of growth and magnitude of absorption enhancement due to the secondary coating on BC was measured, revealing that growth of coatings is diffusion-limited. Particle composition measurements reveal that condensed SOA onto BC seed particles is nearly identical to nucleated SOA from the same parent hydrocarbon. Measurements of coating thickness and optical properties provide insight to single-particle SOA growth and volatility.
" }, { "name": "Ngo, John Tuan", "degree": "PhD", "year": "2012", "title": "Noncanonical Amino Acids in the Interrogation of Cellular Protein Synthesis", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01122012-225941177", "creators": [ { "name": { "family": "Ngo", "given": "John Tuan" }, "id": "Ngo-John-Tuan", "display_name": "Ngo, John Tuan" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "orcid": "0000-0002-3671-9354", "role": "chair", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Mazmanian", "given": "Sarkis K." }, "id": "Mazmanian-S-K", "orcid": "0000-0003-2713-1513", "role": "member", "display_name": "Mazmanian, Sarkis K." }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "biochem" ], "doi": "10.7907/XNEA-GM53", "abstract": "Proteins in living cells can be made receptive to bioorthogonal chemistries through metabolic labeling with appropriately designed noncanonical amino acids (ncAAs). In the simplest approach to metabolic labeling, an amino acid analog replaces one of the natural amino acids specified by the protein\u2019s gene (or genes) of interest. This approach, often termed \u201cresidue-specific incorporation,\u201d allows the ncAA to be incorporated in controlled proportions into positions normally occupied by the natural amino acid residue. Chapter I of this thesis describes how this strategy has been used to track cellular protein synthesis with reactive ncAAs. In procedures similar to isotopic labeling, translationally active ncAAs are incorporated into proteins during a \"pulse\" in which newly synthesized proteins are tagged. The set of tagged proteins can be distinguished from those made before the pulse by bioorthogonally ligating the ncAA side chain to probes that permit detection, isolation, and visualization of the labeled proteins.
\r\n \r\nChapter II of this thesis describes how the selectivity of the method can be enhanced through the use of mutant aminoacyl tRNA synthetases (aaRSs) that permit incorporation of ncAAs not used by the endogenous biomachinery. Expression of a mutant synthetase in a portion of cells within a complex cellular mixture restricts labeling to that subset of cells. In multicellular environments, this approach permits the identification of the cellular origins of labeled proteins. The work in Chapter III illustrates how the extent of temporal and spatial resolution of protein labeling can be enhanced through controlled expression of mutant synthetases. Use of characterized promoters to direct transcription of mutant synthetase genes can limit labeling to relevant cells and physiological states in settings of increased complexity. Chapter IV presents a novel strategy with which ncAAs can be uniquely incorporated at the N-terminal positions of nascent proteins while excluded from insertion at internal positions. This approach permits \"site-selective\" tagging of cellular proteins, and its use in tagging and visualization of cell-cycle dependent protein synthesis is described.
\r\n\r\nThe work described throughout this thesis was designed with the objective of providing powerful and versatile methods for the study of protein synthesis in complex multicellular systems, including live animals. Thus, Chapter V considers how these strategies might be used to dissect protein synthesis in living animals.
" }, { "name": "Nichols, Eva Megan", "degree": "Senior Thesis", "year": "2012", "title": "Structure and Reactivity of Copper Dipyridyl Carbinol- and Rhenium Diphosphine Complexes", "advisor": "Agapie, Theodor", "url": "https://resolver.caltech.edu/CaltechTHESIS:06142012-152459600", "creators": [ { "name": { "family": "Nichols", "given": "Eva Megan" }, "id": "Nichols-Eva-Megan", "display_name": "Nichols, Eva Megan" } ], "advisors": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "advisor", "display_name": "Agapie, Theodor" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0P52-4M77", "abstract": "Two series of terphenyl-based ligands were designed and synthesized, and the reactivity of their transition metal complexes was examined in the context of small molecule activation.
\r\n\r\nLigands bearing pyridyl donors and pendant hydroxyl groups were synthesized in order to accommodate multiple copper centers with varying steric environments. Copper(I) complexes of these ligands were prepared and characterized, in which copper is coordinated only via the pyridyl nitrogen donors. Treatment of the Cu(I) species with O2 or deprotonation of the ligand followed by metallation with Cu(II) generates multinuclear copper cores supported by bridging alkoxides. Mono-, di-, tetra-, and hexanuclear copper complexes have been synthesized by changing the protonation state and backbone geometry of the ligand. The resulting copper complexes have been characterized by a variety of techniques including single-crystal X-ray diffraction and 1H NMR spectroscopy.
\r\n\r\nRhenium(I) carbonyl coordination chemistry was explored using a series of terphenyl diphosphine ligands with varying steric properties and substituents. Structural differences between complexes of the meta and para ligand variants have been characterized by single crystal X-ray diffraction and 31P-NMR spectroscopy. Cyclic voltammetry studies reveal differences in redox properties, though neither complex appears to exhibit catalytic activity under CO2. Subsequently, we investigate the chemistry of rhenium complexes of 2-methoxy-5-tert-butyl- or 2-methoxy-5- dimethylamino modified ligands.
" }, { "name": "O'Leary, Leslie Esther", "degree": "PhD", "year": "2012", "title": "Mixed Functionality Semiconductor Surfaces: Formation, Characterization, Interfacial Dynamics, and Applications", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012012-205928241", "creators": [ { "name": { "family": "O'Leary", "given": "Leslie Esther" }, "id": "OLeary-Leslie-Esther", "display_name": "O'Leary, Leslie Esther" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "member", "display_name": "Greer, Julia R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y5DE-5W95", "abstract": "The properties of any semiconductor device rely on the charge separation characteristics at interfaces within that device. The charge separation characteristics include relative energetics, interfacial electronic states, and the presence or absence of insulating layers. More importantly, the interfacial properties determine the maximum solar conversion efficiency for a photoelectrochemical or photovoltaic device. Solution-based halogenation/alkylation chemistry was used to functionalize Si surfaces. The chemistry was adapted to allow for the controlled formation of multicomponent molecular monolayers. Functional molecules were incorporated by the mixed monolayer approach, and lowered densities of surface electronic defect states and increased resistance toward the formation of deleterious Si oxides were observed. Heck coupoling reactions were developed at thiophene-containing monolayers. Thiophene terminated Si(111) surfaces had defect frequencies of > 1 defect per 1,000 surface atoms, too large for solar energy conversion applications, while multicomponent CH3/thiophene monolayers had defect densities of < 1 per 500,000 surface atoms. Robust secondary chemistry at Si(111) with facile charge transfer to covalently linked molecules with preservation of surface electronic properties was shown for the first time. Molecular adsorbates with interesting electronic dipoles, such as bromothiophene, were incorporated into mixed monolayers. The electron distribution across the surface dipole caused a shift in the work function of Si by > 600 mV. The fundamental mechanism of Wf shift was elucidated by a combined ab initio and experimental study, and the dependence of Si band-edge positions on pH was relieved using Si-C bonds. Designer surface chemistry was used to covalently link Si microwires within a exible PDMS matrix, and a direct correlation between the surface bonding mechanism and interfacial adhesion strength was unambiguously observed. The formation and electronic properties of Si/PEDOT junctions were studied, where PEDOT was covalently linked to the Si surface via electropolymerization initiation at a mixed molecular monolayer containing 2,2':5',2\"-terthien-5\"-yl- groups. Low resistance, ohmic contacts were made at p-Si. Aldehyde groups were also incorporated into mixed monolayers. Facile, low-temperature atomic layer deposition (ALD) of Al2O3, MnO2,and TiO2 on aldehyde-functionalized Si was achieved. Neither surface oxidation nor surface electronic defects formed during ALD, which has not been shown previously.
" }, { "name": "Oblad, Paul Frederick", "degree": "PhD", "year": "2012", "title": "Toward the Upgrading of Hydrocarbons: Synthesis, Characterization, and Reactivity of Platinum and Palladium Complexes", "advisor": "Bercaw, John E.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292011-105052667", "creators": [ { "name": { "family": "Oblad", "given": "Paul Frederick" }, "id": "Oblad-Paul-Frederick", "display_name": "Oblad, Paul Frederick" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "co-advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZEHM-9S69", "abstract": "Herein, hydroxyl-dimers of platinum and palladium supported by diimine ligands have been prepared and studied. It was found that they are capable of activating allylic, benzylic, and aromatic carbon-hydrogen bonds. The kinetics of the C-H activation of cyclohexene with the platinum system and of indene with the palladium system were studied. In each case the rate-limiting step was found to be associative substitution. The catalytic dehydrogenation of cyclohexene to benzene with the palladium hydroxyl-dimer was investigated. The chemical oxidation of the \u03b73-organometallic products synthesized via C-H activation of cyclohexene and indene with platinum and palladium, respectively, was explored. Treatment of these products with strong halogenating oxidants resulted in the liberation of halogenated substrates and bridging halide metal complexes. Uncharged platinum and palladium polypyrazoleborate complexes were synthesized and characterized. The kinetics of the degenerative ligand exchange of DMSO with palladium methyl DMSO complexes ligated with a polypyrazoleborate or a diimine ligand were studied and it was found that the associative substitution mechanism through which the diimine ligated complexes proceeds was unavailable to the polypyrazoleborate palladium complex. In the polypyrazoleborate system ligand exchange proceeded through a dissociative mechanism. The C-H activation substrate scope of the platinum and palladium hydroxyl-dimers was further explored. The diimine platinum hydroxyl-dimer was found to activate an allylic C-H bond in cyclopentene and form an \u03b73-cyclopentenyl complex when heated with acid and dilute stoichiometric amounts of cyclopentene. Conversely, dehydrogenation of cyclopentene to a platinum-bound \u03b75-cyclopentadiene resulted from the treatment of the platinum hydroxyl-dimer with super-stoichiometric amounts of cyclopentene at room temperature. This difference in reactivity with the same substrate may be due to the relative reactivities of allylic versus homoallylic C-H bonds. Further evidence of a homoallylic C-H activation mechanism was demonstrated by treating the diimine platinum hydroxyl-dimer with neo-hexene to form a cyclometalated neo-hexenyl platinum complex. The diimine palladium hydroxyl-dimer was also found to catalytically oligomerize and isomerize olefins. Furthermore, the catalytic activity was supported by the presence of oxygen and stable in the presence of water. Most likely the oligomerization proceeded through a palladium hydride that can decompose to palladium(0) complex, which can be reoxidized by oxygen. The photochemical oxidation of platinum complexes with Ru(bipy)_3^(2+) was also investigated. Finally, the coordination chemistry of the tris(triphenylphosphino)silyl ligand was explored with cobalt, ruthenium, nickel, and platinum. " }, { "name": "Olmon, Eric Daniel", "degree": "PhD", "year": "2012", "title": "Investigating DNA-Mediated Charge Transport by Time-Resolved Spectroscopy", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282011-143721555", "creators": [ { "name": { "family": "Olmon", "given": "Eric Daniel" }, "id": "Olmon-Eric-Daniel", "display_name": "Olmon, Eric Daniel" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6GDE-2707", "abstract": "In all organisms, oxidation threatens the integrity of the genome. Numerous studies have suggested that DNA-mediated charge transport (CT) may play an important role in the sequestration, detection, and repair of oxidative damage. To fully understand the mechanism of DNA-mediated CT, it is necessary to characterize transient intermediates that arise during the reaction and to determine the lifetimes of these intermediates. Time-resolved spectroscopy is the most appropriate experimental method for such observations. Each intermediate has a characteristic spectrum. By observing time-dependent changes in the absorption spectrum of the sample, it is therefore possible to determine what species are present at a particular time and how long it exists in solution. Experiments presented here involve the use of time-resolved spectroscopy to better understand the process of DNA-mediated CT.
\r\n\r\nThe study of DNA-mediated CT requires a robust and consistent method for triggering the CT reaction. The metal complexes that have traditionally been used for this purpose provide several advantages over organic phototriggers: they are synthetically versatile, they are stable in solution, they exhibit rich photophysics, and many are strong photooxidants. However, the spectroscopic features used to follow the photochemical processes triggered by these probes are generally broad optical bands. These can be difficult to resolve in samples that contain several absorbing species. For this reason, we have developed a Re photooxidant bearing a set of vibrationally active carbonyl ligands that can be covalently tethered to DNA. Unlike many absorption bands in the visible range, the vibrational absorption bands of these ligands are narrow, well-resolved, and specific. Such probes can be used to follow the complex photophysical pathways observed in biochemical systems with good precision, making them useful for the study of DNA-mediated CT.
\r\n\r\nSpecifically, the complex [Re(CO)3(dppz)(py′-OR)]+ (dppz = dipyrido[3,2-a:2′,3′-c]-phenazine; py′-OR = 4-functionalized pyridine) offers IR sensitivity and can oxidize DNA directly from the excited state. The behavior of several covalent and noncovalent Re-DNA constructs was monitored by time-resolved IR (TRIR) and UV/visible spectroscopies, as well as biochemical methods, confirming the ability of the complex to trigger long-range oxidation of DNA. Optical excitation of the complex leads to population of metal-to-ligand charge transfer excited states and at least two distinct intraligand charge transfer excited states. Several experimental observations are consistent with charge injection by excited Re*. These include similarity between TRIR spectra and the spectrum of reduced Re observed by spectroelectrochemistry, the appearance of a guanine radical signal in TRIR spectra, and the eventual formation of permanent guanine oxidation products. The majority of reactivity occurs on the ultrafast time scale, although processes dependent on slower conformational motions of DNA, such as the accumulation of oxidative damage at guanine, are also observed.
\r\n\r\nThe photooxidation activity of this Re complex was compared directly to that of other metallointercalators that have been used previously in our laboratory to oxidize DNA. The complexes [Rh(phi)2(bpy′)]3+ (phi = 9,10-phenanthrenequinone diimine; bpy′ = 4-methyl-4′-(butyric acid)-2,2′-bipyridine), [Ir(ppy)2(dppz′)]+ (ppy = 2-phenylpyridine; dppz′ = 6-(dipyrido[3,2-a:2′,3′-c]phenazin-11-yl)hex-5-ynoic acid), and [Re(CO)3(dppz)(py′-OH)]+ (py′-OH = 3-(pyridin-4-yl)-propanoic acid) were each covalently tethered to DNA. Biochemical studies show that upon irradiation, the three complexes oxidize guanine by long-range DNA-mediated CT with the efficiency: Rh > Re > Ir. Comparison of spectra obtained by spectroelectrochemistry after bulk reduction of the free metal complexes with those obtained by transient absorption (TA) spectroscopy of the conjugates suggests that excitation of the conjugates at 355 nm results in the formation of the reduced metal states. Electrochemical experiments and kinetic analysis of the TA decays verify that the primary factors responsible for the trend observed in the guanine oxidation yield of the three complexes are the thermodynamic driving force for CT, variations in the efficiency of back electron transfer, and coupling to DNA.
\r\n\r\nThe ability of redox-active DNA-binding proteins to act as hole sinks in DNA-mediated CT systems was also studied by time-resolved spectroscopy. Such experiments are designed to provide support for the utilization of DNA-mediated CT in biological systems. In studies involving the cell cycle regulator p53, photoexcitation results in the formation of a weak transient band at 405 nm. This band, which is not observed in samples lacking the protein, resembles the primary spectral feature of the tyrosine cation radical. Although the signal is weak and reproducibility is inconsistent, these results suggest that photolysis of the sample leads to DNA-mediated oxidation of tyrosine in p53. Similar experiments were conducted on the transcriptional activator SoxR. Here, the presence of dithionite, required in solution to keep the protein reduced, complicates the photochemistry of the system considerably. Regardless, a weak absorbance at 418 nm that develops following photolysis at 355 nm provides evidence for the DNA-mediated oxidation of the protein. The behavior of the base excision repair protein endonuclease III was also observed in the presence of DNA and metal complex oxidants. In flash-quench studies, addition of the protein results in the formation of a strong negative signal at 410 nm in TA traces. In studies involving direct photooxidation by Rh, Ir, and Re complexes, no new transients are detected upon the addition of protein, but changes in the intensities of the resultant TA spectra and in the steady-state absorbance spectra following photolysis indicate that DNA-mediated oxidation of the protein may be taking place.
\r\n\r\nThe experiments described here comprise several new developments in the story of DNA-mediated CT. First, proof of concept has been given for a valuable new vibrationally-active Re probe. Further modifications on the characteristics of this complex and further study by time-resolved vibrational spectroscopy will allow us to observe DNA-mediated CT with high spectral resolution. Second, comparison between this Re probe and established photooxidants shows that the Re complex is a strong photooxidant in its own right and that this complex can be added to our growing toolbox of CT phototriggers. Third, time-resolved studies involving redox-active proteins have provided preliminary direct evidence for the ability of these proteins to serve as CT probes themselves. Further refinement of the experimental methods used in these experiments will allow us to observe such processes with greater sensitivity, increasing our knowledge of the mechanism and applications of DNA-mediated CT.
\r\n" }, { "name": "Puskar, Nyssa Leigh", "degree": "PhD", "year": "2012", "title": "Structure-Function Studies of Nicotinic Acetylcholine Receptors Using Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02172012-141718925", "creators": [ { "name": { "family": "Puskar", "given": "Nyssa Leigh" }, "id": "Puskar-Nyssa-Leigh", "display_name": "Puskar, Nyssa Leigh" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YK2P-K088", "abstract": "This dissertation primarily describes structure-function studies of the nicotinic acetylcholine receptors (nAChRs). These studies use a combination of unnatural amino acid mutagenesis and electrophysiology to determine the specific molecular interactions required for neurotransmitter binding to nAChRs. Chapter 2 examines the mode of agonist activation for the \u03b14\u03b22 nAChR, the receptor responsible for nicotine addiction. This study investigates the molecular interactions that differentiate the \u03b14\u03b22 receptor from other receptor subtypes and endow it with the ability to mediate nicotine addiction. We report that the high affinity for nicotine at the \u03b14\u03b22 receptor is a result of a strong cation-\u03c0 interaction and a strengthened backbone hydrogen bond to a conserved tryptophan (TrpB) of this receptor. We also establish that a point mutation just four residues away from TrpB appears to influence the shape of the agonist binding site, such that it can differentiate the agonist binding mode of the \u03b14\u03b22 and muscle-type receptors. Chapter 3 extends studies of the point mutation near TrpB, termed the \u201cloop B glycine.\u201d We examine the muscle-type, \u03b14\u03b22, and \u03b17 subtypes and show that the identity of this residue strongly correlates with agonist potency. Low-potency receptor subtypes have a glycine at the loop B site, while high-potency receptors have a lysine at this site. We establish that mutation of this residue can to convert a low-potency receptor to a high-potency receptor and vice versa. Chapter 4 investigates the agonist binding mechanism of the \u03b14\u03b24 receptor. We show both ACh and nicotine make a strong cation-\u03c0 interaction to TrpB, and nicotine makes a strong hydrogen bond to the backbone carbonyl of TrpB. Additionally, chimeric \u03b2 subunits are used to examine the influence of the complementary binding component on receptor pharmacology for the \u03b14\u03b22 and \u03b14\u03b24 receptors. Last, chapter 5 is a methodology-based project focused on optimizing the incorporation of unnatural amino acids into mammalian cells. Using HEK293T cells, we successfully suppressed an amber stop codon using HSAS, an in vivo aminoacylated tRNA. Additional studies will pursue the viability of in vitro aminoacylated tRNAs for nonsense suppression in mammalian cells." }, { "name": "Romero, Philip Anthony", "degree": "PhD", "year": "2012", "title": "Statistical Models of the Protein Fitness Landscape: Applications to Protein Evolution and Engineering", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172012-160452929", "creators": [ { "name": { "family": "Romero", "given": "Philip Anthony" }, "id": "Romero-Philip-Anthony", "orcid": "0000-0002-2586-7263", "display_name": "Romero, Philip Anthony" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "biochem" ], "doi": "10.7907/7W9R-Y338", "abstract": "Understanding the protein fitness landscape is important for describing how natural proteins evolve and for engineering new proteins with useful properties. This mapping from protein sequence to protein function involves an extraordinarily complex balance of numerous physical interactions, many of which are still not well understood. Directed evolution circumvents our ignorance of how a protein\u2019s sequence encodes its function by using iterative rounds of random mutation and artificial selection. The selection criteria is based on experimental measurements, which permits the optimization of protein sequence properties that are not understood. While directed evolution has been useful for exploring protein fitness landscapes, these searches have been relatively local in comparison to the vast space of possible protein sequences. Here, we present several classes of statistical models that map protein sequence space on a larger scale. We use these simple models to interpret data from SCHEMA recombination libraries, understand the evolutionary benefit of intragenic recombination, and design optimized protein sequences. By training on directly on experimental data, these models implicitly capture the numerous and possibly unknown factors that shape the protein fitness landscape. This provides an unrivaled quantitative accuracy across a massive number of protein sequences.
\r\n" }, { "name": "Song, Hang", "degree": "PhD", "year": "2012", "title": "Recognition of Nucleic Acid Mismatches by Luminescent Ruthenium Complexes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11072011-185116656", "creators": [ { "name": { "family": "Song", "given": "Hang" }, "id": "Song-Hang", "display_name": "Song, Hang" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4TM6-BR89", "abstract": "Deficiencies in DNA mismatch repair (MMR) have been implicated in the development of several forms of cancers, and MMR-deficient cells tend to be resistant to commonly employed cancer therapeutics such as cisplatin. Mismatch-targeting metalloinsertors developed in our laboratory have shown great promise as therapeutic and diagnostic agents for MMR-deficient cancers. In this work, we examine fundamental aspects of binding interactions of octahedral rhodium and ruthenium complexes to DNA mismatches, and strive to develop a luminescent sensor for mismatches inside cells.
\r\n\r\nWe first demonstrate that the mismatch binding affinity of rhodium metalloinsertors directly correlates with their antiproliferative effect against MMR-deficient colorectal carcinoma cells. Smaller ancillary ligands on the rhodium center facilitate binding to mismatches via metalloinsertion from the narrow minor groove of DNA. Complexes with higher mismatch binding affinity in turn selectively inhibit the growth of MMR-deficient cells compared to MMR-proficient ones. This correlation suggests that DNA mismatches are indeed the biological target of rhodium metalloinsertors inside cells.
\r\n\r\nBesides rhodium metalloinsertors, luminescent ruthenium complexes are found to bind DNA mismatches as well. Mismatch binding is accompanied by enhanced luminescence intensity. We determined two crystal structures of \u0394-Ru(bpy)2dppz2+ bound to oligonucleotide duplexes. For an oligonucleotide containing AA mismatches, the atomic-resolution structure revealed that the ruthenium complex binds to DNA mismatches also through metalloinsertion: the complex inserts a planar ligand into the mismatched site from the minor groove, ejecting the mismatched bases out of the helix. Several binding geometries of the complex intercalated between well-matched DNA were also observed.
\r\n\r\nTo improve the mismatch selectivity of luminescent ruthenium complexes, we tethered the complexes to organic dye molecules in an effort to amplify mismatch-associated luminescence signal through resonance energy transfer. We also modified the structure of the inserting ligand in an attempt to improve the binding affinity to mismatches over well-matched DNA. Coupling mismatch binding to luminescence response has proved most challenging in these endeavors.
\r\n\r\nFinally, we venture into the realm of RNA. Unlike their nonspecific binding to DNA, ruthenium complexes bind poorly to well-matched RNA but quite avidly to RNA mismatches. As a result, mismatched RNA produces a higher luminescence signal from bound ruthenium. We subsequently applied the ruthenium complex to image RNA mismatches inside live HeLa cells using fluorescence microscopy.
" }, { "name": "Sontz, Pamela Alisa", "degree": "PhD", "year": "2012", "title": "DNA-mediated Charge Transport in a Biological Context: Cooperation among Metalloproteins to Find Lesions in the Genome", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242012-110320685", "creators": [ { "name": { "family": "Sontz", "given": "Pamela Alisa" }, "id": "Sontz-Pamela-Alisa", "display_name": "Sontz, Pamela Alisa" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9YT4-7181", "abstract": "Damaged bases in DNA are known to lead to errors in replication and transcription, compromising the integrity of the genome. A molecular wire, DNA conducts charge with shallow distance dependence, yet mismatches and lesions attenuate this process. We have proposed a model where repair proteins, containing redox-active [4Fe4S] clusters, utilize DNA charge transport (CT) to scan the genome for lesions. Based on this model, proteins are predicted to redistribute onto strands where DNA CT is inhibited. Using single-molecule atomic force microscopy (AFM) we have probed the redistribution of EndoIII, a base excision repair protein that contains a [4Fe4S] cluster. Consistent with the model, we find a redistribution of EndoIII onto DNA strands (3.8 kbp) containing C:A mismatch, which is not a specific substrate of EndoIII but inhibits CT. Proteins with mutations making them deficient in DNA-mediated CT do not similarly redistribute onto mismatched strands.
\r\n\r\nVarious DNA-binding proteins, such as those involved in repair and pathways that maintain the integrity of DNA, have been found to contain FeS domains and other redox cofactors. We are discovering proteins from alternate repair pathways that may also utilize DNA CT to find damage. XPD, a 5\u2032-3\u2032 helicase involved in nucleotide excision repair, contains a conserved [4Fe4S] cluster and exhibits a DNA-bound redox potential that indicates it is able to carry out DNA CT. In AFM studies, we observe also the redistribution of XPD onto strands containing a mismatch. We further demonstrate that an XPD mutant, L325V, defective in carrying out DNA CT, does not redistribute onto mismatched strands.
\r\n\r\nDNA CT between distinct repair proteins bound to DNA was also probed by AFM. When XPD and EndoIII are mixed together, they coordinate in relocalizing onto mismatched strands. However, when a CT-deficient mutant of either repair protein is combined with the CT-proficient repair partner, no relocalization occurs. These data not only indicate a general link between the ability of a repair protein to carry out DNA CT and its ability to redistribute onto DNA strands near lesions but also provide evidence for coordinated DNA CT between repair proteins in their search for damage in the genome.
\r\n" }, { "name": "Sprague, Matthew Kiran", "degree": "PhD", "year": "2012", "title": "Cavity Ringdown Spectroscopy, Kinetics, and Quantum Chemistry of Atmospherically Relevant Reactions", "advisor": "Okumura, Mitchio; Sander, Stanley P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282012-184532561", "creators": [ { "name": { "family": "Sprague", "given": "Matthew Kiran" }, "id": "Sprague-Matthew-Kiran", "display_name": "Sprague, Matthew Kiran" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "co-advisor", "display_name": "Sander, Stanley P." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "member", "display_name": "Sander, Stanley P." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/T8BQ-D871", "abstract": "This thesis describes laboratory experiments and electronic structure calculations on three chemical systems relevant to tropospheric ozone chemistry: peroxynitrous acid (HOONO), hydroxymethylperoxy radical formed from HO2 + HCHO (R1), and products of alkoxy isomerization (R2). R1 and R2 were studied experimentally using a gas flow cell that combined UV photolysis with cavity ringdown spectroscopy (CRDS). All chemical systems were studied using electronic structure calculations and kinetics modeling.
\r\n\r\nHOONO is one of the products of the reaction OH + NO2, and acts as a temporary reservoir for HOx and NOx in the atmosphere. Torsional excitation of HOONO will break its internal hydrogen bond, leading to sequence band formation in the OH stretch spectrum. Chapter 3 describes a calculated 3-dimensional potential energy surface to examine torsional mode coupling and sequence band formation. We apply these results to previous CRDS kinetics studies of HOONO.
\r\n\r\nThe reaction of HO2 with carbonyls is believed to be a major sink of HOx and carbonyl compounds at reduced temperatures. R1 is the simplest of these reactions. Despite numerous previous studies, considerable uncertainty exists on the activation energy and rate constant of R1. Chapters 4-6 describe CRDS and electronic structure studies on the isomerization product, hydroxymethylperoxy. CRDS was used to make the first measurements of the OH stretch and A-X electronic spectra, and the kinetics of hydroxymethylperoxy chemistry. Electronic structure calculations were used to simulate the spectroscopic bands and examine the conformers of hydroxymethylperoxy and 2-hydroxyisopropylperoxy.
\r\n\r\nAtmospheric alkoxy radicals can isomerize or react with O2, and each pathway has a different impact on ozone chemistry. Chapters 7-10 describe cavity ringdown spectroscopy, kinetics, and electronic structure calculations on the n-butoxy and 2-pentoxy isomerization products, specifically δ-HOC4H8\u2022, δ-HOC4H8OO\u2022, δ-HO-1-C5H10\u2022, and δ-HO-1-C5H10OO\u2022. CRDS was used to make the first measurements of the A-X electronic spectrum of δ-HOC4H8OO\u2022 and clean OH stretch spectra of all four radicals. Relative kinetics data previously obtained using CRDS were reanalyzed to include the effects of additional alkoxy reactions. Electronic structure calculations were performed to explain the observations that the OH stretch absorption cross section differs between HOR\u2022 and HOROO\u2022.
" }, { "name": "Tadross, Pamela Michele", "degree": "PhD", "year": "2012", "title": "Exploiting the Reactivity of Arynes in the Total Synthesis of Natural Products", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11092011-100634353", "creators": [ { "name": { "family": "Tadross", "given": "Pamela Michele" }, "id": "Tadross-Pamela-Michele", "display_name": "Tadross, Pamela Michele" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0HAZ-QF41", "abstract": "Within 14 years of the seminal experiments of J. D. Roberts leading to the first proposal of the structure of benzyne, synthetic organic chemists recognized the potential to exploit this highly reactive intermediate (and its substituted variants) in the synthesis of natural products. More specifically, it was recognized that arynes offered the strategic advantage of rapidly functionalizing an aromatic ring by forming multiple carbon\u2013carbon or carbon\u2013heteroatom bonds in a single operation, often in a regioselective manner. Herein are reported three separate efforts aimed at constructing natural products by aryne-based methodologies. In each of the studies described in the following chapters, the implementation of new aryne technologies developed in our group to natural product synthesis has resulted in concise, convergent, and general strategies to our targets.
\r\n\r\nThe first project discussed in this work is the enantioselective total synthesis of (\u2013)-curvularin by an acyl-alkylation reaction of a protected resorcinylic silyl aryl triflate aryne precursor with a \u03b2-ketolactone. Application of this strategic disconnection resulted in a six-step convergent synthesis of the polyketide natural product, the shortest to date. These efforts also resulted in the syntheses of curvulin and diplodialide C.
\r\n\r\nIn our efforts toward the total synthesis of two naturally occurring HIV integrase inhibitors, integrastatins A and B, we attempted to utilize a sequence involving an acyl-alkylation followed by an ortho-Fries-type rearrangement to access the tetracyclic core of the natural products. However, this proved to be a significant challenge and led to the development of an alternative route to the tetracyclic integrastatin core by a Wacker cyclization of a diol onto a pendant olefin.
\r\n\r\nFinally, ongoing progress toward the synthesis of the bis-tetrahydroisoquinoline natural product jorumycin is detailed. In a departure from the efforts toward curvularin and the integrastatins, jorumycin has been targeted through the application of a combination of aryne annulation and acyl-alkylation/condensation methodologies aimed at the synthesis of a functionalized bis-isoquinoline intermediate. Reduction of this key bis-isoquinoline to a bis-tetrahydroisoquinoline and subsequent lactamization provided the pentacyclic core of jorumycin and related natural products in only two steps from simple isoquinoline building blocks.
" }, { "name": "Takaoka, Ayumi", "degree": "PhD", "year": "2012", "title": "Investigations on Low-Valent Group 8 and 9 Metalloradicals", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202012-105759966", "creators": [ { "name": { "family": "Takaoka", "given": "Ayumi" }, "id": "Takaoka-Ayumi", "display_name": "Takaoka, Ayumi" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "chair", "display_name": "Agapie, Theodor" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZN62-KX32", "abstract": "Tetradentate, monoanionic, tris(phosphino)silyl ligands were chelated to group 8 and 9 transition metals to stabilize complexes with unusual oxidation states and/or geometries. Initial studies with the [SiPPh3]\u2212 ligand on ruthenium established the flexibility of this ancillary ligand in stabilizing complexes with strongly trans influencing ligands in trans dispositions. A related ligand scaffold, [SiPiPr3]\u2212, was subsequently used to stabilize mononuclear complexes of Ru(I) and Os(I), the first examples to be isolated and thoroughly chracterized. EPR spectroscopy and DFT calculations supported their metalloradical character, and further studies highlighted their reactivity in both one- and two-electron redox processes. The ability of the [SiPiPr3]\u2212 scaffold to stabilize d7 metalloradicals of group 8 metals was extended to group 9 metals, and a series of d7 complexes of cobalt, rhodium, and iridium were synthesized in which their ancillary ligands, oxidation states, spin states, and geometry are conserved. Similar to the previously reported [SiPiPr3]Fe(N2) complex, the related [SiPiPr3]Ru(N2) complex was shown to exhibit N\u2212N coupling of organic azides to yield azoarenes catalytically. Detailed mechanistic studies conclusively showed that the Ru(III) imide species, whose iron analog is the key intermediate in the [SiPiPr3]Fe system, is not involved in the mechanism for the [SiPiPr3]Ru system. Instead, a mechanism in which free nitrene is released during the catalytic cyle is favored. Finally, hybrid ligands with multiple thioether donors in place of phosphine donors on the [SiPR3]\u2212 scaffold were synthesized to stabilize a number of dinitrogen complex of iron. These complexes featured rare examples of S\u2212Fe\u2212N2 linkages." }, { "name": "Tham, Douglas Weng Wah", "degree": "PhD", "year": "2012", "title": "Silicon Nanostructure Photovoltaics", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222012-210013999", "creators": [ { "name": { "family": "Tham", "given": "Douglas Weng Wah" }, "id": "Tham-Douglas-Weng-Wah", "display_name": "Tham, Douglas Weng Wah" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "chair", "display_name": "Haile, Sossina M." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2B6T-Q315", "abstract": "Photovoltaic devices consisting of highly periodic, ultradense, silicon nanowire arrays and nanohole arrays have been fabricated with nominal nanowire widths of 20 nm, nanohole sizes of 12 nm, and lattice pitches of 32 nm, deep in the subwavelength regime for visible light. We have developed a set of surface passivation protocols that provide the extremely low surface recombination velocities typical of thick, high-quality, furnace-grown thermal silicon dioxide, but within an ultrathin layer on the order of 5 \u2013 10 nm thick. With this high quality oxide passivation, these devices exhibit good photovoltaic performance that rivals or exceeds all comparable devices reported in the literature. Using a collection of characterization techniques, including optical microscopy, scanning electron microscopy, cross-sectional transmission electron microscopy, and spectroscopic ellipsometry, we characterize the structure and morphology of these nanostructure arrays. The high perfection of the arrays enables absorptance calculations to be performed using rigorous coupled-wave analysis, which solves Maxwell\u2019s equations for periodic structures. The calculations show that these deep subwavelength nanostructures behave as homogeneous optical materials with effective refractive indices determined by the structural parameters. We solve approximate models to estimate their refractive indices. When the spectral responses of these devices were measured, their external quantum efficiencies track the calculated absorptances, except for a small multiplicative offset at shorter wavelengths due to a greater than unity internal quantum efficiency, which we estimate by dividing the absorptance into the external quantum efficiency. " }, { "name": "Theofanis, Patrick Lauren", "degree": "PhD", "year": "2012", "title": "The Quantum Electron Dynamics of Materials Subjected to Extreme Environments", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-115237724", "creators": [ { "name": { "family": "Theofanis", "given": "Patrick Lauren" }, "id": "Theofanis-Patrick-Lauren", "display_name": "Theofanis, Patrick Lauren" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BJ5N-QV45", "abstract": "Quantum wavepacket molecular dynamics simulations are used to study the effects of extreme environments on materials. The electron forcefield (eFF) method provides energies and forces from which wavepackets can be propagated in time under conditions ranging from standard temperature and pressure to tens of thousands of Kelvin and hundreds of GPa of pressure with strain rates as high as 1 km per second. Using this technique nanometer scale systems with hundreds of thousands of particles can be simulated for up to hundreds of picoseconds.
\r\n\r\nHigh strain rate fracture in solids is accompanied by the emission of electrons and photons, though atomistic simulations have thus far been unable to capture such processes. The eFF method for nonadiabatic dynamics accounts for electron emission and large potential differences consistent with the experiments, providing the first atomistic description of the origin of these effects. The effects that we explain are (1) loading of a crack leads to a sudden onset of crack propagation at 7 GPa followed by uniform velocity of the crack at 2500 km/sec after initiation, and (2) voltage fluctuations in the 10\u2013400 mV range, charge creation (up to 1011 carriers/cm2), and current production (up to 1.3 mA). The development of an effective core potential for eFF enabled this large scale study.
\r\n\r\nUsing the eFF wavepacket molecular dynamics method, simulations of the single shock Hugoniot are reported for crystalline polyethylene (PE). The eFF results are in good agreement with previous DFT theories and experimental data which is available up to 80 GPa. We predict shock Hugoniots for PE up to 350 GPa. In addition, we analyze the phase transformations that occur due to heating. Our analysis includes ionization fraction, molecular decomposition, and electrical conductivity during isotropic compression. We find that above a compression of 2.4 g/cc the PE structure transforms into a Lennard-Jones fluid, leading to a sharp increase in electron ionization and a significant increase in system conductivity. eFF accurately reproduces shock pressures and temperatures for PE along the single shock Hugoniot.
" }, { "name": "Thomas, Renee Michelle", "degree": "PhD", "year": "2012", "title": "The Design, Synthesis, and Application of Ruthenium Metathesis Catalysts for the Preparation of Small Molecules and Polymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082012-070058810", "creators": [ { "name": { "family": "Thomas", "given": "Renee Michelle" }, "id": "Thomas-Renee-Michelle", "display_name": "Thomas, Renee Michelle" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VTAR-5J81", "abstract": "Olefin metathesis is a widely used method for constructing carbon\u2013carbon double bonds. This methodology has broad applications in organic and polymer chemistry, and the continued design of highly efficient catalysts has been critical to the success of this reaction. The main goal of this thesis was to design and synthesize new catalysts for better selectivity and for improved properties for targeted applications, as well as to explore different ligand structures for optimal catalyst performance in olefin metathesis.
\r\n\r\nThe application of ruthenium catalysts for the ring-opening metathesis polymerization of challenging monomer 1,5-dimethyl-1,5-cyclooctadiene in the presence of a chain transfer agent is discussed in chapter 2. A variety of complexes were explored to find the ideal catalyst for this transformation, enabling the synthesis of telechelic polyisoprene, which has extensive applications in block copolymerization.
\r\n\r\nChiral N-alkyl, N-aryl NHC ruthenium catalysts were designed and synthesized to improve the enantioselectivity during asymmetric ring-opening cross-metathesis. Mechanistic studies of these catalysts revealed a preference for methylidene propagation compared to previous NHC catalysts. Chapter 3 describes these studies, in addition to the screening of a variety of chiral ligands for optimal enantioselectivity. Some of these catalysts gave very high enantioselectivity, comparable to the best reported ruthenium catalysts. Insights into the stability of these complexes as a propagating methylidene led to investigating them in applications where propagation as a methylidene is desirable.
\r\n\r\nN-aryl, N-alkyl NHC ruthenium catalysts were designed and synthesized for improved selectivity during ethenolysis reactions, which require a ruthenium methylidene species to react with an internal olefin to yield a terminal olefin and a ruthenium alkylidene species. Subsequent reaction of this ruthenium alkylidene species with ethylene gives the other terminal olefin. This reaction can be applied to the internal olefin of seed oils to generate valuable products that are typically derived from petroleum sources, thus providing an environmentally friendly route to the same products. An important component of ethenolysis catalysts is stability to existing as a methylidene, a property of the N-aryl, N-alkyl NHC ruthenium catalysts described in chapter 4.
\r\n \r\nChapter 5 describes the design and synthesis of sterically hindered N-aryl, N-alkyl NHC ruthenium catalysts for application in latent metathesis. These complexes also show excellent stability at elevated temperatures for extended periods of time.
\r\n\r\nAppendix A contains NMR spectra for catalysts described in chapter 4, as well as X-ray crystal structures for two of the catalysts.
\r\n\r\nAppendix B contains NMR spectra for catalysts described in chapter 5, as well as X-ray crystal structures for two of those catalysts.
\r\n" }, { "name": "Tonks, Ian Albert", "degree": "PhD", "year": "2012", "title": "Fundamental Studies of Early Transition Metal-Ligand Multiple Bonds: Structure, Electronics, and Catalysis", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12192011-112528810", "creators": [ { "name": { "family": "Tonks", "given": "Ian Albert" }, "id": "Tonks-Ian-Albert", "display_name": "Tonks, Ian Albert" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FYGA-KK18", "abstract": "Two major topics are covered: the first section is focused on the structure, electronics, stoichiometric reactivity and catalysis of nonmetallocene early transition metal complexes that often contain metal-ligand multiple bonds (Chapters 2-4); the second section is dedicated to the development of hydrazide(2-) ligands for group 5 elements, which were heretofore unexplored as ligands for group 5 (Chapters 5-6).
\r\n\r\nA series of tantalum imido and amido complexes supported by a pyridine linked bis(phenolate) (ONO) ligand has been synthesized. Characterization of these complexes via X ray crystallography reveals both Cs and C2 binding modes of the bis(phenolate)pyridine ligand. DFT calculations and molecular orbital analyses of the complexes have revealed that the preference for Cs symmetric ligand binding is a result of Ta-O \u03c0 bonding: in cases where Ta-O \u03c0 bonding is overridden by stronger Ta N \u03c0 bonding, C2 symmetric ligand binding is preferred because this is the lowest energy geometric conformation.
\r\n\r\nTitanium and zirconium complexes supported by a related pyridine bis(anilide) ligand (NNN = pyridine 2,6 bis(N-mesitylanilide)) have been synthesized. The ligand geometry of these complexes is dictated solely by chelate ring strain rather than metal-ligand \u03c0-bonding. These complexes were tested as propylene polymerization precatalysts, with most complexes giving low to moderate activities (10^2-10^4 g/mol*h) for the formation of polypropylene.
\r\n\r\n(ONO)TiX2 complexes are highly active precatalysts for the intermolecular hydroamination of internal alkynes with primary arylamines and some alkylamines. (ONO)TiBn2 also cyclotrimerizes dimethylacetylene. During the cyclotrimerization reaction the Ti(IV) precatalyst is reduced to Ti(II), which is the active species for catalysis. The mechanism of formation of TiII has been investigated and an (ONO)Ti(II) species has been trapped by ethylene and crystallographically characterized.
\r\n\r\nHydrazide complexes (dme)TaCl3(NNPh2) and (dme)NbCl3(NNPh2) (dme = 1,2 dimethoxyethane) were synthesized. Unlike the corresponding imido derivatives, (dme)TaCl3(NNPh2) is dark blue due to an LMCT that has been lowered in energy as a result of an N\u03b1-N\u03b2 antibonding interaction that raises the HOMO. Reaction of (dme)TaCl3(NNPh2) with a variety of neutral, mono and dianionic ligands generates the corresponding ligated complexes retaining the k-1 bound [TaNNPh2] moiety.
\r\n\r\nFurthermore, a series of colorful terminal hydrazide complexes of the type (dme)MCl3(NNR2) (M = Nb, Ta; R = alkyl or aryl) or (MeCN)WCl4(NNR2) have been synthesized. Perturbing the electronic environment of the \u03b2 nitrogen significantly impacts the lowest-energy charge transition in these complexes, and in the W complexes leads to metal based reduction. The photophysics of these complexes highlights the importance of the difference in reduction potential between metal centers, and could lead to differences in ligand- and/or metal-based redox chemistry in early transition metal hydrazidos, especially in the context of N2 fixation.
\r\n\r\nFinally, the hydroxy-bridged dimer [(COD)IrOH]2 (COD = 1,5-cyclooctadiene) cleanly C-H activates indene and cyclopentadiene to form (COD)Ir(\u03b73-indenyl) and (COD)Ir(\u03b75-C5H5), respectively. The kinetics of the formation of (COD)Ir(\u03b73-indenyl) has been investigated, and the mechanism involves coordination of indene to the dimeric [(COD)IrOH]2 followed by rate determining C-H activation from the dimer-indene unit.
\r\n" }, { "name": "Turner, Ryan Matthew", "degree": "PhD", "year": "2012", "title": "Reshaping Elastomers with Light: First Principles Model of Diffusion-Induced Deformation", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192012-094254839", "creators": [ { "name": { "family": "Turner", "given": "Ryan Matthew" }, "id": "Turner-Ryan-Matthew", "display_name": "Turner, Ryan Matthew" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Selinger", "given": "Robin L. B." }, "id": "Selinger-R-L-B", "role": "member", "display_name": "Selinger, Robin L. B." } ], "option_major": [ "chemeng" ], "doi": "10.7907/RVVD-2J26", "abstract": "Elastomeric photopolymers are a new class of materials originally developed at Caltech for use as intraocular lenses. These materials consist of a host network swollen with short-chain, photoreactive \"macromers.\" Using a light source for selective photopolymerization, gradients in free macromer molecules are created, driving diffusion-induced shape change. Although models exist for external flow of solvent into a swelling gel or for gel deswelling caused by externally imposed forces, no known model exists to account for reaction-induced diffusion-deformation for a force-free material in which solvent can neither enter nor leave. To predict this unique reaction-diffusion-induced shape change, we propose a simple \"two-component\" model which treats macromer as converting directly into network strands. This model is first shown to be in good agreement with experimental data on the equilibrium swelling of elastomeric photopolymers. We then use mixture theory to develop constitutive laws for the system stress and the flux of macromer by ensuring that the second law of thermodynamics holds. Finally, we implement the theory to a variety of problems - including a finite-element model of the light-adjustable lens - in each case systematically detailing the relative importance of the material parameters on the magnitude and rate of shape change. We determined that the shape change depends upon the rate of consumption of macromer (specified by the initial extent of reaction profile and the initial volume fraction of macromer) and is independent of the network modulus or the macromer molar mass. In addition, we found that the macromer molar mass serves only to determine the rate at which the deformation proceeds, whereas the network modulus serves to determine the magnitude of the internal forces experienced in the photopolymer." }, { "name": "Weintrob, Edward Charles", "degree": "PhD", "year": "2012", "title": "Synthesis, Characterization, and Reactivity Studies of Pyridine Bis(anilide) Iron Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08112011-151147364", "creators": [ { "name": { "family": "Weintrob", "given": "Edward Charles" }, "id": "Weintrob-Edward-Charles", "display_name": "Weintrob, Edward Charles" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/M1Y4-RM69", "abstract": "The unifying concept within this thesis is the investigation of pyridine bis(anilide) (NNN) iron complexes. Within this topic, chapter 1 speaks to the motivation behind studying these complexes, and how they relate to problems within iron catalysis in general. Chapter 2 introduces the general ligand design and the features which are thought to give unique and desirable properties to the complexes derived from it. The mesityl susbstituted ligand [MesNNN]H2 and subsequently ferrous ([MesNNN]Fe(THF)) and ferric ([MesNNN]FeI and ([MesNNN]Fe)2O) complexes are synthesized. The properties of the complexes are investigated using a variety of characterization techniques. Such techniques include paramagnetic 1H NMR spectroscopy, X-ray crystallography, Evans method, cyclic voltammetry, DFT calculations, and UV-vis spectrscopy. A detailed explanation of the challenges and solutions involved in using paramagnetic NMR are discussed. Crystallographic data indicate that the ligand framework confers a quite unusual geometry about the iron center, especially for the ferrous derivative [MesNNN]Fe(THF). The factors involved in this geometry are discussed, and DFT calculations supplement this discussion. Chapter 3 focuses on the reactivity of the iron complexes. Various oxidants and reductants were employed which interconvert the iron derivatives in chapter 2. Organometallic derivatives [MesNNN]FeR (R = hydride, alkyl, aryl) were not accessible, likely due to homolytic processes. L ligand exchange for [MesNNN]Fe(THF) was investigated. Ethylene reversibly binds, while cyclohexene does not. Trimethylphosphonium methylidene displaces THF to generate [MesNNN]FeCH2PMe3. Although the I oxidation state was accessible for [MesNNN]Fe(THF) electrochemically, attempts to chemically produce Fe I complexes based on the NNN ligand led to multiple products. Chapter 4 focuses on the intramolecular C-H activation of [MesNNN]Fe(THF) with RN3 to afford [MesNNN-NHR]Fe (R = SiMe3, adamantyl). The kinetics of the reaction with Me3SiN3 was investigated in detail, and a mechanism was proposed. Iron complexes based on the pincer ligands [tBuNNN] and [ONO] were investigated. " }, { "name": "Yu, Jen-Kan", "degree": "PhD", "year": "2012", "title": "Nanostructured Silicon Thermoelectrics", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252012-235254880", "creators": [ { "name": { "family": "Yu", "given": "Jen-Kan" }, "id": "Yu-Jen-Kan", "display_name": "Yu, Jen-Kan" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HPEF-BM21", "abstract": "The thesis discusses the thermoelectric properties of silicon nanostructures with a particular focus on their heat transport phenomenon. The aim of this thesis work is to design ultra-low thermal conductivity materials based on fundamental phonon physics. Silicon nanowires and silicon nanomeshes are the model nanostructure systems investigated in this thesis.
\r\n \r\nDegenerately boron-doped silicon nanowires (20 nm x 20 nm cross section) exhibit thermal conductivity, depending on the temperature of interest, roughly two orders of magnitude smaller than bulk silicon with similar impurity concentration. The reduction in thermal conductivity is presumably from increased boundary scattering of the thermal phonons. For smaller nanowire systems (e.g., 10 nm x 20 nm cross section), thermal conductivity lower than the amorphous limit is also observed. Dimensional crossover of the thermal phonons in these ultra-small nanowire systems is proposed to explain the thermal conductivity reduction. Thermoelectric figure-of-merit ZT~1, a two order of magnitude improvement is achieved in 20 nm x 20 nm silicon nanowires at 200K.
\r\n\r\nSilicon nanomeshes are designed to further reduce the thermal conductivity of silicon. The 2-D hole-array is patterned on the silicon nanomesh film as Bragg reflectors to slow down the phonon group velocity. From the direct thermal conductivity measurement via suspended microstructure platform, the coherent scattering mechanism effectively reduces the thermal conductivity of silicon by a factor of two from the nanowire value. In essence, the phononic metamaterial approach essentially creates a new class of silicon-based material with distinct phonon properties, in other words, the theoretical lower limit of thermal conductivity of silicon based on bulk dispersions no longer applies to the phononic nanomeshes. In addition, silicon nanomeshes exhibit bulk-like electrical conductivity rendering them potential high efficiency thermoelectrics.
\r\n\r\nIn Chapter 1, an introduction to the lattice thermal conductivity is given to point out the key parameters affecting the phonon transport, e.g., scattering mechanisms, phonon dispersions and phonon density-of-states. The thermoelectrics fundamentals are given in Chapter 2, as are the experimental results on silicon nanowires. The fabrication and measurement methodologies are also explained in this chapter. In Chapter 3, the phonon transport mechanism of the silicon nanomesh, a new class of phononic metamaterial, is investigated. A coherent phonon scattering mechanism is used to explain the unexpected phonon behaviors. A complete fabrication process flow is also developed in this chapter in order to fully release the nanostructure from the substrate for precise and accurate thermal conductivity measurement. In the last part of the thesis (Chapter 4), the phononic nanomesh approach is extended to a nanomesh superlattice structure. The architectural design is to incorporate interfacial thermal resistance or the Kapitza resistance to further reduce the thermal conductivity of silicon. In addition, device architecture consisting of self-assembled quantum dots is proposed to enhance the thermoelectric efficiency by energy-filtering mechanism.
\r\n" }, { "name": "Zhu, Zhaoyan", "degree": "PhD", "year": "2012", "title": "Studies in Recombination and Dissociation Reactions for Collisional Energy Transfer and Electron Transfer of Nanocrystals and Dye Molecules", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132012-142451725", "creators": [ { "name": { "family": "Zhu", "given": "Zhaoyan" }, "id": "Zhu-Zhaoyan", "display_name": "Zhu, Zhaoyan" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/C23D-SR83", "abstract": "This dissertation consists of three parts. In the first part, the effect of the large impact parameter near-elastic peak of collisional energy transfer for unimolecular dissociation/bimolecular recombination reactions and deviation from equilibrium case is studied. To this end the conventional single exponential model, a bi-exponential model that fits the literature classical trajectory data better, a model with a singularity at zero energy transfer, and the most realistic model, a model with a near-singularity, are fitted to the trajectory data in the literature. A theory is developed for the population distribution as a function of the energy E of a dissociating model, and used to calculate the three-body low pressure recombination rate constant. In the second part, the electron transfer process in the single quantum dot fluorescence blinking phenomenon is studied. The DCET (diffusion controlled electron transfer) model has been modified to explain the exponential cutoff of the power law time distribution of the bright state and the quadratic dependence of the exponential tail on the excitation intensity. Based on ensemble measurements it is proposed that an exponential tail for the dark state time distribution for long time experiments exists for single trajectory experiments. In the last part, we develop a general MLE (maximum likelihood estimation) method to analyze experimental data with a potential distribution of power law form which can be extended to a power law with an exponential tail and more generally, many other distribution forms." }, { "name": "Zuckerman, Jonathan Eric", "degree": "PhD", "year": "2012", "title": "Targeting Tumors and the Kidney with siRNA Nanoparticles and Evaluation of Extracellular MicroRNA-based Methodologies to Track Their Activity", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182012-134600511", "creators": [ { "name": { "family": "Zuckerman", "given": "Jonathan Eric" }, "id": "Zuckerman-Jonathan-Eric", "display_name": "Zuckerman, Jonathan Eric" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Ribas", "given": "Antoni" }, "id": "Ribas-A", "role": "member", "display_name": "Ribas, Antoni" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "biochem" ], "doi": "10.7907/P4FF-NQ42", "abstract": "The goal of my thesis work is to discover new ways to enable the use of nanoparticle therapeutics to treat human disease. The work presented here touches on several areas in medicine and is united by a common theme: engineering ways to make, use, and evaluate therapeutics that maximize the benefit to the patient and minimize the harm. I have explored three interrelated strategies to achieve my objectives: (1) the use of targeted-nanoparticle-based therapeutics to deliver therapeutic entities to specific sites in the body, (2) the use of a highly specific type of therapeutic, siRNA, and (3) the evaluation of strategies for using extracellular microRNAs to non invasively monitor therapeutic activity and disease response to that activity.
\r\n\r\nIn Chapter 2, I present the first evidence of targeted-nanoparticle delivery of siRNA to solid tumors following systemic administration to patients. My coworkers and I demonstrate both dose-dependent accumulation of the siRNA nanoparticles and evidence of gene knockdown via the canonical RNAi mechanism.
\r\n\r\nChapters 3 \u2013 5 describe the therapeutic potential of targeted nanoparticles (one version used in the clinic and described in Chapter 2) for: (i) targeting ribonucleotide reductase subunit M2 in human melanoma cell lines (Chapter 3), (ii) Herceptin-targeted nanoparticles containing siRNA against Her2 in Her2(+) breast cancer (Chapter 4), and (iii) siRNA targeting the \u201cundruggable\u201d protein N-Ras for N-Ras mutant melanomas (Chapter 5).
\r\n\r\nChapters 6 \u2013 8 focus on the interaction of nanoparticles with the kidney. Chapter 6 explores a previously unknown phenomenon of size-dependent glomerular accumulation of nanoparticles. In Chapter 7, a new mechanism of clearance for polycation-polymer-based nucleic acid delivery systems is demonstrated, based on interactions between polymer components in the nanoparticle and the anionic surface of the renal filtration barrier, explaining the rapid clearance of these siRNA nanoparticle systems. Chapter 8 illustrates targeted-nanoparticle delivery of siRNA to the kidney.
\r\n\r\nIn Chapter 9, I test the hypothesis that analysis of tumor-secreted microRNAs within patient blood samples can be used as real-time markers of drug pharmacodynamics. Specifically, I focus on efforts to characterize microRNA expression patterns following pharmacologic inhibition of the oncogene BRAF in melanoma cells and their secreted exosomes.
" }, { "name": "Ahmad, Habibullah", "degree": "PhD", "year": "2011", "title": "Microfluidics Platforms for Quantitative, Multiplexed Protein Detection", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072011-185553467", "creators": [ { "name": { "family": "Ahmad", "given": "Habibullah" }, "id": "Ahmad-Habibullah", "display_name": "Ahmad, Habibullah" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Scherer", "given": "Axel" }, "id": "Scherer-A", "role": "member", "display_name": "Scherer, Axel" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/04A6-YT31", "abstract": "This thesis describes the development of microfluidic platforms that enable cheap, facile, rapid, and multi-parameter protein sensing. The first section of this work describes two strategies for high density DNA microarray patterning: microcontact printing and flow patterning. A protocol is provided for micron-scale alignment of multiple PDMS stamps to a single substrate, and a simple strategy to allow very low aspect-ratio stamping is enumerated.
\r\n\r\nThe second section describes the formation of high density antibody microarrays using flow patterned DNA microarrays in conjunction with DEAL chemistry, and applies these microarrays to biological measurements. The platform\u2019s performance is first characterized using a human chorionic gonadotropin assay, and is subsequently used to stratify 22 cancer patients from frozen serum samples by quantifying the levels of twelve serum proteins. A microfluidic plasma separation device is then detailed to allow for similar measurements from fresh finger pricks of blood.
\r\n\r\nThe third section of this work outlines improvements to the flow patterning platform through two alternate schemes: covalent attachment and DMSO patterning. Both protocols are shown to dramatically increase the consistency of microarray elements across a single chip when compared to the initial method. Theoretical simulations are used to describe the mechanism by which DMSO enhances patterning consistency.
\r\n\r\nThe fourth section describes the design and fabrication of a robotics system that is capable of autonomously interfacing and manipulating PDMS substrates, and its application to producing barcode microarrays. The resulting substrates show unprecedented consistency from chip to chip, and we demonstrate through massively parallel single-cell measurements that data derived from different substrates is statistically indistinguishable.
\r\n\r\nFinally, we introduce an integrated software and hardware package designed to facilitate and automate microfluidic control at the laboratory level. We further provide the technical details of a related system which optimizes and comprehensively automates microfluidic blood assays such that even non-technical users who have never worked with microfluidics can regularly obtain the same standard of data that is produced in the lab.
\r\n" }, { "name": "Babiskin, Andrew Harris", "degree": "PhD", "year": "2011", "title": "Development of RNA-Based Genetic Control Elements for Predictable Tuning of Protein Expression in Yeast", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202011-212047218", "creators": [ { "name": { "family": "Babiskin", "given": "Andrew Harris" }, "id": "Babiskin-Andrew-Harris", "display_name": "Babiskin, Andrew Harris" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "chair", "display_name": "Smolke, Christina D." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZVTW-9B37", "abstract": "The proper functioning of many biological processes and synthetic genetic networks depends on the precise tuning of expression levels of key protein components. With growing interests in eukaryotic hosts and the increasing complexity of networks in synthetic biology, there is a need for the expansion of the genetic toolbox, particularly for the bioprocessing and biosynthesis applications in the yeast Saccharomyces cerevisiae. The available control elements in yeast generally focus on the regulation of transcription through alternative promoter systems. Synthetic RNA-based control elements placed in the untranslated regions (UTRs) of transcripts have the ability to regulate the posttranscriptional mechanisms of translation initiation and transcript stability. Such posttranscriptional elements have the added advantage of being coupled to any promoter for enhanced control strategies.
\r\n\r\nTwo types of posttranscriptional elements were examined in this thesis. The first type is a class of RNA hairpins baring AGNN tetraloops that are cleaved by the S. cerevisiae RNase III enzyme Rnt1p. By locating these hairpins in the 3\u2019 UTR of a transcript, the endonucleolytic cleavage due to Rnt1p activity resulted in the rapid degradation of the transcript. We developed two libraries of RNA hairpins based on the randomization of critical regions in Rnt1p substrates that affect the enzyme\u2019s ability to associate and/or cleave the hairpin. The modulation of the strength of binding and cleavage by Rnt1p resulted in changes in the steady-state transcript levels and thus protein levels. Through integration of an aptamer into the stem of an Rnt1p hairpin, we were able to develop a riboswitch based upon the direction inhibition of Rnt1p cleavage through association of the ligand in the sites of cleavage. The second type of posttranscriptional elements examined is the placement of internal ribosome entry sites (IRESes) in the 5\u2019 UTR that initiate translation independent of the 5\u2019 cap through direct interaction with the ribosomal machinery. We propose that the activity of small sequential IRESes can be tuned through varying the complementarity with the 18S ribosomal RNA (rRNA) to advance the creation of yeast multicistronic vectors. The application of Rnt1p hairpins and IRESes provide a key tool in synthetic biology for the construction of complex genetic networks in yeast where the predictable tuning of gene expression is necessitated.
\r\n" }, { "name": "Baldwin, Steven M.", "degree": "PhD", "year": "2011", "title": "Investigation of the Role of Hydrides in Zirconocene Catalyzed Olefin Polymerization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182010-211348487", "creators": [ { "name": { "family": "Baldwin", "given": "Steven M." }, "id": "Baldwin-Steven-M", "display_name": "Baldwin, Steven M." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/P2XG-AD12", "abstract": "The structure and reactivity of zirconocene hydrides in the presence of aluminum alkyls is investigated for both neutral species and cationic species. Unbridged zirconocene dichlorides react with HAliBu2 to yield trihydride dialuminum clusters of the general formula (RnC5H5-n)2Zr(\u03bc-H)3(AliBu2)3(\u03bc-Cl)2. Bridged zirconocenes instead predominantly yield a dihydride monoaluminum cluster of the general form Me2E(RnC5H4-n)2Zr(Cl)(\u03bc-H)2AliBu2 where E = Si or C. For tert-butyl substituted zirconocenes the terminal Cl is replaced by a H. It is shown that steric factors dictate which hydride is formed.
\r\n\r\nA single type of cationic trihydride dialuminum cluster of general formula [(RnC5H4-n)2Zr(\u03bc-H)3(AliBu2)+] is formed for all zirconocene hydrides upon addition of [Ph3C][B(C6F5)4] regardless of which class of neutral hydride was formed. For {(SBI)Zr} and {(Me2Si)2(C5H3)2Zr} the resulting cations were crystallographically characterized where SBI stands for Me2Si(indenyl)2. [(SBI)Zr(\u03bc-H)3(AliBu2)]+ reacts with propene to make isotactic polypropene while the Me-substituted analogue [(SBI)Zr(\u03bc-H)3(AliMe2)]+ is a catalyst for hydroalumination. These trihydride cations are shown to be dormant species in polymerization reactions. [(SBI)Zr(\u03bc-H)3(AliBu2)]+ is identified as the hydride observed by Babushkin and Brintzinger (Babushkin, D. E.; Brintzinger, H. H. Chem. Eur. J. 2007, 13, 5294) upon addition of AliBu3 or HAliBu2 to a mixture of (SBI)ZrCl2 and methylaluminoxane.
\r\n" }, { "name": "Cao, Peigen", "degree": "PhD", "year": "2011", "title": "Surface Chemistry at the Nanometer Scale", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252011-091250250", "creators": [ { "name": { "family": "Cao", "given": "Peigen" }, "id": "Cao-Peigen", "display_name": "Cao, Peigen" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7EFV-V231", "abstract": "This thesis describes research towards understanding surface chemical and physical processes, as well as their effects on the underlying substrate properties, at the nanometer and atomic scales. We demonstrate a method to tune the density of etch pits on Si(111) during the chlorination process so as to change the surface reactivity. Subsequent grafting of an azide group to replace chlorine demonstrates an example of non-oxidative passivation of silicon surfaces with new functionalities. Depending upon the solvent used in the azidation process, it is shown to yield different azidation kinetic rates, different final azide coverages, and different surface-area distributions. Scanning tunneling spectroscopy studies show that both chlorination and azidation processes significantly modify the surface electronic structures, with the former leading to a non-zero density of states at the Fermi level.\r\n
\r\nOur studies on a new class of corrugation, i.e., wrinkles, in exfoliated graphene on SiO2 show that a \"three-for-six\" triangular pattern of atoms is exclusively and consistently observed on wrinkles, suggesting the local curvature of the wrinkle is a perturbation that breaks the six-fold symmetry of the graphene lattice. Lower electrical conductance is also found on the top of wrinkles compared to other regions of graphene. The wrinkles are characterized by the presence of midgap states, which is in agreement with recent theoretical predictions. A general method is also reported for reliably fabricating ultrahigh-density graphene nanoribbon (GNR) arrays. We have clearly observed how the properties of GNRs evolve as a function of number of graphene layers. The band gap (and so the on-off ratio) decreases as the number of layers increases. These results suggest that, in addition to single layer graphene, properties of GNRs of different thicknesses can also be harnessed for engineering GNRs as different building blocks towards FET applications.\r\n
\r\nA novel imaging technique, graphene-templated scanning probe microscopy, has been developed and applied for the study on the condensation process of water and small organic molecules on mica. We found that these molecular adlayers grow epitaxially on the mica substrate in a layer-by-layer fashion. In particular, submonolayers of water form atomically flat, faceted islands of height 0.37 plus or minus 0.02 nm, in agreement with the height of a monolayer of ice. The second adlayers also appear ice-like, and thicker layers appear liquid-like. This general mechanism, however, is not universal. Exclusively three-dimensional droplets of water are observed on chemically modified (hydrophobic) mica surfaces, suggesting a 3D growth mechanism.\r\n
\r\nThis thesis also includes my work on the design of a quartz-tuning-fork-based force sensor and related electronics for applications on low-temperature atomic force microscopy. Results show that the force-sensor-global-feedback circuit detector system induced lowest noise floor. The high detection sensitivity of this system demonstrates its ability to be used in frequency-modulated AFM at cryogenic temperatures. Surface topographic imaging of H-terminated Si(111) has been achieved at low temperatures.\r\n
" }, { "name": "Chen, Mike Ming Yu", "degree": "PhD", "year": "2011", "title": "Directed Evolution of Cytochrome P450 for Small Alkane Hydroxylation", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042011-114651954", "creators": [ { "name": { "family": "Chen", "given": "Mike Ming Yu" }, "id": "Chen-Mike-Ming-Yu", "display_name": "Chen, Mike Ming Yu" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/T154-RW89", "abstract": "Methane is an ideal alternative to petroleum refining as a chemical feedstock source since it is highly abundant an inexpensive. However, the lack of selective methane oxidation catalysts has limited such utilization. Starting from cytochrome P450 CYP102A1 (BM3) from Bacillus megaterium, which prefers C12-C20 fatty acids as its substrates, I investigated several protein engineering approaches to shift the enzyme\u2019s substrate specificity toward small gaseous alkanes, with the ultimate goal of methane. By continuing previous directed evolution efforts in our group, a variant with wild-type-like affinity and catalytic efficiency for propane, P450PMO, was isolated. To alleviate the loss of protein thermostability (~10 \u00b0C) as a result of this approach, mutations were targeted to the BM3 active site with site saturation mutagenesis, targeted mutagenesis with a reduced set of amino acids, and computationally guided library designs. From these enzyme libraries, variants were identified that replicated much of the P450PMO activities with a minimal number of mutations while maintaining wild-type thermostability.
\r\n\r\nContinuing the protein engineering with a high throughput ethane hydroxylation screen, variants with improved in vitro ethane hydroxylation activity were obtained. However, in whole-cell ethane bioconversions, BM3-derived variants could not match the activity of a natural P450 alkane hydroxylase, CYP153A6. To investigate the oxidation capability of the P450 oxo-ferryl porphyrin radical intermediate directly, I employed a variety of terminal oxidants to support P450 alkane hydroxylation reactions abridging the P450 catalytic cycle. In this study, the CYP153A6 oxo-ferryl intermediate was able to oxidize methane in reactions using iodosylbenzene, which demonstrated that direct methane-to-methanol conversion by a P450 heme porphyrin catalyst at ambient conditions is possible and does not necessarily require the use of additional effectors to alter the active site geometry.
\r\n" }, { "name": "Chen, Yvonne Yu-Hsuan", "degree": "PhD", "year": "2011", "title": "Genetic Control of T-Cell Proliferation with Synthetic RNA Regulatory Systems", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12172010-180148854", "creators": [ { "name": { "family": "Chen", "given": "Yvonne Yu-Hsuan" }, "id": "Chen-Yvonne-Yu-Hsuan", "display_name": "Chen, Yvonne Yu-Hsuan" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "chair", "display_name": "Smolke, Christina D." }, { "name": { "family": "Jensen", "given": "Michael C." }, "id": "Jensen-M-C", "role": "member", "display_name": "Jensen, Michael C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/AP1T-QM29", "abstract": "Adoptive T-cell therapy, or the use of autologous T cells to seek and destroy diseased cells, is a promising treatment option for opportunistic diseases, virus-associated malignancies, and cancers. However, the safety and efficacy of adoptive T-cell therapy depend, in part, on the ability to sustain and tightly regulate the proliferation of transferred T cells in vivo. The emerging field of synthetic biology provides powerful conceptual and technological tools for the construction of regulatory systems that can interface with and reprogram complex biological processes such as cell growth. Here, we present the development of RNA-based regulatory systems that can control T-cell proliferation in a ligand-dependent manner, and examine the construction of integrated control systems capable of fine-tuned programming of cellular behavior.
\r\n\r\nWe systematically investigate the translation of ribozyme-based regulatory devices from yeast to mammalian cells and identify design parameters critical to the portability of regulatory devices across host organisms. We report the construction of ligand-responsive ribozyme switch systems capable of modulating the transgenic expression of growth-stimulatory cytokines in mammalian lymphocytes. We demonstrate the ability of ribozyme switch systems to regulate T-cell proliferation in primary human central memory T cells and in animal models. We further develop ligand-responsive, miRNA-based devices to regulate the endogenous expression of cytokine receptor chains and the functional output of cytokine signaling pathways, highlighting the ability to construct integrated T-cell proliferation control systems employing various regulatory mechanisms to modulate multiple components in relevant signaling pathways. Finally, we describe efforts in the generation of novel RNA aptamers to clinically suitable molecules, which can serve as the molecular inputs for ligand-responsive, RNA-based control systems in therapeutic applications.
\r\n\r\nThe regulatory systems developed in this work are designed to be modular and transportable across host organisms and application contexts, thus providing a template for future designs in RNA-based genetic regulation. This work demonstrates the capability of RNA-based regulatory systems to advance next-generation treatment options for critical diseases, and highlights the potential of synthetic biological systems to achieve novel and practical functions in diverse applications.
\r\n" }, { "name": "Chhabra, Puneet Singh", "degree": "PhD", "year": "2011", "title": "Studies of Chamber Organic Aerosol using an Aerodyne High-Resolution Time-of-Flight Aerosol Mass Spectrometer", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182011-094338191", "creators": [ { "name": { "family": "Chhabra", "given": "Puneet Singh" }, "id": "Chhabra-Puneet-Singh", "display_name": "Chhabra, Puneet Singh" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "co-advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2FKC-Y116", "abstract": "Secondary organic aerosol (SOA) contributes a substantial fraction to total ambient particulate mass. SOA is a complex mixture of different organic species formed via many gas- and particle-phase reaction pathways. The Aerodyne aerosol mass spectrometer (AMS) has become a standard tool in measuring the bulk chemical composition of SOA in realtime. In addition to acquiring mass spectra of SOA, the high-resolution time-of-flight AMS, or HR-ToF-AMS, can distinguish and quantify ions with the same nominal mass but different elemental compositions. This thesis presents results from several studies in which the HR-ToF-AMS is used to chemically characterize SOA generated in chamber experiments.
\r\n\r\nGlyoxal is a common oxidation product of both biogenic and anthropogenic volatile organic compounds (VOCs) and is known to partition into wet inorganic aerosol. Chamber studies of glyoxal uptake onto ammonium sulfate aerosol are conducted to better understand the mechanisms controlling glyoxal uptake onto ambient aerosol. Organic growth due to glyoxal uptake was found to be reversible under dark conditions. HR-ToF-AMS spectra provide evidence for glyoxal dimers and trimers existing in the particle phase. HR-ToF-AMS spectra indicate the irreversible formation of carbon-nitrogen compounds in the aerosol. Organosulfates are not detected under dark conditions; however, active photochemistry was found to occur within aerosol during irradiated experiments. Carboxylic acids and organic esters are identified within the aerosol. An organosulfate, which had been previously assigned as glyoxal sulfate in ambient samples and chamber studies of isoprene oxidation, is observed only in the irradiated experiments. Comparison with a laboratory-synthesized standard and chemical considerations strongly suggest that this organosulfate is glycolic acid sulfate, an isomer of the previously proposed glyoxal sulfate.
\r\n\r\nDevelopments in HR-ToF-AMS data analysis have allowed for the measurement of the elemental composition of SOA. Additional graphical representations of AMS spectra and elemental composition have been developed to explain the oxidative and aging processes of SOA. It has been shown previously that oxygenated organic aerosol (OOA) components from ambient and laboratory data fall within a triangular region in the f44 vs. f43 space, where f44 and f43 are the ratios of the organic signal at m/z 44 and 43 to the total organic signal, respectively; we refer to this model as the \"triangle plot.\" Alternatively, the Van Krevelen diagram has been used to plot the elemental composition of SOA and describe the evolution of functional groups in SOA. The variability of SOA formed in chamber experiments from twelve different precursors in both \"triangle plot\" and Van Krevelen domains are investigated. Spectral and elemental data from the high-resolution Aerodyne aerosol mass spectrometer are compared to offline species identification analysis and FTIR filter analysis to better understand the changes in functional and elemental composition inherent in SOA formation and aging. SOA formed under high- and low-NOx conditions occupy similar areas in the \"triangle plot\" and Van Krevelen diagram, and SOA generated from already-oxidized precursors starts higher on the \"triangle plot.\" The most oxidized SOA come from the photooxidation of methoxyphenol precursors which yielded SOA O/C ratios near unity. \u221d-pinene ozonolysis and naphthalene photooxidation SOA systems have had the highest degree of mass closure in previous chemical characterization studies and also show the best agreement between AMS elemental composition measurements and elemental composition of identified species. In general the elemental composition of chamber SOA follows a slope shallower than -1 on the Van Krevelen diagram. From the spectra of SOA studied, the triangular region originally constructed with ambient OOA components with chamber aerosol can be reproduced. Ambient data in the middle of the triangle represent the ensemble average of many different SOA precursors, ages, and oxidative processes.
" }, { "name": "Choi, Chung Hang Jonathan", "degree": "PhD", "year": "2011", "title": "Pharmacological Behavior of Systemically Administered Nanoparticles of Defined Properties: Mechanistic Investigations at the Organ, Tissue, and Cellular Levels", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02162011-153857988", "creators": [ { "name": { "family": "Choi", "given": "Chung Hang Jonathan" }, "id": "Choi-Chung-Hang-Jonathan", "display_name": "Choi, Chung Hang Jonathan" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Webster", "given": "Paul" }, "id": "Webster-P", "role": "member", "display_name": "Webster, Paul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/33C2-FY20", "abstract": "The objective of this thesis is to establish design rules for nanoparticle properties that enable their in vivo transport to target destinations. Gold nanoparticles containing surface-engrafted polyethylene glycol (PEG) chains are prepared with controlled physicochemical properties (hydrodynamic size, surface charge, targeting ligand density). Upon systemic injection into mice, the transport of nanoparticles is monitored by blood pharmacokinetics as well as distribution at the organ, tissue, and subcellular levels from the same injection in an individual animal.
\r\n\r\nAt a constant, slightly negative surface charge (ca. -10 mV), most PEGylated gold nanoparticles (PEG-AuNPs) deposit in the liver, spleen, and kidney of normal mice 24 hours after injection. Increasing retention in the liver (Kupffer cells) and spleen correlate positively with increasing nanoparticle diameter over the range of 25-165 nm, largely due to phagocytic uptake. Accumulation in the kidney is size-dependent, but shows a maximum uptake at ca. 75 \u00b1 25 nm that also gives the highest deposition in the mesangium (uptake by mesangial cells).
\r\n\r\nTumor-bearing mice received injections of PEG-AuNPs of near-constant size (ca. 75 nm) and surface charge (ca. -10 mV) but with variable amounts of ligands that target cancer cells (0-144 ligands per nanoparticle). Independent of ligand content, nanoparticles accumulate in the tumor by the enhanced permeation and retention effect to the same magnitude, and adjacent to leukocytes. Nanoparticles only enter cancer cells in significant amounts when they contain targeting ligands above a threshold amount (between 18 and 144 ligands per nanoparticle).
\r\n\r\nMechanistic studies from model nanoparticles provide insights for the delivery of therapeutic nanoparticles. Systemic administrations of targeted, cyclodextrin-based, siRNA-containing nanoparticles are investigated in animals and humans (Phase I clinical trial). A fluorescent chemical stain with exposed adamantane molecules for binding into the cyclodextrin cups of the targeted nanoparticles is created, allowing for the examination of tumor tissue sections from animals and patient biopsies. Results from both animal and human tissues reveal intracellular, dose-dependent accumulation of targeted nanoparticles in cancer cells of the tumor.
" }, { "name": "Clark, Paul Gregory", "degree": "PhD", "year": "2011", "title": "Synthesis of Interlocked Molecules by Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292010-112948436", "creators": [ { "name": { "family": "Clark", "given": "Paul Gregory" }, "id": "Clark-Paul-Gregory", "display_name": "Clark, Paul Gregory" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8C88-RT79", "abstract": "A large body of work in the Grubbs group has focused on the development of functional-group tolerant ruthenium alkylidene catalysts that perform a number of olefin metathesis reactions. These catalysts have seen application in a wide range of fields, including classic total synthesis as well as polymer and materials chemistry. One particular family of compounds, interlocked molecules, has benefitted greatly from these advances in catalyst stability and activity. This thesis describes several elusive and challenging interlocked architectures whose syntheses have been realized through the utilization of different types of ruthenium-catalyzed olefin metathesis reactions.\r\nRing-closing olefin metathesis has enabled the synthesis of a [c2]daisy-chain dimer with the ammonium binding site near the cap of the dimer. A deprotonated DCD possessing such a structural attribute will more forcefully seek to restore coordinating interactions upon reprotonation, enhancing its utility as a synthetic molecular actuator. Dimer functionalization facilitated incorporation into linear polymers, with a 48% size increase of an unbound, extended analogue of the polymer demonstrating slippage of the dimer units. Ongoing work is directed at further materials studies, in particular, exploring the synthesis of macroscopic networks containing the DCD units and analyzing the correlation between molecular-scale extension-contraction manipulations and resulting macro-scale changes.
\r\n\r\nA \"clipping\" approach to a polycatenated cyclic polymer, a structure that resembles a molecular \"charm bracelet\", has been described. The use of ring-opening metathesis polymerization of a carbamate monomer in the presence of a chain transfer agent allowed for the synthesis of a linear polymer that was subsequently functionalized and cyclized to the corresponding cyclic analogue. This cyclic polymer was characterized through a variety of techniques, and subjected to further functionalization reactions, affording a cyclic polyammonium scaffold. Diolefin polyether fragments were coordinated and \"clipped\" around the ammonium sites within the polymer backbone using ring-closing olefin metathesis, giving the molecular \"charm bracelet\". Confirmation of the interlocked nature of the product was achieved via 1H NMR spectroscopy and two-dimensional diffusion ordered NMR spectroscopy.
\r\n\r\nA simple strategy for a one-pot, multi-component synthesis of polyrotaxanes using acyclic diene metathesis polymerization was developed. The polyrotaxanes were characterized by traditional 1H NMR spectroscopy as well as size exclusion chromatography, and the interlocked topology was confirmed using two-dimension diffusion-ordered NMR spectroscopy. The dynamic, self-correcting nature of the ADMET polymerization was also explored through the equilibration of a capped polyammonium polymer in the presence of dibenzo-24-crown-8 ether and olefin metathesis catalysts. The efficiency and ease with which these mechanically interlocked macromolecules can be assembled should facilitate rapid modulation to achieve versatile polyrotaxane architectures.
\r\n\r\nFlexible, switchable [c2]daisy-chain dimers (DCDs) were synthesized, where the macromer ammonium binding site was adjacent to the crown-type recognition structure and separated from the cap by an alkyl chain. A DCD of this topology is expected to have an extended structure in the bound conformation (when the ammonium was coordinated to the crown). Several different macromer candidates were designed to allow access to DCDs with flexible alkyl chains between the ammonium binding site and the cap, and a number of synthetic routes were explored in an effort to access these challenging materials. While the first generation DCD structure proved to be unstable due to a labile ester linkage, work is continuing toward the development of several cap structures in an effort to replace the ester linkage with an ether linkage, which, in the second generation model systems, has proven much more stable to the acidic and basic conditions necessary to induce switching of the dimeric architecture.
\r\n\r\nOne of the efforts in our lab is directed at the synthesis of 18F-labeled nanoparticles to be used as tumor imaging agents in positron emission tomography. We have been working to optimize fluorine incorporation while minimizing NP crosslinking. Because of evidence of NP side-reactions with the potassium carbonate base, we have begun to use potassium benzoate solid-state beads. To analyze the fluorinated NPs, various sorbents were explored. It was found that silica sorbents rapidly reacted and bound to the NPs, while the NPs remained unreactive and mobile on alumina. Further analysis of the NPs has been accomplished using 2D-DOSY NMR spectroscopy. Future work with the NPs will involve a systematic evaluation of the role of water on the extent of fluorination, as well as functionalization of the NPs with Cy5.5 dye for use in studies on eyes to be done in collaboration with researchers at the Mayo Clinic.
\r\n" }, { "name": "Clark, Peter Michael", "degree": "PhD", "year": "2011", "title": "New Tools for Studying O-G1cNAc Glycosylation and Chondroitin Sulfate Proteoglycans and Studies on the Roles of O-G1cNAc Glycosylation on the Transcription Factor CREB", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01132011-095304695", "creators": [ { "name": { "family": "Clark", "given": "Peter Michael" }, "id": "Clark-Peter-Michael", "display_name": "Clark, Peter Michael" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Kennedy", "given": "Mary B." }, "id": "Kennedy-M-B", "role": "member", "display_name": "Kennedy, Mary B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FTJS-8M82", "abstract": "The addition and removal of the monosaccharide N-acetyl-D-glucosamine (GlcNAc) to serine and threonine residues of proteins has emerged as a critical regulator of cellular processes. However, studies of O-GlcNAc in such complex systems as the brain have been limited, in part due to the lack of tools. Here we report the development of new tools for studying O-GlcNAc, and the application of these and other tools for studying the roles of O-GlcNAc in the brain.
\r\n\r\nWorking from a previously established chemoenzymatic method, we designed an isotopic labeling strategy for probing the dynamics of O-GlcNAc glycosylation using quantitative proteomics. With this tool, we show that O-GlcNAc is dynamically modulated on specific proteins by excitatory stimulation of the brain in vivo. Separately, we improved this chemoenzymatic strategy by integrating [3+2] azide-alkyne cycloaddition chemistry to attach biotin and fluorescent tags to O-GlcNAc residues. These tags allow for the direct fluorescence detection, proteomic analysis, and cellular imaging of O-GlcNAc modified proteins. With this strategy, we identified over 146 novel glycoproteins from the mammalian brain.
\r\n\r\nThe transcription factor cAMP-response element binding protein (CREB) is critical for numerous functions in the brain, including neuronal survival, neuronal development, synaptic plasticity, and long-term memory. We show that CREB is highly glycosylated in the brain and discover new glycosylation sites on CREB in neurons. One of these sites is dynamically modulated and is important for regulating CREB. Removal of this glycosylation site alters CREB-mediated functions in vitro and in vivo. These studies are the first demonstration that O-glycosylation at a specific site on a specific protein is critical for neuronal function and behavior.
\r\n\r\nChondroitin sulfates (CS) are sulfated linear polysaccharides important in neuronal development and viral invasion. Depending on their sulfation patterns, CS molecules differ dramatically in their functions. We developed a computational method to model the structure and function of CS. Using this approach, we show that different CS tetrasaccharides have distinct solution structures. We also modeled the CS binding site on a variety of proteins and discovered that CS may be important in modulating protein-protein interactions.
" }, { "name": "Crounse, John D.", "degree": "PhD", "year": "2011", "title": "Atmospheric Reactive Trace Gas Observations in Field and Chamber Studies Using CF\u2083O\u207b Chemical Ionization Mass Spectrometry", "advisor": "Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172011-160342650", "creators": [ { "name": { "family": "Crounse", "given": "John D." }, "id": "Crounse-John-D", "orcid": "0000-0001-5443-729X", "display_name": "Crounse, John D." } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JMSN-NF98", "abstract": "This dissertation describes the development of chemical ionization mass spectrometry (CIMS) instrumentation and methods utilizing the CF3O- reagent ion for the sensitive, specific, and direct detection of many oxygenated volatile organic compounds (OVOC) and inorganic reactive trace gases in the atmosphere. These species include HNO3, HONO, HO2NO2, SO2, HCN, H2O2, CH3OOH, CH3(O)OOH, HC(O)OH, CH3C(O)OH, HC(O)CH2OH, CH3C(O)CH2OH, organic hydroperoxides (ROOH), and many additional multifunctional species (e.g., hydroxynitrates, hydroxycarbonyls, hydroxyhydroperoxides, carbonylnitrates, carbonylhydroperoxides, etc.).
\r\n\r\nCF3O--tandem mass spectrometry (MSMS) is demonstrated to be useful for distinguishing and individual quantification of certain isobaric compounds, as well as solving instrumental background problems for certain species. This technology is applied in field studies conducted from aircraft and ground-based platforms and to chamber studies investigating VOC oxidation and organic aerosol formation mechanisms. Comparisons with simultaneous observations from other instrumentation for several species show good agreement with CIMS observations. CF3O--CIMS observations of HCN (a biomass burning tracer) from aircraft are used to quantify the impact of biomass burning emissions to the Mexico City region in March 2006. Biomass burning emissions are shown to contribute significantly to a number of gas and aerosol phase pollutants even in the midst of the large anthropogenic pollution emissions from Mexico City. The analysis of the photochemical aging of a fire plume over the Yucatan Peninsula (March 2006) is also reported. Observations indicate intense chemistry occurring within the fire plume evidenced by high OH levels, fast production of H2O2 and conversion of NO and NO2 (NOx) into peroxyacetylnitrate (PAN) and aerosol nitrate. This rapid chemistry is likely driven by photolysis of HONO, which is observed to be emitted in high amounts from these fires.
\r\n\r\nThe CIMS methods are applied to studies of VOC oxidation and organic aerosol formation conducted in chamber experiments. Specifically, new insights gained from the study of isoprene oxidation under high and low NOx conditions are reported. We quantify the formation of small carboxylic acids as well as C5-hydroxynitrates from the oxidation of isoprene under high NOx conditions. Under low NOx conditions, we show that C5-hydroxyhydroperoxides are formed in high yield. Subsequent oxidation of these hydroxyhydroperoxides is shown to occur through a unique HOx neutral mechanism that generates C5-epoxydiols, a likely precursor to organic aerosol.
\r\n\r\nWe utilize the high sensitivity and specificity of CF3O- -CIMS to study novel intermolecular hydrogen-shift isomerization processes in peroxy radicals formed during isoprene oxidation. We find these rates to be substantially slower than recent theoretical predictions; however, we find these isomerization rates to be fast enough that they are important in atmospheric isoprene oxidation in regions where lifetimes become long. Globally, we estimate 8-11% of isoprene peroxy radicals react through 1,6-H-shift isomerization reactions.
" }, { "name": "Dempsey, Jillian Lee", "degree": "PhD", "year": "2011", "title": "Hydrogen Evolution Catalyzed by Cobaloximes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252011-134049886", "creators": [ { "name": { "family": "Dempsey", "given": "Jillian Lee" }, "id": "Dempsey-Jillian-Lee", "display_name": "Dempsey, Jillian Lee" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XK4M-DZ27", "abstract": "Cobaloximes are among a promising class of small molecules which catalytically evolve hydrogen at modest overpotentials. Motivated by the imminent need to develop efficient solar energy conversion processes, a number of research groups have recently revisited the catalytic activity of cobaloximes, which was initially reported by Espenson almost three decades ago. Both Espenson\u2019s seminal work and the studies reported during this recent resurgence are chronicled in the introductory Chapter 1. The next three chapters introduce photochemical methods for detecting catalytic intermediates and determining kinetics associated with the elementary steps of hydrogen evolution. Four catalytic pathways are considered; each beginning with the reduction of a CoII-diglyoxime to generate CoI, which reacts with a proton donor to produce a CoIII-hydride. In a homolytic pathway, two CoIII-hydrides react in a bimolecular step to eliminate H\u2082. Alternatively, in a heterolytic pathway, protonation of CoIII-hydride produces H\u2082 and CoIII. The CoIII-hydride may also be reduced further to a CoII-hydride, which can react via analogous heterolytic or homolytic pathways. In Chapter 2, kinetics of electron transfer reactions of a Co-diglyoxime complex are presented. These experimental results, along with a detailed thermodynamic analysis of proposed hydrogen evolution pathways, shed new light on the barriers and driving forces of the elementary reaction steps involved in proton reduction. A strong thermodynamic preference for a CoIII-hydride homolytic pathway over a CoIII-hydride heterolytic route is identified as the key finding from this work. In Chapter 3, phototriggered hydride generation utilized in conjunction with time-resolved spectroscopy is introduced as a novel method for mechanistic investigations. Here, excited-state proton transfer from an organic photoacid to a CoI-diglyoxime triggers the formation of the reactive CoIII-hydride. This and the subsequent reactivity of CoIII-hydride are monitored spectroscopically. The reaction kinetics are consistent with a heterolytic route for hydrogen evolution that proceeds via a CoII-hydride intermediate. Chapter 4 extends these mechanistic investigations to aqueous media by employing photoionization and pulse radiolysis methods to trigger CoII-diglyoxime reduction. Chapters 5 and 6 focus on the design and construction of second generation cobaloximes. In Chapter 5, the thermodynamic preference for bimolecular reactivity of two CoIII-hydrides is probed with a binuclear cobaloxime. A covalent alkyl tether is used to decrease the volume required for diffusional collisions. Electrocatalytic activity is consistent with a rate-limiting step associated with the formation of the hydride, as seen in mononuclear catalysts, and thus no enhancement of catalytic activity is observed. However, as an efficient water splitting device may require the tethering of catalysts to an electrode surface, this ligand should allow binuclear association of immobilized catalysts. A strategy for covalently grafting cobaloxime derivatives to silicon electrodes is introduced in Chapter 6. A terminal olefin is incorporated into a glyoxime backbone, a functionality amenable to surface-based coupling reactions. The bifunctional cobaloxime is an active catalyst, and initial efforts to prepare the chemically modified electrode are discussed. Three appendices are provided, including work on the photochemical generation of powerful OsII reductant, electron transfer reactions of N,N\u2019,3,3\u2019-tetramethyl-4,4\u2019-bipyridinium, and annotated MATLAB scripts utilized for kinetics analysis.
" }, { "name": "Enquist, John Andrew", "degree": "PhD", "year": "2011", "title": "Total Synthesis of Cyanthiwigin Natural Products via Double Asymmetric Catalytic Alkylation and Investigations into the Nature of Double Asymmetric Processes", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122010-101531793", "creators": [ { "name": { "family": "Enquist", "given": "John Andrew" }, "id": "Enquist-John-Andrew", "display_name": "Enquist, John Andrew" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/V11W-RH98", "abstract": "Since the initial isolation of the cyathane molecules in 1970, considerable synthetic interest has been invested into the preparation of these diterpenoid natural products. Owing to the biological activity and intriguing molecular architecture of these compounds, the members of the cyathane family of natural products have emerged as appealing targets for total synthesis. After a brief summary of the isolation and bioactivity properties of these diterpene compounds, previous synthetic efforts toward these molecules are reviewed.
\r\n\r\nA concise and versatile approach toward the preparation of the cyanthiwigin family of cyathane natural products is described. By leveraging a unique double asymmetric catalytic alkylation procedure it is possible to quickly establish two of the most critical stereocenters of the cyanthiwigin framework with high levels of selectivity and expediency. The synthesis additionally employs a tandem ring-opening and cross-metathesis reaction, and an aldehyde-olefin radical cyclization process, to rapidly arrive at the tricyclic cyathane core of the cyanthiwigin molecules. From this unifying intermediate, the preparation of cyanthiwigins B, F, and G are attained swiftly and without the need for protecting groups.
\r\n\r\nThe nature of double asymmetric transformations is investigated from a historical, mathematical, and experimental perspective. The initial findings of Langenbeck and Horeau concerning the enantioenriching effects of scalemic duplication are described, with a specific focus on the impact of this phenomenon on total synthesis. A thorough mathematical examination, based on the work of Kagan, is then presented for situations involving double asymmetric transformations of prochiral starting materials. Expressions relating the final quantities of the stereoisomeric products to the intermediary selectivity of each stereoselective process are presented based on these formulae.
\r\n\r\nFinally, experiments designed to probe the selectivity of each stage of stereoselective bond construction in a double asymmetric process are presented. The compiled results are scrutinized in keeping with the previously derived equations, and these findings are analyzed to understand the nature of the double asymmetric processes in question.
" }, { "name": "Ernst, Russell J.", "degree": "PhD", "year": "2011", "title": "The Biological Activity of Rhodium Metalloinsertors", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272011-113632785", "creators": [ { "name": { "family": "Ernst", "given": "Russell J." }, "id": "Ernst-Russell-J", "display_name": "Ernst, Russell J." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "orcid": "0000-0002-3671-9354", "role": "member", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "biochem" ], "doi": "10.7907/3K6K-JX55", "abstract": "Mismatches in DNA occur naturally during replication and as a result of endogenous DNA damaging agents, but the mismatch repair (MMR) pathway acts to correct mismatches before subsequent rounds of replication. The loss of MMR carries dire consequences, including increased mutation rates, carcinogenesis, and resistance to a variety of clinical anti-cancer agents, such as cisplatin and DNA alkylators. Rhodium metalloinsertors previously developed in our laboratory bind to DNA mismatches with high affinity and specificity, and represent a promising strategy to target mismatches in cells. Thus, uncorrected mismatches can be exploited to provide a basis of discrimination between MMR-deficient, cancerous cells and MMR-proficient, healthy cells.
\r\n\r\nHere we describe the application of rhodium metalloinsertors to inhibit cellular proliferation selectively in MMR-deficient cells compared to those that are MMR-proficient. The colorectal carcinoma cell lines HCT116N and HCT116O serve as an isogenic model system for MMR deficiency. We show that the \u0394-isomer of an octahedral rhodium complex containing a bulky chelate ligand for insertion into a DNA mismatch is active both in targeting base mismatches in vitro and in inhibiting DNA synthesis selectively in the HCT116O cell line.
\r\n\r\nA family of derivative complexes with varying ancillary ligands has also been synthesized, and both DNA mismatch binding affinities and anti-proliferative activities against the HCT116 cell lines have been determined. DNA photocleavage experiments reveal that all complexes bind to the mismatched sites with high specificities; DNA binding affinities to oligonucleotides containing single base CA and CC mismatches, obtained through photocleavage titration or competition, vary from 104 to 108 M-1 for the series of complexes. Significantly, binding affinities are found to be inversely related to ancillary ligand size and directly related to differential inhibition of the HCT116 cell lines. The observed trend in binding affinity is consistent with the metalloinsertion mode where the complex binds from the minor groove with ejection of mismatched base pairs. The correlation between binding affinity and targeting of the MMR-deficient cell line suggests that rhodium metalloinsertors exert their selective biological effects on MMR-deficient cells through mismatch binding in vivo.
\r\n\r\nIn particular, rhodium metalloinsertors bearing dipyridylamine ancillary ligands are shown to exhibit accelerated cellular uptake. This increased uptake allows us to observe additional cellular responses to these agents, including disruption of the cell cycle, monitored by flow cytometry assays, and induction of necrosis, monitored by dye exclusion and caspase inhibition assays, that also occur preferentially in the HCT116O cell line. Finally, these cellular responses provide insight into the mechanisms underlying the selective activity of this novel class of targeted anti-cancer agents, and are consistent with the idea that repair proteins are activated in response to DNA mismatch binding.
\r\n" }, { "name": "Ferry, Vivian Eleanor", "degree": "PhD", "year": "2011", "title": "Light Trapping in Plasmonic Solar Cells", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202011-180941490", "creators": [ { "name": { "family": "Ferry", "given": "Vivian Eleanor" }, "id": "Ferry-Vivian-Eleanor", "display_name": "Ferry, Vivian Eleanor" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AMD4-Q845", "abstract": "Subwavelength nanostructures enable the manipulation and molding of light in nanoscale dimensions. By controlling and designing the complex dielectric function and nanoscale geometry we can affect the coupling of light into specific active materials and tune macroscale properties such as reflection, transmission, and absorption. Most solar cell systems face a trade-off with decreasing semiconductor thickness: reducing the semiconductor volume increases open circuit voltages, but also decreases the absorp- tion and thus the photocurrent. Light trapping is particularly critical for thin-film amorphous Si (a-Si:H) solar cells, which must be made less than optically thick to enable complete carrier collection. By enhancing absorption in a given semiconductor volume, we can achieve high efficiency devices with less than 100 nm of active region.
\r\n\r\nIn this thesis we explore the use of designed plasmonic nanostructures to couple incident sunlight into localized resonant modes and propagating waveguide modes of an ultrathin semiconductor for enhanced solar-to-electricity conversion. We begin by developing computational tools to analyze incoupling from sunlight to guided modes across the solar spectrum and a range of incident angles. We then show the potential of this method to result in absorption enhancements beyond the limits for thick film solar cells. The second part of this thesis describes the integration of plasmonic nanos- tructures with a-Si:H solar cells, showing that designed nanostructures can lead to enhanced photocurrent over randomly textured light trapping surfaces, and develops a computational model to accurately simulate the absorption in these structures. The final chapter discusses the fabrication of a high-efficiency (9.5%) solar cell with a less than 100 nm absorber layer and broadband, angle isotropic photocurrent enhance- ment. Moreover, we discuss general design rules where light trapping nanopatterns are defined by their spatial coherence spectral density.
" }, { "name": "Fitch, Anthony G.", "degree": "PhD", "year": "2011", "title": "The Photoelectrochemistry of Solution Grown Zinc Oxide Nanowire Arrays", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:02212011-102830400", "creators": [ { "name": { "family": "Fitch", "given": "Anthony G." }, "id": "Fitch-Anthony-G", "display_name": "Fitch, Anthony G." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DVMD-SW60", "abstract": "ZnO nanowire arrays were synthesized by a simple wet chemical method, and the effects of substrate, solution composition, and time on the attributes of the wire arrays were explored. Optimized wire arrays were used as photoanodes for water oxidation and in dye-sensitized solar cells with fast redox couples. The results for the wire arrays as photoanodes for water oxidation were compared to single crystals. Both ZnO electrodes exhibited poor cathodic kinetics with the aqueous solution, resulting in a non-ideal behavior of the semiconductor-liquid junction and substantial losses in the fill factor. Surprisingly, the wire arrays approached the efficiency of the single crystal, 0.18% vs 0.22% respectively. In the dye senitized solar cell, the ZnO nanowires developed a Schottky junction and allowed the use of fast redox couples. Unfortunately, the efficiencies measured were low, but results suggest the potential for substantial gains in the efficiency and versatility of the dye-sensitized solar cell." }, { "name": "Gahlmann, Andreas", "degree": "PhD", "year": "2011", "title": "Ultrafast Electron Diffraction: Pulsed Laser Desorption Enables Time-Resolved Structural Determination of Thermally Labile Chromophores", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04042011-112659805", "creators": [ { "name": { "family": "Gahlmann", "given": "Andreas" }, "id": "Gahlmann-Andreas", "orcid": "0000-0001-7521-6787", "display_name": "Gahlmann, Andreas" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Jensen", "given": "Grant J." }, "id": "Jensen-G-J", "role": "member", "display_name": "Jensen, Grant J." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YACJ-HG30", "abstract": "The construction and utilization of the fourth-generation ultrafast electron diffraction apparatus, UED4, is the subject of this thesis. With UED4 and its novel and universal sample delivery method based on laser desorption, we were able to vaporize thermally labile molecular samples and determine their ground-state structures and the structures of their photochemical and photophysical reaction products. Each component part of the new UED4 apparatus is described, and the experimental and computational procedures used to extract structural information from the time-resolved diffraction patterns are presented.
\r\n\r\nSeveral molecules were studied in their ground states and photoinduced excited states or product states on the time scale of picoseconds and nanoseconds. With UED3, nitrobenzene was shown to undergo intramolecular rearrangement prior to NO loss in an ultrafast fragmentation reaction. In indole, the chromophore of the amino acid tryptophan, the involvement of a dark structure, formed on the picosecond time scale, was revealed in the nonradiative decay pathway of the initially excited state. By determining the ground state structures of the thermally labile nucleobases uracil and guanine, the first use of surface-assisted laser desorption in a pulsed electron diffraction experiment was reported using the newly developed UED4 apparatus. The determined structures of the photochemically generated species of the photochromic molecule 6-nitro-BIPS further demonstrated the capability of laser desorption electron diffraction to function as a time-resolved experiment. Finally, the fragmentation reaction of the amino acid tryptophan upon UV laser irradiation was studied with UED4. The ability to deliver increasingly large and conformationally heterogeneous molecules into the gas phase now provides new challenges and opportunities of both experimental and theoretical nature for the field of ultrafast electron diffraction.
" }, { "name": "Garcia-Berrios, Edgardo", "degree": "PhD", "year": "2011", "title": "Investigation of Composites of Carbon Black and Metallocycles, and Functionalized Transition-Metal Nanoparticles as Chemiresistive Vapor Sensors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232011-115151777", "creators": [ { "name": { "family": "Garcia-Berrios", "given": "Edgardo" }, "id": "Garcia-Berrios-Edgardo", "display_name": "Garcia-Berrios, Edgardo" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WSN1-HP60", "abstract": "An electronic nose is a man-made implementation of an olfactory system that is comprised of an array of broadly cross-reactive sensors. Electronic noses are used in the food industry, environmental monitoring, explosive detection and medical diagnosis. Our laboratory has focused in the development and implementation of arrays of low power, inexpensive chemiresistive thin films, that are able to identify and quantify a diverse collection of vapors and mixtures of vapors. Novel bioinspired sensors, and array chamber architectures are constantly been developed and improved to fulfill the desired performance of such arrays in different applications. This work details the development and the sensing performance of novel sensor materials based on composites of carbon black and metalloporphyrins, and organically-functionalized gold (Au) and titanium (IV) dioxide (TiO2) nanoparticles.
\r\n\r\nComposites of carbon black and metalloporphyrin complexes were developed and optimized to sensitively detect and classify a series of organic vapors. Such sensors films also exhibited a high sensitivity towards trace levels of ammonia (NH3(g)) and 2,4,6-trinitrotoluene (TNT) in air. Such composites broaden the types of materials that can be used for this type of low-power chemiresistive vapor sensing, and broaden the types of analytes that can be sensitively detected to include inorganic gases and explosives, as well as organic vapors.
\r\n\r\nAu and TiO2 nanoparticles were synthesized and functionalized with a variety of ligands. These materials allowed for molecular control of the interparticle physicochemical properties such as electron transfer. Details about the performance of each unique functionalized Au or TiO2 nanoparticle film upon exposure to a variety of organic vapors was described as a function of ligand length, structure and other physicochemical properties. The discrimination performance for arrays of such sensors was also evaluated.
" }, { "name": "Hutchens, Shelby Brooke", "degree": "PhD", "year": "2011", "title": "Deformation Behavior and Mechanical Analysis of Vertically Aligned Carbon Nanotube (VACNT) Bundles", "advisor": "Greer, Julia R.; Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-141718914", "creators": [ { "name": { "family": "Hutchens", "given": "Shelby Brooke" }, "id": "Hutchens-Shelby-Brooke", "orcid": "0000-0003-0349-1792", "display_name": "Hutchens, Shelby Brooke" } ], "advisors": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "advisor", "display_name": "Greer, Julia R." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "orcid": "0000-0002-9675-1508", "role": "chair", "display_name": "Greer, Julia R." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Daraio", "given": "Chiara" }, "id": "Daraio-C", "orcid": "0000-0001-5296-4440", "role": "member", "display_name": "Daraio, Chiara" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/BPW6-Z145", "abstract": "Vertically aligned carbon nanotubes (VACNTs) serve as integral components in a variety of applications including MEMS devices, energy absorbing materials, dry adhesives, light absorbing coatings, and electron emitters, all of which require structural robustness. It is only through an understanding of VACNT\u2019s structural mechanical response and local constitutive stress-strain relationship that future advancements through rational design may take place. Even for applications in which the structural response is not central to device performance, VACNTs must be sufficiently robust and therefore knowledge of their microstructure-property relationship is essential. This thesis first describes the results of in situ uniaxial compression experiments of 50 micron diameter cylindrical bundles of these complex, hierarchical materials as they undergo unusual deformation behavior. Most notably they deform via a series of localized folding events, originating near the bundle base, which propagate laterally and collapse sequentially from bottom to top. This deformation mechanism accompanies an overall foam-like stress-strain response having elastic, plateau, and densification regimes with the addition of undulations in the stress throughout the plateau regime that correspond to the sequential folding events. Microstructural observations indicate the presence of a strength gradient, due to a gradient in both tube density and alignment along the bundle height, which is found to play a key role in both the sequential deformation process and the overall stress-strain response. Using the complicated structural response as both motivation and confirmation, a finite element model based on a viscoplastic solid is proposed. This model is characterized by a flow stress relation that contains an initial peak followed by strong softening and successive hardening. Analysis of this constitutive relation results in capture of the sequential buckling phenomenon and a strength gradient effect. This combination of experimental and modeling approaches motivates discussion of the particular microstructural mechanisms and local material behavior that govern the non-trivial energy absorption via sequential, localized buckle formation in the VACNT bundles." }, { "name": "Huynh, Joyce", "degree": "PhD", "year": "2011", "title": "Factors Governing Photodynamic Cross-Linking of Ocular Coat", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202011-143758537", "creators": [ { "name": { "family": "Huynh", "given": "Joyce" }, "id": "Huynh-Joyce", "display_name": "Huynh, Joyce" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Schwartz", "given": "Daniel S." }, "id": "Schwartz-Daniel-S", "role": "member", "display_name": "Schwartz, Daniel S." } ], "option_major": [ "chemeng" ], "doi": "10.7907/GQ57-4J30", "abstract": "This thesis addresses the challenge of minimizing toxicity of therapeutic protein-protein cross-linking of the cornea and sclera. Protein-protein cross-links include disulfide bonds, enzymatic cross-links and non-enzymatic cross-links. Disulfide bonds and enzymatic cross-links are closely regulated in the body. Non-enzymatic cross-links accumulate in an uncontrolled manner, often leading to deleterious effects. Clinically, non-enzymatic cross-links can be inserted in a controlled manner, both temporally and spatially, using photo-activation to achieve effects ranging from killing tumors to stabilizing ocular shape.
\r\n\r\nThe shape of the eye is maintained by the ocular coat\u2014the cornea and sclera. Diseases that result in progressive shape changes can lead to blindness (degenerative myopia) or necessitate a corneal transplant (keratoconus and post-LASIK ectasia). Photodynamic corneal cross-linking, pioneered by Wollensak et al. using riboflavin activated by near-ultraviolet light (riboflavin/UVA), halts the progression of keratoconus; if applied to the sclera, it might halt the progression of degenerative myopia, as well. However, this treatment suffers from severe cytotoxicity. The literature to date implicitly assumes that photodynamic cross-linking is inherently toxic. The present research demonstrates that protein-protein cross-linking can be achieved with minimal toxicity using eosin Y activated by visible light (eosin Y/visible).
\r\n\r\nAt a molecular level, both eosin Y/visible and riboflavin/UVA are shown to act through a singlet oxygen mechanism; therefore, they are expected to produce similar covalent modifications of collagenous tissues. Real-time measurements of the increase in elastic modulus during irradiation show that the eosin Y/visible and riboflavin/UVA produce similar rates of cross-linking. The transport coefficients of both eosin Y and riboflavin were measured for both sclera and de-epithelialized cornea. The diffusivity and partition coefficient values, together with the cross-linking kinetics, were used in a predictive model of the cross-linking profile as a function of treatment parameters. The predictive model also serves as an optimization tool for guiding the selection of treatment parameters in pre-clinical studies. In contrast to the dramatic toxicity of the riboflavin/UVA treatment (which kills all of the keratocytes and the endothelium in the rabbit model), the eosin Y/visible treatment achieves comparable cross-linking with negligible phototoxicity.
\r\n" }, { "name": "Jaru-Ampornpan, Peera", "degree": "PhD", "year": "2011", "title": "Post-Translational Membrane Protein Targeting by the Chloroplast Signal Recognition Particle", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05242011-165030719", "creators": [ { "name": { "family": "Jaru-Ampornpan", "given": "Peera" }, "id": "Jaru-Ampornpan-Peera", "orcid": "0000-0002-4610-2235", "display_name": "Jaru-Ampornpan, Peera" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "biochem" ], "doi": "10.7907/RDKZ-8094", "abstract": "Post-translational transport of membrane proteins poses enormous challenges to the cells. The transport factors must accurately select and deliver the cargos to the appropriate target membranes. In addition, they have to provide chaperone for their hydrophobic cargos. To understand capacity and limitation of a post-translational transport factor, we studied one of the most efficient membrane protein transport pathways, the delivery of light-harvesting chlorophyll-binding (LHC) proteins to the thylakoid membrane. This targeting reaction is mediated by the chloroplast Signal Recognition Particle (cpSRP) and its receptor. Although the core SRP GTPases are close homologues of those in cytosolic SRP pathways, the unique features of cpSRP that might reflect its adaptation to the challenges in post-translational targeting include (i) the lack of the otherwise universally conserved SRP RNA, and (ii) the exclusive presence of a novel protein, cpSRP43. In the first part of this thesis, we define the thermodynamic and kinetic framework for the GTPase cycles of cpSRP and its receptor and uncover the molecular bases that enable their intrinsically fast interactions, such that they can bypass an SRP RNA, an essential accelerator for the cytosolic SRP\u2013receptor interaction. The second part of the thesis is devoted to characterization of the chaperone function of cpSRP43. We show that cpSRP43 specifically and effectively prevents and reverses the aggregation of its cargo, LHC proteins. We further investigate the molecular mechanism of this novel disaggregase activity, using a combination of biochemical and structural approaches. In summary, this dissertation aims to understand how cpSRP and its receptor adapt to their unique requirements in efficiently transporting a family of highly abundant membrane proteins. " }, { "name": "Knapp, David", "degree": "PhD", "year": "2011", "title": "Chemistry and Electronics of the Ge(111) Surface", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152010-142322737", "creators": [ { "name": { "family": "Knapp", "given": "David" }, "id": "Knapp-David", "display_name": "Knapp, David" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CGA1-QJ35", "abstract": "The halogenation/alkylation procedure that has been proven to chemically and electrically passivate the Si(111) surface has been adapted for application to Ge(111). Removal of the Ge(111) surface oxide with 6\u20139 M HF(aq), followed by exposure to Br2 vapor, then alkylmagnesium or alkyllithium reagents yields air stable surfaces with surface recombination velocities (SRVs) as low as 40 cm/sec\u22121 at \ufb02at-band conditions. Surface charges with a density on the order of 1012 cm\u22122 cause a negative surface potential of almost 300 mV in n-type CH3 -Ge(111) samples prepared with this method. The oxidized surface shows a strongly positive surface potential in atmospheric conditions. A negative surface potential is also present in CH3 -Si(111), but the wider bandgap prevents this from causing inversion conditions in extrinsic samples. Ge(111) surfaces alkylated with a larger organic group, such as ethyl or decyl, displayed a weaker surface potential and higher surface recombination velocity as the surface was brought near \ufb02at-band. Mercury contacts to alkylated n-type substrates form rectifying junctions with barrier heights of 0.6 \u00b1 0.1 eV. Contacts to p-type substrates or to oxidized n-type substrates show no measurable recti\ufb01cation. X-ray photoelectron spectroscopy (XPS) con\ufb01rms that the area concentration of surface-bound carbon on CH3 -Ge(111) surfaces is equal to that of CH3 -Si(111) surfaces. Other passivation methods were less successful.
\r\n\r\nEvery atop Ge atom of an ideal CH3-Ge(111) should be capped and the Ge-C bonds should be directed normal to the surface plane. Infrared absorption spectroscopy (IRAS) of methyl-terminated surfaces prepared from HF-etched precursors did not display distinguishable absorption peaks, but if the Ge substrate is \ufb01rst treated with an anisotropic etch before the HF etch, IRAS con\ufb01rms the methyl group orientation with the polarization-dependent \u201cumbrella\u201d mode absorption at 1232 cm\u22121 and a polarization-independent rocking mode at 755 cm\u22121. Well-ordered CH3-Ge(111) surfaces displayed less surface charging while maintaining the low SRVs, indicating that such surfaces are successfully passivated.
\r\n\r\n" }, { "name": "Kushiro, Keiichiro", "degree": "PhD", "year": "2011", "title": "Directing Cellular Traffic Using Geometric and Biomolecular Signal Alterations", "advisor": "Asthagiri, Anand R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122010-134624507", "creators": [ { "name": { "family": "Kushiro", "given": "Keiichiro" }, "id": "Kushiro-Keiichiro", "display_name": "Kushiro, Keiichiro" } ], "advisors": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "advisor", "display_name": "Asthagiri, Anand R." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "role": "member", "display_name": "Bronner, Marianne E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." } ], "option_major": [ "biochem" ], "doi": "10.7907/61Y2-AC28", "abstract": "Directed cell migration plays a principal role in various aspects of important cellular phenomena such as wound healing, development and cancer metastasis. Although the mechanism of gradient stimulus leading to directed cell migration is well understood and exploited, the geometrical and topographical cues that cause directed migration has been largely unexplored. With the advent of accessible microfabrication techniques to precisely control the topography of the extracellular matrix (ECM) on substrates, researchers are just starting to study the complex mechanical signals that can alter directed cell motility. A key challenge now is to parse out the precise factors that affect directional movement of cells on certain micropatterns, use that understanding to design strategies to enhance the motility and bias of directed cell migration, and further apply these concepts to multiple cell types and higher-order cell systems.
\r\n\r\nHere, we investigate the tunability of directional bias through various geometrical manipulations using quantitative analysis of cell movement on micropatterns. We observe that MCF-10A epithelial cells in general jump with an unnaturally high bias between teardrop-based islands with specific gap distance, asymmetry and positional placement. Throughout the studies, we observe that lamellipodial protrusions and unilamellar morphology play a crucial role in dictating not only the directional bias of epithelial cells, but also their speed and persistence, and find that moderate alteration of Rac1 signal leads to an unexpected flip of bias. We further extend the concept of directional bias to design patterns to successfully control cell flux and effectively partition cell population, as well as induce unilamellar morphology in different cell types to promote directed cell motility. We also investigate the combinatorial effect of hybrid micropatterns in enhancing motility and unravel the unique properties and possible mechanisms behind directed cell motility on teardrop-based micropatterns.
\r\n\r\nOur results demonstrate a new type of directed cell motility using a micropattern that involves the use of physical constraints to stabilize the unilamellar morphology and guidance of the unilamella in the correct direction through purely geometrical cues. These studies offer multiple design strategies to modulate the cell motility and directional bias on micropatterns for various applications, such as tissue engineering.
\r\n" }, { "name": "Lancaster, Kyle Matthew", "degree": "PhD", "year": "2011", "title": "Outer-Sphere Effects on the Copper Sites of Pseudomonas Aeruginosa Azurins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09082010-131422449", "creators": [ { "name": { "family": "Lancaster", "given": "Kyle Matthew" }, "id": "Lancaster-Kyle-Matthew", "orcid": "0000-0001-7296-128X", "display_name": "Lancaster, Kyle Matthew" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "orcid": "0000-0002-9692-7614", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9HZZ-XE74", "abstract": "This thesis describes structural, spectroscopic, and reactivity studies of mutants of the cupredoxin azurin from Pseudomonas aeruginosa. Emphasis is given to the effects of outer-sphere coordination on spectroscopic observables and reduction potentials. Among the key findings are that the characteristics of the classical \"type 1\" copper site can be largely reproduced in the absence of canonically necessary cysteine thiolate ligation. Mutants exhibiting this behavior have been classified as \"type zero\" copper proteins.
" }, { "name": "Lee, I-Ren", "degree": "PhD", "year": "2011", "title": "Femtosecond Time-resolved Spectroscopy of Gas-phase Anions: Electron Solvation and Isolated Chromophore Dynamics", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12082010-143906786", "creators": [ { "name": { "family": "Lee", "given": "I-Ren" }, "id": "Lee-I-Ren", "display_name": "Lee, I-Ren" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BAYG-2G33", "abstract": "This thesis presents the studies of ultrafast dynamics of negatively charged molecules and clusters in the gas phase using femtosecond photoelectron spectroscopy. The core motifs of two distinct complex systems \u2014 solvated electrons and protein chromophores \u2014 were studied in the gas phase.
\r\n\r\nFor the solvated electron systems \u2014 hydrated electrons and ammoniated electrons \u2014 were studied in finite-sized clusters in the gas phase. Interestingly, the results show a significant difference. In the hydrated electron, ground-state vibrational cooling is evident by the transient photoelectron spectra, while, in the ammoniated electron, a coherent motion with a 500-fs relaxation is observed. The difference is attributed to the cage rigidity, which results in different solvent motions for the electron\u2019s interaction with water (libration) or ammonia (phonon-like).
\r\n\r\nThe photocycle of the photoactive yellow protein (PYP) has been studied extensively, but the dynamics of the isolated chromophore responsible for the transduction of phototacticity is less known. The anionic chromophore model molecule was investigated in the gas phase using femtosecond photoelectron spectroscopy and the results indicate that the protein function is in directing efficient conversion to the cis-structure and in impeding radical formation within the protein. Finally, a classic system of conformational twisting, stilbene, was studied in its anionic radical state. Ultrafast conversions from both trans- and cis- isomers are accompanied with coherent oscillation, in contrast to observations in the solution phase, and this suggests that a major solvent retardation take place. Dynamic studies of the photochemistry of gas-phase anions are very scarce due to the experimental difficulties. However, our results successfully resolve the photophysics and photochemistry of the isolated species and, thereby, elucidate the effect of solution.
" }, { "name": "Louie, Mary W. C.", "degree": "PhD", "year": "2011", "title": "Electrocatalysis in Solid Acid Fuel Cells", "advisor": "Haile, Sossina M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232011-144137426", "creators": [ { "name": { "family": "Louie", "given": "Mary W. C." }, "id": "Louie-Mary-W-C", "display_name": "Louie, Mary W. C." } ], "advisors": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "advisor", "display_name": "Haile, Sossina M." } ], "committee": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "chair", "display_name": "Haile, Sossina M." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Bhattacharya", "given": "Kaushik" }, "id": "Bhattacharya-K", "role": "member", "display_name": "Bhattacharya, Kaushik" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1HK1-2M22", "abstract": "Solid state electrochemical reactions play a crucial role in many energy conversion devices, yet the pathways of many reactions remain unknown. The elusiveness of the reaction mechanisms is due, in part, to the complexity of electrochemical reactions; because electrochemical reactions require the interaction of many species (e.g., ions, electrons, and adsorbates) across multiple phases (e.g., electrolyte, catalyst, and gas phases), elucidation of the reaction pathway can quickly become complicated. In this work, we develop and utilize model catalyst | electrolyte systems, that is, structures of reduced complexity, to study electrode reactions in solid acid fuel cells which operate at intermediate temperatures of ~ 250 \u00baC. We employ AC impedance spectroscopy to explore the reaction pathway for hydrogen electro-oxidation over Pt thin films sputter-deposited atop the proton-conducting solid acid electrolyte CsH2PO4. We observed that hydrogen electro-oxidation occurs by diffusion of hydrogen through Pt, taking advantage of the entire Pt | CsH2PO4 interfacial area rather than being confined to the triple-phase sites. This insight opens up new avenues for developing high performance electrodes with low Pt loadings by eliminating the requirement that Pt-based electrodes be comprised of high triple-phase site densities long considered to be critical for Pt electrocatalysis. Indeed, even for flat, planar electrodes of very thin Pt films, we obtained a Pt utilization that is significantly higher than in typical composite electrodes.
\r\n\r\nWe also demonstrate the efficacy of a new tool for probing the spatial heterogeneity of electrochemical reactions at the metal | electrolyte interface. We characterized oxygen electro-reduction kinetics at the nanoscale Pt | CsHSO4 interface at ~ 150 \u00baC using conducting atomic force microscopy in conjunction with cyclic voltammetry and AC impedance spectroscopy. Not only did we find the electrochemical activity for oxygen electro-reduction to vary dramatically across the electrolyte surface but the current-voltage data, when analyzed in the Butler-Volmer framework, exhibited a strong counter-correlation between two key kinetic parameters, the exchange coefficient and exchange current. Specifically, the exchange current spanned five orders of magnitude while the exchange coefficient ranged between 0.1 and 0.6. Such a correlation has not been observed before and points to the power of atomic force microscopy for electrochemical characterization at electrolyte | metal | gas boundaries in general.
\r\n\r\nAs reduction in microstructural complexity is a key advantage in model electrode | electrolyte systems, we also sought to understand the bulk properties of solid acid compounds, specifically, the relationship between microstructure and the superprotonic phase transition, the latter of which lends solid acid compounds their high proton conductivities at intermediate temperatures. We found a correlation between phase transformation hysteresis and crystallographic compatibility of the high- and low-temperature phases of the Cs1\u2013xRbxH2PO4 solid solution series. Therefore, it is to be expected that hysteresis, and therefore microcrack formation, can be minimized during phase transformation via the principle of crystallographic compatibility. This is confirmed in single crystals of CsHSO4, which was found to have higher crystallographic compatibility, lower hysteresis, and significantly fewer microcracks formed during phase transition compared to CsH2PO4. The apparent applicability of the theory of crystallographic compatibility implies a new tool for identifying solid acid compounds with suitable microstructures for fuel cell application and for model electrode | electrolyte systems.\r\n
\r\n" }, { "name": "Ma, Sandy", "degree": "PhD", "year": "2011", "title": "Progress Toward the Cortistatin A Carbocyclic Core and the Development of the Catalytic Enantioselective Alkylation of 3-Helooxindoles", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122010-162444550", "creators": [ { "name": { "family": "Ma", "given": "Sandy" }, "id": "Ma-Sandy", "display_name": "Ma, Sandy" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZF1G-Y610", "abstract": "Biologically active natural products often contain interesting and complex structural features and functionalities that make them attractive targets for synthetic chemists. As such, these natural products can serve as inspiration for the development of new reaction methodology.
\r\n \r\nCortistatin A contains a unique rearranged steroidal core and possesses potent anti-angiogenic activity. These features have made cortistatin A the target of many synthetic efforts, including ours. The progress toward the synthesis of the cortistatin A carbocyclic core via an enyne-ene metathesis is discussed. Our studies towards the construction of the cortistatin A carbocyclic core yielded an interesting result, wherein an attempted SN2 inversion of a secondary mesylate afforded product with retention of stereochemistry.
\r\n\r\nOxindole derived motifs are also prevalent in biologically active molecules. More specifically, 3,3-disubstituted oxindoles can be used to access pyrrolidinylspirooxindole and pyrrolidinoindoline cores. Herein, the development of a catalytic enantioselective malonate alkylation of 3-halooxindoles to access enantiopure 3,3-disubstituted oxindoles is detailed. We then demonstrate that the enantiopure 3,3-disubstituted oxindoles derived from this novel transformation can be used towards the construction of pyrrolidinylspirooxindole and pyrrolidinoindoline cores.
\r\n" }, { "name": "Meyer, Michael Elliott", "degree": "PhD", "year": "2011", "title": "Palladium(II)-Catalyzed Oxidation Reactions in Natural Product Synthesis: Efforts toward Bielschowskysin and Phalarine", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08042010-151446303", "creators": [ { "name": { "family": "Meyer", "given": "Michael Elliott" }, "id": "Meyer-Michael-Elliott", "display_name": "Meyer, Michael Elliott" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/J3YQ-SP42", "abstract": "Two types of oxidative transformations, an oxidative kinetic resolution and an oxidative heterocyclization, have been developed by several laboratories using palladium(II)-catalysis to provide enantioenriched products. The main drawback of these asymmetric transformations is the limited substrate scope for each set of conditions. To address this, the Stoltz laboratory developed a unique platform utilizing palladium(II)-catalysis that provides a highly effective oxidative kinetic resolution of secondary alcohols and an asymmetric oxidative heterocyclization of phenols. Key to this platform is the use of (\u2013)-sparteine as the chiral ligand and O2 as the stoichiometric oxidant. Both of these methodologies will be featured in this thesis as they were applied toward the total synthesis of complex natural products.
\t\r\n\r\nOur palladium(II)-catalyzed oxidative kinetic resolution was used to access an enantioenriched intermediate in our efforts toward the synthesis of bielschowskysin, a polycyclic diterpenoid. A key disconnection in our strategy was formation of the cyclobutane core of bielschowskysin from a cyclopropane intermediate. After considerable experimentation, we were able to synthesize a cyclopropane intermediate that could be used for future research.
\r\n\r\nIn separate work, we hoped to use two palladium(II)-catalyzed oxidative heterocyclization reactions to provide the core of phalarine, a polycyclic alkaloid. The synthesis of a key intermediate relied on a Stille coupling reaction of a complex 4,5,7-substituted indole and a nitro-arene. Model cyclization studies on an aniline substrate gave inconclusive results, while a model of a phenolic substrate has shown that cyclization onto styrenyl olefins is possible.
\r\n" }, { "name": "Miller, Alexander James Minden", "degree": "PhD", "year": "2011", "title": "Emissive Monocopper Amidophosphine Complexes and Lewis Acid-Assisted Reductive Coupling of Carbon Monoxide", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12072010-151616905", "creators": [ { "name": { "family": "Miller", "given": "Alexander James Minden" }, "id": "Miller-Alexander-James-Minden", "display_name": "Miller, Alexander James Minden" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/SPH6-R695", "abstract": "Two major themes are presented, in roughly chronological order: the synthesis and characterization of photoluminescent copper complexes are described, followed by studies on the selective conversion of synthesis gas (CO and H2) to oxygenates. With the latter comprising the majority of the work, it is the subject of the introductory Chapter 1. In Chapter 2, the photoluminescent copper chemistry is introduced, and the synthesis and photophysics of monomeric amidophosphine complexes of copper is presented. The copper complexes are exceptional luminophores, with quantum efficiency up to 70% and lifetimes up to 150 \u03bcs. In Chapter 3, homogeneous CO hydrogenation is pursued using a strategy reliant on the incorporation of pendent Lewis acidic groups into the secondary coordination sphere of a metal carbonyl complex. This design feature promotes facile C\u2013H and C\u2013C bond formation, with transition metal hydrides as the hydrogen source. A structure-function study investigating the specific role of the Lewis acid determined that thefirst C\u2013H bond formation is not particularly sensitive to the acid, whereas the second C\u2013H bond formation and C\u2013C coupling are both highly sensitive to the length of the tether between the metal and the borane. In Chapter 4, this chemistry is extended to utilize dihydrogen directly as a reductant, in a \"frustrated Lewis pair\" (FLP) mechanism. A strong phosphazene base is too bulky to interact with the pendent borane, but can heterolytically cleave dihydrogen in concert with the borane to generate a borohydride that transforms the carbonyl ligands into a metal-bound C2 organic fragment. In Chapter 5, Lewis acidic boranes are again employed as promoters of reductive chemistry, this time for CO2 reduction. The same late transition metal hydrides that were employed for CO reduction, such as [HNi(dmpe)2][BF4] (dmpe = 1,2-bis(dimethylphosphino)ethane), are able to reduce CO2 gas when used in concert with the appropriate borane, affording a borane-formate adduct. In Chapter 6, the \"frustrated Lewis pair\" concept is extended to a different problem: the dehydrogenation of amine-boranes, which are candidates for hydrogen storage applications. Treatment of amine-boranes with the FLP tBu3P/B(C6F5)3 effects rapid and quantitative transfer of H2 from the amine-borane, forming cyclic aminoborane products along with [tBu3PH][HB(C6F5)3]. Appendices are provided, including early work on Br\u00f8nsted acid-assisted CO reduction, speciation of trialkylborohydrides, tabulating NMR impurities in deuterated solvents of interest to the organometallic chemist, and crystallographic tables.\r\n" }, { "name": "Muzikar, Katy Ann", "degree": "PhD", "year": "2011", "title": "Repression of DNA-Binding-Dependent Glucocorticoid Receptor-Mediated Gene Expression", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12142010-165109760", "creators": [ { "name": { "family": "Muzikar", "given": "Katy Ann" }, "id": "Muzikar-Katy-Ann", "display_name": "Muzikar, Katy Ann" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FKCV-KP50", "abstract": "Gene expression is controlled by transcription factors that regulate the rates at which genes are expressed either by recruiting or inhibiting protein complexes that bind to the promoters or enhancers of target genes. Molecules that can specifically modulate these protein-DNA interfaces show promise as tools for understanding gene regulation pathways and may have application in human medicine. Hairpin pyrrole-imidazole polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells, disrupt protein-DNA interactions, and downregulate endogenous gene expression. This thesis describes the use of polyamides to modulate gene expression in order to probe gene regulation mechanisms of several different biologically relevant systems. A polyamide is designed to target the glucocorticoid receptor transcription factor DNA binding site located in the promoter of the glucocorticoid-induced leucine zipper gene. This polyamide is shown to bind with high affinity to the promoter sequence, modulate the expression of this gene, and disrupt the binding of the protein to the gene\u2019s promoter. Examination of the global effects of this polyamide on mRNA transcription is used to elucidate a list of genes that are regulated by a glucocorticoid receptor protein-DNA dependent mechanism. Also in this thesis, the specificities of a Cy3-labeled polyamide known to downregulate expression of the Vascular Endothelial Growth Factor is examined using DNA microarrays composed of hairpins harboring all 524,800 unique 10 base pair DNA sequences. We experimentally verify the correlation of Cy3 fluorescence intensity with quantitative DNase I footprint-derived binding affinities. Additionally, progress is made towards the polyamide-mediated inhibition of Myc/Max transcription factor gene regulation. " }, { "name": "Palmer, Joshua Henry", "degree": "PhD", "year": "2011", "title": "Iridium Corroles: Synthesis, Properties, and Electronic Structure", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02152011-145456588", "creators": [ { "name": { "family": "Palmer", "given": "Joshua Henry" }, "id": "Palmer-Joshua-Henry", "display_name": "Palmer, Joshua Henry" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7CAD-6P44", "abstract": "The synthesis, properties, and electronic structures of a family of iridium corrole complexes are discussed in detail. These compounds represent the first well-characterized examples of third-row metals being inserted successfully into the small corrole binding pocket; they possess a planar macrocycle, which neither saddles nor ruffles upon bromination, and are bound at the axial positions by either two amine ligands or one phosphine. Unlike their well-studied cobalt and rhodium analogues, whose redox activity is restricted primarily to the corrole ring, iridium corroles can be oxidized to produce an electron paramagnetic resonance spectrum that has extremely anisotropic g tensor components, implying mixing of the 5d orbitals into the oxidized ground state and opening the door to possible higher-valent iridium complexes. Detailed experimental and computational studies are presented showing that this oxidized ground state is actually mostly corrole-based, as has been found in the past for numerous other supposedly high-valent corrole compounds, but the percentage of iridium character varies from 10 to 18% and tracks with the electron-donating ability of the ligand. Additionally, the unique (among corrole complexes) near-IR phosphorescence of Ir(III) corroles is presented and discussed. Iridium(III) corroles phosphoresce with lifetimes ranging from hundreds of nanoseconds to a few microseconds at room temperature, with slightly longer lifetimes at low temperature. Unfortunately, the quantum yields of phosphorescence are low, 1% or less, and this appears to be due to an exceptionally slow set of radiative rates for the corroles. An examination of the reactivity of ammine-ligated Ir(III) corroles is also described. These compounds can be oxidized in the presence of an ammonia source to form novel six-coordinate iridium(III) azaporphyrins in an unprecedented chemical transformation. The characterization and properties of these iridium azaporphyrin complexes are detailed as well, with a focus on nuclear magnetic resonance characterization techniques and a discussion of the red phosphorescence of the azaporphyrins. " }, { "name": "Phillips, John Wilson", "degree": "PhD", "year": "2011", "title": "Biological Activity of a Py-Im Polyamide Androgen Receptor Antagonist", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022011-172257819", "creators": [ { "name": { "family": "Phillips", "given": "John Wilson" }, "id": "Phillips-John-Wilson", "display_name": "Phillips, John Wilson" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "biochem" ], "doi": "10.7907/MPH7-D492", "abstract": "Py-Im polyamides are cell-permeable, programmable, sequence-specific, DNA minor groove-binding small molecules. When designed to bind a DNA sequence that matches the consensus DNA-binding sequence of a transcription factor, they can be used to block the binding of that transcription factor to its response element in vitro and in cell culture. We have used this approach to inhibit the genotropic activity of the endogenous transcription factors HIF1\u03b1, glucocorticoid receptor (GR), and androgen receptor (AR). In this work, we report the completion of a library of hairpin Py-Im polyamides targeted to all possible 5\u2019-WGNNNW-3\u2019 (W = A or T) sequences. These compounds bind their target DNA sequences with high affinity. One compound from this set targets the sequence 5\u2019-WGWWCW-3\u2019, which matches the DNA binding consensus sequence of GR and AR and has been shown to inhibit the gene regulatory activity of these proteins in cell culture. Herein, we show that a cyclic derivative of this compound maintains its activity against AR-driven gene expression in hormone-sensitive LNCaP prostate cancer cells. As androgen receptor signaling is crucial to prostate cancer growth and metastasis even in its recurrent form, we next examine the activity of the AR/GR antagonist in a tissue culture model of castration-resistant prostate cancer. In this model, the polyamide retains its activity against AR-driven mRNA expression, but it fails to inhibit the binding of AR to its response element. The polyamide-mediated repression is also accompanied by significant cell stress and cytotoxicity, which are explored in the final two chapters of this thesis. The former investigates a role for polyamides as inhibitors of DNA Topoisomerase II. Despite in vitro evidence indicating polyamides prevent Topoisomerase II binding, no evidence for this is found in cell culture. The final chapter reveals that polyamide-mediated cytotoxicity is likely due to inhibition of DNA synthesis. This occurs at concentrations similar to those used for transcription factor inhibition, suggesting that S-phase disturbance accompanies efforts to regulate gene expression with polyamides." }, { "name": "Pryce, Imogen Mary", "degree": "PhD", "year": "2011", "title": "Resonant Metallic Nanostructures for Active Metamaterials and Photovoltaics", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282011-153554049", "creators": [ { "name": { "family": "Pryce", "given": "Imogen Mary" }, "id": "Pryce-Imogen-Mary", "display_name": "Pryce, Imogen Mary" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Scherer", "given": "Axel" }, "id": "Scherer-A", "role": "member", "display_name": "Scherer, Axel" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1RB7-ME80", "abstract": "Electromagnetic metamaterials are composites consisting of sub-wavelength structures designed to exhibit particular responses to an incident electromagnetic wave. In general, the properties of a metamaterial are fixed at the time of fabrication by the dimensions of each unit cell and the materials used. By incorporating dynamic components to the metamaterial system, a new type of tunable design can be accessed.
\r\n\r\nThis thesis describes the design and development of resonant metallic nanostructures for use in active metamaterials. We begin by examining passive systems and introduce concepts that are critical for the design of more complex, tunable structures. We show how a simple metamaterial design, a plasmonic nanoparticle array, can be used to enhance the photocurrent of an ultrathin InGaN quantum well photovoltaic cell. We then explore how more complex resonator shapes can be coupled together in a single unit cell in order to access more complex resonant behavior.
\r\n\r\nIn the second half of this thesis, we use several material systems as the basis for the design of active metamaterials. We demonstrate the first tunable metamaterial at optical frequencies using vanadium dioxide, a phase transition material. We exploit this material's transition from a semiconducting to a metallic state and show how a novel fabrication scheme can be used to achieve a frequency tunable resonant response. We then abandon traditional hard and brittle substrates and develop a lithographic transfer process for adhering metallic nanostructures to highly compliant polymeric substrates. Mechanical deformation is then used to distort the resonator shapes and achieve resonant tunability of a full linewidth. This system is exploited to demonstrate interesting resonant hybridization phenomena, such as Fano resonance modulation, and sets the stage for the more elusive goal of driving two resonant nanostructures into contact. Finally, we describe the use of compliant tunable metamaterials as both refractive index sensors and surface enhanced infrared absorption (SEIRA) substrates. The results highlight the promise of post-fabrication tunable compliant metamaterial sensors and the potential for integration with spectroscopic devices in remote sensing and microfluidic device applications.
" }, { "name": "Pye, Havala Olson Taylor", "degree": "PhD", "year": "2011", "title": "Investigations of Global Chemistry-Climate Interactions and Organic Aerosol Using Atmospheric Modeling", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08172010-150049831", "creators": [ { "name": { "family": "Pye", "given": "Havala Olson Taylor" }, "id": "Pye-Havala-Olson-Taylor", "display_name": "Pye, Havala Olson Taylor" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WCT5-RM26", "abstract": "Aerosol, or particulate matter (PM), is an important component of the atmosphere responsible for negative health impacts, environmental degradation, reductions in visibility, and climate change. In this work, the global chemical transport model, GEOS-Chem, is used as a tool to examine chemistry-climate interactions and organic aerosols.
\r\n\r\nGEOS-Chem is used to simulate present-day (year 2000) and future (year 2050) sulfate, nitrate, and ammonium aerosols and investigate the potential effects of changes in climate and emissions on global budgets and U.S. air quality. Changes in a number of meteorological parameters, such as temperature and precipitation, are potentially important for aerosols and could lead to increases or decreases in PM concentrations. Although projected changes in sulfate and nitrate precursor emissions favor lower PM concentrations over the U.S., projected increases in ammonia emissions could result in higher nitrate concentrations.
\r\n\r\nThe organic aerosol simulation in GEOS-Chem is updated to include aerosol from primary semivolatile organic compounds (SVOCS), intermediate volatility compounds (IVOCs), NOx dependent terpene aerosol, and aerosol from isoprene + NO3 reaction. SVOCs are identified as the largest global source of organic aerosol even though their atmospheric transformation is highly uncertain and emissions are probably underestimated. As a result of significant nighttime terpene emissions, fast reaction of monoterpenes with the nitrate radical, and high aerosol yields from NO3 oxidation, biogenic hydrocarbons reacting with the nitrate radical are expected to be a major contributor to surface level aerosol concentrations in anthropogenically influenced areas such as the United States. Globally, 69 to 88 Tg/yr of aerosol is predicted to be produced annually, approximately 22 to 24 Tg/yr of which is from biogenic hydrocarbons.
" }, { "name": "Romano, Christine Anne", "degree": "PhD", "year": "2011", "title": "DNA-Mediated Charge Transfer Between [4Fe-4S] Cluster Glycosylases", "advisor": "Barton, Jacqueline K.; Newman, Dianne K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04032011-125158842", "creators": [ { "name": { "family": "Romano", "given": "Christine Anne" }, "id": "Romano-Christine-Anne", "display_name": "Romano, Christine Anne" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "co-advisor", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "co-advisor", "display_name": "Newman, Dianne K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/63TC-FN74", "abstract": "The work performed herein describes three proteins: Uracil DNA glycosylase (UDG) from Archaeoglobus fulgidus, MutY, and Endonuclease III (EndoIII) from Escherichia coli. They are DNA repair glycosylases that contain [4Fe-4S] clusters. While the catalytic mechanisms of many BER enzymes have been studied in detail, questions remain about how these enzymes search the vast amount of cellular DNA to find their substrates, and why some require a [4Fe-4S] cluster. The iron-sulfur cluster is not necessary for catalysis, and it only displays a physiologically relevant midpoint potential when bound to DNA. We have proposed that UDG, MutY, and EndoIII use their [4Fe-4S] clusters to participate in DNA-mediated charge transport (CT), and that these proteins mediate long-range electrochemical signaling in order to detect DNA damage.
\r\n\r\nThis scheme for DNA damage detection assumes that CT occurs efficiently between the DNA helix and the [4Fe-4S] cluster of the bound protein. In order for efficient CT to occur, a pathway of amino acids must be present that facilitates CT between the DNA and the iron-sulfur cluster. For each of the enzymes mentioned, this pathway was explored through mutagenesis. In UDG, MutY, and EndoIII, several amino acids thought to be important for CT were mutated and the resulting proteins were characterized biochemically. Their CT capabilities were analyzed by cyclic voltammetry on DNA-modified electrodes. In these experiments, the mutants\u2019 signal intensities were quantified and compared to those of wild-type enzyme. An attenuated signal relative to wild-type protein may indicate that the mutant is deficient in CT and that the targeted amino acid is part of the protein-DNA CT pathway in the native enzyme. Many mutants were also screened by enzymatic assays and circular dichroism spectroscopy to further characterize their DNA-binding properties and structural stability.
\r\n\r\nThe A. fulgidus UDG mutants examined, C17H, C85S, and C101S, all contained mutations in the cysteine residues that ligate the [4Fe-4S] cluster. These mutants were designed to determine how the iron-sulfur cluster coordination environment affects protein-DNA CT. The mutants exhibited varying signal strengths relative to WT UDG on DNA-modified electrodes. C85S produced a weaker signal, indicating a CT deficiency. The signal intensity from C101S was within error of that of WT, and the signal from C17H was larger than that of WT, possibly indicating that this mutant is less structurally stable than WT UDG.
\r\n \r\nIn E. coli MutY, position Y82 aligns with Y165 in MUTYH, a residue in which mutations have been found in many colorectal cancer patients. To better understand the correlation between protein-DNA CT and colorectal cancer, the MutY mutants Y82C and Y82L were prepared and characterized. Y82C exhibited a CT deficiency relative to WT MutY, whereas Y82L did not. These data indicate that Y82 forms part of the CT pathway in native E. coli MutY, but that other long-chain amino acids, such as leucine, can also mediate CT efficiently at this position.
\r\n \r\nSeveral different mutants of E. coli EndoIII were examined. First, the Y82 position was targeted, since the aligning MUTYH residue has been found mutated in colorectal cancer patients and because this residue is located near the protein-DNA interface. Five mutations were made at or near the Y82 position, and their cyclic voltammetry signals demonstrated that aromatic amino acids best mediate CT at this position. Other residues towards the interior of the protein, Y75, Y55, and F30 were also mutated to alanines. These mutants exhibited CT deficiencies, implicating the residues as part of a potential CT pathway. Residues W178 and Y185, located near the [4Fe-4S] cluster of EndoIII, were also mutated to alanines. The resulting mutants produced larger signals than that of WT EndoIII. These mutants were later shown by circular dichroism spectroscopy to be less stable structurally than WT EndoIII. All of the mutants mentioned exhibited enzymatic properties similar to those of WT, suggesting that they are able to bind DNA and excise damage nucleobases as well as the native enzyme. Several of these mutants were also used in a mutagenesis-based experiment to assay how EndoIII variants help MutY search for DNA lesions, although data from these experiments showed no significant differences in mutation rate between strains expressing different EndoIII variants.
\r\n \r\nIn total, the mutagenesis studies performed here helped determine the characteristics of BER enzymes that enable them to mediate DNA-protein CT. All these enzymes must contain a stable, well-protected metallocluster that charge can access through a series of CT-facilitating amino acids. In discovering several residues important for protein-DNA CT in UDG, MutY, and EndoIII, we have strengthened support for the hypothesis that these enzymes facilitate DNA-mediated CT in vivo. These enzymes may in fact be part of a much larger array of redox-active DNA-binding proteins that communicate electrochemically to help each other detect and repair DNA lesions inside the cell.
\r\n" }, { "name": "Saouma, Caroline Thalia Abdunnur", "degree": "PhD", "year": "2011", "title": "Iron Mediated Reduction Schemes for Dinitrogen and Carbon Dioxide", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01242011-170306838", "creators": [ { "name": { "family": "Saouma", "given": "Caroline Thalia Abdunnur" }, "id": "Saouma-Caroline-Thalia-Abdunnur", "display_name": "Saouma, Caroline Thalia Abdunnur" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/46C3-BY97", "abstract": "Several mono- and diiron species that coordinate NxHy ligands have been prepared and studied, to serve as structural, spectroscopic, and/or reactivity mimics to intermediates to an alternating reduction scheme for N\u2082 (i.e., Mn-N\u2261N \u2192 Mn-HN=NH \u2192 Mn-H\u2082N-NH\u2082 \u2192 Mn + 2 NH\u2083). The reaction between [PhBPR\u2083]FeMe ([PhBPR\u2083] = (PhB(CH\u2082PR\u2082)\u2083-; R = Ph, CH\u2082Cy) and hydrazine affords {[PhBPR\u2083]Fe}\u2082(\u03bc-\u03b7\u00b9: \u03b7\u00b9-N\u2082H\u2084)(\u03bc\u00b2- \u03b7\u00b2:N\u2082H\u2082). In one instance (R = Ph), the stepwise oxidation of coordinated hydrazine to diazene, and diazene to dinitrogen is achieved, giving {[PhBPPh\u2083]Fe}\u2082(\u03bc-\u03b7\u00b9:\u03b7\u00b9-N\u2082H\u2082)(\u03bc-\u03b7 2: \u03b7 2-N2H2) and {[PhBPPh\u2083]Fe}\u2082(\u03bc-NH)\u2082, respectively.
\r\n\t\r\nAs an extension to this work, a family of complexes which feature the same auxiliary ligands (i.e., [PhBPCH2Cy\u2083]Fe(OAc)), that are all iron(II), and that only differ in the oxidation state of the nitrogenous ligand has also been prepared: {[PhBPCH2Cy\u2083]Fe(OAc)}\u2082(\u03bc-N\u2082), {[PhBPCH2Cy\u2083]Fe(OAc)}\u2082(\u03bc-N\u2082H\u2082), {[PhBPCH2Cy\u2083]Fe(OAc)}\u2082(\u03bc-N\u2082H\u2084), and {[PhBPCH2Cy\u2083]Fe(OAc)(NH\u2083).
\r\n\t\r\nTo determine whether similar species could be isolated at a single iron site, the coordination chemistry of the more crowded \u201c[PhBPmter3]Fe\u201d fragment was investigated and compared to that of the \u201c[PhBPPh3]Fe\u201d scaffold. Treatment of [PhBPmter3]FeMe with hydrazine generates the unusual 5-coordinate hydrazido complex, [PhBPmter3]Fe(\u03bc2-N2H3), which features an Fe=N \u03c0 bond. Both 5- and 6-coordinate iron complexes that coordinate hydrazine were also synthesized, and the oxidation of these hydrazine and hydrazido(-) species was explored. In most instances, oxidation results in disproportionation of the N2Hy ligand, and [PhBPR3]Fe(NH3)(OAc) (R = Ph, mter) is isolated.
\r\n\t\r\nA 5-coordinate diiron diazene redox pair of complexes, {[PhBPPh3]Fe(CO)}2(\u03bc-\u03b71:\u03b71-N2H2)0/- was also prepared and studied. The electronic structure of the Fe-NH-NH-Fe core in these complexes is unusual in that it features a highly activated diazene ligand, which is unprecedented for mid-to-late transition metals. Combined structural, spectroscopic, and computation studies indicate that there is much \u03c0-covalency within the Fe-NH-NH-Fe core, which has a similar electronic structure as butadiene.
\r\n\t\r\nWith regards to CO2 reduction, the ability of iron(I) to mediate the one- and two- electron reductions of CO2 was explored. The reaction between [PhBPCH2Cy3]Fe(PCy)3 and CO2 is solvent dependent, with oxalate formation to generate {[PhBPCH2Cy3]Fe}2(\u03bc-\u03b72:\u03b72-oxalato) being favored in THF, and decarbonylation to give {[PhBPCH2Cy3]Fe}2(\u03bc-O)(\u03bc-CO) occurring exclusively in MeCy. Studies aimed at understanding this unusual solvent-induced selectivity are presented.
\r\n" }, { "name": "Scott, Valerie J.", "degree": "PhD", "year": "2011", "title": "Investigations of C-H Activation and the Conversion of Methanol to Triptane", "advisor": "Bercaw, John E.; Labinger, Jay A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02272011-102614437", "creators": [ { "name": { "family": "Scott", "given": "Valerie J." }, "id": "Scott-Valerie-J", "display_name": "Scott, Valerie J." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "advisor", "display_name": "Labinger, Jay A." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/P0A0-JV28", "abstract": "Broadly speaking, this thesis represents research towards understanding the mechanisms and important species related to small molecule conversion, namely methane to methanol and methanol to higher hydrocarbons. The first section is on understanding the catalytic formation of methanol from methane, with specific interest in using gold (Au). While this transformation is known to occur catalytically, very little is understood about how it happens. To study this reaction, well-defined Au-complexes were synthesized and reactions relevant to the possible catalytic cycles were examined. In doing so, the first simple Au(III)-monoalkyl complex was generated and characterized: (Idipp)AuI2Me, where Idipp = 1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene). Kinetics experiments demonstrated that the complex reductively eliminates methyl iodide, which is relevant to the functionalization step in CH activation. At low concentrations of iodide, the reductive elimination happens faster, from an unobserved 3-coordinate intermediate. However, at high iodide concentrations, the pathway is still consistent with reductive elimination, but from a 5-coordinate intermediate. This is in contrast to the related platinum-system, as well as to density functional theory calculations done on the Au-system.
\r\n \r\nThe second section studies the C-H activation step alone by close examination of the microscopic reverse: protonation of a metal-alkyl. It had previously been noted that the observed kinetic isotope effects (KIEs) were unusually high for the protonolysis of a few Pd complexes and one Pt complex. It was hypothesized that these high KIEs and involvement of quantum mechanical tunneling may indicate a change in the mechanism of the protonolysis reaction, from protonation at the metal center and reductive coupling to direct protonation of the M-Me bond. The experiments described here were designed to explicitly test this theory and demonstrated that no correlation can be made between mechanism and tunneling.
\r\n\r\nThe third section is focused on the study of the conversion of methanol to highly branched alkanes that make good fuel additives, namely 2,2,3-trimethylbutane (triptane), amidst other alkanes, olefins, and aromatics. Catalyzed by ZnI2 or InI3 at high temperatures, the reaction is hydrogen deficient: aromatics are formed as unsaturated by-products necessary for alkane generation. While the product distributions are somewhat different for the two different catalysts, the general mechanism is the same. While typical InI3 reactions generate more alkanes, more aromatics, and fewer olefins than ZnI2 reactions, longer reaction times and higher temperatures make the ZnI2 reaction look like the InI3 profile. Furthermore, InI3 can activate alkanes; it was found that InI3 can \u201cupgrade\u201d other alkanes with methanol. Notably, a 1:1 mixture of 2,3-dimethylbutane and methanol can be converted into triptane with good selectivity and little aromatic formation; ZnI2 can carry out similar chemistry at higher temperatures. Quantification of the iodine-containing products in each reaction mixture was attempted because of its relevance to the system\u2019s industrial viability and found that these concentrations were significantly higher than would be acceptable in an industrial setting.
\r\n" }, { "name": "Sha, Yao", "degree": "PhD", "year": "2011", "title": "The Mechanisms of the Fuel Cell Oxygen Reduction Reaction on Pt and Other 8-11 Column Metal Surfaces", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112011-205842246", "creators": [ { "name": { "family": "Sha", "given": "Yao" }, "id": "Sha-Yao", "display_name": "Sha, Yao" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7VD4-FY21", "abstract": "To better understand and improve the cathode process for Proton exchange membrane fuel cell, we studied systematically the mechanism of oxygen reduction reaction (ORR) on group 8\u201311 metals and their alloys using density functional theory calculations. To address the contribution of solvent effect, we developed a practical implicit solvation model based on Poisson-Boltzmann equation. We discovered that solvation changed greatly the reaction barriers and hence the pathways preferences. The two well known mechanisms O2-diss and OOH-form mechanisms become impossible with water solvation. Instead, we found three new alternative mechanisms, namely, O2-diss-hydr, OOH-form-hydr, and high-H mechanisms. We showed that the oxygen hydrolysis Oad + H2Oad -> 2OHad plays an important role in the ORR which leads to the preferred O2-diss-hydr mechanism. We also developed a method to study the processes involving electron transfer between the solvent and the electrode. We found that direct OH formation from Oad and H3O+ has a high barrier of 0.70eV and is hence unlikely to be the dominant way of forming OHad at the operating potential of 0.8V. The potential dependent barrier leads to an overall optimal operating potential of 0.68V. We also studied the ORR on Pt3Ni alloys and found that the sublayer Ni atoms imposes an inhomogeneity in surface binding sites. The different binding energies make the barriers coverage dependent. Pt3Ni can only outperform Pt at higher coverage. We also showed the general approach of studying an unknown alloying system using Pd-Cu system as an example. We studied the structural, surface cleavage, and binding site preferences for various types of PdCu alloys. We predicted that 1:1 PdCu alloy with L11 structure and layered surface is a better catalyst than pure Pd and Cu, which agrees with later experiments. " }, { "name": "Shanata, Jai Anand Pattur", "degree": "PhD", "year": "2011", "title": "Single-Molecule Studies of Ion Channels Expressing Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082011-080856211", "creators": [ { "name": { "family": "Shanata", "given": "Jai Anand Pattur" }, "id": "Shanata-Jai-Anand-Pattur", "display_name": "Shanata, Jai Anand Pattur" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2Y28-RP86", "abstract": "The nicotinic acetylcholine receptors are pentameric ligand-gated ion channels that mediate fast synaptic transmission in the brain and peripheral nervous system. After an introduction (Chapter 1), Chapter 2 describes my development of techniques to combine single-channel and whole-cell recording with nonsense suppression. Having established the feasibility of the combined use of single-channel and whole-cell recording, in Chapter 3 we developed a method to identify the functional interactions of amino acids that are physically far apart in a protein. This is fundamentally a whole-cell recording method to find allosteric interactions in ion channels. The significance of this method is strongly supported by single-channel measurements. Additionally, the relationship between the single-channel gating equilibrium constant, theta, and the whole-cell measurement of EC50 is considered.
\r\n\r\nIn Chapter 4, I describe my progress towards measuring the channel opening rate of the fetal and adult muscle-type nicotinic acetylcholine receptors. Multiple different agonists are used, including acetylcholine, choline, and tetramethylammonium. Single-channel data are reported for the wild-type receptors as well as for receptors with the unnatural amino acid 5-F-Trp (monofluoro-Trp). Data are reported for multiple concentrations for a mutated fetal nAChR, and QuB is used to fit various possible models and estimate theta for this mutant.
\r\n\r\nA major aim of this dissertation was to use single-molecule studies of ion channels expressing unnatural amino acids to provide even more convincing evidence for cation-pi interactions at the binding sites of ligand-gated ion channels, specifically the neuronal nicotinic acetylcholine receptor. Chapter 5 describes the combined application of single-channel, whole-cell, and unnatural amino acid mutagenesis to the specific question of how two molecules\u2014nicotine and Chantix\u00ae (varenicline)\u2014bind to the alpha4beta2 brain receptor. In Chapter 6, I describe single-channel experiments that establish a method for distinguishing between the two known stoichiometries of the wild type alpha4beta2 brain receptor. Specifically, I identify a difference in the rectification properties of the high and low affinity receptors.
\r\n" }, { "name": "Sherden, Nathaniel Haynes", "degree": "PhD", "year": "2011", "title": "Mechanistic Investigations into the Palladium-Catalyzed Decarboxylative Allylic Alkylation of Ketone Enolates Using the PHOX Ligand Architecture\r ", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05312011-072858726", "creators": [ { "name": { "family": "Sherden", "given": "Nathaniel Haynes" }, "id": "Sherden-Nathaniel-Haynes", "display_name": "Sherden, Nathaniel Haynes" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QEAX-9N40", "abstract": "Palladium-catalyzed asymmetric allylic alkylation has become a large and important field for chemical synthesis. Many methodologies in this field offer mild conditions under which challenging and important molecular features can be reliably synthesized, including chiral all-carbon quaternary stereocenters. As a result, palladium- catalyzed asymmetric allylic alkylation has found significant use in total synthesis, and growing use in industry. While the general process of palladium-catalyzed asymmetric allylic alkylation has been studied for decades, there have been a number of recent modifications and developments, such as asymmetric versions of decarboxylative allylic alkylation procedures that are not yet well understood. The development of future implementations and improvements to palladium-catalyzed asymmetric allylic alkylation and related methodologies is expected to be facilitated by a better understanding of these more recent developments, and thus further mechanistic investigation is warranted.
\r\n\r\nReported herein is a set of investigations into the palladium-catalyzed decarboxylative asymmetric allylic alkylation of ketone enolates using the PHOX ligand architecture. By monitoring the reaction via 31P NMR, a series of previously unidentified key intermediates is discovered. Two representatives of these key intermediates are isolated and characterized. The solution behavior of these species under reaction-like conditions is studied along with a few novel and related complexes. The role of these intermediates and their impact on the behavior of the reaction and product formation is discussed.\tPreviously confounding experimentally observed behavior for this methodology is rationalized via the properties elucidated for these discovered intermediates.
" }, { "name": "Sohn, Chang Ho", "degree": "PhD", "year": "2011", "title": "New Reagents and Methods for Mass Spectrometry-based Proteomics Investigations", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02162011-180032183", "creators": [ { "name": { "family": "Sohn", "given": "Chang Ho" }, "id": "Sohn-Chang-Ho", "display_name": "Sohn, Chang Ho" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HRF2-FJ21", "abstract": "New chemical reagents and methods have been employed for mass spectrometry (MS)-based proteomics investigations. Many chemical reagents are synthesized to be covalently attached to biomolecules, especially peptides and proteins. The properties of the resulting peptide conjugates are characterized by various tandem mass spectrometric techniques (e.g., collision-induced dissociation (CID), electron capture dissociation (ECD), electron transfer dissociation (ETD), infrared multiphoton dissociation (IRMPD), and free radical initiated peptide sequencing (FRIPS)). In Chapter 2, the effect of high electron affinity tags in ECD and ETD is investigated using their peptide conjugates. The initial intramolecular electron transfer from the high-lying Rydberg states to the covalently attached high electron affinity tag occurs in competition with the Coulomb stabilized \u03c0* orbitals of the amide bonds in the model peptides. This leads to the inhibition of the normal sequence of ECD and ETD processes, yielding no backbone fragmentations. In Chapter 3, selective disulfide bond cleavages are observed by the FRIPS method. A newly prepared TEMPO-based FRIPS reagent is labeled to model peptides containing disulfide bonds and subject to CID to monitor free radical induced cleavages. Highly selective C\u2013S and S\u2013S bond cleavages are observed and their reaction mechanisms are proposed. In Chapter 4, novel Caltech isobaric tags (CITs) for protein quantification are developed and validated using various model samples. A newly discovered low-energy gas-phase fragmentation pathway, a nucleophilic substitution of the N3 in the 1,2,3-triazole ring generated by copper-catalyzed azide-alkyne cycloaddition (CuAAC) inspired us to create CITs. This selective cleavage is applied to the formation of the reporter ions to quantify protein expression level in cells. Chapter 5 describes clickable cross-linkers (CXLs) developed for elucidation of three-dimensional protein structures and protein-protein interactions (PPIs). In CXLs, cross-linking reactions are separated from the conjugation of affinity tags, avoiding steric hindrance. Cross-linked peptides are enriched from the complex mixture of yeast lysate and cross-linked ubiquitin digests using avidin affinity chromatography, showing high sensitivity of the CXL-based analysis. The low-energy pathway used for CIT reagents is also adopted to produce the reporter ion, filtering MS/MS scans of cross-linked peptides from those of unmodified peptides." }, { "name": "Spencer, Kathleen Marie", "degree": "PhD", "year": "2011", "title": "Constraining Anthropogenic and Biogenic Emissions using Chemical Ionization Mass Spectrometry", "advisor": "Wennberg, Paul O.; Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262011-132849976", "creators": [ { "name": { "family": "Spencer", "given": "Kathleen Marie" }, "id": "Spencer-Kathleen-Marie", "display_name": "Spencer, Kathleen Marie" } ], "advisors": [ { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "advisor", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "co-advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XRFJ-2Q92", "abstract": "Numerous gas-phase anthropogenic and biogenic compounds are emitted into the atmosphere. These gases undergo oxidation to form other gas-phase species and particulate matter. Whether directly or indirectly, primary pollutants, secondary gas-phase products, and particulate matter all pose health and environmental risks. In this work, ambient measurements conducted using chemical ionization mass spectrometry are used as a tool for investigating regional air quality.
\r\n\r\nAmbient measurements of peroxynitric acid (HO\u2082NO\u2082) were conducted in Mexico City. A method of inferring the rate of ozone production, PO3, is developed based on observations of HO\u2082NO\u2082, NO, and NO\u2082. Comparison of this observationally based PO3 to a highly constrained photochemical box model indicates that regulations aimed at reducing ozone levels in Mexico City by reducing NOx concentrations may be effective at higher NOx levels than predicted using accepted photochemistry.
\r\n\r\nMeasurements of SO\u2082 and particulate sulfate were conducted over the Los Angeles basin in 2008 and are compared to measurements made in 2002. A large decrease in SO\u2082 concentration and a change in spatial distribution are observed. Nevertheless, only a modest reduction in sulfate concentration is observed at ground sites within the basin. Possible explanations for these trends are investigated.
\r\n\r\nTwo techniques, single and triple quadrupole chemical ionization mass spectrometry, were used to quantify ambient concentrations of biogenic oxidation products, hydroxyacetone and glycolaldehyde. The use of these techniques demonstrates the advantage of triple quadrupole mass spectrometry for separation of mass analogues, provided the collision-induced daughter ions are sufficiently distinct. Enhancement ratios of hydroxyacetone and glycolaldehyde in Californian biomass burning plumes are presented as are concentrations of these compounds at a rural ground site downwind of Sacramento.
" }, { "name": "Takematsu, Kana", "degree": "PhD", "year": "2011", "title": "Cavity Ringdown Spectroscopy of the Nitrate and Peroxy Radicals", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012011-114553466", "creators": [ { "name": { "family": "Takematsu", "given": "Kana" }, "id": "Takematsu-Kana", "orcid": "0000-0002-2334-336X", "display_name": "Takematsu, Kana" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8SB5-HR07", "abstract": "The chemistry of the Earth's atmosphere consists of complex networks of reactions. Photooxidation of volatile organic compounds (VOCs) in the atmosphere initiates free radical formation. These radicals attack other VOCs to form pollutants and secondary organic aerosols. Quantitative understanding of the radicals and reactions is needed for accurate modeling of the atmosphere. Many species are difficult to study due to low concentrations and short lifetimes. Spectroscopic methods in the ultraviolet and visible regions either do not have the sensitivity or the specificity to characterize these reactions. The work here examines the chemistry and physics of atmospheric radicals by using the sensitive and fast spectroscopic technique cavity ringdown spectroscopy (CRDS), to detect transient species in the near-infrared (NIR) region.
\r\n\r\nThe nitrate radical NO\u2083 is a major nighttime oxidant in the troposphere. It is also a classic example of the breakdown of the Born-Oppenheimer approximation. The radical was first observed a century ago in atmospheric measurements. The structures of the three lowest electronic state however are still not well understood. Difficulties arise from the non-adiabatic Jahn Teller and Pseudo-Jahn-Teller effects. In Chapter 3, we examine the electronic-dipole forbidden à \u2190 X̃ transition of NO\u2083 in the NIR to elucidate the à state of NO\u2083. In Chapter 4, we examine the role of NO\u2083 in atmospheric reactions by detecting the peroxy radical intermediate of the oxidation of 2-butene by NO\u2083.
\r\n\r\nThe chlorine atom Cl is highly reactive and has been historically considered a coastal or marine layer oxidant. Studies now indicate that Cl atoms can play significant roles in urban mainland chemistry. Isoprene and 2-methyl-3-buten-2-ol (MBO232) are two important biogenic VOC emissions. Isoprene alone is responsible for emissions of 500 Tg C y\u207b\u00b9. The peroxy radical intermediates of the oxidation of isoprene and MBO232 by Cl have never been detected using absorption spectroscopy. Chapter 5 includes the first preliminary CRD spectra of the à \u2190 X̃ transition of Cl-isoprenyl and Cl-MBO232 peroxy radials in the NIR. We also outline kinetic experiments to measure the rates of reaction between the Cl-substituted peroxy radicals and nitric oxide (NO) and hydroperoxy radical (HO\u2082) under high and low NO\u2093 conditions in the troposphere.
\r\n" }, { "name": "Van Deventer, James A.", "degree": "PhD", "year": "2011", "title": "Biophysics and Protein Engineering with Noncanonical Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272011-162341841", "creators": [ { "name": { "family": "Van Deventer", "given": "James A." }, "id": "Van-Deventer-James-A", "display_name": "Van Deventer, James A." } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "orcid": "0000-0002-0021-889X", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/VT2B-8B33", "abstract": "Noncanonical amino acids are tools for expanding and altering the chemical functionalities available within proteins. Much recent work has focused on developing biosynthetic means for incorporating noncanonical amino acids into proteins, and applications of noncanonical amino acids to many problems in science and engineering are emerging. The first portion of this thesis describes established methods to incorporate noncanonical amino acids into proteins and efforts to exploit the properties of noncanonical amino acids in areas such as protein structure determination, protein and organism evolution, modulation of the immune system, and proteomics. Researchers\u2019 creative and successful use of this growing toolkit suggests that noncanonical amino acids will continue to be a valuable asset for dissecting biological problems and imparting proteins with new chemical and physical properties.
\r\n\r\nBiophysical studies with noncanonical amino acids provide a platform for studying the effects of atom-by-atom manipulations of amino acid side chains on protein properties. The middle portions of this thesis describe work to better understand how protein properties are affected by subtle amino acid side chain manipulations. This work was aided greatly by the establishment of homoisoleucine as a translationally active analog of leucine in bacterial cells. The small side chain differences between leucine, homoisoleucine, and the fluorinated amino acid trifluoroleucine allow for detailed studies on how amino acid side chain size and fluorination affect protein stability and hydration dynamics. Replacement of leucine by homoisoleucine in coiled-coil peptides stabilizes these proteins, as shown by elevation of the coiled coil thermal denaturation temperature. The stabilization observed when homoisoleucine replaces leucine in the peptides is greater than when trifluoroleucine replaces leucine, suggesting that expansion of side chain volume may play a role in protein stabilization irrespective of hydrocarbon or fluorocarbon character.
\r\n\r\nStudies of water-protein interactions using designed coiled coils containing surface-exposed leucine, homoisoleucine, or trifluoroleucine residues enabled systematic examination of the roles that side chain size and fluorination play in dictating solvation dynamics. Fluorinated side chains appear to exert a large electrostatic drag on nearby water molecules. These results have important implications for the design and engineering of fluorinated proteins due to the critical role water-protein interactions play in many protein properties and functions.
\r\n\r\nThe final portion of this thesis details efforts to engineer the binding properties and chemical reactivity of antibody fragments with noncanonical amino acids. The properties of the single chain variable fragment form of a model anti-digoxin antibody have been studied after replacement of the protein\u2019s methionine residues with methionine analogs containing alkyne, azide, and aliphatic side chains. Experiments with antibody fragments displayed on the surface of Escherichia coli cells revealed that replacement of the methionine residues of the fragment with an analog containing an alkyne side chain reduced the fluorescence levels of cells treated with a fluorescently labeled antigen to background levels, indicating loss of binding function. Replacement of methionine with analogs containing aliphatic and azide side chains left the fluorescence of cells unchanged and reduced by a factor of 0.6, respectively. Fluorescence-activated cell sorting of libraries of cell surface-displayed antibody fragments enabled the isolation of clones functional in multiple amino acid contexts. Cells displaying variants containing alkyne, azide, and aliphatic analogs and treated with fluorescently labeled antigen were more fluorescent than cells displaying the methionine form of the parent antibody fragment by factors of roughly 1.7, 3.5, and 1.3, respectively. Furthermore, the amino acid context used during high-throughput screening experiments appears to affect the frequencies of mutations occurring at various positions within the antibody fragment construct. High-throughput sequencing revealed that populations isolated in different amino acid contexts exhibit mutational rates differing by greater than twenty percent at some residues in the protein.
\r\n\r\nCharacterization of soluble fragments indicated that each noncanonical amino acid used in this study modulates the binding kinetics of antibody fragments in a distinct fashion. Perhaps most interestingly, fragments containing the azide-containing analog azidohomoalanine exhibit improved binding kinetics relative to their methionine-containing counterparts. Replacement of methionine by azidohomoalanine in several variants lowers the dissociation constant of the fragment by up to a factor of two. Chemical conjugation of azide-containing fragments to fluorescent dyes and biotin proved facile with strain-promoted cycloaddition reactions. Quantifications of the extent of reaction using fluorescent dyes revealed that approximately 0.4 dyes had been conjugated per protein, and the resulting conjugates were found to retain their binding function in kinetic and Western blotting assays. Experiments in which azide-containing fragments were displayed on the surface of Escherichia coli cells and subjected to strain-promoted cycloadditions demonstrated that the extent of chemical modification and antigen binding can be monitored simultaneously and used to isolate cells displaying functional, modified proteins. These experiments demonstrate how noncanonical amino acids can be used to modulate multiple properties of antibody fragments and illustrate the feasibility of developing and screening libraries of chemically modified proteins. Evolved, functional bioconjugates may be applicable to a variety of outstanding diagnostic and therapeutic problems.
" }, { "name": "Vermesh, Ophir", "degree": "PhD", "year": "2011", "title": "Highly Informative Analytical Platforms for Rapid, Non-Invasive Diagnosis and Stratification of Patients with Cancer", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272011-115528661", "creators": [ { "name": { "family": "Vermesh", "given": "Ophir" }, "id": "Vermesh-Ophir", "display_name": "Vermesh, Ophir" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "co-chair", "display_name": "Heath, James R." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/40BR-TW68", "abstract": "As the tissue that contains the largest representation of the human proteome, blood is the most important fluid for clinical diagnostics. However, although changes of plasma protein profiles reflect physiological or pathological conditions associated with many human diseases, only a handful of plasma proteins are routinely used in clinical tests. Reasons for this include the intrinsic complexity of the plasma proteome, the heterogeneity of human diseases and the rapid degradation of proteins in sampled blood. The first part of this thesis reports an integrated microfluidic system, the integrated blood barcode chip (IBBC) that can sensitively sample a large panel of protein biomarkers over broad concentration ranges and within 10 minutes of sample collection. It enables on-chip blood separation and rapid measurement of a panel of plasma proteins from quantities of whole blood as small as those obtained by a finger prick. The device holds potential for inexpensive, noninvasive and informative clinical diagnoses, particularly in point-of-care settings.
\r\n\r\nProteomic approaches, on which the IBBC platform is based, have shown great promise in recent years for correctly classifying and diagnosing cancer patients. However, no large antibody-based microarray studies have yet been conducted to evaluate and validate plasma molecular signatures for detection of glioblastoma and monitoring of its response to therapy. In the second part of this thesis, plasma samples from 46 glioblastoma patients (72 total samples) are compared with those of 47 healthy controls with respect to the plasma levels of 35 different proteins known to be generally associated with tumor growth, survival, invasion, migration, and immune regulation. Average-linkage hierarchical clustering of the patient data stratified the two groups effectively, permitting accurate assignment of test samples into either GBM or healthy control groups with a sensitivity and specificity as high as 90% and 94%, respectively (when test samples within unbiased clusters were removed). The accuracy of these assignments improved (sensitivity and specificity as high as 94% and 96%, respectively) when the cluster analysis was repeated on increasingly trimmed sets of proteins that exhibited the most statistically significant (p < 0.05) differential expression. The diagnostic accuracy was also higher for test samples that fell into more homogeneous clusters. Intriguingly, test samples that fell within perfectly homogeneous clusters (all members belonging to the same group) could be diagnosed with 100% accuracy. Using the same 35-protein panel, we then analyzed plasma samples from GBM patients who were treated with the chemotherapeutic drug Avastin (Bevacizumab) in an effort to stratify patients based on treatment-responsiveness. Specifically, we compared 52 samples from (25) patients who exhibited tumor recurrence with 51 samples from (21) patients who did not exhibit recurrence. Again, several proteins were highly differentially expressed and cluster analysis provided effective stratification of patients between these two groups (sensitivity and specificity of 90% and 96%, respectively).
\r\n" }, { "name": "Walker, Don", "degree": "PhD", "year": "2011", "title": "Corrole Sensitized Solar Cells", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09282010-221227791", "creators": [ { "name": { "family": "Walker", "given": "Don" }, "id": "Walker-Don", "display_name": "Walker, Don" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XQBW-D585", "abstract": "The performance of dye sensitized solar cells (DSSC) was investigated as a function of electrolyte composition and dye sensitizer. Electrolytes consisting of increasing concentrations of bromide and tri-bromide effectively increased the current of DSSCs while conserving an increase in open circuit voltage. Corroles were used to investigate their efficacy as light absorbers for DSSCs. Electronic spectroscopy of corroles demonstrated that the spectra of corroles could be red shifted through \u03b2 substitution. Also, the changes in the electronic spectra of corroles was not affected by adsorption to TiO2. Electrochemical data concluded that the functionalization of the \u03b2 positions of the corroles did not significantly affect the corrole's redox potentials. FTIR spectroscopy confirmed that the corroles were chemically adsorbed onto TiO2. Photoelectrochemical measurements concluded that the corroles are efficient sensitizers for DSSCs. A highly efficient corrole utilizing sulfonic acid binding groups was discovered. Also, a corrole with a malonic acid binding group was 70% as efficient as one of the best performing dye sensitizers in DSSCs.\r\n" }, { "name": "Whited, Charlotte A.", "degree": "PhD", "year": "2011", "title": "Tuning Nitric Oxide Synthase: Investigating the Thiolate \"Push\" and No Release", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042011-174816761", "creators": [ { "name": { "family": "Whited", "given": "Charlotte A." }, "id": "Whited-Charlotte-A", "display_name": "Whited, Charlotte A." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PZAY-WQ64", "abstract": "All heme thiolate enzymes have conserved hydrogen bonding networks surrounding the axial thiolate ligand. In order to understand the role of this proximal hydrogen bonding network in nitric oxide synthases (NOS), three mutants of the NOS enzyme from Geobacillus stearothermophilus were expressed and characterized. The wild type enzyme has a tryptophan residue at position 70 that \u03c0-stacks with the porphyrin ring and donates a long hydrogen-bonding interaction to the thiolate ligand of the heme iron. The native Trp was replaced with His, Phe, and Tyr. These three residues were selected to investigate the two effects of the Trp, H-bonding and Pi-stacking. Several different spectroscopic techniques were used to investigate the stability and properties of these mutant enzymes. The identity of each mutant was confirmed by mass spectrometry. Both UV-visible absorption and circular dichroism spectroscopies were used to assess the stability of the new proteins. It was shown using binding assays, generation of the ferrous-CO species, and redox titrations that the \u03c3-donating abilities of the thiolate are increased after removal of the hydrogen bonding group in the Trp. Finally, electron paramagnetic resonance spectroscopy and Evans method nuclear magnetic resonance spectroscopy were used to characterize the spin state of the iron center in each mutant, reflecting the increased \u03c3-donating capabilities of the thiolate upon removal of the hydrogen bonding group. The reduction potential of wild type and W70H were determined by chemical titration to be -362 and -339 mV vs. NHE, respectively. This is the first report of the reduction potential of any bacterial nitric oxide synthase.
\r\n\r\nThe reactivity of each the wild type enzyme and the three new mutants was tested using stopped-flow mixing coupled with UV-visible absorption spectroscopy and the Griess Assay. Autoxidation rates measured by stopped-flow suggest that the Tyr and Phe mutants do indeed have significantly more negative reduction potentials, but that the His mutant is particularly slow to oxidize. The Griess Assays showed that all four enzymes produce nitrite in solution, when provided with substrate, cofactor and hydrogen peroxide (as a source of reducing equivalents). In single turnover experiments, however, only three of the four enzymes showed evidence of ferric-NO production. The His mutant showed no intermediate absorbance near 440 nm (which would be indicative of ferric-NO formation), suggesting that it releases NO- rather than the radical species NO\u2219. The role of this hydrogen bond is concluded to be an electronic one, rather than playing any part in positioning the heme. It prevents formation of the inactive P420 species, and tunes the reduction potential to one high enough to be reduced by a reductase but low enough to still deliver an electron to the redox active cofactor, tetrahydrobiopterin, at the end of catalysis.
\r\n\r\nThe rate at which NO is released by each NOS enzyme varies greatly among isoforms and species, over nearly two orders of magnitude. One residue (an isoleucine located above the heme in bacterial enzymes) involved in the gating of NO release has been previously identified by Stuehr. However, this single residue does not account for the entirety of the differences among the forms of NOS. Another residue, a histidine at position 134 in NOS from Geobacillus stearothermophilus (gsNOS), was hypothesized to also participate in gating NO release based on an observed correlation between rates of NO release and the bulk of side chains at this position. Each single point mutation, H134S and I223V, and the double mutant were expressed in gsNOS and their reactivity toward the diatomic molecules CO and NO were studied. CO rebinding was investigated using laser flash photolysis and NO release using stopped flow UV-visible spectroscopy. The presence of both monomer and dimer was observed in solution, and position 134 was shown to be another key residue in gating NO release. Wild type gsNOS contains both the bulkier Ile223 and His134 and has the slowest measured NO release (0.039 s-1) of all NOS enzymes. A new, more accurate kinetics model for turnover is proposed. Each single mutation increased NO release substantially, while the double mutant has a rate constant of 1.0 s-1, nearly as fast as mammalian iNOS at 2.3 s-1, identifying position 134 as another important factor determining rate constants for NO release.
\r\n" }, { "name": "Yang, Fan", "degree": "PhD", "year": "2011", "title": "Biochemical and Biophysical Characterizations of Immunoglobulin Superfamily Receptors Neogenin and L1", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242010-143824484", "creators": [ { "name": { "family": "Yang", "given": "Fan" }, "id": "Yang-Fan", "display_name": "Yang, Fan" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q8ET-K632", "abstract": "Immunoglobulin (Ig) superfamily receptors function in a wide variety of developmental and metabolic processes. We are particularly interested to characterize two Ig superfamily receptors neogenin and L1. The first chapter of the thesis gives a brief review of the biological significance of neogenin and L1 and what has been learned in their functions. In Chapter 2, we described the localization of the hemojuvelin-binding epitope of neogenin to the membrane proximal fifth and sixth fibronectin type III (FNIII) domains, with the sixth FNIII domain contributing the majority of the binding. Chapter 3 presents the crystal structure of this hemojuvelin-binding fragment at 1.8 \u00c5, revealing a nearly linear domain arrangement. Hemojuvelin binding sites have been mapped to one face of the sixth FNIII domain based on sequence alignment between neogenin and DCC (Deleted in Colorectal Cancer), a molecule related to neogenin but does not bind to hemojuvelin. These results should also be informative in understanding the interaction between neogenin and repulsive guidance molecule (RGM), the closest homologue of hemojuvelin. The interaction between neogenin and RGM is known to regulate neuronal survival. Chapter 4, the second part of the thesis, describes our studies of L1-mediated homophilic adhesion using biophysical approaches. We built a basis shape model to describe L1-mediated homophilic adhesion between L1-coated giant unilamellar vesicles and flat substrate. Using confocal microscopy techniques, we were able to reconstruct the three-dimensional shape of an adhered vesicle. We developed an algorithm in order to derive adhesion strength from the configurations of adhered vesicles based on our basis shape model using energy minimization approach." }, { "name": "Yang, Jennifer Chuen-Hsien", "degree": "PhD", "year": "2011", "title": "Following Motion of Early Heart Development at the Cellular Level Using Confocal Microscopy in Transgenic Quail Embryos", "advisor": "Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312010-135100976", "creators": [ { "name": { "family": "Yang", "given": "Jennifer Chuen-Hsien" }, "id": "Yang-Jennifer-Chuen-Hsien", "display_name": "Yang, Jennifer Chuen-Hsien" } ], "advisors": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "chair", "display_name": "Gharib, Morteza" }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Collazo", "given": "Andres" }, "id": "Collazo-A", "role": "member", "display_name": "Collazo, Andres" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "biochem" ], "doi": "10.7907/Y0YB-2312", "abstract": "The heart has fascinated scientists for centuries, from the days of Leonardo da Vinci to the modern scientist. As tools have developed over the years, we have begun to create a different perspective of how the heart develops and functions from original ideas. Genetics, molecular biology, and microscopes have allowed us to examine the heart with a level of detail that could not have been imagined by da Vinci.
\r\n\r\nThe heart is a complex organ to study due to its innate nature of contracting and relaxing for the entire life of an organism. The motions of systole and diastole complicate any measurements and analysis that can be done. In general, most research has been done in either fixed tissue or dead organisms, neither being ideal for studying a live heart. But current research aims to change our knowledge of cardiogenesis through dynamic imaging of live tissue. With the progress made in the last few years, we have had to revise many of our assumptions about heart development and pumping mechanics. Now, we are at a new stage of research that requires the quantification of cardiogenesis to understand the requirements of heart development to prevent future diseases from occurring.
\r\n\r\nThe following work divides the heart into three areas: 1-dimensional dynamic imaging and analysis of contractions and relaxation to achieve temporal resolution, 4-dimensional modeling of a beating heart during tube formation and early looping to observe individual cellular motion, and 4-dimensional fate mapping of the developing heart tube to visualize development with cellular resolution. With these three perspectives, we are able to quantify the movements of the myocardium and endocardium during development while the heart is beating. This novel approach will give us a wealth of information never seen before.
\r\n\r\nWe use transgenic Japanese quail to highlight the nuclei of individual endothelial cells in the vasculature to analyze the inner tube of the heart, and another transgenic with a ubiquitous marker that fluoresces in every cell of the embryo. The quail heart is comparable to the human heart in that both have 4-chambered hearts, yet the quail is a much easier organism to study. The embryo is transparent and develops outside the mother. The quail embryo can be imaged ex ovo on inverted microscopes, allowing for ease of setup in a controlled environment.
\r\n\r\nWith the use of dynamic imaging and innovative computer software, we were able to reconstruct the live heart while it is beating and developing. By dynamically imaging the endocardium and myocardium, we were able to study the interactions between the two layers by offering unsurpassed visual access to the morphogenetic events of cardiogenesis. Questions that have remained elusive are now being answered with extensive analysis from the data collected. Quantification of cardiogenesis is possible and a detailed fate-map has been produced from this research.
\r\n" }, { "name": "Agnew, Heather Dawn", "degree": "PhD", "year": "2010", "title": "Rapid Construction of Protein Capture Agents with Chemically Designed Stability and Antibody-Like Recognition Properties", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03092010-121643566", "creators": [ { "name": { "family": "Agnew", "given": "Heather Dawn" }, "id": "Agnew-Heather-Dawn", "display_name": "Agnew, Heather Dawn" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1HJG-AQ59", "abstract": "This thesis describes technologies for the rapid and scalable production of high-affinity, high-specificity protein capture agents which possess the affinities and specificities of antibodies, but also exhibit improved chemical, biochemical, and physical stability. I will discuss how the chemical flexibility of comprehensive, one-bead-one-compound (OBOC) libraries of oligopeptides may be combined with iterative in situ click chemistry to select multi-ligand capture agents. Large OBOC libraries form the basis of individual peptide ligands, and also permit chemically designed stability through the incorporation of artificial (azide or acetylene) and non-natural amino acid building blocks. The in situ click chemistry method then utilizes the target protein as the catalyst, or template, for assembling its own biligand via formation of a 1,2,3-triazole linkage between two individual ligands (azide and acetylene). This process can be repeated to produce triligands, tetraligands, and other higher-order multi-ligands with an accompanying increase in affinity and specificity through cooperative interactions. Once found, multi-ligand capture agents can be produced in gram amounts via conventional synthetic methods such as the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC). This is a general and robust strategy for the inexpensive, high-throughput construction of protein capture agents that can be exploited to detect protein biomarkers in multi-parameter clinical diagnostic assays.
\r\n\r\nWhile high-affinity protein capture agents represent a significant technology advance, they are just one component of what is necessary for highly multiplexed measurements of protein biomarkers. It is also important to develop or optimize the actual assay platforms that can enable sensitive multi-parameter protein measurements using these capture agents. Silicon nanowire (SiNW) nanoelectronic sensors can provide quantitative, label-free multi-parameter measurements of protein biomarkers in real time. However, SiNW sensors can be challenging to deploy because unprotected Si forms a native oxide layer that can significantly reduce the detection sensitivity of the nanowire sensors via dielectric shielding. Another technical challenge is the development of chemistries which allow for the selective encoding of nanowire surfaces with the capture agents. To overcome these challenges, the final part of this thesis presents a general method to functionalize organic and biological molecules on highly passivated Si(111) surfaces with minimal surface oxidation.
" }, { "name": "Allan, Kevin McCormack", "degree": "PhD", "year": "2010", "title": "Development of Versatile Strategies for Aryne Annulation: Applications in Methodology and Natural Product Total Synthesis", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04272010-110655339", "creators": [ { "name": { "family": "Allan", "given": "Kevin McCormack" }, "id": "Allan-Kevin-McCormack", "display_name": "Allan, Kevin McCormack" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Virgil", "given": "Scott C." }, "id": "Virgil-S-C", "role": "member", "display_name": "Virgil, Scott C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VPEN-7M75", "abstract": "Since the elucidation of its structure in 1953, benzyne has been the focus of intense interest within the chemical community. Due to an unusually high degree of ring strain, benzyne displays reactivity uncharacteristic of common alkynes, including a tendency to react under mild metal-free conditions. This reactivity is exploited in the development of three novel methods for the synthesis of heterocyclic structures.
\r\n\r\nThe first synthetic methodology includes two orthogonal annulation reactions taking place between functionalized enamines and arynes. The substitution at the nitrogen atom of the enamine determines the path of reactivity. Carbamates undergo a formal [3 + 2] cycloaddition with arynes to give rise to indolines, while amides undergo a formal [4 + 2] cycloaddition and dehydration to form isoquinolines. The latter reaction is applied to a three-step synthesis of the antispasmotic pavine alkaloid, papaverine.
\r\n\r\nThis isoquinoline-forming aryne annulation reaction is further employed in a concise asymmetric total synthesis of the tetrahydroisoquinoline antitumor antibiotic, (\u2013)-quinocarcin. In addition to this key transformation, the synthetic route features an auxiliary-mediated diastereoselective dipolar cycloaddition to set the absolute stereochemistry and a novel two-step reduction to form the tetrahydroisoquinoline. In total, this strategy has enabled the shortest total synthesis of this important alkaloid reported to date.
\r\n\r\nThe second methodology involves the synthesis of 3-hydroxyisoquinolines and 2-hydroxy-1,4-naphthoquinones from \u03b2-ketoesters using an aryne acyl-alkylation reaction in combination with an in-situ condensation. This technology enables the preparation of highly functionalized polyaromatic ring systems in two steps from readily available carboxylic acid starting materials. As a demonstration of its utility, this method is employed in a rapid synthesis of the P,N-ligand, QUINAP.
\r\n\r\nFinally, the development of a pair of three-component coupling reactions between arynes, isocyanides, and a third relay species is described. Phenyl esters and quinones lead to iminoisobenzofurans, while alkynes furnish iminoindenones. Procedures for the subsequent hydrolysis of these products are provided, thereby giving access to synthetically useful ortho-ketobenzamide and indenone compounds.
" }, { "name": "Anderson, Amos Gerald", "degree": "PhD", "year": "2010", "title": "Quantum Monte Carlo: Faster, More Reliable, and More Accurate", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-08122009-151332", "creators": [ { "name": { "family": "Anderson", "given": "Amos Gerald" }, "id": "Anderson-Amos-Gerald", "display_name": "Anderson, Amos Gerald" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KVTV-N754", "abstract": "The Schroedinger Equation has been available for about 83 years, but today, we still strain to apply it accurately to molecules of interest. The difficulty is not theoretical in nature, but practical, since we're held back by lack of sufficient computing power. Consequently, effort is applied to find acceptable approximations to facilitate real time solutions. In the meantime, computer technology has begun rapidly advancing and changing the way we think about efficient algorithms. For those who can reorganize their formulas to take advantage of these changes and thereby lift some approximations, incredible new opportunities await.
\r\n\r\nOver the last decade, we've seen the emergence of a new kind of computer processor, the graphics card. Designed to accelerate computer games by optimizing quantity instead of quality in processor, they have become of sufficient quality to be useful to some scientists. In this thesis, we explore the first known use of a graphics card to computational chemistry by rewriting our Quantum Monte Carlo software into the requisite \"data parallel\" formalism. We find that notwithstanding precision considerations, we are able to speed up our software by about a factor of 6.
\r\n\r\nThe success of a Quantum Monte Carlo calculation depends on more than just processing power. It also requires the scientist to carefully design the trial wavefunction used to guide simulated electrons. We have studied the use of Generalized Valence Bond wavefunctions to simply, and yet effectively, captured the essential static correlation in atoms and molecules. Furthermore, we have developed significantly improved two particle correlation functions, designed with both flexibility and simplicity considerations, representing an effective and reliable way to add the necessary dynamic correlation. Lastly, we present our method for stabilizing the statistical nature of the calculation, by manipulating configuration weights, thus facilitating efficient and robust calculations.
\r\n\r\nOur combination of Generalized Valence Bond wavefunctions, improved correlation functions, and stabilized weighting techniques for calculations run on graphics cards, represents a new way for using Quantum Monte Carlo to study arbitrarily sized molecules.
" }, { "name": "Bower, Kiowa San", "degree": "PhD", "year": "2010", "title": "Chemical-Scale Studies of the 5-HT\u2083 and D2 Dopamine Receptors ", "advisor": "Dougherty, Dennis A.; Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142010-163350106", "creators": [ { "name": { "family": "Bower", "given": "Kiowa San" }, "id": "Bower-Kiowa-San", "display_name": "Bower, Kiowa San" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "co-advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "biochem" ], "doi": "10.7907/17AK-6J11", "abstract": "During synaptic transmission in the central nervous system, neuroreceptors transduce a chemical signal into an electrical signal, a process that is mediated by both ligand-gated ion channels (LGICs) and G-protein coupled receptors (GPCRs). The work in this thesis examines structure-function relationships within these receptors, with a focus on elucidating the mechanism of molecular recognition during ligand binding. We utilize conventional and unnatural amino acid mutagenesis, structural derivatives of agonists, and homology models to identify specific interactions and the role of binding site residues in ligand binding and receptor activation. The technique of unnatural amino acid mutagenesis allows us to study these processes in greater detail than would otherwise be possible, even at the scale of a chemical bond.
\r\n\r\nChapter 2 covers structure-function investigations of a ligand-gated ion channel, the 5-HT\u2083 receptor, with a goal of understanding agonist binding and receptor activation. The project examines residues in close proximity to the ligand-binding site and focuses on polar interactions with hydrophilic residues. We identify 5-fluorotryptamine (5-FT) as a partial agonist of the 5-HT\u2083 receptors and show that size and electronegativity are important at the 5\u2019 position for efficient channel opening. Our investigation of the compound 1-OT revealed it to be an agonist of equal potency to the native agonist (5-HT), demonstrating that the indolic proton of serotonin is not essential to its activation of the receptor. A study focusing on loop A residues led us to refine our homology model and propose that Glu129 faces into the binding pocket, where, through its ability to hydrogen bond, it plays a critical role in ligand binding. Further studies of binding site residues identified an ionic interaction that likely participates in the conformational changes associated with receptor gating and characterized several other residues that play critical roles in receptor activation. Finally, we compare and contrast the behaviors of two structurally distinct agonist classes, 5-HT and its related structures, and m-chlorophenylbiguanide (mCPBG) and identify several residues that play critical roles in modulating agonist binding and gating in response to these agonists.
\r\n\r\nChapter 3 describes a study examining the binding site and the mechanism of agonist activation of a GPCR, the D2 dopamine receptor. A number of aromatic amino acids thought to be near the agonist binding site were evaluated. Incorporation of a series of fluorinated tryptophan derivatives at a conserved tryptophan of the D2 receptor establishes a cation-\u03c0 interaction between the agonist dopamine and this residue (W6.48), suggesting a reorientation of W6.48 on agonist binding, consistent with proposed \"rotamer switch\" models.
\r\n\r\nFinally, chapter 4 describes a project that seeks to extend the nonsense suppression methodology to include mammalian expression systems. Progress is made developing techniques for efficient transfection of cells in culture.
\r\n" }, { "name": "Braakman, Rogier", "degree": "PhD", "year": "2010", "title": "Gas-Phase Terahertz Spectroscopy and the Study of Complex Interstellar Chemistry", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09252009-142627047", "creators": [ { "name": { "family": "Braakman", "given": "Rogier" }, "id": "Braakman-Rogier", "orcid": "0000-0002-4485-8450", "display_name": "Braakman, Rogier" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R2KK-E302", "abstract": "Terahertz spectroscopy holds great promise in the advancement of the field of astrochemistry. The sensitive observation of interstellar THz radiation is expected to lower detection limits and allow the study of larger and more complex species than is currently possible at millimeter wavelengths, which will place further constraints on chemical models and permit a direct comparison to the organic compounds seen in carbonaceous chondrites. With the successful recent launch of the Herschel Space Telescope, which will give high-fidelity access to interstellar THz radiation for the first time, and the completion of the Atacama Large Millimeter Array (ALMA) by 2013, the THz astronomy era is upon us. Unfortunately, laboratory THz spectroscopy presents significant challenges and will be soon be lagging behind the newly available observational platforms. Technologies to extend the capabilities of high-resolution spectroscopic systems into the THz domain are actively being pursued on many fronts, but affordable systems that are broadly tunable, sensitive and achieve the necessary resolution are not yet available. The work in this thesis should therefore be seen as part of the effort in the transition from centimeter-/millimeter-wave to THz spectroscopy that is currently taking place in the astrochemistry community.
\r\n\r\nAs part of this thesis, observational searches for the complex organics hydroxyacetone (CH\u2083COCH\u2082OH), 2-cyanoethanol (OHCH\u2082CH\u2082CN) and methoxyacetonitrile (CH\u2083OCH\u2082CN) were attempted at millimeter wavelengths. The unsuccessful nature of these searches highlight the current limits of studying interstellar chemistry using pure rotational spectroscopy. The characterization of the laboratory spectra of these molecules is nonetheless important as it will aid in the assignment and description of the rotational substructure and band shapes of their THz torsional spectra, features that may allow their interstellar detection; and this thesis presents methods by which such complex spectra may be rapidly and efficiently collected and fit using automated spectrometers and modern software tools.
\r\n\r\nThe description of the spectrum of hydroxyacetone is furthermore of interest due to the presence of the very low barrier to internal rotation in this molecule. Many interstellar compounds, both known and potential future targets, have functional groups capable of internal rotation in their structure; and so the effort in understanding the complex effects of the low barrier rotor in this case will benefit the general effort to further understand internal rotation.
\r\n\r\nIn searching for new interstellar molecules, both at millimeter wavelengths and at higher THz frequencies, characterization of the complete spectra of known interstellar molecules is of great importance to allow substraction of their contribution to observational spectra. In this thesis, the ground-state rotational spectrum of methanol, the most important \"interstellar weed\", is catalogued and described in detail through most of the THz region that will be accessible with Herschel and ALMA.
\r\n\r\nLastly, as part of the effort to increase the sensitivity of THz spectrometers, the use of Fabry-Perot cavities at these frequencies is explored. Such resonant cavities hold the potential to significantly increase the possible path lengths in spectroscopic system and to allow novel and sensitive detection techniques. Optimal configurations and the limits on achievable path lengths and Q-factors of such cavities are discussed, as are the possible extensions of Fourier Transform MicroWave (FT-MW) techniques to THz frequencies.
" }, { "name": "Bray, Jenelle Kiara", "degree": "PhD", "year": "2010", "title": "The Development and Application of Computational Methods for the Prediction of G Protein-Coupled Receptor Structures", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-09032009-105125", "creators": [ { "name": { "family": "Bray", "given": "Jenelle Kiara" }, "id": "Bray-Jenelle-Kiara", "display_name": "Bray, Jenelle Kiara" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1655-ES74", "abstract": "Computational methods for the prediction of G protein-coupled receptor (GPCR) structures were applied to serotonin receptors, and new methods were developed to predict an orphan GPCR structure. First, the MembStruk procedure was used to predict the structures of the serotonin 2b and 2c receptors. Ligand binding sites for agonists and antagonists were predicted for both receptors. In addition, the SAR data for a series of psilocybin analogs bound to serotonin 2c were predicted. There was good agreement with binding and mutagenesis experiments.
\r\n\r\nA new structure prediction procedure called SuperBiHelix was developed to predict an ensemble of low-lying structures. SuperBiHelix samples the tilt and sweep angles of the transmembrane helices along with the rotation of the helices along the helical axes. The procedure was validated on the \u03b22-adrenergic receptor and A2A adenosine receptor crystal structures. This procedure was then used to predict the structure of GPR88, an orphan receptor. GPR88 has been identified as a novel target for psychiatric disorders. Three lipids were predicted to bind to GPR88. The head group of a lipid would bind to R113(3) and R116(3) at the extracellular side of the receptor. The lipid tail would bind in an aliphatic pocket in the TM2-TM3-TM6-TM7 region. The predicted bound complexes offer good suggestions for binding and mutagenesis experiments that could help validate the proposed structures.
\r\n" }, { "name": "Brunelli, Nicholas Anthony", "degree": "PhD", "year": "2010", "title": "Sizing Aerosol Particles Between One and Three Nanometers", "advisor": "Giapis, Konstantinos P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12172009-101652286", "creators": [ { "name": { "family": "Brunelli", "given": "Nicholas Anthony" }, "id": "Brunelli-Nicholas-Anthony", "orcid": "0000-0003-0712-8966", "display_name": "Brunelli, Nicholas Anthony" } ], "advisors": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "advisor", "display_name": "Giapis, Konstantinos P." } ], "committee": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "chair", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/YNE5-2G91", "abstract": "The measurement of nanoparticle size is of primary importance to the fields of aerosol science and nanotechnology. Size affects the aerosol dynamics and impacts the optical, magnetic, and catalytic properties of nanoparticles. The size range from 1 to 10 nm is of particular interest because quantum effects and ambient aerosol nucleation occur in this range. Differential Mobility Analyzers are the primary instruments used currently to measure the size of aerosol particles, but diffusion impairs significantly their ability to size in the lower range (1\u20133 nm).
\r\n\r\nA primary focus of this thesis work has been to design, construct, and test a Radial Differential Mobility Analyzer, termed \"nano-RDMA,\" capable of measuring nanoparticles in the 1 to 12.5 nm size range with high resolution and transmission. The nano-RDMA was calibrated using electrospray techniques to aerosolize molecular ions for mobility analysis. The instrument was determined to have significantly improved resolution and transmission than the commercially available nano-DMA. Simulations of the nano-RDMA operation were performed to determine how the resolution could be improved.
\r\n\r\nThe nano-RDMA has been employed to characterize in-situ size distributions of particles produced in an atmospheric pressure microplasma reactor. The operating parameters of the microplasma (i.e., plasma current, flow rate, precursor concentration, and precursor composition) were investigated to determine the effect on particle size distribution. The microplasma was further examined as a calibration source for narrow size distributions. Iron nanoparticles produced with the microplasma were used to grow nanotubes catalytically. A correlation was established between the size of the grown carbon nanotubes and the catalytic particles produced in the microplasma.
\r\n\r\nThe nano-RDMA was also used as a size characterization and selection device in particle overgrowth experiments. Silicon nanoparticles produced in the microplasma were introduced into two different processing stages: a second microplasma and a furnace. The nano-RDMA permitted quick evaluation of how the operating conditions of the second processing stage affected overgrowth. The broad size distributions indicated that agglomeration was contributing to the measured size distribution, leading to the adoption of a Tandem DMA (TDMA) arrangement for overgrowth experiments. Limiting the size distribution with the first nano-RDMA permitted homogeneous overgrowth of silicon nanoparticles.
\r\n\r\nThe microplasma was also investigated as a possible calibration source using the TDMA arrangement. While the microplasma produced a stable size distribution with a high concentration of nanoparticles, the measured resolution was lower than expected. The TDMA arrangement permitted studies of the thermal annealing of silicon nanoparticles. The particle size was observed to decrease with increasing temperature in a manner consistent with hydrogen evolution.
" }, { "name": "Cable, Morgan Leigh", "degree": "PhD", "year": "2010", "title": "Life in Extreme Environments: Lanthanide-Based Detection of Bacterial Spores and Other Sensor Design Pursuits", "advisor": "Ponce, Adrian; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102010-145436548", "creators": [ { "name": { "family": "Cable", "given": "Morgan Leigh" }, "id": "Cable-Morgan-Leigh", "orcid": "0000-0002-3680-302X", "display_name": "Cable, Morgan Leigh" } ], "advisors": [ { "name": { "family": "Ponce", "given": "Adrian" }, "id": "Ponce-A", "role": "co-advisor", "display_name": "Ponce, Adrian" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Ponce", "given": "Adrian" }, "id": "Ponce-A", "role": "member", "display_name": "Ponce, Adrian" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0NFE-Y329", "abstract": "Bacterial spores, or endospores, are produced by certain genera of bacteria under stress and are considered to be one of the most resilient forms of life on Earth. Detection of endospores is vital in areas ranging from bioburden reduction to homeland security. Rapid bacterial spore detection is achieved by targeting dipicolinic acid (DPA), a chemical marker unique to endospores. An improvement on the current bacterial spore detection assay based on sensitized lanthanide luminescence is presented through the implementation of a dipicolinate-specific Tb3+ receptor site. The use of a chelating ligand such as DO2A (1,4,7,10-tetraazacyclododecane-1,7-bisacetate) can increase both the sensitivity and selectivity of the assay. The luminescent series of Ln(DO2A)(DPA)- complexes (Ln = Sm, Eu, Tb and Dy) is fully characterized in terms of structure, photophysics and stability, and the Tb(DO2A)+ binary complex in particular is investigated as a sensing complex for bacterial spores. The \u2018ligand enhancement\u2019 observed in all cases improves dipicolinate binding affinity by approximately one order of magnitude over the lanthanide ion alone. Binding of the DO2A ligand also appears to generate a \u2018gadolinium break\u2019 effect, creating a discrepancy in binding affinity in the lanthanide series and rendering the terbium complex the most effective dipicolinate receptor site of all investigated. We have also extended the application of this receptor site design technology to the targeted detection of other aromatic analytes of biological relevance, such as salicylates and catecholamines. Our work indicates that construction of effective receptor site complexes is not governed by net electrostatic considerations, and that local charge variations from the ligand-induced perturbation of lanthanide electron density may play a significant role. This work sets the stage for the development of the next-generation terbium(macrocycle) complex for bacterial spore detection, with the aim of constructing a solid-state endospore microsensor for applications ranging from sterilization validation to life detection in extreme environments." }, { "name": "Campbell, Tammy Y.", "degree": "PhD", "year": "2010", "title": "Sonochemical Decomposition of Perfluorinated Surfactants: Chain Length Effects", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05232010-212126893", "creators": [ { "name": { "family": "Campbell", "given": "Tammy Y." }, "id": "Campbell-Tammy-Y", "display_name": "Campbell, Tammy Y." } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HDZ3-X116", "abstract": "The sonochemical degradation kinetics of the aqueous perfluorochemicals (PFCs) perfluorobutanoate (PFBA), perfluorobutanesulfonate (PFBS), perfluorohexanoate (PFHA) and perfluorohexanesulfonate (PFHS) have been investigated. Surface tension measurements were used to evaluate chain-length effects on equilibrium air-water interface partitioning. The PFC air-water interface partitioning coefficients, \u039a^(PF)_(eq), and maximum surface concentrations, \u0393^(PF)_(max), were determined from the surface pressure equation of state for PFBA, PFBS, PFHA and PFHS. Relative \u039a^(PF)_(eq) values were dependent upon chain length \u039a^(PFHS)_(eq) \u2245 2.1K^(PFHA)_(eq) \u2245 3.9K^(PFBS)_(eq) \u2245 5.0K^(PFBA)_(eq), whereas relative \u0393^(PF)_(max) values had minimal chain length dependence \u0393^(PFHS)_(max) \u2245 \u0393^(PFHA)_(max) \u2245 \u0393^(PFBS)_(max) \u2245 2.2\u0393^(PFBA)_(max). The rates of sonolytic degradation were determined over a range of frequencies from 202 to 1060 kHz at dilute (< 1 \u03bcM) initial PFC concentrations. Under all conditions, the time-dependent PFC sonolytic degradation was observed to follow pseudo-first order kinetics suggesting bubble-water interface populations were below saturation. The PFHX (where X = A or S) sonolysis rate constant was observed to peak at an ultrasonic frequency of 358 kHz, similar to PFOX. In contrast, the PFBX degradation rate constants had an apparent maximum at 610 kHz. Degradation rates observed for PFHX are similar to previously determined PFOX rates, k^(PFOX)_(app,358) \u2245 k^(PFHX)_(app,358). PFOX is sonolytically pyrolyzed at the transiently cavitating bubble-water interface suggesting that rates should be proportional to equilibrium interfacial partitioning. However, relative equilibrium air-water interfacial partitioning predicts that K^(PFOX)_(eq) \u2245 5K(PFHX)_(eq). This suggests that at dilute PFC concentrations, adsorption to the bubble-water interface is sonochemically mediated. PFC sonochemical kinetics are slower for PFBS and further diminished for PFBA as compared to longer analogs suggesting that PFBX surface films are of lower stability due to their greater water solubility. Furthermore, application of a Langmuir type kinetic model on the basis of a heterogenous solution system is applied in evaluating the sonochemical effects on surface activity and the absolute rates over four orders of magnitude of initial PFYX (Y = H or B, X = A or S). Investigations on the effects of ultrasound power densities at 83.3, 167, 250, and 333 W L^(-1) have been carried out. Rate constants exhibit a linear increase with increasing power density for all species, thus rates can be increased by simply increasing the power density. Degradation rates are compared at single frequency exposures of 202, 358, and 610 kHz and compared to dual frequency exposures at 20 + 202 and 20 + 610 kHz under the same power conditions (250 W L^(-1). A synergistic enhancements in degradation rates for PFOS (~12%) and PFOA (~23%) were observed for 20 + 202 kHz simultaneous exposure. Frequency and power are parameters that can affect the sonochemical efficiency by modifying peak collapse temperature and by controlling the size and population of transiently cavitating bubbles." }, { "name": "Carbone, Martina Nini", "degree": "PhD", "year": "2010", "title": "Characterization of the Functional Diversity and Evolvability of Chimeric Enzymes Assembled by Structure-Guided SCHEMA Recombination", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272010-170914354", "creators": [ { "name": { "family": "Carbone", "given": "Martina Nini" }, "id": "Carbone-Martina-Nini", "display_name": "Carbone, Martina Nini" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Adami", "given": "Christoph Carl" }, "id": "Adami-C-C", "orcid": "0000-0002-2915-9504", "role": "member", "display_name": "Adami, Christoph Carl" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/QE98-1921", "abstract": "In nature proteins evolve by a combination of point mutagenesis and recombination. This process has generated hundreds of fascinating and structurally complex protein folds capable of performing a myriad of important and diverse biochemical functions. This has inspired protein engineers to mimic natural protein evolution in the library to construct synthetic proteins with new or improved properties. Here I show that homologous protein recombination can be used in the library to engineer novel enzymes with new catalytic activities and altered substrate specificities. I also propose that homologous recombination can be used in the laboratory to overcome the challenge of improving the native activities of wild-type proteins. In nature recombination may have helped proteins escape local maxima of the fitness landscape by introducing many homologous mutations to which proteins are highly tolerant. Protein engineers can possibly use it for the same purpose. I validate this hypothesis computationally with highly simplified protein models, and I attempt an experimental verification of this theory with cellulases. " }, { "name": "Carpenter, John Reeves, III", "degree": "PhD", "year": "2010", "title": "I. Synthesis and Testing of a Supported Shilov Oxidation Catalyst and II. Influence of Structural Features on Zeolite Characterization by Constraint Index Testing", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292009-141737581", "creators": [ { "name": { "family": "Carpenter", "given": "John Reeves, III" }, "id": "Carpenter-John-Reeves", "display_name": "Carpenter, John Reeves, III" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WGZA-R541", "abstract": "This thesis is composed of two separate projects invoking the use of heterogeneous catalyst, one focused on catalyst development and another on characterization.
\r\n\r\nThe first project concentrates on the development of a heterogeneous catalyst for alkane oxidation utilizing Shilov chemistry. Three techniques for creating heterogeneous catalyst are compared using Wacker oxidation: supported molten salts, supported aqueous phases (SAP), and ion-exchanged zeolites. From the Wacker oxidation study the supported aqueous phase catalyst was identified as the best potential method for developing a Shilov oxidation catalyst.
\r\n\r\nInitial work focused on oxidation of ethanesulfonate loaded onto the SAP catalyst. Similar turnovers were achieved on the SAP catalyst as have been seen in the homogeneous system. The reaction parameters of liquid loading, oxygen pressure, reactant concentration, copper (II) chloride concentration, and acid addition were investigated. While the SAP catalyst was successful in the oxidation of ethanesulfonate, attempts to perform ethane oxidation in a flow system were not. The loss of chloride ions is believed to lead to the deactivation.
\r\n\r\nThe second project investigates anomalous Constraint Index (CI) results for zeolites containing cages that are relatively larger than their pore opening. The CI test utilizes the competitive cracking of 3-methylpentane and n-hexane to classify structures as having small, medium, or large pores. However, structures like SSZ-23, SSZ-25, SSZ-28 and SSZ-35 with these large cages have CI results consistent with a larger pore classification than the pores in them.
\r\n\r\nIncomplete hemi-cages on the external surface may provide a nonselective active site that would result in lower CI results. This work looks at this possibility by comparing SSZ-25 and SSZ-35 with ZSM-5 and BEA* that are normally behaving medium- and large-pore structures respectively. The surface is passivated by a dealumination treatment and the CI test is compared on the parent and treated samples. No evidence of activity on the external surface having an influence on the CI test is observed. Several techniques are also used to further investigate accessibility. Finally we observed that for structures with multiple distinct features, different fouling rates in each feature may result in observable changes in the CI value over time.
\r\n" }, { "name": "Carrera, Diane Elizabeth", "degree": "PhD", "year": "2010", "title": "The Development of Br\u00f8nsted Acid Catalysis Technologies and Mechanistic Investigations Therein", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022010-164832965", "creators": [ { "name": { "family": "Carrera", "given": "Diane Elizabeth" }, "id": "Carrera-Diane-Elizabeth", "display_name": "Carrera, Diane Elizabeth" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZGS8-QT92", "abstract": "The enantioselective reductive amination of ketones with Hantzsch ester has been achieved through Br\u00f8nsted acid catalysis. A novel triphenylsilyl substituted BINOL-derived phosphoric acid catalyst has been developed for this transformation, imparting high levels of selectivity when used with methyl ketones and aromatic amines. A stereochemical model for the observed selectivity based on torsional effects has been developed through molecular modeling and is further supported by a single crystal x-ray structure of an imine-catalyst complex.
\r\n\r\nMechanistic studies have revealed the importance of catalyst buffering and drying agent on reaction efficiency while a Hammett analysis of acetophenone derivatives offers insight into the key factors involved in the enantiodetermining step. Kinetic studies have shown that imine reduction is rate-determining and follows Michaelis-Menten kinetics. Determination of the Eyring parameters for the imine reduction has also been accomplished and suggests that the phosphoric acid catalyst behaves in a bifunctional manner by activating both the imine electrophile and the Hantzsch ester nucleophile.
\r\n\r\nThe intermolecular addition of vinyl, aromatic, and heteroaromatic potassium trifluoroborate salts to non-activating imines and enamines can also be accomplished through Br\u00f8nsted acid activation. This analog of the Petasis reaction shows a wide substrate scope and is amenable to use with a variety of carbamate protected nitrogen electrophiles in the first example of metal-free 1,2-additions of trifluoroborate nucleophiles. The mechanistic underpinnings of benzyl trifluoroborate addition has also been explored and, in contrast to what is seen with \u03c0-nucleophilic species, appears to proceed through an intramolecular alkyl-transfer mechanism.
" }, { "name": "Chan, Arthur Wing Hong", "degree": "PhD", "year": "2010", "title": "Chamber Studies and Modeling of Secondary Organic Aerosol Formation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182010-161102525", "creators": [ { "name": { "family": "Chan", "given": "Arthur Wing Hong" }, "id": "Chan-Arthur-Wing-Hong", "orcid": "0000-0001-7392-4237", "display_name": "Chan, Arthur Wing Hong" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/61XH-D105", "abstract": "Secondary organic aerosol (SOA), formed from atmospheric oxidation of gas-phase hydrocarbons, comprise a large fraction of ambient particulate matter. Significant uncertainties exist in identifying the sources and mechanisms responsible for SOA formation, making it difficult to understand its impact on global climate and local air quality. Laboratory chambers have been a valuable tool to study underlying chemical mechanisms of SOA formation and to quantify SOA formation from select hydrocarbons in a controlled environment. However, a good understanding of the chemical processes involved is required to be able to extrapolate data acquired from smog chamber studies. This thesis presents results from experimental investigation of SOA formation from atmospherically important compounds, and model simulations of kinetic mechanisms involved in SOA formation.
\r\n\r\nThe distinguishing mechanism of SOA formation is the partitioning of semivolatile hydrocarbon oxidation products between the gas and aerosol phases. While SOA formation is typically described in terms of partitioning only, the rate of formation and ultimate yield of SOA can also depend on the kinetics of both gas- and aerosol-phase processes. Here a general equilibrium/kinetic model of SOA formation is presented to provide a framework for evaluating the extent to which the controlling mechanisms of SOA formation can be inferred from laboratory chamber data. Current atmospheric models systematically underpredict SOA formation, suggesting that in current models, 1) signicant SOA precursors could be missing and 2) SOA forming processes could be misrepresented. Aerosol formation from oxidation of 2-methyl-3-buten-2-ol (MBO) and polycyclic aromatic hydrocarbons (PAHs), two important classes of compounds previously assumed to be an insignicant SOA source, is studied. Upon photooxidation, MBO produces glyoxal (an important SOA intermediate), but the yields are too low to be atmospherically important. Photooxidation of napthalene and other 2-ring PAHs leads to substantial amounts of aerosol, and can account for a large fraction of SOA formed from oxidation of diesel exhaust and other primary emissions.
\r\n\r\nIsoprene is a signicant source of atmospheric organic aerosol; however, the oxidation pathways that lead to SOA have remained elusive. Under remote low-NOx conditions, epoxydiols are formed from gas-phase photooxidation of isoprene, and are found to undergo reactive uptake to lead to low-volatility compounds, such as C5-methyltetrols and organosulfates observed in ambient particulate matter. Under urban high-NOx conditions, methacrolein, an important C4 aldehyde formed from isoprene oxidation, is found to form SOA via reaction with NO2 to form peroxy methacryloyl nitrate, which subsequently forms low-volatility oligoester products. As a result of radical chemistry of aldehydes, SOA formation from isoprene depends critically on the NO2/NO ratio, and the implications on ambient aerosol formation are discussed.
" }, { "name": "Chen, George Shuxiong", "degree": "PhD", "year": "2010", "title": "Mechanisms of C-H Bond Activation by Platinum(II)", "advisor": "Bercaw, John E.; Labinger, Jay A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12012009-210811032", "creators": [ { "name": { "family": "Chen", "given": "George Shuxiong" }, "id": "Chen-George-Shuxiong", "display_name": "Chen, George Shuxiong" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "co-advisor", "display_name": "Labinger, Jay A." } ], "committee": [ { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "chair", "display_name": "Labinger, Jay A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/G7TZ-QS84", "abstract": "The rates of C\u2013H bond activation for various alkanes by [(N\u2013N)PtII(CH\u2083)(TFE-d\u2083)]\u207a (N\u2013N = Ar\u2013N=C(CH\u2083)\u2013C(CH\u2083)=N\u2013Ar; Ar = 3,5-di-tert-butylphenyl; TFE-d\u2083 = CF\u2083CD\u2082OD) were studied. Both linear and cyclic alkanes give the corresponding [(N\u2013N)PtII(H)(alkene)]\u207a cation. Second-order rate constants for cycloalkane activation (CnH2n) are proportional to the size of the ring (k ~ n). For cyclohexane, the deuterium kinetic isotope effect (kH/kD) of 1.28(5) is consistent with the proposed rate determining alkane coordination to form a C\u2013H \u03c3 complex. Comparing the relative rates of cyclic and linear alkanes indicates that the platinum center is relatively unselective with respect to different C\u2013H bonds: the rate constants (per C\u2013H bond) for the substrates examined all fall into a narrow range, and there does not appear to be any significant preference for either primary or secondary C\u2013H bonds.
\r\n\r\nThe protonolysis of platinum(II) methyl complexes was investigated by both experiment and computation. Experimental results showed that protonolysis of (COD)PtII(CH\u2083)\u2082 (COD = 1,5 \u2013 cyclooctadiene) by trifluoroacetic acid gave abnormally large (greater than 10) kinetic isotope effects (kH/kD) at room temperature and higher. The temperature dependence of kH/kD for the protonolysis of (COD)PtII(CH\u2083)\u2082 gave Arrhenius parameters outside semi-classical limits. On the other hand, protonolysis of (tmeda)PtII(CH\u2083)Cl (tmeda = N,N,N\u2019,N\u2019\u2013tetramethyl\u2013ethylenediamine) by trifluoroacetic acid gave normal kinetic isotope effects and classical Arrhenius parameters. Density functional theory (DFT) was used to examine the mechanism of protonolysis of these two systems, and the results were found to be consistent with experimental observations. Based on our experimental and computational work, we propose that protonolysis of methylplatinium(II) complexes can occur through either a concerted or stepwise pathway that is highly ligand dependent; more electron-rich ligands will favor the stepwise mechanism, while electron-deficient ligands with stronger trans influence will favor the concerted mechanism. Finally, we propose that the presence of abnormally large KIEs is an indication for a concerted pathway, and that there is a connection between the magnitude and temperature dependence of the KIE and mechanism.
\r\n\r\nIn aqueous solution, [PtII(glycinato)Cl\u2082]\u207b catalyzes oxidation by [PtIVCl\u2086]\u00b2\u207b of the methyl group of p-toluenesulfonate to the corresponding alcohol and aldehyde, with no further oxidation to the carboxylic acid. Both rate and selectivity are improved in comparison to the original Shilov system that employs [PtIICln(H\u2082O)4-n]2-n as the catalyst.
\r\n" }, { "name": "Farkas, Michelle Elizabeth", "degree": "PhD", "year": "2010", "title": "Structural Variations on the Turn Unit of DNA-Binding Hairpin Py-Im Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-145249345", "creators": [ { "name": { "family": "Farkas", "given": "Michelle Elizabeth" }, "id": "Farkas-Michelle-Elizabeth", "display_name": "Farkas, Michelle Elizabeth" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RVY7-BR84", "abstract": "Modulation of gene expression by small molecules is a challenge in the field of chemical biology. Hairpin pyrrole-imidazole polyamides are a class of programmable small molecules that bind to the minor groove of DNA, and have been shown to inhibit gene expression by interfering with transcription factor-DNA interfaces. When considering the biological implications of these molecules, improvement of sequence-specificities and binding affinities is of great interest. The work described herein focuses on modifications to the turn sub-unit of hairpin polyamides, and subsequent effects on the biophysical and biological characteristics of these molecules. The substitution of a \u03b3-2,4-diaminobutyric acid with an \u03b1-2,4-diaminobutyric acid hairpin turn moiety resulted in greater selectivity, and diminished reactivity for polyamide-alkylator conjugates. These molecules have been utilized in generating site-specific damage in histone H4 genes in cancer cells. Employment of 3,4-diaminobutyric acid in the turn unit has resulted in increased DNA affinities for polyamides targeting particular sequences. These molecules are also promising in their abilities to tolerate modifications that improve cellular uptake but would otherwise severely diminish binding." }, { "name": "Fisher, Daniel Ross", "degree": "PhD", "year": "2010", "title": "Development and Applications of Quantum Monte Carlo", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152009-120706357", "creators": [ { "name": { "family": "Fisher", "given": "Daniel Ross" }, "id": "Fisher-Daniel-Ross", "display_name": "Fisher, Daniel Ross" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4YCS-9T88", "abstract": "Quantum Monte Carlo is a relatively new class of electronic structure methods that has the potential to calculate expectation values for atomic, molecular, and materials systems to within chemical accuracy. QMC scales as (ON3 or better with the size of the system, which is much more favorable than traditional electronic structure methods capable of comparable accuracy. In addition, the stochastic nature of QMC makes it relatively easy to parallelize over multiple processors.
\r\n \r\nQMC calculations use the Metropolis algorithm to sample the electron density of the system. This method has an inherent equilibration phase, during which the configurations do not represent the desired density and must be discarded. Because the time spent on equilibration increases linearly with the number of processors, this phase limits the efficiency of parallel calculations, making it impossible to use large numbers of processors to speed convergence.
\r\n \r\nThis thesis presents an algorithm that generates statistically independent walker configurations in regions of high probability density, shortening the length of the equilibration phase and ensuring the accuracy of calculations. Shortening the length of the equilibration phase greatly improves the efficiency of large parallel calculations, which will allow QMC calculations to use the next generation of homogeneous, heterogeneous, and distributed computing resources to conduct highly accurate simulations on large systems.
\r\n\r\nThe most common formulation of diffusion Monte Carlo has two sources of error: the time step used to propagate the walkers and the nodes of the trial function. In order to explore these sources of error, DMC calculations were carried out on three pericyclic hydrocarbon reactions using Hartree-Fock, generalized valence bond, and multiconfiguration self-consistent field trial functions and time steps ranging from 10-4 to 10-2 au. The results are compared to values from experiment and high quality ab initio calculations, as well as the recently developed X3LYP, M06, and XYG3 density functionals. The appropriate time step and trial functions for the reactants, transition states, and products are identified to begin to develop guidelines for researchers carrying out calculations on larger systems.
\r\n" }, { "name": "Folinsky, Anna Barr", "degree": "PhD", "year": "2010", "title": "Investigating Molecular Size Variations in Thin Film Chemical Vapor Sensors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252010-102954788", "creators": [ { "name": { "family": "Folinsky", "given": "Anna Barr" }, "id": "Folinsky-Anna-Barr", "display_name": "Folinsky, Anna Barr" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EGMC-C788", "abstract": "Vapor sensing arrays composed of broadly responsive, chemically sensitive detectors have been explored for many years. They have been used in fields ranging from good quality control, to environmental monitoring and explosives detection, to disease diagnostics. All of these tasks require high sensitivity and fine discrimination ability. As new challenges arise, the ability to understand the performance and improve the availability of array components becomes paramount.
\r\n\r\nThis work details progress in gaining greater understanding of certain chemical substrates used in sensor arrays. Specifically, arrays using insulator/carbon black composite sensors have been prepared using either polymer or non-volatile small organic molecules as the insulating, chemically sensitive component. The crystallinity of the small molecules as compared to the polymers was determined to cause the differing formulation requirements between the polymers and the small molecules.
\r\n\r\nAdditionally, arrays of sensors composed of varying molecular weights of a given polymer were examined. Very low molecular weights of polystyrene, a high glass transition temperature polymer, exhibited improved behavior and response times compared to higher molecular weights. Finally, arrays composed of varied length carboxylic and dicarboxylic acids were studied. Of these two homologous series, the arrays composed of carboxylic acids provided better discrimination than did those composed of dicarboxylic acids, suggesting the utility of sensor materials containing multiple accessible functional groups.
\r\n\r\nThese studies, taken together, suggest several new ways to increase the number of compounds and chemical functionalities available to use in chemical vapor sensors. Increased sensor choice allows construction of more broadly responsive and finely discriminating sensor arrays, thereby increasing the general utility of composite vapor sensor arrays.
" }, { "name": "Gagnon, Alexander C.", "degree": "PhD", "year": "2010", "title": "Geochemical Mechanisms of Biomineralization from Analysis of Deep-Sea and Laboratory Cultured Corals", "advisor": "Adkins, Jess F.; Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102010-102555148", "creators": [ { "name": { "family": "Gagnon", "given": "Alexander C." }, "id": "Gagnon-Alexander-C", "display_name": "Gagnon, Alexander C." } ], "advisors": [ { "name": { "family": "Adkins", "given": "Jess F." }, "id": "Adkins-J-F", "role": "advisor", "display_name": "Adkins, Jess F." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "co-advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "role": "member", "display_name": "Eiler, John M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Adkins", "given": "Jess F." }, "id": "Adkins-J-F", "role": "member", "display_name": "Adkins, Jess F." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/N1MW-8Q84", "abstract": "The ocean is a major component of global heat transport and represents a large exchangeable reservoir of CO\u2082. The importance of these effects on climate can be quantified with records of ocean temperature, chemistry and dynamics spanning past climate change. One approach to reconstruct past ocean conditions relies on the chemical composition of CaCO\u2083 skeletons from coral. Despite the utility of these geochemical proxies, several lines of evidence suggest that biomineralization, the process corals use to build their skeletons, also influences composition, complicating the interpretation of past records. Coral grown under constant environmental conditions, either collected from the deep-sea or cultured in the laboratory, are used to quantify and spatially map the effects of biomineralization on skeletal composition.
\r\n\r\nIn modern deep-sea coral, Mg/Ca increases with decreasing Sr/Ca in most the skeleton, consistent with closed-system (Rayleigh) precipitation. Results also show composition strongly follows skeletal architecture. Centers of calcification (COCs) are small regions of disorganized crystals thought to be the initial stage of skeletal extension. Unlike the rest of the skeleton, Mg/Ca ratios vary more than two fold within the COCs while Sr/Ca is near constant. Our data provide new constraints on a number of possible mechanisms for this effect.
\r\n\r\nIn a complementary set of experiments the nanoSIMS, a new instrument capable of accurate sub-micron compositional analysis, is applied to adult cultured surface coral (1) mapping the pattern of metal ion incorporation in new growth and showing that the calcifying fluid is likely in direct exchange with seawater; and (2) testing the sensitivity of Me/Ca ratios to aragonite saturation \u03a9. Despite a large range of \u03a9 and calcification rates, the average Sr/Ca of nanoSIMS spot measurements in cultured coral are within 1.2% (2 sigma std. dev. of the 5 means). These data suggest that temperature is a more significant control on Sr/Ca than aragonite saturation between \u03a9 = 2.5--5. Within the framework of a closed-system (Rayleigh) model for biomineralization the results constrain explanations for the sensitivity of coral calcification rates to ocean acidification, improving our understanding of how anthropogenic CO\u2082 will impact coral reefs.
" }, { "name": "Genereux, Joseph Charles", "degree": "PhD", "year": "2010", "title": "Exploring DNA-Mediated Charge Transport with Fast Radical Traps", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062010-125002622", "creators": [ { "name": { "family": "Genereux", "given": "Joseph Charles" }, "id": "Genereux-Joseph-Charles", "orcid": "0000-0002-5093-7710", "display_name": "Genereux, Joseph Charles" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R0CF-GF80", "abstract": "The \u03c0-stack of DNA is competent for mediating charge transport (CT), both by single-step and multi-step mechanisms. The yield of long-range single-step CT from photoexcited 2-aminopurine to guanine across adenine tracts has a shallow, periodic distance dependence, with increasing amplitude and decreasing slope with temperature. To measure total CT yield, herein we employ the fast radical traps N2-cyclopropylguanine (CPG), and N6-cyclopropyladenine (CPA), which are similar to the unmodified bases, but undergo rapid decomposition upon oxidation. We find that decomposition of CPG by a photoexcited rhodium intercalator across an adenine tract has similar periodic distance dependence to quenching of 2-aminopurine by guanine, and the same temperature dependence as well. In contrast, decomposition of CPG by photoexcited 2-aminopurine is monotonic with respect to adenine tract length, and also competes with back electron transfer (BET). Eliminating BET by separating 2-aminopurine from the adenine tract with three high-potential inosines restores the non-monotonic distance dependence. We also determined decomposition of CPA along adenine tracts by photoexcited rhodium, and found the CT yield to be distance-independent, demonstrating that the periodicity associated with guanine oxidation is with respect to adenine tract length, not donor-acceptor separation. This length-dependent periodicity, and the associated temperature dependence, support a model of conformational gating in the formation of CT-active domains along the DNA.
\r\n\r\nDNA-mediated electrochemistry is facile in self-assembled monolayers on electrodes, and redox-active dyes are reduced through the DNA \u03c0-stack at potentials far lower than those of the individual bases. Since cytosine is the most readily reduced base, we incorporated CPC into DNA monolayers to assay for bridge occupation, and CPC decomposition was not observed.
\r\n\r\nTo explore the relative contributions of single-step and multi-step mechanisms to CT yield across adenine tracts, we compared quantum yields previously collected from 2-aminopurine fluorescence quenching experiments to those of CPG decomposition. For seven or eight intervening adenines, single-step CT accounts for the entire CT yield, while for four to six adenines, multi-step CT is the dominant mechanism. We interrupted multi-step CT by substituting CPA for an adenine on the bridge, and found the total CT yield across five or six intervening adenines is lowered to the single-step CT yield. Blocking single-step CT by replacing the terminal guanine with redox-inactive inosine does not affect CPA decomposition on the bridge. These results imply that single-step and multi-step CT processes are not in direct competition for these assemblies, consistent with the model of conformationally gated CT-active states.
\r\n" }, { "name": "Gleitsman, Kristin Rule", "degree": "PhD", "year": "2010", "title": "Chemical-Scale Studies of the Nicotinic Acetylcholine Receptor: Insights from Amide-to-Ester Backbone Mutagenesis", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102010-211900670", "creators": [ { "name": { "family": "Gleitsman", "given": "Kristin Rule" }, "id": "Gleitsman-Kristin-Rule", "display_name": "Gleitsman, Kristin Rule" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZYZF-9E22", "abstract": "This thesis describes the use of peptide backbone amide-to-ester mutations to study the structure and function of ligand-gated ion channels. The research described herein has been done on the muscle nicotinic acetylcholine receptor, a prototypical ligand-gated ion channel in the cys-loop superfamily. Backbone mutagenesis in these proteins provides insight into specific intermolecular interactions that are critical to function, as well as answering more fundamental questions about the role of the peptide backbone in long-range conformational changes in these allosteric receptors.
\r\n\r\nChapter 2 describes the identification of a key hydrogen bond near the binding site that is involved in the gating pathway. We found that the backbone N-H of a loop C residue makes a hydrogen bond to an anionic side chain of the complementary subunit upon agonist binding. The hydrogen bonding partner is not the residue predicted by structural data, but instead an aspartate that was originally believed to participate directly in agonist binding.
\r\n \r\nIn chapter 3 we consider the involvement of the peptide backbone in the binding-induced conformational changes that lead to channel gating. Single backbone mutations in the \u03b2-sheet-rich extracellular domain were well tolerated, whereas two proximal backbone mutations led to nonfunctional receptors. These results support a model in which backbone movements in the outer \u03b2-sheet are important for receptor function.
\r\n\r\nChapter 4 describes a new method - elucidating long-range functional coupling in allosteric receptors (ELFCAR) - that should be broadly applicable to determining functional roles of residues in allosteric receptors.
\r\n\r\nChapters 5 and 6 describe electrophysiological and computational investigations into the role of amide-to-ester mutations in the aromatic binding box of the nicotinic receptor. Echoing the results of chapter 3, these mutations largely reveal an overall tolerance of backbone mutations in the binding site.
\r\n \r\nFinally, in chapter 7, we explore the use of ester and N-methyl backbone modifications to uncover the role of conformational changes at an unusual vicinal disulfide bond near the tip of the C-loop. Using ab initio calculations, we demonstrate that N-methylation and esterification of this ring structure in model peptides dramatically impacts its cis-trans conformational preferences.
\r\n" }, { "name": "Golisz, Suzanne Rose", "degree": "PhD", "year": "2010", "title": "Organometallic Reaction Mechanisms: Olefin Polymerization Catalysis and C-H Bond Activation by Early Transition Metal Bisphenolate Complexes and Protonolysis of Bipyrimidine Platinum Methyl Complexes ", "advisor": "Bercaw, John E.; Labinger, Jay A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072010-114755605", "creators": [ { "name": { "family": "Golisz", "given": "Suzanne Rose" }, "id": "Golisz-Suzanne-Rose", "display_name": "Golisz, Suzanne Rose" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "co-advisor", "display_name": "Labinger, Jay A." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BBBN-SA63", "abstract": "Mechanistic aspects of organometallic transformations such as polymerization, C H activation, and protonolysis have been examined. Relationships between catalyst geometry and polymer microstructure were defined. The mechanism of an intramolecular C H activation process was found to involve two competing pathways. The protonolysis of platinum methyl complexes was investigated for kinetic isotope effects and observation of intermediates.
\r\n\r\nBisphenolate ligands with pyridine and benzene diyl linkers were synthesized and metalated with group 4 and 5 transition metals. The solid state structures of some of the group 4 complexes were solved. The titanium, zirconium, hafnium, and vanadium complexes were tested for propylene, 1 hexene, and ethylene/1 octene polymerization activities with methylaluminoxane as co catalyst. Titanium and zirconium (IV) precatalysts with pyridine diyl linkers provided mixtures of isotactic and atactic polypropylene while titanium (IV) precatalysts with benzene diyl linkers gave atactic polypropylene only. The hafnium (IV) precatalyst with a pyridine diyl linker generated moderately isotactic polypropylene.
\r\n\r\nA titanium dibenzyl complex featuring a ligand with two phenolates linked by a benzene diyl was found to undergo thermal decomposition to give toluene and a cyclometalated dimeric complex. The thermal decomposition followed first order kinetics and was studied at a number of temperatures to determine the activation parameters. Deuterated isotopologs were synthesized to measure the kinetic isotope effects. The complexes with deuterium in the benzyl methylene positions decomposed slower than the protio analogs. Isotopologs of toluene with multiple deuteration positions were observed in the product mixtures. These data are consistent with competing \u03b1-abstraction and \u03c3-bond metathesis.
\r\n \r\nThe protonolysis of bipyrimidine ligated platinum (II) complexes was explored. The bipyrimidine platinum dimethyl complex (bpm)PtMe\u2082 was shown to undergo protonation at the metal upon addition of trifluoroacetic acid (tfa) to give a platinum (IV) hydride intermediate which reductively eliminated methane to give (bpm)PtMe(tfa). Using a mixture of deutero and protio acid, all isotopologs of methane were observed. The protonation of (bpm)PtMe(tfa) was less straightforward as no intermediates were found, and CH\u2084, CH\u2083D, and CH\u2082D\u2082 were observed upon addition of a mixture of deutero and protio acid. The protonation of a nitrogen of the bpm ligand was also examined and determined improbable under the present conditions.
\r\n" }, { "name": "Hunt, Heather Kristine", "degree": "PhD", "year": "2010", "title": "I. Development of Facile Route to Fluoride-Mediated, Pure-Silica Zeolite Thin Films. II. Removal of Structure-Directing Agents from Molecular Sieves via the Use of Photolabile Structure-Directing Agents", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10082009-183206738", "creators": [ { "name": { "family": "Hunt", "given": "Heather Kristine" }, "id": "Hunt-Heather-Kristine", "orcid": "0000-0001-8412-2774", "display_name": "Hunt, Heather Kristine" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Greer", "given": "Julia R." }, "id": "Greer-J-R", "role": "member", "display_name": "Greer, Julia R." }, { "name": { "family": "Yan", "given": "Yushan" }, "id": "Yan-Yushan", "role": "member", "display_name": "Yan, Yushan" } ], "option_major": [ "chemeng" ], "doi": "10.7907/P09Y-2K69", "abstract": "This thesis consists of two projects related to the development of new routes to zeolite films. In an effort to expand the known library of pure-silica zeolites accessible in planar conformation, Part I details the development of a new synthetic technique, the vapor phase transport of fluoride, to produce pure-silica zeolite films with the LTA, CHA, STT, ITW and \u2013SVR topologies. The films are characterized by X-ray diffraction, field emission scanning electron microscopy, X-ray energy dispersive analyses, and mechanical testing. Such pure-silica zeolite films could be useful in a variety of applications, due to their porosity, crystallinity, and general stability. For example, these materials could be employed as low dielectric constant materials, which are needed for microprocessors as the feature size is continually reduced. Upon investigation of the aforementioned zeolite powders and films, we find that the materials with the LTA topology have the lowest dielectric constant of all the pure-silica zeolites. Additionally, all the zeolites investigated, except STT, give k-values lower than predicted from their structures using the Bruggeman effective medium model, which has been commonly employed and found able to predict dielectric constants of amorphous silicas.
\r\n\r\nThe second part of this thesis presents the development of an alternative method to thermal combustion to remove organics from zeolite pores, which can degrade zeolite films, using a photolabile structure-directing agent that can be removed from the zeolite pore space using UV photolysis. Here, the synthesis, photocleavage, and structure-directing ability of two different photolabile molecules (8,8-dimethyl-2-(2-nitrophenyl)-1,4-dioxa-8-azoniaspiro[4.5]decane hydroxide (P-SDA 1) and 1-(2-nitrobenzyl)-1H-imidazole (P-SDA 2)), are presented and discussed. Cleavage of the photolytic P-SDA 1 is demonstrated in a homogeneous solution, and intercalated into a dealuminated zeolite FAU. The structure-directing ability of P-SDA 1 is evaluated via attempts to synthesize silicate and aluminosilicate zeolites, resulting in the formation of amorphous and layered materials. The structure-directing ability of P-SDA 2 is evaluated via attempts to produce aluminophosphate zeolites, resulting in several unknown crystalline phases, in addition to dense and hydrated phases. Lastly, complete photocleavage of P-SDA 2 within the crystalline, aluminophosphate materials is also demonstrated. \r\n
" }, { "name": "Krout, Michael Raymond", "degree": "PhD", "year": "2010", "title": "Progress Toward the Asymmetric Total Synthesis of Variecolin and Gas-Phase Studies of the Twisted Amide 2-Quinuclidone", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282010-090825123", "creators": [ { "name": { "family": "Krout", "given": "Michael Raymond" }, "id": "Krout-Michael-Raymond", "orcid": "0000-0002-0539-6986", "display_name": "Krout, Michael Raymond" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9765C9X", "abstract": "Biologically active natural products and pharmaceuticals often present intriguing structural features that can challenge the state of the art in catalysis and synthetic methodology for their preparation. The identification of unique targets thus stimulates the development of new strategies and methods for chemical synthesis. The complex architecture representative of the variecolin family of sesterterpenes has inspired our pursuit of new tactics that has enabled the expansion of methods from our laboratory.
\r\n\r\nFirst, progress toward the asymmetric total synthesis of variecolin is discussed. Our convergent synthetic approach bisects the target into two complex fragments to address the main structural challenges. A microwave-promoted tandem Wolff/Cope rearrangement of vinyl cyclobutyl diazocarbonyls has been developed that provides access to functionalized, fused eight-membered rings and is used to construct the central B ring of variecolin. In addition, the utility of our Pd-catalyzed enantioselective alkylation method is extended to a new vinylogous ester substrate class to produce a quaternary ketone in excellent yield with high selectivity that is an exceptional substrate for an efficient ring contraction to the cyclopentene D ring system. The successful asymmetric preparation of our two devised fragments has facilitated initial studies toward their coupling and completion of variecolin.
\r\n\r\nSecond, a preliminary examination of the substrate scope for the asymmetric alkylation of the vinylogous \u03b2-ketoester substrate class is described. Derivatives that perturb substrate electronics display enhanced reactivity and selectivity, generating products with excellent selectivities and expanding the potential of this versatile class of substrates. Furthermore, their utility is underscored as the key enantioselective transformation en route to the synthesis of the sesquiterpenoid (+)-carissone.
\r\n\r\nFinally, gas-phase studies of the twisted amide 2-quinuclidone are described. Proton affinity experiments have quantified its high basicity, which is comparable to a tertiary amine. A gas-phase synthesis of 2-quinuclidione via elimination of water and subsequent fragmentation further highlight the unusual characteristics of extremely twisted amides.
\r\n" }, { "name": "Kuhn, Kevin Michael", "degree": "PhD", "year": "2010", "title": "Understanding and Improving Efficiency in Ruthenium Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07142009-090835", "creators": [ { "name": { "family": "Kuhn", "given": "Kevin Michael" }, "id": "Kuhn-Kevin-Michael", "display_name": "Kuhn, Kevin Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XT5J-TA64", "abstract": "Olefin metathesis has become an increasingly important and powerful reaction. The development of the well-defined ruthenium alkylidene complexes, in particular, has broadened the scope and utility of the olefin metathesis reaction in both organic synthesis and polymer science. Despite these advances, complete control of the parameters (activity, stability, and selectivity) that affect efficiency in olefin metathesis remains a major challenge, and the development of more efficient catalysts for a variety of applications remains a very important goal. With that in mind, this thesis primarily focuses on understanding the requirements for and improving the efficiency of ruthenium-based olefin metathesis.
\r\n\r\nIn chapter two, a series of ruthenium olefin metathesis catalysts bearing N-heterocyclic carbene (NHC) ligands with varying degrees of backbone and N-aryl substitution were prepared. These complexes show greater resistance to decomposition through C-H activation of the N-aryl group, resulting in increased catalyst lifetimes. This work utilized robotic technology to examine the activity and stability of each catalyst in metathesis, providing insights into the relationship between ligand architecture and catalyst efficiency.
\r\n\r\nIn chapter three, the high-throughput assay developed in the previous chapter was utilized to screen a series of ruthenium catalysts for the ring-closing metathesis (RCM) of acyclic carbamates to form the corresponding di-, tri-, and tetrasubstituted five-, six-, and seven-membered cyclic carbamates. While disubstituted cyclic olefins were easily formed by a variety of catalysts, NHC-bearing catalysts were required to produce trisubstituted cylic olefin products at low catalyst loadings. Furthermore, only catalysts bearing small N-aryl bulk on the NHC ligands were found to effectively accomplish the RCM reaction for sterically challenging substrates, providing a reminder that more-efficient catalysts still need to be developed.
\r\n\r\nA process for the preparation of symmetric and unsymmetric imidazolinium chlorides that involves reaction of a formamidine with dichloroethane and a base is described in chapter four. This method makes it possible to obtain numerous imidazolinium chlorides under solvent-free reaction conditions and in excellent yields with purification by simple filtration.
\r\n\r\nIn chapter five, both chiral triazolylidenes and cyclic alkyl amino carbenes (CAACs) were chosen as ligands for the preparation of chiral ruthenium olefin metathesis catalysts. These C1 symmetric ligands were chosen to create non-conformationally flexible environments in proximity to the ruthenium center, potentially bringing chirality extremely close to the site of catalysis. These new motifs for ligand architecture show great promise. The moderate enantioselectivies obtained for AROCM and ARCM indicate potential utility toward both synthetic methodology and mechanistic insight.
\r\n\r\nFinally, appendix A describes the preparation of a series of ruthenium olefin metathesis catalysts bearing acenapthylene-annulated NHC ligands with varying degrees of N-aryl substitution. Initial evaluation of their performance in olefin metathesis demonstrated that these complexes show greater resistance to decomposition, resulting in increased catalyst lifetimes. While this work has significant potential, the results are preliminary.
\r\n" }, { "name": "Lee, Paul Eulehwann", "degree": "PhD", "year": "2010", "title": "Activation of Transcription from a Distance: Investigations on the Oxidation of SoxR by DNA-Mediated Charge Transport\r ", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192010-175848794", "creators": [ { "name": { "family": "Lee", "given": "Paul Eulehwann" }, "id": "Lee-Paul-Eulehwann", "display_name": "Lee, Paul Eulehwann" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/44P4-C408", "abstract": "In enteric bacteria, the cellular response to oxidative stress caused by superoxide is activated by soxR, which encodes a redox-active transcription factor that contains a [2Fe2S] cluster and binds DNA with high affinity. Here we describe how SoxR may detect global changes in oxidative stress while bound to DNA at a single location through DNA-mediated charge transport. A unique property of DNA is its ability to delocalize charge along its base stack, allowing oxidative damage to be funneled to specific sites of low oxidation potential. Charge transport also has the potential to access proteins with redox-active moieties.
\r\n\r\nElectrochemical studies presented here demonstrate that the redox couple of the [2Fe2S] clusters of SoxR can be accessed through the DNA, and that when the protein is bound to DNA, is shifted almost 0.5 V positive to its potential measured in solution in the absence of DNA. SoxR in its reduced form is found to inhibit guanine damage by repairing guanine radicals formed in DNA by the use of various photoactive metallointercalators, by donating an electron from one of its [2Fe2S]\u207a clusters and filling the guanine radical hole. RT-PCR is used to monitor the amount of soxS mRNA produced in cells that have taken up the DNA binding photooxidant [Rh(phi)2bpy]\u00b3\u207a and are treated with light. Cells thus treated to generate guanine radicals express soxS, evidence that SoxR is being oxidized. An in vitro assay is furthermore used to examine directly the DNA-mediated oxidation of SoxR by measuring its transcriptional activity. [Rh(phi)2bpy']\u00b3\u207a, tethered to DNA 80 bp from the soxS promoter, induces transcription by activating SoxR upon irradiation. These results demonstrate not only that guanine radicals can act to oxidize SoxR, but that the resulting oxidized, DNA-bound protein is biologically active. Thus, transcription can be activated from a distance through DNA-mediated charge transport.
\r\n\r\nThe ability of DNA to conduct charge along its base stack allows offers a general strategy for DNA-mediated signaling of oxidative stress, as it allows information about oxidative events to be transmitted quickly and directly to the proteins responsible for turning on the genes necessary for cell survival.
\r\n" }, { "name": "Liu, Yu", "degree": "PhD", "year": "2010", "title": "Biochemical Reactions in Confined Space", "advisor": "Collier, C. Patrick", "url": "https://resolver.caltech.edu/CaltechETD:etd-06262009-144008", "creators": [ { "name": { "family": "Liu", "given": "Yu" }, "id": "Liu-Yu", "display_name": "Liu, Yu" } ], "advisors": [ { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "advisor", "display_name": "Collier, C. Patrick" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/W9H8-8T44", "abstract": "The understanding of biological systems relies on the accurate description of the interaction among biomolecules. This knowledge can be obtained by in vitro assays involving interacting partners with well-defined compositional, spatial, and temporal constraints. The distinguishing features of living systems, namely, low copy number, crowded environment, and spatial compartmentalization, are usually absent in most in vitro experiments reported in the literature. This thesis discusses the implications of low copy number and spatial constraints using theoretical and computational methods in some model systems. Furthermore, two experimental platforms, based on the recent development of microfluidic techniques, are described in detail. In the first implementation, micronsized chambers fabricated using soft lithography provide a high-throughput reactor array whose size and composition can be configured to mimic the in vivo environment. The second design reports the generation and manipulation of femtoliter-volume water-in-oil droplets. A model biochemical reaction catalyzed by beta-galactosidase is observed in both reactors with precisely defined initiation time, opening the way to monitor transient kinetics in addition to steady-state behavior. Additionally, the enzymatic activity exhibits a negative correlation with the size of water-in-oil droplets when the nominal concentrations of reagents are kept the same. This surprising result is analyzed in detail by carefully designed control experiments, and attributed to the shear-induced redistribution of surfactant employed to stabilize the water/oil interface. Specifically, smaller droplets experience bigger shear stress, which change the surface concentration of surfactant and allow for the nonspecific binding of proteins to the interface. Surface-bound enzymes are denatured, leading to reduced catalytic activity. This highly dynamic process is hardly detectable by other methods such as tensiometry or direct fluorescence imaging of the interface." }, { "name": "Mack, Brendan Cahill", "degree": "PhD", "year": "2010", "title": "Biodegradable Filaments for Controlled Ophthalmic Drug Delivery", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09042009-115118", "creators": [ { "name": { "family": "Mack", "given": "Brendan Cahill" }, "id": "Mack-Brendan-Cahill", "display_name": "Mack, Brendan Cahill" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wright", "given": "Kenneth" }, "id": "Wright-K", "role": "member", "display_name": "Wright, Kenneth" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NFRZ-BY29", "abstract": "The focus of this thesis is the wet-spinning, in-vitro characterization, and in-vivo implantation of drug loaded filaments for ophthalmic, controlled-release applications. Filaments of ca. 200-300 micrometers in diameter are comprised of the copolymer poly(d,l-lactide-co-glycolide), with various lactide to glycolide ratios, and either the antibiotic levofloxacin or the steroid dexamethasone. The objective of this work is to develop implantable filaments that can provide long release of drugs in the eye and then dissolve in order to replace eye drops, since poor patient compliance can limit the utility of drops.
\r\n\r\nFilament formation by wet-spinning is examined in Chapter 2. Mass transfer during filament coagulation is experimentally probed. The experimental plan explores the effect of drug on the mass flux of solvent and antisolvent. Drug retention during extrusion is examined in the context of mass transport, as well as solid-state and solution-state thermodynamics. Chapter 3 presents data that show how the composition of the filaments affects the thermal, mechanical, and release properties. By manipulating various aspects of filament formulation (drug content, polymer type, etc.), release rate and mechanical properties can be greatly changed. The development of an in-vivo model (rabbit) to verify in-vitro results is described in Chapter 4. Drug release into the tear film and mechanical stability are determined for one filament using three different implantation techniques. Large exposed sections of filament are necessary for drug release into the tear fluid and filament ends must be secured for in-vivo mechanical stability. In-vivo results correlate well to in-vitro results for both drug release and mechanical life span. A method of combining the properties of different single component filaments through side-by-side multicomponent wet-spinning is described in Chapter 5. Single component properties are maintained by this method, so mechanical and release properties of various monocomponent filaments described in Chapter 3 can be combined into a single filament. This thesis shows that wet-spinning is a versatile method of producing drug loaded filaments with various drug encapsulation and release properties, and that these filaments are well suited for ophthalmic controlled release applications.
\r\n" }, { "name": "Mankad, Neal P.", "degree": "PhD", "year": "2010", "title": "Copper and Iron Complexes with Unusual Coordination Geometries Enforced by Phosphine Chelates", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112010-172248190", "creators": [ { "name": { "family": "Mankad", "given": "Neal P." }, "id": "Mankad-Neal-P", "display_name": "Mankad, Neal P." } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6F4J-WE60", "abstract": "Chelating phosphine ligands were used to enforce targeted coordination geometries onto complexes of iron and copper, thereby imparting molecular properties distinct relative to species studied previously in other geometries. The bulky bis(phosphino)borate ligand [Ph\u2082B(CH\u2082PtBu\u2082)\u2082]\u207b was used to provide trigonal planar complexes of Cu. This structural motif provided a rare opportunity for a single framework to stabilize Cu complexes in three discrete oxidation levels and allowed for the study of unique ligands including diazoalkanes, a diphenylcarbene, diarylamides, and a diarylaminyl radical. In the latter case, physical measurements (multiedge XAS and multifrequency EPR spectroscopy) and theoretical methods (DFT) were used to quantitate the delocalization of spin density between the Cu center and the NAr\u2082 unit, providing a comprehensive electronic structure picture for L\u2082CuER\u2082 (E = C or N) complexes in this system. In separate studies, trigonal bipyramidal Fe complexes were generated using the bulky, anionic tris(phosphino)silyl ligands [(2-R\u2082PC\u2086H\u2084)\u2083Si]\u207b (R = Ph or iPr). Low-valent Fe species in this system were found to activate dinitrogen, providing labile N\u2082 ligands trans to the silyl donor, including the first instance of a terminally bound N\u2082 ligated to a paramagnetic Fe center. Subsequent reactions involving these FeI-N\u2082 species and organoazides provided entry to unusual catalytic N-N coupling reactions. These reactions were found to involve reactive FeNAr intermediates, destabilized by virtue of the trigonal bipyramidal coordination geometry, which subsequently coupled bimolecularly in the N-N bond-forming step. The effects of perturbing previously studied C\u2083-symmetric pseudotetrahedral iron complexes to their trigonal bipyramidal analogues proved key to uncovering the chemistry of interest." }, { "name": "Matson, John B.", "degree": "PhD", "year": "2010", "title": "Applications and Extensions of Living Ring-Opening Metathesis Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09092009-091741", "creators": [ { "name": { "family": "Matson", "given": "John B." }, "id": "Matson-John-B", "orcid": "0000-0001-7984-5396", "display_name": "Matson, John B." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4QZ8-CS23", "abstract": "Living ring-opening metathesis polymerization (ROMP) is a polymerization method that has recently become popular in the synthesis of complex polymers due to advances in olefin metathesis catalyst design. The unrivaled degree of functional group tolerance of the method, coupled with a high level of control and synthetic ease, make living ROMP a valuable tool in the assembly of complex nanostructures and functional polymers. Work in this thesis details methods for applying living ROMP in the assembly of complex nanostructures and extending the uses of living ROMP to end-functionalized polymers and to polymers synthesized in a catalyst economical manner.
\r\n\r\nChapter 2 describes the synthesis and radiofluorination of fluorine-18 functionalized nanoparticles assembled from polynorbornene block copolymers synthesized via living ROMP. The block copolymers include a hydrophobic photo-crosslinkable block made from a novel cinnamate-containing norbornene, as well as a hydrophilic block made from a PEGylated norbornene. Chapter 3 illustrates another application of ROMP-based nanoparticles in which polynorbornene block copolymers are assembled into Janus (hemispherical) nanoparticles.
\r\n\r\nA method for end-capping ROMP polymers using a symmetrical alpha\u2013bromoester-containing cis-olefin terminating agent is described in Chapter 4. Subsequent atom transfer radical polymerization (ATRP) from the functionalized chain end confirms complete end-functionalization and was used to synthesize mechanistically incompatible block copolymers. Chapter 5 extends this polymer end-functionalization approach to additional functional groups, including alcohols, bromides, thioacetates, fluorescent compounds, biotin, and others.
\r\n\r\nA thorough study of pulsed-addition ROMP (PA-ROMP) performed using a Symyx robotic system is presented in Chapter 6. Extending the end-capping methodology described in Chapters 4 and 5 to the synthesis of additional polymer chains led to a homo- and block copolymerization strategy that can produce more than one polymer chain per molecule of metal initiatior. The PA-ROMP strategy reduces catalyst consumption as much as sevenfold in the synthesis of polynorbornenes.
\r\n\r\nAppendix 1 describes the synthesis and ROMP of several norbornene monomers, including a copper-64 chelating norbornene, that were not addressed in the previous chapters but that may be useful for future studies on functional ROMP polymers and nanostructures. Appendix 2 contains additional mathematical details on PA-ROMP.
\r\n" }, { "name": "May, Andrew Friedrich", "degree": "PhD", "year": "2010", "title": "High-Temperature Transport in Lanthanum Telluride and Other Modern Thermoelectric Materials", "advisor": "Snyder, G. Jeffrey; Haile, Sossina M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192010-092441990", "creators": [ { "name": { "family": "May", "given": "Andrew Friedrich" }, "id": "May-Andrew-Friedrich", "orcid": "0000-0003-0777-8539", "display_name": "May, Andrew Friedrich" } ], "advisors": [ { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "advisor", "display_name": "Snyder, G. Jeffrey" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "co-advisor", "display_name": "Haile, Sossina M." } ], "committee": [ { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "chair", "display_name": "Haile, Sossina M." }, { "name": { "family": "Snyder", "given": "G. Jeffrey" }, "id": "Snyder-G-J", "role": "member", "display_name": "Snyder, G. Jeffrey" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Johnson", "given": "William Lewis" }, "id": "Johnson-W-L", "role": "member", "display_name": "Johnson, William Lewis" } ], "option_major": [ "chemeng" ], "doi": "10.7907/W5AZ-JF32", "abstract": "This manuscript discusses the materials physics of thermal and electrical transport in the solid state. In particular, the focus is on thermoelectric materials, which enable the direct conversion between thermal and electrical energy. The ability of simple approximations and semiclassical models to describe transport is explored in a variety of systems. In some cases, the traditional models provide a very accurate description of the transport for the compositions of interest to thermoelectric applications. This is the case for n-type Ba8Ga16-xGe30+x, where a single, parabolic band model captures the electrical transport and thus allows the accurate prediction of optimal composition for energy conversion. This is not found to be true in La3-xTe4, and more than one parabolic conduction band is required to describe the electrical transport. In this case, the use of ab initio electronic band structure calculations provided critical knowledge for physical models to be developed. The influence of structure on thermal transport is also examined in detail. The compounds considered typically possess low lattice thermal conductivity, with values often being less than or equal to 1 W/m/K at 300 K. This can generally be associated with large unit cells, where the high number of atoms per unit cell results in a large number of optical modes, which carry little heat due to their low group velocities. Phonon scattering is also considered, and the cation vacancies in La3-xTe4 are found to reduce the lattice thermal conductivity by over 100% at room temperature. Finally, the resulting thermoelectric efficiency is discussed, where leg efficiencies near 20% of the Carnot efficiency are predicted in segmented legs. The work detailed here has led to the continued development of La3-xTe4 by the Jet Propulsion Laboratory, where it is a top candidate for future use in deep-space power-generation systems." }, { "name": "McMenimen, Kathryn Anna", "degree": "PhD", "year": "2010", "title": "Chemical-Scale Studies of Ligand-Gated Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042009-210441548", "creators": [ { "name": { "family": "McMenimen", "given": "Kathryn Anna" }, "id": "McMenimen-Kathryn-Anna", "orcid": "0000-0002-4108-7355", "display_name": "McMenimen, Kathryn Anna" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JVHN-2536", "abstract": "The studies discussed in this dissertation are aimed at the chemical-scale interactions involved in neuroreceptor structure and function. Unnatural amino acids were incorporated into several ligand-gated ion channels. Two different ionotropic glutamate receptors (iGluRs), the N-methyl-D-aspartate (NMDA) receptor and the \u03b1\u2013amino-3-hydroxy-5-methyl- 4-isoxazolepropionic acid (AMPA) receptor were studied, along with an acetylcholine receptor - the nicotinic acetylcholine receptor (nAChR), and all were analyzed with electrophysiology\u2013an assay of receptor function.
\r\n\r\nIn Chapter 2, a highly conserved tryptophan (Trp607) in the ion channel pore of the NMDA receptor was investigated for its role during extracellular Mg\u00b2\u207a block. Previous studies hypothesized that a cation-\u03c0 interaction between NR2BW607 and Mg\u00b2\u207a contributed to the receptor blockade. However, our studies suggest that Trp607 is not involved in a cation-\u03c0 interaction with Mg\u00b2\u207a, instead it is a structural component of the pore. NR2B Trp607 acts as a steric \"plug,\" preventing Mg\u00b2\u207a permeation through the ion channel. These studies were the first to incorporate unnatural amino acids into a glutamate receptor, extending the scope of nonsense suppression methodology to a new class of neuroreceptors.
\r\n\r\nChapter 3 describes the incorporation of unnatural amino acids into the ligand binding domain (LBD) of NMDA and AMPA receptors. Previous structural studies of AMPA receptors established the overall topology of the LBD to be a clamshell, two domains clamp down around a central cleft. Further studies utilizing agonists that induce full receptor activation and partial receptor activation demonstrate a relationship between cleft closure and agonist efficacy, which is the ability to activate a receptor. Full agonists correlate with more cleft closure than partial agonists, which induce less cleft closure. To examine this relationship, we used unnatural amino acid mutagenesis to convert an NR2-conserved tyrosine to homotyrosine and an NR1 glutamine to homoglutamine, residues designed to disrupt clamshell closure by expanding the side chain without altering its functionality. The development of our functional probe demonstrates that the clamshell closure mechanism, previously shown for AMPA receptors, likely also applies to NMDA receptors, but to different degrees in the NR1 and NR2 subunits.
\r\n\r\nFinally, in Chapter 4 we use unnatural amino acids, mutagenesis, and computational simulations to probe the binding interactions that are involved in agonist selectivity at the muscle-type nicotinic acetylcholine receptor. Acetylcholine (ACh) and nicotine, both agonists for nAChRs, have a high potency for neuronal receptors. However, nicotine is a weak agonist for the muscle-type nAChRs, yet the amino acids that contribute to the binding site remain the same between both types of receptors. These studies use mutagenesis and unnatural amino acids to introduce changes in the muscle-type receptor to increase nicotine potency. Although some of the mutations increase nicotine potency, none of the mutations result in a muscle-type receptor with nicotine potency as great as the neuronal receptors. A second set of studies generated a mouse muscle homology model and used molecular dynamics to simulate movements in the receptor with and without agonist bound. These structures demonstrate the importance of a hydrogen-bonding network that contributes to the pre-organization of the aromatic box.\r\n
" }, { "name": "Mohr, Justin Thomas", "degree": "PhD", "year": "2010", "title": "Enantioselective Reactions of Palladium Enolates", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-053625648", "creators": [ { "name": { "family": "Mohr", "given": "Justin Thomas" }, "id": "Mohr-Justin-Thomas", "orcid": "0000-0002-7005-3322", "display_name": "Mohr, Justin Thomas" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9RF5S1C", "abstract": "Synthetic efforts directed at preparing certain target molecules highlight deficiencies in the synthetic technology currently available to chemists. Enolates are among the most important synthetic intermediates for synthesis, but general means for enolate functionalizations are not available for many transformations. In order to address these limitations in synthetic technology, novel enantioselective transformations are developed and applied to total syntheses of biologically active natural products.
\r\n\r\nFirst, to address the challenge of generating all-carbon quaternary stereocenters, a palladium-catalyzed allylic alkylation reaction is discovered and optimized for allyl enol carbonate and silyl enol ether substrate classes. Certain enolate precursors are not accessible using these substrates, and therefore a method employing racemic allyl \u03b2-ketoester substrates is developed. In addition to solving the problem of regiospecific enolate generation, these transformations are conceptually interesting due to the stereoablative enantioconvergent mechanism.
\r\n\r\nStudies of the mechanism of the above transformation suggest the intermediacy of a chiral palladium enolate. Since enolate functionalization reactions are valuable to synthetic chemistry and general protocols are rare, different electrophiles are explored in addition to the allyl electrophiles used in quaternary center formation. These studies lead to the discovery of enantioselective protonation reactions generating tertiary stereocenters.
\r\n\r\nTo demonstrate the importance of enantioselective enolate functionalization reactions in synthesis, the allylic alkylation reaction is applied in the total synthesis of cassiol and the formal synthesis of platencin.
\r\n" }, { "name": "Mueller, Jonathan Edward", "degree": "PhD", "year": "2010", "title": "Structures, Energetics and Reactions of Hydrocarbons on Nickel", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-132424180", "creators": [ { "name": { "family": "Mueller", "given": "Jonathan Edward" }, "id": "Mueller-Jonathan-Edward", "orcid": "0000-0001-8811-8799", "display_name": "Mueller, Jonathan Edward" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RVXX-Z341", "abstract": "To better understand and improve reactive processes on nickel surfaces such as the catalytic steam reforming of hydrocarbons, the decomposition of hydrocarbons at fuel cell anodes, and the growth of carbon nanotubes, we have performed atomistic studies of hydrocarbon adsorption and decomposition on low index nickel surfaces and nickel catalyst nanoparticles. Quantum mechanics (QM) calculations utilizing the PBE flavor of density functional theory (DFT) were performed on all CHx and C2Hy species to determine their structures and energies on Ni(111). In good agreement with experiments, we find that CH is the most stable form of CHx on Ni(111). It is a stable intermediate in both methane dehydrogenation and CO methanation, while CH(2,ad) is only stable during methanation. We also find that nickel surface atoms play an important catalytic role in C-H bond formation and cleavage. For the C2Hy species we find a low surface coverage decomposition pathway proceeding through CHCHad, the most stable intermediate, and a high surface coverage pathway which proceeds through CCH3,ad, the next most stable intermediate. Our enthalpies along these pathways are consistent with experimental observations.
\r\n\r\nTo extend our study to larger systems and longer time scales, we have developed the ReaxFF reactive force field to describe hydrocarbon decomposition and reformation on nickel catalyst surfaces. The ReaxFF parameters were fit to geometries and energy surfaces from DFT calculations involving a large number of reaction pathways and equations of state for nickel, nickel carbides, and various hydrocarbon species chemisorbed on Ni(111), Ni(110) and Ni(100). The resulting ReaxFF description was validated against additional DFT data to demonstrate its accuracy, and used to perform reaction dynamics (RD) simulations on methyl decomposition for comparison with experiment. Finally ReaxFF RD simulations were applied to the chemisorption and decomposition of six different hydrocarbons (methane, acetylene, ethylene, benzene, cyclohexane and propylene) on a 468 atom nickel nanoparticle. These simulations realistically model hydrocarbon feedstock decomposition and provide reaction pathways relevant to this part of the carbon nanotube growth process. They show that C-C \u03c0 bonds provide a low barrier pathway for chemisorption, and that the low energy of subsurface C is an important driving force in breaking C-C bonds.
" }, { "name": "Neidholdt, Evan Lyle", "degree": "PhD", "year": "2010", "title": "Novel Pyroelectric and Switched Ferroelectric Ion Sources in Mass Spectrometry: Implementation and Applications", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-222225209", "creators": [ { "name": { "family": "Neidholdt", "given": "Evan Lyle" }, "id": "Neidholdt-Evan-Lyle", "display_name": "Neidholdt, Evan Lyle" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/M86B-8T98", "abstract": "Instrumentation development for ambient mass spectrometry is an ever-changing and ever-growing field, often emphasizing the development of field-portable, ruggedized instrumentation. This thesis presents work in the area of ion source development. Specifically, two novel ionizers for mass spectrometry are constructed, implemented, and tested on a variety of systems. The first, the ambient pressure pyroelectric ion source (APPIS) comprises a z-cut lithium niobate or lithium tantalate pyroelectric crystal which is subjected to thermal cycling. Thermal cycling and the pyroelectric effect result in the buildup of excess charge on the z-faces of the material. For a temperature change of only 30 K, an electrical potential as high as 70,000 V could be built up if no discharging occurs. At ambient pressure, electrical discharges occur between the oppositely charged crystal faces and regions of different potentials on the same crystal face. Monitoring of the discharges using an inductive pickup reveals that the time frame of ion production corresponds to that of electrical activity on the crystal face. Additionally, the ions observed in the mass spectra differ when different ambient gas compositions are present. This, and comparison to APCI experiments reveals that ionization with APPIS is a gas phase process and observed product ion species are highly dependent on ambient gas composition. An application of APPIS, whereby APPIS is used as an ion source for the detection of chemical warfare agents, is presented. Agents in the V and G classes possess amine functionality, and as a result have relatively high proton affinities and are well suited to ionization and detection using chemical ionization with APPIS. Simulants for the nerve agents VX and Tabun were detected as singly protonated species using APPIS.
\r\n\r\nA second ion source for ambient mass spectrometry is also presented, the switched ferroelectric plasma ionizer (SwiFerr). The source comprises a 1 mm thick plate of barium titanate with an electrode on one face and a grounded metallic grid on the opposite face. If an audio frequency high voltage waveform is applied to the electrode, domain structure is formed and the high electric fields across domain walls give rise to electron emission and plasma formation. At ambient pressure, the plasma produces chemical ionization reagent ions which participate in proton transfer reactions with trace species in ambient air. The source is useful for examining organic vapors and solid samples. Solid sampling is achieved through use of a pneumatic aspirator, which can aspirate powders into the SwiFerr source for analysis. Powders of the drugs loperamide and ibuprofen were ionized and detected using SwiFerr. A second-generation SwiFerr source has been designed and implemented, and is described. The second-generation source is constructed in a unibody fashion, such that the rear electrode, grid, and electrical contact wires are attached as a single unit using conductive adhesives. This allows for a source which is further miniaturized and capable of insertion into a standard Swagelok fitting, for ease of integration into existing instrumentation. The source is particularly sensitive, and an application involving detection of trace explosives is presented. Nanogram quantity samples of TNT were ionized and detected with SwiFerr after volatilization using a rudimentary thermal desorption apparatus. Sensitive detection of TNT suggests use of SwiFerr in applications where sensitive detection in field portable instrumentation is desired. To this end, plans for a stand-alone power supply for this ionizer as well as a supply designed for operating the source in a constant discharge mode at low power are presented in an appendix.
\r\n\r\nAdditional work not related to ion source development is also presented in this thesis. Chapter 6 presents advances in free radical initiated peptide sequencing (FRIPS). The 20 amino acid basis set has been analyzed for reactivity with acetyl radical, and distinct reactivity classes are observed. Chapter 7 presents a study of regioselective cleavage at aspartic acid residues by various cations. Selective cleavage at aspartic acid is observed for any cation which is not mobile along the peptide backbone, and fragmentation proceeds through a salt bridge mechanism.
" }, { "name": "Noell, Aaron Craig", "degree": "PhD", "year": "2010", "title": "Laboratory Studies of the Self and Cross Reactions of Atmospheric Peroxy Radicals", "advisor": "Okumura, Mitchio; Sander, Stanley P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252010-225602127", "creators": [ { "name": { "family": "Noell", "given": "Aaron Craig" }, "id": "Noell-Aaron-Craig", "orcid": "0000-0001-6244-174X", "display_name": "Noell, Aaron Craig" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "co-advisor", "display_name": "Sander, Stanley P." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "member", "display_name": "Sander, Stanley P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/B844-DA56", "abstract": "My studies focused on the self and cross reactions of peroxy radicals (RO\u2082). These are important gas phase reactions in the atmosphere when concentrations of nitrogen oxides are low. Hydroperoxide products of these reactions can undergo further reaction to form aerosol precursors, making RO\u2082 reactions critical to aerosol formation as well. The occurrence of multiple simultaneous reactions is frequently unavoidable when working with radical reactions. Self reactions of RO\u2082 further complicate matters by producing another peroxy radical (HO\u2082) through one of their product channels. Time resolved spectroscopic probes in the ultraviolet and near-infrared, specifically targeting each reactant, were used to measure the rate coefficients for the self and cross reactions of HO\u2082 and ethyl peroxy radicals (C\u2082H\u2085O\u2082). In addition the product branching fraction leading to HO\u2082 was determined for the C\u2082H\u2085O\u2082 self reaction with results very different from the literature.
\r\n\r\nFurther work on the self reaction branching fractions of methyl peroxy, ethyl peroxy, and propyl peroxy was done to try and resolve the discrepancy with the literature. A photoionization mass spectrometry technique was used to monitor all of the stable reaction products on the timescale of the reaction. The literature work had used end product studies after the reactions had completed to measure all of the stable products. Results from the photoionization studies appear to agree with the spectroscopic work for the C\u2082H\u2085O\u2082 self reaction, indicating that additional secondary chemistry may have skewed the results in the literature.
\r\n\r\nAerosol nucleation observed in low temperature experiments on the HO\u2082 self reaction was another area of work. Radical chemistry is the main driver of gas phase atmospheric cycles, but is not currently thought to be at the center of new particle formation. Radical-molecule complexes between HO\u2082 and a number of species including methanol, water, and acetone could act as particle seeds at low temperature due to the stability of their hydrogen bonds. Most of the nucleation work described is on the HO\u2082 - methanol complex, but all three were investigated. Lastly, the experimental calibrations and general procedures that went on throughout all this work are described.
" }, { "name": "Norton, Valerie Ann", "degree": "PhD", "year": "2010", "title": "Efficient Generation of Hyperpolarized Molecules Utilizing the Scalar Order of Parahydrogen", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05212010-154212167", "creators": [ { "name": { "family": "Norton", "given": "Valerie Ann" }, "id": "Norton-Valerie-Ann", "display_name": "Norton, Valerie Ann" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Reisman", "given": "Sarah E." }, "id": "Reisman-S-E", "role": "member", "display_name": "Reisman, Sarah E." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/57FW-1060", "abstract": "This dissertation describes methods that polarize the spin of a specific nucleus in molecules synthesized by molecular addition of parahydrogen to a precursor molecule. Nuclear magnetic resonance (NMR) pulse sequences are designed to perform efficient transfer of spin order by way of the scalar spin couplings between the two nascent protons and a heteronuclear spin label target. The result is an increase in the NMR signal from that nucleus by several orders of magnitude, approaching unity polarization. Algorithms are presented to effect the desired unitary evolution of this three-spin system over the range of couplings found in diverse molecules and in the presence of interfering spins. These methods are explored theoretically and comparisons are made to select the most advantageous method given a specific problem.
\r\n\r\nIssues concerning the choice of target molecule, portable equipment, and automation are discussed. Some design choices made for convenience in one aspect of the execution of the methods raise difficulties in other aspects. These difficulties are elucidated and methods of mitigation are discussed.
\r\n\r\nPulse design issues are elucidated with numerical calculations which confirm analytical results for the time dependence obtained in the multiply rotating frame approximation. Failures of this approximation at low frequencies are explored numerically leading to novel pulse sequence design rules which ameliorate undesirable phenomena peculiar to low field NMR, enabling its employment for this and other applications requiring precise control of the spin degrees of freedom. Experimental results, primarily aimed at biomedical applications, are reviewed.
\r\n" }, { "name": "Pascal, Tod Augustin", "degree": "PhD", "year": "2010", "title": "New Approaches to Accurate Predictions of Free Energies: From Proteins to Organic Nanostructures", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262009-204842274", "creators": [ { "name": { "family": "Pascal", "given": "Tod Augustin" }, "id": "Pascal-Tod-Augustin", "orcid": "0000-0003-2096-1143", "display_name": "Pascal, Tod Augustin" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "co-chair", "display_name": "Heath, James R." }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "orcid": "0000-0002-5899-7523", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P0JH-QM60", "abstract": "Although computer simulations have been applied to the calculation of solvation free energies for a wide range of molecules, reliable calculations including explicit consideration of entropy and quantum effects (zero-point energy corrections) are less common, owing to the enormous computational effort required by standard perturbation methods. Accurate calculations of entropies are essential if computer simulations are to become more useful tools for obtaining molecular insights into solvation and ligand binding phenomena.
\r\n\r\nWe report on the extension of a method of calculating exact entropies and quantum effects from standard MD simulations. This novel method is applied to the investigation of three model cases: 1) the folding of a DNA three-way junction 2) the efficacy of binding in a protein-protein interaction, critical in the pathogenesis of bacterial meningitis in neonates and 3) the free energy of water molecules at two extreme surfaces, as model systems for an investigation of the hydrophobic effect. We develop a scheme to partition the free energy into the per-atom components, and show that the water molecules in the first hydration shell have unique character. Understanding their nature is critical to discovering the underlying physics in these systems.
" }, { "name": "Pribisko Yen, Melanie Anne", "degree": "PhD", "year": "2010", "title": "Unfolded States of Heme Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06242011-125949350", "creators": [ { "name": { "family": "Pribisko Yen", "given": "Melanie Anne" }, "id": "Pribisko-Yen-Melanie-Anne", "display_name": "Pribisko Yen, Melanie Anne" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WWS3-C929", "abstract": "Cytochromes adopt discrete structures when the heme cofactor is present. Since the heme provides crucial contacts in the native protein, this hydrophobic prosthetic group plays an important role in the folding mechanism and introduces interesting features into the folding landscape. Since the iron-porphyrin is sensitive to protein structure and environment, it also acts an optical probe and will be used in photophysical and photochemical studies of three alpha-helical proteins in the electron transport family of cytochromes: both horse heart and Saccharomyces cerevisiae iso-1 cytochrome c (cyt c), Rhodopseudomonas palustris cytochrome c' (cyt c'), and the engineered cytochrome cb\u2085\u2086\u2082(cyt cb\u2085\u2086\u2082) from E. coli cytochrome b\u2085\u2086\u2082.
\r\n\r\nThe work in this thesis expands upon previous research in the Gray Group that has shown heterogenous unfolded populations in these three alpha-helical proteins. Triplet state decay kinetics of Zn-substituted cytochrome c (Zn-cyt c) reveal the level of solvent exposure of the heme through an isotope effect and bimolecular quenching of lifetimes. Differences of the GuHCl, urea, and thermally-induced unfolded states between Zn- and Fe-cyt c, cyt c' and cb\u2085\u2086\u2082 were uncovered, revealing a distinct hydrophobic effect. The inability of elevated temperature to disrupt hydrophobic pockets was studied further for DNS(C102)-cyt c through FET kinetics that reveal a significant compact population at high temperature. Finally, initial experiments on macromolecular crowding of cyt c revealed only a slight effect on the equilibrium unfolded states.
" }, { "name": "Puckett, Cindy Ann", "degree": "PhD", "year": "2010", "title": "The Cellular Uptake of Luminescent Ruthenium Complexes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062010-122905478", "creators": [ { "name": { "family": "Puckett", "given": "Cindy Ann" }, "id": "Puckett-Cindy-Ann", "display_name": "Puckett, Cindy Ann" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2484-1405", "abstract": "Transition metal complexes have enormous potential as diagnostic and therapeutic agents, but their internalization and distribution in living cells are only poorly understood. Here, we perform one of the few systematic explorations of the uptake efficiency and mechanism of a class of metal complexes: luminescent dipyridophenazine (dppz) complexes of ruthenium(II). Substitution of the ancillary ligands permits variation in the overall complex charge, size, and hydrophobicity. We find that internalization of these complexes occurs mostly through passive diffusion, driven by the membrane potential, and that hydrophobicity, rather than size, is the most important determinant of compound accumulation. Across different cell types with all compounds, mostly uneven cytoplasmic staining is observed with near exclusion from the nucleus. Conjugation to cell-penetrating peptides, such as D-octaarginine, increases uptake efficiency, but leads to trapping in endosomes below a threshold concentration. Above this threshold concentration, substantial staining of the nucleus as well as the cytosol is observed. An appended fluorescein tag lowers the threshold concentration, indicating the importance of payload to the internalization and distribution of cell-penetrating peptides. Shorter peptides, including the nuclear targeting signal RrRK (where r = D-arginine), are also studied, though none have as high a degree of uptake nor as low a threshold concentration as the octaarginine conjugate. These studies provide a basis for the future design and optimization of metal complexes for biological application. " }, { "name": "Putnam, Morgan Charles", "degree": "PhD", "year": "2010", "title": "Si Microwire-Array Solar Cells", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072010-170215356", "creators": [ { "name": { "family": "Putnam", "given": "Morgan Charles" }, "id": "Putnam-Morgan-Charles", "display_name": "Putnam, Morgan Charles" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/JSVM-J029", "abstract": "By allowing for the fabrication of flexible crystalline-Si (c-Si) solar cells that employ ~1/100th) the Si of a traditional wafer-based c-Si solar cell, while maintaining high photovoltaic efficiencies, vertically aligned arrays of c-Si microwires provide a novel photovoltaic geometry that has the potential to dramatically reduce the cost of solar electricity. In this thesis we report on 1) the growth of Si microwire arrays, 2) the chemical and electrical characterization of Si microwire arrays, and 3) the fabrication of Si microwire-array solar cells.
\r\n\r\nUsing the vapor-liquid-solid (VLS) growth mechanism in combination with photolithographic patterning, vertically aligned arrays of Si microwires, with nominally identical heights and diameters, were fabricated over areas > 1 cm2. Chemical characterization of the Si wires was then performed using secondary ion mass spectrometry to measure the incorporation of the Au VLS-catalyst into the Si wire. The incorporation of the VLS-catalyst into the Si wires at its thermodynamic equilibrium concentration suggested that the use of Cu as a VLS-catalyst was less likely to limit the photovoltaic performance of Si microwire-array solar cells. Switching to the Cu-catalyzed growth of Si wires, in-situ doping with BCl3 was used to demonstrate control of the electrically active dopant concentration from 8 x 1015 to 4 x 1019 dopants cm-3. Scanning photocurrent measurements were then made to measure the minority-carrier diffusion length. The observation of 10 \u03bcm minority-carrier diffusion lengths indicated that solar cells with efficiencies of 17.5% should be possible. With the knowledge that highly efficient solar cells were possible, methods for the fabrication of a p-n junction and a transparent top contact in a solid-state solar cell were developed. This culminated in the demonstration of Si microwire-array solar cells with Air Mass 1.5 Global photovoltaic conversion efficiencies of up to \u03b7 = 7.9%. Through improved device processing and the use of an amorphous Si passivation layer at the top contact, ~15% efficient solar cells should be possible.
\r\n" }, { "name": "Roizen, Jennifer Lyn", "degree": "PhD", "year": "2010", "title": "Progress Toward an Enantioselective Total Synthesis of Ineleganolide", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11172009-113840501", "creators": [ { "name": { "family": "Roizen", "given": "Jennifer Lyn" }, "id": "Roizen-Jennifer-Lyn", "orcid": "0000-0002-6053-5512", "display_name": "Roizen, Jennifer Lyn" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z93F4MMN", "abstract": "Investigations toward an enantioselective total synthesis of ineleganolide (1) are disclosed. These studies have driven the development of a novel asymmetric ketone alkylation to form C(\u03b1)-tetrasubstituted carbonyl compounds. Products of these alkylations have been converted to \u03b1-hydroxy ketones, acids, and esters, completing an asymmetric formal synthesis of (\u2013)-quinic acid.
\r\n\r\nAdditionally, one of these products, a chloroalkene, has been advanced in the synthesis of the [6\u20137\u20135\u20135]-fused core of ineleganolide. The chloroalkene can be converted through a mild oxidative bromination, Wittig olefination, and Luche reduction sequence to rapidly access the enantioenriched cyclopentenol fragment of ineleganolide. Two of these alcohols can be coupled with a cyclohexenone-derived carboxylic acid to append the six-membered ring fragment. These flexible vinylogous \u03b2-ketoesters can be advanced to a rigid [5\u20135\u20133]-fused cyclopropane.
\r\n\r\nAt the outset of this work, we envisioned the advancement of a [5\u20135]-fused cyclopropane through a tandem Wolff/Cope rearrangement to access the [6\u20137\u20135\u20135]-fused core of ineleganolide. Synthetic studies toward this rearrangement are described. Additionally, we explore a translactonization/Cope rearrangement and a cyclopropanation/Cope/epoxidation cascade sequence to access the [6\u20137\u20135\u20135]-fused scaffold. In the course of these efforts, a rich body of chemistry has been developed exploring translactonizations in cis-substituted cyclopentane diols, including the translactonization/Cope cascade.
\r\n" }, { "name": "Smirnova, Diana Sergeievna", "degree": "PhD", "year": "2010", "title": "Application of Two-Dimensional Correlation Analysis to Explosives Detection and Polymer Crystallization", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112009-132932", "creators": [ { "name": { "family": "Smirnova", "given": "Diana Sergeievna" }, "id": "Smirnova-Diana-Sergeievna", "display_name": "Smirnova, Diana Sergeievna" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7PAR-VK52", "abstract": "This thesis presents two novel applications of two-dimensional (2D) correlation analysis: (1) long standoff detection of explosives and (2) morphology development in semicrystalline materials.
\r\n\r\nDue to the dangers of improvised explosive devices (IEDs), effective detection of explosives at standoff distances can save lives. A scheme based on 2D correlation analysis in conjunction with thermal modulation is proposed to overcome weak signals that plague long standoff detection. Implementation of 2D correlation analysis results in significant enhancement of explosive signals relative to background. Effective separation of explosive features resulting from their unstable nature compared to common contaminants is demonstrated for two biogenic compounds. Several aspects of 2D correlation analysis are examined to optimize effectiveness of detection.
\r\n\r\nUltimate physical properties of semicrystalline materials are directly related to their morphology through molecular characteristics and processing conditions. The effects of different molecular characteristics on morphology of model hydrogenated polybutadienes are examined by 2D correlation analysis of x-ray scattering data.
\r\n\r\nModel short-chain branched (SCB) polyethylenes are found to crystallize in three regimes during quiescent temperature ramps. \"Primary-irreversible\" crystallization occurs at the highest temperatures as primary lamellae propagate through unconstrained melt. During \"secondary-irreversible\" crystallization at intermediate temperatures, secondary lamellae grow in the largest non-crystalline regions between primary lamellae. \u201cReversible\u201d crystallization at low temperatures is marked by the formation of fringed micelles. This is the first time that a physical justification is presented for the separation of the irreversible crystallization into primary- and secondary-irreversible regimes.
\r\n\r\nEach regime is identified by unique features in 2D correlation plots. Two-dimensional correlation analysis provides unique insight into subtle changes in morphology, such as the development of density heterogeneities in non-crystalline regions.
\r\n\r\nThe presence of short-chain branches is found to have a profound, diminishing effect on the formation of oriented structures in response to flow-induced crystallization, which is further examined through blends containing linear and SCB polyethylene. Evidence presented suggests that a buildup of chain defects at the growth front results in a transition from oriented to isotropic crystallization. It is proposed that size of crystal structures can be controlled by dictating the amount of copolymer incorporated during crystallization.
\r\n" }, { "name": "Spurgeon, Joshua Michael", "degree": "PhD", "year": "2010", "title": "Wire Array Solar Cells: Fabrication and Photoelectrochemical Studies", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:12142009-114256569", "creators": [ { "name": { "family": "Spurgeon", "given": "Joshua Michael" }, "id": "Spurgeon-Joshua-Michael", "orcid": "0000-0002-2987-0865", "display_name": "Spurgeon, Joshua Michael" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." } ], "option_major": [ "chemeng" ], "doi": "10.7907/PTMZ-C585", "abstract": "Despite demand for clean energy to reduce our addiction to fossil fuels, the price of these technologies relative to oil and coal has prevented their widespread implementation. Solar energy has enormous potential as a carbon-free resource but is several times the cost of coal-produced electricity, largely because photovoltaics of practical efficiency require high-quality, pure semiconductor materials. To produce current in a planar junction solar cell, an electron or hole generated deep within the material must travel all the way to the junction without recombining. Radial junction, wire array solar cells, however, have the potential to decouple the directions of light absorption and charge-carrier collection so that a semiconductor with a minority-carrier diffusion length shorter than its absorption depth (i.e., a lower quality, potentially cheaper material) can effectively produce current. The axial dimension of the wires is long enough for sufficient optical absorption while the charge-carriers are collected along the shorter radial dimension in a massively parallel array. This thesis explores the wire array solar cell design by developing potentially low-cost fabrication methods and investigating the energy-conversion properties of the arrays in photoelectrochemical cells.
\r\n\r\nThe concept was initially investigated with Cd(Se, Te) rod arrays; however, Si was the primary focus of wire array research because its semiconductor properties make low-quality Si an ideal candidate for improvement in a radial geometry. Fabrication routes for Si wire arrays were explored, including the vapor-liquid-solid growth of wires using SiCl4. Uniform, vertically aligned Si wires were demonstrated in a process that permits control of the wire radius, length, and spacing. A technique was developed to transfer these wire arrays into a low-cost, flexible polymer film, and grow multiple subsequent arrays using a single Si(111) substrate. Photoelectrochemical measurements on Si wire array/polymer composite films showed that their energy-conversion properties were comparable to those of an array attached to the growth substrate. High quantum efficiencies were observed relative to the packing density of the wires, particularly with illumination at high angles of incidence. The results indicate that an inexpensive, solid-state Si wire array solar cell is possible, and a plan is presented to develop one.
\r\n" }, { "name": "Surratt, Jason Douglas", "degree": "PhD", "year": "2010", "title": "Analysis of the Chemical Composition of Atmospheric Organic Aerosols by Mass Spectrometry", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122010-020001934", "creators": [ { "name": { "family": "Surratt", "given": "Jason Douglas" }, "id": "Surratt-Jason-Douglas", "orcid": "0000-0002-6833-1450", "display_name": "Surratt, Jason Douglas" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PVWD-HZ44", "abstract": "Although secondary organic aerosol (SOA) makes up a substantial fraction of the organic mass observed in tropospheric fine particulate matter, there remain significant uncertainties in the true impact of atmospheric aerosols on climate and health due to the lack of full knowledge of the sources, composition, and mechanisms of formation of SOA. This thesis demonstrates how the detailed chemical characterization of both laboratory-generated and ambient organic aerosol using advanced mass spectrometric techniques has been critical to the discovery of previously unidentified sources (i.e., role heterogeneous chemistry) of SOA.
\r\n\r\nThe focal point of this thesis is given to the detailed chemical characterization of isoprene SOA formed under both high- and low-NOx conditions. Until recently, the formation of SOA from isoprene, the most abundant non-methane hydrocarbon emitted into the troposphere, was considered insignificant owing to the volatility of its oxidation products. In conjunction with the chemical characterization of gas-phase oxidation products, we identify the role of two key reactive intermediates, epoxydiols of isoprene (IEPOX) and methacryloylperoxynitrate (MPAN), that are formed during isoprene oxidation under low- and high-NOx conditions, respectively. Increased uptake of IEPOX by acid-catalyzed particle-phase reactions is shown to enhance low-NOx SOA formation. The similarity of the composition of SOA formed from the photooxidation of MPAN to that formed from isoprene and methacrolein demonstrates the role of MPAN in the formation of isoprene high-NOx SOA. More specifically, the further oxidation of MPAN leads to SOA by particle-phase esterification reactions. Reactions of IEPOX and MPAN in the presence of anthropogenic pollutants could be a substantial source of \"missing urban SOA\" not included in current SOA models.
\r\n\r\nIncreased aerosol acidity is found to result in the formation of organosulfates, which was a previously unrecognized source of SOA. By comparing the tandem mass spectrometric and accurate mass measurements collected for both the laboratory generated and ambient aerosol, previously uncharacterized ambient organic aerosol components are found to be organosulfates of isoprene, \u03b1 pinene, \u03b2 pinene, and limonene-like monoterpenes, demonstrating the ubiquity of organosulfate formation in ambient SOA. We estimate that the organosulfate contribution to the total organic mass fraction in certain locations could be substantial (upwards of 30%).
\r\n\r\n" }, { "name": "Swan, James W.", "degree": "PhD", "year": "2010", "title": "Colloids in Confined Geometries: Hydrodynamics, Simulation and Rheology", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05262010-140604509", "creators": [ { "name": { "family": "Swan", "given": "James W." }, "id": "Swan-James-W", "orcid": "0000-0002-4244-8204", "display_name": "Swan, James W." } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/JJ28-7641", "abstract": "The hydrodynamics of colloids in confined geometries is studied hierarchically beginning with the exact solutions for a spherical particle translating, rotating and deforming in the presence of a plane wall at low Reynolds number. The many-bodied hydrodynamic interactions among a collection of spherical particles near a plane wall are computed and used to study the Brownian motion of confined suspensions. The method of reflections is used to describe the motion of a single spherical particle embedded in the fluid constrained by two, parallel plane walls. From this, tables which are independent of the channel width are generated describing the particle\u2019s response to various force moments. This same approach is expanded to describe the hydrodynamic interactions among the particles comprising a colloidal dispersion confined in a channel. The simulations arising from this theory depict the short-time self-diffusivity, sedimentation rate and high frequency viscosity of suspensions of varying volume fractions in channels of varying widths. A theory for the scattering of evanescent waves by colloidal dispersions is developed and cast in the form of the diffusivity measured by classical light scattering. A series of simulations is conducted to predict the short- time self-diffusivity and the collective diffusivity measured by evanescent wave dynamic light scattering. The thesis concludes with a discussion of how the developed simulations and theories can be extended to make dynamic measurements as well as a brief consideration of some remaining, open questions." }, { "name": "Swaroop, Manuj", "degree": "PhD", "year": "2010", "title": "The Bulk Viscosity of Suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05282010-012507201", "creators": [ { "name": { "family": "Swaroop", "given": "Manuj" }, "id": "Swaroop-Manuj", "display_name": "Swaroop, Manuj" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "role": "member", "display_name": "Hunt, Melany L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/HQGZ-DV22", "abstract": "Particles suspended in a fluid are known to undergo variations in the local concentration in many flow situations; essentially a compression or expansion of the particle phase. The modeling of this behavior on a macroscopic scale requires knowledge of the effective bulk viscosity of the suspension, which has not been studied before. The bulk viscosity of a pure compressible fluid is defined as the constant of proportionality that relates the difference between the mechanical pressure and the thermodynamic pressure to the rate of compression. The bulk viscosity of a suspension is defined analogous to that for a pure fluid as the constant of proportionality relating the deviation of the trace of the macroscopic stress from its equilibrium value to the average rate of compression. The compression flow drives the suspension microstructure out of equilibrium and the thermal motion of the particles tries to restore equilibrium. The Peclet number (Pe), defined as the expansion rate made dimensionless with the Brownian time-scale, governs the departure of the microstructure from equilibrium. The microstructural forcing in compression is monopolar for small Pe resulting in a significantly slower spatial and temporal response of the microstructure compared to shearing or diffusive motion.
\r\n\r\nWe have determined the effective suspension bulk viscosity for all concentrations and all rates of compression, accounting for the full thermodynamic and hydrodynamic interactions that particles experience at the micro-scale. Current simulation techniques were enhanced to enable the dynamic simulation of compression flows in a suspension. A 'compression thinning' of the suspension is observed at small rates of compression and there is some 'compression thickening' at large compression rates. The bulk viscosity diverges as the volume fraction nears maximum packing and is in fact larger than the shear viscosity. Existing models for multiphase flows must therefore include the bulk viscosity term to properly simulate variations in particle concentration.
\r\n\r\nAn understanding of bulk viscosity effects in suspensions will enable the modeling of certain aggregation and separation behavior and lead to more accurate models for multiphase flows where there are variations in the particle concentration, such as filtration or fluidization.
" }, { "name": "Tai, Hwan-Ching", "degree": "PhD", "year": "2010", "title": "Characterization of the Brain Proteasome and its Interacting Proteins and their Regulation by Neuronal Activity", "advisor": "Schuman, Erin Margaret", "url": "https://resolver.caltech.edu/CaltechTHESIS:12092009-103613738", "creators": [ { "name": { "family": "Tai", "given": "Hwan-Ching" }, "id": "Tai-Hwan-Ching", "orcid": "0000-0003-0668-9163", "display_name": "Tai, Hwan-Ching" } ], "advisors": [ { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "advisor", "display_name": "Schuman, Erin Margaret" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Zinn", "given": "Kai George" }, "id": "Zinn-K-G", "orcid": "0000-0002-6706-5605", "role": "member", "display_name": "Zinn, Kai George" }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DGMA-1K68", "abstract": "Despite the importance of proteasome-mediated proteolysis in synaptic plasticity, protein quality control, and cell regulation, little is known about proteasome composition and regulation in the brain. This thesis represents the first detailed study of mammalian brain proteasomes. Using a new affinity purification method, 26S proteasomes were isolated from the cytosolic and the synaptic compartments of the rat cortex. The proteins associated with the 26S proteasome were purified and analyzed by tandem mass spectrometry. A total of 30 proteasome-interacting proteins were identified in the brain. Several differences were seen in the spectrum of proteasome-associated proteins in the cytosol and the synaptosome. For example, the proteasome-associated protein ECM29 was found only in the cytosolic 26S proteasome, and the ubiquitin-binding factor TAX1BP1 only in the synaptic 26S proteasome. These findings allowed for further investigations into the interplay between proteasome regulation and synaptic plasticity.
\r\n\r\nNeuronal exposure to the neurotransmitter NMDA caused the degradation of 19S particles, resulting in lower levels of 26S proteasomes. The levels of ubiquitin conjugates also decreased, as did two proteasome-bound ubiquitin ligases, UBE3A/E6-AP and HUWE1/ARF-BP1, both of which have been linked to neurogenetic disorders associated with mental retardation. Thus, in the brain, proteasomes have a characteristic set of associated proteins that may serve as regulators or cofactors. Moreover, the content and pattern of associated proteins can vary with synaptic activity, in a manner likely to influence synaptic plasticity.
" }, { "name": "Witman, Jennifer Elisabeth", "degree": "PhD", "year": "2010", "title": "The T-Shaped Anisotropic Molecule Model: A Unique Perspective on the Glass Transition and Gelation in Low Valence, Directional, Network Forming Liquids", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:04122010-145555532", "creators": [ { "name": { "family": "Witman", "given": "Jennifer Elisabeth" }, "id": "Witman-Jennifer-Elisabeth", "display_name": "Witman, Jennifer Elisabeth" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Miller", "given": "Thomas F." }, "id": "Miller-T-F", "orcid": "0000-0002-1882-5380", "role": "member", "display_name": "Miller, Thomas F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/0XET-0H46", "abstract": "Glass and gel formers exhibit unusual mechanical characteristics and amorphous phases which are highly dependent on their thermal history. We introduce a lattice model with T-shaped molecules that exhibits glassy and gel-like states without introducing artificial frustration. This system has a large number of degenerate energy minima separated by small barriers leading to a broad, kinetically-explored landscape. It particularly replicates valence-limited materials, which can form self-assembled materials with highly controlled physical properties. Despite its remarkable simplicity, this model reveals some of the fundamental kinetic and thermodynamic properties of the glass transition and of gel formation.
\r\n\r\nA dearth of low temperature experimental and simulation measurements has inhibited investigation in this field. We overcome this difficulty by using a modified Metropolis Monte Carlo method to quickly provide equilibrium samples. Then kinetic Monte Carlo techniques are used to explore the properties of the equilibrium system, providing a touchstone for the non-equilibrium glassy states.
\r\n\r\nFully-dense simulation samples reveal a fragile-to-strong crossover (FSC) near the mean-field (MF) spinodal. At the FSC, the relaxation time returns to Arrhenius behavior with cooling. There is an inflection point in the configurational entropy. This behavior resolves the Kauzmann Paradox which is a result of extrapolation from above the inflection point. In contrast, we find that the configurational entropy remains finite as the temperature goes to zero. We also observe different kinetics as the system is quenched below the FSC, resulting in non-equilibrium, amorphous states with high potential energy persisting for long periods of time. Simulation samples remain at non-equilibrium conditions for observation times exceeding those permitting complete equilibration slightly above the FSC. This suggests the FSC would often be identified as the glass transition without indication that there is true arrest or a diverging length scale. Indeed, our simulations show these samples do equilibrate if sufficient time is allowed. To elucidate the complex, interdependent relation time and length scales at the FSC will require careful consideration of the spatial-dynamic heterogeneity.
\r\n\r\nDynamic mean-field simulations at high density and in the solvated regime reveal a rich range of morphological features. They are consistent with simulated and experimental results in colloidal systems. Stability limits of decreasing length scales beneath the phase separation bimodal coincide into a single curve, which terminates at the fully-dense MF spinodal, suggesting that gelation and vitrification are the same phenomena. Our work indicates that gelation is, therefore, a result of phase separation arrested by a glass transition.
" }, { "name": "Xia, Yan", "degree": "PhD", "year": "2010", "title": "Syntheses of Polymers with Diverse Architectures via Metathesis Polymerization and Investigation of Their Structure-Property Relationships", "advisor": "Grubbs, Robert H.; Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05192010-182707354", "creators": [ { "name": { "family": "Xia", "given": "Yan" }, "id": "Xia-Yan", "display_name": "Xia, Yan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "co-advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WTBS-F528", "abstract": "Metathesis polymerization using highly active, functional-group-tolerant catalysts is a powerful and versatile method for polymer synthesis. This thesis focuses on the preparation of a variety of advanced polymer architectures using well-defined ruthenium-based metathesis catalysts and the study of materials properties dictated by those unique macromolecular structures.
\r\n\r\nChapter 1 introduces olefin metathesis, metathesis polymerization, and recent developments in living/controlled polymerization and polymer functionalization. The goal is to provide a summary of the current toolbox of polymer chemists. The second part of Chapter 1 describes using these tools to synthesize different macromolecular architectures.
\r\n\r\nChapters 2 and 3 describe ring-expansion metathesis polymerization (REMP) using cyclic catalysts. Chapter 2 focuses on catalyst development, while Chapter 3 focuses on the REMP mechanism and cyclic polymer characterization.
\r\n\r\nChapters 4 and 5 focus on brush polymers. Chapter 4 describes the syntheses of linear and cyclic brush polymers using ring-opening metathesis polymerization (ROMP) and REMP of macromonomers (MMs), respectively. Chapter 5 describes the efficient synthesis of brush copolymers and the study of their melt state self-assembly into highly ordered nanostructures.
\r\n\r\nChapter 6 describes the synthesis and electro-optic response of well-defined liquid crystalline (LC) gels that were made from controlled end-linking of telechelic LC polymers. These gels possessed very fast, reversible electro-optic switching; the degree of response was closely related to network structure.
" }, { "name": "Yeung, Laurence Yip-Lun", "degree": "PhD", "year": "2010", "title": "Photochemical and Dynamics Studies of Oxygen Isotope Exchange Reactions of CO\u2082", "advisor": "Okumura, Mitchio; Eiler, John M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222009-120450275", "creators": [ { "name": { "family": "Yeung", "given": "Laurence Yip-Lun" }, "id": "Yeung-Laurence-Yip-Lun", "orcid": "0000-0001-9901-2607", "display_name": "Yeung, Laurence Yip-Lun" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "co-advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "role": "co-advisor", "display_name": "Eiler, John M." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Chen", "given": "Pin" }, "id": "Chen-Pin", "role": "member", "display_name": "Chen, Pin" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Eiler", "given": "John M." }, "id": "Eiler-J-M", "role": "member", "display_name": "Eiler, John M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/TQKB-3T76", "abstract": "This dissertation describes laboratory studies of three oxygen isotope exchange reactions \u2014 O(1D) + CO2, O2 + CO2, and O(3P) + CO2 \u2014 and their importance to oxygen cycling in the upper atmosphere. First, we studied the isotope exchange reaction O(1D) + CO2, which is believed to govern the oxygen-isotope budget of CO2 in the stratosphere. Our combined field, laboratory, and modeling study of the exceptionally rare 16O13C18O isotopologue revealed that O(1D) + CO2 explains only part of the stratospheric CO2 isotopologue budget, not all of it as previously thought: O(1D) + CO2 could not explain the large enrichments of 16O13C18O (i.e., of the \"Δ47\" tracer) at high Northern latitudes. Mesospheric and heterogeneous chemistry of CO2 were proposed as possible sources of this meridional variation in 16O13C18O. Therefore, we performed crossed-molecular-beam experiments to investigate the chemistry of CO2 at hyperthermal collision energies; this class of reaction could be important in the upper atmosphere, where low gas densities and high rates of photochemistry increase the relative probability of hyperthermal reactions. Our experimental and theoretical study of the O2 + CO2 isotope exchange reaction showed that the reaction can occur through a short-lived CO4 reaction complex, which leads to O2 + CO2 products that are highly internally excited, but possibly still in their ground electronic state. Our study of O(3P) + CO2 collisions at hyperthermal energies showed that O(3P) + CO2 isotope exchange can occur in the upper atmosphere, proceeding through a short-lived CO3 reaction complex. The O(3P) + CO2 → O2 + CO reaction was also observed, and our data suggest that it can proceed through a 'stripping' mechanism or a CO3 complex. These reactions demonstrate new ways in which oxygen can be cycled through CO2 in the atmosphere; their isotope effects, manifest in the isotopic composition of atmospheric CO2, may impose independent constraints on atmospheric transport and biosphere-atmosphere interactions. " }, { "name": "Zeglis, Brian Matthew", "degree": "PhD", "year": "2010", "title": "Investigations into the Generality of Metalloinsertion at DNA Defects", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06162009-143222", "creators": [ { "name": { "family": "Zeglis", "given": "Brian Matthew" }, "id": "Zeglis-Brian-Matthew", "display_name": "Zeglis, Brian Matthew" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0YRQ-3W54", "abstract": "Metalloinsertors are substitutionally inert, octahedral transition metal complexes that bind to thermodynamically destabilized mismatched sites in duplex DNA with high affinity and selectivity. The complexes approach DNA from the minor groove, eject the mismatched bases into the major groove, and replace the displaced bases in the helical \u03c0-stack with their own sterically expansive ligands. Herein, we describe a series of five investigations aimed at elucidating the generality of metalloinsertion at DNA defects.
\r\n\r\nIn an effort to develop a diagnostic for mismatched DNA, a bifunctional, mismatch-specific conjugate with rhodium metalloinsertor and fluorophore subunits has been constructed. A proof-of-concept conjugate was successfully produced that displays an almost fourfold fluorescence enhancement in the presence of mismatched versus matched DNA.
\r\n\r\nTo investigate the range of metal complexes capable of mismatch-specific metalloinsertion, a ruthenium bisdipyridyl complex bearing the heptacyclic eilatin ligand has been synthesized and characterized. Electrophoresis competition experiments illustrate that the complex does display mismatch-preferential, though not necessarily mismatch-selective, binding.
\r\n\r\nTo probe the generality of metalloinsertion at other common thermodynamically destabilized DNA defects, the binding of rhodium metalloinsertors at abasic sites and single base bulges has been studied. It was determined that metalloinsertors bind abasic sites with high affinity and specificity, without regard to the identity of the unpaired base and with little dependence on the sequence context of the defect. Single base bulge recognition proved more elusive, with both the identity of the unpaired base and the sequence context influencing recognition.
\r\n\r\nTo determine the structural generality of metalloinsertion, single crystal X-ray diffraction was employed to determine the structure of \u0394-Rh(bpy)2(chrysi)3+ bound to an oligonucleotide duplex containing two A\u2022A mismatches. Two structures were obtained at <2 \u00c5 resolution, and each provides an archetypical picture of metalloinsertion: the bulky rhodium complex inserts into the mismatched site from the minor groove, ejecting the mismatched bases and replacing the displaced base pair with its own sterically expansive ligand.
\r\n\r\nFinally, two mismatch-specific conjugates have been designed for chemotherapeutic applications: a metalloinsertor-oxaliplatin conjugate for the selective delivery of platinum chemotherapeutics to mismatch repair deficient cells and a metalloinsertor-Auger electron emitter conjugate for the selective irradiation of mismatch-containing DNA.
" }, { "name": "Zhang, Xin", "degree": "PhD", "year": "2010", "title": "Multistate GTPases Control Cotranslational Protein Targeting", "advisor": "Shan, Shu-ou", "url": "https://resolver.caltech.edu/CaltechTHESIS:05272010-004616557", "creators": [ { "name": { "family": "Zhang", "given": "Xin" }, "id": "Zhang-Xin", "display_name": "Zhang, Xin" } ], "advisors": [ { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "advisor", "display_name": "Shan, Shu-ou" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/28HP-FJ94", "abstract": "The cotranslational protein targeting process transports roughly one-third of proteins in a cell\u2019s genome from the cytoplasmic space to the membrane compartments. This process is regulated by the signal recognition particle (SRP) and its receptor (SR). I aim to understand how the complex assembly and activation of GTP hydrolysis during the SRP-SR interaction are controlled so that the SRP machinery functions as a molecular switch to regulate the series of molecular events in space and time. Using a combination of biochemical and biophysical approaches, this dissertation has defined the kinetic and thermodynamic framework of the SRP-SR interaction and has elucidated the regulatory role of the SRP-SR interaction on the protein targeting process. In particular, this dissertation demonstrates that the function of the SRP machinery is governed by a series of ordered conformational changes during SRP-SR interaction that culminate in their activation of GTP hydrolysis. Further, these conformational changes closely monitor and actively respond to the biological cues so that they provide discrete control points at which regulation can be exerted on the protein targeting reaction spatially and temporally. The paradigm provided in this dissertation offers a mechanistic view of another fascinating system in which multistate protein machineries control critical biological processes with exquisite order." }, { "name": "Alabi, Christopher Akinleye", "degree": "PhD", "year": "2009", "title": "I. Synthesis and Proton Conductivity Studies of Mesostructured Organosilicates and Bitriazole-Polymer Composites. II. Targeted Nanoparticles for siRNA Delivery", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262009-145437", "creators": [ { "name": { "family": "Alabi", "given": "Christopher Akinleye" }, "id": "Alabi-Christopher-Akinleye", "orcid": "0000-0003-2654-018X", "display_name": "Alabi, Christopher Akinleye" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9SNH-2A91", "abstract": "The underlying theme of the research outlined in both parts of this report is centered on the ability to use synthetic design as a probe to investigate and answer fundamental mechanistic questions in an effort to improve the function of materials employed in energy and biological research. Specifically in the field of energy research, we have designed a new strategy aimed at improving the proton conductivity of organically modified silica-based polymer electrolyte membranes for use in direct methanol fuel cells. Our design involves the incorporation of the desired organic functional group into a siloxane-modified polymerizable surfactant that can be used in mesoporous silicate synthesis. This approach takes advantage of the silicate assembly mechanism, which places surfactants exclusively within the pores of the silicate at high loadings. The desired functional group is revealed upon selective cleavage after hydrothermal silicate synthesis. We have used this approach to synthesize organosilicates with different sized organic groups displaying high organic acid densities and have studied their proton conductivity under fully hydrated conditions. Under these conditions, structural diffusion via a percolated water network is the dominant mechanism of proton transport.
\r\n\r\nWith regards to membranes for use in hydrogen fuel cells that operate best at temperatures above the dew point of water, the need for an alternative to water as the proton conducting medium is desired. Towards this end, we designed a new nitrogen-containing heterocycle (NCH), 4,4-1H-1H-bi-1,2,3-triazole (bitriazole) capable of mimicking water in the solid state and have investigated its ability to conduct protons in the presence of polyethylene oxides under anhydrous conditions. With numerous chemical tools at our disposal, we probed the mechanism of proton conduction and confirmed the bitriazole proton to be the source of anhydrous proton conductivity. Our data suggests structural diffusion as the dominant transport mechanism via synergistic interactions between bitriazole and polyethylene oxides in the polymer-rich region of the composite material that is encapsulated by a crystalline nonconductive bitriazole framework.
\r\n\r\nIn the second part of this report, we shift our focus to the investigation of antibody-mediated targeting, using our well-established cyclodextrin polycation (CDP) nanoparticles containing therapeutic oligonuleotides, to epitopes expressed at the surface of cancer cells as a means of increasing site-specific therapeutic delivery. To do this, we synthesized fragments of anti-CD20 (rituximab) and conjugated them to flexible poly(ethylene glycol) (PEG) linkers with terminal adamantane groups that can interact with the cyclodextrins on the surface of the CDP nanoparticle via the formation of an inclusion complex. With the PEGylated antibody fragments in hand, we investigate, via a B-cell lymphoma model, the binding characteristics of the targeting ligands as well as their effect on the binding, internalization, and efficacy of the targeted CDP-nucleic acid therapeutic nanoparticles.
\r\n" }, { "name": "Allen, Benjamin Daniel", "degree": "PhD", "year": "2009", "title": "Development and Validation of Optimization Methods for the Design of Protein Sequences and Combinatorial Libraries", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05012009-112749", "creators": [ { "name": { "family": "Allen", "given": "Benjamin Daniel" }, "id": "Allen-Benjamin-Daniel", "display_name": "Allen, Benjamin Daniel" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/SNJJ-0Q88", "abstract": "To facilitate the design of protein sequences with desired properties, simulation techniques have been developed to allow large portions of amino acid sequence space to be evaluated by computer. These computational protein design methods apply optimization algorithms to sort through the enormity of sequence space and find desirable variants.
\r\n\r\nSimple modifications to the stochastic optimization algorithm FASTER enhanced its performance by two orders of magnitude without loss of accuracy, and rendered it more efficient than its major competitor by a factor of 10. These improvements allowed higher-quality amino acid solutions to be found more quickly, and accelerated the pace at which users could perform cycles of design and model adjustment.
\r\n\r\nThis success prompted research into techniques for a protein design formulation that allows simulation in the context of multiple states simultaneously. This multi-state design can be used to wield explicit control over structural, binding, or catalytic specificity, and changes the scope of design goals that can be addressed by computation. Evaluation of multi-state FASTER indicated that it performed radically better than its major competitor in a variety of design contexts, and that in most cases it found solutions better than those that could ever be found using a lesser method.
\r\n\r\nMulti-state optimization using FASTER was applied to test the influence of various types of input structural data on the design of a small protein. To facilitate this evaluation, methods for the design and high-throughput stability screening of combinatorial libraries were developed. Screening of libraries based on single structures and structural ensembles indicated the success of multi-state modeling. Our results also suggested that the exhaustive screening of designed libraries can help to elucidate the origins of design model failures. Finally, they showed that success of a design procedure does not hinge on its ability to correlate experimental and simulated measures of fitness, and prompted greater consideration of design methods that target explicitly conformational specificity.
\r\n" }, { "name": "Archer, Raymond Humphrey", "degree": "PhD", "year": "2009", "title": "Molecular Sieve Synthesis Using Imidazolium Structure Directing Agents", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022009-100039", "creators": [ { "name": { "family": "Archer", "given": "Raymond Humphrey" }, "id": "Archer-Raymond-Humphrey", "display_name": "Archer, Raymond Humphrey" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/GJT6-1C73", "abstract": "The synthesis of high-silica molecular sieve SSZ-70 is investigated through a guest/host study of imidazolium structure directing agents (SDAs). The original borosilicate synthesis is extended to pure-silica and aluminosilicate compositions using six imidazolium SDAs. Physical characterization using powder X-ray diffraction (XRD), 29Si solid-state NMR, electron microscopy, thermogravimetric analysis, and nitrogen adsorption shows SSZ-70 to be layered with similarity to MCM-22 (MWW). Aluminum-containing SSZ-70 is evaluated for catalytic activity using the constraint index (CI) test and shows a similar cracking rate to SSZ-25 (MWW structure). Distinct differences in CI as a function of time on stream are observed between MWW and SSZ-70 materials. Additional molecular sieve phases observed in this guest/host study included Theta-1 (TON), ZSM-5 (MFI), ZSM-23 (MTT), ZSM-12 (MTW), Beta, Mordenite (MOR), CIT-5 (CFI), SSZ-16 (AFX), and SSZ-35 (STF).
\r\n\r\nAttempts to synthesize Beta enriched in chiral polymorph A are investigated in a second guest/host study using five chiral imidazolium SDAs. Two SDAs successfully gave Beta, but no enrichment in polymorph A is observed. The remaining SDAs do not direct the formation of any molecular sieve phases. Molecular modeling indicates both SDAs occupy the straight [100]/[010] 12 membered ring (MR) pores of Beta. In this configuration, no chirality could be projected across the [001] fault planes and this offers an explanation for not observing enrichment. Modeling shows careful consideration must be given to efficiently filling the entire void volume when large SDAs are used. Additional molecular sieve phases observed in the guest/host study are EU-1 (EUO) and MOR.
\r\n\r\nFinally, attempts to synthesize novel materials using supramolecular SDAs are described. Supramolecular SDAs are created through adamantyl/beta-cyclodextrin inclusion complex formation. Both 2:1 and 1:1 inclusion complex stoichiometries are attempted. Significant cyclodextrin degradation occurs at temperatures above 90\u00b0C and no structure-directing effect can be attributed to the cyclodextrin. Molecular sieve phases observed in the study are SSZ-16 (AFX), MOR, B-SSZ-13 (CHA), VPI-8 (VET), and SSZ-24 (AFI).
\r\n" }, { "name": "Bayer, Travis Scott", "degree": "PhD", "year": "2009", "title": "Synthetic Regulation and Genetic Control of an Ecological Strategy", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10162008-131654", "creators": [ { "name": { "family": "Bayer", "given": "Travis Scott" }, "id": "Bayer-Travis-Scott", "display_name": "Bayer, Travis Scott" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "member", "display_name": "Elowitz, Michael B." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "biochem" ], "doi": "10.7907/3GDB-C409", "abstract": "The construction of synthetic gene regulatory circuits inside living cells has illuminated how organisms process environmental signals, and has suggested that biological systems can be engineered for useful purposes. However, these lines of inquiry are limited by a lack of technologies for programming gene expression and an understanding of the adaptive or ecological consequences of manipulating gene expression. Here, I describe the design of noncoding RNA regulators of gene expression in Saccharomyces cerevisiae. These regulators are able to regulate gene expression in response to a small molecule ligand, which offers the ability to tailor control devices for a variety of applications. In light of this, an open question is the dependence of organism fitness on the levels of a regulator, which has seldom been measured. I found that the expression level of a transcriptional regulator of nitrogen metabolism mediates a trade-off between growth in resource abundant and resource limited environments in S. cerevisiae. Redundancy in the metabolic pathways of ammonia assimilation allowed noise, or random fluctuations in the amount of protein present, to dictate whether cells specialized in maximizing fitness in abundant or limiting environments. These results show how gene expression may be programmed via noncoding RNA regulators, and that the manipulation of regulator levels can affect the strategy by which organisms adapt to their environments.\r\n" }, { "name": "Beisel, Chase Lawrence", "degree": "PhD", "year": "2009", "title": "Engineering Ligand Control of RNA Interference", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212009-144705", "creators": [ { "name": { "family": "Beisel", "given": "Chase Lawrence" }, "id": "Beisel-Chase-Lawrence", "orcid": "0000-0003-0650-9943", "display_name": "Beisel, Chase Lawrence" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "chair", "display_name": "Smolke, Christina D." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/CBRX-PG36", "abstract": "RNA is a rich and versatile substrate for the construction of information processing devices. These devices detect the levels of specified intracellular biomolecules and control cellular behavior accordingly. With few superficial constraints on the identity of the recognized biomolecule or the targeted gene, RNA-based information processing devices can be rapidly implemented toward various applications in medicine and biotechnology. To advance the design and implementation of RNA-based information processing devices, we delineated general design principles and applied these principles to the construction of devices that operate through RNA interference (RNAi).
\r\n\r\nRNAi represents an endogenous enzymatic pathway present in humans and other eukaryotes that mediates targeted gene silencing. The pathway has garnered recent interest as a revolutionary biological research tool and as a targeted therapeutic strategy. While RNAi has left an indelible mark on the scientific community, exerting greater control would advance the applicability and safety of this already impressive gene silencing mechanism. Toward this goal, we engineered ligand control of three types of RNAi effectors in mammalian cells: small interfering (si)RNAs, small hairpin (sh)RNAs, and microRNAs (miRNAs). Engineering frameworks enabled facile replacement of the biomolecule sensory and gene targeting domains, thus lending to rapid implementation as biosensors or autonomous control devices. Experimental and computational characterization studies provided a comprehensive understanding of device behavior, thereby facilitating forward design.
\r\n\r\nNaturally-occurring analogs of RNA-based information processing devices are riboswitches. Riboswitches predominantly mediate dynamic feedback in metabolism and share many traits with current examples of engineered information processing devices. Various experimental characterization studies of riboswitches showed that kinetics underlying events such as conformational switching and ligand binding have a substantial impact on device performance, although these factors remain to be comprehensively evaluated or considered when formulating design principles for synthetic riboswitch construction. We explored the contribution of kinetic factors to riboswitch performance in silico, where model predictions matched experimental observations, including results from our ligand-responsive RNAi effectors. From our modeling results, we developed a general set of design principles that guide riboswitch assembly and performance tuning.
" }, { "name": "Chapman, Stephen Allen", "degree": "PhD", "year": "2009", "title": "Quantitative Performance and Tradeoffs in the MAP Kinase Signaling Module", "advisor": "Asthagiri, Anand R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02202009-142419", "creators": [ { "name": { "family": "Chapman", "given": "Stephen Allen" }, "id": "Chapman-Stephen-Allen", "display_name": "Chapman, Stephen Allen" } ], "advisors": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "advisor", "display_name": "Asthagiri, Anand R." } ], "committee": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "chair", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "chemeng" ], "doi": "10.7907/YVHW-Z764", "abstract": "Intracellular signal transduction networks propagate and integrate the information that cells sense from environmental stimuli. The quantitative performance of signaling networks regulates cell decisions, and aberrations in network performance lead to pathologies such as cancer. The mitogen-activated protein (MAP) kinase cascade is a highly-conserved signaling module that regulates diverse cellular processes, such as proliferation, differentiation, and apoptosis in eukaryotic species ranging from yeast to human. While the principal components and mechanisms that define the MAP kinase module are well established, our understanding of and ability to tune its quantitative performance is limited. Here, we probe more deeply how the quantitative properties of the MAP kinase module may be affected by variations in the expression levels of the key constituents of the cascade\u2014kinases, phosphatases and scaffolds.
\r\n\r\nUsing a computational approach, we delineate how four quantitative properties\u2014responsiveness to input, dynamic range of output, signal amplification, and signal lifetime\u2014depend on the relative abundances of the two core components of the MAPK module, kinases and phosphatases. We identify a reduced metric termed the \u2018resistance to activation\u2019 that predicts the quantitative properties of the module across a wide range of parameter values. Its predictive utility extends to dynamic properties such as signal lifetime, which often dictates the MAP kinase\u2019s effect on cell function. Our analysis highlights tradeoffs in design, as not all quantitative attributes of the module can be simultaneously optimized. Thus, the resistance to activation captures the fundamental principles that determine cascade behavior and can be exploited to guide quantitative redesign of the MAP kinase module.
\r\n\r\nIn addition to the expression levels of kinases and phosphatases, scaffolds play a key role in signal propagation through the MAP kinase module. Protein scaffolds bring together multiple components of a signaling pathway, thereby promoting signal flux along a common physical \u201cbackbone.\u201d Scaffolds figure prominently in natural signaling pathways and are emerging as a promising platform for synthetic circuits. To better understand how scaffolding quantitatively affects signal transmission, we conducted an in vivo experimental sensitivity analysis of MAP kinase response to broad perturbations in the expression level of Ste5, an exemplar scaffold of the yeast mating pathway. Our results demonstrate that the expression level of Ste5 significantly affects several quantitative aspects of signal propagation, including signal throughput, pathway ultrasensitivity, and baseline leakage. These new insights into the quantitative role of scaffolding in MAP kinase signaling suggest advantages and limitations in designing synthetic scaffold-based regulatory networks.
\r\n" }, { "name": "Chen, Wei-Chen", "degree": "PhD", "year": "2009", "title": "Isotope Effects in Chemical Processes of Atmospheric Interest", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01222009-173227", "creators": [ { "name": { "family": "Chen", "given": "Wei-Chen" }, "id": "Chen-Wei-Chen", "display_name": "Chen, Wei-Chen" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WCH2-W090", "abstract": "The thesis is focused on the theoretical study of the isotope effects in three atmospheric reactions, the CO+OH reaction, the photolysis of N\u2082O, and the ozone formation. The CO+OH reaction is investigated by using both Rice-Ramsperger-Kassel-Marcus theory and its nonstatistical modification, which was prompted by existing molecular-beam data on incomplete intramolecular energy transfer in the HOCO* intermediate. The resulting calculations show reasonable agreement with most experimental data, except the O isotope effect. Two predictions are made: the temperature dependence of the OD+CO reaction; and the rate constant kv decreasing with increasing CO vibrational quantum number v from v = 0 to v = 1. In both experiments and our calculation, the kinetic oxygen isotope effect is different from the expected value (i.e. the mass-dependent slope), which may be due to the H-tunneling. An experiment that avoids a possible role of vibrationally excited OH radicals as reactants in the O isotope effect is also suggested to remove the discrepancy in the O isotope effect between the experiments and calculations.
\r\n\r\nThe UV photolysis of the greenhouse gas N\u2082O and its isotope effects are important in atmospheric chemistry. Based on the multidimensional reflection principle using the available ab initio data on the molecule for the potential energy surfaces and the transition dipole moments, we provide an accurate but not computationally intensive method in obtaining the absorption cross section. The present calculated fractionation gives good agreement with the experimental absorption cross section in the low-energy region, where the experimentally observed isotopic fractionation occurs. We also suggest a single effective mass, a linear combination of two main coordinates for the photolysis, to determine the slope of a multi-element isotope plot and to yield approximate agreement between the experimental data and a \"mass-dependent\" fractionation, which range from 0.47 to 3.28.
\r\n\r\nA modified ab initio potential energy surface is used for calculations of ozone recombination and isotopic exchange rate constants. The calculated low-pressure isotopic effects on the ozone formation reaction are consistent with the experimental results and with the theoretical results obtained earlier [J. Chem. Phys. 116, 137 (2002)]. This result showed that they are relatively insensitive to the properties of the PES.
\r\n" }, { "name": "Chenoweth, David Michael", "degree": "PhD", "year": "2009", "title": "Synthesis and Structural Studies of Cyclic Py-Im Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282009-211225", "creators": [ { "name": { "family": "Chenoweth", "given": "David Michael" }, "id": "Chenoweth-David-Michael", "orcid": "0000-0002-0819-4669", "display_name": "Chenoweth, David Michael" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PZEC-VA33", "abstract": "The work presented in this thesis is focused on the molecular recognition of DNA by minor groove binding polyamides. Methods and strategies for the solution-phase synthesis of hairpin and cyclic pyrrole-imidazole polyamides are presented with optimized protocols requiring little to no chromatography. These synthetic strategies have led to the design of cyclic polyamides targeted to the androgen response element and are shown to be biologically active and cell permeable in cell culture experiments in addition their binding affinities rival that of most polyamide architectures. The structural elucidation of an \u03b1-amino-turn-linked cyclic polyamide is presented at 1.17 \u00c5 resolution providing insight into the detailed molecular recognition process and allosteric modulation responsible for the inhibition of transcription factor-DNA binding. Additionally, structural elucidation of a \u03b2-amino-turn-linked cyclic polyamide, highlighting the conformational differences compared to the \u03b1-amino-turn linked structure is presented. A structural basis for the inability of polyamides to bind dsRNA is also proposed based on biophysical, structural, and modeling data. In addition to these studies a new class of programmable oligomers targeting the DNA sequence 5\u2019-WGGGGW-3\u2019 were shown to inhibit DNA binding of the Nf-kB transcription factor by EMSA gel shift. Compounds synthesized in this study were found to possess unique fluorescent properties with the ability to modulate their fluorescence by binding their targeted dsDNA, leading to sequence specific fluorescent detection reagents. Efforts toward the templated-assembly of polyamides using higher-order DNA structure (NCP) are also reported and the development of a new pro-fluorescent class of heterocycle, which has the potential to be used as a chemical reporter of ligation events is described.\r\n" }, { "name": "Cohen, Justin Delgado", "degree": "PhD", "year": "2009", "title": "Programming Protein Patterns on DNA Nanostructures with Pyrrole-Imidazole Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11232008-171327", "creators": [ { "name": { "family": "Cohen", "given": "Justin Delgado" }, "id": "Cohen-Justin-Delgado", "display_name": "Cohen, Justin Delgado" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CZ2K-MJ03", "abstract": "Molecular recognition of DNA has important applications for gene regulation, molecular biology, and DNA nanotechnology. Pyrrole-imidazole polyamides are a unique class of molecules with the ability to bind to DNA in a programmable manner. These small molecule analogues of distamycin A can be programmed to target virtually any DNA sequence with high affinity and specificity. Originally characterized for their ability to bind to B-form DNA, polyamides are also able to target DNA in architectures such as the nucleosome core particle (NCP) and two-dimensional DNA nanostructures including DX-arrays and DNA origami. In addressing DNA nanostructures, polyamide-biotin conjugates can be used to create nanoscale molecular assemblies in a bottom-up approach to self-assembly. The ability to address unique sequences on a DNA nanostructure with different polyamides makes it possible to create unique arrangements of protein on a single 2-dimensional DNA template. Polyamides targeted to the NCP can be used for a variety of exciting applications including NCP-templated ligation reactions, gene regulation, and as tools for X-ray crystallography. The programmability of polyamides makes them an ideal tool for addressing a variety of DNA architectures for varying applications.\r\n" }, { "name": "Culler, Stephanie June", "degree": "PhD", "year": "2009", "title": "Reprogramming Alternative Splicing Using Cis-Acting Intronic Control Elements", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-142907", "creators": [ { "name": { "family": "Culler", "given": "Stephanie June" }, "id": "Culler-Stephanie-June", "display_name": "Culler, Stephanie June" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HVGX-RJ21", "abstract": "Alternative splicing is a process by which multiple protein isoforms are generated from a single coding region by altering the ways in which exons are joined together. This pathway is used by cellular systems to both increase proteomic diversity from a limited number of genes and to precisely control gene expression. Bioinformatics and comparative genomics approaches have provided significant sequence and functional insight into the regulatory sequences that occur within exonic regions of a transcript. In vitro and in vivo strategies have also been developed to screen for exonic splicing enhancers and silencers (ESEs and ESSs) from small, randomized libraries. Much less is known about intronic splicing enhancers and silencers (ISEs and ISSs), although recent bioinformatics approaches are beginning to shed some light on these regulatory sequences. A thorough understanding of both exonic and intronic regulators is necessary to enable the programming of alternative splicing patterns, which will provide a powerful tool for interrogating and manipulating cellular function.
\r\n\r\nWe developed a generalizable in vivo screening strategy for generating intronic splicing regulatory elements (ISREs). Our high-throughput approach employed a systematic screening strategy with extensive genome-wide bioinformatic analyses and experimental characterization which included a small-scale RNAi screen. Using this approach, we identified ISRE consensus motifs, characterized the splicing regulatory networks (SRNs) associated with these regulatory elements and generated a model for ISRE regulatory function. Highlighting the complexity of SRNs, we found that cis-acting intronic regulatory sequences function through combinatorial effects from multiple elements and trans-acting factors, and that the immediate transcript context has a dominant effect on ISRE function. Overall, this screening strategy provides a general method for generating regulatory sequences of alternative splicing events, which provide powerful tools for gene expression control.
\r\n\r\nWe next extended from our studies on cellular screening strategies for generating splicing regulatory elements, to build novel platforms that support the construction of protein-responsive alternative splicing control elements. Protein-binding RNA aptamers were inserted into key intronic locations of an alternatively spliced transcript to enable the detection of intracellular protein concentrations and to translate detection events to the regulation of alternative splicing patterns and thus gene expression. We demonstrate that these RNA elements can serve as autonomous control devices by linking endogenous nuclear protein levels to gene expression events and external stimuli to complex cellular phenotypes. These synthetic alternative splicing regulators can be implemented combinatorially to regulate alternative splicing patterns in response to multiple inputs. In addition, we applied these synthetic regulators to the rewiring of endogenous signal transduction pathways and building of novel regulatory networks for user-defined phenotypes. Our work provides an early example of a novel class of RNA-based \u201cintelligent\u201d therapeutics by directing increased signaling through pathways associated with disease to the triggering of apoptosis. These programmable sensing-actuation molecules will be broadly applied in health and medicine towards the early diagnosis and treatment of disease.
" }, { "name": "Eastwood, Amy Lynn", "degree": "PhD", "year": "2009", "title": "Investigating Structure-Function Relationships in Ion Channels Using Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01062009-133603", "creators": [ { "name": { "family": "Eastwood", "given": "Amy Lynn" }, "id": "Eastwood-Amy-Lynn", "display_name": "Eastwood, Amy Lynn" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/86B5-SV57", "abstract": "Ion channels are proteins that traverse the cell membrane and form gated pores that open and close in response to various stimuli. In order to experimentally probe aspects of ion channel functionality, we performed subtle structure function studies using the in vivo nonsense suppression method, which allows for the incorporation of synthetically accessible unnatural amino acids and hydroxy acids into an ion channel at a site of interest.
\r\n\r\nFluorinated aromatic amino acids are good probes for a cation-\u03c0 interaction because fluorine substituents reduce the binding affinity of the aromatic for a cation in a linear, step-wise fashion. In collaboration with Professor Richard Horn at the Thomas Jefferson University, we substituted a series of fluorinated phenylalanines for important tyrosines in the Shaker B K\u207a channel and experimentally determined that TEA was binding to the residues through a cation-\u03c0 interaction. We also determined that Ca\u00b2\u207a binds to and blocks the NaV1.4 channel through a cation-\u03c0 interaction with a tyrosine at the top of the pore of this channel. We found that tetrodotoxin, another channel blocker, also binds to this same residue through a cation-\u03c0 interaction. Finally, we proved that lidocaine and other local anesthetics bind to a phenylalanine at the bottom of the pore of this channel through a cation-\u03c0 interaction.
\r\n\r\nAn important aspect of our work is the development of unnatural amino acids that can be used in the study of ion channels through the in vivo nonsense-suppression methodology. We determined that D-amino acids could not be incorporated into ion channels using this method. We synthesized several novel fluorescent-MTS reagents to be used in FRET studies. We probed the sterics around phenylalanines using the unnatural amino acid 3,5-dimethylphenylalanine. We also attempted to incorporate 4-amino-phenylalanine, but, unfortunately, we never saw the enhanced binding of a cationic ligand that was our expected phenotype.
\r\n\r\nFinally, we also designed and synthesized two \u03b1-hydroxy acids capable of site-specific proteolysis upon UV irradiation. We used a tripeptide model system to isolate and characterize the cleavage fragments, proving that these two residues are indeed capable of site-specific proteolysis through the predicted mechanism.
\r\n" }, { "name": "Ebner, David Christopher", "degree": "PhD", "year": "2009", "title": "Development and Applications of the Palladium-Catalyzed Enantioselective Oxidation of Secondary Alcohols ", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09192008-185009", "creators": [ { "name": { "family": "Ebner", "given": "David Christopher" }, "id": "Ebner-David-Christopher", "display_name": "Ebner, David Christopher" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2KEA-TT16", "abstract": "The development of new methods for the preparation of chiral alcohols is vital due to the presence of alcohols in natural products, pharmaceuticals, and a variety of synthetic materials, as well as their versatility as synthetic intermediates. Until recently, oxidative kinetic resolution has been a relatively underdeveloped strategy for obtaining enantioenriched alcohols.
\r\n\r\nThe development of a palladium-catalyzed aerobic system for the enantioselective oxidation of secondary alcohols is described. This mild method utilizes (\u2013)-sparteine as a chiral ligand to resolve a wide range of benzylic, allylic, and cyclopropylcarbinyl alcohols to high enantiomeric excesses with excellent selectivity. The resolution of pharmaceutical intermediates and the Claisen rearrangement of resolved allylic alcohols demonstrate the utility of the method.
\r\n\r\nMechanistic insights have driven further catalyst development. Anionic ligand modification has provided more efficient catalysts for the resolution of a broader array of substrates. Neutral ligand studies have led to an enantioselective alcohol oxidation system with a diamine pseudo-enantiomeric to (\u2013)-sparteine, allowing access to enantioenriched alcohols in either enantiomeric series.
\r\n\r\nThis methodology has been applied to the enantioselective total synthesis of (\u2013)-amurensinine via a selective C\u2013H insertion, an aryne C\u2013C insertion, and an oxidative kinetic resolution with (\u2013)-sparteine. Use of an alternative diamine in the resolution results in a formal synthesis of (+)-amurensinine.
\r\n" }, { "name": "Elowe, Paul Richard", "degree": "PhD", "year": "2009", "title": "The Selective Oligomerization of Ethylene Using Chromium Diphosphine Catalysts and the Synthesis and Reactivity of Group 7 Carbonyl Derivatives Relevant to Synthesis Gas Conversion", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07252008-141614", "creators": [ { "name": { "family": "Elowe", "given": "Paul Richard" }, "id": "Elowe-Paul-Richard", "display_name": "Elowe, Paul Richard" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/S7NA-Y054", "abstract": "The work presented in this thesis explores two distinct fields of organometallic chemistry with a common goal of selectively transforming cheap and abundant feedstocks to value-added chemicals using homogeneous catalysts.
\r\n\r\nChapter 1 presents the synthesis and characterization of a series of bis(diphenylphosphino)amine ligands and their corresponding chromium(III) trichloride complexes. The isolated chromium complexes are precursors to highly active catalysts for the selective oligomerization of ethylene to 1-hexene and 1-octene. The unique feature of the ligands presented herein is the presence of coordinating functionalities tethered to the nitrogen backbone. These act as hemilabile donors, which stabilize the active species and/or transition states during catalysis. This increased stability leads to more productive catalysts. Furthermore, important solvent and additive effects have been investigated. While reactions in non-polar solvents exhibit poor activity at lower ethylene pressures, those in more polar solvents are highly active and generate very little undesired polymer. Varying the solvent has a significant impact on 1-hexene/1-octene selectivity as well. Experiments with potentially coordinating additives result in a higher tendency for 1-octene formation. An investigation of catalyst decomposition is also discussed.
\r\n\r\nChapter 2 presents synthetic, structural and reactivity studies on a series of Group 7 carbonyl derivatives relevant to synthesis gas conversion. Reduction of the carbonyl precursors with a hydride source generates the corresponding formyl species. This reaction is facilitated when more electrophilic carbonyl complexes are employed. Neutral and cationic Fischer carbene complexes were prepared by the reaction of the formyl species with boranes and alkyltriflates, respectively. Further reduction of Group 7 methoxycarbenes with a hydride leads to the formation of a reactive methoxymethyl species. Dimethyl ether release is obtained from treatment of a manganese methoxymethyl species with a hydride. Moreover, subjecting manganese methoxymethyl complexes to an atmosphere of CO generates acyl complexes via migratory insertion. Preliminary mechanistic details are presented.
\r\n" }, { "name": "Gama, Cristal Ivette", "degree": "PhD", "year": "2009", "title": "Understanding the Chemical Basis of Neuronal Development and Communication: I. The Role of Fucose \u03b1(1-2) Galactose Carbohydrates in Neuronal Growth. II. Structure-Function Analysis of Chondroitin Sulfate in the Brain", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10302008-123855", "creators": [ { "name": { "family": "Gama", "given": "Cristal Ivette" }, "id": "Gama-Cristal-Ivette", "display_name": "Gama, Cristal Ivette" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Kennedy", "given": "Mary B." }, "id": "Kennedy-M-B", "role": "member", "display_name": "Kennedy, Mary B." }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." } ], "option_major": [ "biochem" ], "doi": "10.7907/CDGH-MJ49", "abstract": "Although carbohydrates are known to participate in many processes including inflammation and cancer metastasis, their functional roles are only beginning to be understood on a molecular level. Unlike DNA and proteins, carbohydrate structures are not template-encoded and are challenging to detect in vivo and manipulate for structure-function analyses. New tools are needed to complement biochemical and genetic approaches to advance our understanding of carbohydrates and their physiological roles. We seek to understand the roles of carbohydrates in regulating the structure and function of proteins in the brain. Our focus is on two modifications that are important in neuronal communication and development: fucosylation (Part I) and chondroitin sulfate modifications (Part II).
\r\n\r\nIn Part I, we describe our progress in elucidating the molecular mechanisms by which fucosyl saccharides regulate neuronal communication. Previous studies have shown that preventing formation of fucose\u03b1(1-2)galactose saccharides causes reversible amnesia in animals, suggesting that these sugars play essential roles in learning and memory. However, proteins expressing the fucose\u03b1(1-2)galactose epitope or proteins binding this epitope have not been identified. Using chemical probes, we established that fucose\u03b1(1-2)galactose associated proteins participate in a novel carbohydrate-mediated pathway for regulating neuronal growth. Additionally, we found that fucose\u03b1(1-2)galactose glycoproteins are prevalent in developing brain and that synapsin Ia/Ib are the major fucose\u03b1(1-2)galactose glycoproteins in adult brain. In our attempts to identify Fuc\u03b1(1-2)Gal lectins, we have established that multivalent polymers enhance our ability to capture and characterize such proteins.
\r\n\r\nIn Part II, we describe our efforts toward understanding the role of chondroitin sulfate glycosaminoglycans in neuronal development. Chondroitin sulfate glycosaminoglycans are structurally complex and heterogeneous in nature, thus hampering efforts to understand their precise biological roles. It is thought that chondroitin sulfate activity is dictated by a sulfation code, where distinct sulfation sequences are spatially and temporally regulated. We have developed a chemical approach to evaluate the structure-activity relationship of chondroitin sulfate as it effects neuronal growth. We generated the first synthetic library of well-defined chondroitin sulfate oligosaccharides containing various sulfation sequences and have demonstrated that the chondroitin sulfate-E sequence is a stimulatory motif that promotes the growth of several neuron types. Moreover, we determined that chondroitin sulfate-E stimulation was facilitated through activation of the midkine/PTP\u03b6 and BDNF/TrkB pathways.
" }, { "name": "Gorodetskaya, Irina A.", "degree": "PhD", "year": "2009", "title": "Nonlinear Polymeric Architectures via Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262009-232200", "creators": [ { "name": { "family": "Gorodetskaya", "given": "Irina A." }, "id": "Gorodetskaya-Irina-A", "display_name": "Gorodetskaya, Irina A." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WRYR-4674", "abstract": "The research presented in this thesis focuses on application of olefin metathesis to the construction of hyperbranched and cyclic macromolecules. The olefin metathesis reaction is briefly reviewed in Chapter 1, along with its applications in polymer synthesis. A very mild, simple, and modular, olefin metathesis-based hyperbranched polymerization route is presented in Chapter 2. This method utilizes the cross metathesis selectivity of the functional group tolerant N-heterocyclic carbene ruthenium catalyst towards different types of alkenes, and it can be applied to the polymerization of many easily prepared ABn monomers. Moreover, the same method can be used to post-synthetically functionalize such polymers for realization of their substrate carrying potential. Chapter 3 describes one such functionalization example\u2014a pyrene analyte is attached to a metathesis derived hyperbranched polymer. This modification of the polymer provides insight into its solution structure relative to a linear analog. In addition, molecular weight control of the metathesis hyperbranched polymerization is discussed in detail in Chapter 4. The careful choice of the catalysts loading and the use of a multifunctional core are found to be important parameters in preparation of polymers which span a range of molecular weights.
\r\n\r\nEven well-established materials, such as polyethylene, can benefit from olefin metathesis and the unusual polymeric architectures it can efficiently create. For example, a cyclic polymer which lacks end groups, as opposed to having many end groups like a hyperbranched polymer, is expected to possess unique physical properties. The preparation of cyclic and linear polyethylenes and the study of their relative rheological properties are described in Chapter 5. The polymerization methodology outlined in this chapter takes advantage of ring-expansion metathesis polymerization\u2014a facile method for the synthesis of cyclic macromolecules. Some efforts directed at molecular weight control of this cyclic polymerization are also discussed.
\r\n" }, { "name": "Gorodetsky, Alon A.", "degree": "PhD", "year": "2009", "title": "Electrical Detection of DNA Binding Proteins", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102008-101354", "creators": [ { "name": { "family": "Gorodetsky", "given": "Alon A." }, "id": "Gorodetsky-Alon-A", "display_name": "Gorodetsky, Alon A." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VPKN-CV38", "abstract": "The base pair stack of double helical DNA has proven to be an effective medium for charge transport. The \u03c0-stacked DNA base pairs can mediate charge transport (CT) chemistry over distances as long as 20 nm, and the reaction is exquisitely sensitive to DNA sequence-dependent conformation and dynamics. This sensitivity to perturbations in DNA structure and base pair stacking makes DNA-mediated charge transport chemistry an ideal methodology for the electrical detection of base mismatches, lesions, and protein binding. Efforts toward expanding the scope of electrochemistry at DNA-modified surfaces for biosensing applications are presented here." }, { "name": "Hanek, Ariele Patrice", "degree": "PhD", "year": "2009", "title": "Chemical-Scale Investigations of Cys-Loop Neurotransmitter Gated Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-112657", "creators": [ { "name": { "family": "Hanek", "given": "Ariele Patrice" }, "id": "Hanek-Ariele-Patrice", "display_name": "Hanek, Ariele Patrice" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FSYX-Y861", "abstract": "Cys-loop ligand gated ion channels mediate rapid synaptic transmission in the mammalian central and peripheral nervous system. Proper functioning of this superfamily of receptors is critical to brain function and as such the proteins are implicated in a number of neuropathies and are a target for many pharmaceuticals. A central concern is how these receptors recognize and bind their neurotransmitter agonists as well as how these binding events lead to a conformational change spanning a distance of at least 50 \u00c5. Using the nonsense suppression methodology, we are able to incorporate unnatural amino acids into these proteins and identify the precise molecular interactions involved in neurotransmitter binding and the conformational changes that take place during channel activation.
\r\n\r\nIn chapters two through four we investigate the role of the nicotinic acetylcholine receptor (nAChR) \u03b11 loop 2 residues in channel activation. Using conventional mutagenesis, we have identified several residues that are part of a global electrostatic network. This is the first study to present an element of activation that is universal to the entire Cys-loop superfamily. Using unnatural amino acids, we identify the pro-S methyl group of \u03b1Val46 as a critical element in the activation pathway of the muscle type nicotinic acetylcholine receptor, thereby validating a proposed the pin-into-socket mechanism for this residue.
\r\n\r\nWe switch our focus from the excitatory nAChR to the inhibitory glycine (Gly) and \u03b3-aminobutyric acid type A (GABAA) receptors in chapter 5. By incorporating successively fluorinated phenylalanine analogs into the binding site of both the GlyR and GABAAR we were able to identify a cation-\u03c0 interaction at \u03b11Phe159 of the GlyR and \u03b22Tyr97 of the GABAAR, providing further evidence that the cation-\u03c0 interaction is conserved across the superfamily.
\r\n\r\nFinally we investigate the mechanisms of GABA activation and flurazepam (FLZM) potentiation in the GABAAR. Incorporation of a photo-activated backbone cleaving unnatural amino acid reveals that an unstructured linker connecting loops A and E of the GABAAR \u03b11 subunit is critical to GABA but not pentobarbital activation. We further investigate this region of the receptor and its role in GABA activation and flurazepam potentiation using conventional mutagenesis and incorporation of \u03b1-hydroxy acids. The data indicate that GABA activation and FLZM potentiation are differentially affected by side chain mutations in this region, but not by backbone mutations. Loss-of-function due to incorporation of alpha-hydroxy acids strongly suggests the unstructured linker becomes more structured during channel activation.
\r\n" }, { "name": "Hawkins, Kristy Michelle", "degree": "PhD", "year": "2009", "title": "Metabolic Engineering of Saccharomyces cerevisiae for the Production of Bensylisoquinoline Alkaloids", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10302008-210903", "creators": [ { "name": { "family": "Hawkins", "given": "Kristy Michelle" }, "id": "Hawkins-Kristy-Michelle", "display_name": "Hawkins, Kristy Michelle" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "chair", "display_name": "Smolke, Christina D." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/BQF7-QZ35", "abstract": "The engineering of synthetic metabolic pathways in microbial hosts holds much promise for the synthesis of new chemicals and materials, including a variety of natural and non-natural products. The benzylisoquinoline alkaloids (BIAs) represent a large and structurally diverse class of plant secondary metabolites that exhibit a broad range of pharmacological activities. The reconstitution of a BIA biosynthetic pathway in an engineered microbial host offers several advantages over isolation from plants, including the targeted production of key intermediate molecules, rapid biomass accumulation, ease of purification, and the availability of genetic tools for strain engineering and pathway optimization.
\r\n\r\nHere we describe the development of a synthetic BIA pathway in an engineered yeast host which incorporates heterologous enzymes from a variety of organisms. The BIA backbone is derived from two molecules of tyrosine and is assembled through a heterologous pathway comprising enzymatic activities from plants, bacteria, and humans. Simultaneous efforts have focused on the downstream portion of this pathway to convert a commercially available substrate to the major branch point intermediate reticuline. By synthesizing both stereoisomers of reticuline from a racemic substrate, we have demonstrated production of BIA metabolites along the diversified sanguinarine/berberine and morphinan branches. Further optimization, scale-up, and a combination of bioconversions and chemical synthesis will potentially revolutionize drug discovery and manufacturing of these compounds.
\r\n" }, { "name": "Hsu, Carey Frank", "degree": "PhD", "year": "2009", "title": "Completion of a Programmable DNA-Binding Small Molecule Library", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11032008-191338", "creators": [ { "name": { "family": "Hsu", "given": "Carey Frank" }, "id": "Hsu-Carey- Frank", "display_name": "Hsu, Carey Frank" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PG0R-3X44", "abstract": "Hairpin pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. These cell-permeable small molecules have been shown to enter the nuclei of live cells and downregulate endogenous gene expression. We complete here a library of 27 hairpin Py-Im polyamides that bind 7-base-pair sequences of the general form 5\u2019-WWGNNNW-3\u2019 (where W = A or T, N = W, G, or C). A table of binding affinities and sequence contexts for this completed 27-member library has been assembled for the benefit of the chemical biology community interested in molecular control of transcription. Quantitative fluorescence-based methods have been developed to determine the nuclear concentration of polyamide-fluorescein conjugates in cell culture. Confocal laser scanning microscopy and flow cytometry techniques are utilized to plot calibration curves, from which the nuclear concentration can be interpolated. Although confocal microscopy and flow cytometry generate disparate values, taken together these experiments suggest that the polyamide concentration inside the cell nucleus is lower than it is outside the cell. To further our understanding of C-terminal tail linkage effects on sequence specificity, the equilibrium association constants of hairpin polyamide conjugates were measured by quantitative DNase I footprint titration experiments. These results indicate that linkers and functional R groups on the tails of hairpin polyamide conjugates have recognition properties that should be considered in the design of these molecules to target DNA binding sites. Furthermore, these \u03b2-alanine-C\u2083-linked polyamide conjugates are shown to decrease hypoxia-inducible transcription of vascular endothelial growth factor (VEGF) in cultured HeLa cells. In addition, polyamide conjugates designed to target the Oct4 octamer DNA element modulate the expression levels of Oct4-driven genes in P19 mouse embryonal carcinoma cells and R1 mouse embryonic stem (ES) cells.\r\n" }, { "name": "Jacobs, Claire Sigrid", "degree": "PhD", "year": "2009", "title": "Structural Modifications to DNA-Binding Polyamides for Improved Biological Activity in Cell Culture", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272009-161836", "creators": [ { "name": { "family": "Jacobs", "given": "Claire Sigrid" }, "id": "Jacobs-Claire-Sigrid", "display_name": "Jacobs, Claire Sigrid" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HMMN-YW83", "abstract": "Polyamides are a class of synthetic small molecules that recognize DNA in a sequence-specific fashion through a network of hydrogen bonds formed with bonding partners in the floor of the minor groove. The binding affinity of polyamides is comparable to that of numerous DNA-binding proteins, and polyamides have been shown to displace DNA-binding proteins. As such, they present a powerful opportunity to modulate expression levels of genes vital to human health. The cellular permeability and biological activity of polyamides has presented an impediment in moving from in vitro to in vivo work that was partially removed by the discovery that fluorescein dyes facilitate cell entry. The work described here details recent advances in modifications to the C-terminal polyamide linker, linkage and tail groups that improve the endogenous inducible gene regulation activity of polyamides in cell culture.\r\n" }, { "name": "Keeffe, Jennifer Rae", "degree": "PhD", "year": "2009", "title": "Engineering Cyanovirin-N for Enhanced Viral Neutralization", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12232008-110031", "creators": [ { "name": { "family": "Keeffe", "given": "Jennifer Rae" }, "id": "Keeffe-Jennifer-Rae", "orcid": "0000-0002-5317-6398", "display_name": "Keeffe, Jennifer Rae" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/QSJH-5X56", "abstract": "Cyanovirin-N (CVN) is an 11-kDa lectin originally isolated from the cyanobacterium Nostoc ellipsosporum during a high-throughput screen for novel anti-HIV activities. In addition to having anti-HIV activity, CVN has since been shown to neutralize a number of other enveloped viruses including influenza and Ebola. This antiviral activity is attributed to two homologous carbohydrate binding sites that specifically bind \u03b1(1-2)-linked oligomannose glycosylation sites present on many envelope glycoproteins. Because of its broad ability to neutralize enveloped viruses, CVN is a promising target as a potential therapeutic or prophylactic.
\r\n\r\nIn this work, we oligomerized CVN to determine whether an increase in the number of carbohydrate binding sites has an effect on its viral neutralization activity. To create obligate dimers, we covalently linked multiple copies of CVN through flexible polypeptide linkers. Using HIV-1 as our viral system, we found that a tandem repeat of two CVN molecules (CVN\u2082) increased the efficacy of HIV-1 neutralization by up to 10-fold. An additional benefit was not seen when CVN was trimerized. We also show here that CVN and the CVN\u2082 variants show extensive cross-clade reactivity and higher neutralization efficacy than the most broadly reactive neutralizing antibodies. To determine whether any major structural changes or differences in domain swapping occurred because of the linkage, we solved the crystal structures of three dimeric variants and showed that all variants are intramolecularly domain-swapped.
\r\n\r\nAdditionally, we present in this thesis a novel CVN-Fc chimera, a \"lectibody,\" which shows antiviral activity similar to wild-type CVN. This variant is dimerized through the Fc region of an antibody and has the additional benefit of incorporating Fc-mediated effector functions, which may be therapeutically advantageous. Initial results on the lectibody indicate that domain swapping of CVN has an integral role in the antiviral function as well as in the overall folding and stability of the molecule. Future work on this variant to assay the effector functions as well as create a monodispersive, stable variant are underway.
\r\n\r\nAlthough CVN is already a promising candidate for antiviral therapeutics, we show here that engineering CVN to add additional functionalities or creating variants with an increased number of active sites can significantly enhance the potential benefit of these molecules.
" }, { "name": "Kekenes-Huskey, Peter Michael", "degree": "PhD", "year": "2009", "title": "A Monte Carlo-Based Torsion Construction Algorithm for Ligand Design", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-131419", "creators": [ { "name": { "family": "Kekenes-Huskey", "given": "Peter Michael" }, "id": "Kekenes-Huskey-Peter-Michael", "orcid": "0000-0001-7286-3022", "display_name": "Kekenes-Huskey, Peter Michael" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/A1MQ-3116", "abstract": "A wealth of computational strategies [1,2,3,4,] is available for predicting the binding site and affinities of a putative ligand inside a target receptor. Although numerous techniques focus on the orientation of ligands or fragments thereof, few methods have delved into improving the accuracy of generating reliable ligand conformations within predicted binding modes. In an effort to comprehensively sample the torsion space available to a flexible ligand and focus on low-energy conformations, a recursive, Metropolis Monte Carlo (MC)-based rotamer design protocol has been developed. This approach recursively samples adjacent rotatable bonds from a defined anchor and directs the search along low-energy pathways, such that high-affinity conformations of the ligand can be identified. Furthermore, this program applies spatial constraints within the search that restrict the solutions to structurally dissimilar conformations, thus encouraging a diverse solution set. The performance of moleculeGL has been evaluated for a set of 55 co-crystals, for which the number of rotatable bonds ranged from 2 to 32. Approximately 80 percent of the structures are predicted within 2.0 A2 root mean square deviations (RMSD) with respect to the crystal structure, starting from an arbitrary ligand conformation. This level of accuracy suggests the program's applicability to the design of pharmacaphore substituents, for which the position of a chemically active pharmacaphore is well-known." }, { "name": "Kim, Hyungjun", "degree": "PhD", "year": "2009", "title": "Multiscale and Multiphysics Computational Frameworks for Nano- and Bio-Systems", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212009-221851", "creators": [ { "name": { "family": "Kim", "given": "Hyungjun" }, "id": "Kim-Hyungjun", "orcid": "0000-0001-8261-9381", "display_name": "Kim, Hyungjun" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0PFF-R531", "abstract": "Multiscale and multiphysics simulation strategy is important to investigate complex problems in nature because it provides a systematic method to understand underpinning physics of the systems depending on the size. In this thesis, we discuss how such multiscale and multiphysics simulation framework can explain and rationalize the experimental observations in several nano- and biosystems. Furthermore, we exhibit the computational simulation methods that play major roles to rationally design novel materials with desired properties in next generation nano electronic devices, alternative energy materials, life science, and so on.
\r\n\r\nChapter 1 reviews the significance of multiscale and multiphysics simulation strategy. In this chapter, we briefly discuss the multiscale and multiphysics natures in nano- and bio-systems, and detailed examples are contained in the next chapters. Chapter 2 introduces an electric field induced conformational change mechanism, which is responsible for the unique current-voltage (I-V) behavior of nano device, negative differential resistance (NDR). In Chapter 3, the on/off kinetics of the Stoddart-Heath rotaxane-based programmable molecular electronic switch is discussed in terms of the free energy quantities. Chapter 4 explores sodium diffusion through the aluminum-doped zeolite BEA system, and the effect of water uptake amount is thoroughly discussed. This has importance for the application of zeolite to proton exchange membranes for fuel cells (PEMFC). In Chapters 5 and 6, the ion mobilities of tertiary and quaternary ammonium cations (precursors for lipids), and phosphatidylcholine (PC) lipid cations are investigated, respectively. In order to compute the ion mobilities of the precursors and entire lipids, we develop a modified trajectory (TJ) method dealing with the complicated integrals of interaction terms. QM and MD simulations are performed to determine the structures and charge distributions. In Chapter 7, we study how the model lung system of lipid monolayer with surfactant protein B (SP-B) responds to ozone introduction. In parallel with the field induced droplet ionization (FIDI) mass spectrometry study, MD simulations identify the distinct ozone reaction mechanism at the interface, and the role of SP-B at the pulmonary surfactant (PS) system on the oxidative stresses.
\r\n\r\nFrom these studies, we suggest various multiscale and multiphysics modeling approaches depending on the characteristics of systems and objectives. These efforts allow us to overcome the limited time- and length-scales of the monoscale simulations. In addition, we expect that an establishment of such multiscale modeling procedures will invoke interdisciplinary studies by tightly combining the developments occurring independently across fields.
\r\n" }, { "name": "Knowles, Robert Randolph", "degree": "PhD", "year": "2009", "title": "Asymmetric Organocatalysis in Complex Target Synthesis: Progress Towards the Total Synthesis of Diazonamide A", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10282008-080437", "creators": [ { "name": { "family": "Knowles", "given": "Robert Randolph" }, "id": "Knowles-Robert-Randolph", "display_name": "Knowles, Robert Randolph" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/40HC-7C37", "abstract": "Progress towards the total synthesis of the marine natural product diazonamide A is described. The synthesis was conceived around an iminium-catalyzed alkylation/cyclization cascade that stereoselectively installs the central C(10) quaternary carbon stereocenter and the complete furanoindoline core of the natural product in an asymmetric, organocatalytic manner. The manner in which this idea was brought to bear is illustrated, with the remainder of the work focused on devising and executing strategies toward the synthesis of the two twelve-membered macrocycles of the target structure. Considerable efforts were made in this regard, and highlights include execution of a Witkop photo-annulation, development of a novel and highly selective magnesium-mediated macroaldolization reaction to close a thirteen-membered ring, a Suzuki biaryl macrocyclization, an unusual oxidative ring contraction, and the development of a new DAST-mediated method for the synthesis of 4-acyl oxazoles. Five distinct approaches towards the endgame of the synthesis are described. In all cases these approaches came only a single synthetic operation from the assured completion of the natural product, but none proved ultimately viable.
\r\n\r\nAlso described is work focused on replacing a late-stage auxiliary-based aldol reaction in a previously completed MacMillan group synthesis of the macrolide antibiotic erythronolide B, with a substrate-controlled, diastereoselective variant. The overarching synthetic strategy and forward synthesis will be described along with a detailed discussion of the aforementioned, late stage aldol reaction to install the C(1)-C(2) portion of the seco acid.
\r\n" }, { "name": "Leigh, Brian Scott", "degree": "PhD", "year": "2009", "title": "Electron Transfer Through Organic and Biological Molecules", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08042008-115533", "creators": [ { "name": { "family": "Leigh", "given": "Brian Scott" }, "id": "Leigh-Brian-Scott", "display_name": "Leigh, Brian Scott" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EYKS-R134", "abstract": "The function of solvent in facilitating long-range coupling in donor/bridge/acceptor complexes is not well understood. There are exceptional challenges inherent to the measurement of the electron transfer coupling properties of solvents. By immobilizing the donor and acceptor in a glass to eliminate the effects of diffusion, statistical methods of analysis can be employed to study electron transfer between randomly dispersed donor and acceptor molecules over long distances. Toluene and 2-methyltetrahydrofuran form glasses that can solubilize donor and acceptor molecules at 77 K. Exponential decay constant of 1.23 per angstrom, for electron tunneling through a frozen toluene glass, and 1.62 per angstrom through 2-methyltetrahydrofuran glass have been found. Identification of the electronic coupling sites on the surfaces of proteins is usually achieved by inspection of a crystal structure. These coupling spots have been experimentally observed by employing mixed self-assembled monolayer electrodes and a variety of mutants. The electron transport protein azurin has a well defined reduction potential on self-assembled monolayer electrodes (0.16 V vs. saturated Ag/AgCl). When a point mutation is made at position 48, electron transfer ceases. This disruption of electron transfer occurs because the mutation forces conformational changes that disrupt a critical hydrogen bond between asparagine-47 and cysteine-112. This hydrogen bond is a key element for electron transfer into and out of the protein. " }, { "name": "Lin, Alexander Pei-Den Peter", "degree": "PhD", "year": "2009", "title": "Noninvasive Imaging of Carotid Arterial Strain Using Displacement-Encoded MRI", "advisor": "Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072009-232351", "creators": [ { "name": { "family": "Lin", "given": "Alexander Pei-Den Peter" }, "id": "Lin-Alexander-Pei-Den-Peter", "display_name": "Lin, Alexander Pei-Den Peter" } ], "advisors": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "chair", "display_name": "Gharib, Morteza" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." }, { "name": { "family": "Tyszka", "given": "Julian Michael" }, "id": "Tyszka-J-M", "role": "member", "display_name": "Tyszka, Julian Michael" }, { "name": { "family": "Wen", "given": "Han" }, "id": "Wen-Han", "role": "member", "display_name": "Wen, Han" } ], "option_major": [ "biochem" ], "doi": "10.7907/Q7NT-XN05", "abstract": "Stroke is the leading cause of disability in the United States and the third leading cause of death. These \u201cbrain attacks\u201d occur when atherosclerosis, the progressive process of thickening and hardening of arterial walls, develops in the carotid arteries, leading to stenosis or thrombosis that cuts off the vital supply of blood and oxygen to the brain. These atherosclerotic plaques have been shown to form in regions of excessive stretching or strain. Furthermore, intravenous ultrasound studies (IVUS) have demonstrated that strain plays a role in determining those plaques most likely to rupture, the so-called vulnerable plaques. However, IVUS is an invasive technique that poses risks for patients and requires specialized methods that are not readily available in most hospitals. Therefore, the objective of this thesis is to develop a noninvasive method of measuring strain in the carotid artery that may provide an early diagnosis of stroke.
\r\n\r\nMagnetic resonance imaging (MRI) is a powerful noninvasive method of imaging the human body. An MRI technique called displacement encoding with stimulated echoes, or DENSE-MRI, has been shown to accurately measure strain in the human heart. This thesis describes the adaptation of the DENSE-MRI technique to the carotid arteries, validation and optimization of the DENSE-MRI pulse sequence, and in vivo strain measurements in human subjects. The results show the successful adaptation of this method in the carotid arteries and that strain measurements are accurate, reproducible, and robust. In particular, utilization of a single-shot pulse sequence effectively removes flow-sensitive artifacts that permit strain mapping at the bifurcation and in the internal and external carotid arteries, areas where plaque is most likely to form. Furthermore, it is shown that strain changes with age and may be a more sensitive diagnostic measure as patients with atherosclerosis show significantly lower strain values.
\r\n\r\nThe primary contributions of this thesis are the achievement of quantitative measurements of strain in the carotid arteries and the development of a robust method of measuring strain in atherosclerosis that may facilitate the early diagnosis of stroke so that treatment can be provided before the devastating effects of the disease can take their course.
\r\n" }, { "name": "Lin, Bo-Lin", "degree": "PhD", "year": "2009", "title": "A Combined Experimental and Computational Study of Ligand Effects on C-H Bond Activation by Palladium and Platinum Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04022009-144521", "creators": [ { "name": { "family": "Lin", "given": "Bo-Lin" }, "id": "Lin-Bo-Lin", "display_name": "Lin, Bo-Lin" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PD2Z-QZ56", "abstract": "Abnormally large kinetic hydrogen/deuterium isotope effects (KIEs, ~ 20) are measured for the protonolysis of several dimethylpalladium(II) complexes with various bidentate ligands by trifluoroethanol (TFE) at room temperature. Analyses of semiclassical KIE theory suggest that the occurrence of hydrogen tunneling needs to be invoked in order to explain these KIE values, which is further supported by the KIE-temperature-dependence study for the protonolysis of (dppe)Pd(CH\u2083)\u2082 by CF\u2083CD\u2082OD/CF\u2083CH\u2082OH.
\r\n\r\nDensity functional theory (DFT) computation suggests that protonation at the MII-C bond is kinetically preferred over protonation at the metal center for the protonolysis of (COD)Pt(CH\u2083)\u2082 by TFA and the dimethylpalladium(II) complexes by TFE in dichloroethane. The computation further indicates the significant contribution of hydrogen tunneling in the abnormally large KIEs observed experimentally.
\r\n\r\nThe monomethylpalladium(II) complex, (COD)Pd(CH\u2083)Cl (COD = 1,5-cyclooctadiene), undergoes both benzene C-H activation and migratory insertion of olefin, with the former faster than the latter, at room temperature under the assistance of an anionic \u03b2-diketiminate ligand, to yield \u03b7\u00b3-(2-R-cyclooctenyl)palladium(II) \u03b2-diketiminate (R = methyl or phenyl).
\r\n\r\nDFT computation result suggests that bisindolide-type ligands and carbenearyl-type ligands are likely to lead to faster benzene C-H bond activation as well as lower relative VIII barrier heights of the C-H bond activation versus the insertion of olefins than those in monomethyl palladium(II) with \u03b2-diketiminate.
\r\n\r\nSeveral pyridine-like ligands were found to improve Pd(OAc)\u2082-catalyzed allylic oxidation of allylbenzene to cinnamyl acetate by p-benzoquinone in acetic acid. The best ligand examined, bipyrimidine, was used to identify the catalyst precursor for this system, (bipyrimidine)Pd(OAc)\u2082, which was fully characterized. Mechanistic studies suggest the reaction takes place through disproportionation of (bipyrimidine)Pd(OAc)\u2082 to form a bipyrimidine-bridged dimer, which reacts with olefin to form a PdII-olefin adduct, followed by allylic C-H activation to produce (\u03b7\u00b3-allyl)PdII species. The (\u03b7\u00b3-allyl)PdII intermediate undergoes a reversible acetate attack to generate a Pd\u2070-(allyl acetate) adduct, which subsequently reacts with p-benzoquinone to release allyl acetate and regenerate (bipyrimidine)Pd(OAc)\u2082. No KIE is observed for the competition experiment between allylbenzene-d\u2080 and allylbenzene-d\u2085(CD\u2082=CD-CD\u2082-C\u2086H\u2085), suggesting that allylic C-H activation is not rate determining. Catalytic allylic acetoxylations of other terminal olefins as well as cyclohexene were also effected by (bipyrimidine)Pd(OAc)\u2082.
\r\n" }, { "name": "Maiolo, James Reynold, III", "degree": "PhD", "year": "2009", "title": "Photoelectrochemistry of Microstructured Silicon Materials for Solar Energy Applications", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-05142009-130434", "creators": [ { "name": { "family": "Maiolo", "given": "James Reynold, III" }, "id": "Maiolo-James-Reynold", "display_name": "Maiolo, James Reynold, III" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1WDR-M120", "abstract": "In the face of mounting evidence that CO2 emissions from the burning of fossil fuels is a key contributor to anthropogenic global climate change, the search for a carbon-neutral energy source that is scalable and economically viable has become a key research target. Orthogonalization of the directions of light absorption and charge carrier collection in solar cell absorber materials, as in arrays of wires with radial junctions, has the potential to enable the use of low-purity and low-cost materials in efficient solar cells. This work focuses on the use of structured silicon materials as the absorber in semiconductor/liquid junction photoelectrochemical cells in order to verify the potential of structured materials to enable efficient and inexpensive solar cells.\r\n\r\nMacroporous Si was used as a physical model system for wire-array solar cells. Using high-purity starting materials, it was found that increasing the surface area by porous etching did not dramatically lower the observed energy conversion efficiency, and efficiencies in excess of 10% were observed even for the longest pores studied. The open-circuit voltage (V[subscript oc]) was lowered in samples with long pores, however, verifying the principle that a reduction in V[subscript oc] is expected with increased junction area due to a decreased flux of minority carriers through the junction. This will be an important design principle for building structured solar cells. In addition, diffusion of Au impurities into macroporous Si was used to explore the effect of employing a structured junction in poor quality materials.\r\n\r\nWire array solar cells produced by chemical vapor deposition were also measured in liquid junction cells. Initial studies showed significant photocurrent and photovoltage over the control substrate. Improved arrays having longer wires showed significantly higher photocurrents, giving energy conversion efficiencies as high as 1.5% in the liquid junction cell, and it has been shown that the photoelectrochemical properties of the wire array samples are due to the CVD-grown wires rather than the silicon substrate used. These results are an important first step toward understanding and building efficient, low-cost solar cells using structured materials.\r\n" }, { "name": "Maskarinec, Stacey Ann", "degree": "PhD", "year": "2009", "title": "Engineering Protein-Based Biomaterials with Biological and Mechanical Cues to Direct Cellular Behavior", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102009-170632", "creators": [ { "name": { "family": "Maskarinec", "given": "Stacey Ann" }, "id": "Maskarinec-Stacey-Ann", "display_name": "Maskarinec, Stacey Ann" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "role": "member", "display_name": "Ravichandran, Guruswami" } ], "option_major": [ "chemistry" ], "doi": "10.7907/751E-J376", "abstract": "Biomaterials play critical roles in tissue engineering, reconstructive surgery, and regenerative medicine. Constructing biomaterials through protein engineering offers a unique and powerful solution to the challenges posed by the creation of well-defined, multi-functional materials that must provide structural support, as well as guide cell and tissue behavior. This thesis describes the construction, characterization, and application of protein-based biomaterials composed of photoreactive artificial extracellular matrix (aECM) proteins. These proteins consist of mechanical and biological motifs derived from natural proteins: an elastin-like backbone containing a photocrosslinking site dictates the mechanical properties of the material, and an RGD binding domain from fibronectin mediates cell attachment. aECM proteins were assembled at the genetic level and expressed in a bacterial host. Manipulation of an aminoacyl-tRNA synthetase of the expression strain permitted the incorporation of the photoreactive noncanonical amino acid, para-azidophenylalanine (pN3Phe), within the elastin subunit of the protein.
\r\n\r\nAn evaluation of the mechanical and biological properties of photoreactive aECM proteins has been performed. Nanoindentation experiments using atomic force microscopy (AFM) demonstrated that the elastic moduli of photocrosslinked protein films lie within the range of native elastins and that the mechanical properties of films can be tuned by altering the incorporation of pN3Phe in the protein or adjusting the irradiation dosage. Cell spreading experiments showed that cell attachment to protein films is sequence-specific to the presence of the RGD cell-binding domain. Patterning of protein films using standard photolithography methods allowed for the generation of cellular arrays.
\r\n\r\nA molecular characterization of cellular response to engineered aECM proteins has been initiated using mRNA microarrays and the proteomic technique, BONCAT (bio-orthogonal noncanonical amino acid tagging). These methods provide information regarding changes in the cellular expression of mRNA transcripts and proteins in response to the biochemical composition of protein-based materials.
\r\n\r\nCell-mediated deformation of the extracellular matrix in all three spatial dimensions was tracked and quantified using a newly developed method that combines time-lapse laser scanning confocal imaging and digital volume correlation. Analysis of the displacement profiles of migrating cells illustrates that, in addition to in-plane (x,y) forces, cells also exert significant normal (z) forces. A new \"push-pull\" aspect of cell migration was detected in the normal displacement profiles of monitored cells suggesting that cells simultaneously \"push\" and \u201cpull\u201d the underlying matrix while exploring their microenvironment.
\r\n" }, { "name": "McKeen, John Charles", "degree": "PhD", "year": "2009", "title": "Proton and Ion Conductivity in Microporous Materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272009-144416", "creators": [ { "name": { "family": "McKeen", "given": "John Charles" }, "id": "McKeen-John-Charles", "display_name": "McKeen, John Charles" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Yazami", "given": "Rachid" }, "id": "Yazami-R", "role": "member", "display_name": "Yazami, Rachid" }, { "name": { "family": "Yan", "given": "Yushan" }, "id": "Yan-Yushan", "role": "member", "display_name": "Yan, Yushan" } ], "option_major": [ "chemeng" ], "doi": "10.7907/N0GH-3B50", "abstract": "Two separate but related investigations on proton and ion conductivity in microporous materials are presented. In the first study, the effect of hydroxyl group density on the proton conductivity in a family of sulfonic-acid functionalized microporous materials with the *BEA framework topology is investigated. Pure silica, aryl sulfonic acid-functionalized microporous materials are synthesized with high concentration of hydroxyl groups from tetraethylammonium hydroxide and aluminum-containing gels and by post synthetic modification of zinc containing CIT-6, and they exhibit proton conductivities of ~5*10\u207b\u00b3 S/cm. Pure-silica materials with nearly defect free structures (low hydroxyl group density) are synthesized from tetraethylammonium fluoride containing gels and by post synthetic modification of CIT-6, and exhibit proton conductivities an order of magnitude lower, ~5 x 10\u207b\u2074 S/cm, than the samples with a high \u2013OH density. Propyl sulfonic acid, ethyl phosphoric acid, and carboxylic acid containing pure-silica zeolite beta, MCM-41, and MCM-48 are also prepared and investigated for use as solid proton conductors. Strong acids are necessary for fast proton transport in hydrated systems. The proton conductivities of the functionalized solids decrease accordingly with the strength of the organic acids in solutions, and little difference is observed between microporous and mesoporous solids when functionalized to the same level.
\r\n\r\nIn the second study, the ion conducting properties of the microporous, zincosilicate VPI-9 (Si/Zn = 4.0) containing the alkali cations Li\u207a, Na\u207a, K\u207a, Rb\u207a, and Cs\u207a, and the alkaline earth cations Mg\u00b2\u207a, Ca\u00b2\u207a, and Sr\u00b2\u207a are studied using impedance spectroscopy. Monovalent cation exchanged samples Li- and Na-VPI-9 lose X-ray crystallinity upon vacuum dehydration at 450 \u00b0C, while K-, Rb-, and Cs-VPI-9 remain crystalline and exhibit conductivities of 1.7 x 10\u207b\u2074, 3.5 x 10\u207b\u2074, and 4.9 x 10\u2074 S/cm, respectively, at 450 \u00b0C in vacuum. While K-VPI-9 is less conductive than K-X, Rb- and Cs-VPI-9 are more conductive than corresponding zeolite X samples. Divalent cation exchanged sample Mg-VPI-9 also loses X-ray crystallinity, while Ca-, and Sr-VPI-9 remain crystalline and exhibit conductivities of 2.3 x 10\u207b\u2076 S/cm and 7.7 x 10\u2077 S/cm, respectively, at 450 \u00b0C, greatly exceeding the conductivity of correspondingly divalent exchanged zeolite X materials. Dense, crystalline zincosilicate samples with the compositions K\u2082ZnSixO\u2082(x=1) (x = 2 - 5), Rb\u2082ZnSi\u2085O\u2081\u2082, and Cs\u2082ZnSi\u2085O\u2081\u2082 are also prepared and exhibit much lower conductivities than their microporous counterparts.
\r\n" }, { "name": "Murphy, Shane Michael", "degree": "PhD", "year": "2009", "title": "Analysis of the Chemical Composition of Atmospheric and Chamber Generated Aerosol Using Mass Spectrometry", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-113717", "creators": [ { "name": { "family": "Murphy", "given": "Shane Michael" }, "id": "Murphy-Shane-Michael", "orcid": "0000-0002-6415-2607", "display_name": "Murphy, Shane Michael" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6B9K-AT89", "abstract": "This thesis presents results demonstrating the use of particulate composition measurements to determine the mechanisms of aerosol formation in both chamber and field studies. Aerosol composition measurements are also used to theoretically estimate the water-uptake behavior and ability to nucleate cloud droplets of atmospheric aerosol; these estimates are compared with in-situ airborne measurements. Common to all studies presented is the use of online aerosol mass spectrometry, a technique with high time resolution and minimal artifacts.
\r\n\r\nChemical mechanisms involved in particle formation from the photooxidation of isoprene were explored in chamber studies using both online and offline mass spectrometry. The yield of aerosol and the nature of oliogmers formed was found to depend on the NOx concentration. Peroxides were found to be important under low-NOx conditions while under high-NOx conditions the majority of the particulate mass was found to derive from reaction products of methacrolein.
\r\n\r\nParticle formation from photooxidation of aliphatic amines was shown to be a feasible route of secondary organic aerosol formation in the atmosphere. Chamber studies at low relative humidity demonstrated that particle formation is primarily the result of acid-base reactions between amines and nitric or sulfuric acid, though diverse oxidized organic compounds are also formed. Thermodynamic calculations show that certain amines can compete with ammonia to form aminium salts at atmospherically relevant concentrations. An airborne field study near a major bovine source in the San Joaquin Valley, CA gave evidence of particulate amine formation in the atmosphere.
\r\n\r\nThe composition of particulate emissions from ships was studied during a joint shipboard and airborne field project in the Eastern Pacific. Particulate emissions were found to contain significantly higher levels of organic material than accounted for in current inventories. Observed hydrophobic organic material is concentrated in smaller particles and acts to suppress hygroscopic growth and activity of ship-exhaust particles as cloud condensation nuclei.
\r\n\r\nOngoing research involves quantifying the impact of reactions within cloud droplets on the organic composition of aerosols. A recently completed field campaign investigated the role of particle chemistry in determining if aerosols can act as ice crystal nuclei.
\r\n" }, { "name": "Murrey, Heather Elizabeth", "degree": "PhD", "year": "2009", "title": "Identification and Characterization of the Plasticity-Relevant Fucose-\u03b1(1-2) Galactose Glycoproteome from Mouse Brain", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12182008-145714", "creators": [ { "name": { "family": "Murrey", "given": "Heather Elizabeth" }, "id": "Murrey-Heather-Elizabeth", "display_name": "Murrey, Heather Elizabeth" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." } ], "option_major": [ "biochem" ], "doi": "10.7907/QG38-9P18", "abstract": "Fuc\u03b1(1-2)Gal carbohydrates have been implicated in cognitive processes such as learning and memory. However, a molecular level understanding of their functions has been lacking. This thesis describes multiple chemical and biological approaches that we have undertaken to elucidate the molecular mechanisms by which fucosyl sugars mediate neuronal communication. We demonstrate that Fuc\u03b1(1-2)Gal carbohydrates play an important role in the regulation of synaptic proteins and neuronal morphology. We identify synapsins Ia and Ib as prominent Fuc\u03b1(1-2)Gal glycoproteins in rat hippocampus, and fucosylation protects synapsin I from proteolytic degradation by the calcium-activated protease calpain. Synapsin fucosylation has important consequences on neuronal growth and morphology, with defucosylation leading to stunted neurites and delayed synapse formation. In addition, we identify the Fuc\u03b1(1-2)Gal proteome from mouse olfactory bulb using lectin affinity chromatography. We discover four major classes of Fuc\u03b1(1-2)Gal glycoproteins, including the immunoglobulin superfamily of cell adhesion molecules, ion channels and solute carriers/transporters, ATP-binding proteins, and synaptic vesicle-associated proteins. Protein fucosylation is regulated by FUT1 in mouse olfactory bulb, and olfactory bulb development is impaired in FUT1-deficient mice. In particular, FUT1 KO animals exhibit defects in the olfactory nerve and glomerular layers of olfactory sensory neurons expressing the fucosylated cell adhesion molecules NCAM and OCAM. Lastly, we explore the molecular mechanisms of protein fucosylation by metabolic labeling with alkynyl- and azido-fucose derivatives. We demonstrate that fucosylated glycoconjugates are present along both axons and dendrites of developing neuronal cultures, as well as in the Golgi body. We identify the fucosylated proteome from cultured cortical neurons, and demonstrate that proteins such as NCAM, the MARCKS family of proteins, and the inositol 1,4,5 triphosphate receptor are fucosylated. In addition, we can label fucosylated glycans in vivo, which will have important consequences for studies on the dynamics of protein fucosylation in living animals. Cumulatively, our studies suggest important functional roles for fucosyl-carbohydrates in the nervous system, and implicate an extended role for fucose in the molecular mechanisms that may underlie synaptic plasticity and neuronal development.\r\n" }, { "name": "Papadantonakis, Kimberly Marshall", "degree": "PhD", "year": "2009", "title": "Exploration of Physisorbed Monolayers for Molecular-Scale Surface Patterning", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-07222008-144633", "creators": [ { "name": { "family": "Papadantonakis", "given": "Kimberly Marshall" }, "id": "Papadantonakis-Kimberly-Marshall", "orcid": "0000-0002-9900-5500", "display_name": "Papadantonakis, Kimberly Marshall" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Brunschwig", "given": "Bruce S." }, "id": "Brunschwig-B-S", "role": "member", "display_name": "Brunschwig, Bruce S." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JZCK-B721", "abstract": "Many simple organic molecules, such as straight-chain alkanes and simple aromatics, spontaneously assemble into highly ordered monolayers at solid\u2013liquid interfaces. These monolayers are composed of molecules that lie flat at the interface without forming chemical bonds to the surface of the solid. These monolayer structures are highly ordered and produce patterns with features on the scale of just a single nanometer in length. The exploitation of this physisorption phenomenon may provide a promising route toward an inexpensive nanometer-scale surface patterning technique. However, two fundamental challenges must be overcome before physisorbed monolayers can be useful in surface-patterning applications: (1) absence of control over the particular pattern formed by the molecules; and (2) pattern impermanence.
\r\n\r\nThis document opens with an introductory chapter that contains background on physisorbed monolayers and a brief description of scanning tunneling microscopy, the experimental technique which is commonly used to study monolayers. The second and third chapters present details on the results of experiments with a monolayer templating technique. This templating technique involves replacement of the molecules comprising a monolayer of either normal alkanes or symmetrical thioethers by symmetrical ethers. The ethers are forced to conform to the structure of the existing template monolayer, which differs from the structure of an ether monolayer formed in the absence of the template. The monolayer templating technique offers researchers a limited method for exercising control over the surface patterns formed by particular molecules.
\r\n\r\nThe challenge of pattern impermanence is addressed in the fourth chapter of this document. The molecules comprising physisorbed monolayers are free to exchange with molecules in the solution contacting the surface, thus the orientation of the monolayer structure within a particular surface region can change with time. A technique analogous to traditional lithographic methods that may allow physisorbed monolayers to be used for permanent surface patterning is described. The technique would employ physisorbed monolayers as surface masks while other molecular species chemically bond to regions of the surface left uncovered by the masking monolayer. Descriptions of the progress made toward the development of the patterning technique, and of the substantial challenges encountered during efforts to develop such a patterning method close the chapter.
\r\n" }, { "name": "Privett, Heidi Kathleen", "degree": "PhD", "year": "2009", "title": "An Iterative Approach to de novo Computational Enzyme Design and the Successful Application to the Kemp Elimination", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272009-091024", "creators": [ { "name": { "family": "Privett", "given": "Heidi Kathleen" }, "id": "Privett-Heidi-Kathleen", "display_name": "Privett, Heidi Kathleen" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1402-XZ32", "abstract": "The development of reliable methods for the 'on demand\" de novo design of an enzymatic catalyst for an arbitrary chemical reaction has been an elusive goal of the computational protein design community. Recent successful results of de novo computational enzyme design have been encouraging, but the activity of the enzymes produced so far is still well below that of natural enzymes and the generalizability of these methods has yet to be established.
\r\n\r\nPresented in this thesis are methods that we have developed for the computational design of enzyme active sites as well as results from the evaluation of these methods through a test case, the Kemp elimination. Initial Kemp elimination designs were shown to be inactive. However, in the course of refining these design procedures, we carried out extensive theoretical and experimental evaluation of several of these inactive designs, which allowed us to identify the causes of the inactivity and led to adjustments of our design procedure. These modified methods were then successfully used to design four distinct enzymes for this reaction in three inert scaffolds including the scaffold that housed the previously inactive designs. In addition, we demonstrate that molecular dynamics simulations can accurately predict the activity of designed Kemp elimination enzymes and can be used as a reliable prescreening step, allowing us to focus our experimental efforts on designs that are most likely to be active.
\r\n\r\nThe work presented here demonstrates that the cyclic evaluation and redesign of both active and inactive enzymes was instrumental in the identification and resolution of deficiencies in our computational methods and directly resulted in de novo designed enzymes with novel and increased activity.
\r\n" }, { "name": "Puckett, James William", "degree": "PhD", "year": "2009", "title": "Microarray and Genome-wide Sequencing Approaches to Characterizing DNA Binding Molecules", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282009-145527", "creators": [ { "name": { "family": "Puckett", "given": "James William" }, "id": "Puckett-James-William", "display_name": "Puckett, James William" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E3NT-SC46", "abstract": "Hairpin and linear beta-alanine linked pyrrole-imidazole (Py-Im) polyamides are programmable oligomers that bind the DNA minor groove sequence-specifically with affinities comparable to those of DNA-binding proteins found in nature. These small molecules have been observed to localize within the nucleus of living cells and modulate endogenous gene expression. Herein, we demonstrate the utility of a linear beta-alanine linked pyrrole-imidazole polyamide to upregulate frataxin mRNA and protein expression in a cell line derived from a Friedreich\u2019s Ataxia patient. We examine the binding affinities and specificities of additional linear beta-alanine linked polyamides. We examine binding specificities of a Cy3-fluorescently labeled version of the frataxin\u00ad expression modulating-polyamide and a Cy3-labeled polyamide known to downregulate expression of the Vascular Endothelial Growth Factor using DNA microarrays composed of hairpins harboring all 524,800 unique 10 bp DNA sequences. We experimentally verify the correlation of Cy3 fluorescence intensity with quantitative DNase I footprint derived binding affinities. We find that Cy3 dye placement on the polyamide tail versus labeling of an internal pyrrole does not significantly alter DNA specificity. Finally, we examine the genome-wide binding preferences of Androgen Receptor (AR) in LNCaP cells using ChIP-Seq (chromatin immunoprecipitation followed by high-throughput DNA sequencing). We observe the canonical ARE motif to be present in a majority of the immunoprecipitated binding regions. We observe a secondary sequence motif that may be the dimerization of AR with a forkhead protein, an interaction known in the literature but without a defined sequence motif. We also define AR occupancy with respect to location in and about known genes. We correlate gene expression profiles from mRNA microarray data with the ChIP-Seq data." }, { "name": "Rodriguez, Erik Ali", "degree": "PhD", "year": "2009", "title": "In Vivo Incorporation of Multiple Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01122009-153110", "creators": [ { "name": { "family": "Rodriguez", "given": "Erik Ali" }, "id": "Rodriguez-Erik-Ali", "orcid": "0000-0001-9143-2535", "display_name": "Rodriguez, Erik Ali" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9H38-9661", "abstract": "Unnatural amino acid (UAA) incorporation is an invaluable technique that is seeing increased use. THG73 is an amber suppressor tRNA used to incorporate > 100 residues at the UAG, amber stop codon, in Xenopus oocytes. We have found that yeast Phe frameshift suppressors (YFFS) can incorporate UAAs at the CGGG and GGGU quadruplet codons in vitro and in vivo, allowing simultaneous incorporation of three UAAs in the nicotinic acetylcholine receptor (nAChR). The YFFS are more \u201corthogonal\u201d than the amber suppressor tRNA, THG73, but the frameshift suppressors incorporate UAAs less efficiently than THG73. A library of tRNAs derived from THG73 has produced an amber suppressor that is \u201corthogonal\u201d and suppresses similarly to THG73. An analogous opal suppressor tRNA allows incorporation of UAAs at the UGA, opal stop codon. The use of the amber, opal, CGGG, and GGGU codons should allow for the simultaneous incorporation of four UAAs in vivo. Bioorthogonal labeling of UAAs is useful for the addition of large fluorophores. We incorporated p-AcPhe at \u03b170 of the nAChR and labeled with biotin and Cy5.5 hydrazide. Biotin and Cy5.5 hydrazide consistently labeled three proteins on oocytes not expressing \u03b170p-AcPhe and isn\u2019t useful for site-specific labeling of ketone containing UAAs in oocytes. We explored the known subunit stoichiometry of the nAChR (2\u03b1:\u03b2:\u03b3:\u03b4) expressed in oocytes and detected each subunit with the HA tag by Western blot. The \u03b1-subunit is present in excess of the other subunits in a ratio of \u2248 3:1, which is expected to be 2:1. UAAs are being sold commercially for detection of protein-protein interactions in eukaryotic cells. The UAAs are heterogeneously incorporated and little is known about the effect on protein function and stability. We heterogeneously incorporated UAAs into the nAChR and detected changes in function by shifts in EC50. Many UAAs altered the function of the nAChR. Incorporation of photo-reactive UAAs allowed for detection of cross-linking by Western blot. Heterogeneously incorporated UAAs also altered the functional nAChR expression on the surface of oocytes. Site-specific and heterogeneous incorporation of multiple UAAs are useful techniques for novel experiments to explore protein function, FRET experiments, cross-linking, and protein expression." }, { "name": "Rohde, Rosemary Dyane", "degree": "PhD", "year": "2009", "title": "Developing High-Affinity Protein Capture Agents and Nanotechnology-Based Platforms for in vitro Diagnostics", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06032009-230415", "creators": [ { "name": { "family": "Rohde", "given": "Rosemary Dyane" }, "id": "Rohde-Rosemary-Dyane", "display_name": "Rohde, Rosemary Dyane" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/G70V-TC49", "abstract": "In this thesis, I describe projects that were aimed at improving ways to capture proteins for clinical diagnostics. Nanoelectronic sensors, such as silicon nanowires (SiNWs), can provide label-free quantitative measurements of protein biomarkers in real time. One technical challenge for SiNWs is to develop chemistry that can be applied for selectively encoding the nanowire surfaces with capture agents, thus making them sensors that have selectivity for specific proteins. Furthermore, because of the nature of how the sensor works, it is desirable to achieve this spatially selective chemical functionalization without having the silicon undergo oxidation. This method is described here and provides a general platform that can incorporate organic and biological molecules on Si (111) with minimal oxidation of the silicon surface.
\r\n\r\nThe development of these devices is, in part, driven by early diagnosis, treatment, monitoring, and personalized medicine\u2014 all of which are increasingly requiring quantitative, rapid, and multiparameter measurements. To begin achieving this goal, a large number of protein biomarkers need to be captured and quantitatively measured to create a diagnostic panel. One of the greatest challenges towards making protein-biomarker-based in vitro diagnostics inexpensive involves developing capture agents to detect the proteins. A major thrust of this thesis is to develop multi-valent, high-affinity and high-selectivity protein capture agents using in situ click chemistry. In situ click chemistry is a tool that utilizes the protein itself to catalyze the formation of a biligand from individual azide and alkyne ligands that are co-localized. Large one-bead one-compound (OBOC) libraries of peptides are used to form the body of these ligands, also providing high chemical diversity with minimal synthetic effort. This process can be repeated to identify a triligand, tetraligand, and so forth. Moreover, the resulting multiligand protein capture agents can be produced in gram-scale quantities with designed control over chemical and biochemical stability and water solubility. This is a general and robust method for inexpensive, high-throughput capture agent discovery that can be utilized to capture the relevant biomarker proteins for blood protein diagnostics.
\r\n" }, { "name": "Shapiro, Ian Ross McKay", "degree": "PhD", "year": "2009", "title": "Observation of Single-Molecule Rotational Diffusion at Microsecond Timescale by Polarized Fluorescence Correlation Spectroscopy", "advisor": "Collier, C. Patrick", "url": "https://resolver.caltech.edu/CaltechETD:etd-06052009-140716", "creators": [ { "name": { "family": "Shapiro", "given": "Ian Ross McKay" }, "id": "Shapiro-Ian-Ross-McKay", "display_name": "Shapiro, Ian Ross McKay" } ], "advisors": [ { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "advisor", "display_name": "Collier, C. Patrick" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "co-chair", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KVDR-9429", "abstract": "This work presents a series of experimental and numerical studies of macromolecular organic, inorganic and biological structures, in all instances focusing on the behavior characteristic of individual discrete molecular elements. Chapters 1 and 2, beginning on pages 1 and 31, respectively, describe fabrication, use and numerical analysis of of single-walled carbon nanotube probes for amplitude-modulation atomic force microscopy. These studies reach the conclusion that the molecular structure and nanoscale surface interaction potential unique to carbon nanotubes collectively give rise to atomic force microscopy imaging artifacts manifesting as apparent lateral topographic resolution signi\ufb01cantly better than that predicted by the probe and sample structures.
\r\n\r\nChapter 3 (p. 61) presents a brief review of single-molecule microscopy, describes a generalized mathematical formalism for focusing polarized visible-spectrum electromagnetic radiation, and delineates the construction of a custom two-channel scanning confocal \ufb02uorescence microscope system with single-photon detection capability for spectral- and polarization-resolved studies of individual mobile \ufb02uorophores. This Chapter includes a theory-based optical analysis of the confocal probe volume structure and photoluminescence collection efficiency from 3D-polarized single-dipole emitters. The latter analysis was aided by introducing a modi\ufb01ed Jones formalism using non-square matrix representation for polarization state changes in the speci\ufb01c context of confocal optics. Proper calculation of the expected confocal probe volume dimensions was essential for accurately interpreting experimental data in the following chapter. Additionally, the quantitative understanding that followed from analysis of 3D polarization state measurement by orthogonally polarized detection channels was critical to both the interpretation of experimental data and the numerical generation of simulated data in Chapter 5.
\r\n\r\nChapter 4 (p. 125) presents a generalized formalism for correlation analysis of the \ufb02uorescence signal collected using the two-channel microscopy system described in Chapter 3. Particular focus was directed toward the theoretical auto- and cross-correlation traces anticipated from polarization-sensitive bivariate time series of photoluminescence emission from freely-rotating transition dipoles. Chapter 4 also presents population-resolved data collected from single F\u00a8orster resonance energy transfer \ufb02uorphore pairs conjugated to DNA oligomers as they undergo cleavage by restriction endonucleases. The endonuclease enzyme Michaelis constants KM measured for EcoRI and BglI via \ufb02uorescence burst analysis were in agreement with prior literature. The success of these experiments provide concrete con\ufb01rmation of the microscope\u2019s \ufb02uorescence emission sensitivity and detection channel selectivity in the context of single-molecule experiments.
\r\n\r\nChapter 5 describes a polarized \ufb02uorescence correlation spectroscopy (PFCS) investigation of liquid phase rotational diffusion by colloidal CdSe semiconductor nanocrystals possessing two-dimensional nondegenerate photoluminescence transition dipoles, as well as red \ufb02uorescent protein (monomeric DsRed) and rhodamine-labeled phospholipids that possess more conventional one-dimensional \ufb02uorescence transition dipoles. The experimental PFCS data collected from these samples is in close agreement with simulated PFCS data produced by a Monte Carlo rotational diffusion numerical routine that incorporates the microscope 3D polarization state sensitivity calculated in Chapter 3.
\r\n\r\nAppendices beginning on page 221 include a matrix-based description of arbitrary 3D rotation that was used in the rotational diffusion simulations, Matlab code transcripts (p. 227), and an additional mathematical formalism based on information theoretic precepts (p. 242) for assessing directed causal relationships in bivariate time series data.
\r\n" }, { "name": "Sheriff, Bonnie Ann", "degree": "PhD", "year": "2009", "title": "Silicon Nanowires and Silicon/Molecular Interfaces for Nanoscale Electronics", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06302008-165534", "creators": [ { "name": { "family": "Sheriff", "given": "Bonnie Ann" }, "id": "Sheriff-Bonnie-Ann", "display_name": "Sheriff, Bonnie Ann" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "chair", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q13E-NB40", "abstract": "This thesis describes the utilization of silicon nanowires and molecular films towards the realization of nanoscale electronics. The key enabling technology is the method in which the silicon nanowires are produced\u2014the superlattice nanowire pattern transfer (SNAP) method. The SNAP method allows for the simultaneous formation and alignment of metal or semiconducting nanowires using a template-mediated approach.
\r\n\r\nHigh-performance n- and p-type silicon nanowire field-effect transistors (FETs) were demonstrated. These FETs exhibited consistent performance and strong performance metrics such as high on/off ratios, high on-currents, high mobilities and low subthreshold swings. Due to the nanowire\u2019s large surface-area-to-volume ratio, surface states were shown to dominate performance, especially for the n-type FETs. Reducing the number of surface states improved performance significantly.
\r\n\r\nN- and p-type silicon nanowire FETs were integrated into complementary symmetry (CS) logic circuits. This required the development of a pattern doping technique that allowed for spatial control of doped regions. The inverter circuit was fabricated and tested. A gain of ~ 5 was consistently measured from 7 working inverter circuits. This demonstration provided the foundation for the eventual fabrication and characterization of the other Boolean logic functions.
\r\n\r\nA methodology was developed that optimizes the design of high-performance logic circuits constructed from Si NW p- and n-type FETs. Circuit performance can be predicted from individual fabricated NW FETs before prototype circuits are manufactured, resulting in a faster and more efficient design process. These results suggest design options for fabricating high performance NW circuits, which can then be implemented experimentally. The effectiveness of this methodology is shown by optimizing the gain of Si NW complementary symmetry inverter from an initially measured value of 8 to a gain of 45.
\r\n\r\nLastly, methods to covalently attach electronically interesting molecules via microcontact printing onto gold and silicon substrates were developed. In these studies, the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was used to form the covalent attachment. It was observed that the reaction would proceed readily by replacing the Cu catalyst in the stamp ink by a Cu coating on the stamp directly. This reaction proceeded quickly on both azide-terminated monolayers on Au and Si(111) substrates.
" }, { "name": "Stockdill, Jennifer Lynn", "degree": "PhD", "year": "2009", "title": "Forays into the Synthesis of Zoanthenol: Intriguing Patterns in Reactivity and Selectivity", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01022009-165956", "creators": [ { "name": { "family": "Stockdill", "given": "Jennifer Lynn" }, "id": "Stockdill-Jennifer-Lynn", "orcid": "0000-0003-4238-6530", "display_name": "Stockdill, Jennifer Lynn" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WYAG-4S28", "abstract": "The zoanthamine family of alkaloids has attracted the attention of synthetic chemists for over two decades, beginning with the first report of their isolation in 1984. Not only are these stereochemically dense polycyclic compounds structurally fascinating, but they also display interesting and important biological activities. Foremost among these is the potent anti-osteoporotic effect of norzoanthamine. To date, norzoanthamine remains the only member to have succumbed to total synthesis, by Miyashita and co-workers in 2004. Our studies began by targeting zoanthenol, a structurally similar natural product that possesses the key stereochemical challenges of norzoanthamine, while offering unique opportunities for strategic development as compared to the other family members.\r\n\r\nThe synthetic work described herein focuses on approaches to the tricyclic core of zoanthenol, specifically employing an approach by which the stereochemical complexity of the C ring, marked by the challenging vicinal all-carbon quaternary centers, is addressed early in the synthesis. These functionalized C ring synthons are then tethered to an aromatic A ring synthon, and methods to form the final bond of the B ring are explored. Special attention is given to the acid-mediated Friedel-Crafts cyclization approach. In addition to the acid-mediated cyclization approach, an alternative cyclization method is discussed wherein the A ring is substituted with a halogen in order to enable generation of a radical. This radical then undergoes a 1,4-addition into a fully substituted enone to close the B ring and provide the desired stereochemistry both of the two new stereocenters that are generated in the cyclization.\r\n\r\nIn these efforts, we have learned a great deal about the factors governing selectivity and reactivity in these systems. For each case, stereochemical models are discussed and key structural requirements for future investigations are outlined.\r\n" }, { "name": "Tanrikulu, Ismet \u00c7ag\u02d8ler", "degree": "PhD", "year": "2009", "title": "Discovery of Aminoacyl-tRNA Synthetase Mutants for the Incorporation of Non Canonical Amino Acids into Proteins", "advisor": "Tirrell, David A.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232009-204358", "creators": [ { "name": { "family": "Tanrikulu", "given": "Ismet \u00c7ag\u02d8ler" }, "id": "Tanrikulu-Ismet-\u00c7ag\u02d8ler", "orcid": "0000-0002-7165-0399", "display_name": "Tanrikulu, Ismet \u00c7ag\u02d8ler" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "biochem" ], "doi": "10.7907/E7D5-HN96", "abstract": "Efficient in vivo incorporation of a noncanonical amino acid into proteins often requires engineering new aminoacyl-tRNA synthetase (AARS) activity into the cell, usually by modifying a natural aaRS. Although experimental methods, relying on mutagenesis and library screening, have identified many successful mutant aaRS-substrate pairs in the recent years, computational approaches have reported only a few successes. Here we compare the results of computational and experimental screens of an E. coli methionyl-tRNA synthetase (MetRS) saturation-mutagenesis library for binding (in silico), and activation and cell-surface display (in vivo) of azidonorleucine (Anl).
\r\n\r\nThree positions (L13, Y260, and H301) in the methionine binding pocket of E. coli MetRS were randomized, and the resulting library was screened for MetRS activity toward Anl, based on a screening strategy previously established in our group. This strategy relies on the introduction of reactive side chains into surface-exposed sites on outer-membrane protein C (OmpC), and their subsequent labeling with reactive, fluorescent probes. We have discovered a large diversity of MetRS mutants that allow the incorporation of Anl into proteins in vivo. The extent of OmpC expression and the amount of available Anl during the screen have substantial effects on the outcome of the screens. In addition to displaying improved activities toward Anl, identified mutants also show an improved discrimination against Met. We have shown that the degree of cell-surface labeling in vivo correlates well with the measured rates of Anl activation in vitro, which reflects the success of the screen design.
\r\n\r\nComputational analysis of the experimentally identified mutants revealed a good agreement between computed binding energies and in vitro activation data. To better test the computation model, we performed an in silico screen for Anl binding on a saturation-mutagenesis library comparable to the experimental library. Computational screen predominantly selects mutants that interact with Anl through hydrogen bonds, whereas the hydrophobic residues are selected more often by the experimental screen. We identify that experimental mutants try to optimize packing at the Y260 and H301 sites, but not at the L13 site. We discuss possible explanations for these results. Combined results from computation and experiments suggest the importance of various factors in ligand recognition and in vivo selection of MetRS mutants. We explore the implications of these factors to the future efforts in the engineering of new MetRS activities.
\r\n" }, { "name": "Torrice, Michael McCann", "degree": "PhD", "year": "2009", "title": "Chemical-Scale Studies of the Nicotinic and Muscarinic Acetylcholine Receptors", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08072008-103726", "creators": [ { "name": { "family": "Torrice", "given": "Michael McCann" }, "id": "Torrice-Michael-McCann", "display_name": "Torrice, Michael McCann" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4WKT-NB09", "abstract": "This dissertation describes three chemical-scale studies of neuroreceptor structure and function. Incorporation of unnatural amino acids into two acetylcholine receptors\u2014the nicotinic acetylcholine receptor (nAChR) and the M\u2082 muscarinic acetylcholine receptor (M\u2082AChR)\u2014and an electrophysiology assay of receptor function were performed in each of the studies. The nAChR is a ligand-gated ion channel (LGIC) and the M\u2082AChR is a G-protein-coupled receptor (GPCR).
\r\n\r\nIn Chapter 2, a highly conserved aspartate residue (D89) that is near the agonist binding site of the nAChR was probed for its role in agonist binding. We found that the side chain of D89 establishes a redundant network of hydrogen bonds and preorganizes the agonist binding site by positioning a critical agonist-binding residue, tryptophan 149 (W149). Previous studies of a D89N mutant led to the proposal that a negative charge at D89 was essential for receptor function. However, our studies show that neutral side chains at position 89 function well, only if an unfavorable electrostatic clash is avoided.
\r\n\r\nChapter 3 describes our attempts to incorporate unnatural amino acids into the M\u2082AChR, a GPCR. GPCR activity is assayed through second messenger signaling pathways, unlike the direct readout assays of LGICs. These second messenger pathways require significant amounts of optimization to create assays that produce reliable and robust data. In our experiments, variability of dose-response relationship data between batches of cells was the most significant concern. Several factors were investigated to reduce this batch-to-batch variability. After a reliable means to assay M\u2082AChR function was found, we performed a preliminary search for tryptophan residues in the agonist binding site that form a cation-pi interaction with acetylcholine.
\r\n\r\nFinally, in Chapter 4, we discuss the use of hydroxy acids to scan the \u03b1-M1 transmembrane helix of the nAChR for residues that undergo structural rearrangements during gating. Hydroxy acids disrupt hydrogen bonding in protein backbones and thus provide a means to detect backbone interactions that form or break during gating. The hydroxy acid analog of valine, valic acid (Vah), was incorporated at ten positions along the \u03b1-M1 helix. Backbone mutations at five residues on the intracellular side of a conserved proline (P221) produced shifts in dose-response relationships.
\r\n" }, { "name": "Vecitis, Chad David", "degree": "PhD", "year": "2009", "title": "Chemical Reactions at Aqueous Interfaces", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03162009-190807", "creators": [ { "name": { "family": "Vecitis", "given": "Chad David" }, "id": "Vecitis-Chad-David", "display_name": "Vecitis, Chad David" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1X15-EG53", "abstract": "Interfaces or phase boundaries are a unique chemical environment relative to individual gas, liquid, or solid phases. Interfacial reaction mechanisms and kinetics are often at variance with homogeneous chemistry due to mass transfer, molecular orientation, and catalytic effects. Aqueous interfaces are a common subject of environmental science and engineering research, and three environmentally relevant aqueous interfaces are investigated in this thesis: 1) fluorochemical sonochemistry (bubble-water), 2) aqueous aerosol ozonation (gas-water droplet), and 3) electrolytic hydrogen production and simultaneous organic oxidation (water-metal/semiconductor). Direct interfacial analysis under environmentally relevant conditions is difficult, since most surface-specific techniques require relatively \u2018extreme\u2019 conditions. Thus, the experimental investigations here focus on the development of chemical reactors and analytical techniques for the completion of time/concentration-dependent measurements of reactants and their products. Kinetic modeling, estimations, and/or correlations were used to extract information on interfacially relevant processes.
\r\n\r\nWe found that interfacial chemistry was determined to be the rate-limiting step to a subsequent series of relatively fast homogeneous reactions, for example: 1) Pyrolytic cleavage of the ionic headgroup of perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) adsorbed to cavitating bubble-water interfaces during sonolysis was the rate-determining step in transformation to their inorganic constituents carbon monoxide, carbon dioxide, and fluoride; 2) ozone oxidation of aqueous iodide to hypoiodous acid at the aerosol-gas interface is the rate-determining step in the oxidation of bromide and chloride to dihalogens; 3) Electrolytic oxidation of anodic titanol surface groups is rate-limiting for the overall oxidation of organics by the dichloride radical. We also found chemistry unique to the interface, for example: 1) Adsorption of dilute PFOS(aq) and PFOA(aq) to acoustically cavitating bubble interfaces was greater than equilibrium expectations due to high-velocity bubble radial oscillations; 2) Relative ozone oxidation kinetics of aqueous iodide, sulfite, and thiosulfate were at variance with previously reported bulk aqueous kinetics; 3) Organics that directly chelated with the anode surface were oxidized by direct electron transfer, resulting in immediate carbon dioxide production but slower overall oxidation kinetics. Chemical reactions at aqueous interfaces can be the rate-limiting step of a reaction network and often display novel mechanisms and kinetics as compared to homogeneous chemistry.
\r\n" }, { "name": "Walker, Ron", "degree": "PhD", "year": "2009", "title": "Functionalized Polymers from Ring-Opening Metathesis Polymerization Through Monomer Design", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10082008-161705", "creators": [ { "name": { "family": "Walker", "given": "Ron" }, "id": "Walker-Ron", "display_name": "Walker, Ron" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/GC6K-CG98", "abstract": "The focus of the research presented in this thesis deals with the synthesis and development of functionalized polymers using ring-opening metathesis polymerization (ROMP). The approach taken in developing the polymers presented within, feature the careful design and synthesis of a number of functionalized and unique monomers. A basic history and overview of olefin metathesis and polymer science is given in Chapter 1.
\r\n\r\nChapters 2 and 3 describe the development of controlled polymer architectures for use as barrier materials. This work was done in collaboration with Kuraray, Inc, which is a major manufacturer of commercial barrier materials. Also the structure-property relationships of these materials were studied to better understand how polymer architecture affects polymer properties.
\r\n\r\nChapter 4 discusses the controlled living ROMP of highly strained trans-cyclooctene. The knowledge and understanding of solvent effects during ROMP was also explored as a means to attenuate the rate of propagation during ROMP. Block copolymers containing polynorbornene and PCO were also synthesized and hydrogenated to form block copolymers containing blocks of linear, narrowly dispersed polyethylene.
\r\n\r\nChapter 5 describes the development of photodegradable polymer. By incorporating photodegradable links into a polymer chain, using ROMP, the polymer chain may be degraded upon irradiation with light.
" }, { "name": "Weinberg, David Richard", "degree": "PhD", "year": "2009", "title": "Investigations into the Requirements for Homogeneous Platinum- and Iridium-Catalyzed Oxidative C-H Bond Functionalization\r ", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02042009-144339", "creators": [ { "name": { "family": "Weinberg", "given": "David Richard" }, "id": "Weinberg-David-Richard", "display_name": "Weinberg, David Richard" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TAYG-C375", "abstract": "Investigations have been performed to determine the requirements for homogeneous platinum- and iridium-catalyzed oxidative alkane functionalization. Previous platinum-catalyzed systems have involved initial C-H bond activation to generate a platinum(II)-alkyl, followed by two-electron oxidation of this species to activate the alkyl towards nucleophilic displacement from the metal center. The factors affecting C-H bond activation by platinum(II) complexes and oxidation of alkylplatinum(II) complexes have been probed, while the possibility of using a diphenolate imidazolyl-carbene ligand to stabilize iridium complexes in a variety of oxidation states has been explored.
\r\n\r\nRelative oxidation and protonation rates for trichloro(methyl)platinum(II) dianion have been screened under a variety of conditions, using several different oxidants. Both one- and two-electron oxidants were shown to compete effectively with protonation of trichloro(methyl)platinum(II) dianion, including CuCl2, CuBr2, FeCl3, Na3[H3PMo9V3O40], Br2, Na2IrCl6, and (NH4)2Ce(NO3)6. Oxidation by copper(II) proved to be highly dependent on the counteranion.
\r\n\r\nDisodium (2,2\u2019-biindolyl)dimethylplatinum(II) has been synthesized for the purpose of probing the C-H bond activation chemistry of electron rich platinum(II) complexes. This complex decomposes rapidly in air, and deuterolysis of both platinum-methyls as well as the 2,2\u2019-biindolyl ligand occurs when it is dissolved in methanol-d4. Methide abstraction from (2,2\u2019-biindolyl)dimethylplatinum(II), either by protonolysis or by reaction with B(C6F5)3, generates monomethylplatinum(II) species capable of activating C-H and C-D bonds.
\r\n\r\nIn the search for ligands capable of stabilizing iridium complexes in a variety of oxidation states, the first iridium complexes containing a diphenolate imidazolyl-carbene ligand have been synthesized. 1,3-Di(2-hydroxy-5-tert-butylphenyl)imidazolium chloride was synthesized and then reacted with chloro-1,5-cyclooctadiene iridium(I) dimer to generate potassium (1,5-cyclooctadiene){1,3-di(2-hydroxy-5-tert-butylphenyl)imidazolyl}iridium(I). Oxidation of this complex with two equivalents of ferrocenium(III) hexafluorophosphate generates (acetonitrile)(1,5-cyclooctadiene){1,3-di(2-hydroxy-5-tert-butylphenyl)imidazolyl}iridium(III) hexafluorophosphate. Reaction of this complex with dihydrogen generates a species capable of catalyzing olefin hydrogenations. Heating (acetonitrile)(1,5-cyclooctadiene){1,3-di(2-hydroxy-5-tert-butylphenyl)imidazolyl}iridium(III) hexafluorophosphate with greater than two equivalents of tricyclohexylphosphine in acetonitrile followed by treatment with tetramethylammonium chloride results in (chloro)bis(tricyclohexylphosphine){1,3-di(2-hydroxy-5-tert-butylphenyl)imidazolyl}iridium(III). As indicated by cyclic voltammetry and bulk electrolysis, this complex undergoes two reversible one-electron oxidations in methylene chloride at -0.22 V and at 0.58 V.
\r\n" }, { "name": "Whited, Matthew Thomas", "degree": "PhD", "year": "2009", "title": "Synthetic and Mechanistic Studies of Small-Molecule Activation at Low-Valent Iron, Cobalt, and Iridium Centers", "advisor": "Grubbs, Robert H.; Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05062009-173812", "creators": [ { "name": { "family": "Whited", "given": "Matthew Thomas" }, "id": "Whited-Matthew-Thomas", "orcid": "0000-0002-1193-9078", "display_name": "Whited, Matthew Thomas" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-T", "role": "member", "display_name": "Agapie, Theodor" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4N3R-5194", "abstract": "The preparation of transition-metal systems for catalytic multielectron transformations of small molecules remains a significant challenge for synthetic chemists. The realization of new transformations often depends critically on the design of frameworks capable of stabilizing unusual oxidation states and molecular geometries, providing a frontier molecular-orbital landscape that is well suited to interact with the molecules of interest. This thesis has sought to address two particularly noteworthy challenges in the field of small-molecule activation, dinitrogen reduction and C\u2013H bond functionalization, through judicious ligand choice and design.
\r\n\r\nChapters 2 and 3 describe the syntheses of new tri- and tetradentate hybrid ligands incorporating a single X-type donor (amido or silyl) and multiple phosphine donors designed to stabilize low oxidation states at iron and cobalt and support dinitrogen reduction and other multielectron redox transformations. While the amidophosphine ligands do allow access to unusual monovalent iron and cobalt complexes, the isolation of dinitrogen adducts supported by these ligands remains elusive and the weakness of the silicon\u2013nitrogen bond makes the complexes prone to decomposition. In contrast, the tris(phosphino)silyl ligands presented in Chapter 3 afford straightforward access to the first terminally bonded dinitrogen complexes of monovalent iron, and the structure of these and related complexes are described along with preliminary experiments showing that protonolysis of the iron(I)\u2013dinitrogen complexes produces hydrazine in reasonable stoichiometric yields.
\r\n\r\nChapters 4 through 7 address the functionalization of ether and amine C\u2013H bonds by a double C\u2013H activation route. Chapter 4 describes the investigation of reactivity of low-valent, pincer-supported iridium species with a variety of ethers, leading to a number of selective C\u2013H, C\u2013C, and C\u2013O bond cleavage events, affording in several cases iridium carbene complexes by double C\u2013H activation and loss of dihydrogen.
\r\n\r\nChapter 5 presents an exploration of the electronic structure of the unusual square-planar iridium(I) alkoxycarbenes and their nucleophilic activation of several heterocumulene substrates, leading to multiple-bond metathesis events promoted by metal- rather than ligand-initiated reactivity. Chapter 6 describes the discovery of new atom and group transfer reactions from diazo reagents to the alkoxycarbenes and the implementation of these reactions in an unprecedented catalytic cycle for C=E bond formation by multiple C\u2013H activations.
\r\n\r\nChapter 7 explores the related reactivity of a low-valent pincer iridium complex with methyl amines and the reactivity of the resulting iridium(III) dihydrido aminocarbenes, which is shown to diverge substantially from that observed for the iridium(I) carbene species.
\r\n" }, { "name": "Wiencko, Heather L.", "degree": "PhD", "year": "2009", "title": "Adrenergic Receptors: Model Systems for Investigation of GPCR Structure and Function", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292009-094239", "creators": [ { "name": { "family": "Wiencko", "given": "Heather L." }, "id": "Wiencko-Heather-L", "display_name": "Wiencko, Heather L." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S3RC-RZ59", "abstract": "Membrane proteins mediate intercellular communication, resulting in changes in the membrane and within the cell itself. One superfamily of integral membrane proteins, G-protein coupled receptors (GPCRs), are responsible for a vast diversity of processes. Their conformational flexibility and membrane environment pose challenges for direct structural characterization, and to date only five of the more than 1,000 known GPCRs have been characterized by high-resolution crystallography.
\r\n\r\nThe nine adrenergic GPCRs mediate the stress response throughout the body, and are implicated in diseases including hypertension and asthma. While they are among the best studied families of GPCRs, much remains to be learned about selectivity and activation. The first section of this work describes the ab initio structure prediction of the turkey beta-1 receptor and validation using a series of stabilizing mutations. This work preceded the currently available turkey beta-1 structure but shows good agreement, especially in the binding site. It validates the latest methods developed for GPCR structure prediction, emphasizes the role of a neutral charge scheme in energy determination, and explores a structure validation strategy based on stabilizing mutations rather than ligand docking. The next section uses the experimental beta-1 crystal structure as a starting point for nanosecond timescale molecular dynamics, exploring the roles of ligand binding in helix movement that contribute to the transition to an active state. These simulations reveal the early steps in receptor activation, beginning with tilting motions of transmembrane helices 5 and 6 and movement of transmembrane helix 1 closer into the protein core. The last section presents homology models of the human adrenergic receptors for which there are not yet crystal structures. The receptors most closely related to the target structures show the best results, while the less related ones will require further refinement. The best structures provide insight into the binding site of subtype selective antagonists, and can serve as the foundation for future studies. Over the course of these explorations, new subtleties in adrenergic structure have been illuminated, and may drive further exploration into selective binding and the activation mechanism of these and other receptors.
" }, { "name": "Woodka, Marc Dominic", "degree": "PhD", "year": "2009", "title": "Increased Classification Rates of Chemical Vapor Detectors Using Novel Sensor Types and Optimized Sensing Geometries", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-09292008-153208", "creators": [ { "name": { "family": "Woodka", "given": "Marc Dominic" }, "id": "Woodka-Marc-Dominic", "display_name": "Woodka, Marc Dominic" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Perona", "given": "Pietro" }, "id": "Perona-P", "role": "member", "display_name": "Perona, Pietro" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZMTF-DV91", "abstract": "Broadly responsive vapor sensor arrays, or so-called \"electronic noses,\" have been explored and/or used for many years as a means to detect the vapors present in the headspace of a variety of targets, such as coffees, wines, vinegars, oils, explosives, and nerve agents, and for disease diagnosis. Electronic nose sensing modalities often exhibit a response that is linear with concentration, and additive with respect to multiple vapors. Ideally, one could simply train an array towards the pure vapors of interest, and use that pure vapor training to identify either pure vapors or vapor mixtures during field-testing. This, however, has proven difficult, and has limited the utility of this vapor detection approach for a number of applications.
\r\n\r\nThis thesis utilized a low-cost, low-power sensing modality, insulator \u2013 carbon black composite chemiresistors, and exploited their linear response properties to enhance the classification rates of both pure vapors and vapor mixtures, based on pure vapor training. Sensors utilizing non-polymeric, small organic molecules as the insulating component were demonstrated to offer enhanced separation between pure vapor response clusters, and lower detection limits, relative to the traditional use of polymers as the insulating phase. These sensors were then used in a sensing geometry that induced a space- and time, or spatiotemporal (ST) dependence, to the sensor response, which increased the amount of chemical information extracted from the sensor response. This ST response information allowed for the correct classification of vapor mixtures consisting of up to 5 components, with training on only pure vapors.
\r\n\r\nA mass uptake model for the ST response of the sensors was developed, and vapor detection and mixture analysis was simulated for chamber geometries and vapor delivery flow rates spanning several orders of magnitude. The data were first used to define an optimized ST sensing regime for mixture analysis, based on two dimensionless Peclet number analogs. The data were then used to identify the inherent properties of the pure vapor training data that allowed for mixture analysis to be performed at high levels, specifically that the minimum resolution factor between all binary vapor combinations in the training library was sufficiently high.
\r\n\r\nFinally, the utility of the ST response was demonstrated to offer enhanced pure-vapor classification rates, relative to the traditional steady state approach typically employed with broadly responsive array-based sensing. These enhanced classification rates were demonstrated using a number of classification algorithms, including a bioinspired algorithm based on Fisher\u2019s Linear Discriminant. In summary, the results demonstrated herein quantify, in different ways, what is required for classification optimization, and in doing so increase the utility of this approach to vapor detection for a number of applications.
\r\n" }, { "name": "Xu, Ke", "degree": "PhD", "year": "2009", "title": "Nonlinear Electrical Properties of One-Dimensional Nanostructures", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012009-021047", "creators": [ { "name": { "family": "Xu", "given": "Ke" }, "id": "Xu-Ke", "orcid": "0000-0002-2788-194X", "display_name": "Xu, Ke" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BPK0-3V37", "abstract": "A general method is first reported for reliably fabricating highly-ordered conventional superconductor nanowire arrays, with good control over nanowire cross section (down to 10 nm by 11 nm) and length (up to 200 microns). Nanowire size effects are systematically studied through electrical measurements and explained with theories. A comprehensive investigation of influence of nanowire length on superconductivity is reported for the first time.
\r\n\r\nWe further demonstrate the preparation and electrical properties of high-temperature superconductor nanowires. We find that high-temperature superconductivity can be retained in nanowires ~10 nm in width and >100 microns in length. All nanowires exhibit a superconducting transition above liquid nitrogen temperature, and a transition temperature width that depends strongly upon the nanowire dimensions.
\r\n\r\nThe experience gained from the above projects has allowed for the fabrication of superconductor films patterned with ultrahigh-density (pitch ~30 nm) two-dimensional arrays of nano-holes. Significantly enhanced critical currents are observed in such systems.
\r\n\r\nWe then describe a method for the assembly of nanoparticles into granular solids that can be tuned continuously from two dimensions to one dimension, and establish how electron transport evolves between these limits. We find that the energy barriers to transport increase in the one-dimensional limit, in both the variable-range-hopping and sequential-tunneling regimes. Furthermore, in the sequential-tunneling regime, we find an unexpected relationship that is peculiar to one-dimensional systems, between the temperature and the voltage at which the conductance becomes appreciable. These results are explained by extrapolating existing theories to one dimension.
\r\n\r\nWe also describe an approach to combine the geometric confinement of a Si nanowire and the electric field confinement from an array of ultrahigh-density top gates to form a concatenated array of coupled quantum dots. Reproducible confinement and coupling effects are observed.
\r\n\r\nWe have achieved single-atomic resolution in our scanning tunneling microscopy studies of graphene sheets on SiO2 substrates, from which we discovered significant changes in electronic states for bended regions in graphene sheets. We have also carried out the first systematic study on local conductance variations in graphene. Our results suggest large local variations in both the morphology and the electrical properties of graphene.
\r\n" }, { "name": "Yang, Ding-Shyue (Jerry)", "degree": "PhD", "year": "2009", "title": "Ultrafast Electron Crystallography: Principles and Applications", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05082009-170032", "creators": [ { "name": { "family": "Yang", "given": "Ding-Shyue (Jerry)" }, "id": "Yang-Ding-Shyue-Jerry", "orcid": "0000-0003-2713-9128", "display_name": "Yang, Ding-Shyue (Jerry)" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Yeh", "given": "Nai-Chang" }, "id": "Yeh-Nai-Chang", "role": "member", "display_name": "Yeh, Nai-Chang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y61P-2B24", "abstract": "During the last 20 to 30 years, the development and application of time-resolved experimental techniques with a femtosecond temporal resolution have brought to us much knowledge about the fundamental processes in physics, chemistry and biology. Nevertheless, standard spectroscopic methods have their limitation in the determination of the transient structures during ultrafast dynamics at the atomic level, because the spatial resolution is restricted by the wavelength of the probe pulse used. In contract, with the scheme of femtosecond optical initiation and electron probing and through the diffraction phenomenon, ultrafast electron crystallography (UEC) was recently developed as a time-resolved structure-probing technique for condensed-matter studies. The short wavelength and small pulse duration of the highly accelerated electrons used provide the atomic-scale spatiotemporal resolution. In addition, the large electron\u2013matter interaction enables the detection of small transient changes as well as the investigation of surface and interfacial phenomena.
\r\n\r\nThis thesis describes the principles of UEC and its applications to a variety of systems, ranging from nanometer-scale structures to highly correlated materials and to interfacial assemblies. By using a prototype semiconducting material, we elucidated the fundamental processes at work in different parts of the femtosecond-to-nanosecond time range; this investigation led to a conceptual change from the consideration of laser-induced heating to the examination of nonequilibrium structural modifications as a result of the transient dynamical changes in, e.g., carriers, the crystal potential, and phonons. On the basis of such an understanding, we observed and understood the colossal unidirectional expansion induced by the photoexcitation of nanostructures to be a potential-driven result rather than a thermal one.
\r\n\r\nFor highly correlated materials, we showed the effectiveness of UEC in resolving the transient intermediate structures during phase transformations as well as identifying new phases in the nonequilibrium state. An important breakthrough made by UEC was the confirmation of the anisotropic involvement of lattice in the electron pairing mechanism for high-temperature superconductors. In interfacial assemblies, we also found a nonequilibrium phase transformation in water and the phenomenon of ultrafast annealing for a better order in a self-assembled monolayer. With these successful experiences, we expect more condensed-matter studies by UEC to come.
\r\n" }, { "name": "Anderson, Donde R.", "degree": "PhD", "year": "2008", "title": "Ruthenium Olefin Metathesis Complexes: Catalyst Development and Mechanistic Studies", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08142007-151304", "creators": [ { "name": { "family": "Anderson", "given": "Donde R." }, "id": "Anderson-Donde-R", "display_name": "Anderson, Donde R." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6B6N-2V77", "abstract": "The field of olefin metathesis has grown to include organometallic chemists who strive to develop more efficient catalysts and to understand their mechanism of activity and decomposition, synthetic organic chemists who construct complex molecules utilizing existing catalysts and continually find challenging reactions in need of more efficient catalysts, and polymer chemists who utilize current catalysts to synthesize polymers with an ever-widening array of functional groups and structures in a controlled manner. This thesis describes the exploration of new ligands for olefin metathesis catalysts and the investigation of the model compounds of olefin metathesis reaction intermediates.
\r\n\r\nChapter 2 describes the synthesis, characterization, activity and kinetic selectivity of ruthenium olefin metathesis complexes bearing cyclic (alkyl)(amino)carbenes (CAACs). The activity of phosphine-free CAAC-ruthenium complexes is significantly affected by steric interactions. By decreasing the steric bulk of the ligand, a new catalyst with activity comparable to that of existing NHC-ruthenium (N-heterocyclic carbene) complexes has been synthesized. Additionally, these complexes exhibit unusual E/Z-diastereoselectivity and ethenolysis selectivity relative to previously studied NHC-ruthenium complexes.
\r\n\r\nChapter 3 describes the exploration of 3- and 6-membered carbenes as ligands for ruthenium olefin metathesis complexes. Stable silver-cyclopropenylidene adducts were synthesized and utilized as carbene transfer reagents in the presence of ruthenium precursors. Although good conversions were observed, isolation of cyclopropenylidene-ruthenium complexes was unsuccessful. Ruthenium complexes of 6-membered \u2018borazine\u2019-like carbenes were isolated, characterized and evaluated for ring-closing metathesis activity.
\r\n\r\nChapter 4 describes the development of a model system to study ruthenium-olefin complexes relevant to the mechanism of olefin metathesis. Upon addition of the ligand precursor 1,2-divinylbenzene to (H\u2082IMes)(py\u2082)(Cl)\u2082Ru=CHPh (H\u2082IMes = 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene), two ruthenium-olefin adducts are formed. Based on \u00b9H NMR spectroscopy experiments and X-ray crystallographic analysis, the solution phase and solid-state structure of these complexes is assigned. Exploration of the generality of these observations through variation of the N-heterocyclic carbene ligand and the ligand precursor are also presented.
\r\n\r\nAppendix 1 describes the screening of transitional-metal salts and ligands for the non-oxidative hydration of styrene. Appendix 2 describes the investigation of a prior report of intramolecular olefin hydroalkoxylation with ruthenium, copper and silver salts. Appendix 3 describes the evaluation of chiral NHCs as ligands for ruthenium and rhodium hydrosilylation catalysts. Appendix 4 describes the investigation of tin(II) halides as ligands for ruthenium olefin metathesis catalysts. Appendix 5 contains X-ray crystallographic analysis parameters of the structures presented in this thesis.
\r\n" }, { "name": "Archer, Melissa Jane", "degree": "PhD", "year": "2008", "title": "Multijunction Solar Cells on Epitaxial Templates ", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-103359", "creators": [ { "name": { "family": "Archer", "given": "Melissa Jane" }, "id": "Archer-Melissa-Jane", "display_name": "Archer, Melissa Jane" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "King", "given": "Richard" }, "id": "King-Richard", "role": "member", "display_name": "King, Richard" }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9CFK-G982", "abstract": "Future ultrahigh efficiency multijunction solar cells will employ designs that feature three or four or more subcells utilizing lattice-mismatched structures to achieve an optimal band gap sequence for solar energy conversion. While lattice-mismatched multijunction cells have been fabricated recently using metamorphic growth approaches, use of direct wafer bonding techniques to enable lattice mismatch accommodation at the subcell interfaces allows considerably more design freedom and inherently higher-quality, defect-free active regions. This thesis presents new results on wafer bonding and layer transfer for integration of materials with large lattice mismatch, as well as modeling work to better understand the key material parameters in the design of new multijunction solar cells.
\r\n\r\nGaInP/GaAs dual junction solar cells on Ge/Si templates were fabricated using wafer bonding and ion implantation induced layer transfer techniques. Following layer transfer, the surface of the ~1.4 um thick transferred Ge(100) has an as-transferred RMS roughness of ~20 nm and a near surface layer containing a high density of ion implantation-induced defects. The RMS roughness has been reduced to <1 nm. In addition, the effects of changing the strain state of the template substrate on the performance of the devices has been explored by comparing devices grown on Ge/Si and Ge/sapphire. The CTE mismatch between Si and GaAs/GaInP materials induces a tensile strain, whereas the sapphire substrate induces a compressive strain.
\r\n\r\nAn analytical p-n junction device physics model for GaInP/GaAs/InGaAsP/InGaAs four junction solar cells was developed. Real behavior of solar cells is accounted for by including: free carrier absorption, temperature and doping effects on carrier mobility, as well as two recombination pathways: Shockley-Read-Hall recombination from a single mid gap trap level and surface recombination. Upper bounds set by detailed balance calculations can be approached by letting the parameters approach ideal conditions. Detailed balance calculations always benefit from added subcells, current matching requirements in series connected p-n multijunctions indicate a minimum performance required from added subcells for net contribution to the overall device. This model allows novel solar cell structures to be evaluated by providing realistic predictions of the performance limitations of these multijunction devices.
\r\n" }, { "name": "Beatty, Kimberly Elizabeth", "degree": "PhD", "year": "2008", "title": "Imaging the Proteome: Metabolic Tagging of Newly Synthesized Proteins with Reactive Methionine Analogues", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03052008-105142", "creators": [ { "name": { "family": "Beatty", "given": "Kimberly Elizabeth" }, "id": "Beatty-Kimberly-Elizabeth", "orcid": "0000-0002-2303-8779", "display_name": "Beatty, Kimberly Elizabeth" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PTNQ-DJ39", "abstract": "Many strategies have been described for identifying proteins isolated from tissues, cells, or organelles, but the cellular proteome undergoes complex dynamic changes in response to disease or environment. A more complete analysis of the proteome requires complementary, time-resolved images of cellular proteins. In one method for obtaining dynamic proteomic data, cellular proteins are selectively tagged with small, reactive amino acid analogues. Co-translational incorporation of reactive methionine (Met) analogues [e.g., azidohomoalanine (Aha) or homopropargylglycine (Hpg)] is reminiscent of conventional pulse-labeling with radioactive amino acids; the endogenous cellular machinery places reactive Met analogues at sites normally occupied by Met within proteins. Susceptibility to tagging is determined not by the identity of the protein, but rather by the extent to which the protein is translated during exposure to the analogues. The analogue is then labeled using a copper-catalyzed or strain-promoted azide-alkyne ligation; both ligations enable selective, minimally invasive protein labeling in complex biological mixtures. In my dissertation research, I have developed new methods to tag and dye-label proteins in order to visualize one or more subsets of the proteome. In this thesis, I will first describe the tagging of newly synthesized proteins with reactive analogues in bacterial (Chapter 2) and mammalian cells (Chapter 3). In recent work, I have further expanded the method to enable two-fluorophore labeling of two distinct protein populations (Chapter 4). Two-dye labeling of proteins should enable changes in the proteome to be tracked over time. Finally, I will describe how the dye-labeling method has been adapted for live cell compatibility through the use of cyclooctyne-conjugated fluorophores (Chapters 5 and 6). Labeling in live cells will enable dynamic processes to be monitored in real time. Proteomic visualization is complementary to proteomic identification, and it should be useful for examining many different aspects of biological systems, including translational responses to disease or environment.\r\n" }, { "name": "Beeson, Teresa Diane", "degree": "PhD", "year": "2008", "title": "Development of Enantioselective Organocatalytic Technologies for the Alpha-Functionalization of Aldehydes and Ketones", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262008-115504", "creators": [ { "name": { "family": "Beeson", "given": "Teresa Diane" }, "id": "Beeson-Teresa-Diane", "display_name": "Beeson, Teresa Diane" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YYTK-TP61", "abstract": "The development of an expeditious and room-temperature conversion of aliphatic aldehydes to chiral terminal epoxides is described. \u03b1-Chloroaldehydes were prepared via asymmetric enamine catalysis with an imidazolidinone catalyst followed by in situ reduction and cyclization to generate the terminal epoxide. Epoxides with a variety of aliphatic groups and functionalities were produced in 75 minutes with good yields and excellent selectivities.
\r\n\r\nThe catalytic enantioselective direct \u03b1-fluorination of aldehydes and ketones is also reported. \u03b1-Fluoroaldehydes were conveniently prepared via enamine catalysis with an imidazolidinone catalyst and N-fluorobenzenesulfonimide (NFSI) as an electrophilic fluorine source. The method tolerated a wide variety of aldehyde substrates and functional groups. Catalyst loadings as low as 1 mol% generated the fluorinated products in good yield and excellent enantioselectivity. Additionally, various catalyst architectures were studied to apply the \u03b1-fluorination reaction to ketone substrates. Cinchona alkaloid-derived catalysts were found to successfully facilitate the \u03b1-fluorination of ketones in high yields and excellent enantioselectivities.
\r\n\r\nAlso presented is the advent of SOMO catalysis, a new mode of organocatalytic activation based on the catalytic generation of radical cations. A secondary amine catalyst reacts with an aldehyde to transiently generate an enamine that, in turn, undergoes a single-electron oxidation to yield a stabilized radical cation that is subject to enantiofacial discrimination. While the parent enamine reacts only with electrophiles, the radical cation combines with SOMO nucleophiles at the same reacting center, thereby enabling a diverse range of previously unknown asymmetric transformations. As a first example and proof of principle, the development of the direct and enantioselective \u03b1-allylation of aldehydes using SOMO catalysis is described.
\r\n" }, { "name": "Boal, Amie Kathleen", "degree": "PhD", "year": "2008", "title": "DNA-Mediated Charge Transport in DNA Repair", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022008-092549", "creators": [ { "name": { "family": "Boal", "given": "Amie Kathleen" }, "id": "Boal-Amie-Kathleen", "orcid": "0000-0002-1234-8472", "display_name": "Boal, Amie Kathleen" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "chair", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CMWB-6C92", "abstract": "The double-helical structure of deoxyribonucleic acid (DNA) imparts upon this important biological molecule both the ability to store genetic information within a cell and also the capacity to serve as medium for charge transport. DNA-mediated charge transport is now a very well-studied phenomenon but biological roles for these reactions have not been explored. It has been demonstrated that DNA-mediated charge transport can funnel oxidative DNA damage to sites of low oxidation potential in a number of biologically relevant environments ranging from reconstituted nucleosome core particles, to isolated nuclei and mitochondria from HeLa cells. DNA-mediated charge transport may also play a role in transcriptional activation or repression as modulated by redox-active transcription factors. Here we examine how DNA-mediated charge migration could also provide a pathway for protein-protein communication among DNA repair enzymes, a pathway that might serve as a scheme for rapid lesion detection inside the cell." }, { "name": "Boukai, Akram Issam", "degree": "PhD", "year": "2008", "title": "Thermoelectric Properties of Bismuth and Silicon Nanowires", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01172008-141725", "creators": [ { "name": { "family": "Boukai", "given": "Akram Issam" }, "id": "Boukai-Akram-Issam", "display_name": "Boukai, Akram Issam" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QEE9-4H11", "abstract": "Thermoelectric materials convert temperature differences into electricity and vice versa. Such materials utilize the Seebeck effect for power generation and the Peltier effect for refrigeration. In the Seebeck effect, a temperature gradient across a material causes the diffusion of charged carriers across that gradient, thus creating a voltage difference between the hot and cold ends of the material. Conversely, the Peltier effect explains the fact that when current flows through a material a temperature gradient arises because the charged carriers exchange thermal energy at the contacts. Thermoelectrics perform these functions without moving parts and they do not pollute. This makes them highly reliable and more importantly attractive as renewable energy sources, especially at a time when global warming is a growing concern. However, thermoelectrics find only limited use because of their poor efficiency.
\r\n \t\r\nThe efficiency of a thermoelectric material is determined by the dimensionless figure of merit,ZT = S\u00b2\u03c3T/\u03ba , where S is the thermoelectric power, defined as the thermoelectric voltage, V, produced per degree temperature difference \u0394T , \u03c3 is the electrical conductivity, \u03ba is the thermal conductivity, and T is the temperature. To maximize ZT, S must be large so that a small temperature difference can create a large voltage, \u03c3 must be large in order to minimize joule heating losses, and \u03ba must be small to reduce heat leakage and maintain a temperature difference. Maximizing ZT is challenging because optimizing one physical parameter often adversely affects another. The best commercially available thermoelectric devices are alloys of Bi2Te3 and have a ZT of 1 which corresponds to a carnot efficiency of ~10%. My research has focused on achieving efficient thermoelectric performance from the single component systems of bismuth and silicon nanowires.
\r\n\r\nBismuth nanowires are predicted to undergo a semi-metal to semiconductor transition below a size of 50 nm which should increase the thermopower and thus ZT. Limited experimental evidence by other groups has been acquired to support this claim. Through electric field gating measurements and by tuning the nanowire size, we have shown that no such transition occurs. Instead, surface states dominate the electric transport at a size smaller than 50 nm and bismuth remains a semimetal.
\r\n\r\nBulk silicon is a poor thermoelectric due to its large thermal conductivity. However, silicon nanowires may have a dramatically reduced thermal conductivity. By varying the nanowire size and impurity doping levels, ZT values representing an approximately 100-fold improvement over bulk silicon are achieved over a broad temperature range, including a ZT ~ 1 at 200K. Independent measurements of S, \u03c3, and \u03ba, combined with theory, indicate that the improved efficiency originates from phonon effects. The thermal conductivity is reduced and the thermopower is enhanced. These results are expected to apply to other classes of semiconductor nanomaterials.
\r\n" }, { "name": "Butler, Mark Cheiron", "degree": "PhD", "year": "2008", "title": "Novel Methods for Force-Detected Nuclear Magnetic Resonance", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06112008-065533", "creators": [ { "name": { "family": "Butler", "given": "Mark Cheiron" }, "id": "Butler-Mark-Cheiron", "display_name": "Butler, Mark Cheiron" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S5K2-NH54", "abstract": "This thesis is concerned with the problem of extending methods for force-detected nuclear magnetic resonance (NMR) to the nanoscale regime. A magnetic mechanical resonator can be used both as a sensitive detector of spins and a means of inducing spin relaxation between detected transients. At the mK temperatures achievable in a dilution refrigerator, spin-lattice interactions are \"frozen out,\" and resonator-induced relaxation can replace spin-lattice relaxation in returning the spins to equilibrium between detected transients. We analyze resonator-induced spin relaxation and the sensitivity of schemes which use a nanoscale mechanical resonator to detect spins.
\r\n\r\nRelaxation equations are derived from first principles, and a physical interpretation of the processes contributing to resonator-induced relaxation is given. The intrinsically quantum mechanical nature of the relaxation is highlighted by comparing the quantum mechanical relaxation equations with analogous equations derived using a semiclassical model in which all spin components have a definite value simultaneously. In the case where the spins all experience the same field, the semiclassical spins cannot become polarized as a result of their interaction with the resonator, and a quantum mechanical model is necessary even for a qualitative description of the polarization process.
\r\n\r\nResonator-induced relaxation of spin systems is complicated by the fact that an indirect spin-spin interaction is present when all spins are coupled to the same resonator, since the resonator's field at a given spin is determined by the interactions which have occurred between the resonator and the other spins of the system. This indirect interaction can prevent the spins from relaxing to a thermal state characterized by a spin temperature. We present a physical interpretation of the mechanism by which an indirect spin-spin torque develops during resonator-induced relaxation, and we estimate the magnitude of this torque and the time T_corr required for it to induce strong spin-spin correlations. A perturbation in the spin Hamiltonian which periodically reverses the direction of the indirect torques within a time period shorter than T_corr will prevent the development of resonator-induced correlations and allow the spins to relax to a thermal state.
\r\n\r\nThe mechanisms by which the spin Hamiltonian H_s modifies resonator-induced relaxation are characterized. In the case where the eigenstates of H_s are weakly perturbed from product states, the system will relax exponentially to thermal equilibrium with the resonator, provided that resonator-induced couplings between populations and certain zero-quantum coherences are suppressed by terms in H_s which shift the frequencies of these coherences sufficiently far from zero. Analysis of longitudinal relaxation in example systems containing three dipole-dipole coupled spins shows that the relaxation occurs in two stages governed by different physical processes, and the three-spin systems do not relax to a thermal state. For substantially larger dipole-dipole coupled system (e.g., N = 50), we propose the hypotheses that the secular dipolar Hamiltonian will quickly equalize the population of states which lie in the same eigenspace of I_z. Simulations of the longitudinal relaxation predicted by this hypothesis suggest that a single resonator could efficiently relax dipole-dipole coupled systems to a thermal state.
\r\n\r\nArguments based on general properties of the master equation suggest that the transverse relaxation induced by the mechanical resonator could occur on a shorter time scale than that of the longitudinal relaxation. We derive conditions which guarantee that the time constant for transverse relaxation will be 2/R_h, where 1/R_h is the time constant for resonator-induced longitudinal relaxation of a single-spin sample to thermal equilibrium. Under these conditions, transverse relaxation can be interpreted as the \"lifetime broadening\" associated with the shortened lifetime of energy eigenstates due to coupling with the resonator. For a two-spin system, however, we show analytically that \"turning on\" the dipolar coupling can accelerate resonator-induced transverse relaxation, and we give an interpretation of the mechanism by which this occurs. Simulations of four-spin systems also show that the presence of dipolar couplings can substantially accelerate resonator-induced transverse relaxation, and that this accelerated relaxation can be distinguished from so-called radiation damping. In addition, we find that spin-locking limits the rate of resonator-induced transverse relaxation. In the case where the spin-locking field is large enough to average the dipolar Hamiltonian and the superoperator responsible for resonator-induced relaxation, we have T_1rho = 2/R_h.
\r\n\r\nWe propose a general definition of signal-to-noise ratio (SNR) which can be used to compare the sensitivity of methods that measure the amplitude of a signal with the sensitivity of methods that yield a continuous record of a signal. This definition is used to compare the sensitivity of three schemes for detecting the NMR signal of a sample consisting of a few spins: spin-locked detection of a transverse dipole, detection of a freely-precessing dipole, and detection of a correlated product. The dependence of SNR and acquisition time on resonator parameters is analyzed. We find that when the time constant for decay of the signal during the detection period is 2/R_h, with instrument noise substantially larger than spin noise, the only resonator parameter which appears in the SNR expressions is the ratio of the mechanical frequency to the temperature. This result suggests, in particular, that SNR for spin-locked detection will be insensitive to details of resonator design.
\r\n\r\nA torsional mechanical resonator design is presented. We discuss the advantages of using soft magnetic material and eliminating relative motion between the sample and the resonator, as well as the validity of the models used to characterize the resonator. The possibility of using non-metallic magnetic material as the source of the resonator's magnetic field is introduced. A numerical example is presented for which the calculated time constant for the longitudinal relaxation of a single-spin sample is 1/R_h = 0.77 s. Simulations of detected NMR spectra for two-spin samples suggest the possibility of chemical studies in which force-detected NMR spectroscopy is used with single-spin sensitivity.
\r\n\r\nThe final chapter studies the possibility of using hyperpolarized spins to cool a single mechanical mode. Numerical examples suggest that cooling would be negligible for resonators of size scale ~ 10 um or larger. In the regime characterized by these examples, substantial cooling requires sufficiently strong spin-resonator coupling that neither a mechanical mode nor a spin mode can be distinguished in the spin-resonator system; instead, the modes of the system include equal contributions from the spins and the mechanical resonator. The spin-resonator correlations responsible for cooling make a significant contribution to the symmetric correlation function of the resonator coordinate, with the result that the noisy \"thermal torque\" acting on the resonator is increased rather than diminished by the presence of the hyperpolarized spins.
\r\n" }, { "name": "Canaria, Christie Anne", "degree": "PhD", "year": "2008", "title": "Self-Assembled Monolayers for the Study of Biological Targets ", "advisor": "Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06062008-103127", "creators": [ { "name": { "family": "Canaria", "given": "Christie Anne" }, "id": "Canaria-Christie-Anne", "display_name": "Canaria, Christie Anne" } ], "advisors": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Lansford", "given": "Rusty" }, "id": "Lansford-R", "role": "member", "display_name": "Lansford, Rusty" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/39DF-7V92", "abstract": "Understanding the interactions of biological molecules with solid supports is vital for the development of detection systems and assay platforms. These relationships are frequently quite complex, involving hydrophobic interactions, electrostatic interactions, van der Waals forces, and covalent chemical bonds. We can exploit these interactions in a solid support device by modifying the surface substrate with thin films and monolayers. Self-assembled monolayers (SAMs) are powerful tools for functionalizing and imparting chemical character to surfaces. In this thesis, alkylthiol reagents are utilized to build SAMs on gold (Au) substrates. This work characterizes and studies monolayer formation. In addition, I use SAMs to generate surfaces specific for binding proteins, DNA, and cells. The popular biotin-streptavidin motif is used to demonstrate protein binding, as well as characterize monolayer composition as a result of solvent effects. Novel reagent syntheses are presented for both biotinylated alkylthiols and triethylene-glycol alkylthiols. Together, these two reagents generate substrates which bind specific proteins, while repelling non-specific ones. An additional reagent, \u201cDMT-coated controlled porous glass (CPG),\u201d was designed and synthesized for the generation of custom sequence oligonucleotides. Phosphoramidite syntheses using this modified CPG yield oligos with a 3\u2019 alkylthiol modification. SAMs generated with this reagent demonstrate specific binding of complement strands. Both electrochemical techniques and restriction enzymes (where appropriate) provide methods for releasing monolayer-bound species. Lastly, I employ SAMs to generate substrates amenable to cell capture and cell adhesion. Binding B- and T-cell lymphocytes is achieved, demonstrating SAM-coated Au as a substrate for cell panning. Chemokine vascular endothelial growth factor (VEGF) is also bound to SAMs, generating surfaces amenable to cell adhesion and motility. Cells plated on higher surface concentrations of VEGF migrate faster, and I show the effect is specific to cells with VEGF receptors. Overall, this thesis explores the formation and utilization of SAMs for capturing and studying biological targets. The findings here may be transferred in the future into bio-sensing devices and arrays." }, { "name": "Caspi, Daniel David", "degree": "PhD", "year": "2008", "title": "The Adaptive Nature of Palladium Reactivity in Synthesis", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212008-145524", "creators": [ { "name": { "family": "Caspi", "given": "Daniel David" }, "id": "Caspi-Daniel-David", "display_name": "Caspi, Daniel David" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N37A-5970", "abstract": "Both Pd(0) and Pd(II) have had, and continue to have, far-reaching impacts on organic synthesis. The versatile nature of palladium, in conjunction with the mechanistic understanding and predictive models that have been elucidated, has permitted a wealth of exploration into the seemingly endless potential of this metal. The utility of palladium is described in the context of the syntheses of the pharmaceutical agents Prozac\u00ae, and Singulair\u00ae, as well as the natural products dragmacidin F and telomestatin.
\r\n\r\nFirst, the palladium-catalyzed aerobic oxidative kinetic resolution for the enantioselective preparation of a variety of pharmaceutical substances, including Prozac\u00ae, and Singulair\u00ae is described. In this regard, the versatility of this resolution is further demonstrated by the diversity of the substrates chosen for this study, and for the first time this work extends the utility of the resolution to include amino alcohol derivatives and highly functionalized benzylic alcohols.
\r\n\r\nSecondly, an enantiodivergent strategy for the total chemical synthesis of both (+)- and (\u2013)-dragmacidin F from a single enantiomer of quinic acid has been developed and successfully implemented. Although unique, the synthetic routes to these antipodes share a number of key features, including novel Pd(0) reductive isomerization reactions, Pd(II)-mediated oxidative carbocyclization reactions, halogen-selective Suzuki couplings, and high-yielding late-stage Neber rearrangements.
\r\n\r\nFinally, progress toward the total synthesis of the potent telomerase inhibitor telomestatin is described. Palladium-mediated cross-coupling reactions are employed to assemble oligooxazole intermediates from oxazole building blocks. Additionally, this strategy utilizes a minimum number of protecting groups, and proposes a unique aryl\u2013aryl macrocyclization as the last step of the synthesis. In addition to the biological relevance of the desired target, a successful total synthesis of telomestatin would also enable rapid access to the preparation of telomestatin analogs. This would allow for the investigation of key interactions between telomestatin and the G-quadruplex.
\r\n" }, { "name": "Connor, Rebecca Elizabeth", "degree": "PhD", "year": "2008", "title": "N-Terminal Modification and Codon Reassignment with Non-Canonical Amino Acids in Proteins", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03052008-065324", "creators": [ { "name": { "family": "Connor", "given": "Rebecca Elizabeth" }, "id": "Connor-Rebecca-Elizabeth", "display_name": "Connor, Rebecca Elizabeth" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Varshavsky", "given": "Alexander J." }, "id": "Varshavsky-A-J", "role": "member", "display_name": "Varshavsky, Alexander J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "role": "member", "display_name": "Shan, Shu-ou" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ERVA-Q969", "abstract": "Proteins are ubiquitous macromolecules that effect and control all the processes of life from reproduction to respiration to physical motion. These diverse molecules also provide physical structure and defensive mechanisms. The twenty canonical amino acids can be found in virtually every protein; however, in some organisms, the set of endogenous amino acids also contains residues outside the \u201ccanon,\u201d such as pyrrolysine, selenocysteine, and formylmethionine. Although a range of chemistries is available through natural side-chain diversity, some functionalities such as halogens, ketones, azides, alkenes, and alkynes are not found in nature. The introduction of a broader range of chemical functionality into proteins and protein-based materials through the use of non-canonical amino acids represents a challenging goal for protein engineering. The persistence of all the amino acids throughout protein sequences also presents a challenge for biochemical modification at a particular location. The insertion of a non-natural amino acid at a single location on a protein can allow specific modification without further affecting the natural protein sequence. The focus of this thesis is on a new method for the post-translational site-specific introduction of non-canonical amino acids to the N-terminus of proteins in vitro and progress made towards developing a complementary in vivo method using the E. coli L,F-transferase. Addition of non-proteinogenic functionality to the coat proteins of M13 bacteriophage using non-canonical amino acids is also explored.\r\n" }, { "name": "Cordova-Figueroa, Ubaldo M.", "degree": "PhD", "year": "2008", "title": "Directed Motion of Colloidal Particles via Chemical Reactions: Osmotic Propulsion", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-200411", "creators": [ { "name": { "family": "Cordova-Figueroa", "given": "Ubaldo M." }, "id": "Cordova-Figueroa-Ubaldo-M", "orcid": "0000-0003-4891-5325", "display_name": "Cordova-Figueroa, Ubaldo M." } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/W8X1-FQ17", "abstract": "Recent experiments showing reaction-driven propulsion at nanoscales have appeared as a possible mechanism for the transport of particles that may help us to not only understand chemo-mechanical transduction in biological systems, but also to create novel artificial motors that mimic living organisms and which can be harnessed to perform desired tasks. Reaction-driven propulsion consists of the generation of a localized potential gradient by an on-board surface chemical reaction. In this study, we propose and investigate a model for self-propulsion of a colloidal particle --- the osmotic motor --- immersed in a dispersion of ``bath\" particles. The non-equilibrium concentration of bath particles induced by a surface chemical reaction creates an osmotic pressure imbalance on the motor causing it to move. The departure of the bath particle concentration distribution from equilibrium is governed by the Damkohler number Da --- the ratio of the speed of reaction to that of diffusion --- which is employed to calculate the driving force on the motor, and from which the self-induced osmotic velocity is determined via application of Stokes drag law. To illustrate the significant physics in osmotic propulsion, a first-order surface reaction on a portion of the motor's surface is assumed, for the most part, in this work. The implications of these features for different bath particle concentrations and motor sizes are discussed. Furthermore, we investigate the role played by the distribution of reactions on the motor's surface. Different responses are expected depending on the amount of reactive surface in the limiting behaviors of the reaction speed. Lastly, we consider a motor with constant production of particles on a hemisphere as a model that resembles actin-based motility of biological cells and organelles.
\r\n\r\nThis research demonstrates that such an osmotic motor is possible and addresses such questions as: How fast can the motor move? How large of a force can it generate? What is the efficiency of such an osmotic motor? All motor behaviors discussed in this work are shown, after appropriate scaling, to be in good agreement with Brownian dynamics simulations.
\r\n" }, { "name": "David, Ralph Leonard Ameri", "degree": "PhD", "year": "2008", "title": "Associative Polymers as Antimisting Agents and Other Functional Materials via Thiol-ene Coupling", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-194010", "creators": [ { "name": { "family": "David", "given": "Ralph Leonard Ameri" }, "id": "David-Ralph-Leonard-Ameri", "display_name": "David, Ralph Leonard Ameri" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Sarohia", "given": "Virendra" }, "id": "Sarohia-V", "role": "member", "display_name": "Sarohia, Virendra" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9AHR-A213", "abstract": "Associating polymers of varying molecular design were studied as potential additives to aviation fuel, aimed to suppress misting and thereby reduce the fuel\u2019s fire hazard in crash scenarios. Molecular architectures investigated varied from random placement along polymer chains of associating groups (referred to throughout this work as \u201cstickers\u201d) to selective clustering of the stickers at chain ends. Linear chains possessing associating functional groups grafted at random positions along the entire chain were investigated first. Model polymers with matched backbone length were synthesized to examine the effects of degree of functionalization and type of interaction (self-associating or donor-acceptor) on shear and extensional rheology of both dilute and semi-dilute solutions in non-polar hydrocarbon solvents. We found that intramolecular associations dominate the behavior of self-associating chains even in semi-dilute concentrations, leading to chain collapse and reduced shear and extensional viscosities. Mixtures of donor-acceptor chains show much more favorable intermolecular pairing in dilute solutions (as evidenced by the formation of large aggregates), but nevertheless display reduced solution elasticity and extensional viscosity relative to unmodified homologues: sticker pairing interfered with the stretching of the chains in elongational flow. Molecular designs that overcome chain collapse by clustering stickers at the ends of polymer chains were studied next. We showed by theoretical modeling that symmetric linear chains displaying strongly associating endgroups suffer instead from loop formation, which traps the bulk of the polymer into small cyclic aggregates with low mist-control properties. Therefore, we suggest molecular architectures that preclude formation of cyclic supramolecules by employing several different donor-acceptor pairs that do not affect one another (\u201corthogonal\u201d pairs). This presents a synthetic challenge, i.e., the development of simple and rapid protocols for the preparation of functional polymer materials of controlled architecture and functionality. We developed such convenient protocols (fast, non-wasteful, and scalable procedures) for the functionalization of polybutadiene by thiol-ene addition to yield functional polymers of narrow polydispersity. These powerful, versatile synthetic tools can potentially be applied to add any side-group onto any polymer, copolymer, or block copolymer displaying pendant vinyl groups, with exciting potential applications in fields ranging from organic electronics to drug delivery." }, { "name": "Giurumescu, Claudiu Adrian", "degree": "PhD", "year": "2008", "title": "Quantitative Insights into Developmental Signals and Phenotypes in C. elegans", "advisor": "Asthagiri, Anand R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08022007-141737", "creators": [ { "name": { "family": "Giurumescu", "given": "Claudiu Adrian" }, "id": "Giurumescu-Claudiu-Adrian", "display_name": "Giurumescu, Claudiu Adrian" } ], "advisors": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "advisor", "display_name": "Asthagiri, Anand R." } ], "committee": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "chair", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/FVD0-R331", "abstract": "Design of biomaterials and cellular scaffolds for tissue-engineering applications and regenerative medicine requires a precise understanding of the principles underlying multicellular patterning. Adhesion, migration, division, differentiation, and apoptosis are characteristic cellular behaviors, the engineering of which has the potential to allow creation of custom, multicellular structures. These cellular events occur naturally during embryonic and postembryonic development of multicellular organisms. Development thus offers the opportunity to learn about the design principles and molecular mechanisms that guide cellular patterning.
\r\n\r\nA key finding in developmental biology is that a limited set of conserved molecular signaling pathways act at multiple times and locations throughout the embryo to introduce cell-fate asymmetries in homogenous populations of cells. In turn, these asymmetries serve as starting points for the patterning of new organs. These signaling pathways interact quantitatively at multiple levels, including signaling cues, post-translational regulation, and gene-regulatory networks, to guide multicellular patterning.
\r\n\r\nHow does the quantitative performance of these signaling networks ensure the intended phenotype pattern? How do changes in the quantitative performance of these networks, possibly over the course of evolution, give rise to new phenotypes? These are the central questions pursued in this thesis.
\r\n\r\nIn order to answer such questions, we used vulva formation in the nematode Caenorhabditis elegans as a model system of cellular patterning. We formulated a mathematical model of the molecular network underlying cellular-fate specification in this system. Computational analysis of this molecular network reveals that cell\u2013cell coupling through lateral LIN-12/Notch signaling amplifies the perception of the gradient in the epidermal-growth-factor-like soluble cue, LIN-3. Thus, the gradient in LIN-3 concentration produces an even steeper difference in LIN-3-mediated intracellular signals between adjoining cells. Such gradient amplification may be particularly important in converting a shallow, graded-specification signal into a spatial pattern of distinct fate choices.
\r\n\r\nThrough quantitative perturbations of interaction strengths between components of the vulval patterning network, we further show that our modeling approach can correctly predict phenotype patterns observed in C. elegans mutation studies. This study generated a framework for quantitative analysis of molecular networks that links quantitative molecular perturbations to patterning outcomes. This framework will prove useful in the analysis of other systems involving cellular fate decisions and in tissue engineering applications where the generation of precise cell patterns is needed. We demonstrate the generality of our approach through an application to evolutionary developmental biology. Since molecular connectivity of the vulva patterning network of several closely related Caenorhabditis species is preserved, we correctly predict the quantitative diversification that must have occurred in this network during species evolution.
" }, { "name": "Guidry, Erin Nicole", "degree": "PhD", "year": "2008", "title": "Interlocked Molecules Using Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252007-174232", "creators": [ { "name": { "family": "Guidry", "given": "Erin Nicole" }, "id": "Guidry-Erin-Nicole", "display_name": "Guidry, Erin Nicole" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XBXB-6931", "abstract": "Olefin metathesis has been employed in the efficient syntheses of a [2]catenane with the templation being provided by the recognition between a secondary ammonium ion and a crown ether. In one approach, a crown ether precursor has been clipped around an NH2+ center situated in a macrocyclic ring, yielding the mechanically interlocked compound. In the other approach, the reversible nature of olefin metathesis allows for a magic ring synthesis to occur wherein two free macrocycles can be employed as the stationary materials, leading to the formation of the same [2]catenane.
\r\n\r\nA strategy for the formation of mechanically interlocked polymers is presented. Ring-closing olefin metathesis has been shown to provide a very high yielding route to [c2]daisy-chains suitably functionalized to allow their one-step conversion to bis-olefins which can be used as monomers in ADMET polymerizations to afford mechanically interlocked polymers. Metathesis, in two different guises is making a hitherto unreachable goal in synthesis a reality.
\r\n\r\nA method for the production of cyclic polyammonium ions is presented which utilizes a polymer cyclization of azide terminated linear polymer based on the \u201cclick\u201d reaction. An azide terminated polymer was prepared using ROMP in the presence of chain transfer agents (CTA). Formation of cyclic polycateanes was explored utilizing the mutual recognition between secondary ammonium ions and crown ether macrocyles. The product of the RCM of linear crown ether dienes around cyclic polyammonium ions was investigated using 2D-DOSY.
\r\n\r\nThe ring-opening metathesis polymerization of a [2]catenane was investigated, using both a cyclic metathesis catalyst and bulky metathesis catalysts for the formation of cyclic polycatenanes and polyrotaxanes respectively. While it was found that the [2]catenane monomer could function as a ROMP monomer, no interlocked polymers were observed as products from the polymerization. Linear impurities present in either or both the [2]catenane monomer and the metathesis catalysts are believed to be responsible for the formation of the non-interlocked polyether and free macrocycle. These results highlight the critical role of purity to the successful formation of cyclic or linear interlocked polymer using a ROMP process.
" }, { "name": "Jordan, Jason Paul", "degree": "PhD", "year": "2008", "title": "The Development of Water-Soluble Olefin Metathesis Catalysts Containing an N-Heterocyclic Carbene Ligand", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07182007-154911", "creators": [ { "name": { "family": "Jordan", "given": "Jason Paul" }, "id": "Jordan-Jason-Paul", "display_name": "Jordan, Jason Paul" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B57A-ZS49", "abstract": "This research describes the development of new olefin metathesis catalysts that are stable and active in water. Earlier water-soluble metathesis catalysts rely on phosphine ligands functionalized with ionic groups. In contrast to these bis(phosphine) complexes, the catalysts reported in this research harness the increased stability and activity provided by N-heterocyclic carbene (NHC) ligands. As a result, these catalysts display an activity and stability that are unprecedented in aqueous olefin metathesis.
\r\n\r\nInitial efforts to produce the desired water-soluble metathesis catalysts employed poly(ethylene glycol) (PEG) to generate a complex that was soluble in water (Chapter 2). This catalyst was capable of the ring-opening metathesis polymerization (ROMP) of a challenging endo-norbornene monomer, which an earlier bis(phosphine) complex catalyzed poorly. While demonstrating the potential of NHC ligands to improve the activity of water-soluble metathesis catalysts, this catalyst was not sufficiently stable to mediate metathesis transformations involving acyclic olefins in water.
\r\n\r\nA careful examination of the described PEG catalyst inspired a few strategies to produce olefin metathesis catalysts with improved activities in water (Chapter 3). This strategic vision was honed by studies examining the effect of water on the decomposition of catalysts that contain an NHC ligand (Chapter 4). These studies indicated that phosphine ligands play an active role in the aqueous decomposition of ruthenium methylidene complexes, which are vital complexes for metathesis reactions involving terminal olefins. With these results in hand, incorporating NHC ligands into phosphine-free ruthenium complexes was pursued as a promising approach to producing active metathesis catalysts that are stable in water.
\r\n\r\nCatalysts supported by both isopropoxybenzylidene and NHC ligands were modified to include ammonium salts (Chapter 5). The water-soluble catalysts produced were stable in water and competently initiated aqueous ROMP. More importantly, these catalysts readily catalyzed the ring-closing metathesis of [alpha],[omega]-dienes in water. The described catalysts were also able to homodimerize allyl alcohol and homoallyl alcohol in water, which are among the few known examples of cross metathesis in neat water.
" }, { "name": "Kadaba, Neena Sujata", "degree": "PhD", "year": "2008", "title": "Structural Studies of the E. coli Methionine ABC Transporter and Its Cognate Binding Protein", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052008-121818", "creators": [ { "name": { "family": "Kadaba", "given": "Neena Sujata" }, "id": "Kadaba-Neena-Sujata", "display_name": "Kadaba, Neena Sujata" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3DRS-F441", "abstract": "ATP binding cassette (ABC) transporters use ATP hydrolysis to facilitate the transfer of diverse substrates across the membrane. Members of the methionine uptake transporter family, thought to be of considerable biological interest, have not been structurally characterized thus far. The crystal structure of the methionine importer MetNI from Escherichia coli has been solved to 3.7 \u00c5 resolution. The inward-facing conformation of this transporter adopts a more extreme arrangement than seen previously. While the permease domain consists of just five transmembrane helices per monomer, the ATP-binding cassette domain possesses a C-terminal domain in addition to the conserved architecture shared amongst this family. Analysis of the C-terminal extension has revealed a regulatory domain found in other proteins involved in amino acid metabolism, and further classifies this protein as part of the ACT family. Methionine binding in this region suggests a novel mechanism for regulation of transport that possibly stabilizes the inactive conformation of this family of transporters, as this domain is positioned between the nucleotide binding domains. Additionally, crystallization studies of the cognate binding protein to the MetNI system, MetQ were successful. The structure of the MetQ binding protein from E. coli was solved to 1.8 \u00c5 resolution, revealing a bi-lobed structure consistent with many other substrate binding proteins, yet possessing a few differences when compared with previously characterized methionine binding proteins from other organisms. The substrate binding pocket revealed a bound L-methionine residue, which shares key features with other methionine binding proteins and appears to be appropriately selective for L-methionine binding. These combined studies have provided insight into the methionine uptake system and into the ABC transporter mechanism of transport. \r\n" }, { "name": "Kam, Victor Wai Tak", "degree": "PhD", "year": "2008", "title": "Methods in Computational Protein Design", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302008-164022", "creators": [ { "name": { "family": "Kam", "given": "Victor Wai Tak" }, "id": "Kam-Victor-Wai-Tak", "display_name": "Kam, Victor Wai Tak" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S7KW-0M44", "abstract": "In silico design of protein has generated enormous interest with the rapid advances in computational power. Biological systems are known for their complexity, and we have made a series of computational developments that allow us to perform computational protein design. In this work we present a methodology for the design and prediction of protein active sites.
\r\n\r\nWe begin by presenting SCREAM, a program developed to accurately position sidechains in proteins. We show how using an improved scoring function and placement algorithm allow us to achieve better accuracy in the placement and prediction of sidechains in proteins compared to other methods.
\r\n\r\nWe then describe the development of an accurate treatment for describing hydrogen bonding. This is done by refining the hydrogen bond term in the force field DREIDING. We also need to properly describe electrostatics effects in proteins, and to this end, we introduce neutralized residues for proteins. We found that this improves the variance in our predictions dramatically.
\r\n\r\nFinally, having established the components described above, we describe a protein design methodology encompassing the above methods and tools. We show predictions we made and those having been verified by experiments.
\r\n" }, { "name": "Katz, Jordan E.", "degree": "PhD", "year": "2008", "title": "Metal Oxide-Based Photoelectrochemical Cells for Solar Energy Conversion", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-10192007-190231", "creators": [ { "name": { "family": "Katz", "given": "Jordan E." }, "id": "Katz-Jordan-E", "orcid": "0000-0002-6242-2124", "display_name": "Katz, Jordan E." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/29VB-HV45", "abstract": "In order to address the need for CO2-free energy, recent trends in global CO2 emissions and energy production are analyzed, and the photoelectrochemical properties of two types of metal oxide-based solar cells are presented.
\r\n\r\nThe effects of potential-determining cations (Li+, H+) in the electrolyte of TiO2-based dye-sensitized solar cells, using Ru(H2L\u2019)2(NCS)2, where H2L\u2019 is 4,4\u2019-dicarboxylic acid-2,2\u2019bipyridine, as a sensitizer was investigated using current density vs potential (J-E), spectrochronocoulometric, and spectroscopic methods. Photoelectrochemical cells with lower concentrations of the cations Li+ and H+ had increased open-circuit voltages (Voc), and decreased short-circuit current densities (Jsc). Spectrochronocoulometric methods indicated that the energy of states in TiO2 shifted by approximately -1 V when in contact with electrolytes lacking small cations. Spectral response measurements indicated that the loss of photocurrent was accompanied by a nearly monotonic drop in the external quantum yield across all wavelengths.
\r\n\r\nTransient absorption spectroscopy was used to measure the kinetics of interfacial electron transfer of the same system. No dependence was observed on the ultrafast dynamics of electron injection on cations used in ClO4--based solutions. However, in solutions of TBA+ with I3-/I-, femtosecond, but not picosecond, dynamics were observed. In contrast, for solutions with Li+ and ClO4-, I- or I-/I3-, both femtosecond and picosecond dynamics were observed. Nanosecond-resolved spectroscopy results show that the absence of small cations did not affect the rate of recombination, while the regeneration rate of [RuIII(H2L\u2019)2(NCS)2]+ was decreased. Results indicate that both the ground and excited state reduction potentials of the sensitizer shift as a function of small cations in solution, along with the energy of states in TiO2. The efficiency of electron injection is thus largely unchanged; rather a decrease in the regeneration rate accounts for the loss of Jsc.
\r\n\r\nFinally, a novel, high-throughput, combinatorial approach for the synthesis and screening of mixed-metal oxides for use as water-splitting photocatalysts was developed. The methodology relies on inkjet printing to form quantitative mixtures of aqueous metal oxide precursors. After pyrolysis, the photoelectrochemical properties of metal oxides can be fully characterized in an automated high-speed system, including measurement of the Voc and J-E curves.
\r\n" }, { "name": "Keith, Jason M.", "degree": "PhD", "year": "2008", "title": "Palladium Mediated Activation of Molecular Oxygen", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272008-095638", "creators": [ { "name": { "family": "Keith", "given": "Jason M." }, "id": "Keith-Jason-M", "orcid": "0000-0002-5292-397X", "display_name": "Keith, Jason M." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K4AY-P498", "abstract": "In developing environmentally benign chemistries, it is most important to use dioxygen directly in lieu of toxic and/or corrosive stoichiometric oxidants. Unfortunately, for many processes such as direct oxidations this has not yet become practical. To help develop such processes, we elucidate here the mechanism for the reaction of molecular oxygen with palladium-hydride complexes in nonpolar solvent using quantum mechanics for several PdII complexes, specifically focusing on the pathways proceeding through Pd0 and on the direct insertion of oxygen into the Pd-H bond. All the chapters presented herein focus on different aspects of the total problem as follows:
\r\n\r\nChapter 1: Activation of Molecular Oxygen by ((\u2012)-Sparteine)PdHCl: Direct Insertion presents the first proposal of a hydrogen atom abstraction from a palladium-hydride complex by triplet oxygen that demonstrates the feasibility of this mechanism.
\r\n\r\nChapter 2: Activation of Molecular Oxygen by [1,3-(CH2PtBu2)2-C6H3]PdH examines the reaction of an experimentally isolated palladium-hydride complex from which formation of Pd0 has been deemed unlikely, thus proving the previously predicted insertion mechanism to be active in a known system.
\r\n\r\nChapter 3: Activation of Molecular Oxygen by ((\u2012)-Sparteine)PdHCl: Pd0 presents a thorough investigation of possible base-assisted reductive elimination pathways that can lead to the formation of Pd0 in the ((\u2012)-Sparteine)PdHCl system, and it demonstrates that the direct insertion mechanism is in fact the process involved in this system.
\r\n\r\nChapter 4: Activation of Molecular Oxygen by ((\u2012)-Sparteine)Pd(OAc)H: Pd0 vs. Direct Insertion examines the substitution of the OAc ion for Cl in ((\u2012)-Sparteine)PdH system. The acetate ligand\u2019s ability to act as a base while chelating the Pd significantly lowers the energy involved in the Pd0 pathway, switching the calculated preference to the Pd0 pathway.
\r\n\r\nChapter 5: Activation of Molecular Oxygen by (Pyridine)2Pd(OAc)H: Pd0 vs. Direct Insertion examines the reaction of (Pyridine)2Pd(OAc)H with O2. The calculated mechanisms present feasible cis/trans isomerisation and demonstrate that the Pd0 pathway is the favored pathway for both the cis and the trans cases.
\r\n\r\nAppendix: Enantioselective Oxidations of Secondary Alcohols by (\u2013)-Sparteine-PdII Complexes examines the mechanism of specific Pd oxidation catalysis focusing on alcohol binding, deprotonation to form the corresponding alkoxide and the subsequent beta-hydride elimination.
\r\n" }, { "name": "Keith, John Andrew", "degree": "PhD", "year": "2008", "title": "Computational Insight into Homogeneous Organopalladium Catalysis", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05012008-092352", "creators": [ { "name": { "family": "Keith", "given": "John Andrew" }, "id": "Keith-John-A", "orcid": "0000-0002-6583-6322", "display_name": "Keith, John Andrew" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FAS9-DV26", "abstract": "An investigation of modern computational simulation techniques and their results in describing two notable organopalladium reactions are discussed. First, a methodology for computational quantum chemistry simulations of homogeneous catalysis is presented. We find that through careful consideration of electronic and thermodynamic energy contributions, practical methods are available to accurately study complicated reaction mechanisms and to make educated predictions about their chemistry. We apply this technique to develop the first full analysis of the Wacker Process, olefin oxidation by PdCl2 catalysts, effectively uniting nearly 50 years of research into one mechanistic model. Key findings include the identification of competitive rate determining steps that are dependent on ion concentrations and the inaccessibility of [beta]-hydride elimination during product formation. The second analysis addresses the unique performance of the enantioselective Tsuji-allylation reaction, a reaction the great potential in the fields of asymmetric catalysis and natural product synthesis. In this reaction, calculations point towards enantioselectivity determined after the rate determining step. Intriguingly, we find that C-C coupling is facile in a variant to canonical reductive elimination containing characteristics of both reductive cheletropic and Claisen rearrangements. Lastly, a model is presented to direct improved catalyst design. In total, this dissertation presents an outline for practical quantum chemical simulation of complicated and elaborate organopalladium reactions.\r\n" }, { "name": "Kim, Hugh Inkon", "degree": "PhD", "year": "2008", "title": "Fundamental and Applied Studies of the Structures and Reaction Dynamics of Biomolecules Using Mass Spectrometry and Ion Mobility Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05092008-165701", "creators": [ { "name": { "family": "Kim", "given": "Hugh Inkon" }, "id": "Kim-Hugh-Inkon", "orcid": "0000-0002-6210-3107", "display_name": "Kim, Hugh Inkon" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Kanik", "given": "Isik" }, "id": "Kanik-I", "orcid": "0000-0002-7912-2865", "role": "member", "display_name": "Kanik, Isik" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QQFG-WG57", "abstract": "Chapter 1 reviews studies of non-covalently bound metal complexes related to the structures and reactions of biomolecules in the gas phase, chapter 2 introduces the Route 66 method for identifying disulfide linkages in peptides using mass spectrometry. Collisional activation of singly charged cationic alkali and alkaline earth metal complexes of peptides with disulfide linkages results in highly selective elimination of hydrogen disulfide (H\u2082S\u2082). Further activation of the product yields amino acid sequence information in the region previously short-circuited by the disulfide bond. In chapter 3, we demonstrate applications of this methodology by identifying three disulfide linkages in insulin with a peptic digest using the Route 66 method. In chapters 4 and 5, gas phase reactions triggered by the bimolecular collision of a water molecule with collisionally activated anionic and cationic sodiated dicarboxylic acid clusters are examined. The water molecule serves as a proton donor for a dicarboxylate anion in the cluster and introduces energetically favorable dissociation pathways, such as the decomposition of the malonate ion, to yield an acetate ion and CO\u2082.
\r\n\r\nTo further explore the utility of IMS in the identification of organic compounds on other planetary bodies, pursuant to NASA objectives, ion mobilities are investigated for different classes of biomolecules. Chapters 6 and 7 report the reduced ion mobilities of protonated amino acid cations and deprotoanted carboxylate anions, respectively, determined in both N\u2082 and CO\u2082 drift gases. A 12-4 potential model for the ion-neutral interaction is used to investigate the high correlation observed between masses and mobilities of the ions. Computational analysis employing a 12-4 model supports ring conformations for multicarboxylate anions consistent with higher ion mobility values than calculated for extended structures. In Chapter 8, the ion mobilities of tertiary and quaternary ammonium cations in N\u2082 are reported along with their high mass-mobility correlation. We also detail the sensitivity of the collision cross sections of molecular ions to the ion-neutral interactions using the classical ion-neutral collision model and the computational trajectory method. The shape asymmetry of the ammonium cations plays an important role in determining the observed correlation between mass and mobility.
" }, { "name": "Lai, Bert Tsunyin", "degree": "PhD", "year": "2008", "title": "Characterizing \u03b1-Synuclein Membrane Bound Structure", "advisor": "Gray, Harry B.; Winkler, Jay Richmond", "url": "https://resolver.caltech.edu/CaltechETD:etd-05062008-171457", "creators": [ { "name": { "family": "Lai", "given": "Bert Tsunyin" }, "id": "Lai-Bert-Tsunyin", "display_name": "Lai, Bert Tsunyin" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "co-advisor", "display_name": "Winkler, Jay Richmond" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZWH6-3B84", "abstract": "A feature of Parkinson's disease is the presence of fibrillar protein deposits composed mostly of \u03b1-synuclein and calcium ions in the brain\u2019s substantia nigra region. Although \u03b1-synuclein is natively unfolded, the N-terminal region of the protein is highly helical in the presence of membrane mimics, such as acidic phospholipid vesicles and SDS micelles. The C-terminal region of \u03b1-synuclein is known to bind to calcium ions and modulates aggregation. In this thesis, the structure of \u03b1-synuclein variants, incorporated with tryptophan and 3-nitrotyrosine as donor and energy acceptor pairs, have been characterized in the presence of SDS micelles, small unilammelar vesicles, and calcium ions by various techniques. Distance distributions extracted from time-resolved fluorescence energy-transfer measurements provide site-specific information on the protein conformations. In addition, similar studies using mutants linked to early onset Parkinson\u2019s disease were also performed to investigate the structural effect caused by these mutations. Furthermore, single tryptophan mutants have been designed as fluorescent reporters. The locations of these different tryptophan residues in the bilayer were probed by lipids labeled with bromine and dinitrophenol quenchers. Finally, preliminary studies of the intramolecular structure of \u03b1-synuclein aggregates have been carried out, while elucidation of intermolecular \u03b1-synuclein aggregate structures was made possible by the synthesis of new dyes that allow for long-range fluorescent energy transfer.\r\n" }, { "name": "Lee, Sandra", "degree": "PhD", "year": "2008", "title": "Development of Iminium-Activation Technologies and the Total Synthesis of (+)-Frondosin B", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08132007-171008", "creators": [ { "name": { "family": "Lee", "given": "Sandra" }, "id": "Lee-Sandra", "display_name": "Lee, Sandra" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/83M6-7R38", "abstract": "The enantioselective imidazolidinone-catalyzed epoxidation of \u03b1,\u03b2-unsaturated aldehydes has been accomplished via a novel 1,4-heteroconjugate addition reaction using hypervalent iodine reagents. Development of an \u201cinternal syringe pump\u201d protocol for the slow release of iodosobenzene from an iminoiodinane source provides high levels of reaction efficiency and enantiomeric control in the asymmetric epoxidation of electron-deficient olefins. Fundamental to our studies were 15N NMR experiments that elucidated the oxidation pathways that lead to catalyst depletion, thereby providing a mechanistic rational for the utilization of iminoiodinanes, which circumvent these catalyst depletion pathways.
\r\n\r\nWe further established iminium catalysis as a valuable strategy for asymmetric synthesis in an organocatalytic addition of trifluoro(organo)borates and boronic acids to \u03b1,\u03b2-unsaturated aldehydes. Inspired by the Petasis reaction and guided by rational mechanistic considerations, we discovered a new mode of reactivity for organoboronates and a metal-free \u201ccoupling\u201d procedure for enantioselective C\u2013C bond construction. From a practical standpoint, this methodology stands to benefit from the structural diversity and wide commercial availability of several hundred organoboron reagents accessible to organic chemists. Furthermore, the low toxicity and the air and moisture stability of potassium organotrifluoroborates reagents make this powerful new organocatalytic process operationally trivial.
\r\n\r\nA five-step total synthesis of (+)-frondosin B highlights the stereoselective construction of a natural product target using an organocatalytic conjugate addition of a trilfluoro(organoboronate) reagent. This key step unambiguously established the absolute configuration of the frondosin B to be the (R)-enantiomer and led to the reassignment of naturally occurring frondosin B, thus resolving an existing discrepancy in the literature. To date, this work represents the most effective synthesis of frondosin B, which is accessible in only five steps and in a 32% overall yield.
" }, { "name": "Mackel, Michael John", "degree": "PhD", "year": "2008", "title": "Hydrophilic Polymers in Gels and Solutions: Surface Properties and Structure", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05192008-134942", "creators": [ { "name": { "family": "Mackel", "given": "Michael John" }, "id": "Mackel-Michael-John", "display_name": "Mackel, Michael John" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5ZVF-6156", "abstract": "Changes in the wetting properties of thin films of polyethyleneglycol (PEG) end-capped with fluoroalkyl groups are measured when the films are equilibrated at various relative humidity (RH). At high RH, the advancing contact angle on the surfaces is 20\u00ba higher than the advancing contact angle measured at low RH. The surprising transition to non-wetting character at high RH is attributed to fluoroalkyl groups ordering at the air-hydrogel interface when they are liberated by dissolution of PEG crystallites above 85% RH.
\r\n\r\nNext, the structure and tribology of a semi-interpenetrating hydrogel of agarose and an anionic polysaccharide (either hyaluronic acid or dextran sulfate) were studied. The porous structure of agarose allows incorporation of up to 2% dextran sulfate without weakening the gel\u2019s mechanical properties. Addition of the polyelectrolyte endows the gels with shape memory upon drying and reswelling; the gel can be dehydrated and rapidly swollen back to its original dimensions. The addition of both dextran sulfate and hyaluronic acid (HA) increases the lubricity of agarose when tested against hydrophilic clean glass or hydrophobic fluorinated glass. Migration of the polyelectrolytes out of the gel is believed to make the gels self-lubricating.
\r\n\t\r\nFinally, hydrophilic polymers were functionalized with photoresponsive hyrophobes in an attempt to control polymer self-assembly with light. Micelles of PEG end-capped with azobenzene molecules showed no change in size when the solutions were irradiated with UV light. PEG block copolymers were also functionalized with azobenzene and used to modify gold surfaces, but photoresponsive contact angles could not be measured. Finally, acrylamides copolymerized with the vinyl derivatives of malachite green were also studied, but the copolymers proved unsuitable for use at moderate pH.
\r\n" }, { "name": "Margelefsky, Eric Louis", "degree": "PhD", "year": "2008", "title": "Cooperative Catalysis by Bifunctionalized Mesoporous Silica", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04252008-104916", "creators": [ { "name": { "family": "Margelefsky", "given": "Eric Louis" }, "id": "Margelefsky-Eric-Louis", "display_name": "Margelefsky, Eric Louis" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9FET-BR51", "abstract": "The objective of my work was to prepare heterogeneous catalysts that can perform cooperative catalysis. Cooperative catalysis occurs when the presence of two or more functional groups provide an acceleration of a chemical reaction beyond what is possible when either of the two species is used independently. New catalytic materials were synthesized by functionalizing mesoporous silica (SBA-15) with two different functional groups with the groups distributed either randomly or arranged into heterodimeric pairs. The dependence of catalytic activity and selectivity on the surface arrangement (random vs. paired, distance between paired species) was investigated for several different condensation reactions.
\r\n\r\nCatalysts featuring both sulfonic acid and thiol groups were investigated for the synthesis of various bisphenols. Paired alkylsulfonic acid/thiol catalysts outperformed randomly-distributed catalysts in the synthesis of bisphenol A and bisphenol Z. The distance between the two groups in the acid/thiol pair was varied and the activity and selectivity were found to diminish rapidly as the acid/thiol distance grows. Paired arylsulfonic acid/thiol catalysts outperformed randomly-distributed catalysts in the synthesis of bisphenol Z, whereas the synthesis of bisphenol A was insensitive to spatial arrangement.
\r\n\r\nThe second reaction investigated was the aldol reaction in order to investigate the possibility of acid/base cooperativity. A catalyst containing alkylsulfonic acid and primary amines grouped into pairs were generated by opening surface sultone rings with ammonia. This material was catalytically inactive in the aldol reaction due to acid/base neutralization, whereas randomly-distributed acid-base materials exhibit good catalytic activity. Primary amine/carboxylic acid cooperativity was also investigated, both with homogeneous amino acids and bifunctional heterogeneous silicas. While amine/acid cooperativity was conclusively demonstrated with the homogeneous catalysts, in the heterogeneous case the cooperativity due to surface silanol groups actually overshadowed the effect of the carboxylic acids.
\r\n\r\nThe results obtained provide evidence that the spatial arrangement of disparate functional groups on the surface of a heterogeneous catalyst can have profound effects on the activity and selectivity of the catalyst.
\r\n" }, { "name": "McFadden, Ryan Michael", "degree": "PhD", "year": "2008", "title": "Applications of Palladium-Catalyzed Enantioselective Decarboxylative Alkylation in Natural Products Total Synthesis", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12172007-134752", "creators": [ { "name": { "family": "McFadden", "given": "Ryan Michael" }, "id": "McFadden-Ryan-Michael", "display_name": "McFadden, Ryan Michael" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GQ1E-RW28", "abstract": "The catalytic enantioselective preparation of all-carbon quaternary stereocenters within rings via alkylation is a major challenge in synthetic organic chemistry. Many important natural products and biologically active pharmaceuticals contain this motif. We have developed palladium-catalyzed decarboxylative alkylations capable of generating all-carbon quaternary stereocenters in good yield with high enantioselectivity.
\r\n\r\nAlkylated products are readily elaborated to synthetically useful cyclic scaffolds. The enantioselective decarboxylative alkylation is thus utilized to prepare intermediates previously reported in the total syntheses of classic natural products. Herein, we disclose modern formal syntheses of (\u2013)-Thujopsene, (-\u2013)-Dysidiolide, and (\u2013)-Aspidospermine.
\r\n\r\nThe longer-term goal was to apply this new enantioselective catalysis to the total syntheses of natural products with novel carbocyclic architectures. Our methodology is demonstrated during the first protecting group-free enantioselective total synthesis of (+)-dichroanone, a 4a-methyltetrahydrofluorene. The [6-5-6] tricyclic natural products family has members with important biological activity, and our route to (+)-dichroanone may provide general access to related compounds. During our synthetic endeavors, a novel Kumada-benzannulation approach to the aromatic portion of (+)-dichroanone was developed, along with a unique synthesis of a hydroxy-p-benzoquinone from a phenol. The absolute stereochemistry of the natural product was verified for the first time during our total synthesis.
\r\n\r\nSignificant progress has been made toward the total synthesis of the marine meroterpenoid liphagal, a potent and selective phosphatidylinositol 3-kinase alpha inhibitor. The enantioselective decarboxylative alkylation has been employed, and an acetylene [2 + 2] photoaddition / ring-opening sequence is used to construct the 7-membered ring. New understanding about the reactivity of [6-7] bicyclic scaffolds has been gathered, and the information applied during preparation of liphagal\u2019s benzofuran motif. Our efforts have led to a functionally diverse array of liphagal analogues, which may be used for structure-activity-relationship studies with phosphatidylinositol 3-kinases.
\r\n" }, { "name": "Mohanty, Sarina", "degree": "PhD", "year": "2008", "title": "Akt Phosphorylation of Drosophila Heat-Shock Factor: A Signature for Stress Resistance", "advisor": "Parker, Carl Stevens", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302008-150414", "creators": [ { "name": { "family": "Mohanty", "given": "Sarina" }, "id": "Mohanty-Sarina", "display_name": "Mohanty, Sarina" } ], "advisors": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "advisor", "display_name": "Parker, Carl Stevens" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Dunphy", "given": "William G." }, "id": "Dunphy-W-G", "role": "member", "display_name": "Dunphy, William G." } ], "option_major": [ "biochem" ], "doi": "10.7907/Z9CV4FQJ", "abstract": "The heat-shock response is vital to cellular homeostasis. Drosophila melanogaster heat-shock factor (dHSF) is the primary transcriptional activator in the stress response pathway for induction of heat-shock-mediated gene transcription. This work investigates the potential for dHSF to undergo post-translational modification by phosphorylation and lysine tagging, specifically, direct phosphorylation by kinases and covalent-lysine tagging by ubiquitin, acetyl, and SUMO groups. Direct phosphorylation of, and binding to, dHSF was demonstrated by Akt/PKB kinase. Knock-down of this kinase by RNAi resulted in a heat-shock phenotype for dHSF and the acquired DNA-binding ability characteristic of activated transcription factor. Site-directed mutagenesis of lysines within a putative nuclear localization sequence (NLS) revealed two potential sites for regulation of dHSF activation by post-translational modification. The functional consequences of synergistic Akt phosphorylation and lysine modifications are discussed \u2013 this work implicates a role for direct kinase phosphorylation in regulating the stability of dHSF." }, { "name": "Natraj, Vijay", "degree": "PhD", "year": "2008", "title": "Radiative Transfer Modeling for the Retrieval of CO\u2082 from Space", "advisor": "Yung, Yuk L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05062008-111214", "creators": [ { "name": { "family": "Natraj", "given": "Vijay" }, "id": "Natraj-Vijay", "orcid": "0000-0003-3154-9429", "display_name": "Natraj, Vijay" } ], "advisors": [ { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "advisor", "display_name": "Yung, Yuk L." } ], "committee": [ { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "chair", "display_name": "Yung, Yuk L." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/XSPZ-5F22", "abstract": "The Orbiting Carbon Observatory (OCO) mission was proposed to deliver the first temporally and spatially resolved global observations of CO2 to improve our understanding of the sources and sinks of CO\u2082. A retrieval algorithm was developed to obtain the column-averaged dry-air mixing ratio of CO\u2082 (XCO\u2082) from spectroscopic measurements of absorption in the 0.76 \u00b5m O2 A band and two near-infrared (NIR) bands of CO\u2082 centered at 1.61 \u00b5m and 2.06 \u00b5m. An aerosol optical-property database was developed to aid with the retrievals. Principal-component analysis was used to speed up radiative transfer (RT) computations. To test the algorithm, column O\u2082 was retrieved from measurements of absorption in the O2 A band over the sea surface. Using a single sounding, the column O\u2082 was retrieved with an error of around 1%. Polarization was shown to have a significant impact on the retrieval-error budget. A new model based on computing two orders of scattering (2OS) was developed to compute polarization in the OCO spectral regions. The multiple-scattering, scalar model Radiant was combined with the 2OS model to create the R-2OS OCO RT model. Tests with simulated backscatter measurements at the OCO validation sites showed that the R-2OS model reduced the biases in retrieved XCO\u2082 to much lower than 1 ppm in most scenarios, compared to errors as high as 10 ppm using the scalar model. Aerosol vertical distribution, thin cirrus and surface bidirectional reflection need further study.\r\n" }, { "name": "Nickols, Nicholas George", "degree": "PhD", "year": "2008", "title": "Endogenous Gene Regulation by DNA Binding Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06212007-155330", "creators": [ { "name": { "family": "Nickols", "given": "Nicholas George" }, "id": "Nickols-Nicholas-George", "orcid": "0000-0002-3131-9212", "display_name": "Nickols, Nicholas George" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YH4W-4H67", "abstract": "Cells integrate stimuli through networks of proteins that affect programs of gene expression. The expression of genes is controlled by transcription activators and repressors that recruit or inhibit the recruitment of transcription complexes to the promoters of target genes. Molecules that can specifically modulate these protein-DNA interfaces could have significant applications in human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) comprise a class of programmable DNA-binding ligands capable of binding to a broad repertoire of DNA sequences with affinities and specificities comparable to those of natural DNA-binding proteins. Numerous polyamide-dye conjugates localize in the nuclei of cultured cells. Multiple studies have shown that polyamides are capable of displacing DNA binding proteins from their target sites in a sequence specific manner. Early experiments in viral systems showed that polyamides can be active in cell culture. This thesis describes the use of polyamides to modulate the activity of two transcription activators: hypoxia inducible factor 1 (HIF-1) and androgen receptor (AR). Direct inhibition of the HIF-1-DNA and AR-DNA interfaces has relevance to human cancer. A polyamide that targets the hypoxia response element (HRE) binds its target site with high affinity and inhibits the expression of Vascular Endothelial Growth Factor (VEGF) and other HIF-1 induced genes in cultured cells. Similarly, a polyamide that targets the androgen response element binds its target site with high affinity and inhibits the expression of prostate specific antigen (PSA) and other androgen-induced genes in cultured cells. In both systems, the inhibition of target genes is consistent with a decrease in the occupancy of the transcription factor at relevant loci. The genome-wide effect of the HRE-targeted polyamide was compared to that of siRNA against HIF-1\u03b1. Remarkably, a comparable number of genes were affected by the HRE targeted polyamide as by the siRNA. The effect of the ARE targeted polyamide was compared to the synthetic antiandrogen bicalutamide. The polyamide and bicalutamide had a comparable effect on PSA expression, and genome-wide expression analysis reveals that both affected a similar number of transcripts. In addition, HIF-1\u03b1 siRNA and bicalutamide affected nearly all genes induced by hypoxia or androgen, respectively, while the HRE- and ARE- targeted polyamides affected a subset of each pathway that could be consistent with the DNA binding preferences of the polyamides. The data suggest that polyamides can be used to modulate the activity of selected transcription factor pathways." }, { "name": "Olson, Clifford Anders", "degree": "PhD", "year": "2008", "title": "mRNA Display Selection Using a Combinatorial 10FnIII Protein Library for Detection and Modulation of Cellular Processes", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01082008-160438", "creators": [ { "name": { "family": "Olson", "given": "Clifford Anders" }, "id": "Olson-Clifford-Anders", "display_name": "Olson, Clifford Anders" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "chair", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Baltimore", "given": "David L." }, "id": "Baltimore-D-L", "role": "member", "display_name": "Baltimore, David L." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Aberolla-Illa", "given": "Jose" }, "id": "Aberolla-Illa-J", "role": "member", "display_name": "Aberolla-Illa, Jose" } ], "option_major": [ "biochem" ], "doi": "10.7907/9RCG-P320", "abstract": "For years, the natural diversity intrinsic to the mammalian immune system has been harnessed for the generation of specific macromolecular recognition tools. With the development of in vitro selection techniques, the ability to create tailor-made, high affinity peptide-based reagents has become more powerful. The directed evolution of peptides and proteins has many applications in proteomics and functional genomics research. Combinatorial peptide libraries based on stable protein scaffolds with diversity contained within defined regions of the domain\u2019s surface enable the evolution of novel molecules. One scaffold utilized for in vitro selection experiments is the 10th fibronectin type III domain of human fibronectin. This domain is similar to the immunoglobulin fold, although it does not contain disulfides and therefore may be more appropriate for intracellular expression. We have created a new combinatorial library based on this domain and have determined that it is able to tolerate diversity within two loops. Our structured fibronectin library was used for selecting novel, high-affinity reagents by mRNA display. We applied this library towards two important systems, the NF-kappaB pathway and the SARS coronavirus. In both experiments, we generated high-affinity binders which were functional both in vitro and in vivo. A modification-specific, phospho-IkappaBalpha-binding fibronectin was selected with an affinity of 18 nM. The phospho-IkappaBalpha binder was over 1000-fold specific for the phosphorylated state and was able to inhibit IkappaBalpha degradation in vivo. High-affinity SARS nucleocapsid-binding fibronectins were also selected which were able to inhibit virus replication by over 1000-fold when expressed in SARS infected cells. Both selections demonstrate the utility of the fibronectin library for generating novel protein affinity reagents." }, { "name": "Otey, Christopher Richard", "degree": "PhD", "year": "2008", "title": "Structural and Functional Exploration of an Artificial Family of Cytochromes P450", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-06112008-094638", "creators": [ { "name": { "family": "Otey", "given": "Christopher Richard" }, "id": "Otey-Christopher-Richard", "display_name": "Otey, Christopher Richard" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "biochem" ], "doi": "10.7907/MZQM-N011", "abstract": "Protein families are comprised of numerous sequences that adopt a similar three-dimensional structure and functional properties. The superfamily of cytochromes P450 are an excellent example of a common structural scaffold being utilized for a variety of biological functions. This functional diversity is achieved in Nature through millions of years of evolution to create new and diverse sequences. We have used site-directed recombination guided by the computation algorithm SCHEMA to create an artificial family of cytochromes P450 in the laboratory. Members of this family possess unique properties such as altered activity profiles, increased thermostability and the ability to accept new substrates.
\r\n\r\nWe developed screening tools for the rapid analysis of hundreds of individual P450s. These high-throughput assays include the 4-aminoantipyrine (4-AAP) assay which is capable of detecting the hydroxylation of an aromatic ring. High-throughput carbon monoxide binding facilitates the rapid detection of P450s that correctly incorporate a heme cofactor and are thus properly folded and potentially functional. Finally, a substrate binding assay which measures a spectral shift that occurs when a substrate binds in a P450 active site is described.
\r\n\r\nFourteen double-crossover chimeras created from the bacterial P450s CYP102A1 and CYP102A2 were constructed to calibrate the P450 scaffold for SCHEMA, a computational algorithm used to minimize structural disruption in chimeric proteins. We found that only chimeras with high levels of structural disruption as measured by SCHEMA were unfolded. Among the fourteen chimeras we also observed three different activity profiles based on peroxygenase kinetic assays with the substrates p-nitrophenoxydodecanoic acid (12-pNCA), 2-phenoxyethanol and allyloxybenzene.
\r\n\r\nWe applied this calibration to create an artificial family comprising ~3,000 chimeric heme P450 proteins that correctly fold and incorporate a heme cofactor by recombining three cytochromes P450 at seven crossover locations chosen to minimize structural disruption. Members of this protein family differ from any known sequence at an average of 72 and by as many as 109 amino acids. Most (>73%) of the properly folded chimeric P450 heme proteins are catalytically active peroxygenases; some are more thermostable than the parent proteins. A multiple sequence alignment of 955 chimeras, including both folded and not, was analyzed using logistic regression analysis (LRA) to identify key structural contributions to cytochrome P450 heme incorporation and peroxygenase activity and suggests possible structural differences between parents CYP102A1 and CYP102A2.
\r\n\r\nThirty-four members of this artificial family were assayed for functional diversity on a set of eight substrates. P450 chimeras were able to exceed the parents in total activity on all eight substrates and were grouped into five different groups based on activity profiles using K-means clustering. Activity profiles on eight substrates were then performed in high throughput to produce a data set of 330 chimeras. The mean percent standard deviation of the activity assays showed the reproducibility of these high-throughput data and further analysis may reveal information about sequence-structure-function relationships.
\r\n\r\nThe products of the catalytic reactions of four chimeric P450s with substrates of human P450s, some of which are drug compounds, were analyzed by HPLC in order to determine their identity. Chimeras were able to produce authentic human metabolites of chlorzoxazone, zoxazolamine and propranolol, showed peroxidase acitivty on 4-aminobiphenyl and produced an unknown product with tolbutamide. Finally, the peroxygenase activity of a mutant P450 heme domain is able to be further altered and enhanced using directed evolution. After two rounds of directed evolution and screening with the 4-AAP assay, we found mutants with altered substrate specificities and an overall enhancement of activity.
\r\n\r\nThe design and high-throughput methodologies described here can be used to create artificial protein families and to discover new and useful protein sequences. Like natural protein families, artificial protein families can be used to identify regions of protein sequence and structure that are important for folding and function. This is especially useful for analyzing protein families with few members or for validating tools for structure prediction and for protein sequence-structure-function analysis. Artificial protein families are also rich in sequence diversity and can provide sources of novel protein function. Using the high-throughput methodologies described here, chimeric P450s with enhanced activity, altered activity profiles, and the ability to hydroxylate drug-like compounds to produce authentic human metabolites were discovered in our artificial family of P450s. These methodologies will hopefully be extended to the study of other protein families and to the creation and discovery of increasingly valuable protein catalysts.
" }, { "name": "Poon, Yan Shuen", "degree": "PhD", "year": "2008", "title": "The Characterization and Structure of Mechanosensitive Channels of Small Conductance", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-144531", "creators": [ { "name": { "family": "Poon", "given": "Yan Shuen" }, "id": "Poon-Yan-Shuen", "display_name": "Poon, Yan Shuen" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EBZ2-5D39", "abstract": "This thesis describes the investigation of the mechanosensitive channel of small conductance (MscS). The Escherichia coli MscS structure shows a homoheptameric ion channel with each monomer consisting of 3 transmembrane (TM) helices leading into the cytoplasmic domain. TM3 from each of the 7 subunits form the pore that opens up into a cytoplasmic cage, thought to be a molecular sieve. In order to further knowledge regarding the mechanism behind bacterial mechanosensation, several approaches were employed. Homologs from organisms indigenous to environments with temperatures ranging from 30\u00b0C to 95\u00b0C were cloned, expressed, and characterized. Chimeras were constructed between MscS homologs from 6 hyperthermophilic organisms and E. coli MscS, exchanging the transmembrane and cytoplasmic domains. Each protein is engineered with an N-terminal His6 tag and a C-terminal FLAG epitope. 4 homologs were found to be cytotoxic while 3 chimeras failed to rescue the osmotic-shock sensitivity of an E. coli mutant strain lacking endogenous mechanosensitive ion channel activity.
\r\n\r\nStudies revolving around the various homologs and chimeras led to the crystallization of the Helicobacter pylori MscS homolog. H. pylori MscS shares approximately 35% in sequence identity and was crystallized in space group P212121 with cell dimensions a = 123.0 A, b = 147.4 A, c = 179.4 A. Diffraction data was collected at the Stanford Synchrotron Radiation Laboratory at beamline 12-2 to 4.75 A resolution. A molecular replacement solution was achieved using the program PHASER with the E. coli MscS model (PDB: 2OAU). The refined structure shows a similar overall topology with E. coli MscS demonstrating a homoheptameric channel. The cytoplasmic domain maintains the same structure while TM1 and TM2 display slightly tighter packing with the pore. The structure of the pore suggests that H. pylori and E. coli MscS are crystallized in the same state.
\r\n" }, { "name": "Poulin-Kerstien, Katherine G.", "degree": "Masters", "year": "2008", "title": "Exploring Peptides as Template Scaffolds for Directed Olefin Metathesis Oligomerization", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-230530609", "creators": [ { "name": { "family": "Poulin-Kerstien", "given": "Katherine G." }, "id": "Poulin-Kerstien-Katherine-G", "display_name": "Poulin-Kerstien, Katherine G." } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/226t-1843", "abstract": "[No Abstract]" }, { "name": "Robichaud, David Joseph", "degree": "PhD", "year": "2008", "title": "High-Resolution Study of the O\u2082 A-Band using Frequency Stabilized Cavity Ring-Down Spectroscopy", "advisor": "Okumura, Mitchio; Chen, Pin", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212008-152946", "creators": [ { "name": { "family": "Robichaud", "given": "David Joseph" }, "id": "Robichaud-David-Joseph", "orcid": "0000-0002-8925-9013", "display_name": "Robichaud, David Joseph" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Chen", "given": "Pin" }, "id": "Chen-Pin", "role": "co-advisor", "display_name": "Chen, Pin" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Miller", "given": "Charles E." }, "id": "Miller-C-E", "role": "member", "display_name": "Miller, Charles E." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q6GB-R592", "abstract": "This thesis describes laboratory measurements of the O\u2082 A-band spectrum using frequency stabilized cavity ring-down spectroscopy (FS-CRDS). The FS-CRDS allowed the collection of high-resolution (<1 MHz) spectra in conjunction with the exception sensitivity of the CRDS technique. Line positions were measured with an accuracy better than 2 x 10 \u207b\u2075 cm \u207b\u00b9 by calibrating our spectra against the hyperfine components of \u00b3\u2079K D lines. Line parameters were determined using a variety of lineshape models from the standard Voigt profile to models incorporating speed dependence and collisional narrowing. Clear deviations are shown between the observed and Voigt profiles, while the other profiles considered were found to fit the observed lineshapes well. Line intensities obtained using the Galatry profile are compared with previously measured values and found to be approximately 1% smaller than intensities found in current databases. Many of the other lineshape parameters are in good agreement with previous measurements. However, the pressure-induced shifts of the current work are considered much more accurate than other studies. Finally we report on the line parameters of each of the isotopologues of O\u2082. " }, { "name": "Saliba, Katie Rose", "degree": "PhD", "year": "2008", "title": "Methodologies for the Rapid Synthesis of Hexoses and Their Application Towards a Differentially-Protected Chondroitin Sulfate Tetrasaccharide", "advisor": "MacMillan, David W. C.; Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-230310", "creators": [ { "name": { "family": "Saliba", "given": "Katie Rose" }, "id": "Saliba-Katie-Rose", "display_name": "Saliba, Katie Rose" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HWFJ-P813", "abstract": "Carbohydrates play many roles in biology, but their study has been hindered by the paucity of methods available to rapidly access hexoses. In 2004, the MacMillan laboratory published a two-step aldol methodology that allows access to the erythrohexoses allose, glucose, and mannose. Described herein is the development of two methodologies to access hexoses. First, the two-step aldol methodology for accessing the erythrohexoses was expanded to allow access to a differentially-protected mannosamine and gulose. Also described is the discovery of a one-step aldol methodology for accessing hexoses, which has allowed access to a protected allose and gulose.
\r\n\r\nThis methodology was applied to the synthesis of a differentially-protected chondroitin sulfate di- and tetrasaccharide. Chondroitin sulfate is a complex linear polysaccharide composed of alternating glucuronic acid and galactosamine residues that are heterogeneously sulfated. Combining the aldol methodology with a Cerny epoxide methodology developed in the Hsieh-Wilson laboratory, a core disaccharide was accessed. Model studies confirmed each position could be accessed selectively. Elaboration of this disaccharide to the protected tetrasaccharide was hindered by an unfavorable rearrangement during the tetrasaccharide coupling, so a second core disaccharide was synthesized. This core disaccharide was elaborated to a common intermediate to confirm that it should still allow selective access to each position, and then the disaccharide was elaborated towards the desired protected tetrasaccharide.
" }, { "name": "Shao, Fangwei", "degree": "PhD", "year": "2008", "title": "DNA-Mediated Hole and Electron Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06282007-105808", "creators": [ { "name": { "family": "Shao", "given": "Fangwei" }, "id": "Shao-Fangwei", "orcid": "0000-0003-2007-3920", "display_name": "Shao, Fangwei" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VZ0J-W403", "abstract": "Since the elucidation of the double helical structure of DNA, it has been proposed that the dynamic [pi]-stacking base pair array may mediate charge migration, hole transport (HT), and electron transport (ET). In this thesis work, both DNA-mediated HT and ET are investigated to explore their mechanisms by using kinetically fast electron/hole traps: cyclopropylamine-substituted bases, especially N4-cyclopropylcytosine (CPC), and N2-cyclopropylguanine (CPG). Both biochemical reaction with a variety of photooxidants and electrochemistry show that the modified bases, CPC and CPG, have similar redox properties as the natural DNA bases and are irreversible kinetic traps by ring opening on the picosecond time scale.
\r\n\r\nIn DNA assemblies containing either [Rh(phi)2(bpy')]3+ (Rh) or an anthraquinone derivative (AQ), two high energy photooxidants, appreciable oxidative damage at a distant CPC is observed, which shows that hole migration must involve also the higher energy pyrimidine bases. The damage yield is modulated by lower energy guanine sites on the same or complementary strand. Significantly, the efficiency in trapping at CPC is similar to that at flanking CPG. Thus, HT is not simply a function of the relative energies of the isolated bases, but instead may require orbital mixing among the bases. Hole migration through DNA involves occupation of all the DNA bases with radical delocalization.
\r\n\r\nThe oxidation of CPC via distant photooxidants has been found also to be sensitive to intervening structure and sequences. AQ-modified DNA assemblies of identical base composition but different base sequence have been probed. Single and double base substitutions within A-tracts modulate CPC decomposition. In fact, the entire sequence within the DNA assembly is seen to govern CPC oxidation, not simply the bases intervening between CPC and the tethered photooxidant.
\r\n\r\nThese data are reconciled in a mechanistic model of conformationally gated hole transport through delocalized DNA domains. Oxidation of CPG separated from a tethered photooxidant by A-tracts with a series of lengths over 50 A exhibits a nonmonotonically periodic distance dependence and shows that the domain sizes in the A-tract is 4-5 base pairs. Sequence-dependent DNA structure and dynamics are essential to the transient formation of the domains and hole propagation among the domains. This dynamic, delocalized model provides a basis to reconcile and exploit DNA HT chemistry.
\r\n\r\nJust as long-range hole transport through DNA has now been established, DNA-mediated electron transport has not been as well characterized. Three iridium complexes have therefore been designed in order to initiate both photooxidative and photoreductive reaction of DNA and allow direct comparison between the two. Redox potentials of excited Ir complexes are determined by both triplet energy (E0-0) and ground state redox potentials. Two of the iridium complexes prepared have excited state potentials that are suffcient to oxidize purines, but not pyrimidines. The excited state oxidation potentials of three Ir complexes are around -1.0 V and would be able to reduce DNA pyrimidines. Both CPC and CPG in DNA can be decomposed by photoirradiation with the noncovalently bound iridium complexes. In particular, two of the complexes have the potential to probe oxidation of purines and reduction of pyrimidines in DNA.
\r\n\r\nStudies were also conducted using one of the iridium complexes covalently tethered to DNA oligonucleotides. Hence the metal complex serves as both a photooxidant and photoreductant in the study of DNA-mediated hole and electron transport. In the Ir-tethered DNA assemblies, a metal complex stabilizes the DNA duplex through its intercalative, functionalized dppz ligand. Cyclopropylamine-substituted bases, CPC and CPG, are used as kinetic fast electron and hole traps to probe the resulting charge migration processes after direct photoirradiation of the assemblies. Reductive decomposition of CPC via ET as well as the oxidation of CPG via HT is observed. Thus, the iridium tethered DNA containing cyclopropylamine-substituted bases provides a unique model system to explore the two DNA-mediated charge transport processes through the same DNA bridges. For the first time, ET and HT can be initialized by the same photoredox probe employing the identical electronic interaction mode with DNA.
\r\n\r\nA flash quench technique was also applied to Iridium-tethered DNA in order to generate the ground state photoreductant and initiate photoreduction using 5'-bromo-uridine (BrU) as the electron trap. Efficiencies of BrU reduction in Ir-DNA upon flash quench technique was found to be comparable to that of CPG oxidation upon direct photoirradiation of Ir-DNA. Furthermore, in Ir-tethered DNA assemblies containing CPG or BrU as either the hole or electron trap, the sequence dependence of HT versus ET through an A-tract was examed. When CPG and BrU are placed in either purine or pyrimidine strands in A-tract, decomposition of both modified bases are observed. Thus, transient electron occupancy during ET, as well as hole occupancy during HT, are distributed onto both purine and pymidine strands in A-tract. Additionally, BrU decomposes in a more efficient fashion when it is located on a thyime-containing strands, which indicates that DNA-mediated ET prefers to pyrimidine strands rather than purine strands.
\r\n" }, { "name": "Shih, Crystal", "degree": "PhD", "year": "2008", "title": "Electron Tunneling and Hopping Through Proteins", "advisor": "Gray, Harry B.; Winkler, Jay Richmond", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122008-105452", "creators": [ { "name": { "family": "Shih", "given": "Crystal" }, "id": "Shih-Crystal", "display_name": "Shih, Crystal" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "co-advisor", "display_name": "Winkler, Jay Richmond" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0E5A-1W62", "abstract": "Long-range electron tunneling is a central component of processes that are essential for biological function. While many studies have been made to understand electron transfer in proteins, biologically efficient electron transfer at distances exceeding 25 \u00c5 remains unobserved in these experiments and hence unresolved. It is proposed that long-range electron transfer is in actuality multistep electron tunneling. What is reported in this thesis is the design, synthesis, and study of many protein systems for the purpose of studying multistep electron tunneling in azurin.
\r\n\r\nIn each system, a histidine has been introduced on the protein for attachment of a high-potential ruthenium or rhenium sensitizer ([Ru(trpy)(tfmbpy)]2+ or [Re(dmp)(CO)3]+); a nitrotyrosine, tryptophan, or tyrosine is placed between the two metal centers on the tunneling pathway. The electron transfer is triggered with the excitation of the metal label with laser light, and the kinetics are monitored, for the most part, by time-resolved UV-VIS spectroscopy.
\r\n\r\nThe first system to empirically demonstrate multistep electron tunneling in proteins was discovered; ultrafast electron transfer is observed between the copper and rhenium centers in the Re124/W122 system; the system was structurally characterized and studied by time-resolved UV-VIS and IR spectroscopies. A two-step tunneling model is proposed; the data sets for the different methods utilized are all in excellent agreement with the model.
\r\n\r\nSystematic perturbations were made to the working hopping system. It was discovered that nitrotyrosine can participate as an intermediate, but studies to demonstrate its participation in multistep tunneling are not yet fully realized. A second hopping system was discovered in the development of the Re126/W122 system.
\r\n" }, { "name": "Sorooshian, Armin", "degree": "PhD", "year": "2008", "title": "Aerosol Composition and Hygroscopicity Studies: Instrument Development/Characterization, Ambient and Laboratory Measurements, and Modeling", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05072008-174726", "creators": [ { "name": { "family": "Sorooshian", "given": "Armin" }, "id": "Sorooshian-Armin", "orcid": "0000-0002-2243-2264", "display_name": "Sorooshian, Armin" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/FMCM-4Q81", "abstract": "Aerosols influence climate by altering the global energy balance via scattering and absorbing solar radiation (direct effects), and by their effect on the reflectance of clouds and occurrence of precipitation (indirect effects). Aerosols also influence biogeochemical cycles, lead to diminished environmental visibility, and harm human health. This thesis focuses on advancing knowledge of critical properties, specifically composition and hygroscopicity, which govern the role of aerosols in climatic and environmental change. The methods used in this work include a combination of instrument development/characterization, ambient and laboratory measurements, and modeling.
\r\n\r\nAn instrument was developed to quantify the water-soluble composition of aerosols. The particle-into-liquid sampler (PILS) grows ambient particles into droplets that grow sufficiently large to be collected by inertial impaction. After being collected in vials, the liquid sample can be analyzed with a variety of analytical methods including ion chromatography. Results from characterization tests are presented, which summarize instrument accuracy, precision, size and time resolution, and uncertainties. An instrument model was developed to simulate operation of the PILS; the model considers plumbing transmission efficiencies, droplet growth, mixing effects, and volatilization losses. Model predictions and measurements are compared and are shown to exhibit good agreement.
\r\n\r\nA second instrument, termed the differential aerosol sizing and hygroscopicity spectrometer probe (DASH-SP), was developed to quantify aerosol hygroscopic growth and refractive index. This technique employs size classification of dry aerosol particles, equilibrates the classified particles to multiple relative humidities, and then measures the sizes of the grown particles using optical particle counters. Similar to the PILS, results from an extensive set of characterization test are presented. DASH-SP measurements of growth factor for various inorganic and organic acid salts are reported and compared to thermodynamic predictions.
\r\n\r\nAirborne aerosol measurements from four separate field campaigns are presented. The main topics of investigation from the ambient experiments include the following: (1) in-cloud production of secondary organic aerosol; (2) a characterization of the sources and character of water-soluble aerosol composition during the 2006 Gulf of Mexico Atmospheric Composition and Climate Study (GoMACCS); and (3) a comprehensive airborne characterization of aerosol from a massive bovine source.
\r\n" }, { "name": "Stafford, Ryan Leonard", "degree": "PhD", "year": "2008", "title": "Design of Protein-DNA Dimerizers", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08232007-154048", "creators": [ { "name": { "family": "Stafford", "given": "Ryan Leonard" }, "id": "Stafford-Ryan-Leonard", "display_name": "Stafford, Ryan Leonard" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PF5M-KF68", "abstract": "Genes are regulated by proteins called transcription factors that bind to DNA in a sequence-specific manner and modulate the rate of transcription. Mutated transcription factors often lead to abnormal gene expression, developmental defects, and disease. This thesis describes the design of chemicals called protein-DNA dimerizers that mimic natural transcription factor protein-DNA complexes. In the long-term, it is hoped that these dimerizers will be able to engage or even replace mutant transcription factors and artificially regulate gene expression in living cells. Specifically, programmable DNA binding pyrrole-imidazole polyamides conjugated to YPWM peptide motifs incorporating various linker domains facilitate the binding of a natural transcription factor, extradenticle, to DNA. From a design point of view, it has been explored what the minimum size and shape (branched or linear) is that will ultimately be optimal for cell uptake with adequate functional potency in the transcriptional apparatus. Branched dimerizers are shown to function with a minimal WM dipeptide protein-binding domain in vitro up to 37 degrees C, and linear dimerizers are shown to function with WMK tripeptides up to 20 degrees C. Collectively, branched and linear dimerizers can facilitate protein binding to DNA from 2 base pair overlap sites to ones that reach 6 base pairs apart. Polyamide-WM-fluorescein conjugates are also found to be cell permeable in several cell lines including HeLa, MCF-7, and PC3. These studies provide insight into the importance of linker length and composition, binding-site spacing and orientation, and the protein binding domain content that are important for the optimization of protein DNA-dimerizers suitable for biological experiments." }, { "name": "Traub, Matthew C.", "degree": "PhD", "year": "2008", "title": "Chemical Functionalization and Electronic Passivation of Gallium Arsenide Surfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-07172007-124916", "creators": [ { "name": { "family": "Traub", "given": "Matthew C." }, "id": "Traub-Matthew-C", "display_name": "Traub, Matthew C." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2A4E-HV45", "abstract": "Chemically controlled, low defect-density surfaces are essential for the incorporation of gallium arsenide into solar conversion and optoelectronic devices. Detailed X-ray photoelectron spectroscopic (XPS) studies have been conducted on chemically functionalized GaAs(111)A surfaces. Quantitative analysis of this surface after HCl(aq) etching reveals that it is completely free of observable oxide and As(0) contaminants, and is terminated with nearly a full monolayer of Cl. These surface Ga-Cl bonds have been reacted with the phosphine reagents PCl3 and PEt3, both of which introduce P atoms onto the surface. Direct reaction of PCl3 with the oxide-terminated surface leads to surfaces that are nearly oxide free but contain measurable amounts of As(0). Steady-state photoluminescence (PL) intensity measurements were used to evaluate the effectiveness of these techniques at passivating surface carrier recombination. Consistent with the chemical observations, etched and functionalized surfaces showed enhanced PL, while surfaces functionalized directly with PCl3 did not.\r\n\r\nThe effects of surface functionalization were explored on GaAs nanocrystals chemically synthsized with an oxide capping layer. Transmission electron microscopy and powder X-ray diffraction demonstrated that the particles were anisotropically etched by treatment with HCl(aq). XPS measurements showed that the Cl-terminated particles were almost entirely free of oxide but contained significant As(0) contamination. Further functionalization of the particles with N2H4 or NaSH replaced surface Cl atoms with N or S moieties but did not remove this As(0). The corresponding band gap PL of these particles was quite weak. Annealing the functionalized particles lead to the disappearance of the As(0) and strong enhancement of the PL intensity. These results imply that surface As(0) is a dominant carrier trap on nanoscale GaAs surfaces and should be broadly applicable for improving the performance of GaAs nanocrystals and nanowires.\r\n\r\nFinally, Fermi\u2019s golden rule has been used to develop relationships between rate constants for electron transfer in donor-bridge-acceptor and electrode-bridge-acceptor systems and resistances across metal-bridge-electrode and metal-bridge-tip junctions. This formulation was used to predict resistances for alkanethiolate, oligophenylene, and DNA bridges from reported donor-acceptor electron-transfer measurements in these systems. These predicted values were compared to reported resistances measured for these molecules." }, { "name": "Tsai, Sherry Mon-Yue", "degree": "PhD", "year": "2008", "title": "Alpha-Diaminobutyric Acid-Linked Hairpin Polyamide-Alklylator Conjugates ", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10152007-175458", "creators": [ { "name": { "family": "Tsai", "given": "Sherry Mon-Yue" }, "id": "Tsai-Sherry-Mon-Yue", "display_name": "Tsai, Sherry Mon-Yue" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3S8Y-YD79", "abstract": "The ability to control gene expression through the use of DNA sequence-specific, cell-permeable molecules holds therapeutic promise. Pyrrole-imidazole polyamides are a class of synthetic ligands that can be programmed to bind a broad repertoire of DNA sequences with affinities and specificities comparable to natural DNA-binding proteins. These ligands are generally linked via a turn moiety, resulting in a \u2018hairpin\u2019 structure. Conjugation of polyamides to the non-specific DNA alkylator chlorambucil produces molecules capable of the sequence-specific alkylation of DNA that can arrest gene transcription. We have identified \u03b1-diaminobutyric acid (\u03b1-DABA) as a new turn moiety that can give polyamide-chlorambucil conjugates distinctive biological properties in cellular and small animal models; this may be due to their increased DNA alkylation specificities relative to the standard \u03b3-DABA-linked conjugates. A general characterization of \u03b1-DABA-linked polyamides and their conjugates is reported.
\r\n\r\nAlso described is the development of a modular synthesis of chondroitin sulfate (CS) glycosaminoglycans \u2014 a class of linear, sulfated oligosaccharides that play critical roles in neuronal development, cell division, and spinal cord injury. CS structure in vivo is complex and heterogeneous, hampering efforts to understand its precise biological roles. Access to CS molecules of precisely defined structures is critical to understanding their structure-function relationships. The reported synthetic route is capable of accessing CS structures of defined lengths and sulfation motifs, providing a new approach to understanding these important molecules.
\r\n" }, { "name": "Tuttle, Jamison Bryce", "degree": "PhD", "year": "2008", "title": "Development of Enantioselective Organocatalytic Hydrogenation Methods and Progress toward the Total Synthesis of (+)-Minfiensine", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04292008-113738", "creators": [ { "name": { "family": "Tuttle", "given": "Jamison Bryce" }, "id": "Tuttle-Jamison-Bryce", "display_name": "Tuttle, Jamison Bryce" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/SJGJ-2K48", "abstract": "The development of an enantioselective organocatalytic hydrogenation reaction utilizing the LUMO-lowering activation of \u03b1,\u03b2-unsaturated aldehydes has been developed. This strategy employs an imidazolidinone catalyst to activate the alkene towards conjugate reduction of the pendant \u03b2,\u03b2-disubstituted alkene by a Hantzsch dihydropyridine. This is the first general methodology that utilizes disubstituted alkenes for iminiuim activation chemistry and stereoconvergently reduces mixtures of olefin geometric isomers to favor an enantioenriched product. Furthermore, the reagents are air and moisture stable making this new process operationally trivial.
\r\n\r\nBy exploiting the aforementioned mode of reactivity, enones have been successfully reduced utilizing a privileged imidazolidinone catalyst. These studies led to the discovery of a novel Hantzsch dihydropyridine that exhibits a dramatic increase in reactivity. Further comparison of these Hantzsch derivatives provides interesting physical and structural data that may account for the observed differences.
\r\n\r\nA rapid entry into the tetracyclic framework of minfiensine utilizing our group\u2019s organocascade cyclization methodology was undertaken. This strategy demonstrates the first example of a 2,3-dialkyl substituted indole starting material successfully reacting under our pyrroloindoline-forming conditions. Various strategies for introducing an allyl silane moiety for use as a SOMOphile to furnish the final ring of the pentacycle were pursued. Numerous attempts were unsuccessful, and studies for introducing the allylsilane post-cyclization were undertaken. These experiments have led to the construction of a vicinal diol that should be two transformations away from attempting the key SOMO cyclization. If successful, the resulting intermediate will be six steps away from the final natural product.
\r\n" }, { "name": "Vizcarra, Christina Luisa", "degree": "PhD", "year": "2008", "title": "Development and Evaluation of Protein Design Methods for Functional Targets", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-140215", "creators": [ { "name": { "family": "Vizcarra", "given": "Christina Luisa" }, "id": "Vizcarra-Christina-Luisa", "display_name": "Vizcarra, Christina Luisa" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/G16E-JZ97", "abstract": "Computational protein design seeks to identify amino acid sequences that will fold into a specified three-dimensional structure. Extending this technique from identification of sequences that retain a native structure to the design of sequences that will carry out a function has been a significant challenge. Modeling the energetics of catalysis and binding requires considerations that may not be necessary for the design of folded, stable proteins. I have investigated models for protein electrostatics with the goal of improving current methods for the design of functional molecules. The work in this thesis is focused on the Poisson-Boltzmann model, a dielectric continuum model that describes the effect of solvent polarization on the electrostatic potential in a protein. I found that this model is amenable to design calculations, as judged by its ability to be decomposed into terms that are used in sequence selection.
\r\n\r\nAside from energy estimation, there are a number of assumptions that are made in protein design in order to make the problem computationally tractable. Because of these assumptions, and also because of incomplete models of protein function, it is expected that many proteins sequences will need to be experimentally characterized to find one that meets a difficult design goal. To this end, I examined methods for using computational tools to produce libraries of protein sequences. These studies showed that (1) structure-based, computational library design methods can be used to generate libraries with a high number of folded proteins and (2) computational design is a promising tool for generating highly mutated proteins with a diverse range of functions.
" }, { "name": "Win, Maung Nyan", "degree": "PhD", "year": "2008", "title": "Engineering RNA Devices for Gene Regulation, Biosensing, and Higher-Order Cellular Information Processing", "advisor": "Smolke, Christina D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282008-142750", "creators": [ { "name": { "family": "Win", "given": "Maung Nyan" }, "id": "Win-Maung-Nyan", "display_name": "Win, Maung Nyan" } ], "advisors": [ { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "advisor", "display_name": "Smolke, Christina D." } ], "committee": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "chair", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/H6J4-P729", "abstract": "The proper regulation of gene expression is critical to many biological processes occurring in the cell. It is becoming increasingly apparent that post-transcriptional processing pathways play significant roles in regulating the expression of various genes in both prokaryotic and eukaryotic organisms, where they direct a variety of complex cellular functions. A striking example of a biological communication and control system directing sophisticated gene expression regulation through precise molecular recognition is the class of RNA regulatory elements, called riboswitches, comprised of distinct sensor (ligand-binding) and actuator (gene-regulatory) functions that control gene expression in response to changing levels of specific target ligand concentrations.
\r\n\r\nInspired by these natural examples, numerous synthetic riboswitch systems have been developed and have made profound contribution to the field of riboswitch engineering. However, these early examples of synthetic riboswitches pose one or more challenges, such as portability of the switch design across different cellular systems and modularity and programmability of the components comprising the switch molecule. Therefore, we set out to develop a modular and extensible RNA-based gene-regulatory platform that will provide a framework for the reliable design and construction of gene regulatory systems that can control the expression of specific target genes in response to effector molecules of interest. The platform is called the \u201cribozyme switch\u201d and composed of distinct functional components, which are modularly coupled and functionally independent of each other. Through this platform, ribozyme switch devices that enable up- or down-regulation of target gene expression were developed. Design modularity and response programmability of the switch platform were also demonstrated. We also exhibited the versatility of the platform in implementing application-specific control systems for small molecule-mediated regulation of cell growth and non-invasive in vivo sensing of metabolite production.
\r\n\r\nThrough the ribozyme switch platform, we further constructed higher-order RNA devices that enable complex cellular information processing operations, including logic control (AND, NOR, and NAND gates), advanced computation (bandpass filter and signal shift in the output swing), and cooperativity (signal gain). Finally, we extended the small ribozyme switch platform responsive to small molecules to a different class of ligand molecules, proteins, by developing protein-responsive gene regulators and cellular biosensors. In addition to engineering RNA devices for programming cellular function, we also developed a high-throughput method for functional characterization of small molecule-binding RNA aptamers, which enables robust, accurate, and rapid characterization of such RNA aptamers. This method can be very useful as we (and others) develop RNA aptamers for small molecules of specific interest, which can be subsequently integrated into the ribozyme switch platform as sensing elements for specific applications. Together, these research developments hold synergistic values for the reliable construction of \u2018designer\u2019 gene-regulatory systems for various biotechnological and medical applications.
" }, { "name": "Xiu, Xinan Joanne", "degree": "PhD", "year": "2008", "title": "Structure-Function Studies of Nicotinic Acetylcholine Receptors Using Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12142007-125144", "creators": [ { "name": { "family": "Xiu", "given": "Xinan Joanne" }, "id": "Xiu-Xinan-Joanne", "display_name": "Xiu, Xinan Joanne" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" } ], "option_major": [ "biochem" ], "doi": "10.7907/HWGS-7Z13", "abstract": "Nicotinic acetylcholine receptors (nAChR) are an important family of ligand gated ion channels found throughout the CNS and the PNS. They have been indicated in a series of physiological functions and pathological states. nAChRs have received extensive study in the past as a prototype of the Cys loop LGIC member. Growing interest in developing subtype specific agents targeting nAChRs to treat neurological diseases require more detailed structural and functional information in the numerous members of the nAChR family.
\r\n\r\nWe performed structure-function studies on the chemical scale of several of the most important members of this family using a powerful combination of conventional mutagenesis and unnatural amino acid incorporations. Chapter 2 describes our research in studying the channel gating mechanism of the prototypic nAChR, the muscle type (\u03b1\u2081)\u2082\u03b2\u03b3\u03b4. We studied thoroughly the gating interface of the receptor and concluded that the overall charging pattern of the gating interface, and not any specific pairwise electrostatic interactions, controls the gating process in the Cys loop superfamily. Chapter 3 reports our studies in the ligand binding mechanism of the most prevalent neuronal type \u03b14\u03b22 and \u03b17 nAChR. We identified a cation-\u03c0 interaction and a hydrogen bond employed by nicotine with the \u03b14\u03b22 receptor. These two key interactions are absent or significantly diminished in both the muscle type receptors and in the \u03b17 form of neuronal receptor. In Chapter 4 we studied the ligand binding mechanism of a relatively newly characterized neuronal receptor, \u03b14\u03b24.
\r\n\r\nFrom these studies, we found that in the Cys loop superfamily, homology in amino acid sequences and structures do not translate into a shared functional mechanism. In fact, different sets of chemical interactions are adopted between ligands and the receptor, and between amino acids within the ion channel proteins, both in ligand binding and channel gating.
\r\n\r\nIon channels are membrane bound multi-subunit macromolecules. We are able to carry out such exhaustive detailed structure-function studies by means of the fast developing methodology of unnatural amino acid incorporation by nonsense suppression. This thesis also describes our effort to improve the efficiency of nonsense suppression. In particular, we designed multiple 21nt small interfering RNA (siRNA) targeting release factor 1 (eRF1) in both HEK cells and Xenopus oocytes, and monitored the nonsense suppression efficiency change in vivo and in vitro by RNA PCR, Western blotting, fluorescence, and electrophysiology (Chapter 5).
\r\n" }, { "name": "Yoo, Tae Hyeon", "degree": "PhD", "year": "2008", "title": "Proteins of Novel Composition: Synthesis, Evolution, Dynamics", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03202008-163647", "creators": [ { "name": { "family": "Yoo", "given": "Tae Hyeon" }, "id": "Yoo-Tae-Hyeon", "orcid": "0000-0003-1448-3165", "display_name": "Yoo, Tae Hyeon" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/MKAG-YJ31", "abstract": "Recent efforts from several laboratories have expanded the repertoire of noncanonical amino acids that can be incorporated into recombinant proteins, either by amino acid replacement or by nonsense or frameshift suppression. The recruitment of new amino acid constituents endows the protein engineering field with powerful tools, and raises the prospects for creating novel proteins. In particular, global replacement of one of the canonical amino acids by a non-canonical analog would be expected to cause marked changes in protein structure, dynamics, and function.
\r\n\r\nRegardless of many possible advantages such as enhanced stability or reactivity, it seems likely that global replacement will in many cases compromise protein folding and function, since both protein structure and protein folding pathways have evolved in a context defined by the canonical amino acid side chains. In order to address the problem, we examined the laboratory re-evolution of the green fluorescent protein (GFP) following global replacement of its Leu residues by 5,5,5-trifluoroleucine (Tfl). The reduced fluorescence of bacterial cells expressing fluorinated GFP was recovered through eleven rounds of random mutagenesis of the GFP gene and screening via fluorescence-activated cell sorting. The mutant protein in fluorinated form showed improved photophysical properties, resistance to acid denaturation, and folding efficiency both in vivo and in vitro.
\r\n\r\nIn order to expand our understanding the roles of fluorinated constituents in protein environments, we studied the hydration dynamics at fluorinated protein surfaces by installing Tfl at surface-exposed positions of several coiled-coil proteins and monitoring the fluorescence Stokes shift of Trp with femtosecond resolution. Installing a Tfl residue near the Trp probe retarded the hydration dynamics. These results show that the strong but static dipole moment of the C-F bond interacts with water molecules in a quite different way from the C-H bond, and is instead more similar to polar (or charged) molecules.
\r\n\r\nThe ability of engineering aminoacyl-tRNA synthetases is critical in successful incorporation of analogues into proteins. We have developed a high-throughput method of screening methionyl-tRNA synthetase (MetRS) libraries for global incorporation of noncanonical amino acids. A variant of GFP was engineered to permit incorporation of analogues into its Met sites with minimal loss of fluorescence. Using this variant as a translational reporter, we screened a library of E coli MetRS variants for activity toward 6,6,6-trifluoronorleucine, and identified a MetRS mutant that enabled high-yield expression of recombinant proteins with quantitative replacement of Met with Tfn.
\r\n\r\nThe work explored in this thesis addresses three aspects of protein engineering using noncanonical amino acids: evolution of proteins with novel compositions, effects of unnatural chemical constituents on the protein hydration dynamics, and engineering aaRS for incorporation of new analogues. Even though the results shown here are restricted to fluorinated amino acids, we believe that these approaches can be applied to any noncanonical amino acid. These methodologies and the expanded understanding of noncanonical amino acids in protein environments will accelerate the creation of novel proteins with many copies of abiological constituents.
" }, { "name": "Zhang, Cheng-Zhong", "degree": "PhD", "year": "2008", "title": "Interplay Between Long-Range And Short-Range Interactions In Polymer Self-Assembly And Cell Adhesion", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechETD:etd-11022007-232906", "creators": [ { "name": { "family": "Zhang", "given": "Cheng-Zhong" }, "id": "Zhang-Cheng-Zhong", "orcid": "0000-0001-8825-7158", "display_name": "Zhang, Cheng-Zhong" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "chemeng" ], "doi": "10.7907/GCH8-4A59", "abstract": "Interplay between long-range and short-range interactions is a common theme in soft and biological matter, which results in complicated self-assembly behaviors. We study two examples of this interplay: reversible gelation of associating polymers and ligand-receptor interactions in membrane adhesion. In associating polymer solutions, the competition between the conformation flexibility of polymer chains and the enthalpic monomer interactions results in phase-separated micro-structures at the mesoscopic scale; both gelation and the microphase order-disorder transition are manifestations of this self-assembly. We further establish that reversible gelation is similar to the glass transition: both are characterized by ergodicity breaking, aperiodic micro-structures, and non-equilibrium relaxations over a finite temperature range. In the study of ligand-receptor interactions between surfaces, we emphasize the interplay between specific ligand-receptor binding, and generic physical interactions. We find that both the finite spatial extension of receptors and their mobilities affect their binding affinity. As a special case of the interplay between receptor binding and generic interactions, we study the dynamics of membrane adhesion that is mediated by receptor binding but fulfilled through membrane deformations. We calculate the energy barrier of the adhesion as a result of membrane bending deformations and the double-well adhesion potential, and analyze the different scenarios according to the shape of the adhesion potential by scaling arguments.\r\n" }, { "name": "Agapie, Theodor", "degree": "PhD", "year": "2007", "title": "Synthetic, Reactivity, and Mechanistic Studies Relevant to Olefin Oligomerization and Polymerization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04092007-132543", "creators": [ { "name": { "family": "Agapie", "given": "Theodor" }, "id": "Agapie-Theodor", "orcid": "0000-0002-9692-7614", "display_name": "Agapie, Theodor" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R42C-K778", "abstract": "Chapters 2 and 3 present synthetic, structural, and mechanistic studies relevant to the selective trimerization of ethylene to 1-hexene using a chromium diphosphine catalyst system. The studied diphosphines, PNPL=(o-L-C\u2086H\u2084)\u2082PN(Me)P(o-L-C\u2086H\u2084)\u2082, display a PNP backbone with phosphine-aryl groups ortho-substituted with ethers, amines, or thioethers (L=OMe, NMe2, or SMe). Chromium(0) and chromium(III) complexes have been prepared, characterized structurally, and tested for catalytic activity, highlighting the importance of the pendant ether groups. A chromacyclopentane model complex, (PNPO4)Cr(o,o-biphenyldiyl)Br, has been isolated using the parent phosphine system (PNPO4, L=OMe). Starting with this model system, the olefin trimerization reaction has been investigated using trans-, cis-, and gem-d2-ethylene as well as mixtures of C\u2082D\u2084 and C\u2082H\u2084. The selectivity of \u03b1-olefin insertion into the chromacyclopentane mimic and that of \u03b2-H elimination from chromacycloheptanes have been studied. The relative rates of insertion of terminal and internal olefins into the chromacyclopentane moiety have been measured.
\r\n\r\nChapters 4, 5, and 6 present synthetic studies of tantalum, titanium, and zirconium complexes supported by a new tridentate bisphenolate framework, along with applications to olefin polymerization and mechanistic studies of organometallic transformations based on these architectures. The utilized ligand framework involves a bisphenol connected at the ortho positions via semirigid, ring-ring (sp\u00b2-sp\u00b2) linkages to a flat ring (pyridine, thiophene, furan, or benzene). These ligands were found to coordinate to metals in a mer fashion to give a variety of binding geometries. A tantalum system supported by the benzene bridged bisphenolate was found to undergo intramolecular CH activation faster than metal-alkyl protonolysis by a pendant phenol, un unprecedented process for early metals. An \u03b1-H abstraction reaction has afforded access to a tantalum benzylidene supported by the pyridine linked bisphenolate. Isotope labeling studies and variable temperature kinetics measurements were used to investigate the mechanisms of these transformations. Group 4 complexes supported by the present bisphenolates were found to have interesting catalytic behavior for the propylene polymerization and oligomerization, upon activation with excess MAO. The propylene polymerization activity of present zirconium complexes is excellent, exceeding 10\u2076 g polypropylene / (mol Zr \u2022 h), in some cases.
\r\n\r\nChapter 7 presents the synthesis and study of group 3 dialkyl complexes supported by tetradentate L2N-phenolates (L = S, N, O). These complexes were found to undergo a non-dissociative ligand exchange process in solution. The mechanism of this process was studied by using variable temperature NMR spectroscopy.
" }, { "name": "Arjara, Gitrada", "degree": "PhD", "year": "2007", "title": "Refolding a \u03b2-Barrel Membrane Protein\r \r ", "advisor": "Gray, Harry B.; Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292007-061922", "creators": [ { "name": { "family": "Arjara", "given": "Gitrada" }, "id": "Arjara-Gitrada", "display_name": "Arjara, Gitrada" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Clemons", "given": "William M." }, "id": "Clemons-W-M", "role": "member", "display_name": "Clemons, William M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4PSM-AS02", "abstract": "The field of membrane protein folding is relatively new compared to soluble protein folding. This thesis describes spectroscopy investigations of the refolding and dynamics of a \u03b2-barrel membrane protein. The amphiphilic, \u03b2-barrel outer membrane protein A (OmpA) refolds and inserts directly into a lipid vesicle or micelle from a denatured state in aqueous urea solution. Spectroscopic probes used to study this system are native tryptophans located at positions 7, 15, 57, 102, and 143. Steady-state and time-resolved fluorescence measurements were performed using single tryptophan mutants of full-length OmpA (325 residues) and the truncated, transmembrane domain (176 residues). Both full-length and truncated mutants exhibit similar tryptophan emission lifetimes, suggesting that the transmembrane microenvironment is not greatly perturbed by the presence of the C-terminus.
\r\n\r\nWhile the microenvironments of folded full-length and truncated OmpA appear similar, the dynamics of refolding at each tryptophan position exhibit subtle differences when the C-terminus is present. Specifically, we observe that tryptophan-102, which faces the pore interior, inserts and folds the fastest while tryptophan-7, which does not cross the bilayer, is the slowest. Fluorescence anisotropy decays also indicate that tryptophan-7 is the most flexible residue compared to the other tryptophans. Temperature studies below the lipid gel-liquid transition temperature have also been performed. In the lipid gel phase, OmpA adsorbs to the surface of the vesicles but contains immediate \u03b2-sheet structure upon folding as well as very hydrophobic tryptophan environments. It is still uncertain from ensemble measurements whether this species is a true intermediate.
\r\n\r\nFluorescence energy transfer kinetics have successfully determined the intramolecular distance between tryptophan-7 and cysteine-175 labeled with a dansyl fluorophore. These results reveal that the barrel ends of OmpA come into contact early in the refolding process and remain close together up to the final assembly of the barrel. We also have evidence that the adsorbed species at low temperatures is not an intermediate in the folding pathway since no energy transfer is observed for this species. These spectroscopic investigations have provided the foundation for further fundamental studies to dissect the molecular mechanism of the folding pathway of OmpA as well as other integral membrane proteins.
" }, { "name": "Augustyn, Katherine Emily", "degree": "PhD", "year": "2007", "title": "Fundamental Mechanisms and Biological Applications of DNA-Mediated Charge Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282007-225441", "creators": [ { "name": { "family": "Augustyn", "given": "Katherine Emily" }, "id": "Augustyn-Katherine-Emily", "display_name": "Augustyn, Katherine Emily" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "member", "display_name": "Collier, C. Patrick" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AYHS-7Q13", "abstract": "The Pi-stacked array of heterocylic aromatic DNA base pairs provides an intriguing medium for facilitating the transport of migrating charges. The mechanism of hole transport through this dynamic molecule has been extensively investigated using a wide range of techniques. In particular, our group has taken advantage of the octahedral metal complexes of rhodium (III) and ruthenium (II) to probe charge transport reactions through DNA at long range. These intercalating photooxidants, which are extremely well coupled to the DNA ?-stack, can provide us with mechanistic information through a variety of biochemical and spectroscopic techniques. Here we continue to investigate the mechanism of DNA-mediated charge transport on fast time scales using a variety of hole traps and photooxidants and examine this interesting chemistry in a biological context. DNA-mediated charge transport across three different adenine tracts lengths is monitored using a probe interior to the bridge, N6-cyclopropyladenine, CPA. Upon oxidation, the cyclopropylamine-subsituted deoxynucleoside decomposes rapidly, and the efficiency of decomposition can be used as a kinetically fast measurement of hole occupancy. This trap, incorporated serially across the bridge, can be oxidized by a distally bound photooxidant, [Rh(phi)2(bpy\u2019)]3+ (phi = 9,10-phenanthrenequinone diimmine) without significant attenuation in yield over a distance of 5 nm. These results are consistent with complete delocalization across the DNA bridge. Photooxidation of N2-cyclopropylguanine, CPG, within duplex DNA is used to probe DNA charge transport reactions initiated by the covalently bound photooxidants, [Rh(phi)2(bpy\u2019)]3+ and anthraquinone. Duplexes containing the photooxidant separated from the CPG trap by an increasing number of intervening bases are examined in order to probe DNA charge transport reactions with this kinetically fast hole trap as a function of distance and sequence. Charge transport events through sequences containing various length adenine tracts as well as most mixed sequence bridges do not simply decay exponentially nor geometrically as a function of distance. In particular, for variable-length A-tracts, decomposition decreases in a periodic fashion with increasing distance between the photooxidant and the trap; the period is ~4-5 base pairs. Results obtained from charge injection studies using 2-aminopurine as a fluorescent probe have shown a similar periodic distance dependence. These periodicities are not observed in measurements of oxidative DNA damage using double guanine sites as a slow, irreversible hole trap. Thus, CT through DNA must be probed on multiple time scales to provide mechanistic information. These results are consistent with our model for DNA CT through transient delocalized DNA domains defined by sequence-dependent base pair dynamics. While mechanistic investigations are critical for a fundamental understanding of how charges migrate through DNA, it is important to consider the biological consequences of this process. A biological role for DNA-mediated CT has been investigated in the context of the transcription factor, p53, a tumor suppressor protein involved in myriad cellular pathways such as apoptosis and growth arrest. DNA assemblies containing an anthraquinone photooxidant tethered to the 5\u2019 end of sequences containing p53 binding sites were constructed to examine the binding affinity as a function of photooxidation. We demonstrate that through photoinduced DNA-mediated CT, the p53 protein becomes oxidized and exhibits differential binding for various promoter sequence including Gadd45, p21, and Mdm2. Additionally, insertion of a mismatch intervening between the photooxidant and the p53 binding site serves to attenuate this change in binding affinity associated with photooxidation. MALDI-TOF mass spectrometric analysis of p53 tryptic digests following irradiation of the DNA bound protein provides further evidence that a chemical change occurs, consistent with oxidation of a cysteine residue in the DNA binding domain. Dipyridophenazine complexes of ruthenium (II) have been used extensively to spectroscopically investigate DNA-mediated charge transport. A novel tris heteroleptic dipyridophenazine complex of ruthenium (II), [{Ru(phen)(dppz)(bpy\u2019-his)}{Ru(NH3)5}]5+, containing a covalently tethered ruthenium pentaammine quencher coordinated through a bridging histadine has been synthesized and characterized spectroscopically and biochemically in a DNA environment and in organic solvent. Capable of undergoing intramolecular photoinduced electron transfer, the steady-state and time-resolved luminescence measurements indicate that the tethered-quencher complex is quenched relative to the parent complexes [Ru(phen)(dppz)(bpy\u2019]2+ and [Ru(phen)(dppz)(bpy\u2019-his)]2+ in DNA and acetonitrile. Intercalated into guanine containing DNA, [{Ru(phen)(dppz)(bpy\u2019-his)}{Ru(NH3)5}]5+, upon excitation and intramolecular quenching, is capable of injecting charge into the duplex as evidenced by EPR detection of guanine radicals. DNA-mediated charge transport is also evidenced using a kinetically fast cyclopropylamine-substituted base as a hole trap that undergoes irreversible oxidative ring opening on the picosecond time scale. Guanine oxidation is not observed in measurements using guanine radical as a slow, irreversible hole trap indicating that back electron transfer reactions are competitive with hole injection into the duplex. Moreover, transient absorption measurements reveal a novel photophysical reaction pathway for [{Ru(phen)(dppz)(bpy\u2019-his)}{Ru(NH3)5}]5+ in the presence of DNA, competitive with the intermolecular flash-quench process. These results illustrate the remarkable redox chemistry occurring within a bimolecular ruthenium complex intercalated in duplex DNA." }, { "name": "Austin, Ryan James", "degree": "PhD", "year": "2007", "title": "Solving Molecular Recognition Problems with Evolvable Peptide Motifs", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05072007-135522", "creators": [ { "name": { "family": "Austin", "given": "Ryan James" }, "id": "Austin-Ryan-James", "display_name": "Austin, Ryan James" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "biochem" ], "doi": "10.7907/H8BY-M951", "abstract": "Specific protein-nucleic acid and protein-protein recognition events are frequently mediated through the flexible binding surfaces of these polymers. The functional plasticity and sequence conservation of these surfaces suggests that they are highly evolvable molecular recognition sites. It may therefore be possible to develop discriminate ligands for many protein and nucleic acid targets by directed evolution of consensus ligand scaffolds or motifs. Here we review and present work on the development and use of peptide motifs to evolve high-specificity ligands toward flexible RNA-hairpin and G protein targets. The evolvabilities of these motifs and the compact arrangement of specificity-determining elements in selected sequences, demonstrate the economy of motif-based directed evolution approaches." }, { "name": "Balcerski, William Clifford", "degree": "PhD", "year": "2007", "title": "Applications of Semiconductor Photocatalysis for Both Degradation of Organics and Hydrogen Production", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212007-230239", "creators": [ { "name": { "family": "Balcerski", "given": "William Clifford" }, "id": "Balcerski-William-Clifford", "display_name": "Balcerski, William Clifford" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/23VK-VS37", "abstract": "Diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) was used to study illuminated TiO2 surfaces under both vacuum conditions and in the presence of organic molecules (decane and methanol). In the presence of a hole scavenger, electrons are trapped at Ti(III)-OH sites, and a free electrons are generated. These free electrons are seen to decay by either exposure to oxygen or to heat; in the case of heating, reinjection of holes into the lattice by loss of sorbed hole scavenger leads to a decrease in Ti(III)-OH centers. Decane adsorption experiments lend support to the theory that removal of hydrocarbon contaminants is responsible for superhydrophilic TiO2 surfaces. Oxidiation of methanol led to formation of surface bound formic acid.
\r\n\r\nTitanium dioxide was then doped with nitrogen atoms via high temperature treatment with ammonia, toward the goal of developing a catalyst capable of using visible light to degrade organic substrates. Catalyst efficiency was tested by monitoring formate degradation to CO\u2082 and H\u2082O under visible light using ion chromatography. However, reduced photocatalytic activity in the UV region, as well as a strong synthesis temperature dependence on catalytic efficiency, was observed. The N-doped TiO\u2082 surface was probed with diffuse infrared Fourier transform spectroscopy (DRIFTS), leading us to conclude that Ti-N triple bond defect sites control visible light activity and lead to an apparent reduction in overall crystallinity.
\r\n\r\nVisible light photocatalytic H\u2082 production was then studied. Microporous and mesoporous silicas (Zeolite-Y, Zeolite-L, SBA-15) and niobium oxides (KNbO\u2083, K\u2084Nb\u2086O\u2081\u2087) were combined with nanoparticulate CdS particles and Ni to form hybrid photocatalysts that produced H2 from water/ethanol solutions under visible light irradiation. Silica cavity size, which determines CdS particle size, and photocatalytic activity were found to be correlated. Photocatalytic activity was seen to decrease under acidic or basic conditions with an associated negative ionic strength effect. In the niobate catalysts, Ni doping was shown to lead to higher-energy Nb-O bonding states and to compete with Cd for ion exchange sites. XPS analysis indicated loss of Cd\u00b2\u207a ion from the metal oxide supports occured during the course of the photochemical reaction, with apparent retention of bound CdS for most catalysts.
" }, { "name": "Bartlett, Derek William", "degree": "PhD", "year": "2007", "title": "An Engineering Approach to Cancer Therapy Using Systemically Delivered siRNA", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05172007-150701", "creators": [ { "name": { "family": "Bartlett", "given": "Derek William" }, "id": "Bartlett-Derek-William", "display_name": "Bartlett, Derek William" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Rossi", "given": "John J." }, "id": "Rossi-J-J", "role": "member", "display_name": "Rossi, John J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/TS5S-FD74", "abstract": "The next generation of cancer therapeutics will specifically target processes responsible for the growth and survival of cancer cells. Among the most promising of these molecularly targeted therapeutics are small interfering RNAs (siRNAs). These siRNAs serve as the effectors of RNA interference, a naturally occurring and highly specific mechanism for regulating gene expression through sequence-specific degradation of messenger RNA. While these siRNAs have shown potential in vitro and in preclinical animal models, safe and effective systemic delivery remains one of the greatest challenges hindering their clinical application. This thesis describes an engineering approach to address the challenge of systemic delivery of siRNAs for cancer therapy.
\r\n\r\nAnalysis of the kinetics of siRNA-mediated gene silencing reveals that gene inhibition by unmodified siRNAs can last for one week in rapidly dividing cells and up to one month in cells with minimal division. Additionally, chemical modifications to enhance siRNA nuclease stability do not prolong intracellular siRNA activity. These data, when used in combination with results from a mathematical model of siRNA function, demonstrate that dilution from cell division, and not intracellular nuclease stability, is the dominant factor governing the duration of gene inhibition by siRNAs.
\r\n\r\nCyclodextrin-containing polycations (CDP) can self-assemble with siRNAs to form nanoparticles with desirable properties for systemic application. Characterization of these nanoparticles demonstrates that they can contain several thousand siRNAs, protect the siRNA payload from nuclease degradation, and be modified with transferrin targeting ligands that show multivalent binding to cell surface receptors.
\r\n\r\nMultimodality in vivo imaging with positron emission tomography (PET) and bioluminescent imaging (BLI) is used to monitor the biodistribution and function of the siRNA nanoparticles after intravenous administration in live mice. Attachment of targeting ligands to the surface of the nanoparticles enhances gene inhibition within the tumor, although the biodistribution and tumor localization are not dependent on the amount of targeting ligand. The targeting ligand likely serves to augment nanoparticle uptake by the tumor cells. When the siRNA nanoparticles are used to deliver therapeutic siRNAs to achieve tumor growth inhibition in disseminated and subcutaneous murine cancer models, schedule-dependent anti-tumor effects are observed.
" }, { "name": "Behenna, Douglas Carl", "degree": "PhD", "year": "2007", "title": "Progress Toward the Synthesis of (+)-Zoanthenol and the Development of an Asymmetric Tsuji Allylation Reaction", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10312006-164725", "creators": [ { "name": { "family": "Behenna", "given": "Douglas Carl" }, "id": "Behenna-Douglas-Carl", "display_name": "Behenna, Douglas Carl" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/46KF-QE46", "abstract": "The stereoselective synthesis of all carbon quaternary stereocenters is an important problem in synthetic chemistry due to their common occurrence in bioactive compounds. The zoanthamine class of marine natural products highlights the challenge in constructing such stereocenters. After a summary of the isolation, structure determination, and biological activities of the zoanthamine natural products, published approaches toward their chemical synthesis are reviewed.
\r\n\r\nSynthetic strategies toward the carbocyclic portion of zoanthenol focus on the synthesis of the three challenging quaternary stereocenters located on the central C ring. An unusual acid-mediated SN' cyclization of a nucleophilic arene with an allylic alcohol forms the B ring and diastereoselectively constructs the benzylic C(12) quaternary stereocenter. However, difficulties with late-stage installation of the remaining C(9) quaternary stereocenter compelled the use of C ring synthons containing the vicinal C(9) and C(22) stereocenters installed at an early stage in the synthesis. Desymmetrization of a meso-anhydride containing vicinal quaternary stereocenters accomplishes this goal in an enantioselective fashion. Several C ring synthons bearing the vicinal quaternary stereocenters are elaborated with A ring fragments, and several methods for the formation of the C(11)-C(12) bond in these systems are explored. Ultimately, a radical conjugate addition strategy provides the carbocyclic core of zoanthenol with the correct relative configuration of all three quaternary stereocenters.
\r\n\r\nThese efforts toward the synthesis of zoanthenol highlight the difficulty in generating enantioenriched alpha-quaternary cycloalkanones derived from ketones with multiple acidic alpha-hydrogens. The first direct catalytic enantioselective access to such products is achieved by the application of chiral bidentate phosphinooxazoline (PHOX) ligands to Tsuji\u2019s non-enantioselective allylation reactions. Cyclic allyl enol carbonates, silyl enol ethers, and allyl beta-ketoesters all provide uniformly excellent yields and high enantioselectivity in the reaction. The limitations on the substrate scope of the reaction are discussed. Preliminary studies into the mechanism of these allylation reactions with prochiral enolate fragments suggest that they occur by a different mechanism than the outer-sphere nucleophilic attack commonly proposed in the alkylation of prochiral allyl fragments.
\r\n" }, { "name": "Berlin, Jacob Myar", "degree": "PhD", "year": "2007", "title": "Design Of Olefin Metathesis Catalysts: From Enantioselective Reactions To Tetrasubstituted Olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02192007-153310", "creators": [ { "name": { "family": "Berlin", "given": "Jacob Myar" }, "id": "Berlin-Jacob-Myar", "orcid": "0000-0001-7498-766X", "display_name": "Berlin, Jacob Myar" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q27D-HY48", "abstract": "The widespread use of olefin metathesis in organic and polymer chemistry has been due in large part to the emergence of highly active stable ruthenium catalysts for this transformation. To date, the most successful catalysts for asymmetric olefin metathesis reactions are molybdenum based. It is expected that the development of more effective ruthenium-based catalysts for asymmetric olefin metathesis reactions will dramatically expand the synthetic utility of these reactions. Chapter 2 of this thesis describes the synthesis of novel chiral ruthenium-based olefin metathesis catalysts. These catalysts are applied to asymmetric ring-closing metathesis in chapter 3 and asymmetric ring-opening cross metathesis along with the first examples of asymmetric cross metathesis in chapter 4.
\r\n\r\nAnother area in which the use of ruthenium-based catalysts is limited is the preparation of very sterically encumbered olefins. One example of this limitation is ring-closing metathesis to form tetrasubstituted olefins, chapter 5 describes the synthesis of a family of ruthenium-based catalysts that demonstrate improved activity for this transformation.
" }, { "name": "Bloom, Jesse D.", "degree": "PhD", "year": "2007", "title": "Hidden Dimensions in Protein Evolution: Stability, Mutational Robustness, and Evolvability", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232007-094635", "creators": [ { "name": { "family": "Bloom", "given": "Jesse D." }, "id": "Bloom-Jesse-D", "orcid": "0000-0003-1267-3408", "display_name": "Bloom, Jesse D." } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Adami", "given": "Christoph Carl" }, "id": "Adami-C-C", "orcid": "0000-0002-2915-9504", "role": "member", "display_name": "Adami, Christoph Carl" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "orcid": "0000-0002-7699-0173", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3MNT-7W93", "abstract": "Proteins are evolvable in the sense that they are readily able to acquire new or improved functions through the process of mutation and selection. Here, I examine what properties influence the ability of proteins to evolve new functions. I show that proteins with similar biochemical properties can differ substantially in their capacities to withstand mutations and evolve new functions. Specifically, more stable proteins are both more mutationally robust and more evolvable, due to improved tolerance for mutations. This fact can be exploited in protein engineering. I then show how evolutionary theory can be modified to describe how a protein's mutational robustness changes during the normal course of neutral genetic drift. One of the main theoretical predictions is that proteins evolving in larger populations will gain excess stability and mutational robustness, a prediction which I confirm experimentally. Finally, I turn to the question of how neutral genetic drift can alter \"promiscuous\" protein functions that are not under selection. I show that promiscuous functions can change significantly during genetic drift, a phenomenon that may aid in the evolution of beneficial new functions. Overall, this work establishes two mechanisms whereby initially neutral mutations can influence the course of future evolution." }, { "name": "Bois, Justin S.", "degree": "PhD", "year": "2007", "title": "Analysis of Interacting Nucleic Acids in Dilute Solutions", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-211446", "creators": [ { "name": { "family": "Bois", "given": "Justin S." }, "id": "Bois-Justin-S", "orcid": "0000-0001-7137-8746", "display_name": "Bois, Justin S." } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "advisor", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Winfree", "given": "Erik" }, "id": "Winfree-E", "role": "member", "display_name": "Winfree, Erik" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "role": "member", "display_name": "Pierce, Niles A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2JCJ-SX75", "abstract": "Motivated by the growing demand for analysis tools for diverse natural and engineered DNA and RNA systems, we develop a general theory and set of computational algorithms to perform thermodynamic analysis of dilute reactive solutions and then apply these techniques to interacting nucleic acids. The theory correctly accounts for the effects of indistinguishability in partition function calculations for complexes of interacting strands. With partition functions in hand, the unique complex concentrations corresponding to thermodynamic equilibrium are obtained by solving a convex programming problem. Partition function and concentration information can then be used to calculate equilibrium base-pairing observables corresponding to experimentally measurable properties. The underlying physics and mathematical formulation of these problems lead to an interesting blend of approaches, including ideas from graph theory, group theory, dynamic programming, combinatorics, convex optimization, and Lagrange duality.
\r\n\r\nTo make these analysis tools available to researchers worldwide, we present NUPACK, a web-based software suite for thermodynamic analysis of nucleic acids. Its efficacy is demonstrated in example calculations and the results are shown to be in agreement with experiment.
\r\n\r\nFinally, the thermodynamic properties of a DNA-based triggered self-assembly device [1] are analyzed using NUPACK and extensions of its tools. The computational results complement experimental studies, exposing novel properties about the system and dictating further research.
" }, { "name": "Bunimovich, Yuri Leonid", "degree": "PhD", "year": "2007", "title": "Silicon Nanowires as Biological Sensors and Highly Efficient Thermoelectric Materials", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-151027", "creators": [ { "name": { "family": "Bunimovich", "given": "Yuri Leonid" }, "id": "Bunimovich-Yuri-Leonid", "orcid": "0000-0002-7920-8781", "display_name": "Bunimovich, Yuri Leonid" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Roukes", "given": "Michael Lee" }, "id": "Roukes-M-L", "role": "member", "display_name": "Roukes, Michael Lee" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EY6H-XK94", "abstract": "Silicon nanowires are of significant interest because of their novel properties which afford new functions. Here, we study silicon nanowires fabricated via a well established top down approach called superlattice nanowire pattern transfer (SNAP). In the first part of the thesis, nanowires are utilized for biological sensing of DNA and proteins in an electrolyte solution. Important electronic and surface properties are considered as means to optimize the device sensitivity. The removal of silicon-oxide interface is shown to improve the limit of detection by two orders of magnitude. The sensitivity can be further improved by the reduction of the doping level to 1017 cm-3. In this way, sub-femtomolar concentration of oligonucleotides in physiological conditions can be detected. While the Debye screening is circumvented by the electrostatic adsorption of primary DNA on the amine-terminated monolayer, the detection of proteins is limited by the size of the antibodies. In low ionic strength solution, ~10\u00b5M, human IL2 cytokine is detectable at 1 to 10pM concentrations. Furthermore, a model is developed which allows the determination of kinetic parameters and absolute analyte concentrations from the real-time resistance of the nanowires. This model is consistent with Langmuir model, and could, in principle, be used to determine the amount of low abundance biological molecules at concentrations below those detectable with other label-free methods, such as surface plasmon resonance technique. In addition, a novel electrochemical technique is developed which allows the spatially-selective functionalization of silicon nanowires and the construction of a small library of proteins. In the second part, the discovery of highly efficient thermoelectric materials based on silicon nanowires is discussed. A relatively simple, scalable, and single component system of silicon nanowires with figure of merit of ~1 at room temperature is developed. ZT can be tuned at various temperatures to exceed unity by varying nanowire size and/or impurity doping level. Such enhancement in ZT compared to the bulk value is achieved by significantly perturbing the phonon-mediated heat transport in a nanowire. Decreased thermal conductivities and longer lifetimes of long-wavelength phonons in a nanowire are major reasons for an increased thermoelectric efficiency of these structures." }, { "name": "Byers, Jeffery Allen", "degree": "PhD", "year": "2007", "title": "Synthetic and Mechanistic Studies into the Kinetic Resolution of \u03b1-olefins Using C\u2081\u208b and C\u2082\u208b Symmetric Zirconocene Polymerization Catalysts", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05162007-152948", "creators": [ { "name": { "family": "Byers", "given": "Jeffery Allen" }, "id": "Byers-Jeffery-Allen", "orcid": "0000-0002-8109-674X", "display_name": "Byers, Jeffery Allen" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/H55G-7C87", "abstract": "Mechanistic and synthetic investigations into the kinetic resolution of racemic \u03b1-olefins by polymerization catalysis using C\u2081\u208b and C\u2082\u208bsymmetric zirconocenes are reported. The importance of chain end control as a stereocontrol element was probed with ethylene and propylene copolymerizations catalyzed by the C\u2081\u208bsymmetric catalyst, {1,2-(SiMe\u2082)\u2082(\u03b7\u2075-3,5-C\u2085H\u2081(CHMe\u2082)\u2082)(\u03b7\u2075-4-C\u2085H\u2082((S)-CHMeCMe\u2083)]}ZrCl\u2082/MAO. Selectivity factors and pentad analysis of racemic \u03b1-olefin and propylene polymerizations catalyzed by a similar C\u2081\u208bsymmetric catalyst, {1,2-(SiMe\u2082)\u2082(\u03b7\u2075-3,5-C\u2085H\u2081(CHMe\u2082)\u2082)(\u03b7\u2075-4-C\u2085H\u2082((S)-CHEtCMe\u2083)]}ZrCl\u2082/MAO, indicate that site epimerization does not limit selectivity during kinetic resolution.
\r\n\r\nTo avoid some of the issues involved with the C\u2081\u208bsymmetric catalysts, a route to enantiopure C\u2082\u208bsymmetric zirconocenes was pursued. With the aid of the chiral auxiliary, (R)-N2,N2\u2019-di-p-tolyl-1,1\u2019-binaphtyl-2,2\u2019-diamine, enantiospecefic synthesis of (S,S)-{C\u2082H\u2084 -1,2-(1-indene)\u2082}ZrCl\u2082 was accomplished and its use for kinetic resolution was investigated. Although synthetically useful selectivities were not observed, it was determined that the C\u2082\u208bsymmetric catalyst does not racemize during polymerization, which substantiates a more thorough investigation of catalysts based on {C\u2082H\u2084 -1,2-(1-indene)\u2082}ZrCl\u2082.
" }, { "name": "Choi, Jang Wook", "degree": "PhD", "year": "2007", "title": "Bistable [2]Rotaxane Based Molecular Electronics: Fundamentals and Applications", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-194737", "creators": [ { "name": { "family": "Choi", "given": "Jang Wook" }, "id": "Choi-Jang-Wook", "orcid": "0000-0001-8783-0901", "display_name": "Choi, Jang Wook" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/X6Q6-HD24", "abstract": "Bistable [2]rotaxanes are a unique class of supramolecules that have two constitutional isomers. Upon sandwiched between two electrodes, these two isomeric states show different conducting states, thus behaving as molecular switches. In this thesis, I describe how the bistable [2]rotaxanes have been investigated to ensure that the switching characteristics in solid-state devices are those of the bistable [2]rotaxanes and not those of extraneous elements. In addition, integration of these molecules onto ultradense nanowire arrays to constitute a memory circuit is presented.
\r\n\r\nThe bistable [2]rotaxanes have been examined in various environments to study kinetics and ground-state thermodynamics between both isomeric states. In the kinetic study, as molecules are embedded in more viscous environments (solution\u2192polymer gel\u2192solid-state device), a key step in switching cycle slows down significantly, thus reflecting the environments where the molecules are surrounded. In thermodynamic study, one of the major units in the molecular structure was modified and then equilibrium population ratio between both isomeric states was monitored at various temperatures. In both solution and solid-state devices, the population ratio of the modified [2]rotaxane was more sensitive to temperature. This result is very critical in that the properties of devices can be tailored by manipulating the structure of molecular components.
\r\n\r\nThe bistable [2]rotaxanes were integrated into crossbar nanowire arrays to constitute a memory circuit. Ultra-dense nanowire arrays used as electrodes are generated by superlattice nanowire pattern transfer (SNAP) method. Due to extremely narrow pitch (~33 nm) of the SNAP nanowire arrays, the device sets a remarkable record in memory density (~1011 Bits/cm2). Although the circuits were found to have large numbers of defects, those defects were identified through electronic testing and the working bits were configured to form a fully functional random access memory for storing and retrieving information.
\r\n\r\nFinally, nanofluidic devices have been developed by utilizing the SNAP method. Due to small channel dimensions (< Debye screening length), passage of ions was modulated by electrostatic interactions between the ions and the nanochannel walls. Devices are being developed to quantify isoelectric points of peptides so that ultimately, the device could function as a protein identifier at a single molecule level.
" }, { "name": "Fern\u00e1ndez-Ballester, Lucia", "degree": "PhD", "year": "2007", "title": "Formation of Oriented Precursors in Flow-Induced Polymer Crystallization: Experimental Methods and Model Materials", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05082007-152644", "creators": [ { "name": { "family": "Fern\u00e1ndez-Ballester", "given": "Lucia" }, "id": "Fern\u00e1ndez-Ballester-Ballester-Lucia", "orcid": "0000-0001-6956-5104", "display_name": "Fern\u00e1ndez-Ballester, Lucia" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HMNK-HP78", "abstract": "This thesis presents new insights into the early events of formation of oriented precursors in flow-induced crystallization of polymers, specifically isotactic polypropylene. Experimental approaches are developed to follow the creation of thread-like precursors during flow. The use of model bimodal polymers provides insight on the role of long chains in the mechanism of formation of oriented precursors. The addition of very long chains (3500 kg/mol) at low concentration (< 1% wt) dramatically reduced the stress required to trigger formation of thread-like precursors, which opened a wide range of conditions in which to discover how oriented precursors form. The combination of powerful new methods and model materials exposed a kinetic and mechanistic step prior to propagation of oriented precursors that had not been addressed in prior literature. Furthermore, the present model systems provide a bridge to the flow-induced crystallization phenomena that occur in commercial resins, making it very likely that these well-defined polymers will reveal the underlying physics that governs the effects of flow on morphology and final properties of polymers, and providing a rational basis for molecular design of polyolefins to expand the envelope of accessible properties.
\r\n\r\nThe phenomenological effects of flow on polymer crystallization have been known for decades, manifested dramatically in most processing techniques due to the high stresses imposed onto the polymer melt. Processing flows can accelerate the kinetics of crystallization by orders of magnitude, and can induce the formation of highly oriented crystallites that, in turn, impact the final material properties in the solid state. The formation of oriented thread-like precursors is at the heart of these effects of flow on polymer crystallization; however, the fundamental mechanisms underlying their development remain elusive. This lack of understanding frustrates the formulation of a predictive model that relates the polymer molecular characteristics and the imposed processing conditions to the ensuing crystallization kinetics, the final morphology, and hence, the ultimate material properties. Here, we develop experimental approaches that provide insight into the physics of formation of the oriented precursors, which identify the essential elements required in a truly predictive model of flow-induced crystallization.
\r\n\r\nIn this work, we build on experimental capabilities of imposing well-defined flow and thermal histories onto a polymer melt, and of utilizing small quantities of material so that model polymers can be investigated, which allows us to isolate the effect of specific molecular characteristics and flow conditions. Our apparatus provides us with real-time measurements that probe a range of shear stresses throughout a slit flow channel; thus, we develop a \"depth sectioning method\" as a strategy to isolate the contribution to the real-time signal that arises from a specific level of shear stress. This method is of utmost importance since the formation of thread-like precursors depends strongly on stress. To separate the development of oriented precursors during flow from the growth of oriented crystallites on them, we develop an experimental approach, the \"temperature-jump,\" inspired by classical nucleation studies.
\r\n\r\nWe use a small concentration of ultra-high molecular weight isotactic polypropylene in a matrix of shorter chains to examine the role of long chains in the creation of thread-like precursors. The use of such high molecular weight chains has revealed a richer behavior than could be observed in earlier studies, indicating that there are two stages in thread formation, kick-off and propagation, and that the stress requirement for the first step is more stringent than for the second. The data are consistent with the hypothesis that the interaction of long chains with the tip of a shish creates a local orientation that is not found elsewhere in the flowing melt.
\r\n\r\nFinally, we combine the two experimental approaches to perform measurements that capture the development of the threads during flow. For intermediate shearing times, our results are well described by the most promising model currently available, the \"recoverable strain model,\" and lay the groundwork for determining the velocity of propagation of threads at different shearing stresses. Also, it suggests that some modifications to the recoverable strain model should be included to correctly capture kick-off and saturation of the formation of threads. The experimental tools described here can be extended to other model materials, for example, to expose the effects of long chain length > 3500 kg/mol and of the stereo-regularity of the long chains. A larger parameter space can be surveyed in the future to provide additional data to test predictive models that connect molecular characteristics of a resin to structure formation under processing conditions.
" }, { "name": "Funk, Timothy William", "degree": "PhD", "year": "2007", "title": "Chemo- and Stereoselective Olefin Metathesis in Small Molecule Synthesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06152006-110234", "creators": [ { "name": { "family": "Funk", "given": "Timothy William" }, "id": "Funk-Timothy-William", "orcid": "0000-0002-8828-1446", "display_name": "Funk, Timothy William" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/25WJ-J768", "abstract": "The major goals of the work described in this thesis were to expand the selectivity of ruthenium metathesis catalysts to include chemo- and stereoselective reactions and to apply those reactions to the synthesis of important organic compounds.
\r\n\r\nChapter 2 describes efforts to synthesize trisubstituted vinyl boronates using the cross-metathesis of 1,1-disubstituted vinyl pinacol boronates. The reactions with methyl-substituted substrates afforded products in modest yields (up to 60%), and the reactions were typically highly selective for the Z-alkene. As the size of the substituent increased, the yields and stereoselectivities decreased. The lack of reactivity of certain ruthenium catalysts in the formation of trisubstituted alkenes lent insight into how to develop a chemoselective reaction where a monosubstituted olefin would exclusively react in the presence of a more highly substituted olefin.
\r\n\r\nChapter 3 describes how conjugated dienes were synthesized by taking advantage of the large reactivity difference between monosubstituted alkenes and 1,1-disubstituted alkenes. The cross-metathesis reactions were highly chemo- and stereoselective, and only the E-isomer of the products was formed. Additionally, further functionalization of the diene products was shown to be possible in a one pot cross-metathesis/Suzuki coupling process.
\r\n\r\nThe research presented in chapters 4 and 5 focused on the asymmetric ring-closing metathesis of achiral trienes using chiral ruthenium catalysts. Chapter 4 describes how substitution on the chiral catalyst and the substrate affected the enantioselectivity of the ring-closing reaction. It was discovered that certain five, six, and seven membered rings could be made in up to 92% ee with the chiral ruthenium catalysts. The application of asymmetric ring-closing metathesis in the synthesis of (+)-5-epi-citreoviral is presented in chapter 5. The absolute configuration of one chiral center was set using asymmetric ring-closing metathesis, and the remaining three stereocenters were set from that chiral center.
\r\n\r\nIn addition, there are two appendices. Appendix 1 contains comments on the formation of tetrasubstituted olefins using unhindered ruthenium catalysts. The results from research directed toward the generation of a cis-selective olefin metathesis catalyst bearing a bidentate ligand are described in appendix 2.
" }, { "name": "Galownia, Niki Chiyomi", "degree": "PhD", "year": "2007", "title": "Signaling in Context: Parsing the Adhesion-Dependence of Growth Factor Signaling", "advisor": "Asthagiri, Anand R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04222007-221859", "creators": [ { "name": { "family": "Galownia", "given": "Niki Chiyomi" }, "id": "Galownia-Niki-Chiyomi", "display_name": "Galownia, Niki Chiyomi" } ], "advisors": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "advisor", "display_name": "Asthagiri, Anand R." } ], "committee": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "chair", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Q5RF-8K30", "abstract": "Intracellular signaling induced by adhesion and soluble growth factors is a significant contributor to cellular function. The serine/threonine kinase, extracellular signal-regulated kinase (Erk), is a prominent point of signaling crosstalk between adhesion and growth factors. Despite extensive effort, the effect of individual growth factors on adhesion-dependent Erk signaling remains unclear due to considerable protocol differences and qualitative analyses. To address these issues, we developed an experimental technique to compare systematically the crosstalk between adhesion and individual growth factors and a quantitative protocol for measuring the magnitude and dynamics of Erk signaling.
\r\n\r\nUsing these methods, we demonstrate that: (1) Adhesion to fibronectin desensitizes Erk activation for cells stimulated by either PDGF (platelet-derived growth factor) or bFGF (basic fibroblast growth factor), but not by EGF (epidermal growth factor); (2) EGF, but not PDGF or bFGF, induces adhesion-dependent Erk activation enhancement; and (3) for adherent cells, either EGF or PDGF stimulation generates transient Erk activation, while bFGF stimulation mediates sustained Erk activation. This data reveal that there are significant differences in the adhesion-dependence of growth factor signaling. The most striking observation was that adhesion desensitizes cells to low doses of specific growth factors (PDGF and bFGF). Studies conducted to uncover the underlying mechanism(s) revealed that adhesion-mediated desensitization of Erk activation exhibits rapid kinetics and occurs at or above the level of Ras activation, but does not involve Sos hyperphosphorylation.
\r\n\r\nTo further probe the mechanisms responsible for generating different Erk signaling dynamics, we constructed a simple coarse-grain model of Erk activation and deactivation pathways. These pathways are represented by four distinct motifs: activation, constitutive direct-deactivation, feedback-mediated direct-deactivation, and feedback-decoupling. Our model predicts that transient and sustained Erk signaling dynamics require specific combinations of the four signaling motifs. These predictions suggest that differences in the Erk activation motif are most likely responsible for the experimentally observed characteristics of adhesion-dependent EGF-mediated Erk signaling. Furthermore, the model indicates either feedback-decoupling deactivation or direct-deactivation as the mechanisms responsible for the observed transient-versus-sustained signaling dynamics induced by different growth factors.
" }, { "name": "Goodwin, Nicole Cathleen", "degree": "PhD", "year": "2007", "title": "Application of Iminium Activation Technologies To Natural Product Synthesis: Total Synthesis of the Spiculisporic Acids, Progress Towards the Total Synthesis of Cylindrocyclophane F, and Formal Synthesis of Cylindrocyclophane A", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07242006-134454", "creators": [ { "name": { "family": "Goodwin", "given": "Nicole Cathleen" }, "id": "Goodwin-Nicole-Cathleen", "orcid": "0000-0002-6093-7175", "display_name": "Goodwin, Nicole Cathleen" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/C7D7-XN63", "abstract": "The first enantioselective, catalytic vinylogous Mukaiyama-Michael reaction of siloxyfurans with simple alpha,beta-unsaturated aldehydes has been reported using chiral imidazolidinones. This methodology provides access to enantioenriched gamma-butenolides, a privileged motif in organic synthesis. The utility of this organocatalytic Mukaiyama-Michael reaction was highlighted by the total syntheses of (--)-spiculisporic acid and (--)-5-epi-spiculisporic acid.
\r\n\r\nInvestigations into the total syntheses of cylindrocyclophanes A and F necessitated the development of a novel B-alkyl Suzuki cross-coupling of trimethylanilinium salts using a nickel(0) catalyst and bulky phosphine ligand. This methodology study revealed a very competitive nickel-catalyzed demethylation pathway, which produced dimethylaniline byproducts. A possible explanation for this side reaction is discussed. This technology was applied to a dimerization strategy for the C\u2082-symmetric cylindrocyclophane F. Synthesis of a dimerization precursor included an enantioselective organocatalytic 1,4-addition of 3,5-dimethoxy-N,N-dimethylaniline into an \u03b1,\u03b2-unsaturated aldehyde. However, the B-alkyl Suzuki cross-coupling was unsuccessful in promoting a dimerization.
\r\n\r\nNext, the synthesis of cylindrocyclophane A was explored using an alternative ring-closing metathesis dimerization strategy. A dimerization precursor was to be assembled via the cross-coupling of trimethylanilinium salts with potassium (vinyl)trifluoroborate salts, whose syntheses featured an organocatalytic 1,4-conjugate reduction of a \u03b2,\u03b2-disubstituted enal. This cross-coupling strategy revealed olefin isomerization as a major side-reaction in the nickel-catalyzed Suzuki dimerization, making this route a non-productive approach to the natural product.
\r\n\r\nLastly, formal synthesis of cylindrocyclophane A was accomplished using (i) a nickel-catalyzed Stille cross-coupling of an activated vinyl stannane with a judiciously chosen trimethylanilinium salt and (ii) an asymmetric palladium-catalyzed allylic alkylation of an acyclic ketone. The latter represents the first example of application of the Pd\u2082(dba)\u2083/t-Bu-PHOX catalyst system to effect an asymmetric allylic alkylation on an acyclic system with good stereoselectivity. This route constituted a formal synthesis of cyclindrocyclophane A in eight linear steps, making it more efficient than the published route to the same advanced intermediate reported by Smith, which was synthesized in eleven steps.
" }, { "name": "Graham, Nicholas Alexander", "degree": "PhD", "year": "2007", "title": "Crosstalk Between Soluble Factors and Cell-Cell Interactions: Implications for Cell Cycle Control and Tumor Development", "advisor": "Asthagiri, Anand R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232007-111928", "creators": [ { "name": { "family": "Graham", "given": "Nicholas Alexander" }, "id": "Graham-Nicholas-Alexander", "orcid": "0000-0002-6811-1941", "display_name": "Graham, Nicholas Alexander" } ], "advisors": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "advisor", "display_name": "Asthagiri, Anand R." } ], "committee": [ { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "chair", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/DJ7K-MW95", "abstract": "Precise and dynamic control of cell behaviors, including proliferation, adhesion, and migration, is required for proper tissue organization and homeostasis. A key element to understanding how these cellular functions are controlled lies in uncovering the topology of the molecular signaling networks that couple environmental signals to cellular responses. In this study, we have parsed the signaling networks involved in cell cycle regulation and tumor development and uncovered novel mechanisms of crosstalk between soluble factors and cell-cell interactions.
\r\n\r\nOur findings demonstrate that extracellular cues, including the epidermal growth factor (EGF), stimulate proliferative signaling through beta-catenin, an intracellular protein that participates in both cell adhesion at the plasma membrane and transcription of cell cycle genes in the nucleus. In fact, EGF-mediated beta-catenin transcriptional activity is an essential signal for proliferation of normal epithelial cells. Additionally, in a cancer cell system, we discover that EGF cooperates with Wnt 3a, a classical agonist of beta-catenin transcriptional activity, to induce greater signaling than either ligand alone. Notably, EGF and Wnt 3a activate transcription using different sub-cellular pools of beta-catenin. Because hyperactive beta-catenin signaling drives proliferation in cancer, this suggests that attenuation beta-catenin signaling may require different therapeutic strategies for EGF- and Wnt-driven tumors.
\r\n\r\nSince beta-catenin signaling can be antagonized by binding to the cell-cell contact protein E-cadherin at the plasma membrane, proliferative signals mediated by beta-catenin may regulate growth suppression at high density, a property of normal cells that is often lost during tumorigenesis. Indeed, in non-tumorigenic epithelial cells, we demonstrate that E-cadherin is upregulated in contexts where beta-catenin signaling and DNA synthesis are suppressed. Additionally, exogenous E-cadherin suppresses proliferation with a strict requirement for beta-catenin binding. Future studies to test the hypothesis that E-cadherin regulates the growth of normal cells will benefit from a quantitative assay developed to measure E-cadherin:beta-catenin complexes. Such quantitative measurements are likely to be important because contact-mediated growth suppression by E-cadherin is coupled with a density-dependent, ligand-depletion mechanism that concomitantly regulates proliferation.
\r\n\r\nFinally, we demonstrate that EGF and other soluble factors synergistically control cell-cell interactions governing organization of normal epithelial cells into multicellular structures. Notably, this behavior resembles the program initiated during metastatic cancer, thus illustrating the flexibility of the epithelial phenotype even in non-cancerous cells. Together, these studies illustrate how the topology of molecular signaling networks can couple environmental cues including soluble extracellular factors and cell-cell interactions to regulate fundamental cellular functions.
" }, { "name": "Green, Jonathan Earl", "degree": "PhD", "year": "2007", "title": "Ultra-Dense Nano- and Molecular-Electronic Circuits", "advisor": "Heath, James R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05312007-142846", "creators": [ { "name": { "family": "Green", "given": "Jonathan Earl" }, "id": "Green-Jonathan-Earl", "display_name": "Green, Jonathan Earl" } ], "advisors": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "advisor", "display_name": "Heath, James R." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HCQH-2S48", "abstract": "This thesis describes research towards the realization of large-scale, ultra-dense nanowire-based circuits. The primary means for the construction of such circuits is the superlattice nanowire pattern transfer (SNAP) technique. This technique was optimized for the fabrication of large nanowire arrays containing over 1000 nanowires at narrow pitch and aligned over millimeter length scales. Silicon nanowire arrays were fabricated with wire widths down to ten nanometers, and with precisely-controlled electronic properties and bulk-like resistivity values through the use of diffusion doping and the selection of high-quality silicon-on-insulator substrates.
\r\n\r\nA binary tree demultiplexer circuit allows the unique addressing of N nanowires from within an ultra-dense array using of order 2xlog2(N) control wires. An implementation of this circuit was experimentally demonstrated to bridge from the submicrometer dimensions of lithographic patterning to the nanometer-scale dimensions of SNAP patterning. This circuit utilized field-effect gating by relatively large control wires to address individual nanowires from within a 150-nanowire array patterned at a wire width and pitch of 13 and 34 nanometers, respectively.
\r\n\r\nSilicon- and metal-nanowire arrays were integrated with [2]rotaxane molecular materials for the fabrication of an ultra-dense, 160,000-bit crosspoint molecular electronic memory circuit. This circuit is patterned at a record density of 1x10^11 bits per square centimeter (device-pitch of 33 nanometers), and contains bistable, electrochemically addressable [2]rotaxane switching molecules as the data storage elements within the individual crosspoint junctions. Defective junctions could be readily identified through electronic testing and isolated through software coding. The working bits could then be configured to form a functional memory circuit. The molecular-mechanical nature of the switching mechanism was confirmed through volatility measurements.
\r\n\r\nAn optimized two-step chlorination/methylation protocol was used to methyl passivate thin (~20-nanometer) silicon(111)-on-insulator microelectronic device surfaces, that were then demonstrated to be stable in air for arbitrarily long periods, and to resist oxidation due to common microelectronic fabrication procedures and wet-chemical treatments. Additionally, temperature-dependent mobility data showed that methylated silicon-on-insulator surfaces can be prepared with bulk-like mobility characteristics through careful optimization of the methylation reaction protocol.
\r\n" }, { "name": "Hamann, Thomas William", "degree": "PhD", "year": "2007", "title": "Interfacial Electron-Transfer Reactions at Semiconductor Electrodes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-05022007-055147", "creators": [ { "name": { "family": "Hamann", "given": "Thomas William" }, "id": "Hamann-Thomas-William", "orcid": "0000-0001-6917-7494", "display_name": "Hamann, Thomas William" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mc8e-x717", "abstract": "Differential capacitance versus potential and current density vs. potential measurements were used to determine the energetics and kinetics, respectively, of the interfacial electron-transfer processes of n-type ZnO electrodes in contact with aqueous solutions. The electron-transfer rate constant, ket, vs. driving force was investigated employing a series of non-adsorbing, one-electron, outer-sphere redox couples with formal reduction potentials spanning approximately 900 mV in the band-gap region. The data were well-fit by a parabola generated using classical Marcus theory with a reorganization energy, \u03bb, of 0.67 eV. The dependence of ket on \u03bb was determined using a series of compounds with similar formal reduction potentials, but reorganization energies that span approximately 1 eV. The interfacial electron-transfer rate constant decreases as the reorganization energy of the acceptor species increases and a plot of the logarithm of the electron-transfer rate constant vs. (\u03bb+\u0394G0'2/4\u03bbKBT is linear with a slope of \u2248-1. Changes in solution pH were used to shift the band-edge positions of ZnO electrodes relative to solution-based electron acceptors having pH-independent redox potentials. This strategy allowed investigation of the pH-induced driving-force dependence of ket in the normal and inverted regions. It was further found that introduction of the tert-butyl functionality on osmium tris-bipyridyl decreased the self-exchange rate constant, determined from NMR line-broadening measurements, by a factor of 50 and the interfacial electron-transfer rate constant by 100, compared to that of the analogous methyl-substituted complex. The results indicate that the tert-butyl group can act as a spacer on an outer-sphere redox couple to significantly decrease the electronic coupling of the electron-transfer reaction both in self-exchange and interfacial electron-transfer processes. Methyl-terminated, n-type, (111)-oriented Si surfaces in contact with an electron acceptor having a pH-independent redox potential were used to verify that the band edges of the modified Si electrode were fixed with respect to changes in solution pH. These results, taken together, provide strong evidence that interfacial electron-transfer rate constants at semiconductor electrodes are in excellent agreement with the predictions of a Marcus-type model of interfacial electron-transfer reactions." }, { "name": "Hejl, Andrew", "degree": "PhD", "year": "2007", "title": "Controlling Olefin Metathesis through Catalyst and Monomer Design", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02072007-103257", "creators": [ { "name": { "family": "Hejl", "given": "Andrew" }, "id": "Hejl-Andrew", "display_name": "Hejl, Andrew" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/F0HK-YQ26", "abstract": "The olefin metathesis reaction has become a widely used method for the construction of new carbon-carbon double bonds. The development of well-defined, ruthenium-based catalysts with high air- and moisture-stability and functional group tolerance has allowed synthetic chemists to exploit this reaction in many areas. The main goal of this thesis was to better understand the impact of changes in catalyst and monomer structure on the olefin metathesis reaction.
\r\n\r\nThe introduction of chelating alkylidene ligands to olefin metathesis catalysts has resulted in systems with high activity and stability that, for the most part, are active at or below room temperature. However, for some applications, catalysts that react only at higher temperatures are desirable. Chapter 2 describes the synthesis of latent olefin metathesis catalysts with chelating alkylidenes with a range of donor ligands: including phosphines, pyridines, imines, amines, and thioethers. The nature of the donor ligand was found to have a large impact on the catalyst initiation rate.
\r\n\r\nChapter 3 describes mechanistic studies of the initiation of catalysts with chelating alkylidenes. In all cases, the rate-limiting step of catalyst initiation was found to be association of the incoming olefin, not dissociation of the donor ligand. Further investigations support a mechanism where dissociation of the chelated ligand occurs prior to olefin coordination, but is fast and reversible.
\r\n\r\nChapter 4 presents a detailed study of the ring-opening metathesis polymerization (ROMP) of low-strain monomers with ruthenium-based catalysts. The effects of monomer concentration and catalyst dependence are described for unsubstituted cycloolefins. The ROMP of low-strain olefins with polar substituents is also examined, and a predictive model for ROMP feasibility is proposed.
\r\n\r\nAppendix 1 introduces a set of six reactions with specific reaction conditions to establish standards for comparing olefin metathesis catalysts. The reactions were selected on the basis of their ability to provide a maximum amount of information describing catalyst activity, stability, and selectivity, while being operationally simple. Seven of the most widely used ruthenium-based olefin metathesis catalysts were evaluated using these standards. These conditions are useful tools for the comparison and evaluation of new olefin metathesis catalysts.
" }, { "name": "Henze, Daven Ker", "degree": "PhD", "year": "2007", "title": "Forward and Inverse Analysis of Chemical Transport Models", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05312007-133239", "creators": [ { "name": { "family": "Henze", "given": "Daven Ker" }, "id": "Henze-Daven-Ker", "orcid": "0000-0001-6431-4963", "display_name": "Henze, Daven Ker" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Li", "given": "Qinbin" }, "id": "Li-Q", "role": "member", "display_name": "Li, Qinbin" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Schneider", "given": "Tapio" }, "id": "Schneider-T", "role": "member", "display_name": "Schneider, Tapio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/5647-T777", "abstract": "Assessing the discrepancy between modeled and observed distributions of aerosols is a persistent problem on many scales. Tools for analyzing the evolution of aerosol size distributions using the adjoint method are presented in idealized box model calculations. The ability to recover information about aerosol growth rates and initial size distributions is assessed given a range of simulated observations of evolving systems. While such tools alone could facilitate analysis of chamber measurements, improving estimates of aerosol sources on regional and global scales requires explicit consideration of many additional chemical and physical processes that govern secondary formation of atmospheric aerosols from emissions of gas-phase precursors. The adjoint of the global chemical transport model GEOS-Chem is derived, affording detailed analysis of the relationship between gas-phase aerosol precursor emissions (SOx, NOx, and NH3) and the subsequent distributions of sulfate - ammonium - nitrate aerosol. Assimilation of surface measurements of sulfate and nitrate aerosol is shown to provide valuable constraints on emissions of ammonia. Adjoint sensitivities are used to propose strategies for air quality control, suggesting, for example, that reduction of SOx emissions in the summer and NH3 emissions in the winter would most effectively reduce non-attainment of aerosol air quality standards. The ability of this model to estimate global distributions of carbonaceous aerosol is also addressed. Based on new yield data from environmental chamber studies, mechanisms for incorporating the dependence of secondary organic aerosol (SOA) formation on NOx concentrations are developed for use in global models. When NOx levels are appropriately accounted for, it is demonstrated that sources such as isoprene and aromatics, previously neglected as sources of aerosol in global models, significantly contribute to predicted SOA burdens downwind of polluted areas (owing to benzene and toluene) and in the free troposphere (owing to isoprene)." }, { "name": "Heo, Jiyoung", "degree": "PhD", "year": "2007", "title": "Computational Studies of Orphan G Protein-Coupled Receptors", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102006-144154", "creators": [ { "name": { "family": "Heo", "given": "Jiyoung" }, "id": "Heo-Jiyoung", "orcid": "0000-0001-9953-6400", "display_name": "Heo, Jiyoung" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rmmr-sj52", "abstract": "G protein-coupled receptors (GPCRs) play an essential role in cell communications and sensory functions. Consequently, they are involved in wide variety of diseases and are targets for many drug therapies. Particularly important is the large number of orphan GPCRs, which may play important, albeit unknown, functions in various cells. To understand their respective physiological roles, it is important to identify their endogenous ligands, and to find small molecule ligands that would serve as selective agonists or antagonists. The mas-related gene G protein-coupled receptors (Mrg receptors) belong to the orphan GPCR family, which is expressed in a specific subset of sensory neurons known to detect painful stimuli, suggesting that they could be involved in pain sensation or modulation.
\r\n\r\nThe primary focus of this thesis is to predict the 3D structure and binding site of Mrg receptors and to identify novel ligands that would be potential agonists or antagonists. We predict the 3D structure for the mouse MrgC11 (mMrgC11) and the binding site for five chiral FMRF-NH2 ligands. We correctly predict the relative binding observed for these five ligands. We find that Tyr110 (TM3), Asp161 (TM4), and Asp179 (TM5) are particularly important to binding the ligands. Subsequently, we carry out mutagenesis experiments followed by intracellular calcium release assays that demonstrate the dramatic decrease in activity for the Y110A, D161A, and D179A mutants predicted by our model.
\r\n\r\nThe all-atom molecular dynamics simulation of the mMrgC11/F-(D)M-R-F-NH2 complex structure in explicit water and infinite lipid membrane system shows that some conformational fluctuations are present, but no significant instability is detected, thus validating our structure prediction method.
\r\n\r\nThe virtual screening with the combination of QSPR and docking methods is carried out for the predicted mMrgC11 receptor. The compounds showing the antagonistic effect are identified by competitive functional assays. These hit compounds are certainly good staring points in designing better agonists or antagonists.
\r\n\r\nThe binding site of rat MrgA receptor that shows differential binding between adenine and guanine is also predicted. The predicted binding affinity correlates with the availability of the hydrogen bonds to two Asn residues, which would be primary mutation candidates to validate the structure.
" }, { "name": "Hong, Soon Hyeok", "degree": "PhD", "year": "2007", "title": "Improvement of Olefin Metathesis Efficiency through Understanding Catalyst Stability", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04022007-122855", "creators": [ { "name": { "family": "Hong", "given": "Soon Hyeok" }, "id": "Hong-Soon-Hyeok", "orcid": "0000-0003-0605-9735", "display_name": "Hong, Soon Hyeok" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QMZ9-3Y05", "abstract": "The recent development of ruthenium olefin metathesis catalysts, which show high activity and functional group tolerance, has expanded the scope of olefin metathesis. To improve efficiency of the ruthenium-catalyzed olefin metathesis, this dissertation describes: (1) mechanistic study to understand decomposition pathways of ruthenium olefin metathesis catalysts for the development of more stable and efficient catalysts, (2) a method to prevent an undesirable side reaction for the improvement of selectivity of ruthenium-catalyzed olefin metathesis, and (3) a novel ruthenium catalyst to increase olefin metathesis efficiency in aqueous media for potential biological applications and environmentally friendly approaches to this chemistry.
\r\n\r\nChapter 2 describes the first well-characterized decomposition products, dinuclear ruthenium hydride complex and methylphosphonium salt, from an N-heterocyclic carbene-based ruthenium catalyst under typical metathesis conditions. In Chapter 3, the decomposition study was expanded to other widely used ruthenium olefin metathesis catalysts. Phosphine-involvement in the decomposition was consistently observed whether or not an olefin was present. The presence of other decomposition modes for phosphine-free ruthenium catalysts was also described. Chapter 4 addresses another decomposition pathway of an N,N\u2019-diphenylbenzimidazol-2-ylidene-based catalyst via C--H activation. Chapter 6 describes the development of a novel poly(ethylene glycol)-supported water-soluble catalyst, which is active and stable in aqueous media. Chapter 7 describes an efficient, practical, and environmentally friendly method to remove residual ruthenium-containing byproducts by simple aqueous workup from olefin metathesis products using the poly(ethylene glycol)-supported catalyst.
" }, { "name": "Khair, Aditya Satish", "degree": "PhD", "year": "2007", "title": "Particle Motion in Colloidal Dispersions: Applications to Microrheology and Nonequilibrium Depletion Interactions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02122007-130627", "creators": [ { "name": { "family": "Khair", "given": "Aditya Satish" }, "id": "Khair-Aditya-Satish", "orcid": "0000-0001-6076-2910", "display_name": "Khair, Aditya Satish" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Squires", "given": "Todd M." }, "id": "Squires-T-M", "role": "member", "display_name": "Squires, Todd M." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RWKF-E288", "abstract": "Over the past decade, microrheology has burst onto the scene as a technique to interrogate and manipulate complex fluids and biological materials at the micro- and nano-meter scale. At the heart of microrheology is the use of colloidal 'probe' particles embedded in the material of interest; by tracking the motion of a probe one can ascertain rheological properties of the material. In this study, we propose and investigate a paradigmatic model for microrheology: an externally driven probe traveling through an otherwise quiescent colloidal dispersion. From the probe's motion one can infer a 'microviscosity' of the dispersion via application of Stokes drag law. Depending on the amplitude and time-dependence of the probe's movement, the linear or nonlinear (micro-)rheological response of the dispersion may be inferred: from steady, arbitrary-amplitude motion we compute a nonlinear microviscosity, while small-amplitude oscillatory motion yields a frequency-dependent (complex) microviscosity. These two microviscosities are shown, after appropriate scaling, to be in good agreement with their (macro)-rheological counterparts. Furthermore, we investigate the role played by the probe's shape --- sphere, rod, or disc --- in microrheological experiments.
\r\n\r\nLastly, on a related theme, we consider two spherical probes translating in-line with equal velocities through a colloidal dispersion, as a model for depletion interactions out of equilibrium. The probes disturb the tranquility of the dispersion; in retaliation, the dispersion exerts a entropic (depletion) force on each probe, which depends on the velocity of the probes and their separation. When moving 'slowly' we recover the well-known equilibrium depletion attraction between probes. For 'rapid' motion, there is a large accumulation of particles in a thin boundary layer on the upstream side of the leading probe, whereas the trailing probe moves in a tunnel, or wake, of particle-free solvent created by the leading probe. Consequently, the entropic force on the trailing probe vanishes, while the force on the leading probe approaches a limiting value, equal to that for a single translating probe.
" }, { "name": "Khidekel, Nelly", "degree": "PhD", "year": "2007", "title": "A Chemoenzymatic Strategy toward Understanding O-GlcNAc Glycosylation in the Brain", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03022007-083916", "creators": [ { "name": { "family": "Khidekel", "given": "Nelly" }, "id": "Khidekel-Nelly", "display_name": "Khidekel, Nelly" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "biochem" ], "doi": "10.7907/MT8P-JB95", "abstract": "Posttranslational modification to proteins represents a fundamental mechanism by which protein function is extended and elaborated. In the brain, modifications such as phosphorylation play critical roles in mediating neuronal communication and development. Unique among carbohydrate modifications is the addition of a single monosaccharide, N-acetyl-D-glucosamine, to serine and threonine residues of proteins (O-GlcNAc glycosylation). The modification shares intriguing features with phosphorylation, including its intracellular and dynamic nature. The enzyme responsible for adding the modification to proteins is necessary for life at the single cell level and O-GlcNAc glycosylation has been linked to nutrient sensing, gene expression, and in the brain, to neurodegeneration. Despite tantalizing evidence for the modification\u2019s importance, understanding O-GlcNAc glycosylation has been hampered by insufficient strategies to study it at single-protein level as well as across the proteome. Here we describe the development of a new, chemoenzymatic strategy to facilitate the discovery of O-GlcNAc proteins, as well as the first studies aimed at understanding O-GlcNAc proteome-wide, in the brain.
\r\n\r\nOur approach capitalizes on an engineered enzyme and synthetic unnatural substrate to specifically 'tag' O-GlcNAc-modified proteins for rapid and sensitive detection. We applied the methodology to the discovery of low-abundance, endogenous O-GlcNAc proteins from cells. We also combined the approach with mass spectrometry for the isolation of O-GlcNAc peptides and the mapping of glycosylation sites, the first step toward functional analysis of the modification. Overall, our efforts led to the identification of nearly fifty new O-GlcNAc proteins, several of which serve as targets for mechanistic study. Many of the proteins function in the control of transcription and translation, highlighting the proposed role for O-GlcNAc in regulating gene expression. Additionally, we provide evidence that O-GlcNAc glycosylation is particularly prevalent on proteins at the nerve terminal, or synaptosome, where it may function to control vesicle cycling and neurotransmitter release. Finally, our work has also led to the first bioanalytical, quantitative assays for O-GlcNAc dynamics in both cells and tissue. Here, we have shown that O-GlcNAc is reversible in neuronal tissue and can respond rapidly and robustly to neuronal stimulation in vivo.
" }, { "name": "Kwon, Inchan", "degree": "PhD", "year": "2007", "title": "Protein Engineering via Site-Specific Incorporation of Nonnatural Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01222007-010333", "creators": [ { "name": { "family": "Kwon", "given": "Inchan" }, "id": "Kwon-Inchan", "orcid": "0000-0003-0806-4116", "display_name": "Kwon, Inchan" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XVPN-9P37", "abstract": "Nonnatural amino acid incorporation has been one of the most important protein engineering techniques. Particularly site-specific incorporation of nonnatural amino acids would allow design of artificial proteins containing a nonnatural amino acid with minimal perturbation of their native properties. Site-specific incorporation of phenylalanine (Phe) analogs and tryptophan (Trp) analogs, such as p-bromophenylalanine (pBrF), p-iodophenylalanine, p-azidophenylalanine, 6-chlorotrytophan, 6-bromotryptophan, 5-bromotrytophan, and benzothienylalanine, into proteins in Escherichia coli has been realized by E. coli strains outfitted with a mutant yeast phenylalanyl-tRNA suppressor (ytRNAPheCUA) and a mutant yeast phenylalanyl-tRNA synthetase (yPheRS (T415G)) with a point mutation in the active site of the enzyme. In order to reduce Trp and lysine (Lys) misincorporation at an amber codon, the ytRNAPheCUA_UG containing the optimized sequence and the yPheRS (T415A) showing higher specificity toward pBrF were developed. Combining ytRNAPheCUA_UG and yPheRS (T415A) allowed incorporation of pBrF into murine dihydrofolate reductase in response to an amber codon with at least 98% fidelity.
\r\n\r\nRe-assignment of degenerate sense codons offers the prospect of a substantially expanded genetic code and a correspondingly enriched set of building blocks for natural and artificial proteins. Here we describe the use of a mutant yeast phenylalanine transfer RNA (ytRNAPheAAA) containing a modified anticodon to break the degeneracy of the genetic code in E. coli. By using an E. coli strain co-transformed with ytRNAPheAAA and a mutant yPheRS (T415G), we demonstrated efficient replacement of Phe by L-3-(2-naphthyl)alanine (2Nal) at UUU, but not at UUC codons.
\r\n\r\nHowever, this method had two limitations. First, the yPheRS (T415G) also activated Trp, which led to Trp misincorporation. Second, 2Nal was misincorporated at UUC Phe codons, due to the relaxed codon recognition of AAA anticodon in the ytRNAPheAAA. High-throughput screening of a yPheRS library led to a more selective yPheRS variant (yPheRS_naph). The rationally designed ytRNAPheCAA, which has the CAA anticodon recognizing only a UUG (Leu) codon, allowed incorporation of 2Nal only at UUG codon. Combined use of yPheRS_naph and ytRNAPheCAA achieved multiple-site-specific incorporation of 2Nal into proteins. These results illustrate a general method for increasing the number of distinct, genetically-encoded amino acids available for protein engineering.
" }, { "name": "Lamarre-Vincent, Nathan", "degree": "PhD", "year": "2007", "title": "Identification and Functional Analysis of O-G1cNAc Glycosylation on the Transcription Factor cAMP-Response Element Binding Protein", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292007-183523", "creators": [ { "name": { "family": "Lamarre-Vincent", "given": "Nathan" }, "id": "Lamarre-Vincent-Nathan", "display_name": "Lamarre-Vincent, Nathan" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZEXB-6889", "abstract": "The survival and development of organisms requires the ability of cells to communicate with the environment and with surrounding cells. This demand has led to the evolution of a number of methods used for communication. Chief among these is the ability to modify protein function with post-translational modifications (PTMs). PTMs allow cells to use a single protein for a variety of tasks and link protein activity with a specific environmental or cellular cue. Modification of transcription factors has arisen as a key model for the study of PTMs and their effects on cell processes. PTMs modulate transcriptional activity required for key processes such as development, differentiation and cell survival.
\r\n\r\nThe eukaryotic transcription factor cAMP-response element binding protein (CREB) is a transcription factor that confers dynamic control of a number of cellular processes including neuronal and pancreatic cell survival, gluconeogenesis and neuronal long-term potentiation. CREB is activated by phosphorylation of single serine residue. The observation that a number of kinase signaling cascades converge on CREB has led to the question of how cells deal with the apparent loss of signal identity that occurs as a result of this convergence. In this thesis I describe the identification, characterization and functional analysis of a novel PTM of CREB, O-GlcNAc glycosylation, that provides an additional level of control of CREB activity. CREB glycosylation moderates phosphorylation-dependent CREB activity and reduces CREB-dependent gene expression in pancreatic [beta]-cells, and as a result promotes [beta]-cell death, as observed in type II diabetes. CREB glycosylation offers us an example of how cells use multiple PTMs to control protein function and how dysfunction in the regulation of these modifications may contribute to disease states.
" }, { "name": "Lee, Lori Wai Hang", "degree": "PhD", "year": "2007", "title": "Chemical Scale Investigations of the Gating Mechanism of Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01152007-080704", "creators": [ { "name": { "family": "Lee", "given": "Lori Wai Hang" }, "id": "Lee-Lori-Wai-Hang", "display_name": "Lee, Lori Wai Hang" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bv54-5p15", "abstract": "The studies contained in this dissertation are aimed at utilizing chemistry to understand neurobiology and neuronal communication. Chapters 2 and 3 both address the gating of ion channels, describing structure-function studies to shed light on the gating mechanisms of two classes of ion channels. Chapter 2 studies the gating mechanism of the mechanosensitive channel of small conductance (MscS), which is voltage modulated. Elucidating the mechanism of voltage sensation in MscS may provide insight into how voltage-gated channels translate a change in membrane potential to channel gating. The research discussed in Chapter 2 is aimed at elucidating the role of two arginine residues, in the TM1 and TM2 of MscS, in voltage sensing. We generated two MscS mutants, Arg46Ala and Arg74Ala, to evaluate the effects of \"neutralizing\" the charged side chain on the voltage sensing ability of the channel. The mutants were evaluated using single channel analysis in E. coli spheroplasts. Our preliminary results indicated a potentially significant role for Arg46 in the voltage sensitivity of MscS, however this data set is not extensive due to inconsistency in the spheroplasts preparation.
\r\n\r\nIn Chapter 3, we utilized nonsense suppression to incorporate unnatural amino acids to study the gating of the cation-selective Cys-loop family of ion channel receptors. Specifically, it describes work aimed at elucidating the role of cis-trans isomerization of a proline residue in the gating mechanism of the serotonin-gated 5-hydroxy-tryptamine receptor 3A (5-HT3A) and the nicotinic acetylcholine receptor. A series of proline analgues, of varying cis preference were incorporated at proline 308 in the M2-M3 loop of the 5-HT3A receptor using in vivo nonsense suppression methodology in a Xenopus oocyte expression system. Electrophysiological analysis of the mutant channels revealed a linear relationship between the cis preference of the proline analog and the EC50 of the mutant channel\u2014suggesting that proline 308 may serve as a hinge during the gating 5-HT3A. From these data, we proposed a model of gating for the 5-HT3A receptor. Initial results from similar studies in nAChR suggests that the analogous proline does not play a role in its gating.
\r\n\r\nLastly, Chapter 4 addresses the role of fucose-galactose carbohydrates in learning and memory. It aims to identify lectins to fucose-alpha(1-2)-galactose as well as identify the corresponding glycoproteins bearing fucose-alpha(1-2)-galactose. Chemical probes were synthesized and used to study fucose-alpha(1-2)-galactose binding proteins. One of the probes was used to demonstrate the existence of fucose-alpha(1-2)-galactose binding proteins in hippocampal neurons. Furthermore, initial results from experiments with a photoreactive probe suggested that the design of our probe is sufficient to isolate fucose-alpha(1-2)-galactose binding proteins from the brain. Additionally, we were able to use antibodies specific to fucose-alpha(1-2)-galactose epitopes to examine fucose-alpha(1-2)-galactose bearing glycoproteins in the brain. Overall, results from both studies utilizing chemical probes and molecular probes strongly suggest that the modifications of proteins with fucose-alpha(1-2)-galactose epitopes and the expression of fucose-alpha(1-2)-galactose binding proteins are developmentally regulated.
" }, { "name": "Liu, Jian", "degree": "PhD", "year": "2007", "title": "Microfluidic Devices for Genetic Analysis and Gene Expression Studies", "advisor": "Quake, Stephen R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04122007-134232", "creators": [ { "name": { "family": "Liu", "given": "Jian" }, "id": "Liu-Jian", "orcid": "0000-0002-0095-8978", "display_name": "Liu, Jian" } ], "advisors": [ { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "role": "advisor", "display_name": "Quake, Stephen R." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "role": "member", "display_name": "Quake, Stephen R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xnm0-4a75", "abstract": "Microfluidic devices hold the promise of becoming the next-generation laboratory platforms by offering many possible benefits in chemistry, biology, and medicine. However, microfluidics is still in its infancy at present, requiring a great deal of work before it can become more than an active research field in academia. This thesis describes efforts by the author in developing microfluidic technologies for applications in genetics. Section I describes the development of miniaturized devices for genetic analysis. Successful nucleic acid amplifications by polymerase chain reaction (PCR) have been demonstrated within a reaction volume as small as 700 picoliters. In section II, the concept of a microfluidic matrix chip is described and has been experimentally realized to solve the \"macroscopic/microfluidic\" interface problem. The matrix chip also provides a flexible platform to perform combinatorial tests with high throughput performance. Section III presents an application example of the microfluidic matrix chip in gene expression studies, providing quantitative profiles of gene isoforms by alternative splicing in a high throughput manner. In the section IV, a microfluidic chaotic mixer has been developed to accelerate the process and enhance the hybridization signals of DNA microarray experiments. These devices represent significant advances in microfluidics, with the following goals achieved: improved sensitivity and reliability of assays, reduction of consumption of reagents or analytes into desired economies of scale, and dramatic reduction of the time and complexity of \"hands-on\" manipulations, therefore providing experimental results in a high throughput manner." }, { "name": "Liu, Tao", "degree": "PhD", "year": "2007", "title": "Electrochemical Studies of Electron Transfer in DNA Films with Covalently Tethered Intercalators", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08312006-131856", "creators": [ { "name": { "family": "Liu", "given": "Tao" }, "id": "Liu-Tao", "display_name": "Liu, Tao" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MMSW-4A41", "abstract": "The base stack within double-helical DNA provides an efficient pathway for charge transport. This DNA-mediated charge transport chemistry has been shown to be exquisitely sensitive to minor perturbations in DNA structure and base stacking both in solution and on surfaces. As a result, electrochemical studies on DNA-modified electrodes may provide a novel approach to the development of sensitive, but inexpensive DNA sensing devices. Using intercalated, covalently bound daunomycin as a redox probe, we have examined ground state charge transport in DNA films on gold electrodes. DNA-mediated electron transfer is found to occur over a distance as long as 100 \u00c5 in the film. Moreover, while the introduction of one or even two breaks in the sugar-phosphate backbone yields no detectable effect on electron transfer, a CA base-pair mismatch significantly attenuates the electron transfer yield. These results confirm that the base pair stack is the pathway for DNA mediated charge transfer, not the sugar-phosphate backbone. Based on these studies, we have developed a method to electrochemically monitor the trapping of double- stranded DNA with a 6-base overhang on a gold electrode modified with double- stranded DNA probes containing a complementary overhang. The trapping of the double-stranded target can be monitored by the reduction of daunomycin crosslinked to the target. A CA mismatch in the target duplex can also be detected by the diminished reduction signal.
\r\n\r\nIt has been shown that the electronic coupling between an intercalator and the pi-stack of DNA is critically important for the reduction of the intercalator through DNA-mediated charge transport. Using covalently tethered anthraquinone derivatives as the redox probe, we have investigated also the influence of the binding mode of the intercalator on its reduction in DNA films. The results of these studies underscore the importance of direct interaction between the redox probe and the pi-stack in order to observe efficient DNA-mediated electrochemistry through DNA films. These studies have also shown that the covalent linkage has a significant effect on the intercalation of the probe to the base stack of DNA.
\r\n\r\nIn an effort to develop a redox probe that has effective electronic coupling with the pi-stack while being covalently tethered to a DNA strand with a stable linkage, we have crosslinked Nile blue, a redox active DNA intercalator with high DNA binding affinities, to the 5\u2019-end of oligonucleotides. The covalently tethered Nile blue is shown to be sensitive probe for DNA-mediated electron transfer on the gold surface. An intervening CA mismatch has been detected in both tightly packed and loosely packed films of DNA\u2013Nile blue conjugate. We have also coupled the reduction of Nile blue to an electrocatalytic cycle involving freely diffusing ferricyanide, which significantly enhances the sensitivity to intervening mismatches. Furthermore, using Nile blue as the covalently tethered probe, we have developed a method for DNA mismatch detection that eliminates sample modification and has a potential for high throughput assays. These studies may provide a practical approach to diagnostic devices for mutation detection with high sensitivity and low expense.
" }, { "name": "Millward, Steven Wesley", "degree": "PhD", "year": "2007", "title": "The Design, Synthesis, and Evolution of Macrocyclic mRNA Display Libraries Containing Unnatural Amino Acids", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05142007-161158", "creators": [ { "name": { "family": "Millward", "given": "Steven Wesley" }, "id": "Millward-Steven-Wesley", "orcid": "0000-0002-3231-7075", "display_name": "Millward, Steven Wesley" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "biochem" ], "doi": "10.7907/THV4-2A51", "abstract": "Combinatorial design is a powerful method for generating ligands that disrupt protein-protein interactions, particularly in the absence of structural information. mRNA display is powerful in vitro biological display technique that enables the synthesis and evolution of trillion-member peptide libraries. Previously, mRNA display libraries were limited to linear peptides composed entirely from natural (protegenic) amino acids. This work describes the redesign of mRNA display libraries to include chemical functionalities that hitherto have remained the province of traditional chemical libraries and natural products. The incorporation of unnatural (nonproteogenic) amino acids through nonsense suppression and selection for the unnatural chemical functionality demonstrated that suppression technologies were compatible with biological display. The incorporation of N-methylated amino acids by sequential sense suppression was shown to generate unnatural oligomers with improved proteolytic resistance. Post-translational macrocyclization was shown to be an effective and general strategy to constrain displayed peptides without the use of redox-labile disulfide bonds. Co-translational unnatural amino acid incorporation and post-translational macrocyclization were combined into a new technological platform and employed in the selection of a high-affinity cyclic ligand for G[alpha]i1. This new technology represents a significant step toward the evolution of natural product-like compounds from trillion-member combinatorial libraries." }, { "name": "Mollner, Andrew Keeler", "degree": "PhD", "year": "2007", "title": "Cavity Ringdown Spectroscopy Studies of Atmospheric Reactions: Peroxynitrous Acid Formation and Alkoxy Radical Isomerization", "advisor": "Okumura, Mitchio; Sander, Stanley P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-095914", "creators": [ { "name": { "family": "Mollner", "given": "Andrew Keeler" }, "id": "Mollner-Andrew-Keeler", "display_name": "Mollner, Andrew Keeler" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "co-advisor", "display_name": "Sander, Stanley P." } ], "committee": [ { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "chair", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "member", "display_name": "Sander, Stanley P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HSF6-WM41", "abstract": "This thesis describes laboratory experiments investigating atmospheric reactions using cavity ringdown spectroscopy (CRDS). The reactions studied were the formation of peroxynitrous acid (HOONO) in the termolecular association reaction OH + NO\u2082 (R1) and the isomerization of alkoxy radicals. Experiments were conducted in a gas flow cell combining UV photolysis to initiate reactions with infrared CRDS for the detection of products.
\r\n\r\nFormation of the weakly bound HOONO in the atmosphere reduces the yield of nitric acid (HONO\u2082) from R1 and lowers the efficiency of R1 as a sink for radicals. The cis-cis conformer of HOONO was detected through its fundamental \u03bd\u2081(OH stretch) spectrum centered at 3306 cm\u207b\u00b9. The integrated absorbance of the \u03bd\u2081 bands for HOONO and HONO\u2082 were measured with CRDS and used to calculate the branching ratio (BR = kHOONO / kHONO2) of R1. Initial experiments using a microwave discharge to initiate R1 measured BR at 298 K and 14 torr, but were limited to low pressures by the discharge. BR was then reinvestigated using pulsed laser photolysis to initiate R1. BR was measured over the range 20\u2013760 torr at 298 K.
\r\n\r\nIn support of these branching ratio measurements, a detailed study of the spectroscopy of HONO\u2082 was conducted. CRDS experiments with moderate resolution (1 cm\u207b\u00b9) are known to give incorrect absorbances and line shaes when measuring spectral features with much narrower linewidths. However, the magnitude of these CRDS errors when probing a highly congested spectrum such as that of HONO\u2082 was unknown. We observed reductions in the HONO\u2082 integrated intensity up to 60% and quantified these errors as a function of concentration and pressure.
\r\n\r\nAlkoxy radicals (RO) are an important class of intermediates in the oxidation of hydrocarbons, and they react via several mechanisms. For longer chain RO isomerization (forming HOR) becomes a major pathway, but isomerization rates have never been directly measured. Continuing work described in Eva Garland\u2019s thesis, we measured the infrared spectrum of alkoxy radical isomerization products (HOR and HORO2) formed within 100 \u00b5s. We then used this spectrum to measure the relative rate of isomerization to reaction with oxygen for n-butoxy and 2-pentoxy radicals.
" }, { "name": "Ng, Nga Lee", "degree": "PhD", "year": "2007", "title": "Chamber Studies of Secondary Organic Aerosol Formation", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-210716", "creators": [ { "name": { "family": "Ng", "given": "Nga Lee" }, "id": "Ng-Nga-Lee", "orcid": "0000-0001-8460-4765", "display_name": "Ng, Nga Lee" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/XFEN-5Q08", "abstract": "Atmospheric oxidation of volatile organic compounds leads to the formation of secondary organic aerosol (SOA). Laboratory chambers provide a controlled environment for investigating aerosol formation and evolution. This thesis presents results on aerosol formation from a wide range of parent organic compounds under a variety of experimental conditions.
\r\n\r\nThe effect of particle-phase acidity on aerosol formation is explored in a series of alkene ozonolysis experiments. Oligomeric species are detected regardless of the particle-phase acidity, indicating the ubiquitous existence of particle-phase reactions. As acidity increases, larger oligomers are formed more abundantly and aerosol yields also increase. Volatile organic compounds generally not considered to be SOA precursors, including isoprene and glyoxal, have been shown to lead to aerosol formation. Uptake of glyoxal into particles is evidence that small molecules can potentially produce aerosol via reactive absorption. Although there is strong evidence that heterogeneous reactions play an important role in SOA formation, the detailed mechanisms remain poorly understood. In a comprehensive study on aerosol formation from biogenic hydrocarbons, it is found that data on aerosol growth as a function of the amount of hydrocarbon reacted provide important insights into the general aerosol formation mechanisms by identifying rate-determining steps and whether SOA is formed from first- or second-generation products.
\r\n\r\nThe mechanism of aerosol formation by isoprene is specifically investigated over a range of NOx concentrations. Aerosol yields are found to decrease substantially with increasing NOx. The same NOx dependence is observed for monoterpenes ([alpha]-pinene), as well as aromatic hydrocarbons (m-xylene, toluene, and benzene). It is suggested that peroxy radical chemistry plays the central role in the observed NOx dependence. The NOx dependence for larger compounds is, however, different from that of isoprene, monoterpenes, and aromatics. For sesquiterpenes such as longifolene and aromadendrene, aerosol yields increase with increasing NOx concentration. The reversal of the NOx dependence of SOA formation for the sesquiterpenes appears to be the result of formation of relatively nonvolatile organic nitrates, and/or the isomerization of large alkoxy radicals that leads to less volatile products.
" }, { "name": "Nguyen, Yen Hoang Le", "degree": "PhD", "year": "2007", "title": "Wiring Inducible Nitric Oxide Synthase", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262006-134259", "creators": [ { "name": { "family": "Nguyen", "given": "Yen Hoang Le" }, "id": "Nguyen-Yen-Hoang-Le", "display_name": "Nguyen, Yen Hoang Le" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fgsb-4m91", "abstract": "The \"wires project\" in the Gray group has been focused on characterizing short-lived intermediates of Fe heme enzyme catalytic cycles by designing and synthesizing photosensitizers (wires) that bind to the protein active site with high affinity. The heart of this thesis is on rhenium channel binding and ruthenium surface binding wires for inducible nitric oxide synthase (iNOS). Binding and inhibition studies were conducted, electron transfer (ET) kinetics were studied, and iNOS catalytic activity was assayed for nitric oxide (NO) production.
\r\n\r\nBoth channel and surface binding wires bind to iNOS with low micro molar affinity. Channel binding wires bind at the active site, closely interacting with the protoporphyrin IX iron heme (Fe heme). Characteristic spectral shifts of Fe heme perturbation were observed. The surface binding wires bind presumably at the hydrophobic patch of the oxygenase domain where the reductase domain was proposed to dock during electron transfer processes. The surface binding wire interacts closely with the Fe heme from the surface of the protein, but still close to where spectral shifts of the Fe heme were observed; however, the surface binding wire does not displace other channel binding wires, indicative of a second binding site.
\r\n\r\nUpon photo-excitation of all rhenium wires, the resting state Fe(III) heme is reduced to Fe(II) heme in less than 10 ns, characterized by transient absorption spectroscopy. This ET rate is orders of magnitude faster than Fe(III) reduction by the reductase domain (kET = 1 s-1) under biological conditions. In some cases, the wires were observed to ligate the Fe(II), creating a six-coordinate Fe(II) complex. The fully coordinated Fe(II) species is prevented from binding oxygen, and the catalytic mechanism is terminated. Another electron cannot be injected, and there is no production of NO. In the cases where the wire was shorter, ligation of the Fe(II) species was not observed. The Fe(II) remains five-coordinate, leaving room for oxygen to bind and for the mechanism to continue. In this case, NOS catalytic activity was assayed for the production of NO by photo-excitation of the wires. Complications of photodecomposition of NO indicators presented a challenge in data analysis. It is possible that a very small amount of NO was produced by photo-excitation of the wire; unfortunately, nothing definitely can be concluded. A new method to assay for NOS catalytic activity was proposed.
\r\n\r\nBoth channel and surface binding wires led to many insights on substrate binding modes at the protein active site and on the surface; ET mechanisms were redefined, including amino acid radicals participating in electron transfer processes; and future directions for new wire were designed with hopes of accomplishing the long standing goal of characterizing high-valent Fe species.
" }, { "name": "Niemer, Rachel K.", "degree": "PhD", "year": "2007", "title": "Computational Studies of the Structure and Function of Two Lipid-Activated G Protein-Coupled Receptors", "advisor": "Goddard, William A., III; Vaidehi, Nagarajan", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292007-060906", "creators": [ { "name": { "family": "Niemer", "given": "Rachel K." }, "id": "Niemer-Rachel-K", "orcid": "0000-0002-6238-8544", "display_name": "Niemer, Rachel K." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Vaidehi", "given": "Nagarajan" }, "id": "Vaidehi-N", "role": "advisor", "display_name": "Vaidehi, Nagarajan" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Vaidehi", "given": "Nagarajan" }, "id": "Vaidehi-N", "role": "member", "display_name": "Vaidehi, Nagarajan" } ], "option_major": [ "chemistry" ], "doi": "10.7907/djy6-nw49", "abstract": "Phospholipids are pleiotropic intercellular signaling molecules that have been implicated in various pathologies, including tumorigenesis. Both lysophosphatidic acid (LPA) and sphingosine-1-phosphate (S1P), among other phospholipids, use G protein coupled receptors (GPCRs) to transduce extracellular signals. Other families of GPCRs have successfully been utilized by the pharmaceutical industry, and further understanding of the phospholipid-receptor interaction can highlight potential therapeutic targets in these signaling pathways.
\r\n\r\nThis thesis presents research into the interaction between specific G protein-coupled receptors, lysophosphatidic acid receptor-2 (LPA2) and sphingosine-1-phosphate receptor 1 (S1P1), and their ligands, in an attempt to further validate our method of GPCR structure prediction and to understand subtype specificity within this family of lipid receptors. Although the first principles method of GPCR structure prediction has quite successfully predicted the protein structure of small molecule receptors, lipid receptors create a unique challenge. The surface area on the inside of a small molecule receptor contains a large percentage of polar groups, easily differentiating the inner surface from the highly hydrophobic outer surface. Lipid receptors do not show as dramatic a distinction, as the inner surface is significantly hydrophobic to bind the lipid ligand.
\r\n\r\nHerein we propose and test a new method of orienting the seven transmembrane helices of a GPCR relative to one another through an analysis of the lipid solubility of each residue in conjunction with an optimization of the inter-helical hydrogen bonding associations. We predict structures for LPA2 and S1P1 that replicate the relative binding of different lipids within the LPA and S1P lipid families. The interaction energies between the receptors and the tested ligands correlates well with ligand efficacy, and qualitative analysis of functional group-residue interactions further validates our model for both LPA2 an S1P.
" }, { "name": "Scruggs, Neal Robert", "degree": "PhD", "year": "2007", "title": "Coupling Polymer Thermodynamics and Viscoelasticity to Liquid Crystalline Order: Self-Assembly and Relaxation Dynamics of Block Copolymers in a Nematic Solvent", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02202007-131552", "creators": [ { "name": { "family": "Scruggs", "given": "Neal Robert" }, "id": "Carty-Neal-Robert-Scruggs", "orcid": "0000-0003-1329-4506", "display_name": "Scruggs, Neal Robert" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/68XG-G726", "abstract": "The discontinuous change in solvent quality of a liquid crystal (LC) solvent, 5CB, at the nematic-isotropic phase transition produces abrupt changes in the phase behavior of solutions of coil and LC-polymers and in the self-assembly of coil-LC block copolymers. Nematic 5CB is strongly selective for a side-group liquid crystal polymer (SGLCP) and isotropic 5CB is a good solvent for both SGLCP and a random coil (polystyrene, PS). In nematic 5CB, unfavorable LC-PS interactions drive phase separation in SGLCP-PS-LC ternary solutions and drive micellization of PS-SGLCP diblocks. In isotropic 5CB, rich phase behavior occurs in both ternary solutions and block copolymer solutions. Despite the fact that isotropic 5CB is a good solvent for both SGLCP and PS, segregation can occur due to the asymmetric solvent effect (i.e., the preference of the solvent for the SGLCP). In concentrated isotropic solutions, unfavorable SGLCP-PS interactions become dominant.
\r\n\r\nIn binary solutions of SGLCP and 5CB, the delicate thermodynamic balance between LC order and polymer entropy manifests itself in a non-monotonic concentration dependence of the solutions' clearing points. The frustration between LC order and polymer entropy in an SGLCP melt is partially relieved by the addition of small molecule LC, greatly increasing the polymer's configurational freedom and stabilizing the nematic phase. In dilute solutions, the polymer adopts an anisotropic conformation because of its coupling to the LC solvent's prevailing director field; the sense and the magnitude of the anisotropy depend on the architecture of the SGLCP (end-on or side-on mesogens).
\r\n\r\nCoil-SGLCP-coil triblock copolymers self-assemble in 5CB to form liquid crystalline gels in which nematic order is coupled to an associative polymer network. The network's dynamic restructuring couples to fluctuations in the LC's local order to provide an additional relaxation process that is not present in SGLCP solutions or LC elastomers, and the importance of this process is highly dependent on the underlying anisotropy of the SGLCP-based network. The network furthermore provides a memory of the LC orientation state: when the LC is reoriented by electric-magnetic fields or mechanical shear, the network structure prevents the orientation from relaxing back to a random distribution when the aligning force is removed.
" }, { "name": "Son, Soojin", "degree": "PhD", "year": "2007", "title": "Biosynthetic Approaches to Protein Engineering Using Fluorinated Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09172008-144626", "creators": [ { "name": { "family": "Son", "given": "Soojin" }, "id": "Son-Soojin", "display_name": "Son, Soojin" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4dsq-m054", "abstract": "Non-canonical amino acids provide a new set of building blocks and a potential route to new chemistries that extend beyond those achieved through the 20 common amino acids. Among various methods developed for this purpose, residue-specific incorporation in vivo has the potential to economically engineer proteins of various sizes with altered physical and chemical behavior. The work presented in this thesis explored the incorporation of fluorinated aliphatic residues and their effect on protein structure, stability, and function.
\r\n\r\nIn Chapter 2, two fluorinated amino acids, 5,5,5-trifluoroisoleucine (5TFI) and 4,4,4-trifluorovaline (4TFV), were incorporated in vivo into mutant GCN4 proteins. Both 5TFI and 4TFV showed replacement levels higher than 88%, as indicated by quantitative amino acid and MALDI-MS analysis. The incorporation of 5TFI into a-positions of the coiled-coil protein raised the thermal denaturation temperature (Tm) by 27\u00b0C from that of its isoleucine counterpart. However, when valines were replaced by 4TFV in the same positions, Tm only increased by 4\u00b0C. Similar trends were observed in response to chemical denaturation by guanidine hydrochloride; \u0394\u0394Gfolding upon incorporation of 5TFI and 4TFV was -2.1 and -0.3 kcal/mol, respectively. Secondary and higher order structures as well as biological activity were retained in the presence of both 5TFI and 4TFV. These results indicate that, even when introduced into the same positions within the protein, the effect of fluorination differs depending on which amino acid is fluorinated.
\r\n\r\nIn Chapter 3, the stereochemical effects of 5,5,5-trifluoroleucine (5TFL) were studied using (2S, 4R)-5',5',5'-trifluoroleucine and (2S, 4S)-5',5',5'-trifluoroleucine. The results from in vitro activation assays correlated well with efficiency of their incorporation in vivo. The (2S, 4S) isomer, whose kcat/Km was 100-fold lower than that of leucine, was incorporated at high levels, with 91% replacement of the encoded leucine residues in a de novo engineered coiled-coil protein A1. The (2S, 4R) isomer exhibited 9- fold lower kcat/Km than the (2S, 45) isomer, resulting in a slightly lower level of incorporation, 80%. The secondary structure of A1 was undisturbed upon the incorporation of either isomer and their impact on thermostability was similar, with an increase of 11\u00b0C in Tm as compared to that of A1 containing leucine. However, the equimolar mixture of A1 containing (2S, 45)-TFL and A1 containing (2S, 4R)-TFL displayed a further increase in Tm of 3\u00b0C. Although this further enhancement in thermostability was modest, it may be attributed to the ability of the coils to pack more compactly into dimers due to the stereochemical differences.
\r\n\r\nIn Chapter 4, laboratory evolution was utilized to recover the catalytic activity of chloramphenicol acetyltransferase (CAT) after replacement of isoleucine by 5TFI. Upon global incorporation of 5TFI into CAT, the catalytic efficiency, k cat/Km, was reduced by more than 2-fold, from 10.2 \u00b1 0.8 \u03bcM-1 to 3.9 \u00b1 0.5 \u03bcM-1 min -1. Four rounds of random mutagenesis, enrichment, and screening were performed, yielding a 7-fold fluorinated mutant, tfi-G4, whose activity in fluorinated form was 2.8-fold higher than that of the fluorinated parent enzyme, tfi-WT. The total number of isoleucines decreased only by one in the 7-fold mutant, and the gap in activity between the hydrogenated (ile-G4) and fluorinated (tfi-G4) forms narrowed. Despite similar secondary structure, the incorporation of fluorinated amino acids decreased the stability of CAT for both the wild- type and G4 pairs based on both functional and structural analysis. Fluorinated forms were more sensitive towards thermal and chemical denaturation. However, both forms of G4 enzymes had increased stabilities as compared to their wild-type counterparts. This resulted in tfi-G4 exhibiting similar thermostability as that of ile-WT. Although structural changes were noted at both high and low pH, the pKa of the catalytically essential histidine (His-193) was not affected by the incorporation of 5TFI. Based on these results, the incorporation of 5TFI appears to be adversely affecting protein folding, which resulted in decreased activity and stability. However, laboratory evolution effectively recovered these losses and yielded a fluorinated enzyme that performed similarly to the wild-type.
\r\n\r\nFinally, in Chapter 5, the effect of fluorination on sensitivity to proteolytic degradation was explored. GCN4 proteins containing either 5TFI (tfi-INL) or 4TFV (tfv-VNL) as well as CAT proteins containing either 5TFI (tfi-G2) or 5TFL (tfl-L2A1) were treated with two proteases, trypsin and elastase. As evidenced by gel electrophoresis and densitometry analysis, the half life of tfi-INL in the presence of elastase was 4 times that of its hydrogenated counterpart INL. The increased resistance was less significant upon incorporation of 4TFV as well as in response to trypsin. The opposite trend was observed in the analysis of CAT mutants. Both of the fluorinated CAT mutants were more susceptible to elastase and trypsin as compared to their hydrogenated counterparts. Upon incorporation of fluorinated amino acids, two factors that affect proteolytic degradation are altered, the stability of the protein as well as substrate recognition and hydrolysis by the protease. It appears that changes in both of these factors contributed to the observed rates of proteolysis.
\r\n\r\nThe work explored in this thesis has expanded our understanding of fluorinated amino acids and their effects on proteins. Based on these insights, we are continuing to expand the use of fluorinated amino acids (and other non-canonical amino acids) to control protein structure, function, and stability.
\r\n\r\n\r\n" }, { "name": "Su, Julius Tsu-li", "degree": "PhD", "year": "2007", "title": "An Electron Force Field for Simulating Large Scale Excited Electron Dynamics", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05032007-151410", "creators": [ { "name": { "family": "Su", "given": "Julius Tsu-li" }, "id": "Su-Julius-Tsu-li", "display_name": "Su, Julius Tsu-li" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d8a3-e876", "abstract": "We introduce an electron force field (eFF) that makes simulation of large scale excited electron dynamics possible and practical. The forces acting on thousands of electrons and nuclei can be computed in less than a second on a single modern processor.
\r\n\r\nJust as conventional force fields parameterize the ground state potential between nuclei, with electrons implicitly included, electron force fields parameterize the potential between nuclei and simplified electrons, with more detailed degrees of freedom implicitly included. The electrons in an electron force field are Gaussian wave packets whose only parameters are its position and its size.
\r\n\r\nUsing a simple version of the electron force field, we compute the dissociation and ionization behavior of dense hydrogen, and obtain equations of state and shock Hugoniot curves that are in agreement with results obtained from vastly more expensive path integral Monte Carlo methods. We also compute the Auger dissociation of hydrocarbons, and observe core hole decays, valence electron ionizations, and nuclear fragmentation patterns consistent with experiment.
\r\n\r\nWe show we can describe p-like valence electrons using spherical Gaussian functions, enabling us to compute accurate ionization potentials and polarizabilities for first row atoms, and accurate dissociation energies and geometries of atom hydrides and hydrocarbons.
\r\n\r\nWe show also that we can describe delocalized electrons in a uniform electron gas using localized eFF orbitals. We reproduce the energy of a uniform electron gas, including correlation effects; and following the historical development of density functional theory, we develop a preliminary eFF that can compute accurate exchange and correlation energies of atoms and simple molecules.
" }, { "name": "Tully, Sarah Erin", "degree": "PhD", "year": "2007", "title": "Synthesis and Biological Activity of Chondroitin Sulfate Biopolymers", "advisor": "Hsieh-Wilson, Linda C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12132006-122200", "creators": [ { "name": { "family": "Tully", "given": "Sarah Erin" }, "id": "Tully-Sarah-Erin", "display_name": "Tully, Sarah Erin" } ], "advisors": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "advisor", "display_name": "Hsieh-Wilson, Linda C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/c6pj-np35", "abstract": "Chondroitin sulfate glycosaminoglycans are ubiquitously expressed linear, sulfated polysaccharides involved in cell growth, neuronal development and spinal cord injury. The different sulfation motifs presented by chondroitin sulfate may regulate its activity, but efforts to understand the precise biological roles of this glycosaminoglycan have been hampered by its complexity and heterogeneity. Here, we report the synthesis of well-defined chondroitin sulfate oligosaccharides through a convergent approach that permits installation of sulfate groups at precise positions along the carbohydrate backbone, biological evaluation of the synthetic molecules, and generation of antibodies that recognize the distinct sulfation motifs.
\r\n\r\nUsing the chondroitin sulfate oligosaccharide library, we demonstrate that specific sulfation patterns act as molecular recognition elements for growth factors, and modulate neuronal growth. We identified a chondroitin sulfate tetrasaccharide, CS-E, which stimulates the growth and differentiation of multiple neuron types. Through use of carbohydrate microarrays, we found that the CS-E tetrasaccharide binds to a variety of proteins involved in promoting neurite outgrowth. A CS-E disaccharide, an unsulfated tetrasaccharide, and three other sulfated tetrasaccharides, CS-A, CS-C, and CS-R, were also investigated, and showed little effect on neurite outgrowth and reduced growth factor binding compared to the CS-E tetrasaccharide. These studies represent the first, direct investigations into the structure-activity relationships of chondroitin sulfate using homogeneous synthetic molecules, define a tetrasaccharide as a minimal motif required for function, and reveal the importance of sulfation in chondroitin sulfate bioactivity.
\r\n" }, { "name": "Ueda, Christine Terumi", "degree": "PhD", "year": "2007", "title": "Targeting Human Telomerase RNA via Biochemical and in vitro Selection Methods", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09052006-214421", "creators": [ { "name": { "family": "Ueda", "given": "Christine Terumi" }, "id": "Ueda-Christine-Terumi", "display_name": "Ueda, Christine Terumi" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2NK8-KK06", "abstract": "Telomerase is an enzyme responsible for the maintenance of eukaryotic chromosome ends. The two main components required for activity are a protein subunit, the human telomerase reverse transcriptase (hTERT), and an RNA subunit, the human telomerase RNA (hTR). While telomerase is not active in most normal human cells, roughly 85% to 90% of oncogenic cells display increased telomerase activity. An understanding of the biochemistry of telomerase will aid in the development of molecules that will lead to antitumor-specific therapies. The first part of the work presented here describes a biochemical analysis of an RNA-RNA interaction between two catalytically important domains of hTR. The interactions were characterized via mobility-shift assay, mutation analysis, and UV cross-linking experiments. The data argue for a revised model for the structure of hTR, and point to possible three-dimensional contacts present in the telomerase complex. The next part of this thesis describes an in vitro selection against the catalytically important RNA stem-loop P6.1 in hTR. The in vitro selection was performed using mRNA display, which allows us to isolate RNA-binding peptides from libraries containing trillions of unique sequences. Unexpectedly, the selected peptide binds with high affinity and specificity to the relatively rare dimeric form of the P6.1 stem-loop rather than the more abundant monomeric conformation. Characterization of this novel RNA-peptide interaction was performed via circular dichroism, steady-state fluorescence, mobility-shift assay, and surface plasmon resonance. The data highlight the power of mRNA display to isolate high affinity ligands from large libraries of molecules." }, { "name": "Verduzco, Rafael", "degree": "PhD", "year": "2007", "title": "Self-Assembled Liquid Crystal Polymer Gels", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-153627", "creators": [ { "name": { "family": "Verduzco", "given": "Rafael" }, "id": "Verduzco-Rafael", "orcid": "0000-0002-3649-3455", "display_name": "Verduzco, Rafael" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VAAF-0809", "abstract": "The combination of liquid crystals (LCs) with polymer networks results in fascinating materials in which the elasticity of the polymer network is coupled to LC order, and they hold promise for a variety of applications which depend on an optical or a mechanical response to external stimuli. Unfortunately, the methods for preparing LC networks are limited. In this work, we present two types of LC gels with novel network architectures: a physical gel made by polymer self-assembly in an LC solvent and a chemical gel made by crosslinking telechelic side-group liquid crystalline polymers (SGLCPs). The physical gel thermoreversibly transitions to a liquid on heating, and it can be uniformly aligned using electric, magnetic, or flow fields. The gel exhibits a fast electro-optical response, making it potentially viable for display applications. The physical gel also reveals novel equilibrium and dynamic properties that arise due the coupling between LC order and the polymer network. When confined between cell substrates prohibiting macroscopic shape change, it exhibits a temperature-sensitive striped texture transition. We provide a theoretical model that captures the striped texture by accounting for the compromise between nematic rubber elasticity and LC elasticity. Dynamic light scattering studies reveal two distinct director relaxation modes, in contrast to covalent gels, which show a single relaxation mode. We argue that the slower dynamics arise from the coupling between the director and the physically associated network which restructures on long time scales. We also investigate the self-assembled micellar structure of the gel via neutron scattering and rheometry studies, and these studies reveal that the gels' structure changes dramatically across the nematic-to-isotropic phase transition. Finally, we investigate model LC networks made by crosslinking telechelic SGLCPs using \"click\" chemistry. These chemical networks can be swollen in a small-molecule LC, and they exhibit a low-threshold electro-optic response and a temperature dependent size. These novel physical and chemical LC gels provide insight into the role of network structure in determining the material properties of liquid crystalline elastomers and gels.\r\n" }, { "name": "Zeidan, Ryan K.", "degree": "PhD", "year": "2007", "title": "Design of New Multifunctional Materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212007-101608", "creators": [ { "name": { "family": "Zeidan", "given": "Ryan K." }, "id": "Zeidan-Ryan-K", "display_name": "Zeidan, Ryan K." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CK8E-7H82", "abstract": "Research in areas of science and technology critical to society, such as energy, medicine, electronics, protective equipment, and consumer goods relies on the ability to create new materials with desirable properties. The diversity in the properties of these materials is enormous. An important factor in the quest for developing exciting new materials is the ability to use synthetic chemistry to prepare new materials starting from a molecular point of view. It is this approach that I use in this work.
\r\n\r\nI have used principles of synthetic organic chemistry to guide the molecular design of materials that contain a variety of functionalities. This thesis describes three types of designed functional materials. First, new heterogeneous catalysts have been prepared that incorporate two organic functional groups in a manner that allows for cooperativity between them in catalyzing organic reactions, giving increases in reaction rates and selectivities. In particular, thiol/sulfonic acid bi-functional mesoporous materials have been prepared that give significant enhancements in reactivity and selectivity towards bisphenol A synthesis. These enhancements arise from interactions between thiol and sulfonic acid sites due to their proximity on the surface of the catalyst. Acid-base bi-functional materials have also been synthesized that exhibit excellent reactivity in the aldol condensation between acetone and 4-nitrobenzaldehyde. These catalysts are particularly important as the acid and base groups are mutually incompatible in solution and provide reactivity not achievable without immobilization on the surface of solids. Second, a method for incorporating traceable and quantifiable labels onto cyclodextrins and cyclodextrin containing polymers has been designed that utilizes the reactivity between the primary alcohols on cyclodextrins and ethylene oxide gas, and allows the cyclodextrins to be labeled for use in animal biodistribution studies. Third, polymers bearing aromatic disulfide groups have been prepared that can be degraded through a dual-trigger mechanism requiring simultaneous photochemical and hydrogen peroxide activation.
" }, { "name": "Zhang, Kechun", "degree": "PhD", "year": "2007", "title": "Engineering Protein-Based Materials Through Coiled-Coil Motifs", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232007-144117", "creators": [ { "name": { "family": "Zhang", "given": "Kechun" }, "id": "Zhang-Kechun", "orcid": "0000-0002-7139-2799", "display_name": "Zhang, Kechun" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/324A-2K76", "abstract": "Natural biomaterials are highly organized from the molecular to the macroscopic level in a hierarchical manner, requiring synthetic technologies to achieve this level of complexity. A biosynthetic approach to material design has emerged as an attractive option. In particular, proteins represent a promising class of molecules for creating new materials due to their determined sequence and structure. The research described in this thesis focuses on engineering protein-based materials using coiled-coil motifs. The coiled coil is a common protein architecture consisting of two or more \u03b1-helices wrapped around one another to form a supercoil. Despite its simple conformation, the coiled-coil motif plays diverse roles in biological systems functioning as sensors, recognition elements, scaffolds, levers, rotating arms and springs.
\r\n\r\nFirst, a designed parallel heterodimeric leucine zipper pair was used as the protein capture domain to construct an artificial polypeptide scaffold for surface functionalization. By using a mutant E. coli phenylalanyl-tRNA synthetase, the photoreactive amino acid para-azidophenylalanine was incorporated. This protein polymer was spin-coated and photocrosslinked to octyltrichlorosilane-treated surfaces. The resulting protein films were shown to immobilize recombinant proteins through association of coiled coil heterodimer. Furthermore, in conjunction with microfluidic chips that were specifically designed for on-chip mixing using laminar flow, gradients of leucine zipper tagged proteins were formed in the microchannels and immobilized on the engineered protein films. This provides a general technique for producing surface-bound multicomponent gradients. The adhesion of human umbilical vein endothelial cells cultured on a surface-bound gradient of cell binding ligands generated by this technique was examined. In addition, to generate protein walkers that have different lateral mobility rates on a surface, several variants of the leucine zipper pair with tunable heterodimerization affinities were designed and synthesized to allow diversity in the association strength of proteins linked to a surface.
\r\n\r\nThe coiled-coil motif was also used to construct protein hydrogels. Hydrogels formed from a triblock artificial protein bearing dissimilar helical coiled-coil end domains (P and A) erode more than one hundred fold slower than hydrogels formed from those bearing the same end domains (either P or A). The reduced erosion rate is a consequence of the fact that looped chains are suppressed because P and A tend not to associate with each other. Thus, by harnessing selective molecular recognition, discrete aggregation number and orientational discrimination of coiled-coil protein domains, the erosion rate of hydrogels can be tuned over several orders of magnitude.
\r\n\r\nFinally, a biosynthetic approach was developed to control and probe cooperativity in multiunit biomotor assemblies by linking molecular motors to artificial protein scaffolds using the heterodimeric leucine zipper pair. This approach provides precise control over spatial and elastic coupling between motors. Cooperative interactions between monomeric kinesin-1 motors attached to protein scaffolds enhance hydrolysis activity and microtubule gliding velocity. However, these interactions are not influenced by changes in the elastic properties of the scaffold, distinguishing multimotor transport from that powered by unorganized monomeric motors. These results highlight the role of supramolecular architecture in determining mechanisms of collective transport.
" }, { "name": "Ashley, Eric Robert", "degree": "PhD", "year": "2006", "title": "The First Total Synthesis of (\u2013)-Lemonomycin and Progress toward the Total Synthesis of (+)-Cyanocycline A", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11152005-155011", "creators": [ { "name": { "family": "Ashley", "given": "Eric Robert" }, "id": "Ashley-Eric-Robert", "orcid": "0000-0002-0513-3342", "display_name": "Ashley, Eric Robert" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QM4S-3B86", "abstract": "The first total synthesis of (\u2013)-lemonomycin has been accomplished. The synthesis features a novel, auxiliary-controlled asymmetric dipolar cycloaddition, a highly convergent Suzuki coupling, a diastereoselective enamide hydrogenation to set the C(3) stereochemistry, and a convergent, efficient, and completely diastereoselective Pictet-Spengler cyclization with a glycosyloxy acetaldehyde.
\r\n\r\nThe total synthesis of (+)-cyanocycline A has been approached along two routes. Both routes feature dipolar cycloaddition reactions with alkyne-containing substrates and completely diastereoselective hydrogenations to set the C(4) stereochemistry. Proposals for the advancement of late-stage intermediates to the natural product are included.
" }, { "name": "Austin, Joel Francis", "degree": "PhD", "year": "2006", "title": "The Development of Organocatalytic Reactions Pertaining to Indoles", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06132005-145346", "creators": [ { "name": { "family": "Austin", "given": "Joel Francis" }, "id": "Austin-Joel-Francis", "display_name": "Austin, Joel Francis" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Leonard", "given": "Nelson J." }, "id": "Leonard-N-J", "role": "member", "display_name": "Leonard, Nelson J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CDXN-8R73", "abstract": "An improved imidazolidinone catalyst for the LUMO-lowering activation of [alpha],[beta]-unsaturated aldehydes has been designed, synthesized and evaluated. This new catalyst allows hitherto infeasible reactions to proceed with high fidelity.\r\n\r\nA new strategy for the synthesis of C-3 chiral indoles has been developed. This strategy employs the use of the aforementioned imidazolidinone catalyst to activate [alpha], [beta]-unsaturated aldehydes toward a Friedel-Crafts reaction with a variety of indoles. This is the first and only example in the literature were an indole is alkylated by an [alpha], [beta]-unsaturated aldehyde enantioselectively and catalytically. This methodology allows for the rapid synthesis of this priviledged pharmacophore.\r\n\r\nBy exploiting the indolium ion intermediate produced during the asymmetric Friedel-Crafts alkylation of indoles, a cascade cyclization was found to occur in the first enantioselectivive catalytic construction of the pyrroloindoline architecture. This direct route provides rapid access to this valuable core motif. This research has led to interesting observances in terms of indole facial selectivity that can be rationalized by an understanding of the cation-[pi] interaction.\r\n\r\nAfter numerous unsuccessful attempts to apply the direct pyrroloindoline construction to the synthesis of vicinally quaternary adducts, exploration of the higher reactivity of oxindoles was undertaken. This study has led to the first construction of vicinally quaternary stereogenic carbons via an organocatalyzed protocol." }, { "name": "Bagdanoff, Jeffrey Thomas", "degree": "PhD", "year": "2006", "title": "Development of the Enantioselective Oxidation of Secondary Alcohols and Natural Products Total Synthesis", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08182005-120859", "creators": [ { "name": { "family": "Bagdanoff", "given": "Jeffrey Thomas" }, "id": "Bagdanoff-Jeffrey-Thomas", "display_name": "Bagdanoff, Jeffrey Thomas" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z94F1NQK", "abstract": "Oxidation is a fundamental process in chemistry and biology. In synthetic chemistry, there are several methods for the asymmetric oxidation of organic substrates. Classically, these methods have focused on the delivery of a heteroatom from a reagent or catalyst to a prochiral substrate. What have historically been underdeveloped are enantioselective oxidation methods that do not involve the transfer of a heteroatom, but rather are defined by the enantioselective dehydrogenation of an organic substrate. This type of oxidative transformation was investigated using a palladium(II) catalyst system.
\r\n\r\nA palladium-catalyzed oxidative kinetic resolution of secondary alcohols was developed. Key features of the catalytic system include the use of (\u2013)-sparteine as the source of chiral relay, and molecular oxygen as the sole stoicheometric oxidant. Under the described catalytic system, a number of benzylic and allylic alcohols have been oxidized in an enantioselective manner, to provide a ketone and residual alcohol in high enantiomeric excess and excellent yield.
\r\n\r\nSubsequent to the original system, the systematic investigation of a number of mechanistic hypotheses involving the role of exogenous bases and H-bonding additives prompted the discovery of new reaction conditions displaying greatly enhanced reactivity, selectivity, atom economy, and generality. The net result of these improvements was a catalytic system effective in oxidative desymmetrization of a number of complex meso-diols. Ultimately, these advances have permitted our method to be applied towards a number of synthetic endeavors, including the key step in the total synthesis of the natural product alkaloid (\u2013)-lobeline.
\r\n" }, { "name": "Biteen, Julie Suzanne", "degree": "PhD", "year": "2006", "title": "Plasmon-Enhanced Silicon Nanocrystal Luminescence for Optoelectronic Applications", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-05312006-163455", "creators": [ { "name": { "family": "Biteen", "given": "Julie Suzanne" }, "id": "Biteen-Julie-Suzanne", "orcid": "0000-0003-2038-6484", "display_name": "Biteen, Julie Suzanne" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "chair", "display_name": "Heath, James R." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B77G-WS08", "abstract": "On the path toward the realization of silicon-based optical emitters for integrated microelectronics, this thesis studies the optoelectronic properties of silicon nanocrystals as a function of their surface passivation and their interactions with plasmonic materials. The first part of the thesis utilizes controlled oxidation exposures and photoluminescence spectroscopy to verify previous theoretical and computational predictions of oxygen-related surface states that effectively narrow the energy band gap of small silicon nanocrystals. The focus of the second half of the thesis is on experimental and computational studies of enhanced luminescence from silicon nanocrystals in the near field of noble metal nanostructures.
\r\n\r\nSurface plasmon enhancement is a technique that has only recently been applied to semiconductor nanocrystal luminescence. This thesis thoroughly investigates the emission of silicon nanocrystals coupled to gold and silver nanostructures to achieve a new level of understanding of the enhancement effect. By pairing silicon nanocrystals to metal nanostructures, up to ten-fold increases in the luminescence intensity are realized, concomitant with enhancements of the radiative decay rate, the absorbance cross section, and the quantum efficiency. Moreover, coupling at the plasmon resonance frequency is used to tune the nanocrystal emission spectrum. A computational exploration of these experimental observations indicates that the enhancement effects can be ascribed to emission in the concentrated local field that results from the excitation of metal particle plasmon modes. Finally, the process of coupling silicon nanocrystal emitters to plasmonic metals is applied to a silicon-nanocrystal light-emitting diode, and enhanced electroluminescence is realized.
" }, { "name": "Cashin, Amanda Leigh", "degree": "PhD", "year": "2006", "title": "Chemical Scale Investigations of Drug-Receptor Interactions at the Nicotinic Acetylcholine Receptor", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03022006-172355", "creators": [ { "name": { "family": "Cashin", "given": "Amanda Leigh" }, "id": "Cashin-Amanda-Leigh", "display_name": "Cashin, Amanda Leigh" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RX9T-1069", "abstract": "Biological signaling pathways employ a vast array of integral membrane proteins that process and interpret the chemical, electrical, and mechanical signals that are delivered to cells. Among these proteins, ligand gated ion channels (LGIC) are therapeutic targets for Alzheimer\u2019s disease, Schizophrenia, drug addiction, and learning and memory. High-resolution structural data on neuroreceptors are only just becoming available, yet the functional importance of particular structural features can be challenging.
\r\n\r\nThe primary focus of the present work is to gain a chemical scale understanding of the ligand-receptor binding determinants of LGICs. In particular, these studies explore drug-receptor interactions at the nicotinic acetylcholine receptor (nAChR), the most extensively studied members of the Cys-loop family of LGICs. The present study utilizes in vivo nonsense suppression methodology to perform chemical scale investigations of nAChR agonist activity.
\r\n\r\nThe binding of three distinct agonists\u2013-acetylcholine (ACh), nicotine, and epibatidine--to the nicotinic acetylcholine receptor (nAChR) has been probed using unnatural amino acid mutagenesis. ACh makes a cation-pi interaction with Trp a149, while nicotine employs a hydrogen bond to a backbone carbonyl in the same region of the agonist binding site. The nicotine analogue epibatidine achieves its high potency by taking advantage of both the cation-pi interaction and the backbone hydrogen bond.
\r\n\r\nNonsense suppression was also utilized to probe the importance of residues outside of the binding box in nAChR function. These studies demonstrate a structural role of the highly conserved aD89 residue in stabilizing the agonist binding site near aW149. In addition to outer shell residue, aK145 is shown to be important for proper nAChR function. In combination with additional evidence from other recent advances, this site is proposed to be important in initiating the nAChR channel gating pathway.
\r\n\r\nResidues outside the aromatic binding site were also examined through computational protein design studies. Results from these studies identify outer shell mutations 116Q and 57R (AChBP numbering) that enhance nAChR specificity for nicotine, over ACh and epibatidine compared to wild-type receptors.
\r\n\r\nFinally, a series of cationic polyamides were shown to enhance polyamide affinity while maintaining specificity by varying the number, relative spacing, and linker length of aminoalkyl side chains.
" }, { "name": "Ceres, Donato Marino", "degree": "PhD", "year": "2006", "title": "Electron Transfer at DNA-Modified Electrodes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06202006-113417", "creators": [ { "name": { "family": "Ceres", "given": "Donato Marino" }, "id": "Ceres-Donato-Marino", "display_name": "Ceres, Donato Marino" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "orcid": "0000-0001-5356-4385", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vdyv-zf71", "abstract": "The DNA pi stack provides an efficient pathway for transport of electron and electron holes. Ground-state electron transport is furthermore extremely sensitive to subtle DNA structural perturbations, such as a single base mismatch, that alter pi-stacking. As a result, DNA-modified electrodes have allowed the development of highly sensitive diagnostic devices for the detection of base mismatches, lesions, and mutations. We have been able to apply DNA-mediated charge transduction, using a methylene blue/ferricyanide electrocatalytic cycle, in a DNA chip format for the detection of a single base mismatches at a microelectrode. Electrocatalysis is detected at DNA-modified electrodes down to 40 um electrode in diameter, where 108 DNA molecules are responsible for the electron transduction. This exquisite sensitivity both for mismatch detection irrespective of sequence context and to a small number of molecules is an important requisite for the development of a device able to detect multiple genetic variations in the absence of DNA amplification.
\r\n\r\nWe have also investigated in detail the electrochemical properties of DNA films. DNA is a highly charged molecule and, when self-assembled on a gold surface in a dense array, its properties are similar to those of polyelectrolyte films. We have found that the structure of the DNA film is sensitive to ion concentration and identity. Variations of the electrostatic potential across the film can sensitively affect both thermodynamics and kinetics of redox reporters incorporated in the film. Methylene blue reduction in the DNA film occurs via a two electron, one proton process. The Pourbaix diagram is linear in the case of a monovalent anionic buffer, while it is curved in phosphate buffer. Electron transfer kinetics are also affected by the relative concentration of divalent anions: at low pH the film is compressed in the linker portion and the rate of electron transfer is faster. Based on this understanding of the electrostatic balance inside the DNA film, a new analytical tool for monitoring hybridization events on gold surfaces has been developed using electrochemical impedance spectroscopy of ferricyanide.
\r\n\r\nIn order to explore the electron transport properties of DNA films mechanistically scanning tunneling microscopy (STM) has also been employed. These experiments provide a first opportunity to examine DNA conductivity under physiological conditions. These STM experiments on DNA films show that DNA, when perpendicularly oriented with respect to the surface, is coupled to the STM tip and the local density of states contribute to the measured tunneling current. At positive biases, when the surface is positive, the DNA is tilted towards the surface and as a result decoupled from the tip; the DNA appears \"transparent\" and the underlying surface instead is imaged. Also important is the integrity of the base stack. When the percentage of DNA duplexes containing a single base mismatch in the film is increased, the conductivity of the film decreases. The STM tip, being held at a constant current, approaches the DNA film until, at a critical mismatch content, the tip must penetrate the film and image resolution is lost. The current versus voltage characteristic of the DNA film has furthermore been determined through a new scanning tunneling spectroscopic technique that provides highly stable and reproducible measurements. We find that DNA duplex films under physiological conditions exhibit negative differential resistance, which is a feature that is typical of resonant electron tunneling via energetically localized molecular orbitals. This observation provides an experimental evidence for the existence of localized states within the DNA HOMO-LUMO gap that can be responsible for the ground state electron transport observed in electrochemical experiments.
" }, { "name": "Collins, Cynthia Hollie", "degree": "PhD", "year": "2006", "title": "Directed Evolution of the Transcriptional Activator LuxR", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-12272005-160649", "creators": [ { "name": { "family": "Collins", "given": "Cynthia Hollie" }, "id": "Collins-Cynthia-Hollie", "orcid": "0000-0003-1647-860X", "display_name": "Collins, Cynthia Hollie" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "chair", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Leadbetter", "given": "Jared R." }, "id": "Leadbetter-J-R", "orcid": "0000-0002-7033-0844", "role": "member", "display_name": "Leadbetter, Jared R." }, { "name": { "family": "Elowitz", "given": "Michael B." }, "id": "Elowitz-M-B", "orcid": "0000-0002-1221-0967", "role": "member", "display_name": "Elowitz, Michael B." } ], "option_major": [ "biochem" ], "doi": "10.7907/61qd-8j79", "abstract": "LuxR-type proteins are responsible for density-dependent transcriptional regulation in quorum-sensing systems that employ acyl-homoserine lactones (acyl-HSLs) as signal molecules. The Vibrio fischeri lux operon, which includes LuxR, has been well studied and shown to function in E. coli. The components of the lux operon have been used to engineer de novo genetic circuits because they provide a versatile intercellular communications system. We have used directed evolution to engineer LuxR to generate new components for engineering genetic circuits with a wide range of communications functions and to explore the evolution of LuxR specificity and response.
\r\n\r\nWe developed and validated a screening system to identify mutants of LuxR that activate gene expression with non-cognate acyl-HSLs. We screened libraries of luxR mutants for variants exhibiting increased gene activation in response to octanoyl-HSL (C8HSL). Eight LuxR variants were identified that showed a 100-fold increase in sensitivity to C8HSL. These variants displayed increased sensitivities to a broadened range of acyl-HSLs while maintaining a wild-type or greater response to LuxR\u2019s cognate signal, 3-oxo-hexanoyl-homoserine lactone (3OC6HSL).
\r\n\r\nTo generate a LuxR with a new signaling specificity, we used a dual selection system to identify LuxR variants that either activate gene expression (ON) or do not (OFF) under desired sets of conditions. The dual selection system was evaluated prior to its use, and a 490-fold enrichment in functional clones per round of ON/OFF selection was observed. We used the dual selection system to identify a LuxR variant that responds to straight-chain acyl-HSLs, but no longer responds to 3OC6HSL. A single mutation in the N terminal signal-binding domain reduces the response to acyl-HSLs having a carbonyl substituent at the third carbon of the acyl chain.
\r\n\r\nWe used the dual selection system to identify LuxR variants that activate transcription upon binding to a promoter containing a mutated operator site. An amino acid position critical for modulating the DNA-binding specificity of LuxR for the new DNA target was identified. The dual selection system provides a rapid and reliable method for identifying LuxR variants that have the desired response, or lack thereof, to a given set of acyl-HSL signals or DNA targets.
" }, { "name": "Doss, Raymond Michael", "degree": "PhD", "year": "2006", "title": "Programmable Oligomers for DNA Recognition", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202008-110622", "creators": [ { "name": { "family": "Doss", "given": "Raymond Michael" }, "id": "Doss-Raymond-Michael", "display_name": "Doss, Raymond Michael" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/F0X3-Q612", "abstract": "As the amount of information about the genetic construct of the human body continues to grow, the ability to manipulate genes via the use of synthetic molecules becomes an increasingly attractive concept. Polyamides developed in the Dervan Lab are capable of doing just this by binding in the minor groove of DNA in a highly specific manner. Not only are polyamides able to specifically target sequences of DNA, but they are able to do so at affinities which make them competitive with endogenous transcriptional machinery.
\r\n\r\nThe complex nature of the DNA minor groove structure, however, has forced the evolution of traditional imidazole, pyrrole and hydroxypyrrole polyamides into newly developed oligomers \u2014 compounds which have been shown to bind sequences of DNA that have been traditionally difficult to target. In going from polyamides to oligomers, these compounds have seen a variety of changes brought about by the search for ring systems capable of conveying improved binding properties. Several new recognition elements have been uncovered and characterized with respect to their DNA affinity and specificity. Experiments testing the capabilities of these oligomers have shown that such compounds demonstrate great potential for targeting many new, biologically relevant sequences of DNA thus showing promise as potential 2nd generation therapeutics.
\r\n" }, { "name": "Duimstra, Joseph Anthony", "degree": "PhD", "year": "2006", "title": "Modulation of Magnetic Properties in Magnetic Resonance Imaging Contrast Agents and Molecular Magnetic Materials", "advisor": "Meade, Thomas J.; Fraser, Scott E.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04222006-220215", "creators": [ { "name": { "family": "Duimstra", "given": "Joseph Anthony" }, "id": "Duimstra-Joseph-Anthony", "display_name": "Duimstra, Joseph Anthony" } ], "advisors": [ { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "advisor", "display_name": "Meade, Thomas J." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "advisor", "display_name": "Fraser, Scott E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "member", "display_name": "Meade, Thomas J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vc42-nh03", "abstract": "This dissertation focuses on fundamental research in two areas of magnetism, the technologically advanced field of magnetic resonance imaging (MRI) and the nascent discipline of molecular magnetic materials. Contrast agents for MRI based on the gadolinium(III) ion were designed and studied to gain insight into the parameters that may be modulated to control contrast agent efficacy. Two parameters in particular, the inner-sphere coordination environment and the electronic relaxation of the gadolinium(III) ion, were examined. Investigations into the electronic relaxation of the gadolinium(III) ion led to insights that were applied to the synthesis and evaluation of a low dimensional magnetic material based on ruthenium(III) and nickel(II) ions.
\r\n\r\nManipulation of the gadolinium(III) coordination sphere provided the basis for an MRI contrast agent designed to be sensitive to the oncologically relevant enzyme beta-glucuronidase. This agent functions by restricting water access to the inner-sphere coordination sites of the gadolinium(III) ion. The design, synthesis, magnetic properties and biochemistry of the agent are described in detail. The agent displays good enzyme kinetics and complicated coordination equilibria with water and carbonate ion.
\r\n\r\nA second approach to modulating contrast agent efficacy consisted of varying the electronic relaxation time of the gadolinium(III) ion. Towards this goal, ligand frameworks were designed and synthesized to influence the relaxation time of the gadolinium(III) ion via remote redox activity. Structural characterization and in vitro assays of these ligand-metal constructs indicated more robust ligands were required for complex stability. Initial steps toward a ligand that fulfills these requirements proved successful.
\r\n\r\nThe structural data from the electronic relaxation studies led to the synthesis of a one-dimensional coordination polymer comprised of chelated ruthenium(III) and nickel(II) ions bridged by cyanide ligands. The compound was studied by X-ray crystallography and its magnetic properties indicated that the ions were ferromagnetically coupled.
" }, { "name": "Feenstra, Jonathan Stuart", "degree": "PhD", "year": "2006", "title": "Ultrafast Electron Diffraction: Direct Determination of Structural Dynamics of Molecular Excited States", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232006-084250", "creators": [ { "name": { "family": "Feenstra", "given": "Jonathan Stuart" }, "id": "Feenstra-Jonathan-Stuart", "display_name": "Feenstra, Jonathan Stuart" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QCFT-AK63", "abstract": "Ultrafast electron diffraction (UED) has been applied to determine the structures of isolated molecules and the dynamics of their excited states. Preceding the experimental accounts is a detailed discussion of the theoretical methodology behind UED in the Caltech labs. The procedure is explained by which electron scattering signal is measured and processed to allow the direct determination of structural dynamics (the signature feature of this experiment). The apparatus itself is also broken down into its component parts and discussed.
\r\n\r\nUED has the capability of studying both ground and excited state systems, which will be demonstrated by example. A number of molecules were studied in their ground states (chlorobenzene, bromobenzene, iodobenzene, 2-fluoropyridine, acetylacetone, benzaldehyde, acetophenone, and methylbenzoate). The structures were determined and compared with structures derived by theoretical calculations and with the results of previous gas electron diffraction inquiries. The molecular structures of 2-fluoropyridine, acetophenone, and methylbenzoate had not been previously experimentally determined. The structure of ground-state acetylacetone is discussed in detail as it represents an old problem involving the influence of intramolecular hydrogen bonding.
\r\n\r\nAcetylacetone, benzaldehyde, and acetophenone were also studied after excitation by a femtosecond laser pulse. Acetylacetone was observed to fragment \u2013 losing the hydroxyl radical. Calculations were performed to further explore the dynamics and mechanism. For excited benzaldehyde and acetophenone, a bifurcation of pathways was structurally resolved. Both molecules have photophysical and photochemical channels from the excited state. The photophysical channels result in the formation of a structure possessing a quinoid ring. The photochemical channels differed \u2013 for benzaldehyde, molecular dissociation resulting in benzene and carbon monoxide, and for acetophenone, homolytic bond cleavage resulting in methyl and benzoyl radicals. The structures of all species were determined as were the time scales involved. Calculations were used to assist in the determination of the excited state decay mechanisms.
" }, { "name": "Fry, Juliane Loraine", "degree": "PhD", "year": "2006", "title": "Spectroscopy and Kinetics of Atmospheric Reservoir Species: HOONO, CH\u2083C(O)OONO\u2082, CH\u2083OOH, and HOCH\u2082OOH", "advisor": "Okumura, Mitchio; Wennberg, Paul O.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04292006-175538", "creators": [ { "name": { "family": "Fry", "given": "Juliane Loraine" }, "id": "Fry-Juliane-Loraine", "orcid": "0000-0003-1799-5828", "display_name": "Fry, Juliane Loraine" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "advisor", "display_name": "Wennberg, Paul O." } ], "committee": [ { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "chair", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/B5C5-2F63", "abstract": "This thesis reports experimental and theoretical studies of the spectroscopy and kinetics of four atmospheric reservoir species: peroxynitrous acid (HOONO), peroxyacetyl nitrate (PAN, CH\u2083C(O)OONO\u2082), methyl hydroperoxide (MHP, CH\u2083OOH), and hydroxymethyl hydroperoxide (HMHP, HOCH\u2082OOH). Reservoir species are so named because they temporarily or permanently sequester reactive radicals (such as OH, HO\u2082, or NO\u2082), reducing the oxidative strength of the atmosphere and allowing transport of pollutants to remote regions.
\r\n\r\nTwo conformers, cis-cis and trans-perp HOONO, are identified in the 2vOH region by vibrational overtone initiated photodissociation spectroscopy, and the isomerization barrier from the less stable trans-perp to cis-cis HOONO is determined experimentally, statistically, and ab initio to be ~ 40 kJ/mol. This low barrier indicates that only cis-cis HOONO is atmospherically important. The complex vibrational spectroscopy of cis-cis HOONO is assigned with the aid of a simple two-dimensional OH-stretch/torsion coupling model of the planar, partially hydrogen-bound molecule. Combined with nonuniform quantum yield, this model explains the major features in the cis-cis HOONO spectrum. Its application to the fundamental region suggests an upward adjustment of the atmospherically important HOONO/HONO\u2082 product branching ratio in the OH + NO\u2082 association reaction. The rotational spectrum and dipole moment of cis-cis HOONO and DOONO are measured in the submillimeter region to characterize the molecular structure of HOONO and enable a quantitative atmospheric search.
\r\n\r\nThe overtone initiated photodissociation of PAN is studied in the 3vOH and 4vOH regions. No photodissociation is observed experimentally; statistical modeling is employed to estimate the importance of this process in PAN.
\r\n\r\nThe UV photodissociation of MHP and HMHP is studied in the 300 \u2013 350 nm region and extrapolated to 400 nm to calculate total UV photolysis rates.
\r\n\r\nThe overtone initiated photodissociation of HMHP is studied in the 4vOH and 5vOH regions. The rich spectroscopy of this two-OH-chromophore molecule is assigned with the help of a one-dimensional anharmonic oscillator model on each OH stretch of three ab initio identified HMHP conformers. This modeling allows estimation of the (unknown) dissociation threshold for HMHP.
\r\n\r\nLastly, an atmospheric search for HOONO, likely the most atmospherically important of the four molecules studied herein, is proposed and outlined.
\r\n" }, { "name": "Grimm, Ronald L.", "degree": "PhD", "year": "2006", "title": "Fundamental Studies of the Mechanisms and Applications of Field-Induced Droplet Ionization Mass Spectrometry and Electrospray Mass Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10092005-222651", "creators": [ { "name": { "family": "Grimm", "given": "Ronald L." }, "id": "Grimm-Ronald-L", "orcid": "0000-0003-0407-937X", "display_name": "Grimm, Ronald L." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E8EV-W425", "abstract": "This thesis explores the evaporation and Rayleigh discharge dynamics of highly charged micron-sized droplets and explores new methodologies for extracting ions for mass analysis from neutral droplets using strong electric fields in a technique termed field-induced droplet ionization.
\r\n\r\nA phase Doppler anemometer characterizes individual highly charged droplets moving through a uniform, mild electric field within an ion mobility cell according to size, velocity, and charge. Repeated reversals of the electric field allow multiple characterizations on selected droplets. This \"ping-pong\" technique provides droplet histories that determine the solvent evaporation and Rayleigh discharge behavior. The ping-pong experiment characterizes volatile droplets of the hydrocarbon solvents n-heptane, n-octane, and p-xylene as well as two-component droplets of either 2-methoxyethanol, tert-butanol, or m-nitrobenzyl alcohol with methanol. On average, hydrocarbon droplets eject 18% of their net charge into progeny droplets with an undetectable loss in mass. Rayleigh discharge events in the polar, binary droplets release between 20 and 35% of the net charge with a correspondingly undetectable loss in mass.
\r\n\r\nIn other experiments, strong electric fields elongate neutral droplets along the field axis. Field-induced droplet ionization (FIDI) occurs at sufficient field strengths as the droplets eject opposing jets of positively and negatively charged progeny droplets. Images of droplets from a vibrating orifice aerosol generator illustrate this phenomenon, and mass spectrometric sampling of the progeny droplets demonstrates that they are a viable source of desolvated gas-phase ions. Switched electric field experiments relate the timescale of droplet elongation and progeny droplet formation in FIDI to the timescale of oscillations of droplets in sub-critical field strengths. FIDI mass spectra are presented for several species, including tetraheptyl ammonium cation, deprotonated benzene tetracarboxylic acid, and multiply protonated cytochrome c.
\r\n\r\nDroplets may serve as reactors before being sampled by FIDI-MS. FIDI-MS probes the products of heterogeneous reactions between solution-phase oleic acid or a lysophosphatidic acid and gas-phase ozone.
" }, { "name": "Harkins, Seth Beebe", "degree": "PhD", "year": "2006", "title": "The Synthesis and Study of Redox-Rich, Amido-Bridged Cu\u2082N\u2082 Dicopper Complexes", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08132005-093856", "creators": [ { "name": { "family": "Harkins", "given": "Seth Beebe" }, "id": "Harkins-Seth-Beebe", "display_name": "Harkins, Seth Beebe" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1X2Q-3P72", "abstract": "A Cu2N2 diamond core structure supported by an [SNS]- ligand exhibits a fully reversible one-electron redox process between a reduced CuICuI, {(SNS)Cu}2, and a class III delocalized Cu1.5Cu1.5 state, {(SNS)Cu}2][B(C6H3(CF3)2)4] ([SNS]- bis(2-t-butylsulfanylphenyl)amide). The Cu\u00b7\u00b7\u00b7Cu distance compresses appreciably (~0.13 \u00c5) upon oxidation; a metal-metal distance of 2.4724(4) \u00c5 is observed in the mixed-valence molecule that is nearly identical to the dicopper CuA site found in cytochrome c oxidase. The rate of electron self-exchange ks) between the CuICuI and the Cu1.5Cu1.5 complexes was estimated to be \u2265 107 M-1s-1 by 1H NMR line-broadening analysis. The unusually large magnitude of ks reflects the minimal structural reorganization that accompanies CuICuI \u2194 Cu1.5Cu1.5 interchange.
\r\n\r\nA second generation of {(PNP)CuI}2 dimer supported by a [PNP]- ligand also has been investigated ([PNP]- = bis(2-(diisobutylphosphino)phenyl)amide). The highly emissive {(PNP)CuI}2 is characterized by a long-lived excited state (\u03c4 > 10 \u03bcs) with an unusually high quantum yield (\u03c6 > 0.65) at ambient temperature. Removal of an electron from the {(PNP)CuI}2 dimer yields a nearly isostructural, Cu1.5Cu1.5 complex {(PNP)Cu}2][B(C6H3(CF3)2)4]. With a highly reducing excited state reduction potential (~ -3.2 V vs. Fc+/Fc) as well as the availability of two reversible redox processes, these bimetallic copper systems may be interesting candidates for photochemically driven two-electron redox transformations.
\r\n\r\nStudies of Cu2N2 diamond core complexes supported by the [tBu2-PNP]- ligand revealed that the dicopper complex {(tBu2-PNP)Cu}2 can not only be oxidized by one electron to {(tBu2-PNP)Cu1.5}2][B(C6H3(CF3)2)4], but also by two-electrons to {(tBu2-PNP)Cu}2][SbF6]2 ([tBu2-PNP]- = bis(2-diisobutylphoshino-4-tbutylphenyl)amide). These Cu2N2 complexes show remarkably low structural reorganization for all oxidation states as evidenced by the solid-state molecular-structures. Based on these studies of [{(tBu2-PNP)Cu}2][SbF6]2, we propose a formulation of one CuI and one paramagnetic CuIII nuclei in compressed-tetrahedral environments in the Cu2N2 core. Spectroscopic, redox, and magnetic data are consistent with a highly covalent M2N2 core supported by a rigid ligand scaffold. These complexes are excellent mimics of the entatic state found in bimetallic copper proteins.
" }, { "name": "Hart, Jonathan Ross", "degree": "PhD", "year": "2006", "title": "Synthesis and Applications of Bulky Rhodium(III) Intercalators for the Recognition of DNA Mismatches", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06092006-062410", "creators": [ { "name": { "family": "Hart", "given": "Jonathan Ross" }, "id": "Hart-Jonathan-Ross", "orcid": "0000-0002-3905-225X", "display_name": "Hart, Jonathan Ross" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/sh3b-2f25", "abstract": "The recognition of DNA base mismatches is of considerable interest for both the diagnosis and treatment of mismatch repair-deficient cancers. Two new mismatch recognition complexes have been synthesized. The first, [Rh(bpy)2(phzi)]3+ (phzi=benzo[a]phenazine-5,6-quinone diimine), recognizes DNA mismatches with high specificity and affinity, 1 x 107 Mm-1, two orders of magnitude stronger than [Rh(bpy)2(chrysi)]3+ (chrysi=chrysene-5,6-quinone diimine), the parent complex that binds single thermodynamically-destabilized base-mismatch sites in duplex DNA. The second, [Rh(bqdi)2(chrysi)]3+, is able to recognize more stable mismatches such as the G-G mismatch.
\r\n\r\nThese complexes have been applied in a variety of ways. A method has been developed for the discovery of new single nucleotide polymorphisms, SNPs, within a sequence of interest amplified from pooled genomic DNA. SNPs are readily detected using these mismatch selective molecules without false positives; allele frequencies as low as 0.05 can be detected.
\r\n\r\nUpon photoexcitation, the rhodium(III) diimine complexes cleave DNA by hydrogen atom abstraction from the sugar to yield 3'-phosphate terminated DNA that is inactive for enzymatic modification. This 3'-phosphate can be removed using T4-polynucleotide kinase opening up the possibility of enzymatic modification at the site of rhodium cleavage. The cleavage site can be fluorescently labeled. Terminal transferase can also be used to attach a homopolymer tail tagging the damage site, allowing the amplification of the DNA up to the damaged site.
\r\n\r\nThis assay can also be employed towards the development of early cancer diagnostics. Some cancers are deficient in the repair of DNA base mismatches. As a consequence, these cells have an increased number of mismatches within their genome. These mismatches in extracted genomic DNA were cleaved using mismatch-specific rhodium complexes. The cleavage sites were labeled with radioactivity, allowing the number of mismatch sites to be quantitated. A significant number of sites were cleaved in the mismatch repair deficient DU145 cell line, 1 base/3000 bp, while no sites were cleaved in the mismatch repair proficient cell line SW620. This method may present a new method for the detection of mismatch repair deficiency.
\r\n\r\nThese mismatch-specific complexes also are shown to have an antiproliferative effect on mismatch repair deficient cell lines. Mismatch repair deficiency is a contributing factor in both hereditary and sporadic human cancers. Both [Rh(bpy)2(chrysi)]Cl3 and [Rh(bpy)2(phzi)]Cl3 show a stronger antiproliferative effect against MMR deficient cells than proficient cells. Effects of stereoisomers, incubation time, and UV irradiation are also demonstrated.
" }, { "name": "Hodyss, Robert P.", "degree": "PhD", "year": "2006", "title": "Methods for the Analysis of Organic Chemistry on Titan", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01122006-105657", "creators": [ { "name": { "family": "Hodyss", "given": "Robert P." }, "id": "Hodyss-Robert-P", "orcid": "0000-0002-6523-3660", "display_name": "Hodyss, Robert P." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NRTF-GH89", "abstract": "Tholins are brownish, sticky residues formed by the energetic processing of mixtures of gases abundant in the cosmos, such as CH4, N2, and H2O, either with ultraviolet light or electrical discharge. This thesis describes investigations of the tholins produced by the processing of mixtures of N2 and CH4, as a model of photochemical processes occurring in the atmosphere of Titan. These compounds are mixed with liquid water during impacts or cryovolcanism, in melt pools which eventually freeze. The melt pools are interesting sites for astrobiological research, containing a wealth of organic material interacting over long time periods in a liquid water solvent. Studies of the near infrared reflectance spectrum and the fluorescent properties of the tholins are presented, yielding information on the composition of the tholins and a means of finding organic deposits on the surface of Titan. Tholin decomposition on heating is extensively investigated, partly to ascertain the utility of pyrolysis as a technique for tholin characterization. Tholins are found to undergo significant chemical change at temperatures as low as 100 \u00b0C, releasing large quantities of ammonia, while at higher temperatures, cyclizing and aromatizing reactions occur. Pyrolysis is thus not a good technique for the characterization of tholins. The development of two instruments for tholin characterization are also discussed: a gas chromatograph with an ultraviolet absorption detector, for functional group analysis of the tholins, and sensors designed for the determination of enantiomeric excess." }, { "name": "Holunga, Dean Marcu", "degree": "PhD", "year": "2006", "title": "Aerosol Technologies for Fabrication, Collection, and Deposition of Engineered Nanoparticles", "advisor": "Flagan, Richard C.; Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-09252008-110728", "creators": [ { "name": { "family": "Holunga", "given": "Dean Marcu" }, "id": "Holunga-Dean-Marcu", "orcid": "0000-0003-1101-2448", "display_name": "Holunga, Dean Marcu" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." } ], "option_major": [ "chemeng" ], "doi": "10.7907/42Z7-PY73", "abstract": "We demonstrate a turbulent mixing reactor capable of producing highly monodisperse, \u03c3G \u2248 1.1, heterogeneous oxide-coated silicon nanoparticles from pyrolytic decomposition of silane. Particle concentrations approach 10\u2079 cm\u207b\u00b3 as measured with a radial differential mobility analyzer and fA resolution electrometer. Turbulent mixing power, induced by locally high-momentum jets that actually remain below turbulent Reynolds numbers, induce mechanical mixing within a pathlength comparable to the diameter of the major flow channel. Timescales for transport are enhanced orders of magnitude above laminar processes, enabling nanoparticle evolutionary processes such as densification and crystallization to complete in the absence of significant agglomeration. Use of multiple jets in series may well enable the homogeneous introduction of additional reagents to facilitate additional heterogenous particle development.
\r\n\r\nParticles formed in the Inconel reactor were further studied using both transmission electron microscopy and photoluminescence measurements. Spherical particle morphology with faceted and unfaceted crystalline cores were observed, and thermal oxides appeared uniform. Particle purity and a high quality passivation of the particles were demonstrated by photoluminescence, although particles occasionally required additional processing to complete O\u2082 passivation. Photoluminescence measurements are in good agreement with models of quantum-confined exciton recombination, both in emitted wavelength and photoluminescence decay. Particle contamination studies using Electron Energy Loss Spectroscopy and Energy Dispersive X-Ray Spectroscopy found no evidence of metal contamination within particles studied for both native oxide and thermal oxide-coated particles. A phenomenological comparison of size information from the radial differential mobility analyzer and photoluminescence spectra demonstrated that thermally grown oxide shells and native oxide shell have initially opposite trends in the variation of thickness with particle size, although over time, native oxide shells thicken considerably.
\r\n\r\nA thermophoretic deposition chamber was designed for uniform deposition on wafers ranging in size from 100 mm\u2013300 mm and over a range of flowrates from 500 sccm to 15000 sccm. A power-law hyperbolic inlet nozzle was shown theoretically to minimize separation. A uniform axial temperature gradient is developed using programmable temperature controlled heaters along with active cooling. Characterization by atomic force microscopy studies on 150 mm wafers demonstrated uniform coverage both radially and in the azimuth, in good agreement with model results. Deposition uniformity is predicted on larger wafers, up to 300 mm.
\r\n\r\nPyrolysis reactions in small diameter tubular reactors foul the reactors\u2019 walls continuously, with deposition morphology ranging from thin-films to dendritic, filter-like structures. The particle number concentration decays linearly with time. Hybridization of the turbulent mixing reactor with high energy seed reactors, such as a microplasma discharge, shows promise that may significantly reduce fouling, maintain or increase particle number concentration, maintain or increase particle monodispersity, expand chemistries available, and retain the ability to produce heterogeneous particles.
\r\n\r\nLaminar flow reactors are well suited to the production of monodisperse, \u03c3G \u2248 1.1, aerosols. The rate of pyrolytic decomposition of silane precursor is kept relatively slow during a gentle thermal ramp wherein the low temperature favors vapor deposition growth over additional nucleation. The resulting reduction in silane inhibits further nucleation as the temperature is increased. Slow flowrates, wherein diffusional losses of precursor assists the inhibition of additional nucleation, also contributed to maintaining lower nucleation rates, but are not necessary to achieve monodispersity or higher yield.
\r\n\r\n" }, { "name": "Larsen, Catharine Ho\u00e0ng-Mai", "degree": "PhD", "year": "2006", "title": "Investigating Imidazolidinone Catalysts: Enantioselective Organocatalytic Diels-Alder Reactions, Conjugate Additions to Access Non-Natural \u221d-Amino Acids, and Bimodal Catalyst Activation for the Development of Organo-Cascade Reactions", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142005-105810", "creators": [ { "name": { "family": "Larsen", "given": "Catharine Ho\u00e0ng-Mai" }, "id": "Larsen-Catharine-Ho\u00e0ng-Mai", "display_name": "Larsen, Catharine Ho\u00e0ng-Mai" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2WS6-B577", "abstract": "The MacMillan group focuses on the development of new strategies that harness the power of simple organic compounds to catalyze asymmetric reactions. To this end, we have designed amine catalysts which activate alpha,beta-unsaturated aldehydes via the reversible formation of chiral iminium ions (in analogy to LUMO-lowering activation by reversible metal-substrate complexation). Kinetic studies highlight the importance of the acid co-catalyst and identified a more reactive imidazolidinone catalyst complex, which improved enantioselectivities and vastly expanded the substrate scope of the first highly enantioselective organocatalytic Diels\u2013Alder reaction. Exploration of the crucial components of catalyst architecture led to the development of the second-generation imidazolidinone that not only catalyzes cycloadditions, but a variety of other reactions of aldehydes with excellent selectivity.
\r\n\r\nComplementary to the 1,2-addition observed with Lewis acids, the alternative mode of activation offered by iminium catalysis allows for 1,4-addition of heterocycles to alpha,beta-unsaturated aldehydes. Using a chiral amine catalyst, the first asymmetric conjugate addition of oxazoles generates protected quaternary alpha-amino acids with an adjacent tertiary stereocenter, a widely applicable motif in biology, materials science, and medicine. Finally, having demonstrated that imidazolidinones can activate both electrophiles (LUMO-lowering) and nucleophiles (HOMO-raising), these iminium and enamine catalysis cycles can be linked for tandem nucleophilic addition/electrophilic trapping of enals. In a single synthetic operation, this enantioselective conjugate addition/alpha-halogenation sequence takes achiral starting materials and selectively connects them, creating multiple stereocenters across the newly formed bonds.
\r\n" }, { "name": "Link, Aaron James", "degree": "PhD", "year": "2006", "title": "Azide-Bearing Amino Acids in Protein Engineering and Proteomic Profiling", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09132005-120123", "creators": [ { "name": { "family": "Link", "given": "Aaron James" }, "id": "Link-Aaron-James", "display_name": "Link, Aaron James" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Shan", "given": "Shu-ou" }, "id": "Shan-Shu-ou", "orcid": "0000-0002-6526-1733", "role": "member", "display_name": "Shan, Shu-ou" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/XXA2-5K11", "abstract": "The utility of non-canonical amino acids in protein engineering has grown substantially over the past decade. Proteins containing these unnatural building blocks often have radically different biochemical or spectral characteristics than their wild-type counterparts. Furthermore, proteins may be endowed with chemical reactivity not found in the natural proteome upon the introduction of non-canonical amino acids. Successful incorporation of a non-canonical amino acid into recombinant proteins in E. coli is often dependent on engineering of the aminoacyl-tRNA synthetase (aaRS) activity of the cell. The bulk of the work described herein has focused on developing a system to rapidly screen libraries of mutant aaRS to identify clones capable of efficiently incorporating novel reactive non-canonical amino acids. The system is based on the display of reactive amino acid side chains on the surface of E. coli cells upon metabolic incorporation of the amino acid into recombinant outer membrane protein C (OmpC) and the subsequent covalent biotinylation of the reactive side chains. The cells are then stained with fluorescent avidin, thus rendering the cells incorporating the amino acid fluorescent and readily identifiable and sortable by flow cytometry.
\r\n\r\nThe feasibility of such a system was proven by incorporating the methionine surrogate azidohomoalanine (AHA) into OmpC and subsequently biotinylating the reactive azide groups via copper-catalyzed azide-alkyne ligation. Using an improved copper catalyst, low levels of incorporation of translationally inefficient amino acids azidoalanine, azidonorvaline, and azidonorleucine into OmpC were also detected. A saturation mutagenesis library of the methionyl-tRNA synthetase (MetRS) was designed, and cells transformed with this library were screened for the ability to incorporate the long chain amino acid azidonorleucine into recombinant proteins efficiently. Several MetRS mutants were identified with such activity using the cell surface display system. MetRS containing a single amino acid mutation, leucine 13 to glycine (L13G) that occurs in each of the three mutants discovered in the screen, is very efficient at incorporating azidonorleucine into proteins.
\r\n\r\nIn the last part of the work described in this thesis, azidohomoalanine was used to tag newly-synthesized proteins in mammalian cells, thus endowing the newly-synthesized proteins with unique bioorthogonal chemical reactivity. Following covalent biotinylation via the azide-alkyne ligation, these proteins could be selectively enriched for by avidin chromatography and identified using shotgun proteomic approaches. Nearly 200 newly-synthesized proteins were identified unequivocally in just a two-hour window. This technique promises to develop into a highly useful tool for the examination of proteome dynamics.
\r\n" }, { "name": "Liu, Julie Chih-I", "degree": "PhD", "year": "2006", "title": "Endothelial Cell Response to Artificial Extracellular Matrix Proteins", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03242006-134157", "creators": [ { "name": { "family": "Liu", "given": "Julie Chih-I" }, "id": "Liu-Julie-Chih-I", "display_name": "Liu, Julie Chih-I" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "role": "member", "display_name": "Bronner, Marianne E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ABQJ-TR83", "abstract": "Artificial extracellular matrix (aECM) proteins were designed originally for use in small-diameter vascular grafts. Current synthetic grafts fail primarily due to (i) a compliance mismatch between the prostheses and surrounding tissue and (ii) the inability to support the growth of an endothelial cell monolayer. To address these issues, biomimetic proteins were engineered with elastin-like repeats to confer elastomeric behavior and fibronectin cell-binding domains to promote endothelialization. Lysine residues or the non-canonical amino acid, para-azidophenylalanine (pN3phe), serve as crosslinking sites.
\r\n\r\nHuman umbilical vein endothelial cell (HUVEC) adhesion to aECM proteins was sequence-specific. Cells bind more strongly and exhibit faster spreading kinetics on aECM proteins containing the RGD versus the CS5 sequence. Furthermore, HUVECs on the former protein exhibited well-formed stress fibers and organized the alpha-v-beta-3 but not the alpha-5-beta-1 integrin into focal adhesions.
\r\n\r\nAlthough biomaterial design has focused on the sequences of cell-binding domains, elements remote to these bioactive sequences were found to affect cell response to aECM proteins. Proteins containing identical CS5 cell-binding domains differed in their placement of lysine residues that serve as crosslinking sites. Cell adhesion and spreading were more robust on proteins in which lysine residues were located at the termini versus within the elastin cassettes.
\r\n\r\nCrosslinked films of aECM proteins with RGD sequences adhered HUVECs in a sequence-specific manner. Poly(ethylene glycol) was covalently attached to films to reduce nonspecific cell interactions. Increasing the density of RGD in a film resulted in increased cell adhesion and spreading but did not have a significant effect on migration rates.
\r\n\r\naECM proteins were made photoreactive through the incorporation of pN3phe. Upon exposure to ultraviolet radiation through a patterned mask, proteins were patterned on a non-adhesive background. These two-dimensional patterns then served as templates for cell adhesion.
\r\n\r\nA new technique for studying cells on aECM proteins was developed. Cells were pulsed with homopropargylglycine. Newly synthesized proteins labeled with alkyne-containing amino acids were ligated to 3-azido-7-hydroxycoumarin. Fluorescence microscopy was used to visualize these proteins in a wide variety of mammalian cell types.
" }, { "name": "Lu, Connie Chih", "degree": "PhD", "year": "2006", "title": "The Chemistry of Tris(phosphino)borate Manganese and Iron Platforms", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012006-151944", "creators": [ { "name": { "family": "Lu", "given": "Connie Chih" }, "id": "Lu-Connie-Chih", "orcid": "0000-0002-5162-9250", "display_name": "Lu, Connie Chih" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0DND-1J03", "abstract": "The coordination chemistry of monovalent and divalent manganese complexes supported by the anionic tris(phosphino)borate ligand [PhBPiPr3] is presented. The halide complexes, [PhBPiPr3]MnCl and [PhBPiPr3]MnI, have been characterized by XRD, SQUID magnetometry, and EPR spectroscopy. The halide [PhBPiPr3]MnI serves as a precursor to manganese azide, alkyl, and amide species: [PhBPiPr3]Mn(N3), [PhBPiPr3]Mn(CH2Ph), [PhBPiPr3]Mn(Me), [PhBPiPr3]Mn(NH(2,6-iPr2Ph)), [PhBPiPr3]Mn(dbabh), and [PhBPiPr3]Mn(1-Ph(isoindolate)). Collectively, they represent an uncommon motif of low-coordinate polyphosphine-supported manganese species. Some of our synthetic efforts to generate [PhBPiPr3]Mn?Nx species are described, as are theoretical DFT studies that probe the electronic viability of these multiply bonded target structures.
\r\n\r\nTwo tris(phosphino)borate ligands, [PhBPter3] and [PhBPCH2Cy3] are introduced that feature terphenyl and methylcyclohexyl groups on the phosphine arms, respectively. The iron chlorides, [PhBPter3]FeCl and [PhBPCH2Cy3]FeCl, have been prepared as precursors to iron nitrides. Addition of the nitride transfer reagent Li(dbabh) to [PhBPCH2Cy3]FeCl produced the terminal nitride, [PhBPCH2Cy3]Fe(N). The 15N NMR spectrum of the labeled species, [PhBPCH2Cy3]Fe(15N), contains a peak at 929 ppm, consistent with a terminal nitride functionality. Mossbauer spectroscopy of the nitride shows a low isomer shift value of 0.34(1) mm/s and an exceptionally large quadrupole splitting of 6.01(1) mm/s.
\r\n\r\nReduction of [PhBPCH2Cy3]FeCl generates a masked iron(I) species that is highly reactive. Combustion analysis of this species is consistent with \"[PhBPCH2Cy3]Fe.\" Other physical methods including VT NMR, EPR, and IR spectroscopies suggest the presence of a paramagnetic species in equilibrium with a diamagnetic species. The paramagnetic component is postulated to be an Fe(III) hydride, wherein a ligand C-H bond has been cyclometalated at the metal center. The reactivity of \"[PhBPCH2Cy3]Fe\" is consistent with iron(I). For example, its reaction with PMe3 and 1-adamantylazide affords the phosphine adduct, [PhBPCH2Cy3]Fe(PMe3), and the iron imide, [PhBPCH2Cy3]Fe(NAd), respectively. Interestingly, \"[PhBPCH2Cy3]Fe\" undergoes redox reactions with benzene to give initially a benzene adduct, {[PhBPCH2Cy3]Fe}2(mu-eta3:eta3-C6H6), which decomposes to {[PhBPCH2Cy3]Fe}2(mu-eta5:eta5-6,6'-bicyclohexadienyl) via radical C-C bond coupling. Finally, \"[PhBPCH2Cy3]Fe\" readily reduces CO2 at rt to give as the major product {[PhBPCH2Cy3]Fe}2(mu-CO)(mu-O), wherein a C=O bond has been cleaved. The minor product has not been definitively established, but one possibility is the oxalate-bridged dimer {[PhBPCH2Cy3]Fe}2(mu-eta2:eta2-O2CCO2) that results from reductive coupling of two CO2 molecules.
\r\n" }, { "name": "Mangion, Ian Kyle", "degree": "PhD", "year": "2006", "title": "Development of Organocatalytic Direct Aldol Transformations, Total Syntheses of Brasoside and Littoralisone, and Progress Toward the Total Synthesis of Diazonamide A", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232006-210214", "creators": [ { "name": { "family": "Mangion", "given": "Ian Kyle" }, "id": "Mangion-Ian-Kyle", "display_name": "Mangion, Ian Kyle" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1TPK-9277", "abstract": "The enantioselective amine-catalyzed direct aldol reaction of aldehdyes has been accomplished for the first time using an imidazolidinone organocatalyst. That imidazolidinone catalyst, initially developed for LUMO-lowering activation of alpha, beta-unsaturated aldehydes, provides new insight into amine-mediated aldol transition states. The concepts developed in this study have been applied toward the development of an unprecedented enantioselective Type II direct aldol. In the course of these studies the amino acid proline was also found to be a highly effective catalyst for this transformation. These catalyst systems form the basis for a novel approach to polyketide and polyglycolate architectures, structural motifs having broad representation amongst natural product isolates.
\r\n\r\nThis enamine catalysis strategy was then applied towards the total synthesis of the iridoid natural products brasoside and littoralisone. Direct aldol chemistry was applied towards the synthesis of a substituted carbohydrate structure, and a recently developed enantioselective oxyamination reaction installed a key stereocenter. Stereocontrolled synthesis of the bicyclic core common to the iridoid class of natural products required the development of a new, kinetically controlled organocatalytic intramolecular Michael reaction. A [2+2] photocycloaddition completed the first total synthesis of littoralisone, and demonstrated a likely biosynthetic link to brasoside, which may well be a natural precursor.
\r\n\r\nAn iminium-mediated addition-cyclization cascade reaction has been applied toward the total synthesis of the marine natural product diazonamide A. This strategy has provided stereoselective, catalytic access to the crucial C-10 quaternary carbon stereocenter for the first time. A novel intramolecular soft enolization aldol macrocyclization formed a precursor to the A-ring oxazole, which was subsequently completed in a newly discovered DAST-mediated cyclodehydration. Closure of the fourteen-membered biaryl macrocycle has been accessed through an unusual Suzuki macrocyclization, and completion of diazonamide A should be accessible in four further steps.
\r\n" }, { "name": "May, Jeremy Allen", "degree": "PhD", "year": "2006", "title": "I. Synthesis and Utilization of Diazocompounds for Applications in Solution-Phase and Gas-Phase Chemistry. II. Progress Toward the Communesin Alkaloids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03062006-135435", "creators": [ { "name": { "family": "May", "given": "Jeremy Allen" }, "id": "May-Jeremy-Allen", "orcid": "0000-0003-3319-0077", "display_name": "May, Jeremy Allen" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "chair", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/dkek-2c97", "abstract": "Advances in the synthesis and use of diazo compounds are first discussed. The development of non-carbonyl stabilized diazo equivalents has allowed for carbene reactivity to be localized at carbons not adjacent to carbonyls. Consequently, a new tandem sequence, the Bamford-Stevens/Claisen reaction, has been developed that incorporates selective Z-enol ether formation with a thermal- or Lewis acid-promoted Claisen reaction. Bamford-Stevens/Claisen/Carbonyl Ene and Bamford-Stevens/Claisen/Cope reactions have also been realized.
\r\n\r\nAlso discussed is the application of diazocompounds to gas-phase chemistry with peptides. Crown ethers are used for binding to primary amines, and a diazomalonate is incorporated for generation of a highly reactive carbene within a non-covalent complex. Intermolecular insertion reactions can then occur in these complexes. Electrospray ionization mass spectrometry and density functional theory (DFT) are utilized to evaluate the reactions for small molecules and peptides, as well as metal-promoted Wolff Rearrangement in the gas phase.
\r\n\r\nFinally, the biosynthesis of the calycanthaceous alkaloids is examined. The development of an approach to the alkaloid communesin B is presented. The approach is based on considerations of a possible biosynthetic sequence involving an oxidative coupling of tryptamine with a derivative of the ergot alkaloid aurantioclavine. Structure revision is also suggested for the recently isolated microfilament disrupting alkaloid nomofungin. Crystallographic evidence is presented for products from the proposed inverse-demand Diels-Alder reaction.
" }, { "name": "Meyer, Michelle Margaret", "degree": "PhD", "year": "2006", "title": "Exploring Protein Sequence Space Using Computationally Directed Recombination", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-112358", "creators": [ { "name": { "family": "Meyer", "given": "Michelle Margaret" }, "id": "Meyer-Michelle-Margaret", "orcid": "0000-0001-7014-9271", "display_name": "Meyer, Michelle Margaret" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "biochem" ], "doi": "10.7907/YJPE-CD11", "abstract": "Evolution has provided us with many protein sequences. However, these sequences represent a very small fraction of the possible sequences. In the laboratory, scientists have explored areas of sequence space not represented by natural proteins both to better understand natural proteins, and to create new proteins with desirable properties. The principle mechanism used to explore protein sequence space is mutagenesis. However, recombination of homologous genes can also explore regions of sequence space rich with folded and functional proteins.
\r\n\r\nIn this work we demonstrated using a beta-lactamase model system that a computation energy function (SCHEMA) can predict which of the chimeras made by recombining distantly related proteins are likely to fold. SCHEMA uses protein sequence and structure information to identify pairwise amino acid interactions disrupted by recombination. Using SCHEMA we designed libraries of chimeric beta-lactamases. These libraries were intended to have a high fraction of folded variants, while incorporating many amino acid substitutions compared with the parental proteins. The chimeras in these libraries were characterized to determine whether they retain the parental function and what new substrate specificities could be obtained.
\r\n\r\nTo identify critical variables for determining whether a chimera functions, we used logistic regression analysis to analyze functional and nonfunctional chimeras. From this analysis it is apparent that both two-body (pairwise) and one-body terms play a significant role in determining whether a chimera functions. We also used random mutagenesis to restore functionality to nonfunctional chimeras showing that a thermostabilizing mutation can rescue approximately 5% of the nonfunctional chimeras. The one-body terms that appear significant for determining whether a chimera functions are not explicitly counted by SCHEMA when predicting chimera folding. To estimate the effects on chimera folding represented by the one-body terms, we developed an additional measure to predict chimera folding based on just the chimera amino acid sequence and a multiple sequence alignment of homologous proteins. This measure is predictive of chimera folding alone, and when combined with the pairwise SCHEMA energy increases the accuracy of the folding predictions compared to SCHEMA.
" }, { "name": "Michalak, David Jason", "degree": "PhD", "year": "2006", "title": "Physics and Chemistry of Silicon Surface Passivation", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-05082006-074414", "creators": [ { "name": { "family": "Michalak", "given": "David Jason" }, "id": "Michalak-David-Jason", "orcid": "0000-0002-1226-608X", "display_name": "Michalak, David Jason" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ge4q-ky47", "abstract": "Low interfacial electron-hole recombination rates are essential for low-noise electronic devices and high-efficiency solar energy converters. This recombination rate is dependent on both the surface electrical trap state density, NT,s, and the surface concentrations of electrons, ns, and holes, ps. A reduction in NT,s is often accomplished through surface chemistry, and lower recombination rates, through lower NT,s values, have been demonstrated in this work for surfaces chemically treated to produce methoxylated, Si-O-CH3, overlayers. The H-Si(111) surfaces can react with methanol quickly in the presence of an oxidant or slowly in neat anhydrous methanol. Mechanisms have been proposed for both reactions.
\r\n\r\nLow recombination rates can also be achieved through control of the surface physics; a large ns or ps can lower recombination rates. To date, low recombination rates have often been attributed only to a reduction in NT,s, without a direct measurement of ns and ps, partly because the importance of ns and ps has not been fully recognized and partly because an accurate evaluation of ns and ps can be very difficult. Surface recombination rates of silicon immersed in liquids containing various redox species (e.g., Fc+/0, I2, Me10Fc+/0, or CoCp2+/0) were studied using an rf photoconductivity decay apparatus and compared with ns and ps values obtained from Mott-Schottky and other analysis techniques. The results demonstrate that the observed recombination rates can only be correlated with NT,s values when ns [approx.] ps. In all other cases, the recombination rate was low due to a large ns or ps even for surfaces with large NT,s values.
\r\n\r\nThe full impact of this work was further realized through a study of the recombination rates of H-Si immersed in solutions of 48% HF, 40% NH4F, and buffered HF (BHF), because such measurements are often performed for in situ monitoring of the surface quality during wafer processing steps. Our results demonstrate that only HF contacts can be used for in situ monitoring because ns [approx.] ps. For NH4F or BHF contacts, low recombination rates were observed only because ns \u00bb ps, and NT,s cannot be inferred from these measurements.
" }, { "name": "Min, Endy Yeo-Jung", "degree": "PhD", "year": "2006", "title": "Kinetic Resolution of Chiral \u221d-Olefins Using Enantiopure Ziegler-Natta Polymerization Catalysts", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11162005-125732", "creators": [ { "name": { "family": "Min", "given": "Endy Yeo-Jung" }, "id": "Min-Endy-Yeo-Jung", "display_name": "Min, Endy Yeo-Jung" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZD0X-9Y24", "abstract": "Towards the goal of kinetic resolution of chiral olefins, a series of enantiopure C1 symmetric metallocenes has been synthesized for use in the polymerization of chiral olefins. The new precatalysts were based on the parent precatalyst {(SiMe2)2[[eta]5-C5H(CHMe2)2][[eta]5-C5H2((S)-CHMeCMe3)]}ZrCl2, (S)-2, which has a doubly, silylene-linked ligand framework. The new precatalysts include {(SiMe2)2[[eta]5-C5H(CHEt2)2][[eta]5-C5H2((S)-CHMeCMe3)]}ZrCl2, (S)-3, {(SiMe2)2[[eta]5-C5H(CHCy2)2][[eta]5-C5H2((S)-CHMeCMe3)]}ZrCl2, (S)-4 (Cy = cyclohexyl), {(SiMe2)2[[eta]5-C5H(CHTMS2)2][[eta]5-C5H2((S)-CHMeCMe3)]}ZrCl2, (S)-5 (TMS = trimethylsilyl), and {(SiMe2)2[[eta]5-C5H(CHMe2)2][[eta]5-C5H2((S)-CHEtCMe3)]}ZrCl2, (S)-6.\r\n\r\nThe zirconocene dichlorides (S)-2, (S)-3, (S)-4, and (S)-5 have an enantiopure 3,3-dimethyl-2-butyl (\"methylneopentyl\") substituent on the \"upper\" cyclopentadienyl ligand. The zirconocene dichloride (S)-6 has an enantiopure 2,2-dimethyl-3-pentyl (\"ethylneopentyl\") substituent on the \"upper\" cyclopentadienyl ligand.\r\n\r\nWhen activated with methylaluminoxane (MAO), these metallocenes show unprecedented activity for the polymerization of racemic monomers bearing substitution at the 3- and/or 4-positions. In addition, due to the optically pure nature of these single site catalysts, polymerization of racemic monomers serves as a transition metal mediated kinetic resolution strategy. The polymeric product is enriched with the faster reacting enantiomer, while the recovered monomer is enriched with the slower reacting enantiomer. The two components are easily separated, thus affecting the resolution. A modest kinetic resolution was achieved (s = kfaster/kslower = ca. 2) with most olefins surveyed. In the case of 3,4-dimethyl-1-pentene and 3,4,4-trimethyl-1-pentene, high levels of separation were obtained (s > 12). X ray crystal structure determinations for (S)-2, (S)-3, and (S)-4 have been used to examine the prevailing steric interactions expected in the diastereomeric transition states for propagation during polymerization. In comparison to (S)-2, slight improvements in the selectivity of 3-methyl-1-hexene and 3,5,5-trimethyl-1-hexene were observed with polymerizations using (S)-3. Likewise, the polymerizations of 3-methyl-1-pentene and 3,5,5-trimethyl-1-hexene using (S)-6 showed a modest increase in selectivity, relative to (S)-2. The kinetic resolution of chiral olefins containing a polar functionality also has been attempted with (S)-2. Although the selectivity of these polymerization experiments is yet to be determined, preliminary work indicates that NMR can be used to analyze the (S)-Mosher esters of the olefins to obtain the enantiomeric excess." }, { "name": "Mishra, Swaroop", "degree": "PhD", "year": "2006", "title": "Intracellular Considerations in the Development of Non-Viral Nucleic Acid Delivery Systems for Systemic Administration", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09222005-123557", "creators": [ { "name": { "family": "Mishra", "given": "Swaroop" }, "id": "Mishra-Swaroop", "display_name": "Mishra, Swaroop" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Webster", "given": "Paul" }, "id": "Webster-P", "role": "member", "display_name": "Webster, Paul" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7MP8-JJ24", "abstract": "Non-viral nucleic acid delivery systems must condense nucleic acids into small particles, confer protection from degrading factors in serum and in cells, achieve uptake to targeted cells, direct nucleic acids to appropriate intracellular destinations, release this cargo to permit its action, and exhibit minimal toxicity. The nature of synthetic vectors allows for facile addition of new features, but these modifications can affect performance in unanticipated ways. The effective combination of functional components necessitates a systems approach, where the materials design simultaneously considers the functional environment of and the various barriers to delivery. This thesis facilitates and promotes a systems approach by undertaking development of an improved mechanistic understanding of non-viral gene transfer in vitro, emphasizing elucidation of delivery vehicles\u2019 interactions with and behavior within cells. Special attention is given to the gene delivery behavior of cyclodextrin-containing polycations.
\r\n\r\nSimple modifications to delivery systems can have unanticipated consequences. In Chapter 2, it is shown that greater distance between toxicity-reducing cyclodextrin moieties and amidine charge centers increases both the transfection efficiency and toxicity of a polycationic vector. Chapter 3 shows data demonstrating that modification with poly(ethylene glycol) for extracellular salt-stabilization alters non-viral gene delivery particles\u2019 intracellular trafficking and resulting gene expression. Taken together, the results reveal that non-viral gene delivery vehicles behave as assembled, multifunctional systems.
\r\n\r\npH-buffering components exhibit complex behavior in non-viral gene delivery. In Chapter 4, the intracellular activity of such components is quantified using confocal microscopy. Analysis of chloroquine and its chemical analogues demonstrates in Chapter 5 that chloroquine improves non-viral gene transfer through pH-buffering as well as through enhanced nucleic acid unpackaging and its own interactions with nucleic acids. Chapter 6 gives results that characterize delivery behavior of analogous vectors with and without pH-buffering capacity and show that factors beyond buffering activity contribute to improved transfection efficiency. Collectively, these results emphasize consideration of new system components\u2019 effects on all functions of a non-viral gene delivery system.
\r\n\r\nA systems approach requires comprehensive consideration of the gene delivery process. Chapter 7 reviews current understanding of intracellular barriers to non-viral gene delivery, and Chapter 8 offers recommendations for future work.
\r\n" }, { "name": "Mock, Marissa Lee", "degree": "PhD", "year": "2006", "title": "Protein Modification Through in vivo Incorporation of Noncanonical Amino Acids", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252005-154242", "creators": [ { "name": { "family": "Mock", "given": "Marissa Lee" }, "id": "Mock-Marissa-Lee", "display_name": "Mock, Marissa Lee" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Smolke", "given": "Christina D." }, "id": "Smolke-C-D", "role": "member", "display_name": "Smolke, Christina D." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/H54E-3292", "abstract": "Traditional techniques of polymer synthesis produce macromolecules with statistical distributions of chain length, composition, stereochemistry, and sequence. Nature has evolved a complex system for polypeptide synthesis that gives essentially complete control of chain length and monomer sequence. Using the natural protein biosynthesis machinery to produce protein polymers provides not only a unique opportunity to study the effects of such molecular characteristics on material properties, but also the possibility of readily incorporating bioactive domains into protein-based materials.
\r\n\r\nThe objective of this thesis work was to expand upon the set of amino acids available for incorporation into proteins in vivo and to explore applications of the novel chemistries and physical properties provided by the new analogs.
\r\n\r\nChapter 2 describes the incorporation of new unsaturated analogues of isoleucine, the alkene 2-amino-3-methyl-4-pentenoic acid and the alkyne 2-amino-3-methyl-4-pentynoic acid, by the wild type E. coli biosynthetic apparatus. Incorporation was found to be sensitive to side chain stereochemistry in the case of the alkene analog; the translational activity of the pairs of enantiomers (SS, RR and SR, RS) were markedly different. We concluded that, although the SS-isomer is a good analogue, the SR-isomer is not incorporated into proteins by this expression host.
\r\n\r\nChapter 3 focuses on the incorporation of a fluorine-containing noncanonical amino acid, 5,5,5-trifluoroisoleucine, into artificial extracellular matrix proteins. The fluorinated proteins displayed altered solubility phase behavior and were more resistant to degradation by the physiologically relevant protease elastase, yet retained the ability to adhere endothelial cells in a sequence specific manner.
\r\n\r\nChapter 4 describes the incorporation of the photoreactive noncanonical analog p-azidophenylalanine into artificial extracellular matrix proteins. Films of the azide-containing proteins were crosslinked upon short exposure to ultraviolet radiation. Using simple patterned masks, we demonstrated the ability to pattern protein films by only exposing certain regions. When protein patters were produced on a non-adhesive background, endothelial cells selectively adhered to the protein regions to create stable cell patterns.
" }, { "name": "Morrill, Christie", "degree": "PhD", "year": "2006", "title": "Application of Transition Metal Catalysis to Small Molecule Synthesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08222005-162934", "creators": [ { "name": { "family": "Morrill", "given": "Christie" }, "id": "Morrill-Christie", "display_name": "Morrill, Christie" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QRWG-BM33", "abstract": "Over the past decade, transition metal catalysis has developed into a new field in organic synthesis, enabling numerous synthetic transformations that were previously not feasible. This thesis describes the application of both ruthenium and rhenium catalysis to the synthesis of several classes of small molecules. Ruthenium-catalyzed ring-opening cross-metathesis of five- through eight-membered ring cycloolefins was investigated for the synthesis of functionalized dienes (Chapter 1). Unsubstituted, trisubstituted, and allyl-substituted cycloolefins were studied. Regioselective reactions could be achieved with the use of unsymmetrical cycloolefins. Ruthenium-catalyzed cross-metathesis was explored for the synthesis of both di- and trisubstituted vinyl boronates (Chapter 2). These reactions proceeded efficiently for a wide variety of functionalized alkenes and generally exhibited high E-stereoselectivity. The resultant vinyl boronate products were stereoselectively converted into both Z-vinyl bromides and E-vinyl iodides. The rhenium-catalyzed 1,3-isomerization of allylic alcohols was employed in the synthesis of various allylic alcohols (Chapter 3). Two different strategies were developed to promote high product selectivity in these reactions: conjugated product synthesis and N,O-bis(trimethylsilyl)acetamide-promoted product trapping. These reactions enabled the synthesis of allylic alcohols with conjugated or non-conjugated, di- or trisubstituted, and electron-rich or electron-deficient alkene components. Partial chirality transfer was observed during the 1,3-isomerization of certain enantioenriched allylic alcohols. The fundamental reaction properties observed during these studies were all consistent with the operation of a mechanism involving a chair-like transition state, which contains a partially cationic allyl moiety, as the primary reaction pathway." }, { "name": "Mu, Tingwei", "degree": "PhD", "year": "2006", "title": "A Chemical-Scale Study on the Ligand-Binding Site of a Serotonin-Gated Ion Channel", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08292005-210930", "creators": [ { "name": { "family": "Mu", "given": "Tingwei" }, "id": "Mu-Tingwei", "orcid": "0000-0002-6419-9296", "display_name": "Mu, Tingwei" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VSEF-4856", "abstract": "Signal transmission is a combination of electrical and chemical processes. Upon binding neurotransmitters, ligand-gated ion channels open to allow ion flux, which converts chemical signals to electrical signals. In this thesis, experiments in conjunction with computations are utilized to study the mechanism of the ligand-binding process.
\r\n \r\nThe target receptor is a serotonin-gated chloride channel, the MOD-1 receptor. From the viewpoint of a chemist, we explore the specific orientation of the agonist inside the binding pocket and the specific non-covalent interactions responsible for binding. In Chapter 3, computational chemistry is used to build a homology model of MOD-1 using the acetylcholine binding protein template. We proceed to dock the agonist into the binding pocket. The binding pattern from the model provides guidance for the ensuing experimental studies.
\r\n\r\nUnnatural amino acid mutagenesis is a powerful tool to modify the structure of the protein at the chemical level. Systematic perturbations can be introduced at a specific amino acid. Therefore, specific non-covalent interactions, such as hydrogen bonding and cation-pi interactions can be probed. In Chapter 2, we prove that cation-pi interactions between the agonist serotonin and Trp 226 in loop C of MOD-1 play a key role in binding the ligand. Surprisingly, this cation-pi site in MOD-1 is different from that in the serotonin type 3 receptor although these two receptors both bind serotonin, and they are highly homologous. In Chapter 4, we further show that hydrogen bonds between serotonin and Gln 228 and Asn 223 in MOD-1 are important in the binding process. Both conventional and unnatural amino acid mutagenesis are used in conjunction with serotonin analogues. The results from these thorough structure-function studies confirm aspects of the hydrogen bond pattern described in the model.
\r\n\r\nIn Chapter 5, we apply another strategy called the tethered agonist approach to further probe the agonist binding site. This is another elegant example of the effectiveness of the nonsense suppression method.
" }, { "name": "Nemanick, Eric Joseph", "degree": "PhD", "year": "2006", "title": "Chemical and Electrical Passivation of Single Crystal Silicon Surfaces Through Covalently Bound Organic Monolayers", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-09292005-152710", "creators": [ { "name": { "family": "Nemanick", "given": "Eric Joseph" }, "id": "Nemanick-Eric-Joseph", "orcid": "0000-0002-4650-6491", "display_name": "Nemanick, Eric Joseph" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GNSW-GJ84", "abstract": "The formation of and passivation by alkyl monolayers on Si(111) and Si(100) surfaces was studied. Crystalline Si(111) and Si(100) surfaces were alkylated in a two-step chlorination/alkylation process using both straight chain alkyl groups CH\u2083, C\u2082H\u2085, C\u2084H\u2089, and C\u2088H\u2081\u2087, as well sterically bulky alkyl groups such as (CH\u2083)\u2082CH-(iso-propyl), (CH\u2083)\u2083C-(tert-butyl), and C\u2086H\u2085-(phenyl) moieties to form well defined alkyl monolayers on the surface. X-ray photoelectron spectroscopic (XPS) data in the C 1s region of such surfaces exhibited a low energy emission at 283.6 binding eV, consistent with carbon bonded to Si, demonstrating a Si-C covalent bond. The C 1s XPS data indicated that larger alkyl groups were present at lower coverages than methyl groups on both the CH\u2083-terminated Si(111) surfaces as well as CH\u2083-terminated Si(100) surfaces. Despite the lower monolayer percent coverage, no Cl was detected after alkylation on either surface. Functionalization with even the bulky alkyl groups effectively inhibited the oxidation of the Si surfaces in air and produced low (< 100 cm s\u207b\u00b9) surface recombination velocities, indicating a low density of electronically active surface trap states. Transmission infrared spectroscopy indicated that the Si(111) surfaces were partially H-terminated after the functionalization reaction for groups larger than CH\u2083. High resolution soft X-ray photoelectron spectroscopic (SXPS) measurements of the Si 2p region of the alkylated Si(111) and Si(100) surfaces show monolayer coverage of SiCl and SiCH\u2083 on the Si(111) surface, with mixtures of species on H-term Si(111) as well as H-term Si(100) surfaces. Bulkier alkyl groups such as C\u2082H\u2085 and phenyl on both Si(111) and Si(100) surfaces as well as on CH\u2083-terminated Si(100) show broad Si 2p peaks with binding shifts indicative of hybrid surfaces composed of both Si-R groups and SiH/SiH\u2082 species. To model surface packing of these alkyl groups on the Si(111) surface, molecular dynamics modeling was employed using Cerius. The energies for various packing densities and packing patterns were calculated and referenced versus the reactant energy for each surface. From this it was concluded that 100% of the Si(111) surface should be CH\u2083-terminated, with lower packing densities for C\u2082H\u2085 between 50-80%, 50-66.7% for C\u2088H\u2081\u2087, 33.3-40% for tert-butyl, 33.3-50% for iso-propyl, and 50-66.7% for phenyl. A single electron transfer (SET) mechanism for the reaction of alkyl Grignards with the Cl-terminated surface is proposed. Application of a reducing potential, -2.5 V vs. Ag\u207a/Ag, to Cl-terminated Si(111) electrodes in tetrahydrofuran resulted in the complete elimination of Cl, as measured by XPS. The data are consistent with a mechanism in which the reaction of alkyl Grignard reagents with the Cl-terminated Si(111) surfaces involves electron transfer from the Grignard reagent to the Si, loss of chloride to solution, and subsequent reaction between the resultant silicon radical and alkyl radical to form a silicon-carbon bond. Sites sterically hindered by neighboring alkyl groups abstract a H atom to produce Si-H bonds on the surface.
" }, { "name": "Nickerson, Charles Sellers", "degree": "PhD", "year": "2006", "title": "Engineering the Mechanical Properties of Ocular Tissues", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03172005-145045", "creators": [ { "name": { "family": "Nickerson", "given": "Charles Sellers" }, "id": "Nickerson-Charles-Sellers", "display_name": "Nickerson, Charles Sellers" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0R13-2109", "abstract": "Age and disease can cause changes in the mechanical properties of ocular tissues, which compromise visual acuity and can lead to blindness. Thus, there is great interest in understanding the mechanical properties of ocular tissues and in developing appropriate therapeutic strategies. The goal of this thesis is to discover and manipulate the molecular mechanisms that determine the bulk physical properties of the vitreous and the cornea. Both tissues are ordered biocomposites of fibrous collagen embedded in soft matrices of proteoglycans (PGs) and glycosaminoglycans (GAGs). The hydration state, mole fraction, and organization of these components determine the mechanical properties of their respective tissues. We describe the use of a novel \"cleat geometry\" for rheometry in shear to quantitatively measure the rheological properties of vitreous and other soft biomaterials. Where as the mechanical strength of these tissues has traditionally been attributed to their collagenous components, results from coordinated mechanical and biochemical analyses suggest that PGs and GAGs also make significant contributions. We hypothesize that hyaluronan contributes to the mechanical properties of the vitreous through a Donnan swelling mechanism that induces a state of tension in the collagen network. We hypothesize that the PG/GAG matrix plays a significant role in the mechanics of the cornea by restricting the translation and deformation of the collagen fibrils.
\r\n\r\nOur therapeutic goal in the vitreous is liquefaction: we seek pharmacological agents capable of separating the vitreous from the retina and destabilizing the network without damaging the adjacent tissues (retina and lens). We present evidence that using urea to disrupt hydrogen bonds may provide clinical benefits by inducing posterior vitreous detachment and reducing the shear modulus of the vitreous.
\r\n\r\nOur therapeutic goal in the cornea is to stabilize its mechanical properties against the softening associated with keratoconus. We report a clinically-relevant rise in the modulus of corneas treated with glyceraldehyde to induce crosslinking through glycation. We hypothesize that the mechanically-relevant crosslinks are those that change the properties of the soft PG/GAG matrix and its coupling to the collagen fibrils, rather than the much more numerous crosslinks that form within fibrils.
" }, { "name": "Nowatzki, Paul John", "degree": "PhD", "year": "2006", "title": "Characterization of Crosslinked Artificial Protein Films", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042006-205243", "creators": [ { "name": { "family": "Nowatzki", "given": "Paul John" }, "id": "Nowatzki-Paul-John", "display_name": "Nowatzki, Paul John" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Ravichandran", "given": "Guruswami" }, "id": "Ravichandran-G", "role": "member", "display_name": "Ravichandran, Guruswami" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/AAWE-NV35", "abstract": "Genetically engineered artificial proteins are promising candidates for new biomaterials because their amino acid sequences can be precisely controlled. This work describes the characterization of crosslinked films of biomimetic artificial extracellular matrix (aECM) proteins with hybrid functions designed to meet materials needs in applications such as small diameter vascular grafts and corneal tissue implants. Elastin-derived polypeptides give the proteins flexibility, while RGD and CS5 peptide domains from fibronectin serve to adhere cells.
\r\n\r\nTechniques were sought to crosslink aECM proteins in ways that resulted in tunable mechanical properties. Hexamethylene diisocyanate was used to crosslink aECM proteins into uniform, transparent, highly-extensible hydrogel films with low water contents characteristic of native elastin. Their elastic moduli, 0.1 \u2013 1.1 MPa, depended on crosslinker concentration and aECM protein length, and spanned the observed range of elastin fibers.
\r\n\r\nThe suitability of biomaterials implants depends strongly on their susceptibility to proteolytic degradation in vivo. It was shown that small sequence changes in the elastin-like portion of aECM proteins were sufficient to decrease their rate of degradation by elastase sevenfold, illustrating a simple method to tune the protease sensitivity of designed proteins. The effects were seen in both soluble proteins and crosslinked films analyzed by measuring their decrease in elastic modulus during degradation.
\r\n\r\nAn aECM protein was examined for its effectiveness as a corneal onlay, or permanent contact lens. The protein was crosslinked into transparent, elastic, water-rich lenses and was implanted into rabbit corneas. The onlays were stable and well-tolerated, and full re-epithelialization occurred within 4-7 days. Histological examination revealed normal regenerating epithelial cell morphology on the anterior surface, good interfaces between the onlay and surrounding tissue, and only minimal inflammation.
\r\n\r\nTo create substrates for studying the coordinating effects of mechanical and biological signals on cell behavior, thin films were made from a photoreactive aECM protein containing the non-canonical amino acid para-azidophenylalanine. Atomic force microscopy (AFM) nanoindentation was used to calculate elastic modulus, and the technique was confirmed by bulk tensile measurements and finite element simulations. Film modulus could be tuned either by differential irradiation or variable incorporation of para-azidophenylalanine.
" }, { "name": "Olsen, Adam Paul", "degree": "PhD", "year": "2006", "title": "Scanning Activity Gravimetric Analysis (SAGA) of Aqueous Polyethylene Oxide", "advisor": "Flagan, Richard C.; Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-133416", "creators": [ { "name": { "family": "Olsen", "given": "Adam Paul" }, "id": "Olsen-Adam-Paul", "display_name": "Olsen, Adam Paul" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "co-chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/5X91-2F81", "abstract": "This thesis introduces a new technique\u2014scanning activity gravimetric analysis (SAGA)\u2014for investigating phase transitions in semicrystalline polymers. Isothermal growth and dissolution of polymer crystallites within picogram to milligram samples are manifested by mass changes in response to changes in the activity of sorbed solvent vapor. Single charged particles are levitated and weighed in an electrostatic field, providing access to highly supersaturated states. Phase transitions are inferred from simultaneous equilibrium sorption and light scattering measurements. Analogous to differential scanning calorimetry, scanning solvent activity up and down exposes broad transitions between the semicrystalline solid state and the dissolved state, which are influenced by sample history. We demonstrate dissolution and crystallization of nanogram samples of polyethylene oxide by controlling the activity of sorbed water vapor and observe self-nucleation of crystallites from partially states and fully dissolved states.
\r\n\r\nMemory effects in semicrystalline polymers have been documented for a variety of systems in which the rate of crystallization depends on the temperature and duration of a prior melting step. We report analogous observations of memory effects in aqueous solution droplets of polyethylene oxide. Remnants of the crystalline phase\u2014clusters of chain folded molecules\u2014that are too small to be detected by gravimetric or optical means persist for long times in solution after macroscopic crystals have been dissolved, and they then serve as athermal nuclei when the concentration of the polymer solution droplet is increased. These remnants evolve under certain conditions toward increasing or decreasing thickness, as indicated by a shift in the conditions at which they effectively catalyze crystal growth. Although memory effects in semicrystalline polymers have usually been attributed exclusively to sluggish kinetics of melting or dissolution, thermodynamic considerations may also play an important role. A simple model describing the free energy of a lamellar crystal based on insights of Janeschitz-Kriegl captures the metastability of lamellar remnants and their evolution in thickness. The qualitative successes of the model lend support to the thermodynamic rationalization of memory effects in semicrystalline polymers.
" }, { "name": "Pape, Eric A", "degree": "PhD", "year": "2006", "title": "Light adjustable macromer-doped elastomers : the thermodynamics, transport, and photochemistry of silicones", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12012005-203446", "creators": [ { "name": { "family": "Pape", "given": "Eric A" }, "id": "Pape-E-A", "display_name": "Pape, Eric A" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Sandstedt", "given": "Christian A." }, "id": "Sandstedt-C-A", "role": "member", "display_name": "Sandstedt, Christian A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/342T-6796", "abstract": "Novel elastomeric photopolymer systems that exhibit macroscopic optical and mechanical changes when polymerized were designed and synthesized. These photopolymers consist of a well-defined polydimethylsiloxane matrix, an UV absorbing photoiniator, and a reactive macromer with methacrylate endgroups and a siloxane based midblock. Model elastomer matrices were synthesized, swollen with macromer, macromer was photopolymerized, and mechanical, transport, and thermodynamic behaviors of the resulting photoelastomers were measured.\r\n\r\nModulus increases of 50 to 150% were seen for sequential interpenetrating networks (IPNs) formed by photopolymerizing different length macromers in model networks. Modulus change was independent of network structure but highly dependent on macromer length and extent of macromer doping. With increased macromer doping, the modulus increase seen on photopolymerization changed from a theoretical dispersed phase behavior to bicontinuous phase behavior. Unexpectedly, mechanical properties were independent of photopolymerization conditions; increased photoinitiator content and irradiation intensity did not alter cured photopolymer modulus.\r\n\r\nSwelling behavior for model networks and IPNs was independent of network precursor molecular weight and polymer volume fraction at network preparation. As macromer molecular weight increased, experimental scaling behavior approached theoretical values. For photopolymerized IPNs, macromer was a poorer solvent than in model networks. Macromer containing phenyl groups also showed significant decreases in solubility.\r\n\r\nDiffusivity values ranged from 2x10^-11 to 2x10^-12 m2/s for 1 to 5kg/mol macromer molecular weight in both model and interpenetrating networks, were dependent on penetrant molecular weight and host network modulus, and were independent of thermodynamic interaction parameters. Diffusivities of bimodal molecular weight distributions indicated dependence on host network modulus due to molecular sieving.\r\n\r\nPhotopolymerization of macromer swollen in networks showed unusual reaction kinetics. Although reaction rates scaled linearly with reactive endgroup concentration for a specific macromer molecular weight, they exhibited variable dependence on initiation rate for different photoiniator concentrations and irradiation intensities. High irradiation intensity and photoinitiator concentration led to reaction rate independence on the initiation rate. Different macromer molecular weights showed unique reaction trajectories; maximum reaction rates and the time and extent of conversion at which they occur are not explained with simple scaling behavior. Chain length dependent termination measurements were used to describe reaction rate trajectories." }, { "name": "Rissman, Tracey Alayne", "degree": "PhD", "year": "2006", "title": "Theory, Field Measurements, and Laboratory Experiments Concerning the Cloud Condensation Nucleus Properties of Organic and/or Insoluble Aerosol Components", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262006-115411", "creators": [ { "name": { "family": "Rissman", "given": "Tracey Alayne" }, "id": "Rissman-Tracey-Alayne", "display_name": "Rissman, Tracey Alayne" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/FEP1-P208", "abstract": "Predicting how the future climate of Earth will change as a result of increasing human emissions is one of the greatest problems facing science today. The earth\u2019s climate is the result of a delicate balance between incoming and outgoing radiation. Anthropogenic emissions of aerosol particles into the atmosphere have the potential to affect the earth\u2019s climate in significant ways through both direct and indirect effects on the earth\u2019s radiative balance. One of the largest uncertainties in aerosol radiative forcing is associated with the relationship between atmospheric aerosols and cloud formation, properties, and lifetime. Clouds form by water condensing on small particles (aerosols) in the air (referred to as cloud condensation nuclei, or CCN), and how the increasing levels of atmospheric particles will affect Earth\u2019s clouds and its hydrologic cycle represents one of the key problems in the science of climate. Through theoretical, field, and laboratory investigations, the results presented here reinforce the importance of atmospheric aerosol chemical composition in determining the ability of an aerosol particle to act as a CCN. A study that incorporates surface tension and limited solubility effects, especially of organic compounds, in parameterizations of cloud droplet activation indicate that these chemical effects can rival those of the meteorological environment. An inverse CCN/aerosol closure study of field measurements indicates that assumptions of simple chemistry and mixing state in the interpretation and analysis of field cloud condensation nuclei (CCN) measurements may not necessarily be sufficient and/or realistic, depending heavily on the location of the field study. Properties of organic compounds, such as functional groups, extent of dissociation, and solubility were found to influence the CCN activity of the compounds in laboratory experiments with pure organic aerosols. However, the importance of careful planning of laboratory experiments, in consideration of the properties of the organic compounds, was reinforced and results were carefully interpreted to avoid experimental bias in the conclusions." }, { "name": "Solares, Santiago de Jesus", "degree": "PhD", "year": "2006", "title": "Multi-Scale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy and Density Functional Theory Characterization of Functionalized and Non-Functionalized Silicon Surfaces", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122006-102528", "creators": [ { "name": { "family": "Solares", "given": "Santiago de Jesus" }, "id": "Solares-Santiago-de-Jesus", "orcid": "0000-0003-0895-8160", "display_name": "Solares, Santiago de Jesus" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XZR1-C472", "abstract": "This dissertation focuses on two theoretical research topics: Multiscale Simulations of Single-Walled Carbon Nanotube Atomic Force Microscopy (AFM, chapters 1 through 3) and Density Functional Theory Characterization of Functionalized and non-functionalized Silicon Surfaces (chapters 4 through 8). The first topic presents the development of an AFM simulation methodology, based on first principles, which incorporates the atomistic details of probe, sample, and impurities in the construction of the images. It also includes studies of the influence of common artifacts (such as elastic deformations and imaging multistability) and probe structure (tilt angle and number of walls in the carbon nanotube probe) on image quality. The second topic concerns the structure and energetics of reconstructed and unreconstructed silicon (111) surfaces (either functionalized with groups such as methoxy and methyl or without functionalization) and non-functionalized copper-silicon surfaces and crystals. These studies lead to novel findings such as the formation of a full stacking fault on the methylated Si(111) surface in the presence of large etch pits and the quantification of the surface energy path of the Si(111) 1x1 \u2192 DAS 7x7 reconstruction. Most of this work was done in collaboration with experimental groups and is in agreement with the most current experimental results." }, { "name": "Spronk, Steven Adrian", "degree": "PhD", "year": "2006", "title": "Investigations of Ion Channels with Computational Simulations and Biochemical Experiments", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03132006-112152", "creators": [ { "name": { "family": "Spronk", "given": "Steven Adrian" }, "id": "Spronk-Steven-Adrian", "display_name": "Spronk, Steven Adrian" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z399-V061", "abstract": "Chapter one describes studies of the voltage-dependent hydration and conduction properties of the hydrophobic pore of the mechanosensitive channel of small conductance, MscS. A detailed picture of water and ion properties in small pores is important for understanding the behavior of biological ion channels. Several recent modeling studies have shown that small, hydrophobic pores exclude water and ions even if they are physically large enough to accommodate them, a mechanism called hydrophobic gating. This mechanism has been implicated in the gating of several channels, including MscS. Although the pore in the crystal structure of MscS is wide and was initially hypothesized to be open, it is lined by hydrophobic residues and may represent a nonconducting state. Molecular dynamics simulations were performed on MscS to determine whether or not the structure can conduct ions. Unlike previous simulations of hydrophobic nanopores, electric fields were applied to this system to model the transmembrane potential, which proved to be important. Although simulations without a potential resulted in a dehydrated, occluded pore, the application of a potential increased the hydration of the pore and resulted in current flow through the channel. The calculated channel conductance was in good agreement with experiment. Therefore, it is likely that the MscS crystal structure is closer to a conducting than to a nonconducting state.
\r\n\r\nChapter two describes work toward a method using protein transduction domains (PTDs) to deliver tRNA to cultured mammalian cells. In vivo incorporation of unnatural amino acids using nonsense suppression is a powerful technique to study proteins. However, one challenge to the method is that the amount of unnatural protein that can be produced is directly limited by the amount of unnatural aminoacyl-tRNA presented to the cellular translation machinery. Therefore, the success of this technique depends heavily on the ability to deliver aminoacyl-tRNA, which is produced in vitro, into cells. Currently, the most commonly used system involves injection of a Xenopus oocyte. It is desirable to transfer the technology to a mammalian expression system, but because mammalian cells are so much smaller than oocytes, injection is not a practical delivery method, so other techniques must be utilized. An intriguing possibility is the use of PTDs, small peptides that greatly enhance the internalization of extracellular material. Several PTD-based approaches for tRNA delivery were attempted: covalent ligation of tRNA to a PTD, noncovalent complexation of tRNA and PTDs, and production of a fusion protein containing a PTD and a tRNA-binding domain. However, none of these methods was useful in delivering tRNA into mammalian cells in culture.
\r\n\r\nChapter three describes efforts to develop a high throughput assay for gating of the mechanosensitive channel of large conductance, MscL. The bacterial ion channel MscL is an ideal starting point for understanding the molecular basis of mechanosensation. However, current methods for the characterization of its mutants, patch clamp and bacterial growth analysis, are difficult and time consuming, so a higher throughput method for screening mutants is desired. We have attempted to develop a fluorescence assay for detecting MscL activity in synthetic vesicles. The assay involved the separation of two solutions\u2014one inside and one outside the vesicles\u2014that are separately nonfluorescent but fluorescent when mixed. It was hoped that MscL activity due to downshock of the vesicles would bring about mixing of the solutions, producing fluorescence. The development of the assay required the optimization of several variables: the method for producing a uniform vesicle population containing MscL, the fluorescence system, and the lipid and protein composition of the vesicles. However, no MscL activity was ever detected even after optimization, so the assay was not fully developed. The probable cause of the failure was the inability of current techniques to produce a sufficiently uniform vesicle population.
" }, { "name": "Tambar, Uttam Krishan", "degree": "PhD", "year": "2006", "title": "Convergent Methods for Synthesizing Rings in the Context of Natural Product Synthesis: I. Development of a Tandem Stille-Oxa-Electrocyclization Reaction, and Progress Toward the Total Synthesis of Saudin. II. Development of the Direct Acyl-Alkylation of Arynes, and Its Application Toward the Total Synthesis of Amurensinine", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12212005-185814", "creators": [ { "name": { "family": "Tambar", "given": "Uttam Krishan" }, "id": "Tambar-Uttam-Krishan", "orcid": "0000-0001-5659-5355", "display_name": "Tambar, Uttam Krishan" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PMHT-S093", "abstract": "Cyclic molecular structures are ubiquitous in chemistry. Efficient and convergent methods to synthesize these rings are of great importance, specifically in the context of natural product synthesis. The development of two methods for the synthesis of the core structures of the natural products saudin and amurensinine are described.
\r\n\r\nFirst, the development of the tandem Stille-oxa-electrocyclization will be discussed in the context of synthetic efforts with saudin. The labdane diterpenoid saudin was isolated in 1985 by Mossa and Cassady from the leaves of the Clutia richardiana (L.) family Euphorbiaceae. The natural product was found to induce hypoglycemia in mice and therefore could be an appealing lead structure for the development of new agents to treat diabetes. A diastereoselective tandem Stille-oxa-electrocyclization reaction has been developed, which provides access to the core structure of saudin in a rapid and convergent manner. Additionally, this new reaction has been extended to the convergent preparation of related polycyclic pyran systems. Progress has been made on the advancement of these complex pyran systems toward the synthesis of saudin.
\r\n\r\nSecondly, the development of the direct acyl-alkylation of arynes will be described in the context of the total synthesis of the isopavine natural product amurensinine. The isopavine alkaloids are promising lead structures for the treatment of neuronal disorders such as as Parkinson\u2019s disease, Down\u2019s syndrome, Alzheimer\u2019s disease, amyotrophic lateral sclerosis, and Huntington\u2019s chorea. All members of this family of natural products contain a seven-membered benzannulated carbocycle. To address the challenge of synthesizing the isopavines, an efficient and mild acyl-alkylation of arynes has been developed. The method forms ortho-disubstituted aromatic products that would otherwise be difficult to synthesize. Additionally, the method is used to synthesize medium-sized benzannulated carbocycles, such as the seven-membered ring structure in the isopavine alkaloids, by the ring-expansion of cyclic beta-ketoesters. Overall, the transformation results in the formation of two new C\u2013C bonds by the net insertion of an aryne into the alpha,beta C-C sigma-bond of a beta-ketoester. This reaction has been applied in the total synthesis of amurensinine.
\r\n" }, { "name": "Thomas, Christine Marie", "degree": "PhD", "year": "2006", "title": "Novel Reactivity at Iron Centers Supported by Poly(phosphino)borate Ligands", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05162006-201134", "creators": [ { "name": { "family": "Thomas", "given": "Christine Marie" }, "id": "Thomas-Christine-Marie", "orcid": "0000-0001-5009-0479", "display_name": "Thomas, Christine Marie" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/AGQC-8E07", "abstract": "The reactivity of the iron(II) alkyl species [PhBPiPr3]FeMe ([PhBPiPr3] = PhB(CH2PiPr2)3-) towards Si-H bonds is presented. Reaction of [PhBPiPr3]FeMe with primary aryl silanes results in the unusual \u03b73 silane adducts [PhBPiPr3]Fe(H)(\u03b73-H2SiMeR). X-ray crystallography, Mossbauer spectroscopy, and theoretical calculations confirm this structural assignment; however, solution NMR experiments suggest a degree of fluxionality in solution.
\r\n\r\nLow valent, tris(phosphino)borate iron platforms have been shown to facilitate the activation of white phosphorus, P4. The iron(I) precursors {[PhBPiPr3]Fe}2(\u03bc-N2) and [PhBPPh3]Fe(PPh3) react with P4 to quantitatively generate {[PhBPiPr3]Fe}2(\u03bc-P4) and {[PhBPPh3]Fe}2(\u03bc-P4), respectively. These unique iron(II) dimers bridged by square P42- units have been characterized structurally and spectroscopically, and their reactivity has been examined. A simplified electronic structure calculation is presented to aid in discussion of bonding within these complexes.
\r\n\r\nMotivated by the versatility of the tris(phosphino)borate ligands, a new family of tripodal hybrid bis(phosphino)pyrazolylborate ligands, [PhBPtBu2(pz')]- ([PhBPtBu2(pz')]- = PhB(CH2PtBu2)2(pz')-), has been prepared and characterized. The synthesis, spectroscopy, and solid-state structures of four-coordinate, pseudo-tetrahedral iron(II) and cobalt(II) halide complexes supported by these ligands is presented. To compare the electron-releasing ability of these ligands with their [PhBPR3] analogues, the cyclic voltammetry of these complexes is introduced. Potential routes to a terminal cobalt or iron nitride complex via extrusion of N2 from coordinated azide and metathesis with the N-atom transfer reagent Li(dbabh) are investigated.
\r\n\r\nReduction of the [PhBPtBu2(pz')]MX halide complexes in the presence of excess phosphine generates low valent [PhBPtBu2(pz')]MI(PMe3) precursors. These precursors react with organic azides to generate cobalt(III) and iron(III) imides. Initial reactivity studies indicate that these imides are more moderately more reactive than the corresponding tris(phosphino)borate complexes. The electrochemistry of the [PhBPtBu2(pz')]FeIII(NR) imides features a quasi-reversible to fully reversible oxidation event, dependent on choice of pyrazolyl substituents and scan rate. This oxidation can be achieved chemically to generate the isolable cationic iron(IV) imides, [PhBPtBu2(pz')]FeIV(NR)+. The structural and spectroscopic characterization of these highly unusual complexes is discussed.
\r\n" }, { "name": "Thurman, Derek Wade", "degree": "PhD", "year": "2006", "title": "Molecular Aspects of Flow-Induced Crystallization of Polypropylene", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12032005-115154", "creators": [ { "name": { "family": "Thurman", "given": "Derek Wade" }, "id": "Thurman-Derek-Wade", "display_name": "Thurman, Derek Wade" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wew1-af68", "abstract": "Polyolefins, semicrystalline polymers also known as thermoplastics, are highly desirable because of their material properties, low cost, and ease in processing. The flow and thermal history experienced during processing are known to affect dramatic changes in crystalline kinetics and morphology, dictating the final material properties of solidified products. However, the underlying physics that control crystalline orientation and kinetics is not well understood. To optimize processing conditions and maximize material performance, it is desirable to understand how the interplay of molecular character and flow conditions shape crystalline microstructure.
\r\n\r\nIn the last decade, advances in catalyst technology have produced well defined materials enabling the systematic study of molecular influences on flow-induced crystallization. We investigate bimodal blends of polypropylenes (PP) in which we vary the molecular character (concentration, molecular weight, regularity) of the high molecular weight mode. We apply a number of in situ characterization tools (rheo-optics, rheo-WAXD) to the development of transient structure and interpret our findings in light of ex situ examination (polarized light microscopy, TEM) of the final morphology.
\r\n\r\nBlending a well-characterized high molecular weight isotactic polypropylene into a \"base iPP\" at various concentrations (c), we determined that blends with less than 1% of chains with Mw five times larger than the Mw of the base resin profoundly affected the crystallization kinetics and crystalline morphology of a sheared melt. Beyond unambiguously demonstrating the important role of long chains in the formation of anisotropic crystallization under flow, this approach allowed us to be specific about the length that is meant by \"long chains\" and the concentration of these chains in the melt. Varying the concentration from below to above c* revealed that the effect of the long chains involves cooperative interactions, evident in the non-linear relationship of the long chain concentration, particularly as c approaches the long chain-long chain overlap concentration. The long chains greatly enhance the formation of threadlike precursors but only mildly enhance the formation of pointlike precursors.
\r\n\r\nIn studying a series of blends in which the Mw of the long chain mode was varied, we found that increasing the Mw of the long chain portion of a bimodal blend increased the tendency to form threadlike precursors to oriented crystallization. This was highlighted by a marked decrease in the threshold stress necessary to induce oriented crystalline growth and is related to the separation in time scales between the slowest relaxing chains and the average. Thus, the propagation of shish varies strongly with the separation in time scales between the slowest relaxing chains and the average. Below a threshold ratio of relaxation times (tau_L/tau_S ~ 100) addition of long chains did not change the behavior from that of Base-PP itself.
\r\n\r\nOur analysis of real-time rheo-optical and rheo-WAXD experiments combined with depth dependent information from a novel \"depth sectioning\" analysis technique uncovers several keys to understanding how anisotropic crystallization is induced by flow. Threads first form near the channel wall, where stress is highest, and grow in length with prolonged flow. After sufficient time, thread length per unit volume saturates, perhaps due to collisions with other threads or crystalline overgrowth from those threads. Prior to saturation, when crystalline overgrowth is negligible, the thread propagation appears to be linear with shearing time. The propagation of threads varies in a nonlinear manner with stress. Finally, we identify a promising set of conditions that can be used to measure the thread propagation velocity for this material if the appropriate length scale can be assigned by microscopy.
\r\n\r\nWe examined the effects of long chain regularity on the formation of threadlike precursors, showing that addition of molecular level defects to the high end of the molecular weight distribution effectively raises the threshold stress and mitigates the formation of oriented precursors induced by flow. Our study included a model bimodal blend of isotactic and atactic polypropylene as well as large scale bimodal blends of isotactic polypropylene and a propylene-ethylene copolymer fit for pilot-scale production of nonwoven fabrics. It is noteworthy that the qualitative behavior observed in the melt-spinning process accords well with the trends evident in isothermal shear-induced crystallization. This has value in two respects. Scientifically, it is significant that idealized flow and thermal conditions may well reveal the physics relevant to polymer processing, which involves mixed shear and extension under non-isothermal conditions. Technologically, the ability to screen different resin compositions on a small scale can be used to optimize flow-induced crystallization characteristics prior to scale up.
" }, { "name": "Tobias, Alexander Vincent", "degree": "PhD", "year": "2006", "title": "Directed Evolution of Biosynthetic Pathways to Carotenoids with Unnatural Carbon Backbones", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-08232005-174620", "creators": [ { "name": { "family": "Tobias", "given": "Alexander Vincent" }, "id": "Tobias-Alexander-Vincent", "orcid": "0000-0002-5866-5254", "display_name": "Tobias, Alexander Vincent" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WF0Q-2J98", "abstract": "Over the course of evolution, nature continually discovers new small molecules through the alteration of biosynthetic enzymes and pathways by mutation and gene transfer. Hundreds of these natural products have proven indispensable to medicine, culture, and technology, greatly contributing to increases in the length and quality of human lives. Chemists have found that the \"chemical space\" surrounding natural products is especially rich in functional molecules, and synthesis of natural product analogs has uncovered many with new or improved properties.
\r\n\r\nInspired by nature's search algorithm, we and others have conducted our own evolution of carotenoid biosynthetic pathways in the laboratory. Chapter 1 comprehensively reviews the motivations, accomplishments, and challenges of this research area as of early 2005, and describes in detail how biosynthetic routes to dozens of new carotenoids have been established.
\r\n\r\nTo expand the number of carotenoid backbones beyond the C30 and C40 carbon scaffolds that give rise to the ~700 known natural carotenoids, we subjected a carotenoid synthase, the enzyme responsible for carotenoid backbone synthesis, to directed evolution. Chapter 2 describes the evolution of the C30 carotenoid synthase CrtM from Staphylococcus aureus for the ability to synthesize C40 carotenoids. This work also resulted in novel carotenoids with C35 backbones. We later found that some of the CrtM mutants generated in this laboratory evolution experiment, as well as several second-generation variants, are also capable of synthesizing unnatural C45 and C50 carotenoid backbones when supplied with appropriate prenyl diphosphate precursors.
\r\n\r\nChapter 3 describes the creation of full-fledged pathways to carotenoid pigments based on the C45 and C50 scaffolds. Coexpression of the carotenoid desaturase CrtI from Erwinia uredovora resulted in the biosynthesis of at least 10 new C45 and C50 carotenoids with different systems of conjugated double bonds. We also present evidence of an unnatural asymmetric C40 carotenoid pathway beginning with the condensation of farnesyl diphosphate (FPP, C15PP) and farnesylgeranyl diphosphate (FGPP, C25PP). In addition to clarifying how CrtM and CrtI achieve their product specificities, this work also sheds light on the molecular mechanisms used by evolution to access new chemical diversity and the selective pressures that have shaped natural product biosynthesis.
" }, { "name": "Trend, Raissa M.", "degree": "PhD", "year": "2006", "title": "Concerning the Mechanism and Selectivity of Palladium(II)-Catalyzed Aerobic Oxidation Reactions", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03202006-120555", "creators": [ { "name": { "family": "Trend", "given": "Raissa M." }, "id": "Trend-Raissa-M", "display_name": "Trend, Raissa M." } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/M4CC-BR50", "abstract": "Oxidation is one of the most fundamental and important processes in nature. It would be advantageous to chemically replicate the high substrate specificity and selectivity observed in oxidative enzymes. Several such synthetic processes have been developed that involve the transfer of a heteroatom to a substrate in an asymmetric fashion. Enantioselective oxidative dehydrogenations, which do not involve transfer of a heteroatom, are much less common. Reactions of this type have recently been developed for the oxidative kinetic resolution of secondary alcohols using palladium(II) catalysis, dioxygen, and the chiral ligand (\u2013)-sparteine.
\r\n\r\nThis general approach (palladium(II), dioxygen, ligand) was applied to the development of oxidative heteroatom/olefin cyclizations to form dihydrobenzofurans, cyclic ethers, lactones and lactams. The nonenantioselective reaction employs pyridine as a ligand. These conditions could be extended to the enantioselective cyclization of allyl-appended phenols through the use of (\u2013)-sparteine as a ligand.
\r\n\r\nThe mechanism of the oxidative heteroatom/olefin cyclizations was explored via stereospecifically deuterium-labeled substrates. These studies indicate that the stereochemistry of oxypalladation for primary alcohol substrates is syn, whether a mono- or bidentate ligand is used. In contrast, cyclizations of deuterium-labeled carboxylic acid substrates undergo anti oxypalladation.
\r\n\r\nThe origins of stereoselectivity in the oxidative kinetic resolution of secondary alcohols using the C1 symmetric ligand (\u2013)-sparteine were investigated through structural and reactivity studies of a variety of ((\u2013)-sparteine)palladium(II) complexes. A model for the observed selectivity was developed, and is supported by theoretical calculations. Experiments with the C2 symmetric diastereomers of (\u2013)-sparteine highlight the special properties of (\u2013)-sparteine that make it a uniquely effective ligand in the kinetic resolution.
\r\n" }, { "name": "Varutbangkul, Varuntida", "degree": "PhD", "year": "2006", "title": "Ambient and Laboratory Studies of Aerosol Size Distributions and Hygroscopicity", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242006-175333", "creators": [ { "name": { "family": "Varutbangkul", "given": "Varuntida" }, "id": "Varutbangkul-Varuntida", "display_name": "Varutbangkul, Varuntida" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/KQ8A-2Q95", "abstract": "The optical properties, health effects, atmospheric lifetime, and climate impact of ambient aerosols are influenced directly by their size distribution, chemical composition, and phase. The aerosol hygroscopicity, which is also a function of composition, governs the size and phase changes of these particles when subjected to varying ambient relative humidities (RH). This thesis presents results from a wide variety of studies involving laboratory and ambient measurements of aerosol size distributions and water uptake properties in the subsaturated regime. Time evolutions of particle size and hygroscopic growth were investigated for various secondary organic aerosol (SOA) systems generated in a smog chamber from ozonolysis of cycloalkenes and photooxidation of biogenic terpenes. SOA yields were measured at various initial parent hydrocarbon concentrations and correlated with the structure of the parent compound. The amount of water uptake of the aerosol at a reference RH was found to inversely correlate with the SOA yield. The hygroscopicity of many atmospherically relevant pure organic species was also studied using an unconventional particle generation scheme employing a nonaqueous solution. Experimental results were compared with predictions from an equilibrium thermodynamic model. In these works, organic aerosols are shown to exhibit complex hygroscopic growth, dependent on the particle chemistry, phase, and surrounding RH. Implications of the experimental techniques used on the observation of particle growth, deliquescence, and efflorescence are discussed. A number of other studies incorporating aircraft-based measurements of aerosol size distributions and hygroscopicity with other ambient measurements into various cloud microphysics models are also presented." }, { "name": "Waltman, Andrew Willis", "degree": "PhD", "year": "2006", "title": "N-Heterocyclic Carbene Ligands for Nickel Ethylene Polymerization Catalysts:Toward the Incorporation of Polar Comonomers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06122005-180419", "creators": [ { "name": { "family": "Waltman", "given": "Andrew Willis" }, "id": "Waltman-Andrew-Willis", "display_name": "Waltman, Andrew Willis" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5G0D-JD41", "abstract": "The development of a catalyst capable of incorporating vinyl-functionalized polar olefins (methyl acrylate, acrylonitrile) into a linear polyethylene backbone is one of the most prominent challenges in organometallic chemistry. Recent developments in group 10 catalysts (Ni and Pd) have shown promise; however, there remains no system capable of this goal. Our group has developed a series of neutral Ni complexes which are excellent catalysts for the polymerization of ethylene but are rapidly deactivated in the presence of methyl acrylate and other polar olefins. This thesis presents our studies toward the cause of catalyst deactivation by these olefins, and describes the design of novel Ni complexes based on the findings of the deactivation study.
\r\n\r\nTo determine the cause of deactivation by polar olefins, our neutral Ni catalysts were allowed to react with methyl acrylate (MA). Examination of the products revealed that, upon coordination of MA, the catalysts form chelated enolate complexes which are susceptible to deactivating protonolysis across Ni\u2013C bonds. Furthermore, it was determined that MA itself is a potential source of hydrogen atoms for this cleavage, implying protolytic deactivation is unavoidable result whenever olefins capable of chelation are introduced to the catalysts. Therefore, it was decided that chelation should be made less favorable through the use of more electron-donating ligands. For this purpose, N-heterocyclic carbenes (NHCs) were chosen.
\r\n\r\nNHCs are stable carbenes which have found increasing use as electron-rich ligands for transition metals. In order to make viable catalysts, NHC ligands capable of chelation through a phenoxide moiety were required. An efficient synthesis of these ligands was developed, and they were successfully ligated to Pd. However, it was found that upon attempted ligation to Ni, a series of unexpected and undesired compounds were obtained, one of which is the apparent result of an unprecedented C\u2013N cleavage of the NHC heterocycle. Unfortunately, when a targeted Ni complex was finally synthesized, it proved inactive toward ethylene polymerization. Finally, it was shown that group 4 (Ti and Zr) complexes of the novel NHC ligands are good catalysts for ethylene polymerization, as well as the copolymerization of ethylene with other olefins.
\r\n" }, { "name": "Beene, Darren Lee", "degree": "PhD", "year": "2005", "title": "Chemical Scale Investigations of Ligand-Gated Ion Channels Using Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262005-153907", "creators": [ { "name": { "family": "Beene", "given": "Darren Lee" }, "id": "Beene-Darren-Lee", "display_name": "Beene, Darren Lee" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/B6A3-VT59", "abstract": "The Cys loop receptors, a family of ligand-gated ion channels, mediate fast synaptic transmission throughout the peripheral and central nervous systems. These are large multisubunit proteins, whose primary function is to transduce a chemical signal, binding of a neurotransmitter, into an electrical signal, ion flux across the cell membrane. These receptors have been implicated in several disease states and represent major therapeutic targets. The work presented in this thesis focuses on the chemical-scale elucidation of Cys loop receptors. The main approach of this work is the structure-function study using in vivo nonsense suppression methods. This technique allows for the site-specific incorporation of an unnatural amino acid into a protein expressed in a living cell.
\r\n\r\nNonsense suppression methods were used to incorporate a series of fluorinated tryptophan derivatives into the binding site of the 5-HT3R. This study identified a cation-pi interaction between Trp 183 and the neurotransmitter, serotonin. A similar study using fluorinated phenylalanine derivatives identified a cation-pi binding site at Tyr 198 in the GABAC receptor. These studies build on previous work from our research group and provide further evidence that the cation-pi interaction is a common feature in ligand recognition by Cys loop receptors.
\r\n\r\nNonsense suppression was also used to examine the role of several tyrosine residues in the 5-HT3R. Here the findings demonstrated that the side chains of Tyr 143 and 153 make functionally important hydrogen bonds. These data were used to refine several computational models of serotonin docked into the binding site.
\r\n\r\nStructure-function studies of two conserved prolines in the M2-M3 loop showed that this region of the receptor is involved in the conformational changes associated with receptor activation. The data also provide preliminary evidence that Pro 308 may serve as hinge for the gating movement of the M2 helix.
" }, { "name": "Benitez, Diego", "degree": "PhD", "year": "2005", "title": "Theoretical Study of the Mechanism of Olefin Metathesis and Synthesis of Cyclic Polymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302005-112828", "creators": [ { "name": { "family": "Benitez", "given": "Diego" }, "id": "Benitez-Diego", "orcid": "0000-0003-1212-6957", "display_name": "Benitez, Diego" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/eas9-x408", "abstract": "The research presented in this thesis focuses on the study of the metathesis reaction and applications to synthetic polymeric structures. More specifically, how targeted changes in the polymerization reactants and catalyst provide very unique and useful macromolecular architectures.
\r\n\r\nChapter 1 describes the synthesis of acetoxy end-functionalized polynorbornenes. By introducing 1,4-bis(acetoxy)-2-butene as chain transfer agent (CTA) during a Ruthenium mediated ring opening metathesis polymerization (ROMP) of norbornene (NBE), the respective end-functionalized polymers with molecular weights controllable up to 30 kDa could be obtained in high yield.
\r\n\r\nChapter 2 describes a new synthetic route to cyclic polymers and their characterization. In this approach, the ends of growing polymer chains remain attached to a cyclic Ru catalyst throughout the entire polymerization process. This effectively excludes all types of linear intermediates, which were a major drawback of previous approaches to cyclic polymers.
\r\n\r\nChapter 3 describes the synthesis of cyclic poly-butadiene and the importance of the monomer purity. Techniques for characterizing and determining the purity of cyclic polymers are also discussed.
\r\n\r\nChapter 4 describes a quantum mechanical (QM) study of the mechanism of chloride isomerization of a ruthenium metathesis catalyst with density functional theory (DFT) with the B3LYP hybrid functional. This isomerization is relevant to the mechanism of metathesis and it serves as validation to further studies of the mechanism with the same method.
" }, { "name": "Best, Timothy Patrick", "degree": "PhD", "year": "2005", "title": "Localization of DNA-Binding Polyamides in Living Cells", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172004-184202", "creators": [ { "name": { "family": "Best", "given": "Timothy Patrick" }, "id": "Best-Timothy-Patrick", "display_name": "Best, Timothy Patrick" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MQ0D-8P65", "abstract": "Regulation of the processing of genes into nucleic acids and proteins is a substantial goal in medicine. Small molecules that could enter cells, localize to the nucleus, and bind chromosomal DNA sequence-specifically and with high affinity would be important tools for gene regulation. Pyrrole-imidazole polyamides are small molecules that bind the minor groove of DNA in a sequence-specific fashion according to a set of pairing rules, and with affinities rivaling natural transcription factors. Several in vitro experiments have shown that by directly competing with transcription factors for binding sites in gene promoter regions, polyamides can act to inhibit transcription of those genes. Polyamides bearing transcription activation domains can bind to promoter regions, recruit the transcriptional machinery to the gene, and activate transcription in vitro. Attempts to reproduce these results in vivo were largely unsuccessful, perhaps due to poor cellular trafficking properties of polyamides and polyamide-peptide conjugates.
\r\n\r\nIt was found that polyamides bearing the Bodipy fluorophore localize primarily to the cytoplasm of cells, or were excluded from cells altogether. In attempts to overcome this quality, peptides shown to improve cellular trafficking were appended to the polyamides. These peptides were generally not successful at inducing uptake, and were in many cases toxic to the cells. Small molecules were also appended to polyamides, likewise to improve uptake properties, but met with limited success. Surprisingly, the addition of a fluorescein or fluorescein-like fluorophore to polyamides permit them to localize to the nuclei of all cell lines tested, in a molecular content- and shape-dependent manner. This technology has been applied to several in vivo experiments, including the inhibition of androgen receptor binding to its cognate element in gene promoter regions.
" }, { "name": "Betley, Theodore Alexander", "degree": "PhD", "year": "2005", "title": "Coordination Chemistry from Trigonally Coordinated Iron Platforms: Chemistry Relevant to Dinitrogen Reduction", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-103515", "creators": [ { "name": { "family": "Betley", "given": "Theodore Alexander" }, "id": "Betley-Theodore-Alexander", "orcid": "0000-0001-5946-9629", "display_name": "Betley, Theodore Alexander" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PY23-ME66", "abstract": "The synthesis for a sterically encumbered, strong-field tris(diisopropylphosphino)borate ligand, [PhBPiPr3] ([PhBPiPr3] = [PhB(CH2PiPr2)3]-), is reported to probe aspects of its conformational and electronic characteristics within a host of complexes. To this end, the Tl(I) complex, [PhBPiPr3]Tl, was synthesized, characterized, and used to install the [PhBPiPr3] ligand onto complexes of Fe, Co, and Ru. The spectroscopic, electrochemical, magnetic, and structural features of these complexes are compared with similar examples.
\r\n\r\nTrigonally coordinated \"[PhBPiPr3]M\" platforms (M = Fe, Co) support both pi-acidic (N2) and pi-basic (NR2-) ligands at a fourth binding site. Methylation of monomeric [M0(N2)-] species successfully derivatizes the beta-N atom of the N2 ligand and affords the diazenido product [MII(N2Me)]. Addition of RN3 to MI(N2)MI results in oxidative nitrene transfer to generate [PhBPiPr3]M\u2261NR with concomitant N2 release.
\r\n\r\nA tetrahedrally coordinated L3Fe-Nx platform that accommodates both terminal nitride (L3FeIV\u2261N) and dinitrogen (L3FeI-N2-FeIL3) functionalities is described. The diamagnetic L3FeIV\u2261N species featured has been characterized in solution under ambient conditions by multinuclear NMR (1H, 31P, and 15N) and infrared spectroscopy. The terminal nitride complex oxidatively couples to generate the previously reported L3FeI-N2-FeIL3 species.
\r\n\r\nThe [PhBPiPr3] ligand can support a single iron or cobalt center in a pseudo-tetrahedral environment in which dinitrogen is bound in the fourth coordination site. Zero-valent metal-dinitrogen complexes have the general formula, [[PhBPiPr3]M(mu-N2)]2[Mg2+], while bridging structures can also be obtained as neutral [MI]\u2014N2\u2014[MI] or as anionic [(M)2(N2)]- species. The nature of the structural distortions observed in both [M(mu-N2)]2[Mg2+] and [Mn]\u2014N2\u2014[Mn] complexes are described. Magnetic characterization of the neutral and mixed-valence dimeric complexes reveal the complexes remain ferromagnetically coupled over all temperatures investigated.
\r\n\r\nThe coordination chemistry of group VIII metals featuring the bis(8-quinolinyl)amine (HBQA) ligand is presented. The electrochemical behavior of Fe, Ru, and Os complexes bearing the BQA ligand is reported and compared to related ligand platforms. Halide and phosphine ligand exchange reactions are examined from complexes of the type (BQA)MX(PR3)2 (M = Ru, Os). Carbonyl and dinitrogen complexes of Ru and Os are prepared from halide abstraction from divalent Ru and Os precursors. The spectroscopic and structural features of these complexes are compared with similar examples.
\r\n" }, { "name": "Bittner, Wendy Belliston", "degree": "PhD", "year": "2005", "title": "Ultrafast Photoreduction of Nitric Oxide Synthase by Electron Tunneling Wires", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05192005-234308", "creators": [ { "name": { "family": "Bittner", "given": "Wendy Belliston" }, "id": "Bittner-Wendy-Belliston", "display_name": "Bittner, Wendy Belliston" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e82v-jn92", "abstract": "The Gray group has a long-standing interest in the study of methods for rapid delivery of electrons to enzyme active sites. This thesis describes picosecond to nanosecond reduction of the heme active site of the inducible nitric oxide synthase oxygenase domain (iNOSoxy) bound to Re- and Ru-diimine electron-tunneling wires. The Re wires have the form [(4,7-dimethylphenanthroline)ReI(CO)3L]+ where L is a perfluorinated biphenyl bridge connecting a rhenium-ligated imidazole or aminopropylimidazole to a distal imidazole (F8bp-im (1) and C3-F8bp-im (2)) or F (F9bp (3) and C3-F9bp (4)). All four bind tightly (micromolar to nanomolar Kd) in the active site channel of iNOSoxy. Upon excitation with 355 nm light, the bound rhenium of 1, 2, or 4 is quenched in fewer than 200 ps, possibly by electron donation from a nearby tryptophan residue. When a through-bond pathway from the rhenium to the heme iron exists, the active site Fe(III) is then reduced to Fe(II) within 300 ps, approximately ten orders of magnitude faster than the naturally occurring reduction. The Ru-diimine wire, [(4, 4\u2019, 5, 5\u2019-tetramethylbipyridine)2Ru(bpyF9bp)]2+ (5), also binds tightly to iNOSoxy. The binding of 5 is independent of tetrahydrobiopterin, arginine, imidazole, and 1, indicating that tmRu-F9bp resides on the surface of the enzyme. Reductive flash-quench studies have shown that the bound wire is capable of reducing the imidazole-bound active-site heme in approximately 50 ns, fully seven orders of magnitude faster than the comparable in vivo process. This work represents the first demonstration of electron-tunneling wires that specifically target and rapidly reduce an enzyme without blocking the active site channel." }, { "name": "Borths, Christopher J.", "degree": "PhD", "year": "2005", "title": "Investigations in Enantioselective Catalysis. Development of Novel Asymmetric Organocatalytic Reactions", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07072004-222212", "creators": [ { "name": { "family": "Borths", "given": "Christopher J." }, "id": "Borths-Christopher-J", "display_name": "Borths, Christopher J." } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bhq4-ep12", "abstract": "A new strategy for the catalysis of organic transformations using iminium ion activation has been developed. Using this strategy, the first asymmetric organocatalytic Diels-Alder reaction has been developed. This methodology has demonstrated the possibility of an imidazolidinone salt to function as an effective asymmetric catalyst for a wide variety of chemical transformations.
\r\n\r\nThe iminium ion activation strategy has also proved successful for conjugate additions, and an asymmetric organocatalytic Mukaiyama-Michael reaction has been developed using the principles of LUMO-lowering catalysis. A more reactive and selective chiral imidazolidinone catalyst was developed, and this secondary amine has extended the range of transformations possible with iminium ion catalysis.
\r\n\r\nProgress has been made towards the development of an enantioselective organocatalytic alpha-oxidation of ketones. Proline catalysis has been demonstrated to effectively catalyze the asymmetric alpha-oxidation of cyclohexanone, but extension of this methodology to other ketones has not been successful. These studies have further demonstrated the utility of proline as a catalyst, and provide a platform for the extension of HOMO-raising catalysis to other organic transformations.
\r\n" }, { "name": "Borths, Elizabeth Loraine", "degree": "PhD", "year": "2005", "title": "Structural and Biochemical Characterization of the Vitamin B\u2081\u2082 ABC Transporter, BtuCD-F", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032005-142802", "creators": [ { "name": { "family": "Borths", "given": "Elizabeth Loraine" }, "id": "Borths-Elizabeth-Loraine", "display_name": "Borths, Elizabeth Loraine" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "biochem" ], "doi": "10.7907/kkkr-tk81", "abstract": "BtuCD-F is a binding protein-dependent ABC transporter system that uses the power of ATP hydrolysis to pump vitamin B\u2081\u2082 into the cytoplasm of E. coli. The crystal structure of BtuF, the protein that binds vitamin B\u2081\u2082 and delivers it to the transporter, BtuCD, has been solved by x-ray crystallography. BtuF is a bi-lobed protein and B\u2081\u2082 is bound in a deep cleft formed at the interface between the two lobes. A stable complex between BtuF and BtuCD is demonstrated to form in vitro and was modeled using the individual crystal structures. Two conserved surface glutamates from BtuF may interact with conserved arginine residues on the periplasmic surface of the BtuCD transporter, playing a role in docking and the transmission of conformational changes.
\r\n\r\nBtuCD has also been reconstituted in vitro into proteoliposomes. In the presence of ATP, BtuCD proteoliposomes can mediate uptake of vitamin B\u2081\u2082 in a BtuF dependent fashion. In the absence of ATP, B\u2081\u2082 appears to become sequestered between BtuF and BtuCD. The ATPase activity of BtuCD was examined in proteoliposomes as well as in detergent solution. BtuCD has a significant basal rate of hydrolysis under all conditions tested, and B\u2081\u2082-bound and apo-BtuF can stimulate that rate. Interestingly, the rate of ATP hydrolysis, as well as the effect of BtuF, vitamin B\u2081\u2082 and sodium ortho-vanadate on that rate, is different in each detergent and lipid environment. These results indicate that ABC transporters are highly sensitive to their environment and underline the importance of detergent or lipid choice in functional reconstitution and membrane protein crystallization experiments. Our results lead us to propose a revised model of the ABC transport cycle.
" }, { "name": "Brown, Sean Pomeroy", "degree": "PhD", "year": "2005", "title": "Iminium and Enamine Activation: Methods for Enantioselective Organocatalysis", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-174252", "creators": [ { "name": { "family": "Brown", "given": "Sean Pomeroy" }, "id": "Brown-Sean-Pomeroy", "display_name": "Brown, Sean Pomeroy" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SPVW-N190", "abstract": "Further development of an organocatalytic LUMO-lowering activation strategy utilizing chiral imidazolidinone salts has been described. Enantioselective catalytic Friedel-Crafts alkylations of furans and thiophenes have been achieved with good yields and high levels of enantioselectivity. Furthermore, this methodology has been utilized to access enantioenriched a-chiral esters.
\r\n\r\nThe organocatalytic iminium activation strategy has been applied to the development of an enantioselective Mukaiyama-Michael reaction for the construction of the g-butenolide architecture. This reaction is viable due to imidazolidinone catalysts' ability to partition silyloxyfurans to react through an unprecedented 1,4-addition manifold to a,b-unstaturated aldehydes. This Mukaiyama-Michael methodology has also been extended to provide access to a-amino acids by use of silyloxyoxazoles.
\r\n\r\nEnamine activation of aldehydes has provided the first direct asymmetric a-oxidation of carbonyls. This proline catalyzed HOMO-raising activation strategy affords high levels of reaction efficiency and enantioselectivity. Moreover, the function of proline solubility has been investigated to explain an unusual kinetic and enantioselective profile.
\r\n\r\nThe imidazolidinone framework, developed for iminium activation, was also demonstrated to participate in enamine activation of aldehydes to perform the enantioselective a-chlorination of aldehydes. A first generation catalyst provided good yields and high enantioselectivities at -30 \u00b0C. Design of a second generation catalyst afforded high levels of reaction efficiency and enantioselectivity at ambient temperature.
" }, { "name": "Brown, Steven Douglas", "degree": "PhD", "year": "2005", "title": "The Chemistry of Tris(phosphino)borate Supported Iron-Nitrogen Multiply-Bonded Linkages", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05312005-201150", "creators": [ { "name": { "family": "Brown", "given": "Steven Douglas" }, "id": "Brown-Steven-Douglas", "display_name": "Brown, Steven Douglas" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/46DN-YH09", "abstract": "The metallation of FeX2 (X = Cl, Br, I) salts with the strong-field [PhBP3] ([PhBP3] = PhB(CH2PPh2)3-) ligand is presented. The resulting four-coordinate, 14-electron species, [PhBP3]FeX, have been thoroughly characterized and feature high-spin (S = 2) electronic ground-states. X-ray diffraction analysis of [PhBP3]FeCl establishes a monomeric structure in the solid state.
\r\n\r\nThe one electron reduction of [PhBP3]FeCl in the presence of a triphenylphosphine cap affords a rare example of four-coordinate iron(I). This species, [PhBP3]Fe(PPh3), serves as a synthetic surrogate to a low-valent \"[PhBP3]Fe(I)\" subunit that is readily oxidized in the presence of organic azides. The resulting S = 1/2 iron(III) imides of general formula [PhBP3]Fe\u2261NR may be subsequently reduced by one electron to yield the anionic S = 0 derivatives. Exposure of the former to an atmosphere of CO results in cleavage of the Fe\u2261NR linkage to yield [PhBP3]Fe(CO)2 and free isocyanate (O=C=N-R). Dicarbonyl [PhBP3]Fe(CO)2 is itself an imide precursor and is gradually converted back to [PhBP3]Fe\u2261NR upon exposure to excess organic azide.
\r\n\r\nTolyl imide [PhBP3]Fe?N-p-tolyl readily reacts with H2 under mild conditions to undergo a step-wise Fe-Nx bond scission process to ultimately release free p-toluidine. Initially formed is the S = 2 iron(II) anilide, [PhBP3]Fe(N(H)-p-tolyl), which has been independently prepared and shown to release p-toluidine in the presence of H2. In benzene solvent the final iron containing product of the hydrogenation process is diamagnetic [PhBP3]Fe(?5-cyclohexadienyl), which is presumably formed from benzene insertion into a low-valent iron-hydride intermediate.
\r\n\r\nReduction of the ferromagnetically coupled dimer, {[PhBP3]Fe(N3)}2, yields the bridging nitride species, [{[PhBP3]Fe}2(\u03bc-N)][Na(THF)5]. This compound features two high-spin iron(II) metal centers that are so strongly antiferromagnetically coupled that a diamagnetic S = 0 ground-state is exclusively populated at room temperature. X-ray diffraction analysis reveals a bent Fe-N-Fe linkage that quantitatively releases ammonia in the presence of excess protons. Reactivity with CO and H2 is also presented, and for the latter, complete rupture of the Fe-N-Fe manifold is not observed as the presence of an additional metal center (when compared with the iron(III) imides) favors the formation of the diamagnetic bridging imide-hydride species, [{[PhBP3]Fe}2(\u03bc-NH)(\u03bc-H)][Na(THF)5].
" }, { "name": "Carpen, Ileana Cristina", "degree": "PhD", "year": "2005", "title": "Studies of Suspension Behavior: I. Instabilities of Non-Brownian Suspensions. II. Microrheology of Colloidal Suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022005-131439", "creators": [ { "name": { "family": "Carpen", "given": "Ileana Cristina" }, "id": "Carpen-Ileana-Cristina", "display_name": "Carpen, Ileana Cristina" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Squires", "given": "Todd M." }, "id": "Squires-T-M", "role": "member", "display_name": "Squires, Todd M." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/857a-gg43", "abstract": "Complex fluids are present in a multitude of forms: polymers, foods, paints, inks, biological materials, pharmaceuticals, cosmetics, etc. Many of these are suspensions, which have a particulate phase suspended in a solvent phase. This multiphase character gives a rich variety of behaviors, making suspensions interesting and useful materials but difficult to process. We investigate two different aspects of suspension behavior: instabilities in suspension flows and the use of microrheology in colloidal suspensions.
\r\n\r\nWe look at two different mechanisms that generate instabilities and pattern formation in suspension flows. In the first, a jump in normal stresses at the interface between two fluids may lead to growing perturbations of the interface that ultimately give rise to migration of the particle phase into enriched regions. Fluids with a negative second normal stress difference, such as suspensions, can be unstable with respect to transverse or spanwise perturbations. The mechanism appears to be generic, although the details will depend on the specific system. The second mechanism may affect suspensions whose particle phase is not density-matched to the fluid. In this case, a flow can be unstable to spanwise perturbations of the particle phase when the shearing motion generates a density profile that increases with height. This is a Rayleigh--Taylor-like instability, due to having heavier material over light. As with the first instability, this mechanism may play an important role in pattern formation in multiphase flows.
\r\n\r\nThe second aspect of suspension behavior we examine is the application of microrheology to colloidal suspensions. Microrheology has great promise for the study of soft, heterogeneous materials, but is not as well understood as traditional rheology. Most methods use tracer particles to investigate a medium, sometimes passively---tracking random motion (well established but restricted to the linear viscoelastic regime)---and more rarely actively---applying an external force to drive the tracers and access the medium's nonlinear response. Active microrheology is not well understood, and we study it by simulating a prototypical example, the motion of a particle due to an imposed force through a colloidal suspension. The deformation of the microstructure results in resistance to the tracer\u2019s motion. This system displays 'force-thinning', analogous to the 'shear-thinning' in a macrorheologically sheared suspension, but the comparison is not exact, and care needs to be taken in the use and application of microrheological results. Comparable length scales between the measurement device (the tracer) and the medium lead to interesting effects and distinctions between types of microrheological methods.
" }, { "name": "Chung, Serena Hsin-Yi", "degree": "PhD", "year": "2005", "title": "Global Distribution, Radiative Forcing, and Climate Impact of Carbonaceous Aerosols", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02012005-131605", "creators": [ { "name": { "family": "Chung", "given": "Serena Hsin-Yi" }, "id": "Chung-Serena-Hsin-Yi", "orcid": "0000-0001-5030-5871", "display_name": "Chung, Serena Hsin-Yi" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Schneider", "given": "Tapio" }, "id": "Schneider-T", "role": "member", "display_name": "Schneider, Tapio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/d2ff-ad43", "abstract": "This thesis is motivated by the need to better understand and quantify the climate effects of carbonaceous aerosols, i.e., black carbon (BC) and organic carbon (OC). Global three-dimensional distribution of carbonaceous aerosols is simulated online in a general circulation model (GCM). The carbonaceous aerosol model includes primary BC, primary OC, five groups of biogenic volatile organic compounds (BVOCs), and fourteen semi-volatile products of BVOC oxidation by O3, OH, and NO3, which condense to form secondary organic aerosols (SOAs) based on an equilibrium partitioning model. Human activities since the preindustrial period are predicted to have increased global burdens of BC and OC by an order of magnitude and almost tripled the SOA production rate. Based on an older emission inventory for BC, the direct radiative forcing of increased atmospheric BC burden is estimated to warm the atmosphere by 0.51 to 0.8 W m-2, depending on how BC is mixed with other tropospheric aerosols. For OC, the estimated anthropogenic direct radiative forcing at top of the atmosphere (TOA) is -0.1 to -0.2 W m-2, depending on the water-uptake property of OC. When BC, OC and sulfate are combined, the estimated direct radiative forcing at TOA is -0.39 to -0.78 W m-2. Using an updated emission inventory, direct radiative forcing of anthropogenic BC at TOA is estimated to be +0.33 and +0.6 W m-2, for BC mixed externally and internally with present-day level of sulfate, respectively. Using a GCM coupled to a mixed-layer ocean model, these estimated forcings for BC are predicted to warm surface air temperature by 0.2 to 0.37 K. The temperature increase is the largest over northern high latitutdes during winter and early spring. Even though the predicted global-averaged warming due to BC is less than that of greenhouse gases, significant regional differences do exist, such as substantial warming in central and eastern Russia predicted for BC. In addition to temperature increase, direct radiative forcing of anthropogenic BC is also predicted to lead to a change in the hydrological cycle by shifting the intertropical convergence zone northward." }, { "name": "Deev, Andrei", "degree": "PhD", "year": "2005", "title": "Cavity Ringdown Spectroscopy of Atmospherically Important Radicals", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechETD:etd-03172005-154741", "creators": [ { "name": { "family": "Deev", "given": "Andrei" }, "id": "Deev-Andrei", "display_name": "Deev, Andrei" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YQBN-RX97", "abstract": "Many radicals, due to their electronic structure, have low-lying electronic states transitions to which lie in the near-IR. They often carry more information about the molecules than the transitions in the UV. However, these transitions even in the most important atmospheric radicals have not been thoroughly investigated due to their weakness and low attainable concentrations of radicals. This thesis describes the application of cavity ringdown spectroscopy to detection of near-IR states of some atmospherically important radicals.
\r\n\r\nThe near-IR cavity ringdown spectrometer constructed for these experiments is described in detail and characterized. The pulsed near-IR laser radiation was generated by sequential Raman shifting of the output of a tunable dye laser in hydrogen. The constructed multi-pass Raman cell extended the tunable range of the available dye laser continuously from the visible to 6000 cm\u207b\u00b9 with 0.15 cm\u207b\u00b9 resolution. The sensitivity of the instrument is \u22480.5 % of the mirror loss.
\r\n\r\nThe near-IR \u00c3 \u2190 X~ transition in peroxy radicals offers detection specificity for at least small radicals. The sensitivity of this transition to hydrogen atom substitution has been explored. The spectra of chloro-ethyl, -propyl, -butyl and -butenyl peroxy radicals in the 7000-8600 cm\u207b\u00b9 region are reported. The origin bands of the electronic transition were found to be shifted by 200 cm\u207b\u00b9 to the red. The spectra have more complex structure than those of unsubstituted homologues. DFT calculations predicted multiple conformers for C\u2082H\u2084ClO\u2082 and C\u2083H\u2086ClO\u2082 with the energies within 2 kcal/mol. Tentative assignment of the C\u2082H\u2084ClO\u2082 spectrum is presented. The integrated cross-section for the transition in chloro-ethyl peroxy radical is estimated from the known rate of self-reaction.
\r\n\r\nThe first full absorption spectrum of the \"dark\" \u00c3 \u00b2E' \u2190 X~ \u00b2A'\u2082 transition of the nitrate radical NO\u2083 in the 6000-10700 cm\u207b\u00b9 region is reported. \u03bd\u2082, \u03bd\u2083, and \u03bd\u2084 progressions and several combination bands are assigned. A more accurate estimate for the position of the \"dark\" origin is given. Analysis of the partially resolved rotational contours suggests that NO\u2083 undergoes static Jahn-Teller distortion in some of the vibronic states.
" }, { "name": "Dirks, Robert Michael", "degree": "PhD", "year": "2005", "title": "Analysis, Design, and Construction of Nucleic Acid Devices", "advisor": "Pierce, Niles A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-133116", "creators": [ { "name": { "family": "Dirks", "given": "Robert Michael" }, "id": "Dirks-Robert- Michael", "display_name": "Dirks, Robert Michael" } ], "advisors": [ { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "display_name": "Pierce, Niles A." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VZ43-FM66", "abstract": "Nucleic acids present great promise as building blocks for nanoscale devices. To achieve this potential, methods for the analysis and design of DNA and RNA need to be improved. In this thesis, traditional algorithms for analyzing nucleic acids at equilibrium are extended to handle a class of pseudoknots, with examples provided relevant to biologists and bioengineers. With these analytical tools in hand, nucleic acid sequences are designed to maximize the equilibrium probability of a desired fold. Upon analysis, it is concluded that both affinity and specificity are important when choosing a sequence; this conclusion holds for a wide range of target structures and is robust to random perturbations to the energy model. Applying the intuition gained from these studies, a process called hybridization chain reaction (HCR) is invented, and sequences are chosen that experimentally verify this phenomenon. In HCR, a small number of DNA or RNA molecules trigger a system wide configurational change, allowing the amplification and detection of specific, nucleic acid sequences. As an extension, HCR is combined with a pre-existing aptamer domain to successfully construct an ATP sensor, and the groundwork is laid for the future development of sensors for other small molecules. In addition, recent studies on multi-stranded algorithms and improvements to HCR are included in the appendices. Not only will these advancements increase our understanding of biological RNAs, but they will also provide valuable tools for the future development of nucleic acid nanotechnologies." }, { "name": "Edelson, Benjamin S.", "degree": "PhD", "year": "2005", "title": "Nuclear Localization of Polyamide-Fluorescein Conjugates in Cell Culture", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03162007-135225", "creators": [ { "name": { "family": "Edelson", "given": "Benjamin S." }, "id": "Edelson-Benjamin-S", "display_name": "Edelson, Benjamin S." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XQYG-DW76", "abstract": "Chapter 1: Distamycin A is a crescent-shaped natural product that preferentially binds to (A,T) sequences in the minor grove of DNA as 1:1 and 2:1 ligand-DNA complex [1,2]. Analogs of the N-methylpyrrole (Py) rings of these polyamides afford a set of five-membered heterocycles that can be combined\u2014as unsymmetrical ring pairs\u2014in a modular fashion to recognize predetermined DNA sequences with affinity and specificity comparable to DNA-binding proteins (Figures 1 and 2) [3,4]. We describe here recent advances in the field of DNA-binding polyamides, including structural verification of binding models, new heterocycles for recognition, cellular and nuclear uptake properties, and recent biological applications.
\r\n\r\nChapter 2: A series of hairpin pyrrole-imidazole polyamide-fluorescein conjugates were synthesized and assayed for cellular localization. Thirteen cell lines, representing eleven human cancers, one human transformed kidney cell line, and one murine leukemia cell line, were treated with 5 \u00b5M polyamide-fluorescein conjugates for 10-14 h, then imaged by confocal laser scanning microscopy. A conjugate containing a [beta]-alanine residue at the C-terminus of the polyamide moiety showed no nuclear localization, while an analogous compound lacking the [beta]-alanine residue was strongly localized in the nuclei of all cell lines tested. The localization profiles of several other conjugates suggest that pyrrole-imidazole sequence and content, dye choice and position, linker composition, and molecular weight are determinants of nuclear localization. The attachment of fluorescein to the C-terminus of a hairpin polyamide results in an approximate 10-fold reduction in DNA-binding affinity, with no loss of binding specificity with reference to mismatch binding sites.
\r\n\r\nChapter 3: A pivotal step forward in chemical approaches to controlling gene expression is the development of sequence-specific DNA-binding molecules that can enter live cells and traffic to nuclei unaided. DNA-binding polyamides are a class of programmable, sequence-specific small molecules that have been shown to influence a wide variety of protein-DNA interactions. We have synthesized over 100 polyamide-fluorophore conjugates and assayed their nuclear uptake profiles in thirteen mammalian cell lines. The compiled dataset, comprising 1300 entries, establishes a benchmark for the nuclear localization of polyamide-dye conjugates. Compounds in this series were chosen to provide systematic variation in several structural variables, including dye composition and placement, molecular weight, charge, ordering of the aromatic and aliphatic amino-acid building blocks, and overall shape. Nuclear uptake does not appear to be correlated with polyamide molecular weight or with the number of imidazole residues, although the positions of imidazole residues affect nuclear access properties significantly. Generally negative determinants for nuclear access include the presence of a [beta]-Ala-tail residue and the lack of a cationic alkyl amine moiety, whereas the presence of an acetylated 2,4-diaminobutyric acid-turn is a positive factor for nuclear localization. We discuss implications of this data on the design of polyamide-dye conjugates for use in biological systems.
" }, { "name": "Elgammal, Ramez Ahmed", "degree": "PhD", "year": "2005", "title": "Theoretical and Experimental Investigations in MEMS-Based Force-Detected NMR", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02182006-145814", "creators": [ { "name": { "family": "Elgammal", "given": "Ramez Ahmed" }, "id": "Elgammal-Ramez-Ahmed", "orcid": "0000-0002-6382-6817", "display_name": "Elgammal, Ramez Ahmed" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4FSQ-YP59", "abstract": "This thesis describes a method of mechanically detecting magnetic resonance. The detector consists of a ferromagnet harmonically bound to a mechanical resonator and measures a magnetic force of interaction with a nearby sample via dipole-dipole coupling. Flexural modes of vibration of the resonator are induced by inversion of the sample magnetization at the mechanical resonance frequency of the device. In this method, a nominally homogeneous field at the sample allows coherent spectroscopy over the entire sample volume.
\r\n\r\nSensitivity analyses suggest that encoding an NMR signal into mechanical oscillations favors inductive detection at the micron scale and below with Brownian motion of the detection being the predominant source of noise and azimuthal eddy currents being the predominant source of damping. As such, the design issues of a MEMS-based spectrometer optimized for 50 micron samples have been investigated. Finite element methods were used and the results for magnetic softening effects, mechanical stresses, field homogeneity, magnet design, radiofrequency excitation, and the utility of capacitive transduction to provide tuning of the oscillator\u2019s mechanical resonance frequency and active shimming are discussed. A piezeoelectrically actuated microvalve is proposed as part of a microfluidic device to allow shuttling of liquid samples. We present a new means of fiber-optic interferometry for geometrically confined regions in which the light exits transverse to core axis. The use of a composite magnetic array of packed nanoparticles may reduce the damping by 104.
\r\n\r\nThe portability of the spectrometer will allow in situ spectroscopy and towards that end 14N overtone experiments were simulated. Force-detection of this transition is superior not only at reduced size scales, but over a broad range of magnetic field strengths. The line narrowing observed by detecting the overtone transition should allow detailed spectroscopic analysis not possible by observing the quadrupolar broadened first-order spectrum. Simulations for a representative class of tholins suggest that the overtone linewidths is of order tens of kHz.
\r\n\r\nWe conclude by discussing the feasibility of nanoscale NMR using torque detection of spin-locked, transverse magnetization, include a derivation of the signal-to-noise and detector optimization, and comment on the fundamental limitations of quantum statistical noise.
" }, { "name": "Fechter, Eric James", "degree": "PhD", "year": "2005", "title": "Design of Sequence-Specific DNA Intercalators", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06052005-164552", "creators": [ { "name": { "family": "Fechter", "given": "Eric James" }, "id": "Fechter-Eric-James", "display_name": "Fechter, Eric James" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/d0v0-pb71", "abstract": "Small molecules that bind specific DNA sequences may have powerful therapeutic applications by influencing the mechanisms of abnormal gene expression. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) specifically bind the minor groove of DNA and have been shown to inhibit many protein-DNA complexes. However, some major groove-binding proteins can co-occupy the same DNA sequences as polyamides. Presented here are polyamide-intercalator conjugates that specifically bind target regions of DNA and deliver a non-specific intercalator to an adjacent site. The studies detail intercalative unwinding of specific DNA sequences to allosterically inhibit any protein:DNA complex. The evolution of sequence-specific polyamides to bisintercalate DNA and cause larger distortion of the helix is described. The success of hybrid molecules containing mixed DNA binding modes led to the development of a bis-polyamide-intercalator motif, modeled after the natural product actinomycin D, which is capable of specifically binding extended sequences of DNA. Also described is a polyamide-intercalator series which shows large fluorescence enhancement upon specific DNA binding and may be useful in detecting specific DNA sequences within living cells." }, { "name": "Ferreira, Eric Matthew", "degree": "PhD", "year": "2005", "title": "The Design and Development of Palladium-Catalyzed Aerobic Oxidative Transformations", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252005-205358", "creators": [ { "name": { "family": "Ferreira", "given": "Eric Matthew" }, "id": "Ferreira-Eric-Matthew", "orcid": "0000-0001-9412-0713", "display_name": "Ferreira, Eric Matthew" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z9K64G2R", "abstract": "Oxidation is a fundamental process in chemistry and biology. In synthetic chemistry, several developments have been made in catalytic asymmetric oxidative transformations that involve a heteroatom transfer from a reagent to a substrate (e.g., epoxidations, dihydroxylations). Enantioselective oxidations that do not involve a heteroatom transfer have been relatively less explored. These types of oxidative transformations were investigated using a general palladium(II) catalyst system.
\r\n\r\nA palladium-catalyzed oxidative kinetic resolution of secondary alcohols was developed. This catalytic system utilizes (\u2013)-sparteine as the chiral ligand and molecular oxygen as the sole stoichiometric oxidant. Benzylic and allylic alcohols can be resolved to high enantiomeric excesses in excellent yields. The same selective process has been applied to the desymmetrization of meso diols.
\r\n\r\nThis general palladium(II) oxidative system was applied to intramolecular Wacker oxidations to form a variety of heterocycles. Lactones, lactams, tetrahydrofurans, dihydrobenzofurans, and dihydrobenzopyrans were all accessed by this methodology. Importantly, this work provided entry into the development of asymmetric variants. Highly enantioselective cyclizations of phenolic substrates were realized with a palladium-sparteine catalyst, analogous to the kinetic resolution chemistry. The heterocyclization chemistry was employed in the context of the total synthesis of the Cephalotxaxus alkaloids.
\r\n\r\nOxidative annulations for the synthesis of carbocycles were developed utilizing this general palladium system. Indoles with pendant olefin tethers were oxidatively cyclized under palladium(II) catalysis to form annulated indoles. Electron-rich aromatic systems were also investigated, culminating in the syntheses of benzofurans and dihydrobenzofurans. These reactions were demonstrated to proceed by an initial C-H bond functionalization event, followed by olefin insertion and beta-hydride elimination.
\r\n\r\nEnantioselective heterocyclizations using the general oxidative system were further explored. Promising results were realized in the heterocyclizations of sulfonamide-based compounds. Key experiments allowed for a firmer understanding of how the reaction was progressing, and specifically, how enantioselectivity was being induced by the palladium catalyst.
\r\n" }, { "name": "Galownia, Jonathan Michael", "degree": "PhD", "year": "2005", "title": "I. Synthesis, Characterization, and Base Catalysis of Novel Zeolite Supported Super-Basic Materials. II. Oxidative Dehydrogenation of Ethane Over Reduced Heteropolyanion Catalysts", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-230657", "creators": [ { "name": { "family": "Galownia", "given": "Jonathan Michael" }, "id": "Galownia-Jonathan-Michael", "display_name": "Galownia, Jonathan Michael" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/QZ7V-5W65", "abstract": "This thesis is composed of two separate and unrelated projects. The first part of this thesis outlines an investigation into the synthesis and characterization of a novel zeolite supported super-base capable of carbon-carbon olefin addition to alkyl aromatics. A zeolite supported basic material capable of such reactions would benefit many fine chemical syntheses, as well as vastly improve the economics associated with production of the high performance thermoplastic polyester polyethylene naphthalate.
\r\n\r\nThe thermal decomposition of alkali\u2014metal azides impregnated in zeolite X is investigated as a novel route to the synthesis of a zeolite supported super-base. Impregnation of the alkali\u2014metal azide precursor is shown to result in azide species occluded within the pores of the zeolite support by using high speed, solid-state 23Na MAS and 2D MQMAS NMR, FTIR, and TGA characterization methods. Addition of alkali\u2014metal azides to the zeolite results in redistribution of the extra-lattice cations in the zeolite framework. Thermal decomposition of impregnated azide species produces further cation redistribution, but no neutral metallic clusters are detected by high speed, solid-state 23Na MAS NMR following thermal activation of the materials. Instead, it is possible that inactive ionic clusters are formed. The thermally activated materials do not promote base catalysis for the isomerization of 1-butene, the ethylation of toluene and o-xylene, and the alkenylation of o-xylene with 1,3-butadiene to produce 5-ortho-tolyl-pent-2-ene (5-OTP). The lack of catalytic activity in the materials is attributed to failure of the materials to form neutral metallic clusters during thermal treatment, possibly due to preferential formation of NMR silent ionic clusters. The formation of neutral metallic clusters is found to be insensitive to synthesis technique and activation procedure. It is concluded that the impregnation of alkali\u2014metal azides in zeolite X does not provide a reliable precursor for the formation of zeolite supported super-basic materials.
\r\n\r\nThe second part of this thesis describes the oxidative dehydrogenation of ethane over partially reduced heteropolyanions. Niobium and pyridine exchanged salts of phosphomolybdic (NbPMo12Pyr) and phosphovanadomolybdic (NbPMo11VPyr) acids are investigated as catalyst precursors to prepare materials for catalyzing the oxidative dehydrogenation of ethane to ethylene and acetic acid at atmospheric pressure. The effects of feed composition, steam flow, temperature, and precursor composition on catalytic activity and selectivity are presented for both ethane and ethylene oxidation. Production of ethylene and acetic acid from ethane using the catalytic materials exceeds that reported in the literature for Mo-V-Nb-Ox systems under atmospheric or elevated pressure. Production of acetic acid from ethylene is also greater than that observed for Mo-V-Nb-Ox systems. Addition of vanadium reduces catalytic activity and selectivity to both ethylene and acetic acid while niobium is essential for the formation of acetic acid from ethane. Other metals such as antimony, iron, and gallium do not provide the same beneficial effect as niobium. Molybdenum in close proximity to niobium is the active site for ethane activation while niobium is directly involved in the transformation of ethylene to acetic acid. A balance of niobium and protonated pyridine is required to produce an active catalyst. Water is found to aid in desorption of acetic acid, thereby limiting deep oxidation to carbon oxides. A reaction scheme is proposed for the production of acetic acid from ethane over the catalytic materials.
" }, { "name": "Garg, Neil Kamal", "degree": "PhD", "year": "2005", "title": "The Total Synthesis of Dragmacidins D and F", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03222005-133937", "creators": [ { "name": { "family": "Garg", "given": "Neil Kamal" }, "id": "Garg-Neil-Kamal", "display_name": "Garg, Neil Kamal" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q4GM-9610", "abstract": "The dragmacidins are an emerging class of bis(indole) natural products isolated from deep-water marine organisms. Although there has been a substantial effort to prepare the simple piperazine dragmacidins, little synthetic work has been done in the area of the pyrazinone-containing family members, dragmacidins D, E, and F. These compounds are particularly interesting due to their complex structures and broad range of biological activity.
\r\n\r\nA highly convergent strategy to access dragmacidin D has been developed. In this approach, sequential halogen-selective Suzuki couplings were used to assemble the carbon scaffold of the natural product. After executing a highly optimized sequence of final events, the first completed total synthesis of dragmacidin D was achieved.
\r\n\r\nAn enantiodivergent strategy for the total chemical synthesis of both (+)- and (-)-dragmacidin F from a single enantiomer of quinic acid has been developed and successfully implemented. Although unique, the synthetic routes to these antipodes share a number of key features, including novel reductive isomerization reactions, Pd(II)-mediated oxidative carbocyclization reactions, halogen-selective Suzuki couplings, and high-yielding late-stage Neber rearrangements.
\r\n\r\nThe formal total syntheses of dragmacidin B, trans-dragmacidin C, and dihydrohamacanthin A are described. In addition, preliminary studies involving a novel approach for the preparation of dragmacidin E are reported.
" }, { "name": "Hall, Spencer Eugene", "degree": "PhD", "year": "2005", "title": "Development of a Structure Prediction Method for G-Protein Coupled Receptors", "advisor": "Vaidehi, Nagarajan; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-235052", "creators": [ { "name": { "family": "Hall", "given": "Spencer Eugene" }, "id": "Hall-Spencer-Eugene", "display_name": "Hall, Spencer Eugene" } ], "advisors": [ { "name": { "family": "Vaidehi", "given": "Nagarajan" }, "id": "Vaidehi-N", "orcid": "0000-0001-8100-8132", "role": "advisor", "display_name": "Vaidehi, Nagarajan" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Vaidehi", "given": "Nagarajan" }, "id": "Vaidehi-N", "orcid": "0000-0001-8100-8132", "role": "member", "display_name": "Vaidehi, Nagarajan" }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JN28-5F55", "abstract": "G-Protein Coupled Receptors (GPCRs) form a major target class of membrane proteins for therapeutic drug design, and the challenge is to design subtype specific drugs. Hence the knowledge of three-dimensional structure is critical to drug design for GPCRs. Since GPCRs are membrane bound proteins, there is only one crystal structure for a GPCR, namely bovine rhodopsin. The prediction of structure and function of G-protein-coupled receptors will allow for designing drugs with minimal side effects.
\r\n\r\nThe focus of my thesis is the development of computational methods for prediction of structure of GPCRs and application of these methods (MembStruk) for a class of important drug targets such as chemokine receptors. MembStruk method is a hierarchical method ranging from coarse grain optimization of the trans-membrane helices to fine grain optimization of the structure in explicit lipid bilayer. The first two chapters of the thesis details the computational steps involved in MembStruk and its application to validating the method for bovine rhodopsin. The first chapter presents the method development in the most current version of the MembStruk method, version 4.30, and its application to bovine rhodopsin. The final predicted structure for bovine rhodopsin deviates from the crystal structure trans-membrane main chain atoms by 2.66 A coordinate root mean square deviation (CRMSD), and the residues in the binding site of 11cis-retinal is only 1.37 A CRMSD from the crystal structure for the main chain atoms. The second chapter of this thesis details the computational methods for optimization of the rotation and translation of the trans-membrane regions. These methods of rotation and translation of transmembrane helices has been further extended to the comparison of structures of two membrane proteins, and applied to the comparison of crystal structures of bovine rhodopsin and bacteriorhodopsin. The third chapter details the graphical user interface that has been developed to automate the various steps of the MembStruk method.
\r\n\r\nOlfactory receptors are GPCRs and the molecular analysis for the recognition of odorants is very important in understanding the mechanism of olfaction. In a blind study prior to experiments, in collaboration with Dr. Bozza of Rockefeller University, I applied the MembStruk method to understanding the binding of odorants to rat and mouse olfactory receptor I7. Chapter 4 describes the application of the MembStruk method to rat and mouse I7 olfactory receptor and the binding of 65 odorants to this receptor. The last chapter describes the use of MembStruk method in predicting the structure and function of important drug targets, namely chemokine receptors CCR5 and CXCR4.
\r\n" }, { "name": "Heidel, Jeremy David", "degree": "PhD", "year": "2005", "title": "Targeted, Systemic Non-Viral Delivery of Small Interfering RNA in vivo", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252005-114817", "creators": [ { "name": { "family": "Heidel", "given": "Jeremy David" }, "id": "Heidel-Jeremy-David", "display_name": "Heidel, Jeremy David" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Rossi", "given": "John J." }, "id": "Rossi-J-J", "role": "member", "display_name": "Rossi, John J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/F5AX-3Y24", "abstract": "Armed with the complete sequence of the human genome and an ever-increasing array of biological techniques, researchers continue to learn more about the genetic basis of diseases. For two decades, scientists and physicians have been developing therapeutic strategies for treating many diseases at the genetic level, creating the field of \"gene therapy.\" For those diseases caused by loss-of-function mutations in a specific gene, delivery of a wild-type copy of that gene to affected cells can reduce or eliminate the disease phenotype. Viruses, having evolved to be extremely effective at delivering nucleic acids (i.e., their own genes for viral production) to cells, have been modified to include therapeutic genes of interest. While such viral gene therapy vectors are the most efficient vectors developed, concerns about their safety and immunogenicity have prompted many to investigate non-viral vector alternatives. Cationic polymers and lipids have emerged as leading non-viral vector materials. Our laboratory has developed a class of cyclodextrin-containing polycations (CDPs) that condense DNA into complexes that can be endocytosed by cells, achieve expression of their genetic payload in those cells, and may be modified to target particular cell types within an animal.
\r\n\r\nIn the past five years, scientists have discovered a new mechanism for the reduction of gene expression in mammalian cells via sequence-specific cleavage of a particular messenger RNA (mRNA); this phenomenon is known as RNA interference (RNAi). Since RNAi is triggered by nucleic acids (small interfering RNA (siRNA) duplexes), I hypothesized that CDPs may be suitable vectors for the delivery of siRNA. In my thesis work, the safety of synthetic siRNA duplexes is examined both in cultured cells and in vivo. Using a number of different siRNA sequences, two different strains of mice, and three different methods of administration, I fail to observe any cytokine (IL-12 or IFN-a) responses, morphological changes, or alterations in complete blood counts (CBCs) or liver enzyme levels.
\r\n\r\nThe ability of CDP to serve as a delivery vehicle for siRNA is also explored. I demonstrate that CDP/siRNA complexes can be formed that are small enough to be endocytosed, can be modified to ensure stability in physiological fluid, and protect the siRNA payload from serum nuclease degradation. Finally, down-regulation of specific target genes, including genes implicated in disease, is shown in vitro and in mice. An endogenous reporter gene (luciferase) in the livers of transgenic mice is down-regulated by galactosylated CDP/siRNA formulations that target hepatocytes. The level of a chimeric oncogene, EWS-Fli1, is reduced by polyplex formulations in cultured Ewing\u2019s sarcoma cells and by transferrin-targeted formulations in tumor-bearing mice; this in vivo down-regulation corresponds to an inhibition of tumor growth. These results suggest that CDP-containing siRNA formulations have the potential for development into therapeutics.
" }, { "name": "Ja, William Wei-Hua", "degree": "PhD", "year": "2005", "title": "Peptide Modulators of G Protein Signaling", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032005-161114", "creators": [ { "name": { "family": "Ja", "given": "William Wei-Hua" }, "id": "Ja-William-Wei-Hua", "orcid": "0000-0002-4003-7356", "display_name": "Ja, William Wei-Hua" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." }, { "name": { "family": "Deshaies", "given": "Raymond Joseph" }, "id": "Deshaies-R-J", "role": "member", "display_name": "Deshaies, Raymond Joseph" }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WMQ9-8086", "abstract": "The hundreds of transmembrane proteins that make up the superfamily of G protein-coupled receptors (GPCRs) mediate signaling from an enormous variety of extracellular stimuli\u2014including odorants, pheromones, peptides, lipids, and neurotransmitters\u2014to intracellular heterotrimeric G proteins. The identification of specific modulators of G protein signaling is highly relevant to drug discovery; approximately 50% of currently marketed drugs target a GPCR. Here, we use mRNA display to identify novel and potent peptide ligands for G protein targets. mRNA display is a robust technique that facilitates the isolation of peptides with specific activities (e.g., binding to a target of interest) from large libraries containing trillions of unique molecules. We first targeted the heterotrimeric G protein, Gi(alpha)1, with peptide combinatorial libraries. Isolated peptides bind with high affinity to Gi(alpha)1 and can potentially affect downstream signaling in a pathway-specific manner. A potent peptide core motif interacting with G(alpha) subunits was identified and used to construct new mRNA display libraries for the isolation of class- and/or state-specific G(alpha)-binding peptides. We have also identified a novel peptide (the RWR motif) that interacts with the Drosophila GPCR, Methuselah. These peptides are potent antagonists to Methuselah-mediated signaling and, as mutants of Methuselah are associated with longevity, may be useful in lifespan and aging studies of the fruit fly. Overall, these efforts demonstrate the successful use of mRNA display as an efficient and facile method for generating new solutions to molecular design problems." }, { "name": "Jenkins, David Matthew", "degree": "PhD", "year": "2005", "title": "Low Spin Pseudotetrahedral Cobalt Tris(phosphino)borate Complexes", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02102005-144940", "creators": [ { "name": { "family": "Jenkins", "given": "David Matthew" }, "id": "Jenkins-David-Matthew", "orcid": "0000-0003-2683-9157", "display_name": "Jenkins, David Matthew" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5WNW-R611", "abstract": "A synthetic protocol is developed for the preparation of a thallium complex featuring the tris(phosphino)borate ligand [PhBP3] ([PhBP3] = [PhB(CH2PPh2)3]-). The transmetallating reagent, [PhBP3]Tl, is characterized by single crystal X-ray diffraction and solution NMR spectroscopy, and is the first example of a stable homoleptic Tl(I)-phosphine complex.
\r\n\r\nThe synthesis and characterization of [PhBP3]Co-X (X = I, Br or Cl) is discussed. These halide complexes are structurally characterized and magnetic investigations establish that they are low spin when monomeric. The low spin iodide complex is a monomer in solution and in the solid state. The other halides exhibit a monomer/dimer equilibrium that complicates their magnetic behavior. Theoretical calculations help provide a rationale as to why these pseudotetrahedral species are low spin. A classic high spin species supported by [PhBP3] is compared to the low spin complexes.
\r\n\r\nSpin state control involving pseudotetrahedral [PhBP3]Co(II) complexes is explored. Both high and low spin, as well as spin crossover, complexes are synthesized and structurally characterized. The complexes are discussed in terms of the relationship between local geometry and spin state. Changing the axial or tripodal ligand can cause a different spin state to be favored. Since the energy difference between the states is small, ligand changes at remote positions from the metal center have a significant effect on spin crossover phenomena. Theoretical calculations help illuminate why the low spin state is preferred for many of the complexes.
\r\n\r\nThe first examples of cobalt imide complexes ([PhBP3]Co\u2261NR (R = aryl or alkyl)) are prepared and they are supported by the [PhBP3] ligand. These diamagnetic species are evaluated by NMR and single crystal X-ray diffraction. Theoretical studies suggest that they have a similar molecular orbital bonding scheme as the previously prepared group 9 imides.
\r\n\r\nA cobalt \u03bc2-bridging nitride complex (([PhBP3]Co)2(\u03bc-N)) is synthesized and structurally characterized. This mixed-valence species is evaluated by magnetometry to determine its ground state, which is low spin (S = \u00bd).
\r\n\r\nSeveral cobalt diazoalkane complexes are prepared. These diamagnetic species adopt two different bonding modes depending on the nature of the diazoalkane ligand.
" }, { "name": "Jones, Elizabeth Anne Vincent", "degree": "PhD", "year": "2005", "title": "Blood Flow and The Mammalian Embryo", "advisor": "Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-102319", "creators": [ { "name": { "family": "Jones", "given": "Elizabeth Anne Vincent" }, "id": "Jones-Elizabeth-Anne-Vincent", "display_name": "Jones, Elizabeth Anne Vincent" } ], "advisors": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "chair", "display_name": "Fraser, Scott E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Bronner", "given": "Marianne E." }, "id": "Bronner-M-E", "orcid": "0000-0003-4274-1862", "role": "member", "display_name": "Bronner, Marianne E." }, { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "member", "display_name": "Gharib, Morteza" } ], "option_major": [ "chemeng" ], "doi": "10.7907/TTW7-YY07", "abstract": "Hemodynamics, or blood fluid dynamics, is of great importance in vascular biology and its role is well recognized in events ranging from atherosclerosis to wound healing. The importance of hemodynamics during embryonic development, however, is less clear. The early vertebrate vasculature is established through two processes; vasculogenesis, which is the de novo formation of vessels and angiogenesis, which is the sprouting of new vessels from existing vessels and the remodeling of existing vessels. The latter process, angiogenesis and vascular remodeling, is dependent on blood flow and does not occur if cardiac output is blocked. As well, if blood flow is altered, such as with mutations that affect cardiac contraction, the early vessels also fail to remodel. Flowing blood imparts a physical force, called shear stress, on the endothelial lining of the blood vessels. Many genes known to be regulated by shear stress are important for vascular remodeling in the embryo. In this work, we investigate the role of shear stress on the remodeling process.
\r\n\r\nStudying the role of shear stress in embryos requires the ability to measure changes in both fluid dynamics and vascular morphology as well as methods to alter shear stress levels. In this work, we use an optical technique for the quantitative analysis of hemodynamics during early organogenesis in the mouse embryo. We established the morphological changes that occur in the vasculature during remodeling and link these to the fluid dynamics that are present. We establish the mechanical cues that are available to the endothelial cells and the type of flow present at various stages of development. In order to understand how these mechanical cues affect embryonic development, we examine altered shear stress during development using a mutant mouse model in which the atrial cardiac contraction is lacking as well as inducing specific changes in shear stress through chemical manipulation of the embryonic cardiovascular system. These studies establish a link between the pattern of blood flow within the vasculature and the stage of cardiovascular development and enable analysis of the influence of mechanical forces during development.
" }, { "name": "Kapinus, Vadym A.", "degree": "PhD", "year": "2005", "title": "Photophysical Properties of Protonated Aromatic Hydrocarbons", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01252005-123917", "creators": [ { "name": { "family": "Kapinus", "given": "Vadym A." }, "id": "Kapinus-Vadym-A", "display_name": "Kapinus, Vadym A." } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3A85-DC20", "abstract": "Polycyclic aromatic hydrocarbons (PAHs) and their derivatives are among the likely candidates for diffuse interstellar band (DIB) carriers. In diffuse interstellar clouds molecules are expected to be ionized, and PAHs in particular are predicted to be in protonated form. Protonated PAHs are closed-shell ions with electronic transitions that are red-shifted compared to neutral PAHs.
\r\n\r\nThis thesis presents an experimental and theoretical analysis of two-, three-, and four-ring protonated PAHs. The energetics of protonated PAH isomers in their ground electronic state and the proton tunneling barriers were calculated using density functional theory. The loss of an H atom or H2 molecule from a protonation site were identified as the most favorable dissociation channels for protonated PAHs. They were found to be within a few kcal/mol of each other in energy, and about 45-60 kcal/mol above the ground state.
\r\n\r\nThe Configuration Interaction Singles (CIS) method was used to estimate the positions of the electronic transitions for protonated PAHs. Red shifts up to 150 nm were predicted for protonated naphthalene, anthracene, phenanthrene and pyrene. This places the S1 \u2190 S0 transitions of protonated PAHs well into the DIB wavelength region.
\r\n\r\nExperimentally, a robust hydrogen discharge source was designed to produce protonated PAHs. Laser photodissociation of protonated PAHs was studied with an excimer laser/reflectron time-of-flight mass spectrometer. Small protonated PAHs were found to be very photostable. Nanosecond pulse length photodissociation was multiphoton even at short wavelengths (193 nm). For protonated anthracene, the dissociation threshold was estimated to be 13 -- 15 eV, much higher than the predicted thermodynamic threshold of 2.5 -- 3.0 eV. This was attributed to intramolecular vibrational relaxation (IVR) upon electronic excitation.
\r\n\r\nCluster photodissociation was used to locate the electronic transitions of protonated anthracene between 420 and 540 nm. Clusters with water molecules were produced in a two-valve mixing discharge source. Their photodissociation spectrum was recorded using a novel hybrid cavity optical parametric oscillator. The observed absorption bands (20 nm FWHM) are too wide to account for the DIBs. This spectral broadening most likely results from rapid IVR induced by the high density of states in protonated PAHs.
" }, { "name": "Klamo, Sara Bernadine", "degree": "PhD", "year": "2005", "title": "Direct Examination of Initiation and Propagation Kinetics of Zirconocene-Catalyzed Alkene Polymerization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-144620", "creators": [ { "name": { "family": "Klamo", "given": "Sara Bernadine" }, "id": "Klamo-Sara-Bernadine", "display_name": "Klamo, Sara Bernadine" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z24R-FF38", "abstract": "Zirconocene precatalysts with sterically bulky alkyl groups were designed in order to obtain models for the propagating species in zirconocene-catalyzed alkene polymerization. Alkyllithium reagents Li(CH2CEt3) and Li(CH2CMe2CH2Ph) were prepared and utilized in methyl alkylzirconocene synthesis. Dialkyl and methyl alkylzirconocenes of the form [(eta-5-C5H5) (eta-5-C5Me5)Zr(R)2], [(eta-5-C5H5)2Zr(R)(CH3)], and [(eta-5-C5H5)(eta-5-C5Me5)Zr(R)(CH3)] (where R = CH2CMe3, CH2SiMe3, CH2CEt3,CH2CMe2CH2Ph) were synthesized and fully characterized by NMR spectroscopy and in some cases X-ray diffraction. The molecular structures determined display the bent sandwich coordination mode common for zirconocenes. The observed structural parameters are slightly perturbed by the steric influence of the bulky alkyl group.
\r\n\r\nA direct examination of propagation kinetics for alkene polymerization using the zirconocenium initiator, [(eta-5-C5H5)(eta-5-C5Me5)Zr(CH2CMe3)]+[CH3B(C6F5)3]-, is reported. Propagation rate constants (kp) for the polymerization of propene and a series of 1-alkenes catalyzed by [(eta-5-C5H5)(eta-5-C5Me5)Zr(CH2CHR)nCH2CMe3)]+[CH3B(C6F5)3]- were measured by 1H NMR spectroscopy in toluene-d8 at low temperature. The kp obtained for propene and other alkenes decreases with increasing chain length and steric influence. The overall activation parameters for propagation determined from an Eyring analysis are (delta)H(activation) = 8.5(3) kcal/mol and (delta)S(activation) = -25(2) eu. The propagation rate was found to increase in the presence of [CH3B(C6F5)3]- counteranion and in a polar toluene-d8-chlorobenzene-d5 solvent system. The experimental results are most consistent with propagation mechanism that does not involve the formation of outer-sphere ions for alkene polymerization by this catalyst system.
\r\n\r\nPropene initiation kinetics have been examined for a series of alkylzirconocene initiators, [(eta-5-C5H5)(eta-5-C5Me5)Zr(R)]+[CH3B(C6F5)3]- (R = CH3 (5), CH2CMe3 (1), CH2SiMe3 (4)). Measurement of ki for the neopentyl initiator reveals that the rate of initiation is on the order of propagation for this catalyst. This initiator with a polymeryl like alkyl group serves as a model of the propagating species in propene polymerization. The catalyst initiation behavior has been investigated and the observed relative rates of propene initiation are not always predicted by ground-state (zirconium-carbon bond strength or extent of ion-pairing) considerations. The catalysts 4 and 5 are both poor initiators with ki << kp and show less than 50% initiation in the presence of excess propene at -60 C in toluene-d8.
" }, { "name": "Kwan, Brian Joseph", "degree": "Masters", "year": "2005", "title": "Development of Sequential Olefin Cross Metathesis-Organocatalysis Methodology", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12202004-085725", "creators": [ { "name": { "family": "Kwan", "given": "Brian Joseph" }, "id": "Kwan-Brian-Joseph", "display_name": "Kwan, Brian Joseph" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nv3a-nj90", "abstract": "No abstract." }, { "name": "Lambert, Bruce Michael", "degree": "PhD", "year": "2005", "title": "Force-Detected, Single-Molecule Spectroscopy and Imaging Using Nanoscale Mechanical Resonators", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-194621", "creators": [ { "name": { "family": "Lambert", "given": "Bruce Michael" }, "id": "Lambert-Bruce-Michael", "display_name": "Lambert, Bruce Michael" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SN22-ZZ77", "abstract": "Novel methods for spectroscopic probing of single-molecules are described that sense the optically induced, molecular dipole through the force/torque it generates on a submicron mechanical probe. The probe comprises a mechanical resonator with a high-Q mode of oscillation at frequency vh, to which is attached a nanoparticle with dipole moment p. This dipole is either the optically induced dipole of a metal nanoparticle irradiated at plasmon resonance, or the static dipole moment of a ferroelectric nanocrystal. The electric force or torque between the probe dipole and molecular dipole drives the motion of the resonator at the resonance frequency. Three novel optical scattering mechanisms, which encode the mechanical motion into the phase, amplitude, or polarization of the light scattered by the resonator are investigated and quantified. A novel single-molecule sensor will also be described that comprises a mechanical torsional resonator with an attached ferroelectric nanoparticle. The observable quantity is the shift in the oscillation frequency of the mechanical resonator as a molecule becomes polarized by the rf near-field of the ferroelectric particle. The ferroelectric particle couples electrostatically to a nearby nanoscale capacitor which is used to electrically drive and detect the resonant mechanical motion. Due to this coupling, the electric and mechanical coordinates, which specify the state of this electromechanical device, are no longer the eigenmodes of the system. This gives rise to interesting dynamical effects that are best analyzed using the Lagrange formulation of mechanics. Finally, we discuss experimental progress toward fiber-optic interferometric detection of submicron mechanical resonators." }, { "name": "Lee, Hyunjoo", "degree": "PhD", "year": "2005", "title": "A New Strategy for Synthesizing Zeolites and Zeolite-Like Materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122005-144223", "creators": [ { "name": { "family": "Lee", "given": "Hyunjoo" }, "id": "Lee-Hyunjoo", "orcid": "0000-0002-4538-9086", "display_name": "Lee, Hyunjoo" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/N5NX-2T83", "abstract": "Zeolite and molecular sieve materials are broadly used as ion-exchangers, adsorbents and catalysts in the chemical industry. Zeolites are typically synthesized by using organic molecules as structure-directing agents (SDA). The SDA should be removed from the pore cavity of the zeolite framework to create microporous void space before the zeolite can be used for further purposes. Porous zeolites have been prepared by calcination, or extraction in very limited cases. However, calcination has several undesired aspects mainly resulted from a high temperature. A combustion-free methodology is developed in this work by using a new concept for the SDAs. An organic molecule that can be easily cleaved into smaller fragments and subsequently recombined into the original molecule by simple treatments can be used as a 'recyclable SDA'. That is, after synthesizing a zeolite using this type of organic molecule as the SDA, the molecule can be fragmented in the pore cavity, and its fragments removed due to their smaller size. The recovered fragments are then recombined into the original SDAs, which can be used for further zeolite syntheses. The cyclic ketal molecule, 8,8-dimethyl-1,4-dioxa-8-azaspiro[4,5]decane, is used here to prove this new methodology. The ketal is fragmented into its corresponding ketone and diol molecules after structure-directing the synthesis of the zeolite, ZSM-5. The fragments are successfully removed by ion-exchange, and the prepared porous ZSM-5 shows equivalent porosity, catalytic activity and shape selectivity as conventional ZSM-5. In some cases, the SDA can be so tightly packed inside the pore cavity that the small reagent molecules required for fragmentation by acid hydrolysis have no access to the pore cavity. Therefore, the original methodology was expanded to provide a solution for this problem by utilizing two different kinds of organic molecules, a SDA and a pore-filling agent (PFA), during the zeolite syntheses. The removal of the PFA by simple extraction generates the necessary space inside the pore cavity for agents necessary for the hydrolysis to transport into the zeolite. Using this methodology, ZSM-5, ZSM-12, VPI-8 and MOR are successfully synthesized with various ketal SDAs whose hydrolysis depends on the hydrophilicity and pore connectivity of the synthesized zeolites." }, { "name": "Li, Youyong", "degree": "PhD", "year": "2005", "title": "Atomistic Simulation of Macromolecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-12072004-021118", "creators": [ { "name": { "family": "Li", "given": "Youyong" }, "id": "Li-Youyong", "orcid": "0000-0002-5248-2756", "display_name": "Li, Youyong" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NW1Q-1E81", "abstract": "This thesis focuses on the atomistic simulation of polymers/dendrimers material properties and development/applications of Monte Carlo methods for macromolecules. The main topics and their outlines are listed as following.
\r\n\r\n1) Structures and properties of crystalline polymers from theory. Although crystalline polymers such as nylon are important industrial materials, it is difficult to get the details of the various structures/properties and the conversion between them from the experiment. Using molecular modeling, we successfully predicted the complicated structures/properties and illustrated the process of forming the polymer crystal and conversion mechanism among those structures.
\r\n\r\n2) Packing mechanism of self-assembly dendrimer balls with soft coronas. Using the vibrational density of state (DoS) derived from molecular dynamic simulations, we investigate the free energy of the liquid crystal formed by soft dendrimer balls. We find that the preferred lattice for soft balls is different from the hard balls and illustrate the mechanism.
\r\n\r\n3) Development of CCBTX Monte Carlo method for polymer and dendrimer. Although computer simulation has developed as a powerful research tool to study polymer/dendrimer materials properties recently, it has been hampered by the difficulties of sampling amorphous polymer/dendrimer configurations efficiently. We develop the efficient Continuous Configurational Biased TX (CCBTX) method to generate high-quality amorphous polymer and dendrimer atomistic structures directly. The code is implemented in C++ and ported in python environment, which provides friendly interface.
\r\n\r\n4) Thermodynamic functions, critical exponents, and theta temperatures of polymer chains from CCBB Monte Carlo method. We examine the thermodynamic properties (entropy, energy, end-to-end distance) of isolated polymer chains with the Monte Carlo method.
" }, { "name": "Marques, Michael Anthony", "degree": "PhD", "year": "2005", "title": "The Molecular Recognition of DNA by Novel Heterocycles", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252005-143409", "creators": [ { "name": { "family": "Marques", "given": "Michael Anthony" }, "id": "Marques-Michael-Anthony", "display_name": "Marques, Michael Anthony" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/GHEJ-A648", "abstract": "With a rapid movement toward personalized genetic medicine, tailoring treatment to individual patient needs based on their genetic code is becoming an important goal. The ability to develop small molecules capable of reprogramming the cellular machinery at the genetic level is one approach to the difficult challenge of treating diseases that result from aberrant gene expression. Inspired by the architecture of the natural products netropsin and distamycin, polyamides are capable of binding the DNA minor groove with high affinity and fidelity. Originally composed of five-membered heterocyclic carboxamides, polyamides have evolved in both form and function. A search has been initiated to develop new DNA specific oligomers that have different electronic and geometric properties. Alteration of these properties may lead to a new class of compounds, capable of targeting DNA sequences that have previously been shown to be difficult to recognize. Second-generation compounds containing novel heterocyclic recognition elements, within the context of both 5-membered heterocyclic carboxamides and fused 6-5 benzimidazole analogues, have recently been developed. These molecules have successful DNA recognition profiles as well as favorable cell uptake properties, important considerations when searching for effective pharmacophores. These new classes of rationally designed oligomers offer one approach to the challenging problem of regulating gene expression." }, { "name": "Meinhold, Peter", "degree": "PhD", "year": "2005", "title": "Engineering Cytochrome P450 BM-3 for Selective Hydroxylation of Alkanes", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-06032005-113204", "creators": [ { "name": { "family": "Meinhold", "given": "Peter" }, "id": "Meinhold-Peter", "display_name": "Meinhold, Peter" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Newman", "given": "Dianne K." }, "id": "Newman-D-K", "orcid": "0000-0003-1647-1918", "role": "member", "display_name": "Newman, Dianne K." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "biochem" ], "doi": "10.7907/aats-ca30", "abstract": "Cytochromes P450 are of potential synthetic value because they hydroxylate a large array of substrates, often with high regio- and enantioselectivity. In contrast to most P450s, the BM-3 variant from Bacillus megaterium is soluble, easily expressed in E. coli, and does not require additional electron transfer proteins. A highly efficient enzyme for its preferred reaction, hydroxylation of medium-chain (C12 to C18) fatty acids, BM-3 is a good candidate for engineering for applications requiring activity on other substrates.
\r\n\r\nUsing iterations of random mutagenesis, recombination, and high throughput screening, we engineered P450 BM-3 mutants to hydroxylate linear alkanes as short as propane. Activity towards linear alkanes was further increased by changing two key active site residues. The resulting mutants hydroxylate linear alkanes with high regioselectivity and, notably, enantioselectivity.
\r\n\r\nWe further engineered these enzymes with guidance from the crystal structure of substrate-bound P450 BM-3. Eleven active-site residues were chosen for saturation mutagenesis, and the resulting mutants were screened for improved activity towards alkanes, as measured by total product formation. Substitutions at these positions generally did not affect correct folding of the enzyme, and a large fraction of folded proteins retained similar levels of activity as their predecessor. Moreover, several of the 11 selected amino acid substitutions yielded mutants that were both more active and produced various combinations of product regioisomers.
\r\n\r\nRecombination of these beneficial active-site mutations generated BM-3 variants that catalyze: (a) regio- and enantioselective hydroxylation of linear alkanes; (b) terminal hydroxylation of linear alkanes; (c) regio- and enantioselective hydroxylation of heterocyclic compounds; and (d) ethane hydroxylation.
\r\n\r\nThe selective conversion of ethane to ethanol, not previously reported for any P450, is catalyzed by the most active mutant from this library. In nature, this reaction is solely observed for methane monooxygenases (MMOs) and related enzymes in alkane-assimilating bacteria.
\r\n\r\nAdditionally, we have found that the reductase domain can be engineered to increase the efficiency of these reactions. Our progress in converting BM-3 from a fatty-acid hydroxylase into an enzyme able to selectively hydroxylate smaller alkanes, including ethane, is an important step towards our ultimate goal, achieving selective BM-3 catalyzed conversion of methane to methanol.
" }, { "name": "Murphy, John Frank", "degree": "PhD", "year": "2005", "title": "Methods for Collection and Processing of Gene Expression Data", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252004-101813", "creators": [ { "name": { "family": "Murphy", "given": "John Frank" }, "id": "Murphy-John-Frank", "display_name": "Murphy, John Frank" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "orcid": "0000-0002-4925-7523", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Wold", "given": "Barbara J." }, "id": "Wold-B-J", "orcid": "0000-0003-3235-8130", "role": "member", "display_name": "Wold, Barbara J." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/8p8e-2147", "abstract": "Examination of the transcriptional messages encoded in the manifold of mRNA molecules within a cell is a central task of molecular biology and functional genomics. This examination can be broken down into two parts: collection of gene expression data, and analyses of those data. Here, a new method for collecting gene expression data, and two new methods for analyzing those data are presented.
\r\n\r\nA new method for quantifying gene expression denoted as the Mass-spectrometric Analysis of Gene Expression (MAGE) is developed. MAGE relies on novel conjugates of DNA oligonucleotide 30-mers; each unique sequence is conjugated via photolabile linker to an N-substituted glycine oligomer (peptoid) of unique mass. Deuterated bromoacetic acid is incorporated into some peptoids yielding two chemically identical probe conjugates of different molecular weights for each nucleic acid sequence of interest. Mixtures of these probes, along with 3' adjacent biotin-labeled oligonucleotides, are used to interrogate a target mixture of cDNA. Following hybridization, the two adjacent probes are ligated to enhance the specificity of the identification, and to enable the use of a biotin-affinity column for removal of confounding peptoid tags. The resulting mixture is exposed to longwave ultraviolet light to release the peptoid tags, that are quantified using MALDI-TOF mass spectrometry using the isotopically labeled peptoids as internal standards. These individual components of MAGE are demonstrated.
\r\n\r\nA strategy for simplification and visualizing of high-dimensional gene expression data, as well as a strategy for inferring the presence of clusters within those data, is formulated and implemented. In order to visualize high-dimensional gene expression data, principle components analysis is used with subsequent mapping of the data onto an orthogonal set of basis functions known as Andrews curves. This analysis method is demonstrated by visualizing of breast cancer tumor data and yeast sporulation data. In order to cluster gene expression data, the expectation-maximization algorithm is employed to optimize the parameters of a mixture model of Lorentzian distributions. The difference between Lorentzian and Gaussian mixture models is first demonstrated with artificial data, and then applied to yeast sporulation data. The results indicate that mixtures of Lorentzian distributions may have significant utility for gene expression analysis.
\r\n\r\nThe tools demonstrated here offer unique advantages when compared to the current suite of experimental and analytical tools employed by investigators of functional genomics.
\r\n" }, { "name": "Nielsen, Robert J.", "degree": "PhD", "year": "2005", "title": "Computational Strategy in Catalyst Design", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-06052005-221223", "creators": [ { "name": { "family": "Nielsen", "given": "Robert J." }, "id": "Nielsen-Robert-J", "orcid": "0000-0002-7962-0186", "display_name": "Nielsen, Robert J." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/60VH-AQ40", "abstract": "The strategy and efficacy of applying computational tools to the development of new catalytic cycles is discussed using the enantioselective palladium-catalyzed aerobic oxidation of secondary alcohols as a model case. The key interactions responsible for the unique reactivity of ((\u2013)-sparteine)PdX2 complexes (X = chloride, acetate) in kinetic resolutions of secondary alcohols are elucidated using density functional theory with the Poisson-Boltzmann polarizable continuum solvent model. Enantioselectivities in these reactions are found to follow directly from calculated energies of diastereomeric beta-hydride elimination transition states incorporating (R) and (S) substrates. This relationship reveals an important role of the anion, namely to communicate the steric interaction of the ligand on one side of the PdII square plane and the substrate on the other side. When no anion is included, no enantioselectivity is predicted. Locating these transition states in different solvents shows that higher dielectrics stabilize the charge separation between the anion and metal and draw the anion farther into solution. Thus the solvent influences the barrier height (rate) and selectivity of the oxidation.
\r\n\r\nBased on this understanding, computational assays for selectivity, reaction rate and stability are developed and used to screen possible mimics of the natural product (\u2013)-sparteine which could be synthesized in both antipodes. Derivatives of the bispidine and bispidinone structures are predicted to have high selectivity but poor stability on palladium. Experimental results verify that catalytically active (bispidine)PdX2 complexes do not form.
\r\n\r\nMechanisms by which palladium diacetate complexes of N-heterocyclic carbenes may oxidize alcohols (a reaction known to occur with no enantioselectivity) are examined computationally. The strong trans effect of the carbene distinguishes the behavior of these complexes from other palladium catalysts. No traditional beta-hydride elimination is predicted to be capable of generating the high deuterium kinetic isotope effect measured using this catalyst. Instead, the low-energy pathway consistent with previous experimental observations (KIE, activation parameters, kinetics) is a \"reductive\" beta-hydride elimination, in which the beta-hydrogen of the alcohol is transferred directly to a bound acetate ligand. Assuming that relative energies of transition states of this type will determine enantioselectivity, new, chiral carbene ligands are hypothesized and screened. Careful placement of stereocenters and steric bulk has led to ligands with high predicted enantioselectivity and stability.
\r\n\r\nRecurring factors in the induction of selectivity by asymmetric ligands are observed. Strengths and weaknesses of quantum chemistry as applied to catalytic cycles are discussed, along with the synergy of theory and experiment. Common pitfalls and areas in need of improvement are highlighted.
" }, { "name": "Northrup, Alan Bowers", "degree": "PhD", "year": "2005", "title": "Design and Development of New Enantioselective Organocatalytic Transformations, a Two-Step Synthesis of Carbohydrates, and Progress toward the Total Synthesis of Callipeltoside C", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09242004-095741", "creators": [ { "name": { "family": "Northrup", "given": "Alan Bowers" }, "id": "Northrup-Alan-Bowers", "display_name": "Northrup, Alan Bowers" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/g84s-an43", "abstract": "The LUMO-lowering activation of a,b-unsaturated ketones has been accomplished through the development of a new imidazolidinone organocatalyst. That new imidazolidinone catalyst provided the first enantioselective catalytic Diels-Alder reaction with simple ketone dienophiles. Significantly, that catalyst is able to activate both cyclic and acyclic a, b-unsaturated ketones in this cycloaddition process.
\r\n\r\nA new strategy for the synthesis of two privileged structural motifs, the polyketide and polyglycolate architectures, has been developed based on the direct aldehyde aldol reaction. Two different catalysts are presented that are capable of performing the enantioselective direct aldol cross coupling of two distinct aldehyde components. Imidazolidinones have been shown for the first time to initiate the HOMO-raising activation of both saturated and a, b-unsaturated aldehyde substrates. Using an imidazolidinone catalyst, the first direct enantioselective catalytic aldol coupling of two aldehydes is described and provides synthetically valuable b-hydroxy dimethylacetals. Later, proline was found to be an exceptionally effective catalyst for the direct aldehyde aldol reaction. In contrast to imidazolidinone catalysts, proline affords b-hydroxyaldehyde products that are primed for use directly in subsequent aldol reactions.
\r\n\r\nUtilizing those direct aldehyde aldol methodologies, a two-step synthesis of 2,4,6-O-protected carbohydrates has been developed. Importantly, this modular strategy is capable of producing highly enantioenriched differentially protected forms of glucose, mannose, allose, mannosamine, as well as unnatural hexose derivatives. Furthermore, this method for sugar synthesis has been applied to the construction of differentially protected 13C6-labeled glucose, mannose, and allose in just four steps from labeled ethylene glycol.
\r\n\r\nThe enantioselective catalytic direct aldehyde aldol reaction was further applied toward the total synthesis of the marine natural product callipeltoside C. Several key fragments have been successfully synthesized and coupled to form macrolactone precursors. Nozaki-Hiyama-Kishi ring closure across the C-9/C-10 bond, however, affords exclusively the undesired C-9 epimer. Therefore, completion of the total synthesis will require a revised order for fragment assembly.
\r\n" }, { "name": "Owen, Jonathan Scharle", "degree": "PhD", "year": "2005", "title": "A Study of Ligand Substitution and its Importance in the C-H Activation of Methane and Methanol", "advisor": "Bercaw, John E.; Labinger, Jay A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022005-124848", "creators": [ { "name": { "family": "Owen", "given": "Jonathan Scharle" }, "id": "Owen-Jonathan-Scharle", "orcid": "0000-0001-5502-3267", "display_name": "Owen, Jonathan Scharle" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "co-advisor", "display_name": "Labinger, Jay A." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1SHC-4G39", "abstract": "Pyridinium and indolium-derived aminocarbene complexes of platinum and palladium were prepared by oxidative addition of pyridinium and 2-chloro-indolium carbene precursors. These complexes were synthesized in order to study the degree to which aminocarbene ligands pi-bond with the transition-metals to which they are bound. X-Ray crystal structures show minimal multiple bonding in the indole examples and a measurable shortening of the pyridine-2-ylidene Pt\u2013C distance (1.959(3) A) compared with typical Pt\u2013C bonds (2.01(1) A). The kinetics of associative DMSO substitution trans to the pyridine-2-ylidene ligand indicate a stabilization of the trigonal bipyramidal transition structure that is due to pi-acidity of the carbene carbon. This pi-acidity is responsible for 4-orders of magnitude acceleration in the associative substitution rate compared with a structurally similar phenyl donor.
\r\n\r\nThe relative rates of methane, methanol and dimethylether C\u2013H activation by [(N-N)PtMe(TFE-d3)]+ ((N-N) = ArN=C(Me)-C(Me)=NAr Ar = 3,5-di-tert-butylphenyl, TFE-d3 = CF3CD2OD) were studied by 1H and 13C NMR spectroscopy. Methane activation kinetics were conducted at 300-1000 psi of methane pressure in single crystal sapphire NMR tubes (k = 1.6 \u00b1 0.4 x 10-3 M-1s-1, 330 K; k = 2.7 \u00b1 0.2 x 10-4 M-1s-1, 313 K). Deuterium scrambling studies indicate that displacement of TFE-d3 from the platinum center by methane's C\u2013H bond is slower than the subsequent C\u2013H oxidative cleavage and hence the rate-determining step in methane C\u2013H activation. The kinetics of methanol and dimethylether C\u2013H activation were studied with 1H NMR spectroscopy and shown to be inhibited by a preequilibrium binding of the substrates oxygen lone-pair to the metal center. A small kinetic isotope effect (kH/kD = 1.4 \u00b1 0.1) and the observed concentration dependence suggest that the reaction proceeds by rate determining displacement of the coordinated trifluoroethanol by the C-H bonds of methanol (k = 2.0 \u00b1 0.2 x 10-3 M-1s-1, Keq = 0.0042 \u00b1 0.0006, 330 K). A similar concentration dependence is observed in the activation of dimethylether (k = 5.5 \u00b1 0.5 x 10-4 M-1s-1, Keq = 0.020 \u00b1 0.002, 313 K). Comparison of these second order rate constants (k(Methane)/k(Methanol) = 1/1.3, 330 K; k(Methane)/k(Dimethylether) = 1/2, 313 K) shows that the selectivity of this ligand substitution step matches the selectivity previously reported by our group for oxidizing methyl and hydroxymethyl groups with aqueous tetrachloroplatinate (1/1.5). These data strongly suggest a similar rate-determining step under the Shilov conditions.
" }, { "name": "Petersson, Ernest James", "degree": "PhD", "year": "2005", "title": "Investigations of Ion Channel Structure and Function. I. Studies of Nicotine Binding to the Acetylcholine Receptor. II. Development of Tools for Studying Learning and Memory with Unnatural Amino Acids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-172213", "creators": [ { "name": { "family": "Petersson", "given": "Ernest James" }, "id": "Petersson-Ernest-James", "orcid": "0000-0003-3854-9210", "display_name": "Petersson, Ernest James" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/yhty-re87", "abstract": "This dissertation can be divided into two main sections:
\r\n\r\nI. In previous studies, we have used fluorinated tryptophan derivatives to conclusively identify a cation-pi interaction with Trp 149 in the binding of acetylcholine (ACh) to the muscle-type nicotinic acetylcholine receptor (nAChR). We have incorporated mimics of ACh, termed tethered agonists, in the binding site to produce self-activating channels. Using tertiary tethered agonists that would only become cations and activate the channel when protonated, we identified a perturbed pKa for the binding pocket, which has implications for the binding of tertiary agonists like nicotine (Nic). It has been shown that Nic does not participate in a straight-forward cation-pi interaction as ACh does. We have examined a hydrogen bond between the Nic pyrrolidine N-H and the backbone carbonyl of Trp149 by introducing an ester linkage at this point, weakening the carbonyl H-bond accepting ability. Calculations performed on hydrogen bound complexes of ACh, Nic, and the Nic analog epibatidine (Epi) explain the trends observed for ligand activation of the nAChR. Expanding upon this study, we have performed molecular dynamics (MD) simulations of models of the ligand binding domain of the nAChR. Ligand-bound structures from these simulations have been taken on to quantum mechanical/molecular mechanical (QMMM) calculations to model the effects of unnatural amino acid mutations in an environment that simulates the full nAChR binding pocket.
\r\n\r\nII. The nAChR is essential to neurotransmission at the junction between nerve and muscle cells, and it plays an important role in many central nervous system processes. However, its role in learning and memory is limited, at least in our current molecular models of these events. In a sense, the formation of a memory consists of the strengthening of some synaptic connections and the weakening of others. These processes, termed long term potentiation (LTP) and depression (LTD) respectively, are primarily governed by modifications to glutamate receptors (GluRs). We have developed tools for studying the mechanism and timecourse of these modifications (of phosphorylation in particular), and we have demonstrated the first incorporation of unnatural amino acids into a GluR.
" }, { "name": "Popielarski, Stephen R.", "degree": "PhD", "year": "2005", "title": "I. Structural Effects of Carbohydrate-Containing Polycations on Gene Delivery. II. Development of a Nanoparticle-Based Model Delivery System to Guide the Rational Design of Gene Delivery to the Liver\r ", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03302005-120327", "creators": [ { "name": { "family": "Popielarski", "given": "Stephen R." }, "id": "Popielarski-Stephen-R", "display_name": "Popielarski, Stephen R." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/rskv-rf12", "abstract": "Linear cationic beta-cyclodextrin (b-CD)-based polymers can bind with plasmid DNA to form colloid-sized composite particles that transfect cultured cells. In the first part of this thesis, synthetic variations of the b-CD structure are used to probe structure-function gene delivery properties. The type of cyclodextrin and its functionalization are investigated by synthesizing numerous 3A,3B-dideoxy-3A,3B-diamino-b- and g-CD monomers, which are polymerized with dimethyl suberimidate to yield amidine-based polycations. The nature of the spacer between the CD-ring and the primary amines of each monomer is found to influence both molecular weight and polydispersity of the polycations. When complexed with plasmid DNA, polycations with longer alkyl regions between the CD and the charge centers show increased transfection efficiency and toxicity in BHK-21 cells. More hydrophilic spacers resulted in lower toxicity, and g-CD-based polycations were less toxic than otherwise identical b-CD-based polycations.
\r\n\r\nIn the second part of this thesis, a model delivery system is developed that can mimic the size and surface properties of the cyclodextrin-based gene-delivery particles, and this system is used to define design constraints that should be applied to next generation gene delivery particles targeted to the liver. Gal-50 and Gal-140 are galactosylated 50 nm and 140 nm nanoparticles that have the same surface galactose density, while MeO-50 and MeO-140 are methoxy-terminated 50 nm and 140 nm nanoparticles. All four particles have the same surface charge and resist aggregation in serum.
\r\n\r\nIn freshly isolated hepatocytes, Gal-50 nanoparticles are taken up to a greater extent than are MeO-50, but both 50 nm beads are taken up to a much greater extent than are either of the 140 nm nanoparticles. TEM and immunohistochemistry confirm that Gal-140 nanoparticles are primarily internalized by Kupffer cells, though isolated examples of a few Gal-140 in hepatocytes can also be found. On the other hand, Gal-50 nanoparticles are overwhelmingly found in vesicles throughout the cytoplasm of hepatocytes, with only isolated examples of Kupffer cell uptake. As such, it is clear that slightly anionic, galactose-PEGylated nanoparticles should be about 50 nm in diameter to preferentially target hepatocytes while they should be about 140 nm in diameter to selectively target Kupffer cells.
" }, { "name": "Poulin-Kerstien, Adam Thomas", "degree": "PhD", "year": "2005", "title": "DNA-Templated Dimerizations of Minor Groove-Binding Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252005-100011", "creators": [ { "name": { "family": "Poulin-Kerstien", "given": "Adam Thomas" }, "id": "Poulin-Kerstien-Adam-Thomas", "display_name": "Poulin-Kerstien, Adam Thomas" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/em7t-g660", "abstract": "Polyamides have emerged as a class of small molecules capable of binding the minor groove of DNA with high affinity and sequence specificity that have potential applications in molecular biology and human medicine. In efforts towards the use of polyamides in living cells, we report research directed towards DNA-templated formations of polyamide dimers. We find that formation of polyamide dimers, linked both turn-to-turn and turn-to-tail, can be templated via a 1,3-dipolar cycloaddition using a targeted sequence of DNA. The dimer products formed in situ may prove to have interesting biological effects.
\r\n\r\nAlso reported in this thesis are several uses of polyamides as molecular tools. We find that polyamide-biotin conjugates are able to selectively bind and capture targeted pieces of DNA via streptavidin-coated magnetic beads, effectively enriching mixtures of DNA fragments in the fragment of interest. Such molecules may find utility in the identification of DNA-protein complexes. In a second utility we report the use of polyamide-maleimide and chlorambucil conjugates to impart sequence specificity on nonspecific DNA enzymes for crystallographic studies.
" }, { "name": "Qi, Xin", "degree": "PhD", "year": "2005", "title": "Unnatural Amino Acid Incorporation to Rewrite the Genetic Code and RNA-Peptide Interactions", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-133323", "creators": [ { "name": { "family": "Qi", "given": "Xin" }, "id": "Qi-Xin", "display_name": "Qi, Xin" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YNYY-KE32", "abstract": "My general research direction is the interface between organic chemistry and biology. Interesting biological systems inspire target-oriented organic synthesis, new methodology development, and molecular design of novel materials. On the other hand, chemical synthesis prepares important biologically active compounds to be used in understanding involved mechanism and engineering biological systems.
\r\n\r\nWe designed and synthesized a series of peptide-acridine conjugates based on the modular design principle to target RNA structures. Some of the peptide-acridine conjugates have substantially improved RNA-binding affinity and specificity relative to the peptide alone. We also generated various high-affinity inhibitors of the tRNA synthetases\u2014aminoacyl sulfamide to create synthetic blanks in our translation extracts. The gaps were filled with chemically aminoacylated orthogonal tRNAs. This unnatural strategy enables peptides and proteins to be constructed containing a single novel residue at specific locations and will facilitate the mRNA display-based protein selection. To test the versatility of ribosome, we have constructed a series of puromycin analogs with natural and unnatural amino acids side chains and tested the effects of side chain characteristics of amino acid moiety on the activity of puromycin analogs. We found that amino acids of different stereo characteristics can be incorporated via puromycin route, and larger hydrophobic amino acids render higher potency.
\r\n\r\nOverall, these efforts demonstrate the successful use of a combination of molecular design as an efficient and facile method for generating new solutions to biological problems.
" }, { "name": "Rutenberg, Isaac Michael", "degree": "PhD", "year": "2005", "title": "Functionalized Polymers and Surfaces via Ring-Opening Metathesis Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08132004-132724", "creators": [ { "name": { "family": "Rutenberg", "given": "Isaac Michael" }, "id": "Rutenberg-Isaac-Michael", "orcid": "0000-0003-0969-4523", "display_name": "Rutenberg, Isaac Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5Z6Y-G191", "abstract": "The research presented in this thesis focuses on the preparation of functionalized polymers using olefin metathesis polymerization methods. A portion of this research is also devoted to the development of applications for metathesis-derived polymers.
\r\n\r\nThree distinct types of olefin metathesis polymerizations can be recognized within this work. Ring-opening metathesis polymerization (ROMP) is the most prevalent type, followed by acyclic diene metathesis (ADMET) polymerization and a hybrid of the ROMP and ADMET mechanisms known as ring-opening-insertion metathesis polymerization (ROIMP).
\r\n\r\nMany of the concepts that appear throughout this thesis are introduced in Chapter 1. Olefin metathesis occupies a central role in each of the subsequent chapters; detailed descriptions of the mechanism and important olefin metathesis catalysts are provided. The chapter also includes background information regarding polymers, polymer properties and the application of ROMP in the construction of electronic devices.
\r\n\r\nAlthough the utility of ADMET does not yet seem to match that of ROMP, valuable information can be obtained from ADMET polymerizations. In an effort to elucidate catalytic activity, Chapter 2 details a comparison of the ADMET polymerizations of terminal and non-terminal dienes.
\r\n\r\nExperimental investigations involving ROIMP, a novel method for the production of A,B-alternating copolymers, is presented in Appendix A. The mechanism of ROIMP is conceptually very different from the mechanisms of either step growth or chain growth polymerizations. Efforts toward understanding the mechanism of ROIMP using a mathematical model are discussed in Chapter 3.
\r\n\r\nPolymeric chain transfer agents (PCTAs) suitable for ROMP reactions are polymers that contain a single, metathesis-active olefin. These polymers are the focus of Chapter 4 and can be used in the preparation of novel block copolymers. As an example, Appendix B presents the preparation of block copolymers consisting of polyacetylene and various commodity polymers.
\r\n\r\nFinally, the development of applications for surface-initiated ROMP (SI-ROMP) is discussed in Chapter 5 and Appendix C. Polymer films prepared using SI-ROMP are shown to be viable dielectric layers in thin-film transistors, and research is presented involving microcontact printing and dip pen nanolithography as methods for forming patterned SI-ROMP polymer films.
\r\n" }, { "name": "Sanders, Daniel Paul", "degree": "PhD", "year": "2005", "title": "Development of Fluorinated Monomers and Polymers for Advanced Photolithographic Applications", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12092004-165229", "creators": [ { "name": { "family": "Sanders", "given": "Daniel Paul" }, "id": "Sanders-Daniel-Paul", "orcid": "0000-0001-5736-2801", "display_name": "Sanders, Daniel Paul" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/g8b9-hh25", "abstract": "The incorporation of fluorine into photoresist materials imparts a variety of highly desirable properties for deep ultraviolet lithography at 193 nm and 157 nm. Chief amongst these benefits are the high optical transparency of partially fluorinated materials and the high acidity of fluorocarbinols. Yet, significant challenges remain to incorporate the large amount of fluorine necessary for high transparency into functionalized norbornene monomers without adversely affecting transition metal polymerization processes.
\r\n\r\nChapters 2 details the synthesis and characterization of a series of partially fluorinated tricyclo[4.2.1.0(2,5)]non-7-ene (TCN) monomers. The fused cyclobutane ring serves as an additional scaffold onto which additional fluorinated groups can be incorporated in order to increase transparency at 157 nm without adversely affecting the polymerization behavior of the monomer. The synthesis and imaging of TCN-based photoresist polymers is detailed in Chapter 3.
\r\n\r\nChapters 4 and 5 introduce a series of 3-oxa-tricyclonon-7-ene and 4-oxa-tricyclonon-8-ene monomers synthesized from quadricyclane and fluorinated ketones. In Chapter 5, addition and ring-opening metathesis polymers of fluorinated oxatricyclononenes are shown to offer transparencies similar to a hexafluorocarbinol-functionalized norbornene addition polymer, revealing the effect of the alicyclic backbone structure on transparency at 157 nm. 4-Oxatricyclononenes are valuable comonomers for the elevation of glass transition temperatures in ROMP polymers, while low molecular weight ROMP copolymers of 3-oxatricyclonene are being evaluated as crosslinking agents in negative tone resist formulations.
\r\n\r\nChapter 6 details the use of cross-metathesis and ring-opening cross-metathesis in the synthesis of multifunctional monomers and oligomers for 193 nm immersion and 157 nm lithography. Cross-metathesis with unsaturated hexafluorocarbinols is a facile method to generate functionalized olefins without using the hexafluoroacetone. These developments culminate in the synthesis of difunctional norbornenes containing both ester and hexafluorocarbinol functionalities which display dramatically increased transparency at 157 nm and will potentially afford unique dissolution behavior.
\r\n\r\nFinally, chapter 7 explores the synthesis of trisubstituted olefins via ruthenium-catalyzed cross-metathesis. 2-Methyl-2-butene is a convenient isobutylene surrogate in the formation of prenyl groups via cross-metathesis. Understanding of the reactivity of second-generation metathesis catalysts with 1,1-disubstituted and trisubstituted olefins has prompted the exploration of ring-opening cross-metathesis of low strain cyclic olefins and three component cross-metathesis reactions with high product selectivity.
" }, { "name": "Sarisky, Catherine Ann", "degree": "PhD", "year": "2005", "title": "Exploration of the Determinants of Protein Structure and Stability by Protein Design", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272005-121337", "creators": [ { "name": { "family": "Sarisky", "given": "Catherine Ann" }, "id": "Sarisky-Catherine-Ann", "orcid": "0000-0002-7692-2517", "display_name": "Sarisky, Catherine Ann" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "chair", "display_name": "Roberts, Richard W." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RBSA-R089", "abstract": "Optimization of Rotamers by Iterative Techniques (ORBIT) has been used to calculate novel sequences for several small proteins. A partial sequence design (20 of 28 residues) is described for the zinc finger Zif268 (beta-beta-alpha) motif. The designed peptide folds without a metal cofactor, despite its small size and the avoidance of the disulfides and unnatural amino acids that are often used to stabilize peptide structures. The utility of ORBIT for predicting the relative stabilities of a series of beta-beta-alpha peptides was investigated. A good correlation between theoretical and experimental stabilities was observed except when the turn residues were changed. This observation led to the discovery that some of these peptides had an unexpected turn conformation. This information was used to design a peptide that is more stable than the original peptide sequence produced with ORBIT.
\r\n\r\nThe tolerance of ORBIT for altered backbone coordinates was investigated using the protein domain G-beta1. It was determined that altering the coordinates of the backbone template used in ORBIT altered the sequences selected, but that the fold did not change as a result. The G-beta1 domain was also used to parameterize a methionine inclusion penalty, allowing the inclusion of methionine in ORBIT design calculations while preventing indiscriminate inclusion of methionine at sites where a less flexible side-chain will fit.
\r\n\r\nLastly, some preliminary work on using ORBIT to design DNA binding interfaces is discussed.
" }, { "name": "Sharma, Shantanu", "degree": "PhD", "year": "2005", "title": "Prediction of Structure and Antagonist Binding Site in Human and Rodent Chemokine Receptor 1", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-143543", "creators": [ { "name": { "family": "Sharma", "given": "Shantanu" }, "id": "Sharma-Shantanu", "display_name": "Sharma, Shantanu" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/j4zd-ny21", "abstract": "Chemoattractant cytokines (chemokines) are small proteins that are known to play a key role in the development of numerous autoimmune and inflammatory diseases. The signal transduction cascade responsible for this pathology is initiated by chemokine binding to a G-protein coupled receptor (GPCR). Since therapeutic intervention would involve inhibition of ligand binding, it follows that detailed understanding of the structures and binding sites of these receptors would lead to the rational design of such drugs. However, GPCRs are a class of integral membrane proteins whose structures are extremely difficult to determine via the conventional method of X-ray crystallography. Additionally, homology models based on the crystal structure of bovine rhodopsin (BR) have offered little structural insight into the remotely homologous chemokine receptors. In light of this information, our laboratory has developed a novel computational approach to predicting the structures and ligand binding sites of GPCRs with no information from the atomic coordinates of the crystal structure of BR.
\r\n\r\nIn this thesis we describe the use of the MembStruk procedure to predict the structure of human, mouse, and rat chemokine receptor 1 (CCR1). Interhelical interactions that stabilize the conformation of each receptor are discussed in detail, and where appropriate comparisons are made to information gleaned from the crystal structure of BR. The side chain placements of conserved residues are found to be different across the human and rodent species, accounting for binding differentials not previously explained by homology models. To improve the binding of a low affinity small molecule antagonist, point mutation candidates in human CCR1 are predicted.
\r\n\r\nValidation of the human CCR1 structure is achieved through prediction of the antagonist binding site, to which a series of known antagonists are docked and scored for comparison to experimental structure-activity data. The ligand binding energies are in excellent agreement with the experimentally known trend in binding affinities, and results from a virtual ligand screening calculation (Dr. Sabine Schlyer, Berlex/Schering AG) also support the validity of the structural model. This work in this thesis provides the basis for the design of receptor-specific antagonists to human and rodent CCR1, thus accelerating the drug discovery process.
" }, { "name": "Shen, Wei", "degree": "PhD", "year": "2005", "title": "Structure, Dynamics, and Properties of Artificial Protein Hydrogels Assembled Through Coiled-Coil Domains", "advisor": "Tirrell, David A.; Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05132005-114413", "creators": [ { "name": { "family": "Shen", "given": "Wei" }, "id": "Shen-Wei", "display_name": "Shen, Wei" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "co-chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NXST-MZ65", "abstract": "The structure-property relationships of an artificial protein hydrogel, which was constructed from a triblock protein (designated AC10A) that contained two associative leucine-zipper endblocks and a water-soluble random coil midblock, were investigated to provide guidelines for the rational design of new generations of artificial protein hydrogels. The leucine zipper A domain is composed of six heptad repeating units designated as abcdefg, where the a and d positions are occupied by hydrophobic residues, and the e and g positions are mainly occupied by glutamic acid residues. In contrast to hydrogels formed from synthetic hydrophobically modified polymers, the normalized plateau storage modulus G/nkT of the AC10A gel was below 13% at all concentrations examined. This indirect evidence that AC10A tends to form a substantial fraction of looped configurations was supported by a fluorescence quenching experiment: significant quenching occurred in labeled d-AC10A-a (d=tryptophan at the N-terminus, a=coumarin at the C terminus) chains mixed with a great excess of unlabelled AC10A chains in a solution. The strong tendency to form loops originates in large part from the compact size of the random coil midblock domain (mean RH, C10~20 A, determined from quasi-elastic light scattering of C10). Despite the small aggregation number of the leucine zipper domains (tetrameric aggregates, determined from multi-angle static light scattering of AC10 diblock), the average center-to-center distance between aggregates in a 7% w/v AC10A solution is roughly 3 times the radius of gyration and 1.5 times the average end-to-end distance of the C10 domain. To avoid the energy penalty for stretching the C10 domain to form bridges, the chains tend to form loops. The importance of loops explains the nonmonotonic effect of pH on modulus and the decrease in modulus with increasing ionic strength. It also led to the design concept of increasing the midblock length or charge density to increase storage modulus.
\r\n \r\nDynamic properties of the AC10A hydrogel show correlation between network relaxation behavior and molecular exchange kinetics of the associative domain. The longest stress relaxation time changes from ca. 70 seconds at pH 8.0 to ca. 1000 seconds at pH 7.0, determined by creep measurements on 7% w/v gels. In a parallel manner, the characteristic time of the leucine zipper strand exchange varies from ca. 200 seconds at pH 8.0 to ca. 4500 seconds at pH 7.0, determined by fluorescence de-quenching after mixing a fluorescein-labeled leucine zipper solution (in which fluorescence was quenched) with a great excess of an unlabeled leucine zipper solution. Both time scales vary strongly with pH due to the associated change in charge on the e and g residues of the leucine zipper.
\r\n\r\nThe observed structure-property relationships suggest that the rapid dissolution that occurs with AC10A hydrogels in open systems originates from the tendency of the protein to form loops, the small aggregation number of the associative domains, and the transient nature of association. For applications in which materials are surrounded by excess fluids, we demonstrated two molecular design approaches to avoid the rapid dissolution. One way to slow dissolution is to suppress loops by engineering a triblock protein with dissimilar associative endblocks, PC10A, such that P associates only with P and A associates only with A. A PC10A gel erodes 500 times more slowly and exhibits a 5-fold increase in modulus compared to an AC10A gel at the same concentration. Alternatively, hydrogel stability in open systems can be improved by engineering a cysteine residue into each leucine zipper domain to allow covalent bond formation following physical association of leucine zippers. Asymmetric placement of the cysteine residue in each leucine zipper domain suppresses locking-in loops and creates linked \"multichains\". The increased valency of the building units stabilizes the hydrogels in open systems, while the physical nature of their association retains the reversibility of gelation. The gel networks dissolve at pH 12.2, where the helicity of the leucine zipper domains is reduced by ca. 90%, and re-form upon acidification.
\r\n\r\nThe ability to form robust artificial protein hydrogels in open systems opens the way to biomedical applications. Therefore, we examined their toxicity and incorporated an RGD cell-binding domain into the midblock backbone. Viability assays for mammalian 3T3 fibroblast cells cultured in the presence of the AC10A protein revealed no evidence of toxicity. Anchorage-dependent epithelial cells spread well on hydrogel films bearing an RGD cell-binding domain. In contrast, cells remained round on films without the cell-binding domain; significant apoptosis was induced. Encapsulated 3T3 fibroblast cells remained viable inside the hydrogel for at least 12 hours, suggesting that these materials have proper permeability for transferring oxygen, nutrients, and metabolic waste. The hydrogel containing the RGD domain was micropatterned on a PEG-modified glass surface and limited cell adhesion to the hydrogel region.
\r\n" }, { "name": "Sisk, Brian Christopher", "degree": "PhD", "year": "2005", "title": "Computational Optimization of Chemical Vapor Detector Arrays", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-02152005-125249", "creators": [ { "name": { "family": "Sisk", "given": "Brian Christopher" }, "id": "Sisk-Brian-Christopher", "orcid": "0000-0003-3156-9673", "display_name": "Sisk, Brian Christopher" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z3K5-C749", "abstract": "Arrays of broadly responsive, chemically sensitive detectors have been used for many years as a means of detecting a wide array of vapors. These systems have been used in fields ranging from analysis of wines and coffees to land mine and nerve agent detection to disease diagnosis. Despite their successes, these systems have been plagued by problems, namely a lack of sensor diversity, miniscule libraries of previously-recognized analytes, significant sensor drift, and weak signal processing capabilities compared to the mammalian olfactory system.
\r\n\r\nThis work details progress toward the alleviation of those problems with regard to arrays of polymer/carbon-black composite chemiresistor detectors developed at Caltech. Specifically, it has been determined that larger sensor arrays allow the suitable recognition of more analytes, and a greater chance of successful discrimination between a given analyte others to which it is similar. Additionally, new classes of percolative, low carbon-black sensors have been developed that yield far higher sensitivities and stronger responses than traditional sensors, as well as responses that are exponential with concentration. Such sensors allow for recognition of analytes using lower precision electronics than was previously realizable. A method for calibrating the system with few analyte exposures has also been developed from an analysis of the correlations between sensor/analyte response changes with time over groups of analytes and sensors.
\r\n\r\nFurther work has allowed algorithmic optimizations to assign functional group identities and certain physiochemical information such as molar volume and octanol/water partition coefficients to analytes that are completely unknown to the system, using a model built upon other known analytes. Additionally, a comparison of linear and nonlinear classifiers is performed to identify data characteristics that might be more suited to linear classifiers such as Fisher's Linear Discriminant or nonlinear ones such as Artificial Neural Networks.
\r\n\r\nThese improvements to chemical vapor detector arrays and the processing of their data allow the extraction of more useful information and the minimization of time spent training and calibrating the system. By constructing more appropriate sensor arrays, establishing non-comprehensive but extensive analyte response libraries, choosing useful algorithmic classifiers, and performing timely and mimimal calibration, the utility of detector systems can be maximized while minimizing maintenance.
" }, { "name": "Spakowitz, Andrew James", "degree": "PhD", "year": "2005", "title": "Semiflexible Polymers: Fundamental Theory and Applications in DNA Packaging", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechETD:etd-11162004-120143", "creators": [ { "name": { "family": "Spakowitz", "given": "Andrew James" }, "id": "Spakowitz-Andrew-James", "orcid": "0000-0002-0585-1942", "display_name": "Spakowitz, Andrew James" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "chair", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Phillips", "given": "Robert B." }, "id": "Phillips-R", "orcid": "0000-0003-3082-2809", "role": "member", "display_name": "Phillips, Robert B." } ], "option_major": [ "chemeng" ], "doi": "10.7907/GGY2-SZ67", "abstract": "Much is understood about the behavior of perfectly flexible and perfectly rigid polymer chains; however, many polymers, for example DNA, are somewhere in between these two limiting cases. Such polymers are termed semiflexible, and their molecular elasticity can play a significant role in single-chain behavior as well as contribute to collective effects. Using analytical theory and numerical methods, we address several problems that focus on the equilibrium and dynamic behavior of semiflexible polymers to gain a deeper understanding of their fundamental physics. We consider the equilibrium statistical behavior of semiflexible polymers under the influence of external fields, confinement, and the collective influence of a nematic liquid-crystal phase. We then turn to the dynamics of a deformed elastic thread, addressing instances of instability and the subsequent nonlinear relaxation. Once we establish an understanding of these physical effects, we discuss the role that they play in DNA packaging, specifically focusing on the role of twist in DNA packaging in chromatin and the formation of an ordered conformation within a viral capsid." }, { "name": "Srinivasan, Ramesh", "degree": "PhD", "year": "2005", "title": "Structural Dynamics of Complex Molecules by Ultrafast Electron Diffraction : Concepts, Methodology and Applications", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122005-083103", "creators": [ { "name": { "family": "Srinivasan", "given": "Ramesh" }, "id": "Srinivasan-Ramesh", "display_name": "Srinivasan, Ramesh" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DTG2-5932", "abstract": "The central theme in ultrafast electron diffraction (UED) is the elucidation of the structural dynamics of transient molecular entities. With properly timed sequences of ultrafast electron pulses, it is now possible to image complex molecular structures in the four dimensions of space and time with resolutions approaching 0.01 [angstroms] and 1 ps, respectively. Reaching this spatiotemporal resolution on the atomic scale has been the driving force behind the development and application of the third generation UED instrument\u2013-the subject of this dissertation. The current state-of-the-art in resolutions and sensitivity, together with theoretical advances, has made possible the direct determination of transient structures, leading to studies of diverse molecular phenomena hitherto not accessible to other techniques. By freezing structures on the ultrafast timescale, we are able to develop concepts that correlate structure with dynamics. Examples include structure-driven radiationless processes, dynamics-driven reaction stereochemistry, and non-equilibrium structures exhibiting negative temperature, bifurcation, or selective energy localization in bonds. These successes in the studies of complex molecular systems, even without heavy atoms, establish UED as a powerful method for mapping out temporally changing molecular structures in chemistry, and potentially, in biology." }, { "name": "Sumner, Heather Ann", "degree": "PhD", "year": "2005", "title": "Gas Phase Reaction Dynamics and Design of Molecular Clusters and Bioconjugates", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242005-144900", "creators": [ { "name": { "family": "Sumner", "given": "Heather Ann" }, "id": "Sumner-Heather-Ann", "display_name": "Sumner, Heather Ann" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/AVWS-B055", "abstract": "Chapter 1 serves as an introduction to the design of molecular clusters and bioconjugates that exhibit interesting reactivity in the gas phase. In Chapter 2, gas-phase reactions of clusters of alkylammonium ions with triphosphate, DNA, and peptides are examined. Alkylation of both phosphate and carboxylate groups is observed. In Chapter 3, the gas phase reactions of methyl phosphate noncovalently bound clusters are studied in detail. The presence of sodium ions in methyl phosphate clusters stabilizes the clusters, facilitating intermolecular condensation reactions between methyl phosphates.
\r\n\r\nIn Chapter 4, the first gas-phase phosphorylation of molecules containing hydroxyl substituents is reported. Gas-phase reactions of triphosphate with hydroxyl-containing molecules result in phosphorylation of the hydroxyl substituent. In the absence of a hydroxyl substituent, the C-terminus of a peptide can be phosphorylated. Otherwise, hydroxyl residues are selectively phosphorylated.
\r\n\r\nChapter 5 considers the possibility of free radical initiated peptide sequencing, or FRIPS, in the gas phase. A free radical initiator is conjugated to the N-terminus of peptides or proteins, forming a bioconjugate. Collision-induced dissociation of the conjugated species results in free radical formation. The free radical then fragments on further collisional activation to yield backbone fragmentation products. This technique may allow selective cleavage of peptides at specific amino acid residues, with applications to gas-phase proteomics sequencing efforts.
\r\n\r\nChapters 6 deals with experiments conducted on solvated ions, specifically focusing on the evaporation kinetics and the relative intensities of differently solvated species. Water cluster distributions are used to discriminate between isomers and enantiomers. Chapter 6 also includes data on the reaction of t-butyl chloride in water clusters, as well as data on doubly charged cationic species showing pairwise evaporation of water.
\r\n\r\nChapter 7 uses H/D exchange experiments to examine the behavior of sodiated glycine oligomers, ranging from Gly1 to Gly5. It is found that H/D exchange dynamics do not directly reflect the structure of sodiated glycine oligomers, as the solvation energy provided by the exchange reagent can allow the ion-molecule complex to access high-energy states. Therefore, interpretations of H/D exchange results should be conducted with detailed examinations of possible exchange mechanisms.
" }, { "name": "Takahashi, Terry Torao", "degree": "PhD", "year": "2005", "title": "In Vitro Selection of RNA Binding Peptides", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-163739", "creators": [ { "name": { "family": "Takahashi", "given": "Terry Torao" }, "id": "Takahashi-Terry-Torao", "display_name": "Takahashi, Terry Torao" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "biochem" ], "doi": "10.7907/9X0X-PG47", "abstract": "RNA is recognized to play an increasing number of roles in the cell: transcription regulation, translation, and catalysis. Peptides that bind RNA would therefore be useful as biochemical tools and lead compounds for therapeutics. Existing genetic methods of isolating RNA binding peptides are prone to biases and can only search millions of sequences. In vitro selections using mRNA display provide an avenue to discover specific, high affinity peptides that bind to any RNA target from libraries composed of trillions of molecules.
\r\n\r\nHere, we describe initial experiments to optimize the mRNA display selection cycle for the isolation of RNA binding peptides. We use this optimized cycle to show that enrichment of specific sequences is possible using mRNA display, and select mutants of the lambda N peptide which bind in a different conformation than wild-type. Characterization of these peptides demonstrates that affinity is not enough for in vivo activity; binding in a correct conformation is also important.
\r\n\r\nBased on these experiments, we designed a strategy to isolate RNA binding peptides to targets for which no natural ligand is known. We test this strategy and isolate peptides that bind to functionally important domains of telomerase RNA with nanomolar affinity and high specificity. Using mutagenic PCR and additional rounds of selection, we increase the specificity of several peptides for telomerase RNA and also isolate other peptides which bind an important domain of the Hepatitis C Virus internal ribosome entry site.
" }, { "name": "Udit, Andrew K.", "degree": "PhD", "year": "2005", "title": "P450 BM3 Electrochemistry and Electrocatalysis", "advisor": "Arnold, Frances Hamilton; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05112005-100825", "creators": [ { "name": { "family": "Udit", "given": "Andrew K." }, "id": "Udit-Andrew-K", "orcid": "0000-0002-4454-7687", "display_name": "Udit, Andrew K." } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wr4v-d345", "abstract": "Cytochromes P450 catalyze monooxygenations of relatively inert substrates. The significance of this activity in physiology and industry has inspired many to capture this activity in vitro. However, practical applications of P450s will continue to be hindered by the need for reducing equivalents from NAD(P)H. While electrochemical methods provide a potential solution, the difficulty in achieving good electronic coupling to the heme remains an enormous obstacle.
\r\n\r\nFlavocytochrome P450 BM3 is soluble, well-characterized, and easily manipulated, making it a good target for in vitro applications. Bioelectrocatalysis was first attempted with holo BM3 using a novel electrochemical mediator, 1,1\u2019-dicarboxycobaltocene (Mred). Absorption spectroscopy confirmed electron transfer (ET) from Mred to the cofactors, while electrolyses resulted in Mred-mediated hydroxylation of lauric acid by both the holo (16.5 nmol product / nmol enzyme / min) and heme proteins (hBM3) (1.8 nmol product / nmol enzyme / min).
\r\n\r\nSubsequent bioelectrocatalysis was attempted with the more stable hBM3. We achieved direct electrochemistry of hBM3 by wiring it through engineered surface Cys387 to a basal plane graphite electrode (BPG) with 1-pyreneiodoacetamide (Py). AFM images revealed that only pyrene-wired enzyme molecules adsorb to BPG. ko for the BPG-Py-hBM3 system was 650 \u00b1 50/s. Rotated-disk electrode (RDE) experiments show that the BPG-Py-hBM3 system catalyzes the four-electron reduction of dioxygen to water. Analogous experiments were performed with enzyme labeled at Cys62, which is spatially adjacent to Cys387 but does not provide a similar well-coupled through-bond pathway to the heme. Surprisingly, the Cys62 mutant showed similar electrode kinetics, demonstrating that the pyrene tether does not provide a unique pathway, but probably anchors the protein onto the electrode surface in a favorable docking mode for ET.
\r\n\r\nExtensive electrochemical characterization of hBM3 was conducted in various surfactant films on BPG. Cyclic voltammetry of hBM3 in SDS films revealed the Fe(III/II) redox couple at -330 mV (vs. Ag/AgCl, pH 7.4), and ko of 40/s. Although voltammetry confirmed catalytic dioxygen reduction by Fe(II), substrate oxidation was not observed.
\r\n\r\nVoltammetry of hBM3 mutant 1-12G in DDAPSS films revealed Fe(III/II) (-202 mV) and Fe(II/I) (-1082 mV) redox couples of the heme (pH 7). Catalytic activity included dioxygen reduction by Fe(II), and reductive dehalogenation by Fe(I). Voltammetry on hBM3 in DDAPSS revealed that hBM3 and 1-12G display distinct redox properties. Absorption spectra in solution showed the Fe(III) Soret at 418 nm for hBM3, and a split Soret for 1-12G at 390 and 418 nm. Voltammetry of the proteins within DDAPSS films revealed nearly identical Fe(III/II) potentials (~ -200 mV), but significant differences in ko, 250 vs. 30 per second, and Fe(III/II) \u2013 CO potentials, -140 mV vs. -115 mV, for hBM3 vs. 1-12G. Catalytic dioxygen reduction by the proteins on RDEs was analyzed using Levich and Koutecky-Levich treatments. Calculated values of n, 2.7 vs. 4.7, and kobs, 1400000 vs. 100000/M/s, for hBM3 vs. 1-12G suggest that the two proteins differ strikingly in their reaction with dioxygen.
\r\n\r\nUsing the prototypical cytochrome P450 CAM (CAM), we attempted to generate high-valent species of P450 in DDAB films. Performing rapid-scan (50 V/s) voltammetry revealed a couple (E) at 831 mV. E was not observed at scan rates less than 30 V/s at room temperature; however, at four degrees Celsius E could be reversibly generated at 1 V/s. E was found to be sensitive to imidazole in solution and to variations in pH, suggesting that the redox reaction is occurring at the metal center (i.e., Fe(IV/III)) rather than at the porphyrin macrocycle. Electrolyses revealed that the electrochemically generated high-valent species is only capable of performing S-oxidation, converting thioanisole to methyl phenyl sulfoxide.
" }, { "name": "Weaver, Jeremy John", "degree": "PhD", "year": "2005", "title": "Corroles", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04122005-152030", "creators": [ { "name": { "family": "Weaver", "given": "Jeremy John" }, "id": "Weaver-Jeremy-John", "display_name": "Weaver, Jeremy John" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8DS8-QS11", "abstract": "Corroles, porphyrin analogues, are the center of a rapidly growing field of research. By virtue of a missing meso-carbon, corroles retain the aromaticity of porphyrins, but become tribasic ligands in place of the dibasic porphyrin. This thesis is a study of synthetic methods for corroles, as well as their photophysical properties and potential applications.
\r\n\r\nNew synthetic methodologies for the free-base molecules have been used to obtain corroles with pentafluorophenyl meso substituents in both water-soluble and non-water-soluble forms. Closed-shell metallocorrole complexes have been synthesized by introducing Ga(III) and Sn(IV) ions into the macrocycle. Likewise, an open shell transition metal corrole utilizing Mn(III) has been made. Problems arising from making a third type of closed shell metallocorrole by introduction of In(III) are also discussed. Among other characterizations of these complexes, Gouterman\u2019s four-orbital model for porphyrins is reinterpreted under the reduced symmetry of the corrole macrocycle to explain the absorption and singlet emission spectra of the molecules. Evidence of a triplet excited state is also presented.
\r\n\r\nThe application of corrole complexes to other aspects of chemistry is then examined in two different areas. The interactions of the water-soluble corroles with human serum albumin were investigated to assess their usefulness as diagnostic agents and drugs for cancer research. These highly colored compounds have also been introduced as the dye component of dye-sensitized solar cells, and various aspects of the cells, including overall efficiency, have been tested.
\r\n\r\nThis thesis concludes with a summary of results obtained from collaborations on the interactions of corroles in cellular systems and synthetic attempts toward new types of water-soluble corroles, including an imidazole substituted chromium corrole and a sulfonated manganese nitrido corrole.
" }, { "name": "Webb, Lauren J.", "degree": "PhD", "year": "2005", "title": "Chemical Characterization and Charge Carrier Dynamics of Crystalline Silicon(III) Surfaces Modified with Surface-Bound Organic Functional Groups", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262005-123044", "creators": [ { "name": { "family": "Webb", "given": "Lauren J." }, "id": "Webb-Lauren-J", "orcid": "0000-0001-9999-5500", "display_name": "Webb, Lauren J." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DM8E-JA05", "abstract": "Investigations of the chemical structure and charge carrier properties of alkylated crystalline silicon(111) surfaces are presented. Hydrogen-terminated Si(111) surfaces were alkylated with a series of saturated hydrocarbons through a chlorination/alkylation procedure and characterized using surface-sensitive techniques. High-resolution soft X-ray photoelectron spectroscopy (SXPS) identified 1 monolayer of H, Cl, and C on the H-, Cl- and CH3-terminated surfaces, respectively. Surfaces functionalized with bulkier alkyls showed Si 2p binding energy shifts that suggest that unalkylated Si atoms are bonded to hydrogen. Alkylated Si(111) surfaces were further characterized using transmission infrared spectroscopy (TIRS). The Si-Cl stretching and bending motions were identified at 583 and 528 cm-1, respectively. On the methyl-terminated Si(111) surface, a CH3 symmetrical bending vibrational mode at 1257 cm-1 polarized perpendicular to the surface was observed. On the C2H5-terminated surface, a Si-H stretching and bending motion at 2080 and 627 cm-1, respectively, were observed, confirming that unalkylated Si atoms are terminated with H atoms. Structural morphology of the CH3-terminated Si(111) surface was investigated by low energy electron diffraction (LEED), which found that this surface retained a flat, unreconstructed (1 x 1) structure. Scanning tunneling microscopy (STM) images of CH3-Si(111) were obtained at 4.7 and 77 K. The functionalized surface preserved the atomically flat morphology of freshly etched H-Si(111), and at 4.7 K individual methyl H atoms were clearly resolved for the first time.
\r\n\r\nElectronic passivation of the alkylated Si(111) surface was investigated through measurement of surface charge carrier recombination velocities (S), through time-resolved radio frequency (rf) photoconductivity decay methods. While unpassivated H- and Cl-terminated surfaces reacted rapidly in an air ambient to yield S>1400 cm s-1, alkylated surfaces preserved S<200 cm s-1 even when exposed to air for a period of weeks.
\r\n\r\nFinally, the two-step chlorination/alkylation route was compared to three other Si(111) surface functionalization techniques: (1) chlorination with Cl2(g) followed by alkylation with an alkylmagnesium halide reagent, (2) Lewis acid-mediated reduction of a terminal alkene, and (3) anodization of the H-terminated Si(111) surface in diethyl ether containing 3.0 M CH3MgI. The chemical properties and charge carrier recombination rates of each surface were measured as a function of time exposed to air.
" }, { "name": "Widicus Weaver, Susanna Leigh", "degree": "PhD", "year": "2005", "title": "Rotational Spectroscopy and Observational Astronomy of Prebiotic Molecules", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05162005-153745", "creators": [ { "name": { "family": "Widicus Weaver", "given": "Susanna Leigh" }, "id": "WidicusWeaver-Susanna-Leigh", "orcid": "0000-0001-6015-3429", "display_name": "Widicus Weaver, Susanna Leigh" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "orcid": "0000-0002-8198-793X", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CN1R-H437", "abstract": "It is now widely believed that prebiotic molecules were delivered to the early Earth by planetesimals and their associated interplanetary dust particles. Yet the formation pathways for these molecules are not clear. Amino acids and sugars have been found in carbonaceous chondrites, but only much simpler species have been detected in the interstellar medium (ISM). Prebiotic organics could have formed in the ISM and been directly incorporated into planetesimals, or simpler species could have formed in the ISM and then been incorporated into planetesimals, undergone further processing, and been delivered to Earth. Limits on interstellar chemistry must therefore be established through observational astronomy before potential prebiotic formation pathways can be assessed. These observations require laboratory spectroscopic investigation of the species of interest.
\r\n\r\nThis thesis is an interdisciplinary study involving laboratory rotational spectroscopy and astronomical observations of several key prebiotic molecules. The laboratory work has focused on obtaining the rotational spectra of the simplest three-carbon ketose sugar, 1,3-dihydroxyacetone, and its structural isomers methyl glycolate and dimethyl carbonate, as well as aminoethanol, the predicted interstellar precursor to alanine. The pure rotational spectral analysis of the low-lying torsional states of the simplest alpha-hydroxy aldehyde, glycolaldehyde, has also been completed. The original Balle-Flygare Fourier transform microwave spectrometer was used to obtain the microwave spectra, while both the Jet Propulsion Laboratory and Caltech direct absorption flow cell spectrometers were used for additional direct absorption millimeter and submillimeter studies.
\r\n\r\nThe results of these laboratory experiments were used to guide observational searches with the Caltech Submillimeter Observatory, the Owens Valley Millimeter Array, and the Green Bank Telescope toward the hot core sources Sgr B2(N-LMH), Orion Hot Core/Compact Ridge, and W51 e1/e2. Evidence has been found for the presence of dihydroxyacetone and methyl glycolate in Sgr B2(N-LMH).
\r\n\r\nThese results have important implications for interstellar grain surface chemistry, and proposed additions to grain surface chemical models are also discussed. Reactions involving surface radicals and molecules containing carbonyl groups can efficiently compete with the simple grain surface reactions included in previous models. Such aldehyde abstraction reactions should be considered as pathways to complex carbonyl-containing species on interstellar grain surfaces.
" }, { "name": "Zahler, James Michael", "degree": "PhD", "year": "2005", "title": "Materials Integrations for High-Performance Photovoltaics by Wafer Bonding", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022005-234526", "creators": [ { "name": { "family": "Zahler", "given": "James Michael" }, "id": "Zahler-James-Michael", "display_name": "Zahler, James Michael" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/05F0-K740", "abstract": "The fundamental efficiency limit for state of the art triple-junction photovoltaic devices is being approached. By allowing integration of non-lattice-matched materials in monolithic structures, wafer bonding enables novel photovoltaic devices that have a greater number of subcells to improve the discretization of the solar spectrum, thus extending the efficiency limit of the devices. Additionally, wafer bonding enables the integration of non-lattice-matched materials with foreign substrates to confer desirable properties associated with the handle substrate on the solar cell structure, such as reduced mass, increased thermal conductivity, and improved mechanical toughness. This thesis outlines process development and characterization of wafer bonding integration technologies essential for transferring conventional triple-junction solar cell designs to potentially lower cost Ge/Si epitaxial templates. These epitaxial templates consist of a thin film of single-crystal Ge on a Si handle substrate. Additionally, a novel four-junction solar cell design consisting of non-lattice matched subcells of GaInP, GaAs, InGaAsP, and InGaAs based on InP/Si wafer-bonded epitaxial templates is proposed and InP/Si template fabrication and characterization is pursued.
\r\n\r\nIn this thesis the detailed-balance theory of the thermodynamic limiting performance of solar cell efficiency is applied to several device designs enabled by wafer bonding and layer exfoliation. The application of the detailed-balance theory to the novel four-junction cell described above shows that operating under 100 suns at 300 K a maximum efficiency of 54.9% is achievable with subcell bandgaps of 1.90, 1.42, 1.02, and 0.60 eV, a material combination achievable by integrating two wide-bandgap subcells lattice matched to GaAs and two narrow-bandgap subcells lattice matched to InP.
\r\n\r\nWafer bonding and layer transfer processes with sufficient quality to enable subsequent material characterization are demonstrated for both Ge/Si and InP/Si structures. The H-induced exfoliation process in each of these materials is studied using TEM, AFM, and FTIR to elucidate the chemical states of hydrogen leading to exfoliation. Additionally, the electrical properties of wafer-bonded interfaces between bulk-Ge/Si and bulk-InP/Si structures are show Ohmic, low-resistance electrical contact. Further studies of p-p isotype heterojunctions in Ge/Si indicate that significant conduction paths exist through defects at the bonded interface. The first known instance of epitaxy of III-V compound semiconductors on wafer-bonded Ge/Si epitaxial templates is demonstrated. Additionally InGaAs is grown on InP/Si templates that have been improved by removal of damage induced by the ion implantation and exfoliation processes.
" }, { "name": "Allen, Matthew John", "degree": "PhD", "year": "2004", "title": "Delivery and Activation of Contrast Agents for Magnetic Resonance Imaging", "advisor": "Meade, Thomas J.; Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12122003-094113", "creators": [ { "name": { "family": "Allen", "given": "Matthew John" }, "id": "Allen-Matthew-John", "orcid": "0000-0002-6868-8759", "display_name": "Allen, Matthew John" } ], "advisors": [ { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "advisor", "display_name": "Meade, Thomas J." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "co-advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "member", "display_name": "Meade, Thomas J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6V70-FK81", "abstract": "Magnetic Resonance Imaging (MRI) has become a powerful tool for noninvasive imaging of living specimens. Magnetic resonance contrast agents containing the paramagnetic ion gadolinium(III) are used to enhance regions, tissues, and cells that are magnetically similar but histologically distinct. To increase the effectiveness of contrast agents, agents responsive to biological phenomena and directed to specific regions need to be developed. These two improvements are related in that many biologically significant molecules are located in specific locations. Therefore, the design, synthesis, and testing of advanced contrast agents are described.
\r\n\r\nMany interesting biological targets for imaging reside inside the cell membrane. As the current generation of contrast agents is strictly extracellular, a method of intracellular delivery is required in the development of MRI contrast agents. I have developed cationic, polyarginine-oligomers to deliver gadolinium(III)-based contrast agents into the interior of cells. Delivery was confirmed and studied using methods including inductively coupled plasma-mass spectrometry, MRI, and two-photon laser microscopy to image lanthanide-based MRI contrast agents.
\r\n\r\nA second approach focused on the synthesis of a series of contrast agents designed to cross the blood brain barrier and label A[Beta]-plaques associated with Alzheimer's disease. These agents were found to permeate cell membranes, and the intracellular properties of these agents are compared to the polyarginine agents. Finally, attempts towards the creation of an advanced MRI contrast agent that is chemically activated by matrix metalloproteinases are described.
\r\n" }, { "name": "Bhattacharya, Pratip K.", "degree": "PhD", "year": "2004", "title": "Structure and Reactivity of Metal Complexes Bound to DNA", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122004-052751", "creators": [ { "name": { "family": "Bhattacharya", "given": "Pratip K." }, "id": "Bhattacharya-Pratip-K", "orcid": "0000-0002-0625-252X", "display_name": "Bhattacharya, Pratip K." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "co-chair", "display_name": "Roberts, Richard W." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZANY-J082", "abstract": "Establishing correlations among structure, dynamics and reactivity is a fundamental problem in biological chemistry. Here, this problem is explored in the context of the design and reactivity of different metallointercalators bound to DNA.
\r\n\r\nFirst, the effects of intervening mismatches on DNA structure, dynamics and DNA charge transport reactivity is examined. The \u03c0-stacked DNA base pairs mediate charge transport chemistry over long molecular distances in a reaction that is exquisitely sensitive to DNA sequence dependent conformation and dynamics. To examine the long-range charge transport as a function of intervening base mismatches, a series of DNA oligonucleotides were synthesized that incorporate a ruthenium intercalator, [Ru(phen)(bpy')(dppz)]\u00b2\u207a (phen = 1,10 phenanthroline; bpy' = 4-butyric acid-4'-methylbipyridine; dppz = dipyrido[3,2-a:2',3'-c]phenazine) linked covalently to the 5' terminus of one strand and containing two 5'-GG-3' sites in the complementary strand. Single base mismatches were introduced between the two guanine doublet steps, and the efficiency of transport through the mismatches was determined through measurements of the ratio of oxidative damage at the guanine doublets distal versus proximal to the intercalated ruthenium oxidant. Differing relative extents of guanine oxidation were observed for the different mismatches. The damage ratio of oxidation at the distal versus proximal site for the duplexes containing different mismatches varies in the order GC ~ GG ~ GT ~ GA > AA > CC ~ TT ~ CA ~ CT. The extent of distal/proximal guanine oxidation in different mismatch-containing duplexes was then compared with the helical stability of the duplexes, electrochemical data for intercalator reduction on different mismatch-containing DNA films, and base-pair lifetimes for oligomers containing the different mismatches derived from \u00b9H NMR measurements of the imino proton exchange rates. The exchange kinetics of the imino protons were measured from selective longitudinal relaxation times, and the effect of the mismatch was observed on the base pair lifetime up to a distance of two neighboring base pairs. The overall order of base-pair lifetimes in the selected sequence context of the base pair was as follows: GC > GG > AA > CC > TT. While a clear correlation is evident both with helix stability and electrochemical data monitoring reduction of an intercalator through DNA films, guanine damage ratios was found to correlate most closely with base-pair lifetimes. These results underscore the importance of base dynamics in modulating long-range charge transport through the DNA base-pair stack.
\r\n\r\nIn a related \u00b9H NMR structural study of the ruthenium intercalator, [Ru(phen)(bpy')(dppz)]\u00b2\u207a covalently tethered to a short eightmer DNA duplex, d(ACGAGCAC)\u2022d(GTICTCGT) with a nine carbon linker, the type of construct used in charge transport experiments, a very fast exchange was observed. Comparison of the NOESY data obtained from the NMR study of this system and control samples comprising of the duplex with only linker and the duplex alone, led to the conclusion that the nine carbon linker is positioned between the second and fourth bases from the point of its origin. The absence of any site specificity of the metal complex in the oligonucleotide complicates the structural characterization by NMR study. This led us to conceive of a more general strategy of obtaining structural information of metal complexes that bind non-specifically to DNA based on paramagnetic NMR.
\r\n\r\nThe selective paramagnetic relaxation of oligonucleotide proton resonances of two short self-complementary oligonucleotides; d(GTCGAC)\u2082 and d(GTGCAC)\u2082 by Ni(phen)\u2082(L)\u00b2\u207a where L= dipyridophenazine (dppz), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq) and phenanthrenequinone (phi) was examined to obtain structural insight into the non-covalent binding of these metal complexes to DNA. In the oligonucleotide d(GTCGAC)\u2082, preferential broadening of the G1H8, G4H8, T2H6, and C3H6 proton resonances was observed with Ni(phen)\u2082(dppz)\u00b2\u207a, Ni(phen)\u2082(dpq)\u00b2\u207a and Ni(phen)\u2082(phi)\u00b2\u207a. In the case of the sequence d(GTGCAC)\u2082, where the central two bases are juxtaposed from the previous one, preferential broadening was observed instead for the A5H2 proton resonance. Thus, a subtle change in the sequence of the oligonucleotide can cause significant change in the binding location of the metal complex in the oligonucleotide. Owing to comparable changes for all metal complexes and sequences in broadening of the thymine methyl proton resonances, the switch in preferential broadening was attributed to a change in site location within the oligomer rather than to an alteration of groove location. Therefore, even for DNA-binding complexes of low sequence-specificity, distinct variations in binding as a function of sequence are apparent and can be monitored using paramagnetic probes.
\r\n\r\nFinally, \u00b9H NMR spectroscopy was employed to study the binding of [Rh(bpy)\u2082chrysi]\u00b3\u207a (chrysi = 5,6-chrysenquinone diimine), a metal complex which specifically targets mismatches, to a ninemer oligonucleotide d(GCCTCAGGC)\u2082 containing centrally placed CC mismatch. Evidence supports intercalation by the metal complex within the mismatch site (i) upfield chemical shifts and significant broadening of the chrysi resonances and (ii) an increase in duplex melting temperature in the presence of the metal complex. To simplify the NMR spectra, the \u0394 isomer of [Rh(d\u2088\u208bbpy)\u2082chrysi]\u00b3\u207a was employed in NMR experiments with DNA. A break in the connectivity in the NOE walk is observed between T\u2084 and C\u2085, thereby marking the binding site of the metal complex at the CC mismatch. Intermolecular NOE's place the metal complex in the major groove of the oligonucleotide.
\r\n\r\nThus through a series of experiments in this thesis, attempts have been made to correlate the structure and dynamics of metal complexes bound to DNA. Truly, metal complexes bound to DNA provide an interesting system to study structure, function and dynamics in a single package.
" }, { "name": "Brewer, Rhett Ty", "degree": "PhD", "year": "2004", "title": "Quantitative Biaxial Texture Analysis with Reflection High-Energy Electron Diffraction for Ion Beam-Assisted Deposition of MgO and Heteroepitaxy of Perovskite Ferroelectrics", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-08182003-150957", "creators": [ { "name": { "family": "Brewer", "given": "Rhett Ty" }, "id": "Brewer-Rhett-Ty", "display_name": "Brewer, Rhett Ty" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Bhattacharya", "given": "Kaushik" }, "id": "Bhattacharya-K", "role": "member", "display_name": "Bhattacharya, Kaushik" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Haile", "given": "Sossina M." }, "id": "Haile-S-M", "role": "member", "display_name": "Haile, Sossina M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/J5PY-RS79", "abstract": "To facilitate ferroelectric-based actuator integration with silicon electronics fabrication technology, we have developed a route to produce biaxially textured ferroelectrics on amorphous layers by using biaxially textured MgO templates.
\r\n\r\nUsing a kinematical electron scattering model, we show that the RHEED pattern from a biaxially textured polycrystalline film can be calculated from an analytic solution to the electron scattering probability. We found that diffraction spot shapes are sensitive to out-of-plane orientation distributions and in-plane RHEED rocking curves are sensitive to the in-plane orientation distribution. Using information from the simulation, a RHEED-based experimental technique was developed for in situ measurement of MgO biaxial texture. The accuracy of this technique was confirmed by comparing RHEED measurements of in-plane and out-of-plane orientation distribution with synchrotron x-ray rocking curve measurements.
\r\n\r\nBiaxially textured MgO was grown on amorphous Si3N4 by ion beam-assisted deposition (IBAD). MgO was e-beam evaporated onto the amorphous substrate with a simultaneous 750-1200 eV Ar\u207a ion bombardment at 45\u00b0 from normal incidence. We observed a previously unseen, dramatic texture evolution in IBAD MgO using transmission electron microscopy (TEM) and RHEED-based quantitative texture measurements of MgO. The first layers of IBAD MgO are diffraction amorphous until the film is about 3.5 nm thick. During the next 1 nm of additional growth, we observed rapid biaxial texture evolution. RHEED and TEM studies indicate that biaxially textured MgO film results from a solid phase crystallization of biaxially textured MgO crystals in an amorphous matrix.
\r\n\r\nBiaxially textured perovskite ferroelectrics were grown on biaxially textured MgO templates using sol-gel, metallorganic chemical vapor deposition (MOCVD), and molecular beam epitaxy (MBE). Through RHEED-based biaxial texture analysis we observed that the heteroepitaxial ferroelectric in-plane orientation distribution, deposited using ex situ techniques (not performed in the same high vacuum growth environment where the MgO was deposited), narrowed significantly with respect to the in-plane orientation distribution of its MgO template (from 11\u00b0 to 6\u00b0 FWHM). Evidence from cross section TEM and RHEED suggest that atmospheric moisture degrades the crystallinity of highly defective, misaligned MgO grains and that heteroepitaxially grown ferroelectrics preferentially nucleate on well-aligned grains and over grow misaligned regions of MgO.
" }, { "name": "Carrico, Isaac Sheridan", "degree": "PhD", "year": "2004", "title": "Protein Engineering Through in vivo Incorporation of Phenylalanine Analogs", "advisor": "Tirrell, David A.; Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechETD:etd-09082003-110526", "creators": [ { "name": { "family": "Carrico", "given": "Isaac Sheridan" }, "id": "Carrico-Isaac-Sheridan", "display_name": "Carrico, Isaac Sheridan" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "co-advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/VDX0-Z265", "abstract": "Proteins mediate the bulk of biochemical functions within the cell. These biopolymers control processes utilizing specific arrangements of the natural twenty amino acids. Expanding the set of amino acids available could both aid in the study of these macromolecules as well as significantly increase their functional capabilities. A set of enzymes known as aminoacyl tRNA-synthetases lies at the heart of the fidelity of translation, the process by which genetic information gets decoded into proteins. These synthetases accurately charge a specific tRNA with its cognate amino acid in the presence of the other nineteen natural amino acids. Interestingly these enzymes demonstrate a much higher level of promiscuity with unnatural amino acids. However, acceptable amino acids are limited to those that bear steric and electronic resemblance to the natural analog.
\r\n\r\nOur efforts to expand the substrate set of phenylalanyl-tRNA (PheRS) synthetase are described in Chapters 2-4. We redesigned the catalytic site of PheRS computationally. These results combined with an already known mutant allowed us to rationally create a third mutant. All three mutants were characterized for their ability to activate a large panel of unnatural amino acids in vitro. Further, we were able to confirm the in vivo incorporation of a number of these analogs. In vitro and in vivo results were consistent and defined an expanded substrate set for the described mutants. This substrate set includes a number of analogs that are dramatically different from phenylalanine both sterically and electronically, as well as a number which contain chemical moieties valuable to protein engineering efforts.
\r\n\r\nOne example is para-azidophenylalanine (pN\u2083Phe), which provides access to photochemistry as well as modified Staudinger ligations and copper mediated electrocyclizations. In Chapter 5 we describe utilization pN\u2083Phe as a photocrosslinking reagent. Our aim was to create photochemically crosslinkable artificial extracellular matrix proteins for the production of synthetic vascular grafts. These proteins, produced in E. coli, were diblocks of endothelial cell binding domains and structural domains including the pN\u2083Phe site. Photochemical crosslinking of these constructs provided moduli well within the range presented by the natural vascular wall. Chapter 6 describes our ability to photopattern films composed of the above protein. Photopatterning provided a means to spatially array endothelial cells, based upon a number of controllable processing parameters of such films.
\r\n\r\nThe final chapter details the utilization of incorporated unnatural amino acids, particularly para-iodophenylalanine, para-acetylphenylalanine and homopropargylglycine, to access Pd(0) catalyzed cross-coupling chemistry. We demonstrated this chemistry exhibits the characteristics necessary for chemoselective ligations. Further, we demonstrated the selective modification of proteins incorporating all of the above analogs.
" }, { "name": "Casperson, Julie Diane", "degree": "PhD", "year": "2004", "title": "Design and Characterization of Layered Tunnel Barriers for Nonvolatile Memory Applications", "advisor": "Atwater, Harry Albert", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262004-111123", "creators": [ { "name": { "family": "Casperson", "given": "Julie Diane" }, "id": "Casperson-Julie-Diane", "display_name": "Casperson, Julie Diane" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "display_name": "Atwater, Harry Albert" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Heath", "given": "James R." }, "id": "Heath-J-R", "role": "member", "display_name": "Heath, James R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/D90P-6821", "abstract": "The main limitations of floating gate memory devices (Flash memory) are the long program (microsecond) and erase times (~ 1 \u00b5s) inherent to the charging of floating gates using Fowler-Nordheim tunneling. An alternative to the integration of homogeneous dielectric tunnel barriers present in standard Flash memory is to use layered tunnel barriers made of high-k heterostructures. This allows for an effective lowering in barrier height under applied bias, resulting in shorter write/erase times while maintaining long retention times.
\r\n\r\nTo assess these types of dielectric structures, tunneling probability simulations were performed using an effective mass-model, allowing us to predict current-voltage (I-V) characteristics and optimize the layered tunnel barrier structure. Based on our results, we correlated dielectric constants and band offsets with respect to silicon in order to help identify possible materials from which to construct these layered barriers. This survey allowed for the determination of promising high-k materials heterostructures: Si\u2083N\u2084 / Al\u2082O\u2083 / Si\u2083N\u2084 / Si\u2083N\u2084 and HfO\u2082 / Al\u2082O\u2083 / HfO\u2082.
\r\n\r\nWe performed a series of physical and electrical characterization experiments on single-layer as well as two- and three-layer structures of Si\u2083N\u2084, Al\u2082O\u2083, and HfO\u2082. Transmission electron microscopy and I-V measurements were used to correlate the physical effects of high-temperature annealing on the electrical properties of the films, allowing us to determine the ideal processing conditions. Construction of Fowler-Nordheim plots from experimental I-V data gave qualitative evidence of barrier lowering in the multi-layer structures.
\r\n\r\nWe developed a bias-dependent photoemission technique for quantitative determination of the band-offsets between silicon and our dielectric barriers, which is found to be highly dependent on the applied bias. For SiO\u2082 (and other single-layer materials), image potential barrier lowering simulations predict the barrier profile as a function of voltage, allowing us to report the band-offsets for these materials in a more complete way than was previously possible. Also, by characterizing multi-layer structures of HfO\u2082 and Al\u2082O\u2083, we have been able to quantitatively measure the effective barrier height of these structures over a wide range of biases and prove barrier lowering. Analysis by an electrostatic model allowed us to accurately simulate the barrier lowering results over all voltage ranges.
" }, { "name": "Choi, Tae-Lim", "degree": "PhD", "year": "2004", "title": "Olefin Metathesis: a Versatile Tool for the Synthesis of Small to Large Molecules", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05262004-173345", "creators": [ { "name": { "family": "Choi", "given": "Tae-Lim" }, "id": "Choi-Tae-Lim", "orcid": "0000-0001-9521-6450", "display_name": "Choi, Tae-Lim" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FD0X-D313", "abstract": "In olefin metathesis, the designing of better catalysts has been the key to the success of its utility. Throughout the history of olefin metathesis research, the development of new and improved catalysts has brought new applications and new strucures that are accessible by olefin metathesis routes. With the developmet of highly active catalyst containing an N-heterocyclic carbene, the field of olefin metathesis is currently in a period of renaissance opening up the versatile synthesis of both small orgainc molecules to macromolecules. Following four chapters describle recent applications towards the synthesis of molecules with various sizes.\r\n" }, { "name": "Cirino, Patrick Carmen", "degree": "PhD", "year": "2004", "title": "Laboratory Evolution of Cytochrome P450 Peroxygenase Activity", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-06062003-164310", "creators": [ { "name": { "family": "Cirino", "given": "Patrick Carmen" }, "id": "Cirino-Patrick-Carmen", "orcid": "0000-0002-7245-6205", "display_name": "Cirino, Patrick Carmen" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/KWGR-DF47", "abstract": "The ability of the cytochrome P450 heme monooxygenases to catalyze difficult oxidation reactions, often with high specificity and selectivity, makes them attractive for numerous biotechnological applications. However they are generally limited by low turnover rates and low stability, and their minimum requirements for catalysis include a cofactor as source of electrons (NAD(P)H), partner proteins for electron transfer, and dioxygen. Some P450s are capable of supporting low levels of peroxygenase activity, in which a peroxide is utilized to drive catalysis via a \"shunt\" pathway. This mechanism for substrate oxidation, although inefficient and not generally utilized in nature, simplifies P450 catalysis by eliminating the need for NAD(P)H.
\r\n\r\nOur goal was to engineer an efficient P450 peroxygenase which utilizes hydrogen peroxide (H\u2082O\u2082). Directed evolution is a powerful enzyme engineering methodology which mimics nature's algorithm for evolution. Enzyme libraries are generated via DNA mutagenesis or recombination techniques, and variants with improved function are isolated using an appropriate screen or selection. Using this strategy, in combination with site-directed mutagenesis, we have created P450 BM-3 heme domain variants with more than 100-fold improved H\u2082O\u2082-driven hydroxylation activity compared to wild-type, showing both an improved kcat as well as a lower Km for H\u2082O\u2082. Thermostability was also improved by directed evolution.
\r\n\r\nWe have engineered a cell-free, biomimetic hydroxylase that requires only H\u2082O\u2082 to exploit the hydroxylating power of P450 BM-3. Peroxide-mediated inactivation as a result of heme destruction remains a major obstacle and presents an important enzyme engineering challenge. This research has broadened the potential applications of P450 biocatalysis by exploiting the versatility of heme-containing proteins.
" }, { "name": "Delaney, Sarah", "degree": "PhD", "year": "2004", "title": "Oxidative DNA Damage by Long-Range Charge Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05182004-181406", "creators": [ { "name": { "family": "Delaney", "given": "Sarah" }, "id": "Delaney-Sarah", "orcid": "0000-0002-8366-3808", "display_name": "Delaney, Sarah" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9Q0X-TZ17", "abstract": "Ever since the elucidation of the double helical structure of DNA, it has been proposed that the stack of base pairs within the double helix may mediate charge transport (CT) reactions. In fact, CT through DNA can result in chemistry at a distance, yielding oxidative DNA damage at a site remote from the bound oxidant. DNA CT chemistry depends upon coupling within the stacked base pair array, and this chemistry is remarkably sensitive to sequence-dependent DNA structure and dynamics. Using a variety of octahedral transition metal complexes, DNA CT has been probed to explore mechanistic considerations and biological possibilities.
\r\n\r\nInteractions with DNA by a family of ruthenium(II) complexes bearing the dipyridophenazine (dppz) ligand or its derivatives have been examined. An intercalative binding mode has been established based on luminescence enhancements in the presence of DNA, excited state quenching, fluorescence polarization values and enantioselectivity. Oxidative damage to DNA by these complexes using the flash/quench method has also been examined. A direct correlation between the amount of guanine oxidation obtained via DNA CT and the strength of intercalative binding was observed. These results support the importance of close association and intercalation for DNA-mediated CT. Electronic access to the DNA base pairs, provided by intercalation of the oxidant, is a prerequisite for efficient CT through the DNA pi-stack.
\r\n\r\nUsing polypyridyl ruthenium complexes, a reductive flash/quench scheme in DNA has also been explored. The flash/quench scheme previously utilized in DNA studies involves an oxidative quencher and allows for examination of electronic hole transport through DNA. In contrast, a reductive flash/quench technique would allow for direct observation of electron transport through the base stack. In our studies, p-methoxydimethylaniline and potassium iodide have proven to be effective reductive quenchers of dipyridophenazine complexes of ruthenium. However, by transient absorption spectroscopy, high performance liquid chromatography, gel electrophoresis, and electron paramagnetic resonance we are unable to observe any DNA reduction products with the ruthenium complexes examined. Rates of back electron transfer may in fact be faster than trapping of the anion radical, thus hindering observation of long-range damage.
\r\n\r\nThe oxidative flash/quench technique was applied in probing DNA CT in a range of DNA assemblies containing a tethered ruthenium intercalator and methylindole (M), a low potential nucleobase analog, where radical formation at a distance as a function of DNA sequence could be examined both by laser spectroscopy and biochemical methods. Hole injection and subsequent formation of the methylindole radical cation were observed at a distance of over 30 \u0160at rates > 10e7 s-1 in assemblies containing no guanine bases intervening the ruthenium intercalator and GMG oxidation site. Radical yield was, however, strikingly sensitive to an intervening base mismatch; no significant methylindole radical formation was evident with an intervening AA mismatch. Also critical is the sequence at the injection site; this sequence determines initial hole localization and hence the probability of hole propagation. With guanine rather than inosine near the site of hole injection, decreased yields of radicals and long-range oxidative damage are observed. The presence of the low energy guanine site in this case serves to localize the hole and increase the probability of back reaction at the injection site therefore diminishing CT through the base pair stack.
\r\n\r\nDNA assemblies containing a pendant dppz complex of Ru(II) along with two oxidative traps, a site containing the nucleoside analog methylindole (5?-GMG-3?) and a 5?-GGG-3? site, were constructed to explore charge equilibration across the base pair stack. In these assemblies the base radicals form with a rate of 10e7 s-1. Interestingly, the rate of base radical formation does not change upon the addition of a second radical trap, the 5?-GGG-3? site; however the yield of methylindole oxidation is significantly lower. This observation indicates that the 5?-GGG-3? site is effective in competing for the migrating charge and provides a second trapping site. Importantly, switching the orientation of the two trapping sites does not affect the yield of oxidized products at either site. Therefore, in DNA both forward and reverse charge transport occur so as to provide equilibration across the duplex on a time scale that is fast compared to trapping at a particular site. Further evidence of charge equilibration results from incorporating an intervening base-stacking perturbation and monitoring the fate of the injected charge. These experiments underscore the dynamic nature of DNA charge transport and reveal the importance of considering radical propagation in both directions along the DNA duplex.
\r\n\r\nDNA conjugates containing adjacent duplex and guanine quadruplex assemblies have been designed to explore CT into quadruplex architectures. The quadruplex assemblies have been characterized structurally using circular dichroism and by assaying for chemical protection. Using an intercalating rhodium photooxidant, noncovalently bound or tethered to the duplex end, oxidizing radicals are found to be trapped in the folded quadruplex. Damage is observed almost exclusively at the external tetrads of the quadruplex. Little damage of the center tetrad is observed, due most likely to lowered efficiency of radical trapping within the quadruplex core. This pattern of damage is distinct from that observed for repetitive G sequences within duplex DNA. The data indicate, furthermore, that in the conjugates examined, the guanine quadruplex provides a more effective trap than a 5?-GG-3? guanine doublet within duplex DNA. Additionally, within these assemblies, sufficient base-base overlap must exist at the duplex/quadruplex junction to allow for charge migration. This funneling of damage to the quadruplex, as well as the unique pattern of damage within the quadruplex, requires consideration with respect to the analysis of oxidative DNA damage within the cell.
" }, { "name": "Deng, Wei-Qiao", "degree": "PhD", "year": "2004", "title": "Computation Aided Design in Molecular Nanotechnology", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05282004-161503", "creators": [ { "name": { "family": "Deng", "given": "Wei-Qiao" }, "id": "Deng-Wei-Qiao", "orcid": "0000-0002-3671-5951", "display_name": "Deng, Wei-Qiao" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Goodwin", "given": "David G." }, "id": "Goodwin-D-G", "role": "member", "display_name": "Goodwin, David G." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3EKY-3J53", "abstract": "We use multi-scale simulation strategy to understand, improve and rationally design novel materials with desired properties in molecular nanotechnology. The areas we have studied cover from molecular electronics, nano-structured materials to carbon nanotube technology.
\r\n\r\nIn term of molecular and nano-electronics, first we used quantum mechanics to characterize the structure and current-voltage (I-V) performance of the Stoddart-Heath rotaxane-based programmable electronic switch. This methodology established a basis for iterative experimental-theoretical efforts to optimize systems for molecule-based electronics. We extended this switch principle and rationally designed an ultrafast molecular switch, proton-hopping molecular switch. Second we developed a kinetic model to study the hole mobility in organic semiconductor. After screening several designs, we presented a nano-bracelet as a competitive organic semiconductor.
\r\n\r\nWe studied several topics related to the applications of nano-structured materials in fuel cell technology. Based on our simulation, we proposed a new kind of carbon-based materials for hydrogen storage. It can satisfy the target set up by the Department of Energy, USA. We develop a kinetic model to study the proton diffusion in proton exchange membrane of hydrogen fuel cell. We validated our proposed system, fluorinated imidazole impregnated nafion, as the candidate that can transfer proton above 100 0C at water-free media.
\r\n\r\nIn term of carbon nanotube technology, we explored the reason why bimetallic catalysts are 10-100 times better than mono-metals at assisting single wall carbon nanotube growth. Based on our proposed two-stage growth mechanism, we screened and designed a better catalysis.
" }, { "name": "Dong, Vy Maria", "degree": "PhD", "year": "2004", "title": "Novel Variants of the Zwitterionic Claisen Rearrangement and the Total Synthesis of Erythronolide B", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252004-175803", "creators": [ { "name": { "family": "Dong", "given": "Vy Maria" }, "id": "Dong-Vy-Maria", "orcid": "0000-0002-8099-1048", "display_name": "Dong, Vy Maria" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/AR3C-3566", "abstract": "This dissertation describes the development of three novel variants of the zwitterionic Claisen rearrangement. Initial studies demonstrate an efficient and diastereoselective ketene-Claisen rearrangement catalyzed by metal salts. This process involves the condensation of ketenes and allylic amines to form zwitterionic enolates which undergo [3,3]-sigmatropic rearrangements to afford alpha,beta-disubstituted-gamma,delta-unsaturated amides. The scope of this chemistry is further expanded through the development of a Lewis acid-catalyzed acyl-Claisen rearrangement which employs acid chlorides as ketene surrogates. Based on these studies, a new tandem acyl-Claisen rearrangement for the construction of structurally complex 1,7-dioxo-acyclic architectures is achieved. The versatility of this tandem transformation for macrolide antibiotic synthesis is demonstrated through a concise total synthesis of erythronolide B, in 24 linear steps." }, { "name": "Elmore, Donald Eugene, Jr.", "degree": "PhD", "year": "2004", "title": "Investigations of Ion Channel Structure-Function Relationships Using Molecular Modeling and Experimental Biochemistry", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212004-144036", "creators": [ { "name": { "family": "Elmore", "given": "Donald Eugene, Jr." }, "id": "Elmore-Donald-Eugene-Jr", "orcid": "0000-0002-8723-8710", "display_name": "Elmore, Donald Eugene, Jr." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/47GW-HT46", "abstract": "Ion channels are integral membrane proteins found in all cells that mediate the selective passage of specific ions or molecules across a cell membrane. These channels are important in a diverse range of physiological processes, including signal transmission in the nervous system, sensory perception, and regulation of vital systems, such as circulation. This thesis discusses the use of computational chemistry methods, such as molecular dynamics (MD) and ab initio calculations, and experimental biochemical techniques, such as site-directed mutagenesis, in vivo bacterial assays, chemical cross-linking, and circular dichroism spectroscopy, in tandem to elucidate ion channel structure-function relationships. This research was catalyzed by the solving of atomic resolution crystal structures of the mechanosensitive channels of large and small conductance (MscL and MscS) by the Rees group. Although interesting themselves, these bacterial channels also provide good model systems for considering more complex eukaryotic channels.
\r\n\r\nMscL is an ion channel gated only by membrane tension. Initial studies of MscL verified the relevance of the crystal structure conformation under physiological conditions and compared different MscL homologues. Other work began to elucidate potentially unique structural and functional roles of the M. tuberculosis MscL C-terminal helical bundle. As well, interactions between the MscL channel protein and surrounding lipid and the potential relevance of helical kinking in MscL gating pathways were investigated. MscS is also gated by membrane tension, but its gating can be modulated by changes in transmembrane potential. Thus, studies on MscS began to identify the specific amino acid residues that are responsible for giving the channel its voltage sensitivity. Finally, computations predicting the conformation of nicotine in different solvent environments are discussed. Nicotine is a small molecule ligand that binds to and gates nicotinic acetylcholine receptors, and a thorough understanding of nicotine structure could aid efforts to elucidate receptor structure-function relationships and design new pharmaceuticals.
" }, { "name": "Foister, Shane", "degree": "PhD", "year": "2004", "title": "Shape Selective Recognition of the DNA Minor Groove by Hairpin Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05112004-101833", "creators": [ { "name": { "family": "Foister", "given": "Shane" }, "id": "Foister-Shane", "display_name": "Foister, Shane" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "role": "member", "display_name": "Quake, Stephen R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9WK2-3T81", "abstract": "Polyamides composed of N-methylpyrrole (Py), N-methylimidazole (Im), and 3-hydroxy-N-methylpyrrole (Hp) are crescent-shaped ligands that bind predetermined DNA sequences with affinities and specificities rivaling naturally occurring proteins. Inherent limitations of the thymine-selective Hp residue, including reduced affinity, diminished stability in aqueous solution, and loss of specificity in N-terminal pairings, have restricted the array of DNA sequences that can be specifically targeted with polyamides. The work described in this thesis addresses two major areas of research: the development of fluorescent conjugates of minor groove-binding polyamides as tools for genomic analysis and expansion of the minor groove recognition code by designing internal and N-terminal replacements for Hp.
\r\n\r\nFluorophore-polyamide conjugates were designed using different fluorescent probes, different sites of probe attachment with respect to the polyamide, and different chemical linkers separating the above moieties. Ring conjugates, connecting tetramethylrhodamine or cyanine probes to the N-methyl position of Py rings exhibited reasonable affinities and specificities for the cognate DNA sequences, and displayed fluorescent enhancement upon association with the minor groove. The cyanine conjugates, though less quenched than their TMR counterparts, also demonstrated the capacity for fluorescence resonance energy transfer (FRET). The advantages offered by polyamides relative to oligonucleotide-based probes for DNA detection suggest that polyamides might be useful tools for genomic analysis.
\r\n\r\nThe utility of polyamides as diagnostic tools or as therapeutic agents would be greatly enhanced by the development of novel thymine-specific residues. Efforts toward this end have employed two general design strategies for Hp replacement. One approach has sought to remove the hydroxyl recognition element in favor of purely shape selective discrimination of the T.A base pair, while other efforts have examined alternative hydroxy-substituted aromatic scaffolds that possess greater stability than Hp. Both of these approaches are discussed in the context of N-terminal, internal, and multiple recognition of T.A base pairs.
" }, { "name": "Gordon, Michael Joseph", "degree": "PhD", "year": "2004", "title": "Low-Energy Ion Beamline-Scattering Apparatus with Application to Charge Exchange Collisions at Surfaces", "advisor": "Giapis, Konstantinos P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01022004-085659", "creators": [ { "name": { "family": "Gordon", "given": "Michael Joseph" }, "id": "Gordon-Michael-Joseph", "orcid": "0000-0003-0123-9649", "display_name": "Gordon, Michael Joseph" } ], "advisors": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "advisor", "display_name": "Giapis, Konstantinos P." } ], "committee": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "chair", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Corngold", "given": "Noel Robert" }, "id": "Corngold-N-R", "role": "member", "display_name": "Corngold, Noel Robert" } ], "option_major": [ "chemeng" ], "doi": "10.7907/w315-sr88", "abstract": "Ion-surface interactions are important in a variety of fields such as plasma physics, surface analysis, and semiconductor manufacturing. However, the low-energy regime (50 eV - 1 keV) has been generally avoided by the research community because of the experimental challenges associated with providing sufficient ion beam current at low impact energy to conduct surface scattering studies. This energy regime is a useful range to study because threshold physical and chemical processes occur at low energies. We have set out to probe this neglected energy range by developing an ion scattering system to investigate a wide variety of ion-surface interaction phenomena below 1 keV. This thesis describes the design and construction of our system and its application to charge exchange collisions at surfaces.
\r\n\r\nOur design philosophy has been to take an inductively coupled plasma (ICP) source and couple it to a high-voltage ion beam transport line with magnetic mass- filtering to provide a clean ion beam surface probe with high current (>100 uA/cm\u00b2) and tunable energy (~50 eV - 1 keV). Space charge repulsion between the ions, which usually precludes high current at low energy, is circumvented using the accel-decel scheme for transport. In this arrangement, ions are created at the desired collision energy in the plasma source, extracted and accelerated to high transport energy (to fight space charge forces), and then decelerated back down to their original creation potential right before impacting the grounded target. In this way, the beam current is high, the collision energy is easily tunable (just by floating the whole plasma source above ground), and the target is always kept grounded. The ICP-based beamline is a generic and robust system because any ion created in the plasma can be individually singled out and delivered to the target as a clean surface probe composed of only one species and one charge state.
\r\n\r\nThe particle flux leaving the target surface is analyzed with a hybrid scattered product detector which allows simultaneous mass and energy filtering. The detector combines an electron-impact ionizer, hemispherical electrostatic sector, and quadrupole mass filter in series with single ion detection capabilities so that small signals of both ions and neutrals can be analyzed. Energy dispersion, followed by mass dispersion, is an effective combination because overlapping signals can be separated easily (i.e., multiple charge states or a mix of ion species leaving the target).
\r\n\r\nThe performance of the entire scattering system has been evaluated in an investigation of Ne+ scattering off lighter target materials (Mg, Al, Si , and Ti), where the scattered particle flux can contain inelastic Ne\u207a and Ne\u207a\u207a exit channels as a result of charge exchange between the projectile and target nuclei. Specifically, we have seen a sudden \"turn-on\" in Ne\u207a\u207a generation as the collision energy is raised above a threshold value. This turn-on seems indicative of inelastic loss channels that open up as the distance-of-closest-approach gets smaller during the hard collision. Values for the inelastic loss in the center-of-mass frame for Ne\u207a and Ne\u207a\u207a have been evaluated with our system for collision energies up to 1.3 keV and compared with literature data at higher energies. The inelasticity values we see in the threshold region are too small to be readily explained by the mechanisms proposed for higher collision energies in the literature for both Ne\u207a and Ne\u207a\u207a. Finally, a simple orbital overlap model is presented which suggests that Ne\u207a\u207a generation is coincident with a required atomic orbital overlap between the projectile and target atom L-electron shells, which signify that the Ne 2p orbital is promoted through the 4f\u03c3 molecular orbital at some threshold internuclear distance.
" }, { "name": "Greene, Blake Bennet", "degree": "Masters", "year": "2004", "title": "Progress Toward the Total Synthesis of Salvadione-A and Related Diterpenoids", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252004-084128", "creators": [ { "name": { "family": "Greene", "given": "Blake Bennet" }, "id": "Greene-Blake-Bennet", "display_name": "Greene, Blake Bennet" } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AAPZ-W246", "abstract": "Herein, we report our progress toward the total synthesis of salvadione-A, a structurally complex triterpenoid isolated from Salvia bucharica. We document a model system of our tandem Claisen/Cope/Diels-Alder strategy. Additionally, we describe the evolution of our strategy toward the synthesis of three structurally related diterpenoids-coulterone, cyclocoulterone, and komaroviquinone--from a cyclopropanation/Friedel-Crafts route to an anionic homo-Fries/intramolecular Barbier cyclization pathway.\r\n" }, { "name": "Gstrein, Florian", "degree": "PhD", "year": "2004", "title": "Electron-Transfer Processes at Semiconductor/Liquid Interfaces and Metal/Nanogap Junctions", "advisor": "Lewis, Nathan Saul; Roukes, Michael Lee; Hone, James C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242004-181514", "creators": [ { "name": { "family": "Gstrein", "given": "Florian" }, "id": "Gstrein-Florian", "display_name": "Gstrein, Florian" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Roukes", "given": "Michael Lee" }, "id": "Roukes-M-L", "role": "co-advisor", "display_name": "Roukes, Michael Lee" }, { "name": { "family": "Hone", "given": "James C." }, "id": "Hone-J-C", "role": "co-advisor", "display_name": "Hone, James C." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Roukes", "given": "Michael Lee" }, "id": "Roukes-M-L", "role": "member", "display_name": "Roukes, Michael Lee" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1NT2-FB12", "abstract": "It is shown that n-ZnO/H\u2082O-A/A\u207b junctions (A/A\u207b = [Co(bpy)\u2083]\u00b3\u207a/\u00b2\u207a or [OsL\u2082L']\u00b3\u207a/\u00b2\u207a) display energetic and kinetic behavior of unprecedented ideality. The rate constant of the junction with the highest driving force increased when the driving force was lowered, which indicates that the junction operated in the inverted regime. The driving force was varied by shifting the conduction-band edge of the semiconductor with pH. The contact with the lowest driving force was found to operate in the normal regime of charge transfer. These results provide the first experimental indication that semiconductor/liquid contacts can operate in the inverted regime. Junctions having a similar driving force but different reorganization energies show the expected dependence of the rate constant on the reorganization energy.
\r\n\r\nLow surface-recombination velocities (SRVs) were observed for systems with an accumulation of holes or electrons at the Si surface. Formation of the charge-carrier accumulation layer was confirmed by a solution-gated transistor method. Digital simulations revealed that SRVs < 10 cm s\u207b\u00b9 can be produced by surfaces with trap densities as large as 10\u00b9\u00b2 cm\u207b\u00b2 provided that the surface is in accumulation or inversion. The degree of band bending and SRVs of Si(111) in contact with a variety of aqueous fluoride solutions were determined for the first time at open circuit. An accumulation of electrons at the surface is responsible for the low effective SRVs in NH\u2084F and buffered HF solutions. The protonation of basic defect sites is important for the low SRV of Si(111)/H\u2082SO4(aq) and Si(111)/HF(aq) contacts.
\r\n\r\nThe J-E characteristics of electron-tunnel junctions formed by the electromigration of metal nanowires without a molecule bridging the gap were explored in detail. The low-temperature J-E curves of some junctions showed regions of zero conductivity near zero bias, while such features were absent in the data collected for other junctions. A common pattern was discerned in that the low-bias resistances of all junctions decreased by at least an order of magnitude with increasing temperature according to Abeles' model for electron tunneling in granular metal junctions. These findings were consistent with the Coulomb blockade effect and can be attributed to metal islands in the gap.
" }, { "name": "Heilshorn, Sarah Christine", "degree": "PhD", "year": "2004", "title": "Design and Characterization of Artificial Extracellular Matrix Proteins for Use as Small-Diameter Vascular Grafts", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242004-103633", "creators": [ { "name": { "family": "Heilshorn", "given": "Sarah Christine" }, "id": "Heilshorn-Sarah-Christine", "orcid": "0000-0002-9801-6304", "display_name": "Heilshorn, Sarah Christine" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Asthagiri", "given": "Anand R." }, "id": "Asthagiri-A-R", "role": "member", "display_name": "Asthagiri, Anand R." }, { "name": { "family": "Wold", "given": "Barbara J." }, "id": "Wold-B-J", "role": "member", "display_name": "Wold, Barbara J." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/BX95-3X10", "abstract": "Synthetic small-diameter vascular grafts often fail within three years of implantation. The underlying causes of graft failure are thought to be i) a mismatch in the mechanical properties between the graft and host material and ii) an inability of the graft to support the adhesion of endothelial cells. To address these two issues, artificial extracellular matrix (aECM) proteins contain elastin-like regions to provide physical integrity and cell-binding domains derived from fibronectin to promote endothelial cell attachment. Using recombinant protein technology, a family of artificial proteins was created with differing ratios of elastin-like regions to cell-binding domains, with variable placement of amino acid crosslinking residues, and with differing identity of cell-binding domain.
\r\n\r\nHuman umbilical vein endothelial cells (HUVEC) adhere in a sequence-specific manner to aECM proteins, secrete basal levels of key fibrinolytic regulators, and are capable of resisting a physiologically relevant detachment force. HUVEC spread more quickly and adhere more firmly to aECM proteins that contain the RGD versus the CS5 cell-binding domain. Decreasing the density of RGD cell-binding domains results in decreased HUVEC adhesion. Furthermore, amino acid selection even at sites up to 16 residues away from the cell-binding domain impacts HUVEC spreading and adhesion. HUVEC also adhere more strongly to stiffer aECM films. Therefore, the identity, density, and context of the cell-binding domain as well as the elastic modulus of the substrate are all important variables in influencing cell-substrate interactions.
\r\n\r\nProper amino acid sequence choice also influences the susceptibility of aECM proteins to elastase proteolysis; modifying 3% of the amino acid side chains results in a 7-fold reduction in degradation rate. An alternative strategy to decrease degradation involves incorporation of the noncanonical amino acid, 5,5,5-trifluoroisoleucine, into the favored proteolytic cut site, isoleucine. Replacing 82% of the isoleucines results in a twofold reduction in degradation rate without compromising sequence-specific HUVEC adhesion. Incorporation of another noncanonical amino acid, para-azidophenylalanine, allows synthesis of photoreactive proteins that can be patterned using photolithography. These protein patterns retain their ability to adhere HUVEC and produce stable cell patterns after 48 hours in medium supplemented with serum.
\r\n" }, { "name": "Jen, Wendy Sandra", "degree": "PhD", "year": "2004", "title": "Development of New Asymmetric Organocatalytic Methods and Progress Towards the Total Synthesis of Guanacastepene A", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10282003-135857", "creators": [ { "name": { "family": "Jen", "given": "Wendy Sandra" }, "id": "Jen-Wendy-Sandra", "display_name": "Jen, Wendy Sandra" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3PZD-1K08", "abstract": "The development of a new iminium-activation approach towards asymmetric organic catalysis is described. This strategy has been successfully applied to a 1,3-dipolar cycloaddition reaction to produce the first enantioselective catalytic [3+2]cycloaddition between nitrones and a,b-unsaturated aldehydes. This methodology highlights the ability of this new organocatalytic strategy to access chemical transformations not attainable though traditional Lewis acid catalysis.
\r\n\r\nWe have also applied this iminium-activation strategy towards the successful development of an enantioselective organocatalytic intramolecular Diels-Alder (IMDA) reaction. This variant of the IMDA reaction is capable of accessing a range of stereochemically complex [4.3.0] and [4.4.0] ring systems in good yields and with excellent selectivities. Furthermore, we have successfully developed the first asymmetric Type II intramolecular Diels-Alder cyclization. Finally, the utility of this methodology was demonstrated in the efficient total synthesis of (-)-solanapyrone D where an asymmetric organocatalytic IMDA reaction comprised the pivotal bond construction.
\r\n\r\nProgress has been made towards the total synthesis of guanacastepene A. Significant efforts were directed towards a pursuing a 3-component coupling/intramolecular Diels-Alder approach towards the natural product. IMDA precursors were synthesized in an efficient and convergent manner. It was found, however, that these substrates were unable to undergo the desired cyclization. By modifying our synthetic approach towards guanacastepene A, we found that the stereochemically complex cyclohexene portion of the natural product could be synthesized via an intermolecular Diels-Alder. Therefore recent efforts have been directed towards the pursuing a more convergent intermolecular Diels-Alder/ conjugate addition/ Dieckman condensation strategy towards guanacastepene A.
" }, { "name": "Kalani, M. Yashar S.", "degree": "PhD", "year": "2004", "title": "Structure and Function Studies of the Human Dopamine Receptors", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05042004-203854", "creators": [ { "name": { "family": "Kalani", "given": "M. Yashar S." }, "id": "Kalani-M-Yashar-S", "orcid": "0000-0002-5923-1255", "display_name": "Kalani, M. Yashar S." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Wilson, Linda C." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Vaidehi", "given": "Nagarajan" }, "id": "Vaidehi-N", "role": "member", "display_name": "Vaidehi, Nagarajan" }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "biochem" ], "doi": "10.7907/T6NV-7W30", "abstract": "Dopamine neurotransmitter and its receptors play a critical role in cell signaling process responsible for information transfer in neurons functioning in the nervous system. Development of improved therapeutics for such disorders as Parkinson's and schizophrenia would be significantly enhanced with the availability of the three-dimensional (3-D) structure for the dopamine receptors and of the binding site for dopamine and other agonists and antagonists. In this thesis, I report the 3-D structures of the 5 subtypes of the human dopamine receptors, predicted from primary sequence using first principles theoretical and computational techniques. I use the term \"first principles\" to mean that we do not use the high resolution crystal structure of rhodopsin as a template, nor do we use homology modeling or threading of any kind to determine the structure. Predicting the binding sites, and the relative binding affinities of endogenous ligands and various pharmaceuticals to the 5 receptors validates the predicted structures. These structures correctly predict the critical residues for binding dopamine and several antagonists, identified by mutation studies and give relative binding affinities that correlate well with experiment. The predicted binding site for dopamine and agonists is located between transmembrane helices (TM) 3, 4, 5, and 6, while the best antagonists bind to a site involving TM helices 2, 3, 4, 6, and 7 with minimal contacts to TM 5. We identify characteristic differences between the binding sites of agonists and antagonists, as well as factors that cause differential binding to the 5 subtypes of the human dopamine receptors.
\r\n\r\nThis thesis consists of five chapters that have, or will shortly result in publications. The first chapter is a brief introduction to the field, the motivation for the project, my scientific contributions, and contribution of others on the team. Chapter two introduces the methods and their successes at reproducing experimentally known results for the human D2 dopamine receptor; it discusses, in great detail, the active site of pharmaceutical agonists and antagonists to the human D2 dopamine receptor, and highlights the strengths and shortcomings of homology modeling for membrane bound proteins; this chapter will be submitted for publication to the Journal of Molecular Biology. Chapter three reports the results of a blind study performed in collaboration with Aventis Pharmaceuticals. For this study, we were provided with the two-dimensional structure of 9 antagonists and were asked to predict their binding sites, binding affinities, and to explain the differential binding of the ligands to the human D2 and D3 dopamine receptors and the human a1A adrenergic receptor. The results of this study are in preparation for submission to the Journal of Medicinal Chemistry. Chapters four and five of the thesis give preliminary results of comparative studies of the agonist and antagonist binding sites of the five subtypes of the human dopamine receptors. Chapter 6 contains results of another blind study on the G2A receptor with Professor Owen Witte.
\r\n\r\nIn addition to the six main chapters, this thesis contains 6 independent appendices that report results of similar studies in other systems. The first 2 appendices are work that has already been published. The remaining 4 appendices will shortly result in publications, but at this time, they are not publication worthy; these appendices represent data that has been analyzed but has not been written in paper format.
\r\n\r\nIn addition, I would like to make note of the studies that I have conducted on the 9 subtypes of the human adrenergic receptors with Mr. Peter Freddolino, the 4 human histamine receptors that were conducted with Mr. Freddolino and Mr. Maziyar Kalani, and the 4 G2A-like lipid receptors conducted with Mr. Rene Trabanino, Dr. Radu, Dr. Yang, and Professor Owen Witte of the Howard Hughes Medical Institute at the David Geffen School of Medicine at the University of California, Los Angeles.
" }, { "name": "Kempe, Michael David", "degree": "PhD", "year": "2004", "title": "Rheology and Dynamics of Side-Group Liquid Crystalline Polymers in Nematic Solvents", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202003-103429", "creators": [ { "name": { "family": "Kempe", "given": "Michael David" }, "id": "Kempe-Michael-David", "orcid": "0000-0003-3312-0482", "display_name": "Kempe, Michael David" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/W41E-KB03", "abstract": "To form a liquid crystalline (LC) gel that retains the ability to respond rapidly to applied fields, it is necessary to work with low polymer concentrations. In turn, to form a dilute polymer network it is necessary to use very long polymers that are soluble in the small molecule LC. This research focuses on the synthesis of ultra-long side-group liquid crystalline polymers (SGLCPs), their properties when dissolved in nematic hosts, and the self-assembly of a nematic gel using an ABA triblock with an SGLCP midblock and LC-phobic end-blocks. Typically, LCs are made from small molecules that can be quickly reoriented. In applications such as artificial muscles, flexible displays, or compensating films, a more robust LC gel is desired. Prior routes to LC gels, typically using in situ polymerization, suffer from director misorientation, lack of control over cross-link density, polymer network inhomogeneity, undesired phase separation, and slow responses to applied fields. The present research (at the intersection of block copolymers, gels, and LCs) has demonstrated that an optically uniform LC gel with fast reorientational response can be achieved using a self-assembling ABA triblock copolymer.
\r\n\r\nTo provide the fundamental underpinning for the design of a self-assembling gel, we first advanced the synthesis of model SGLCPs that have well-defined length even at high degrees of polymerization. The polymerization method must provide narrow length distribution, be applicable to block copolymers, and preferably enable chains of varied side-group structure to be prepared. These requirements were met by starting from an anionically produced prepolymer and attaching the mesogen in a second step (a ?polymer analogous? approach). Homopolymers were made and characterized to determine how polymer structure affects solubility, rheological response, electro-optic response and chain conformation. This showed that cyanobiphenyl (CB) side-groups provide excellent solubility in CB-based small molecule LCs even for SGLCPs an order of magnitude longer than those investigated in solution previously; that ultra-long SGLCPs have unprecedented effects on the flow behavior of LC solutions, and that the anisotropy (R^/R?1.6) is insensitive to spacer length and degree of polymerization.
\r\n\r\nThe size of a polymer is related to the concentration necessary to form a gel network; however, there have been few studies of SGLCP dimensions in LC solvents. Since it is the polymer backbone conformation that is of interest, researchers use polymers labeled on the backbone to avoid scattering from the side groups. Unfortunately in a dilute solution this provides unacceptably low scattered intensity. Therefore, we demonstrate a method for measuring the dimensions of an unlabeled SGLCP in a perdeuterated nematic solvent, in which scattering originates from both the backbone and the pendant side groups. Since it is the backbone conformation that is of interest, we developed a method to mathematically account for scattering due to the side groups.
\r\n\r\nInformation gained from homopolymer studies guided the design of ABA block copolymers for nematic gels. We demonstrated that an optically uniform nematic gel can form in a small molecule LC even at low polymer concentrations using a triblock composed of an SGLCP center block and end-blocks that microphase separate to form physical cross-links. The key to making a dilute gel was using well-solvated, very long SGLCP midblocks. The necessity of cross-linking very dilute chain ends is prohibitive using covalent linking, but facile using end-blocks that spontaneously aggregate. In contrast to prior LC gels, these dilute gels maintain both the optical uniformity and fast reorientational responses of the small molecule LC host.
" }, { "name": "Kessler, Jacqueline Elizabeth", "degree": "PhD", "year": "2004", "title": "Gas and Dust Chemistry in Planet-Forming Disks", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222003-092836", "creators": [ { "name": { "family": "Kessler", "given": "Jacqueline Elizabeth" }, "id": "Kessler-Jacqueline-Elizabeth", "display_name": "Kessler, Jacqueline Elizabeth" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MGC6-WR47", "abstract": "As analogs to the solar nebula, circumstellar disks offer a unique opportunity to study the conditions during the star and planet formation process. Interpretation of molecular line observations is dependent on the development of extensive models of the chemistry and radiative transfer in accretion disks. In this study, several millimeter-wave molecular lines were observed toward a sample of disks encircling T Tauri and Herbig Ae stars with the Owens Valley Millimeter Array. The intent of these studies is the quantitative examination of the chemistry of the biogenic elements (C, N, O, S) in accretion disks. Toward this goal, radiative transfer models were modified for direct comparison with the observations to aid in the interpretation of molecular line emission and comparison with the predictions of chemical models, as discussed in Chapter 2. Chapter 3 presents a survey of CN, HCN, CO and HCO+ in 7 Herbig Ae and T Tauri star disks, which was performed in order to probe the effects of UV fields on disk chemistry. In this study, CN and HCO+ are found to be sensitive to the strength of the local UV field. The first interferometric studies of deuterium in disks were performed and are discussed in Chapter 4. HDO and DCN were detected toward the T Tauri disk LkCa 15 and the Herbig Ae disk HD 163296. The deuterium enrichments are similar to that of molecular clouds, hot cores, and comets, consistent with comet formation in the outer regions of disks. The distribution of HDO in LkCa 15 was found to be similar to predictions from chemical models, which suggest a steep gradient as a function of disk radius. Chapter 5 presents Keck LWS observations of the 8-13 micron silicate emission feature toward several T Tauri and Herbig Ae stars at various stages of the star formation process indicate an evolutionary trend similar to that previously seen with ISO for disks around intermediate mass stars. However, emission from crystalline silicates was only detected toward one low mass star, Hen 3-600A, possibly indicating that crystallization processes occur less frequently, or are more difficult to observe at mid-infrared wavelengths, in these disks. Finally, in Chapter 6, a summary of protoplanetary disk chemistry is presented and the future of the field is discussed." }, { "name": "Lambert, Tristan Hayes", "degree": "PhD", "year": "2004", "title": "Development of the Lewis Acid Catalyzed Allenoate-Claisen Rearrangement. Investigations of Enantioselective Catalysis of the Allenoate-Claisen Rearrangement. Studies Towards the Total Synthesis of Erythrolide E", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12112003-091509", "creators": [ { "name": { "family": "Lambert", "given": "Tristan Hayes" }, "id": "Lambert-Tristan-Hayes", "orcid": "0000-0002-7720-3290", "display_name": "Lambert, Tristan Hayes" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/QVJB-E506", "abstract": "The development of a new Lewis acid catalyzed sigmatropic reaction is described. This process, termed the allenoate-Claisen rearrangement, involves the metal-catalyzed condensation of an allenic ester with a tertiary allylic amine. The zwitterionic intermediate resulting from this condensation undergoes facile [3,3] bond reorganization to provide \u03b2-amino-\u03b1,\u03b2,\u03b5,\u03b6-unsaturated-\u03b3,\u03b4-disubstituted ester products. The allenoate-Claisen reaction has been demonstrated to allow for the production of a diverse range of Claisen adducts in high yield and with very high diastereoselectivities. Perhaps most notably, this process is amenable to the rapid generation of quaternary carbon stereogenicity with nearly complete stereocontrol.
\r\n\r\nInvestigations of an enantioselective catalytic variant of the allenoate-Claisen rearrangement have been initiated. Enantioselectivities of up to 49% have been achieved with the use of a titanium bis(binaphthyl) catalyst and a bidentate chelating allenic partner. The effects of solvent and method of catalyst preparation on enantioselectivity are described.
\r\n\r\nProgress towards the total synthesis of the briarane diterpene, erythrolide E, has been made. Using acyl-Claisen methodology developed in the MacMillan laboratories, both key fragments of the erythrolide framework have been prepared in racemic fashion. In addition, a highly enantioselective route to the core fragment has been developed using an enantioselective organocatalytic Diels-Alder reaction and Ireland-Claisen methodology.
" }, { "name": "Lesko, Timothy Michael", "degree": "PhD", "year": "2004", "title": "Chemical Effects of Acoustic Cavitation", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262004-184449", "creators": [ { "name": { "family": "Lesko", "given": "Timothy Michael" }, "id": "Lesko-Timothy-Michael", "display_name": "Lesko, Timothy Michael" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TY3J-F564", "abstract": "A novel high-frequency, high-power, pilot-plant scale sonochemical reactor was developed and used to study the degradation of organic pollutants in aqueous solutions. The degradation rates of trichloroethylene, dichloromethane, and phenol were found to exceed those of similar frequency, small-scale bench reactors by factors ranging from 2.5 to 7. Experiments with 10 \u00b5M methyl orange in the large reactor operating at different total volumes exhibited a linear dependence between the observed sonolytic rate constants and the applied power density. Likewise, steady-state \u2022OH-radical (aq) in each reactor were calculated and shown to correlate with the applied power density in the vessel.
\r\n\r\nThe sonochemical decomposition of phenol was further studied in a bench-scale ultrasound reactor combination with ozonolysis. The addition of ozone during sonication did not affect the first-order degradation rate constants of phenol compared to the linear combination of separate sonication and ozonation experiments. However, enhancement of the degradation rates of the total organic carbon (TOC) by 43% was observed for sonolytic ozonation compared to the separate sonication and ozonolysis experiments. The synergistic action of O\u2083 (aq) and ultrasound enhanced oxalate degradation rates 16-fold compared to the simple linear addition of the two independent systems. Several degradation pathways are considered which may account for the rate enhancements observed when ultrasonic irradiation is applied concurrently with ozonolysis.
\r\n\r\nIn addition, the decomposition of aqueous ozone in the presence of hydrogen peroxide was investigated. H\u2082O\u2082 enhances the reactivity of O\u2083 (aq) by reactions that remain obscure. Several free-radical degradation mechanisms for O\u2083 decomposition correctly predict the ozone-decay kinetics in pure water but vastly overestimate reaction rates in the presence of H\u2082O\u2082. Results from solvent deuteration experiments in neat water are compatible with a chain-process driven by electron transfer and/or O-transfer processes. However, the large kinetic isotope effect (KIE) found in the O\u2083/H\u2082O\u2082 system provides compelling evidence for an elementary reaction (O\u2083 + HO\u2082\u207b) involving H-O\u2082\u207b bond cleavage and does not support appreciable radical production from the O\u2083 + HO\u2082\u207b reaction. The magnitude of the observed KIE is consistent with a hydride transfer process yielding a closed-shell trioxide HO\u2083\u207b, the conjugate anion of H\u2082O\u2083.
" }, { "name": "Luo, Wen-I", "degree": "Masters", "year": "2004", "title": "The Role of Fucose in Learning and Memory: the Identification of a Fucosylprotein, Synapsin I, in the Rat Brain and the Characterization of its Fucosylation", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262013-154211086", "creators": [ { "name": { "family": "Luo", "given": "Wen-I" }, "id": "Luo-Wen-I", "display_name": "Luo, Wen-I" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P7ZV-C811", "abstract": "Previous studies have shown that the glycoproteins containing the fucose moiety are involved in neuronal communication phenomena such as long-term potentiation and memory formation. These results imply that fucose containing glycoproteins might play an important role in learning and memory. To understand the role of fucose in neuronal communication, and the mechanisms by which fucose may be involved in information storage, the identification of fucosylproteins is essential. This report describes the identification and characterization of fucosylproteins in the brain, which will provide new insights into the role of the fucose involved molecular interactions.\r\n" }, { "name": "Mayo, Elizabeth Idonia", "degree": "PhD", "year": "2004", "title": "Kinetics and Thermodynamics of Dye (Group VIII Metal)\u2013Sensitized Nanocrystalline Titanium Dioxide Photoelectrodes", "advisor": "Gray, Harry B.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-06042004-153530", "creators": [ { "name": { "family": "Mayo", "given": "Elizabeth Idonia" }, "id": "Mayo-Elizabeth-Idonia", "display_name": "Mayo, Elizabeth Idonia" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E9WY-1N05", "abstract": "This thesis reports a comprehensive series of experiments involving complementary kinetics and thermodynamic measurements directed at isolating the important individual reactions in dye-sensitized nanocrystalline titanium dioxide solar cells (DSSCs). These experiments were done in conjunction with steady-state photoelectrochemical measurements; a combination which allowed a greater understanding of the overall mechanisms and driving forces of these systems.
\r\n\r\nAlternative two-electron redox couples were studied and efficiency increases of >40% were achieved when compared to similar systems using iodide/triiodide. Surface treatment with carboxylic acids minimized direct reduction of the redox couple by electrons in the titanium dioxide, and interestingly, the photocurrent also increased resulting in overall efficiency increases as high as 20%. Bridging ligands were used in an attempt to minimize recombination of the injected electrons with the resulting oxidized dyes, but DSSCs with these sensitizers showed poor conversion efficiencies and no distance dependence for injection or recombination was observed. The lack of distance dependence was attributed to the flexible single carboxyl anchoring group. To further investigate the effect of binding mode, a series of carboxyl-modified ruthenium bipyridyl sensitizers were studied. A single carboxyl anchoring group resulted in unstable DSSCs due to enhanced desorption as well as poor photon-to-current conversion efficiencies. These dyes injected efficiently into TiO\u2082 on the nanosecond timescale, and regeneration of the oxidized sensitizers competed effectively with recombination. Consequently, individual kinetics measurements could not explain the decreased steady-state performance. The regeneration rates of these dyes in solution were found to rapid, approaching the diffusion controlled limit. The regeneration rate was dependent on the number and electron-withdrawing nature of the pendant groups, with the rate decreasing with increasing number of electron withdrawing substituents. Iridium dyes with cyclometalating ligands were shown to be efficient sensitizers in DSSCs, with quantum yields on the order of a ruthenium analogue having similar spectral overlap. Overall, the repeated inconsistencies between the steady-state behavior and the measured individual kinetics processes indicate that the current kinetic model is insufficient to accurately predict photoelectrochemical behavior.
" }, { "name": "Monahan, Sarah Lynn", "degree": "PhD", "year": "2004", "title": "Site-Specific Incorporation of Unnatural Amino Acids into Receptors Expressed in Mammalian Cells", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252004-153512", "creators": [ { "name": { "family": "Monahan", "given": "Sarah Lynn" }, "id": "Monahan-Sarah-Lynn", "display_name": "Monahan, Sarah Lynn" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/B00K-QH65", "abstract": "Unnatural amino acid incorporation into proteins by nonsense suppression has proven to be a valuable tool for structure-function studies. Using the in vivo nonsense suppression methodology, information on ligand binding and ion channel gating mechanisms has been obtained on a variety of ion channels. To date, such studies have been limited to the Xenopus oocyte heterologous expression system. There would be clear benefits to expanding the technology to a mammalian cell expression system. This would provide a more relevant environment for many proteins of mammalian origin and would allow for studies of cell-specific signal transduction pathways.
\r\n\r\nWe describe here unnatural amino acid incorporation into channels and receptors expressed in mammalian cells. Presented is a general method to deliver mRNA or DNA that codes for a protein of interest, amber suppressor tRNA, and a reporter gene to mammalian cells. Chapter 2 describes in detail the screening of several suppressor tRNAs, as well as various transfection methods tested for tRNA delivery including electroporation, lipofection, peptide-mediated transfection and biolistics. It was found that electroporation was the best method to deliver tRNA to adherent cells, and that THG73 was the most efficient suppressor tRNA. Chapter 3 describes studies, aimed at optimizing the protocol, that involved co-electroporation of a human serine amber suppressor tRNA with the DNA or mRNA corresponding to the protein of interest into adherent cells. This leads to highly efficient delivery of these components and efficient nonsense suppression. We demonstrate this for both enhanced green fluorescent protein and nicotinic acetylcholine receptor expression in CHO-K1 cells. We also show that the approach is successful in cultured hippocampal neurons. Finally, Chapter 4 demonstrates the application of the electroporation method to the delivery of aminoacyl-tRNA to cells for unnatural amino acid incorporation into the nicotinic acetylcholine receptor. When chemically aminoacylated with natural or unnatural amino acids, THG73 delivers the amino acid site-specifically into receptors expressed in CHO-K1 cells. Electrophysiology clearly reveals the expected shift in dose-response relations, establishing that the desired unnatural amino acid has been incorporated. In conclusion, we describe the first general method for unnatural amino acid incorporation in mammalian cells.
" }, { "name": "Paik, Daniel Hern", "degree": "PhD", "year": "2004", "title": "Femtosecond Time-Resolved Spectroscopy of Anionic Systems: Dynamics of Mesoscopic Solvation and Gas-Phase Organic Reactions", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272004-213231", "creators": [ { "name": { "family": "Paik", "given": "Daniel Hern" }, "id": "Paik-Daniel-Hern", "display_name": "Paik, Daniel Hern" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/W687-V550", "abstract": "This thesis work presents the femtosecond time-resolved spectroscopy of anionic systems ranging from gas-phase organic molecules to the finite-sized molecular clusters. The subject matter in this thesis is twofold: Mesoscopic solvation of anionic clusters and transition state dynamics of neutral organic molecules.
\r\n\r\nSolvation dynamics in the finite sized clusters were investigated at the molecular level of details. The main objective of the cluster study was to follow the evolution of cluster properties as function of cluster size. Ultrafast processes exhibited in the cluster systems were investigated by utilizing the femtosecond time-resolved anion photoelectron spectroscopy. The bond rupture and solvent evaporation of homogeneous and heterogeneous clusters were studied, and the correlation between the dissociation rates and the cluster size is obtained. Gas-phase analogues of solvated systems were studied, and the key steps involved in the solvation dynamics are highlighted.
\r\n\r\nDirect probing of the transition state dynamics in the ground state is studied with femtosecond time resolution. The transition state of the ring inversion reaction of cyclooctatetraene was directly accessed by the vertical detachment from the planar anion. The subsequent nuclear motion was then probed by ionization mass spectrometry. The oscillatory feature observed in the transients reflects trajectories of motion (resonance) along the reaction coordinate, and comparison with theory is reported. This work demonstrated the applicability of the charge reversal scheme to a complex organic system and suggests the possibility of studying ground-state thermal organic reactions with their transition states resolved in real time.
" }, { "name": "Paras, Nick Anthony", "degree": "PhD", "year": "2004", "title": "Enantioselective Organocatalytic Friedel-Crafts Alkylations of Heterocycles and Electron-Rich Benzenes", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012004-190154", "creators": [ { "name": { "family": "Paras", "given": "Nick Anthony" }, "id": "Paras-Nick-Anthony", "orcid": "0000-0001-5742-4056", "display_name": "Paras, Nick Anthony" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EFG2-7V87", "abstract": "The development of the first organocatalytic asymmetric Friedel-Crafts alkylation is described in the context of conjugate additions of pyrroles to a,b-unsaturated aldehydes. Catalytic amounts of chiral imidazolidinone salts are used to activate the electrophile component via reversible formation of iminium ions. Ensuing conjugate additions of pyrroles afford aldehyde products in good yield and high enantiopurity using a range of alkyl-, aryl-, and heteroatom-substituted enals and nucleophiles. This reaction demonstrates the feasibility of using iminium catalysis to promote reactions of electron-deficient olefins beyond simple cycloaddition reactions. Observations were also made regarding the role of Bronsted acid cocatalysts in these organocatalytic reactions. The synthetic utility of asymmetric conjugate additions of pyrroles was demonstrated in a concise, enantioselective synthesis of the analgesic Ketorolac.
\r\n\r\nAn enantioselective organocatalytic conjugate addition of electron-rich benzenes to a,b-unsaturated aldehydes has been developed. A new chiral secondary amine promotes exclusive para-alkylation of dialkylamino-substituted benzenes in good yield and with a high degree of stereocontrol. The process tolerates a range of substitutents on the electrophile component as well as a high degree of flexibility in the ortho- and meta-positions on the benzene ring. Particularly, the unique ability of this methodology to efficiently generate bisbenzyllic stereocenters by addition of electron-rich benzenes to cinnamaldehyde derivatives is demonstrated.
\r\n\r\nA general procedure for the cleavage of dialkylamino substituents from aromatic rings has also been developed. To accomplish this cleavage, a dialkylaniline is first converted to the corresponding quaternary ammonium salt with methyl iodide or methyl trifluromethanesulfonate. In a second step, dissolving metal reduction of the salt liberates the deaminated arene in high yields for the overall process. A range of alkyl, aryl, and heteroatom substitutions at the ortho, meta, and para positions were tolerated without significant decrease in reaction efficiency or yield. Deamination of aniline substrates bearing stereogenic centers para to the dialkylamino functionality proceeded with complete retention of enantiopurity. The combined utility of the asymmetric aniline alkylation and the new deamination methodology was demonstrated in the first enantioselective synthesis of the anticholinergic drug (R)-Tolterodine.
" }, { "name": "Robinson, Noah Edward", "degree": "PhD", "year": "2004", "title": "Investigations of Peptide and Protein Deamidation", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09212004-154502", "creators": [ { "name": { "family": "Robinson", "given": "Noah Edward" }, "id": "Robinson-Noah-Edward", "display_name": "Robinson, Noah Edward" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JHAP-JG47", "abstract": "This work concerns the peptide and protein deamidation of asparaginyl, Asn, and glutaminyl, Gln, residues to aspartyl and glutamyl residues, respectively. This is accompanied by a change in charge and increase of one unit in mass. Isomerization also often takes place. This reaction--which occurs spontaneously and non-enzymatically in many proteins under physiological conditions--has been hypothesized to be a general molecular clock, which could be used as a timer for protein turnover, development, or aging, and for the controlled conversion of one protein into another. Since this hypothesis was first proposed, amide molecular clocks have been demonstrated in several biological systems. These include the timing of protein turnover in rat cytochrome c and aldolase; the counting of individual enzyme molecule catalytic cycles in triosephosphate isomerase; and the resetable time-dependent monitoring of DNA repair in Bcl-XL.
\r\n\r\nThe objective of this work is to increase the understanding of peptide and protein deamidation, especially the prediction of deamidation rates for specific amides in proteins. This capability has been developed for Asn residues in proteins of known three-dimensional structure, and the sequence information required to do this for Gln residues has also been obtained. This work provides stability information to protein chemists and needed information to those who continue to investigate the molecular clock hypothesis.
\r\n\r\nThe problem was attacked in two phases. The first consisted of experimental work to determine the rate of deamidation as a function of primary sequence near the amide. All 400 possible peptides of the type GlyXxxAsnYyyGly were synthesized and the deamidation rates of 323 of these were measured. An additional 67 asparaginyl containing peptides that had a variety of lengths and forms were also measured in order to assess the efficacy of pentapeptides in this work. Also, a similar set of 400 peptides were synthesized with Gln in place of Asn. The deamidation rates of 52 of the Gln peptides have been measured and, from these rates, the rates of the other Gln peptides have been inferred. With the addition of rates for 34 peptides with blocked Cys, a total of 476 individual rate experiments on peptides have been carried out in 0.15 M Tris buffer at pH 7.4, 37.00 [degrees]C. Additional rate experiments were conducted on solution effects and on properties of the experimental system.
\r\n\r\nThe second phase involved using experimental data from the literature--on relative instabilities of specific amides in proteins under specified solvent conditions and on protein three-dimensional structures--to quantify the effect that secondary, tertiary, and quaternary protein structure has on primary structure deamidation rates.
\r\n\r\nFactors that determine deamidation rates include structural components as well as electronic effects. It happens that the primary sequence component is so large that it is possible to separate it from the rest of the problem and measure it alone. The secondary, tertiary, and quaternary effects were then considered. It was found that, on average, 60% of the rate is accounted for by primary sequence, while the remaining 40% is ascribable to secondary, tertiary, and quaternary structure in those proteins for which suitable deamidation observations are available. For all proteins, the estimated values are 50% and 50%. For individual amides, these percentages vary over a wide range.
\r\n\r\nA procedure was developed through which the quantitative deamidation rate of any amide in a protein for which the three-dimensional structure is known can be calculated. These estimated rates are accurate to within about a factor of two or better for most amides with half-times less than 100 days. They can be used to predict the fastest amides in a protein to greater than 95% reliability. This reliability is remarkable, considering the fact that deamidation half-times vary from less than 1 day to over 100 years in 37.00 [degrees]C, pH 7.4, 0.15 M Tris buffer. The procedure was calibrated with only relative amide instabilities. It was then evaluated with absolute deamidation rates.
\r\n\r\nDetails of this work are given in the pages which follow. The result was a computerized procedure through which deamidation rates for every Asn of every protein in the PDB Protein Database were calculated and analyzed.
\r\n\r\nThis work provides two discoveries of biological importance.
\r\n\r\nFirst, the assumption of genetic determination of deamidation rates, which has until now been dependent upon scattered and largely qualitative observations, has been placed upon firm quantitative foundation with a thorough understanding of the effects of primary, secondary, and tertiary structure.
\r\n\r\nSecond, this quantitative understanding has permitted reliable estimation of the distribution functions of deamidation rates in thousands of proteins. These rates show that a substantial fraction of proteins are genetically programmed to deamidate in biologically relevant timed intervals even though most of the genetically available structures deamidate more slowly. This quantitative preference for fast deamidation times relative to slow deamidation times is an entirely new discovery. The fact that this property is present within the thousands of proteins of currently known three-dimensional structure markedly strengthens the molecular clock hypothesis.
\r\n" }, { "name": "Scherman, Oren Alexander", "degree": "PhD", "year": "2004", "title": "Enhancing Materials Through Controlled Architectures with Ring-Opening Metathesis Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02272004-034648", "creators": [ { "name": { "family": "Scherman", "given": "Oren Alexander" }, "id": "Scherman-Oren-Alexander", "orcid": "0000-0001-8032-7166", "display_name": "Scherman, Oren Alexander" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E1BS-HG72", "abstract": "The focus of the research presented in this thesis is the synthesis of functional polymers and construction of controlled molecular architectures through a polymerization process referred to as ring-opening metathesis polymerization (ROMP). A brief overview of polymer chemistry as well as ring-olefin metathesis polymerization is discussed in introductory Chapter 1.
\r\n\r\nChapters 2 and 3 discuss new synthetic routes to polyacetylene and polyacetylene block-copolymers from cyclooctatetraene and a new ruthenium olefin metathesis catalysts. Polyacetylene is an intractable material, as are most organic conducting polymers. Chapter 3, however, introduces a novel route to soluble telechelic polyenes and polyacetylene block-copolymers.
\r\n\r\nThe construction of organic overlayers on semiconductor surfaces is important in the area of anti-fouling coatings as well as in organic electronic applications. Chapter 4 introduces a new route to polymer-covered silicon surfaces through a covalent Si-C linkage. ROMP of norbornene from a surface-attached ruthenium catalyst produces uniform polynorbornene overlayers with controlled thickness ranging from 10 \u00c5 to 5.5 \u00b5m. The work discussed in Chapter 5 elaborates on surface-initiated ROMP by constructing thin-film top-contact field effect transistors with a polynorbornene dielectric layer.
\r\n\r\nChapter 6 explores the synthesis of polar-functionalized linear polymers from cyclopentene and cycloheptene derivatives. The challenge of polymerizing low-ring strain monomers via ROMP is also discussed. A method to a priori discern a monomer's ability to undergo ROMP is outlined in this chapter as well.
\r\n\r\nChapters 7 and 8 describe the synthesis of both regioregular and stereoregular polar-functionalized linear ethylene vinyl alcohol (EVOH) co-polymers by the ROMP of rationally designed, symmetric monomers. These polymers were made with the goal of producing materials with enhanced oxygen barrier properties. Controlling material architecture imparts a dramatic effect on both the solution and solid state morphologies of EVOH and the synthetic challenges and results are discussed.
\r\n\r\nFinally, Chapter 9 complements Chapters 7 and 8, and investigates the reason behind enhanced oxygen barrier properties of EVOH through molecular dynamics simulations. For EVOH polymers that differs only by the syn or anti orientation of neighboring diols, a clear difference is observed for the hydrogen bonding clusters. Moreover, the free volume accessible to any solute molecules is extremely low identified by a probe radius of less than 0.6 \u00c5.
" }, { "name": "Schofer, Susan Jessica", "degree": "PhD", "year": "2004", "title": "The Effect of Ligand Array on Stereocontrol and Molecular Weight in Metallocene-Catalyzed \u03b1-Olefin Polymerization and (PNP)CrPh\u2083 Complexes as Well-Defined Ethylene Trimerization Catalysts", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06042004-173118", "creators": [ { "name": { "family": "Schofer", "given": "Susan Jessica" }, "id": "Schofer-Susan-Jessica", "display_name": "Schofer, Susan Jessica" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/F04S-0S62", "abstract": "A series of neutral and cationic group 4 and neutral group 3 model complexes of the Me\u2082Si(\u03b7\u2075-C\u2085H\u2084)(\u03b7\u2075-3-(CMe\u2083)-C\u2085H\u2083)(tBuSp) ligand have been prepared: tBuSpZrCl\u2082(1), tBuSpZr(CH\u2082SiMe\u2083)\u2082 (8), tBuSpZrMe\u2082 (9), [tBuSpZrH\u2082]\u2082 (10), tBuSpZrMeCl (11), tBuSpZrMe(CH\u2082CMe\u2083) (12), tBuSpZrMe(CH\u2082SiMe\u2083) (13), tBuSpScCl(THF) (14), tBuSpScCH(SiMe\u2083)\u2082 (17), [tBuSpScH] (18), and tBuSpTiCl\u2082 (19). The kinetically preferred isomers of 12 and 13 have been identified, and in both cases the syn isomer is preferred. We have obtained solid state structures of [tBuSpZrH\u2082]\u2082 (10), tBuSpZrMeCl (11), tBuSpZrMe(CH\u2082CMe\u2083) (12), and tBuSpScCl(THF) (14). Complexes 12 and 13 isomerize to form predominantly the thermodynamically preferred anti isomers. The ratio of isomers observed for [tBuSpZrMe]\u207a[MeB(C\u2086F\u2085)\u2083]\u207b (21) and [tBuSpZrCH\u2082SiMe\u2083]\u207a[Me B(C\u2086F\u2085)\u2083]\u207b (22) suggests that the tBuSp ligand does not distinguish very well between different groups in the metallocene wedge ([delta]G = 0.27-0.89 kcal/mol). The tBu group is not an effective stereodirector in the ground state structures and the remarkable stereodirecting capability of this ligand in propylene polymerizations must be reconciled by its effect on transition state energies.
\r\n\r\nA series of scandocene tetramethylaluminate have been prepared, including Ind\u2082Sc(\u03bc-Me)\u2082AlMe\u2082 (1), Cp\u2082Sc(\u03bc-Me)\u2082AlMe\u2082 (2), Cp*CpSc(\u03bc-Me)\u2082AlMe\u2082 (3), and meso-DpSc(\u03bc-Me)\u2082AlMe\u2082 (4). These complexes display characteristic terminal and bridging methyl resonances in solution at room temperature, indicating static structures. Complexes 1-4 oligomerize 1-pentene to form a range of oligomers. The tetramethylaluminate complexes initiate oligomerization from a scandium-methyl species after dissociation of AlMe\u2083, and the primary mechanism of chain transfer is \u03b2-hydrogen elimination. Complexes 1-4 react with L donors (L = DMAP, THF, PMe\u2083) to form (RnCp)\u2082ScMe(L) compounds (5-9).
\r\n\r\nTo study the chromium-based ethylene trimerization catalyst involving the diphosphine ligand (o-MeO-C\u2086H\u2084)\u2082PN(Me)P(o-MeO-C\u2086H\u2084)\u2082 (PNPOMe (1)), we have synthesized (PNPOMe-d\u2081\u2082)CrPh\u2083 (11), (PNPSMe-d12)CrPh\u2083, (12), and (PNPOMe-d12)CrPh2Cl (14) containing deuterated PNP ligands. Activation of 11 by protonation with H\u207a(OEt\u2082)\u2082B[C\u2086H\u2083(CF\u2083)\u2082]\u2084- in the presence of ethylene provides an active trimerization catalyst that gives similar selectivity and activity to 1-hexene as the originally reported system and represents the first examples of an active, well-defined trimerization catalyst based on chromium. The trimerization of a 1:1 mixture of C\u2082H\u2084 and C\u2082D\u2084 gives only C\u2086D\u2081\u2082, C\u2086D\u2088H\u2084, C\u2086D\u2084H\u2088, and C\u2086H\u2081\u2082, the 1-hexene isotopomers without H/D scrambling, which is consistent with a trimerization mechanism involving metallacyclic intermediates.
" }, { "name": "Starck, Shelley Ruth", "degree": "PhD", "year": "2004", "title": "Exploring the Proteome: Insights into Eukaryotic Protein Synthesis Using Puromycin Analogs", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012004-235945", "creators": [ { "name": { "family": "Starck", "given": "Shelley Ruth" }, "id": "Starck-Shelley-Ruth", "display_name": "Starck, Shelley Ruth" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WKXS-KM18", "abstract": "Puromycin is a protein synthesis inhibitor that acts as a structural analog of an aminoacyl-tRNA. The ribosome mistakenly inserts puromycin in place of aminoacyl-tRNA resulting in truncated proteins containing the drug at their C-terminus. Herein, the puromycin reaction is re-examined in a cell-free eukaryotic translation extract and in live cells. The framework for puromycin reactivity in terms of potency, product distribution, and mechanism is studied in vitro. These insights are used to develop a series of fluorescent puromycin-based reagents to detect protein expression in living cells that does not require transfection, radiolabeling, or the prior choice of a candidate gene. Further, puromycin is used to examine the stereo- and regiochemical nature of protein synthesis both in vitro and in vivo. These data indicate that the ribosome tolerates a broader range of substrates than previously recognized, including D-amino acids. Overall, these studies yield a series of insights about protein synthesis and the ribosome, including mechanistic observations, the development of reagents to explore the proteome, and a theory about the evolution of amino acid homochirality" }, { "name": "Thomas, John Christopher", "degree": "PhD", "year": "2004", "title": "Ligand Design, Coordination Chemistry, and Mechanistic Studies of (Phosphino)Borates and their Platinum, Nickel, and Copper Complexes", "advisor": "Peters, Jonas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012004-115510", "creators": [ { "name": { "family": "Thomas", "given": "John Christopher" }, "id": "Thomas-John-Christopher", "display_name": "Thomas, John Christopher" } ], "advisors": [ { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "advisor", "display_name": "Peters, Jonas C." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/GCAQ-8D59", "abstract": "Synthetic methods are presented for the preparation of various substituted bis(phosphino)borates. A relatively general protocol based on the delivery of a nucleophilic phosphine-containing carbanion to a borane electrophile has been developed. Preparative methods for the synthesis of substituted diarylchloroboranes from dimethyldiaryltin reagents provide the borane electrophiles. Methyldialkyl- or methyldiarylphosphines are selectively deprotonated at the phosphine-methyl using alkyl lithium bases to form the carbanion nucleophiles. The reaction of diverse phosphine-containing carbanions with diarylchloroboranes results in bis(phosphino)borates selectively substituted at the borate, at the phosphine, or at both positions. In addition to the generated lithium salts of the bis(phosphino)borates, cation-exchange protocols provide methods for preparing ammonium and thallium bis(phosphino)borate salts. Structural data for some of these derivatives are presented.
\r\n\r\nThe electronic properties of transition metals coordinated by bis(phosphino)borates are explored through NMR and IR spectroscopies. The spectroscopic features of platinum(II) dimethyl and methyl carbonyl complexes are examined for trends based on the substitution pattern of the (phosphino)borate ligand. These trends indicate that phosphine substituents have a more significant impact than borate substituents on electronics of the metal center. Structural and spectroscopic comparisons of structurally similar platinum(II) dimethyl and methyl carbonyl complexes indicate that the anionic bis(phosphino)borate ligand renders platinum(II) more electron-rich than structurally similar neutral phosphine donors. Related spectroscopic studies of anionic and neutral molybdenum(0) tetracarbonyl complexes provide results analogous to those found when comparing neutral and cationic platinum(II) systems.
\r\n\r\nComparative studies on the ligand exchange and benzene C-H activation chemistry of structurally similar platinum(II) complexes convey the similarities and differences between zwitterionic and cationic systems. Examination of THF ligand self-exchange by magnetization transfer shows a change in mechanism between the neutral and cationic species. Both bis(phosphino)borate-ligated and neutral bis(phosphine) platinum methyl solvento complexes undergo a benzene C-H activation to form the corresponding phenyl solvento complex; however, the rates of reaction and ultimate products differ. Extensive isotopic studies indicate that the zwitterionic system forms observable intermediates prior to benzene C-H activation, some of which are attributable to ligand metalation processes.
\r\n\r\nStructural and spectroscopic studies of a phenyl-substituted tris(phosphino)borate on platinum are presented. Alkyl- and hydride-containing platinum(II) and platinum(IV) species have been synthesized. The structural and spectroscopic features of these complexes are compared to related tris(pyrazolyl)borate systems on platinum.
\r\n\r\nCoordination and reaction chemistry of an isopropyl-substituted tris(phosphino)borate on nickel are discussed. Complexes in the Ni(II), Ni(I), and Ni(0) oxidation states have been prepared. This system is compared through structural, spectroscopic, and electrochemical methods to related phenyl-substituted tris(phosphino)borate chemistry on nickel. Reactivity studies aimed at preparing Ni(III) and Ni(IV) complexes containing metal-ligand multiple bonds through group-transfer reactions are presented. Theoretical studies using density functional methods are used to probe several target species containing multiply-bonded ligands.
\r\n\r\nThe coordination chemistry of copper(I) is explored using bis(phosphino)borates. Both aryl- and alkyl-substituted bis(phosphino)borates provide access to copper(I) complexes. A tert-butyl-substituted bis(phosphino)borate is particularly useful for preparing a family of three-coordinate compounds. The spectroscopic and structural features of these complexes are compared with similar, previously described examples.
" }, { "name": "Trabanino, Rene Jouvanni", "degree": "PhD", "year": "2004", "title": "Prediction of Structure, Function, and Spectroscopic Properties of G-Protein-Coupled Receptors: Methods and Applications", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05202004-174324", "creators": [ { "name": { "family": "Trabanino", "given": "Rene Jouvanni" }, "id": "Trabanino-Rene-Jouvanni", "display_name": "Trabanino, Rene Jouvanni" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VHED-4063", "abstract": "G-protein-coupled receptors are of great pharmaceutical interest, comprising the majority of targets for currently marketed drugs. The theme of my thesis is the development of the structure prediction method, MembStruk, for the superfamily of G-protein-coupled receptors. The first part of this thesis focuses on the methods and their validation. There are several steps involved in MembStruk that are detailed and tested for membrane proteins with known structures in the first few chapters (Chapters 2-6). Specifically, the first principles methods for predicting the transmembrane helical ranges and the helix hydrophobic centers are tested. The program for predicting the transmembrane helical ranges, TM2ndS, ranks in the top two when comparing performance with other top prediction methods. And because it is based on general principles, it can be applied robustly for membrane protein families for which little structural information is available. The simulation of the EC-II closing is also tested on bovine rhodopsin. The use of the MembStruk method on bovine rhodopsin as a validation case is presented in detail (Chapter 2). The large majority (71%) of the residues involved in binding in rhodopsin are predicted and the protein structure itself is 2.84 \u00c5 coordinate root mean square error in the transmembrane main chain atoms from the crystal structure.
\r\n\r\nThe second part of the thesis discusses applications on various G-protein-coupled receptor systems. The application of the MembStruk method to other peptide chemokine G-protein-coupled receptors like CCR1 and CCR5 is discussed in Chapter 9. The fundamental scientific problems of G-protein-coupled receptor modulation of absorption and relaxation properties of a bound chromophore (retinal) are addressed and results are presented for the predictions of these properties.
\r\n\r\nThe prediction of structure and function of G-protein-coupled receptors would allow for structure-based drug design and a rational approach to reducing drug cross-reactivity across receptor families.
" }, { "name": "VanReken, Timothy Mark", "degree": "PhD", "year": "2004", "title": "Understanding the Relationship between Aerosols and Clouds: Field Investigations and Instrument Development", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11142003-134303", "creators": [ { "name": { "family": "VanReken", "given": "Timothy Mark" }, "id": "VanReken-Timothy-Mark", "orcid": "0000-0002-2645-4911", "display_name": "VanReken, Timothy Mark" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Jonsson", "given": "Haflidi H." }, "id": "Jonsson-H-H", "role": "member", "display_name": "Jonsson, Haflidi H." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/TGKK-QB38", "abstract": "The research presented in this thesis is part of the ongoing effort to better understand the role of atmospheric aerosols in the development of clouds. Cloud condensation nuclei (CCN) are the subset of the aerosol population that can activate and grow into cloud droplets under suitable atmospheric conditions. The supersaturation at which a given CCN will activate is dependent on the particle's size and composition, but the details of the relationship are not completely understood. CCN observations from the CRYSTAL-FACE (Cirrus Regional Study of Tropical Anvils and Cirrus Layers- Florida Area Cirrus Experiment) field campaign are presented in Chapter 2. These measurements are compared to predictions based on measured aerosol size distributions with an assumed chemical composition to determine whether activation theory is sufficient to describe what is observed. The analysis indicates that, in cases like those included in the study, CCN concentrations can be accurately predicted from the size distribution even in the absence of detailed chemical compositional data.
\r\n\r\nA case study is described in Chapter 3 to demonstrate the potential importance of anthropogenic aerosols in the development of clouds. During a CRYSTAL-FACE flight, an aerosol plume was encountered in the boundary layer near the base of a large mixed-phase convective cloud. Evidence suggests that an oil-burning power plant south of Miami was the likely source of the plume. The convective cloud was probed at higher altitudes, and a spatial gradient was observed in the ice particle concentrations. The evidence linking the plume in the boundary layer to the upper-level trends is inconclusive, but worthy of further study.
\r\n\r\nThe measurement of CCN in the atmosphere is difficult, and improved instrumentation would significantly improve our ability to obtain the detailed information necessary to understand the relationship between aerosols and clouds. The concept for an improved CCN spectrometer is outlined in Chapter 4; this new design would expand the resolvable range of supersaturations for which data can be obtained. The dependence of the instrument's performance on various design parameters is evaluated, and a configuration is proposed that would be a significant improvement over currently available instrumentation.
" }, { "name": "Wang, Pin", "degree": "PhD", "year": "2004", "title": "Expanding the Biosynthetic Capacity of the Aminoacyl-tRNA Synthetases", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12172003-140435", "creators": [ { "name": { "family": "Wang", "given": "Pin" }, "id": "Wang-Pin", "display_name": "Wang, Pin" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemeng" ], "doi": "10.7907/99W6-8F08", "abstract": "Incorporation of non-natural amino acids into proteins in vivo can provide biological materials with new chemical functions and improved physical properties. Examples include new posttranslational modification chemistry by introducing azide and ketone moieties into recombinant proteins, and novel strategies for engineering hyper-stable proteins by incorporating fluorinated side chains. Implementing such methods requires manipulation of protein biosynthesis to specifically alter the genetic code. The rules of the genetic code are established by the aminoacylation reaction, where the aminoacyl-tRNA synthetases (aaRS) catalyze the attachment of the amino acids to their cognate tRNAs. Thus manipulation of cellular aminoacylation reactions could potentially expand the available set of amino acid building blocks for protein engineering and biomaterials engineering.
\r\n\r\nBy simple depletion of the cellular pool of isoleucine and utilization of isoleucine auxotrophic hosts, we were able to force the endogenous isoleucyl-tRNA synthetase to join 5,5,5-trifluoroisoleucine (5TFI) to tRNAIle and assign it to isoleucine codons in vivo. Murine interleukin 2 containing 5TFI retains its biological activity. We showed that engineering of bacterial expression hosts can allow a single RNA message to be read in different ways, depending on the relative rates of competing aminoacylation reactions. Specifically, we showed that the 2S,3R-form of 4,4,4-trifluorovaline can be assigned either to isoleucine or to valine codons, depending on whether the bacterial host overexpresses the isoleucyl- or the valyl-tRNA synthetase. When an amino acid analog of interest is not recognized by the corresponding wild-type aaRS, we can either identify the appropriate modification of the amino acid as a promising ligand or design new synthetase activity. We describe an attempt to develop a virtual ligand screening method to find non-natural amino acids that can serve as ligands for the phenylalanyl-tRNA synthetase and our computational results correlate well with experimental results in vitro and in vivo. We also present a computational method for identifying the sites of mutations to relax the substrate specificity of the E. coli phenylalanyl-tRNA synthetase (ePheRS). One designed variant of ePheRS allows the efficient in vivo incorporation of aryl ketone functionality into proteins in vivo. Proteins outfitted with ketone functionality can be chemoselectively ligated with hydrazide reagents under mild conditions. Three designed mutants of ePheRS were subjected to extensive examination, and a broad activation profile toward many non-natural aromatic amino acids was observed. E. coli host strains were established to over-express these mutant ePheRSs, enabling the re-assignment of the Phe codons to many non-natural amino acids. By rational attenuation of the editing function of a leucyl-tRNA synthetase, oxonorvaline was incorporated into a recombinant protein in Escherichia coli.
\r\n\r\nThe work described above addresses the multi-site incorporation of new amino acids into proteins in vivo, which can be utilized to engineer the overall properties of biomacromolecules such as protein stability. The second component of this thesis focused on the site-specific incorporation of novel amino acids into proteins in vivo, which can be applied to problems that require local change of protein behavior. We have refined a previously described system, where we introduce a mutant form of yeast PheRS co-transformed with a cognate suppressor tRNA, allowing incorporation of several aromatic amino acids into proteins in response to an amber codon. The results firmly demonstrate the general strategy of importing an exogenous synthetase/tRNA pair to achieve site-specific incorporation of non-natural amino acids into proteins in vivo.
" }, { "name": "Ward, Donald William", "degree": "PhD", "year": "2004", "title": "Stereoselective Ruthenium-Catalyzed Olefin Metathesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07152003-183214", "creators": [ { "name": { "family": "Ward", "given": "Donald William" }, "id": "Ward-Donald-William", "display_name": "Ward, Donald William" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zxw4-av70", "abstract": "Ruthenium complexes ligated with N-heterocyclic carbenes, such as (IMesH2)(PCy3)(Cl)2Ru=CHPh [IMesH2 = 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene], constitute the latest class of olefin metathesis catalysts and are particularly desirable for their high activity and tolerance of most common functional groups. This thesis primarily describes studies aimed at understanding and controlling the stereoselectivity of this type of complex, including enantioselectivity and cis/trans selectivity.
\r\n\r\nChapter 2 describes the basic design of novel chiral N-heterocyclic carbene ruthenium complexes active for olefin metathesis. A series of catalysts based on this design is prepared and studied by variable-temperature NMR spectroscopy and X-ray crystallography.
\r\n\r\nChapter 3 relates the utilization of these chiral ruthenium-based olefin metathesis catalysts in enantioselective desymmetrization reactions of achiral trienes to produce cyclic ethers. Selectivity trends are identified and catalysts are optimized with the best result showing a 90% enantiomeric excess of product. A stereochemical model is proposed based on the outcome of these reactions.
\r\n\r\nChapter 4 relates efforts to develop a useful test for measuring the inherent stereoselectivity of a wide array of ruthenium-based olefin metathesis catalysts by converting them to relatively inactive Fischer-alkylidenes in a single-turnover reaction with dihydrofuran. A group of approximately twenty olefin metathesis catalysts is tested with this technique, and the resulting data are found to correlate well with the results of the ring-closing metathesis of macrocycles. Several trends are discussed, and a stereochemical model consistent with the results of these reactions is described.
\r\n\r\nChapter 5 details a novel route for the synthesis of telechelic polymers through the ring-opening metathesis polymerization (ROMP) of highly strained bicyclic monomers.
" }, { "name": "Wiener, John Jacob Moely", "degree": "PhD", "year": "2004", "title": "Design and Development of New Enantioselective Catalytic Reactions and Progress towards the Total Synthesis of Callipeltoside", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01282004-181526", "creators": [ { "name": { "family": "Wiener", "given": "John Jacob Moely" }, "id": "Wiener-John-Jacob-Moely", "display_name": "Wiener, John Jacob Moely" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "chair", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KA4F-XJ24", "abstract": "The development of a new enantioselective catalytic anti aldol reaction is described. In this Lewis acid-catalyzed process, a chiral metal-ligand enolate complex is accessed through soft-enolization and reacts with an aldehyde to form aldol adducts in good enantioselectivity and anti diastereoselection. Mechanistic studies confirm the non-Mukaiyama pathway involving a reactive metal enolate species. Investigations have shown that the choice of amine base has a remarkable effect on the mechanism and outcome of the reaction.
\r\n\r\nThe development of the first enantioselective organocatalytic [1,3]-dipolar cycloaddition reaction is also reported. In this imidazolidinone-catalyzed process, nitrones react with a,b-unsaturated aldehydes to form chiral isoxazolidines in excellent yield, enantioselectivity, and diastereoselection. The scope of this process appears quite general with respect to both the nitrone and aldehyde components of the reaction. A second-generation imidazolidinone catalyst offers improved reaction rates and selectivities and has also facilitated the development of the first exo selective organocatalytic [1,3]-dipolar and Diels-Alder cycloaddition reactions.
\r\n\r\nA synthetic approach towards the marine natural product callipeltoside A is described. The synthesis relies upon rapid construction of the stereochemical backbone through a novel tandem amino-sulfide acyl-Claisen rearrangement. Subsequent elaboration towards the macrolide has involved a highly diastereoselective reductive opening of a spirocyclic intermediate, highly diastereoselective Ireland Claisen rearrangement, and synthesis of the tetrahydropyran moiety through a palladium catalyzed carbonylative cyclization. Completion of the synthesis has yet to be achieved due to difficulties in removal of a benzyl ether protecting group.
" }, { "name": "Wight, Andrea Palmisano", "degree": "PhD", "year": "2004", "title": "I. Synthesis, Characterization, and Base Catalysis of Organic-Functionalized Molecular Sieves. II. Selective Oxidation of Ethane via Heteropolyanion-Containing Solid Catalysts", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252004-102344", "creators": [ { "name": { "family": "Wight", "given": "Andrea Palmisano" }, "id": "Wight-Andrea-Palmisano", "display_name": "Wight, Andrea Palmisano" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/DCKV-0007", "abstract": "This thesis is composed of two separate and unrelated projects. The first project examines the preparation of functional groups that can serve as immobilized bases in molecular sieves. Many heterogeneous, base catalysts are not able to promote diverse reaction types that require strong bases as catalysts. Additionally, some of the stronger solid base catalysts are sensitive to carbon dioxide and moisture in air and therefore are not easily suitable for recycling. Organic-functionalized molecular sieves possess an organic moiety within the pore space of a molecular sieve by incorporation of an organosilane directly into the synthesis gel of the molecular sieve. Previous work reported by Davis and co-workers demonstrated the incorporation of an acid site in zeolite Beta (*BEA type) and its use in shape-selective acid catalysis.
\r\n\r\nHere, a phosphonium functionality is prepared from halogen-containing alkyl groups in *BEA to allow the incorporation of a strong base (OH-) within the molecular sieve for base catalysis. Characterization of the phosphonium-containing material prepared is accomplished. Shape-selective chemical reactions and ion-exchanges are presented, and the results of these experiments suggest that the functional groups are located within the molecular sieve pore space, although the exact structure of these moieties is not conclusively obtained.
\r\n\r\nThe second part of this thesis examines the use of niobium- and pyridine-exchanged heteropolyanions as catalyst precursors for the selective oxidation of light alkanes with dioxygen. The versatility of many oxidation catalysts is limited, thereby restricting potential usefulness. Alkenes, typically used as feedstock, are becoming costly as their demand for use in many other industrial processes increases. The use of light alkanes as reactants for selective oxidation would allow one to take advantage of an under-utilized and relatively inexpensive feedstock for selective oxidation.
\r\n\r\nNiobium- and pyridine-exchanged heteropolyanions (HPAs) have been shown to produce highly active and selective catalysts for the oxidation of propane and n-butane to acrylic acid and maleic acid, respectively, by Davis and co-workers. Specifically, molybdophosphoric acid and molybdovanadophosphoric acid were exchanged with niobium oxalate and pyridine to produce the exchanged HPAs (denoted NbPMo12pyr and NbPMo11Vpyr, respectively). Preliminary work in these studies indicates that the exchanged HPAs may also be effective for the oxidation of ethane to acetic acid. The application of this catalyst system to the selective oxidation of ethane to acetic acid and ethylene is explored here.
\r\n\r\nThe exchanged heteropolyanions give higher ethane conversion at elevated pressures (230 psig and 280oC) but better yields at atmospheric pressure and 380oC. Variations of steam flow rates or reaction temperatures are not observed to improve acetic acid space-time-yield (STY). Lower gas-hourly-space-velocity (GHSV) causes the ethylene and acetic acid to over-oxidize to COx. The maximum STY of acetic acid using NbPMo12pyr is 0.021 mmol/min/g catalyst at 380oC, 0 psig, and flows of 16: 8: 16: 20 mL/min of ethane: oxygen: helium: steam.
\r\n\r\nAt elevated pressure (230 psig) the addition of vanadium into the Keggin ion precursor is shown to decrease conversion (from 6.0% to 2.2%) but improve selectivity to ethylene (from 23.2% to 46.8%). The formation of acetic acid is not affected (0.002 mmol/min/g catalyst). At atmospheric pressure the addition of vanadium into the Keggin precursor does have a favorable affect on the acetic acid formation. NbPMo11Vpyr is shown to have a maximum acetic acid production of 0.062 mmol/min/g catalyst at 380oC, 0 psig, and flows of 16: 8: 16: 20 mL/min of ethane: oxygen: helium: steam.
\r\n\r\nThe addition of both Nb and pyridine to the HPA is crucial for active catalyst formation, for reactions both at atmospheric pressure and 230 psig. Substitution of other metals for Nb does not yield materials that give significant ethane conversion.
\r\n\r\nHigher ethane/oxygen ratios increase the selectivity to acetic acid over NbPMo12pyr at atmospheric pressure. The oxidation of ethylene over NbPMo12pyr is accomplished, and the results indicate that acetic acid is formed from ethylene during the oxidation of ethane. D2O is substituted as the source of steam, and the observation that acetic acid contains deuterium shows that the steam in the feed is involved in its formation.
\r\n\r\nThe data obtained from NbPMo11Vpyr suggest that this precursor can give a catalyst that is active and selective for producing ethylene and acetic acid from ethane and dioxygen. Further experimentation is necessary to optimize performance.
" }, { "name": "Williams, Tashica Tr\u00e9shun", "degree": "PhD", "year": "2004", "title": "Fundamental Aspects of DNA-Mediated Charge Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04082004-161537", "creators": [ { "name": { "family": "Williams", "given": "Tashica Tr\u00e9shun" }, "id": "Williams-Tashica-Tr\u00e9shun", "display_name": "Williams, Tashica Tr\u00e9shun" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/83ec-2t89", "abstract": "The \u03c0-stacked array of DNA base pairs has fascinated scientists since its structural delineation. Here are described fundamental studies to probe how this \u03c0-stacked array mediates DNA charge transport (CT). Intercalators, such as dipyridophenazine (dppz) complexes of ruthenium and phenanthrenequinone diimine (phi) complexes of rhodium, serve as powerful and systematic probes of DNA CT in these studies.
\r\n\r\nIn a series of rhodium-tethered DNA assemblies, with varying A/T sequences intervening between guanine doublet sites (5'-GG-3'), long-range oxidative DNA damage is examined. The guanine doublet sites are known as sites of low oxidation potential in DNA, and the rhodium complex serves as a spatially separated, potent photooxidant. Although these studies are inconsistent with a mechanism involving guanine hopping and tunneling through A/T sequences, these data illustrate that the sequence of bases is an important determinant in attenuating oxidative damage yields of CT. Based on these data, we propose hopping among domains defined by sequence-dependent structure. Additional studies are also described using rhodium-tethered DNA assemblies to examine how different ionic distributions around the DNA duplex modulate DNA CT. In the rhodium-DNA conjugates, differences in long-range oxidative damage yield were observed depending on the position of pendent charges on the oligomer.
\r\n\r\nA direct comparison of DNA CT utilizing a variety of oxidants has also been performed. CT is assayed both through determination of the yield of oxidative guanine damage and, in derivative DNA assemblies, by analysis of the yield of a faster oxidative trapping reaction, ring-opening of N2-cyclopropylguanine (CPG) within the DNA duplex. We find clear differences in oxidative damage ratios at the distal versus proximal 5'-GG-3' depending upon the photooxidant employed. There is also a correlation seen between absolute yield of oxidative damage and distal/proximal damage ratio; photooxidants that produce higher distal/proximal damage ratios have lower yields. These differences observed among photooxidants as well as the complex distance dependence are attributed to differences in rates of back electron transfer (BET).
\r\n\r\nA study of the overall effect of bridge energetics on DNA CT has also been performed by constructing rhodium-DNA assemblies containing varying numbers of inosine, a guanine base analog with a higher oxidation potential, between two 5'-GG-3' sites. For the rhodium conjugates, only a slight diminution in distal oxidative yield with increasing distance is observed, suggesting direct charge injection by rhodium into higher energy sites of the intervening bridge.
\r\n\r\nThese results, taken together, provide insight into salient parameters that govern DNA CT, in particular how energetics, charge distribution, and sequence-dependent DNA structure and dynamics modulate charge migration through DNA.
" }, { "name": "Zacharias, Niki Marie", "degree": "PhD", "year": "2004", "title": "Chemical-Scale Manipulation of Ion Channels: in vivo Nonsense Suppression and Targeted Disulfide Crosslinking", "advisor": "Dougherty, Dennis A.; Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01042004-210542", "creators": [ { "name": { "family": "Zacharias", "given": "Niki Marie" }, "id": "Zacharias-Niki-Marie", "orcid": "0000-0002-9364-6016", "display_name": "Zacharias, Niki Marie" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "co-advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/y4ay-ph28", "abstract": "The study of the three-dimensional shape and structure-function relationships of ion channels is a very challenging field of research. Ion channels are integral-membrane proteins that when open allow ions to flux across the cell membrane. The structure and function of ion channels are dependent on the cell membrane that surrounds them. Because an ion channel must be embedded in a cell membrane, many techniques used to probe the structure of soluble proteins cannot be used in the study of ion channels.
\r\n\r\nOne versatile technique that has been shown to be quite valuable in the structure-function studies of ion channels is the in vivo nonsense suppression method for unnatural amino acid incorporation. This technique allows one to site-specifically incorporate an unnatural amino acid or hydroxy acid into a protein in a living cell. To date more than 60 amino acids and hydroxy acids have been incorporated into proteins using in vivo nonsense suppression. The method has been shown to accommodate a wide variety of unnatural amino acids and hydroxy acids. Chapter One will discusses the in vivo nonsense suppression method in greater detail.
\r\n\r\nA key component of this work is the design and synthesis of new unnatural amino acids that have novel properties. Chapter 2 discusses the synthesis and uses of 5-(o-nitrobenzyl)selenyl-2-hydroxypentanoic acid (NBSeOH). NBSeOH is used to site-specifically cleave a peptide backbone. The o-nitrobenzyl protecting group is photochemically removed to reveal a selenium anion. The selenium anion then initiates an intramolecular SN2 displacement that cleaves the backbone of the protein. Preliminary data reveals that NBSeOH can be incorporated into a protein in vivo and in vitro, and photolysis of proteins and peptides containing NBSeOH does lead to protein backbone cleavage.
\r\n\r\nChapter 4 discusses how the in vivo nonsense suppression method was used to incorporate unnatural amino acids containing a quaternary ammonium moiety to mimic the quaternary ammonium on acetylcholine. These unnatural amino acids were used to probe the nicotinic acetylcholine receptor?s binding site. These unnatural amino acids are called tethered agonists because when they were incorporated into four different positions on the nicotinic acetylcholine receptor partial opening of the channel occurred even when agonist was not present. These tethered agonists were used to obtain distance information about where acetylcholine binds within the receptor.
\r\n\r\nAnother technique used to probe the structure of ion channels is targeted disulfide crosslinking. In the targeted disulfide crosslinking method, cysteine residues are introduced at various locations throughout a protein and oxidized to see whether disulfide bond formation can occur. Since only cysteine residues close in space will form a disulfide bond, this method can reveal fine structural aspects of a protein. The method was used to study the pore lining structure of the nicotinic acetylcholine receptor. Several cysteine mutants were made using mutagenesis and then studied in functional channels expressed in Xenopus oocytes. The channels were then exposed to oxidizing agents, and the ability of these mutant channels to form disulfide bonds was evaluated. Chapter 3 describes the work dealing with the targeted disulfide crosslinking experiments in the nicotinic acetylcholine receptor.
" }, { "name": "Zepernick, John F.", "degree": "Masters", "year": "2004", "title": "The Development of a Tandem Stille-Oxaelectrocyclization Reaction", "advisor": "Stoltz, Brian M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10022012-135626882", "creators": [ { "name": { "family": "Zepernick", "given": "John F." }, "id": "Zepernick-John-F", "display_name": "Zepernick, John F." } ], "advisors": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "advisor", "display_name": "Stoltz, Brian M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hc53-h270", "abstract": "No abstract." }, { "name": "Abrol, Ravinder", "degree": "PhD", "year": "2003", "title": "Theory of Electronically Nonadiabatic Quantum Reaction Dynamics", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-12052002-203732", "creators": [ { "name": { "family": "Abrol", "given": "Ravinder" }, "id": "Abrol-Ravinder", "orcid": "0000-0001-7333-6793", "display_name": "Abrol, Ravinder" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6NQY-2K60", "abstract": "In most quantum descriptions of chemical reactions, the Born-Oppenheimer (BO) approximation is invoked that separates the motion of light electrons and heavy nuclei, thereby restricting the motion of those nuclei to a single adiabatic electronic state. Intersections between neighboring electronic states are more common in molecular systems of interest to chemistry and biology than in diatomic molecules. The picture is further complicated due to nonadiabatic couplings which can be present in these systems even in the absence of intersections between electronic states. These couplings are solely responsible for all nonadiabatic effects in chemical and biological processes. For understanding these nonadiabatic effects, the BO picture needs to be replaced by the general Born-Huang (BH) description, in which the nuclei can sample an arbitrary number of electronic states.
\r\n\r\nA general BH treatment is presented for a polyatomic system evolving on n adiabatic electronic states. All nonadiabatic couplings are considered in this adiabatic representation. These couplings can be singular for electronically degenerate nuclear geometries. The presence of these nonadiabatic couplings (even if not singular) can lead to numerical inefficiencies in the solution of the corresponding nuclear motion Schr\"odinger equation. This problem is circumvented by going to a diabatic representation, in which these couplings are not only never singular but are also minimized over the entire dynamically important nuclear configuration space. This BH description is applied to the benchmark triatomic system H\u2083 by obtaining an optimal diabatic representation of its lowest two adiabatic electronic states. A two-electronic-state quantum dynamics formulation is also presented, which, in addition to providing reaction cross sections over a broad energy range, will also enable a quantitative test of the validity of the BO approximation.
" }, { "name": "Ackerman, Lily Joy", "degree": "PhD", "year": "2003", "title": "Ancillary Ligand Effects in Niobocene Olefin Hydride Complexes and Hydrocarbon Oxidation by Palladium(II) Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212003-130334", "creators": [ { "name": { "family": "Ackerman", "given": "Lily Joy" }, "id": "Ackerman-Lily-Joy", "display_name": "Ackerman, Lily Joy" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FZMS-V955", "abstract": "To examine the effects of cyclopentadienyl and olefin substitution on preferred stereochemistry, the preparation of a series of singly bridged ansa-niobocene olefin hydride complexes is described. These complexes serve as stable transition state analogues for the much more kinetically labile group 4 metallocenium cationic intermediates in metallocene-catalyzed olefin polymerization. Characterization of the thermodynamically preferred isomers of niobocene olefin hydride complexes reveals that placement of a single alkyl substituent on the cyclopentadienyl ligand array may have a moderate effect on the stereochemistry of olefin coordination.
\r\n\r\nUsing dynamic NMR methods the rates of hydrogen exchange following intramolecular ethylene insertion into the metal-hydride bond have been measured for singly and doubly bridged group 5 ansa-metallocene complexes. The singly bridged ansa-niobocenes exchange up to 3 orders of magnitude faster than unbridged complexes. However, the doubly bridged ansa-tantalocene complex exchanges at a rate comparable to that previously reported for the unlinked and much slower than a singly bridged complex. These \"ansa-effects\" were investigated by DFT calculations on model complexes. The computed exchange pathway showed the presence of an agostic ethyl intermediate. The calculated barriers for hydrogen exchange of model unbridged, singly bridged, and doubly bridged niobocenes correlate with the experimental results.
\r\n\r\nN,N'-Diaryl-diimine-ligated Pd(II) dimethyl complexes undergo protonolysis with tetrafluoroboric acid (aq) in trifluoroethanol (TFE) to form cationic monomethyl complexes and methane. The cations activate benzene C-H bonds at room temperature. Kinetic analyses reveal trends similar to those observed for the analogous Pt complexes: the C-H activation step is rate determining and is inhibited by water, which is consistent with a mechanism in which benzene substitution proceeds by a solvent- (TFE-) assisted associative pathway. After benzene C-H activation under 1 atm dioxygen, the products of the reaction are biphenyl and a dimeric hydroxide complex. The Pd(0) formed in the reaction is reoxidized by dioxygen after the oxidative C-C bond formation. Toluene and trifluorotoluene were investigated as substrates to examine the regioselectivity of arene coupling.
\r\n" }, { "name": "Austin, Daniel Ephraim", "degree": "PhD", "year": "2003", "title": "Impact-Ionization Mass Spectrometry of Cosmic Dust", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11072002-135150", "creators": [ { "name": { "family": "Austin", "given": "Daniel Ephraim" }, "id": "Austin-Daniel-Ephraim", "display_name": "Austin, Daniel Ephraim" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Ahrens", "given": "Thomas J." }, "id": "Ahrens-T-J", "role": "member", "display_name": "Ahrens, Thomas J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2E8R-G492", "abstract": "In situ characterization of cosmic dust grains typically involves impact-ionization time-of-flight mass spectrometry. Considering the performance and limitations of previous instruments, I designed and tested a novel, compact time-of-flight mass spectrometer for cosmic dust analysis. The instrument, Dustbuster, incorporates a large target area with a reflectron, simultaneously optimizing mass resolution, particle detection, and ion collection. Dust particles hit the 65-cm\u00b2 target plate and are partially ionized by the impact. The resulting ions, with broad energy and angular distributions, are accelerated through the modified reflectron, focusing ions spatially and temporally to produce high-resolution spectra.
\r\n\r\nInitial performance tests of the Dustbuster used laser desorption ionization of embedded metal and mineral samples to simulate particle impacts. Mass resolution (mass/peakwidth) in these experiments ranged from 60 to 180, permitting resolution of isotopes. Subsequent experiments included hypervelocity microparticle impacts. Charged iron and copper microparticles, accelerated to 2-20 km/s in a 2 MV van de Graaff accelerator, impacted the Dustbuster. Mass resolution in these experiments ranged from 150 to 300 for iron and copper. Hydrogen, carbon, and oxygen ions appeared in many spectra. Field-induced emission of electrons immediately before impact is a possible cause of ion formation from species with high ionization potentials. The implications of this ionization effect are discussed in relation to interpretation of mass spectra from other in situ dust analyzers.
\r\n\r\nAnother time-of-flight instrument, originally designed as an energy analyzer, shows promise as a high-resolution mass spectrometer for high-flux cosmic dust environments.
\r\n\r\nIce is an important component of particulates ejected from comets and other icy bodies in the solar system. Due to limited experimental data on ice particle impacts, I built an ice particle source based on a vibrating orifice aerosol generator connected directly to vacuum. Ice particles produced in this manner can be electrostatically accelerated for impact ionization studies.
\r\n\r\nHypervelocity impact vaporization may have played a key role in the mass extinction that occurred at the Cretaceous-Tertiary (K-T) boundary. In order to study the speciation of gases that may have been produced in such an asteroid impact, I designed a specialized orthogonal extraction mass spectrometer for future laboratory impact experiments.
" }, { "name": "Bielawski, Christopher William", "degree": "PhD", "year": "2003", "title": "Tailoring Polymer Synthesis with Designer Ruthenium Catalysts", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11072002-184043", "creators": [ { "name": { "family": "Bielawski", "given": "Christopher William" }, "id": "Bielawski-Christopher-William", "orcid": "0000-0002-0520-1982", "display_name": "Bielawski, Christopher William" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X0T4-9940", "abstract": "The research presented in this thesis focuses on applying ring-opening metathesis polymerization (ROMP) toward the synthesis of advanced macromolecular architectures. Chapter 1 provides an overview of the olefin metathesis reaction and evaluates the various synthetic tools currently employed for preparing complex polymeric structures.
\r\n\r\nChapters 2 and 3 summarize the performance of various Ru-based catalysts in ROMP. Chapter 2 focuses on complexes coordinated with various N-heterocyclic carbene ligands while Chapter 3 focuses on their phosphine ligated analogs and methods to improve their initiation efficiency. The scope and utility of these catalysts in various ROMP reactions are discussed.
\r\n\r\nChapters 4 and 5 describe the synthesis of acetoxy, hydroxy, and vinyl end-functionalized polybutadienes (PBDs) and polynorbornenes. By including allyl acetate, 1,4-bis(acetoxy)-2-butene, or 2-butene-1,4-diol as chain transfer agents (CTAs) during a Ru mediated ROMP of cyclooctadiene (COD) or norbornene (NBE), the respective end-functionalized polymers with molecular weights controllable up to 30 kDa could be obtained in high yield.
\r\n\r\nChapter 6 describes a one-pot synthesis of triblock copolymers composed of mechanistically incompatible segments. Bis(allyl chloride) and bis(2-bromopropionate) end-functionalized telechelic PBDs were synthesized by the ROMP of COD in the presence of the corresponding difunctional CTAs. These telechelic PBDs were subsequently used as difunctional macroinitiators for the atom transfer radical polymerization (ATRP) of styrene or methyl methacrylate (MMA) to form the respective block copolymers.
\r\n\r\nChapter 7 describes the synthesis of a multifunctional Ru complex which was found to be capable of mediated both the ROMP of COD and the ATRP of MMA to form diblock copolymers. Depending on the reaction conditions, the complex was found to catalyze both polymerizations either in tandem or simultaneously. Introduction of hydrogen at the conclusion of the polymerizations resulted in quantitative saturation of the polymer backbone.
\r\n\r\nChapters 8 and 9 describe a new synthetic route to cyclic polymers. In this approach, the ends of growing polymer chains remain attached to a cyclic Ru catalyst throughout the entire polymerization process. This effectively excludes all types of linear intermediates, which were a major drawback of previous approaches to cyclic polymers. Techniques for characterizing and determining the purity of cyclic polymers are also discussed.
" }, { "name": "Boon, Elizabeth Marshall", "degree": "PhD", "year": "2003", "title": "Electrochemical Sensors Based on DNA-Mediated Charge Transport Chemistry", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08222002-162219", "creators": [ { "name": { "family": "Boon", "given": "Elizabeth Marshall" }, "id": "Boon-Elizabeth-Marshall", "orcid": "0000-0003-1891-839X", "display_name": "Boon, Elizabeth Marshall" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PFXM-7M76", "abstract": "The base pair stack within double helical DNA provides an effective medium for charge transport. The \u03c0-stacked DNA base pairs mediate charge transport chemistry over long molecular distances in a reaction that is exquisitely sensitive to DNA sequence-dependent conformation and dynamics. This sensitivity to minor perturbations in DNA structure and base stacking makes DNA-mediated charge transport chemistry an ideal platform for DNA sensing. Electrochemical methods through DNA-modified electrode surfaces that exploit this sensitivity for efficient biosensing are described. Gold electrodes are modified with DNA double helices and used to monitor the electrochemistry of bound redox-active intercalators. The efficiency of electrochemical reduction of the intercalated redox-probe, in a DNA-mediated reaction, provides an indicator of base stacking within the surface-bound duplexes. Perfectly stacked DNA is capable of mediating the electrochemical reduction, while duplexes containing \u03c0-stacking perturbations, such as single base mismatches, do not support current flow to the intercalator.
\r\n\r\nAll single base mismatches, including thermodynamically stable GT and GA mismatches, as well as many common base damage products can be detected within DNA and DNA/RNA hybrid duplexes using this assay. Moreover, mismatches can be detected as a small percentage of a perfectly matched film, making it possible to detect mutations associated with genetic disorders in only a small fraction of cells. This assay is also compatible with DNA based chip technology. Furthermore, electrochemistry at DNA films is found to provide a novel and sensitive method for probing protein dependent changes in DNA structure and enzymatic reactions.
\r\n\r\nThe efficient transport of charge through self-assembled monolayers of thiol-terminated duplexes on gold therefore offers an extremely sensitive probe for the integrity of DNA sequences. Completely new approaches to single base mismatch detection as well as assaying protein-DNA interactions and reactions on surfaces are now available. This technology is generally applicable as a tool for directly measuring base pair stacking in nucleic acid duplexes.
" }, { "name": "Brandt, Gabriel Shaw", "degree": "PhD", "year": "2003", "title": "Site-Specific Incorporation of Synthetic Amino Acids into Functioning Ion Channels", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202003-221429", "creators": [ { "name": { "family": "Brandt", "given": "Gabriel Shaw" }, "id": "Brandt-Gabriel-Shaw", "orcid": "0000-0002-9148-8042", "display_name": "Brandt, Gabriel Shaw" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3PYX-4P72", "abstract": "Synthetic amino acids may be introduced into functioning proteins by means of nonsense suppression, using tRNA aminoacylated with unnatural amino acids. This technique can be extended to living cells through micro-injection of mRNA and tRNA into Xenopus laevis oocytes. Introduction of synthetic amino acids into proteins has been used, broadly, for three purposes. First, sensitive probes have been incorporated into proteins, using side chain chemistry unavailable to naturally encoded amino acids. Second, reactive side chains have been developed which can drive conformational rearrangements of the protein. Third, natural post-translational modifications of protein side chains have been mimicked. The work presented here applies all of these approaches to the study of ion channels. A series of fluorinated Trp residues was incorporated into the nicotinic acetylcholine receptor (nAChR) to probe electrostatic effects on cation-pi mediated binding of nicotine and other agonists. Site-specific protein backbone cleavage of the nicotinic acetylcholine and purinergic P2X\u2082 receptors was undertaken, along with intersubunit photo-crosslinking in the nAChR. Caged tyrosine was employed to study tyrosine phosphorylation of an important modulatory site in the potassium channel Kir2.1. Finally, caged phosphoamino acid analogs were synthesized for further characterization of the effects of phosphorylation on ion channels." }, { "name": "Briglin, Shawn Michael", "degree": "PhD", "year": "2003", "title": "Spatial, Temporal, and Chemical Aspects of Vapor Detection Using Conductive Composite Chemically Sensitive Resistors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-02262003-004639", "creators": [ { "name": { "family": "Briglin", "given": "Shawn Michael" }, "id": "Briglin-Shawn-Michael", "display_name": "Briglin, Shawn Michael" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XHF4-YX71", "abstract": "We have investigated the vapor response properties of chemically sensitive thin film resistors prepared from conductor-insulator composites. A new sensor type was developed from alkylamine-capped gold nanocrystals, and films of this composite, which are composed of nanometer-scale gold cores separated by regions of insulating alkylamine chains, exhibit small reversible resistance increases upon exposure to vapors such as water, acetone, or toluene. However, these films exhibit large irreversible resistance decreases in exposure to vapors possessing the thiol (-SH) functionality. The resistance change is shown useful for determination of the mercaptan concentration, and readily permits the detection of methylmercaptan at concentrations as low as 4 ppb (parts per billion), and hydrogen sulfide at concentrations as low as 9 ppm (parts per million). We have also investigated the geometric, spatial, and temporal response properties of chemically sensitive resistors prepared from polymer-carbon black composites in exposure to common organic vapors. The reversible resistance responses of these detectors were evaluated with short rise-time pulses of vapor, and detectors formed from very thin (< 200 nm) films of polyethylene-co-vinyl acetate (PEVA)-carbon black composites produced steady-state responses within 17 ms for methanol exposures and within 90 ms for toluene, acetone, or n-hexane. In accord with Fickian diffusion, the response times of PEVA-carbon black detectors were proportional to the square of the film thicknesses in the range 510 nm to 5700 nm, and the response vs. time profiles were well fit by a simple finite difference model based on Fickian diffusion. The temporal response also provides useful information for the identification or discrimination of solvent vapors beyond that available solely in the steady-state response employed in previous studies of this sensor type. We also demonstrate that there is an optimum detector volume to produce the highest signal/noise ratio for a given composite when exposed to a fixed volume of analyte vapor, and we show that useful information and optimizations can be obtained from the spatiotemporal response profile of an analyte moving in a controlled path across an array of chemically identical, but spatially nonequivalent, detectors.\r\n" }, { "name": "Chatterjee, Arnab Kumar", "degree": "PhD", "year": "2003", "title": "Investigations into the Selectivity of Olefin Cross-Metathesis Using Ruthenium Alkylidene Catalysts: Electronic and Steric Matching of Substrates", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122002-142629", "creators": [ { "name": { "family": "Chatterjee", "given": "Arnab Kumar" }, "id": "Chatterjee-Arnab-Kumar", "display_name": "Chatterjee, Arnab Kumar" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/K2NX-3592", "abstract": "Olefin cross-metathesis (CM) is a thermodynamically controlled metathesis reaction that is governed by statistical product distributions and a mixture of olefin stereoisomers. In fact, while the reaction allows for the functionalization of alpha-olefins under mild conditions, it has not been used widely due to a lack of selective processes. The research effort disclosed here has provided some new solutions to the selectivity issues involved with CM. These including the use of olefins with altered steric and electronic properties allowing for selective olefin functionalization by CM. After an introduction to state-of-the-art CM in Chapter 1, the discussion continues with CM work in earlier generation ruthenium catalyst systems (Chapter 2). The next two chapters reveal new substrate scope in CM using more active ruthenium based catalysts developed in this group, including the synthesis of trisubstituted olefins (Chapter 3) and directly functionalized olefins (Chapter 4). Once discoveries in expanding substrate scope were accomplished, the final chapter outlines an empirical model for understanding the electronic and steric factors in CM selectivity across a variety of olefin metathesis catalysts. This model provides a method to determine if selective CM can be performed for target-oriented synthetic efforts. In addition, a better understanding of selectivity issues allows for the discovery of new reaction platforms and expands the synthetic utility of CM. These are discussed in Chapter 5 and describe CM as a method to install structural elements as well as to synthesize reagents for subsequent transformation. " }, { "name": "Cheng, Timothy Casey", "degree": "PhD", "year": "2003", "title": "Investigations into the Enzymology and Biotechnology of the Hyperthermophilic Carboxypeptidase (PfuCP) from the Archaeon Pyrococcus furiosus", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05272003-203637", "creators": [ { "name": { "family": "Cheng", "given": "Timothy Casey" }, "id": "Cheng-Timothy-Casey", "display_name": "Cheng, Timothy Casey" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R8WE-R336", "abstract": "A novel metallocarboxypeptidase (PfuCP) from the hyperthermophilic archaeon Pyrococcus furiosus was purified and characterized to investigate its dependence on metal ion cofactors and to evaluate its suitability as a biotechnological tool for protein sequencing at elevated temperatures.
\r\n\r\nThe crystal structure reveals a dimer of primarily a-helical subunits that bears no resemblance to the \u03b1/\u03b2-hydrolase morphology of typical carboxypeptidases and which defines a new family of HEXXH metalloproteases (M32) based on primary sequence alignments. A deep active site groove appears to function not only in size-selection of substrates but also in modulating the activity and substrate affinity through complicated allosteric effects involving ambient ligands which may play a role in regulatory metabolism.
\r\n\r\nTwo forms of the enzyme were observed; one which retains stabilizing metal(s) that confer structural thermostability and a remarkable retention of activity to the dimer, and another demetallated form which has lost stability with regards to both dimeric integrity and activity. Difficulties in expressing a properly folded recombinant necessitated refolding of the expressed clone from inclusion bodies and further suggest that in vivo the stabilizing metal(s) may participate in folding a metastable enzyme.
\r\n\r\nThe apparent paradox of activation by only Co\u00b2\u207a and not Zn\u00b2\u207a is resolved into two issues, uncompetitive inhibition by the latter as seen in steady-state kinetic experiments, and intrinsic, electronic aspects of a catalytic Co\u00b2\u207a. Several explanations are proposed for the intrinsic rate enhancement of Co\u00b2\u207a over Zn\u00b2\u207a including the ability of Co\u00b2\u207a to modulate the potential energy surface for both reactants and transition states by virtue of its greater mobility within the protein framework.
\r\n\r\nThe broad amino acid specificity and rapid digestion by PfuCP in peptide sequencing trials show promise, and high-temperature protein sequencing has now been demonstrated for the first time.
" }, { "name": "Christensen, Lance Eric", "degree": "PhD", "year": "2003", "title": "Laboratory Studies of Atmospherically Important Gas-Phase Peroxy Radical Reactions", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechETD:etd-05152003-115814", "creators": [ { "name": { "family": "Christensen", "given": "Lance Eric" }, "id": "Christensen-L-E", "display_name": "Christensen, Lance Eric" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6QP1-YM37", "abstract": "Peroxy radicals (HO\u2082, RO\u2082) are important intermediates in Earth's atmosphere. They are intermediates in the oxidation of alkanes and CO in combustion and atmospheric chemical processes. In earth's atmosphere, the rates of their self and cross reactions are often the dominant loss processes when NOx concentrations fall below tens of pptv. These reactions have proven difficult to study in laboratory experiments, due to complex secondary chemistry and ambiguities in radical detection.
\r\n\r\nThis thesis describes a new laser-photolysis apparatus to measure the rates of peroxy radical reactions under atmospheric conditions that employs simultaneous UV direct absorption and IR wavelength-modulation spectroscopy to detect the peroxy radicals. Prior kinetic measurements of gas-phase peroxy radical reactions have typically employed flash-photolysis methods coupled with detection of the radicals only by UV absorption spectroscopy. However, uncertainties can arise because several different species often contribute to the absorption signal. The IR channel provides an independent means of monitoring HO\u2082 radicals by detection of specific rovibrational transitions.
\r\n\r\nWith this apparatus, the rates of the reactions HO\u2082 + NO\u2082, HO\u2082 + CH\u2083O\u2082, CH\u2083O\u2082 + CH\u2083O\u2082, and HO\u2082 + HO\u2082 were studied at temperatures from 219 K to 300 K. Our measurements have, in some cases, led to significant revision of previously accepted rate constants, mechanisms, or product yields, especially at conditions relevant to the upper atmosphere. The new rate coefficients for the HO\u2082 + HO\u2082 reaction are shown to account for a long-standing discrepancy in modeled vs. observed hydrogen peroxide in the stratosphere.
\r\n\r\nA key finding has been the observation that many previous measurements of HO\u2082 reactions at low temperatures have suffered from problems due to complexation between HO\u2082 and methanol, a precursor used to generate HO\u2082. Direct kinetic evidence is presented for the formation of the HO\u2082\u2022CH\u2083OH complex; the rate coefficients, equilibrium constant, and enthalpy of reaction for HO\u2082 + CH\u2083OH \u2194 HO\u2082\u2022CH\u2083OH were measured. These results are the first direct study of the chaperone effect proposed to explain the enhancement of the observed rates of the HO\u2082 self-reaction by hydrogen-bonding species.
\r\n\r\nThe effects of methanol enhancement on the HO\u2082 + NO\u2082, HO\u2082 + CH\u2083O\u2082, CH\u2083O\u2082 + CH\u2083O\u2082, and HO\u2082 + HO\u2082 reaction rates were measured. For the HO\u2082 + NO\u2082 reaction, overlapping, time-dependent signals in the UV due to the equilibrium between NO\u2082 and N\u2082O\u2084 were observed that may not have been properly accounted for in previous measurements. Other studies of NO\u2082 reactions conducted at temperatures below 250 K may be subject to similar errors. In the CH\u2083O2 + CH\u2083O2 reaction, detection of HO\u2082 products has raised questions concerning the product yields and reaction mechanisms.
" }, { "name": "Dunn, Alexander Robert", "degree": "PhD", "year": "2003", "title": "Sensitizer-Linked Substrates as Probes of Heme Enzyme Structure and Catalysis", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302003-172047", "creators": [ { "name": { "family": "Dunn", "given": "Alexander Robert" }, "id": "Dunn-Alexander-Robert", "orcid": "0000-0001-6096-4600", "display_name": "Dunn, Alexander Robert" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Collier", "given": "C. Patrick" }, "id": "Collier-C-P", "role": "member", "display_name": "Collier, C. Patrick" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/RW1J-6665", "abstract": "Ruthenium-diimine sensitizers (Ru-wires) with the structure [Ru(L2)L']2+, where L' is a perfluorobiphenyl bridge connecting 4,4'-dimethylbipyridine to the substrate adamantane or the heme ligand imidazole, bind to cytochrome P450cam with micromolar dissociation constants. Ru-wires can be used to trigger redox reactions on timescales faster than those achievable using conventional stopped-flow techniques: photoinduced heme reduction with an imidazole-terminated Ru-wire occurs in 40 ns. The large variation in ET rates among the Ru-diimine:P450 conjugates strongly supports a through-bonds model of Ru:heme electronic coupling.
\r\n\r\nThe Ru-wires also bind the murine inducible nitric oxide synthase (NOS) oxidase domain, both in the active site and to the hydrophobic surface patch that interacts with the NOS reductase domain. Rhenium-diimine probes with the structure [Re(4,7-dimethyl phenanthroline)(CO)3L]+, where L = imidazole-C12F8-imidazole (Re-im) or imidazole-C12F9 (Re-F9bp), bind in the NOS active site. Re-im (Kd = 6 nM) ligates the heme iron. Re-F9bp (Kd = 3.4 micromolar) produces a partial low- to high-spin conversion of the heme. Compounds with properties similar to the Ru- and Re-diimine probes may provide novel means of NOS inhibition.
\r\n\r\nLuminescent dansyl probes were designed to target cytochrome P450cam. D-4-Ad (dansyl-C4-adamantane) luminescence is quenched by Forster energy transfer upon binding (Kd = 0.83 micromolar), but is restored when the probe is displaced from the active site by camphor. In contrast, D-8-Ad (Kd ~ 0.02 micromolar) is not displaced from the enzyme even in the presence of a large excess of camphor. Probes with properties similar to those of D-4-Ad potentially could be useful for screening P450 inhibitors.
\r\n \r\nCrystal structures of P450cam bound to ruthenium diimine and danysl probes reveal an open enzyme conformation that allows substrate access to the active center via a 22-A deep channel. Interactions of the probes with the channel illustrate the importance of exploiting protein dynamics in inhibitor design. Movements of the F, G and B' helices couple to conformational changes in active site residues implicated in proton pumping and dioxygen activation. Common conformational states among P450cam and homologous enzymes indicate that the structural flexibility of the F/G helix region allows the 54 human P450s to oxidize diverse substrates.
" }, { "name": "Gosavi, Shachi Sharadchandra", "degree": "PhD", "year": "2003", "title": "Electron Transfer at Metal Surfaces", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192003-095722", "creators": [ { "name": { "family": "Gosavi", "given": "Shachi Sharadchandra" }, "id": "Gosavi-Shachi-Sharadchandra", "orcid": "0000-0001-7219-8333", "display_name": "Gosavi, Shachi Sharadchandra" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KK8A-ZF26", "abstract": "In recent years there has been considerable interest in electrode processes at metal surfaces with alkanethiol monolayers attached to them. One effect of the monolayer is that the electron transfer rate from the redox reagent in solution to the metal (gold or platinum are commonly used) becomes clearly nonadiabatic and the effect of the density of states of the metal on such a rate can be investigated.
\r\n\r\nWe develop a way of writing the wave function of a semi-infinite metal using tight-binding matrix elements and the 'Z-transform', a discrete Laplace transform. Using these k-dependent metal wave functions we calculate the coupling matrix element between the metal and the redox reagent and thus the electron transfer rate constant. We then study the effect of changing the density of electronic states at the Fermi level (DOS) of a metal on the rate of nonadiabatic electron transfer by changing the metal.
\r\n\r\nThe DOS of platinum is about 7.5 times that of gold, the difference being mainly due to the d-band of Pt. Inspite of this difference, the calculated electron transfer rate constant increases only by a factor of about 1.8. Bands which are weakly coupled (e.g., the d-band of Pt in the present case) contribute much less to the rate constant than is suggested by their density of states. Thereby, the rate constant is approximately independent of the density of states in two cases: adiabatic electron transfer and nonadiabatic electron transfer when the extra density of states is due to weakly coupled bands. Our results are in agreement with experiments performed with systems similar to those used in our calculations.
\r\n\r\nWe next employ our method to calculate the temperature dependence of the electronic contribution to the nonadiabatic electron transfer rate constant at metal and semiconductor electrodes. We find that the electronic contribution in metals is proportional to T, and under conditions for the maximum rate constant, that at semiconductor electrodes is also proportional to T, but for different reasons than in the case of metals (Boltzmann statistics and transfer at the conduction band edge for the semiconductor vs. Fermi-Dirac statistics and transfer at the Fermi level, which is far from the band edge, of the metal).
\r\n \r\nOn a different topic, we study the inverse photoemission spectra at metal electrode-liquid interfaces. In such experiments, an electron transfer redox agent was used to inject electrons or holes into a metal and create excited electronic states of the metal. Emission thus occurs in competition with energy loss and radiationless transitions. Some of the excited states decay radiatively and gave a frequency-dependent spectrum. The spectrum may be analysed to probe the electronic structure of the metal above and below its Fermi level. The experimental technique, known in the literature as charge transfer inverse photoemission spectroscopy (CTRIPS), is treated theoretically here.
\r\n\r\nWe give a possible explanation of the data using a model, experimental band structures (from vacuum inverse photemission) and surface states from solution electroreflectance (ER) experiments and propose experiments that could be performed to further clarify the mechanism of electron transfer.
" }, { "name": "Holt, Jason Knowles", "degree": "PhD", "year": "2003", "title": "Hot-Wire Chemical Vapor Deposition of Silicon and Silicon Nitride for Photovoltaics: Experiments, Simulations, and Applications", "advisor": "Atwater, Harry Albert; Goodwin, David G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11262002-143938", "creators": [ { "name": { "family": "Holt", "given": "Jason Knowles" }, "id": "Holt-Jason-Knowles", "display_name": "Holt, Jason Knowles" } ], "advisors": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "advisor", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Goodwin", "given": "David G." }, "id": "Goodwin-D-G", "role": "advisor", "display_name": "Goodwin, David G." } ], "committee": [ { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "role": "chair", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Goodwin", "given": "David G." }, "id": "Goodwin-D-G", "role": "member", "display_name": "Goodwin, David G." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z9S6-8J66", "abstract": "Hot-wire chemical vapor deposition is a promising technique for deposition of thin amorphous, polycrystalline, and epitaxial silicon films for photovoltaic applications. Fundamental questions remain, however, about the gas-phase and surface-kinetic processes involved. To this end, the nature of the wire decomposition process has been studied in detail by use of mass spectrometry. Atomic silicon was the predominant radical formed for wire temperatures above 1500 K, and catalysis was evident for SiH3 production with the use of a new wire. Aged wires appear to produce radicals by a non-catalyzed route and chemical analysis of these wires reveal large quantities of silicon at the surface, consistent with the presence of a silicide layer. This study is the first of its kind to correlate radical desorption kinetics with filament aging for the hot-wire chemical vapor deposition technique.
\r\n\r\nThreshold ionization mass spectrometry revealed large quantities of the SiH2 radical, attributed to heterogeneous pyrolysis on the walls of the reactor. At dilute (1%) silane pressures of up to 2 Torr, a negligible amount of ions and silicon agglomerates (Si2, Si2H, Si2H6) were detected. Density functional theory calculations reveal an energetically favorable route for the reaction of Si and SiH4, producing Si2H2 and H2. The trace amounts of Si2H2 observed experimentally, however, may suggest that an intermediate spin state transition involved in this reaction is slow under the hot-wire conditions used. Monte Carlo simulations of the hot-wire reactor suggest SiH3 is the predominant growth species under conditions leading to amorphous and polycrystalline growth. The flux of atomic hydrogen, rather than the identity of the precursor, appears to be the more important factor in governing the amorphous-to-microcrystalline transition that occurs upon hydrogen-dilution. Two-dimensional Monte Carlo simulations were used to model a hot-wire reactor for the first time, showing that filament arrays can be used to improve film growth uniformity. Under conditions where agglomerate formation does not occur, continuum simulations predict a maximum growth rate of 10 nm/s for dilute (1%) silane conditions and a rate of 50 nm/s for pure silane.
\r\n\r\nHot-wire chemical vapor deposition was used to deposit silicon nitride films with indices of refraction from 1.8-2.5 and hydrogen content from 9-18 atomic %. By tuning the SiH4/NH3 flow ratio, films in which the hydrogen was predominantly bound to N or Si could be produced, each of which reveal different hydrogen release kinetics. Platinum-diffused silicon samples, capped by a hydrogenated silicon nitride layer revealed, upon annealing at 700oC, platinum-hydrogen complexes with a bulk concentration of 1014 cm-3. This constitutes the first direct evidence for bulk silicon passivation by hydrogen release from a silicon nitride layer and hydrogen complex formation. Photovoltaic cells employing a hot-wire nitride layer were found to have comparable electrical properties to those using plasma nitride layers.
\r\n\r\nFinally, a method for in situ generation of SiH4 by atomic hydrogen etching was evaluated. Using a cooled crystalline silicon target in an H/H2 ambient produced negligible etching, while a cooled amorphous silicon film target was etched at a rate of up to 14 nm/min. In the latter case, net deposition at 0.6 nm/min onto a heated Ge(100) substrate resulted. A method for more efficient etching of crystalline silicon materials was proposed.
" }, { "name": "Joern, John Michael", "degree": "PhD", "year": "2003", "title": "Engineering Dioxygenases by Laboratory Evolution: A Comparison of Evolutionary Search Strategies", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-02042003-160317", "creators": [ { "name": { "family": "Joern", "given": "John Michael" }, "id": "Joern-John-Michael", "display_name": "Joern, John Michael" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemeng" ], "doi": "10.7907/61KV-P379", "abstract": "Due to the unique and difficult chemistry they perform, the aromatic ring-hydroxylating dioxygenases are of interest as industrial catalysts. Unfortunately, an application-specific array of problems limits their utility. To address these problems through laboratory evolution, I developed methods for high-throughput screening of tens of thousands of dioxygenase variants. These methods rely on a phenol detection reagent (Gibbs reagent) and can be applied to liquid cultures or to growing bacterial colonies expressing variant enzymes.
\r\n\r\nRecombination of genes encoding homologous enzymes (\"family shuffling\") has emerged as a promising tool for evolutionary protein engineering. Using the dioxygenases as a model system, I have investigated the value of recombination as a search strategy for laboratory evolution. Chimeric dioxygenase libraries constructed by DNA shuffling are first evaluated for biases that limit sequence diversity using a probe hybridization approach in lieu of sequencing. This analysis shows that crossovers preferentially occur in regions with high sequence identity and that certain parent sequences can be preferred at particular gene positions.
\r\n\r\nHigh-throughput functional screening allowed characterization of substrate specificity for hundreds of dioxygenase chimeras. These data are coupled with sequence data to reveal sequence-function relationships and demonstrate the utility of recombination as a tool for functional genomics. One region of sequence is shown to be a primary determinant of substrate specificity for the enzymes studied. Furthermore, several sets of variant enzymes with similar functionality are shown to have sequence similarities.
\r\n\r\nRecombination and random mutagenesis are compared as search strategies for generating functionally-diverse dioxygenases. I screened similarly sized libraries of chimeric and mutant dioxygenases for variants with altered substrate specificity or activity toward n-hexylbenzene, which is not accepted by the parent enzymes. Both recombination and random mutagenesis gave rise to enzymes with altered substrate specificity, although such enzymes were more frequent in the chimeric libraries and more distinct specificities were found in the chimeric libraries. Only chimeras were active toward n-hexylbenzene. These results support the view that recombination is an effective search strategy for evolving substrate specificity, and may be more effective than random mutagenesis.
" }, { "name": "Juang, Agnes", "degree": "PhD", "year": "2003", "title": "Effects of Surface Modification on Charge-Carrier Dynamics at Semiconductor Interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-08062002-192958", "creators": [ { "name": { "family": "Juang", "given": "Agnes" }, "id": "Juang-Agnes", "display_name": "Juang, Agnes" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z8ZM-QH98", "abstract": "Understanding the basic concepts of semiconductor junctions is an important step towards the development of efficient solar energy conversion devices. The work described in this dissertation includes both the investigation of semiconductor/liquid junctions and the modification of semiconductor surfaces for achieving chemical control over physical properties.
\r\n\r\nThe interfacial charge-carrier dynamics of n-GaAs/acetonitrile junctions has been investigated. Differential capacitance barrier height measurements and steady-state current density?potential (J?E) measurements were used to evaluate the degree of partial Fermi-level pinning. The presence of irreversible chemical and/or electrochemical changes on n-GaAs electrodes immersed in acetonitrile/coboltacene-coboltacenium solutions was examined using x-ray photoelectron spectroscopy (XPS) and cyclic voltammetric studies that were designed to probe surface reactions.
\r\n\r\nChemical modifications of semiconductor surfaces can provide a reliable mean to control physical properties of semiconductor interfaces. The growth of robust polymer films that are covalently attached to Si surfaces via a Si-C linkage was demonstrated. Uniform polymer overlayers of different thicknessess were formed using a general method combining chlorination/Grignard reaction with ring-opening metathesis polymerization (ROMP). The surfaces of these modified Si were characterized by x-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM), ellipsometry, and/or profilometry. The charge-carrier dynamics at these modified Si/air interfaces was investigated using transient photoconductivity decay method. Time-dependent photoconductivity measurements further confirmed the ability for polymer-terminated Si to maintain low surface recombination velocities once exposed to the air.
" }, { "name": "Julian, Ryan Roy", "degree": "PhD", "year": "2003", "title": "Molecular Recognition of Biomolecules in the Gas Phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04292003-134947", "creators": [ { "name": { "family": "Julian", "given": "Ryan Roy" }, "id": "Julian-Ryan-Roy", "orcid": "0000-0003-1580-8355", "display_name": "Julian, Ryan Roy" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8D4X-RE68", "abstract": "The first chapter introduces the most relevant noncovalent forces for gas phase experiments. Chapters 2-5 contain work on small clusters of biologically relevant molecules. In Chapter 2, it is shown that the unusual properties of arginine lead to extensive noncovalent clustering of this amino acid, when sampled by ESI-MS. The stability of the zwitterionic form of arginine for clusters without a net charge is addressed by theoretical methods in Chapter 3.
\r\n\r\nIn Chapter 4, the properties of the unusually abundant serine octamer are examined. Experiments demonstrate that this octamer has a strong preference to be homochiral. A structure for the serine octamer is proposed that is cubic and has a zwitterionic core. The results gathered from the serine octamer demonstrate that a homochiral preference can exist for very small clusters or \"nanocrystals.\"
\r\n\r\nThe first gas phase synthesis for ATP is given in Chapter 5. ATP is easily synthesized in the gas phase from a cluster of three AMP molecules bound by a sodium salt bridge. Subsequent CAD spectra following the gas phase synthesis are identical to those obtained from an authentic sample of ATP in separate experiments.
\r\n\r\nChapters 7-9 deal with the molecular recognition of amino acid side chains in ESI-MS experiments. The ability of 18C6 to recognize and selectively attach to lysine residues is explored. Recognition of arginine side chains is accomplished in a similar manner by utilizing the larger dibenzo-30-crown-10 ether (DB30C10). The two techniques are mutually compatible, allowing for both crowns to be added to the same solution.
\r\n\r\nChapters 10-11 combine the recognition of 18C6 with various chemical functionalities in order to mediate peptide chemistry in the gas phase. In Chapter 10, a new class of molecules termed ?molecular mousetraps? is described. The mousetraps combine the recognition of 18C6 with the chemical reactivity of diazo groups. The resulting molecules are capable of noncovalently attaching to any molecule that contains a protonated primary amine. CAD can be utilized to activate the complex. In Chapter 11, the mousetraps are utilized in experiments with peptides. It is shown that covalent attachment can be achieved in a quantitative fashion.
" }, { "name": "Kelly, Melissa Ann", "degree": "Masters", "year": "2003", "title": "Some New Measurements of the Ground and v\u2082 = 1 States of HDO in the Region 200 \u2013 750 GHz", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09162002-140330", "creators": [ { "name": { "family": "Kelly", "given": "Melissa Ann" }, "id": "Kelly-Melissa-Ann", "display_name": "Kelly, Melissa Ann" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P33F-HD20", "abstract": "To facilitate measurements of HDO in molecular clouds, late-type stars and planetary atmospheres, several new lines of HDO were measured between 200 and 750 GHz. The measurements were done in a one-meter gas flow cell, with specially constructed diode multiplier sources and a liquid helium cooled InSb hot-electron bolometer. The lines measured were of very low intensity, thanks to their higher J and K values. Both a-type and b-type transitions were observed, in the vibrational ground state (000) and the first excited bending state (010). These lines were added to existing HDO spectral lines and fit using a least-squares regression of an Euler series Hamiltonian that has proven useful in the analysis of molecules with large vibrational amplitudes. The results were comparable in precision to existing analyses. The data will be beneficial to two upcoming remote sensing missions designed to investigate the far IR and microwave regions: SOFIA, an airborne observatory that will carry a 2.5m telescope and detectors into the upper atmosphere, and the Herschel space observatory, a cryogenically cooled 3.5m telescope that will operate at the L2 Lagrangian point some 1.5 million km from the Earth." }, { "name": "Kent, David Randall, IV", "degree": "PhD", "year": "2003", "title": "New Quantum Monte Carlo Algorithms to Efficiently Utilize Massively Parallel Computers", "advisor": "Gray, Harry B.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252003-134943", "creators": [ { "name": { "family": "Kent", "given": "David Randall, IV" }, "id": "Kent-David-Randall-IV", "display_name": "Kent, David Randall, IV" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "chair", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bruck", "given": "Jehoshua" }, "id": "Bruck-J", "role": "member", "display_name": "Bruck, Jehoshua" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/V64A-V618", "abstract": "The exponential growth in computer power over the past few decades has been a huge boon to computational chemistry, physics, biology, and materials science. Now, a standard workstation or Linux cluster can calculate semi-quantitative properties of moderately sized systems. The next step in computational science is developing better algorithms which allow quantitative calculations of a system's properties.
\r\n\r\nA relatively new class of algorithms, known collectively as Quantum Monte Carlo (QMC), has the potential to quantitatively calculate the properties of molecular systems. Furthermore, QMC scales as O(N\u00b3) or better. This makes possible very high-level calculations on systems that are too large to be examined using standard high-level methods.
\r\n\r\nThis thesis develops (1) an efficient algorithm for determining \"on-the-fly\" the statistical error in serially correlated data, (2) a manager-worker parallelization algorithm for QMC that allows calculations to run on heterogeneous parallel computers and computational grids, (3) a robust algorithm for optimizing Jastrow functions which have singularities for some parameter values, and (4) a proof-of-concept demonstrating that it is possible to find transferable parameter sets for large classes of compounds.
" }, { "name": "Leskowitz, Garett Michael", "degree": "PhD", "year": "2003", "title": "Force-Detected Nuclear Magnetic Resonance Independent of Field Gradients", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-175447", "creators": [ { "name": { "family": "Leskowitz", "given": "Garett Michael" }, "id": "Leskowitz-Garett-Michael", "display_name": "Leskowitz, Garett Michael" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "co-chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8GH1-CC08", "abstract": "This thesis describes a new method of magnetic resonance detection based on mechanical displacements caused by magnetic forces, which is general with respect to sample and pulse sequence. A spin-bearing sample placed inside a flexible magnet assembly distorts that assembly in proportion to the sample's magnetization. Radio-frequency fields that modulate the sample's spin magnetization at this detector's mechanical resonance frequency encode magnetic resonance spectra into the detector's trajectory. A key insight is that such mechanical detection can be performed within optimized detectors with no need for field gradients inside the sample volume, circumventing the deleterious consequences of such gradients for sensitivity and resolution. The new method is called Better Observation of Magnetization, Enhanced Resolution, and No Gradient (BOOMERANG), and its sensitivity is predicted to exceed that of inductive detection at microscopic size scales.\r\n\r\nA prototype BOOMERANG spectrometer optimized for 3 mm diameter liquid and solid samples is described. The device uses direct digital synthesis of radio-frequency waveforms in its operation and fiber-optic interferometry to detect picometer-scale motions of a detector magnet. This magnet is bound to a tuned mechanical oscillator inside a magnet assembly designed for homogeneity of the magnetic field in the sample. Several types of time-domain FT-NMR spectra on test samples are presented. The data confirm theory and design principles.\r\n\r\nThe favorable scaling of BOOMERANG's sensitivity and the numerous potential uses for NMR at reduced size scales motivate construction of spectrometers optimized for microscopic samples. Geometric concerns in scaling down BOOMERANG are addressed quantitatively. At size scales where the number of spins is such that mean magnetization is smaller than fluctuations, such fluctuations, if not accounted for, can dominate the noise regardless of the physical detection method used. A measurement paradigm using correlations of these fluctuations to encode spectra is proposed to suppress this quantum noise, and the sensitivity of this method, which we call Correlated Observations Narrow Quantum Uncertainty, Enhancing Spectroscopic Transients (CONQUEST), is analyzed. BOOMERANG and CONQUEST promise to extend the applicability of nuclear magnetic resonance (NMR) for chemical analysis to samples and problems that are currently inaccessible by NMR due to poor sensitivity." }, { "name": "Li, Lintong", "degree": "PhD", "year": "2003", "title": "The Tethered Agonist Approach to Mapping Ion-Channel Proteins: Toward a Structural Model for the Agonist-Binding Site of the Nicotinic Acetylcholine Receptor", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07312002-120928", "creators": [ { "name": { "family": "Li", "given": "Lintong" }, "id": "Li-Lintong", "display_name": "Li, Lintong" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/AMDZ-XE24", "abstract": "The integral membrane proteins of neurons and other excitable cells are generally resistant to high-resolution structural tools. In this thesis we present our efforts to probe the structure of the agonist-binding site of the nicotinic acetylcholine receptor (nAChR) using the tethered agonist approach, which combines chemical synthesis, the nonsense suppression methodology for unnatural amino acid incorporation and electrophysiology.
\r\n\r\nIn Chapter 2, we present the results of incorporating a series of tethered quaternary ammonium derivatives of tyrosine into the nAChR using the in vivo nonsense suppression methodology for incorporating unnatural amino acids site-specifically. At three sites, a constitutively active receptor results, but the pattern of activation as a function of chain length is different. At position alpha149, there is a clear preference for a three-carbon tether, while at position alpha93 tethers of 2-5 carbons are comparably effective. At position gamma55/delta57, all tethers except the shortest one can activate the receptor. Based on these and other data, a model for the binding site of the receptor can be developed by analogy to the acetylcholine esterase crystal structure.
\r\n\r\nIn Chapter 3, we report evidence that the N-terminal extracellular domain of nAChR is closely related to acetylcholine binding protein (AChBP), whose crystal structure was solved in May 2001. Based on the model obtained from docking acetylcholine into the structure of AChBP, we designed and incorporated a new tethered agonist, lysyl-carbamylcholine. Incorporation of this tethered agonist at several positions produced constitutively active receptors, with significant activity seen at alpha192, alpha193, and gamma119/delta121. These results demonstrated that the loop E residue gamma119/delta121 on the complementary subunit is very near the agonist-binding site. We also investigated the role of an intersubunit hydrogen bond, which was seen in the crystal structure of AChBP. Incorporation of tryptophan analogs that abolish the hydrogen bonding abilities slowed the desensitization of the receptor, which implied that this hydrogen bond might play a key role in the allosteric transitions of desensitization.
\r\n\r\nIn Chapter 4, we describe our efforts to prepare a short tethered agonist and the results of incorporating it into nAChR at alpha198 by chemical modification of cysteine mutants introduced by nonsense suppression methodology. Methanethiosulphonate ethyltrimethylammonium (MTSET) modification resulted in constitutive activity, which suggested the closeness of alpha198 to the agonist-binding site.
\r\n\r\nIn Chapter 5, methods in molecular biology, electrophysiology and molecular docking, and the synthesis of amino acids and dinucleotide dCA-amino acids are summarized.
" }, { "name": "Li, Shuwei", "degree": "PhD", "year": "2003", "title": "In Vitro Selection of mRNA-Display Libraries Containing Unnatural Amino Acids", "advisor": "Roberts, Richard W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05182003-185245", "creators": [ { "name": { "family": "Li", "given": "Shuwei" }, "id": "Li-Shuwei", "display_name": "Li, Shuwei" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "advisor", "display_name": "Roberts, Richard W." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/NVCQ-JS95", "abstract": "The mRNA display library provides a strategy to make up to 1013 unique peptides that fuse with their own genes via a covalent link. In this thesis, several strategies to prepare mRNA display libraries containing unnatural side chains are described. Chapter 1 is a short introduction and application of mRNA-display technology. Chapter 2 describes a chemical derivatization strategy to append an unnatural side chain to libraries. Chapter 2 introduces the incorporation of unnatural amino acids via non-sense codon suppression. Chapter 4 focuses on the catalytic selection with mRNA display libraries. These libraries should facilitate the discovery of novel ligands with functionalities beyond those provided by the 20 naturally occurring amino acids." }, { "name": "Lyubovitsky, Julia Gennadievna", "degree": "PhD", "year": "2003", "title": "Mapping the Cytochrome C Folding Landscape", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102003-004657", "creators": [ { "name": { "family": "Lyubovitsky", "given": "Julia Gennadievna" }, "id": "Lyubovitsky-Julia-Gennadievna", "display_name": "Lyubovitsky, Julia Gennadievna" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/W2R9-Y195", "abstract": "The solution to the riddle of how a protein folds is encoded in the conformational energy landscape for the constituent polypeptide. Employing fluorescence energy transfer kinetics, we have mapped the S. cerevisiae iso-1 cytochrome c landscape by monitoring the distance between a C-terminal fluorophore and the heme during folding. Within 1 ms after denaturant dilution to native conditions, unfolded protein molecules have evolved into two distinct and rapidly equilibrating populations: a collection of collapsed structures with an average fluorophore-heme distance (r) of 27 A and a roughly equal population of extended polypeptides with r > 50 A. Molecules with the native fold appear on a timescale regulated by heme ligation events (~300 ms, pH 7). The experimentally derived landscape for folding has a narrow central funnel with a flat upper rim on which collapsed and extended polypeptides interchange rapidly in a search for the native structure.
\r\n\r\nNonnative states of proteins are involved in a variety of cellular processes, including translocation of proteins across membranes and formation of amyloid fibrils. Probes that report on the structural heterogeneity of a polypeptide ensemble could resolve ambiguities in the classification of these states. We have shown that added anions shift the equilibrium between the compact and extended polypeptide structures that are present during refolding of Saccaromyces cerevisiae iso-1 cytochrome c. Specifically, at high salt concentrations (>= 700 mM), all the polypeptides are compact with a mean C-terminal fluorophore-heme separation quite close to that in the native protein (25 A). Addition of chemical detaturants, on the other hand, tends to shift the equilibrium towards unfolded structures.
\r\n\r\nFolding of modified Fe(II) cyt c was probed by fluorescence in presence of imidazole with NADH as photochemical sensitizer. At very high imidazole concentrations (400 mM), protein was still found to fold but the rate that coincides with Met80 ligation was slowed down significantly.
\r\n\r\nReductive flash-quench/scavenge experiments, in which ascorbic acid was used to scavenge MeODMAA+, were shown to keep ferrocyt c reduced for up to 500 ms. Electron injection into unfolded modified yeast Fe(III)cyt c was fast in comparison to injection using NADH as photochemical sensitizer. The overall electron transfer process was reversible. This photoreduction system could be used to trigger folding of Fe(II) cyt c to monitor the changes in dansyl fluorescence intensity on ms time scales.
" }, { "name": "Maurer, Joshua Ahab", "degree": "PhD", "year": "2003", "title": "I. Structure-Function Analysis of the Mechanosensitive Channel of Large Conductance. II. Design of Novel Magnetic Materials using Crystal Engineering", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10202002-002307", "creators": [ { "name": { "family": "Maurer", "given": "Joshua Ahab" }, "id": "Maurer-Joshua-Ahab", "orcid": "0000-0002-6663-0721", "display_name": "Maurer, Joshua Ahab" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DNFY-8G73", "abstract": "The work presented here encompasses two distinct areas, with the first section addressing structure-function relationships in the mechanosensitive channel of large conductance (MscL) from bacteria. A high-throughput fluorescent screening technique has been developed for the E. coli homologue of MscL. This technique has been applied to a large library of random E. coli MscL mutations to provide insights into channel function. Additionally, attempts have been made to characterize the functionally important regions of MscL and comparisons have been made between the E. coli and M. tuberculosis homologues of MscL.
\r\n\r\nThe second section addresses the design of novel magnetic materials. The guanidinium sulfonate \"Ward lattice\" from crystal engineering has been used to develop a new family of frustrated magnetic materials.
" }, { "name": "Meier, Alexandre Edouard", "degree": "PhD", "year": "2003", "title": "Gallium and Chromium Corroles", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04082003-142034", "creators": [ { "name": { "family": "Meier", "given": "Alexandre Edouard" }, "id": "Meier-Alexandre-Edouard", "display_name": "Meier, Alexandre Edouard" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JAKV-8V97", "abstract": "We report on the synthesis and characterization of various chromium and gallium complexes of the corrole 1,5,15-trispentafluorophenylcorrole (tpfc)H3. We synthesized a chromium(V)oxo compound by reaction between (tpfc)H3 and Cr(CO)6 in refluxing toluene. Characterization of the compound via EPR and MS revealed a d1 metal species. Hyperfine splittings for the compound are A(53Cr) 1.64 mT, A(14N) 0.30 mT. Combined with the X-ray bond lengths (Cr-O, 1.545(2) \u00c5 Cr-N, 1.969/1.991 \u00c5 those data suggest that the stability of the Cr-O bond is mainly due to the strong N->Cr s donation. The compound (tpfc)Cr(O) provided the starting point for all other oxidation states we made and isolated.
\r\n\r\nBy treatment with dioxinium hexachloroantimonate we were able to form the ligand radical chromium(V) oxo species, which was shown by EPR to be in its triplet ground state. By treatment with cobaltocene, we were able to isolate the chromium(IV) oxo species, which was proven diamagnetic via NMR. Reaction with phosphines, gave rise to the chromium(III) species, which is hexa-coordinated. The two axial ligands could be either pyridine, or triphenylphosphine oxide, and were readily exchanged with one another.
\r\n\r\n\r\nThe reactivity of (tpfc)Cr(O) was found to be quite low, exhibiting a rate constant of 9.7 M-1s-1 for reaction with triphenylphosphine. The chromium(III) counterpart was readily reoxidized in air, with a mechanism involving a five coordinate intermediate as the reactive species.
\r\n\r\n\r\nIn a bid to increase reactivity, we examined the effect of bromination at the b position on reactivity. To ascertain the electronic effects, we prepared a series of gallium corroles with various degrees of bromination. After characterization via MS and 2D NMR, electrochemical as well as UV-Vis measurements demonstrated that there is little steric deformation of the ligand framework upon increased bromination, which leads to a maximum of activity at maximum bromination.
\r\n\r\n\r\nWe then successfully prepared the octabromo chromium corrole (Br8-tpfc)Cr(py)2. The oxidized compound (Br8-tpfc)Cr(O) was indeed reactive enough to oxidize various styrenes, albeit slowly (rates in the range:4.1?10-5-62 ?10-5 M-1 s-1). More surprisingly, the chromium(III) counterpart was found to oxidize in air, back to the oxo. The reoxidation is painfully slow, due in part to the difficulty in dissociating an axial ligand, and part to the low reactivity of the five-coordinate species. To speed up the reoxidation, we switched to adding TFA to (Br8-tpfc)Cr(py)2, in a bid to drive the ligand dissociation via trapping of the free pyridine.
\r\n\r\n\r\nThe presence of an acid indeed leads to dramatically improved rates of air reoxidation of the compound, but at the same time, TFA was shown to play a non-innocent role in the process. We then proceeded to get rid of all the axial ligands altogether by treating the compound with HCl. The compound obtained displayed catalytic activity in the oxygenation of styrenes (~10 turnovers). The low turnover is due to product inhibition of the catalyst.
" }, { "name": "Miller, Jeremiah Edward", "degree": "PhD", "year": "2003", "title": "Radical Formation and Electron Transfer in Biological Molecules", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292003-131114", "creators": [ { "name": { "family": "Miller", "given": "Jeremiah Edward" }, "id": "Miller-Jeremiah-Edward", "display_name": "Miller, Jeremiah Edward" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M27B-4W56", "abstract": "Multi-step electron transfer is increasingly recognized as a means for moving charge in biological systems over long distances rapidly. Many postulated multi-step mechanisms rely on the formation of organic radicals (amino-acid radicals, nucleobase radicals) as intermediate electron or ?hole? carriers. In this thesis, the multi-step mechanism for electron transfer in both proteins and DNA is investigated. These two systems form a natural complement; the role of electron transfer in DNA with regard to lesion repair is still unknown, as are the electron transfer events in the proteins that mediate the repair. Rhenium-labeled mutant Pseudomonas aeruginosa azurins serve as model systems for this phenomenon in proteins. The photo-active rhenium label in these azurins can be oxidized by a flash/quench reaction to provide a potent oxidant capable of generating a variety of radicals in the protein matrix. Three mutants (with one tryptophan residue each) were constructed to investigate the effect of tryptophan radicals on charge transfer in proteins. The properties of tryptophan radicals in three protein environments have been investigated; including a kinetically stable tryptophan radical that persists for more than 5 hrs at room temperature. The variation in these radicals plays a significant role in their effect on the oxidation of the remote copper center in azurin. The stable radical greatly reduces the rate of electron transfer from copper relative to the rhenium-labeled wild-type analogs, while another radical plays no role in copper oxidation. In order to examine multi-step electron transfer in DNA, a series of photo-active ruthenium and rhenium-thymine complexes were constructed. By attaching the metal complexes at the sugar of the deoxyribonucleic acid, they were incorporated into DNA strands by solid-state synthetic techniques. Two different ruthenium-labeled DNA strands were produced in this way; one with a single guanine base and one with two side by side guanine bases. The strand containing a guanine-guanine sequence showed formation of a guanine radical by EPR under flash/quench conditions, while the strand containing a single guanine remained EPR silent. These strands represent an excellent template to examine a system which may or may not exhibit multi-step charge transfer." }, { "name": "Mo, Chunhui", "degree": "PhD", "year": "2003", "title": "Synaptic Learning Rules for Local Synaptic Interactions: Theory and Application to Direction Selectivity", "advisor": "Koch, Christof", "url": "https://resolver.caltech.edu/CaltechETD:etd-05222003-170638", "creators": [ { "name": { "family": "Mo", "given": "Chunhui" }, "id": "Mo-Chunhui", "display_name": "Mo, Chunhui" } ], "advisors": [ { "name": { "family": "Koch", "given": "Christof" }, "id": "Koch-C", "orcid": "0000-0001-6482-8067", "role": "advisor", "display_name": "Koch, Christof" } ], "committee": [ { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "chair", "display_name": "Fraser, Scott E." }, { "name": { "family": "Koch", "given": "Christof" }, "id": "Koch-C", "orcid": "0000-0001-6482-8067", "role": "member", "display_name": "Koch, Christof" }, { "name": { "family": "Schuman", "given": "Erin Margaret" }, "id": "Schuman-E-M", "orcid": "0000-0002-7053-1005", "role": "member", "display_name": "Schuman, Erin Margaret" }, { "name": { "family": "Laurent", "given": "Gilles J." }, "id": "Laurent-G-J", "orcid": "0000-0002-2296-114X", "role": "member", "display_name": "Laurent, Gilles J." }, { "name": { "family": "Quartz", "given": "Steven R." }, "id": "Quartz-S-R", "role": "member", "display_name": "Quartz, Steven R." } ], "option_major": [ "biochem" ], "doi": "10.7907/EAK1-BQ32", "abstract": "This thesis is organized in two parts, both concerned with local synaptic interactions within the dendritic tree. The first part is focused on how specific synaptic arrangements that can be used to compute direct ion selectivity can be learned in an unsupervised manner. The second part consists of a double synaptic veto model that can account for the observed reverse-phi selectivity of direction-selective cells. We propose an activity-based, local learning model that may account for the direction selectivity in neurons in the visual cortex based on the local veto operation among excitation and inhibition. We implement the learning rule with local calcium concentration changes and a BCM type learning curve (Bienenstock, Cooper and Munro, 1982). Our biophysical simulations suggest that a model cell implementing our learning algorithm develops direction selectivity organically after unsupervised training. The learning rule is also applicable to cells with multiple direction-selective subunits on dendrites and is stable under a number of starting conditions.
\r\n\r\nReverse-phi motion is the illusory reversal of perceived direction of movement when the stimulus contrast is reversed in successive frames. Livingstone (2000) showed that direction-selective cells in striate cortex of the alert macaque monkey showed reversed excitatory and inhibitory regions when two different contrast bars were flashed sequentially during a two-bar interaction analysis. We carry out detailed biophysical simulations of a direction-selective cell model implementing a synaptic shunting scheme. Our results suggest that a simple synaptic-veto mechanism with strong direction selectivity for normal motion cannot account for the observed reverse phi-motion effect. A direct interaction between the ON and OFF pathway, missing in the original shunting-inhibition model, is essential to account for the reversal of response. We propose a double synaptic-veto mechanism in which ON excitatory synapses are gated by both delayed ON inhibition at their null side and by delayed OFF inhibition at their preferred side. The converse applies to OFF excitatory synapses. Mapping this scheme onto the dendrites of a direction-selective neuron permits the model to respond best to normal motion in its preferred direction and to reverse-phi motion in its null direction.
" }, { "name": "Morgan, John Philip", "degree": "PhD", "year": "2003", "title": "Ruthenium-Based Olefin Metathesis Catalysts Coordinated with NHeterocyclic Carbene Ligands: Synthesis and Applications", "advisor": "Grubbs, Robert H.; Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222002-204928", "creators": [ { "name": { "family": "Morgan", "given": "John Philip" }, "id": "Morgan-John-Philip", "display_name": "Morgan, John Philip" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "role": "chair", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JFPH-1020", "abstract": "The improved synthesis and olefin metathesis activity of N-heterocyclic carbene (NHC)-coordinated ruthenium alkylidenes of the form (NHC)(L)x(Cl)2Ru=CHR (x = 1 or 2) are reported. In order to circumvent the handling of highly sensitive free carbenes, N-heterocyclic carbene \"adducts\" were prepared in high yields by the reaction of nucleophilic bases with N,N'-diarylimidazolium salts. Most notably, the addition of trichloromethyl anion to N,N'-dimesityl-4,5-dihydroimidazolium chloride produced an air-, moisture-, and temperature-stable crystalline adduct, 2-trichloromethyl-4,5-dihydro-imidazolidine. When this species is heated above the critical temperature of 55 degrees C in the presence of (PCy3)2(Cl)2Ru=CHPh, a single, clean phosphine substitution reaction occurs to form the NHC-coordinated benzylidene (NHC)(PCy)3(Cl)2Ru=CHPh in 84% isolated yield. This procedure has been successfully scaled up to industrial production and remains the most effective catalyst synthesis to date.
\r\n\r\nThe NHC-coordinated catalysts show dramatically expanded activity relative to their bis-phosphine counterparts. The high yielding, trans-stereoselective cross metathesis of various acroyl substrates is the first example of the ruthenium-catalyzed metathesis of olefins directly substituted with electron-withdrawing functionality. Ring-opening cross metathesis of acroyl species with relatively high ring strain cyclooctadiene and norbornene monomers has also been achieved in good yields and perfect regioselectivity when the norbornene is asymmetrically substituted with a bridgehead methyl group.
\r\n\r\nFurther expansion of the substrate scope was achieved when the catalyst's phosphine ligand was replaced with more weakly bound 3-bromopyridine (3-Br-pyr) ligands. The resulting catalyst (NHC)(3-Br-pyr)2(Cl)2Ru=CHPh produced synthetically useful yields (>= 67%) in the cross metathesis of acrylonitrile and terminal olefins (as opposed to less than 30% yield with the phosphine-coordinated catalyst). NHC-coordinated catalysts therefore allow both electron-rich and electron-poor olefins to undergo metathesis in the same pot, potentially leading to synthetically valuable products containing electronically differentiated olefins.
\r\n\r\nThe lower activity of phosphine-coordinated catalysts relative to those coordinated with 3-bromopyridine can be addressed by the addition of \"phosphine scavengers\" to the former. Higher pKa carboxylic acids (such as acetic and benzoic acids) are capable of accelerating catalysis as effectively as the much stronger hydrochloric acid, without concomitant catalyst decomposition. These properties make carboxylic acids the optimal choice for use with sensitive organic substrates.
\r\n" }, { "name": "Nenes, Athanasios", "degree": "PhD", "year": "2003", "title": "Toward an Understanding of the Indirect Climatic Effect of Aerosols", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06022003-074653", "creators": [ { "name": { "family": "Nenes", "given": "Athanasios" }, "id": "Nenes-Athanasios", "orcid": "0000-0003-3873-9970", "display_name": "Nenes, Athanasios" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/S02W-0573", "abstract": "This thesis is motivated by the need to improve our understanding of the aerosol indirect effect. The activation of aerosol into cloud droplets has been extensively studied, using a comprehensive numerical cloud droplet activation model. Using this model, the effect of water vapor mass transfer limitations on the cloud droplet activation process was first studied; it was found that mass transfer limitations are important for activation under polluted conditions. The potential effect of (currently unresolved) \"chemical effects\" on cloud droplet number (e.g., the presence soluble gases and surface active species) was also assessed. It was seen that small changes in aerosol and gas-phase composition can have a strong effect on cloud droplet number, and should be included in future estimates of the aerosol indirect effect.
\r\n\r\nA comprehensive aerosol activation parameterization was developed for use in a first-principle assessment of the aerosol indirect effect. This new parameterization introduces the concept of \"population splitting,\" in which the droplets are separated into two populations, each with its own growth characteristics. The effect of water vapor mass transfer limitations is explicitly introduced. The parameterization allows for treatment of chemical effects. The new parameterization shows excellent and robust agreement with a detailed numerical parcel model.
\r\n\r\nPreviously unidentified mechanisms of aerosol-cloud interactions were also explored. Aerosol, when it contains black carbon, can absorb light and heat the droplet enough to affect its activation behavior. This can affect cloud properties in numerous and counterintuitive ways; black carbon heating can dissipate clouds, but may also increase cloud lifetime (and lead to a climatic cooling) by decreasing the probability of drizzle formation.
\r\n\r\nFinally, the performance of instruments used for measuring the concentration of cloud condensation nuclei (CCN) was assessed. Each design exhibits different limitations and sources of uncertainty, but all show decreased ability to measure CCN of low critical supersaturation (<0.1%). The performance of the instrumentation can be very sensitive to the operating conditions. Therefore, an in-depth theoretical understanding of the instrumentation is necessary; otherwise, CCN measurements may be subject to considerable uncertainty.
" }, { "name": "Quezada, Cindy Mar\u00eda", "degree": "PhD", "year": "2003", "title": "Histidine Phosphorylation in Bacterial Chemotaxis", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302003-145522", "creators": [ { "name": { "family": "Quezada", "given": "Cindy Mar\u00eda" }, "id": "Quezada-Cindy-Mar\u00eda", "display_name": "Quezada, Cindy Mar\u00eda" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "biochem" ], "doi": "10.7907/8DNJ-GX96", "abstract": "Bacterial chemotaxis, the directed movement of bacteria in a chemical environment, represents one of the best biochemically and structurally characterized signal transduction pathways. The histidine kinase CheA is a central player in this two component regulatory system. Its active site is spread across two domains: the histidine phosphotransfer domain (P1) and the kinase domain (P4). Our efforts focus on elucidating the mechanistic contribution of P1 residues to the autophosphorylation reaction.
\r\n\r\nAn atomic resolution structure (0.98 \u00c5) of the Thermotoga maritima CheA histidine phosphotransfer domain was obtained, affording a unique opportunity to view the environment surrounding His45, the phosphoaccepting histidine, in detail. His45, participates in a hydrogen bonding network including three other residues: Glu67, Lys48, and His64, which are conserved in CheA. Employing a combination of site-directed mutagenesis studies, protein crystallography, and 2D heteronuclear NMR techniques, we explored the functional roles of these residues involved in the largely conserved hydrogen bonding network.
\r\n\r\nOur experiments revealed that the P1 domain provides the nucleophile for phosphate transfer (His45) and the activating glutamate (Glu67) completing a catalytic center observed in the GHL family of ATPases. Glu67 tunes the reactivity of His45 through a hydrogen bond. This interaction activates His45 to the normally unfavored N?1H tautomeric state. As a result, His45 possesses an altered pKa. Upon mutation of Glu67 to a Gln, the chemical properties of His45 change. When existing in the predominantly N\u03b52H tautomeric state, its pKa is similar to that of a solvent exposed histidine and its phosphorylation is dramatically reduced in vitro and in vivo.
\r\n\r\nHence, the phosphoaccepting histidine must exist in the normally unfavored N?1H tautomeric state in order for CheA autophosphorylation to occur. The other two residues, Lys48 and His64, do not affect the reactivity of His45. Instead they contribute towards the structural integrity of the P1 active site. The results obtained in this thesis provide a solid structural and biochemical basis for further understanding the CheA phosphotransfer mechanism and may provide critical insight for the development of novel antibiotic agents.
\r\n" }, { "name": "Rucker, Victor Clay", "degree": "PhD", "year": "2003", "title": "Detection of DNA by Sequence Specific Fluorescent Polyamides", "advisor": "Rutledge, David B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05092003-135830", "creators": [ { "name": { "family": "Rucker", "given": "Victor Clay" }, "id": "Rucker-Victor-Clay", "display_name": "Rucker, Victor Clay" } ], "advisors": [ { "name": { "family": "Rutledge", "given": "David B." }, "id": "Rutledge-D-B", "role": "advisor", "display_name": "Rutledge, David B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rutledge", "given": "David B." }, "id": "Rutledge-D-B", "role": "member", "display_name": "Rutledge, David B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/93KR-9543", "abstract": "This thesis covers the use of hairpin polyamides to achieve, most notably, HIV-1 LTR gene regulation and fluorescent detection of double stranded DNA. In Chapter 2 we discuss our collaboration with Professor David Margolis to study integrated HIV-1 latency in quiescent T-lymphocytes. Understanding latency in HIV-1 infection is of paramount importance for developing anti-HIV-1 therapeutics. Chapter 3 deals with the characterization of a special case of 2-beta-2 polyamide binding in the minor groove, and we discuss the use of (S)-2,4-diaminobutyric acid to influence polyamide specificity and orientation. In Chapter 4 we present data concerning the use of hairpin polyamides that, when unbound to DNA, quench the fluorescence of the xanthene fluorphore to which they are covalently attached. We cover experiments aimed at exploring the uses of this fluorescence phenomenon to optically detect double stranded DNA in a sequence specific manner, an issue of great importance as shown in the literature by the numerous denaturing assays for oligo detection by hybridization. In Chapter 5, the fruits of a collaboration with Alexander Dunn of Professor Gray's group, we attempt to define the mechanism whereby polyamides quench tetramethyl rhodamine fluorescence." }, { "name": "Spessard, Sarah Jane", "degree": "Masters", "year": "2003", "title": "Progress Toward the Total Synthesis of Garsubellin A and Structurally Related Phloroglucin Natural Products", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142025-165919678", "creators": [ { "name": { "family": "Spessard", "given": "Sarah Jane" }, "id": "Spessard-Sarah-Jane", "display_name": "Spessard, Sarah Jane" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1y2w-nn41", "abstract": "Progress toward the polyprenylated phloroglucin garsubellin A is presented. A\r\nhighly diastereoselective single-step cyclization reaction provides access to the\r\nbicyclo[3.3.1]nonane core of this natural product. Further elaboration to a more\r\nfunctionalized analog involves a sequential Claisen rearrangement/Grubbs olefin cross\r\nmetathesis strategy. Additionally, the feasibility of this strategy toward the preparation\r\nof the bis-quaternary carbon array found at the bridgehead positions of the phloroglucinol\r\nnatural products is demonstrated. Enantioselective strategies and model studies will also\r\nbe discussed." }, { "name": "Sun, Lianhong", "degree": "PhD", "year": "2003", "title": "Engineering Galactose Oxidase to Increase Expression Level in E. coli, Enhance Thermostability and Introduce Novel Activities", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-10032002-101924", "creators": [ { "name": { "family": "Sun", "given": "Lianhong" }, "id": "Sun-Lianhong", "orcid": "0000-0002-4042-3011", "display_name": "Sun, Lianhong" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PZ0M-T047", "abstract": "For the first time, we functionally expressed the fungal glycosylated copper-containing enzyme, galactose oxidase, in Escherichia coli. The generation of fully functional GOase confirms that the formation of the unusual thioether bond is an auto-catalytic process involving a self-processing mechanism. This process does not rely on the pro-peptide of native GOase and is not dependent on the auto-cleavage of the precursor peptide during maturation, a question which can not be illustrated with other expression systems. The kinetic parameters of recombinant GOase and native GOase are comparable, but the former is less stable than the latter, revealing that the small contents of carbohydrate in native GOase confer a more rigid structure, but not a beneficial effect on catalytic efficiency to the enzyme. We applied directed evolution to generate GOase variants with improved thermostability, increased catalytic efficiency, and enhanced expression level in Escherichia coli. The final mutants are comparable to fungal GOase in their thermostability, long-term stability and radical stability. We also applied saturation mutagenesis to endow the protein with a novel D-glucose 6-oxidase activity, an activity that has never been reported in nature or laboratory. The resultant mutant M-RQW, with three amino acid substitutions (R330K, Q406T/S and W290H), shows low but significant activity in the selective oxidation of D-glucose's 6-hydroxyl group and has decreased activity towards its native substrate, D-galactose. None of the mutations can be obtained by single nucleotide substitutions. The mutation on W290, a residue proposed to stabilize the radical of GOase, supports the conclusion that W290 restricts substrates from entering the active center of GOase. Moreover, kinetic characterization of the mutant indicates that W290 might facilitate access of D-galactose to the active center. It is also found that radical stability is not only affected by reduction potential, but also structural factors. The synergistic interactions between the R330K and Q406S/T substitutions improve D-glucose accessibility to the active center. Mutant M-RQW can also accept aliphatic secondary alcohols to generate corresponding ketones. This activity, compared with the bioinorganic mimics of GOase, illustrates the flexible, yet robust, active center configuration of GOase. \r\n\r\n\r\n\r\n" }, { "name": "Thorsen, Todd Addison", "degree": "PhD", "year": "2003", "title": "Microfluidic Technologies for High-Throughput Screening Applications", "advisor": "Roberts, Richard W.; Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-12012002-092026", "creators": [ { "name": { "family": "Thorsen", "given": "Todd Addison" }, "id": "Thorsen-Todd-Addison", "display_name": "Thorsen, Todd Addison" } ], "advisors": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "advisor", "display_name": "Roberts, Richard W." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "orcid": "0000-0002-1613-0809", "role": "chair", "display_name": "Quake, Stephen R." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "biochem" ], "doi": "10.7907/QGWY-VX32", "abstract": "In this thesis, I present a strategy for the design and development of microfluidic devices for high-throughput screening applications, such as mutant enzyme libraries expressed in prokaryotic hosts, where a few point mutations at the DNA level translates to hundreds of thousands of enzyme variants. The work falls into three main sections. Section I addresses fundamental research in polymer chemistry, where I explore the suitability of several polymers for microfluidic applications, examining properties such as molding, fluorescence, solvent compatibility, and adhesion/sealing to glass substrates. Section II describes my development of a two-phase microfluidic device, in which I report on crossflow-based dynamic formation of picoliter-sized water droplets in a continuously flowing oil-surfactant stream. A predictive model describing the fluid dynamics of droplet formation in this model is presented as well as its applications in screening bacterial populations. Section III reports the development of multilayer soft lithography technology using silicone rubber to build addressable high-density microfluidic arrays with thousands of integrated mechanical valves. This technology, which introduces the concept of fluidic large scale integration, is presented as a high-throughput parallel method to analyze bacterial enzyme expression at the single cell level. The detection of enzymatic activity in these high-density microarrays is described, comparing a self-constructed solid-state laser apparatus with a modified scanner (Axon Industries) used for looking at DNA arrays.\r\n" }, { "name": "Treadway, Christopher Ryan", "degree": "PhD", "year": "2003", "title": "Spectroscopic Characterization of DNA-Mediated Charge Transfer", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252003-231704", "creators": [ { "name": { "family": "Treadway", "given": "Christopher Ryan" }, "id": "Treadway-Christopher-Ryan", "display_name": "Treadway, Christopher Ryan" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KMWD-4M75", "abstract": "The DNA double helix provides a well-characterized molecular pi stack in which charge transfer rates and efficiencies may be examined. We investigated the phenomenon in a series of DNA duplexes modified with various photo- and redox-active species.
\r\n\r\nCharge transfer dynamics through DNA were distance independent for a series of duplexes modified with 7-deazaguanine and a covalently attached ethidium chromophore. The decay times were grouped into two components: (1) injection of charge into the DNA base stack and (2) a correlated charge transfer corresponding to the reorientation of ethidium within the duplex.
\r\n\r\nUsing the modified bases 2-aminopurine and 7-deazaguanine, intrastrand charge transfer through DNA was observed on the picosecond timescale. Charge transfer rates and quenching yields were also dependent on the reaction?s driving force and the composition of the intervening base stack.
\r\n\r\nThe efficiency of photooxidation of 7-deazaguanine by a ruthenium(II) intercalator in DNA over 7?14 angstroms was shallow and dependent on the chirality of the covalently attached metallointercalator. Nanosecond to subnanosecond decay rates were measured, and the spectroscopic signature of a charge transfer intermediate was observed.
\r\n\r\nA series of ruthenium(II) intercalators with high oxidation potentials was created. Redox reactivity of the compounds with DNA did not correlate directly with oxidation potential and was dependent on DNA binding and luminescence quenching abilities. Thus, redox potential may not be used as the sole predictor of reactivity with the base stack of DNA.
\r\n\r\nFinally, the binding of ruthenium(II) and rhodium(III) intercalators to DNA was investigated with CD and NMR spectroscopies. Data confirmed that metallointercalators do not preferentially bind next to each other along the double helix. Hence, direct contact of reactants is not responsible for fast and efficient charge transfer between metallointercalators bound noncovalently to DNA.
\r\n\r\nThese studies have provided direct measurements of the dynamics of DNA-mediated charge transfer and proven, once again, that the DNA pi stack facilitates fast and efficient charge transfer. Most importantly, the stacking and dynamics of the reactants and DNA bases were found to affect the charge transfer behavior.
" }, { "name": "Trnka, Tina Maria", "degree": "PhD", "year": "2003", "title": "Catalysts for Olefin Metathesis: Ruthenium Alkylidene Complexes with Phosphine and N-Heterocyclic Carbene Ligands", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01302003-225031", "creators": [ { "name": { "family": "Trnka", "given": "Tina Maria" }, "id": "Trnka-Tina-Maria", "display_name": "Trnka, Tina Maria" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PP5B-E858", "abstract": "The objectives of the work described in this dissertation were twofold: (1) to further improve the activity and selectivity of ruthenium-based olefin metathesis catalysts, and (2) to obtain a better understanding of how these catalysts operate.
\r\n\r\nThe first problem was addressed by varying the ligand sphere within the L2X2Ru=CHR framework. Chapter 2 explores the metathesis of directly functionalized olefins, such as 1,1-difluoroethylene and acrylonitrile. Detailed studies revealed that ruthenium alkylidene complexes react readily with these olefins but stop after a single turnover of the catalytic cycle. This effect is caused by electronically deactivating carbene substituents, which dramatically decrease the rate of phosphine dissociation from the metal center and thus prevent catalyst re-initiation.
\r\n\r\nChapter 3 describes complexes where the L ligands are phosphines, N-heterocyclic carbenes (NHCs), imidazoles, or pyridines, where the X ligands are chlorides, and where the carbene moiety is either benzylidene or a cyclic moiety. Improved catalytic activity and selectivity were achieved with complexes containing a combination of phosphine and NHC ligands. The reactivity and stability profiles of these species can be tuned through the stereoelectronic properties of the NHC. To facilitate the use of NHCs in organometallic applications, a synthetic route was developed that employs NHC adducts to protect the reactive carbene centers.
\r\n\r\nChapter 4 describes the reactions of ruthenium alkylidene complexes with alkynes. In the majority of cases, the metathesis polymerization of alkynes is unsuccessful because of competing reactions to form eta3-vinylcarbene and eta5-cyclopentadienyl derivatives. The eta3-vinylcarbene complexes are particularly interesting as models for the olefin-bound intermediate in the olefin metathesis catalytic cycle, and their structures demonstrate that it is possible for the chloride ligands to adopt a cis arrangement that places one of the chlorides trans to the L donor ligand.
\r\n\r\nThe studies in Chapter 5 explore the stereoelectronic properties of phosphine and NHC ligands and provide valuable insights about electronic structure and bonding. This information was obtained by a variety of techniques, including structure-activity studies, kinetics, x-ray crystallography, heteronuclear NMR, infrared spectroscopy, and gas-phase UV photoelectron spectroscopy.
" }, { "name": "Vadehra, Anand", "degree": "Masters", "year": "2003", "title": "DNA-Mediated Charge Transfer in Biological Contexts", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02252025-185802207", "creators": [ { "name": { "family": "Vadehra", "given": "Anand" }, "id": "Vadehra-Anand", "display_name": "Vadehra, Anand" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cqzg-1391", "abstract": "No abstract." }, { "name": "Wang, Jian", "degree": "PhD", "year": "2003", "title": "Instrument Development and Characterization of Atmospheric Aerosol Physical Properties Through Airborne Measurement", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06092005-132829", "creators": [ { "name": { "family": "Wang", "given": "Jian" }, "id": "Wang-Jian", "display_name": "Wang, Jian" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "member", "display_name": "Yung, Yuk L." }, { "name": { "family": "Wennberg", "given": "Paul O." }, "id": "Wennberg-P-O", "role": "member", "display_name": "Wennberg, Paul O." } ], "option_major": [ "chemeng" ], "doi": "10.7907/GNFA-V973", "abstract": "Atmospheric aerosol has significant impact on climate. It influences radiative transfer by scattering and absorbing sunlight and by changing the microphysical structure, lifetime, and amount of the clouds. Due to its short lifetime, the spatial and temporal distributions of tropospheric aerosol are highly inhomogeneous. Aircraft have proven to be an effective platform in characterizing the atmospheric aerosol. To maximize the potential and to reduce the artifacts associated with aircraft sampling, both improvements in existing instruments and developments of new instruments are required.
\r\n\r\nTo increase the speed of submicron aerosol size distribution measurements, a mixing condensation nucleus counter (MCNC) has been developed. By carefully designing the mixing chamber and condenser, the response time of the MCNC was significantly reduced. Our experiments demonstrate that a differential mobility analyzer (DMA) coupled with the developed MCNC can measure complete aerosol size distributions in as little as 2 seconds.
\r\n\r\nThe effects of bends and elbows on the diffusional losses of particle in nanometer range were studied. The results show that the effect of bends and elbows on particle diffusion loss is significant, and for Reynolds number smaller than 250, the enhancement of diffusion losses due to bends and elbows is sensitive to both the relative orientations of the bends and elbows and the lengths of straight tubing between them. Because of this sensitivity, direct calibration or simulation is required to assess nanoparticle penetration efficiencies for any flow system containing bends or elbows at low Reynolds number. When the Reynolds number exceeds 250, the enhancement is insensitive to the actual flow configurations. Experimental results are presented, which can be used for design of aerosol flow systems at Reynolds number larger than 250.
\r\n\r\nTo minimize the airborne sampling bias, an advanced differential mobility analyzer (DMA) system for measuring submicron aerosol size distribution at ambient relative humidity, with special attention to implementation on aircraft, has been developed. The system includes an active RH controller, a cylindrical differential mobility analyzer (CDMA), and a condensation nucleus counter. A cascade controller consisting of two PID modules maintains the RH inside the CDMA at ambient RH by actively adding or removing water vapor from the air stream. The flows are controlled with feedback PID controllers, which compensate for the variation of pressure as the aircraft changes altitude. This system was integrated into the CIRPAS Twin Otter aircraft and used to measure ambient size distributions during the Aerosol Characterization Experiment-Asia (ACE-Asia), carried out from March to May, 2001, in Japan.
\r\n\r\nDuring the ACE-Asia experiment, the above DMA system, together with an aerodynamic particle sizer (APS), was used to characterize aerosol size distributions in East Asia during 19 flights on board of CIRPAS Twin Otter aircraft. Besides providing the aerosol size characteristics, the data were combined with chemical composition and aerosol mixing state measurements to predict the vertical profile of aerosol extinction, which was compared with those derived from simultaneous direct measurements of aerosol optical depth by the NASA 14-channel sunphotometer. Agreement between the predicted and derived aerosol extinction varies for different scenarios, but the discrepancies were generally within the calculated uncertainties.
" }, { "name": "Wehbi, William Amine", "degree": "PhD", "year": "2003", "title": "Amino Acid Radicals in Rhenium-Modified Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302003-153624", "creators": [ { "name": { "family": "Wehbi", "given": "William Amine" }, "id": "Wehbi-William-Amine", "display_name": "Wehbi, William Amine" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HF8D-1W16", "abstract": "Oxidative flash quench of [Re(CO)3(phen)(His)]+ generates a high-potential [Re]2+ oxidant (E\u00b0 (Re2+/+) = 2 eV v. NHE), which has been used to obtain rates of electron transfer of Cu(I) oxidation in rhenium-modified azurins. These rates are enhanced over the [Ru(bpy)2(im)(His)]2+ analogues (E\u00b0 Ru3+/2+ ~ 1 eV), suggesting an alternate mechanism from driving force optimized, singe-step electron tunneling. To test whether other intermediates can be involved, oxidative freeze flash quench of the zinc(II) derivatives were undertaken. These experiments reveal that [Re]2+ can produce the amino acid radicals of tyrosine and cysteine, as detected by EPR. The properties of these radicals in structurally well-defined protein microenvironments in Pseudomonas aeruginosa azurin mutants have focused, in particular, on the g1 component of the g-tensor, which is sensitive to the strength of the hydrogen bond to the radical. The g1 for Tyr48 radical, which resides in a completely hydrophobic pocket and is inaccessible to solvent, is found to be greater than the g1 for the solvent exposed Tyr108 radical. This comparison could not be made for the cysteine radicals as Cys108 formed a sulfenyl radical upon oxidation; the Cys48 radical has been demonstrated to be a thiyl radical species and provides the EPR spectroscopic benchmark for a non-hydrogen bonded thiyl radical.
\r\n\r\nIn azurin mutants without any tyrosine, tryptophan, or cysteine residues, oxidative flash quench results in another organic based radical. This radical is located on the histidine imidazole ring that is coordinated to the rhenium atom. DFT calculations suggest that the spin density resides mainly on the imidazole ring when it is deprotonated. Corrected distances in the tunneling timetable to the imidazole ring from the copper atom predict an identical exponential decay in the electron transfer rates as for the ruthenium-labeled azurins. The rate enhancement is explained in terms of a \"trivial hop\" whereby Re2+ rapidly oxidizes the non-innocent histidine ligand in a proton dependent process; the histidine radical in turn oxidizes the copper atom or tyrosine, cysteine, or tryptophan when zinc is present. This model explains all of the enhanced Cu(I) oxidation rates by [Re]2+ and suggests that for Cu(I) oxidation in azurin, multistep electron tunneling through other amino acid radicals does not occur and that the observed radicals are generated in off-path processes.
\r\n" }, { "name": "Zhang, Deqiang", "degree": "PhD", "year": "2003", "title": "Structure-Based Design of Mutant Proteins: I. Molecular Docking Studies of Amino Acid Binding to Wild-Type Aminoacyl-tRNA Synthetases. II. Structure-Based Design of Mutant Aminoacyl-tRNA Synthetases for Non-Natural Amino Acid Incorporation", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-12182002-190040", "creators": [ { "name": { "family": "Zhang", "given": "Deqiang" }, "id": "Zhang-Deqiang", "display_name": "Zhang, Deqiang" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "chair", "display_name": "Roberts, Richard W." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CN3G-JH45", "abstract": "Protein biosynthesis has precisely controlled accuracy, and aminoacyl-tRNA synthetases (AARSs) play an important role in charging amino acids to their cognate tRNAs with high fidelity. In some cases the misactivation of non-natural amino acids by the wild-type or mutant AARS can be utilized to incorporate these non-natural amino acids into proteins in vivo. Such technique has tremendous potentials in protein engineering and other applications. Therefore, it is essential to understand the amino acid recognition mechanism displayed by AARSs.
\r\n\r\nIn this thesis, computational studies of the selection of natural and non-natural amino acids by AARSs at the binding stage have been conducted for methionyl-tRNA synthetase (Chapter 2), histidyl-tRNA synthetases (Chapter 3), and isoleucyl-tRNA synthetase (Chapter 4). In these chapters, molecular docking and ligand perturbation are used to elucidate the binding discrimination showed by these AARSs.
\r\n\r\nBecause many non-natural amino acids carrying interesting physical and chemical properties on their side chains cannot be incorporated by using the wild-type AARSs, it is necessary to manipulate the activity of AARSs by making mutations in the binding site of amino acids. To this end, we have developed a Clash Opportunity Progressive (COP) protein design tool to redesign the binding site of AARSs. Chapter 5 describes the main steps in COP. Chapters 6 to 8 present the application of COP to different AARSs. In Chapter 6, COP has been applied to design mutant tyrosyl-tRNA synthetase (TyrRS) for recognizing Ome-Tyr, Naph-Ala, and p-keto-Tyr. In Chapter 7, COP has been used to design mutant phenylalanyl-tRNA synthetase for p-keto-Phe. In Chapter 8, tryptophanyl-tRNA synthetase is used as a template to design mutant AARS to recognize NBD-Ala, bpy-Ala, and DAN-Ala.
\r\n\r\nThe appendices are some publications and manuscripts on various other projects. Appendix I is a molecular dynamics study of laboratory-evolved pNBE enzymes with different thermostability. The findings presented here will help us to better understand the determinants in protein stability evolution. Appendix II contains experimental work I have done in the Chan group. Unfolding experiments revealed the existence of intermediates in the equilibration unfolding of RdPf. In Appendix III, femtosecond time-resolved spectroscopy was used to study the fluorescence resonance energy transfer and tryptophan solvation dynamics in RdPf.
" }, { "name": "Adams, Peter Jonathan", "degree": "PhD", "year": "2002", "title": "Representing Tropospheric Aerosols and Their Climatic Effects in Global Models", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122010-125450691", "creators": [ { "name": { "family": "Adams", "given": "Peter Jonathan" }, "id": "Adams-Peter-Jonathan", "display_name": "Adams, Peter Jonathan" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "orcid": "0000-0002-4263-2562", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/10CM-8W55", "abstract": "In order to better understand and quantify the direct and indirect effect of aerosols on climate, an earlier general circulation model (GCM) simulation of tropospheric sulfate has been extended by incorporating aerosol thermodynamics and microphysics. The thermodynamic simulation allows the prediction of nitrate, ammonium, and aerosol water concentrations. It is estimated that nitrate contributes as much to total aerosol mass as sulfate on regional scales in parts of Europe and North America. The direct radiative forcing associated with the sulfate-nitrate-ammonium-water mixture is estimated to be \u20141.14 W M^(-2) for the present day. Based on a future emissions scenario, this could increase to as much as \u20142.13 W^(-2) by the year 2100, an increase that results from increased nitrate concentrations. Although currently a minor contributor to aerosol direct radiative forcing, nitrate is predicted to exceed sulfate in its contribution by the end of the century for this emissions scenario. It is also found that direct radiative forcing estimates are highly sensitive to aerosol behavior at relative humidity above 90%, highlighting the shortcomings of global models in their treatment of aerosol water uptake under partly cloudy conditions. The microphysical simulation allows the prediction of tropospheric aerosol number concentrations and size distributions, key parameters in determining the indirect effect of aerosols on clouds. A two-moment sectional algorithm is used to simulate the microphysical processes of condensation/evaporation and coagulation. It has been tested by performing a simulation of sulfate microphysics. Predicted aerosol number concentrations generally agree with observations to within 25%. The microphysical simulation also reproduces key features of the tropospheric aerosol such as increasing number concentrations with altitude and land-sea contrasts in cloud condensation nuclei concentrations. It is found that there are important uncertainties in the source rates of new particles to the atmosphere, whether from in situ nucleation or emissions of particulates, that can significantly impact predicted aerosol number and cloud condensation nuclei concentrations." }, { "name": "Amashukeli, Xenia", "degree": "PhD", "year": "2002", "title": "Electron-Transfer Reorganization Energies of Isolated Molecules", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04252012-084159781", "creators": [ { "name": { "family": "Amashukeli", "given": "Xenia" }, "id": "Amashukeli-Xenia", "display_name": "Amashukeli, Xenia" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "abstract": "Electron-transferreorganization energies of isolated organic molecules and biologically relevant porphyrins are obtained from analyses of their photoelectron spectra. The\r\nassignments of experimental ionization energies are aided by ab initio calculations, and comparisons between He I and He II ionization data. It is established that in unsymmetrically substituted metalloporphyrins, i.e., Zn(II) protoporphyrin IX, the highest occupied molecular orbital has appreciable nitrogen character (Chapter 3).Quantum-mechanical and semiclassical analyses of vibrational progressions observed in photoelectron spectra yield\r\ngas-phase reorganization energies. Favorable agreement is reached between experimental and calculated values of reorganization energies (Chapters 2 and 3). This observation is not surprising, however, since density functional theory calculations, employed in this thesis, are successful at reproducing experimental molecular geometries. Indeed, X-ray structural parameters of dibenzo[a,c]phenazine are in excellent agreement with calculated results (Chapter 6). Vibrational frequencies of organic molecules are also calculated (Chapter 5) to aid mode-specific quantum mechanical analyses of fine structure observed in photoelectron spectra. Given the success of ab initio calculations of reorganization energies of organic\r\nmolecules, the same computational approach is employed to obtain reorganization energies of six-coordinate metalloporphyrin model systems (Chapter 4). The results show that large reorganization energies are associated with charged ligands, which are most frequently found in protein redox catalytic sites; small reorganization energies, on the other hand, are calculated for the molecules with neutral ligands, commonly located in the protein active\r\nsites that facilitate electron transfer.
\r\n" }, { "name": "Belitsky, Jason Matthew", "degree": "PhD", "year": "2002", "title": "DNA Binding Polyamides in Biological Systems", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252012-151300693", "creators": [ { "name": { "family": "Belitsky", "given": "Jason Matthew" }, "id": "Belitsky-Jason-Matthew", "display_name": "Belitsky, Jason Matthew" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "chair", "display_name": "Roberts, Richard W." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/WNV6-DH45", "abstract": "Small molecules that bind selectively to a DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing\r\nN-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of \"pairing rules\" with affinities and specificities that rival natural transcription factors. By directly competing with a given transcription factor or other DNA binding protein for its binding site, polyamide can cause inhibition of diverse biological processes, such as retroviral integration and gene transcription. Polyamides are presented which inhibit the in vitro integration activities for two retroviruses, M-MuLV and HIV-l. Polyamides are described that inhibit TBP binding to the HER2 promoter, a gene implicated in human breast cancer. Failure to achieve inhibition of HER2 transcription in cell culture led to the surprising discovery that polyamide-fluorescent dye conjugates are cell permeable, but that nuclear localization does not occur in many cell lines. Efforts toward modified polyamides with enhanced nuclear localization properties are presented. In order to extend the number of sequences amenable to high affinity recognition, alteration of the C-terminal polyamide tail has been investigated. The development of conditions for polyamide solid-phase synthesis on a new resin, which allows for the generation of \"truncated tail\" polyamides, is presented. During the original route to one of these compounds, an\r\nunexpected reaction was uncovered that leads to entirely different C-terminal tails." }, { "name": "Chevillet, John Richard", "degree": "Masters", "year": "2002", "title": "Targeting Repeat Sequences with DNA-Binding Small Molecules", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022012-110126423", "creators": [ { "name": { "family": "Chevillet", "given": "John Richard" }, "id": "Chevillet-John-Richard", "display_name": "Chevillet, John Richard" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3YF2-Y771", "abstract": "Recognition of repeat sequences in DNA would have applications in molecular biology. One of the most biologically interesting repeat sequences is the telomeric repeat which composes the ends of eukaryotic chromosomes; in vertebrates 5'-TTAGGG-3'. This sequence has been used as a model to study how DNA-binding polyamide molecules composed of pyrrole (Py) and imidazole (Im) residues bind to repeating sequences. DNase I footprinting shows that the polyamide-fluorophore conjugate IrnImImPy-\u03b3-PyPy((CH_2)_3N,N',N''trimethylbis hexamethylene)triamineOregonGreen488) PyPy-\u03b2-Me can bind the sequence 5'-AGGGTT-3' K_a = 1.8x10^8 M^(-1). \r\nQuantitative fluorescence titrations with varying patterns of telomeric repeat suggest that the molecule can tolerate another polyamide binding contiguously, but not two.\r\nTruncation of the tail of the conjugate to yield the molecule ImImImPy-\u03b3-Py Py((CH_2)_3N,N',N''trimethylbis (hexamethylene)triamine-OregonGreen488) PyPy-Me allows the compound to bind three contiguous sites, suggesting that steric polyamide-polyamide interactions control binding in this manner." }, { "name": "Copeland, Kimberly Davis", "degree": "PhD", "year": "2002", "title": "The Reactions of Metallointercalator-Peptide Conjugates and DNA", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01262012-090632523", "creators": [ { "name": { "family": "Copeland", "given": "Kimberly Davis" }, "id": "Copeland-Kimberly-Davis", "display_name": "Copeland, Kimberly Davis" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MR9T-7W57", "abstract": "A family of metallointercalator-peptide conjugates for reaction with DNA has been constructed. In these chimeras, the metallointercalator provides binding affinity for\r\nDNA and the peptide contributes reactivity. With the goal of creating an artificial nuclease, we have tethered metal-binding peptides to a sequence neutral intercalator,\r\n[Rh(phi)_2bpy']^(3+) (phi = phenanthrenequinone diimine, bpy' = 4-butyric acid-4' -methyl-2,2'-bipyridine). This is a general strategy, and we have observed Zn^(2+)-promoted\r\ncleavage of plasmid DNA with widely different peptides: a designed helical peptide with histidine residues, and a hairpin peptide modeled after the active site of the BamHI\r\nendonuclease. To optimize the peptide composition of our artificial nuclease we created a library of 16,000 conjugates, but no new active conjugates were identified with this combinatorial strategy. To achieve oxidative cleavage of the DNA backbone we have also used our intercalator-peptide conjugates to deliver copper to DNA. Tethered peptides containing histidine residues promote oxidative strand scission in DNA restriction fragments and oligonucleotides in the presence of Cu^(2+) and a reducing agent. Importantly, by comparing the photocleavage pattern of the rhodium intercalator with the copper cleavage pattern of the metal-binding peptide, the interactions of the conjugate with DNA could be dissected. Finally, short peptides were tethered to [Ru(phen)(bpy')(dppz)]^(2+) \r\n(phen = 1,10-phenanthroline, dppz = dipyridophenazine) to\r\ncreate fluorescent DNA crosslinking agents. Through a flash-quench reaction, the ruthenium intercalator generates guanine radicals in a DNA duplex. These guanine\r\nradicals can react with water or oxygen, but also with tethered peptides to produce pennanent DNA-peptide crosslinks. The DNA-peptide crosslinks were detected by gel\r\nelectrophoresis and absorbance measurements, and characterized by mass spectrometry. Although they have low affinity for DNA, untethered peptides could also be crosslinked to DNA using the ruthenium chemistry. The peptide composition influences conjugate binding and the extent and pattern of crosslinking; indeed, positively charged residues were essential for effective crosslinking. Although the flexibility of our tethered peptides\r\nis an obstacle to the rational design of reactive conjugates, we have demonstrated that peptides can mediate a variety of reactions if delivered to DNA by metallointercalators." }, { "name": "Feldmann, Michael Todd", "degree": "PhD", "year": "2002", "title": "Quantum Monte Carlo: Quest to Get Bigger, Faster, and Cheaper", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252012-135136531", "creators": [ { "name": { "family": "Feldmann", "given": "Michael Todd" }, "id": "Feldmann-Michael-Todd", "display_name": "Feldmann, Michael Todd" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Bruck", "given": "Jehoshua" }, "id": "Bruck-J", "orcid": "0000-0001-8474-0812", "role": "member", "display_name": "Bruck, Jehoshua" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Pierce", "given": "Niles A." }, "id": "Pierce-N-A", "orcid": "0000-0003-2367-4406", "role": "member", "display_name": "Pierce, Niles A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4D4F-WZ34", "abstract": "We reexamine some fundamental Quantum Monte Carlo (QMC) algorithms with the goal of making QMC more mainstream and efficient. Two major themes exist: (1) Make QMC faster and cheaper, and (2) Make QMC more robust and easier to use. A fast \"on-the-fly\" algorithm to extract uncorrelated estimators from serially correlated data on a huge network is presented, DDDA. A very efficient manager-worker algorithm for QMC parallelization is presented, QMC-MW. Reduced expense VMC optimization procedure is presented to better guess initial Jast row parameter sets for hydrocarbons, GJ. I also examine the formation and decomposition of aminomethanol using a variety of methods including a test of the hydrocarbon GJ set on these oxygen- and nitrogen-containing systems. The QMC program suite QMcBeaver is available from the authors in its entirety while a user's and developer's manual is attached as supplementary material." }, { "name": "Fu, Anne Yen-Chen", "degree": "PhD", "year": "2002", "title": "Microfabricated Fluorescence-Activated Cell Sorters (\u00b5FACS) for Screening Bacterial Cells", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-05132002-124824", "creators": [ { "name": { "family": "Fu", "given": "Anne Yen-Chen" }, "id": "Fu-Anne-Yen-Chen", "display_name": "Fu, Anne Yen-Chen" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Anderson", "given": "W. French" }, "id": "Anderson-W-F", "orcid": "0000-0003-4043-1684", "role": "member", "display_name": "Anderson, W. French" }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hsieh-Wilson", "given": "Linda C." }, "id": "Hsieh-Wilson-L-C", "orcid": "0000-0001-5661-1714", "role": "member", "display_name": "Hsieh-Wilson, Linda C." }, { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "role": "member", "display_name": "Quake, Stephen R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6HKD-RQ61", "abstract": "In this thesis, I have developed elastomeric microfabricated cell sorting devices using a micromachining technology, \"soft lithography\". Inexpensive elastomeric microfabricated devices were designed to replace flow chambers in conventional fluorescence-activatived cell sorters (FACS). Sorting of cells and other particles was accomplished via different means of flow control. My early work of cell sorting on these devices was accomplished using electrokinetic flow. However, in order to alleviate problems associated with electrokinetic flow, the microfabricated cell sorter was integrated with microvalves and micropumps for pneumatic actuation control. The integrated cell sorter has better capabilities of fine-tuning the flow control, manipulating single cells and is less harmful to the cells than electrokinetic flow. Substantial enrichments of beads and cells were accomplished on these devices. Novel sorting algorithms, which can only be implemented in microfabricated devices, were also demonstrated. Compared with conventional FACS, these microfabricated devices allow for more sensitive optical detection for bacterial cells and DNA, innovative sorting schemes and are disposable to eliminate any cross-contamination from previous runs. Ultimately, these elastomeric microfluidic flow cells provide an inexpensive, robust and effective way to perform cell sorting and can be used as stand-alone devices or as a part of an integrated system for diagnostics and/or cytometric measurements.
\r\n\r\nPresently, the microfabricated cell sorter is enjoying new applications in various fields for high throughput screening, including directed evolution, digital genetic circuits, microbiology and cell biology of gene expression and regulation. In addition, this sorter is not limited only to the detection of optical signals. I have attached the sorter to a high resolution magnetometer, a superconducting quantum interference device (SQUID) microscope, to obtain cytometric data of the magnetic field strengths of magnetotactic bacteria as they flowed through the device.
\r\n\r\nThis thesis lays down the foundation for future work in cell sorting and single cell analysis. Time-course measurements of a single cell for kinetic studies can be implemented using novel sorting schemes. Sample dispensing and any downstream analysis, such as cell lysis and/or polymerase chain reaction, can be carried out immediately after the cells have been sorted. The sorter could also be incorporated with other technologies to measure cellular magnetic or electrical properties. We anticipate that an integrated lab-on-chip, where cell sorting is one of the steps of a complete analysis system, is not far off.
" }, { "name": "Garland, Eva Rose", "degree": "PhD", "year": "2002", "title": "Laboratory Studies of Atmospheric Reactions Using Infrared Cavity Ringdown Spectroscopy", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252012-085741064", "creators": [ { "name": { "family": "Garland", "given": "Eva Rose" }, "id": "Garland-Eva-Rose", "display_name": "Garland, Eva Rose" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NFZF-0E29", "abstract": "Infrared cavity ringdown spectroscopy provides for sensitive spectroscopic detection with a time scale of microseconds. This thesis discusses the implementation of infrared cavity ringdown spectroscopy for studies of atmospheric reactions.
\r\n\r\nChapter 1 details the infrared cavity ringdown spectrometer assembled in our laboratory. Pulsed infrared radiation was generated by pumping an optical parametric amplifier (OPA) with 532 nm light from a doubled Nd:YAG laser, and a tunable dye laser provided the signal frequency. The ringdown decay was fit to an exponential curve to extract a ringdown time from which concentrations of absorbing species could be determined. Initial measurements indicated that our apparatus is a highly sensitive spectroscopic probe of infrared transitions of molecules with absorption linewidths greater than 1 cm^(-1). Our detection limit for the j = 7 line of the v_3 band of methane in a 43 inch cell was 10^(13) molec/cc of methane.
\r\n\r\nChapter 2 describes initial kinetics experiments performed with our apparatus for the reactions of HO_2 + HO_2 and HO_2 + ClO. Our results for the rates of the HO_2 + HO_2 reaction and the HO_2 + ClO reaction agree well with literature values, demonstrating the capabilities of our system for use in kinetic studies. We were unable to observe the formation of the postulated HOOOCI intermediate from the reaction of HO_2 + ClO due to spectral interference from H_2O_2 in the region where HOOOCl is predicted to absorb.
\r\n\r\nChapter 3 discusses studies of the reaction pathways undergone by alkoxy radicals. We found that photolysis of the alkyl nitrite precursor at 248 nm resulted in an\r\nunexpectedly high rate of decomposition of the alkoxy radicals, and we attributed this result to excess energy in the alkoxy radicals following photolysis at this wavelength.\r\nWith photolysis at 351 nm, no decomposition products were detected. At this wavelength, we observed an -OH peak at 3675 cm^(-1) for the n-butoxy and n-pentoxy radicals, which is evidence of the isomerization channel. For the n-butoxy radical, we determined that the ratio of the rate for its reaction with O_2 versus its isomerization (k_(O2)/k_(isom)) was (4.0\u00b10.1)*10^(-20) cm^3 molec^(-1) when probing the isomerization product milliseconds after the generation of the n-butoxy molecule and (3.6\u00b11.4)* 10^(-20) cm^3 molec^(-1) when probing the isomerization product 10-20 \u00b5s after the generation of the nbutoxy\r\nradical. For the n-pentoxy radical, we placed an upper limit on the ratio of k_ (O2)/k_(isom) of 5.6*10^(-21) cm^3 molec^(-1).
\r\n" }, { "name": "Halstenberg, Sven", "degree": "PhD", "year": "2002", "title": "Biologically Engineered Protein-graft-Poly(Ethylene Glycol) Hydrogels: A Cell-Adhesive and Plasmin-Degradable Biosynthetic Material for Tissue Repair", "advisor": "Hubbell, Jeffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022011-083754766", "creators": [ { "name": { "family": "Halstenberg", "given": "Sven" }, "id": "Halstenberg-Sven", "display_name": "Halstenberg, Sven" } ], "advisors": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "advisor", "display_name": "Hubbell, Jeffrey A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XQG0-6825", "abstract": "The goal of the research presented in this dissertation was to create a biomimetic artificial material that exhibits functions of extracellular matrix relevant for improved nerve regeneration.\r\n\r\nTo identify minimal factors necessary for neurite extension in a suitable model system, neural adhesion peptides were photoimmobilized on highly crosslinked poly(ethylene glycol)-based substrates that were otherwise non-adhesive. Neurons adhered in two-dimensional patterns for eleven hours, but no neurites extended. In contrast, human\r\nfibroblasts adhered and spread on regions with photoimmobilized RGDS oligopeptide, but not on RDGS peptide, suggesting that specific integrin-ligand binding accounted for fibroblast adhesion and spreading.\r\n\r\nTo enable neurite extension and nerve regeneration in three dimensions, and to address the need for specifically cell adhesive and cell degradable materials for clinical\r\napplications in tissue repair in general, an artificial protein was recombinantly expressed and purified that consisted of a repeating amino acid sequence based on fibrinogen and antithrombin III. The artificial protein contained integrin-binding RGD sites, plasmin\r\ndegradation sites, and heparin-binding sequences. Furthermore, the protein contained six cysteine residues as grafting sites for poly(ethylene glycol) diacrylate via Michael-type conjugate addition. The resulting protein-graft-poly(ethylene glycol)acrylates were crosslinked by photopolymerization to form hydrogels. Human fibroblasts attached to, invaded, and apparently proliferated in the artificial hydrogel matrices three-dimensionally. Fibroblast penetration was inhibited in a concentration-dependent manner by both soluble cyclo(RGDFV) peptide and aprotinin, a serine-protease inhibitor. Inhibition of fibroblast outgrowth by cyclic RGD peptide suggests that cellular integrins engaged in specific binding to RGD sites present in the artificial protein-graft-poly(ethylene glycol) hydrogels' protein core. Inhibition by aprotinin suggests that serine protease-mediated cleavage of the hydrogel matrix was the mode of cellular ingrowth.\r\n\r\nAlthough three-dimensional ingrowth of fibroblasts into protein-graft-poly(ethylene glycol) hydrogels occurred, only surface neurite outgrowth was observed from chick dorsal root ganglia. Neurite outgrowth depended on the concentration of matrix-bound heparin, suggesting that heparin was necessary to immobilize neuroactive adhesion- and/or growth factors in the hydrogels. Toward three-dimensional neurite outgrowth in protein-graft-poly(ethylene glycol) hydrogels, additional heparin-binding factors can be identified or designed for intentional immobilization in future experiments.\r\n\r\nTogether, the above results show that specific biological functions can be harnessed by protein-graft-poly(ethylene glycol) hydrogels to serve as matrices for tissue repair and\r\nregeneration. In particular, the two design objectives, specific cell adhesion and degradability by cell-associated proteases, were fulfilled by the material. In the future, this and similar artificial protein-graft-poly(ethylene glycol) materials with varying protein elements for improved wound healing might serve as biosynthetic implant materials or wound dressings that degrade in synchrony with the formation of a variety of target tissues." }, { "name": "Hansen, Kirk Charles", "degree": "PhD", "year": "2002", "title": "Using Photolabile Protecting Groups for the Rapid Triggering of Fast Biological Events", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02102012-145747544", "creators": [ { "name": { "family": "Hansen", "given": "Kirk Charles" }, "id": "Hansen-Kirk-Charles", "display_name": "Hansen, Kirk Charles" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XP3F-G534", "abstract": "To circumvent problems associated with rapid mixing we have used photolabile protecting groups for rapid initiation of biochemical processes. Specifically we have utilized laser triggering to initiate electron transfer in quinol-oxidizing enzymes and to study conformational changes in proteins.
\r\n\r\nIn order to probe the reaction chemistry of respiratory quinol-oxidizing enzymes on a rapid time scale, a photoreleasable quinol substrate was synthesized by coupling\r\ndecylubiquinol with the water-soluble protecting group 3',5'-bis(carboxymethoxy)benzoin (BCMB). Photolysis of DQ-BCMB led to the release of the BCMB group in less than\r\n10^(-6) s. The electron transfer from decylubiquinol to the respiratory enzymes Escherichia coli cytochrome bO_3 and mitochondrial cytochrome bc_1 was studied using \"caged\"\r\ndecylubiquinol. Cytochrome bc_1 reacted with photoreleased decylubiquinol with distinct kinetic phases corresponding to rapid b-heme reduction and slower c-heme reduction.\r\nThe discrimination of kinetic phases in the reaction of cytochrome bc_1 with ubiquinol substrates has provided a means of exploring the bifurcation of electron transfer that is central to the operation of the Q-cyde in this enzyme.
\r\n\r\nA general, rapid method for triggering protein unfolding and folding has been developed using the photolabile protecting group 3',5'-dimethoxybenzoin (DMB) and the\r\nphotolabile linker 3'-(carboxymethoxy)benzoin (CMB) respectively. To study unfolding the DMB group was introduced in a site-specific manner to block a mutation known to destabilize the GCN4-p1 coiled-coil. Upon photolysis, the unfavorable interaction is\r\nunmasked and the peptide unfolds allowing for kinetic characterization.
\r\n\r\nThe 35 amino-acid headpiece subdomain of the actin bundling protein Villin was constrained in a non-native state by cyc1ization of the N-terminus to a cysteine residue\r\nintroduced in the middle of the protein. Since destabilization of the native state is accomplished by the conformational constraint of a head-to-side chain cyc1ization, the folding of the Villin headpiece can be initiated by rapid photolysis of the photo labile\r\nlinker. The ensuing folding process was studied in real time, in the absence of added denaturants. This work demonstrates a general methodology for studying early events in protein folding, a process that is crucial for the understanding of how a protein reaches its native state.
" }, { "name": "Hess, Corinna Renate", "degree": "PhD", "year": "2002", "title": "Probing the Active Site of Amine Oxidase with Electron Tunneling Wires", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302012-150944800", "creators": [ { "name": { "family": "Hess", "given": "Corinna Renate" }, "id": "Hess-Corinna-Renate", "display_name": "Hess, Corinna Renate" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2EYM-TW23", "abstract": "Amine oxidases (AO) are copper-containing enzymes that catalyze the conversion of amines to aldehydes. The active site is deeply buried within the protein network, a factor which has precluded many investigations into the mechanism. A series of electron tunneling molecular wires has been synthesized, designed to access the cofactors of amine oxidase by means of the substrate channel. These wires are\r\ncomprised of phenyl-ethynyl units and thus promote rapid rates of electron transfer to the active site. An amine group attached to one end of the oligomer serves as the\r\nchannel-specific functionality, which binds within the channel. Binding of the oligomers to AO was demonstrated through inhibition and fluorescence quenching studies. A\r\nvariety of reporter groups has been attached to the chain end opposite the amine group, allowing us to probe the enzyme using a variety of techniques. A Re terminated complex was designed for electron transfer studies with the enzyme. The photophysics of this complex were investigated in the presence of AO. A thiol terminated wire also has been\r\nsynthesized, which was employed in electrochemical studies of the amine oxidase cofactors. These studies provide evidence for the ability to communicate with the active\r\nsite using the molecular wires. In addition, these complexes fulfilled our primary goal and enabled us to determine a redox potential of the TPQ cofactor." }, { "name": "Hoke, Kevin Richard", "degree": "PhD", "year": "2002", "title": "Electron Tunneling in Blue and Purple Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302012-102554225", "creators": [ { "name": { "family": "Hoke", "given": "Kevin Richard" }, "id": "Hoke-Kevin-Richard", "display_name": "Hoke, Kevin Richard" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6WB9-2805", "abstract": "The CU_A domain is the initial point of entry for electrons into cytochrome c oxidase. In order to explain fast rates of intramolecular electron transfer (ET) over long distances, it has been suggested that the ET reorganization energy is less than 0.6 eV. This issue was investigated by attaching a ruthenium(II)-bisbipyridyl-imidazole complex to a single surface histidine of the Thermus thermophilus CU_A domain. Photoexcitation results in rapid ET between the ruthenium complex and the copper site. This was done over a range of driving forces by employing a series of substituted bipyridines. An analysis of the driving force dependence of the ET rate suggests that the total reorganization energy for this CU_A fragment is about 0.7 eV, almost as high as for azurin. The degree of solvent exposure of the active site may be the factor responsible for the higher reorganization energy.
\r\n\r\nIn addition, the effect of distance on ET rate was investigated. Two variants of ruthenium-modified CU_A were examined, in which the labeled sites are two positions apart. The observed ET rates only differ by an order of magnitude, drastically less than what theory would predict. It appears that geometric factors other than length influence ET coupled through hydrogen bonds.
\r\n\r\nThe role of hydrogen bonds in ET was studied in more detail with ruthenium-modified azurin. Changes in the ET rate were observed for different degrees of deuterium\r\nincorporation in the system. For wild-type azurin, the greatest effect (k_H/k_D \u2248 0.7) is seen when the protein is subjected to rigorous exchange under denaturing conditions, then returned to a normal buffer as a control for the solvent isotope effect on the reorganization energy. This is the expected outcome if deuteration of internal, difficult to exchange hydrogen bonds results in improved coupling along the path.
" }, { "name": "Johnson, Brian P.", "degree": "Masters", "year": "2002", "title": "Multifunctional Conjugates for Fluorescence and Magnetic Resonance Imaging", "advisor": "Meade, Thomas J.; Fraser, Scott E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262025-014025819", "creators": [ { "name": { "family": "Johnson", "given": "Brian P." }, "id": "Johnson-Brian-P", "orcid": "0000-0003-2565-4927", "display_name": "Johnson, Brian P." } ], "advisors": [ { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "orcid": "0000-0001-6202-1155", "role": "advisor", "display_name": "Meade, Thomas J." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "advisor", "display_name": "Fraser, Scott E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mbc4-7j70", "abstract": "Computer-enhanced light microscopy imaging and magnetic resonance imaging (MRI) have emerged as leading techniques for in vivo monitoring of intact organisms. Employing the advantages of both techniques, a set of bifunctional, polymeric imaging agents is presented. A high-molecular weight, membrane impermeable scaffold such as dextran was chosen, so that the imaging agent would be trapped inside cells after injection. The molecular framework is covalently functionalized with multiple units of both gadolinium-diethylenetriaminepentaacetic acid and a fluorescent dye, such as 1,1 'dioctadecyl-3,3,3 ',3 '-tetramethylindocarbocyanine (DiI). The synthesis of this class of reporter probes is versatile, allowing for varying wavelengths of attached fluorophores and types of MRI agents to be used.
" }, { "name": "Lee, Jennifer Chen", "degree": "PhD", "year": "2002", "title": "Mapping Heme Protein Folding Landscapes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08202004-114236", "creators": [ { "name": { "family": "Lee", "given": "Jennifer Chen" }, "id": "Lee-Jennifer-Chen", "display_name": "Lee, Jennifer Chen" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DCQ1-F958", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe folding dynamics of two four-helix bundles, Fe'-cytochrome b[...] (E. coli) and Fe'-cytochrome c' (R.palustris), have been investigated: in each case, folding was triggered by electron transfer (ET) to the unfolded Fe'-protein and probed by transient absorption spectroscopy. Although these two proteins are topologically homologous, they display strikingly different folding kinetics: for FE'-cyt [...], the extrapolated time constant in the absence of denaturant [...] is near the predicted value for intrachain diffusion; in contrast, Fe'-cyt c' folding is heterogeneous over a ms-s time range.
\r\n\r\nNonnative methionine ligands in Fe'-cyt c' contribute to the complex folding kinetics. Removal of either Met-15 or Met-25 leads to simpler kinetics than found in the pseudo-wild-type (Q1A) protein. The amplitude of the intermediate folding phase ([...]) is diminished, suggesting that formation of near-native contacts may facilitate folding.
\r\n\r\nCyt c' has a wild-type Trp-72 residue that can be exploited in fluorescence energy transfer (FET) kinetics measurements. Also, we have crystallographically characterized [...] a Trp-mutant, Q1A/F32W/W72F, in order to probe distances between position-32 and the heme during folding. Analysis of FET kinetics from Trp-72 and Trp-32 shows that there is structural heterogeneity in the denatured protein. Even at high guanidine hydrochloride (GuHCl) concentrations, 50% of the polypeptides adopt compact conformations (25-35A) in cyt c'. A burst phase [...] is revealed when stopped-flow triggered refolding is probed by Trp fluorescence intensity: measurements on the Q1A protein show that 75% of the Trp-72 fluorescence (83% for Trp-32, Q1A/F32W/W72F) is quenched in the mixing deadtime, suggesting that most of the polypeptides have collapsed.
\r\n\r\nElectronically excited Zn-porphyrin in GuHCl-denatured Zn-substituted cytochrome c (Zn-cyt c) reduces [...] about ten times faster than when embedded in the folded protein. Measurements of ET kinetics during folding reveal a burst intermediate in which one-third of the ensemble has a protected Zn-porphyrin and slow ET kinetics; the remaining fraction exhibits fast ET characteristic of a solvent-exposed cofactor. Importantly, our FET (cyt c') and ET (Zn-cyt c) experiments show that collapsed nonnative structures are not substantially more stable than extended polypeptide conformations.
" }, { "name": "Liu, Zenghe", "degree": "PhD", "year": "2002", "title": "Vanadium-Schiff Base Complexes as Catalysts for the Four-Electron Reduction of Dioxygen", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022012-100419178", "creators": [ { "name": { "family": "Liu", "given": "Zenghe" }, "id": "Liu-Zhenghe", "display_name": "Liu, Zenghe" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BV5W-DK24", "abstract": "The coordination chemistry and electrochemistry of complexes of vanadium(III, IV, V) with salen (H_2salen = N,N'-ethylenebis(salicylideneamine)) were first examined. The origin of the puzzling results reported in previous reports in the literature was identified using\r\nmicroelectrode voltammetry and the modifications required are specified. VO(salen) was found to disproportionate in acidified acetonitrile. The equilibrium constant for this disproportionation reaction was measured. The stoichiometry and kinetics of the reaction between O_2 and the V(III)salen\r\ncomplex were examined and a possible mechanism for this four-electron reduction of O_2 is suggested.
\r\nThe study was then expanded to vanadium complexes with fifteen Schiff base (SB) ligands analogous to salen. Electrochemical and spectral characteristics of the complexes were evaluated and compared. With several of the ligands the V(III) complexes are much more stable in\r\nthe presence of acid than is the complex with salen. Equilibrium constants for the disproportionation of the oxovanadium (IV) complexes were evaluated. The vanadium(III) complexes reduce dioxygen to form two oxo ligands. In the presence of acid some of the complexes\r\ninvestigated participate in a catalytic electroreduction of dioxygen.
\r\nThe otherwise slow reaction between O_2 and decamethylferrocene or V^(III)(SB)^+ is significantly accelerated if these three reactants are present. In the absence of acid the reduction of O_2 proceeds stoichiometrically to yield the two oxo groups in (SB)V^(IV)O. In the presence of acid the reaction becomes catalytic and the O_2 is reduced to H_2O. Preliminary results on the kinetics of the O_2 reduction was presented.
\r\nElectrochemical study on vanadium-naphophen (naphophen = N, N'-1, 2-phenylenebis-(2-hydroxy-l-naphthylideneiminate)) complexes in acetonitrile containing excess acetic anhydride was also conducted. V^(IV)O(naphophen) was found to undergo deoxygenation by two equivalents of acid to give V^(IV)(naphophen)^(2+), which had not persisted in\r\nprevious study. Several reactions proposed previously to describe the chemistry of vanadium-Schiff base complexes in acetonitrile were directly demonstrated with this species.
\r\nThe oxovanadium-naphophen complexes were found to\r\nspontaneously adsorb on EPG electrodes. They also exhibited\r\nremarkable stability towards acid after adsorption. Their surface electrochemical behavior was studied and characterized using cyclic voltammetry.
\r\n\r\n" }, { "name": "Madsen, Louis Albert", "degree": "PhD", "year": "2002", "title": "Force-Detected NMR in a Homogeneous Field: Experiment Design, Apparatus, and Observations", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-133554077", "creators": [ { "name": { "family": "Madsen", "given": "Louis Albert" }, "id": "Madsen-Louis-Albert", "display_name": "Madsen, Louis Albert" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MT9P-7J20", "abstract": "Here I present motivation, experimental progress, and theoretical aspects of the BOOMERANG (better observation of magnetization enhanced resolution and no gradient) method of force-detected NMR, a general approach to extending arbitrary NMR experiments to the micron scale and below. Enabling quality of BOOMERANG is that its sensitivity scales much more favorably than traditional inductive detection for small samples. A reduction in the sample size accessible by NMR is strongly motivated by such goals as massively parallel analysis in support of combinatorial chemistry, portability in support of planetary exploration, and the general advantage of highest sensitivity per unit cost.
\r\n\r\nThe key design insight is that the spin-dependent forces are independent of the field homogeneity across the sample. However, throughput is optimized only by providing field homogeneity during detection sufficient to allow coherent control over all target spins in a sample. I present our BOOMERANG design concepts and strategies, which allow detectors with high geometrical efficiency and good prospects for low mechanical dissipation.
\r\n\r\nThe design principles are quantitatively confirmed using a prototype mm-scale spectrometer. Our experimental results, which include proton and fluorine FT-NMR\r\nspectra in solids and liquids, heteronuclear J spectra, and liquid-state spin echoes with sub-Hz linewidths, emphasize BOOMERANG\u2019s general spectroscopic applicability.
\r\n\r\nFabrication of a high-sensitivity spectrometer optimized for 60-micron samples is underway in conjunction with the Microdevices Laboratory (MDL) at the NASA Jet Propulsion Laboratory (JPL). Using state-of-the-art lithography and electrodeposition techniques, we have fabricated magnets and mechanical oscillator structures that show promise for incorporation into spectrometers for in-situ planetary exploration, and for massively parallel analysis.
\r\n\r\nAs the sample size decreases, sensitivity is dominated by quantum-statistical noise in the sample, or spin noise. This fundamental problem is mitigated by the CONQUEST measurement paradigm involving multiple time-correlated measurements on a spin system of interest. This is an essential ingredient in converting polarization\r\nfluctuations to coherent time-domain spectroscopy or to images with arbitrary numbers of spins in each pixel.
\r\n" }, { "name": "Main, Rebekah Mary", "degree": "Masters", "year": "2002", "title": "Studies Towards the Development of New Catalysts for Methane Conversion", "advisor": "Davis, Mark E.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262025-185839420", "creators": [ { "name": { "family": "Main", "given": "Rebekah Mary" }, "id": "Main-Rebekah-Mary", "display_name": "Main, Rebekah Mary" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xxcm-zd60", "abstract": "In efforts to develop new catalysts for the partial oxidation of methane to\r\nmethanol, studies were focused on developing supported aqueous phase (SAP) catalysts\r\nfor this chemistry. The work can be separated into two main projects. First, steps were\r\ntaken to prepare an organometallic SAP catalyst. A water-soluble sulfonated Pt diimine\r\nspecies has been prepared and supported on controlled-pore glass. The compound was\r\ncharacterized by solid state 13C CP-MAS NMR, and observations were made on the\r\ncompounds behavior. This work is carried out in collaboration with research into\r\nhomogeneous organometallic catalysts, and progress in this area is dependent on the\r\ndevelopment of successful homogeneous catalysts. The second project involves using\r\nplatinum/copper salt catalyst for the hydroxylation of alkanes, where dioxygen is the\r\nultimate oxidant. Several homogeneous reactions were carried out to investigate the\r\nreactivity of this catalyst system in solution. The catalysts were found to successfully\r\nhydroxylate sulfonated alkanes as well as ethane and methane, all with multiple platinum\r\nturnovers. Product characterizations were carried out using 1H NMR and GC/MS.\r\nEfforts were also begun to develop a SAP catalyst with the Pt/Cu system, modeled after\r\nthe SAP Pd/Cu Wacker oxidation catalyst." }, { "name": "Marshall, Shannon Alicia", "degree": "PhD", "year": "2002", "title": "Stability and Conformational Specificity in Protein Design: Models for Binary Patterning and Electrostatics", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302012-143643233", "creators": [ { "name": { "family": "Marshall", "given": "Shannon Alicia" }, "id": "Marshall-Shannon-Alicia", "display_name": "Marshall, Shannon Alicia" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4BVY-VN75", "abstract": "Binary patterning (the arrangement of hydrophobic and polar amino acids) and electrostatics are important determinants of the stability and conformational specificity of designed proteins. We have developed methods to to select the optimal binary pattern and model electrostatics in protein design studies. The Genclass method of binary patterning uses a solvent accessible surface generated from backbone coordinates of the target fold and \"generic\" side chains, constructs whose size and\r\nshape are similar to an average amino acid. Each position is classified according to the solvent exposure of its generic side chain. The method was tested by analyzing several proteins in the Protein Data Bank and by experimentally characterizing homeodomain variants whose binary patterns were systematically varied. Selection of the optimal binary pattern results in a designed protein that is monomeric, well-folded, and hyperthermophilic. Homeodomain variants with fewer hydrophobic residues are destabilized, additional hydrophobic residues induce aggregation. The optimal variant was further characterized by nuclear magnetic resonance spectroscopy. Binary patterning, in conjunction with a force field that models folded state energies, appears sufficient to satisfy two basic goals of protein design: stability and conformational specificity.
\r\n\r\nElectrostatic interactions are critical determinants of protein structure and function. Computational protein design algorithms typically use fast methods based on Coulomb's law to model electrostatic interactions. These methods fail to accurately account for desolvation and solvent screening, which strongly attenuate electrostatic interactions in proteins. Using the current force field, we designed a 25-fold mutant with moderate stability similar to the wild type protein. Incorporating two classes of electrostatic interactions using simple rules yielded a nine-fold mutant of the initial design that is over\r\n3 kcal mol^(-1) more stable. The simple electrostatic model used in the ORBIT force field is unable to predict the experimentally determined stabilities of the designed variants. Finite difference Poisson-Boltzmann (FDPB) methods have substantially better predictive power, but are far too slow for problems with high combinatorial complexity. We have developed new strategies for modeling electrostatics in\r\nprotein design problems that utilize one- and two-body decomposable FDPB methods. Computational results indicate that this method has the accuracy and speed required for design calculations.
\r\n" }, { "name": "Nguyen Hackley, Doan Hanh", "degree": "PhD", "year": "2002", "title": "Allosteric Inhibition of Zinc Finger Proteins by DNA Binding Polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-135843100", "creators": [ { "name": { "family": "Nguyen Hackley", "given": "Doan Hanh" }, "id": "Nguyen-Hackley-Doan-Hanh", "display_name": "Nguyen Hackley, Doan Hanh" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/NJ2K-H827", "abstract": "Small molecules that can bind selectively to any predetermined DNA sequence in the human genome could potentially be powerful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of \"pairing rules\" with affinities and specificities similar to many naturally occurring DNA binding proteins. The study of DNA binding polyamides is further expanded by the development of new monomer\r\npairings and new synthetic methods which allow access to polyamides with varying truncated tails. A new pairing of N-methylpyrazole with N-methylpyrrole increased\r\nspecificity substantially without loss in affinity. This result indicates that other ring positions, besides the 3-position, can also greatly impact DNA recognition properties. Polyamides having truncated tails are shown to bind DNA with greater generality at the tail positions while maintaining high affinity, and may allow the targeting of a larger number of biologically relevant DNA sequences. Small molecules that bind DNA may offer a general approach to the chemical down- or up-regulation of gene expression by the inhibition or recruitment of transcription factors, respectively. Polyamide-peptide\r\nconjugates were synthesized and evaluated for their ability to activate transcription. A greater than 30-fold enhancement over basal levels was observed and activation could be correlated to DNA occupancy levels. Cys_2His_2 zinc finger proteins are the most common DNA binding motif in higher eukaryotes. We have elucidated an allosteric mechanism for the inhibition of zinc finger proteins, binding purely in the major groove, by Py/Im polyamides. The inhibition of this large class of proteins greatly enlarges the applicability of these minor groove ligands for gene regulation.\r\n" }, { "name": "Nu\u00f1ez, Megan Elizabeth", "degree": "PhD", "year": "2002", "title": "Oxidation of DNA by Long-Range Charge Transport", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312012-114925650", "creators": [ { "name": { "family": "Nu\u00f1ez", "given": "Megan Elizabeth" }, "id": "Nu\u00f1ez-Megan-Elizabeth", "display_name": "Nu\u00f1ez, Megan Elizabeth" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZQ5T-9Z15", "abstract": "Ever since the double helical structure of DNA was elucidated, it has been proposed that charge might move through the stacked base pairs of the double helix because of the electronic coupling of the \u03c0 orbitals of the nucleotide bases with neighboring bases. Here it is demonstrated that electronic \"holes\" generated\r\nby a one-electron oxidation of DNA can result in permanent lesions on guanine bases up to 200 \u00c5 away from the intercalating oxidant as a result of such charge\r\nmigration. Both rhodium and ruthenium complexes, covalently tethered to the 5' end of a double-stranded oligonucleotide and intercalated into the base stack, can with photoactivation promote oxidation of guanines in 5'-GG-3' sites over this distance. Since charges can move efficiently through the DNA oligonucleotides, it was important to characterize this reaction in more detail, and to extend observations of charge transport through DNA to larger and more complicated DNA assemblies that more closely mimic its structure in vivo.
\r\n\r\nLong-range oxidative damage to guanine doublets in DNA is shown to compete for oxidation with other reactions, such as the repair of thymine dimers. When both thymine dimer lesions and guanine doublets are present, both can be\r\noxidized by a photoexcited rhodium complex, although each in lower yield than in the absence of the other. While the 5-GG-3' may represent the thermodynamically favored site for oxidative reaction, repair of the thymine dimer appears to be kinetically more favorable. Therefore electronic \"holes\" generated on genomic DNA might not of necessity cause DNA damage, but could also be funneled onto proteins or other oxidizible sites.
\r\n\r\nUsing a variety of intercalating photooxidants targeted to a specific site on a restriction fragment by an appended triplex-forming oligonucleotide, the upper distance limits and sequence effects on long-range charge transfer through DNA were examined. Charge migration occurs in both directions from the intercalator and on both DNA strands of the target, but the oxidation is significantly more\r\nefficient to the 3' side of the triplex, over 25-38 base pairs. When intercalators were tethered directly to the 5' terminus of the triplex-forming strand as opposed\r\nto the center, significant amounts of oxidative damage was generated only in the immediate vicinity of the intercalation site, suggesting that the base stack is\r\ndistorted at the 5' end of the triplex region in the duplex/triplex junction. Targeting of photooxidative damage by triplex formation extends previous studies of long-range charge transport to significantly longer DNA sequences through a strategy that does not require covalent attachment of the photooxidant to the DNA being probed.
\r\n\r\nWithin eukaryotic cells most DNA is packaged as nucleosome core particles, made up of ~146 base pairs of DNA wrapped around a core of histone proteins. Photoexcited rhodium complexes were also used to explore charge\r\ntransport through DNA within these structures. Although histone proteins inhibit intercalation of a noncovalent rhodium complex, they do not prevent oxidation of\r\n5'-GG-3' sites, the signature of oxidative charge transport through DNA. Furthermore, some of these sites are not directly accessible to a solution-bound oxidant due to his tones in the major groove, and thus they must be oxidized from a distance. Therefore, although the structure of the nucleosome core particle generally protects DNA from damage from solution-borne molecules, it does not protect the DNA from charge transfer damage through the base pair stack. In\r\nsupport of this assertion, guanine bases within nucleosomal DNA were oxidized at a distance of over 23 base pairs from a covalently-tethered rhodium intercalator.
\r\n\r\nThe environment within the cell nucleus contains a variety of other proteins and small molecules that could potentially influence the migration of charge through DNA. Using the rhodium photochemistry, the oxidation of\r\nguanine by photoexcited rhodium complexes inside of nuclei from cultured human cells was examined and compared with the oxidative damage on bare genomic DNA. Oxidation occurs preferentially at the 5'-guanine of 5'-GG-3' sites, indicative of base damage by DNA-mediated charge transport chemistry. Moreover, oxidative damage occurs at protein-bound sites which are inaccessible to rhodium. Thus, on transcriptionally active DNA within the cell nucleus, DNA-mediated charge transport acts to induce base damage from a distance. Direct interaction of an oxidant is not necessary to generate a base lesion at a specific\r\nsite within the nucleus.
\r\n\r\nAll of these observations indicate that charges can migrate along DNA within the cell. These observations require a reconsideration of cellular mechanisms for DNA damage and repair, and present new avenues for exploration in the design of DNA-based drugs and therapies.
" }, { "name": "Piccione, Patrick Manuel", "degree": "PhD", "year": "2002", "title": "Thermodynamics of Formation of Molecular Sieves", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062010-084034470", "creators": [ { "name": { "family": "Piccione", "given": "Patrick Manuel" }, "id": "Piccione-Patrick-Manuel", "display_name": "Piccione, Patrick Manuel" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Navrotsky", "given": "Alexandra" }, "id": "Navrotsky-Alexandra", "orcid": "0000-0002-3260-0364", "role": "member", "display_name": "Navrotsky, Alexandra" }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/TQVE-FW28", "abstract": "Molecular sieves, porous, crystalline frameworks with pore sizes of molecular dimensions, are of great industrial importance as detergents, catalysts and absorbants. Despite their technological importance, the syntheses of these materials are still not well understood and typically rely on extensive series of trials to produce new framework structures.
\r\n\r\nThermodynamic investigations are undertaken to better understand the energetic differences amongst molecular sieve frameworks and the mechanisms and interactions important in molecular sieve self-assembly. The enthalpies relative to quartz at 298.15 K are determined by high-temperature solution calorimetry for a collection of calcined pure-silica molecular sieves with diverse structural features. Si0_2 molecular sieves are shown to be only modestly (6.8-14.4 kJ/mol) metastable with respect to quartz. A strong linear correlation between enthalpy and molar volume is observed, implying that the overall packing quality determines the relative enthalpies of Si0_2 molecular sieves. Silanol (Si-O-H) defect sites lead to an additional destabilization of no more than 2.4 kJ/mol. The entropies of four pure-silica molecular sieves spanning the entire range of molar volumes available to Si0_2 frameworks are determined by the integration of heat capacity measurements from 5 to 400 K. The entropies of these structures are almost identical (3.2-4.2 J\u2219K^(-1)\u2219mol^(-1) above quartz), hence the empty pore volume and cages do not contribute appreciably to the vibrational density of states. The enthalpy and entropy data are combined to calculate the Gibbs free energies of transition from quartz to eight other silica polymorphs, including four molecular sieves as well as silica glass. At typical synthesis conditions, the available thermal energy is RT = 3.5 kJ/mol. The molecular sieve Gibbs free energies are only slightly larger than RT at 5.5-12.6 kJ/mol above quartz and lie in the same energetic region as the amorphous precursors used for molecular sieve preparation. There are therefore no significant thermodynamic barriers to transformations among silica polymorphs. Thus the role of SDA in molecular sieve syntheses is not the stabilization of otherwise very unstable phases.
\r\n\r\nInteraction enthalpies between inorganic frameworks and organic SDAs are measured by HF solution calorimetry for six molecular sieve/SDA pairs. The enthalpies are only moderately exothermic (-1.1 to -5.9 kJ/mol SiO_2), as expected if the predominant interactions are van der Waals contacts between the hydrophobic silica frameworks and the hydrocarbon portions of the SDAs. Interaction entropies can be estimated for three framework/SDA pairs, and, when used in combination with the interaction enthalpies, allow the calculation of the Gibbs free energies of interaction between these three inorganic/organic pairs. The latter values range from -2.0 to -5.4 kJ/mol SiO_2, smaller in magnitude than twice the available thermal energy at molecular sieve synthesis temperatures. This energy range is comparable to the range observed for the molecular sieve frameworks alone, showing that energetics of both the frameworks and of the molecular sieve/SDA interactions must be considered in order to adequately describe molecular sieve synthesis. The energetics of the synthesis of molecular sieves (considering all components present in the synthesis mixture) are examined here and also reveal small differences between various molecular sieve/SDA combinations. The energetic contribution of the effective dilution experienced by the SDA upon occlusion is similar in magnitude to the other energetic effects. The strong selectivity of organic SDAs experimentally observed in the face of the comparatively small energetic differences suggests that kinetic factors dominate in molecular sieve preparation.
" }, { "name": "Rosario-Ortiz, Fernando L.", "degree": "Masters", "year": "2002", "title": "Determination of the Relative Line Strengths of the A\u00b2A' \u2190 X\u00b2A\" and (200)\u2190(000) transitions of HO\u2082", "advisor": "Okumura, Mitchio; Sander, Stanley P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022012-093757351", "creators": [ { "name": { "family": "Rosario-Ortiz", "given": "Fernando L." }, "id": "Rosario-Ortiz-Fernando-L", "display_name": "Rosario-Ortiz, Fernando L." } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Sander", "given": "Stanley P." }, "id": "Sander-S-P", "role": "co-advisor", "display_name": "Sander, Stanley P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vh44-fh68", "abstract": "The hydroperoxyl radical (HO\u2082) has been one of the most studied triatomic radicals during the past few decades. Its roles in atmospheric chemistry through the HO\u2093 cycle as well as in processes such as combustion have made the study of this radical extremely important. In the past three decades the interest in the spectroscopy of this molecule has increased due in part by the need of detecting this radical in several different environments. Although its UV, mid- and far-IR transitions have been studied extensively, its near-IR transitions have not received much attention until recently. Among the transitions observed in this region, the A\u00b2A' \u2190 X\u00b2A\" first electronic transition and the (200)\u2190(000) first OH overtone transition are two of the most important. These bands offer many advantages for detection of HO\u2082 in kinetic experiments and possibly in situ. Due to the importance of these two bands, information on their intensity is needed to measure accurately the concentration of HO\u2082. An apparatus has been constructed to measure the line strengths of the A \u2190 X electronic transition at 1.43 \u00b5m and the (200)\u2190(000) first OH overtone transition at 1.51 \u00b5m by diode laser absorption spectroscopy." }, { "name": "Rossi, Robert Charles", "degree": "PhD", "year": "2002", "title": "The Electrical Properties of Nanoscale Parallel Semiconductor Interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-07132001-180811", "creators": [ { "name": { "family": "Rossi", "given": "Robert Charles" }, "id": "Rossi-Robert-Charles", "display_name": "Rossi, Robert Charles" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/F9YE-BM08", "abstract": "Nanosphere lithography has been used to prepare a series of ordered, periodic arrays of low barrier height n-Si/Ni nanometer-scale contacts interspersed amongst high barrier height n-Si/liquid contacts. To form the arrays, crystalline bilayers of close-packed latex spheres were deposited onto (100)-oriented n-type single crystal Si surfaces. The spheres formed a physical mask through which Ni was evaporated to produce regularly spaced and regularly sized Si/Ni contacts. By varying the diameter of the latex spheres from 174 nm to 1530 nm, geometrically self-similar Si/Ni structures were produced having triangular Si/Ni regions with edge dimensions of 100 - 800 nm. The resulting Si surfaces were used as electrodes in contact with a methanolic solution of LiClO4 and 1,1'-dimethylferrocene/1,1'-dimethylferrocenium. The current-voltage and photoresponse properties of these mixed barrier height contacts were strongly dependent on the size of the Ni regions, even though the fraction of the Si surface covered by Ni remained constant. Electrodes formed from large-dimension Si/Ni and Si/electrolyte contacts behaved as expected for two area-weighted Schottky diodes operating independently and in parallel, whereas electrodes having nanoscale Si/Ni and Si/liquid contacts behaved in quantitative accord with effective barrier height theories that predict a \"pinch-off\" effect for mixed barrier height systems of sufficiently small physical dimensions.\r\n" }, { "name": "Sierou, Asimina", "degree": "PhD", "year": "2002", "title": "Accelerated Stokesian Dynamics: Development and Application to Sheared Non-Brownian Suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202009-160503", "creators": [ { "name": { "family": "Sierou", "given": "Asimina" }, "id": "Sierou-Asimina", "display_name": "Sierou, Asimina" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/SX3A-8M59", "abstract": "A new implementation of the conventional Stokesian Dynamics (SD) algorithm, called Accelerated Stokesian Dynamics (ASD), is presented. The equations governing the motion of N particles suspended in a viscous fluid at low particle Reynolds number are solved accurately and efficiently, including all hydrodynamic interactions, but with a significantly lower computational cost of O(N ln N). The main differences from the conventional SD method lie in the calculation of the many-body long-range interactions, where the Ewald-summed wave-space contribution is calculated as a Fourier Transform sum, and in the iterative inversion of the now sparse resistance matrix. The ASD method opens up an entire new class of suspension problems that can be investigated, including particles of non-spherical shape and a distribution of sizes, and can be readily extended to other low-Reynolds-number flow problems. The new method is applied to the study of sheared non-Brownian suspensions.
\r\n\r\nThe rheological behavior of a monodisperse suspension of non-Brownian particles in simple shear flow in the presence of a weak interparticle force is studied first. The availability of a faster numerical algorithm permits the investigation of larger systems (typically of N = 512 \u2014 1000 particles), and accurate results for the suspension viscosity, first and second normal stress differences and the particle pressure are determined as a function of the volume fraction. The system microstructure, expressed through the pair-distribution function, is also studied and it is demonstrated how the resulting anisotropy in the microstructure is correlated with the suspension non-Newtonian behavior. The ratio of the normal to excess shear stress is found to be an increasing function of the volume fraction, suggesting different volume fraction scalings for different elements of the stress tensor. The relative strength and range of the interparticle force is varied and its effect on the shear and normal stresses is analyzed. Volume fractions above the equilibrium freezing volume fraction (\u00f8 \u2248 0.494) are also studied, and it is found that the system exhibits a strong tendency to order under flow for volume fractions below the hard-sphere glass transition; limited results for \u00f8 = 0.60, however, show that the system is again disordered under shear.
\r\n\r\nSelf-diffusion is subsequently studied and accurate results for the complete tensor of the shear-induced self-diffusivities are determined. The finite, and oftentimes large, auto-correlation time requires the mean-square displacement curves to be followed for longer times than was previously thought necessary. Results determined from either the mean-square displacement or the velocity autocorrelation function are in excellent agreement. The longitudinal (in the flow direction) self-diffusion coefficient is also determined, and it is shown that the finite autocorrelation time introduces an additional coupled term to the longitudinal self-diffusivity, a term which previous theoretical and numerical results omitted. The longitudinal self-diffusivities for a system of non-Brownian particles are calculated for the first time as a function of the volume fraction.
\r\n" }, { "name": "Sobrero, Aquiles Carlos", "degree": "PhD", "year": "2002", "title": "Surface Structure Determination by Low-Energy Electron Diffraction", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212011-075629318", "creators": [ { "name": { "family": "Sobrero", "given": "Aquiles Carlos" }, "id": "Sobrero-Aquiles-Carlos", "display_name": "Sobrero, Aquiles Carlos" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9b54-km20", "abstract": "Four aspects of low-energy electron diffraction (LEED) have been investigated: interpretation of spot patterns to determine the surface unit cell and possible ambiguities, development of a photographic method for measuring angles of incidence and determining alignment of the LEED instrument, study of reliability factors used for intensity analysis, and justification for equivalent beam averaging.
\r\n\r\nThe interpretation of LEED spot patterns to determine the geometry of the surface unit cell can be involved when there are several symmetrically equivalent structural domains contributing to the pattern. Complex patterns can be deciphered by the algorithm described in Chapter II. The algorithm determines a surface unit cell that is often unique but not always, as where a p(2 x 2) pattern from a fcc(111) surface can be produced by a true (2 x 2) overlayer or by three domains of a (2 x 1) structure. This ambiguity arises on surfaces with 6m symmetry, such as fcc(111) and hcp(0001), for spot patterns with threefold rotational symmetry.
\r\n\r\nIn Chapter III, a broadly applicable photographic method for measuring angles of incidence and determining the alignment of the LEED instruments is described. Two published methods for determining the angle of incidence are special cases of this general procedure. The procedure extends the photographic methods and facilitates the verification of the alignment of the components of the LEED instrument.
\r\n\r\nReliability factors are used to evaluate correspondence between computed and observed LEED intensity spectra. Zanazzi and Jona, Pendry, and Sobrero and Weinberg have proposed reliability factors that are examined in Chapter IV. Chapter V provides a theoretical analysis and shows that averaging over momentum space gives the best resolution of the surface structure while energy averaging smears out information in the intensity spectra.
\r\n\r\nChapter VI provides a theoretical basis for the procedure of equivalent beam averaging, which provides a first-order correction to LEED intensities for systematic error due to angular misalignment of the incident beam and corrects for misorientation (where the actual surface plane is at a slight angle to the desired crystal plane). The potential of higher-order corrections is discussed.
" }, { "name": "Subramanian, Ganesh", "degree": "PhD", "year": "2002", "title": "Inertial Effects in Suspension Dynamics", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07042002-114141", "creators": [ { "name": { "family": "Subramanian", "given": "Ganesh" }, "id": "Subramanian-Ganesh", "display_name": "Subramanian, Ganesh" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Campbell", "given": "Charles Soutter" }, "id": "Campbell-Charles-Soutter", "role": "member", "display_name": "Campbell, Charles Soutter" }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "orcid": "0000-0001-5592-2334", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Corngold", "given": "Noel Robert" }, "id": "Corngold-N-R", "role": "member", "display_name": "Corngold, Noel Robert" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DSMP-HV88", "abstract": "This work analyses the role of small but finite particle inertia on the microstructure of suspensions of heavy particles subjected to an external flow. The magnitude of particle inertia is characterized by the Stokes number, St, defined as the ratio of the inertial relaxation time of a particle to the flow time scale. Fluid inertia is neglected so that the fluid motion satisfies the quasi-steady Stokes equations. The statistics of the particles is governed by a Fokker-Planck equation in position and velocity space. For small St, a multiple scales formalism is developed to solve for the phase-space probability density of a single spherical Brownian particle in a linear flow. Though valid for an arbitrary flow field, the method fails for a spatially varying mass and drag coefficient. In all cases, however, a Chapman-Enskog-like formulation provides a valid multi-scale description of the dynamics both for a single Brownian particle and a suspension of interacting particles. For long times, the leading order solution simplifies to the product of a local Maxwellian in velocity space and a spatial density satisfying the Smoluchowski equation. The higher order corrections capture both short-time momentum relaxations and long-time deviations from the Maxwellian. The inertially corrected Smoluchowski equation includes a non-Fickian term at O(St).
\r\n\r\nThe pair problem is solved to O(St) for non-Brownian spherical particles in simple shear flow. In contrast to the zero inertia case, the relative trajectories of two particles are asymmetric. Open trajectories in 'repels' nearby trajectories that spiral out onto a new stable limit cycle in the shearing plane. This limit cycle acts as a local attractor; in-plane trajectories from an initial offset of O(St\u00b9/\u00b2) or less approach the limit cycle. The topology of the off-plane trajectories is more complicated because the gradient displacement changes sign away from the plane of shear. The 'neutral' off-plane trajectory with zero net gradient displacement acts to separate trajectories spiralling onto contact from those that go off to infinity. The aforementioned asymmetry leads to a non-Newtonian rheology and self-diffusivities in the gradient and voriticity directions that scale as St\u00b2 ln St and St2, respectively.
" }, { "name": "Sundaresan, Vidyasankar", "degree": "PhD", "year": "2002", "title": "Selective Molecular Recognition in Imprinted Polymeric Adsorbents and in Biological Macromolecules", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052011-134334164", "creators": [ { "name": { "family": "Sundaresan", "given": "Vidyasankar" }, "id": "Sundaresan-Vidyasankar", "display_name": "Sundaresan, Vidyasankar" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/jvev-x884", "abstract": "This thesis describes the synthesis and use of molecularly imprinted polymeric adsorbents for use in ligand-exchange chromatographic separations of structurally similar substrates. A general model of stereo selectivity is also described, which can be applied both to chromatographic adsorbents and to biological receptors.
\r\n\r\nCrosslinking polymerization of trimethylolpropane trimethacrylate (TRIM), under controlled conditions yields macroporous polymers bearing surface-accessible unpolymerized methacrylate residues. These residues have been utilized for copolymerization with different functional monomers to obtain composite polymer matrices with surface coatings of functional polymer chains. Surface modification has been carried out by molecular imprinting, using ternary Cu^(2+) complexes of [N-(4-vinylbenzyl)imino]diacetate and bisimidazole templates, with ethylene glycol dimethacrylate as comonomer. Selectivity characteristics similar to bulk-copolymerized polymers have been observed. The physicochemical characteristics of these functional polymer matrices have been evaluated by ^(13)C NMR, X-ray photoelectron spectroscopy, IR spectroscopy, and scanning electron microscopy.
\r\n\r\nThe ability of molecular imprinting to impart enantioselectivity to polymeric adsorbents has been studied using Cu^(2+) complexes of the achiral monomer [N-(4-vinylbenzyl)imino]diacetate and \u03b1-amino acids. Crosslinking polymerization with ethylene glycol dimethacrylate as the comonomer yields polymeric adsorbents capable of enantioresolutions of underivatized \u03b1-amino acids. Chromatographic adsorbents have been prepared by grafting the imprinted polymer on to silica particles. The observed enantioselectivity increases corresponding to the size of the side chain of the amino acid used as template, with the best enantioresolutions being obtained for materials imprinted against phenylalanine (~1.65 for D,L-phenylalanine enantioresolution). Adsorbents imprinted for alanine show negligible enantioselectivity. Cross-selectivity patterns towards non-template amino acids have been investigated, and the ability of an amino acid imprinted material to resolve analogous chiral amines has been demonstrated.
\r\n\r\nThe mechanisms underlying enantioselectivity in imprinted polymers are discussed in terms of the three-point interaction model. This model has been extended to a stereocenter-recognition (SR) model for substrates with multiple stereocenters. For N stereocenters in a linear chain, it has been demonstrated that a minimum of N + 2 interactions need to be distributed over all stereocenters, such that three effective interactions exist per stereocenter. The general applicability of the SR model is demonstrated for biological ligand-receptor interactions, by reinterpreting several previous experimental observations.
" }, { "name": "Tae, Giyoong", "degree": "PhD", "year": "2002", "title": "In situ Forming Hydrogels Using Self-Assembly of Fluoroalkyl-Ended Poly(ethylene Glycol)s", "advisor": "Kornfield, Julia A.; Hubbell, Jeffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07192007-103729", "creators": [ { "name": { "family": "Tae", "given": "Giyoong" }, "id": "Tae-Giyoong", "display_name": "Tae, Giyoong" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "advisor", "display_name": "Hubbell, Jeffrey A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "member", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xrnv-yh71", "abstract": "Telechelic polymers with hydrophilic midblocks (poly(ethylene glycol), PEG) and hydrophobic end groups (fluoroalkyl, Rf) are synthesized and explored as candidates for in situ forming hydrogels for biomedical applications. Relevant physical properties, including phase behavior, rheology and erosion kinetics, are characterized to guide rational design of polymers for specific applications, including controlled release of therapeutic proteins and deposition of biocompatible surface layers. Disruption of the aggregation of the end groups using biocompatible complexing agents or solvents produces a low viscosity liquid that is injectable; self-assembly of the gel once inside the body can be achieved gently by diffusion of the complexing agent or solvent out into the surrounding tissue. By modulating molecular structure, the mechanical and erosion properties of these hydrogels can be systematically varied over a wide range for desired applications.
\r\n\r\nWith increasing fluoroalkyl length relative to PEG length, the phase behavior of these fluoroalkyl-ended PEGs (Rf-PEGs) polymers in aqueous solution changes from singlephase behavior (continuous transition in properties from solution-like to gel-like with increasing concentration), to sol-gel coexistence, to an insoluble precipitate (Chapter 2). For sol-gel coexisting polymers, the equilibrium gel concentration and the modulus of the gel phase are governed by the length of the PEG midblock, whereas the relaxation time is determined by the hydrophobe length. The erosion characteristics of these hydrogels correlate with their phase behavior: the gels of sol-gel coexisting species exhibit surface erosion in an open system with slow dissolution rate controlled by the end-group length, whereas gels showing single-phase behavior exhibit bulk erosion that is relatively fast.
\r\n\r\nAqueous solutions of Rf-PEGs exhibit ordering transitions, with increasing concentration (Chapter 3). The hydrophobic cores of the micelle-like aggregates order into a body-centered-cubic (BCC) structure. The aggregated state of the hydrophobic core is determined by the length of the hydrophobic end group, and is insensitive to the concentration of the polymer solution or the temperature. A shorter PEG length for a given end group produces a much enhanced ordering compared to a longer one. This micelle packing effect is manifested in changes in the viscoelastic properties: the single-relaxation behavior evolves to the appearance of a new low frequency elastic plateau in the dynamic moduli, and a linear response changes to a yielding behavior in creep.
\r\n\t\r\nThe gel phase of sol-gel coexisting polymers can be transformed into an injectable state by the addition of a bio-tolerable organic solvent, such as N-methyl pyrrolidone (NMP), and this solution can be restored to a hydrogel state quickly after injection by removal of the organic solvent by diffusion. Release of Human growth hormone (hGH) using this injectable formulation (Chapter 4) reveals that hGH remains stable inside the hydrogel formed, and more than 2 weeks of prolonged release of hGH pretreated with zinc is obtained using the injectable formulation without irreversible aggregation. For the Rf-PEGs examined here, the release rate of hGH is determined by the rate of diffusion through the hydrogel.
\r\n\r\nThe telechelic Rf-PEGs that exhibit sol-gel equilibrium or precipitated gel phase behavior provide a facile route to hydrophilic modification of poly(tetrafluoroethylene) (PTFE) surfaces that are frequently encountered in biomedical devices (Chapter 5). Dip coating of PTFE into 1 wt % Rf-PEGs in ethanol, followed by immersing into water, converts the surface of PTFE from hydrophobic to hydrophilic. The lifetime of this modification is correlated to the phase behavior of the bulk gel state, and stable in the various ranges of shear rates. An Rf-PEG that is insoluble in water gave a stable modification over a period of weeks in the absence of shear, and persisted for days when subjected to the highest shear stresses encountered in arteries (3-4Pa). Telechelic Rf-PEGs are effective, while monofunctional PEGs with a single fluoroalkyl group are not.
\r\n\r\nThe swelling and drying behaviors of thin films of RfPEGs (~0.1 [mu]m) show abnormalities relative to glassy and semi-crystalline films (Chapter 6). In a humidity ramp test starting from a dry state, thin films of Rf-PEGs show a distinctive hysteresis behavior; as humidity increases, little swelling occurs until ~ 85% humidity, then the film swells rapidly; as the humidity decreases, a rapid deswelling occurs near ~75% humidity. In a humidity step test, following a step-up the mass increase shows an overshoot, followed by a gradual approach to the equilibrium value, whereas the film tracks the equilibrium state very rapidly and monotonically following a step down from high to low humidity.
" }, { "name": "Tang, Yi", "degree": "PhD", "year": "2002", "title": "Protein Engineering Using Unnatural Amino Acids: Incorporation of Leucine Analogs into Recombinant Protein in vivo", "advisor": "Tirrell, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08152006-084149", "creators": [ { "name": { "family": "Tang", "given": "Yi" }, "id": "Tang-Yi", "display_name": "Tang, Yi" } ], "advisors": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "advisor", "display_name": "Tirrell, David A." } ], "committee": [ { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "chair", "display_name": "Tirrell, David A." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4cvy-8295", "abstract": "The incorporation of unnatural amino acids into recombinant proteins is an important tool for understanding protein function, engineering robust proteins and introducing useful building blocks for protein-based materials biosynthesis. While site-directed mutagenesis using natural amino acids allows one to vary protein composition and protein functions, the scope of such manipulations is limited to the twenty naturally occurring amino acids. Important chemical functionalities such as alkenes, alkynes, ketones, halides, and azides are not present in the pool of amino acids specified by the genetic code. Developing methods to insert amino acids containing these orthogonal groups, either site specifically or residue specifically, can lead to new tools in protein chemistry and protein engineering. In this thesis, we will describe the incorporation of leucine analogs into recombinant proteins in vivo. Our objectives are to investigate and relax the substrate specificity of E. coli leucyl-tRNA synthetase towards nonproteinogenic amino acids. Our results show that manipulation of synthetase activity and specificity can provide new opportunities for stabilization and chemoselective modification of proteins.\r\n\r\nSubstitution of leucine residues by 5,5,5-trifluoroleucine at the d-positions of the leucine zipper peptide GCN4-pld increases the thermal stability of the coiled-coil structure. The midpoint thermal unfolding temperature of the fluorinated peptide is elevated by 13\u00b0C at 30 uM peptide concentration. The modified peptide is more resistant to chaotropic denaturants, and the free energy of folding of the fluorinated peptide is 0.5 to 1.2 kcal/mol larger than that of the hydrogenated form. A similarly fluorinated form of the DNA-binding peptide GCN4-bZip binds to target DNA sequences with affinity and specificity identical to those of the hydrogenated forn, while demonstrating enhanced thermal stability. Molecular dynamics simulation on the fluorinated GCN4-pld peptide using the Surface Generalized Born implicit solvation model revealed that the coiled-coil binding energy is 55% more favorable upon fluorination. These results suggest that fluorination of hydrophobic substructures in peptides and proteins may provide new means of increasing protein stability, enhancing protein assembly, and strengthening receptor-ligand interactions.\r\n\r\nTo make fluorination a general method of stabilizing protein structures, we studied in vivo incorporation of trifluoroleucine (Tfl) and hexafluoroleucine (Hfl) in place of leucine using leucine auxotrophic E. coli strains. The target protein is Al, which is a leucine zipper protein that has 74 residues and eight leucines. The leucine residues are buried at the dimer interface and stabilize the protein complex. Tfl supported protein synthesis efficiently and replaced up to 92% of leucines in the protein under normal expression conditions. The yield of fluorinated protein was reduced from 40 mg/L to 20 mg/L. We were able to tune the level of fluorination by altering the concentration of competing leucine in culture media. Tfl-A1 adopted the identical helical secondary structure and dimeric aggregation order. Tm of Tfl-A1 was elevated to 67\u00b0C, a 13\u00b0C increase over A1. The concentration of urea needed to denature 50% (Cm) of protein was elevated from 2.7 M to 7 M. In contrast to Tfl incorporation, the more hydrophobic amino acid Hfl did not support protein synthesis under similar conditions. From in vitro characterization of leucyl-tRNA synthetase (LeuRS) substrate specificity, Hfl was shown to be activated 4100 times slower than leucine (compared to the 240-fold rate attenuation of Tfl). The decreased rate of tRNA(Leu), aminoacylation by Hfl resulted in insufficient amounts of Hfl-tRNA(Leu) during protein synthesis. We raised the cellular LeuRS activity eightfold at the time of protein induction by overexpressing LeuRS under a constitutive promoter during cell growth. Under these conditions, Hfl was effectively incorporated into A1 at ~80% substitution rate. The presence of the nearly perfluorinated side chains in the protein core enhanced protein stability even further. Tm was increased to 76\u00b0C and [Delta]Gf decreased by 3.6 kcal/mol. More remarkably, Cm of Hfl-A1 was not observed within the urea solubility limit.\r\n\r\nTo further broaden the chemical functionality available for protein engineering, we investigated the proofreading mechanism of leucyl-tRNA synthetase (LeuRS). The aaRSs that activate the hydrophobic amino acids leucine, isoleucine and valine employ a proofreading mechanism that hydrolyzes noncognate aminoacyl adenylates and misaminoacylated tRNAs. Discrimination between structurally similar amino acids by these AARSs is believed to operate by a double-sieve principle, wherein a separate editing domain governs hydrolysis based on the size and hydrophilicity of the amino acid side chain. Leucyl-tRNA synthetase (LeuRS) relies on its editing function to correct misaminoacylation of tRNA(Leu) by isoleucine and methionine. Thr252 of E. coli LeuRS has been shown previously to be important in defining the size of the editing cavity. Here we report the isolation and characterization of three LeuRS mutants with point mutations at this position (T252Y, T252L, and T252F). The proofreading activity of the synthetase is significantly impaired when an amino acid bulkier than threonine is introduced. The misaminoacylation rate of tRNA(Leu) by isoleucine and valine increases with increasing size of the amino acid substituent at position 252, and the noncognate amino acids norvaline and norleucine are inserted efficiently at leucine sites of recombinant proteins under conditions of constitutive overexpression of the T252Y mutant in E. coli. In addition, the unsaturated amino acids allylglycine, homoallylglycine, homopropargylglycine and 2-butynylalanine all support protein synthesis. These results demonstrate that programmed manipulation of the editing cavity can allow in vivo incorporation of novel protein building blocks.\r\n" }, { "name": "Urbach, Adam Robert", "degree": "PhD", "year": "2002", "title": "1:1 Motif for DNA Recognition by \u03b2-Alanine Linked Polyamides", "advisor": "Readhead, Anthony C. S.; Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05202002-104244", "creators": [ { "name": { "family": "Urbach", "given": "Adam Robert" }, "id": "Urbach-Adam-Robert", "orcid": "0000-0003-3426-4760", "display_name": "Urbach, Adam Robert" } ], "advisors": [ { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "advisor", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "member", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "orcid": "0000-0002-8587-5097", "role": "member", "display_name": "Roberts, Richard W." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/V6FD-YQ78", "abstract": "Polyamides composed of N-methylpyrrole (Py), N-methylimidazole (Im), and 3-hydroxypyrrole (Hp) amino acids linked by beta-alanine (beta) bind in the minor groove of DNA in 1:1 and 2:1 ligand:DNA complexes. Although the energetics and structure of the 2:1 motif have been explored extensively, there is remarkably less understood about 1:1 recognition beyond the initial studies on netropsin and distamycin. Laemmli and coworkers used beta-linked polyamides, which bind in a 1:1 motif, to effect phenotypic changes in Drosophila melanogaster. The thesis work described here investigates Laemmli's 1:1 motif in order to further understand and exploit this novel mode of DNA recognition.
\r\n\r\ny selectively replacing Py residues with beta it was found that the Im-beta-Im subunit is important for high-affinity binding in 1:1 and 2:1 modes. This study also demonstrates that a single ligand can target very different DNA sequences based on 1:1 or 2:1 binding. This ambiguity of sequence targeting based on stoichiometry was addressed. It was discovered that hairpin and 1:1 binding modes, which are dependent on ligand conformation, are controlled by changing the linker between polyamide subunits.
\r\n\r\nThe possibility of developing a 1:1 recognition code was explored by selectively mutating polyamide residues and DNA base pairs and comparing the association constants for the resulting complexes. It was found that Im residues tolerate all four Watson-Crick base pairs; Py and beta residues are specific for A?T and T?A base pairs; and Hp specifies a single base pair, A?T, in the sequence context 5'-AAAGAGAAGAG-3'. Attempts to improve upon this recognition code using novel heterocyclic amino acids, such as furan, thiophene, thiazole, and hydroxythiophene, are presented. The sequence-dependence of ligand orientation and the effect of ligand size on binding affinity were also explored.
\r\n\r\nThe NMR structure of a 1:1 polyamide:DNA complex was determined. It reveals B-form DNA with a narrow minor groove and large negative propeller twist, which are shown to be stabilized by bifurcated hydrogen bonds between polyamide NH groups and purine N3 and pyrimidine O2 atoms. The first direct evidence is provided for hydrogen bond formation between Im-N3 and guanine NH2 in the 1:1 motif, thus confirming the original lexitropsin model.
" }, { "name": "Villahermosa, Randy Michael", "degree": "PhD", "year": "2002", "title": "Electron Tunneling Through Phenylene Bridges", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232005-084837", "creators": [ { "name": { "family": "Villahermosa", "given": "Randy Michael" }, "id": "Villahermosa-Randy-Michael", "display_name": "Villahermosa, Randy Michael" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qxxp-m840", "abstract": "A series of donor-bridge-acceptor (D-B-A) complexes, [(bpy)2Ru(bpy-(XY)n-G)](PF6)2 (where n = 2 to 5, bpy = 2,2'-bipyridine, XY = 2,5-xylene, and G is 3-ethynyl-4-methoxyN, N-dimethylaniline; abbreviated [Ru-(XY)n-G]2+), were designed, synthesized, and characterized to study electron tunneling through phenylene bridges. [Ru-(XY)n -G]2+ is a versatile D-8-A scaffold that exhibits a strong correlation between xylene conformation and electron transfer properties.
\r\n\r\n[Ru-(XY)n -G](PF6)2 was assembled from three components in a convergent process. Stepwise oligomer growth produced the well-defined bridging ligand, bpy-(XY)n; bipyridine was regioselectively functionalized with a xylene oligomer through multiple cycles of palladium-catalyzed cross-couplings. The donor, synthesized separately, was joined to bpy-(XY)n using an alkyne linkage. Metalation with a (bpy)2Ru fragment finished assembly of the D-8-A complex. The D-B-A series was analyzed with mass spectrometry- and NMR.
\r\n\r\nSpectroscopic, electrochemical, and spectroelectrochemical characterizations of [Ru-(XY)n -G]2+ indicate no significant electronic or chemical difference among the members of the series. UV-visible absorption spectra, with a metal to ligand charge transfer (MLCT) band maximum of 460 nm, resemble the model complexes [Ru(bpy)3]2+ and [Ru-XY-TMS]2+ (where TMS = trimethylsilyl). Representative cyclic voltammograms of [Ru-(XY)3-G]2+ contain reversible redox couples for Ru111m and Gw+, with potentials of 1.24 and 0.59 V (vs. Ag/AgCl). Spectroelectrochemical traces, displaying loss of MLCT intensity and increased absorption centered at 520 nm, indicate the formation of [Ru111-(XY)n -G+]4+.
\r\n\r\nThe flash-quench technique was used to measure the electron transfer rates for [Rum\u00b7(XY)11-G] 3+-+ [Ruu-(XY)n-G+]3+. The rates, 9.0 \u00b1 0.3 x 106, 2 \u00b1 1x105, and \u00b7 6 ::: 1 103 for n == 3 through 5, have a strong dependence on donor-acceptor distance. Estimates of the donor-acceptor distance were used to determine a distance decay constant, J), of 0.84 A-1 \u2022 The typical 13-value for electron tunneling through phenylenes is\r\n0.4 A-1 \u2022 The unusually high ~-value for [Ru-(XY)n -G]2+ is attributed to near-orthogonal dihedral angles between adjacent xylene rings. UV-visible spectra, cyclic voltammograms, and structural information, from molecular modeling calculations and a crystal structure, all support a near-orthogonal twist angle.
\r\n\r\nThe versatility of [Ru-(XY)n-G]2+ as a molecular scaffold was demonstrated in studies on electron transfer reactions in nanocrystalline Ti02 solar cells. Modified to incorporate a terminal carboxyl group, [Ru-(XY)n -BA]2+ (where BA : 4wethynyl-benzoic acid) was synthesized and used as a Ti02 solar cell dye. Utilizing the flash-quench method, the second-order rate constant for dye regeneration with r- ([Rum\u00b7(XY)n-BA] 3+-+ [Ru-(XY)11-BA]2+) in homogenous fluid solution was 1.5 x 1010 M'1s-1 for all three dyes in the series n=O to 2.
" }, { "name": "Wang, Clay Chia Chun", "degree": "PhD", "year": "2002", "title": "Sequence Specific Trapping of Topoisomerase I by Camptothecin Polyamide Conjugates", "advisor": "Readhead, Anthony C. S.; Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05012012-101216772", "creators": [ { "name": { "family": "Wang", "given": "Clay Chia Chun" }, "id": "Wang-Clay-Chia-Chun", "display_name": "Wang, Clay Chia Chun" } ], "advisors": [ { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "advisor", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "member", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/sphn-ma74", "abstract": "Polyamides containing N-methylpyrrole (Py)N-methylimidazole (Im) and 3-hydroxy-1-methylpyrrole (Hp) are cell permeable small molecules that bind as antiparallel pairs in the minor groove of DNA according to a set of \"pairing rules\" with affinities and specificities for predetermined sequences comparable to DNA-binding proteins. Several of these ring pairings have only been demonstrated when placed internal in a hairpin and not for the terminal position in hairpin polyamides. Several series of eight ring hairpin polyamides with modification at the N-terminal position were synthesized and characterized. We observed that at the terminal position (i) the Py/Py pair functions similar to when placed internally preferring A\u2022T and T\u2022A base pairs over O\u2022C and C\u2022O, (ii) the Hp/Py pair could not distinguish between T\u2022A over A-T possibly due to rotation of the terminal Hp to form an intramolecular hydrogen bond between the 3-hydroxyl hydrogen and the carboxamide oxygen which would orient the key hydroxyl recognition element away from the minor groove. A new aromatic pair, 2-hydroxy-6-methoxybenzamidell-methylpyrrole was designed and shown to distinguish T\u2022A from A\u2022T base pairs and both from O\u2022C/C\u2022O and (iii) the Py/Im pair in the classic eight ring hairpin motif showed no preference for C\u2022O base pair possibly due to the mispositioning of the Im residue located at the C-terminal end of the four ring polyamide subunit. Targeting of C\u2022O was accomplished by replacing a pyrrole with a flexible \u03b2-alanine and setting the imidazole back in register.
\r\n\r\nPyrrole-imidazole polyamides that target DNA sequences in the promoter have been shown to inhibit transcription of specific genes in cell culture. When bound to coding region of genes, polyamides do not appear to inhibit gene expression. A possible solution is to design molecule capable of modifying DNA when bound to the coding region. A series of polyamide-camptothecin conjugates were designed to trap the enzyme Topoisomerase I and induce cleavage at predetermined DNA sites. Cleavage yields were shown to be dependent on linker length between the DNA binding polyamide\r\nand the Topo I trapping camptothecin unit with the camptothecin unit with the longest linker showing greatest cleavage yield of over 90%.
\r\n" }, { "name": "Wilson, Rebecca Mary", "degree": "Masters", "year": "2002", "title": "Advances in Organic Catalysis: The Design of a Novel Asymmetric, Organocatalytic Intramolecular Diels Alder Reaction", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08162013-153809045", "creators": [ { "name": { "family": "Wilson", "given": "Rebecca Mary" }, "id": "Wilson-Rebecca-Mary", "display_name": "Wilson, Rebecca Mary" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/emr9-4m89", "abstract": "[Introduction] The Diels-Aider reaction is one of the most powerful and widely exploited methods available for generating six-membered rings. Similarly, the intramolecular Diels-Alder (IMDA), in which the diene and dienophile reacting partners are tethered, has received a great deal of attention from synthetic chemists in recent years. The IMDA usually proceeds with excellent levels of regio- and stereocontrol to generate complex bicyclic systems with up to four contiguous stereocenters from relatively simple precursors. There have been a number of efforts to develop diastereoselective variants of the IMDA, but there are considerably fewer examples of catalytic, asymmetric IMDA variants." }, { "name": "Wong-Foy, Antek Golangco", "degree": "PhD", "year": "2002", "title": "Ancillary Ligand Effects in Zirconium(IV) Aminoborollide and Nitrogen Chelated Pt(II) Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04102012-133622013", "creators": [ { "name": { "family": "Wong-Foy", "given": "Antek Golangco" }, "id": "Wong-Foy-Antek-Golangco", "display_name": "Wong-Foy, Antek Golangco" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6xyc-e660", "abstract": "The preparation of new chloro derivatives of pentamethylcyclopentadienyl aminoborollide complexes of Zr are described. Treatment of the dianions 1.9-1.12 with Cp*ZrCl_3 yields Cp*{\u03b7^5-C_4H_4BN(Si(CH_3)_3)_2}ZrCl\u2022LiCl (1.13), Cp*{\u03b7^5-C_4H_4BNC(CH_3)_3Si(CH_3)_3}ZrCl\u2022Li\u2022CI (1.14). |Cp*{\u03b7^5-C_4H_4BN(Et)CH_2CH_2Net_2}ZrCl_2Li]_2 (1.15), and Cp*{\u03b7^5-2,5-Ph_2C_4H_2BNMe_2}ZrCl\u2022LiCl (1.16). The electronic spectra of these complexes were measured and compared to the parent complex Cp*{\u03b7^5-C_4H_4BN(CHMe_2)_2}ZrCl\u2022LiCl (1.17a) in THF solvent. In general, as the substituents directly bonded to nitrogen increase in size, a blue shift of the low energy, aminoborollide to zirconium charge transfer band (LMCT), occurs. \u03bb_(max) decreases in the order 1.16 > 1.17a > 1.14 > 1.15 ~ 1.13. The anionic portions of complexes 1.13-1.16 have also been structurally characterized by x-ray crystallography. Although the changes are very small, in general a lengthened B-N bond correlates linearly with the observed blue shift of the LMCT band.
\r\n\r\nStudies directed towards the development of a Pt(II)-catalyzcd oxidation of ethylene to ethylene\r\nglycol based on the Shilov system for alkane functionalization is described. The first step is the activation of ethylene towards nucleophilic attack by water to generate a Pt(II) \u03b2-hydroxyalkyl intermediate that is oxidized in a second step to the Pt(IV) \u03b2-hydroxyalkyl. Reductive elimination via an S_N2-type mechanism at the \u03b1-C of the Pt(IV) \u03b2-hydroxyalkyl liberates the oxidized product leaving the reduced Pt(II) center to bind another equivalent of olefin. The first system examined was the methyl ethylene complex [(tmeda)PtMe(\u03b7^2-C_2H_4)][SbF_6,], 2.2. Nucleophilic attack at the bound ethylene was not observed: instead displacement of ethylene occurred. The bound ethylene in the neutral complexes cis-Cl_2PtL(\u03b7^2-C_2H_4), (L =PPh_3 (2.23), AsPh_3 (2.24), Me_2SO (2.25)) and trans-Cl_2Pt(\u03b7^2-C_2CH_4)(C_5H_5N). 2.26 arc susceptible towards attack by OH-. Under catalytic conditions (excess ethylene and H_2O_2) decomposition of 2.23, 2.24, and 2.25 was observed. In 2.26, 1 turnover was observed before decomposition occurred. The hound ethylene in the complex [(tmeda)PtCl(\u03b7^2-C_2H_4)][ClO_4] is activated towards nucleophilic attack by water and OH-, allowing the isolation of the Pt(II) \u03b2-hydroxyalkyl. This is rapidly oxidized to the Pt(IV) \u03b2-hydroxyalkyl by hydrogen peroxide. In the presence of HCl, it undergoes reductive elimination to yield 2-chlorocthanol\r\nand (tmeda)PtCl_2. Unfortunately, this system also showed no catalytic activity.
\r\n\r\nThe dicationic complexes (|(ArN=C(Me)-C(Me)=NAr)Pt(solv)_2 |X_2. (\u039br = 2.6-(CH_3)_2C_6,H_3: 3.5a:\r\nsolv = CH_3CN, X = CF_3SO_3-, BF_4-, SbF_6-; 3.5b: solv = (CH_3)_2CO, X = BF_4-, SbF_6-,) and 3.6\r\n[(CyN=C(H)-C(H)=NCy)Pt(CH_3CN)_2]X_2, (Cy = C_6H_(11) , X= OTf, BF_4-, Pf_6-, SbF_6-) were synthesized from the corresponding Pt dichlorides with 2 equiv. of AgX. The reaction of 3.5a with 1-phenylpyrazole, 2-phenylpyridine, 2-vinylpyridine, and 2-(2-thienyl)pyridine in acetone affords the cyclometalation products 3.11-3.14 via intramolecular C-H activation of an sp^2 C-H bond of the unsaturated sidegroup. Pyridines with saturated groups at the 2-position do not undergo a similar cyclomctalation reaction. 3.6 undergoes cyclometalation of one of the cyclohexyl groups, an example of sp^3 C-H bond activation. The later reaction proceeds only partway to completion, implying that an equilibrium has been reached: in the case where X = OTf, the equilibrium favors the starting dication. Furthermore, the intramolecular C-H activation occurs in trifluoroethanol but not in acetone under comparable conditions in contrast to the reactions of 3.5a with\r\nthe substituted pyridines.
\r\n\r\nThe diaqua complexe [(ArN=C(Me)-C(Me)=NAr)Pt(H_2O)_2]X_2, 4.3. (\u039br = 2.6-(CH_3)_2C_6H_3; X = OTf^-, BF_4^-) decompose in aqueous solution to yield a red-orange precipitate. Spectroscopic characterization of the precipitate by ^1H, IR, and conductivity measurements is consistent with C_(2v), symmetric structure containing hydroxo groups. Confirmation of the dicationic, dinuclear Pt(II) complex, 4.4, where the two Pt centers are bridged by two OH groups was revealed by x-ray crystallography.
" }, { "name": "Wurtz, Nicholas Roland", "degree": "PhD", "year": "2002", "title": "Sequence Specific Alkylation of DNA by Polyamide-Chlorambucil Conjugates", "advisor": "Readhead, Anthony C. S.; Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-150437308", "creators": [ { "name": { "family": "Wurtz", "given": "Nicholas Roland" }, "id": "Wurtz-Nicholas-Roland", "orcid": "0000-0003-2574-9440", "display_name": "Wurtz, Nicholas Roland" } ], "advisors": [ { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "advisor", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "orcid": "0000-0001-9602-6915", "role": "co-advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "orcid": "0000-0003-3352-4532", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Readhead", "given": "Anthony C. S." }, "id": "Readhead-A-C-S", "orcid": "0000-0001-9152-961X", "role": "member", "display_name": "Readhead, Anthony C. S." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "orcid": "0000-0001-9602-6915", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/59jz-2e47", "abstract": "Small molecules that bind selectively to a DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are small molecules that bind DNA according to a set of \"pairing rules\" with affinities and specificities similar to many naturally occurring DNA binding proteins. Two alternate routes of synthesis of polyamides are presented that allowed improved synthesis of commonly used motifs as well as access to polyamides with truncated tails which increase the number of DNA sequences targetable by polyamides with high affinity. Py-Im polyamides may offer a general approach to chemical regulation of gene expression provided inhibition of DNA binding for a variety of transcription factor families can be achieved. Two successful strategies are shown for the inhibition of DNA binding by two such proteins, GCN4 and NF-\u03baB. An alternate method of gene regulation would be inhibition of transcription during the elongation phase by site-specific alkylation in the coding region of genes. A new class of compounds is created by the attachment of a bis (dichloroethylamino)-benzene nonspecific DNA alkylator to polyamides, which alkylate DNA with high yield and specificity. The biological activity and cell permeability of one of these compounds in several systems is studied.
" }, { "name": "Yeh, Andrew Peter", "degree": "PhD", "year": "2002", "title": "Crystallographic Studies of Iron Proteins", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072012-093202232", "creators": [ { "name": { "family": "Yeh", "given": "Andrew Peter" }, "id": "Yeh-Andrew-Peter", "orcid": "0000-0003-4610-4940", "display_name": "Yeh, Andrew Peter" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/25dt-ct33", "abstract": "The crystal structures of a number of iron proteins from various microbes have been determined in order to better understand the structure-function relationship of these proteins. Several of these iron proteins are as follows:
\r\n\r\nSuperoxide Reductase (SOR) from the hyperthermophile Pyrococcus furiosus. SOR is a non-heme mono-iron protein that functions in anaerobic microbes (e.g., Pyrococcus furiosus) as a defense mechanism against reactive oxygen species by catalyzing the reduction of superoxide to hydrogen peroxide. Crystal structures of SOR in both its oxidized and reduced states have been determined and suggest a possible mechanism by which superoxide accessibility may be regulated.
\r\n\r\n\r\n[2Fe-2S] Ferredoxin 4 (Fd4) from the hyperthermophile Aquifex aeolicus. The crystal structure of this [2Fe-2S] ferredoxin has been determined and reveals a thioredoxin-like fold that is novel among iron-sulfur proteins. Protein sequence alignments show that this fold is present as components of more complex anaerobic and aerobic electron transfer systems (e.g., complex I of aerobic respiratory chains). The crystal structures of two variants of this protein in which one of the [2Fe-2S] cysteine ligands was substituted with a serine have also been determined. The structures of these variants provide metric details of unprecedented accuracy for serine-ligated iron-sulfur clusters in proteins.
\r\n\r\n\r\nThe Photosynthetic Reaction Center (RC) from the photosynthetic purple bacterium Rhodobacter sphaeroides. The plimary process of bacterial photosynthesis, which is light-induced trans-membrane charge separation, occurs in the reaction center (RC), an integral membrane protein-pigment complex. We have obtained the crystal structures of the RC bound to the inhibitor stigmatellin in the presence and absence of light to determine any structural change(s) that may be associated with one of its light-induced charge-separated (D^+QA^-) states. In addition, we have determined the crystal structure of the RC complexed with its physiological electron donor, the soluble monoheme protein cytochrome C_2.
" }, { "name": "Yoon, Tehshik Peter", "degree": "PhD", "year": "2002", "title": "The Acyl-Claisen Rearrangement: Development of a Novel Metal-Catalyzed Claisen Rearrangen1ent and Enantioselective Variants of the Acyl-Claisen Rearrangement", "advisor": "MacMillan, David W. C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01282010-153053761", "creators": [ { "name": { "family": "Yoon", "given": "Tehshik Peter" }, "id": "Yoon-Tehshik-Peter", "orcid": "0000-0002-3934-4973", "display_name": "Yoon, Tehshik Peter" } ], "advisors": [ { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "orcid": "0000-0003-3352-4532", "role": "advisor", "display_name": "MacMillan, David W. C." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "orcid": "0000-0003-3352-4532", "role": "member", "display_name": "MacMillan, David W. C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JNTK-2387", "abstract": "The development of a versatile new variant of the Claisen rearrangement is described. In this new Lewis acid-catalyzed process, the condensation of an allylic amine with a ketene (generated in situ from dehydrohaolgenation of an acid chloride) results in formation of a zwitterionic intermediate. Sigmatropic rearrangement via a highly organized cyclic transition state allows stereospecific access to a diverse range of \u03b1,\u03b2-disubstituted-\u03b3,\u03b4-unsaturated amides in excellent yields and diastereoselectivities for a range of alkyl-, aryl-, and heteroatom-substituted substrates. The ability of this new methodology to generate quaternary carbon stereocenters on both cyclic and acyclic carbon frameworks is demonstrated.
\r\n\r\nAn enantioselective variant of the acyl-Claisen rearrangement employing a chiral magnesium(II)-bis(oxazoline) Lewis acid has been developed. The use of chelating acid chlorides provides excellent organizational control over the transition state, allowing the rearrangement of a range of allyl morpholine substrates to proceed in up to 97% ee. Excellent levels of complementary diastereocontrol can be achieved in a predictable and highly selective manner from the rearrangement of the (E)- and (Z)-isomers of the allyl amine substrates. This reaction is also proficient at accessing quaternary carbon stereocenters.
\r\n\r\nThe scope of the enantioselective acyl-Claisen has been expanded by the use of a new chiral boron Lewis acid. This rearrangement does not require chelating acid chloride substrates for good enantioinduction. Thus, a range of \u03b1-alkyl-, \u03b1-alkoxy-, \u03b1-thio-, and \u03b1-halogen-substituted Claisen adducts can be produced in up to 93% ee.
" }, { "name": "Brandow, Christopher Graham", "degree": "PhD", "year": "2001", "title": "Zirconocenes as Models for Homogeneous Ziegler-Natta Olefin Polymerization Catalysts", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192014-141855635", "creators": [ { "name": { "family": "Brandow", "given": "Christopher Graham" }, "id": "Brandow-Christopher-Graham", "display_name": "Brandow, Christopher Graham" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/kxb2-wp19", "abstract": "Using density functional theory, we studied the fundamental steps of olefin \r\npolymerization for zwitterionic and cationic Group IV ansa-zirconocenes and a neutral ansa-\r\nyttrocene. Complexes [H2E(C5H4)2ZrMe]n (n = 0: E = BH2 (1), BF2 (2), AlH2(3); n = +: E = CH2(4), SiH2(5)) and \r\nH2Si(C5H4)2YMe were used as computational models. The largest\r\ndifferences among these three classes of compounds were the strength of olefin binding and the \r\nstability of the \u03b2-agostic alkyl intermediate towards \u03b2-hydrogen elimination. We investigated \r\nthe effect of solvent on the reaction energetics for land 5. We found that in benzene the \r\nenergetics became very similar except that a higher olefin insertion barrier was\r\ncalculated for 1. The calculated anion affinity of [CH3BF3]- was weaker towards 1 than 5. The\r\ncalculated olefin binding depended primarily on the charge of the ansa linker, and the olefin \r\ninsertion barrier was found to decrease steadily in the following order: [H2C(C5H4)2ZrMe]+ > [F2B(C5H4)2ZrMe] \u2248 [H2B(C5H4)2ZrMe] > [H2Si(C5H4)2ZrMe]+ > \r\n[H2Al(C5H4)2ZrMe].
\r\n\r\n\r\nWe prepared ansa-zirconocene dicarbonyl complexes Me2ECp2Zr(CO)2 (E = Si, C), and\r\nt-butyl substituted complexes (t-BuCp)2Zr(CO)2, Me2E(t-BuCp)2Zr(CO)2 (E = Si, C),\r\n(Me2Si)2(t-BuCp)2Zr(CO)2 as well as analogous zirconocene complexes. Both the reduction\r\npotentials and carbonyl stretching frequencies follow the same order: Me2SiCp2ZrCl2>\r\nMe2CCp2ZrCl2> Cp2ZrCl2> (Me2Si)2Cp2ZrCl2. This ordering is a result of both the donating\r\nabilities of the cyclopentadienyl substituents and the orientation of the cyclopentadiene rings.\r\nAdditionally, we prepared a series of analogous cationic zirconocene complexes\r\n[LZrOCMe3][MeB(C6F5)3] (L = CP2, Me2SiCp2, Me2CCP2, (Me2Si)2Cp2) and studied the kinetics of anion dissociation. We found that the enthalpy of anion dissociation increased from 10.3 kcal\u2022mol-1 to 17.6 kcal\u2022mol-1 as exposure of the zirconium center increased.
\r\n\r\nWe also prepared series of zirconocene complexes bearing 2,2-dimethyl-2-sila-4-pentenyl substituents (and methyl-substituted olefin variants). Methide abstraction with B(C6F5) results in reversible coordination of the tethered olefin to the cationic zirconium center. The kinetics of olefin dissociation have been examined using NMR methods, and the effects of ligand variation for unlinked, singly [SiMe2]-linked and doubly [SiMe2]-linked bis(cyclopentadienyl) arrangements has been compared (\u0394G\u2021 for olefin dissociation varies from 12.8 to 15.6 kcal\u2022mol-1). Methide abstraction from 1,2-(SiMe2)2(\u03b75-C5H3)2Zr(CH3)-(CH2CMe2CH2CH = CH2) results in rapid \u03b2-allyl elimination with loss of isobutene yielding the allyl cation [{1,2-(SiMe2)2(\u03b75-C5H3)2Zr(\u03b73-CH2CH=CH2)]+.
\r\n" }, { "name": "Chang, Aileen Yulin", "degree": "PhD", "year": "2001", "title": "Cleavage of DNA by Polamide-Seco-CB1 Conjugates", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142014-154815404", "creators": [ { "name": { "family": "Chang", "given": "Aileen Yulin" }, "id": "Chang-Aileen-Yulin", "display_name": "Chang, Aileen Yulin" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FY0F-DW57", "abstract": "Small molecules that bind to any predetermined DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. Polyamides containing N-methylimidazole (Im) N-methylpyrrole (Py) are cell permeable small molecules that bind DNA according to a set of \"pairing rules\" with affinities and specificities similar to many naturally occurring DNA binding proteins. Py-Im polyamides offer a general approach to the chemical regulation of gene expression. We demonstrate here that polyamide containing a DNA alkylating moiety seco-CBI can specifically direct sequence specific DNA alkylation. We can also control the strand of DNA that is alkylated, depending on the enantiomer of seco-CBI used and the orientation of the polyamide relative to the alkylation site (Chapter 2). This class of molecules has been applied to a gene repair system in collaboration with the Baltimore group at Caltech (Chapter 3). Also reported are additional seco-CBI polyamide conjugates synthesized to study other systems (HIV-1 and COX-2) (Appendix 1).\r\n" }, { "name": "Chong, Sing Hwa", "degree": "PhD", "year": "2001", "title": "Ultrafast Dynamics of Barrier Crossing: Step-Wise Solvation Effect on Isomerization of Trans-Stilbene in Alkane Clusters", "advisor": "Zewail, Ahmed H.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072008-151825", "creators": [ { "name": { "family": "Chong", "given": "Sing Hwa" }, "id": "Chong-Sing-Hwa", "display_name": "Chong, Sing Hwa" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "co-advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5m8y-hz17", "abstract": "The ultrafast spectroscopic study of molecular clusters in supersonic beams can provide valuable information on the structure, energetics and dynamics of molecular aggregates in gas phase and in solution. This information will shed light on important issues such as how molecules interact, how energy flows in solvated systems, and how chemical reactions progress.
\r\n\r\nAlthough microscopic friction and solvation in barrier crossing reactions is of fundamental importance in molecular dynamics, their roles are not well understood. This is mainly due to the fact that few comprehensive investigations of this subject have been performed. In this thesis, the detail studies of a prototypical barrier crossing reaction\u2014the photoisomerization of jet-cooled trans-stilbene\u2014in size-selected n-alkane clusters, using the picosecond pump-probe ionization TOF mass spectrometry and transient technique, are reported. The microcanonical nonradiative decay rate constants at the S1 manifold for trans-stilbene-hexanen and trans-stilbene-octanen (n = 1, 2) complexes, including certain deuterated variants, were measured as a function of excitation energy, with the energy range defined by tuning the pump wavelength from the 0-0 transition of trans-stilbene to ~3200 cm-1 higher in energy. The experimental results were modeled with standard RRKM theory, nonadiabatic RRKM theory and Kramers-type theory for microcanonical systems. It was found that the excess energy dependence results could be accounted for very well by the nonadiabatic RRKM theory, from which analysis the barriers to isomerization for all of the trans-stilbene n-alkane clusters were found to be lower than that of the parent molecule by ~50%. The analysis revealed that not only can the differences in the rates among the four trans-stilbene-hexane1 isotopic species studied (combinations of trans-stilbene-h12 and -d12 with n-hexane-h14 and -d14) be attributed to energy friction, a term describing how energy is \"drained away\" from the reaction coordinate as a result of the change in the vibrational density of states, but the reduction in the nonradiative rates of the 1:2 complexes, relative to that of the 1:1 complexes, can also be attributed to the same energy friction.
\r\n\r\nFinally, in the same studies, the cluster binding energies of trans-stilbene-hexanen and trans-stilbene-octanen were also determined.
" }, { "name": "Debe, Derek Anthony", "degree": "PhD", "year": "2001", "title": "Shaving Levinthal with Occam's Razor: Understanding the Rate Limiting Step in Protein Folding", "advisor": "Chan, Sunney I.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-154318044", "creators": [ { "name": { "family": "Debe", "given": "Derek Anthony" }, "id": "Debe-Derek-Anthony", "display_name": "Debe, Derek Anthony" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p4yc-y834", "abstract": "How do proteins fold? This thesis addresses this simple yet important question by developing a first principles theoretical framework that accurately describes the experimentally observed protein folding rate data. The success of the new theory suggests that single domain proteins fold according two a two- state mechanism consisting of
\r\n(i)\ta random, diffusive search for the native topology, followed by
\r\n(ii)\tnon-random, local conformation changes within the native topology to find the unique native state.
In chapter 1, a popular analogy between protein folding and the game of golf is used to qualitatively illustrate the most important aspects of the new theory. In chapter 2, mean-field computational methods are developed that allow the time involved in the rate limiting diffusive search for the native state to be calculated. Chapters 3 and 4 remove the mean-field restriction from the methods of chapter 2, allowing the folding rate for an arbitrary two-state folding protein to be calculated. Chapter 5 then explores how real proteins deviate from this ideal model by examining the roles that non-random mechanisms such as helix, hydrophobic core, and 13-turn formation play in the early folding process. Finally, chapter 6 develops an empirical model that also capably predicts protein folding rates, adding further support to the proposed folding mechanism.
" }, { "name": "Fang, Xiangdong", "degree": "PhD", "year": "2001", "title": "Developmentally Regulated Transcription Factors in Drosophila melanogaster", "advisor": "Parker, Carl Stevens", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182014-110657424", "creators": [ { "name": { "family": "Fang", "given": "Xiangdong" }, "id": "Fang-Xiangdong", "display_name": "Fang, Xiangdong" } ], "advisors": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9598-2454", "role": "advisor", "display_name": "Parker, Carl Stevens" } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Parker", "given": "Joseph" }, "id": "Parker-J", "orcid": "0000-0001-9598-2454", "role": "member", "display_name": "Parker, Joseph" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "co-chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Wold", "given": "Barbara J." }, "id": "Wold-B-J", "orcid": "0000-0003-3235-8130", "role": "member", "display_name": "Wold, Barbara J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h17r-qa60", "abstract": "During early stages of Drosophila development the heat shock response cannot be induced. It is reasoned that the adverse effects on cell cycle and cell growth brought about by Hsp70 induction must outweigh the beneficial aspects of Hsp70 induction in the early embryo. Although the Drosophila heat shock transcription factor (dHSF) is abundant in the early embryo, it does not enter the nucleus in response to heat shock. In older embryos and in cultured cells the factor is localized within the nucleus in an apparent trimeric structure that binds DNA with high affinity. The domain responsible for nuclear localization upon stress resides between residues 390 and 420 of the dHSF. Using that domain as bait in a yeast two-hybrid system we now report the identification and cloning of a nuclear transport protein Drosophila karyopherin-\u03b13(dKap- \u03b13). Biochemical methods demonstrate that the dKap-\u03b13 protein binds specifically to the dHSF's nuclear localization sequence (NLS). Furthermore, the dKap-\u03b13 protein does not associate with NLSs that contain point mutations which are not transported in vivo. Nuclear docking studies also demonstrate specific nuclear targeting of the NLS substrate by dKap-\u03b13.Consistant with previous studies demonstrating that early Drosophila embryos are refractory to heat shock as a result of dHSF nuclear exclusion, we demonstrate that the early embryo is deficient in dKap-\u03b13 protein through cycle 12. From cycle 13 onward the transport factor is present and the dHSF is localized within the nucleus thus allowing the embryo to respond to heat shock.
\r\n\r\nThe pair-rule gene fushi tarazu (ftz) is a well-studied zygotic segmentation gene that is necessary for the development of the even-numbered parasegments in Drosophila melanogastor. During early embryogenesis, ftz is expressed in a characteristic pattern of seven stripes, one in each of the even-numbered parasegments. With a view to understand how ftz is transcriptionally regulated, cDNAs that encode transcription factors that bind to the zebra element of the ftz promoter have been cloned. Chapter Ill reports the cloning and characterization of the eDNA encoding zeb-1 (zebra element binding protein), a novel steroid receptor-like molecule that specifically binds to a key regulatory element of the ftz promoter. In transient transfection assays employing Drosophila tissue culture cells, it has been shown that zeb-1 as well as a truncated zeb-1 polypeptide (zeb480) that lacks the putative ligand binding domain function as sequencespecific trans-activators of the ftz gene.
\r\n\r\nThe Oct factors are members of the POU family of transcription factors that are shown to play important roles during development in mammals. Chapter IV reports the eDNA cloning and expression of a Drosophila Oct transcription factor. Whole mount in-situ hybridization experiments revealed that the spatial expression patterns of this gene during embryonic development have not yet been observed for any other gene. In early embryogenesis, its transcripts are transiently expressed as a wide uniform band from 20-40% of the egg length, very similar to that of gap genes. This pattern progressively resolves into a series of narrower stripes followed by expression in fourteen stripes. Subsequently, transcripts from this gene are expressed in the central nervous system and the brain. When expressed in the yeast Saccharomyces cerevisiae, this Drosophila factor functions as a strong, octamer-dependent activator of transcription. The data strongly suggest possible functions for the Oct factor in pattern formation in Drosophila that might transcend the boundaries of genetically defined segmentation genes.
" }, { "name": "Gao, Yi Qin", "degree": "PhD", "year": "2001", "title": "Theory of Ozone Isotopic Effects and Various Electron Transfer Reaction", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192014-125137237", "creators": [ { "name": { "family": "Gao", "given": "Yi Qin" }, "id": "Gao-Yi-Qin", "display_name": "Gao, Yi Qin" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fj7v-ht75", "abstract": "Three separate topics, each stimulated by experiments, are treated theoretically in this dessertation: isotopic effects of ozone, electron transfer at interfaces, and intramolecular directional electron transfer in a supramolecular system.
\r\n\r\nThe strange mass-independent isotope effect for the enrichment of ozone, which has been a puzzle in the literature for some 20 years, and the equally puzzling unconventional strong mass-dependent effect of individual reaction rate constants are studied as different aspects of a symmetry-driven behavior. A statistical (RRKM-based) theory with a hindered-rotor transition state is used. The individual rate constant ratios of recombination reactions at low pressures are calculated using the theory involving (1) small deviation from the statistical density of states for symmetric isotopomers, and (2) weak collisions for deactivation of the vibrationally excited ozone molecules. The weak collision and partitioning among exit channels play major roles in producing the large unconventional isotope effect in \"unscrambled\" systems. The enrichment studies reflect instead the non-statistical effect in \"scrambled\" systems. The theoretical results of low-pressure ozone enrichments and individual rate constant ratios obtained from these calculations are consistent with the corresponding experimental results. The isotopic exchange rate constant for the reaction ^(16)O + ^(18)O ^(18)O\u2192+ ^(16)O ^(18)O + ^(18)O provides information on the nature of a variationally determined hindered-rotor transition state using experimental data at 130 K and 300 K. Pressure effects on the recombination rate constant, on the individual rate constant ratios and on the enrichments are also investigated. The theoretical results are consistent with the experimental data. The temperature dependence of the enrichment and rate constant ratios is also discussed, and experimental tests are suggested. The desirability of a more accurate potential energy surface for ozone in the transition state region is also noted.
\r\n\r\nElectron transfer reactions at semiconductor /liquid interfaces are studied using a tight-binding model for the semiconductors. The slab method and a z-transform\r\nmethod are employed in obtaining the tight-binding electronic structures of semiconductors having surfaces. The maximum electron transfer rate constants at Si/viologen^(2-/+) and InP /Me_(2)Fc^(+/O) interfaces are computed using the tight-binding type calculations for the solid and the extended-Huckel for the coupling to the redox agent at the interface. These electron transfer reactions are also studied using a free electron model for the semiconductor and the redox molecule, where Bardeen's method is adapted to calculate the coupling matrix element between the molecular and semiconductor electronic states. The calculated results for maximum rate constant of the electron transfer from the semiconductor bulk states are compared with the experimentally measured values of Lewis and coworkers, and are in reasonable agreement, without adjusting parameters. In the case of InP /liquid interface, the unusual current vs applied potential behavior is additionally interpreted, in part, by the presence of surface states.
\r\n\r\nPhotoinduced electron transfer reactions in small supramolecular systems, such as 4-aminonaphthalimide compounds, are interesting in that there are, in principle,\r\ntwo alternative pathways (directions) for the electron transfer. The electron transfer, however, is unidirectional, as deduced from pH-dependent fluorescence quenching studies on different compounds. The role of electronic coupling matrix element and the charges in protonation are considered to explain the directionality of the electron transfer and other various results. A related mechanism is proposed to interpret the fluorescence behavior of similar molecules as fluorescent sensors of metal ions.
\r\n" }, { "name": "Hung, Shao-Ching", "degree": "PhD", "year": "2001", "title": "Succinate: Ubiquinone Oxidoreductase from Paracoccus denitrificans and Particulate Methane Monooxygenase from Methylococcus capsulatus (Bath): Experimental and Theoretical EPR Studies of the Metal Cofactors", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212014-084556805", "creators": [ { "name": { "family": "Hung", "given": "Shao-Ching" }, "id": "Hung-Shao-Ching", "display_name": "Hung, Shao-Ching" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ze04-mx93", "abstract": "This thesis summarizes the application of conventional and modern electron paramagnetic resonance (EPR) techniques to establish proximity relationships between paramagnetic metal centers in metalloproteins and between metal centers and magnetic ligand nuclei in two important and timely membrane proteins: succinate:ubiquinone oxidoreductase (SQR) from Paracoccus denitrificans and particulate methane\r\nmonooxygenase (pMMO) from Methylococcus capsulatus. Such proximity relationships are thought to be critical to the biological function and the associated biochemistry mediated by the metal centers in these proteins. A mechanistic understanding of biological function relies heavily on structure-function relationships and the knowledge of how molecular structure and electronic properties of the metal centers influence the reactivity in metalloenzymes. EPR spectroscopy has proven to be one of the most powerful techniques towards obtaining information about interactions between metal centers as well as defining ligand structures. SQR is an electron transport enzyme wherein the substrates, organic and metallic cofactors are held relatively far apart. Here, the proximity relationships of the metallic cofactors were studied through their weak spin-spin interactions by means of EPR power saturation and electron spin-lattice (T_1)\r\nmeasurements, when the enzyme was poised at designated reduction levels. Analysis of the electron T_1 measurements for the S-3 center when the b-heme is paramagnetic led to\r\na detailed analysis of the dipolar interactions and distance determination between two interacting metal centers. Studies of ligand environment of the metal centers by electron spin echo envelope modulation (ESEEM) spectroscopy resulted in the identication of peptide nitrogens as coupled nuclei in the environment of the S-1 and S-3 centers.
\r\n\r\nFinally, an EPR model was developed to describe the ferromagnetically coupled trinuclear copper clusters in pMMO when the enzyme is oxidized. The Cu(II) ions in these clusters appear to be strongly exchange coupled, and the EPR is consistent with equilateral triangular arrangements of type 2 copper ions. These results offer the first glimpse of the magneto-structural correlations for a trinuclear copper cluster of this type, which, until the work on pMMO, has had no precedent in the metalloprotein literature. Such trinuclear copper clusters are even rare in synthetic models.
\r\n" }, { "name": "Hwang, Suzie Jean", "degree": "PhD", "year": "2001", "title": "Rational Design of a New Class of Cyclodextrin-Containing Polymers for Gene Delivery", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192010-081828575", "creators": [ { "name": { "family": "Hwang", "given": "Suzie Jean" }, "id": "Hwang-Suzie-Jean", "orcid": "0000-0003-1443-4996", "display_name": "Hwang, Suzie Jean" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Farbstein", "given": "Mark" }, "id": "Farbstein-M", "role": "member", "display_name": "Farbstein, Mark" }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Triche", "given": "Timothy" }, "id": "Triche-T", "role": "member", "display_name": "Triche, Timothy" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jvc2-6q78", "abstract": "The transfer of gene therapy from an academic exercise to a clinical setting demands the development of an efficient, biocompatible gene delivery vector. Current non-viral systems suffer from toxicity, low transfection efficiency, and in vivo instability. In this work, a new class of polymers was designed to address these issues. Linear, polyamidine, \u03b2-cyclodextrin (\u03b2CD)-containing polymers (\u03b2CDPs) are synthesized by polymerizing difunctionalized cyclodextrins with other difunctionalized comonomers. The inclusion of \u03b2CD in the backbone of the polyamidine polymers decreases the IC\u2085\u2080s by three orders of magnitude, resulting in a polymer with very low in vitro and in vivo toxicity. The cationic \u03b2CDPs are able to self-assemble with and condense DNA into small particles (100-150 nm in diameter). When formulated at a positive charge, the complexes are readily internalized by nearly all exposed cultured cells.
\r\n\r\nThe transgene expression from the delivered complexes was increased by fine-tuning the \u03b2CDP structure for optimum reporter gene activity and by modifying the polymer to enhance endosomal release. The function of the \u03b2CDPs was found to be highly dependent on the polymer structure; changes in position of the amidine charge centers by a few angstroms resulted in transfection and toxicity differences of one order of magnitude. The highest transfection is achieved with the \u03b2CDP6 polymer, that contains a 2 methylene spacer between the cyclodextrin and amidine group and a 6 methylene spacer between adjacent amidine functionalities. The conjugation of a pH-sensitive moiety, histidine, to \u03b2CDP6 endgroups also increases transgene expression by 20-fold without a change in polymer toxicity. Flow cytometry and confocal microscopy experiments with fluorescently-Iabeled DNA suggest that histidylation of \u03b2CDP6 enhances transfection by buffering the endosomal pH, thereby delaying lysosomal degradation and allowing for more endosome release.
\r\n\r\nThe \u03b2CDP-based particles (\u03b2CD-polyplexes) were modified for in vivo stability by using the ability of cyclodextrins to form inclusion complexes with hydrophobic guest molecules. Various compounds were conjugated to adamantane, a molecule that has a high cyclodextrin association constant. The adamantane conjugates, when added to preformed \u03b2CD-polyplexes, are able to self-assemble with the \u03b2CD-polyplexes without disrupting the polymer/DNA binding interactions. Using this method, \u03b2CD-polyplexes were modified with adamantane-polyethylene glycol (PEG) conjugates. The PEGylated particles were salt stabilized in a PEG length-dependent manner. In a second example, modification of \u03b2CD-polyplexes with anionic peptide-adamantane conjugates prevented non-specific cellular uptake in cultured cells. The assembly of the three components, DNA, \u03b2CDP, and adamantane-based modifer, results in a particle with the potential for achieving systemic, in vivo gene delivery. Finally, a small molecule, fluorescein, was conjugated to adamantane and co-delivered with \u03b2CD-polyplexes to cultured cells, thus demonstrating the possibility for therapeutic pouches of small molecule and gene-drugs.
" }, { "name": "Ihee, Hyotcherl", "degree": "PhD", "year": "2001", "title": "Ultrafast Electron Diffraction", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072008-112244", "creators": [ { "name": { "family": "Ihee", "given": "Hyotcherl" }, "id": "Ihee-Hyotcherl", "orcid": "0000-0003-0397-5965", "display_name": "Ihee, Hyotcherl" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "role": "member", "display_name": "Stoltz, Brian M." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AZ0P-H612", "abstract": "Molecular dynamics is now routinely studied on femtosecond time scales using various spectroscopies. However, direct structural information of all nuclear coordinates involved in such dynamical processes requires resolution in time by x-ray or electron diffraction. The focus of this laboratory has been the development of ultrafast electron diffraction (UED) for recording structures in motion, which exploits the six-orders-of-magnitude higher scattering cross section of electrons compared with x-rays. Conventional electron diffraction has been developed over the last several decades to become an enormously powerful technique for determining the static structures of molecules in the gas phase; the subsequent plementation of pulsed electron sources has added a temporal dimension to such studies. In UED, a femtosecond (fs) laser pulse is used to initiate a reaction, but unlike other ultrafast spectroscopies, the subsequent laser pulses normally used to probe the progress of the reaction are replaced with ultrashort pulses of electrons. Time-resolved diffraction patterns are then recorded at fixed time delays relative to the zero-of-time. This directly reflects the changing internuclear distances in the species under study.
\r\n\r\nFor these UED studies, there exist a number of significant experimental challenges, including: (i) the problem of independently determining the temporal overlap (zero-of-time) of the pump and probe pulses in situ for clocking the change; (ii) the problem of low electron flux required to minimize space-charge induced temporal broadening of electron pulses; and (iii) the problem of low scattering and sensitivity caused by the absence of long-range order present in solids, and the low density of molecules in gases. These challenges to the realization of UED have been surmounted over the last decade, and UED now approaches the combined spatial and temporal resolution necessary for tracking all nuclear coordinates during the making and breaking of chemical bonds, thereby permitting the direct observation of molecular structural dynamics in real time. In addition, the diffraction-difference method\u2014which employs the subtraction of a reference diffraction signal from the signals recorded over the course of the reaction\u2014can be used to select the contributions resulting only from changes in structure in the species under study, thereby enhancing the sensitivity of UED to chemical change. Contributions only from the products can be also isolated by adding the appropriately scaled parent diffraction signal at negative time to the difference curves, thus canceling out the parent contribution in each curve.
\r\n\r\nThe first reaction studied by UED was the dissociation of CH2I2 into CH2I and I with fs laser pulses. The second-generation apparatus allowed us to see the amplitude change in the scattering intensity on the picosecond time scale resulting from dissociation. Since this work, UED experiments have successfully investigated the course of several prototypical chemical reactions. For example, the molecular structures and branching ratios of the final products were determined in the dissociation of Fe(CO)5 upon two-photon excitation at 310 nm. A simple intermediate, CF2, was generated by fragmentation of CF2I2 and its molecular structure was precisely determined and compared with other experiments and theoretical calculations. Furthermore, the molecular structure of the transient Fe(CO)4 species was elucidated and compared with available theoretical predictions, permitting identification of the specific electronic energy state of the intermediate and the primary reaction pathway. UED was applied to another organometallic compound, namely (C5H5)Co(CO)2 and the molecular structures of the intermediate and final products were observed. A preliminary analysis showed that either C5H5 and other species can be selectively generated depending on the excitation wavelength. Further analysis will elucidate their molecular structures. The elimination of iodine from 1,2-diiodotetrafluoroethane (C2F4I2) was also studied with the second-generation apparatus, providing early results which suggested that the molecular structure of the C2F4I radical intermediate is not bridged in nature, but instead is \"classical,\" resembling the structure of the parent species.
\r\n\r\nThe need for greater sensitivity and resolution, as well as the desire to study more complex reactions, led to the development of our third-generation UED apparatus. This new machine, with vast improvements in pulsed electron flux, repetition rate, detection sensitivity, and experimental stability, permits the direct imaging of complex chemical reactions with unprecedented spatial and temporal resolution. The spatial and temporal resolution of UED approached ~0.01 \u00c5 and ~1 ps, respectively, and we were sensitive to ~1% changes in the mole fractions of the various chemical species over the course of the reaction. In its first application, the non-concerted elimination of iodine from a haloethane (C2F4I2) was re-visited and the molecular structure of the transient (C2F4I) radical was determined for the first time. Two prototypical cyclic hydrocarbons, 1,3,5-cycloheptatriene (CHT) and 1,3-cyclohexadiene (CHD), were also studied with temporal and spatial resolution of ~5 ps and ~0.04 \u00c5 respectively. At high internal energies of ~4 eV, these molecules displayed markedly different behavior. For CHT, wherein excitation resulted in the reformation of the parent, the observed diffraction change was explained with an equipartitioned model of hot structures\u2014indicating rapid energy redistribution (within a few picoseconds). For CHD, photo-induced ring opening was shown to result in hot but highly non-equilibrium structures even up to 400 ps, with energy trapped in large-amplitude motions comprised of torsion and asymmetric stretching. These studies promise a new direction of research for studying transient structural changes both in equilibrium and non-equilibrium complex systems. The results presented here provide the new limit of improved detection sensitivity, versatility, and resolution of UED, as well as the potential for its diverse applications. The extension to even more complex systems, a process that has already begun in our laboratory, represents our next challenge in UED.
\r\n" }, { "name": "Kempf, James G.", "degree": "PhD", "year": "2001", "title": "Probing Quantum Confinement at the Atomic Scale with Optically Detected Nuclear Magnetic Resonance", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08282001-123851", "creators": [ { "name": { "family": "Kempf", "given": "James G." }, "id": "Kempf-James-G", "display_name": "Kempf, James G." } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0JZB-N948", "abstract": "Near-band-gap circularly polarized excitation in III-V semiconductors provides spin-polarized electrons that transfer spin order to lattice nuclei via fluctuations in the contact hyperfine interaction. This process of optical nuclear polarization and the complementary technique of optical detection of nuclear magnetic resonance (NMR) provide extreme sensitivity enhancement and spatial selectivity in structured samples, enabling collection of NMR spectra from samples such as single quantum wells or dots containing as few as ~10^5 nuclei.
\r\n\r\nCombining these advances with novel techniques for high spectral resolution, we have probed quantum-confined electronic states near the interface of a single epitaxially grown Al(1-x)Ga(x)As/GaAs (x = 0.36) heterojunction. Using a novel strategy that we refer to as POWER (perturbations observed with enhanced resolution) NMR, multiple-pulse time suspension is synchronized with bandgap optical irradiation to reveal spectra of effective spin Hamiltonians that are differences between those of the occupied and unoccupied photoexcited electronic state. The underlying NMR linewidth is reduced by three orders of magnitude in these experiments, enabling resolution of an asymmetric line shape due to light-induced hyperfine interactions. The results are successfully fit with the coherent nuclear spin evolution and relaxation theoretically expected for sites distributed over the volume of an electronic excitation weakly localized at a point defect. This analysis establishes a one-to-one relationship, which can be used to follow nuclear spin diffusion, between optical Knight shift and the radial position of lattice nuclei.
\r\n\r\nWe have also introduced POWER NMR techniques to characterize the change in electric field associated with cycling from light-on to light-off states via a linear quadrupole Stark effect (LQSE) of the nuclear spins. Simulations of these NMR spectra in terms of the radial electric fields of either donor-bound electrons or excitons indicate differences, where the bound-exciton model provides a significantly better fit to the data. The same spin physics enabled our measurement of the heterojunction interfacial field, which we find to be less than 1.3 kV/cm at the sites responsible for optical NMR. Other simulations show the promise of optical NMR as a tool in future studies aimed at atomic-level characterization of quantum-confined systems such as quantum dots and wells.
" }, { "name": "Krider, Elizabeth Stratford", "degree": "PhD", "year": "2001", "title": "Synthesis and Spectroscopy of Ruthenium-Modified Nucleic Acids", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202014-093625161", "creators": [ { "name": { "family": "Krider", "given": "Elizabeth Stratford" }, "id": "Krider-Elizabeth-Stratford", "display_name": "Krider, Elizabeth Stratford" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "member", "display_name": "Meade, Thomas J." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s0za-ec86", "abstract": "Redox-active probes are designed and prepared for use in DNA-mediated electron\r\ntransfer studies. These probes consist of ruthenium(II) complexes bound to nucleosides\r\nthat possess metal-binding ligands. Low- and high-potential oxidants are synthesized\r\nfrom these modified nucleosides and display reversible one-electron electrochemical\r\nbehavior. The ruthenium-modified nucleosides exhibit distinct charge-transfer transitions\r\nin the visible region that resemble those of appropriate model complexes. Resonance\r\nRaman and time-resolved emission spectroscopy are used to characterize the nature of\r\nthese transitions.
\r\n\r\nThe site-specific incorporation of these redox-active probes into oligonucleotides\r\nis explored using post-synthetic modification and solid-phase synthetic methods. The\r\npreparation of the metal-binding nucleosides, their incorporation into oligonucleotides,\r\nand characterization of the resulting oligonucleotides is described. Because the insertion\r\nof these probes into modified oligonucleotides using post-synthetic modification is\r\nunsuccessful, solid-phase synthetic methods are explored. These efforts lead to the first\r\nreport of 3'-metallated oligonucleotides prepared completely by automated solid-phase\r\nsynthesis. Preliminary efforts to prepare a bis-metallated oligonucleotide by automated\r\nsynthesis are described.
\r\n\r\nThe electrochemical, absorption, and emissive features of the ruthenium-modified\r\noligonucleotides are unchanged from those of the precursor metallonucleoside. The\r\nabsence of any change in these properties upon incorporation into oligonucleotides and\r\nsubsequent hybridization suggests that the incorporated ruthenium(II) complex is a\r\nvaluable probe for DNA-mediated electron transfer studies.
" }, { "name": "Kua, Jeremy Soo Pin", "degree": "PhD", "year": "2001", "title": "Computational Studies of Heterogeneous and Homogeneous Catalysis by Late Transition Metals", "advisor": "Goddard, William A., III; Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-085252318", "creators": [ { "name": { "family": "Kua", "given": "Jeremy Soo Pin" }, "id": "Kua-Jeremy-Soo-Pin", "orcid": "https://orcid.org/0000-0002-2472-1887", "display_name": "Kua, Jeremy Soo Pin" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "co-advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M9WN-7M53", "abstract": "To design new catalysts that meet the environmental, materials and energy concerns of modern society, it is vital to understand the fundamental mechanisms involved in catalytic reactions. This thesis focuses on using quantum mechanical methods to determine the mechanisms for several critical catalytic processes in chemical industry.
\r\n\r\nLate transition metals are widely used as heterogeneous catalysts involving organic substrates. To lay a foundation for developing an orbital view useful for reasoning about surface reactions, we have developed the interstitial electron model (IEM) for bonding in platinum described in Chapter 1. To test the validity of the model cluster chosen to represent the surface, we studied the chemistry of C\u2081 and C\u2082 hydrocarbons, for which the most single-crystal experimental data is available, as described in Chapter 2.
\r\n\r\nIn Chapter 3, we extend this model to the second and third row Group VIII transition metals (Ir, Os, Pd, Rh, Ru) and develop a thermochemical group additivity framework for hydrocarbons on metal surfaces similar to the Benson scheme so useful for gas phase hydrocarbons. This provides a potentially powerful technique for deriving a mechanistic understanding on complex hydrocarbon reactions on catalytic surfaces, applicable to hydrocarbon reforming processes.
\r\n\r\nAn advantage of direct methanol fuel cells (DMFCs) over the internal combustion engines is to avoid the environmental damage caused by the latter. Chapter 4 describes our studies on electrocatalysis of methanol oxidation in direct methanol fuel cells. In particular, we focus on the role of different metals at the anode as alloys and as promoters for various aspects of the reaction converting methanol and water to CO\u2082 and energy.
\r\n\r\nOne of the most important challenges is to find ways to utilize the enormous resources in methane around the world as the fundamental feedstock for the chemical and energy industries. Perhaps the most promising progress in developing low-temperature highly selective homogeneous catalysts have been the Hg and PtCl\u2082 catalysts from Catalytica. Chapter 5 reports our studies on the stability, thermodynamics, and reaction mechanism of the PtCl\u2082 catalysts, with suggestions of possible modifications necessary to make this process economic.
" }, { "name": "Lai, Re", "degree": "PhD", "year": "2001", "title": "Synthesis and Characterization of ZSM-5 Zeolite Membranes", "advisor": "Gavalas, George R.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-103556", "creators": [ { "name": { "family": "Lai", "given": "Re" }, "id": "Lai-Re", "display_name": "Lai, Re" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "co-advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m5xs-mq20", "abstract": "Synthesis of ZSM-5 zeolite membranes supported on porous alumina substrates was conducted in autoclave reactors. The film morphologies and structures were characterized by scanning electron microscopy, energy dispersive spectroscopy and X-ray diffraction. Gas adsorption was used to estimate the crystalline fraction of the products. The gas permeation properties of the membranes were evaluated for H\u2082, CH\u2084, O\u2082, N\u2082, and n-butane and other gases singly or in mixtures.
\r\n\r\nZSM-5 film formation on alumina and other surfaces in certain clear, tetrapropylammonium(TPA\u207a)-containing synthesis solutions was found to be preceded by a gel layer. The presence of alumina and other substrates of a high Hamaker constant facilitated formation of the surface gel layer and accelerated zeolite crystallization. Aluminum added to the solution or leached from alumina substrates had dual effects, to induce surface gelation and to retard crystallization of that layer as well as crystallization in the bulk solution.
\r\n\r\nGrowth of ZSM-5 membranes was facilitated by using alumina tubes pre-coated with silicalite seeds. Accompanied with gradual growth of an external polycrystalline layer, siliceous deposits accumulated as deep as 100 \u00b5m inside the pores of the support, converting gradually from amorphous to crystalline. Pure gas permeation results are presented for membranes prepared in a solution of composition SiO\u2082: 0.15TPAB4: 0.7NaOH: 98H\u2082O using 0.4 and 2 \u00b5m seeds.
\r\n\r\nOrganic-free hydrogel reaction mixtures were further used to grow ZSM-5 membranes on seeded porous alumina substrates, eliminating the crack-prone calcination step for removing organic TPA\u207a templates from as-synthesized ZSM-5. The optimum composition SiO\u2082: 0.0125Al\u2082O\u2083: 0.2675Na\u2082O: 46H\u2082O was identified to produce membranes with permeation selectivities for H\u2082 over n-butane above 10\u2074 and for O\u2082 over N\u2082 9-10. The permeation was strongly activated with the activation energies increasing sharply with molecular size.
\r\n\r\nParallel synthesis of zeolite films was developed to expedite composition screening. The films prepared in an array reactor of multiple wells each containing 35 micro-liter synthesis solution displayed morphology similar to that produced by the conventional synthesis. The method was applied to explore the composition space of clear, organic-free synthesis solutions for ZSM-5 films growth: SiO\u2082: (700-300)Al\u2082O\u2083: (0.5-0.7)NaOH: 80H\u2082O.
" }, { "name": "Lobo, Julio Danin", "degree": "PhD", "year": "2001", "title": "Experimental Chemical Physics of Droplets and Clusters", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172014-143110747", "creators": [ { "name": { "family": "Lobo", "given": "Julio Danin" }, "id": "Lobo-Julio-Danin", "display_name": "Lobo, Julio Danin" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/84nr-p931", "abstract": "Time-of-flight measurements of energetic He atoms, field ionization of cryogenic liquid\r\nhelium clusters, and time-of-flight and REMPI spectroscopy of radical salt clusters were\r\ninvestigated experimentally. The excited He atoms were generated in a corona\r\ndischarge. Two strong neutral peaks were observed, accompanied by a prompt photon\r\npeak and a charged peak. All peaks were correlated with the pulsing of the discharge.\r\nThe neutral hyperthermal and metastable atoms were formed by different mechanisms\r\nat different stages of the corona discharge. Positively charged helium droplets were\r\nproduced by ionization of liquid helium in an electrostatic spraying experiment. The fluid\r\nemerging from a thin glass capillary was ionized by a high voltage applied to a needle\r\ninside the capillary. Fine droplets (less than 10 \u00b5m in diameter) were produced in showers with\r\ncurrents as high as 0.4 \u00b5A at 2-4 kV. The high currents resulting from field ionization in\r\nhelium and the low surface tension of He I, led to charge densities that greatly exceeded\r\nthe Rayleigh limit, thus resulting in coulombic explosion of the liquid. In contrast, liquid\r\nnitrogen formed a well-defined Taylor cone with droplets having diameters comparable\r\nto the jet (\u2248100 \u00b5m) at lower currents (10 nA) and higher voltages (8 kV). The metal-halide\r\nclusters of calcium and chlorine were generated by laser ablation of calcium metal\r\nin a Ar/CCl4 expansion. A visible spectrum of the Ca2Cl3 cluster was observed from 651\r\nto 630 nm by 1 +1' REMPI. The spectra were composed of a strong origin band at 15\r\n350.8 cm-1 and several weak vibronic bands. Density functional calculations predicted\r\nthree minimum energy isomers. The spectrum was assigned to the 2B2 \u2190 X 2A1\r\ntransition of a planar C2V structure having a ring of two Cl and two Ca atoms and a\r\nterminal Cl atom. The ring isomer of Ca2Cl3 has the unpaired electron localized on one\r\nCa2+ ion to form a Ca+ chromophore. A second electronic band of Ca2Cl3 was observed at 720 nm. The band is sharply different from the 650 nm band and likely due to a\r\ndifferent isomer." }, { "name": "Luo, Lin", "degree": "PhD", "year": "2001", "title": "Partial Oxidation of Propane Over Vanadium-Containing Zeolite Catalysts", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-135122", "creators": [ { "name": { "family": "Luo", "given": "Lin" }, "id": "Luo-Lin", "display_name": "Luo, Lin" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ce5g-3606", "abstract": "Over the past few decades, significant efforts have been devoted to the development of new catalysts and processes for the partial oxidation of cheap and abundant light alkanes directly into oxygenates and olefins. One of the main challenges in the partial oxidation of light alkanes is that they are usually less reactive than the desired products, and further oxidation to total oxidation products, COx, is thermodynamically favored. With a few exceptions, e.g., partial oxidation of n-butane to malefic anhydride by V-P-O and a oxidation of propane to acrylonitrile by V-Al-Sb, catalysts investigated for the partial oxidation of light alkanes consist of complicated elemental compositions of metal oxides that have less than desirable catalytic behavior.
\r\n\r\nCompared to the traditional bulk metal oxides where the active sites selective for partial oxidation of hydrocarbons are usually lattice oxygens, small metal oxide clusters that do not have lattice energies are anticipated to offer oxygen with a lower energetic barrier. Thus, by using metal oxide clusters, the reaction temperature for oxidation of hydrocarbons may possibly be lowered and total oxidation reduced. Zeolites have been shown to be able to provide an excellent matrix for stabilizing metal oxide clusters. Here, a new approach is investigated for the partial oxidation of propane that combines the tunable advantages of zeolites with possibility of high reactivity of metal oxide clusters by using zeolite supported metal oxide clusters as catalysts.
\r\n\r\nVarious methods are employed to synthesize zeolite supported small metal oxide clusters, including ion-exchange-hydrolysis, liquid phase impregnation, vapor phase impregnation, and post-synthesis modification methods. Vanadium is used as the transition metal of interest and is combined with zeolite L, beta and SSZ-33. Vanadium oxide clusters are successfully incorporated inside zeolites and they have remarkably lower reduction temperatures than the bulk metal oxide. These zeolite based catalysts are studied for propane oxidation. The influence of the locations of the vanadium, the acidity of the zeolite matrix, the hydrophobicity of the zeolite framework and the addition of a second metal(Mo and Sb) are discussed. It is found that vanadium oxide cluster catalysts (VxOy/zeolite L, VxOy/zeolite beta, V-Sb/zeolite beta, V-Mo/zeolite beta) are not particularly selective for the partial oxidation of propane at the reaction conditions investigated (contact time 2 s, reaction temperature 350-450\u00b0C, feed gas molar ratio C3H8:O2:H2O:He=4:2:4:5), and most of the vanadium-containing zeolite beta catalysts are as active as V2O5 (as suggested by the turnover frequency).
\r\n\r\nA considerable amount of acetic acid is produced with vanadyl ion-exchanged zeolite beta (VO-H-beta), with a selectivity to acetic acid of 21.1% at propane conversion 1.62% (350\u00b0C). It appears that more valuable oxygenates, e.g., acrylic acid, may have been produced in the reaction and overoxidized to COx, since feeding acrylic acid into this VO-H-beta reaction system at 350\u00b0C results in complete oxidation of the acid to CO\u2093. Motivated by these data, the reaction pathways for propane and propylene oxidation are investigated on this catalyst. For comparison, reaction pathways are also studied with a \"Mitsubishi\" type catalyst, Mo1V0.3Te0.23Nb0.120x, one of the best catalysts for propane partial oxidation to acrylic acid. With VO-H-beta, propylene is the primary product of propane oxidation and acetic acid is a sequential oxidation product of the formed propylene possibly through an acetone intermediate. Mo1V0.3Te0.23Nb0.120x also gives propylene as the primary product of propane oxidation and the propylene thus formed further oxidizes to acrylic acid and acetone. Reactions of individual oxygenate compounds, e.g., propanal, acrolein, etc., suggest a need to further suppress the total oxidation and to improve allylic oxidation feature for the zeolite based catalysts.
" }, { "name": "Machczynski, Michael Christopher", "degree": "PhD", "year": "2001", "title": "Physical Characterization of the Rack Effect and Hydrogen Bond Networks in Blue Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202014-144611863", "creators": [ { "name": { "family": "Machczynski", "given": "Michael Christopher" }, "id": "Machczynski-Michael-Christopher", "display_name": "Machczynski, Michael Christopher" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "co-chair", "display_name": "Richards, John H." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/q0yk-sj10", "abstract": "A summary of previous research is presented that indicates that the purpose of a\r\nblue copper protein's fold and hydrogen bond network, aka, the rack effect, enforce a\r\ncopper(II) geometry around the copper(I) ion in the metal site. In several blue copper\r\nproteins, the C-terminal histidine ligand becomes protonated and detaches from the\r\ncopper in the reduced forms. Mutants of amicyanin from Paracoccus denitrificans were\r\nmade to alter the hydrogen bond network and quantify the rack effect by pKa shifts.
\r\n\r\nThe pKa's of mutant amicyanins have been measured by pH-dependent\r\nelectrochemistry. P94F and P94A mutations loosen the Northern loop, allowing the\r\nreduced copper to adopt a relaxed conformation: the ability to relax drives the reduction\r\npotentials up. The measured potentials are 265 (wild type), 380 (P94A), and 415 (P94F)\r\nmV vs. NHE. The measured pKa's are 7.0 (wild type), 6.3 (P94A), and 5.0 (P94F). The\r\nadditional hydrogen bond to the thiolate in the mutants is indicated by a red-shift in the\r\nblue copper absorption and an increase in the parallel hyperfine splitting in the EPR\r\nspectrum. This hydrogen bond is invoked as the cause for the increased stability of the C-terminal\r\nimidazole.
\r\n\r\nMelting curves give a measure of the thermal stability of the protein. A\r\nthermodynamic intermediate with pH-dependent reversibility is revealed. Comparisons\r\nwith the electrochemistry and apoamicyanin suggest that the intermediate involves the\r\nregion of the protein near the metal site. This region is destabilized in the P94F mutant;\r\ncoupled with the evidence that the imidazole is stabilized under the same conditions\r\nconfirms an original concept of the rack effect: a high energy configuration is stabilized\r\nat a cost to the rest of the protein.
" }, { "name": "Maynard, Heather Dawn", "degree": "PhD", "year": "2001", "title": "New Materials for Biological Applications Prepared by Olefin Metathesis Reactions", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202014-141427716", "creators": [ { "name": { "family": "Maynard", "given": "Heather Dawn" }, "id": "Maynard-Heather-Dawn", "display_name": "Maynard, Heather Dawn" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pb50-kz34", "abstract": "With the advent of well-defined ruthenium olefin metathesis catalysts that are\r\nhighly active and stable to a variety of functional groups, the synthesis of complex\r\norganic molecules and polymers is now possible; this is reviewed in Chapter 1. The\r\nmajority of the rest of this thesis describes the application of these catalysts towards the\r\nsynthesis of novel polymers that may be useful in biological applications and\r\ninvestigations into their efficacy.
\r\n\r\nA method was developed to produce polyethers by metathesis, and this is\r\ndescribed in Chapters 2 and 3. An unsaturated 12-crown-4 analog was made by\r\ntemplate- directed ring-closing metathesis (RCM) and utilized as a monomer for the\r\nsynthesis of unsaturated polyethers by ring-opening metathesis polymerization (ROMP).\r\nThe yields were high and a range of molecular weights was accessible. In a similar\r\nmanner, substituted polyethers with various backbones were synthesized: polymers with\r\nbenzo groups along the backbone and various concentrations of amino acids were\r\nprepared. The results from in vitro toxicity tests of the unsubstituted polyethers are\r\nconsidered.
\r\n\r\nThe conditions necessary to synthesize polynorbornenes with pendent bioactive\r\npeptides were explored as illustrated in Chapter 4. First, the polymerization of various\r\nnorbornenyl monomers substituted with glycine, alanine or penta(ethylene glycol) is\r\ndescribed. Then, the syntheses of polymers substituted with peptides GRGD and SRN, components of a cell binding domain of fibronectin, using newly developed ruthenium initiators are discussed.
\r\n\r\nIn Chapter 5, the syntheses of homopolymers and a copolymer containing\r\nGRGDS and PHSRN, the more active forms of the peptides, are described. The ability of\r\nthe polymers to inhibit human dermal fibroblast cell adhesion to fibronectin was assayed\r\nusing an in vitro competitive inhibition assay, and the results are discussed. It was\r\ndiscovered that the copoymer substituted with both GRGDS and PHSR peptides was\r\nmore active than both the GRGDS-containing homopolymer and the GRGDS free\r\npeptide.
\r\n\r\nHistorically, one of the drawbacks to using metathesis is the removal of the\r\nresidual ruthenium at the completion of the reaction. Chapter 6 describes a method\r\nwhere the water soluble tris(hydroxymethyl)phosphine is utilized to facilitate the removal\r\nof residual ruthenium from RCM reaction products.
\r\n" }, { "name": "Miller, Michael Andrew", "degree": "PhD", "year": "2001", "title": "Laser Synchronized Optical Nuclear Magnetic Resonance via Larmor Beat Detection : Imaging Electronic Wavefunctions in Gallium Arsenide Device Structures", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102007-114331", "creators": [ { "name": { "family": "Miller", "given": "Michael Andrew" }, "id": "Miller-Michael-Andrew", "display_name": "Miller, Michael Andrew" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ARCE-F837", "abstract": "We have accomplished Optical Nuclear Magnetic Resonance (ONMR) experiments in an Al0.36Ga0.64As/GaAs heterojunction sample at ~2K with rf-optical pulse synchronization. The hyperfine coupling of the electron spin to the nuclear spins enable this spectroscopy in several ways, which are discussed herein. Moreover, the interactions experienced by nuclear spins in III-V semiconductors, in general, and the phenomena encountered when they are in the vicinity of a shallow donor or pseudo-donor, specifically, are developed. Furthermore, the most accurate calculation of spin diffusion in a spin-three-halves system to date is developed and presented using a methodology can be readily applied to any spin-larger-than-one-half system to a yield a set of coupled differential equations for a set of orthogonal polarizations. The behavior of these equations under a number of physical situations is also investigated.
\r\n\r\nWe have captured the first ever radially resolved Knight shift images from the nuclei near a point defect in GaAs using laser synchronized ONMR. A deconvolution of these images into their constituent physical interactions has been approximately carried out using the theoretical advances developed and presented in this thesis, yielding the shape and size of the electronic orbital in which the electron is trapped, the occupancy of that electronic orbital, and the quadrupolar interactions in the vicinity of the defect, including the charge state of the defect.
\r\n\r\nComputational approaches include both full, real-time analyses of every one of the hundreds of thousands of nuclei surrounding a defect in GaAs, modeling the time domain evolution for each individual nucleus including its Knight shift, quadrupolar interactions (both secular and nonsecular), individual optical polarization conditions, optical detection weighting, and rigorously exact rf effects, and analyses of a variety of continuous medium approximations. The only computations that fit the experimental spectra are those that calculate spin diffusion along a radial line of spins, and use this approximation to the radial profile of nuclear polarization in a continuous medium approximation. The successful interface of this spin diffusion calculation and the single nucleus calculations, leveraging their individual strengths, is clearly a desirable route to further increase computational accuracy.
" }, { "name": "Mish, Michael Robert", "degree": "PhD", "year": "2001", "title": "The Application of Trimethylsilyl Diazomethane to the Synthesis of Optically Active Pyrazolines and Related Studies", "advisor": "Carreira, Erick Moran", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252014-083524220", "creators": [ { "name": { "family": "Mish", "given": "Michael Robert" }, "id": "Mish-Michael-Robert", "display_name": "Mish, Michael Robert" } ], "advisors": [ { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "advisor", "display_name": "Carreira, Erick Moran" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s6ej-q525", "abstract": "The 1,3-dipolar cycloadditions of trimethylsilyl diazomethane with camphorsultam-derived acrylates are reported as a means for the efficient synthesis of optically active pyrazolines. Trimethylsilyl diazomethane is a safe, commercially available diazoalkane which provides \u03941-pyrazolines 1n good yield and diastereoselectivity when camphorsultam-derived acrylates are used as the reaction dipolarophiles . These initial cycloadducts are subsequently converted to stable, characterizable \u03942-pyrazolines upon desilylation.
\r\n\r\nA manifold of reactions that can be applied to these \u03942-pyrazolines has been developed which includes pyrazoline reduction, N-N bond reduction, addition to the pyrazoline C=N by mild carbon nucleophiles, and both solvolytic and reductive chiral auxiliary removal. Additionally, it has been demonstrated that the pyrazoline reduction products can take part in peptide coupling reactions that allow for the pyrazolidines to serve as proline-like molecules. The development of this methodology is a general solution to the problem of highly substituted, functionalized pyrazoline synthesis. Importantly, the pyrazolines thus provided have been demonstrated to be amenable to reactions that add to their value as synthetic intermediates.
\r\n" }, { "name": "Odom, Duncan T.", "degree": "PhD", "year": "2001", "title": "The Application of Metallointercalators in Recognition of and Charge Transport in Nucleic Acids", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212014-095851500", "creators": [ { "name": { "family": "Odom", "given": "Duncan T." }, "id": "Odom-Duncan-T", "orcid": "0000-0001-6201-5599", "display_name": "Odom, Duncan T." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/yz1f-w961", "abstract": "Metal complexes that utilize the 9,10-phenanthrene quinone diimine (phi) moiety\r\nbind to DNA through the major groove. These metallointercalators can recognize DNA\r\nsites and perform reactions on DNA as a substrate. The site-specific metallointercalator\r\n\u039b-1-Rh(MGP)_2phi^(5+) competitively disrupts the major groove binding of a transcription\r\nfactor, yAP-1, from an oligonucleotide that contains a common binding site. The\r\ndemonstration that metal complexes can prevent transcription factor binding to DNA site-specifically\r\nis an important step in using metallointercalators as therapeutics.
\r\n\r\nThe distinctive photochemistry of metallointercalators can also be applied to\r\npromote long range charge transport in DNA. Experiments using duplexes with regions\r\n4 to 10 nucleotides long containing strictly adenine and thymine sequences of varying\r\norder showed that radical migration is more dependent on the sequence of bases, and\r\nless dependent on the distance between the guanine doublets. This result suggests that\r\nmechanistic proposals of long range charge transport must involve all the bases.
\r\n\r\nRNA/DNA hybrids show charge migration to guanines from a remote site, thus\r\ndemonstrating that nucleic acid stacking other than B-form can serve as a radical bridge.\r\nDouble crossover DNA assemblies also provide a medium for charge transport at\r\ndistances up to 100 \u00c5 from the site of radical introduction by a tethered metal complex.\r\nThis radical migration was found to be robust to mismatches, and limited to individual,\r\nelectronically distinct base stacks. In single DNA crossover assemblies, which have\r\nconsiderably greater flexibility, charge migration proceeds to both base stacks due to\r\nconformational isomers not present in the rigid and tightly annealed double crossovers.
\r\n\r\nFinally, a rapid, efficient, gel-based technique was developed to investigate\r\nthymine dimer repair. Two oligonucleotides, one radioactively labeled, are photoligated\r\nvia the bases of a thymine-thymine interface; reversal of this ligation is easily visualized\r\nby gel electrophoresis. This assay was used to show that the repair of thymine dimers\r\nfrom a distance through DNA charge transport can be accomplished with different\r\nphotooxidants.
\r\n\r\nThus, nucleic acids that support long range charge transport have been shown to\r\ninclude A-track DNA, RNA/DNA hybrids, and single and double crossovers, and a\r\nmethod for thymine dimer repair detection using charge transport was developed.\r\nThese observations underscore and extend the remarkable finding that DNA can serve a\r\nmedium for charge transport via the heteroaromatic base stack.
\r\n\r\n" }, { "name": "Okada, Sheldon Yoshio", "degree": "Masters", "year": "2001", "title": "Synthesis and Biological Applications of Oligopeptide-Substituted Polynorbornenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172018-160205705", "creators": [ { "name": { "family": "Okada", "given": "Sheldon Yoshio" }, "id": "Okada-Sheldon-Yoshio", "display_name": "Okada, Sheldon Yoshio" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/76ch-0t79", "abstract": "Chapter 1
\r\n\r\nSynthetic fibronectin mimics have been constructed usmg functionalised norbomenyl polymers synthesized via ring-opening metathesis polymerization (ROMP). The ROMP reactions were catalyzed by newly developed ruthenium initiators. Prior to the synthesis of the fibronectin mimics, the polymerization reactions of a number of norbornene derivatives with pendent glycine or penta(ethylene oxide) (EO5) units were studied in order to select the derivatives with optimal characteristics: high yields, fast polymerization times, and narrow PDI's. For these initial studies Ru = CHPh(Cl2)(PCy3)2 (1) was used as the initiator. Based on these studies poly(5-norbomene-2-carboxyl) and poly(4-(Exo-3,5-dioxo-10-oxa-4-azatricyclo[5.2.1.0]dec-8-en-4-yl)-butyric acid) were chosen as the ideal backbones for a series of polymers functionalised with pendent arginine-glycine-aspartic acid (RGD) and serine-arginineasparagine (SRN) oligopeptides. The polymers containing a propyl spacer between the pendant group and the backbone were synthesized in an attempt to demonstrate that the presentation of the peptide units could be altered to closely mimic the natural presentation of these peptides in fibronection. Homopolymers and random copolymers containing various combinations of norbomene monomers with pendant EO5 (21 & 14), GRGD/RGD (24 & 29), and SRN (25 & 30) units were made. Copolymers with large RGD or SRN contents (> 10 mol %) could only be synthesised in high yields and narrow PDI's by using the newly developed ruthenium 2,3-dihydroimidazolylidene initiators Ru = CHPh(Cl)2(PCy3)(DHIMes) (2) or Ru = CH-CH = CH2(CH3)2(Cl)2 PCp3)(DIHMes) (3). In addition, the ROMP reactions of the norbornene monomers containing the propyl spacers also required the new initiator 2. Attempts to synthesize these polymers using ruthenium initiator 1 resulted in either low yields, bimodal molecular weight distributions, or a combination of both.
\r\n\r\nChapter 2
\r\n\r\nPolynorbomenes substituted with two different peptide sequences from the RGD containing integrin cell binding domain of fibronectin are potent inhibitors of human foreskin fibroblast cell adhesion to fibronectin-coated surfaces. Ring-opening metathesis polymerization (ROMP) using Ru = CHPh(Cl)2(PCy3)(DHIMes) (1) as an initiator produced polymers substituted with GRGDS and PHSRN peptide sequences. The inhibitory activity was quantified for these polymers and compared to the free peptides and GRGES containing controls. A homopolymer substituted with GRGDS peptides was significantly more active than the free GRGDS peptide (IC50 of 0.18 \u00b1 0.03 and 1.33 \u00b1 0.20 mM respectively), and the copolymer containing both GRGDS and PHSRN was the most potent inhibitor (IC50 of 0.04 \u00b1 0.01 mM). These results demonstrate that significant enhancements of observed biological activity can be obtained from polymeric materials containing more than one type of multivalent ligand and that ROMP is a useful method to synthesize such well-defined copolymers.
\r\n\r\n\r\n" }, { "name": "Ostraat, Michele Louisa", "degree": "PhD", "year": "2001", "title": "Synthesis and Characterization of Aerosol Silicon Nanoparticle Nonvolatile Floating Gate Memory Devices", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072005-081230", "creators": [ { "name": { "family": "Ostraat", "given": "Michele Louisa" }, "id": "Ostraat-Michele-Louisa", "orcid": "0000-0003-2678-6171", "display_name": "Ostraat, Michele Louisa" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Atwater", "given": "Harry Albert" }, "id": "Atwater-H-A", "orcid": "0000-0001-9435-0201", "role": "member", "display_name": "Atwater, Harry Albert" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/FDGV-GS71", "abstract": "Silicon nanoparticle-based floating gate metal-oxide-semiconductor (MOS) field effect devices have potential for terabit cm-2 density nonvolatile memory applications. Aerosol synthesis of silicon nanoparticles is an important route toward the formation of discontinuous silicon nanoparticle floating gate structures that affords excellent control over particle size and size distribution, particle density, and oxide passivation. We have fabricated nanoparticle memory devices in a conventional MOS ultra-large scale integration (ULSI) process with channel lengths from 0.2 - 10 \u00b5m with a silicon nanoparticle floating gate fabricated by aerosol deposition.
\r\n\r\nSiO2 passivated silicon nanoparticles have been synthesized in an ultra clean two-stage aerosol reactor that is interfaced to a 200 mm wafer deposition chamber in a class 100 cleanroom. We synthesize silicon nanoparticles by thermal decomposition of silane gas at 950\u00b0C to produce single crystal, nonagglomerated nanoparticles. The second reactor stage passivated the silicon nanoparticles with a thin thermal oxide grown at 1050\u00b0C. Particles are thermophoretically deposited onto 200 mm silicon wafers with densities from 1013 particles cm-2 at the wafer center to 1011 particles cm-2 at the wafer edge in tens of minutes. We have fabricated floating gate memory devices in which the dielectric layer contains a discontinuous nanoparticle layer containing either (i) 2 -4 nm crystalline core diameter with 1 nm thermal oxide; or (ii) 6 - 15 nm crystalline core diameter with 2 nm thermal oxide. Cross-sectional transmission electron microscopy (TEM) verifies the presence of a silicon nanoparticle floating gate layer and planar TEM confirms nanoparticle morphology, size, and density.
\r\n\r\nAerosol floating gate devices exhibit normal transistor behavior and have promising nonvolatile device performance. Aerosol nanoparticle devices with 0.2 mm channel lengths exhibit threshold voltages < 5 V with large threshold voltage shifts (~ 2 V), submicrosecond program times and millisecond erase times. No degradation in program/erase threshold voltage swing was observed during 105 program and erase cycles, although some threshold voltage shift due to charge trapping was observed. Electrostatic modeling indicates when a discontinuous nanoparticle layer can be modeled as a continuous sheet charge embedded within oxide and when it should be modeled as individual nanoparticles in an array.
" }, { "name": "Pantu, Piboon", "degree": "PhD", "year": "2001", "title": "Methane Conversion to Synthesis Gas over Platinum Supported on Rare Earth Oxides", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062010-111511765", "creators": [ { "name": { "family": "Pantu", "given": "Piboon" }, "id": "Pantu-Piboon", "display_name": "Pantu, Piboon" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/rksa-xc11", "abstract": "The central theme of this research is to study methane conversion to synthesis gas focusing on the redox capabilities of cerium oxide. Reaction of methane with platinum or ruthenium supported on Ce_(1-x)Zr_xO_2 (x=0, 0.2, 0.5) in the absence of gaseous oxygen was studied in a packed-bed reactor at 550-700\u00b0C. The oxidation of methane utilized lattice oxygen of the support, which was subsequently restored by reacting with oxygen in a separate step. Thus, by using theredox property of cerium oxide, methane oxidation can be carried out by air without diluting the product with nitrogen. Addition of ZrO_2 into CeO_2 increased the reducibility of the oxide as well as the rate of methane oxidation but decreased the selectivity to CO and H_2. The rate of oxidation was initially very fast but slowed down as the oxide support became progressively reduced. On the other hand, the selectivity increased with the reduction of the support and sharply rose to over 90% as the support attained 10%,40%, and 65% degree of reduction for the oxide compositions x=0, 0.2, and 0.5, respectively.
\r\n\r\nPartial oxidation of methane to synthesis gas over 0.5wt% Pt/Al_2O_3 and 0.5wt% PtfCeO_2 catalysts was studied in a packed-bed reactor. At temperatures up to 650\u00b0C, the PtfCeO_2 catalyst gave higher conversion and higher selectivity but the activity and selectivity became comparable to those of Pt/Al_2O_3 above 700\u00b0C. The Pt/CeO_2 catalyst also maintained high conversion and high selectivity when the CH_4:O_2 feed ratio varied from 1.7 to 2.3 while the Pt/Al_2O_3 catalyst had considerably lower selectivity under methane-rich conditions. The effect of reducibility of support on the catalytic activity was discussed. A multiple microreactor system for parallel testing of heterogeneous catalysts was developed. The reactor system was composed of nine tubular microreactors housed in a single wider tube and used a multiposition valve to conduct the reaction products sequentially from each microreactor to a mass spectrometer for analysis. The catalyst samples were prepared in the form of thin films coated on quartz rods for convenience of preparation and loading samples in the reactors. The system was tested with the reaction of methane reforming with carbon dioxide over Pt/Ce_(1-x)Gd_xO_(2-0.5x) and Pt/Ce_(1-x)Sm_xO_(2-0.5x) at 650\u00b0C and 700\u00b0C. The measurements showed that Pt/CeO_2 had the highest activity and, generally, the activity increased with cerium oxide content. After exposure to the feed stream for 2-3 hours at 700\u00b0C, most catalysts suffered significant deactivation with the exception of the mixed oxides with 25-85% samarium oxide that maintained relatively stable activity.
" }, { "name": "Pratt, Alison Beth", "degree": "PhD", "year": "2001", "title": "Cell-Responsive Synthetic Biomaterials Formed in situ", "advisor": "Hubbell, Jeffrey A.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08132007-143014", "creators": [ { "name": { "family": "Pratt", "given": "Alison Beth" }, "id": "Pratt-Alison-Beth", "display_name": "Pratt, Alison Beth" } ], "advisors": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "orcid": "0000-0003-0276-5456", "role": "advisor", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "orcid": "0000-0003-0276-5456", "role": "member", "display_name": "Hubbell, Jeffrey A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/HFEF-7F61", "abstract": "Two-way communication between cells and their extracellular matrices plays an important role in establishing and maintaining cell and tissue morphology. Synthetic materials for tissue engineering have so far not been able to mimic these interactions. This work describes a new class of synthetic biomaterials that display the essential characteristics of naturally occurring matrices. The materials can be formed in contact with cells and tissues to create covalently cross-linked hydrogels which are effectively nonporous on the length scale of a cell process. The otherwise nonadhesive gels can be rendered specifically cell-adhesive by incorporation of ligands for cell surface adhesion molecules, such as integrins. The materials are degradable by plasmin, a proteolytic enzyme used by cells during proliferation and migration in natural matrices. Furthermore, the materials can be designed to sequester heparin-binding growth factors.
\r\n\r\nThe materials consist primarily of poly(ethylene glycol) which is cross-linked in situ by selective conjugate addition reactions of its termini, activated with conjugate acceptors such as vinylsulfones, with peptides containing three or more cysteine residues in the form of reduced thiols. The cross-linking peptides are designed such that they are hydrolyzed by plasmin. A simple cell migration assay was developed to evaluate the material design parameters. Human fibroblasts were observed to migrate out of microliter fibrin clots into the synthetic materials in a manner dependent on the type of material and the culture conditions. Inhibiting fibrinolysis with a plasmin-insensitive substrate or with a plasmin inhibitor, [epsilon]-amino-n-caproic acid, inhibited migration. Adding growth factors, FGF-2 or PDGF-BB, that upregulate plasminogen activation increased the rate of cell migration. Decreasing the amount of RGD within the materials decreased the rate and extent of cell migration in a concentration-dependent manner. Replacing the RGD peptide with an RDG peptide decreased the amount of outgrowth.
\r\n\r\nIn a critical size calvarial defect in the rat, the synthetic materials were formed in the presence of an osteoinductive protein, rhBMP-2, and supported de novo bone formation. Materials containing a heparin-based growth factor delivery system promoted significantly more bone than materials without the delivery system. After three weeks, 94% of the defect area was covered with new bone, and the opacity of the new bone was 84% of that of neighboring, uninjured bone.
" }, { "name": "Rostovtsev, Vsevolod Vladimirovich", "degree": "PhD", "year": "2001", "title": "Reactions of Platinum(II) Complexes with Dioxygen: Progress Toward Alkane Functionalization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202014-115036901", "creators": [ { "name": { "family": "Rostovtsev", "given": "Vsevolod Vladimirovich" }, "id": "Rostovtsev-Vsevolod-Vladimirovich", "orcid": "0000-0002-1226-5909", "display_name": "Rostovtsev, Vsevolod Vladimirovich" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Stoltz", "given": "Brian M." }, "id": "Stoltz-B-M", "orcid": "0000-0001-9837-1528", "display_name": "Stoltz, Brian M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jevj-7928", "abstract": "Whereas stoichiometric activation of C-H bonds by complexes of transition metals is\r\nbecoming increasingly common, selective functionalization of alkanes remains a\r\nformidable challenge in organometallic chemistry. The recent advances in catalytic\r\nalkane functionalization by transition-metal complexes are summarized in Chapter I.
\r\n\r\nThe studies of the displacement of pentafluoropyridine in\r\n[(tmeda)Pt(CH_3)(NC_5F_5)][BAr^f_4] (1) with \u03b3- tetrafluoropicoline, a very poor nucleophile,\r\nare reported in Chapter II. The ligand substitution occurs by a dissociative interchange\r\nmechanism. This result implies that dissociative loss of pentafluoropyridine is the rate-limiting\r\nstep in the C-H activation reactions of 1.
\r\n\r\nOxidation of dimethylplatinum(II) complexes (N-N)Pt(CH_3)_2 (N-N = tmeda(1), \u03b1-diimines)\r\nby dioxygen is described in Chapter III. Mechanistic studies suggest a two-step mechanism. First, a hydroperoxoplatinum(IV) complex is formed in a reaction\r\nbetween (N-N)Pt(CH_3)_2 and dioxygen. Next, the hydroperoxy complex reacts with a\r\nsecond equivalent of (N-N)Pt(CH_3)_2 to afford the final product,\r\n(N-N)Pt(OH)(OCH_3)(CH_3)_2. The hydroperoxy intermediate,\r\n(tmeda)Pt(OOH)(OCH_3)(CH_3)_2 (2), was isolated and characterized. The reactivity of 2\r\nwith several dime thylplatinum(II) complexes is reported.
\r\n\r\nThe studies described in Chapter IV are directed toward the development of a\r\nplatinum(II)-catalyzed oxidative alkane dehydrogenation. Stoichiometric conversion of\r\nalkanes (cyclohexane, ethane) to olefins (cyclohexene, ethylene) is achieved by C-H\r\nactivation with [(N-N)Pt(CH_3)(CF_3CH_2OH)]BF_4 (1, N-N is N,N'-bis(3,5-di-t-\r\nbutylphenyl)-1,4-diazabutadiene) which results in the formation of olefin hydride\r\ncomplexes. The first step in the C-H activation reaction is formation of a platinum(II)\r\nalkyl which undergoes \u03b2-hydrogen elimination to afford the olefin hydride complex.\r\nThe cationic ethylplatinum(II) intermediate can be generated in situ by treating\r\ndiethylplatinum(II) compounds with acids. Treatment of (phen)PtEt_2 with\r\n[H(OEt_2)_2]Bar^f_4 at low temperatures resulted in the formation of a mixture of\r\n[(phen)PtEt(OEt_2)]Bar^f_4 (8) and [(phen)Pt(C_2H_4)H] Bar^f_4 (7). The cationic olefin\r\ncomplexes are unreactive toward dioxygen or hydrogen peroxide. Since the success of\r\nthe overall catalytic cycle depends on our ability to oxidize the olefin hydride\r\ncomplexes, a series of neutral olefin complexes of platinum(II) with monoanionic ligands\r\n(derivatives of pyrrole-2-carboxyaldehyde N-aryl imines) was prepared. Unfortunately,\r\nthese are also stable to oxidation.
\r\n" }, { "name": "Royea, William Joseph", "degree": "PhD", "year": "2001", "title": "Investigations of Charge-Carrier Dynamics at Semiconductor/Liquid lnterfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212014-101732487", "creators": [ { "name": { "family": "Royea", "given": "William Joseph" }, "id": "Royea-William-Joseph", "display_name": "Royea, William Joseph" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gc45-ed38", "abstract": "Theoretical and experimental investigations of charge-carrier dynamics at\r\nsemiconductor/liquid interfaces, specifically with respect to interfacial electron transfer\r\nand surface recombination, are presented.
\r\n\r\nFermi's golden rule has been used to formulate rate expressions for charge transfer\r\nof delocalized carriers in a nondegenerately doped semiconducting electrode to localized,\r\nouter-sphere redox acceptors in an electrolyte phase. The treatment allows comparison\r\nbetween charge-transfer kinetic data at metallic, semimetallic, and semiconducting\r\nelectrodes in terms of parameters such as the electronic coupling to the electrode, the\r\nattenuation of coupling with distance into the electrolyte, and the reorganization energy\r\nof the charge-transfer event. Within this framework, rate constant values expected at\r\nrepresentative semiconducting electrodes have been determined from experimental data\r\nfor charge transfer at metallic electrodes. The maximum rate constant (i.e., at optimal\r\nexoergicity) for outer-sphere processes at semiconducting electrodes is computed to be in\r\nthe range 10-17-10-16 cm4 s-1, which is in excellent agreement with prior theoretical\r\nmodels and experimental results for charge-transfer kinetics at semiconductor/liquid\r\ninterfaces.
\r\n\r\nDouble-layer corrections have been evaluated for semiconductor electrodes in both\r\ndepletion and accumulation conditions. In conjuction with the Gouy-Chapman-Stern\r\nmodel, a finite difference approach has been used to calculate potential drops at a\r\nrepresentative solid/liquid interface. Under all conditions that were simulated, the\r\ncorrection to the driving force used to evaluate the interfacial rate constant was\r\ndetermined to be less than 2% of the uncorrected interfacial rate constant.
\r\n\r\nPhotoconductivity decay lifetimes have been obtained for Si(111) in contact with\r\nsolutions of CH3OH or tetrahydrofuran containing one-electron oxidants. Silicon\r\nsurfaces in contact with electrolyte solutions having Nernstian redox potentials > 0 V vs.\r\nSCE exhibited low effective surface recombination velocities regardless of the different\r\nsurface chemistries. The formation of an inversion layer, and not a reduced density of\r\nelectrical trap sites on the surface, is shown to be responsible for the long charge-carrier\r\nlifetimes observed for these systems. In addition, a method for preparing an air-stable,\r\nlow surface recombination velocity Si surface through a two-step, chlorination/alkylation\r\nreaction is described.
" }, { "name": "Sanford, Melanie Sarah", "degree": "PhD", "year": "2001", "title": "Synthetic and Mechanistic Investigations of Ruthenium Olefin Metathesis Catalysts", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12012008-142143", "creators": [ { "name": { "family": "Sanford", "given": "Melanie Sarah" }, "id": "Sanford-Melanie-Sarah", "orcid": "0000-0001-9342-9436", "display_name": "Sanford, Melanie Sarah" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "orcid": "0000-0003-3352-4532", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q96P-VK05", "abstract": "The ruthenium-based catalysts (PCy[subscript 3])[subscript 2](Cl)[subscript 2]Ru=CHPh (1) and (IMesH[subscript 2])(PCy[subscript 3])(Cl)[subscript 2]Ru=CHPh (2) [IMesH[subscript 2] = 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene] show high olefin metathesis activity in the presence of most common functional groups and have been widely used in synthetic chemistry. This thesis describes mechanistic, structural, and synthetic studies aimed at understanding the reactivity of these complexes, and at developing new olefin metathesis catalysts with superior properties.
\r\n\r\nChapter 2 details the effects of ligand variation on the mechanism and activity of ruthenium-based olefin metathesis catalysts. A series of ruthenium complexes of the general formula (L)(PR[subscript 3])(X)[subscript 2]Ru=CHR[superscript 1] were prepared, and the influence of the ancillary ligands L,X, R, and R[superscript 1] on the rates of phosphine dissociation and initiation as well as on the overall catalytic activity was examined.
\r\n\r\nChapter 3 describes the synthesis of a series of ruthenium benzylidenes containing N-heterocyclic carbene ligands. The new complexes, of the general formula (IMesH[subscript 2])(X)[subscript m](L)[subscript n]Ru=CHPh, were prepared using a variety of synthetic methods, and the bis-pyridine adduct (IMesH[subscript 2])(Cl)[subscript 2](C[subscript 5]H[subscript 5]N)[subscript 2]Ru=CHPh served as a particularly valuable synthon in these systems. Several of these compounds were characterized by X-ray crystallography, and the barriers to benzylidene and N-heterocyclic carbene rotation were determined using [superscript 1]H NMR spectroscopy.
\r\n\r\nChapter 4 describes the preparation of a series of four-coordinate ruthenium benzylidenes that serve as analogues of the 14-electron olefin metathesis intermediate (L)(Cl)[subscript 2]Ru=CHPh. These coordinatively unsaturated species have the general formula (L)(OR)[subscript 2]Ru=CHPh, and are stabilized by sterically bulky and \u03c0-donating alkoxide ligands, such as tert-butoxide, hexafluoro-tert-butoxide, and perfluoro-tert-butoxide. The new compounds were characterized by X-ray crystallography, and their reactivity with incoming ligands, including substituted alcohols, phenols, carboxylates, and pyridine, was investigated. In addition, their olefin metathesis activities were examined in the presence and absence of HCl co-catalyst.
\r\n\r\nChapters 5 and 6 describe the synthesis and characterization of neutral and cationic tris(pyrazolyl)borate ruthenium complexes. The new complexes were characterized by NMR spectroscopy and X-ray crystallography, and their olefin metathesis activities were explored.
" }, { "name": "Starr, Jeremy Tyson", "degree": "PhD", "year": "2001", "title": "Studies Directed Toward the Synthesis of Palau'amine and Axinellamines A-D", "advisor": "Carreira, Erick Moran", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212014-142648295", "creators": [ { "name": { "family": "Starr", "given": "Jeremy Tyson" }, "id": "Starr-Jeremy-Tyson", "orcid": "0000-0001-8651-507X", "display_name": "Starr, Jeremy Tyson" } ], "advisors": [ { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "advisor", "display_name": "Carreira, Erick Moran" } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "orcid": "0000-0002-6610-4414", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/114f-cx28", "abstract": "The use of spiro [2.4]hepta-4,6-diene-1-methanol 7 as a general precursor for the\r\nsynthesis of highly functionalized cyclopentyl rings is described. Diene 7 was converted\r\nto its silyl protected 4-nitrile derivative 24 in 46% overall yield. The cyclopropyl ring of\r\n24 reacted with soft carbanionic nucleophiles to give ring opened homo-conjugate\r\naddition products 25a-h in 76-97% yield without loss of optical purity. The addition\r\nproducts could be further manipulated by selective mono-hydrogenation to give 1,2\r\nsubstituted cyclopentenes 26a-e in 85-96% yield.
\r\n\r\nDiene 7 was used as a starting material for studies directed toward the synthesis\r\nof the stereochemically dense chloro-cyclopentyl core of palau'amine 1. Two advanced\r\nintermediates 50 and 72 were synthesized. Attempts to effect intramolecular chlorine\r\ntransfer with 50 were unsuccessful. Attempted intramolecular chlorine transfer with 72\r\nled, instead, to an oxygenated species resulting from oxygen radical trapping.
\r\n\r\nThe enantioselective synthesis of the stereochemically dense chloro-cyclopenty l\r\ncore of axinellamines A-D 2-5 starting from 7 is also described. The core is synthesized\r\nin 4.6% yield over 24 steps. Nakamura's radical dehalogenative hydroxylation is applied\r\nfor the first time to a cyclopropyl carbonyl iodide to give the ring-opened product in 86%\r\nyield. Bolm's meso-anhydride desymmetrization is used to introduce asymmetry in a\r\nnorbornene intermediate. The final step is a diastereoselective intermolecular\r\nchlorination using Barton's methodology to achieve chlorine transfer in 76% yield.
\r\n" }, { "name": "Szczepankiewicz, Steven Henry", "degree": "PhD", "year": "2001", "title": "Surface Chemistry of TiO\u2082 Photocatalysts", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05232006-094537", "creators": [ { "name": { "family": "Szczepankiewicz", "given": "Steven Henry" }, "id": "Szczepankiewicz-Steven-Henry", "display_name": "Szczepankiewicz, Steven Henry" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HABJ-3T48", "abstract": "The surface chemistry of TiO\u2082 photocatalysts have been characterized by infrared spectroscopy, alcalimetric titrations, and photocatalytic reactivity. The fundamental processes governing electron transfer at the surface were investigated by inhibiting the photocatalytic reactions.
\r\n\r\nFree and trapped charge carriers in polycrystalline TiO\u2082 following bandgap irradiation are characterized by diffuse reflectance IR spectroscopy (DRIFTS). Irradiation of anatase in vacuo or in the presence of CD\u2083OD leads to decreased overall reflectance, to an absorbance at 3717 cm\u207b\u00b9, and to the decline of a 3647 cm\u207b\u00b9 band. x persists for days in vacuum or dry O\u2082 and is only bleached by the action of [O\u2082 + H\u2082O(g) + hv]. It is assigned to a Ti(III)O-H vibration ensuing electron trapping at the acidic Ti(IV)OH centers that absorb at 3647 cm\u207b\u00b9. Irradiation under O\u2082 yields a band at 3683 cm\u207b\u00b9 (Y) that corresponds to bound OH radicals. These last indefinitely in vacuo, but decay in a few hours under O\u2082. Since none of the above phenomena occur on defective TiO\u2082-x, materials obtained by thermal annealing under vacuum, photochemical damage to actual catalysts involves concurrent surface reorganization. The presence of the 3717 cm\u207b\u00b9 band is used to confirm this reorganization.
\r\n\r\nThe decreased reflectivity is due to a spectrum-wide absorption signal proportional to \u03bb1.7 (\u03bb = wavelength/\u00b5m), which indicates the presence of free conduction band electrons coupled with acoustic phonons in the lattice. Free electrons appear to decay according to saturation kinetics. The fitted parameters indicate a limited number of reversible trapping states. The concentration of these states appears to be diminished by sequential UV treatments. A broad IR absorption peak centered at 3380 cm\u207b\u00b9 is attributed to an electronic transition from an occupied surface electron trap 0.42 eV below the conduction band. The free carrier decay lifetime is lengthened as the samples are dehydrated.
\r\n\r\nElectric fields generated by photoexcited charge carriers in TiO\u2082 (anatase) produce Stark effect intensity and wavelength shifts for surface TiO-H stretching vibrations. Shallow electron-trapping states, observed as broad absorption bands above 3000 cm\u207b\u00b9, produce an apparently homogeneous electric field. Intensity changes and corresponding wavelength shifts for v(TiO-H) are proportional to the magnitude and polarity of the electric field. O\u2082 is shown to reversibly abstract electrons from shallow trapping states. These results suggest that shallow electron traps are not associated with localized structures, but rather are delocalized across the TiO\u2082 surface.
\r\n\r\nThe effect of poisoning the photocatayst is monitored during the oxidation of a phosphorous-containing organic substrate. The photoassisted oxidation of dimethyl-methyl-phosphonate (DMMP) over UV-irradiated TiO\u2082 is investigated as a simulant for warfare nerve agent detoxification. Adsorption uptake measurements are performed by MS analysis of a fine DMMP aerosol up and downstream of an adsorbant TiO\u2082 film. Photodesorption processes, gas phase intermediates and mineral products are quantified in situ by headspace GC-MS analysis of a static system. Non-volatile intermediates and products are analyzed by HPLC analysis of both aqueous and organic extractions from the Ti02 film. Adsorbed intermediates are characterized and quantified in situ by DRIFTS of TiO\u2082 powders. Specific site binding of DMMIP and catalyst poisoning are observed in the DRIFT spectra. A proposed mechanism suggests rapid detoxification of DMMP as a simulant, but extensive poisoning of the catalyst by the end products.
\r\n\r\nIn a comparative investigation of titania surface chemistry, TiO\u2082 Q particles are synthesized and characterized by transmission electron microscopy, potentiometric titration, infrared analysis, and photocatalytic reactivity. TEM images show small individual particulates of anatase about 2 nm in diameter. Potentiometric titrations confirm the presence of a highly protonated gel layer on the surface of these particles. The infrared spectra indicate that this layer is amorphous. An autocatalytic enhancement of the photocatalysts during photooxidation of methyl orange suggests that reaction intermediates cause the collapse of the hydrated gel layer into a more active surface.
\r\n\r\nTwo supplementary investigations are presented which confirm the previous results. MAS NMR data is presented which shows a paramagnetic influence from surface trapped electrons. The data also suggests localized trapping at a characteristic type of TiOH surface moiety. Theoretical calculations also confirm the band assignments presented in the previous chapters by reproducing the data with the predicted structural assignments.
" }, { "name": "Tezcan, Faik Akif", "degree": "PhD", "year": "2001", "title": "Reactions of Heme Proteins to Solutions and Crystals", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312019-135136732", "creators": [ { "name": { "family": "Tezcan", "given": "Faik Akif" }, "id": "Tezcan-Faik-Akif", "orcid": "0000-0002-4733-6500", "display_name": "Tezcan, Faik Akif" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "orcid": "0000-0002-4453-9716", "role": "member", "display_name": "Winkler, Jay Richmond" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rrqd-9v38", "abstract": "To assess the effects of heme solvation and iron ligation on reduction potentials in c-type cytochromes, we have examined the redox and ligand-binding properties of microperoxidase-8 (MP8). Methionine-, histidine- and amine-coordination to MP8 were found to account for 130, -40 and -10-mV shifts in the Fe(III/II)-potential, respectively. Our finding that reduction potentials increase with decreasing heme-surface exposure suggests that the protein matrix can further tune the reduction potential by 500 mV through water exclusion from the heme pocket.
\r\n\r\nThe 410-mV upshift in the cytochrome c (cyt c) potential as the heme cofactor is moved from a highly-solvated environment to the protein interior signals a 10-kcal/mol greater stability of the reduced form. Consequently, there exists a range of denaturant concentrations where Fe(II)-cyt c is folded and Fe(III)-cyt c is unfolded. Electron injection into the oxidized protein in this range triggers the folding reaction. Using NADH as a redox photosensitizer, cyt c folding can be initiated within 100 \u00b5s. Our results suggest that the folding of cyt c is rate-limited by ligand-substitution events on the iron center.
\r\n\r\nDue to an increased barrier to ligand substitution, folding of Co(III)-substituted cyt cis 5 orders of magnitude slower than Fe-cyt c. The slow folding kinetics of Co(III)-cyt c have allowed the convenient study of protein dynamics with a variety of spectroscopic techniques, revealing previously unresolved folding pathways involving Lys- and His-misligated populations of the unfolded molecule and extremely long-lived folding intermediates.
\r\n\r\nFactors that control electron flow between proteins are not well understood, owing to uncertainties in the relative orientations and structures of the reactants during the short time that tunneling occurs. To circumvent this ambiguity, we have measured the kinetics of electron transfer (ET) between native and Zn-substituted tuna cyt c molecules in crystals of known structure. ET rates (320 s-1 for *Zn-cyt c \u2192 Fe(III)-cyt c; 2000 s-1 for Fe(II)-cyt c \u2192 Zn-cyt c+) over a Zn-Fe distance of 24.1 \u00c5 closely match those for intraprotein ET over similar donor-acceptor separations. Our results indicate that van der Waals interactions and water mediated H-bonds provide effective electronic coupling across a protein-protein interface.
" }, { "name": "Winblade, Natalie Dawn", "degree": "PhD", "year": "2001", "title": "Blocking Adhesion to Cell and Tissue Surfaces via Steric Stabilization with Graft Copolymers Containing Poly(Ethylene Glycol) and Phenylboronic Acid", "advisor": "Hubbell, Jeffrey A.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202002-221541", "creators": [ { "name": { "family": "Winblade", "given": "Natalie Dawn" }, "id": "Winblade-Natalie-Dawn", "orcid": "0000-0003-1293-345X", "display_name": "Winblade, Natalie Dawn" } ], "advisors": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "orcid": "0000-0003-0276-5456", "role": "advisor", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "co-advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "orcid": "0000-0003-0276-5456", "role": "chair", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Hoffman", "given": "Allan S." }, "id": "Hoffman-A-S", "role": "member", "display_name": "Hoffman, Allan S." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/B47A-E319", "abstract": "Graft copolymers were designed to coat biological surfaces and thereby block subsequent adhesion and recognition events with other proteins, cells, and tissues. Inspired by polymeric steric stabilization of colloidal dispersions, the copolymers contain a backbone with affinity for biological surfaces and grafted side-chains that are resistant to adhesion of biological elements. Phenylboronic acid (PBA) moieties in the polymer backbone provided for binding, by forming reversible covalent complexes with cis-diols in oligosaccharides that are ubiquitous on cell surfaces and secreted macromolecules. The PBA moieties were conjugated to a poly-L-lysine (PLL) backbone via a secondary amine linker. Grafted poly(ethylene glycol) (PEG) side-chains provided for resistance of adhesion of proteins and cells. It was hypothesized that these PLL-g-(PEG;PBA) copolymers would spontaneously assemble on biological (e.g., cell or tissue) surfaces, where the PBA-containing backbone would bind to the surfaces and thereby anchor a dense PEG brush on the surface.
\r\n\r\nPLL-g-(PEG;PBA) copolymers were synthesized with varying degrees of PEG and PBA grafting. The pKa of the PBA groups was found to be circa 6, allowing for stronger binding at physiological pH than most PBA groups, which have pKas circa 8.8. The PLL-g-(PEG;PBA) copolymers were found to bind specifically to a mannan resin, where the PEG grafting ratio sterically controlled the binding. The copolymers coated red blood cells and blocked their agglutination by lectins and by blood group antibodies. The copolymers were also found to coat tissue culture polystyrene, adsorbed serum proteins, and extracellular matrix and to prevent the adhesion, spreading, and/or migration of rabbit lens epithelial cells on those surfaces. The copolymers displayed evidence of toxicity in vitro but no toxicity was seen when administered in vivo in models of posterior capsule opacification or peritoneal adhesion formation. PLL-g-(PEG;PBA) was found to interfere with the worsening of peritoneal adhesions following adhesiolysis. The efficacy of the copolymers was a function of the degree of PEG and PBA grafting, and PLL-g-(PEG;PBA) copolymers were found to be more effective than electrostatically-binding PLL-g-PEG copolymers. PLL-g-(PEG;PBA) copolymers have many possible clinical applications where blocking protein or cell interactions with cell, tissue, or biomaterial surfaces via a simple aqueous lavage is desired.
" }, { "name": "Wong, Chi-Kin", "degree": "PhD", "year": "2001", "title": "Spectroscopic Studies of Gas-Phase Molecular Clusters", "advisor": "Okumura, Mitchio; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012014-155631770", "creators": [ { "name": { "family": "Wong", "given": "Chi-Kin" }, "id": "Wong-Chi-Kin", "display_name": "Wong, Chi-Kin" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "co-advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/y9tk-8g51", "abstract": "Spectroscopic investigations of hydrogen-bonding and van der Waals' interactions\r\nm molecular clusters were studied by the techniques of infrared predissociation and\r\nresonance-enhanced multiphoton ionization spectroscopies (REMPI). Ab initio\r\ncalculations were applied in conjunction for data interpretation.
\r\n\r\nThe infrared predissociation spectroscopy of CN^-\u2022(H_2O)_n (n = 2 - 6) clusters was\r\nreported in the region of 2950 - 3850 cm^(-1).\r\nThe hydrogen bondings for the C-site and N-site\r\nbinding, and among the water molecules were identified for n = 2 to 4. A spectral\r\ntransition was observed for n = 5 and 6, implying that the anion was surface-bound onto\r\nthe water aggregates in larger clusters.
\r\n\r\nThe infrared predissociation spectroscopy of Br^-\u2022(NH_3) and I^-\u2022(NH_3)_n (n =1-3)\r\nclusters was reported in the region of 3050-3450 cm^(-1).\r\nFor the Br^-\u2022(NH_3) complex, a\r\ndominating ionic NH stretch appeared at 3175 cm^(-1), and the weaker free NH stretch\r\nappeared at 3348 cm^(-1). The observed spectrum was consistent to the structure in which\r\nthere was one nearly linear hydrogen bond between Br^- and the NH_3 moiety. For the I^-\r\n\u2022(NH_3) complex, five distinct IR absorption bands were observed in the spectrum. The\r\nspectrum was not consistent with basic frequency patterns of three geometries considered\r\nin the ab initio calculations - complex with one, two and three hydrogen bondings\r\nbetween I^- and the NH_3 moiety. Substantial inhomogenous broadening were displayed in\r\nthe spectra for I^-\u2022(NH_3)_n (n =2-3), suggesting the presence of multiple isomers.
\r\n\r\nThe REMPI spectroscopy of the bound 4p ^2\u041f 1/2 and ^2\u041f 3/2 states, and the\r\ndissociative 3d ^2\u03a3^+ 1/2 state in the Al\u2022Ar complex was reported. The dissociative spectrum\r\nat Al^+ channel suggested the coupling of the 4p ^2\u041f 1/2,3/2 states to the repulsive 3d ^2\u03a3^+ 1/2\r\nstate. The spin-electronic coupling was further manifested in the dissociative Al^+\r\nspectrum of the 3d ^2\u03a3^+ 1/2 state. Using the potential energy curves obtained from ab initio\r\ncalculations, a bound \u2192 continuum Franck-Condon-intensity simulation was performed\r\nand compared with the one-photon 3d ^2\u03a3^+ 1/2 profile. The agreement provided evidence\r\nfor the petturbation above the Al(3d)Ar dissociation limit, and the repulsive character of\r\nthe 3d ^2\u03a3^+ 1/2 state.
\r\n" }, { "name": "Yoder, Jeffrey Charles", "degree": "PhD", "year": "2001", "title": "Model Studies of Ziegler-Natta Olefin Polymerization Using Group 3 and Group 4 Metallocenes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072014-140228693", "creators": [ { "name": { "family": "Yoder", "given": "Jeffrey Charles" }, "id": "Yoder-Jeffrey-Charles", "display_name": "Yoder, Jeffrey Charles" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6qry-9x55", "abstract": "Evidence for the stereochemical isomerization of a variety of ansa\r\nmetallocene compounds is presented. For the scandocene allyl derivatives\r\ndescribed here, we have established that the process is promoted by a variety of\r\nsalts in both ether and hydrocarbon solvents and is not accelerated by light. A\r\nplausible mechanism based on an earlier proposal by Marks, et al., is offered as\r\nan explanation of this process. It involves coordination of anions and/or donor\r\nsolvents to the metal center with cation assistance to encourage metalcyclopentadienyl\r\nbond heterolysis, rotation about the Si-Cp bond of the\r\ndetached cyclopentadienide and recoordination of the opposite face. Our\r\nobservations in some cases of thermodynamic racemic:meso ratios under the\r\nreaction conditions commonly used for the synthesis of the metallocene\r\nchlorides suggests that the interchange is faster than metallation, such that the\r\ncomposition of the reaction mixture is determined by thermodynamic, not\r\nkinetic, control in these cases.
\r\n\r\nTwo new ansa-scandocene alkenyl compounds react with olefins resulting\r\nin the formation of \u03b73-allyl complexes. Kinetics and labeling experiments\r\nindicate a tuck-in intermediate on the reaction pathway; in this intermediate the\r\nmetal is bound to the carbon adjacent to the silyllinker in the rear of the\r\nmetallocene wedge. In contrast, reaction of permethylscandocene alkenyl\r\ncompounds with olefins results, almost exclusively, in vinylic C-H bond\r\nactivation. It is proposed that relieving transition state steric interactions\r\nbetween the cyclopentadienyl rings and the olefin by either linking the rings\r\ntogether or using a larger lanthanide metal may allow for olefin coordination,\r\nstabilizing the transition state for allylic \u03c3-bond metathesis.
\r\n\r\nA selectively isotopically labeled propylene, CH2CD(13CH3), was\r\nsynthesized and its polymerization was carried out at low concentration in\r\ntoluene solution using isospecific metallocene catalysts. Analysis of the NMR\r\nspectra (13C, 1H, and 2H) of the resultant polymers revealed that the production\r\nof stereoerrors through chain epimerization proceeds exclusively by the tertiaryalkyl\r\nmechanism. Additionally, enantiofacial inversion of the terminally\r\nunsaturated polymer chain occurs by a non-dissociative process. The\r\nimplications of these results on the mechanism of olefin polymerization with\r\nthese catalysts is discussed.
" }, { "name": "Younkin, Todd Ross", "degree": "PhD", "year": "2001", "title": "Polymerization of Functionalized Olefins with Neutral Group Ten Catalysts", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252014-100408562", "creators": [ { "name": { "family": "Younkin", "given": "Todd Ross" }, "id": "Younkin-Todd-Ross", "display_name": "Younkin, Todd Ross" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/svwr-te86", "abstract": "This thesis describes the preparation, characterization, and application of welldefined\r\nsingle-component group ten salicylaldimine complexes for the polymerization of\r\nethylene to high molecular weight materials as well as the copolymerization of ethylene\r\nand functionalized olefins. After an initial introduction to the field, Chapter 2 describes\r\nthe preparation of PPh3 complexes that contain a series of modified salicylaldimine and\r\nnaphthaldimine ligands. Such complexes were activated for polymerization by the\r\naddition of cocatalysts such as Ni(COD)2 or B(C6F5)3. As the steric demand of the ligand\r\nset increased-the molecular weight, polymerization activity, and lifetime of the catalyst\r\nwas observed to increase. In fact, complexes containing \"bulky\" ligands, such as the\r\n[Anthr,HSal] ligand (2.5), were found to be highly-active single component complexes for\r\nthe polymerization of ethylene. Model hydrido compound were prepared-allowing for a\r\nbetter understanding of both the mechanism of polymerization and one mode of\r\ndecomposition.
\r\n\r\nChapter 3 describes the effect which additives play on neutral NiII polymerization\r\ncatalysts such as 2.5. The addition of excess ethers, esters, ketones, anhydrides, alcohols,\r\nand water do not deactivate the catalysts for polymerization. However, the addition of\r\nexcess acid, thiols, and phosphines was observed to shut-down catalysis. Since excess\r\nphosphine was found to inhibit catalysis, \"phosphine-free\" complexes, such as the\r\nacetonittile complex (3.26), were prepared. The acetonitrile complex was found to be the\r\nmost active neutral polymerization catalyst prepared to date.
\r\n\r\nChapter 4 outlines the use of catalyst 2.5 and 3.26 for the preparation of linear\r\nfunctionalized copolymers containing alcohols, esters, anhydrides, and ethers.\r\nCopolymers can be prepared with \u03b3-functionalized-\u03b1-olefins, functionalized norbornenes,\r\nand functionalized tricyclononenes, with up to 30 mol% comonomer incorporation.
\r\n\r\nChapter 5 outlines the preparation of a series of PtII alkyl/olefin salicylaldimine\r\ncomplexes which serve as models for the active species in the NiII-catalyzed\r\npolymerization process. Understanding the nature of the M-olefin interaction as a the\r\nelectronic and steric properties of the salicylaldimine ligand is varied has allowed for a\r\nnumber of predictions about the design of future polymerization systems.
" }, { "name": "Zhong, Hong A.", "degree": "PhD", "year": "2001", "title": "Ancillary Ligand Effects: From Zirconium(IV)-Catalyzed Homogeneous Propylene Polymerization to Platinum(II)-Mediated C-H Bond Activation", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252014-134849293", "creators": [ { "name": { "family": "Zhong", "given": "Hong A." }, "id": "Zhong-Hong-A", "display_name": "Zhong, Hong A." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "MacMillan", "given": "David W. C." }, "id": "MacMillan-D-W-C", "orcid": "0000-0003-3352-4532", "role": "member", "display_name": "MacMillan, David W. C." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/km2k-bb61", "abstract": "A series of Cs- and C1-symmetric doubly-linked ansa-metallocenes of the general formula {1,1'-SiMe2-2,2'-E-('\u019e5-C5H2-4-R1)-(\u019e5-C5H-3',5'-(CHMe2)2)}ZrC2 (E = SiMe2 (1), SiPh2 (2), SiMe2 -SiMe2 (3); R1 = H, CHMe2, C5H9, C6H11, C6H5) has been prepared. When activated by methylaluminoxane, these are active propylene polymerization catalysts. 1 and 2 produce syndiotactic polypropylenes, and 3 produces isotactic polypropylenes. Site epimerization is the major pathway for stereoerror formation for 1 and 2. In addition, the polymer chain has slightly stronger steric interaction with the diphenylsilylene linker than with the dimethylsilylene linker. This results in more frequent site epimerization and reduced\r\nsyndiospecificity for 2 compared to 1.
\r\n\r\nC1-Symmetric ansa-zirconocenes [1,1 '-SiMe2-(C5H4)-(3-R-C5H3)]ZrCl2 (4), [1,1 '-SiMe2-(C5H4)-(2,4-R2-C5H2)]ZrCl2 (5) and [1,1 '-SiMe2-2,2 '-(SiMe2-SiMe2)-(C5H3)-( 4-R-C5H2)]ZrCl2 (6) have been prepared to probe the origin of isospecificity in 3. While 4 and 3 produce polymers with similar isospecificity, 5 and 6 give mostly hemi-isotactic-like polymers. It is proposed that the facile site epimerization via an associative pathway allows rapid equilibration of the polymer chain between the isospecific and aspecific insertion sites. This results in more frequent insertion from the isospecific site, which has a lower kinetic barrier for chain propagation. On the other hand, site epimerization for 5 and 6 is slow. This leads to mostly alternating insertion from the isospecific and aspecific sites, and consequently, a hemi-isotactic-like polymers. In comparison, site epimerization is even slower for 3, but enchainment from the aspecific site has an extremely high kinetic barrier for monomer coordination. Therefore, enchainment occurs preferentially from the isospecific site to produce isotactic polymers.
\r\n\r\nA series of cationic complexes [(ArN=CR-CR=NAr)PtMe(L)]+[BF4]+ (Ar = aryl; R = H, CH3; L = water, trifluoroethanol) has been prepared. They react smoothly with benzene at approximately room temperature in trifluoroethanol solvent to yield methane and the corresponding phenyl Pt(II) cations, via Pt(IV)-methyl-phenyl-hydride intermediates. The reaction products of methyl-substituted benzenes suggest an inherent reactivity preference for aromatic over benzylic C-H bond activation, which can however be overridden by steric effects. For the reaction of benzene with cationic Pt(II) complexes, in which the diimine ligands bear 3,5-disubstituted aryl groups at the nitrogen atoms, the rate-determining step is C-H bond activation. For the more sterically crowded analogs with 2,6-dimethyl-substituted aryl groups, benzene coordination becomes rate-determining. The more electron-rich the ligand, as reflected by the CO stretching frequency in the IR spectrum of the corresponding cationic carbonyl complex, the faster the rate of C-H bond activation. This finding, however, does not reflect the actual C-H bond activation process, but rather reflects only the relative ease of solvent molecules displacing water molecules to initiate the reaction. That is, the change in rates is mostly due to a ground state effect. Several lines of evidence suggest that associative substitution pathways operate to get the hydrocarbon substrate into, and out of, the coordination sphere; i.e., that benzene substitution proceeds by a solvent- (TFE-) assisted associative pathway.
\r\n" }, { "name": "Zhou, Weijun", "degree": "PhD", "year": "2001", "title": "Dynamics and Shear Alignment Behavior of a Model Thermotropic Liquid Crystalline Polymer", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08292008-110129", "creators": [ { "name": { "family": "Zhou", "given": "Weijun" }, "id": "Zhou-Weijun", "display_name": "Zhou, Weijun" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/dv2d-w145", "abstract": "Although liquid crystalline polymers (LCPs) emerged as important engineering materials in the early 1970s, the current level of understanding still falls short of allowing deliberate manipulation of macroscopic orientation, leading to poor control of morphology and material properties. The flow behavior of rod-like LCP solutions (lyotropic) are fairly well understood, yet little progress has been made on LCP melts (thermotropic) because of the formidable experimental difficulties with commercial thermotropes. A simple extension of the knowledge obtained from rod-like LCP solutions to thermotropic LCPs is unlikely to hold due to the enhanced molecular flexibility and intimate molecular contact in LCP melts.
\r\n\r\nThe primary concern of this thesis is therefore the flow behavior of thermotropic LCPs, with an emphasis on how flow influences orientation and morphology and how this depends on molecular structure. For this purpose we synthesized a model thermotropic LCP selected for its chemical stability, wide nematic range and optical transparency. This main-chain LCP, designated as DHMS-7,9, has alternating mesogen and spacer structure with dihydroxy-[alpha]-methylstilbene as mesogen and two different lengths of alkyl spacers (-C\u2087H\u2081\u2084- and -C\u2089H\u2081\u2088-). A range of molecular weights were prepared to probe the effects of chain flexibility (ratio of chain length of persistence length). Synthesis was scaled up to provide adequate quantities for physical studies (rheology, rheo-conoscopy and rheo-WAXS).
\r\n\r\nThe director response of a monodomain during shear flow is followed by in situ optical conoscopy using a custom-made shear cell. We observe that the director rotates opposite to the vorticity in shear for DHMS-7,9 using planar monodomain samples, demonstrating conclusively that it is flow aligning throughout its nematic temperature range. Director rotation is solely a function of applied strain, independent of shear rate, showing that the Leslie-Ericksen theory is applicable to polymeric nematics for shear rates that are low relative to their molecular relaxation. Comparisons of the observed tumbling parameter of DHMS-7,9 with predictions from available molecular models lead us to infer that molecular flexibility produces shear alignment for this class of thermotropic LCPs. To identify the effect of chain flexibility on the dynamics of this LCP, the rotational viscosity and shear viscosity were measured as functions of molecular weight. Both viscosities showed weaker sensitivity to molecular weight above a characteristic molecular weight, suggesting a crossover to semiflexible character at high molecular weight.
\r\n\r\nRheology and shear orientation behavior of DHMS-7,9 are markedly different from that of nematic lyotropic LCPs. Synchrotron WAXS measurements in steady shear show that molecular orientation is relatively high and nearly independent of shear rate. In transient shear during flow inception, flow reversal, and step up/down shear rate, neither shear stress nor orientation parameter shows multiple oscillations. Thus, both steady and transient responses of DHMS-7,9 are characteristic of flow-aligning liquid crystals, in contrast to tumbling rod-like LCPs, which show complex shear rate dependence in steady shear and oscillatory response to these transient flows.
\r\n\r\nAn interesting feature of DHMS-7,9 is the existence of a mysterious liquid crystalline phase--Phase X. The flow behavior of Phase X is completely different from that of the nematic phase. A striking flip of the orientation from the flow direction to the vorticity direction occurs below a critical shear rate. This orientational flipping is reversible in response to step changes of temperature and/or shear rate. In addition, we found that oscillatory shear flow also induces a similar type of orientational flipping. Examination of the linear viscoelastic properties as a function of orientation in Phase X suggests rheological similarity to layered fluids.
" }, { "name": "Zubris, Deanna Lynn", "degree": "PhD", "year": "2001", "title": "Investigations of the Origin of Stereocontrol in Syndiospecific Ziegler-Natta Polymerizations", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03242014-152154971", "creators": [ { "name": { "family": "Zubris", "given": "Deanna Lynn" }, "id": "Zubris-Deanna-Lynn", "orcid": "0000-0003-1003-9630", "display_name": "Zubris, Deanna Lynn" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j7gk-0s22", "abstract": "In order to expand our understanding of the mechanism of stereocontrol\r\nin syndiospecific \u03b1-olefin polymerization, a family of Cs-symmetric, ansa-group 3\r\nmetallocenes was targeted as polymerization catalysts. The syntheses of new\r\nansa-yttrocene and scandocene derivatives that employ the doubly [SiMe2]-\r\nbridged ligand array (1,2-SiMe2)2{C5H-3,5-(CHMe2)2} (where R = t-\r\nbutyl, tBuThp; where R = i-propyl, iPrThp) are described. The structures of\r\ntBuThpY(\u00b5-Cl)2K(THF)2, tBuThpSc(\u00b5-Cl)2K(Et2O)2, tBuThpYCH(SiMe3)2, Y2{\u00b52-(tBuThp)2}(\u00b52-H)2, and tBuThpSc(\u00b5-CH3)2 have been examined by\r\nsingle crystal X-ray diffraction methods. Ansa-yttrocenes and scandocenes that\r\nincorporate the singly [CPh2]-bridged ligand array (CPh2)(C5H4)(C13H8)(where\r\nC5H4 = Cp, cyclopentadienyl; where C13H8 = Flu, fluourenyl) have also been\r\nprepared. Select meallocene alkyl complexes are active single component\r\ncatalysts for homopolymerization of propylene and 1-pentene. The scandocene\r\ntetramethylaluminate complexes generate polymers with the highes molecular\r\nweights of the series. Under all conditions examined atactic polymer\r\nmicrostructures are observed, suggesting a chain-end mechanism for\r\nstereocontrol.
\r\n\r\nA series of ansa-tantalocenes have been prepared as models for Ziegler-Natta\r\npolymerization catalysts. A singly bridged ansa-tantalocene trimethyl\r\ncomplex, Me2Si(\u03b75-C5H4)2TaMe3, has been prepared and used for the synthesis\r\nof a tantalocene ethylene-methyl complex. Addition of propylene to this\r\nethylene-methyl adduct results in olefin exchange to give a mixture of endo and\r\nexo propylene isomers. Doubly-silylene bridged ansa-tantalocene complexes\r\nhave been prepared with the tBuThp ligand; a tantalocene trimethyl complex and\r\na tantalocene methylidene-methyl complex have been synthesized and\r\ncharacterized by X-ray diffraction. Thermolysis of the methylidene-methyl\r\ncomplex affords the corresponding ethylene-hydride complex. Addition of\r\neither propylene or styrene to this ethylene-hydride compound results in olefin\r\nexchange. In both cases, only one product isomer is observed. Studies of olefin\r\nexchange with ansa-tantalocene olefin-hydride and olefin-methyl complexes have\r\nprovided information about the important steric influences for olefin\r\ncoordination in Ziegler-Natta polymerization.
\r\n\r\n" }, { "name": "Bellmann, Erika", "degree": "PhD", "year": "2000", "title": "Synthesis and Characterization of Hole-Transporting and Electroluminescent Polymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012023-173457731", "creators": [ { "name": { "family": "Bellmann", "given": "Erika" }, "id": "Bellmann-Erika", "display_name": "Bellmann, Erika" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/580c-6t05", "abstract": "This thesis describes research on synthesis and characterization of electroluminescent and hole-transporting polymers for applications in organic light-emitting diodes (OLEDs). The first part of the project focuses on the synthesis of derivatives of the electroluminescent polymer poly(para-phenylenevinylene) (PPV) using ring-opening metathesis polymerization (ROMP) of substituted barrelenes. Barrelenes (a certain kind of bicyclic olefins) have been prepared through multi-step synthetic procedures, and the existing synthetic route was extended to barrelenes without electron-withdrawing groups. ROMP of barrelenes was explored because this polymerization can be living, which allows the preparation of well-defined polymeric products. A new version of a soluble PPV derivative was prepared via this route.
\r\n\r\nThe second part of the project focuses on hole-transporting (HT) polymers. A range of HT polymers were prepared via ROMP and anionic polymerization to explore the influence of different hole mobility and different ionization potential on the performance of a two-layer OLED. OLED devices were fabricated using spin-casting and vacuum vapor deposition, and were characterized in terms of current-voltage behavior and light output. A photo-crosslinkable hole transport layer was demonstrated. The HT polymers have been found to yield improved OLEDs by comparison to analogous small-molecule materials due to better film coverage and better film morphology. The device performance has been found to improve with increasing ionization potential of the hole transport polymer. An optimized device was fabricated, which showed 20 Lm/W efficiency. The best HT polymer was modified further to improve the operational stability of the device by improving the interfacial contact to the anode. A better adhesion to the conducting glass was achieved by preparing trimethoxysilane-containing copolymers via radical polymerization, and developing a procedure to cross-link these copolymers to the anode surface.
\r\n\r\nThe appendix describes a project unrelated to the general topic of materials for OLEDs. It presents a study on four chiral molybdenum-based ROMP-initiators with regard to their ability to yield highly stereoregular polymers.
" }, { "name": "Bremer, Ryan Elwood", "degree": "PhD", "year": "2000", "title": "Inhibition of DNA Major Groove Binding Proteins by Hairpin Polyamides", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08132025-181322821", "creators": [ { "name": { "family": "Bremer", "given": "Ryan Elwood" }, "id": "Bremer-Ryan-Elwood", "display_name": "Bremer, Ryan Elwood" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0rz0-ah38", "abstract": "Small molecules that bind to any predetermined DNA sequence in the human\r\ngenome are potentially useful tools for molecular biology and human medicine.\r\nPolyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) are cell\r\npermeable small molecules that bind DNA according to a set of \"pairing rules\" with\r\naffinities and specificites similar to many naturally occurring DNA binding proteins.\r\nIm/Py polyamides offer a general approach to the chemical regulation of gene expression,\r\nprovided inhibition of DNA binding for a variety of transcription factor families can be\r\nachieved. Polyamides bound in the minor groove have been shown to co-occupy the DNA\r\nhelix with proteins in the major groove. We demonstrate here that polyamides containing\r\na positively charged moiety directed to the DNA backbone can effectively inhibit DNA\r\nbinding by an exclusively major groove protein, potentially by competing with the\r\npositively charged protein side chains for contacts to the negatively charged phosphate\r\nbackbone. The requisite positive patch can be achieved with a naturally derived C-terminal\r\nArg-Pro-Arg tripeptide (Chapter 2) or a simple synthetic diaminoalkyl chain\r\ndelivered from the N-1 of a single pyrrole residue (Chapter 3). The functional repertoire\r\nof poly amides as synthetic ligands for the control of transcription factor binding has been\r\nexpanded to include proteins which bind exclusively in the major groove of DNA. The\r\nbroad targetable sequence repertoire of polyamides, coupled with the ubiquity of\r\nbackbone contacts in protein recognition of DNA, make phosphate neutralization by a\r\npositive patch a promising approach for inhibition of major groove transcription factors.\r\nOther investigations into polyamide:DNA recognition have afforded N=aminoalkylpyrrole-\r\ncontaining polyamides that offer enhanced affinity without\r\ncompromising specificity (Chapter 3), desmethylpyrrole-containing polyamides that\r\nincrease water solubility while retaining subnanomolar affinity (Chapter 4 ), and structural\r\ninsight into the lower affinities observed with Hp-containing polyamides (Chapter 5)." }, { "name": "Carlson, Matt Jeffrey", "degree": "PhD", "year": "2000", "title": "BUFF: A Biological Universal Forcefield Derived from Quantum Mechanics", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-084608026", "creators": [ { "name": { "family": "Carlson", "given": "Matt Jeffrey" }, "id": "Carlson-Matt-Jeffrey", "display_name": "Carlson, Matt Jeffrey" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5kyh-4402", "abstract": "Molecular mechanical simulations of biomolecules require an accurate potential energy function (forcefield) in order to produce meaningful results. Most current forcefields are highly parameterized in order to correctly reproduce high level theory and experiment. Increasingly, new biomolecules are designed and studied that have atypical configurations such as metal centers and nonstandard amino acids. To avoid a lengthy process to develop new parameters for each new system encountered, a generic forcefield is desired. A hierarchical approach is undertaken herein to achieve this flexibility and accuracy.\r\n\r\nBuilding upon the rule based generic forcefields UFF and Dreiding, a new biological universal forcefield, BUFF, is presented for the simulation of proteins and other biological molecules. In addition to its UFF and Dreiding based terms, the BUFF has additional hydrogen bond terms, specialized protein backbone torsions, and a process for deriving charges for amino acids that is independent of other parameterization. These additional parameters have been fit to ab initio quantum mechanical calculations carried out on model systems.\r\n\r\nValidation studies of peptide trimers demonstrate that the BUFF accurately reproduces the quantum mechanical torsional energies. Several other common, highly parameterized forcefields are also applied to the same tripeptide systems, as well as short \u03b1-helical chains and other model systems in order to make a comparison to the BUFF. These studies show that while the BUFF is universal and can be quickly deployed on new systems, such as unnatural amino acids or metal containing systems, it is also at least as accurate as other commonly employed, but highly parameterized, forcefields. The biological universal forcefield described herein is presented as complementary to the MSC forcefield derived for simulations of DNA and other nucleic acids." }, { "name": "Chirik, Paul James", "degree": "PhD", "year": "2000", "title": "Ancillary Ligand Effects on Fundamental Transformations in Metallocene Catalyzed Olefin Polymerization", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112025-205555750", "creators": [ { "name": { "family": "Chirik", "given": "Paul James" }, "id": "Chirik-Paul-James", "orcid": "0000-0001-8473-2898", "display_name": "Chirik, Paul James" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2qx2-9753", "abstract": "The preparation of a series of unlinked and ansa-zirconocene dihydride complexes from hydrogenation of the corresponding dimethyl complexes is described. In general, sterically demanding ligands promote formation of monomeric dihydride complexes. The ansa-zirconocene dihydride, meso-[Equation. See abstract in scanned thesis for details], has been characterized by X-ray diffraction. The monomeric, ansa-zirconocene, rac-[Equation. See abstract in scanned thesis for details] undergoes thermal reductive elimination of dihydrogen forming, BpZr(\u03bc2-N2)ZrBp which displays a side-on coordination of the dinitrogen fragment.
\r\n\r\nRates of olefin insertion and \u03b2-hydrogen elimination have been measured for a series of zirconocene and hafnocene dihydride and alkyl hydride complexes. In both cases, increased cyclopentadienyl substitution slows the rate of insertion or elimination, although the former is more sensitive to steric perturbations. From these studies, the transition state for olefin insertion/\u03b2-hydrogen elimination has been established. Equilibration of zirconocene isobutyl hydride complexes with the corresponding normal butyl hydrides has allowed for determination of the relative ground state energies of the two alkyl hydride metallocenes. These data in combination with the activation barriers for \u03b2-hydrogen elimination have allowed for delineation of ground and transition state effects in these processes. Likewise, ancillary ligand effects on the rate of alkyl isomerization have also been examined with a series of isotopically labeled zirconocene alkyl complexes. In general, increasing the substitution on the cyclopentadienyl rings has little effect on the rates of isomerization.
\r\n\r\nThe preparation of ansa-tantalocene olefin-hydride complexes is described. These complexes serve as models for the transition state for olefin insertion in the corresponding group IV metallocene olefin polymerization catalysts. Preparation of the Ci-symmetric ethylene hydride complex, [Equation. See abstract in scanned thesis for details] affords predominantly (-95 %) of one isomer, where the ethylene ligand is coordinated on the side of the wedge away from the isopropyl substituent. Similar results have been obtained with related tantalocene propylene-hydride and styrene-hydride complexes, the latter being characterized by X-ray diffraction. Additionally, several singly and doubly bridged tantalocene trimethyl complexes have been prepared and characterized by X-ray diffraction.
" }, { "name": "Dmochowski, Ivan Julian", "degree": "PhD", "year": "2000", "title": "Probing Cytochrome P450 with Sensitizer-Linked Substrates", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022026-212838189", "creators": [ { "name": { "family": "Dmochowski", "given": "Ivan Julian" }, "id": "Dmochowski-Ivan-Julian", "orcid": "0000-0001-7162-1347", "display_name": "Dmochowski, Ivan Julian" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/89h6-qd11", "abstract": "The covalent attachment of the photosensitizer [Ru(bpy)3]2+ to a substrate\r\nconstitutes a powerful new method for probing the steric and electronic properties of\r\nburied enzyme active sites. Particularly important targets are oxygenases (cytochromes\r\nP450) involved in drug metabolism and many disease states. The crystal structure of a\r\nP450:Ru-adamantyl complex reveals that the substrate moiety gains access to the active\r\ncenter via a deep channel and rests above the heme much like the natural substrate\r\ncamphor. This structure also identifies significant P450 conformational changes\r\nassociated with substrate binding for the first time: the channel opens via a 6-\u00c5 loop\r\nmovement. Turnover studies show that activity is not significantly diminished in the\r\nP450:Ru-adamantyl complex. Preliminary light-activated substrate turnover experiments\r\nalso show promise.
\r\n\r\nThe binding of Ru-substrates to P450 was measured by time-resolved\r\nluminescence and UV-vis assays. These molecules specifically recognize submicromolar\r\ncytochrome P450cam in the presence of other heme proteins. In the P450:Ru-substrate\r\nconjugates, energy transfer to the heme dramatically accelerates the Ru-luminescence\r\ndecay. Quantifying the fraction of quenched Ru2+* provides an accurate method for\r\ndetermining dissociation constants. In addition, for the P450:Ru-adamantyl complex,\r\nForster analysis of the energy-transfer kinetics yields a Ru-Fe distance (21 \u00c5) virtually\r\nthe same as that measured in the crystal structure. Similar analysis for other Ru-substrates\r\nof varying length shows a narrow range of Ru-Fe distances, indicating\r\nfavorable association of the {Ru(bpy)3}2+ moiety with the protein. The binding of the \u039b\r\nand \u0394 enantiomers of Ru-C9-Ad to P450 was measured, and the results, KD(\u0394/\u039b) ~2,\r\nsuggest that the bipyridyl ligands interact with aromatic residues at the mouth of the\r\nsubstrate channel. Thus, enantiospecific interactions may be exploited in the design of\r\nenzyme-metallosubstrate conjugates.
\r\n\r\nOxidative and reductive quenching of P450:[Ru-(CH2)n-substrate]2+* conjugates in\r\nsolution triggers the injection of holes and electrons from ruthenium to the heme on submillisecond\r\ntime scales. In order to accelerate electron transfer, conjugated\r\n(perfluorobiphenyl-bridged) Ru-probes were synthesized which bind P450 strongly (KD<\r\n1 \u03bcM). Photoexcitation of conjugated Ru-imidazole-P450 complexes reduces the heme\r\non submicrosecond time scales, opening new avenues for the study of short-lived enzyme\r\nintermediates.
" }, { "name": "Elder, Delwin Lerone", "degree": "PhD", "year": "2000", "title": "The Use of Well-Defined Molybdenum ROMP Initiators in the Synthesis of Fluorescent Poly(arylenevinylene) Homopolymers and Copolymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292024-221148036", "creators": [ { "name": { "family": "Elder", "given": "Delwin Lerone" }, "id": "Elder-Delwin-Lerone", "display_name": "Elder, Delwin Lerone" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/sqjn-9q60", "abstract": "We have discovered that ring-opening metathesis polymerization (ROMP\r\ncatalysts of the type Mo(CHMe2Ph)(N-2,6-C6H3i/Pr2)(OCMe(CF3)2)2 (1) may be greatly\r\nactivated by the addition of one or more equivalents of the cocatalyst HOCMe(CF3)2 (hexafluoro-t-butanol, HFB). In general, HFB increases the rate of initiation relative to\r\npropagation for the ROMP of low strain cyclic olefins. The ratio or propagation to\r\ninitiation has been measured and found to decrease by up to three orders of magnitude\r\nupon the addition of HFB to polymerizations of cyclooctene, cyclooctadiene, and 3,4,6-\r\ntrichloro-5-octyl-benzobarrelene (2) initiated by 1. With 2 we were able to measure kp\r\nand ki as well as kp/ki and found that HFB increases both kp and ki, but ki increases to a\r\ngreater degree. High strain cyclic olefins such as norbornene display no such\r\nenhancement of initiation. The mechanism of this \"alcohol effect\" is not yet well\r\nunderstood.
\r\n\r\nNew conjugated poly(1,4-naphthalenevinylene)s (PNVs) disubstituted by\r\nelectron-donating alkoxy substituents (3) have been synthesized by ROMP of new\r\ndialkoxy-benzobarrelene monomers (4) followed by aromatization with DDQ.\r\nPolymerizations were initiated with catalyst Mo(CHCMe2Ph)(N-2,6-C6H3\r\niPr2)(OCMe2(CF3))2 (5) whose performance was superior to initiator 1. This ROMP-Aromatization\r\nRoute is a mild synthesis procedure and provides polymers of controlled\r\nmolecular weight that are low in polydispersity and soluble in common organic solvents.\r\nThe wavelengths of photoluminescence of 3 are from 534-546 nm with quantum\r\nefficiencies of (5-15%).
\r\n\r\nBlock copolymers diester-PPV-block-dialkoxy-PNV (6) and dialkoxy-PNV-block-\r\nalkyl-PNV (7) and random copolymers diester-PPV-random-dialkoxy-PNV (8)\r\nhave been synthesized by the ROMP-Aromatization Route utilizing initiator 2. The\r\ndiester-PPV segments have a larger HOMO-LUMO gap than the dialkoxy-PNV segments\r\nallowing the polymer to be able to execute through-bond (non- Forster) energy transfer.\r\nUpon photoexcitation of the large band gap segments, the block copolymers 6 however\r\ndo not display energy transfer, but the block copolymer 7 and the random copolymers 8\r\ndo display moderate to efficient energy transfer. Remarkably, in the case of 8c,\r\nphotoluminescence is increased by a factor of 2 to 18%, and for 7, the efficiency is\r\nincreased by a factor of 10 to 5%. This copolymer strategy should be a general technique\r\nto increase the quantum efficiency of polyarylenevinylenes.
" }, { "name": "Elliott, Sean Joseph", "degree": "PhD", "year": "2000", "title": "The Copper Centers of Particulate Methane Monooxygenase: Differentiation of C- and E-Clusters", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292025-210442771", "creators": [ { "name": { "family": "Elliott", "given": "Sean Joseph" }, "id": "Elliott-Sean-Joseph", "orcid": "0000-0003-0096-9551", "display_name": "Elliott, Sean Joseph" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Roberts", "given": "Richard W." }, "id": "Roberts-R-W", "role": "member", "display_name": "Roberts, Richard W." } ], "option_major": [ "chemistry" ], "doi": "10.7907/be24-zt04", "abstract": "This dissertation investigates the approximately 15 copper ions of pMMO\r\nfrom M. capsulatus by a variety of spectroscopic, biochemical and molecular\r\nbiological techniques. The first chapters describe spectroscopy studies of the C- and\r\nE-clusters of the protein. The pMMO protein is prepared in a number of chemical\r\nstates which access the differentially oxidized of the C- and E-clusters. Investigation\r\nof these states by X-ray Absorption Spectroscopy (XAS) reveals unique oxidation\r\nstates of pMMO copper ions upon anaerobic preparation, and oxidation with air, pure\r\ndioxygen, or hydrocarbon suicide substrate. Structural implications for the copper\r\nions of the protein are discussed, and a model for the ability of acetylene to highly\r\noxidize pMMO is explored. The differentiation of the copper ions of pMMO is\r\nexplored by the use of proteolytic enzymes and chemical treatment with N,N,N',N'-Ethylenediamine-tetraacetic \r\nacid (EDTA), monitoring the ability of pMMO to form a\r\nCu(II)-ferrocyanide adduct upon treatment with ferricyanide and subsequent electron\r\ntransfer. Soluble, copper-binding domains are found, as well as specific centers that\r\nare buried in the transmembrane domain. The inability of an EDTA-treated\r\npreparation to regenerate a fully oxidized form of the protein indicates that the copper\r\nions bound by pMMO do interact with one via electron transfer. The ability to assess\r\nthe potential ligands of the copper ions of pMMO is determined by Electron Spin\r\nEcho Envelop Modulation (ESEEM) spectroscopy, revealing potential interactions\r\nbetween histidine residues and the enzyme active site.
\r\n\r\nSubsequent chapters probe reported characteristic of the pMMO active site,\r\nthought to be located within the PmoA sub-unit. First, the identity of potential\r\nligands for copper ions bound by the PmoA protein is assessed by a homology of\r\npmoA. Next, the role of ion in pMMO is explored by treatment with NO(g), and it is\r\nconcluded that the resulting signals in the g\u22484.0 region of the Electron Paramagnetic\r\nResonance (EPR) spectrum were due to an iron-nitrosyl adduct. The identity of the\r\niron is assigned to adventitious iron bound to pMMO. A final chapter probes the\r\noverall structure and geometry of the active site by examining the regio- and\r\nstereoselectivity of pMMO-mediated hydroxylation and epoxidation chemistry.
" }, { "name": "Gallivan, Justin Patrick", "degree": "PhD", "year": "2000", "title": "Electrostatic Interactions in Chemistry and Biology", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08252025-211023743", "creators": [ { "name": { "family": "Gallivan", "given": "Justin Patrick" }, "id": "Gallivan-Justin-Patrick", "display_name": "Gallivan, Justin Patrick" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hj9z-mp47", "abstract": "Electrostatic interactions such as hydrogen bonds, salt bridges, and cation-\u03c0 interactions\r\nplay a large role in structural biology. A major goal of this thesis is to build\r\nupon previous studies of the cation-1r interaction to further understand its role in\r\nbiological systems. Put simply, we wish to understand how, when, and why Nature\r\nuses cation-\u03c0 interactions.
\r\n\r\nWe begin by highlighting a cation-1r interaction important in the binding of acetylcholine\r\nto the nicotinic acetylcholine receptor (nAChR). By combining ab initio calculations\r\nand molecular neurobiology, we provide compelling evidence that a cation-\u03c0\r\ninteraction is a major determinant of the recognition of acetylcholine by the nAChR.
\r\n\r\nWe then ask a broader question: To what extent does Nature use cation-\u03c0 interactions\r\nwithin protein structures? By surveying the protein databank, we demonstrate\r\nthat energetically significant cation-\u03c0 interactions are quite common within protein\r\nstructures. To explain why, we ask what advantages cation-\u03c0 interactions have over\r\nother noncovalent interactions commonly found in proteins. Using quantum mechanical\r\ncalculations, we study the strengths of cation-\u03c0 interactions and salt bridges in\r\nboth water and in a range of organic solvents. The results suggest that cation-\u03c0 interactions\r\nmaintain their strength over a wide range of solvents, whereas the strength\r\nof a salt bridge is severely attenuated when it is placed in a high-dielectric solvent.
\r\n\r\nWe then turn our attention to a different type of electrostatic interaction - the interaction\r\nbetween water and hexafluorobenzene. We find that in the gas phase, water\r\nbinds to hexafluorobenzene in a geometry in which the lone pairs of electrons located\r\non the oxygen are directed towards the \u03c0-system of the aromatic. This surprising\r\nresult is easily explained using electrostatics. In addition, we present computational\r\nstudies of the triphenylene\u00b7\u00b7\u00b7perfluorotriphenylene \"supramolecular synthon.\"
\r\n\r\nFinally, we return to the nAChR. A challenge in the study of integral membrane\r\nproteins is determining their transmembrane topology. Here we present a potentially\r\ngeneral method for determining not only the transmembrane topology of a functional\r\nneuroreceptor expressed in a living cell, but also the surface accessibility of individual\r\namino acids.
" }, { "name": "Gordon, David Benjamin", "degree": "PhD", "year": "2000", "title": "Combinatorial Optimization in Computational Protein Design", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07312025-172124033", "creators": [ { "name": { "family": "Gordon", "given": "David Benjamin" }, "id": "Gordon-David-Benjamin", "display_name": "Gordon, David Benjamin" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fzxm-d394", "abstract": "The central objective of computational protein design is to develop computational\r\ntechniques for selecting amino acid sequences that fold into proteins with desired\r\nstructures and functions. The work described here is directed toward addressing issues\r\nthat arise in the development of computational methods for the design of solvent-exposed\r\nportions of beta-sheets. However, it is also demonstrated that the results of these\r\ninvestigations extend beyond specific secondary structures and in fact provide a means to\r\naddress a broad spectrum of design problems. Computational issues arise from the fact\r\nthat when constructing a representation of protein sequence space for analysis, significant\r\nconcessions must be made with respect to the physical model and the search criteria in\r\norder to ensure that the calculation remains tractable. One of the limiting factors driving\r\nthese concessions is the sheer number of combinations of amino acid identities and\r\nconfigurations that must be evaluated. We have therefore pursued the development and\r\nrefinement of high-performance combinatorial search algorithms in order to better enable\r\nimprovement of computational methods. The consequent algorithmic work consists of\r\nenhancement strategies based on combining optimization methods and instilling within\r\nthem heuristics that manifest specialized knowledge of protein design problems. The\r\nresults are significant performance enhancements for the well-established Dead-End\r\nElimination algorithm, as well as two new algorithmic approaches, dubbed Branch and\r\nTerminate and Hybrid Rotamer Optimization." }, { "name": "Griffin, Robert John", "degree": "PhD", "year": "2000", "title": "Experimental and computational studies of secondary organic aerosol formation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12222006-125228", "creators": [ { "name": { "family": "Griffin", "given": "Robert John" }, "id": "Griffin-R-J", "display_name": "Griffin, Robert John" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Dabdub", "given": "Donald" }, "id": "Dabdub-D", "role": "member", "display_name": "Dabdub, Donald" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2F9Q-1772", "abstract": "Organic species are important constituents of tropospheric particulate matter in remote, rural, and urban areas. Such aerosol can be primary (emitted in the particle phase as solids or liquids) or secondary (formed in situ as condensable vapors) in nature. Secondary organic aerosol (SOA) is formed when products resulting from the gas-phase oxidation of a parent organic species partition to the particle phase. This partitioning can occur via condensation onto existing inorganic aerosol (heterogeneous-heteromolecular nucleation), absorption into an existing organic aerosol, dissolution to the aerosol aqueous phase, or homogeneous-heteromolecular nucleation.\n\nSOA yield is defined as the amount of SOA formed per the amount of a parent organic species that is oxidized. This yield depends functionally on stoichiometric and partitioning coefficients for each of the oxidation products formed and the total amount of organic aerosol mass available to act as absorptive media. Appropriate yield parameters are developed for a series of parent organics using smog chamber experiments. The effects of parent organic structure and the oxidizing species on SOA yield are also examined during the smog chamber experiments. Such yield parameters are used to model SOA formation from the oxidation of biogenic organic species on a global and annual scale. Yield parameters can also be used to define a new concept, the incremental aerosol reactivity for parent organic species, which is a convenient way of ranking parent organics in terms of their SOA-forming potentials.\n\nEfforts to improve the simulation of SOA formation in the California Institute of Technology three-dimensional air quality model are also described. The Caltech Atmospheric Chemistry Mechanism was designed to predict concentrations of the highly functionalized secondary organic oxidation products capable of leading to SOA. A module that treats formation of SOA thermodynamically is used to predict the distribution of these products between the gas- and aerosol-phases. The new mechanism and thermodynamic module will used to simulate a smog episode that occurred in 1993 in the South Coast Air Basin of California." }, { "name": "Hung, Hui-Ming", "degree": "PhD", "year": "2000", "title": "Sonochemistry : the mechanism and the application", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09062005-085408", "creators": [ { "name": { "family": "Hung", "given": "Hui-Ming" }, "id": "Hung-H", "display_name": "Hung, Hui-Ming" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "chair", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e2xw-jv23", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe ultrasonic irradiation of chlorinated hydrocarbon and iodide in aqueous solution is studied under various physical conditions. The observed sonochemical rate constants can be analyzed to yield information about the nature of the bubbles which exist during acoustic cavitation and to determine which parameters are significant for enhancing cavitation chemistry.\n\nA significant feature of the sonolytic decomposition of chlorinated hydrocarbon is the dependence on Henry's law constant, [...]. First-order degradation rate constants, [...], for a series of chlorinated hydrocarbons vary as [...] at all frequencies ([...]), change with [...] by less than a factor of two in this range, and peak near 600 kHz for all species. The non-linear dependence of the observed rate constants on [...] indicates that rate constants are not solely determined by equilibrium parameters. Rectified diffusion contributes significantly to the composition of the vapor phase of a cavitation bubble before collapse, particularly for the less volatile substrates.\n\nThe maximum [...] production rates measured by iodine dosimetry depend on frequency, [...], and acoustic intensity in a concerted manner, e.g., the optimal frequency is 358 kHz at 83 W/L, and 205 kHz at 33 W/L. The zero-order production rate of [...] radical increases with acoustic intensity up to 248 W/L before leveling off. A temperature range of 3900 to 4300 K inside the cavitation bubble is estimated from the power dependence data at 205 and 358 kHz.\n\nThe combination of ultrasound and iron metal was used to study the degradation of carbon tetrachloride and nitrobenzene. In the coupled ultrasound and iron system, the contribution to the overall degradation rate of carbon tetrachloride by direct reaction with [...] results in an apparent rate enhancement by a factor of 40. A comparison of the first order degradation rate constants for carbon tetrachloride and nitrobenzene by [...] reduction with/without sonication revealed that the observed enhancement upon the combination of ultrasound and [...] is attributed 1) to the continuous cleaning and chemical activation of the [...] surface by the combined chemical and physical effects of acoustic cavitation, and 2) to accelerated mass transport rates of reactants to the [...] surfaces.\n\nIn addition, a new advanced oxidation process, combination of ultrasound and ozone, was developed to investigate the decomposition of methyl tert-butyl ether (MTBE). The faster rates of MTBE degradation in actual groundwaters by ultrasound/O3 systems are most likely due to the fact that ozone is more effectively converted to hydroxyl radical in high alkalinity groundwater, and that the carbonate radical anion, which is formed from the oxidation of bicarbonate by hydroxyl radical, reacts further with MTBE by a hydrogen-atom abstraction pathway.\n" }, { "name": "Kirkland, Thomas Andrew", "degree": "PhD", "year": "2000", "title": "Expanding the Applications of Transition Metal Alkylidenes and Alkylidynes to Organic Synthesis", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292024-181421142", "creators": [ { "name": { "family": "Kirkland", "given": "Thomas Andrew" }, "id": "Kirkland-Thomas-Andrew", "display_name": "Kirkland, Thomas Andrew" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w770-7r65", "abstract": "The application of olefin and acetylene metathesis to organic synthesis has\r\nincreased greatly since its introduction. The research in this thesis describes the Ring-Closing\r\nMetathesis (RCM) of substituted olefins and enynes, the metathesis of internal\r\nacyclic olefins and the conversion of acid chlorides to acetylenes with tungsten\r\nalkylidynes.
\r\n\r\nIn Chapter 1, the activity of ruthenium alkylidenes and molybdenum alkylidenes\r\nfor the RCM of dienes containing gem-disubstituted olefins was investigated. Dienes\r\nwith sterically-demanding and/or electron-withdrawing substituents were cyclized\r\nsuccessfully with only the molybdenum alkylidene. Dienes with allylic functional groups\r\nyielded functionalized cyclic olefins when treated with either alkylidene.
\r\n\r\nIn Chapter 2 the cyclization of enyne and endiyne substrates using ruthenium\r\nalkylidenes was discussed. The effects of ring size and methyl substitution on the\r\nconversion were determined. A mechanism in which the alkylidene reacts with the olefin\r\nfirst, followed by an intramolecular reaction with the acetylene on an enyne substrate is\r\ndescribed.
\r\n\r\nThe RCM of acyclic dienes containing vicinally substituted olefins was described\r\nin Chapter 3. Water-soluble ruthenium alkylidenes did not cyclize \u03b1,\u03c9-dienes due to the\r\ninstability of the resulting methylidene. The incorporation of a phenyl substituent\r\nresulted in nearly quantitative cyclization. RCM of a water-soluble diene has been\r\nachieved in aqueous solution using this methodology. This methodology has also been\r\nsuccessfully applied to increase RCM yields in organic solvents.
\r\n\r\nThe stereoselectivity of metathesis of acyclic olefins was investigated for several\r\nruthenium alkylidenes in Chapter 4. This was primarily done using cis-2-pentene\r\nmetathesis. Data from cis-2-pentene metathesis was also used to determine relative\r\nmetathesis rates for various alkylidenes and reaction conditions. An alkylidene bearing\r\ntricyclopentyl phosphines (13) was significantly more cis selective than one with\r\ntricyclohexyl phosphines (8). Alkylidene 8 was moderately cis selective for cis-2-pentene \r\nmetathesis and slightly cis selective for trans-2-pentene metathesis.
\r\n\r\nAn investigation into the conversion of acid chlorides to substituted acetylenes\r\nusing tungsten alkylidynes is discussed in Chapter 5. A new route to DIPP tungsten\r\nalkylidynes is described. Several aromatic acid chlorides were converted into acetylenes\r\nusing these alkylidynes in good yields. Finally, attempts at the synthesis of W2(DIPP)6\r\nare described.
" }, { "name": "Kossakovski, Dmitri A.", "degree": "PhD", "year": "2000", "title": "Scanning probe chemical and topographical microanalysis", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02272009-085501", "creators": [ { "name": { "family": "Kossakovski", "given": "Dmitri A." }, "id": "Kossakovski-D-A", "display_name": "Kossakovski, Dmitri A." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/at5p-pe62", "abstract": "The last decade has seen a rapid rise of Scanning Probe Microscopy, SPM, as a prominent and versatile approach for surface studies. SPM instruments are differentiated from the beam-based ones by the fact that they use solid proximal probes for localized analysis. The most commonly used SPM methodology is Atomic Force Microscopy, AFM. In its basic implementation, AFM provides topographical information with nanometer resolution. The most common modifications allow the magnetic, electrostatic, and specific chemical environment to be examined. However, there is no direct way today to perform general chemical analysis with AFM probes.\n\nNear-field Scanning Optical Microscopy, NSOM, is another variation of SPM where sharp tapered optical fibers serve dual purposes, being proximal probes of sample topography, and providing the means for localized light delivery for optical studies with sub-wavelength spatial resolution. Again, NSOM itself does not have a general chemical contrast capability. However, the capability to deliver light to localized area opens the way to a multitude of experiments that can be devised using different aspects of light interaction with the sample.\n\nThis thesis demonstrates several approaches for combined topographical and chemical investigations. Infrared spectroscopy is a sensitive molecular analysis tool. Without scanning proximal probe, IR microscopy has very poor spatial resolution. Enabling methodology for probe fabrication for Near-field Scanning Infrared Microscopy, NSIM, is presented.\n\nThe efforts in combining NSOM with mass spectrometry, which is probably the most general chemical analysis tool, are outlined. We have demonstrated the possibility of simultaneous topographical and molecular imaging.\n\nAnother variation of chemical imaging is the combination of SPM and Laser Induced Breakdown Spectroscopy, LIBS. In this method the elemental composition of samples is obtained by analyzing optical emissions from transient plasma plumes formed by intense laser pulses delivered through fiber probes. We have demonstrated the feasibility of this approach. The instrument that we have developed is an attractive complementary tool for established methods of spatial elemental analysis, such as X-ray Fluorescence. Among its attractive features are operation in ambient conditions, minimal requirements for sample preparation, and ease of use.\n" }, { "name": "Kumaraswamy, Guruswamy", "degree": "PhD", "year": "2000", "title": "The effect of flow history on the crystallization of semicrystalline polymers", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262005-074935", "creators": [ { "name": { "family": "Kumaraswamy", "given": "Guruswamy" }, "id": "Kumaraswamy-G", "display_name": "Kumaraswamy, Guruswamy" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8SJ5-HM09", "abstract": "Semicrystalline polymers constitute well over half of all the polymers produced worldwide. Their material properties depend sensitively on the thermal and flow history experienced during processing which strongly influences the kinetics of phase change and the morphology of the final crystalline microstructure. Therefore, it is of considerable interest to understand the mechanisms of flow effects on the rate and geometry of nucleation and crystal growth.\r\n\r\nMicrostructural development under the influence of flow is controlled by the interplay between melt relaxation processes and crystallization processes: the thermodynamic and kinetic aspects give rise to rich physics that are not well understood. This thesis elucidates key fundamentals of this process. We develop novel instrumentation that improves over prior approaches by examining the development of order at all the length scales of interest (in-situ rheo-optics, synchrotron small angle X-ray scattering (SAXS), and wide angle X-ray diffraction (WAXD), and ex-situ electron and optical microscopy); and by reducing the sample requirement by about three orders of magnitude, opening the way to study of model materials. We investigate a polydisperse, commercial Ziegler-Natta isotactic polypropylene (iPP) using the short term shearing protocol pioneered by the group of Janeschitz-Kriegl which imposes a well defined thermal and flow history on the polymer.\r\n\r\nRheo-optical investigations reveal that imposition of brief intervals of shear (less than a thousandth of the quiescent crystallization time) reduces the crystallization time by two orders of magnitude at a crystallization temperature of 141\u00b0C. Above a critical value of the shear stress, there is a transition to highly oriented growth with increase in shearing duration. This transition is correlated with changes in the transient behavior during flow and the semicrystalline morphology observed exsitu. During flow, we observe the generation of long-lived, highly oriented structures (evident in the transient birefringence) under all conditions that induce subsequent growth of highly oriented crystallites. In turn, the development of oriented crystallites observed in-situ after cessation of flow correlates with development of a \"skin-core\" morphology observed ex-situ.\r\n\r\nThe transient structures that develop during flow are identified as oriented [alpha]-phase crystals by WAXD, and show an unexpected temperature dependence for their time of formation: with increase in temperature, they occur at shorter times after startup of flow. This very unusual temperature dependence is strikingly similar to that for rheological processes, and is in contrast to the exponential increase expected for crystallization time-scales. Thus, the transition to anisotropic nucleation in polymers subjected to flow follows a non-classical kinetic pathway controlled by the formation of a transient, highly oriented metastable melt state.\r\n\r\nIn-situ synchrotron SAXS and WAXD reveal that for shearing conditions that lead to anisotropic morphologies, crystals that are highly oriented in the flow direction develop during shear, templating the formation of crystallites after flow cessation. In the densely nucleated skin regions, ex-situ TEM shows lamellae growing radially from oriented central \"shish\" structures until they impinge to form the \"shish-kebab\" or row-nucleated structures. Under milder shear conditions, the rate of crystallization is gradual compared to strong shearing, and less oriented morphologies develop. Interestingly the ratio of parent to the crosshatched, epitaxial daughter lamellae for the oriented crystallites increases with increase in shearing time, imposed wall shear stress and temperature.\r\n\r\nOur data suggests a mechanistic model for shear-enhanced crystallization: the rheologically-controlled formation of a critical anisotropic distribution of chain segments in the melt upon imposition of flow nucleates oriented crystallites. For intense shearing conditions, these line-nuclei are long and dense. Row nucleated structures develop from these line nuclei as lamellae grow radially to form fully impinged structures. For milder shearing conditions, lower nucleation densities lead to the development of less oriented structures.\r\n" }, { "name": "Mahmoudi Zarandi, Mehrdad", "degree": "PhD", "year": "2000", "title": "Steady and Pulsatile Flow in Curved Vessels", "advisor": "Gharib, Morteza", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232005-081558", "creators": [ { "name": { "family": "Mahmoudi Zarandi", "given": "Mehrdad" }, "id": "Mahmoudi-Zarandi-M", "display_name": "Mahmoudi Zarandi, Mehrdad" } ], "advisors": [ { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "advisor", "display_name": "Gharib, Morteza" } ], "committee": [ { "name": { "family": "Gharib", "given": "Morteza" }, "id": "Gharib-M", "orcid": "0000-0003-0754-4193", "role": "chair", "display_name": "Gharib, Morteza" }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ERAB-MJ26", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAn experimental investigation is carried out on the nature of secondary flow patterns in a curved vessel. This study concentrates on the role of the upstream spatial boundary conditions and the time-periodicity of the formation of the secondary flow patterns in curved vessels. Four sets of studies are made. In the first set, steady flow is compared to a pulsatile flow simulating the physiological conditions in the human aorta. To study the effect of spatial upstream boundary conditions, we investigated the effect of an upstream constriction, which represents the actual physiological conditions in the human aorta. All in vitro studies are carried out in models with dimensions close to those of the human aorta and with the Reynolds number (1400 < Re < 7000), Dean number (1470 < De < 7300) and Womersley number (8.6 < [...] < 12.6) all in a range close to the physiological values. The technique of Digital Particle Image Velocimetry is used to measure instantaneous and average flow fields.\r\n\r\nIn the first stage of this research, an orifice with a stenosis ratio of ~3 = 80% is used to simulate the upstream constriction and study its effect on the secondary flow patterns. It is found that the existence of the upstream constriction profoundly changes the nature of the secondary flow pattern. In the presence of the upstream constriction, the double circulation pattern of Dean flow is substituted with a single circulation pattern.\r\n\r\nNext, to investigate where the transition from one pattern to the other occurs, similar sets of experiments are carried out with constrictions of different sizes corresponding to stenosis ratios of, [...] = 65% and [...] = 88%. In addition, to investigate the sense of rotation for the single circulation pattern, an orifice with an asymmetric opening mounted at different angular positions is used.\r\n\r\nThe comparison of the secondary flow patterns for steady versus pulsatile flow revealed that the flow pattern does not change its main structure due to the time-periodicity of the flow. However, the pulsatile flow in general shows secondary flow rates greater than the steady flow.\r\n\r\nOn the other hand, the spatial boundary conditions are found to be central in determining the secondary flow patterns. First, the presence of an upstream constriction or stenosis ratio of [...] = 65% will result in a single circulation pattern. Therefore, the transition between the double circulation pattern of the non-constrained flow and the single circulation pattern occur at constrictions less than [...] = 65%. Secondary flow velocities and shear rate along the vessel wall are much higher for the flow with an upstream constriction than those for the flow without an upstream constriction. In the presence of an upstream constriction, the axial velocity and secondary flow maximum velocity are of the same order of magnitude.\r\n\r\nThe results of the experiments with the asymmetric orifice show that the sense of rotation depends on the position of the upstream opening with respect to the central axis of the vessel. The clinical data show that the aortic valve opening, even at the full open stage, is less than the maximum diameter of the sinus of valsalva at the base of the human aorta by at least 30% which is equivalent to a stenosis ratio of [...] = 51%. Therefore, our results are important in the understanding of the nature of shear stress development along the vessel walls and in the study of the radial distribution of blood cells in a secondary flow field. Similarly, for industrial application these results are important for the assessment of the transport properties in coiled heat exchangers or fluid-fluid absorption systems. In order to investigate the spatial condition which determines the sense of rotation in single-circulation patterns, a series of experiments were carried out changing the position of orifice opening in [...] increments with respect to anterior-posterior wall axis. These results strongly support the conjecture that the incoming jet impingement on the vessel wall is redirected by the local curvature of the vessel wall into a helical pattern which overcomes the Dean's flow and causes the single-circulation patterns.\r\n\r\nTo summarize, three distinct secondary flow patterns are observed in our experimental study. The first one is the known Dean flow, which is a double-circulation pattern. The second and third patterns, which are discovered for the first time, are the clockwise and counterclockwise single-circulation patterns. The transition from one pattern to another is dependent on the spatial boundary conditions and is independent of the temporal boundary conditions. The secondary flow velocity gradient and hence its shear stress is comparable to the axial flow velocity gradient and shear stress in the single-circulation pattern. For the Dean flow or double-circulation secondary flow pattern, shear stress values are much less than those for the axial flow. This finding can greatly contribute to our understanding of blood flow-related pathology. In addition, the position of the upstream orifice opening with respect to the anterior-posterior vessel wall is an important factor in the design of artificial aortic valves. The dependence of the sense of the rotation of single-circulation patterns on the relative position of orifice opening with respect to the anterior-posterior vessel wall axis suggests that the out of plane curvature of aorta may play an important role in the re-direction of the incoming jet in the arch." }, { "name": "Miller, Stephen Albert", "degree": "PhD", "year": "2000", "title": "Metallocene-mediated olefin polymerization : the effects of distal ligand perturbations on polymer stereochemistry", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05172004-054229", "creators": [ { "name": { "family": "Miller", "given": "Stephen Albert" }, "id": "Miller-S-A", "display_name": "Miller, Stephen Albert" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/51r0-km07", "abstract": "New group IV compounds containing a 9-dialkylaminofluorenide ligand have been prepared. Their properties and reactivity have been investigated. For example, single crystal X-ray analysis of the metallocene (9-(N,N-dimethylamino)fluorenyl)2ZrCl2 (4) reveals a bonding mode that includes a zirconium-nitrogen bond. In combination with methylaluminoxane (MAO), several aminofluorenide complexes afford atactic polypropylene.\n\nA statistical model has been developed that quantifies the unidirectional site epimerization probability, e, for singly- and doubly-bridged C1- symmetric metallocene polymerization catalysts. The unidirectional site epimerization model allows deconvolution of the site sequence probability and the stereochemical probability for producing a given pentad.\n\nHighly stereoregular syndiotactic polypropylene is obtained with the catalyst systems Ph2C(Oct)(C5H4)ZrCl2/MAO (8/MAO) (Oct = octamethyloctahydrodibenzofluorenyl, C-29H36) and Me2C(Oct)(C5H4)ZrCl2/MAO (12/MAO). Melting temperatures as high as 153?C or 154?C are found for the thermally quenched polymers. Distal ligand perturbations are demonstrated to have a dramatic effect on polymer stereochemistry.\n\nPolypropylenes that are isotactic-hemiisotactic or syndiotactic-hemiisotactic can be made with proper R substituent selection in the catalyst system Me2C(Flu)(3-R-C5H3)ZrCl2/MAO or Me2C(Oct)(3-R-C5H3)ZrCl2/MAO, where Flu = fluorenyl (C13H8). The prepared polymers have been subjected to a statistical model which suggests that the metallocenes have one highly selective site (99%) and one site of variable selectivity which is highly dependent on the nature of the R substituent and whether the metallocene contains the Flu or Oct ligand.\n\nControl of the tacticity of isotactic-hemiisotactic polypropylene, as quantified by the parameter a, is achieved by proper R substituent selection in the catalyst system R'2C(3-R-C5H3)(C13H8)MCl2/MAO. For R = 2-adamantyl, R' = Ph, and M = Zr or Hf, a is approximately 0.60 and the polypropylene obtained is elastomeric. Its properties are rationalized by the statistical existence of isotactic stereoblocks among an otherwise amorphous hemiisotactic medium.\n\nFor the C1-symmetric polymerization catalyst Me2C(3-t-butyl-C5H3)(9-C13H8)ZrCl2/MAO, evidence gathered here supports an alternating mechanism in which both sites of the metallocene wedge are utilized for monomer insertion. For an Oct-containing catalyst system with a cyclopentadienyl substituent of R = 2-methyl-2-adamantyl, unprecedentedly high isotacticity (>99% [mmmm]) is observed for a fluorenyl-based metallocene catalyst. Melting temperatures for such isotactic polymers can be as high as 167?C (Tp = 0?C)." }, { "name": "Morgan, Chantal Smith", "degree": "PhD", "year": "2000", "title": "Full Sequence Design of an Alpha-Helical Protein and Investigation of the Importance of Helix Dipole and Capping Effects in Helical Protein Design", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04092019-114920250", "creators": [ { "name": { "family": "Morgan", "given": "Chantal Smith" }, "id": "Morgan-Chantal-Smith", "display_name": "Morgan, Chantal Smith" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "chair", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8wn3-cv27", "abstract": "Our goal is an objective, quantitative design algorithm based on the\r\nphysical chemical forces which determine protein structure and stability. To\r\nthis end, we have developed a cyclical protein design strategy which utilizes\r\ntheory, computation, and experimentation using a variety of protein systems.\r\nWe address the inverse folding problem using a protein design algorithm\r\nwhich objectively predicts protein sequences which are compatible with a\r\ngiven fold.
\r\n\r\nOur protein design methodology was developed using a variety of\r\nproteins, and therefore should be generalizable to many folds and motifs. To\r\ntest the generalizability and expand the size of proteins we have designed,\r\nengrailed homeodomain (enh), a 51-residue helix-turn-helix motif, was used\r\nas a target motif.
\r\n\r\nA series of design calculations and experiments on the thirty surface\r\npositions of enh were performed to probe the importance of the helix dipole\r\nand capping effects in protein design. Rules for which types of residues were\r\nallowed at the helix termini were introduced systematically, resulting in\r\nprogressively more stable proteins. The first design in the series, which had\r\nno considerations for the helix dipole or capping effects, was shown to have\r\nthe same thermal stability as wild-type enh and the protein with the most\r\nstringent rules has a Tm of 75 \u00b0C, 32\u00b0 higher than wild-type and the first\r\ndesign. Therefore, helix dipole and capping effects have a large impact on\r\nour ability to design stable proteins. The ten core residues of enh were\r\nincluded in the design calculation. The resulting protein, a 29-fold mutant of\r\nwild-type, has a Tm of 81 \u00b0C.
\r\n\r\nThe full sequence design of enh was computed stepwise. The eleven\r\nboundary residues were designed in the context of the surface-core design.\r\nThe resulting protein, a 39-fold mutant of wild-type enh, has a melting\r\ntemperature of 114 \u00b0C and is 4.7 kcal/mol more stable than wild-type. The\r\nstructure of the boundary-surface-core design was solved by NMR\r\ntechniques and found to be in excellent agreement with the target structure.\r\nThe top 10 structure have a backbone root-mean-square standard deviation of\r\n0.45 \u00c5 and the root-mean-square standard deviation between the model\r\nstructure and experimental backbones is 1.25 \u00c5.
\r\n\r\nThe side chain selection algorithm was also extended to the design of\r\npeptides to bind tightly to MHC class I proteins. A circular dichroism\r\nspectrometry assay was developed to determine the peptide dissociation\r\nconstants. Three designed peptides were bound more tightly to the MHC\r\nclass I molecule H-2Kd than known peptides. In addition, an investigation of\r\nthe removal of disulfide bonds from toxin folds is discussed.
\r\n\r\n" }, { "name": "Ponce, Adrian", "degree": "PhD", "year": "2000", "title": "Electron tunneling in proteins and water", "advisor": "Gray, Harry B.; Winkler, Jay Richmond", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062014-082923705", "creators": [ { "name": { "family": "Ponce", "given": "Adrian" }, "id": "Ponce-A", "display_name": "Ponce, Adrian" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "co-advisor", "display_name": "Winkler, Jay Richmond" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/deva-c162", "abstract": "The subject of this thesis is electronic coupling in donor-bridge-acceptor systems. In Chapter 2, ET properties of cyanide-bridged dinuclear ruthenium complexes were investigated. The strong interaction between the mixed-valent ruthenium centers leads to intense metal-to-metal charge transfer bands (MMCT). Hush analysis of the MMCT absorption bands yields the electronic-coupling strength between the metal centers (H_(AB)) and the total reorganization energy (\u03bb). Comparison of ET kinetics to calculated rates shows that classical ET models fail to account for the observed kinetics and nuclear tunneling must be considered.
\r\n\r\nIn Chapter 3, ET rates were measured in four ruthenium-modified highpotential iron-sulfur proteins (HiPIP), which were modified at position His50, His81, His42 and His18, respectively. ET kinetics for the His50 and His81 mutants are a factor of 300 different, while the donor-acceptor separation is nearly identical. PATHWAY calculations corroborate these measurements and highlight the importance of structural detail of the intervening protein matrix.
\r\n\r\nIn Chapter 4, the distance dependence of ET through water bridges was measured. Photoinduced ET measurements in aqueous glasses at 77 K show that water is a poor medium for ET. Luminescence decay and quantum yield data were analyzed in the context of a quenching model that accounts for the exponential distance dependence of ET, the distance distribution of donors and acceptors embedded in the glass and the excluded volumes generated by the finite sizes of the donors and acceptors.
\r\n\r\nIn Chapter 5, the pH-dependent excited state dynamics of ruthenium-modified amino acids were measured. The [Ru(bpy)_(3)] ^(2+) chromophore was linked to amino acids via an amide linkage. Protonation of the amide oxygen effectively quenches the excited state. In addition. time-resolved and steady-state luminescence data reveal that nonradiative rates are very sensitive to the protonation state and the structure of the amino acid moiety.
\r\n\r\n" }, { "name": "Sakiyama-Elbert, Shelly Elese", "degree": "PhD", "year": "2000", "title": "Biofunctional polymers for the controlled release of growth factors in the peripheral nervous system", "advisor": "Hubbell, Jeffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08112006-152417", "creators": [ { "name": { "family": "Sakiyama-Elbert", "given": "Shelly Elese" }, "id": "Sakiyama-Elbert-S-E", "display_name": "Sakiyama-Elbert, Shelly Elese" } ], "advisors": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "advisor", "display_name": "Hubbell, Jeffrey A." } ], "committee": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "chair", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "role": "member", "display_name": "Fraser, Scott E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/0k5s-vf32", "abstract": "Fibrin is the natural biomaterial of nerve regeneration. Fibrin possesses the ability to promote cell adhesion and can be degraded locally by cell-regulated proteases. However, fibrin lacks sufficient neuroinductive character to promote nerve regeneration across large gaps. A previously developed method for the incorporation of peptides via the transglutaminase activity of factor XIIIa was used to immobilize cell adhesion sites and growth factors within fibrin matrices that could serve as potential therapeutics for peripheral nerve regeneration.\n\nHeparin-binding domains from several proteins have been shown to promote neurite extension on surfaces. Four different heparin-binding domains were immobilized within fibrin matrices using factor XIIIa and all four domains were found to enhance three-dimensional neurite extension through fibrin. The ability of these domains to enhance neurite extension was found to correlate positively with their relative heparin-binding affinity.\n\nProlonged release of exogenous growth factors over the duration of nerve regeneration could potentially enhance regeneration. Two delivery systems were developed to provide controlled release of exogenous growth factors, where the rate of release could be regulated by cellular activity rather than by diffusion. The first system developed was designed to mimic the ability of the extracellular matrix to sequester heparin-binding growth factors based on interactions with heparin sulfate proteoglycans. It was hypothesized that by immobilizing a high excess of heparin sites within fibrin, diffusion of growth factors from the matrix could be slowed, and this would allow release to be dominated by cell-regulated matrix degradation. The ability of such systems to immobilize growth factors and release them in an active form was assayed using neurite extension from dorsal root ganglia (DRGs).\n\nA second method of delivery was developed consisting of recombinantly expressed nerve growth factor (NGF) fusion proteins containing an exogenous crosslinking substrate. A plasmin-degradable linker was placed between the crosslinking substrate and the NGF domain. These fusion proteins could be immobilized in fibrin using factor XIIIa and released in a native form by plasmin cleavage. Immobilized NGF fusion proteins were found to enhance neurite extension from DRGs within fibrin matrices versus similar concentrations of native NGF in the medium.\n" }, { "name": "Scholl, Matthias", "degree": "PhD", "year": "2000", "title": "Expanding the Scope of Ruthenium-Based Olefin Metathesis Catalysts", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11222019-095315401", "creators": [ { "name": { "family": "Scholl", "given": "Matthias" }, "id": "Scholl-Matthias", "display_name": "Scholl, Matthias" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Peters", "given": "Jonas C." }, "id": "Peters-J-C", "role": "member", "display_name": "Peters, Jonas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/55x3-h359", "abstract": "The development of well-defined ruthenium alkylidene (PCy\u2083)\u2082Cl\u2082Ru=CHPh brought about a revolution in the area of olefin metathesis. The objective of the work presented here is to expand the scope of ruthenium-based olefin metathesis catalysts such as (PCy\u2083)\u2082Cl\u2082Ru=CHPh through the development of novel synthetic organic methods for ring-closing metathesis as well as through modification of the ligand sphere of the ruthenium complexes.
\r\n\r\nChapter 2 describes the application of ruthenium alkylidenes to the catalysis of polycyclization reactions. Several acyclic precursors have been synthesized and reacted with (PCy\u2083)\u2082Cl\u2082Ru=CHPh. These precursors vary in topology and contain acetylenic and/or cycloolefinic metathesis relays. The cyclization reactions proceed in good yields to produce polycyclic polyenes.
\r\n\r\nChapter 3 focuses on the synthesis of racemic and enantiopure targets containing the 6,8-dioxabicycIo [3.2.1]octane skeleton using an intramolecular ruthenium-catalyzed ring-closing metathesis reaction as the key step. The natural product frontalin is synthesized in racemic and enantiopure forms and in excellent yields using this methodology.
\r\n\r\nChapter 4 outlines the preparation of a novel imidazolylidene-substituted ruthenium-based complex starting from (PCy\u2083)\u2082RuCl\u2082(=CHPh). The N-heterocyclic carbene-substituted olefin metathesis initiator exhibits increased ring-closing metathesis activity at elevated temperature compared to that of the parent complex (PCy\u2083)\u2082Cl\u2082Ru(=CHPh). Di-, tri-, and tetra-substituted cycloolefins are successfully prepared from corresponding diene precursors in moderate to excellent yields.
\r\n\r\nChapter 5 describes the preparation of a new family of 1,3-dimesityl-4,5-dihydroimidazol-2-ylidene-substituted ruthenium-based complexes. These air and water tolerant systems exhibit an increased ring-closing metathesis activity at elevated temperature when compared to that of the parent complex (PCy\u2083)\u2082Cl\u2082Ru(=CHPh) as well as to the complexes disclosed previously in Chapter 4. In many instances the activity of these new complexes also rivals or exceeds that of the alkoxy-imido molybdenum-based olefin metathesis catalysts. Applications of chiral N-heterocyclic carbene ruthenium complexes to asymmetric ring-closing metathesis are also briefly discussed.
\r\n\r\nFinally, the synthesis of the Schiff base-substituted ruthenium carbene complexes on a solid support is described in Chapter 6. The activities of the supported complexes are compared to those of their unsupported counterparts. The newly prepared systems are found to be highly stable to air, moisture, and temperature, and exhibit increased catalytic activity in acidic media.
" }, { "name": "Shogren-Knaak, Michael Aaron", "degree": "PhD", "year": "2000", "title": "Incorporating Function into \u03b2\u03b2\u03b1-Motif Peptide Scaffolds", "advisor": "Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechTHESIS:09042025-153842319", "creators": [ { "name": { "family": "Shogren-Knaak", "given": "Michael Aaron" }, "id": "Shogren-Knaak-Michael-Aaron", "orcid": "0000-0001-6526-3977", "display_name": "Shogren-Knaak, Michael Aaron" } ], "advisors": [ { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "orcid": "0000-0002-5749-7869", "role": "advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "orcid": "0000-0002-5749-7869", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wg2w-q908", "abstract": "The generation of functional biomolecules constitutes an important and\r\nchallenging goal in bioorganic chemistry. Efforts to incorporate chemical\r\nfunctionality into a \u03b2\u03b2\u03b1-motif (BBA) peptide scaffold are presented. In the course\r\nof this work we have utilized this system to help determine to what extent folded\r\npeptide scaffolds can support chemical function, which strategies are best suited\r\nto the discovery of functional peptides, and what can be learned about biological\r\ncatalysis. To address these issues several different strategies involving the BBA\r\npeptide scaffold have been explored.
\r\n\r\nInitial efforts focused on using the BBA peptide scaffold to modulate the\r\nreactivity of a non-natural pyridoxamine-associated amino acid (Pam). The Pam\r\nresidue was incorporated at three different positions in the BBA peptide, and\r\ndifferent potential general acid and general base residues were included. These\r\npeptides, BP1-BP6, showed improved transamination rates and stereoselectivity\r\nrelative to a model pyridoxamine compound. Additionally, one peptide, BPS,\r\nmaintained many of the secondary and super-secondary structural features of\r\nthe BBA peptide scaffold. A second generation of Pam-containing peptides,\r\npeptides CBP01-CBP18, was constructed based on BPS to investigate the effects\r\nof systematic amino acid changes in the vicinity of the pyridoxamine\r\nfunctionality. These peptides also exhibited enhanced rates of transamination\r\nand stereoselectivity and showed clear trends in stereoselectivity as a function of\r\nthe amino acid substitutions. Finally, peptide systems utilizing other\r\nmechanisms of influencing pyridoxamine-mediated transamination were\r\ninvestigated.
\r\n\r\nSubsequent work, undertaken in collaboration with Kevin McDonnell,\r\nsought to address some of the limitations of the Pam amino acid approach. This\r\neffort focused on developing high-throughput techniques for finding BBA\r\npeptides capable of mediating aldol condensation. A library of over 100,000\r\ndifferent BBA peptides, the CPLB peptides, was designed to incorporate one of\r\nseveral possible basic residues within a core of many potential residues. These\r\npeptides were synthesized and assayed for their ability to sequester a fluorescent\r\nprobe, DMED, which resembles the reaction intermediates in aldol condensation.\r\nThe \"winners\" of this screen exhibited a high degree of sequence similarity,\r\nexhibiting \u03b2-diaminoproprionic acid (Dap) exclusively as the basic residue, and\r\nfavoring aromatic, hydrophobic amino acids as the neighboring residues.\r\nStructural and functional characterization of one of these \"winners,\" peptide\r\nCPLB-A2, was performed. Despite the inclusion of the Dap group within the\r\nhydrophobic core, this peptide appeared to be a monomeric species with a high\r\ndegree of the secondary and super-secondary structure expected of a BBA\r\npeptide. This peptide demonstrated an enhanced ability to sequester DMED\r\nrelative to Dap-containing model peptides and had the capacity to generate an\r\nenamineone reaction intermediate.
\r\n\r\nIn the course of these efforts, techniques were created to aid in the\r\npurification and characterization of N-terminally capped peptides. An affinity\r\npurification method involving a reversible biotin-based capping group was\r\ndeveloped to aid in the isolation of N-terminal glycolyl-capped peptides. This\r\nmethod proved practical for the efficient parallel purification of peptides. A\r\ncapping method involving an \u03b1-chloroacetyl group was developed to generate\r\nN-terminally capped peptides that were not only stable to standard assay\r\nconditions but also capable of being transformed to a form compatible with\r\nEdman sequencing. This method proved to be effective for the identification of\r\nunknown N-terminally capped peptides.
" }, { "name": "Ulman, Michael", "degree": "PhD", "year": "2000", "title": "Selectivity, activity, and stability of ruthenium-carbene based olefin metathesis initiators", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06172014-104222829", "creators": [ { "name": { "family": "Ulman", "given": "Michael" }, "id": "Ulman-M", "display_name": "Ulman, Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tbb7-wb93", "abstract": "The olefin metathesis reaction has found many applications in polymer synthesis\r\nand more recently in organic synthesis. The use of single component late metal olefin\r\nmetathesis catalysts has expanded the scope of the reaction to many new applications and\r\nhas allowed for detailed study of the catalytic species.
\r\n\r\nThe metathesis of terminal olefins of different steric bulk, different geometry as\r\nwell as electronically different para-substituted styrenes was studied with the ruthenium\r\nbased metathesis initiators, trans-(PCy3)2Cl2Ru=CHR, of different carbene substituents.\r\nIncreasing olefin bulk was found to slow the rate of reaction and trans internal olefins\r\nwere found to be slower to react than cis internal olefins. The kinetic product of a11\r\nreactions was found to be the alkylidene, rather than the methylidene, suggesting the\r\nintermediacy of a 2,4-metallacycle. The observed effects were used to explain the\r\nmechanism of ring opening cross metathesis and acyclic diene metathesis polymerization.\r\nNo linear electronic effects were observed.
\r\n\r\nIn studying the different carbene ligands, a series of ester-carbene complexes was\r\nsynthesized. These complexes were found to be highly active for the metathesis of\r\nolefinic substrates, including acrylates and trisubstituted olefins. In addition, the estercarbene\r\nmoiety is thermodynamically high in energy. As a result, these complexes react\r\nto ring-open cyclohexene by metathesis to alleviate the thermodynamic strain of the\r\nester-carbene ligand. However, ester-carbene complexes were found to be\r\nthermolytically unstable in solution.
\r\n\r\nThermolytic decomposition pathways were studied for several ruthenium-carbene\r\nbased olefin metathesis catalysts. Substituted carbenes were found to decompose through\r\nbimolecular pathways while the unsubstituted carbene (the methylidene) was found to\r\ndecompose unimolecularly. The stability of several derivatives of the bis-phosphine\r\nruthenium based catalysts was studied for its implications to ring-closing metathesis. The\r\nreasons for the activity and stability of the different ruthenium-based catalysts is\r\ndiscussed.
\r\n\r\nThe difference in catalyst activity and initiation is discussed for the bis-phosphine\r\nbased and mixed N-heterocyclic carbene/phosphine based ruthenium olefin metathesis\r\ncatalysts. The mixed ligand catalysts initiate far slower than the bis-phosphine catalysts\r\nbut are far more metathesis active. A scheme is proposed to explain the difference in\r\nreactivity between the two types of catalysts.
" }, { "name": "Anderson, Cheryl Marie", "degree": "PhD", "year": "1999", "title": "Two-dimensional photonic band gap crystals", "advisor": "Giapis, Konstantinos P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082008-170050", "creators": [ { "name": { "family": "Anderson", "given": "Cheryl Marie" }, "id": "Anderson-Cheryl-Marie", "display_name": "Anderson, Cheryl Marie" } ], "advisors": [ { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "advisor", "display_name": "Giapis, Konstantinos P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/17mm-qm12", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA photonic crystal is a periodic dielectric structure that possesses a band of frequencies in which propagating electromagnetic waves are forbidden. Two- dimensional photonic crystals exhibit a band gap for waves traveling in the crystal plane, a property that offers promise for improved operation of optoelectronic devices including semiconductor lasers, light-emitting diodes, and frequency filters.\r\n\r\nA theoretical investigation of two-dimensional photonic band gap crystals has been performed. The plane-wave expansion method is used to solve Maxwell's equations for the electromagnetic frequency bands in several square (Lane group 4mm) and triangular (Laue group 6mm) crystal structures. The size of absolute band gaps is often limited by band degeneracies at lattice symmetry points. By reducing the lattice symmetry, these degeneracies can be lifted to increase the size of existing photonic band gaps, or to create new gaps where none existed for the more symmetric structure. Symmetry analysis also offers a rational approach for exploring and designing new photonic crystal structures. Gap maps for several important crystal structures are presented as a useful reference guide for experimentalists.\r\n\r\nThe utility of photonic crystals for many applications is enhanced through the introduction of a defect into the crystal structure, which creates localized frequency states within the photonic band gap. Defect modes in two-dimensional square photonic crystal structures were studied using a supercell approach. By changing the radius of a single rod, several defect modes with complex electromagnetic field patterns appear within the photonic band gap. The mode frequencies can be tuned by varying the size of the defect rod. The double-rod square structure has two rod types per unit cell, yielding different defect characteristics depending on which rod is altered.\r\n\r\nIn addition, anisotropic etching of patterned silicon has been investigated experimentally using a hyperthermal neutral fluorine atom beam generated by laser- induced detonation of [...]. The detrimental effects of surface charging are eliminated by the use of charge-neutral etch species; however, inelastic scattering of energetic reactive species has a significant effect on the development of the etch profiles, especially at high aspect ratios. Etch profile anomalies including microtrenching and undercutting are observed." }, { "name": "Baird, Eldon Eugene", "degree": "PhD", "year": "1999", "title": "Solid Phase Synthesis of DNA-Binding Small Molecules", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282006-113514", "creators": [ { "name": { "family": "Baird", "given": "Eldon Eugene" }, "id": "Baird-Eldon-Eugene", "orcid": "0009-0009-2775-8704", "display_name": "Baird, Eldon Eugene" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zky0-ha94", "abstract": "Small molecules that bind to any predetermined DNA sequence in the human genome are potentially useful tools for molecular biology and human medicine. A twenty year research effort led by Dr. Peter B. Dervan at the California Institute of Technology has led to the development of \"pairing rules\" to control rationally the sequence-specificity of polyamides that bind in the DNA minor groove. During the course of my Ph.D. research, methodology was developed for the machine-assisted solid phase synthesis of these DNA-binding polyamides (Chapter 2). The large number of polyamides made available by the solid phase synthetic methodology has greatly accelerated the development of this class of molecules. Polyamides prepared by solid phase synthetic methodology have been used by a variety of collaborators to: extend the targetable binding-site size (Chapter 3), recognize predetermined DNA sequences with subnanomolar affinity (Chapter 6), regulate gene expression in human cells (Chapter 7), and recognize all four base pairs in the DNA minor groove (Chapter 8)." }, { "name": "Blackwell, Helen Elizabeth", "degree": "PhD", "year": "1999", "title": "New synthetic applications for ring-closing metathesis and cross-metathesis employing well-defined ruthenium alkylidenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262005-133922", "creators": [ { "name": { "family": "Blackwell", "given": "Helen Elizabeth" }, "id": "Blackwell-H-E", "display_name": "Blackwell, Helen Elizabeth" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XBZ4-CV61", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe development of well-defined ruthenium alkylidene [...] (1) has revolutionized the application of the olefin metathesis reaction in organic synthesis. This thesis describes: (1) the application of ring-closing metathesis (RCM) to the synthesis of constrained cyclic peptides, (2) the conformational analyses of these peptide architectures, and (3) the development of new selective cross-metathesis (CM) methodology employing alkylidene 1.\n\nChapter 2 describes the initial application of RCM to the synthesis of cyclic amino acids and peptide [...]. Introduction of olefin functionality into peptidic structures proved straightforward, and treatment with ruthenium alkylidene 1 generated cyclic amino acids and dipeptides in excellent yields. Tetrapeptide diene analogs of naturally-occurring disulfide [...] proved to be robust substrates for RCM, and the macrocyclic olefin products could be prepared either in solution or on solid support.\n\nChapter 3 describes the application of RCM to the synthesis of macrocyclic hexapeptide [Beta]-sheets. The acyclic hexapeptide diene frameworks were modeled after hexapeptide disulfides reported to adopt [Beta]-sheet conformations. Treatment with ruthenium alkylidene 1, however, afforded only low yields of the desired 20-membered macrocycles: conformational analyses suggested that the hexapeptides adopted a helical rather than [Beta]-sheet conformation in the apolar solvents in which RCM was performed. These peptide systems were redesigned in Chapter 4 so that macrocyclization was favored when the peptides adopted a helical conformation. A series of macrocyclic heptapeptides were prepared in high yield via RCM which were shown to adopt [...]-helical conformations both in solution and in the solid state.\n\nChapter 5 describes new CM methodology involving the coupling of terminal olefins with symmetrically disubstituted olefins to generate heterodimeric cross-products in excellent yields and with high trans selectivity. CM was employed in an initial self-metathesis step to synthesize a variety of disubstituted olefins with diverse functionality, which were then further processed in the CM with terminal olefins. Finally, a new CM application was introduced involving the metathesis of acrolein acetal derivatives with terminal olefins to generate [...] aldehydes.\n" }, { "name": "Brameld, Kenneth A.", "degree": "PhD", "year": "1999", "title": "Molecular modeling of biological systems : from chitinase A to Z-DNA", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-095619938", "creators": [ { "name": { "family": "Brameld", "given": "Kenneth A." }, "id": "Brameld-K-A", "display_name": "Brameld, Kenneth A." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mvyy-4570", "abstract": "Quantum chemical methods and molecular dynamics simulations are used herein to address interesting problems associated with chemical systems of biological relevance. Two such systems are investigated: The mechanisms of family 18 and family 19 chitinases and the development of a force field for simulations of nucleic acids from first principles calculations.
\r\n\r\nChitinases catalyze the hydrolysis of chitin, a \u03b2(1,4)-linked N-acetyl-glucosamine polymer. Family 18 and family 19 chitinases are glycosyl hydrolases with different structures and mechanisms. Using a combination of quantum chemical and molecular dynamics methods, several interesting and unexpected features of the hydrolysis mechanisms of chitinases were discovered. Family 18 chitinases induce substrate distortion forcing the N-acetyl-glucosamine sugar bound at subsite -1 to adopt a boat conformation. Protonation of the \u03b2(1,4)-anomeric oxygen leads to spontaneous bond cleavage and the formation of an oxazoline ion intermediate. The oxazoline ion is stabilized through anchimeric assistance from the neighboring N-acetyl group. In contrast, family 19 chitinases do not induce substrate distortion and utilize an oxocarbenium ion intermediate. The first of two acidic residues in the active site serves to protonate the \u03b2(1,4)-anomeric oxygen while the second acidic residue stabilizes the oxocarbenium ion through a conformational change within a flexible loop of the enzyme. The second acidic residue also coordinates with and activates a water molecule for nucleophilic attack at the Cl' anomeric carbon to complete the hydrolysis mechanism.
\r\n\r\nFor molecular dynamics simulations of biomolecules, it is desirable to use accurate potential energy functions (force fields) which are also generic enough to be parameterized for most any conceivable molecule. A hierarchical approach is undertaken herein to achieve this flexibility and accuracy. To begin, a rule based force field (UFF) forms the foundation upon which additional parameters are added so as to reproduce structural and energetic properties important for nucleic acids. The specific substructures within nucleic acids which require additional parameterization are the phosphodiester backbone, sugar ring pseudorotation, glycosidic bond and base pair hydrogen bonding. The potential energy surfaces for each of these substructures are determined from high level quantum mechanical calculations and the force field parameterized to reproduce these results.
\r\n" }, { "name": "Carter, Scott Reynolds", "degree": "PhD", "year": "1999", "title": "Sequence-specific minor groove binding polyamides : DNA recognition and applications", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04272006-153748", "creators": [ { "name": { "family": "Carter", "given": "Scott Reynolds" }, "id": "Carter-S-R", "display_name": "Carter, Scott Reynolds" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JGMJ-YJ95", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPyrrole-imidazole polyamides bind to the minor groove of DNA with high affinity and specificity. This thesis explores the scope of this DNA recognition motif both in terms of improved recognition and application to problems of DNA detection and purification. Chapter 2 describes conjugates of polyamides with fluorescent dyes. Three cyanine dye butyric acids were synthesized and linked to the polyamide, [...]. These conjugates retain high specificities and high affinities for targeted DNA sequences, and show large fluorescence enhancements upon binding to double stranded DNA. Chapter 3 describes the use of polyamide conjugates as affinity reagents for the purification of double stranded DNA. Specifically, systems composed of biotin and histidine tagged conjugates that can rapidly and efficiently capture restriction fragment DNA are described.\r\n\r\nChapter 4 focuses on the design and synthesis of constrained [...]-aminobutyric acid analogs designed to improve hairpin polyamide binding affinities through reduction of the entropic cost of binding to DNA. Six derivatives were synthesized as Boc protected monomers and were incorporated into polyamides by solid phase synthesis. The affinity and specificity of the compounds were analyzed by quantitative DNAse I footprinting.\r\n\r\nChapter 5 describes preliminary synthetic efforts towards the recognition of G rich DNA sequences with polyamides containing imidazole dimers linked by alkyl chains rather than amides. Regioselective synthesis of an alkyl imidazole dimer suitably protected for solid phase polyamide synthesis is described. This dimer was incorporated into 2 polyamides for the recognition of 5'-WGGGGW-3' sequences. Alkyl substituted polyamides bound comparably to the corresponding amide linked compounds.\r\n\r\nAn appendix summarizes work on the recognition of 5'-WGWGW-3' sequences by pyrrole-imidazole polyamides. [...] and [...] recognize a [...] binding site.\r\n\r\nChapter 6 describes studies of the non-natural base pair between isoguanosine and isocytosine. A synthesis of deoxyisoguanosine (d-isoG) suitably protected for solid phase oligonucleotide synthesis is presented. Transcriptional studies on templates containing diosG showed that it directed the transcription of uridine rather than isoC, providing evidence that isoG can access different tautomeric forms." }, { "name": "Claypool, Christopher L.", "degree": "PhD", "year": "1999", "title": "Why molecules look the way they do in STM : a systematic functional group approach", "advisor": "Marcus, Rudolph A.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-081325550", "creators": [ { "name": { "family": "Claypool", "given": "Christopher L." }, "id": "Claypool-C-L", "display_name": "Claypool, Christopher L." } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AAWF-HM84", "abstract": "A series of functionalized alkanes and/or alkyl alcohols have been prepared and imaged by scanning tunneling microscopy (STM) methods on graphite surfaces. The stability of these ordered overlayers has facilitated reproducible collection of STM images at room temperature with sub-molecular resolution, in most cases allowing identification of individual hydrogen atoms in the alkane chains, but in all cases allowing identification of molecular length features and other aspects of the image that can be unequivocally related to the presence of functional groups in the various molecules of concern. Functional groups imaged in this study include halides (X=F, Cl, Br, I), amines, alcohols, nitriles, alkenes, alkynes, ethers, thioethers, allenes, and disulfides. The dominance of molecular topography in producing the STM images of alkanes and alkanols was established experimentally and also was consistent with quantum chemistry calculations. For molecules in which electronic effects overwhelmed topographic effects in determining the image contrast, a simple model is presented to explain the variation in the electronic coupling component that produces the contrast between the various functional groups observed in the STM images. Additionally, a theoretical model based on perturbation theory has been developed to predict the scanning tunneling microscopy (STM) images of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort and provides images that are in qualitative agreement with experimental results. The computations correlate well with the STM data of functionalized alkanes and allow assessment of the structure and orientation of most of the functionalized alkanes that have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals of the adsorbed molecules, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals, may play an important role in determining e STM image contrast of such systems.\r\n" }, { "name": "Cucullu, Mich\u00e8le Elise", "degree": "Masters", "year": "1999", "title": "Ruthenium Based Catalysts: Catalytic Dehalogenation of Chloroarenes and Syntheses of Bimetallic Carbene Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012023-172614654", "creators": [ { "name": { "family": "Cucullu", "given": "Mich\u00e8le Elise" }, "id": "Cucullu-Mich\u00e8le-Elise", "display_name": "Cucullu, Mich\u00e8le Elise" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a64g-1585", "abstract": "[No Abstract]" }, { "name": "Doleman, Brett James", "degree": "PhD", "year": "1999", "title": "Study and development of an \"electronic nose\" and comparison with mammalian olfaction", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172012-133347649", "creators": [ { "name": { "family": "Doleman", "given": "Brett James" }, "id": "Doleman-B-J", "display_name": "Doleman, Brett James" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R6QQ-NX09", "abstract": "Arrays of broadly responsive vapor detectors (i.e., electronic noses) are receiving\r\nan increasing amount of scientific attention for their potential as analytical devices, as\r\nmodels for studying mammalian olfaction, and perhaps for someday ultimately duplicating\r\nor surpassing the mammalian olfactory sense. Herein, research was primarily focused on\r\nan electronic nose composed of an array of carbon black-polymer composite detectors\r\nwhile arrays of tin oxide detectors and organic conducting polymer detectors were used\r\nonly in a comparison study. The research determined the odorant resolving power of\r\nelectronic nose sensor arrays, explored the dependence of the electronic nose array\r\nresponse intensity on odorant vapor pressure, compared the odorant detection thresholds\r\nand odorant classification properties of the electronic nose to the mammalian olfactory\r\nsense, and attempted to predict human odor quality judgements using electronic nose\r\ndetector responses.
\r\n\r\nThe Fisher linear discriminant statistical metric was utilized to quantify the\r\nperformance of arrays composed of carbon black-insulating polymer composite detectors,\r\ntin oxide detectors and bulk conducting organic polymer detectors in resolving nineteen\r\nodorant vapors. The odorant resolving power of the sensor arrays as a function of the\r\nchemical composition of the detectors and the number of detectors they contained was\r\nstudied. The results provided insights into optimizing the chemical diversity and size of a\r\nchemical vapor sensor array for various tasks.
\r\n\r\nResponse data were collected for a carbon black-polymer composite electronic nose\r\narray during exposure to homologous series of 1-alcohol and n-alkane odorants. The mean\r\nresponse intensity of the electronic nose detectors, and the response intensity of the most\r\nstrongly-driven set of electronic nose detectors, was essentially constant for members of a\r\nchemically homologous odorant series when the concentration of each odorant in the gas\r\nphase was maintained at a constant fraction of the odorant's vapor pressure. A similar\r\ntrend is observed in human odor detection threshold values for these same odorants. The\r\ndata imply that the trends in detector responses and human detection thresholds can be\r\nunderstood based on the thermodynamic tendency to establish a relatively constant\r\nconcentration of sorbed odorant into each of the polymeric films of the electronic nose and\r\ninto the olfactory epithelium of humans at a constant fraction of the odorant's vapor\r\npressure.
\r\n\r\nExperiments were performed to compare the detection thresholds and trends in\r\ndiscrimination abilities of the electronic nose to those of the mammalian olfactory sense,\r\nand to develop models predicting human odor quality judgements from electronic nose\r\ndetector responses. The detection thresholds for the electronic nose and the human nose\r\nwere compared for series of n-alkanes and 1-alcohols. Trends in the odorant-discriminating\r\nabilities of an electronic nose and mammalian noses were compared for\r\nseries of esters, alcohols and carboxylic acids. Electronic nose response data were\r\ncollected for a diverse set of odorants which had previously been quantitatively\r\ncharacterized by human panelists according to many categories of odor quality. The\r\nresponses of the electronic nose detectors were then used in attempts at predicting the\r\nhuman odor quality judgements.
" }, { "name": "Farrow, Neil", "degree": "PhD", "year": "1999", "title": "Investigation of electron transfer in the [alpha]-helical protein cytochrome b [subscript 562]", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-151616", "creators": [ { "name": { "family": "Farrow", "given": "Neil" }, "id": "Farrow-N", "display_name": "Farrow, Neil" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "member", "display_name": "Winkler, Jay Richmond" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8mrb-7d44", "abstract": "Electron transfer rates in the [alpha]-helical protein cytochrome b[562] are investigated using the photoexciteable luminescent labelling compound ruthenium(II)bis(2,2'-bipyridine)(imidazole) attached to surface accessible histidine residues. Three residues on helices A and D and two on helix C were replaced with histidine by site directed mutagenesis to form eight mutant proteins which, together with a wild-type histidine on helix C, were labelled with ruthenium(II)bis(2,2'-bipyridine)(imidazole). Laser excitation of ruthenium(II)bis(2,2'-bipyridine)(imidazole) formed the highly reducing species *ruthenium(II)bis(2,2'-bipyridine)(imidazole) which was either quenched by the heme directly and the back rate (k[b][ET]) to the RuIII monitored by transient absorbance, or was oxidized by an external quencher and the rate from the reduced protein then monitored. Mutants spanned a metal-metal distance range from 14.2 \u00c5 to 25 \u00c5 with the rates ranging from 2.5 x 10[2] s[-1] to 2.2 x 107 s[-1]. A \u00df value of 1.09 \u00c5[-1] is calculated from the data which agrees well with data from azurin and cytochrome c. The results show that the [alpha]-helices together with the extended heme plane provides an efficient homogenous barrier to electron transfer.\r\n\r\nA mutant of cytochrome b[562] with a covalently attached heme via one thioether linkage was expressed. The unfolding characteristics of this protein show it to be more stable to guanidinium unfolding than wild-type protein. The electron transfer rate for this mutant was identical to wild-type indicating minimal perturbation of the heme binding pocket by the mutation. It can be inferred that the side chain of the carboxyl terminal arginine residue and not Arg98 is responsible for stabilizing the His102 ligand histidinate charge." }, { "name": "Foss, David R.", "degree": "PhD", "year": "1999", "title": "Rheological behavior of colloidal suspensions : the effects of hydrodynamic interactions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02132007-143514", "creators": [ { "name": { "family": "Foss", "given": "David R." }, "id": "Foss-D-R", "display_name": "Foss, David R." } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/g6s5-x267", "abstract": "The rheological behavior of hard-sphere colloidal suspensions in simple shear flow is examined theoretically and by dynamic simulation. The Stokesian Dynamics and Brownian Dynamics simulation techniques are used to study suspensions with and without many-body hydrodynamic interactions, respectively. Suspensions near equilibrium, where Brownian motion dominates, and at high shear rates, where hydrodynamic forces dominate, are examined. Steady-state simulations are performed using both simulation algorithms. The Brownian Dynamics system is found to be shear-thinning at low shear rates and undergoes a phase transition at high shear rates to a phase of hexagonally-packed strings aligned in the flow direction. Inclusion of hydrodynamic interactions eliminates the phase transition at high shear rates. Instead, the suspension is found to shear thicken due to a boundary layer of high particle probability that forms near contact where convection balances Brownian diffusion. This increases the role of strong hydrodynamic lubrication forces. Shear thinning and thickening data from many different volume fractions are collapsed using scaling theories. A previous steady-state theoretical analysis of the boundary layer at high shear rates (Brady & Morris 1997) is extended to include unsteady flow conditions. Theoretical results are found to be in agreement with start-up and flow-cessation simulations. A relation between start-up flow at low shear rates and the relaxation of equilibrium fluctuations is made. Equilibrium fluctuations are characterized using the shear-stress autocorrelation function and Green-Kubo formulae. Behavior of this function at short times is related to the behavior in an oscillatory shear flow at high frequencies that is also well-described by a boundary layer where unsteady convection balances Brownian diffusion. A new method for determining the components of the long-time self-diffusion tensor is proposed. Self-diffusion is found to be a decreasing function of volume fraction near equilibrium and an increasing function of volume fraction at high shear rates. Data is in agreement with previous theory and experiment. Due to the buildup of particle probability along the compressional axis relative to the extensional axis in simple shear flow, there is a nonzero off-diagonal component to the long-time self-diffusion tensor which is proportional to the shear rate. This component is positive near equilibrium and negative at high shear rates" }, { "name": "Giardello, Amy Beth", "degree": "PhD", "year": "1999", "title": "Ruthenium Mediated Olefin Metathesis : Materials with Controlled Microstructure and Functionalization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292024-213235529", "creators": [ { "name": { "family": "Giardello", "given": "Amy Beth" }, "id": "Giardello-Amy-Beth", "display_name": "Giardello, Amy Beth" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9r5p-jw46", "abstract": "Methylcyclopentene and cyclooctadiene were copolymerized via ring\r\nopening metathesis polymerization (ROMP) mediated by the well-defined complex\r\n(PCy3)2Cl2Ru=CHPh to produce materials with controlled microstructure and\r\nfunctionalization. The copolymer (COD/3-MCP) composition (10-80 methyls/1000\r\ncarbons) and melting point (Tm) (65 - 110\u00b0C) were controlled by comonomer feed ratio. Polymerizations performed in the presence of chain transfer agent (CTA) cis-2-butene-1,4-diacetate provided telechelic copolymers with controlled chain length (Mn 1500-3500 g/mol), and 13C NMR spectra were used to assign polymer microstructure. The ruthenium carbene was converted in situ to an active olefin hydrogenation catalyst. The effectiveness of this methodology depends on polymer microstructure, solvent, temperature, pressure and additives. Methylene chloride is the best solvent for hydrogenation (200\u00b0C, 800 psi H2, Olefin/Ru \u2248 2000). The structure/property relationships of this family of materials was\r\ninvestigated by numerous methods. The number of backbone methyl branches had a\r\nsignificant effect on the melt transition temperature and enthalpy and zero shear viscosity.\r\nThere was not a demonstrable effect on the energy of activation of flow. However,\r\npreliminary rheo-optical measurements indicate a strong dependence of the stress-optic\r\ncoefficient on methyl branch.
\r\n\r\nThe regiospecific and irreversible reaction of ruthenium carbenes\r\n(PR3)2Cl2RuCHR' (R = PPh3 or PCy3, R' = Ph, CHCPh2, (CH2)4CH3 or\r\npolynorbornene) with electron rich vinyl ethers (EtOCH=CHR, R = H, CH3 (CH2)5CH3,\r\nCH2Ph or Ph ) was also investigated. These reactions were monitored by 1H NMR\r\nspectroscopy and kinetic data was obtained under pseudo first order conditions ([vinyl\r\nether]0[Ru]0 10/1). The half lives (t1/2) for this reaction were calculated from the\r\nobserved kinetic data for [vinyl ether] = 0.15 M. 1H NMR data indicates that the observed metathesis was regiospecific and irreversible yielding a heteroatom stabilized alkylidene\r\nspecies (LnRu=CHOEt). Ruthenium catalysts possessing electron rich alkyl phosphines\r\nwere more reactive towards each substrate. Coordination of a heteroatom from the polymer\r\nbackbone (poly(cyclobutene) with pendant amide or ether groups) significantly inhibited\r\nmetathesis at all temperatures. The analogous triphenylphosphine derivatives were less\r\nreactive and (PPh3)2Cl2RuCH(C7H10)n reacts only with ethyl vinyl ether at 20\u00b0C. At\r\n40\u00b0C metathesis was observed with other less hindered substrates.
" }, { "name": "Hu, Yonglin", "degree": "PhD", "year": "1999", "title": "Crystal Structures of ModA from Escherichia coli and Formaldehyde Ferredoxin Oxidoreductase from Pyrococcus furiosus", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07312025-184818403", "creators": [ { "name": { "family": "Hu", "given": "Yonglin" }, "id": "Hu-Yonglin", "display_name": "Hu, Yonglin" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "orcid": "0000-0002-5749-7869", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j04r-6905", "abstract": "The crystal structures of two proteins, ModA from Escherichia coli and formaldehyde\r\nferredoxin oxidoreductase from Pyrococcus furiosus, are reported in this paper.
\r\n\r\nModA is a periplasmic molybdate binding protein. Crystals of this protein complexed\r\nwith tungstate or molybdate belong to space groups P3221, with cell dimensions\r\nof a=b=82.6\u00c51, c=81.5\u00c5, \u03b1=\u03b2=90\u00b0, and \u03b3=120\u00b0. The structure of ModA was\r\nsolved by the Single Isomorphous Replacement and Anomalous Scattering method\r\nand refined to 1.75\u00c5 resolution for both molybdate- and tungstate-bound crystal\r\nforms. The Rand free R factors are 16.2% and 20.3%, respectively, for the molybdate-bound\r\nmodel, and 16.3% and 18.6%, respectively, for the tungstate-bound model.\r\nBased on the structural comparisons with other periplasmic binding proteins, such as\r\nsulfate and phosphate binding proteins and ModA from Azotobactor vinelandii, the\r\nstructural bases of the high specificity of ModA for molybdate were identified.
\r\n\r\nP. furiosus formaldehyde ferredoxin oxidoreductase (FOR) was crystallized m\r\nspace group P212121, with cell dimensions a=99.03\u00c5, b=171.10\u00c5, c=179.86\u00c5, and\r\n\u03b1=\u03b2=\u03b3=90\u00b0. Its crystal structure was solved by the molecular replacement method,\r\nand refined to 1.85\u00c5 resolution to an R factor of 17.4%, and free R factor of 22.0%.\r\nComplexes of FOR with glutarate, an inhibitor, and P. furiosus ferredoxin, its physiological\r\nelectron acceptor, were solved and refined to 2.4\u00c5 and 2.15\u00c5 resolution,\r\nrespectively. A structural comparison revealed that FOR may have an enzymatic\r\nmechanism similar to that of Desulfovibrio gigas Mop, an unrelated molybdenum-containing\r\nenzyme. Residues related to the substrate specificity of FOR were identified\r\nbased on the FOR-glutarate interactions. From the arrangement of the redox\r\ncenters in the FOR-ferredoxin complex, an electron transfer pathway between these\r\ntwo partners was proposed.
" }, { "name": "Jones, Christopher W.", "degree": "PhD", "year": "1999", "title": "Organic-functionalized molecular sieves (OFMS'S): A new class of materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11152005-152437", "creators": [ { "name": { "family": "Jones", "given": "Christopher W." }, "id": "Jones-C-W", "display_name": "Jones, Christopher W." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6xz1-hh23", "abstract": "Throughout the last two decades, there has been a tremendous interest and growth in molecular sieve science. In particular, substantial attention has been paid to the development of new molecular sieves for catalytic applications, as molecular sieves have the unique ability to promote reactions in a shape-selective manner. To increase the variety of reactions that can be catalyzed by molecular sieves, recent efforts have focused on generating new types of active sites in molecular sieves by incorporating transition metals into the silicate framework or by supporting metal-based species within the micropores. Despite this, there are still many chemistries that can not be carried out over molecular sieve catalysts where significant benefit could be gained if the reaction were to be accomplished in a shape-selective manner. To address this problem, I have prepared a new class of molecular sieves that contain intracrystalline organic functionalities [denoted organic-functionalized molecular sieves (OFMS's)]. Previous attempts to synthesize silicate-based molecular sieves with organic functionalities within the micropores have focused on grafting organic groups onto preformed zeolites. However, this is not a viable route to the production of OFMS's that can function as shape-selective catalysts, as the organic groups preferentially functionalize the external crystal surface. Here, the problems with this approach are circumvented by preparing OFMS's by direct synthesis.\n\nAttempts to synthesize OFMS's directly both in the presence and absence of organic structure-directing agents (SDA's) are described. Pure-silica beta zeolites containing a variety of intracrystalline organic groups are synthesized using tetraethyl ammonium fluoride (TEAF) as the SDA. Porosity is generated by removing the occluded TEAF by solvent-extraction techniques. Following extraction, the exposed organic functionalities are further altered by chemical techniques, e.g., amines to imines, phenethyl groups to phenethylsulfonic acid groups. The ability to perform shape-selective acid catalysis (phenethylsulfonic acid) and shape-selective formation of imines from amines indicates that the organic moieties reside largely in the micropores of the molecular sieve. Several preparation variables have an impact on the nature of the resulting OFMS's, the most of important of which are the synthetic method, silicon source, and extraction method. The effects of these synthetic factors on the crystal size and morphology, porosity and hydrophobicity of the products are discussed." }, { "name": "Katz, Alexander", "degree": "PhD", "year": "1999", "title": "The synthesis and characterization of molecularly imprinted materials", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06272005-135319", "creators": [ { "name": { "family": "Katz", "given": "Alexander" }, "id": "Katz-A", "display_name": "Katz, Alexander" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/w71z-hn73", "abstract": "Current advances in chemical protection strategies, analytical methods such as solid-state NMR and EPR spectroscopies and biological catalysis make it an ideal time to reinvestigate molecular imprinting as a viable method for the synthesis of catalysts for small molecule transformations. In the past, imprinting has been pursued mainly as a method for creating separation media for dealing with issues of adsorption/separation of small molecules. In a few instances, these materials have also been investigated as catalysts. Most imprinted systems to-date have employed non-covalent interactions to achieve functional group positioning, and this type of an approach can lead to other undesired effects such as binding site heterogeneity (as shown in this thesis for one particular system that employs self-assembly to achieve imprinting). Site heterogeneities can be extremely detrimental for selective catalysis. The objective of this work is to determine the origins of site heterogeneity and attempt to overcome these issues in order to synthesize new catalysts via molecular imprinting.\n\nTo gain further insight into the causes responsible for site heterogeneity in imprinted materials, the nature of molecular recognition in an imprinted polymer that is known to exhibit strong binding site heterogeneity is investigated. The system is formed by the self-assembly of a binding monomer and an imprint through non-covalent interactions. Based on observations of bulk phase separation in the system investigated, an alternative mechanism for molecular recognition in the imprinted polymer is proposed. This mechanism involves remaining, occluded imprint molecules that provide for binding via imprint-imprint intermolecular interactions. Support for this mechanism is provided from polymers prepared using a combination of imprint and mimic, which remains covalently bound in the polymer and is shown to increase the rebinding of imprint while not significantly affecting the binding of the opposite enantiomer of the imprint. Elucidation of this mechanism provides insight into the nature of site heterogeneity in imprinted polymer systems.\n\nBased on the findings from the self-assembly system, a new molecular imprinting approach is developed that utilizes the controlled distance method. In this approach, silica is used for the inert crosslinking framework instead of an organic polymer due to its significantly greater mechanical rigidity (300 times more rigid and not susceptible to swelling in organic media). Instead of non-covalent interactions as the driving force for functional group positioning, covalent interactions are used. The method positions several amine functionalities (up to three demonstrated), within the three-dimensional porous structure of silica. This imprinting process is characterized by FTIR and solid state NMR spectroscopies. The imprinted silicas show microporosity specifically resulting from the imprinting process, with the amount of microporosity added consistent with the extent of imprint removal. The imprinted amines which reside in the microporous void space are able to bind molecules such as benzoic acid and acetylacetone and also perform shape-selective catalysis. To ascertain the degree of control over functional group positioning with this imprinting approach, fluorescence measurements with a pyrenebutyric acid probe molecule were performed on the imprinted silicas. The results demonstrate that the imprinting process employed gives local functional group ordering for the case of three amines per site and gives well-isolated functional groups for the case of one amine per site. The imprinted silicas thus provide a foundation from which further investigations towards elucidating quantitative distance information between imprinted functionalities in these materials can be developed." }, { "name": "Kelley, Shana O.", "degree": "PhD", "year": "1999", "title": "Electron transfer through the DNA double helix: spectroscopic and electrochemical studies", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142005-111510", "creators": [ { "name": { "family": "Kelley", "given": "Shana O." }, "id": "Kelley-S-O", "orcid": "0000-0003-3360-5359", "display_name": "Kelley, Shana O." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HZ7H-AD50", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe DNA helix, containing a stacked array of aromatic base pairs, presents a novel medium in which electron transfer mediated by a molecular [pi]-stack can be investigated. To probe electron transfer through DNA, we have constructed duplex assemblies modified with photo- and redox-active probes and applied spectroscopic and electrochemical approaches to the study of DNA-mediated charge transport.\r\n\r\nPhotoinduced electron transfer between intercalators was examined as a function of distance in a series of small DNA duplexes covalently modified with ethidium (Et) and [...]. At distances up to 35 [...], electron transfer occurs on the subnanosecond time scale ([...]). In duplexes containing disruptive base mismatches, large decreases in electron-transfer yields are observed, confirming that the electron transfer pathway proceeds through the stacked base pairs. Hence, it was demonstrated for the first time that DNA-mediated electron transfer between intercalators is exceptionally efficient, only weakly dependent on distance, but highly sensitive to perturbations in base stacking.\r\n\r\nTo investigate a DNA base within the [pi]-stack as a reactant, ethidium-modified duplexes containing the base analogue deazaguanine were synthesized. The photooxidation of deazaguanine by ethidium also proceeds on a subnanosecond time scale ([...]) and exhibits a shallow distance dependence. The efficiency and overall distance dependence is sensitive to the stacking of deazaguanine as determined by flanking sequence. These studies again showed that the DNA base stack can mediate extremely fast, long-range charge transport, and further elucidated that stacking interactions are critical in modulating the efficiency of this phenomenon.\r\n\r\nUsing base-base photochemistry, electron transfer through DNA was probed directly without external donors and acceptors. Using fluorescent analogues of adenine that selectively oxidize guanine, electron transfer through the DNA [pi]-stack was investigated as a function of reactant stacking and energetics. Small variations in each of these factors lead to remarkable changes in the kinetics of DNA-mediated electron transfer and values of [beta], a parameter reflecting the exponential dependence of electron transfer on distance, were measured ranging from [...] to [...]. The DNA base stack was shown to exhibit insulator to \"wire\"-like properties, depending on the structure and energetics of reactants employed to probe this medium.\r\n\r\nTo investigate DNA-mediated electron transfer using electrochemical methods, we assembled DNA films and incorporated intercalating redox-active molecules into the monolayers. Surface characterization techniques were employed to determine the orientation of the DNA helices within the films. With the intercalator daunomycin crosslinked to DNA duplexes immobilized on gold, efficient electron transfer over distances greater than 30 [...] was observed. Base mismatches also attenuate this long-range reaction, providing a new method for the electrochemical detection of genomic mutations.\r\n\r\nThese studies have provided essential measurements of electron transfer in DNA over known, fixed distances. It is now apparent that stacking interactions modulate the efficiency of this phenomenon, an observation that may explain the range of conflicting results reported within this field. Moreover, as experimental evidence increasingly supports the notion that ultrafast charge transport can occur through the DNA helix over long distances, the implications for biological systems can now be considered. Our findings point to the DNA [pi]-stack as not only a carrier of genetic information, but also a pathway which is conducive to charge transport.\r\n" }, { "name": "Kim, Chang Hee", "degree": "PhD", "year": "1999", "title": "Site-Specific Chemical Modification and Crosslinking Studies of U6 snRNA in the Yeast spliceosome", "advisor": "Abelson, John N.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01092024-222740445", "creators": [ { "name": { "family": "Kim", "given": "Chang Hee" }, "id": "Kim-Chang-Hee", "display_name": "Kim, Chang Hee" } ], "advisors": [ { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "advisor", "display_name": "Abelson, John N." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "member", "display_name": "Abelson, John N." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cfw0-z473", "abstract": "Pre-mRNA splicing is an essential step in eukaryotic gene expression. Most eukaryotic genes are interrupted by sequences, called introns, that do not code for sequences in the final protein gene product. Pre-mRNA splicing is the process by which introns are removed and the coding sequences, called exons, are joined together following transcription of a gene into RNA. The spliced mRNA subsequently acts as the coding template for protein synthesis. Pre-mRNA splicing occurs in a large ribonucleoprotein particle called the spliceosome which includes five essential small nuclear RNAs (snRNAs) and more than 50 different proteins. It is thought that the active site of the spliceosome consists of U2, U6 and U5 snRNAs. In order to probe the structure of the catalytic site, we have done an extensive site-specific chemical modification and crosslinking studies of U6 RNA in the yeast spliceosome. From an extensive screen of site-specific 2'-deoxy modifications, we have found four that block the first step of splicing, yet are able to assemble spliceosome complexes which precede the reactive spliceosome, suggesting that the 2'-hydroxyls at these nucleotides may be required for catalysis. In the crosslinking experiments, we found crosslinks between 4-thioU placed in the central conserved sequences in U6 with the 5' splice site of the pre-mRNA, which participates in the first chemical step of splicing. We were able to determine the order of this crosslink by doing the experiment in yeast mutant spliceosomes which were blocked in well-defined stages of splicing. We also found that a conserved nucleotide in the 3' stem-loop of U6 crosslinks to a nucleotide in a region of the actin pre-mRNA intron which is required for its splicing in vitro. We also found crosslinks to snRNAs -- U2 and U4. Certain positions in U6 can crosslink first to U4 snRNA, then subsequently to the pre-mRNA, consistent with the notion that the spliceosome is a dynamic machine." }, { "name": "Lee, Hak-No", "degree": "PhD", "year": "1999", "title": "I. Gas Phase Proton Affinity of Zwitterionic Betaine. II. High Resolution Spectroscopy of Trapped Ions: Concept and Design", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212019-155237296", "creators": [ { "name": { "family": "Lee", "given": "Hak-No" }, "id": "Lee-Hak-No", "display_name": "Lee, Hak-No" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8gqa-0x72", "abstract": "In an ideal experiment, the system being investigated is isolated from the environment. The only external influences allowed on the system are the parameters that the experimenter chooses to vary, in effort to study their effects on the observables. Moreover, these parameters can be controlled with all the accuracy and precision desired by the experimenter. In chemistry, ion cyclotron resonance (ICR) mass spectrometry may come closer to replicating this ideal condition than any other experimental technique. An ion isolated in an ICR trap is under ultra high vacuum, devoid of physical contact with other atomic and molecular systems, as well as with the apparatus itself. Confined to a small volume and for a practically unlimited length of time, its few connections with the external environment, such as temperature and the electric and magnetic trapping fields, are well under the experimenter's control. And since the motion of a charged particle in electric and magnetic fields is completely known, the ion can be manipulated with an unequaled freedom and certainty. In this dissertation, two experimental methods which utilize these unique capabilities of ICR spectrometry are explored.
\r\n\r\nIn Chapter 1, the kinetic method is applied to determine the gas phase proton affinity of the zwitterion betaine, (CH\u2083)\u2083N\u207aCH\u2082CO\u2082\u207b. Protonated dimers of betaine with reference bases of known proton affinities are formed by Cs\u207a bombardment of a glycerol solution in an external ion source FT-ICR. Product distributions resulting from off-resonance collisional activation of isolated adducts are analyzed to yield a value of 242 \u00b1 1 kcal/mol for the gas phase proton affinity of betaine. This is 103 kcal/mol less than that of the isoelectronic tert-butylacetate anion, (CH\u2083)\u2083CCH\u2082CO\u2082\u207b, and the difference can be attributed to the electrostatic dipolar stabilization of the carboxylate anion in betaine. In addition, a general analysis of the kinetic method is presented based on RRKM unimolecular reaction theory. This analysis does not assume a Boltzmann distribution of internal energies in the reactant ion and provides a rationalization for the success of the method even when different experimental techniques are used.
\r\n\r\nWhile ICR has proven to be a powerful technique for studying the chemical properties of gas phase ions, it suffers from a serious weakness which prevents full realization of its unique capabilties: The only observable it measures is the mass. This has kept ICR from being widely used to investigate the physical properties of molecular ions. In Chapter 2, a novel method for obtaining high-resolution r.f. and microwave spectra of ions in ICR trap is proposed. Termed internally resonant ion trapping excitation (IRITE), it uses spatially inhomogeneous a.c. electric fields to couple the internal energy states with the ion's translation motion. The resonance absorption of radiation is detected by its effect on the oscillations of the trapped ions, rather than on the radiation. The theoretical concept behind IRITE is introduced, and an experiment designed to demonstrate its feasibility by observing r.f. transitions in HCl\u207a is discussed in details. Combined with ICR's unsurpassed ability to isolate and manipulate chemical systems, this new technique promises to allow chemists to study phenomena previously unobservable even in neutral molecules.
" }, { "name": "Lin, Chih-hsiu", "degree": "PhD", "year": "1999", "title": "Synthesis and characteristics of hyperbranched polyradicals", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212008-095945", "creators": [ { "name": { "family": "Lin", "given": "Chih-hsiu" }, "id": "Lin-C", "display_name": "Lin, Chih-hsiu" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tthb-mt28", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe design, synthesis and magnetic characterization of hyperbranched polyradicals based on triphenylmethyl are described. The precursor polymers are synthesized via unimolecular polymerization with a A[...]B type monomer employing palladium catalyzed Suzuki coupling reaction. The required dibromo-boronic acid monomers are synthesized by a newly developed selective lithium-iodo exchange reaction. The polytrityl methyl ethers are first converted to polytrityl trifluoroacetates. They are then transformed into corresponding polyradicals with various reductants. Cobaltocene proves to be the best choice. Magnetic characterization of the polyradicals, using SQUID magnetometry, indicates the samples contain small ferromagnetic-coupled radical clusters with spin concentration near 20 percent. In a futile attempt to minimize the defects in these systems, similar polyradicals with various substitutions are made. However, high-spin coupling is observed in a control system with neighboring antiferromagnetic interactions. This unexpected result is rationalized with a new mode of ferromagnetic interaction unique to hyperbranched or \ndentrimer systems. The new model provides new insights and implications to the designing of magnetic materials that is not hitherto appreciated.\n\nA polyradical based on phenoxyl radical is also synthesized and characterized. In order to make the system defect-insensitive, the magnetic interaction is transmitted through a conducting polymer backbone. Although this polyradical has a pretty high spin concentration, the S value is only mediocre. Neither does the defect-insensitive property appear.\n" }, { "name": "Lynn, David Michael", "degree": "PhD", "year": "1999", "title": "Water-Soluable Ruthenium Alkylidene Complexes: Synthesis and Applications to Olefin Metathesis in Protic Solvents", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08212024-214619136", "creators": [ { "name": { "family": "Lynn", "given": "David Michael" }, "id": "Lynn-David-Michael", "display_name": "Lynn, David Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "orcid": "0000-0003-3175-4596", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7910-ds67", "abstract": "This thesis describes the application of well-defined ruthenium alkylidene \r\ncomplexes to olefin metathesis in protic solvents. Chapter 2 describes the application of (Cy3P)2Cl2Ru=CHPh to the living ring-opening metathesis polymerization (ROMP) of functionalized monomers in aqueous emulsions. In these systems, monomers were \r\ndispersed in water using a cationic surfactant, and polymerization was initiated by \r\ninjection of a catalyst solution. These polymerizations were shown to take place in the \r\nabsence of chain transfer and chain termination reactions, passing all experimental \r\ncriteria for living systems.
\r\n\r\nChapter 4 describes the synthesis, characterization, and application of ruthenium \r\nalkylidenes of the type (Cy2RP)2Cl2Ru=CHPh bearing charged phosphine ligands. These \r\ncomplexes were completely soluble and stable in protic, high-dielectric solvents such as \r\nmethanol and water. Interestingly, the alkylidene protons in these new complexes were \r\nfound to exchange with deuterons when they were dissolved in perdeuterated protic \r\nsolvents (as described in Chapter 5).
\r\n\r\nChapter 6 describes the application of these new water-soluble alkylidenes to \r\nROMP in aqueous solution. The propagating alkylidenes in these reactions were found to \r\ndecompose on the time scale of the polymerizations. In the presence of a Bronsted acid, \r\nhowever, polymerization was rapid and quantitative. The effect of the acid in these \r\nsystems was twofold-in addition to eliminating hydroxide ions, catalyst activities were \r\nenhanced by protonation of phosphine ligands. These activated alkylidenes were used to \r\ninitiate living polymerizations in aqueous solution. Both chain termination and chain \r\ntransfer reactions were demonstrated to be absent on the time scale of the\r\npolymerizations, and this living polymerization protocol was used to synthesize water\u00ad \r\nsoluble block copolymers.
\r\n\r\nChapter 7 describes the application of water-soluble alkylidenes to the ring-closing \r\nmetathesis (RCM) of diene substrates in water and methanol. These alkylidenes could not \r\nbe used to cyclize \u03b1,\u03c9-dienes due to the instability of the catalytically-active methylidene \r\ncomplexes in these reactions. Substrates containing an internal olefin, however, were \r\nreadily cyclized. The activities of these alkylidene complexes were found to correlate \r\nwith predicted activities based on analyses of the steric and electronic character of the \r\nphosphine ligands in these complexes (as described in Chapter 3).
" }, { "name": "Miller, Seth Adrian", "degree": "PhD", "year": "1999", "title": "Magnetic Interactions in Molecular Materials", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08052025-203130914", "creators": [ { "name": { "family": "Miller", "given": "Seth Adrian" }, "id": "Miller-Seth-Adrian", "display_name": "Miller, Seth Adrian" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/kqj7-pp77", "abstract": "A series of nitronylnitroxide and imino nitroxide radicals have been\r\nmade that incorporate the benzene-hexafluorobenzene macromolecular\r\nsynthon. These systems were designed to self-assemble into a crystal lattice in\r\nsuch a way that a ferromagnetic interaction is propagated. Sixteen systems,\r\nrepresenting a potential total of thirty-two radicals, were investigated. One\r\nsystem was obtained with a stacking that should propagate a ferromagnetic\r\ninteraction. This system, however, also contains a strong antiferromagnetic\r\npathway, and its magnetic properties are unusual and still incompletely\r\nunderstood.
\r\n\r\nA molecule containing two dicyanoquinonediimine units linked meta\r\nthrough a benzene was synthesized. It was found to be a ground state triplet,\r\nas expected. Several metal complexes were synthesized, and the molecule\r\nwas found to interact ferromagnetically with nickel. Crystals of these systems\r\ncould not be obtained.
\r\n\r\nTwo polymers based on the poly(arenemethide) conducting backbone\r\nwere synthesized. At least one of these polymers was found to be unstable on\r\ndoping. Neither system conducts.
" }, { "name": "Parrish, Cynthia Ann", "degree": "PhD", "year": "1999", "title": "Synthesis of an \u03b1,3-Dehydrotoluene Biradical Precursor with DNA Cleaving Activity and Studies Directed Toward the Total Synthesis of Tetracycline", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09122016-085802807", "creators": [ { "name": { "family": "Parrish", "given": "Cynthia Ann" }, "id": "Parrish-Cynthia-Ann", "display_name": "Parrish, Cynthia Ann" } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "orcid": "0000-0002-5749-7869", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3m0y-w259", "abstract": "The synthesis and characterization of a model of the enediyne antibiotics is\r\ndescribed. The prepared conjugate consists of an \u03b1,3-dehydrotoluene biradical precursor\r\ntethered to an N-methylpyrrolecarboxamide minor groove binding element. The conjugate\r\nis shown to bind and cleave DNA with sequence selectivity. The binding domain is shown\r\nto localize the allene-ene-yne effector domain for sequence-selective DNA cleavage at\r\nmicromolar concentrations of substrate. The time course of DNA cleavage parallels the rate\r\nof cyclization of the bioconjugate in organic solvent to form an \u03b1,3-dehydrotoluene\r\nbiradical. These results indicate that the (Z)-allene-ene-yne functional group is a viable\r\neffector domain for the cleavage of DNA upon mild thermal activation.
\r\n\r\nSynthetic studies directed toward a concise and versatile synthesis of the antibiotic\r\ntetracycline are described. A strategy based on an isobenzofuran Diels-Alder cycloaddition\r\nto assemble the two halves of tetracycline is presented. The synthesis of the phthalide lefthand\r\nhalf is shown in five steps with 56% overall yield from commercially available\r\nstarting materials. Several isobenzofuran Diels-Alder reactions are described that model\r\nthe proposed condensation of the two halves of tetracycline. Specifically, a thermal DielsAlder\r\nreaction is successfully demonstrated with an enone dienophile containing an a-ester\r\nfunctional group. The synthesis of 6-dimethylaminomethyl-2,2-dimethyl-1,3-dioxin-4-one\r\nas a protected and fully functionalized right-hand half of the A ring of tetracycline is\r\ndescribed. Strategies are discussed that aim to utilize this substrate in the synthesis of the\r\nright-hand half of tetracycline. A novel and potentially rapid route involving intermediate\r\n2,4- or 2,5-cyclohexadienones from the oxidation of phenol precursors is briefly\r\nexamined.
" }, { "name": "Sauve, Genevieve", "degree": "PhD", "year": "1999", "title": "Dye sensitization of nanocrystalline titanium dioxide with osmium and ruthenium polypyridine complexes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-04222009-131406", "creators": [ { "name": { "family": "Sauve", "given": "Genevieve" }, "id": "Sauve-G", "display_name": "Sauve, Genevieve" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TR9M-HZ96", "abstract": "The goal of this work is to explore the idea of replacing the ruthenium metal center of polypyridine complexes with osmium to increase the overlap between the spectral response of the \"Gratzel cell\" and the solar spectrum. A series of osmium polypyridine dyes with various ground state reduction potentials has been synthesized, purified, characterized and utilized to sensitize nanoporous titanium dioxide electrodes to solar radiation. The dyes are ML'2(NCS)2, ML'2(CN)2, ML'3^2+ and ML2L'^2+ where M is Os(II) or Ru(II), L is bipyridine and L' is 4,4'-dicarboxy-2,2'-bipyridine. The visible absorption spectra of the Os complexes showed an additional absorption band at longer wavelengths than the Ru complexes. The spectral response and current-voltage properties of electrodes modified with the Os dyes have been compared with their Ru analogs. In general, the Os dye showed a similar maximum external quantum yield, an enhanced response at longer wavelengths, a higher photocurrent density and a similar open-circuit voltage than th Ru analog. The Os complexes thus appear to be promising sensitizers for energy conversion applications. The only discrepancy in this trend was observed for the OsL'2(NCS)2 complex, which showed a much lower maximum external quantum yield, lower photocurrent and lower open-circuit voltage than the Ru analog. Experiments suggest that the regeneration rate of Os(II)L'2(NCS)2 by iodide does not compete effectively with the regeneration rate of the dye by the electron in the TiO2. The ground-state redox potential of Os(II/III)L'2(NCS)2 (+0.42 V vs aq SCE in methanol) may represent a limit on how negative the redox potential of the dye can be to obtain efficient regeneration of the sensitizer by I-/13-. For electrodes with very low dye coverage, the open-circuit voltage was mainly determined by the reduction of I3-, whereas for high dye coverage, the open-circuit voltage also depended on the nature of the complex and on the dye loading level.\n" }, { "name": "Schense, Jason Charles", "degree": "PhD", "year": "1999", "title": "Enzymatic incorporation of bidomain peptides into fibrin matrices for directed enhancement of three-dimensional in vitro neurite outgrowth and in vivo nerve regeneration", "advisor": "Hubbell, Jeffrey A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242008-092332", "creators": [ { "name": { "family": "Schense", "given": "Jason Charles" }, "id": "Schense-J-C", "display_name": "Schense, Jason Charles" } ], "advisors": [ { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "advisor", "display_name": "Hubbell, Jeffrey A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Tirrell", "given": "David A." }, "id": "Tirrell-D-A", "role": "member", "display_name": "Tirrell, David A." }, { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "member", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Patterson", "given": "Paul H." }, "id": "Patterson-P-H", "role": "member", "display_name": "Patterson, Paul H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2q3f-vw87", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nIn this research, fibrin has been enzymatically modified using the transglutaminase, factor XIIIa, to incorporate bioactive domains from extracellular matrix and cell surface proteins. Fibrin was chosen as a base matrix as it is sensitive to cell-derived and cell-regulated protease activity. In order to improve the bioactive character of the fibrin, bi-domain peptides were designed where one domain contained a bioactive sequence and the other contained a factor XIIIa substrate sequence. These factor XIIIa substrates were derived from fibrinogen, [...]-plasmin inhibitor and a nonbiological substrate. Each of these peptides were then covalently incorporated into the fibrin during coagulation through the action of the enzyme, factor XIIIa, with the sequence from [...]-plasmin inhibitor incorporating at levels up to 8.2 mol peptide/mol fibrinogen.\n\nInitially, these enzymatically modified fibrin gels were utilized in an academic study to probe the mechanisms involved in RGD-mediated three-dimensional cell migration. Two separate RGD sequences, one linear and one cyclic, were individually incorporated into fibrin matrices and the effect on neurite migration was measured, and it was shown that both RGD peptides have an adhesive-like, biphasic effect on cell migration. The density of peptide corresponding to maximal neurite outgrowth was lower for the cyclic than the linear peptide. However, since the cyclic RGD is a stronger binding sequence, it is likely that these two peptide densities represent a similar adhesive quality.\n\nDevelopment of enzymatically-modified fibrin matrices was also specifically directed towards enhancement of peripheral nerve regeneration. Peptides were individually incorporated in a concentration series and it was shown that these peptides, including RGD, HAV, IKVAV, YIGSR or RNIAEIIKDI, could improve neurite outgrowth by approximately 20%. A series of formulations were then tested, whereby multiple bioactive peptides were co-cross-linked into fibrin gels. One formulation, which contains the four laminin-derived sequences, RGD, IKVAV, YIGSR and RNIAEIIKDI, incorporated in equimolar densities of 1.7 mol/mol proved to enhance neurite outgrowth by 75% over unmodified fibrin. This formulation was then tested as a filler material for growth guides in peripheral nerve repair. Through these experiments, it was demonstrated that enzymatically modified fibrin is both nontoxic and capable of enhancing nerve regeneration." }, { "name": "Severin, Erik J.", "degree": "PhD", "year": "1999", "title": "Array-based vapor sensing using conductive carbon black-polymer composite thin film detectors", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-12272004-162841", "creators": [ { "name": { "family": "Severin", "given": "Erik J." }, "id": "Severin-E-J", "display_name": "Severin, Erik J." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HHS2-DJ06", "abstract": "A simple, broadly responsive detector array, based on polymer-carbon black composites that can detect, classify, and quantify various vapors and vapor mixtures is described. The individual detector elements of the array are constructed from films consisting of carbon black particles dispersed into insulating organic polymers. The carbon black provides an electrically conductive network in the films, whereas the different organic polymers are the source of chemical diversity between elements in the detector array. Swelling of the polymer upon exposure to a vapor increases the electrical resistance of the film by disrupting the conductive network of carbon black particles, thereby providing a simple means for monitoring the presence of a vapor. The dc electrical resistance change of an individual composite is shown to be consistent with the predictions of percolation theory. The differing gas-solid partition coefficients between vapor analytes for the various polymers of the detector array produce a characteristic pattern of resistance changes for each analyte. The response of these detectors is linear with variations in analyte concentration, allowing quantification as well as identification of a test analyte. This type of detector array can be used to discriminate different classes of analyte molecules (such as aromatics from alcohols) as well as those within a particular class (such as benzene from toluene and methanol from ethanol). Additionally, by using polymers with chiral subunits, enantiomerically different vapors can be discriminated. Principle component data analysis is used to identify and quantify airborne analytes and the relative compositions of simple gas mixtures. Integration of the electrical resistance signals with data analysis software has made sensing and analysis functions possible in a compact, low-power, simple vapor sensor device." }, { "name": "Spangler, Randall Richard", "degree": "PhD", "year": "1999", "title": "Rule-based analysis and generation of music", "advisor": "Goodman, Rodney M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02262008-114413", "creators": [ { "name": { "family": "Spangler", "given": "Randall Richard" }, "id": "Spangler-R-R", "display_name": "Spangler, Randall Richard" } ], "advisors": [ { "name": { "family": "Goodman", "given": "Rodney M." }, "id": "Goodman-R-M", "role": "advisor", "display_name": "Goodman, Rodney M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "cns" ], "doi": "10.7907/YXTQ-4057", "abstract": "We develop a rule-based system for the purpose of analyzing musical examples to extract probabilistic rules of harmony; these rules are then used to generate new harmony in response to a melody input in real-time. A representation of music derived from the figured bass is developed which is suitable for embodying the harmonic content of a piece of music in a format suitable for machine learning. Algorithms are developed to convert music between this representation and standard MIDI files. An efficient algorithm for extracting raw rules from examples is presented, along with a comparison of its behavior to alternative methods such as hashing and hybrid algorithms. Processes to refine the rules produced by the previous algorithm into a more compact representation are shown, including considerations for weighting rules based on the types of errors they make in addition to their accuracy. Psychophysics experiments are performed to measure the perception of harmonic errors. The results of these experiments allow the development of new algorithms to generate rules which make less noticeable errors. The techniques developed above are used to build a rule-based system for real-time accompaniment.\r\n" }, { "name": "Szewczyk, Jason W.", "degree": "PhD", "year": "1999", "title": "Design of ligands for sequence-specific recognition of the minor-major grooves of DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282006-112749", "creators": [ { "name": { "family": "Szewczyk", "given": "Jason W." }, "id": "Szewczyk-J-W", "display_name": "Szewczyk, Jason W." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zt1g-kq41", "abstract": "The two most powerful chemical approaches to date for the sequence-specific recognition of double helical DNA are the pyrrole-imidazole polyamides in the minor groove and oligonucleotide-directed triple-helix formation in the major groove. Described here are the design and synthetic methods to combine the two models for DNA recognition in a single motif. A hairpin polyamide connected to a pyrimidine-oligonucleotide via a simple aliphatic linker was shown to simultaneously recognize the major and minor grooves of DNA at subnanomolar concentrations (Chapter 2). Development of versatile solid phase methodology expanded the protocols for the synthesis of pyrrole-imidazole polyamides to include polyamide-oligonucleotide conjugates. Utilizing the pyrrole-imidazole polyamide moiety as a sequence-specific dimerization domain afforded a class of cooperative polyamide oligonucleotides which bound a 27 bp target with a 2.7 kcal mol(-1) increase in binding energy relative to the unlinked subunits (Chapter 3). Introduction of a new linker design created an extended polyamide-oligonucleotide motif to specifically target 31 contiguous base pairs of DNA at subnanomolar concentrations (Chapter 4). Polyamide-oligonucleotides combine the two binding models to create a paradigm for simultaneous recognition of the major-minor grooves of DNA with synthetic ligands.\n\nFor the pyrrole-imidazole polyamide model, sequence specificity depends on side-by-side aromatic amino acid pairings. An Im/Py pair distinguishes G \u2022 C from C \u2022 G and both of these from A,T base pairs. A Py/Py pair specifies A,T from G,C but does not distinguish A\u2022T from T\u2022A. To break this degeneracy a new aromatic amino acid, 3-hydroxypyrrole (Hp), was synthesized to test for pairings which discriminate A \u2022 T from T \u2022 A. Replacement of a single hydrogen atom with a hydroxy group in a Hp/Py pairing regulates affinity and specificity by an order of magnitude. By incorporation of a third aromatic amino acid, hydroxypyrrole-imidazolepyrrole polyamides form four ring pairings (Im/Py, Py/Im, Hp/Py, Py/Hp) which distinguish all four Watson-Crick base pairs in the minor groove of DNA (Chapter 5)." }, { "name": "Tomooka, Craig Shigeru", "degree": "Masters", "year": "1999", "title": "Use of Manganese(V) Nitrides as Enantioselective Nitrogen-Transfer Reagents", "advisor": "Carreira, Erick Moran", "url": "https://resolver.caltech.edu/CaltechTHESIS:12062017-140954903", "creators": [ { "name": { "family": "Tomooka", "given": "Craig Shigeru" }, "id": "Tomooka-Craig-Shigeru", "display_name": "Tomooka, Craig Shigeru" } ], "advisors": [ { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "advisor", "display_name": "Carreira, Erick Moran" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6t7v-s157", "abstract": "Once activated, manganese(V) nitrides have been shown to efficiently transfer nitrogen to furanoid. glycals. This process, followed by hydrolysis, forms the corresponding amino alcohols in high yield and diastereoselectivity. The isolation of an intermediate oxazoline and the ability to form this oxazoline from the amino alcohol was also discovered. The formation of chiral manganese nitrides is also described. After considerable experimentation, the transfer of nitrogen in these cases resulted in enantiomeric excesses of up to 92% accompanied by high yields." }, { "name": "Trauger, John Wesley", "degree": "PhD", "year": "1999", "title": "Design of DNA-binding polyamides for regulation of gene expression", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282006-111905", "creators": [ { "name": { "family": "Trauger", "given": "John Wesley" }, "id": "Trauger-J-W", "display_name": "Trauger, John Wesley" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q4HD-PT84", "abstract": "Polyamides containing N-methylimidazole and N-methylpyrrole amino acids are synthetic ligands that bind DNA by forming side-by-side complexes in the minor groove. Sequence-specificity depends on side-by-side aromatic amino acid pairings: imidazole (Im) opposite pyrrole (Py) targets a G\u2022C base pair, Py/Im targets C\u2022G and Py/Py targets T\u2022A and A\u2022T. This thesis describes work centered on the design of polyamide motifs that increase the binding site size limit, binding affinity and sequence repertoire of polyamides. In addition, polyamides were designed to bind within the regulatory regions of selected genes, which allowed investigations of polyamides as regulators of gene expression.\n\nIn Chapter Two, [beta]-alanine was found to optimally link three-ring polyamide subunits in an extended conformation, allowing recognition of 9 and 13 base pair sequences. This result extended the binding site size limit of polyamides and identified a useful polyamide building block. Chapter Three describes the ability of C-terminal amino acids to modulate the DNA-binding affinity and specificity of polyamide dimers. Chapters Seven, Eight, Nine and Ten describe additional polyamide motifs for recognition of 9-16 base pair sequences.\n\nChapter Four describes eight-ring hairpin polyamides that bind respective six base pair target sequences with subnanomolar affinity and discriminate match from single-base pair mismatch sites. These results showed that polyamides can bind predetermined DNA sequences with affinity and specificity comparable to DNA-binding gene-regulatory proteins.\n\nIn Chapters Five and Six, studies of hairpin polyamides that incorporate [beta]-alanine ([beta]) residues to correctly position internal imidazoles showed that the choice of a Py/Py, Py/[beta] or [beta/beta] pair depends on the sequence composition of the target site. These results expanded the sequence repertoire of polyamides and contributed to polyamide design guidelines that predict, for a given target sequence, when and where [beta]-alanine residues are needed.\n\nChapter Eleven describes polyamides that bind DNA sequences proximal to transcription factor binding sites within the promoter regions of the 5S rRNA gene, the HIV-1 genome and the HER2/neu gene. The results of biological assays using these polyamides demonstrated that polyamides are cell-permeable, can interfere with transcription factor-DNA interactions and can inhibit the transcription of specific genes and viral replication within living cells.\n" }, { "name": "Unger, Marc Alexander", "degree": "PhD", "year": "1999", "title": "Advances in High-Resolution Probes for Scanning Probe Microscopy", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01282026-190810142", "creators": [ { "name": { "family": "Unger", "given": "Marc Alexander" }, "id": "Unger-Marc-Alexander", "display_name": "Unger, Marc Alexander" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Quake", "given": "Stephen R." }, "id": "Quake-S-R", "orcid": "0000-0002-1613-0809", "role": "member", "display_name": "Quake, Stephen R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xqdw-8009", "abstract": "This thesis describes work designed to improve the resolution of Scanned Probe\r\nMicroscopy (SPM). The work falls into three main sections. Sections I and III are both\r\naimed towards making scanned probes with atomic resolution by attaching a single sharp\r\nmolecule to the end of a tip. Section II is aimed towards making a near-field \"optical\"\r\nprobe in the infrared wavelengths.
\r\n\r\nThe first section centers on the Touchdown Scheme, a path towards attachment of a\r\nsingle sharp molecule at the end of a conventional atomic force microscope (AFM) tip.\r\nThe ability to derivatize the tip with a good monolayer was required. Chapters 2 and 3\r\ndescribe the development and optimization of surface chemistry for this purpose.\r\nIncluded in this development were methods for making chemically patterned surfaces\r\nwith simple photolithography techniques. Chapter 1 describes mathematical methods to\r\nextract intermolecular pair potentials from AFM force measurements.
\r\n\r\nThe second section describes a technique for etching infrared-transmitting fibers to very\r\nsharp points. These sharpened fibers serve as probes in a Near-field Scanning Infrared\r\nMicroscope (NSIM). Making tips by chemical etching is far easier than heat-pulling, and\r\nthe etched probes have a power throughput several orders of magnitude higher than\r\npulled probes.
\r\n\r\nThe third section centers on attempts to attach a single molecule to the end of a single\r\ncarbon nanotube for use as an ultrasharp AFM tip. Bulk derivatization and labeling\r\nchemistry of carbon nanotubes was developed and successfully applied to single mounted\r\nnanotubes. Along the way, several new methods for handling nanotubes were developed.\r\nThese include methods for non-oxidative cleaning, making stable suspensions,\r\nfluorescence staining, and removal from solution without coalescence.
" }, { "name": "Vicic, Michael", "degree": "PhD", "year": "1999", "title": "Rheology and microstructure of complex fluids: dispersions, emulsions and polymer solutions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072005-160903", "creators": [ { "name": { "family": "Vicic", "given": "Michael" }, "id": "Vicic-M", "display_name": "Vicic, Michael" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NEB8-NH16", "abstract": "The rheology and microstructure of complex fluids are intimately related, and this relationship is explored to gain a deeper understanding of the physics of colloidal dispersions, emulsions and polymer solutions.\n\nThe nonequilibrium microstructure and rheological properties of dispersions in steady, simple shear flow are calculated by solving the Smoluchowski equation as a function of dimensionless shear rate. The particles have a purely repulsive interaction with an hydrodynamic radius, a, and a thermodynamic radius, b. For hard spheres, b/a --> l, shear thinning is caused by a decrease in the Brownian contribution since Brownian motion becomes less important with increasing shear. Shear thickening occurs because of an increase in the hydrodynamic viscosity caused by the increased probability of finding particles near contact with increasing shear when particles hydrodynamically interact. The first normal stress difference changes sign since Brownian and hydrodynamic contributions have opposite signs, while the second normal stress difference is always negative. Scaling arguments are made to extend these dilute results for concentrated dispersions. Similar calculations and analyses are performed to study the effects of hydrodynamic interactions and varying b/a ratios on rheology and microstructure.\n\nScaling arguments for the volume-fraction dependence of the bulk stress of emulsions at the critical capillary number are presented along with experimental evidence using an unstabilized emulsion of polymerized castor oil dispersed in polydimethylsiloxane. It is shown that the droplet contribution to both the relative shear viscosity and first normal stress difference is linear in volume fraction for a given viscosity ratio for dilute to moderately-concentrated emulsions in steady, simple shear flow.\n\nStress jump measurements are performed for the first tune for (i) shear startup and (ii) polymer solutions in shear. The startup viscosity of a polymer solution of polyacrylamide in fructose-water at equilibrium is equal to the measured high frequency dynamic viscosity, as expected, since both methods measure the viscous contribution to the viscosity associated with the equilibrium microstructure. Since polymer solutions exhibit stress jumps different from the solvent viscosity, effects of shear on the hydrodynamic viscosity can be investigated." }, { "name": "Wagner, Paul A.", "degree": "PhD", "year": "1999", "title": "Structural Investigation of Zeolites", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192025-175557925", "creators": [ { "name": { "family": "Wagner", "given": "Paul A." }, "id": "Wagner-Paul-A", "display_name": "Wagner, Paul A." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/t8qz-qa09", "abstract": "Microporous materials (including zeolites) that contain molecular-sized pores and\r\ncavities have found wide-spread use in industry as molecular sieves for chemical separations,\r\nas ion-exchangers for detergents and as heterogeneous, shape-selective catalysts. The number\r\nof unique molecular sieve structures discovered over the past few decades has burgeoned and\r\ncurrently is over 121.
\r\n\r\nKnowledge of the crystal structure of these microporous solids can provide important\r\ninsights into their properties that can ultimately lead to the design of desirable materials.\r\nHowever, the structure solution of microporous materials can be challenging because they tend\r\nto form as micron or submicron sized crystals that are too small for single crystal X-ray\r\nanalysis. Thus, the objective of this work is to develop and apply new techniques for solving\r\nthe structures of microporous materials that tend to form micro- and nanocrystals and to utilize\r\nthese structural investigations to gain a more thorough understanding of the zeolite/ organic\r\nstructure directing agent (SDA) interactions that lead to the observed zeolite phase selectivity in\r\ntheir synthesis.
\r\n\r\nIn the absence of single crystal data, structure solution and refinement have typically\r\nrequired the use of powder X-ray data. The difficulty in solving crystal structures from\r\npowder X-ray data is that the three dimensions of information available in a single crystal data\r\nset are collapsed into one dimension (d-spacing) in a powder X-ray data set. If the reflections\r\nin the powder X-ray data are significantly overlapping then solving the crystal structure from\r\nthis data can be extremely difficult. Several techniques are applied here for solving\r\nmicroporous crystal structures from powder X-ray data.
\r\n\r\nThe structure solution of CIT-5 (California Institute of Technology Number 5), a new\r\nhigh-silica molecular sieve synthesized under hydrothermal conditions in the presence of\r\nN(16) methylsparteinium and lithium cations, is obtained though an iterative process of model\r\nbuilding and comparison of the simulated powder X-ray data with the experimental powder X-ray\r\ndata. Rietveld refinement of the synchrotron powder X-ray data supports the symmetry and\r\nspace group assignment for the structure as Pmn21(No.31) with refined unit cell parameters of\r\na=l3.6738(8) \u00c5, b=S.0216(3) \u00c5 and c=25.4883(7) \u00c5 (V=1750.1 \u00c53) and confirms that CIT-5\r\nis the first ordered zeolite to contain one-dimensional extra-large pores circumscribed by\r\n14 tetrahedral-atoms (14 MR).
\r\n\r\nComputational techniques for solving the structures of microcrystals from powder Xray\r\ndata are continuing to increase in sophistication and capability. The crystal structures of\r\ntwo high-silica molecular sieves, SSZ-44 and SSZ-35, are solved using Fourier recycling and\r\nrepresents the first application of this new computational technique for solving novel high-silica\r\nzeolite structures from powder X-ray data. Both materials contain unusual 1-dimensional\r\npores circumscribed by 10 and 18 membered-rings, and are the first high-silica zeolites found\r\nthat possess pores containing greater than 14 membered-rings.
\r\n\r\nElectron diffraction data, obtained from a transmission electron microscope (TEM),\r\nhas inherent advantages over X-ray data for analyzing small crystals due to the stronger\r\ninteraction between the electron beam and matter compared to X-rays. This stronger\r\ninteraction allows a single crystal diffraction data set to be obtained from much smaller\r\ncrystals. Provided that the interaction of the incident electron beam with the crystal is\r\nnearly kinematical direct methods can be used as a powerful tool for obtaining the phase\r\ninformation required to solve the crystal structure.
\r\n\r\nThe development of electron diffraction methods for solving the structure of\r\nnanocrystals is described and the application of this technique to solve the structure of a\r\nlarge-pore, high-silica zeolite, SSZ-48, that contains an occluded organic structure directing\r\nagent is presented. The structure is confirmed by electron diffraction refinement and by\r\nhigh resolution transmission electron microscopy and is found to contain a one-dimensional\r\npore system circumscribed by 12 tetrahedral atoms (12 MR). SSZ-48 is the most complex\r\nthree-dimensional material to be solved at atomic resolution using electron diffraction\r\nmethods and illustrates the power of electron diffraction data for resolving the structures of\r\nmaterials that form crystals too small for standard single crystal X-ray analysis.
\r\n\r\nThese investigations into the structural details of micro- and nanocrystalline\r\nmicroporous materials can be utilized to gain a more thorough understanding of the zeolite/\r\norganic structure directing agent (SDA) interactions that lead to the observed zeolite\r\nsynthesis phase selectivity. Two studies are conducted to probe the relationship between\r\nthe organic structure directing agent and the zeolite framework that is formed from its use.
\r\n\r\nThe first study probes the interaction between the CIT-5 framework and the N(l)-\r\nmethyl-\u03b1-isosparteine SDA I that is found to be a more effective structure directing agent\r\nfor CIT-5 than the diastereomer N(l6)-methylsparteinium II originally used to direct this\r\nnew high-silica zeolite. Molecular modeling calculations reveal that I is capable of forming\r\na greater number of van der Waals interactions with the framework than II thereby\r\nproviding a greater degree of stabilization for the CIT-5 structure as compared to II.
\r\n\r\nFinally, a study into the guest/host interactions between three new zeolite\r\nstructures, SSZ-35, SSZ-36 and SSZ-39 and the 37 organic structure directing agents that\r\nare capable of directing for these zeolites is presented. The size and shape of the organic\r\nSDAs presented in this study are designed in order to obtain novel, open framework\r\nzeolites. The design effort focused on synthesizing large rigid spheroidal SDAs that will\r\npreclude the crystallization of the commonly observed clathrates and straight I-dimensional\r\nchannel system zeolites that result when either small or rigid elongated molecules are\r\nemployed as SDAs. Computational calculations of the organic/inorganic energy of\r\ninteractions provided significant insights into the observed zeolite phase selectivity by the\r\norganic SDAs. The molecular modeling investigations presented here highlight the\r\npotential for developing a rational route to the design of desirable zeolite frameworks.
" }, { "name": "Wang, Guangyang", "degree": "PhD", "year": "1999", "title": "Design and Synthesis of Photoreleasable Ubiquinol and its Biologically Active Analogues", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192025-174058689", "creators": [ { "name": { "family": "Wang", "given": "Guangyang" }, "id": "Wang-Guangyang", "display_name": "Wang, Guangyang" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/str8-et07", "abstract": "Every organism contains a respiratory chain that converts energy from food\r\nmolecules into adenosine triphosphate (ATP) which drives a multitude of biochemical\r\nreactions. A respiratory chain achieves this via a series of integral membrane protein\r\ncomplexes that produce a transmembrane proton gradient as a result of sequential\r\nelectron transfers through these complexes. Ubiquinol and ubiquinol oxidase enzymes are\r\nimportant components of the respiratory chains in most aerobic organisms. The energy\r\nfrom the oxidation of ubiquinol is used to promote the generation of an electrochemical\r\ngradient across the cytoplasmic or mitochondrial membrane for ATP synthesis.
\r\n\r\nStudy of the catalytic mechanisms of ubiquinol oxidase enzymes is very difficult\r\ndue to the structural complexity of these proteins. Since electron input from ubiquinol\r\nplays a very important role in enzyme function, to understand the detailed enzymatic\r\nmechanism of these enzymes, it is critical to understand the kinetics of individual\r\nelectron transfer events in enzymatic turnover. On account of the rapidity of electron\r\ntransfer in these proteins, traditional stopped-flow methods for following the kinetic\r\ncourse of electron transfer reactions are limited, due to the millisecond order of mixing\r\ndead time.
\r\n\r\nPhotochemical initiation of ubiquinol release, a method of circumventing the\r\nmixing limitation, is investigated. The method is based on the photolysis of small\r\norganic protecting groups, or \"cage\" compounds. These cage compounds rendered\r\ninactive quinol-cage complex prior to photolysis by linking to the key functional groups\r\nin ubiquinol or by generating a large steric hindrance that blocks ubiquinol binding.\r\nPhotolysis of the cage-quinol complex rapidly releases the two-electron donor and\r\ntriggers on the enzymatic electron transfer. Such a complex can be used not only in\r\nenzymatic electron transfer study, but also in time-resolved protein conformation change\r\nstudy.
\r\n\r\nThe cage compounds that have been studied for this purpose are based on 3',5'-\r\ndimethoxybenzoin (DMB). Esters of DMB are known to photolyze rapidly (on the sub-nanosecond\r\ntime scale), generating the parent acid and the inert photoproduct 5,7-\r\ndimethoxy-2-phenylbenzofuran. A water-soluble derivative of 3', 5'-dimethoxybenzoin\r\n(DMB),3',5'-bis (carboxylmethoxy)benzoin (BCMB) was linked to the hydroxy group\r\nin ubiquinol via a carbonate linkage. Such a complex has been measured to yield a\r\nphotorelease rate of \r\n990s-1 in detergent solution. Another cage compound, N-hydroxypyridine-\r\n2-thione, was also used to \"cage\" ubiquinol via a carbonate linkage. In\r\nthe presence of efficient hydrogen donor, such as mercaptoethanol, such a complex has\r\nthe potential to photolytically generate ubiquinol in sub-millisecond time scale.
\r\n\r\nA series of ubiquinol analogues were synthesized with a carboxylic acid\r\nfunctionality attached to benzoquinone at different positions. These analogues can be\r\n\"caged\" by BCMB via an ester bond with the potential to trigger electron transfer in sub-microsecond.
\r\n\r\nIn the mean time, efforts have been made to elucidate the controversial photolysis\r\nmechanisms of benzoin compounds by synthetic substitution study and quantum\r\nchemistry calculation. Very efficient synthetic schemes for the preparation of large-size\r\ncombinatorial libraries of benzoins were developed.
" }, { "name": "Weck, Marcus", "degree": "PhD", "year": "1999", "title": "Olefin Metathesis for the Synthesis of Supramolecular Structures", "advisor": "Grubbs, Robert H.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292024-145816529", "creators": [ { "name": { "family": "Weck", "given": "Marcus" }, "id": "Weck-Marcus", "display_name": "Weck, Marcus" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "co-advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/92mk-rc46", "abstract": "The research presented in this thesis combines the versatility of olefin metathesis\r\nwith the concept of supramolecular chemistry. Several supramolecular architectures, such\r\nas liquid crystalline polymers, catenanes, and self-assembled monolayers were designed\r\nwith olefin metathesis.
\r\n\r\nChapter 1 introduces several ABA triblock copolymers synthesized by welldefined,\r\nbimetallic catalysts and norbomene-based monomers. Sequential addition of these\r\nmonomers yielded the triblock copolymers with low polydispersities and controlled\r\nmolecular weight.
\r\n\r\nOne objective of this thesis is the synthesis of side-chain liquid crystalline material\r\nvia ROMP. Therefore the synthesis and polymerization of a number of norbomene and\r\ncyclobutene-based monomers bearing nitrostilbene side-chains is presented. The liquid\r\ncrystalline behavior was determined by differential scanning calorimetry (DSC) and optical\r\npolarized microscopy. The poly(norbomene)s show nematic mesophase behavior whereas\r\nthe poly(cyclobutene)s display enantiotropic smectic A mesomorphism. A 1:1 diblock\r\ncopolymer also shows enantiotropic smectic A mesomorphism. This difference in\r\nmesophase behavior was attributed to varying degrees of backbone rigidity.
\r\n\r\nAs an extension of the work described above, Chapter 3 describes the synthesis and\r\ncharacterization of discotic liquid crystalline material for their use as hole transport\r\nmaterials. Norbornene- and cyclobutene monomers containing triphenylenes were\r\nsynthesized introducing a newly developed strategy for the synthesis of the triphenylene-based\r\nside-chain. The mesomorphic behavior of the polymers was investigated by DSC\r\nand powder diffraction X-ray scattering and was identified as discotic liquid crystalline.
\r\n\r\nIn an effort to synthesize a variety of supramolecular structures via RCM, Chapter 4\r\nillustrates a new strategy for obtaining self-assembled interlocked and intertwined\r\narchitectures. Three different self-assembly approaches based on metal templating,\r\nhydrogen bonding, and \u03c0-\u03c0 interactions followed by RCM to yield catenane or rotaxane\r\nstructures are introduced.
\r\n\r\nThe final chapter presents a new strategy to polymerize directly from surfaces\r\nthrough ROMP. Using a two-step self-assembly approach, a 'molecular wire' molecule\r\ncontaining norbornene and thiol was anchored to gold surfaces pretreated with\r\ndodecanethiol. Addition of a ruthenium catalyst to the functionalized surface followed by\r\naddition of monomer resulted in the synthesis of polymer brushes on the surface. The\r\npolymer brushes were characterized by scanning tunneling microscopy, atomic force\r\nmicroscopy, and scanning electron microscopy.
" }, { "name": "White, Sarah", "degree": "PhD", "year": "1999", "title": "Recognition of All Four Watson-Crick Base Pairs in the Minor Groove of DNA by Synthetic Ligands", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-141420", "creators": [ { "name": { "family": "White", "given": "Sarah" }, "id": "White-Sarah", "display_name": "White, Sarah" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wxsr-8x37", "abstract": "The design of synthetic ligands that read the information stored in the DNA double helix has been a long standing goal at the interface of chemistry and biology. Cell-permeable small molecules which target predetermined DNA sequences offer a potential approach for the regulation of gene-expression. Oligodeoxynucleotides that recognize the major groove of double-helical DNA via triple-helix formation bind to a broad range of sequences with high affinity and specificity. Although oligonucleotides and their analogs have been shown to interfere with gene expression, the triple helix approach is limited to purine tracks and suffers from poor cellular uptake. The subsequent development of pairing rules for minor groove binding polyamides containing pyrrole (Py) and imidazole (Im) amino acids offers a second code to control sequence specificity. An Im/Py pair distinguishes G\u2022C from C\u2022G and both of these from A\u2022T/T\u2022A base pairs. A Py/Py pair specifies A,T from G,C but does not distinguish A\u2022T from T\u2022A. In order to break this degeneracy, a new aromatic amino acid, 3-hydroxypyrrole (Hp), has been added to the repertoire to test for pairings which discriminate A\u2022T from T\u2022A. We find that replacement of a single hydrogen atom with a hydroxy group in a Hp/Py pairing regulates affinity and specificity by an order of magnitude. By incorporation of a third amino acid, hydroxypyrrole-imidazole-pyrrole polyamides form four ring-pairings (Im/Py, Py/Im, Hp/Py, and Py/Hp) which distinguish all four Watson-Crick base pairs in the minor groove of DNA." }, { "name": "Wilhelm, Thomas Edward", "degree": "PhD", "year": "1999", "title": "Easier and More Efficient Methods for the Generation of Metathesis Catalysts: Investigations into Group VI and VII", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062023-220054560", "creators": [ { "name": { "family": "Wilhelm", "given": "Thomas Edward" }, "id": "Wilhelm-Thomas-Edward", "display_name": "Wilhelm, Thomas Edward" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3d4p-py55", "abstract": "Chapter 1:
\r\n\r\nA high yield procedure for generating the ruthenium hydride complexes\r\nRu(H)(H2)Cl(PR3)2 (R=Cyclohexyl, cyclopentyl, isopropyl) in very high yield is\r\npresented. Following a novel insertion-elimination pathway, these hydrides can\r\nreact with propargyl or vinyl halides to make metathesis active vinyl and alkyl\r\ncarbene species with the general formulas (PR3)2Cl2Ru=CH-CH=CR'2 and\r\n(PR3)2Cl2Ru=CHR', respectively. Tertiary propargyl chlorides like 3-chloro-3-\r\nmethyl-1-butyne work best, yielding Ru-vinyl carbenes in extremely high yield.\r\nAn alternate route is to first add an alkyne, and then add HCl to give similar\r\nspecies.
\r\n\r\nIn attempting to learn about the insertion-elimination mechanism, the\r\ncompounds M(H)Cl(CO)(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) were found\r\nto react with 3-chloro-3-methyl-1-butyne to produce the metathesis inactive\r\ncarbenes with general formula cis-Cl2-trans(PCy3)2(CO)M=CHCH=CMe2. Kinetics\r\nofRu(H)Cl(CO)(PiPr3)2 can only be analyzed qualitatively, but from all of\r\nthe available data a mechanism is proposed for the insertion of hydrides into\r\nalkynes and rearrangement to give carbenes. The compounds\r\nM(H)Cl(CO)2(PR3)2 (M=Ru, Os; R=cyclohexyl, isopropyl) show no alkyne insertion.
\r\n\r\nThe osmium analogs Os(H)3Cl(PCy3)2 and (PCy3)2Cl2Os=CH=CH=CMe2\r\nwere investigated for the ability to generate carbenes. The osmium carbene,\r\nhowever, rapidly transforms to the hydrido-carbyne species (PCy3)2Cl2Os(H)(=CCH=\r\nCMe2). It appears that additional stabilization of the osmium system will\r\nbe necessary to prevent such rearrangement.
\r\n\r\nIt is also presented that (PCy3)2Cl2Ru=CHR' reacts with dihydrogen to\r\ngive H3CR', Ru(H)2(C1)2(PCy3)2, and Ru(H)(H2)Cl(PCy3)2. Theoretically, all\r\nRu(H)2(Cl)2(PCy3)2 can be converted to Ru(H)(H2)Cl(PCy3)2. It is thus possible\r\nto go from hydrides to carbenes, and back to hydrides.
\r\n\r\nChapter 2:
\r\n\r\nComplexes of the type M(O)Cl2(PR3)3 (M=W, Mo; R3=PMePh2, PMe2Ph) were\r\nsynthesized using literature procedures, and shown to react with 3,3-\r\ndiphenylcyclopropene to give the \u03b72-olefin complexes M(O)Cl2(PR3)2(\u03b72-\r\ndiphenylcyclopropene). Spectroscopic data suggest a distorted octahedral structure\r\nfor both, with the oxo ligand in the axial position with the olefin cis to it\r\nand the two mutually trans phosphines in the equatorial plane, which was confirmed\r\nfor M=W with an x-ray diffraction study. The olefin complexes react\r\nwith suitable alkoxides to give the oxo-carbene species M(O)(OR)2(PR3)(=CHCH=\r\nCPh2), the first known single component tungsten and molybdenum oxo-alkylidene\r\nmetathesis catalysts, in which the phosphine is readily displaced\r\nwith THF. For these complexes, spectroscopic data suggest a distorted trigonal\r\nbipyramid with the oxo, alkylidene, and one alkoxide ligand in the equatorial\r\nplane, which was confirmed for M=W by a diffraction experiment. These\r\nalkylidene species are active in olefin metathesis reactions, showing comparable\r\nactivity to similar arylimido complexes previously described; polymerization\r\ndata is presented for norbornene and cyclooctene. In addition, the olefin\r\ncomplexes were shown to be active in olefin metathesis at elevated temperatures.
" }, { "name": "Wu, Sheng", "degree": "PhD", "year": "1999", "title": "Development of Broadly Tunable Parametric Light Sources and Their Application to Alkali Metal - Small Molecule Cluster Spectroscopy", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172025-215507596", "creators": [ { "name": { "family": "Wu", "given": "Sheng" }, "id": "Wu-Sheng", "display_name": "Wu, Sheng" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ztvp-j735", "abstract": "Widely tunable laser sources based on second order nonlinear optical (NLO) conversions\r\nand covering the 200 nm to 3 \u03bcm region have been constructed. Considerable\r\neffort is devoted to achieving reasonable linewidth and efficiency, two critical parameters\r\nfor the practical use of NLO materials in spectroscopic and other experiments.\r\nUsing these devices, the ionization behavior of alkali metal - small molecule clusters\r\nis explored. In particular, the spectroscopic results are used to investigate the physics\r\nof salvation between potassium atoms and ions with small molecules.
\r\n\r\nRecent advances in the fabrication of nonlinear optical materials have led to the\r\ndiscovery of several promising crystal candidates for high power applications. These\r\nadvances, coupled with the rapid progress in high power pulsed pump laser technology,\r\nhave made practically possible widely tunable laser sources based on nonlinear\r\noptical conversions. Three major devices have been developed that provide continuous\r\ncoverage from 200 nm to 3 \u03bcm, and which combine reasonable power efficiency\r\nwith a range of linewidths suitable for various spectroscopic measurements.
\r\n\r\nThe design philosophy throughout is to create practical devices that are as simple\r\nand durable as possible. For example, a compact, low cost OPO based on type II\r\nphase matching in BBO and off-the-shelf optics has been fabricated. The type II BBQ\r\nOPO is fully computer controlled, and provides wide tunability (\u2248 410 nm to 3 \u03bcm)\r\nand relatively narrow bandwidth (\u2248 1 cm-1) in the same package. To generate narrow\r\nbandwidth radiation, e.g., close to the transform limit, an extremely simple, unidirectional\r\nOptical Parametric Generator/Optical Parametric Amplifier (OPG/OPA)\r\nis designed based on an intense nanosecond (ns) pump source. Compared with other\r\nCW laser-seeded optical parametric devices, this OPG/OPA design combines simple\r\noperation with a remarkable insensitivity to the matching of the seed laser frequency\r\nto the OPO cavity mode. Numerical models are used to fully characterize the NLO\r\nbehavior of these cavities, and to optimize their performance.
\r\n\r\nFinally, in order to produce UV harmonics of the fundamental oscillators, a\r\nbroadly tunable harmonic generator which effectively covers the 190 to 420 nm region\r\nhas been constructed. The thermal dephasing problem in high average UV power generation\r\nwith NLO crystals is fully explored for the first time, and a new method of\r\novercoming this thermal dephasing problem is proposed and tested. For each of the\r\ndevices, several experiments had been carried out to characterize their performance,\r\nparticularly their wide tunability, ease of operation, and high power scalability.
\r\n\r\nMost importantly for this thesis, fundamental research on the interaction between\r\npotassium and small molecules such as water, ammonia, and benzene has been carried\r\nout with the above mentioned laser sources by collecting the Photo-Ionization\r\nEfficiency (PIE) ion yield and Zero Kinetic Energy Electron - Pulsed Field Ionization\r\n(ZEKE-PFI) spectra of neutral alkali metal-solvent clusters. The tunable sources\r\nmade it possible to rapidly map out the ionization potentials of the different clusters,\r\nand to thereby estimate the binding energies of the neutral and ionic clusters; while\r\nthe ZEKE-PFI spectra of K(NH3) reveal, as expected, a considerable increase in the\r\nangular anisotropy of the intermolecular forces in the charged clusters. Interestingly,\r\nthe measured pair-pair interaction energies of the dimers stand in contradiction to the\r\nion selectivity achieved by biological systems. Many body forces therefore must contribute\r\nsubstantially to the subtle balancing of forces that operate in the condensed\r\nphase, and the results indicate the importance of further characterization of large clusters,\r\nespecially those with mixed constituents such as K(C6H6)n(H2O)m. Additional\r\napplications in fields as diverse as atmospheric science and molecular astrophysics can\r\nbe expected as NLO materials and processes are further refined.
" }, { "name": "Yu, Bo", "degree": "PhD", "year": "1999", "title": "An engineered mutant of G protein [alpha] subunit that binds xanthine nucleotide and not guanine nucleotide", "advisor": "Simon, Melvin I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06172008-140047", "creators": [ { "name": { "family": "Yu", "given": "Bo" }, "id": "Yu-B", "display_name": "Yu, Bo" } ], "advisors": [ { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "advisor", "display_name": "Simon, Melvin I." } ], "committee": [ { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "chair", "display_name": "Simon, Melvin I." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Sternberg", "given": "Paul W." }, "id": "Sternberg-P-W", "role": "member", "display_name": "Sternberg, Paul W." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/K78Q-9K42", "abstract": "This thesis examines the construction and characterization of mutants of G protein [alpha] subunits that bind xanthine nucleotides, but not guanine nucleotides. G proteins play a critical role in transducing extracellular signals across the cell membrane. The mechanisms of G protein-mediated signal transduction are reviewed in chapter 1.\n\nChapter 2 describes the characterization of the first engineered xanthine nucleotide binding mutant of a G[alpha] subunit, Go[alpha]X (Go[alpha]D273N/Q205L). Go[alpha]X switched nucleotide binding specificity; it bound xanthine nucleotides instead of guanine nucleotides. Go[alpha]X formed an heterotrimer with [beta][gamma] subunits when in the XDP form. Binding of XTP induced a conformational change in Go[alpha]X similar to that of the activated wild-type Go[alpha] and promoted its dissociation from the [beta][gamma] complex.\n\nIn chapter 3, we characterized the receptor interaction of Go[alpha]X. It was able to interact with G protein-coupled receptors effectively; the stimulated m2 muscarinic acetylcholne receptor catalyzed the XTP[gamma]S binding of Go[alpha]X, and the Go[alpha]X[beta][gamma] complex induced the high affinity ligand-binding state in the N-formyl peptide receptor. Interestingly, we found that the empty Go[alpha]X, in the nucleotide-free state, formed a stable complex with receptor and inhibited the activity of Go-coupled receptors in COS-7 cells.\n\nIn chapter 4, we extended this study to two other G proteins. We constructed similar xanthine nucleotide binding mutant proteins in G11[alpha] and G16[alpha] and found that G11[alpha]X (G11[alpha]D277N/Q209L) and G16[alpha]X (G16[alpha]D280N/Q213L) bound XTP[gamma]S and not GTP[gamma]S when expressed in COS-7 cells. Empty G11[alpha] and G16[alpha] mutants also interacted with their cognate receptors and blocked their activity. Similar to Go[alpha]X, both G11[alpha]X and G16[alpha]X retained the receptor specificity of their wild-type proteins and can be used to inhibit subsets of G protein-coupled receptors.\n\nIn chapter 5, we constructed recombinant retroviruses encoding G16[alpha]X, and obtained NIH3T3 cell lines stably expressing the empty G16[alpha] mutants by viral infection. We found that G16[alpha]X blocked the activation of the endogenous thrombin and lysophophatidic acid (LPA) receptors in NIH3T3 cells. These experiments proved that retroviral gene expression can be an effective technique for delivering empty G protein mutants into cells.\n" }, { "name": "Zhong, Dongping", "degree": "PhD", "year": "1999", "title": "Femtosecond molecular dynamics of complex reactions", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072008-130657", "creators": [ { "name": { "family": "Zhong", "given": "Dongping" }, "id": "Zhong-Dongping", "display_name": "Zhong, Dongping" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7GR2-YW91", "abstract": "The exploring of complex reactions within femtosecond resolution provides new challenges because the reactions evolve along multiple pathways. New techniques are needed to dissect these complex systems into the elementary reactions. In this thesis, femtosecond-resolved mass spectrometry is successfully developed to achieve temporal, speed, angular and state resolution(s) of the reaction dynamics. With these capabilities, the mechanism and dynamics of the complex reactions are able to be microscopically elucidated for each elementary step by monitoring the temporal evolution of the transition state and final products, measuring the energy deposition among the translational and internal motions of the final products, and resolving the correlation between the structural changes and the energy release.
\r\n\r\nThe complex reactions studied range from unimolecular dissociation, to bimolecular reactions, to cluster solvation, and to nonradiative dynamics. For unimolecular reactions, the level of complexity varies from diatomics to polyatomics, from direct-mode to complex-mode, from one-bond breakage to multi-bond fission. The six different systems were examined and a variety of dynamic behaviors have been revealed, including product rotational and vibrational excitation, electronic and vibrational predissociation, and saddle-point transition-state dynamics.
\r\n\r\nMany kinds of bimolecular reactions were studied, consisting of the major contributions of this thesis. For the first time, the famous electron-donor-acceptor charge-transfer reactions are fully understood. More than ten systems were examined with the different charge-transfer characters and all elementary steps involved are microscopically resolved. Several concepts have been addressed including the reversibility of electron transfer, the nonconcertedness of reverse electron transfer and the bond breakage, the energy dissipation, and the reaction coherence. The reversible electron transfer is found as a general reaction mechanism. The system has been considered as a benchmark textbook example and provides insights into biological charge-transfer processes.
\r\n\r\nThe aromatic nucleophilic substitution reaction was studied. The reaction is involved with many elementary steps and the rate-determining step was identified. The first atom-molecule inelastic collision was clocked in fs resolution and a novel method is presented by femtosecond detachment. The collision complexes are observed and quantum resonance may play a role. The first four-center covalent-covalent bimolecular reaction was studied and the cooperative motion of four centers was observed. The method presented is general and very important, and should be applied to study a variety of covalent-covalent bimolecular reactions.
\r\n\r\nThe solvation ultrafast dynamics were systematically studied for many systems from small to lager clusters by monitoring the temporal evolution and translational energy distributions of the escaped solute. Different solvent structures are identified based on the dramatic temporal behaviors of the exited solute. Finally, the nonradiative dynamics of big organic molecules, using azines as examples, were studied. Different isomers of the valance-bond azines are observed. The conical intersection was found to play a key role on the ultrafast nonradiative dynamics and seems to be a general phenomenon, consistent with the recent ab initio predictions.
\r\n" }, { "name": "Abrams, Michael Benjamin", "degree": "PhD", "year": "1998", "title": "Design, Synthesis, Characterization, and Reactivity of Group III ansa-Metallocenes Containing Bulky Alkyl and Silyl Substituents", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09052025-171738932", "creators": [ { "name": { "family": "Abrams", "given": "Michael Benjamin" }, "id": "Abrams-Michael-Benjamin", "display_name": "Abrams, Michael Benjamin" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2v44-pj33", "abstract": "The preparations of a series of silyl-bridged bis(cyclopentadiene) complexes containing\r\nbulky alkyl and silyl substituents are reported. Incorporation of tertiary alkyl groups are\r\nrequired in order to direct trimethylsilyl groups exclusively adjacent to the silyl linkers. This\r\n1,2,4- substitution is crucial for the directed syntheses of chiral ansa-metallocenes.\r\nTransmetallation of Me2Si{2-SiMe3-4-[2-(2-CH3-C10H14)]-C5H2)22- affords exclusively racemo-chiral) Group III metallocenes, whereas transmetallation of Me2Si{3-[2-(2-CH3-C10H14)]-\r\nC5H3}22- (lacking the \u03b1-TMS groups) proceeds with the opposite enantioselectivity, generating\r\nexclusively mesa- (achiral) metallocenes.
\r\n\r\nTreatment of meso-Me2Si{3-[2-(2-CH3-C10H14)]-C5H3}2MCl-(LiCl)-(THF)2 (meso-\r\nAdpMCl-(LiCl)-(THF)2) with allylmagnesium bromide affords mesa-AdpM(\u019e3-C3H5) (M = Sc,\r\nY). Hydrogenolyses of these mesa-metallocenes generate highly reactive 14-electron d0 metal\r\nhydride complexes. The methyladamantyl substituents on the Cp rings inhibit formation of\r\nbridging hydride dimers, enabling the reactive mesa-AdpMH monomers to react readily with\r\navailable solvent or metallocene C-H bonds.
\r\n\r\nTreatment of [rac-Me2Si{2-SiMe3-4-[2-(2-CH3-C10H14)]-C5H2}2Y(\u03bc-Cl)]2 ([ra c-Abp Y(\u03bcCl)]2) with LiCH(SiMe3)2 affords the bulky yttrium-alkyl complex rac-AbpYCH(SiMe3)2. This\r\nalkyl complex readily polymerizes ethylene, but does not react with cx-olefins.\r\nHydrogenolysis ofrac-AbpYCH(SiMe3)2 generates the homochiral hydride dimer [rac-AbpY(\u03bc-H)]2. \r\nThe bulk of the methyladamantyl substituents inhibits formation of the\r\nheterochiral hydride dimer. Efforts are made to assess the ability of the methyladamantyl\r\ngroups to inhibit the hydride monomer-dimer equilibria that deactivates previously reported\r\ngroup III Ziegler-Natta catalysts. The hydride dimer [rac-AbpY(\u03bc-H)]2 is an ex-olefin\r\nhydrogenation catalyst, but does not oligomerize or polymerize \u03b1-olefins. [rac-AbpY(\u03bc-H)]2\r\nalso reacts readily with dihydrogen, allene, and 2-butyne; examples of \u03c3-bond metathesis,\r\nalkyne insertion, and \u03b2-hydride elimination have been observed for [rac-AbpY] complexes.
\r\n\r\nThe fluxional behavior exhibited by a series of d0-metallocene \u019e3-allyl complexes is\r\ninvestigated. Lineshape analysis of NMR studies performed on these complexes indicates\r\nactivation barriers of ~8-14 kcal/mol for processes involving dissociation of the allyl C=C\r\ndouble bond as the rate determing step. Investigation of Cs-symmetric linked scandocenes and\r\nyttrocenes allows elucidation of a second allyl rearrangement mechanism which operates\r\nconcurrently with olefin dissociation: in-plane rotation rotation of the intact \u019e3-allyl ligand.\r\nAllyl rotation is generally fast relative to the rate of olefin dissociation. Ligand, metal, and\r\nsolvent effects on the observed rates are discussed.
" }, { "name": "Belmares, Michael Paul", "degree": "PhD", "year": "1998", "title": "Molecular Origins of the Thermophysical Properties of Polymers and Modeling of Polymer Permeation by Large Molecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-12172004-155023", "creators": [ { "name": { "family": "Belmares", "given": "Michael Paul" }, "id": "Belmares-Michael-Paul", "display_name": "Belmares, Michael Paul" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vnw1-8367", "abstract": "The molecular origins of the phase transitions of polymers have not been completely understood. The molecular level understanding of polymer behavior is of great technological and scientific value. For example, the melt to glass transition of a polymer Tg is perhaps its most useful quantity describing it. A low Tg polymer will be a useful elastomer and a high Tg polymer will serve for structural purposes. Additionally, sub-glass relaxations are related to polymer aging.
\r\n\r\nBased on a simple poly (ethylene) model, the intramolecular and intermolecular factors governing polymer melting, the glass transition and subglass transitions were investigated through a careful and systematic variation of the torsional potential as well as the cohesive energy of the polymer. The model polymers were studied using constant pressure canonical (Gibbs) dynamics of a system of four polymer chains with one hundred and fifty beads per chain. The advantage of varying systematically the torsional potential is that the morphology of the polymer is controlled, ranging from highly amorphous to highly crystalline, depending on the gauche-trans conformational energy differences. The effect of cohesive energy on the various transitions may also be studied by changing the Van der Waals well depth of each bead in the polymer chain.
\r\n\r\nThe first study presented in this chapter is a semi-crystalline case where the gauche energy was +1.14 kcal/mol more stable than the trans energy, and the trans-gauche barrier was 3.01 kcal/mol. A melting point, a glass transition and a tentatively assigned gamma relaxation were characterized.
\r\n\r\nIn a second study, the effect of the trans-gauche barrier on the phase transitions of a semi-crystalline polymer (gauche energy=+1.14 kcal/mol) was investigated.
\r\n\r\nIn a third study, the effect of the torsional barrier on the glass transition of amorphous polymers (gauche energy=trans energy) was investigated.
\r\n\r\nIn a fourth study, the effects of crystallinity on the phase transitions of polymers was investigated by varying the trans-gauche energy differences while maintaining the trans-gauche barrier constant at 4.03 kcal/mol.
\r\n\r\nIn the fifth and final study, the effect of the cohesive energy on the polymer phase transitions was investigated by changing the Lennard Jones well depth of each bead while maintaining the torsional potential fixed with a gauche energy of 1.14 kcal/mol relative to the trans energy, and a trans-gauche barrier of 4.03 kcal/mol.
\r\n\r\nBased on these studies, new insights on the general thermo-physical properties of polymers were obtained. A summary of the molecular interpretations of the melting point, glass transition, and sub-glass transitions is provided at the conclusion of this study.
\r\n\r\nTherefore, the strength of this study is its ability to produce numerous phase transitions within a single structural polymer model by a systematic variation of the intermolecular and intramolecular forcefield parameters. This allows an effective comparison of the thermodynamics, the kinetics and morphology of each of the polymer cases.
" }, { "name": "Bertsch, Ruth Ann", "degree": "PhD", "year": "1998", "title": "The early events of protein folding : Simulations of polyalanine folding into an alpha-helix", "advisor": "Chan, Sunney I.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-084600422", "creators": [ { "name": { "family": "Bertsch", "given": "Ruth Ann" }, "id": "Bertsch-R-A", "display_name": "Bertsch, Ruth Ann" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vewx-3f78", "abstract": "The kinetics of \u03b1-helix formation in polyalanine and polyglycine eicosamers (20-mers) were examined using the Newton-Euler Inverse Mass Operator (NEIMO) method (Jain et al. (1993) J. Comp. Phys. 106: 258-268), a new type of torsional coordinate molecular dynamics (MD). One hundred fifty-five (155) different MD experiments were carried out on extended (Ala)_(20) under identical conditions for 0.5 ns each, and 129 of the simulations (83%) formed a persistent \u03b1-helix. In contrast, the extended state of (Gly)_(20) only formed a right-handed \u03b1-helix in two of the 20 MD experiments (10%), and these helices were not as long or as persistent as those of polyalanine. This is consistent with the helix propensities of the natural amino acids.\r\n\r\nThe analysis of all 155 simulations show helix formation to be a competition between the rates of \r\n\r\n\t(a) forming local hydrogen bonds (i.e., hydrogen bonds between any residue i and \r\n\t its i + 2, i + 3, i + 4, or i + 5th neighbor) and\r\n\r\n\t(b) forming nonlocal hydrogen bonds (HBs) between residues widely separated in sequence.\r\n\r\nLocal HBs grow rapidly into an \u03b1-helix; but, nonlocal HBs usually retard helix formation by \"trapping\" the polymer in irregular, \"balled-up\" structures. Most trajectories formed some nonlocal HBs, sometimes as many as eight. But, for (Ala)_(20), most of these eventually rearranged to form local HBs that lead to \u03b1-helices. A simple kinetic model describes the rate of converting nonlocal HBs into \u03b1-helices.\r\n\r\nTorsional coordinate MD speeds folding by eliminating bond and angle degrees of freedom and reducing dynamical friction. Thus, the observed times of 80 to 500 ps are likely to be lower bounds on real rates. However, we believe the sequential steps observed here mirror those of real systems. When compensating for the effect of dynamic friction, the half live for \u03b1-helix formation of (Ala)_(20) is estimated to be 209 ps.\r\n\r\nChapters 2 and 3 describe two trajectories of (Ala)_(20) folding into an \u03b1-helix. Different types of analyses are used to understand the process of formation and simplify the megabytes of information available in each trajectory. Chapter 2 illustrates a trajectory that forms an \u03b1-helix fast, whereas Chapter 3 describes a trajectory where helix formation was retarded by nonlocal HBs.\r\n\r\nThese simulations attempt to elucidate the early events of protein folding. As elaborated in Chapter 1, the early events may be vital to controlling folding yield and the folding/aggregation partition.\r\n" }, { "name": "Chen, Zhong-Ren", "degree": "PhD", "year": "1998", "title": "I. Dynamics of Block Copolymer Nanostructures. II. Polymerizability of Cyclic Olefins and Ring-Closing Metathesis", "advisor": "Kornfield, Julia A.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-095827", "creators": [ { "name": { "family": "Chen", "given": "Zhong-Ren" }, "id": "Chen-Zhong-Ren", "orcid": "0000-0002-2929-9566", "display_name": "Chen, Zhong-Ren" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "advisor", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" }, { "name": { "family": "Ko", "given": "Chan U." }, "id": "Ko-Chan-U", "role": "member", "display_name": "Ko, Chan U." }, { "name": { "family": "Doi", "given": "Masao" }, "id": "Doi-Masao", "role": "member", "display_name": "Doi, Masao" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xd1r-aj40", "abstract": "Self-assembly of block copolymers provide versatile means to create nanostructures with potential applications in nanotechnologies. The form and size of these structures are controlled by the type and the length of each block, and the number of blocks. Active processing using symmetry-breaking fields such as flow can extend self-assembled order into the macroscopic dimensions, thus gain desired directional properties, such as transport, optical, and electrical properties.
\r\n\r\nTowards the integrated synthesis and processing of functional block copolymer nanostructures, dynamics and thermodynamics of block copolymer nanostructures must be understood. The dynamics of flow-induced alignment of block copolymers will provide the basis to predict the direction, rate, and degree of alignment, while defect dynamics and thermodynamics will give insight into the possibilities of formation of desired nanostructures. In chapter 1, I will overview key issues of flow-induced alignment based on literature and new results from the first two chapters of the thesis. A three-dimensional mapping summarizes the flow behavior of diblock copolymers in terms of molecular characteristics and processing conditions. Various mechanisms that had been proposed since two decades ago are reviewed and re-evaluated.
\r\n\r\nIn chapter 2, I will present detailed results revealed by a powerful experimental method, which combines in-situ rheo-optical measurements and ex-situ structural characterization by electron microscopy and x-ray scattering. A PS-PI (10K-10K) diblock is used as a model system. Three different trajectories of alignment are investigated: perpendicular alignment and two qualitatively different routes to parallel alignment. At the highest frequencies, symmetry arguments explain the transient development of a bimodal texture en route to alignment of layers parallel to the planes of shear. At lower frequencies, larger scale relaxations introduce rearrangements out of the deformation plane that permit formation of lamellae perpendicular to the shear plane. These explain the change in character of the pathway to parallel alignment and the emergence of perpendicular alignment with decreasing frequency. For each trajectory in general, the initial 'fast' process enhances not only the projection of the orientation distribution that corresponds to the final state, but also increases other projections of the distribution; the late-stage 'slow' process eliminates these other projections and perfects a single alignment.
\r\n\r\nABC triblock copolymer can form a fascinating array of nanostructures. Phase behavior, dynamics of oscillatory-shear alignment, and other issues raised by ABC triblock copolymers, such as dynamics of lamellar perforation in three-nanophase-separated states will be discussed in chapter 3. Both thermotropical and shear-induced phase transitions are observed. Dramatic changes of morphology and alignment behavior are induced simply by switching the permutation of the blocks, molecular size, shear condition, and temperature. In three-nanophase-separated lamellar materials, a new type of defect is found: correlated perforation. As these defects annihilate upon annealing, long range correlations produce striking patterns, including those that resemble a ship's wake. The creation and evolution of these defect structures present challenge and opportunities in developing novel nanostructures.
\r\n\r\nOlefin metathesis by transition metal complex has been a powerful method in polymer and organic synthesis. In chapter 4, I will present a model to predict the ring-chain equilibria in ring-opening-closing reaction. Statistical mechanics and molecular mechanics provide the basic tools in problem formulation and parameter determination. Polymerizability of cyclic olefins are predicted by this model, and agree well with ring-opening metathesis polymerization experiments. We have extended this model to assist ring-closing metathesis of eight-member rings, which can be a useful starting material for drug synthesis.
" }, { "name": "Dahiyat, Bassil I.", "degree": "PhD", "year": "1998", "title": "Protein Design Automation : Principles and Practice", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05132009-113001", "creators": [ { "name": { "family": "Dahiyat", "given": "Bassil I." }, "id": "Dahiyat-Bassil-I", "display_name": "Dahiyat, Bassil I." } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/08j5-w532", "abstract": "We have conceived and implemented a cyclical protein design strategy that couples theory, computation and experimental testing. Our goal is an objective, quantitative design algorithm that is based on the physical properties that determine protein structure and stability and which is not limited to specific folds or motifs. Such a method should escape the lack of generality that has resulted from design approaches based on system-specific heuristics and/or subjective considerations. A critical component of the development of our methods has been their experimental testing and validation. The use of a design cycle coupling theory, computation, and experiment has improved our understanding of the physical chemistry governing protein design and hence enhanced the performance of the design algorithm.\r\n\r\nOur protein design automation algorithm objectively predicts protein sequences likely to achieve a desired fold by using a side-chain selection algorithm that explicitly and quantitatively considers specific side-chain to backbone and side-chain to side-chain interactions. Using a rotamer description of the side chains, we implemented a fast discrete search algorithm based on the Dead End Elimination Theorem to rapidly find the globally optimal sequence in its optimal geometry. We subdivided the sequence selection problem into regions of proteins expected to be dominated by different factors: the tightly packed buried core, the solvent exposed surface, and the boundary between core and surface. We assessed the accuracy of a scoring function or combination of scoring functions by experimentally testing their sequence predictions. Improvements to the scoring function were derived from the experimental data and incorporated into the design algorithm. In this manner, we developed a scoring function for the core of a protein that considers packing interactions and hydrophobic solvation energy. In order to design boundary residues effectively, the usually neglected effect of exposed hydrophobic surface area was addressed. Scoring functions for the design of surface residues were developed that account for hydrogen bonding interactions and secondary structure propensities of amino acids. These potential functions were used to successfully redesign several proteins. The integration of these scoring functions was tested by designing the sequence for an entire protein and solving the NMR solution structure of the designed protein. This work reports the first successful automated design and experimental validation of a novel sequence for an entire protein." }, { "name": "Dias, Eric Lee Kuiokalani", "degree": "PhD", "year": "1998", "title": "Ruthenium-Based Olefin Metathesis Catalysts: Synthesis, Mechanism, and Activity", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012023-164245860", "creators": [ { "name": { "family": "Dias", "given": "Eric Lee Kuiokalani" }, "id": "DIas-Eric-Lee-Kuiokalani", "display_name": "Dias, Eric Lee Kuiokalani" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/30mh-mq42", "abstract": "Several ruthenium-based olefin metathesis catalysts of the formula (PR\u2083)\u2082X\u2082Ru=CHCHCPh\u2082 have been synthesized, and relative catalyst activities were determined by monitoring the ring-closing metathesis of the acyclic diene diethyl diallylmalonate. The following order of increasing activity was determined: X = I < Br < Cl, and PR\u2083 = PPh\u2083 << P\u2071Pr\u2082Ph < PCy\u2082Ph < P\u2071Pr\u2083 < PCy\u2083. Additional studies were conducted with the catalyst (PCy\u2083)\u2082Cl\u2082Ru=CH\u2082 to probe the mechanism of olefin metathesis by this class of catalysts. The data support a scheme in which there are two competing pathways: the dominant one in which a phosphine dissociates from the ruthenium center, and a minor one in which both phosphines remain bound. Higher catalyst activities could be achieved by the addition of CuCl to the reaction.
\r\n\r\nThe carbenes (PCy\u2083)\u2082Cl\u2082Ru=CHR (R = CHCPh\u2082, Ph) react with the bridged-chloride dimers [(p-cymene)RuCl\u2082]\u2082, [(p-cymene)OsCl\u2082]\u2082, and [(\u1d57Bu\u2082Cp)RhCl\u2082]\u2082 to quantitatively form bimetallic, bridged-chloride ruthenium carbenes and and one equivalent of each corresponding piano-stool complex. In the ring-opening metathesis polymerization (ROMP) of 1,5-cyclooctadiene, catalyst activity was found to increase in the order M = Ru < Os < Rh for the ancillary metal centers, with all of the bimetallic catalysts having higher activities. The kinetics of ROMP were studied, and the data support an associative mechanism of olefin metathesis.
\r\n\r\nReaction of excess pyridine with (PCy\u2083)\u2082(Cl)\u2082Ru=CHPh produces the stable, bis(pyridine) adduct (PCy\u2083)(pyr)\u2082(Cl)\u2082Ru(CHPh). In solution, an equilibrium is established with the mono(pyridine) adduct (PCy\u2083)(pyr)(Cl)\u2082Ru(CHPh). Reaction of thallium salts of ,B-diketonates with (PCy\u2083)\u2082ChRu=CHR (R = CHCPh\u2082, Ph) produces the complexes (PCy\u2083)(L)\u2082Ru(CHR) (L = acac, \u1d57Bu\u2082acac; R = CHCPh\u2082, Ph). While the pyridine complexes are stable and completely initiate RCM, the propagating methylidene is very unstable, decomposing as fast as, or faster than, it is formed. The \u03b2-diketonate complexes initiate ROMP in the presence of HCl and RCM in the presence of CuCl.
" }, { "name": "Faglioni, Francesco", "degree": "PhD", "year": "1998", "title": "Quantum chemical computations of heterogeneous selective oxidation, STM images, and multiple bond reactions", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10202009-092753223", "creators": [ { "name": { "family": "Faglioni", "given": "Francesco" }, "id": "Faglioni-F", "display_name": "Faglioni, Francesco" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ksr7-qk84", "abstract": "Chapter one of this thesis describes first principles electronic structure computations performed to understand the mechanism of molecular oxygen activation by vanadyl pyrophosphate. The process is believed to play a key role in the catalytic oxidation of n-butane to maleic anhydride. The results obtained demonstrate that the mechanism involves at least two layers of vanadyl pyrophosphate crystal. Based on the computed energetics for small clusters, we propose an activation mechanism which involves the transfer of one oxygen atom from the first to the second layer of the crystal concerted with dioxygen activation by the first layer.\r\n\r\nChapter two describes a novel ab-initio computational technique, called GVB-RCI, which correctly describes the stretching and dissociation of multiple bonds and provides smooth potential energy surfaces for most chemical reactions. The technique is a special case of Multi Configuration SCF that does not have the Perfect Pairing restriction and still scales well with the size of the system. The capabilities and limitations of GVB-RCI are illustrated in the case of a few simple chemical reactions.\r\n\r\nChapter three contains a theoretical model describing the Scanning Tunneling Microscopy (STM) imaging of molecules adsorbed on graphite. The model is applicable to a variety of different molecules with reasonable computational effort, and provides images that are in qualitative agreement with experimental results. The model predicts that topographic effects will dominate the STM images of alkanes on graphite surfaces. The computations correlate well with the STM data of functionalized alkanes, and allow assessment of the structure and orientation of most of the functionalized alkanes \r\nthat have been studied experimentally. In addition, the computations suggest that the highly diffuse virtual orbitals, despite being much farther in energy from the Fermi level of the graphite than the occupied orbitals of the adsorbed molecules, may play an important role in determining the STM \r\nimage contrast of such systems." }, { "name": "Greenberg, William Anthony", "degree": "PhD", "year": "1998", "title": "Design and synthesis of ligands for recognition of the major and minor grooves of DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282006-114932", "creators": [ { "name": { "family": "Greenberg", "given": "William Anthony" }, "id": "Greenberg-W-A", "display_name": "Greenberg, William Anthony" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/z2xh-y642", "abstract": "The chemical approach to the sequence specific recognition of double stranded DNA in this laboratory focuses on two distinct structural motifs. The first is oligonucleotide-directed triple helix formation. Pyrimidine oligonucleotides bind homopurine duplex sequences in the major groove by formation of T\u2022AT and C+GC base triplets in a parallel orientation relative to the purine target strand. Purine rich oligonucleotides also bind homopurine sequences in the major groove, by formation of G\u2022GC and A\u2022AT or T\u2022AT base triplets, in this case oriented antiparallel to the purine target strand. The lack of ability recognize CG and TA base pairs by either pyrimidine or purine oligonucleotides has resulted in efforts to design nonnatural bases which can recognize these base pairs in the context of triple helices. Such bases would greatly expand the generality of triple helix formation by expanding the range of targetable sequences.\n\nThe second structural motif consists of pyrrole-imidazole polyamides which form 2:1 side-by-side antiparallel complexes in the minor groove of DNA. A set of \"pairing rules\" has been elucidated in which an imidazole-pyrrole pair recognizes a GC base pair, a pyrrole-imidazole pair recognizes CG, and a pyrrole-pyrrole pair is degenerate for both AT and TA base pairs.\n\nThis thesis describes the application of quantitative DNase I footprinting to the evaluation of the energetics of triple helix formation by purine and pyrimidine oligonucleotides containing designed, nonnatural bases, as well the energetics of complex formation between covalently linked H-pin polyamides and the minor groove of DNA. Chapter Two describes the energetics of formation of sixteen triple helical complexes containing only the natural bases A, G, C, and T, which vary at single position within the purine motif. The values obtained set a basis with which to evaluate the energetics of triple helices containing nonnatural bases, and demonstrate the exquisite sensitivity of triple helices to single base mismatches. Chapter Three describes the energetics of formation of purine motif triple helical complexes which contain single substitutions of the nonnatural purines inosine, 2-aminopurine, nebularine, and isoinosine. The results emphasize that new structural space must be explored in order to design bases which will specifically recognize CG and TA base pairs within the purine motif. Chapter Four describes the design and synthesis of methyl-substituted imidazole nucleosides and evaluation of the energetics of formation of purine motif triple helical complexes containing single substitutions of these nonnatural bases. The results suggest that use of small, fivemembered ring heterocycles is likely a good design toward TA recognition, but that hydrophobic interactions between a designed nonnatural base and the 5-methyl group of thymine is not energetically favorable in the context of a purine motif triple helix. Chapter Five describes the design and synthesis of substituted pyrazole nucleosides and evaluation of the energetics of formation of purine motif triple helical complexes containing single substitutions of these nonnatural bases. The pyrazole substitution showed improved specificity towards TA, but at low affinity. This affinity could not be improved by appropriate substitution of an amino group, which instead improved affinity for GC. This points to the difficulty of forming a hydrogen bond to the 04 carbonyl of thymine relative to the more accessible 06 carbonyl of guanine. Chapter Six describes an evaluation of the energetics of formation of pyrimidine motif triple helical complexes containing a previously published nonnatural base and the discovery that as previously prepared, the base retains a benzoyl protecting group in the pyrimidine oligonucleotide. This benzoylated base shows specificity for CG and TA base pairs, similarly to the previously reported, structurally similar D3, which has been shown to bind through an intercalative mode. Independent synthesis of the unprotected base through a new route proved that this base did not bind specifically to any of the four base pairs in the context of a pyrimidine motif triple helix. Chapter Seven describes an evaluation of the energetics of formation of pyrimidine motif triple helical complexes containing a nonnatural base derived from a model heterocycle which was shown to bind isolated CG base pairs in organic solvent. The results suggest that model studies in organic solvent cannot accurately predict the behavior of nonnatural bases in water, in the context of a triple helix, since this base showed no specificity for any base pair by quantitative DNase I footprinting studies. Chapter Eight describes the design and solid phase synthesis of a series of pyrrole-imidazole polyamides which are covalently linked across central pyrrole nitrogens to increase affinity and specificity towards their DNA target sites according to the 2:1 polyamide:DNA binding model. DNase I footprint titration results show that these H-pin polyamides do bind with increased affinity and specificity relative to unlinked analogues, but that hairpin polyamides show a greater improvement, and are thus more optimal designs." }, { "name": "Hastings, Curtis Asa", "degree": "PhD", "year": "1998", "title": "Part A. Studies Directed Toward the Total Synthesis of Chebulagic Acid. Part B. DNA Recognition by Metallointercalator-Peptide Conjugates", "advisor": "Carreira, Erick Moran", "url": "https://resolver.caltech.edu/CaltechTHESIS:08082025-165811908", "creators": [ { "name": { "family": "Hastings", "given": "Curtis Asa" }, "id": "Hastings-Curtis-Asa", "display_name": "Hastings, Curtis Asa" } ], "advisors": [ { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "advisor", "display_name": "Carreira, Erick Moran" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e4be-bd57", "abstract": "Part A. The development of asymmetric allene/enone and allene/enoate\r\nintramolecular [2+2]-photocycloadditions is described. Irradiation of optically active\r\nallenes (89-92% ee) appended to enones and enoates afforded alkylidenecyclobutane\r\nphotoadducts with high levels of asymmetric induction (83 -100%) derived exclusively\r\nfrom the allene fragment. Substrates examined include allenyl alcohols appended to 1,3-\r\ncyclopentanedione, 1,3-cyclohexanedione, and 4-hydroxycoumarin. The absolute sense of\r\ninduction in these reactions was determined by photocycloaddition of an allene containing\r\nan internal stereochemical label. The exa-methylenecyclobutanes obtained upon irradiation\r\nof allene-coumarins were isolated as single olefin diastereomers. A model for the high\r\nlevels of enantioinduction observed in these transformations is presented.
\r\n\r\nThe asymmetric intramolecular allene/enoate [2+2]-photocycloaddition was applied\r\nto the synthesis of the topoisomerase I inhibitor chebulagic acid. The synthetic utility of\r\nthis reaction was demonstrated by the preparation of an advanced intermediate containing\r\nall of the stereochemical information present in the chebulic acid fragment of chebulagic\r\nacid. In the course of these synthetic studies an unusual 8-alkynyl lactone photoproduct\r\nwas obtained upon photocyloaddition of a substrate that was expected to afford a [7.6.6.4]tetracyclic\r\nsystem. A 1,5-hydrogen shift in a biradical intermediate was implicated in the\r\nformation of this product by isotopic labeling studies; the mechanistic implications of these\r\nresults for enantioselectivity in photochemical reactions of optically active allenes tethered\r\nto enones and enoates are discussed.
\r\n\r\nPart B. The DNA recognition properties of peptide conjugates of\r\nphenenthrenequinone diimine complexes of rhodium(III) have been studied. The structural\r\nand thermodynamic basis for the 5'-CCA-3'-selectivity of the metallointercalator-peptide\r\nconjugate [Rh(phi)2(phen')]3+ -AANVAIAAWERAA-CONH2 was investigated. A protocol\r\nfor measuring dissociation constants of DNA cleaving ligands by cleavage titration is\r\ndescribed. Using this protocol, the energetic contribution of the peptide to sequenceselective\r\nbinding was assessed, and evidence for the origin of the enhanced sequenceselectivity\r\nobserved at elevated temperature was obtained. Micromolar quantities of [\u0394Rh-(phi)2(phen')]3+-AANVAIAAWERAA-CONH2 were synthesized to examine the\r\nstructure of the metallointercalator-peptide conjugate and the metallointercalator-peptide\r\nconjugate\u2022DNA complex by NMR. NMR results for the metallointercalator-peptide\r\nconjugate in the absence of DNA are reported.
\r\n\r\nA family of peptide conjugates of [Rh(phi)2(phen')]3+(phi = 9, 10-\r\nphenanthrenequinone diimine, phen' = 5-(amidoglutaryl)-1,10-phenanthroline) was also\r\nsynthesized. The peptide sequences were obtained by single amino acid modification of the\r\n5'-CCA-3'-selective metallointercalator-peptide conjugate [Rh(phi)2(phen')]3+-\r\nAANVAIAAWERAA-CONH2 to explore the correlation between the amino acid sequence\r\nof the peptide and the nucleotide sequence of the DNA target. Changing the position of the\r\nglutamate at position 10 in the sequence of the appended peptide resulted in the\r\nidentification of a 5'-ACA-3'-selective metallointercalator-peptide conjugate,\r\n[Rh(phi)2(phen')3+-AANVAEAAWARAA-CONH2. Locating the glutamate on one face of\r\na putative \u03b1-helix was found to be essential for sequence specificity; peptide conjugates\r\nwith the glutamate at positions 7, 8, 12, and 13 did not afford sequence-selective DNA\r\nrecognition. Further amino acid substitutions were made at positions 6 and 10. Mutating\r\nthe glutamate at position 6 to arginine caused complex changes in the recognition\r\ncharacteristics of the resulting conjugate. To probe the interactions that give rise to\r\nsequence specificity, we have measured thermodynamic dissociation constants for these\r\nsequence-selective metallointercalator-peptide conjugates and [Rh(phi)2(phen')]3+.
\r\n\r\nThe observed sequence preferences are consistent with the model of Sardesai et al.\r\nfor the sequence selectivity of Rh(phi)2(phen')]3+-AANVAIAAWERAA-CONH2. This\r\nmodel states that sequence-specific DNA recognition requires the peptide to adopt an \u03b1-helical\r\nconformation, and that Glu10 makes a critical base-specific contact with the 5'-\r\nterminal cytosine of the recognition sequence. Using the additional sequence-selectivity\r\ndata, this model is refined. This refined model suggests that recognition of the central C\u2022G\r\nbase pair of the 5'-CCA-3' recognition sequence of [Rh]-E10 is accomplished by Ile6\r\nthrough shape-selection, and that recognition of the 5' -terminal A\u2022T base pair of the 5' -\r\nACA-3' recognition sequence of [Rh]-E6 is accomplished by van der Waals contacts\r\nbetween alanine and thymine methyl groups. The implications of these results for the de\r\nnova design of sequence-selective DNA binding peptides are discussed.
" }, { "name": "Hoang, Bac Hoa", "degree": "Masters", "year": "1998", "title": "Progress Towards the Total Synthesis of a Spermine-Conjugated Dynemicin Analog", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08222013-144438603", "creators": [ { "name": { "family": "Hoang", "given": "Bac Hoa" }, "id": "Hoang-Bac-Hoa", "display_name": "Hoang, Bac Hoa" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3g9z-nn03", "abstract": "Progress towards the synthesis of the spermine-conjugated Dynemicin analog 4 is\r\ndescribed. The synthetic route starts with the Michael addition of menthyl acetoacetate to\r\ntrans-ethyl crotonate followed by a Dieckman condensation to form the cyclohexanedione\r\n14 which, through a series of chemical reactions, is transformed into the quinone imine 6.\r\nKey features in the route include the Suzuki coupling reaction of the aryl boronic acid 11\r\nand the enol triflate 12, thermal deprotection/internal amidation of the biaryl 19, cis\r\naddition of the (Z)-enediyne 33 to the quinoline 25, intramolecular acetylide addition to a\r\ncarbonyl within the ketone 29, and an addition/elimination of the cyanophthalide to the\r\nquinone imine 6 to form the anthraquinone 36 utilizing the Kraus and Sugimoto\r\nmethodology." }, { "name": "Hsu, Chao-Ping", "degree": "PhD", "year": "1998", "title": "On the Theory of Electron Transfer Reactions: Superexchange Coupling and Polar Solvation Dynamics", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02162022-191638374", "creators": [ { "name": { "family": "Hsu", "given": "Chao-Ping" }, "id": "Hsu-Chao-Ping", "orcid": "0000-0002-7187-427X", "display_name": "Hsu, Chao-Ping" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/k5yt-g844", "abstract": "A recursion relation is formulated for the Green's function for calculating the effective electron coupling in bridge-assisted electron transfer systems, within the framework of the tight-binding Hamiltonian. The non-perturbative recursion expression relates the Green\u2019s function of a chain bridge to that of a bridge which is one unit less. The method is used to calculate the electronic coupling between a gold electrode and each of the molecules. (\u03b7\u2075-C\u2085H\u2085)Fe(\u03b7\u2075-C\u2085H\u2084)CO\u2082(CH\u2082)\u2099SH and (\u03b7\u2075-C\u2085H\u2085)Fe(\u03b7\u2075-C\u2085H\u2084)(CH\u2082)\u2099SH (n = 3 to 50). At larger numbers of bridge units, the effective coupling strength shows an exponential decay as the number of methylene units increases. This sequential formalism shows numerical stability even for a very long chain bridge and. since it uses only small matrices, requires much less computer time for the calculation. Identical bridge units are not a requirement, and so the method can be applied to more complicated systems, such as proteins. Most of the calculated coupling strengths, if converted to rate constants according to a nonadiabatic expression, agree well with the experimental results.
\r\n\r\nThe time-dependent dynamic Stokes shift function, which describes the solvent response to a sudden change in the charge distribution of a solute molecule, is expressed in terms of experimentally measured dielectric dispersion data of the solvent, using a simple dielectric continuum model. The result is applied to photoexcited coumarin 343 in water, and encouraging agreement with the experimental data is obtained. A simple formula is also derived which includes the effect of a pump pulse of finite duration. Such an effect is negligible when the frequency of a pump pulse is close to the maximum in the absorption spectrum, but a deviation from the standard formula can be expected for the pump pulse tuned to a far wing of the absorption band of the chromophore. To calculate further the time-dependent fluorescence spectral lineshapes, a method is described for incorporating the vibronic transitions of a solute molecule. The intramolecular vibrational relaxation is assumed to be much faster\r\nthan the observation delay time. Calculations are made for coumarin 153 in acetonitrile. The results are again in encouraging agreement with experimental spectra. Results are also given for the dynamic Stokes shift in methanol.
" }, { "name": "Huq, Iftikhar", "degree": "PhD", "year": "1998", "title": "Design and control studies on the fluid catalytic cracking process", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-02012008-111240", "creators": [ { "name": { "family": "Huq", "given": "Iftikhar" }, "id": "Huq-I", "display_name": "Huq, Iftikhar" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7SWK-0M04", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nFluid Catalytic Cracking (FCC) units are widely used in the oil refining industry to crack low value hydrocarbons into a range of higher value hydrocarbons including gasoline. Because of its feed processing flexibility, the FCC process is considered a primary conversion unit in an integrated refinery and optimal FCC operation can have a significant impact on the refinery profitability. Because of its important role in the refinery, the FCC process has recently attracted renewed interest both from academia and industry, with the main emphasis on better understanding and operating the process. In general, several possible alternatives can usually be postulated or envisioned to realize operational improvements, and the critical task is then to rank order these alternatives. Rank ordering the available alternatives requires the utilization of suitable:\r\n\r\n1. process models describing each alternative,\r\n2. tools to quantitatively assess the operational performance achievable with each alternative. \"Operational performance\" here refers to the quality of closed loop process response.\r\nThe different alternatives have often been analyzed and compared through extensive simulations. However, because of stringent environmental and economic requirements, most industrial plants, including the FCC process have evolved into highly complex and integrated processes and ranking through simulation might be infeasible. In ranking design alternatives through simulation, two crucial factors must be considered if the conclusions drawn from such studies are to be reasonably reliable:\r\n\u2022 Detailed case studies need to be conducted for all the alternatives. These case studies typically require considering the effect of a wide range of disturbances, inputs, operating conditions, model structures and parameters, control structures and parameters. It might be necessary to examine many hundreds if not thousands of possible alternatives. Moreover, the effect of many other aspects of practical operation such as plant/model mismatch, process constraints, sensor/actuator failures, etc. on the operational performance must also be considered for each case, and makes the assessment significantly more involved.\r\n\u2022 While qualitative \"good/bad\" indicators might have been sufficient in the past, it is becoming more important to quantitatively rank order the available alternatives in todays highly competitive environment. Indeed, choosing a \"slightly better\" alternative over a \"good\" alternative can have a significant impact on the sustained profitability of the process.\r\n\r\nBecause of the large number of possible cases that must be considered, contradictory conclusions can often be drawn when using such an approach to rank the available alternatives. Such a simulation approach is therefore infeasible except possibly for the simplest of cases. This suggests the utilization of more efficient screening tools to effectively assess the many design alternatives possible for improved process operation while accounting for the practical considerations just discussed. With respect to the requirements (1) and (2) above for ranking the possible alternatives, we note that:\r\n\r\n1. FCC models: The renewed interest in improved FCC operation is partially reflected by the recent publication in the open literature of two first principles models claiming to describe the essential features of the FCC process dynamics (Arbel, Huang, Rinard, Shinnar and Sapre 1995, McFarlane, Reineman, Bartee and Georgakis 1993).\r\n2. Tools for operational performance assessment: The structured singular value (SSV) framework introduced by Doyle (1982) provides a quantitative measure of the achievable operational performance, explicitly accounts for plant/model mismatch, and also permits the approximate incorporation of many of the practical requirements indicated above into the analysis. \r\n\r\nUtilizing the two first principles FCC models and the structured singular value framework, several aspects of the design and control of FCC processes have been addressed in this thesis, with special emphasis on quantitatively ranking possible design/control options from an operational performance improvement viewpoint:\r\n\r\n1. Model IV FCC units differ from other cracking units in that model IV FCC units do not have slide valves in the catalyst circulation lines to enable direct control of catalyst circulation rate through the unit. Reducing fluctuations in catalyst circulation rate is found to significantly improve closed loop performance of this FCC unit. Based on this process insight: (1) an operational modification: operating the regenerator with the catalyst overflow weir always flooded, and (2) a design modification: installing slide valves in the catalyst circulation U- tubes are studied and shown to reduce catalyst flow fluctuations and improve the operational performance of the FCC unit. It is interesting to note that essentially all new FCC units and revamped older FCC units typically include both the above two modifications. To reflect this current FCC operation it is assumed for all the subsequent analysis in this thesis that the above two modifications are already incorporated into the FCC design.\r\n2. A quantitative rank ordering of possible control structures for FCC operation in both partial combustion (PC) mode and complete combustion (CC) mode operation is undertaken. It is argued that intentional transitions between the PC and CC modes is rare. For FCC units operated within design specifications, 2 x 2 control structures are found to be sufficient for effective regulatory control. In particular, it is found that high coking feeds cannot be processed in CC mode operation as the safe upper limit on regenerator temperature can be violated. For PC mode regulation, riser temperature [...] and regenerator dense bed temperature [...] are the most suitable choice for controlled variables. For CC mode regulation, [...] are the most suitable choice for controlled variables, where [...] is the flue gas [...] molar concentration. If higher coking feeds are to be processed, the FCC would need to be refitted with additional process units, as discussed in Point 4 below. For both PC and CC modes, using feed temperature [...] and combustion air rate [...] as manipulated variables is found to provide operational performance levels comparable to those achieved with more conventional control structures typically used in industry (using catalyst circulation rate [...] and combustion air rate). That feed temperature can be an effective manipulated variable can have significant implications for the improved operation of older FCCs (e.g. the Model IV) where catalyst circulation rate cannot be directly manipulated.\r\n3. Decentralized regulatory control of the FCC unit operating in PC mode is examined in detail. Decentralized PI controllers are considered, as they are most often used in the industrial setting. It is found that (1) Decentralized PI controllers can provide satisfactory regulation over the normal FCC operating range. (2) A common regulatory control strategy for PC mode operation is to use decentralized PI controllers for the pairing [...](notation in Point 2). It is shown that \"tightening\" the two PI controllers in fact reduces the process interactions and improves operational performance. This is counterintuitive - typically, detuning the controllers is expected to reduce process interactions and improve performance. (3) Certain FCC operating points are unstable. In the absence of control action, the FCC process would either drift to a stable operating point at a higher regenerator temperature or wind down to the cold state (negligible regenerator combustion and reactor cracking). It is shown that reasonable transitions to unstable operating points can be effectively handled with an appropriately tuned decentralized PI controller. (4) A theoretical development that provides insight into possible changes in the sign of the steady\u2014state and infinite frequency relative gain array (RGA) elements is also presented. It is found to be related to the non\u2014minimal phase behavior of one or more of the following (a) the overall plant, (b) the individual loop transfer functions, (c) the remaining system if some controlled variable and the associated manipulated variable is removed. Stable plants for which pairing for performance can correspond to negative steady\u2014state RGA pairings are thus identified.\r\n4. There is a growing need in the oil refining industry to process higher coking feeds in FCC units. However, FCC units operated in the CC mode might not be able to process sufficiently high coking feeds (as discussed in Point 2 above), and would have to be refitted to accommodate this greater feed processing flexibility. The most significant operating limitation is found to be the upper limit on regenerator temperature. The two possible refitting options considered here to alleviate the impact of this constraint are: (1) converting to partial combustion mode (PC mode) operation by installing a CO boiler and (2) extending complete combustion mode (CCE mode) operation by installing a catalyst cooler. The main objective is to compare the steady\u2014state and dynamic characteristics of these two refitting options. From a steady state viewpoint, it is found that installing the catalyst cooler has a distinct advantage over installing the CO boiler when processing high coking feeds - because the regenerated catalyst is always clean burned. In particular, the product yields as well as overall conversions are typically higher. A comparison of dynamic characteristics suggests that while a simple decentralized control strategy provides satisfactory performance over a wide operating regime in PC mode, a more sophisticated control strategy might be required to achieve tight control over a comparable operating range in CCE mode with the catalyst cooler." }, { "name": "Kusaka, Isamu", "degree": "PhD", "year": "1998", "title": "Molecular Theory of Vapor Phase Nucleation", "advisor": "Seinfeld, John H.; Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechETD:etd-01242008-085938", "creators": [ { "name": { "family": "Kusaka", "given": "Isamu" }, "id": "Kusaka-Isamu", "display_name": "Kusaka, Isamu" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jwwk-0n13", "abstract": "An attempt has been made to establish the foundation of molecular level theory of vapor phase nucleation. We have focused on evaluating the reversible work of cluster formation and followed two major trends in this direction, namely, statistical mechanical density functional theory and molecular level simulation.\r\n\r\nWe applied density functional theory to heterogeneous nucleation onto an ion. Our prime interest is to predict a sign preference of nucleation rate, which has been experimentally observed yet remained inexplicable in the classical framework. The theory indicates that asymmetry in ion-molecule interaction is directly responsible for the sign preference. The predicted sign dependence decreases as the supersaturation is increased. Our results from density functional theory agree well with the existing experimental observations.\r\n\r\nMolecular simulation offers an alternative to molecular level approach. A long-standing issue of fundamental importance in cluster simulation is the precise definition of a cluster. Thus far, all attempts of defining a cluster had introduced ad hoc criteria to determine unambiguously whether a given molecule in the system belongs to vapor or to a cluster for any instantaneous configuration of molecules. From a careful examination of the context in which a cluster should be introduced into nucleation theory, we conclude that such a criterion is unnecessary. Then, we present a new approach to cluster simulation which is free of any arbitrariness involved in the definition of a cluster. Instead, it preferentially and automatically generates the physical clusters, defined as the density fluctuations that lead to nucleation, and determines their equilibrium distribution in a single simulation. The latter feature permits one to completely bypass the computationally demanding free energy evaluation that is necessary in a conventional simulation. The method is applied first to water using the SPC/E model. We then turn to H2SO4/H2O binary system to obtain a large section of the reversible work surface. The resulting surface is markedly different from that in classical theory and indicates that the rate limiting step of stable particle formation in this system is the binary collision of the sulfuric acid hydrates.\r\n" }, { "name": "Kuwata, Keith Tadao", "degree": "PhD", "year": "1998", "title": "Spectroscopic and Computational Studies of Ionic Clusters as Models of Solvation and Atmospheric Reactions", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:06182021-193858046", "creators": [ { "name": { "family": "Kuwata", "given": "Keith Tadao" }, "id": "Kuwata-Keith-Tadao", "orcid": "0000-0002-3542-2081", "display_name": "Kuwata, Keith Tadao" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "member", "display_name": "Yung, Yuk L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/27ng-zt31", "abstract": "Ionic clusters are useful as model systems for the study of fundamental processes in solution and in the atmosphere. Their structure and reactivity can be studied in detail using vibrational predissociation spectroscopy, in conjunction with high level ab initio calculations. This thesis presents the applications of infrared spectroscopy and computation to a variety of gas-phase cluster systems.
\r\n\r\nA crucial component of the process of stratospheric ozone depletion is the action\r\nof polar stratospheric clouds (PS Cs) to convert the reservoir species HCl and chlorine\r\nnitrate (CIONO\u2082) to photochemically labile compounds. Quantum chemistry was used to\r\nexplore one possible mechanism by which this activation is effected:
\r\nCI\u207b + CIONO\u2082 \u2192 CI\u2082 + NO\u2083\u207b (1)
\r\nCorrelated ab initio calculations predicted that the direct reaction of chloride ion with CIONO\u2082 is facile, which was confirmed in an experimental kinetics study. In the reaction a weakly bound intermediate Cl\u2082--NO\u2083\u207b is formed, with ~70% of the charge localized on the nitrate moiety. This enables the Cl\u2082--NO\u2083\u207b cluster to be well solvated even in bulk solution, allowing (1) to be facile on PSCs.
Quantum chemistry was also applied to the hydration of nitrosonium ion (NO\u207a), an important process in the ionosphere. The calculations, in conjunction with an infrared spectroscopy experiment, revealed the structure of the gas-phase clusters NO\u207a(H\u2082O)\u2099. The large degree of covalent interaction between NO\u207a and the lone pairs of the H\u2082O ligands is contrasted with the weak electrostatic bonding between iodide ion and H\u2082O.
\r\n\r\nFinally, the competition between ion solvation and solvent self-association is explored for the gas-phase clusters CI\u207b(H\u2082O)\u2099, and CI\u207b(NH\u2083)\u2099. For the case of water, vibrational predissociation spectroscopy reveals less hydrogen bonding among H\u2082O ligands than predicted by ab initio calculations. Nevertheless, for n\u22655, cluster structure is dominated by water-water interactions, with CI\u207b only partially solvated by the water cluster. Preliminary infrared spectra and computations on CI\u207b(NH\u2083)\u2099 indicate that NH\u2083 preferentially binds to CI\u207b ion instead of forming inter-solvent networks.
" }, { "name": "Liberles, David Alan", "degree": "PhD", "year": "1998", "title": "Sequence specific DNA recognition and bending", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04272006-155123", "creators": [ { "name": { "family": "Liberles", "given": "David Alan" }, "id": "Liberles-D-A", "display_name": "Liberles, David Alan" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D0Q8-6128", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nIntrinsic DNA curvature and protein induced DNA bending play a crucial role in the regulation of many biological processes, including transcription, replication, transposition, viral integration, site-specific recombination, and DNA packaging in nucleosomes. The design of ligands to artifically regulate DNA topology may be important in creating artificial regulators of these processes, with potential utility in biology and human medicine. Much of the work described in this thesis is based upon the ability of a triple helix forming oligonucleotide to recognize double helical DNA. This sequence specific recognition occurs in two motifs and is governed by the formation of specific hydrogen bonds. One limitation of this technique is the inability to recognize pyrimidine bases in the Hoogsteen bonded strand. A novel base, [...], has been previously described with the potential to recognize pyrimidine bases.\n\nChapter 2 describes a thermodynamic analysis of the binding properties of oligonucleotides bearing single and multiple D3 bases in the context of triple helix formation. An NMR structure has indicated the binding mode of [...] as intercalative and the ability of [...] containing oligonucleotides to bend DNA through this intercalative wedge was examined.\n\nChapter 3 describes an alternative experimental approach to triple helix mediated DNA bending. Two third strand binding domains are appended by a linker of variable size to target two cognate binding sites separated by 10 base pairs, or one turn of the helix. Using this experimental approach, large bend angles were obtained, as analyzed electrophoretically.\n\nChapter 4 analyzes the nature of this binding and bending event using the designed third strand ligand. The energetics of bending were examined as were other factors influencing the ability to form a bent structure, including oligonucleotide binding motif, third strand length, sequence composition, pH, ion concentration and valence, target site spacing, and linker composition and orientation to examine the effects of electrostatics and hydrophobicity.\n\nChapter 5 describes the design of a complementary architectural factor to straighten DNA that has been bent by a triple helical ligand. These complementary polyamide ligands recognize DNA sequence specifically and bind in the minor groove of the linker region to straighten DNA. Such molecules may also be useful as artificial regulators of biological processes." }, { "name": "Lim, Ai Ching", "degree": "PhD", "year": "1998", "title": "Investigation of RNA Tertiary Structure and Function by Transition Metal Complexes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102025-233557591", "creators": [ { "name": { "family": "Lim", "given": "Ai Ching" }, "id": "Lim-Ai-Ching", "display_name": "Lim, Ai Ching" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" } ], "option_major": [ "chemistry" ], "abstract": "Phenanthrenequinone diimine (phi) complexes of rhodium(III) were employed to\r\nprobe RNA secondary and tertiary structure. These complexes bind via intercalation in\r\nopen major grooves of RNA and upon irradiation promote strand scission. By probing\r\nboth synthetic and natural molecules containing a variety of tertiary motifs, a systematic and\r\npredictive understanding of the factors involved in RNA recognition by these complexes is\r\nsought. The metal complex Rh(phen)2phi3+ (phen = 1,10-phenanthroline) recognizes and\r\ncleaves synthetic triple helices selectively over double helices. The cleavage sites are\r\ndependent upon maximizing overlap between the phi ligand and the basepairs, and\r\nminimizing charge repulsion between the metal complex and protonated bases. These\r\ncleavage sites have proven useful in explaining rhodium complex cleavage in natural\r\nsystems such as tRNAPhe. With these complexes, we also seek to investigate the\r\ndifferences and similarities in RNA and DNA secondary and tertiary folding, by probing\r\nthe tertiary structure of tDNAPhe compared to tRNAPhe. These complexes have elucidated\r\nthe B-form nature of the DNA duplex as well as the tertiary folding of the DNA molecule,\r\nthus shedding light on the feasibility of using DNA analogs of RNA for structural studies.\r\nThese shape selective probes have also been applied to probe the tertiary structure of HIV\r\nand BIV (TAR (trans-activation response) RNAs. \u0394-Rh(phen)2phi3+ binds with high\r\naffinity (Kb= 6.1 \u00b1 1.3 x 105 M-1) and specificity to sites at and across from a bulge\r\nregion which is the recognition element for the binding of the Tat (trans-activating) peptide.\r\nImportantly, the metal complex recognizes an RNA base-triple the formation of which is\r\nnecessary for transactivation. Derivatives of Rh(phen)2phi3+, Rh(MGP)2phi5+(MGP = 4-\r\nguanidylmethy 1-1, 10-phenanthroline) and Rh(GEB)2phi5+ (GEB = 4-(2-guanidylethyl)-4'methy\r\n1-2,2'-bipyridine) where guanidinium moieties have been added to the ancillary\r\nligands of the rhodium complex, show enhanced affinity and selectivity for HIV and BIV\r\nRNA sequences. This is due to the guanidinium moieties mimicking the arginine side\r\nchains on the native Tat peptide, and making non-specific contacts with the phosphate\r\nbackbone of the RNA. However, even without these functionalities, shape-selection,\r\nmatching the shape of the small metal complex to its nucleic acid target, provides sufficient\r\nselective stabilization for RNA site discrimination. Indeed, these complexes compete\r\neffectively with the specific Tat peptides for their binding sites on their respective TAR\r\nRNAs. These complexes therefore employ shape selection to recognize structural\r\nvariations along the RNA polymer which are important for protein recognition. Shape-selective\r\nrecognition could also be applied to the design of novel small molecules to target\r\nnucleic acid sites with high site-selectivity, in the development of molecules to inhibit\r\nprotein recognition, and, potentially, in the design of new chemotherapeutics." }, { "name": "Martin, Jeremy Isaac", "degree": "PhD", "year": "1998", "title": "Statistical Mechanics of End-Attached Polymer Interfaces", "advisor": "Wang, Zhen-Gang", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-174712767", "creators": [ { "name": { "family": "Martin", "given": "Jeremy Isaac" }, "id": "Martin-Jeremy-Isaac", "orcid": "0000-0001-7233-7217", "display_name": "Martin, Jeremy Isaac" } ], "advisors": [ { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "advisor", "display_name": "Wang, Zhen-Gang" } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4pc9-vz14", "abstract": "This dissertation discusses several closely related problems involving end attached polymers\r\nat interfaces. The studies share a numerical self-consistent field approach which is described\r\nin detail in Chapter 1.
\r\n\r\nIn Chapter 2, we consider irreversible polymer brushes (polymers densely end tethered\r\nto a surface). First, we discuss the adequacy of second virial treatments of interchain\r\ninteractions. Next we examine the extent of interbrush penetration between compressed\r\npolymer brushes, and its effect on the interactions between them. Then we identify scaling\r\nvariables which control the behavior of polymer brushes in polymeric solvents. Finally we\r\ninvestigate brush configurations and interactions in mixed solvents, where nonmonotonic\r\ninteraction profiles are predicted with a longer range weak attraction, and strong repulsion\r\nat shorter separations.
\r\n\r\nIn Chapter 3, we discuss the modification of spreading properties of a liquid on a solid\r\nsurface by the addition of end-adsorbing polymers. An end-adsorption polymer additive\r\ncan lead an otherwise non-spreading liquid to spread. A phase diagram for spreading of a\r\nliquid drop of fixed volume as a function of the concentration of end-adsorbing polymers\r\nand the energy of end-adsorption to the surface is obtained. The equilibrium thickness of\r\na spread film is also calculated, and is shown to be closely related to the thickness of a\r\nself-assembled polymer brush in an unbounded fluid and relatively insensitive to the bare\r\nspreading power of the liquid or the Hamaker constant, which determine the equilibrium\r\nthickness of a film of a simple liquid.
\r\n\r\nFinally, in Chapter 4, we study the interaction forces between two plates in a semi-dilute\r\nsolution of polymers each having one weakly adsorbing end-group. This system exhibits\r\nboth repulsive and attractive interactions of comparable magnitude and well-separated\r\nlength scales. The repulsion has a length scale of the end-to-end distance of the endadsorbed\r\npolymer, and a magnitude which is proportional to the end-adsorption energy\r\nand the volume fraction of the polymer, and inversely proportional the chain molecular\r\nweight. At plate separations of order the correlation length of the solution, a depletion\r\nattraction sets in with a magnitude that scales with the bulk osmotic pressure.
" }, { "name": "Maughon, Bob Robinson, Jr.", "degree": "PhD", "year": "1998", "title": "Synthesis of Functionalized Polymers by Ring-Opening Metathesis Polymerization (ROMP)", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06142018-101514702", "creators": [ { "name": { "family": "Maughon", "given": "Bob Robinson, Jr." }, "id": "Maughon-Bob-Robinson-Jr", "display_name": "Maughon, Bob Robinson, Jr." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" } ], "option_major": [ "chemistry" ], "doi": "10.7907/txks-pt47", "abstract": "In Chapter 1, the ROMP of 5-methacrylate-1-cyclooctene and the copolymerization\r\nof this monomer with cyclooctadiene using the initiator (PCy3)2Cl2Ru=CHCH=CPh2 were\r\ninvestigated to produce polymers with cross-linkable side-chains. The impact of\r\nconcentration, monomer to initiator ratio, and the amount of inhibitor in the polymerization\r\nwas examined. These polymers were cross-linked through the methacrylate side-chains\r\nwith either thermal or photochemical initiation, and the incorporation of these polymers into\r\npoly(methyl methacrylate) (PMMA) to produce AB cross-linked materials was\r\naccomplished. A comparison of the physical properties of PMMA and these new materials\r\ndemonstrated that these materials had higher thermal stability and solvent resistance than\r\npure PMMA.
\r\n\r\n\r\nAs an extension of the work presented in Chapter 1, Chapter 2 illustrated an\r\nalternative approach for the preparation of cross-linkable polymers by ROMP. The\r\nsynthesis of ring-opening metathesis polymerization chain transfer agents bearing\r\nmethacrylate and epoxide end-functionality was accomplished. In the presence of these\r\nchain transfer agents, cyclooctadiene was polymerized via a ruthenium benzylidene\r\ninitiator, (PCy3)Cl2Ru=CHPh, to produce telechelic poly(butadiene)s with either\r\nmethacrylate or epoxide end groups. The impact of initiator concentration, reaction time,\r\nand temperature on the polymer yield and chain transfer agent incorporation was examined.\r\nControl over the polymer molecular weight through the cyclooctadiene/chain transfer agent\r\nratio was demonstrated providing for a range of telechelic poly(butadiene) molecular\r\nweights. Successful cross-linking of these polymers by thermal or photochemical initiation\r\nin the case of the bis(methacrylate)-functionalized telechelic poly(butadiene)s or through\r\nacid catalysis in the case of the bis(epoxide)-functionalized telechelic poly(butadiene)s was\r\naccomplished.
\r\n\r\n\r\nIn an effort to further explore the functional group tolerance of the ruthenium-based\r\nmetathesis initiators developed in our group, the investigation presented in Chapter 3\r\nencompassed the synthesis and living ring-opening metathesis polymerization (ROMP) of\r\nsubstituted cyclobutenes with the functional group tolerant polymerization initiators\r\n(PCy3)2Cl2Ru=CHCH=CPh2 and (PCy3)2Cl2Ru=CHPh. Synthetic methodology was\r\ndeveloped for the synthesis of a wide variety of 3-functionalized cyclobutenes containing\r\nether, ester, alcohol, amine, amide, and carboxylic acid substituents. Coordination of these\r\nfunctional groups to the propagating carbene was observed resulting in the formation of a\r\nchelated propagating species with concomitant loss of one phosphine ligand from the metal\r\ncenter. Studies aimed at understanding this chelation and its effect on the polymerization\r\nwere undertaken. Based on these results, the synthesis of a series of functionalized\r\ncyclobutenes was accomplished which minimized this chelation and allowed for living\r\npolymerizations. A new class of functionalized poly(butadiene) homopolymers and\r\ndiblock copolymers was synthesized and the thermal properties analyzed by\r\nthermogravimetric analysis and differential scanning calorimetry.
\r\n\r\n\r\nIn Chapter 4, the effect of backbone flexibility on the mesomorphic behavior of\r\nside-chain liquid crystalline polymers synthesized by ring-opening metathesis\r\npolymerization was investigated. The synthesis of norbornene and cyclobutene monomers\r\ncontaining a p-nitrostilbene moiety as the mesogenic group and polymerization of these\r\nmonomers with the metathesis initiator (PCy3)2Cl2Ru=CHPh to produce side-chain liquid\r\ncrystalline polymers with low polydispersities and defined molecular weights was\r\naccomplished. The relatively rigid poly(norbornene)s displayed enantiotropic nematic\r\nmesomorphism with glass transitions from 44-64\u00b0C and isotropization temperatures\r\nbetween 108-121\u00b0C, whereas the more flexible poly(butadiene)s showed enantiotropic\r\nsmectic A mesomorphism with glass transition temperatures from 14-31\u00b0C and\r\nisotropization temperatures between 74-111\u00b0C. A diblock copolymer containing a 1:1\r\nmixture of the poly(norbornene) and poly(butadiene) backbones also exhibited a smectic A\r\nmesophase. The dependence of the degree of polymerization and flexible spacer length on\r\nthe phase transitions of these systems was determined demonstrating stabilization of the\r\nmesophase by both increasing molecular weight and flexible spacer length.
\r\n\r\n\r\nA short chapter on the development of methodology for an improved synthesis of\r\n3-methyl-3-phenylcyclopropene was included in Appendix 1. This research was\r\ninvestigated in hopes of developing a more facile and inexpensive procedure for the\r\npreparation of this compound than has been previously reported. Phase transfer catalyzed\r\ndichlorocarbene addition to \u03b1-methylstyrene followed by a selective catalytic Bu3SnH\r\nreduction resulted in the 1-chloro-2-methyl-2-phenylcyclopropane intermediate in excellent\r\nyield. Base-induced elimination of this compound resulted in the desired 3-methyl-3-phenylcyclopropene. \r\nThis approach allowed for the preparation of this cyclopropene on\r\nlarge scale utilizing inexpensive reagents.
\r\n\r\n\r\n\r\n\r\n" }, { "name": "Moore, Teresa Anne", "degree": "PhD", "year": "1998", "title": "Molecular Beam Studies of Stratospheric Photochemistry", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302025-155308477", "creators": [ { "name": { "family": "Moore", "given": "Teresa Anne" }, "id": "Moore-Teresa-Anne", "display_name": "Moore, Teresa Anne" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nkqt-qj82", "abstract": "Photochemistry of chlorine oxide containing species plays a major role in stratospheric\r\nozone depletion. This thesis discusses two photodissociation studies of the key molecules\r\nClONO2 and ClOOCl which were previously thought to only produce Cl-atom ( ozone\r\ndepleting) products at wavelengths relevant to the stratosphere. The development of a\r\nmolecular beam source of ClOOCl and the photodissociation dynamics of the model system\r\nCl2O are also discussed.
\r\n\r\nIn the first chapter, the photochemistry of ClONO2 is examined at 308 run using the\r\ntechnique of photofragment translational spectroscopy. Two primary decomposition\r\npathways, leading to Cl+ NO3 and ClO + NO2, were observed, with a lower limit of 0.33 for\r\nthe relative yield of ClO. The angular distributions for both channels were anisotropic,\r\nindicating that the dissociation occurs within a rotational period.
\r\n\r\nChapter two revisits the photodissociation dynamics of Cl2O at 248 and 308 nm, on\r\nwhich we had previously reported preliminary findings. At 248 nm, three distinct dissociation\r\npathways leading to Cl + ClO products were resolved. At 308 nm, the angular distribution\r\nwas slightly more isotropic that previously reported, leaving open the possibility that Cl2O\r\nexcited at 308 run lives longer than a rotational period.
\r\n\r\nChapter three describes the development and optimization of a molecular beam source\r\nof ClOOCl. We utilized pulsed laser photolysis of Cl2O to generate ClO radicals, and cooled\r\nthe cell to promote three body recombination to form ClOOCl. The principal components in\r\nthe beam were Cl2, Cl2O, and ClOOCl.
\r\n\r\nIn the fourth chapter, the photodissociation dynamics of ClOOCl are investigated at\r\n248 and 308 nm. We observed multiple dissociation pathways which produced ClO + ClO\r\nand 2Cl + O2 products. The relative Cl:ClO product yields are 1.0:0.13 and 1.0:0.20 for\r\nClOOCl photolysis at 248 and 308 run, respectively. The data at 308 nm was more difficult\r\nto interpret because of extensive interference from Cl2 and Cl2O byproducts. The upper limit\r\nfor the relative yield of the ClO + ClO channel was 0.19 at 248 nm and 0.31 at 308 nm.\r\nThese results substantially confirm the current assumption but decrease somewhat the\r\nefficiency of the ClOOCl ozone-depleting catalytic cycle. At 248 run, ClOOCl photolysis\r\nexhibited novel dissociation dynamics which appeared to depend on the symmetry of the\r\nexcited state.
" }, { "name": "Pomykal, Katherine Elizabeth", "degree": "PhD", "year": "1998", "title": "Studies of Charge Transfer at Semiconductor/Liquid Junctions", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:08112025-204826614", "creators": [ { "name": { "family": "Pomykal", "given": "Katherine Elizabeth" }, "id": "Pomykal-Katherine-Elizabeth", "display_name": "Pomykal, Katherine Elizabeth" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v5ck-gf39", "abstract": "Steady-state current-voltage measurements on two types of semiconductor/liquid\r\njunction solar cells are presented. Results of these and other experiments on single-crystal\r\nelectrodes are discussed in terms of present kinetic theory on charge transfer at these\r\njunctions.
\r\n\r\nNanoporous titanium dioxide electrodes have been sensitized with a series of dyes\r\nwith varying ground state reduction potentials. The spectral response and current-voltage\r\nproperties of these electrodes have been measured. The trends can be explained by the\r\ndifferences in absorption spectra and ground state potentials. The effect of pH on the\r\nconduction band edge position of nanoporous titanium dioxide has been examined through\r\ncurrent-voltage measurements and luminescence studies on dye-sensitized electrodes. The\r\nresults are discussed in the framework of current theories on increasing efficiency of these\r\nelectrodes. Studies involving charge separation at the back electrode contact were also\r\nperformed.
\r\n\r\nPredictions of the Marcus/Gerischer theory for photoelectrode stability have been\r\ninvestigated experimentally for n-Si/CH3OH photoelectrochemical cells. Specifically, a\r\nsemiconductor electrode is predicted to be more stable if the reorganization energy of the\r\nstabilizing agent is decreased (in the normal region of the Marcus behavior), thereby\r\nincreasing the rate of minority carrier capture by the stabilizer. This prediction was\r\nquantified experimentally by monitoring the branching ratio between two competing\r\nreactions at a semiconductor/liquid interface. The experimental observations can be\r\nconsistently explained through this predicted influence of the minority carrier acceptor\r\nreorganization energy on the interfacial charge transfer rate constant.
\r\n\r\nInterfacial charge transfer rate constants at indium phosphide/liquid junctions were\r\ninvestigated using current density-potential and differential capacitance-potential methods.\r\nThe measured electron transfer rate constants, ket, for these systems were \u224810-16 cm4 s-1,\r\nin excellent agreement with previous theoretical predictions. Contacts which did not\r\ndisplay bimolecular kinetic behavior still yielded upper bounds on the charge transfer rate\r\nconstants, which were also consistent with limits predicted by theory. The current density potential\r\nbehavior of n-InP and p-InP/Fe(CN)63-/4-(aq) junctions was also examined in\r\norder to assess the validity of prior kinetic measurements on these interfaces.
" }, { "name": "Ramirez, Benjamin E.", "degree": "PhD", "year": "1998", "title": "The CU\u2090 center of cytochrome oxidase : electronic structure calculations and electron-tunneling pathways", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-113407018", "creators": [ { "name": { "family": "Ramirez", "given": "Benjamin E." }, "id": "Ramirez-Benjamin-E", "display_name": "Ramirez, Benjamin E." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/r7t8-xt78", "abstract": "The Cu_A center is a mixed valence, dithoilate-bridged, binuclear copper center that is found in cytochrome oxidase. It serves as the initial acceptor of electrons from cytochrome c. The Cu_A center has distinct UV/Vis and EPR spectroscopic features. It is likely that this site has an extremely low inner-sphere reorganization energy because it very efficiently transfer electrons st low reaction driving forces over long distances (~15-20 \u00c5) in less than a millisecond. We undertook DFT calculations on a Cu_A model complex to examine the structure, spectroscopic assignments and reorganization energy of the center. The optimized structure of the Cu_A model complex closely resembles the structure determined from x-ray diffraction studies. The rms overlap of the optimized structure with the structure derived from EXAFS data is 0.16 \u00c5. Based on the calculated MO diagram, we assign the bands in the UV/Vis absorption spectrum to transitions originating from lower lying doubly-filled orbitals into a \u03c3_(Cu)* singly-occupied HOMO that is primarily Cu d_(x2-y2)/S p_x in character. We find that the character of the HOMO as well as the transition energies and intensities are extremely sensitive to the Cu-S-Cu angle. We also calculated the optimized structure of the reduced center to examine the role of the protein in reducing the inner-sphere reorganization energy. The following picture emerges from the calculations of the coordination geometry: the protein framework imposes a structure, with a low dielectric cavity in which the trigonal geometry of the oxidized form is optimal. In addition, this framework prevents the reduced structure from distorting to its optimal (linear, two-coordinate) structure. This so-called rack effect of the folded protein enables Cu_A and blue copper centers to function as very efficient electron-transfer agents." }, { "name": "Rhodes, Carl", "degree": "PhD", "year": "1998", "title": "Nonlinear modeling and identification for process control", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-02042008-082018", "creators": [ { "name": { "family": "Rhodes", "given": "Carl" }, "id": "Rhodes-Carl", "display_name": "Rhodes, Carl" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Wiggins", "given": "Stephen R." }, "id": "Wiggins-S-R", "role": "member", "display_name": "Wiggins, Stephen R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/96TN-SN45", "abstract": "Ideally, processes to be controlled would behave in a linear manner so that well-developed methods of linear control could be applied directly. However, environmental regulations and increased competition are forcing these processes to operate in regions where the assumptions of linearity tend to break down. There has been a great deal of recent academic interest in the control of nonlinear systems, but there are relatively few applications of these methods in industry. One major reason may be the lack of tools for developing models suitable for nonlinear control schemes.\r\n\r\nA number of tools that can be used in the modeling of nonlinear systems for process control are presented in this thesis. In the first section, the problem of determining the proper regression vector size for black-box modeling is examined. The false nearest neighbors algorithm (FNN) is suggested as a solution for this problem. Extensions, analysis, and numerous applications of the FNN algorithm are given and the algorithm is seen to be a useful tool in the identification of nonlinear models.\r\n\r\nIn the second section of the thesis, the problem of nonlinear model reduction for systems exhibiting large time-scale separations is examined. A method of determining the reduced order manifold of slow dynamics is outlined and it is proved that this algorithm identifies the proper manifold. Some thoughts on how the results of the algorithm can be used for developing reduced models are presented.\r\n\r\nIn the third section, the concept of data-based control is introduced. This method of control attempts to utilize process data directly through local modeling techniques. Some preliminary work in this area is given for trajectory tracking and computing controllable sets and data-based control is successfully applied to an experimental electrical circuit. Finally, some thoughts on possible future work in this field are presented.\r\n" }, { "name": "Wagaman, Michael Wayne", "degree": "PhD", "year": "1998", "title": "Conjugated Electroluminescent Polymers Synthesized by a Ring-Opening Metathesis Polymerization Precursor Route", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07312025-221339661", "creators": [ { "name": { "family": "Wagaman", "given": "Michael Wayne" }, "id": "Wagaman-Michael-Wayne", "display_name": "Wagaman, Michael Wayne" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/65pj-3w78", "abstract": "A variety of substituted poly(para-phenylenevinylene) (PPVs) and poly(l,4-\r\nnaphthalenevinylene) homopolymers, block copolymers and random copolymers have been\r\nsynthesized by a ring-opening metathesis polymerization (ROMP) precursor route. In\r\ngeneral the initiator Mo=CCH(CH3)2Ph(=NAr)(OCCH3(CF3)2)2, 1, was used to polymerize barrelene (bicyclo[2.2.2]octatriene) and benzobarrelene monomers. The\r\nprecursor polymers obtained were then aromatized in solution using 2,3-dichloro-5,6-\r\ndicyanobenzoquinone (DDQ) to produce PPVs and PNVs, many of which are soluble in\r\ncommon organic solvents.
\r\n\r\nTo prepare these polymers, new syntheses of the monomers were first developed as\r\ndescribed in Chapters 1 and 2. The routes developed readily allow the preparation of a\r\nvariety of substituted benzobarrelene and barrelene monomers in multigram quantities. As\r\ndescribed in Chapter 3, several well-defined metathesis initiators were tested to determine\r\nthe one best suited to the synthesis of homopolymers and copolymers of the monomers\r\nprepared. Tuning of the activity of 1 to achieve a living polymerization is also described.
\r\n\r\nIn Chapter 4 the synthesis of PNV and PPV homopolymers, and studies of their\r\nabsorbance and fluorescence properties, are described. These studies show that the\r\ndifferent homopolymers exhibit luminescence from the blue (450 nm) to nearly the red (580\r\nnm) depending on the substituents on the polymer, which were usually alkyl groups,\r\nelectron withdrawing groups (halogens, esters, and perfluoroalkyl groups) or both.\r\nPolymers with electron withdrawing groups were found to be much more stable in air than\r\nunsubstituted PPV and PNV.
\r\n\r\nThe synthesis of PNV and PPV random and block polymers and studies of their\r\nabsorbance and fluorescence properties are described in Chapter 5. In general, polymers\r\nwith a diblock or blocky distribution of monomer units showed migration of excitons\r\n(electron-hole pairs) into the smaller bandgap segments of the polymer. As a result, most\r\nof the luminescence from these materials had a wavelength characteristic of the smaller\r\nbandgap homopolymer. More efficient transport was observed in films and in copolymers\r\nwith shorter block segments.
\r\n\r\nIn Chapter 6 the results of electroluminescence studies with three of the polymers\r\nare described. These measurements show that the polymers prepared exhibit\r\nelectroluminescence. They also reveal that alkylated PNV is a better hole transporter than\r\nelectron transporter but that diester substituted PPV is a better electron transporter and a\r\npoorer hole transporter.
\r\n\r\nFinally, use of a di-t-butylester substituted PPV in conjunction with a photo-acid\r\ngenerator as a photoresist is described in the Appendix.
" }, { "name": "Walkup, Grant Kingsley", "degree": "PhD", "year": "1998", "title": "Fluorescent peptidyl chemosensors for the measurement of divalent metal cation concentrations", "advisor": "Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212012-122025163", "creators": [ { "name": { "family": "Walkup", "given": "Grant Kingsley" }, "id": "Walkup-G-K", "display_name": "Walkup, Grant Kingsley" } ], "advisors": [ { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/q7ve-nc61", "abstract": "Studies toward the production of fluorescent chemosensors for trace divalent\r\nmetal ions have been conducted, with emphasis placed on the attainment of sufficient\r\nanalyte selectivity and sensitivity for the measurement of environmental or biomedical\r\nsamples. One technique that has historically been applied for the design of selective\r\nmetal ion sensors is to prepare biosensors, devices that exploit proteins for their\r\nunmatched specificity in the recognition of small molecules. Alternately, the\r\nconstruction of abiotic chemosensors has been favored by other researchers, but the\r\nsynthetic simplicity and enhanced durability exhibited by these agents comes at the\r\nexpense of analyte-detection selectivity. By applying a strategy that is a hybrid of these\r\napproaches, selective and sensitive chemosensors for divalent zinc, copper, and nickel\r\nhave been prepared. These devices combine the advantageous aspects of biosensors\r\nwithin a peptidyl architecture that by virtue of its synthetic origin contains an expanded\r\nrepertoire of amino acids for metal ion binding and signaling.
\r\n\r\nFluorescent chemosensors for Zn(II) have been prepared that are based upon the\r\nzinc finger domains and enable the quantitation of sub-micromolar concentrations of that\r\nion in the presence of many other divalent ions. In addition, other fluorosensors have\r\nbeen prepared that employ nonnatural alpha-amino acid derivatives that contain the\r\nbidentate metal binding functionality of oxine (8-hydroxyquinoline). These also enable\r\nthe selective detection of sub-micromolar concentrations of Zn(II), but require only seven\r\namino acid residues as opposed to the 25 present in the zinc finger-based sensors.
\r\n\r\nBy exploiting the metal binding properties of the amino terminal Cu(II)- and\r\nNi(II)-binding (ATCUN) motif of the serum albumins, sensors have been prepared which\r\nenable the selective determination of sub-micromolar concentrations of the Cu(II) ion,\r\neven in the presence of elevated concentrations of Ni(II). Sensors for Ni(II) that employ\r\na fluorescence resonance energy transer (FRET) mechanism for analyte detection have\r\nalso been prepared. In addition, studies have been performed to convert these solution based\r\nchemosensing reagents into solid phase-attached devices, in order to perform realtime\r\nmeasurements with regenerable sensing materials.
" }, { "name": "Williamson, Joseph Charles", "degree": "PhD", "year": "1998", "title": "Ultrafast Gas-Phase Electron Diffraction", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112025-231937152", "creators": [ { "name": { "family": "Williamson", "given": "Joseph Charles" }, "id": "Williamson-Joseph-Charles", "orcid": "0000-0002-3711-1682", "display_name": "Williamson, Joseph Charles" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8kj6-m794", "abstract": "The temporal resolution of pump-probe, gas-phase electron diffraction (GED) has\r\nbeen extended to the picosecond time scale, a three order-of-magnitude improvement.\r\nWith such resolution, GED can now be applied to structural studies of fundamental\r\nchemical dynamics, providing complementary information to conventional ps and fs\r\nspectroscopy techniques. This thesis gives a thorough theoretical and experimental\r\ntreatment of ultrafast gas-phase electron diffraction (UGED). Classical Monte-Carlo\r\nsimulations of coherent chemical dynamics were used to demonstrate that the evolution of\r\nmolecular spatial coordinates can be determined with fs GED. Similarly, ps GED can\r\nreveal the structure of short-lived intermediates in kinetic processes. The circular\r\nsymmetry of GED patterns was predicted to break during ps rotational coherences,\r\nrevealing additional structural detail such as bond angles.
\r\n\r\nInstrumentation for UGED was almost entirely home-built. Femtosecond laser\r\npulses were generated in a colliding-pulse, mode-locked ring dye laser and amplified with\r\na four-stage dye cell arrangement pumped by a Nd:YAG laser. The 620-nm output (2 to\r\n3 mJ, 300 fs uncompressed; 30 Hz) was split into pump and probe arms and frequency-doubled.\r\n95% of the laser intensity was focused onto a molecular beam. The remaining\r\n5% was directed onto a back-illuminated 450-A silver cathode, where ultrafast electron\r\npulses were created via the photoelectric effect. The electrons were accelerated with an\r\n18-kV electron gun and focused to a 300-\u03bcm diameter. Space-charge effects forced a\r\ncompromise between electron number density and temporal resolution: streaking\r\nexperiments revealed that a 1-ps pulse contained 1,000 electrons and a 10-ps pulse\r\ncontained 10,000 electrons.
\r\n\r\nThirty centimeters downstream from the exit of the gun, the electrons intersected\r\nthe pump laser at a 90\u00b0 angle, directly underneath the molecular beam orifice. A\r\ntheoretical analysis of the crossed-beam geometry showed that velocity mismatch between\r\nthe pump photons and the probe electrons also affected the temporal resolution of UGED,\r\nmaking a 3-ps contribution. Approximately 10% of the electrons scattered elastically from\r\nsample molecules within the interaction region, and the resulting diffraction pattern was\r\nrecorded with a scintillator / fused fiber optic / image intensifier / charge-coupled device\r\nimaging system housed in a separate vacuum chamber. Single-electron sensitivity across\r\ntwo-dimensions was necessary because of the extremely low electron flux, and the\r\nestimated detective quantum efficiency of the imaging system was better than 0.5.\r\nGround-state GED patterns of CCl4, SF6, CF3I, CH2I2, and C2F4I2 were recorded using ps\r\nelectron pulses. The diffraction data were processed with a software package developed\r\nin the laboratory, and the resulting modified molecular scattering curves agreed well with\r\ntheory. Radial distribution functions were also calculated.
\r\n\r\nTime zero for the pump-probe experiment was identified to within 1 to 2 ps using\r\nphotoionization-induced lensing (PIL) of the unscattered electron beam. The excitation\r\nlaser ionized a small fraction of the molecular beam sample, and a cylindrical coulombic\r\nlens developed within ps as the nascent photoelectrons escaped the interaction region.\r\nThe effects of this lens on the incident 18-ke V electron beam shape was detected by\r\ndirect-bombardment on a charge-coupled device located inside the scattering chamber;\r\nhigh spatial resolution of ~ 15-\u03bcm was necessary to observe PIL-induced changes in the\r\nelectron beam.
\r\n\r\nDiiodomethane was selected as the prototype molecule for the first ultrafast GED\r\ninvestigation. After establishing time zero with PIL, diffraction patterns were recorded at\r\nseveral time steps around t0. The transients showed that approximately 10% of the CH2I2\r\ndissociated into CH2I and an iodine atom following excitation with the 310-nm pump\r\nlaser. The estimated temporal resolution was 5 to 10 ps.
" }, { "name": "Yurkovetsky, Yevgeny", "degree": "PhD", "year": "1998", "title": "I. Statistical mechanics of bubbly liquids. II. Behavior of sheared suspensions of non-Brownian particles", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06222005-110302", "creators": [ { "name": { "family": "Yurkovetsky", "given": "Yevgeny" }, "id": "Yurkovetsky-Y", "display_name": "Yurkovetsky, Yevgeny" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Hunt", "given": "Melany L." }, "id": "Hunt-M-L", "role": "member", "display_name": "Hunt, Melany L." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NMJQ-2X32", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. Statistical mechanics of bubbly liquids. The dynamics of bubbles at high Reynolds numbers is studied from the viewpoint of statistical mechanics. Individual bubbles are treated as dipoles in potential flow. A virtual mass matrix of the system of bubbles is introduced, which depends on the instantaneous positions of the bubbles, and is used to calculate the energy of the bubbly flow as a quadratic form of the bubbles' velocities. The energy is shown to be the system's Hamiltonian and is used to construct a canonical ensemble partition function, which explicitly includes the total impulse of the suspension along with its energy. The Hamiltonian is decomposed into an effective potential due to the bubbles' collective motion and a kinetic term due to the random motion about the mean. An effective bubble temperature - a measure of the relative importance of the bubbles' relative to collective motion--is derived with the help of the impulse-dependent partition function. Two effective potentials are shown to operate: one, due to the mean motion of the bubbles, dominates at low bubble temperatures where it leads to their grouping in flat clusters normal to the direction of the collective motion, while the other, temperature invariant, is due to the bubbles' position-dependent virtual mass and results in their mutual repulsion. Numerical evidence is presented for the existence of the effective potentials, the condensed and dispersed phases and a phase transition.\r\n\r\nII. Behavior of sheared suspensions of non-Brownian particles. Suspensions of non-Brownian particles in simple shear flow of a Newtonian solvent in the range of particle phase concentration, [...], from 0.05 to 0.52, are studied numerically by Stokesian Dynamics. The simulations are a function of [...] and the dimensionless shear rate, [...], which measures the relative importance of the shear and short-ranged interparticle forces. The pair-distribution functions, shear viscosity, normal stress differences, suspension pressure, long-time self-diffusion coefficients, and mean square of the particle velocity fluctuations in the velocity-gradient and vorticity directions are computed, tabulated and plotted. In concentrated suspensions ([...] > 0.45), two distinct microstructural patterns are shown to exist at the highest and lowest shear rates. At [...] = 0.1 the particles form hexagonally packed strings in the flow direction. As [...] increases, the strings are gradually being replaced by non-compact clusters of particles kept together by strong lubrication forces while the particle pair-distribution displays a broken fore-aft symmetry. These changes in the microstructure are accompanied by increases in the shear viscosity, normal stress differences, suspension pressure, longtime self-diffusion coefficients, and fluctuational motion. Agreement is found between the simulation results and the theoretical predictions of Brady and Morris (1997).\r\n" }, { "name": "Zhao, Huimin", "degree": "PhD", "year": "1998", "title": "Enzyme Design by Directed Evolution", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-105832", "creators": [ { "name": { "family": "Zhao", "given": "Huimin" }, "id": "Zhao-Huimin", "display_name": "Zhao, Huimin" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3bcb-4g98", "abstract": "Directed evolution, inspired by Darwinian evolution in Nature, is an effective approach for protein design. An industrially-important enzyme, subtilisin E, has been chosen as the research target. Important methodologies for directed evolution have been developed, including optimizing the error-prone polymerase chain reaction (PCR) to allow easy and precise control of the mutation rate, optimizing DNA shuffling for high fidelity recombination, and developing three new in vitro recombination methods: random priming recombination (RPR), defined primer recombination (DPR) and staggered extension process (StEP) recombination.
\r\n\r\nUsing these techniques, subtilisin E isolated from the mesophilic organism Bacillus subtilis has been rapidly converted into its thermophilic counterpart (without compromising its activity). After five generations of directed evolution, the resulting variant 5-3H5 is as stable as its naturally-occurring thermostable homolog, thermitase, isolated from the thermophilic organism Thermoactinomyces vulgaris. The half-lives of thermal inactivation at 83\u00b0C of both 5-3H5 and thermitase are 3.5 min. Their temperature optima are 76\u00b0C, 18\u00b0C higher than that of wild type subtilisin E. In addition, 5-3H5 is more active than wild type subtilisin E over the whole range of temperatures. The mutations responsible for the enhanced thermostability were identified and mapped into the structure of subtilisin E. Our findings strongly supports the notion that thermal stability is achieved by the cumulative effect of small improvements at many locations within the protein molecule. Thus, not surprisingly, the pursuit of a 'holy grail' of rules for protein thermostabilization was deemed unsuccessful. However, as demonstrated here, directed evolution is a generally applicable, highly effective approach to increase protein thermostability.
\r\n\r\nThe concepts and techniques developed for directed evolution may also be applied to solving problems associated with molecular evolution in Nature. For example, due to significant sequence divergence, identification of the adaptive mutations, neutral mutations and deleterious mutations in evolutionarily-related proteins is a difficult task. We developed a convenient method to identify functional mutations by gene recombination and sequence analysis of a small sampling of the recombined library exhibiting the evolved behavior. As a demonstration, this approach was used to identify the two thermostable mutations out of ten mutations in a laboratory-evolved thermostable subtilisin E variant.
\r\n" }, { "name": "Zuercher, William John", "degree": "PhD", "year": "1998", "title": "Ruthenium-Catalyzed Polycyclization Reactions", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212019-142607353", "creators": [ { "name": { "family": "Zuercher", "given": "William John" }, "id": "Zuercher-William-John", "display_name": "Zuercher, William John" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2857-9b48", "abstract": "Ruthenium carbene Cl\u2082(PCy\u2083)\u2082Ru=CHCH=CPh\u2082 mediates the efficient and selective conversion of acyclic dienynes to fused bicyclic [n.m.0] dienes containing five-, six- and seven-membered rings. Studies with various X-substituted acetylenes (X = H, alkyl, Ph, CO\u2082Me, SnBu\u2083, SiMe\u2083, halogen) suggest that the dienyne metathesis is not only sensitive to these substituents but also to the catalysts employed. Among the various metal alkylidenes examined, only the ruthenium catalyst I exhibited metathesis activity for a range of substrates. In no case, however, were acetylenes with heteroatomic substituents metathesized; these substrates either underwent simple diene RCM or failed to react with the catalyst in a productive fashion. These observations further expand the scope of catalytic RCM for the construction of complex organic compounds.
\r\n\r\nRuthenium alkylidene Cl\u2082(PCy\u2083)\u2082Ru=CHPh has been utilized in the tandem ring-opening/ring-closing metathesis of cycloolefins. This reaction produces a bicyclic molecules conatining nonconjugated dienes. Reactivity of the precursors is dependent upon strain, and thus ring size, of the cycloolefins. Competing oligomerization is observed in substrates having low ring strain; this process is inhibited by increasing dilution of the reaction or by adding alkyl substitution to the acyclic olefins.
\r\n\r\nThe application of ruthenium alkylidene Cl\u2082(PCy\u2083)\u2082Ru=CHPh to the catalysis of polycyclization reactions is detailed. Several acyclic precursors have been synthesized and reacted with the ruthenium alkylidene. These precursors vary in topology and contain either acetylenic or cyclic olefin metathesis relays or both. The cyclization reactions proceed in moderate to good yield to produce polycyclic polyenes when the precursors are subjected to catalytic amounts of the ruthenium complex. Precursors bearing n relay units generate polycycles containing (n + 1) rings.
" }, { "name": "Arkin, Michelle R.", "degree": "PhD", "year": "1997", "title": "Investigations of DNA-Mediated Electron Transfer Reactions with Metallointercalators", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08112025-225322656", "creators": [ { "name": { "family": "Arkin", "given": "Michelle R." }, "id": "Arkin-Michelle-R", "orcid": "0000-0002-9366-6770", "display_name": "Arkin, Michelle R." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4ggg-6x62", "abstract": "The array of \u03c0-stacked base pairs in DNA represents a novel medium for electron transfer\r\nreactions, and metallointercalators have served as useful tools to study this chemistry. Ultrafast\r\nkinetic measurements indicate that photoinduced electron transfer reactions between\r\nM(phen)2(X2dppz)2+ (M = Ru, Os; dppz = dipyrido[3,2-a:2,3-c]phenazine; X = H, CH3) [M(II)]\r\nand Rh(phi)2bpy3+ (phi = phenanthrenequinone diimine) [Rh(III)] can occur with rates> 3 x 1010\r\ns-1. Recombination reactions between M(III) and Rh(II) are also very fast (~ 1010 s-1), and rates\r\nare found to be independent of the loading of \u0394-Rh(phi)2bpy3+ on DNA. However, reaction rates\r\nand efficiencies are highly sensitive to i) the structure and chirality of intercalators and ii) the\r\nsequence and conformation of the DNA double helix. Photoinduced reactions between Ru(II) and\r\nRh(III) bound to the DNA helix and to SOS micelles, which lack the ordered \u03c0-stacked array, are\r\nalso compared. In contrast to DNA, quenching in micelles occurs by diffusion. The details of\r\nintercalation and DNA sequence are thus found to be important characteristics of DNA-mediated\r\nET reactions.
\r\n\r\nTo study long-range reactions through DNA, metallointercalator-DNA conjugates have\r\nbeen prepared. Rh(III) and novel trisheteroleptic complexes of Ru(II) are tethered to the 5'-termini\r\nof oligonucleotides by solid- and solution-phase methods, and these complexes have provided\r\nspectroscopic and photochemical tools to characterize chimeric structures. In addition to\r\nexperiments in which DNA serves as a molecular bridge connecting donor and acceptor, the double\r\nhelix may also serve as a reactant in electron transfer chemistry. Ru(III) oxidants have been\r\ngenerated in situ by a flash-quench methodology and have been found, by transient absorption\r\nspectroscopy, to oxidize G residues in DNA. Furthermore, using a tethered Ru(III)-DNA\r\nconjugate, oxidation products are observed 37 \u00c5 from the metallointercalator. These investigations\r\nof DNA-mediated electron transfer reactions contribute to our understanding of oxidative damage\r\nin DNA and may lead to a novel class of DNA-based biosensors.
" }, { "name": "Bansal, Ashish", "degree": "PhD", "year": "1997", "title": "Surface Modification and Charge Transfer Studies at Silicon and Gallium Arsenide Interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-164213008", "creators": [ { "name": { "family": "Bansal", "given": "Ashish" }, "id": "Bansal-Ashish", "display_name": "Bansal, Ashish" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5k6w-kt74", "abstract": "The thesis describes some chemical modifications of Si and GaAs surfaces, as a\r\nmeans of gaining control over the physical, chemical and electrical properties of these\r\nsurface and of the interfaces formed from these surfaces.
\r\n\r\nThe Current-voltage properties of n-GaAs photoanodes were evaluated in\r\nKOH-Se/2-(aq), CH3CN-ferrocene (Fc)+/0, and CH3CN-methyl viologen (MV)2+/+\r\nsolutions. Chemisorption of transition-metal ions (RhIII, RhIII, CoIII, OsIII) onto GaAs has\r\nbeen shown previously to effect improved photoanode behavior for n-GaAs/KOH-Se/2-\r\n(aq) contacts, but it is not clear whether the chemisorbed metal forms a buried\r\nsemiconductor/metal (Schottky) junction or results in a \"hybrid\" semiconductor/metal/liquid\r\ncontact. Metal ion treated n-GaAs photoanodes displayed different open circuit voltages in\r\ncontact with each electrolyte solution investigated. The role of the chemisorbed metal in the\r\nn-GaAs/KOH-Se/2-(aq) system is, therefore, best described as catalyzing interfacial charge\r\ntransfer at the semiconductor/liquid interface, as opposed to forming a semiconductor/metal\r\nor semiconductor/insulator/metal contact.
\r\n\r\nThe ability to modify Si surf ace without partial oxidation or formation of electrical\r\ndefects is potentially important. However, little is known about the chemistry of these\r\nsurfaces under ambient temperature and pressure. A two-step halogenation/alkylation route\r\nto chemical functionalization of Si(111) surf ace is described, that allows covalent\r\nattachment of alkyl functionalities without concomitant oxidation of the silicon surface. In\r\nthe first step, a hydrogen terminated silicon surface is chlorinated to obtain a chlorine\r\nterminated silicon surface. In the second step, the chlorinated surface is reacted with alkyl\r\nlithium or alkyl Grignard to obtain an alkyl terminated surface. The surface of silicon is\r\nextensively analyzed using a number of techniques such as XPS, HREELS, IRS, AES,\r\nTPD etc. The alkyl terminated surfaces are more resistant to oxidation in air and in contact\r\nwith wet chemical environments than the H-terminated surface.
\r\n\r\nCurrent-voltage and capacitance-voltage measurements of the alkyl terminated\r\nsurfaces in CH3OH-Me2Fc+/0 indicate that the electrical properties of these surfaces are\r\nvery similar to those of a H-terminated surface. The alkyl overlayers provide a small\r\nresistance to charge transfer across the Si/liquid interface but do not shift the band edges or\r\ninduce additional surface recombination. I-V characteristics of n-Si/alkyl/Au MIS devices\r\nindicate that these junctions behave largely liken-Si/Au Schottky junctions. The efficacy of\r\nalkyl overlayers in preventing photooxidation and photocorrosion of n-silicon surfaces was\r\nmeasured in contact with Fe(CN)63-/4-(aq) and with CH3OH-Me2Fc+/0 containing known\r\namounts of water. The alkyl terminated surfaces consistently show better I-V\r\ncharacteristics and lower oxidation than the H-terminated surface, indicating that stability to\r\noxidation had been achieved without any significant compromise in the electrical quality of\r\nthe silicon surface.
" }, { "name": "Baxter-Drayton, Yvette Valencia", "degree": "PhD", "year": "1997", "title": "The Dynamics of Flocculated Dispersions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072025-210544236", "creators": [ { "name": { "family": "Baxter-Drayton", "given": "Yvette Valencia" }, "id": "Baxter-Drayton-Yvette-Valencia", "display_name": "Baxter-Drayton, Yvette Valencia" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vqnw-np85", "abstract": "The rheological behavior of Brownian electrorheological (ER) fluids is studied\r\nas a model for flocculated colloidal dispersions. The ER fluid has the advantages\r\nthat the interparticle potential energy can be varied by simply changing the applied\r\nfield strength, and the microstructure consists of essentially linear chains of particles\r\naligned with the field direction. Studies of the quiescent suspension structure find a\r\ndispersed region, an equilibrium flocculated region, and a kinetically flocculated region\r\nfor low, moderate, and large attractive potential well depths, Umin/kT, respectively.\r\nUnder simple shear flow, the suspension has a high-shear-rate Newtonian viscosity\r\nand a shear thinning viscosity at lower shear rates. For moderate attractive potential\r\nwell depths the suspension has a low-shear viscosity that scales as exp(Umin/kT).\r\nFurthermore, the low-shear limiting behavior is seen at shear rates that scale as\r\nexp(-Umin/kT). The first normal stress difference is also presented. It was found\r\nthat due to the electric field the suspension structure is anisotropic with respect to\r\nthe compressional axis, and the first normal stress difference does not decay with the\r\nshear rate as it does for Brownian hard-spheres, but approaches a low-shear limiting\r\nvalue.
\r\n\r\nA theory is proposed that makes use of the time scale of diffusion for aggregated\r\nparticles out of their mutual potential well, \u03c4 ~ (a2/D)(kT/Umin)exp(Umin/kT),\r\nmuch in the spirit of the Eyring theory, to describe the rheology of the flocculated\r\ndispersion. Here a is the particle radius and D is the diffusivity of an isolated particle.\r\nWhen the shear rate is non-dimensionalized by \u03c4, the reduced viscosity data for all\r\nfield strengths collapse onto a single universal curve. Although we use a relatively\r\nsmall monolayer suspension, our simulation results compare well to the limited experimental\r\nand theoretical work on Brownian ER suspensions. The scaling relationship\r\nfor the low-shear viscosity has also been evidenced in other studies of flocculated\r\ndispersions.
\r\n\r\nThe model is tested for its general applicability by a study of the rheology of\r\na three-dimensional flocculated dispersion with an isotropic potential by molecular\r\ndynamics simulation and by analysis of experimental data obtained independently by\r\nBuscall, McGowan and Morton-Jones for a depletion flocculated dispersion. In both\r\ncases the suspension has a low-shear viscosity that scales exponentially with the pair\r\npotential well depth, and the low-shear limiting behavior was observed at a shear rate\r\nthat scales inverse exponentially with the pair potential well depth, Umin/kT. The\r\nreduced viscosity data collapse onto a single curve when plotted as a function of the\r\nshear rate non-dimensionalized by the escape time scale, and the model was found to\r\npredict the reduced curves.
\r\n\r\n" }, { "name": "Bowman, Frank Morales", "degree": "PhD", "year": "1997", "title": "Ozone and secondary organic aerosol formation from organic precursors", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01092008-152853", "creators": [ { "name": { "family": "Bowman", "given": "Frank Morales" }, "id": "Bowman-F-M", "display_name": "Bowman, Frank Morales" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/y634-fw03", "abstract": "A technique was developed to determine the amount of ozone and other secondary pollutants generated by individual organic components of atmospheric VOC/NO[subscript x] mixtures. This technique was used to investigate the chemical interactions associated with incremental reactivity calculations. It was shown that the incremental reactivity of an individual organic species is a result of changes in the ozone generated by each of the organics present. Incremental reactivities, therefore, are dependent on the nature of the VOC/NO[subscript x] mixture. Aldehydes, alkenes and reactive aromatics were found to have the highest incremental reactivities due to their behavior as radical sources, thereby increasing the rate of reaction of all available organics. Ozone and secondary aerosol formation within the South Coast Air Basin of California during the Southern California Air Quality Study (SCAQS) air pollution episode of August 27-28, 1987 were also analyzed and again the same species were shown to be the most productive compounds in the organic mixture. Less productive compounds, such as CO and alkanes, were also found to be major contributors to ozone concentrations due to their relative abundance. Eight reformulated fuel components were investigated to determine their ozone-forming potential. Most of the fuel oxygenates were found to have relatively low incremental reactivities due to their slow reaction rates and to the formation of relatively unreactive formate and acetate products.\n\nSecondary organic aerosol formation was studied in the Caltech outdoor smog chamber and a model was developed to describe the gas-particle absorptive partitioning of semi-volatile organics. Particle deposition, nucleation and vapor transport to aerosol particles, chamber walls and deposited particles are accounted for by the model. Simulations of a pair of m-xylene/NOX experiments were performed to investigate the nature of aerosol growth. Characteristic transport times indicate that gas-particle equilibrium will typically be established quite rapidly. Additional delays in aerosol formation were shown to result when the condensing semi-volatile products are second-generation, rather than first-generation, products of a parent hydrocarbon. Within a smog chamber, partitioning to chamber walls and deposited particles are shown to be negligible due to unfavorable equilibrium and transport conditions.\n" }, { "name": "Crellin, Kevin Christopher", "degree": "PhD", "year": "1997", "title": "The Investigation of Gas Phase Ion-Molecule Reactions with Fourier Transform Ion Cyclotron Resonance Mass Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222009-123129177", "creators": [ { "name": { "family": "Crellin", "given": "Kevin Christopher" }, "id": "Crellin-Kevin-Christopher", "display_name": "Crellin, Kevin Christopher" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p8bs-x927", "abstract": "The gas-phase chemistry of several chemical systems have been investigated with Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry. The emphasis of these experiments is on organoscandium ion chemistry, but inorganic and organic systems have also been examined. Furthermore, quantum mechanical calculations have been performed on selected systems to help in the interpretation of the experimental data or guide the experiments.\r\n\r\nChapter 1 is a brief review of the experimental aspects of FT-ICR mass spectrometry. The history of the development of FT-ICR is given, and the instrumentation required to perform FT-ICR mass spectrometry is described. The mathematical description of ion motion is discussed, and applied to the description of the excitation and detection of ions. A short explanation of how these aspects are combined to form a standard experimental event sequence is then presented.\r\n\r\nChapters 2-5 present the results of our investigations of the reactivity of organoscandium ions with alkanes and alcohols. In Chapter 2 we examine the reactions of Sc(CH_3)_2^+ with methane, ethane, [2,2-D_2]-propane, [1,1,1,4,4,4-D_6]-n-butane and [2- D]-isobutane, while in Chapter 3 the reactions of CH_3ScCH_2CH_3^+ with methane, ethane, [2,2-D_2]-propane, [1,1,1,4,4,4-D_6]-n-butane, [2-D]-isobutane and n-pentane are observed. In both systems \u03c3-bond metathesis reactions similar to those observed in liquid-phase systems are seen. Site selectivity with the larger alkanes is also observed with the aid of deuterium labeling. In Chapter 4 we return to the Sc(CH_3)_2^+ ion and investigate its reactivity with cyclopentane and cyclohexane. Once again, \u03c3-bond metathesis reactions are observed, this time with secondary C-H bonds rather than primary C-H bonds (as seen with the straight- and branched-chain hydrocarbons). We then change our focus in Chapter 5 to the \u03c3-bond metathesis reactions of Sc(OCD_3)_2^+ with water, ethanol and 1-propanol. Again, \u03c3-bond metathesis reactions were seen. However, in this case ligand exchange equilibria were observed via \u03c3-bond metathesis and used to evaluate the relative bond energies of various Sc^+ alkoxide bonds.\r\n\r\nChapters 6-8 move away from organoscandium systems and into various inorganic and organic systems. In chapter 6 the reaction of Cl^- with C1ONO_2 is examined. This reaction was found to be fast and efficient in the gas phase, which raises the possibility that Cl^- might react directly with C1ONO_2 on water ice films on the surface of type II polar stratospheric cloud particles. Chapter 7 investigates the reactions of nitrobenzene and the explosives 2,4,6-trinitrotoluene (TNT) and 1,3,5-trinitro-1,3,5- triazacyclohexane (RDX) with Si(CH_3)_3^+. Adduct formation and small amounts of characteristic fragmentation (with the TNT and RDX adducts) is observed, suggesting that these types of reactions could be useful as a detection scheme for common explosives. Chapter 8 extends this work to the explosives EGDN (ethylene glycol dinitrate) and PETN (pentaerythritol tetranitrate). These nitrate ester explosives do react with Si(CH_3)_3^+, but no molecular adduct is seen in the FT-ICR mass spectrometer. However, characteristic fragment ions are seen and the PETN-Si(CH_3)_3^+ adduct can be seen in a sector mass spectrometer. The differences in the reactivity of nitro explosives and nitrate ester explosives are also discussed.\r\n" }, { "name": "Drayton, Paul Jeffrey", "degree": "PhD", "year": "1997", "title": "Experimental and theoretical studies of aerosol agglomerates", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01092008-092702", "creators": [ { "name": { "family": "Drayton", "given": "Paul Jeffrey" }, "id": "Drayton-P-J", "display_name": "Drayton, Paul Jeffrey" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/r246-6h84", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe behavior and properties of aerosol agglomerates were experimentally and theoretically probed. Brownian coagulation coefficient rates for titania aerosol agglomerates of mobility diameters from 20 nm to 250 nm were measured. The experimental results agree reasonably well with the predictions of Rogak and Flagan, with the smallest agglomerates showing some enhancement of the coagulation coefficient by electrical image and van der Waals forces.\n\nIn order to analyze the coagulation experiments, the bipolar diffusion charging of aerosol agglomerates was studied. The steady-state bipolar charge distribution of titania agglomerates with primary particle diameters of 6.5 [...] 3 nm, were measured using a Tandem Differential Mobility Analyzer (TDMA) system. The experimental results were compared to an extended Fuchs steady-state charge distribution. The agglomerates were more likely to carry multiple charges than the theory predicted. The extended Fuchs theory was found to be strongly dependent on the properties of the ions.\n\nAlignment of non-spherical particles with the electric field in a DMA, can bias size measurements. To investigate this phenomenon, a theoretical study of agglomerate particle alignment was undertaken. The tendency of a particle to align with the imposed field was found to be characterized by the ratio of the Coulombic to the thermal energies, [gamma]. The electrical mobility ratio [phi], of a linear chain aggregate was calculated to develop the orientation theory. As the number of primary particles increases, [phi] reaches a maximum and then declines. Experimental observations of particle alignment were compared to the theoretical predictions with the experimental data showing alignment effects for [gamma] over 5.0.\n" }, { "name": "Fernandes, Neil Edward", "degree": "PhD", "year": "1997", "title": "Diffusion in mesoporous glass : simulations and experiments", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01092008-135803", "creators": [ { "name": { "family": "Fernandes", "given": "Neil Edward" }, "id": "Fernandes-N-E", "display_name": "Fernandes, Neil Edward" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/HPPB-TJ55", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe diffusivities of simple gases in mesoporous glass were studied by experiment and simulation.\r\n\r\nPorous Vycor[...] glass was modified by deposition of silica on the internal pore surface using consecutive cycles of liquid phase silylation with silicon tetrachloride, and hydrolysis. Macroscopically uniform deposition was achieved by exploiting the self limiting nature of the reaction and the extent of deposition was monitored by the weight change of the samples. Weight increases as high as 24% were recorded and the average pore diameter was estimated to decrease from [...]. Permeation measurements were conducted in the Henry's law region at various levels of deposition for hydrogen, methane, isobutane and nitrogen, at temperatures between 60[degrees]C and 180[degrees]C. The measurements were compared to values calculated with a model using the effective medium approximation to treat network effects and Clausing's correction to account for conductances in pores of finite aspect ratio. The calculated values proved to be inaccurate for hydrogen, overestimating the permeance by a factor of two at high levels of deposition possibly because of non-ideal pore shapes accentuated by the deposition. For nitrogen and methane the agreement between calculations and measurements was better due to a fortuitous cancellation of deviations caused by the enhanced potential energy well within the pores and the non ideal pore shape. The intrapore potential energy effect was especially strong for isobutane and as a result the calculated flux was always less than the experimental.\r\n\r\nIn an effort to understand the importance of the intrapore potential and pore surface roughness on diffusion, molecular dynamics simulations of nitrogen and isobutane in a mesoporous glass pore, under free molecular flow conditions, were conducted for pores of diameter [...], and for temperatures between 200K and 800K. To study the effect of the intrapore potential, the gases were treated as simple Lennard-Jones atoms and the pore was simulated as a perfect cylinder exerting a 9-3 potential, but with its surface roughened by the superposition of spherical Lennard-Jones atoms representing silica tetrahedra. The molecular trajectories were calculated by the application of Nose-Hooverian mechanics and no momentum transfer was allowed between the pore walls and the gas molecules. Random walk behavior resulted from the resulting specular collisions. The effect of the intrapore potential was decoupled into two contributions. The effective diffusivity was respectively increased and decreased by a partitioning effect (or Henry's law adsorption) and a path curvature effect (the trapping of molecules near the surface). In pores of radius [...], both effects were present for temperatures as high as 500K, and were enhanced as the temperature decreased. For nitrogen, the combination of effects canceled over the temperature range of 500-200K and resulted in a temperature dependence similar to that of Knudsen diffusion. For isobutane, the partitioning effect overwhelmed the path curvature effect, resulting in significant surface flows at temperatures as high as 500K. At a temperature of 393K, as the pore radius was reduced from [...], the path curvature effect decreased and the partitioning effect increased. Although the intrapore potential becomes more negative as the pore size decreases, the magnitude of the potential energy barrier trapping molecules near the surface also decreases. The effect of surface roughness was studied through a hard sphere dynamics version of the above simulation. Diffusivities were obtained for various surface coverage of the silica tetrahedra. The specular reflection condition resulted in diffusivities at least twice that of the Knudsen value." }, { "name": "Hammond, Marlys", "degree": "PhD", "year": "1997", "title": "Enantioselective Synthesis of Neocarzinostatin Chromophore Aglycone", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012025-083054910", "creators": [ { "name": { "family": "Hammond", "given": "Marlys" }, "id": "Hammond-Marlys", "display_name": "Hammond, Marlys" } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "orcid": "0000-0001-9602-6915", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k6mz-nt82", "abstract": "An enantioselective synthesis of neocarzinostatin chromophore aglycone (6) is\r\ndescribed. The key features of the synthesis include 1) Sharpless asymmetric epoxidation\r\nof the allylic alcohol 136 to produce epoxy alcohol 137, 2) an intramolecular acetylide\r\naddition within the epoxy aldehyde 138 to furnish alcohol 139, 3) esterification of the diol\r\n171 with the acid 22 and in situ cleavage of the chloroacetate ester to provide ester 172, 4)\r\nelimination of the C-1 alcohol of 175 to afford the olefin 176, and 5) reductive opening of\r\nepoxy alcohol 120 with the combination of iodine, triphenylphosphine, and imidazole to\r\nafford neocarzinostatin chromophore aglycone (6). The synthetic pathway described is\r\nhighly convergent, and should the supply quantities of 6 necessary for ongoing studies\r\ndirected toward the completion of the total synthesis of neocarzinostatin chromophore (1),\r\nas well as the preparation of analogs bearing modified sugar residues." }, { "name": "Hatzimanikatis, Vassily", "degree": "PhD", "year": "1997", "title": "Analysis and design of metabolic reaction networks", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11142005-153634", "creators": [ { "name": { "family": "Hatzimanikatis", "given": "Vassily" }, "id": "Hatzimanikatis-V", "display_name": "Hatzimanikatis, Vassily" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZNCH-WS81", "abstract": "Different mathematical methods can be used for the analysis of metabolic systems and the subsequent engineering of metabolism. The available experimental information dictates the most appropriate mathematical framework for such studies. Several approaches for metabolic system analysis and design are developed in this thesis. It is shown that for several model systems, a (log)linear model shows excellent agreement with the corresponding nonlinear model. The (log)linear model which is developed here describes the dynamical and steady-state responses of the logarithmic deviations of the metabolic variables and functions with respect to a change of the metabolic parameters around a corresponding reference state. The parameters of the (log)linear model are quantities easily estimated from experimental and theoretical tools developed within metabolic control analysis (MCA). A significant advantage of the newly developed (log)linear model is the linearity with respect to logarithms which makes computational analysis easier as compared to the correponding nonlinear model. A second approach introduces a novel, production-oriented optimization framework. Maximizing the performance of a metabolic reaction pathway is treated as a mixed-integer linear programming (MILP) formulation when a (log)linear model of the pathway is available and as a mixed-integer nonlinear programming (MINLP) formulation when a nonlinear model is available. The objective of the MILP and MINLP formulation is to identify changes in regulatory structure and strength, and in cellular content of pertinent enzymes, which should be implemented in order to optimize a particular metabolic process. A regulatory superstructure is proposed that contains all alternative regulatory structures that can be considered for a given pathway. The proposed approach is followed in order to find the optimal regulatory structure for maximization of phenylalanine selectivity in the microbial aromatic amino acid syn thesis pathway. The solution suggests that, from the 8 feedback inhibitory loops in the original regulatory structure of this pathway, inactivation of at least three loops and overexpression of three enzymes will increase phenylalanine selectivity by 42%. Moreover, novel regulatory structures with only two loops, none of which exists in the original pathway, could result in a selectivity of up to 95%." }, { "name": "Herzog, Timothy Allan", "degree": "PhD", "year": "1997", "title": "Deuterium Isotope Effects as Evidence for \u03b1-Agostic Assistance in Ziegler-Natta Catalysts. Design, Synthesis, and Reactivity of a New Class of Highly Syndiospecific Ziegler-Natta Polymerization Catalysts", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192019-173846004", "creators": [ { "name": { "family": "Herzog", "given": "Timothy Allan" }, "id": "Herzog-Timothy-Allan", "display_name": "Herzog, Timothy Allan" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/tv4y-w681", "abstract": "By applying the concept of \"isotopic perturbation of stereochemistry\" to a number of Group III metallocene catalysts, further evidence for an \u03b1-agostic interaction in the chain propagation step of Ziegler-Natta polymerization has been obtained. These results are in accord with the \"modified Green-Rooney\" mechanism. An \u03b1-agostic interaction in the transition state of olefin insertion may contribute to the remarkable stereoselectivities of many Ziegler-Natta catalyst systems since it may restrict the possible orientations of the polymer chain such that it has a more significant impact on the orientation of the inserting olefin.
\r\n\r\nA new class of Group IV metallocene catalysts is presented for the syndiospedfic polymerization of propylene. These catalysts incorporate what are thought to be the key characteristics of syndiospedfic metallocene catalysts: Cs symmetry and rigidly linked cyclopentadienyls of greatly differing size. However, preliminary attempts to develop new syndioselective catalysts have suggested another important characteristic: a pocket in the larger moiety to avoid undesirable steric interactions between the ligand framework and coordinated olefin. In order to accommodate this constraint, a ligand system with a 1,3-dialkylcyclopentadienyl doubly linked to a singly substititued cydopentadienyl was chosen. Group IV metallocenes with these new ligands, in the presence of a cocatalyst (MAO), react rapidly with neat propylene to form highly syndiotactic polypropylene. This is the first example of a stereospecific doubly bridged olefin polymerization catalyst and is the first example of a highly syndiospedfic polymerization catalyst not based on a fluorenyl like ligand. This catalyst system is also very versatile since straightforward changes in the alkyl group of the singly substituted cydopentadienyl and in the reaction conditions lead to dramatic changes in the polymer microstructure. These catalysts should provide an excellent platform for mechanistic study and may be important industrially.
" }, { "name": "Johann, Timothy Wilmot", "degree": "PhD", "year": "1997", "title": "Sequence-Specific Inhibition of DNA Polymerase by Phenanthrene Quinone Diimine Complexes of Rhodium(III)", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08042025-205701232", "creators": [ { "name": { "family": "Johann", "given": "Timothy Wilmot" }, "id": "Johann-Timothy-Wilmot", "orcid": "0000-0003-2212-9684", "display_name": "Johann, Timothy Wilmot" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "member", "display_name": "Parker, Carl Stevens" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fb9e-rw88", "abstract": "The DNA binding characteristics of several phenanthrenequinone\r\ndiimine (phi) complexes of rhodium (III) as well as their ability to inhibit\r\nfunctionally DNA polymerase have been investigated. Affinity constants\r\nhave been determined to be 5x107 M-1 and 1x108 M-1 for \u0394 and \u039b 1Rh(\r\nMGP)2phi5+ binding to the DNA sequences 5'-CATCTG-3' and 5'-\r\nCATATG-3' respectively. The exchange rate, at 21\u00b0C, has been determined to\r\nbe 16 s-1 for the binding of 1-\u039b-Rh(MGP)2phi5+ to 5'-CATATG-3' through the\r\nuse of variable temperature 1H-NMR. Similar 1H-NMR experiments were\r\ncarried out to determine the kinetics of the interaction of 1-\u0394-Rh(MGP)2phi5+\r\nwith a duplex DNA of the sequence 5'-CGCATCTGAC-3'. 1-\u039b-Rh(\r\nMGP)2phi5+, 1-\u0394-Rh(MGP)2phi5+, and Rh(MT)phi3+, which binds to 5'-\r\nTGCA-3', were found to be potent sequence-specific inhibitors of DNA\r\npolymerase. All of these complexes bind to DNA through intercalation. In\r\nexperiments where two templates competed for extension by DNA\r\npolymerase, these complexes were shown to inhibit the extension of\r\ntemplates containing their binding sequences as compared to control\r\ntemplates. Furthermore, in direct competition experiments containing two\r\ntemplates, where each contained a binding sequence for a different metal\r\ncomplex, the relative activity of DNA polymerase on each template was\r\n\"tuned\" by the addition of metal complex specific for that template. \u0394-Rh(\r\nDPB)2phi3+ was also found to be a potent inhibitor of DNA polymerase,\r\nbut not in a template-specific manner. The relative potency of sequence- specific\r\ninhibition shown by 1-\u039b-Rh(MGP)2phi5+, 1-\u039b-Rh(MGP)2phi5+, and\r\nRh(MT)2phi3+ was compared to the binding kinetics, complex size, complex\r\ncharge, binding affinity and binding induced DNA distortion for these\r\ncomplexes. Greater DNA distortion was found to correlate with greater\r\ninhibition. These studies have shown that these molecules not only bind to\r\nDNA in a sequence-specific manner, but can functionally inhibit enzymatic\r\nreactions in a sequence-specific manner as well." }, { "name": "Kenyon, Christopher Neil", "degree": "PhD", "year": "1997", "title": "Time-Resolved and Steady-State Investigations of Carrier Dynamics at the Semiconductor/Liquid Interface", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:07212025-032307531", "creators": [ { "name": { "family": "Kenyon", "given": "Christopher Neil" }, "id": "Kenyon-Christopher-Neil", "display_name": "Kenyon, Christopher Neil" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ef6e-0w18", "abstract": "Fundamental investigations of carrier transport and charge transfer at the\r\nsemiconductor/liquid interface are presented. The application of both steady-state and time-resolved\r\nmethods to these studies is discussed.
\r\n\r\nSmall signal photocurrent transients have been measured for n-Si/CH3OH-dimethylferrocene\r\n(Me2Fc)+/0/Pt and n-Si/Au/CH3OH-Me2Fc+/0/Pt interfaces. The\r\nphotocurrent transients for these interfaces decayed in less than 10 \u03bcs, and were limited by the\r\nseries resistance of the cell in combination with the space charge capacitance of the\r\nsemiconductor. An equivalent circuit model is presented and physically justified in order to\r\nexplain this behavior, and to elucidate the conditions under which photocurrent transients at\r\nsemiconductor electrodes can be expected to yield information regarding the faradaic charge\r\ntransfer rate across the semiconductor/liquid interface. To provide additional support for\r\nthe equivalent circuit representation, transient photocurrent responses are also presented for\r\nn-Si/Pt/NaOH(aq)/Ni(OH)2//Ni, n-TiO2//NaOH(aq)/Ni(OH)2//Ni and n-TiO2//NaOH(aq)Fe(CN)63-/4-fNi(OH)2/Ni contacts.
\r\n\r\nStudies are reported on the behaviors of thin, nearly intrinsically doped Si\r\nelectrodes having interdigitated n+ and p+ back contact points. An analysis of the factors\r\ngoverning the photocurrent directionality and photovoltage in these samples is presented.\r\nAdditionally the back contact geometry has been exploited to perform measurements of the\r\nopen circuit potential of either electrons or holes while the other carrier type was under\r\nelectrical control. In combination with current density-voltage measurements of carriers\r\npassing through the back contact points, these data allowed a comparison of the behavior of\r\na given carrier type when generated by an applied bias (i.e., as majority carriers) relative to\r\ntheir behavior when generated with band gap illumination of the solid (as minority\r\ncarriers). The results have been used to validate certain key predictions of the quasi-Fermi\r\nlevel concept in photo-electrochemistry. In addition, digital simulations that include two-dimensional\r\nrepresentations of the charge density distribution and of the current fluxes in\r\nthe solid have been utilized to provide a quantitative understanding of the observed\r\nexperimental behavior.
\r\n\r\nThe application of time-resolved photoluminescence to the study of InP interfaces is\r\ndescribed. Photoluminescence decay profiles for etched n-type and p-type InP have been\r\nrecorded. These data provide support for a bulk-recombination limited PL lifetime in p-InP,\r\nwhile that of n-InP is evidenced to be dominated by radiative recombination.\r\nAdditional PL decay data are reported for a series of InP/liquid contacts. InP/CH3CN\r\njunctions having Me2Fc+/0, decamethylferrocene+/0 (Me10Fc+/0), methyl viologen\r\n(MV)2+/+, and cobaltocene (COCp2)+/0 as acceptor species have been studied. Quantitative\r\ninformation on the rate constant for charge transfer could not be obtained from these\r\nstudies, but upper limits are suggested, and promising systems for further study are\r\nidentified.
" }, { "name": "Kesselman, Janet M.", "degree": "PhD", "year": "1997", "title": "Fundamental Photoelectrochemical Properties of TIO\u2082/Water Interfaces : Relevance for Hazardous Waste Remediation", "advisor": "Lewis, Nathan Saul; Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07142025-223721756", "creators": [ { "name": { "family": "Kesselman", "given": "Janet M." }, "id": "Kesselman-Janet-M", "display_name": "Kesselman, Janet M." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "advisor", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "co-advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5dmz-sa21", "abstract": "TiO\u2082 photocatalysis is a promising technology for the treatment of aqueous or\r\ngaseous systems contaminated by low levels of organic pollutants. The research\r\ndescribed in this thesis explores fundamental mechanistic and kinetic questions for both\r\nTiO\u2082 photocatalytic and electrocatalytic degradation of aqueous organic contaminants. A\r\nrecurring theme in this thesis is the use of TiO\u2082 electrodes to investigate kinetic and\r\nmechanistic aspects of the TiO\u2082 photocatalytic process. The use of electrodes provides\r\nadditional experimental control of system parameters that is not possible in conventional\r\nTiO\u2082 slurry reactors.
\r\n\r\nThe first study reports the kinetics of oxygen reduction at single-crystal, rutile\r\nTiO\u2082 electrodes as a function of applied potential. Platinum deposits are found to\r\ncatalyze the reduction of oxygen at this surface. Application of a flux-matching condition\r\nto the independently measured reduction and photooxidation currents predicts significant\r\nrecombination losses for TiO\u2082 particles operating under steady-state photocatalytic\r\nconditions.
\r\n\r\nIn a second project, the contributions of direct and hydroxyl radical mediated\r\noxidation pathways are determined at Nb-doped, polycrystalline TiO\u2082 electrodes. In addition to quantifying the branching ratio of these two mechanisms for a variety of\r\norganic substrates, the results suggest that surface interactions are important in\r\ndetermining the predominant reaction pathway in these systems.
\r\n\r\nFinally, the adsorption of 4-chlorocatechol at the TiO\u2082/H\u2082O interface is\r\ninvestigated as a function of pH and solution concentration. Quantitative measurements\r\nof the extent of adsorption are reported as well as spectroscopic evidence for the structure\r\nof the adsorbed complex. Further work correlates observed photocatalytic degradation\r\nrates with the extent of adsorption under various solution conditions.
" }, { "name": "Khodabandeh, Shervin", "degree": "PhD", "year": "1997", "title": "Synthesis of Alkaline-earth Zeolites", "advisor": "Davis, Mark E.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01102008-150302", "creators": [ { "name": { "family": "Khodabandeh", "given": "Shervin" }, "id": "Khodabandeh-Shervin", "display_name": "Khodabandeh, Shervin" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "member", "display_name": "Rossman, George Robert" } ], "option_major": [ "chemeng" ], "doi": "10.7907/35dq-qn66", "abstract": "Zeolite molecular sieves have found extensive applications in ion-exchange, separation and catalytic processes, particularly in the chemical and petroleum industries. Currently, the state-of-the-art in synthesis of high-silica zeolites involves the use of complex organic molecules to direct the formation of zeolitic materials with novel pore structures. While efforts towards preparation of new zeolites using organic molecules as structure-directing agents continues, synthesis of calcium and other alkaline-earth zeolites has not received much attention since the inception of the systematic investigation of zeolite synthesis some 35 years ago. Of the approximate 50 natural zeolites discovered to date, over 20% have eluded synthesis and another 10% have proven exceedingly difficult to synthesize at typical hydrothermal conditions. The overwhelming majority of these zeolites are calcium-dominant. The difficulty encountered in the synthesis of these alkaline-earth zeolites is in direct contrast to their natural occurrence as alteration products of volcanic glasses. Thus, the objective of this work is developing practical methodolgies for the synthesis of alkaline-earth zeolites.
\r\n\r\nHydrothermal transformation of perlite (a natural rhyolitic glass) to calcium zeolites is investigated as a first step towards developing synthesis procedures for the preparation of calcium and other alkaline-earth zeolites from pure starting reagents. In particular, synthetic analogues of the calcium zeolites gismondine, heulandite and epistilbite are obtained as alteration products of perlite glass reacting with calcium-containing solutions. The influence of the solution phase species and their concentrations, the pH and the temperature on the distribution of the zeolite products obtained are discussed. It is observed that the crystallization of heulandite from perlite is preceded by the transient formation of a gismondine-type zeolite most similar to the synthetic zeolite P1. This information is exploited to devise methodology for the preparation of zeolite P1 from pure starting reagents and its subsequent conversion to calcium and other alkaline-earth zeolites upon treatment with solutions containing alkaline-earth cations. Thus, a novel approach for the synthesis of alkaline-earth zeolites based on the hydrothermal conversion of zeolite P1 is developed. Details of the synthesis procedures are enumerated for the preparation of alkaline-earth zeolites CIT-3 (HEU), CIT-4 (BRE), epistilbite (EPI), harmotome (PHI), and yugawaralite (YUG). Transformation of zeolite P1 to alkaline-earth zeolites is governed by factors such as the Si/Al ratio of the starting P1 material, the composition of the solution phase and the presence or absence of seed crystals. The effects of these factors on the products obtained, i.e., phase selectivity, are discussed.
" }, { "name": "Kiely, Andrew F.", "degree": "PhD", "year": "1997", "title": "Pentamethylcyclopentadienyl Aminoborole Complexes of Hafnium", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202019-140851898", "creators": [ { "name": { "family": "Kiely", "given": "Andrew F." }, "id": "Kiely-Andrew-F", "display_name": "Kiely, Andrew F." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n5nr-dx22", "abstract": "The tricyclophosphate ligand, (P\u2083O\u2089)\u00b3\u207b, was investigated as an oxidation resistant ligand for ruthenium chemistry. The silver salt of tricyclophosphate, Ag\u2083(P\u2083O\u2089).H\u2082O, was found to be a useful synthon in the preparation of organic soluble tricyclophosphate salts. The complex [(P\u2083O\u2089)Ru(C\u2086H\u2086)]\u207b was prepared and characterized. In water, it was found that the tricyclophosphate ligand dissociated from the [(C\u2086H\u2086)Ru]\u00b2\u207a dication. Cyclic voltammatry in acetonitrile shows only a small irreversible oxidation at 0.95 V (Vs ferrocene). The rhenium carbonyl complex [(P\u2083O\u2089)Re(C0)\u2083]\u00b2\u207b was also investigated as a precursor to high valent tricyclophosphate rhenium complexes. Based on these results as well as related work by Klemperer and coworkers, it is concluded that the tricyclophosphate ligand is an exceptionally hard one that binds only weakly to transition metals.
\r\n\r\nThe preparations of chloro and allyl derivatives of pentamethylcyclopentadienyl aminoborole hafnium complexes are described. The chloro derivative, Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]HfCl\u2022LiCl, is prepared by treatment of Cp*HfCl\u2083 with Li\u2082(THF){C\u2084H\u2084BN(CHMe\u2082)\u2082}. The structures of the chloro derivatives Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]HfCl\u2022LiCl(Et\u2082O)\u2082 and {Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]HfCl-LiCl}\u2082 were determined by single crystal X-ray analysis. Treatment of Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]HfCl\u2022LiCl with allyl magnesium bromide yields Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]Hf(\u03b7\u00b3-C\u2083H\u2085), whose structure was determined by X-ray analysis. The allyl species was active for the polymerization of ethylene, but not for the polymerization of \u03b1-olefins. Addition of ligands to the allyl derivative results in the formation of Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]Hf(C\u2083H\u2085)(L) (L = PMe\u2083, pyridine, CO). The structure of Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]Hf(\u03b7\u00b3-C\u2083H\u2085)(CO) was determined. Treatment of Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]Hf(\u03b7\u00b3-C\u2083H\u2085)(CO) with PMe\u2083 results in the formation of the dieneolate complex Cp*[C\u2084H\u2084BN(CHMe\u2082)\u2082]Hf(OCHCHCHCH\u2082) (PMe\u2083). The electronic spectra of several aminoborole complexes were investigated and the low energy transitions assigned as borole-metal LMCT transitions. The amphoteric complex Cp*{\u03b7\u2075-C\u2084H\u2084BN(CHMe\u2082)\u2082}HfCl\u2022LiCl heterolytically cleaves H-X bonds to form Cp*{\u03b7\u2075-C\u2084H\u2084BNH(CHMe\u2082)\u2082}HfCl(X) (X = Cl, CCR). Cp*{\u03b7\u2075-C\u2084H\u2084BNH(CHMe\u2082)\u2082}Hf(CCTMS)\u2082 is prepared from Cp*{\u03b7\u2075-C\u2084H\u2084BN(CHMe\u2082)\u2082}Hf(\u03b7\u00b3-C\u2083H\u2085) and two equivalents of (trimethylsilyl)acetylene. Methyl iodide reacts with Cp{\u03b7\u2075-C\u2084H\u2084BN(CHMe\u2082)\u2082}HfCl\u2022LiCl to form Cp*{\u03b7\u2075-C\u2084H\u2083MeBNH(CHMe\u2082)\u2082}HfClI. Control experiments using deuterium labelled substrates show heterolysis occurs with no incorporation of deuterium into the 2,5 positions of the borole heterocycle. The X-ray structure determinations of Cp*{\u03b7\u2075-C\u2084H\u2084BNH(CHMe\u2082)\u2082}HfCl\u2082, Cp*{\u03b7\u2075-C\u2084H\u2084BNH(CHMe\u2082)\u2082}HfCl(CCTMS), and Cp*{\u03b7\u2075-C\u2084H\u2083MeBN(CHMe\u2082)\u2082}HfClI are reported.
" }, { "name": "Kothare, Mayuresh V.", "degree": "PhD", "year": "1997", "title": "Control of Systems Subject to Constraints", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-01162008-153136", "creators": [ { "name": { "family": "Kothare", "given": "Mayuresh V." }, "id": "Kothare-Mayuresh-V", "display_name": "Kothare, Mayuresh V." } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/anhq-xj51", "abstract": "Every operating control system must deal with constraints. On the one hand, the range and rate of change of the input or manipulated variable is limited by the physical nature of the actuator (saturation limits). On the other hand, process state variables or outputs (pressures, temperatures, voltages) may not be allowed to exceed certain bounds arising from equipment limitation, safety considerations, or environmental regulations.
\r\n\r\nA rich theory exists for designing controllers - both linear (H2/H\u221e, LQG, LTR, pole-placement) and nonlinear (nonlinear H\u221e, control, feedback linearization, sliding mode control, gain scheduling). However, none of these popular and fashionable controller design techniques account for the presence of input or output constraints. Although occasionally these constraints may be neglected, in general, they lead to design and operating problems unless they are accounted for properly.
\r\n\r\nIn traditional control practice, overrides or mode selection schemes are used to deal with output constraints: they switch between a \"bank\" of controllers, each of which is designed to achieve a specific objective. In both cases (saturation limit and mode selection), a control input nonlinearity is introduced into the operating system.
\r\n\r\nDespite its significance, the study of the constrained control problem has received far less attention than the traditional unconstrained (linear and nonlinear) control theory. With few exceptions, most of the controller design techniques for constrained systems are by-and-large ad-hoc, with very little guarantees of stability, performance and robustness to plant model uncertainty.
\r\n\r\nThe objective of this thesis is to take a broad approach towards the constrained control problem. One part of the thesis is devoted to the development of a systematic and unifying theory for studying the so-called Anti-Windup Bumpless Transfer (AWBT) problem. The other part aims towards the development of a general novel approach for the synthesis of a robust model predictive control (MPC) algorithm.
\r\n" }, { "name": "Li, Robert Tan", "degree": "PhD", "year": "1997", "title": "Development of Late Transition Metal Catalysts for the Transformation of Olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232025-205751565", "creators": [ { "name": { "family": "Li", "given": "Robert Tan" }, "id": "Li-Robert-Tan", "display_name": "Li, Robert Tan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h7n7-w490", "abstract": "Chapter 1 describes the syntheses and reactivities of a series of\r\nIrCl(CO)(PR3(\u019e2-3,3-diphenylcyclopropene) complexes (PR3 = PMe3, PMe2Ph,\r\nPMePh2, PEt3). In addition, it describes a subsequent reaction of IrCl(CO)(PMe3)2(\u019e2-\r\n3,3-diphenylcyclopropene) in the presence of excess IrCl(CO)(PMe3)2. Spectroscopic\r\ndata support the formation of an iridacyclobutene as part of a bimetallic complex where\r\nthe iridacyclobutene moiety is stabilized by \u019e2-coordination to IrCl(CO)(PMe3)2. The\r\nmechanism of this reaction was studied by kinetic measurements and isotopic labeling\r\nstudies where these studies support formation of this bimetallic complex by direct\r\ninsertion of IrCl(CO)(PMe3)2 into the C-C \u03c3-bond of the cyclopropene moiety.
\r\n\r\nChapter 2 describes the reactions of the iridium dimer, [Ir(COD)Cl]2, with 3,3-\r\ndiphenylcyclopropene to form the bimetallic vinylcarbene complex [Ir(COD)Cl]2=C-C=\r\nCPh2), and examines the activity of this complex in ring-opening metathesis\r\npolymerization (ROMP). This chapter also describes the subsequent reaction of\r\n[Ir(COD)Cl]2(=C-C=CPh2) with AgO2CCX3 (X = F and H) to form\r\n[Ir2(COD)2Cl(O2CX3)](=C-C=CPh2) and describes their reactivity in ROMP.
\r\n\r\nChapter 3 describes the synthesis of Ir and Rh vinylcarbene complexes and examines\r\ntheir activities in olefin metathesis and olefin cyclopropanation. The Ir vinylcarbene\r\nappears to be active solely in olefin metathesis and the Rh vinylcarbene appears to be\r\nactive solely in olefin cyclopropanation. In addition, this chapter investigates the\r\noxidation state effects in the Rh-mediated cyclopropanation reaction by examining the\r\naffinities of the Rh complexes toward olefins as the oxidation state of the Rh metal is\r\nincreased.
\r\n\r\nChapter 4 describes the synthesis of salicylaldimine complexes of Ni(II)-aryls and\r\ntheir reactivity in ethylene polymerization. The effects of varying sterics and electronics\r\nof the salicyclaldimine ligand is discussed. Bulky ligands which block the axial faces of\r\nthe Ni(II) square planar complexes, and provide steric bulk in the plane of the Ni(II)\r\nsquare planar complex, are particularly effective in providing active ethylene\r\npolymerization catalysts that produce linear polymers with high molecular weight.
" }, { "name": "Lin, Susanne Chosein", "degree": "PhD", "year": "1997", "title": "The Molecular Recognition of DNA by Rhodium(III)-Zinc Finger Peptide Chimeras", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07182025-180545892", "creators": [ { "name": { "family": "Lin", "given": "Susanne Chosein" }, "id": "Lin-Susanne-Chosein", "display_name": "Lin, Susanne Chosein" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mss5-wf97", "abstract": "Covalent chimeras of zinc finger peptide domains with\r\nphenanthrenequinone diimine (phi) complexes of rhodium (III) have been\r\ndesigned, synthesized and their DNA recognition characteristics examined. The\r\nrhodium complex binds in the major groove of DNA by intercalation and allows\r\nthe attached peptide to interact with DNA in a sequence-specific manner.\r\nChimeras of [Rh(phi)2(bpy')]3+ (bpy' = 4-(4-carboxybutyl), 4'-methyl-2,2'bipyridine)\r\nand [Rh(phi)2(phen')]3+ (phen' = (5-amidoglutaryl)-1,10-phen-anthroline)\r\nand four different zinc finger peptides (Sp1 finger 2 and 3, ADR1b and\r\nADR1b-Ala) have been successfully synthesized using solid phase coupling\r\nmethodology. Electronic spectroscopy showed the rhodium complex and\r\npeptide to be essentially independent units. A method to successfully fold the\r\npeptide portion of the chimera with zinc has been developed, and 1H HMR\r\nspectroscopy has been used to confirm folding. The resultant chimeras bind\r\ntightly to DNA, and the rhodium intercalator promotes DNA cleavage with\r\nphotoactivation. Analysis of the DNA sites targeted by the chimeras on DNA\r\nrestriction fragments have demonstrated that the peptide can direct new\r\nrecognition. Variations in the rhodium complexes and peptides resulted in\r\ndifferences in specificity as seen by photocleavage. Studies on smaller\r\noligonucleotides containing the recognition sequences have shown the rhodium -\r\nSp1-2 chimera to bind with affinities of 107-108 M-1 for its target sites. Hence,\r\nformation of rhodium(III) - zinc finger chimeras provide a route to establish\r\nhigh affinity DNA binding by a single zinc finger domain. At some sites, the\r\nrhodium complex and zinc finger appeared to bind independently to adjacent\r\nsegments. For the [Rh(phi)2(phen')]3+ - Sp1 - 2 chimeras, a strong high affinity\r\nsite (Ka greater than or equal to 108 M-1) was observed, where it was postulated that the rhodium\r\ncomplex and zinc finger bind to the opposite strands of the GCG binding site in a\r\ncooperative fashion. These rhodium (III) - zinc finger chimeras represent a new\r\nroute to examine the specific interactions of a single zinc finger with DNA in\r\nchemical detail and provide the basis to build a family of sequence-specific DNA\r\nbinding molecules." }, { "name": "Luo, Ji-Ye", "degree": "PhD", "year": "1997", "title": "Stability and Dynamics Studies of Apo-Azurin from Pseudomonas aeruginosa", "advisor": "Mayo, Stephen L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-204744164", "creators": [ { "name": { "family": "Luo", "given": "Ji-Ye" }, "id": "Luo-Ji-Ye", "display_name": "Luo, Ji-Ye" } ], "advisors": [ { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "advisor", "display_name": "Mayo, Stephen L." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Mayo", "given": "Stephen L." }, "id": "Mayo-S-L", "orcid": "0000-0002-9785-5018", "role": "member", "display_name": "Mayo, Stephen L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/je80-hr40", "abstract": "The solution stability and dynamics of apo-azurin from Pseudomonas aeruginosa have\r\nbeen studied. First, the unfolding stability was measured for 20 apo-azurin mutants\r\nmutating at T124 in the context of a \u03b2-sheet host-guest environment. The unfolding free\r\nenergy difference was taken as a measure of the relative \u03b2-sheet propensity for the 20\r\nnaturally occurring amino acids. These data, when combined with data from other\r\nexperimental studies and compared to a statistical analysis of the protein structure data base,\r\nstrongly support intrinsic secondary structure preference as the major determinant of \u03b2-sheet\r\npropensity. Particularly, residues Val, Thr, Ile, Phe, and Tyr as a group are intrinsically\r\nfavored for \u03b2-sheet formation, and residues Pro, Gly, and Asp as a group are intrinsically\r\ndisfavored. The relative contribution of the intrinsic propensity and local context to the \u03b2-sheet\r\nformation was further discussed with the results from mutating S34 to Val and Thr.\r\nThe S34T mutant was more stable than the wild-type protein, but the S34V mutant was less\r\nstable. Secondly, partially perturbed states of different forms of azurin at low pH's were\r\nobserved. Apo-azurin at pH 2.9 is a molten globule-like state, while holo-azurin at pH's as\r\nlow as 2.6 is only partially perturbed. Third, backbone 1H and 15N chemical shift\r\nassignments and solution dynamics of apo-azurin were studied. The overall correlation time\r\nof apo-azurin at 30 \u00b0C was determined to be 5.8 ns, and order parameters were mostly at\r\n0.8-0.95. Residues around the Cu(II) binding site exhibited low order parameters and\r\nsignificant 1H chemical shift difference from those of holo-azurin. Last, the osmolyte\r\nstabilizing effect was studied on RNase A using Hydrogen/Deuterium exchange. Two types\r\nof H/D exchange behavior were observed. The H/D exchange rates of type I residues\r\nbecome slower in the presence of high concentrations of glycine, as expected from the\r\nglobal stability change; the H/D exchange rates of type II residues are not affected, however." }, { "name": "McClurg, Richard Beatty", "degree": "PhD", "year": "1997", "title": "Homogeneous nucleation theory", "advisor": "Goddard, William A., III; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01142008-080911", "creators": [ { "name": { "family": "McClurg", "given": "Richard Beatty" }, "id": "McClurg-R-B", "display_name": "McClurg, Richard Beatty" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z011-9767", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis is composed of a brief preface followed by six chapters addressing various aspects of homogeneous nucleation theory. In the preface, I motivate the need for improved theoretical approaches to resolve the discrepancies between current theory and experiment. The remaining chapters are collected research papers which are in print, in press, or to be submitted as of the writing of the thesis. They were written in collaboration with one or both of my advisors. In Chapter 2, we review current nucleation theories in a statistical mechanical framework. This framework allows us to identify the errors of the various models and to point out internal inconsistencies in some of them. In Chapters 3 and 4, we develop methods to calculate the partition function and thermodynamic properties for noble gas clusters. The methods allow us to describe the asymptotic approach of cluster properties toward the bulk limit with increasing cluster size and to calculate the nucleation rate for supersaturated noble gas vapors. We then apply the methods to the homogeneous nucleation of condensed mercury from a supersaturated vapor in Chapter 5. Chapters 6 and 7 contain portions of the theoretical groundwork needed to extend atomistic nucleation theories to molecular systems. Chapter 6 is a development of a one-dimensional hindered rotor partition function. It sets the stage for the two and three-dimensional hindered rotor partition functions needed to model molecular solids. In Chapter 7 we construct a model for the charge distribution of [...]. We chose this icosahedral molecule as an ideal plastic crystalline substances. The plastic crystals are solids with translational symmetry, but having weak orientational symmetry due largely to their highly symmetric molecular charge distributions. Thus, plastic crystals are ideal hindered rotors in multiple dimensions. I conclude the thesis with some brief comments on my assertion that molecules which form plastic crystals will provide a fruitful common ground for theoretical and experimental investigations of homogeneous nucleation phenomena.\r\n" }, { "name": "Mehta, Aseem", "degree": "PhD", "year": "1997", "title": "New Methods for the Study of Intramolecular and Solvent Dynamics", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02172022-233103988", "creators": [ { "name": { "family": "Mehta", "given": "Aseem" }, "id": "Mehta-Aseem", "display_name": "Mehta, Aseem" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/75xn-rr09", "abstract": "Some of the fastest processes of relevance to chemical physicists occur on pico to femtosecond timescales. In the following chapters two of such fast processes axe investigated with novel theoretical methods to obtain insight into experimental observations at the molecular level.
\r\n\r\nOne of the major topics of interest in chemical physics has been about energy localization in polyatomic molecules. The \"golden rule\" formula states that the rate for the intramolecular relaxation of energy (IVR) that is initially localized in one part of the molecule is proportional to the density of states at that energy. Here, a general mechanism of the energy redistribution out of an initially populated \"light\" or \"bright\" state is elucidated. It is shown that, for a family of acetylenic molecules, the relaxation is due to a sequence of weak off-resonant directly coupled states rather than all the available states. This mechanism shows how the rates of IVR can be significantly slower than those predicted by a naive application of the \"golden rule,\" since mainly only the initial weak off-resonant couplings govern the rate of IVR.
\r\n\r\nAnother topic that has attracted substantial interest in the chemical physics community is that of solvation. Various heavily applied theories of reaction rates, such as the electron transfer theory, have viewed the solvent as a dielectric continuum. Recent experiments and simulations have shown that the very fast solvation response provides interesting information on the molecular nature of the solvent. Here, a new method for doing molecular dynamics (MD) calculations for solvation is developed. This method uses the reaction field method to obtain the long range potential for a small cluster of molecules rather than using the usual Ewald sum technique with periodic boundary conditions (PBC). It is shown, here, that this method may be used successfully for solvent dynamics simulations. This method may prove superior for such calculations as compared to the PBC approach, since it does not impose an artificial isotropy on the problem as is the case with the PBC calculations.
" }, { "name": "Mines, Gary Alan", "degree": "PhD", "year": "1997", "title": "Cytochrome c : Folding Triggered by Electron Transfer. Rates of Heme Oxidation and Reduction at High Driving Forces", "advisor": "Gray, Harry B.; Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07152025-200013414", "creators": [ { "name": { "family": "Mines", "given": "Gary Alan" }, "id": "Mines-Gary-Alan", "display_name": "Mines, Gary Alan" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "co-advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rtx8-jn96", "abstract": "Rates of various intramolecular heme oxidations and reductions in a series of\r\nclosely related RuL2(X)(His33)cytochromes c [L = bipyridine or phenanthroline\r\nderivatives; X = imidazole (im) or cyanide (CN-)] have been measured over a freeenergy\r\nrange of 0.54 to 1.89 eV. The driving-force dependence of Fe2+\u2192Ru3+ electron\r\ntransfer (ET) is well described by semiclassical ET theory with a coupling-limited rate\r\n(kmax) of 2.8 x 106 s-1 and a reorganization energy of 0.74 eV. As predicted by theory,\r\nthe rate of an exergonic (-\u0394G\u00b0 = 1.3 eV) heme reduction reaction,\r\n*Ru2+(bpy)2(im)(His)\u2192Fe3+, falls in the inverted region (k = 2.0 x 105 s-1). In contrast,\r\nthe rates of three highly exergonic heme reductions, *Ru2+(phen)2(CN)(His)\u2192Fe3+ (3.1\r\nx 105 s-1; 1.4 eV), Ru+(4,4'-(CONH(C2H5))2-bpy)2(im)(His)\u2192Fe3+ (2.3 x 105 s-1; 1.44\r\neV), and Ru+(phen)2(CN)(His)\u2192Fe3+ (4.5 x 105 s-1; 1.89 eV), are much higher than\r\nexpected for reactions directly to ground-state products. Agreement with theory is\r\ngreatly improved by assuming that an electronically excited ferroheme\r\n(Fe2+\u2192*Fe2+ ~ 1.05 eV) is the initial product in each of these reactions.
\r\n\r\nIn a separate investigation, rates of folding of ferrocytochromes c from horse\r\n(h-cyt c) and yeast (y-cyt c) were measured over a range of denaturant concentrations\r\n(guanidine hydrochloride, GuHCl) and folding free energies (\u0394Gf) using a new ET\r\ntriggering technique. The backbone structures of the two homologs are similar, but y-cyt\r\nc is ~ 15 kJ mol-1 less stable than h-cyt c and is unfolded at concentrations of GuHCl ~ 1.5\r\nM lower than for h-cyt c. Activation free energies exhibit a linear dependence on GuHCl\r\nand \u0394Gf for both proteins, with folding rates decreasing with increasing concentration of\r\nGuHCl (less negative \u0394Gf). At a given denaturant concentration, the folding rates for y-cyt\r\nc are about an order of magnitude slower than those for h-cyt c, but when the folding\r\nfree energies are matched, folding rates of the two homologs are comparable.
" }, { "name": "Mueller, Leonard John", "degree": "PhD", "year": "1997", "title": "Chemical Exchange in Nuclear Magnetic Resonance", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02212018-140937311", "creators": [ { "name": { "family": "Mueller", "given": "Leonard John" }, "id": "Mueller-Leonard-John", "display_name": "Mueller, Leonard John" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fx7d-jf45", "abstract": "Nuclear magnetic resonance spectra of molecules undergoing chemical exchange \r\nhave traditionally been quantified using a theory that combines a quantum-mechanical treatment of the spin dynamics with a kinetic model for the molecular exchange. This implicit factorization of spin and spatial degrees of freedom is without theoretical justification and yet it has been widely relied upon in chemical studies. In this thesis, a quantum-statistical theory of chemical exchange is presented for the calculation of lineshapes in dynamic nuclear magnetic resonance. In this treatment, the rates describing the exchange of spin coherence are shown to be complex valued due to the incomplete cancellation of the imaginary components of the spectral density of purely spatial perturbations. These imaginary components give rise to the previously unrecognized phenomena of exchange shifts, new contributions to the line positions which depend on spatial rates even in the fast-exchange limit. These shifts can be orders of magnitude greater than the experimental resolution. The same purely spatial fluctuations responsible for chemical exchange determine these shifts through a Hilbert-transform relationship.
\r\n\r\n\r\nNew measurements on the 13C NMR of methylcyclohexane show that, indeed, the traditional theory fails to relate spectra obtained in the regimes of fast and slow exchange. If interpreted using the traditional theory, the fast-exchange line positions in methylcyclohexane lead to an extracted equilibrium constant with an error of up to 30% and differing between isotopomers by up to 30%. With plausible assumptions on the temperature dependence of the chemical shifts and free energy, an overall fit of the fast\u00ad and slow-exchange methylcyclohexane data is unsatisfactory, rigorously excluding the traditional theory. The exchange-shift theory indicates why additional information is needed to fit the fast-exchange line positions and allows a fit consistent with the observed experimental data on methylcyclohexane using a single conformer free energy difference linear in temperature over the entire experimental range.
" }, { "name": "Murray, Michael Mark", "degree": "PhD", "year": "1997", "title": "Synthesis and characterization of high-spin organic materials: prototypes for the polaronic ferromagnet", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02202014-081804882", "creators": [ { "name": { "family": "Murray", "given": "Michael Mark" }, "id": "Murray-M-M", "display_name": "Murray, Michael Mark" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/T6V4-G875", "abstract": "The design, synthesis and magnetic characterization of thiophene-based models for the polaronic ferromagnet are described. Synthetic strategies employing Wittig and Suzuki coupling were employed to produce polymers with extended \u03c0-systems. Oxidative doping using AsF_5 or I_2 produces radical cations (polarons) that are stable at room temperature. Magnetic characterization of the doped polymers, using SQUID-based magnetometry, indicates that in several instances ferromagnetic coupling of polarons occurs\r\nalong the polymer chain. An investigation of the influence of polaron stability and delocalization on the magnitude of ferromagnetic coupling is pursued. A lower limit for mild, solution phase I_2 doping is established. A comparison of the variable temperature data of various polymers reveals that deleterious antiferromagnetic interactions are relatively insensitive to spin concentration, doping protocols or spin state. Comparison of the various\r\npolymers reveals useful design principles and suggests new directions for the development of magnetic organic materials. Novel strategies for solubilizing\r\nneutral polymeric materials in polar solvents are investigated.
\t\r\nThe incorporation of stable bipyridinium spin-containing units into a polymeric high-spin array is explored. Preliminary results suggest that substituted diquat derivatives may serve as stable spin-containing units for the polaronic ferromagnet and are amenable to electrochemical doping. Synthetic efforts to prepare high-spin polymeric materials using viologens as\r\na spin source have been unsuccessful.
\r\n" }, { "name": "Nagel, John Frederick", "degree": "PhD", "year": "1997", "title": "I. The Use of Spherosiloxanes as Molecular Building Blocks for Material and Thin Films. II. A Method of Using SC-Cut Quartz Oscillators for Chemical Sensing", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212025-215725447", "creators": [ { "name": { "family": "Nagel", "given": "John Frederick" }, "id": "Nagel-John-Frederick", "display_name": "Nagel, John Frederick" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "orcid": "0000-0002-7393-298X", "role": "member", "display_name": "Giapis, Konstantinos P." } ], "option_major": [ "chemeng" ], "doi": "10.7907/wkz6-jt81", "abstract": "The ability to prepare a priori ordered materials of a desired structure is a long\r\nstanding goal in materials research. Recently, there has been great interest in the use of\r\nwell-defined molecular precursors that can, in principle, be combined in a regular way\r\nwithout degradation to produce ordered materials. This process has been dubbed \"lego-chemistry.\"\r\nThis work examines the use of spherosiloxanes, a family of polyhedral silicate\r\ncage molecules, as molecular building blocks for the synthesis of bulk microporous\r\nmaterials and microporous thin films.
\r\n\r\nThe process for synthesizing and functionalizing the spherosiloxanes with a variety\r\nof reactive functional ligands is presented. The reactive molecules are characterized\r\nusing a suite of analytical and spectroscopic techniques. In order to achieve some degree\r\nof control over the condensation process, a binary reaction mechanism utilizing nonhydrolytic\r\nreaction conditions is proposed for the production of bulk materials. Experimental\r\nresults from the non-hydrolytic condensation of spherosiloxanes are presented.\r\nThe effects of adding various catalysts to the reaction mixture are described. A multinuclear\r\nsolution NMR study was performed on monomeric silicate analogues of the\r\nspherosiloxanes in order to elucidate the non-hydrolytic reaction pathways. It is found\r\nthat under the conditions of interest ligand exchange predominates over condensation.
\r\n\r\nA reaction scheme and growth mechanism for the production of a microporous\r\nthin film from spherosiloxane precursors is presented and discussed. It is speculated that\r\nsuch an ordered film could function as a framework for the production of a molecular electronic\r\ndevice. The first important steps in this scheme, namely the condensation behavior\r\nof spherosiloxanes on the Si (100) - (2x1) reconstructed surface, are explored through a\r\nvariety of surface characterization techniques. In particular, low temperature STM is used\r\nto record the nature of the species condensed on the surface. An image of a single isolated\r\n(CH3O)8Si8O12 is recorded and its position and orientation are discussed in the context of the reaction scheme. A HREELS/TPD study of the spherosiloxanes on the same surface is\r\nperformed and the results discussed.
\r\n\r\nA new technique for chemical sensing is proposed and is based on the recently\r\ndeveloped SC-cut quartz oscillator used in conjunction with the analytical technique\r\nknown as thermal programmed desorption (TPD). This technique is developed in order to\r\naddress the need to develop new sensing techniques that are sensitive, selective and cost\r\nefficient, for application to the rising threats of terrorism and pollution present today. The\r\ntechnique utilizes two vibrational modes of the crystal, one very sensitive and one relatively\r\ninsensitive to changes in temperature, that are monitored throughout the experiment.\r\nThe two mode sensing allows in principle for the simultaneous monitoring of the mass and\r\ntemperature of the sensor.
\r\n\r\nA system for evaluating the performance of this sensor is designed and built, and\r\nincludes an automated data acquisition and control system. The sensor is tested using a\r\nvariety of chemically selective coatings and analytes. The structure and morphology of\r\nthe coating used is shown to have a significant effect on the oscillation behavior of the\r\ncrystal used. TPD experiments are performed with the sensor in order to evaluate its characteristics.\r\nIn nearly all cases, it is impossible to discern any desorption signal during the\r\nTPD experiment. A dual mode analysis that is used to deconvolute the temperature and\r\nmass responses of the sensor fails to distinguish any desorption signals except from a very\r\nheavily loaded sample, i.e., water on a polyethyleneimine coated crystal where bulk\r\nabsorption occurs. A TPD experiment is performed on a hydrated, PEI coated crystal\r\nusing a Cahn microbalance, and a relationship between the mass loading and frequency\r\nchange is determined for this system. These values are used to calculate the frequency\r\nresponse for a typical coating where only surface adsorption occurs, and the result is\r\nbelow the minimum detection level of the system. Based on these data, it is determined\r\nthat the SC-cut sensor fails to show the sensitivity necessary for application as a practical\r\nsensor device.
" }, { "name": "Rodham, David Allen", "degree": "PhD", "year": "1997", "title": "Spectroscopic Studies of the Gas Phase Complexes Benzene-Ammonia, Sodium-Water, and Sodium-Ammonia", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-185336063", "creators": [ { "name": { "family": "Rodham", "given": "David Allen" }, "id": "Rodham-David-Allen", "display_name": "Rodham, David Allen" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "orcid": "0000-0001-9602-6915", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mcm8-t491", "abstract": "The results of spectroscopic studies of the C6H6(NH3), Na(H2O), and Na(NH3) gas\r\nphase complexes are reported. The goal of these experiments was to obtain information\r\nupon which a more quantitative understanding of the intermolecular interactions\r\nfound within them could be based. These intermolecular interactions, amino-aromatic\r\nhydrogen bonding in the C6H6(NH3) complex and the primarily electrostatic bonding\r\nof Na+ to polar molecules in the Na+(H2O) and Na+(NH3) complexes, form the basis\r\nfor many biologically significant processes.
\r\n\r\nThe C6H6(NH3) dimer was investigated with resonant two-photon ionization (R2PI)\r\nand microwave spectroscopies. Using R2PI via the 610 transition of the benzene in the\r\ncomplex, it was found that the NH3 is located above the benzene plane, on or near\r\nthe benzene C6 axis, and that the monomers undergo free or nearly free internal rotation.\r\nSubsequent high resolution microwave absorption and emission measurements\r\nof the rotational spectrum revealed that the center of mass separation (Rcm-cm) of\r\nthe monomers is 3.59 \u00c5 and that the ammonia C3 axis is tilted 58\u00b0 from the benzene\r\nC6 axis. In this geometry, the ammonia protons interact with the benzene n-cloud in\r\na hydrogen-bonded geometry similar to that observed in high-resolution x-ray crystallography\r\nof protein structures.
\r\n\r\nThe Na(H2O), Na(D2O), Na(NH3), and Na(ND3) complexes were studied with\r\nZEKE-PFI (zero kinetic energy-pulsed field ionization) photoelectron spectroscopy.\r\nSpectra of all four complexes were obtained by single-photon ionization. For the\r\nNa(NH3) and Na(ND3) complexes, two-color (1+1') photoionization was used as well,\r\nwith the \u00c3 2E state serving as the intermediate resonance. Improved values for the\r\nionization energies (IEs) and intermolecular stretching vibrational frequencies of the\r\ncomplexes were determined, while the intermolecular bending vibrational frequencies\r\nof Na(NH3) and Na(ND3) were measured for the first time. From the rotational\r\nstructure observed in the ZEKE-PFI spectra, it was found that the Na-O and Na-N\r\nbond lengths shrink by 5.2 \u00b1 0.5% when the complexes are ionized. The single-photon\r\nZEKE-PFI spectra show transitions only between states of the same vibrational symmetry,\r\nin accord with the selection rule for allowed electronic transitions. Some of\r\nthe two-color ZEKE-PFI spectra, however, show strong transitions between states\r\nof different vibrational symmetry which are attributed to vibronic coupling in the\r\nintermediate state. All of the single-photon spectra as well as the two-color spectra\r\nof Na(NH3) showed unusually strong O-branches, presumably the result of field-induced\r\nrotational autoionization. This effect is commonly observed in ZEKE-PFI\r\nspectroscopy, particularly for species such as Na(H2O) and Na(NH3) which combine\r\nsmall rotational constants with strongly anisotropic ion-electron scattering potentials.
" }, { "name": "Schlessman, Jamie L.", "degree": "PhD", "year": "1997", "title": "Crystal Structure of Azotobachter vinelandii Nitrogenase Iron Protein at 2.2 A\u030a Resolution", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272017-143047601", "creators": [ { "name": { "family": "Schlessman", "given": "Jamie L." }, "id": "Schlessman-Jamie-L", "display_name": "Schlessman, Jamie L." } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8bav-4095", "abstract": "Biological nitrogen fixation by the two-component metalloenzyme nitrogenase \r\nprovides an elegant solution to the problem of reducing abundant, but relatively inert, \r\ndinitrogen to the biologically usable ammonia needed by all organisms. This oxygen \r\nsensitive enzyme, consisting of the separately purifiable nitrogenase iron protein and \r\nmolybdenum iron protein, couples nucleotide hydrolysis to electron transfer to catalyze the \r\nATP-dependent reaction. Iron protein acts as the sole known biological reductant to \r\nmolybdenum iron protein, which contains the actual site of substrate reduction. MgATP \r\nbinding to iron protein induces dramatic conformational changes in the protein's structure \r\nrequired for docking with molybdenum iron protein. Complex formation and dissociation \r\nare essential for nucleotide hydrolysis, electron transfer, and substrate reduction.
\r\n\r\n\r\nWe have determined the crystal structure of Azotobacter vinelandii nitrogenase iron \r\nprotein at 2.2 A\u030a resolution in the absence of nucleotide. Crystals grew in space group\r\nP212121, and represent a new crystal form compared with that of the structure previously determined at 2.9 A\u030a resolution. X-ray diffraction data were collected from a single crystal\r\nusing cryocrystallographic techniques. The structure was solved by molecular replacement, \r\nfollowed by solvent flattening and noncrystallographic averaging. The current model \r\ncontains 575 of 578 possible amino acid residues and 372 solvent molecules, and has been \r\nrefined to R-value of 22.3 % (R-free = 29.0 %) for all data to 2.2 A\u030a, with good stereochemistry.
\r\n\r\n\r\nThe overall topology of nitrogenase iron protein consists of an Fe4S4 cluster symmetrically ligated by two identical subunits of doubly wound \u03b1/\u03b2 structure similar to\r\nthose of other nucleotide binding proteins. A detailed description is provided of those structural features important for iron protein function, including nucleotide binding regions, the Fe4S4 cluster environment, intersubunit interactions, and the molybdenum iron protein\r\nbinding surface. Comparisons are made between the current model and that of C.\r\npasteurianum iron protein, as well as those of two A. vinelandii nitrogenase complexes. \r\nAnalysis of the various iron protein structures provides a framework for considering the \r\nwealth of relevant nitrogenase spectroscopic, biochemical, and genetic information.
\r\n \r\n\r\n" }, { "name": "Singer, Robert Alan", "degree": "PhD", "year": "1997", "title": "Design of Novel Titanium(IV) Schiff Base Complexes for Catalytic, Enantioselective Aldol Additions to Aldehydes", "advisor": "Carreira, Erick Moran", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-181821401", "creators": [ { "name": { "family": "Singer", "given": "Robert Alan" }, "id": "Singer-Robert-Alan", "orcid": "0000-0001-9730-1261", "display_name": "Singer, Robert Alan" } ], "advisors": [ { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "advisor", "display_name": "Carreira, Erick Moran" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "orcid": "0000-0003-1472-490X", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w287-z238", "abstract": "A novel chiral Schiff base ligand derived from 2-amino-2'-hydroxy-1, 1'-binaphthyl\r\nand 3-bromo-5-tbutylsalicylaldehyde has been prepared. When binding the chiral ligand to\r\ntitanium(IV) with 3,5-di-fbutylsalicylic acid, the complex formed functions as an efficient\r\ncatalyst for the Mukaiyama aldol addition reaction. Using only 1-2 mol% of the catalyst,\r\nsilyl ketene acetal additions to aldehydes were carried out in good chemical yield and in\r\nexcellent levels of enantioselectivity. Unsaturated aldehydes tended to produce adducts in\r\n95-99% ee, while aliphatic aldehyde products were typically obtained in 94-95% ee.
\r\n\r\nThe methodology was extended to include dienolate additions to aldehydes by\r\nutilizing silyl enol ethers of dioxinones. Optimal selectivities in the dienolate additions\r\nwere obtained with unsaturated, unbranched aldehydes (90-94% ee). Aromatic and\r\naliphatic aldehydes were usually isolated in 80-84% ee. Since many of the adducts were\r\ncrystalline solids, the optical purity was enhanced by recrystallization. By heating the\r\ndioxinone adduct in the presence of an alcohol or amine, the products were transformed to\r\nmore useful \u03b2-ketoesters or \u03b2-ketoamides.
\r\n\r\nTo demonstrate the utility of the methodology developed, the asymmetric addition\r\nreactions have been applied to the total synthesis of (R)-epinephrine and macrolactin A.\r\nAfter carrying out an enantioselective acetate addition to 3,4-dimethoxybenzaldehyde in\r\n95% ee, the \u03b2-hydroxyester was converted to the amino-alcohol by a Hoffman\r\nrearrangement and a reduction. After deprotecting the catechol, (R)-epinephrine was\r\nobtained in 5 steps overall. Dienolate additions to \u03b2-stannylpropenal were employed to\r\nprepare two key fragments of macrolactin A. The convergent route involved stitching\r\ntogether three fragments with a Stille coupling and a Horner-Emmons olefination.\r\nMacrocyclization was accomplished by an intramolecular Stille coupling.
" }, { "name": "Stahl, Shannon Scot", "degree": "PhD", "year": "1997", "title": "Mechanistic Studies of Alkane Activation by Platinum(II) Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05012018-081029790", "creators": [ { "name": { "family": "Stahl", "given": "Shannon Scot" }, "id": "Stahl-Shannon-Scot", "orcid": "0000-0002-9000-7665", "display_name": "Stahl, Shannon Scot" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/CCAZ-9234", "abstract": "Currently, there is considerable interest in alkane oxidation reactions catalyzed by transition metal complexes. Chapter 1 reviews many of the recent advances in this field involving electrophilic late transition metals. The C-H activation step appears to dictate both the rate and selectivity of these reactions. Unfortunately, however, very little is known about the mechanism of this step.
\r\n\r\nIn chapter 2, mechanistic studies of the protonolysis of several alkylplatinum(II) complexes [(tmeda)PtMeCl, (tmeda)Pt(CH2Ph)Cl, (tmeda)PtMe2, and trans(PEt3)2Pt(CH3)Cl] are described. These reactions model the microscopic reverse of C-H activation by aqueous Pt(II). Kinetics, activation parameters, and isotope effects were determined, and the results support a common mechanistic sequence for all of the reactions: (1) chloride- or solvent-mediated protonation of Pt(II) to generate an alkylhydridoplatinum(IV) intermediate, (2) dissociation of solvent or chloride to generate a cationic, five-coordinate platinum(IV) species, (3) reductive C-H bond formation producing a platinum(II) alkane \u03c3-complex, and (4) loss of alkane either through an associative or dissociative substitution pathway. These studies provide insight into the role of solvent and ancillary ligands in aqueous Pt(II)-mediated C-H activation. The results also support the viability of Pt(II) \u03c3-adducts and alkylhydridoplatinum(IV) intermediates in this reaction.
\r\n\r\nChapter 3 describes the preparation and study of Pt(II) H2-adducts and Pt(IV) dihydride complexes. The species of interest are generated by protonation of hydridoplatinum(II) complexes of the type trans-(PCy3)2Pt(H)X [X = SiH3, H, CH3, Ph, Cl, Br, I, CN, CF3SO3] and [trans-(PCy3)2Pt(H)L][Barf4] [L = CO, 4-picoline; Barf4] = B(3,5-C6H3(CF3)2)4]. The proton attacks one of three different sites on these complexes (hydride, platinum, or the trans ligand), depending on which ligand is trans to hydride. These studies reveal several factors affecting the stability and reactivity of Pt(II) \u03c3-adducts, which thus have implications for C-H activation by Pt(II).
\r\n" }, { "name": "Stowell, Michael H. B", "degree": "PhD", "year": "1997", "title": "Ekmageion", "advisor": "Chan, Sunney I.; Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07112025-210052342", "creators": [ { "name": { "family": "Stowell", "given": "Michael H. B" }, "id": "Stowell-Michael-H-B", "orcid": "0000-0001-7250-1419", "display_name": "Stowell, Michael H. B" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "co-advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "orcid": "0000-0001-9795-4211", "role": "chair", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/y2zf-he43", "abstract": "Membrane proteins compose roughly 30% of the proteins in a living organism.\r\nFurthermore, they are the essential link between the outside world and the cell. A large\r\nnumber of important processes occur in the biological membranes; these include the\r\nproduction of cellular energy, the transmission of nerve impulses, and the perception of\r\nlight and sound. Knowledge of how these systems are constructed and how they function\r\nis critical to understanding the biological world around us as well as ourselves. The studies\r\npresented herein were aimed at gaining an understanding of such systems through the\r\ncombination of both structural and functional analysis of these systems. The results\r\npresented here are the author's efforts to understand such systems and in the process\r\ndevelop methods and techniques which help others understand such systems or related\r\nones. This thesis is divided into two sections. The first section is devoted solely to the\r\ninvestigation of membrane proteins. An introductory discussion on the structure and\r\nstability of membrane proteins is presented followed by studies on the photosynthetic\r\nreaction center, succinate:quinone oxidoreductase, cytochrome c oxidase, and the\r\ndevelopment of methods for studying rapid electron transfer in ubiquinone:cytochrome-c\r\noxidoreductases and ubiquinol oxidases. The second section is a compilation of theoretical,\r\nmethodological, synthetic, and biophysical studies. These include the development of\r\nMIRAS phasing methods using xenon gas, facile synthetic methods for benzoin\r\ncompounds, development of universal photoreduction compounds, theoretical models for\r\nproton pumping mechanisms in ubiquinol oxidases, and structural studies on a leucine-rich\r\nrepeat variant protein." }, { "name": "Tsai, Bao-Liang", "degree": "PhD", "year": "1997", "title": "First principles studies of semiconductor epitaxial growth", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-112630", "creators": [ { "name": { "family": "Tsai", "given": "Bao-Liang" }, "id": "Tsai-B", "display_name": "Tsai, Bao-Liang" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2CV3-2A62", "abstract": "This thesis conducts investigations mainly on the structures, energetics, and reactions of semiconductor as well as oxide surfaces using first principles cluster model approach.
\r\n\r\nThe first part of the research work addresses the issues in the epitaxial growth of Hg1-xCdxTe (MCT) materials. Hg divalent compounds were studied thoroughly using a variety of quantum chemical methods in order to understand the energetics of Hg precursors for growth. The (001) growth surfaces were then examined in detail using cluster model calculations. Based on these results, a novel metal-organic molecular beam epitaxial (MOMBE) growth strategy with favorable energetics for growing MCT using H2C=CH-CH2-Hg-C=C-CH3 is proposed. It is hoped that with this new growth strategy, the Hg vacancy and p-doping problems that currently exist in growth can be avoided.
\r\n\r\nThe second part of the thesis discusses the molecular beam epitaxial (MBE) growth of cubic GaN on the (001) surface using various N sources. Surface reconstructions and the interactions of gas-phase atomic and molecular nitrogens with the surface were elucidated using cluster models. Using these results an energy phase diagram for the growth of GaN has been constructed. It suggests that excited state molecular N2 (3\u03a3u+) is the most favorable of all N species for growth of high quality GaN because it can undergo a dissociative chemisorption process. Ground state atomic N (4S) is also good for growth. The doublet excited states N (2D and 2P) might cause surface N abstraction, leading to N vacancies in the material.
\r\n\r\nFinally, a Fe(OH)3(H20)3 GVB cluster model of crystalline \u03b1-Fe203 was developed. This simple model can describe the local geometry and bonding of Fe in the bulk oxide. Using quantum mechanical calculations, the orientation of the oleic imidazoline (OI) molecule bonding to the oxide surface has been determined. OI class of molecules are used extensively for corrosion inhibitor in oil field pipeline applications. It is found in this work that OI can make very strong bonding to the Fe of the iron oxide. In aqueous environments they can replace water on the pipe surface to form a protective layer to prevent corrosion.
\r\n" }, { "name": "Yan, Yushan", "degree": "PhD", "year": "1997", "title": "Preparation of zeolite ZSM-5 membranes", "advisor": "Gavalas, George R.; Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-141042", "creators": [ { "name": { "family": "Yan", "given": "Yushan" }, "id": "Yan-Yushan", "display_name": "Yan, Yushan" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "co-chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "co-chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Giapis", "given": "Konstantinos P." }, "id": "Giapis-K-P", "role": "member", "display_name": "Giapis, Konstantinos P." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/05FZ-JS07", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nZeolite ZSM-5 membranes were prepared on porous [...] disks by in-situ crystallization using a clear solution of optimized composition [...]. During the synthesis, the disk was fixed horizontally at the air-liquid interface and a continuous polycrystalline zeolite film of about 10 \u00b5m thickness formed on the bottom surface of disk. Extensive experimentation was carried out to find the optimal composition. Pure gas permeation measurements of the most successful preparation yielded hydrogen:isobutane and n-butane:isobutane ratios of 151 and 18 at room temperature and 54 and 31 at 185\u00b0C, respectively.\r\n\r\nElectron probe microanalysis of the cross section of a membrane prepared on a bare alumina disk revealed a layer of crystalline or amorphous silica extending 80 \u00b5m inside the pores of the support. It is believed that this internal layer adds resistance to permeation and degrades selectivity. To limit the excessive penetration of siliceous species into the support pores, a diffusion barrier was introduced into the pores of the support prior to zeolite crystallization by impregnating the disk with a 1:1 molar mixture of furfuryl alcohol and tetraethylorthosilicate, polymerizing the mixture retained in the disk, and carbonizing the resulting polymer. Following carbonization, a partial carbon burnoff was carried out to generate a carbon-free region near the surface of the support. Membranes synthesized using barriers have n-butane flux and n-butane:isobutane selectivity 2.7 x [...] and 45 at 185\u00b0C which are, respectively, about 1.6 and 4 times as large as those of membranes prepared without the use of barriers.\r\n\r\nThe n-butane:isobutane selectivity of ZSM-5 membranes was substantially improved (e.g. 322 vs. 45 at 185\u00b0C) by a post-synthetic coking treatment which was accomplished by impregnating the membranes with liquid 1,3,5-triisopropylbenzene (TIPB) for 24 hours at room temperature and then calcining them in air at 500\u00b0C for 2 hours. Calcination at 500\u00b0C for up to 30 hours does not destroy the high n-butane:isobutane selectivity. Thermogravimetric analysis experiments suggest that microdefects in the zeolite membranes were selectively eliminated by the TIPB coking treatment while the intracrystalline pore space of the ZSM-5 was not affected.\r\n\r\nA model of surface-induced nucleation, crystal growth, and crystal adhesion was proposed for the aforementioned heterogeneous hydrothermal synthesis system. During the synthesis, aluminosilicates in the aged solution interact favorably with and travel toward the [...] surface, resulting in concentration and nucleation in the vicinity of the surface. Some of the nuclei become attached to the surface and grow into a zeolite film while others settle and produce loose zeolite crystals at the bottom of the autoclave. The nutrients for crystal growth is supplied by active gel particles and the synthesis solution. Surface -OH groups on the substrate appear important for crystal adhesion via condensation. As for zeolite membrane formation on a surface of certain area, the location and orientation of the surface as well as the amount of synthesis liquid accessible to the surface are critical for the quality of the zeolite membrane.\r\n" }, { "name": "Yang, Bryant H.", "degree": "PhD", "year": "1997", "title": "Use of pseudoephedrine as a practical chiral auxiliary for asymmetric synthesis", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02202014-095838875", "creators": [ { "name": { "family": "Yang", "given": "Bryant H." }, "id": "Yang-Bryant-H", "display_name": "Yang, Bryant H." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1K2S-P110", "abstract": "The use of pseudoephedrine as a practical chiral auxiliary for asymmetric synthesis is describe. Both enantiomers of pseudoephedrine are inexpensive commodity chemicals and can be N-acylated in high yields to form tertiary amides. In the presence of lithium chloride, the enolates of the corresponding pseudoephedrine amides undergo highly diastereoselective a1kylations with a wide range of alkyl halides to afford \u03b1-substituted products in high yields. These products can then be transformed in a single operation into highly enantiomerically enriched carboxylic acids, alcohols, and aldehydes. Lithium amidotrihydroborate (LAB) is shown to be a powerful reductant for the selective reduction of tertiary amides in general and pseudoephedrine amides in particular to form primary alcohols.
\t\r\n" }, { "name": "Anderson, Kraig Knute", "degree": "PhD", "year": "1996", "title": "An Improved Model for One-Dimensional Polaronic Ferromagnetism: Poly-Meta-Phenylenefuchsone", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10102006-144012", "creators": [ { "name": { "family": "Anderson", "given": "Kraig Knute" }, "id": "Anderson-Kraig-Knute", "display_name": "Anderson, Kraig Knute" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/25a7-sf85", "abstract": "The design, reductive doping, and magnetic characterization of poly-meta-phenylenefuchsone, an improved model for one-dimensional polaronic ferromagnetism, are described. Previous work demonstrated that delocalized radical cations, when linked through appropriate topologies, can exhibit ferromagnetic, or high spin interactions between unpaired electron spins. Consideration of these examples led to the choice of the radical anion of 2,6-di-tert-butylfuchsone as a spin containing unit, due to its relative stability, solubility, spin density, and ease of generation. Electrochemical doping of its polymers is more convenient and effective than chemical doping, resulting in a substantial increase in magnetic properties relative to previous models. The magnetic results are aided by dilution of the doped polymer in a diamagnetic solid, which is interpreted as reducing intermolecular antiferromagnetic interactions. The significant results of this model system provide clear directions for future designs, including improving solubility, spin density, doping efficiency, and defect suppression.
\r\n\r\nA tetraphenoxyl analog to existing quintet tetraradical A was envisioned. The synthesis and oxidation of its precursor tetraphenol I are described, as well as a number of simpler analogs. No evidence of high spin interactions was observed. Instead, the X-ray crystal structure of the product indicates that the oxidized tetraphenol undergoes ring closure of its central cyclobutane ring to form a bicyclobutane, which rapidly rearranges to a ring opened butadiene. The novel feature of this known rearrangement in the current system is that it occurs readily, even under very mild conditions.
" }, { "name": "Andino, Jean Marie", "degree": "PhD", "year": "1996", "title": "Experimental and theoretical studies of reactions important in photochemical smog : aromatics and alkanes", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032007-154253", "creators": [ { "name": { "family": "Andino", "given": "Jean Marie" }, "id": "Andino-J-M", "display_name": "Andino, Jean Marie" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4811-nz89", "abstract": "The development of effective ozone control strategies requires the use of atmospheric models. There is general agreement within the scientific community that several aspects of the chemistry within these models has yet to be fully elucidated, and is influential in their predictions. The work in this thesis is aimed at trying to determine some of the unknown aspects of the mechanisms of important atmospheric species. Specifically, the gas-phase reactions of two large alkanes, 2,2,4-trimethylpentane and 2,2,5-trimethylhexane are investigated. These two alkanes are present in urban air, and are potential aerosol precursors. The chemistry of several aromatic hydrocarbons are also studied using both theoretical and experimental techniques. The effects of NO2 on the photooxidation of toluene, m-xylene, and p-xylene are examined, and mechanisms of each of these organics are thouroughly evaluated through closely coordinated laboratory work and computer modeling. In addition, product studies of the photooxidation of 1,2,4-trimethylbenzene and m-ethyltoluene are conducted. These studies provide the first identification of ring-retained products from 1,2,4-trimethylbenzene, and ring-retained and fragmented products from m-ethyltoluene.\n\nA new indoor experimental reactor was designed to investigate gas-phase reaction kinetics and mechanisms. This new system has served to launch the atmospheric chemistry program at Caltech into a wide variety of new research topics." }, { "name": "Bachrach, Max", "degree": "PhD", "year": "1996", "title": "Electron-Transfer in Covalently Coupled Donor-Acceptor Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152020-011716999", "creators": [ { "name": { "family": "Bachrach", "given": "Max" }, "id": "Bachrach-Max", "display_name": "Bachrach, Max" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan S." }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan S." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tzkw-0q94", "abstract": "A picosecond transient absorption experiment has been constructed and used for the study of intramolecular electron-transfer (ET) in three molecular systems. The first of these is a donor-bridge-acceptor (D(br)A) complex composed of a d\u2078-d\u2078 iridium core covalently coupled to two pyridinium acceptors with flexible phosphonite spacers. Varying the pyridiniums' substituents allows control of the driving-forces (\u0394G\u00b0) of the photoinduced ET reactions from the core's singlet and triplet states. The rates of these reactions have been determined from steady-state and time-resolved emission experiments. Picosecond transient absorption has been used to measure the rates of subsequent charge-recombination, and determine their dependencies on \u0394G\u00b0. The reorganization energy accompanying intramolecular electron-transfer within this system (\u03bb \u2248 0.86 eV) has been determined by fitting the rates of photoinduced and thermal reactions to a single-mode quantum-mechanical ET model.
\r\n\r\nThe rates of all the photoinduced and thermal ET reactions have been measured as a function of temperature (200\u00b0 K - 280\u00b0 K). These data show that the charge-recombination reactions, which lie within the Marcus inverted region (\u0394G\u00b0 > \u03bb), have rates (kBET) that are strongly dependent on temperature. Deuteration of the pyridinium acceptor has a temperature independent effect (kH/kD = 1.2) on kBET, indicating that, although the inverted region reactions within these complexes exhibit behavior that is remarkably classical, quantum-mechanical effects do need to be considered. Both temperature and isotope effects suggest that the molecules' low internal reorganization energies (\u03bbin = 0.006 eV) account for their ET behavior.
\r\n\r\nLess comprehensive studies of two other electron-transfer systems are also reported. Unlike the iridium system, in which the donor-acceptor electronic coupling HAB is less than 100 cm-1, the couplings within these are over 2000 cm-1. It has been found that despite the large amount of coupling between the metals of [(bpy)(tpy)RuIICNRuII(NH3)5]2+ (bpy = 2,2'-bipyridine; tpy = 2,2',2\"-terpyridine), our transient absorption experiment is able to detect formation of a charge-separated state following excitation into the Ru \u2192 immine charge-transfer band. It is proposed that this species can be described as [(bpy)(tpy\u2022-)RuIICNRuIII(NH3)5]2+ and that unusually low coupling between the tpy ligand and the oxidized ruthenium leads to slow (1 x 1010 s-1) charge-recombination.
\r\n\r\nThe ground-state absorption features and excited-state decay kinetics of a series of ferrocene-based D(br)A complexes have also been measured. It is proposed that HAB is much larger than 2000 cm-1 for these complexes, and plays an important role in determining their nonlinear optical properties.
" }, { "name": "Baliga, Ramesh", "degree": "PhD", "year": "1996", "title": "Analysis of Nucleoprotein Complexes Formed by E. coli RecA Protein Using Affinity Cleavage", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12152020-172741079", "creators": [ { "name": { "family": "Baliga", "given": "Ramesh" }, "id": "Baliga-Ramesh", "display_name": "Baliga, Ramesh" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vgxz-vf87", "abstract": "Homologous recombination, a process ubiquitous to most living cells, involves the exchange of strands between two molecules of double-stranded DNA at sites of sequence homology, resulting in the formation of hybrid products. One of the best studied model systems for in vitro studies of homologous recombination is the three-strand reaction catalyzed by the Escherichia coli RecA protein. In the presence of appropriate cofactors, RecA protein polymerizes on single-stranded DNA to form nucleoprotein filaments which can then bind to homologous sequences on duplex DNA. This thesis describes the use of affinity cleavage with oligonucleotides carrying an EDTA moiety appended at a single position, to study the binding of RecA\u2022 oligonucleotide filaments on duplex DNA. Chapter One provides a general overview of protein-DNA recognition, chemical approaches to molecular recognition of B-form DNA (including oligonucleotide-directed triple helix formation) and what is currently known about the role of RecA protein in homologous recombination and DNA repair. Chapter Two describes the technique of affinity cleavage and its optimization for RecA\u2022 oligonucleotide filaments. Chapter Three describes the use of affinity cleavage to observe cooperative binding of nucleoprotein filaments to adjacent sites on duplex DNA and an investigation into the basis for the observed cooperativity. In Chaper Four affinity cleavage with oligonucleotides carrying a single thymidine-EDTA residue at an internal site is used to determine the groove location of the incoming strand, in the threestranded complex formed by recognition of a homologous site on duplex DNA. Finally, in Chapter Five the results from various chemically modified substrates of the three-strand reaction are presented in support of a mechanism of homologous recognition that does not involve formation of a pre-exchange triple helical intermediate.
" }, { "name": "Blake, Robert Edward, Jr.", "degree": "PhD", "year": "1996", "title": "The Synthesis, Characterization and Study of Transition Metal Complexes for the Oxidation and Activation of Hydrocarbons", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052019-113518368", "creators": [ { "name": { "family": "Blake", "given": "Robert Edward, Jr." }, "id": "Blake-Robert-Edward-Jr", "display_name": "Blake, Robert Edward, Jr." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s731-np77", "abstract": "The reaction of previously characterized ruthenium oxo complex, [LOEtRuV(O)(\u00b5-O)]2 with alcohol substrates was undertaken to elucidate the mechanism of the oxidation reaction. Unfortunately, an autocatalytic reaction between the organometallic product, [LOEtRuIV(OH)(\u00b5-O)]2 and the reactant alcohol, as well as catalyst decomposition made exact determinations of rate constants impossible. During the course of this investigation, the free acid form of the ligand, LOEtH, was isolated as a viscous oil. Subsequent investigation of the reactions of [LOEtRuV(O)(\u00b5-O)]2 with other species such as acids, salts and bases demonstrated the inherent instability of the complex. In several cases, initial products were spectroscopically characterized, but isolation of pure compounds was not achieved.
\r\n\r\nGiven the problems with the decomposition of ruthenium complexes which utilized the Klaui ligand, trimetaphosphate was studied as a potentially oxidation-resistant alternative for the development of oxidation catalysts. Attempts were made to prepare salts of the trimetaphosphate ligand which are soluble in nonpolar media and free of water of hydration. Coordination complexes of the trimetaphosphate anion and transition elements were synthesized. The mode of coordination and stability of the ligand was examined by infrared and visible spectroscopy. In all cases, the very weakly coordinating trimetaphosphate anion failed to displace other weakly associated ligands from the metal, failed to adopt the proper coordination geometry or was easily removed from the metal center by water.
\r\n\r\nHexabenzyloxycyclotriphosphatriene was synthesized and thermally rearranged to 1,3,5 - tribenzyl - 2,4,6 tribenzyloxy - 2,4,6 trioxocyclotriphosphazane as per published procedures. Characterization of the rearranged product by NMR techniques revealed the previously undetermined stereochemistry of the product. This ligand precursor has been shown to react with trialkyl silyl chlorides, although the products have not been characterized.
\r\n\r\nCp*2Ta(=NtBu)(THF)[B(C6F5)4] (1) was synthesized according to the method developed previously in our group. A cationic analog to Bergman's Cp2Zr(=NtBu), the reactivity of this complex to hydrocarbon substrates was studied. Contrary to previous reports, this complex does not react with methane, but C-H activation reactions were observed for propyne and phenyl acetylene. In the propyne case, an initial mixture of the [2+2] and C-H activation products was driven to exclusively the C-H activation product thermally. An interesting intramolecular activation of a Cp* methyl group precludes much of the desired C-H activation chemistry. The steric demands of the active site was demonstrated by the observed reaction with ethylene, but the lack of reactivity towards propene. A very interesting dealkylation of the imido group was observed upon reaction with carbon dioxide, which is proposed to involve the intermediacy of a coordinated isocyanate. Cp*2Ta(=NtBu)(THF)[B(C6F5)4] reacts as expected with water, HCl and dihydrogen, and reacts cleanly with methylene chloride to give Cp*2Ta(NHtBu)Cl[B(C6F5)4]. Many of the new compounds have been crystallographically and spectroscopically characterized. The reactivity of this complex can be rationalized in terms of the presence of both electrophilic and nucleophilic sites in the same molecule.
" }, { "name": "Bren, Kara Lynne", "degree": "PhD", "year": "1996", "title": "Structurally Engineered Cytochromes c with Novel Ligand-Binding Properties", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02042014-091755725", "creators": [ { "name": { "family": "Bren", "given": "Kara Lynne" }, "id": "Bren-Kara-Lynne", "orcid": "0000-0002-8082-3634", "display_name": "Bren, Kara Lynne" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/D8HZ-E792", "abstract": "Semisynthesis of horse heart cytochrome c and site-directed mutagenesis of Saccharomyces cerevisiae (S. c.) iso-1-cytochrome c have been utilized to substitute Ala for the cytochrome c heme axial ligand Met80 to yield ligand-binding proteins (horse heart Ala80cyt c and S. c. Ala80cyt c) with spectroscopic properties remarkably similar to those of myoglobin. Both species of Fe(II)Ala80cyt c form exceptionally stable dioxygen complexes with autoxidation rates 10-30x smaller and O2 binding constants ~ 3x greater than those of myoglobin. The resistance of O2-Fe(II)Ala80cyt c to autoxidation is attributed in part to protection of the heme site from solvent as exhibited by the exceptionally slow rate of CO binding to the heme as well as the low quantum yield of CO photodissociation.
\r\n\r\nUV/vis, EPR, and paramagnetic NMR spectroscopy indicate that at pH 7 the Fe(III)Ala80cyt c heme is low-spin with axial His-OH- coordination and that below pH ~6.5, Fe(III)Ala80cyt c is high-spin with His-H2O heme ligation. Significant differences in the pH dependence of the 1H NMR spectra of S. c. Fe(III)Ala80cyt c compared to wild-type demonstrate that the axial ligands influence the conformational energetics of cytochrome c.
\r\n\r\n1H NMR spectroscopy has been utilized to determine the solution structure of the cyanide derivative of S. c. Fe(III)Ala80cyt c. 82% of the resonances in the 1H NMR spectrum of S. c. CN-Fe(III)Ala80cyt c have been assigned through 1D and 2D experiments. The RMSD values after restrained energy minimization of the family of 17 structures obtained from distance geometry calculations are 0.68 \u00b1 0.11 \u00c5 for the backbone and 1.32 \u00b1 0.14 \u00c5 for all heavy atoms. The solution structure indicates that a tyrosine in the \"distal\" pocket of CN-Fe(III)Ala80cyt c forms a hydrogen bond with the Fe(III)-CN unit, suggesting that it may play a role analogous to that of the distal histidine in myoglobin in stabilizing the dioxygen adduct.
" }, { "name": "Campisi, Donna", "degree": "PhD", "year": "1996", "title": "Transition metal complexes as probes of DNA sequence-dependent structure", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09082006-114255", "creators": [ { "name": { "family": "Campisi", "given": "Donna" }, "id": "Campisi-D", "display_name": "Campisi, Donna" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kay4-sz63", "abstract": "Different transition metal complexes have been applied in probing variations in the structure of double helical DNA. The following probes, which all bind DNA noncovalently, have been utilized: Ru(phen)3(2)+, Ru(TMP)3(2)+, Rh(phen)2phi3+, Rh(TMP)2phi3+, Rh(dmbpy)2phi3+, Ru(phen)2dppz2+, Ru(bpy)2dppz2+, and Rh(bpy)2dppz3+ (phen = 1,10 phenanthroline; TMP = 3,4,7,8,-tetramethyl- 1,10-phenanthroline; phi = 9,10-phenanthrenequinone diimine; dmbpy = 5,5'-dimethylbipyridyl; bpy = bipyridyl; dppz = dipyrido[3,2-a;2',3'-c]phenazine). The local structure recognized by [Delta]-Rh(phen)2phi3+ has been defined by comparisons of photocleavage data on crystallographically characterized oligonucleotides with their structural parameters. A quantitative correlation has been determined between [Delta]-Rh(phen)2phi3+ photocleavage and extent of openness in the major groove due to differential propeller twisting, or interpurine angle. Therefore, [Delta]-Rh(phen)2phi3+ has been developed as a probe of DNA propeller twisting in solution. Differences in reaction pathway partitioning between enantiomers of Rh(phen)2phi3+ are attributed to differing extent of shape complementarity with DNA binding sites. Rh(TMP)2phi3+ has been explored in probing DNA mismatches in solution. Both [Delta]-Rh(phen)2phi3+ and Rh(TMP)2phi3+ sensitively mark local structural perturbations in an oligonucleotide, arising from substitution of a CG base pair with TG and AG mismatches. Rh(phen)2phi3+ and Ru(TMP)3(2) have also been applied in probing structural variations in the context of a long DNA strand. A C7 stretch is targeted by Ru(TMP)3(2), an A DNA probe and Rh(phen)2phi3+, a B DNA probe. These results indicate this sequence is heteronomous, containing wide major and minor grooves. [Delta]- and [Lambda]-Rh(phen)2phi3+ also discriminate structural differences between bent and nonbent DNA fragments. Variations in metal complex-DNA interactions have also been examined by a gel electrophoretic mobility assay. Intercalator size, hydrophobicity of ancillary ligands, metal complex charge, and chirality all influence the extent of DNA retardation. Taken together, these studies demonstrate that transition metal complexes can be profitably and uniquely applied towards exploring DNA structural heterogeneity." }, { "name": "Cho, Junhyeong", "degree": "PhD", "year": "1996", "title": "Design of cyclic polyamides for sequence-specific recognition of the minor groove of DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04272006-161449", "creators": [ { "name": { "family": "Cho", "given": "Junhyeong" }, "id": "Cho-J", "display_name": "Cho, Junhyeong" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ksmz-5b60", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nSmall molecules that specifically bind with high affinity to any designated DNA sequence in the human genome would be useful tools in molecular biology and potentially in human medicine. Simple rules have been developed to rationally alter the sequence specificity of minor groove binding polyamides containing N-methylimidazole (Im) and N-methylpyrrole (Py) amino acids. Crescent-shaped polyamides bind as antiparallel dimers with each polyamide making specific contacts with each strand on the floor of the minor groove.\n\nIn Chapter 2, the design of and synthesis of the cyclic polyamide cyclo-(Im-Py-Py-[...]-Py-Py-Py-[...]) is described. The cyclic polyamide binds the 5'-TGTTA-3' site with 40-fold higher affinity than the hairpin polyamide Im-Py-Py-[...]-Py-Py-Py-Dp. These results demonstrate that wholly designed synthetic cyclic polyamides with a molecular weight of 950 can bind designed five base pair sequences at subnanomolar concentration.\n\nIn Chapter 3, in order to develop polyamide ligands to differentiate between A,T-rich sequences, a cyclic polyamide has been synthesized in which two Py-Py-Py units are circled through two [...]-aminobutyric acids ([...]). DNase I footprinting titration experiments reveal that cyclo-(Py-Py-Py-[...]-Py-Py-Py-y) binds the 5'-TATAT-3' sequence with 20-fold higher affinity than distamycin.\n\nIn Chapter 4, experiments are described in which [...] is attached at unique sites of HIV-1 TAR RNA by the chemical synthesis method and autocleavage of [...] is performed. Preliminary results showed that the autocleavage pattern of TAR RNA is changed in the presence of arginine. However, a series of control experiments indicate that the change in the autocleavage pattern is not caused by an RNA conformational change driven by the binding of arginine." }, { "name": "Choi, Wonyong", "degree": "PhD", "year": "1996", "title": "Photooxidative and Photoreductive Degradation of Chlorinated Hydrocarbons on Aqueous Titanium Dioxide Colloids", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-084215", "creators": [ { "name": { "family": "Choi", "given": "Wonyong" }, "id": "Choi-Wonyong", "orcid": "0000-0003-1801-9386", "display_name": "Choi, Wonyong" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/D1KR-1M50", "abstract": "Studies on photocatalytic degradation reactions of chlorinated hydrocarbons on TiO2 colloids are presented in this thesis. Photoreactivities of metal-ion doped quantum-sized TiO2 colloids and photochemical mechanisms of CHCl3 and CCl4 degradation are investigated in detail.
\r\n\r\nA systematic study of 21 metal-ion doped quantum-sized (2-4 nm) TiO2 colloids is performed by measuring their photoreactivities and the transient charge-carrier recombination dynamics. Doping with Fe3+, Mo5+, Ru3+, Os3+, Re5+, V4+, and Rh3+ at 0.1-0.5 atom% significantly increases the photoreactivity for both CHCl3 oxidation and CCl4 reduction while Co3+ and Al3+ doping decreases the photoreactivity. The quantum yields obtained during CW photolyses are quantitatively correlated with the measured transient absorption signals of the charge-carriers.
\r\n\r\nThe photoreductive degradation of CCl4 in TiO2 particulate suspensions in the presence of a variety of organic electron donors (alcohols, carboxylic acids, and benzene derivatives) has been examined. The rate of CCl4 dechlorination can be enhanced significantly when alcohols and organic acids are used as electron donors. It is demonstrated that CCl4 can be fully degraded under both oxic and anoxic conditions. A photodegradation mechanism of CCl4 that includes both one-electron and two-electron transfer is proposed.
\r\n\r\nThe mechanism of photoreduction of CCl4 on illuminated TiO2 surfaces is investigated by selectively trapping transient free radical intermediates. Dichlorocarbene and trichloromethyl radical are trapped with 2,3-dimethyl-2-butene during the photocatalytic degradation of CCl4. The rate of formation of trapped :CCl2 and \u2022CCl3 is found to be a function of [H2O], pH, [CCl4], the nature of the dissolved gas, and light intensity. A two-electron photoreductive pathway (via dichlorocarbene formation) is suggested to be the dominant mechanism leading to the full degradation of CCl4.
\r\n\r\nThe photocatalytic degradation reactions of CHCl3, CHBr3, CCl4, and CCl3CO2- are investigated in aqueous TiO2 suspensions. CHCl3 and CHBr3 are degraded into carbon monoxide and halide ion in the absence of dissolved oxygen. The anoxic degradation proceeds through a dihalocarbene intermediate which is produced by sequential reactions of the haloform molecule with a valence band hole and a conduction band electron. Degradation of haloform is enhanced dramatically at pH >11. This enhancement is ascribed to \"photoenhanced hydrolysis\".
\r\n" }, { "name": "Claverie, J\u00e9r\u00f4me", "degree": "PhD", "year": "1996", "title": "Ring-Opening Metathesis Polymerization with Tungsten Based Catalysts: Kinetics, Thermodynamics and Mechanism", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052019-172741776", "creators": [ { "name": { "family": "Claverie", "given": "J\u00e9r\u00f4me" }, "id": "Claverie-J\u00e9r\u00f4me", "display_name": "Claverie, J\u00e9r\u00f4me" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h6fj-1t43", "abstract": "Ring-opening metathesis polymerization (ROMP) is instrumental in the synthesis of a variety of polymers. Since the appearance of well defined metathesis catalysts, the synthesis and characterization of ROMP polymers has been greatly improved.
\r\n\r\nIn the first chapter, the kinetics and the thermodynamics of such polymerizations are presented. When a living ROMP polymerization is effected in the presence of a chain transfer-agent, the molecular weight distribution is governed by the kinetics of the polymerization. The molecular weight distribution has been evaluated numerically, and the numerical results have been compared to experimental ones. The living polymerization of norbornene by Mo(=CHR)(=N-1,3-i-Pr-C6H3)(O-t-Bu)2 (R = -t-Bu, -C(CH3)2Ph) in the presence of neohexene and styrene has been used as a model experiment. When the ROMP catalyst is too active, chain transfer to the polymer occurs, and the molecular weight distribution is dependent upon the thermodynamics of the polymerization. The theoretical thermodynamic product distribution has been predicted, and compared to experimental results for the polymerization of 1,5-cyclooctadiene (COD) and cyclooctene. The results have been applied to the synthesis of short polyacetylene oligomers by ROMP of sec-butylcyclooctatetraene.
\r\n\r\nIn the second chapter, the synthesis of monodisperse substituted polyacetylenes is described. For this synthesis, one has to use very active ROMP catalysts which appreciably initiate the polymerization. The new class of tungsten vinyl alkylidenes allows such a polymerization. Synthesis, characterization and catalytic properties of tungsten imido and oxo vinyl alkylidenes is described.
\r\n\r\nIn the third chapter, reactivity of tertiary alcohols with tungsten vinyl alkylidenes and neopentylidenes is examined. These alcohols are found in trace amounts in all the samples of these tungsten carbenes. The role of the alcohols in ROMP is studied for polynorbornene, polycyclooctadiene and polyacetylene. Activation of these catalysts has been observed, even by trace amounts of alcohol, and has important consequences in the microstructure of the resulting polymer. Mechanistic implications toward a general scheme of acid activation of the well defined tungsten carbenes is proposed.
" }, { "name": "Colocci, Natalia", "degree": "PhD", "year": "1996", "title": "Cooperative Oligonucleotide-Directed Triple Helix Formation at Adjacent DNA Sites", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222020-002250563", "creators": [ { "name": { "family": "Colocci", "given": "Natalia" }, "id": "Colocci-Natalia", "display_name": "Colocci, Natalia" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/08j6-sd37", "abstract": "Cooperative interactions between DNA-binding ligands are essential for their sequence specificity, binding affinity, and biological activity. Oligonucleotides can bind cooperatively to adjacent sites on double-helical DNA by triple helix formation. The study of the cooperative binding of oligonucleotides to DNA by triple helix formation is important as it provides useful information for the development of new methods leading to the sequence-specific recognition of DNA. As a first step towards this goal, the thermodynamics of the cooperative binding of oligodeoxyribonucleotides to adjacent DNA sites by triple helix formation have been determined by quantitative affinity cleavage titrations (Chapter Two). A 20-fold enhancement in equilibrium association constant is realized for an 11mer pyrimidine oligonucleotide binding in the presence of a neighboring bound site at 24 \u00b0C and pH 7.0 (25 mM TrisOAc, 10 mM NaCl, 1 mM spermine). This corresponds to an increase in binding free energy of 1.8 kcal\u2022mol\u207b\u00b9. This cooperativity is not observed when the two binding sites are separated by one base pair. The observed cooperative energy likely arises from favorable polarization and charge-charge interactions between the terminal bases at the triple-helical junction.
\r\n\r\nIn addition, the energetics of cooperative binding by oligodeoxyribonucleotides to adjacent sites by triple helix formation have been determined as a function of sequence composition at the junction (Chapter Three). The binding affinity of an 11mer in the presence of a neighboring bound oligonucleotide is enhanced by a factor of 12, 17, 61, and 127 when a 5'-TT-3', 5'-\u1d50C\u1d50C-3', 5'-T\u1d50C-3', and 5'-\u1d50CT-3' stack, respectively, is formed at the junction (10 mM Bis-Tris\u2022HCl at pH 7.0, 10 mM NaCl, 250 \u00b5M spermine, 24 \u00b0C) (\u1d50C designates 5-methyl-2'-deoxycytidine). These binding enhancements correspond to an interaction energy between the two oligonucleotides of 1.5, 1.7, 2.5, and 2.9 kcal\u2022mol\u207b\u00b9, respectively. The energetic penalties for a single-base mismatch differ depending on sequence and the location of the mismatch with respect to the 5'- or 3'-side of the junction. In the case of a 5'-TT-3' stack, a T\u2022GC mismatch on the 5'- side of the junction decreases the interaction energy from 1.5 kcal\u2022mol\u207b\u00b9 to 0.6 kcal\u2022mol\u207b\u00b9, whereas a T\u2022GC mismatch on the 3'- side destroys cooperativity. For a 5'-\u1d50CT-3' stack, a \u1d50C\u2022AT mismatch on the 5'-side of the junction decreases the cooperative interaction energy from 2.9 kcal\u2022mol\u207b\u00b9 to 1.7 kcal\u2022mol\u207b\u00b9, whereas a T\u2022GC mismatch on the 3'-side of the junction destroys cooperativity. Most importantly, two 11mer oligonucleotides interacting through a 5'-TT -3' stack binding to adjacent sites on DNA are significantly more sensitive to single-base mismatches than the corresponding 22mer binding to the same two abutting sites.
\r\n\r\nThe use of modified bases, such as 5-(1-propynyl)-2'-deoxyuridine, increases cooperativity between oligonucleotides bound to adjacent sites on DNA, presumably due to an increased stacking energy between the modified bases at the triplex junction (Chapter Four). Oligodeoxyribonucleotides containing 5-(1-propynyl)-2'-deoxyuridine and 5-methyl-2'-deoxycytidine as short as 8 nucleotides in length bind at micromolar concentrations to adjacent 8-bp sites on double-helical DNA at 24 \u00b0C and pH 7.0 (10 mM Bis-Tris\u2022HCl, 10 mM NaCl, 1 mM spermine). Quantitative affinity cleavage titrations reveal that the binding affinity of an 8mer in the presence of a neighboring bound 8mer is enhanced by a factor of at least 40. This corresponds to a remarkable cooperative interaction energy of > 4.5 kcal\u2022mol\u207b\u00b9. In addition, these cooperative interactions allow oligonucleotides as short as 6mers to bind to three adjacent sites on double-helical DNA at near micromolar concentrations (10 mM Bis-Tris\u2022HCl at pH 7.0, 10 mM NaCl, 1 mM spermine, 24 \u00b0C).
\r\n\r\nCooperativity is also observed between purine-rich oligonucleotides (Chapter Five). Quantitative DNase footprinting titration experiments show that the binding affinity of an 11mer purine-rich oligonucleotide in the presence of a neighboring bound oligonucleotide is enhanced by a factor of 81 when a 5'-GG-3' stack is formed at the junction (50 mM TrisOAc at pH 7.0, 10 mM NaCl, 10 mM MgCl\u2082, 24 \u00b0C). This binding enhancement corresponds to an interaction energy between the two oligonucleotides of 2.7 kcal\u2022mol\u207b\u00b9, and is abolished when the two binding sites are separated by one base pair.
\r\n\r\nThe synthesis of pyrimidine oligonucleotide analogs containing 5-(1-propynyl)- and 2'-O-allyl-modified nucleosides (Chapter Six), and the progress towards the synthesis of a novel base, N7-2'-deoxyisoinosine, designed for the recognition of AT base pairs within a parallel isomorphous purine motif (Chapter Seven), are described.
" }, { "name": "Dabdub, Donald", "degree": "PhD", "year": "1996", "title": "Mathematical modeling of air pollution dynamics by parallel computation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12132007-083330", "creators": [ { "name": { "family": "Dabdub", "given": "Donald" }, "id": "Dabdub-D", "display_name": "Dabdub, Donald" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Van de Velde", "given": "Eric" }, "id": "van-de-Velde-E", "role": "member", "display_name": "Van de Velde, Eric" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Keller", "given": "Herbert Bishop" }, "id": "Keller-H-B", "role": "member", "display_name": "Keller, Herbert Bishop" }, { "name": { "family": "Chandy", "given": "K. Mani" }, "id": "Chandy-K-M", "role": "member", "display_name": "Chandy, K. Mani" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/k1ap-np35", "abstract": "The use of massively parallel computers provides an avenue to overcome the computational requirements in the study of atmospheric chemical dynamics. General considerations on parallel implementation of air quality models are outlined including domain decomposition strategies, algorithm evaluation and design, portability, modularity, and buffering techniques used in I/O operations. Results are given for the implementation of the CIT urban air pollution model on distributed memory multiple instruction / multiple data (MIMD) machines ranging from a cluster of workstations to a 512 node Intel Paragon.\r\n\r\nThe central challenge in developing a parallel air pollution model is the implementation of the chemistry and transport operators used in the solution of the atmospheric reaction-diffusion equation. The chemistry operator is generally the most computationally intensive step in atmospheric air quality models. A new method based on Richardson extrapolation to solve the chemical kinetics is presented. The transport operator is the most challenging to solve numerically. Because of its hyperbolic nature non-physical oscillations and/or negative concentrations appear near steep gradient regions of the solution. Six algorithms for solving the advection equation are compared to determine their suitability for use in parallel photochemical air quality models. Four algorithms for filtering the numerical noise produced when solving the advection equation are also compared.\r\n\r\nA speed-up factor of 94.9 has been measured when the I/O, transport, and chemistry portions of the model are performed in parallel. This work provides the computational infrastructure required to incorporate new physico-chemical phenomena in the next generation of urban- or regional-scale air quality models.\r\n\r\nFinally, the SARMAP model is used to model the San Joaquin Valley of California. SARMAP is the updated version of RADM. It can be considered a state-of-the- art regional air pollution model. Like the CIT model, SARMAP incorporates the following atmospheric phenomena: gas-phase chemistry, advection and diffusion. In addition, SARMAP incorporates aqueous-phase chemistry and transport through cumulus clouds. Sensitivity studies performed show a significant dependence of ozone model predictions on boundary conditions." }, { "name": "Dartt, Christopher Bruce", "degree": "PhD", "year": "1996", "title": "Synthesis and characterization of titanium-containing molecular sieves", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12122007-111327", "creators": [ { "name": { "family": "Dartt", "given": "Christopher Bruce" }, "id": "Dartt-Christopher-Bruce", "display_name": "Dartt, Christopher Bruce" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zones", "given": "Stacey I." }, "id": "Zones-S-I", "role": "member", "display_name": "Zones, Stacey I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/0pnv-rt94", "abstract": "The use of zeolites and molecular sieves as catalysts for important organic reactions is reviewed. One emerging area of particular interest is the use of titanium-containing molecular sieves as partial oxidation catalysts and is chosen for further study.\r\n\r\nIn order to elucidate the relationships between the physicochemical properties of titanium-containing molecular sieves and their ability to act as partial oxidation catalysts, titanium-containing pure-silica ZSM-5 (TS-1) materials are synthesized using different methods. The activities of the titanium-containing catalysts for the oxidation of alkanes, alkenes, and phenol at temperatures below 100 [degrees]C using aqueous hydrogen peroxide H2O2 as the oxidant are reported. The relationships between the physicochemical and catalytic properties of these titanium silicates are discussed. The effects of added aluminum and sodium on the catalytic activity of TS-1 are described. The addition of sodium during the synthesis of TS-1 is detrimental to the catalytic activity while sodium incorporation into pre-formed TS-1 is not. The framework substitution of aluminum for silicon appears to decrease the amount of framework titanium.\r\n\r\nThe relationships between catalytic performance and physicochemical properties that are controlled through synthetic methods are further investigated using a series of titanium-containing molecular sieves. Titanium-containing pure-silica ZSM-5 (TS- 1), pure-silica ZSM-48 (Ti-ZSM-48) and zeolite beta (Ti-Al-beta) are synthesized and characterized by X-ray powder diffraction (XRD), elemental analysis, physical adsorption of N2, Fourier transform infrared (FT-IR), FT-Raman, and diffuse reflectance ultraviolet (DR-UV) spectroscopies. TS-1 is synthesized by five different methods. All materials are evaluated for their ability to oxidize 1-hexene and n-octane using aqueous H2O2 as the oxidant. The relationships between the physicochemical and catalytic properties of these titanium-containing zeolites are discussed. TS-1 samples synthesized at high pH are catalytically active and framework titanium is shown to be necessary for olefin epoxidation and alkane hydroxylation to occur. The existence of anatase in active TS-1 samples results in decreased hydrogen peroxide efficiencies in the epoxidation reaction. TS-1 produced at pH=7.4 and Ti-ZSM-48 each contain anatase and are not active. Ti-beta is found to contain framework titanium and be free of anatase. However, at the conditions used in this study these samples are not able to activate 1-hexene or n-octane.\r\n\r\nIn attempts to prepare large pore titanium-containing molecular sieves, postsynthetic incorporation of titanium in the borosilicate SSZ-33 and the direct synthesis of an aluminum-free titanium-containing zeolite Beta (Ti-Beta) are reported. These materials are characterized by XRD, FT-IR, FT-Raman, and DR-UV spectroscopies. The molecular sieves are shown to catalyze the epoxidation of various olefins using aqueous hydrogen peroxide as the oxidant. The physicochemical properties as found by the characterization methods are correlated to the catalytic data and the results compared to a high quality sample of TS-1. The modified SSZ-33 samples contain titanium primarily in the form of isolated tetrahedrally coordinated Ti atoms, although some extra-framework Ti is observed by Raman and DR-UV spectroscopies. Ti-Beta samples show no evidence of extra-framework titanium. For the epoxidation of cis-cyclooctene, the Ti-Beta catalysts give quantitative conversion to epoxide, and both the Ti-Beta and Ti-SSZ-33 catalysts are able to epoxidize substrates too large to be oxidized by TS-1.\r\n" }, { "name": "Day, Michael W.", "degree": "PhD", "year": "1996", "title": "X-Ray Crystallographic Studies on Electron Transfer Proteins; Rubredoxin from Pyrococcus furiosus, Nitrogenase MoFe from Azotobacter vinelandii and Ru(2,2'-bppy)\u2082(imd)His83 Azurin from Pseudomonas aeruginosa", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062019-175229018", "creators": [ { "name": { "family": "Day", "given": "Michael W." }, "id": "Day-Michael-W", "display_name": "Day, Michael W." } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y70P-TJ52", "abstract": "The x-ray crystal structure of the oxidized and the reduced forms rubredoxin from Pyrococcus furiosus, a hyperthermophilic marine Archae, have been solved by molecular replacement and refined by the method of restarined least squares to a maximum resolution of 1.1 \u00c5 for the oxidized form and 1.5 \u00c5 for the reduced form. The oxidized form of the protein crystallizes in the orthorhombic space group P 212121 with unit cell dimensions of a = 33.8 \u00c5, b = 34.6 \u00c5, c = 43.4 \u00c5 and V = 50,755 \u00c53. The reduced form crystallizes in the same space group with the nearly identical unit cell dimensions of a = 33.8 \u00c5, b = 34.5 \u00c5, c = 43.2 \u00c5 and V = 50,375 \u00c53. Data on both forms was collected at -161\u00b0C. Three refinement packages were used in the refinement and the results from each arc discussed as are the possible determinants of the thermal stability. Refinement of the oxidized form (414 protein atoms and 104 solvent oxygens) with TNT or XPLOR resulted in a crystallographic residual of approximately 17% and a model with rms deviations of bond distances and angles from target values of approximately 0.015 \u00c5 and 2.5\u00b0 respectively. Refinement of the oxidized form with SHELXL-93 resulted in a model with 132 solvent oxygens and an R = 13.9% (Rfree = 17.2%) and GOF = 1.08. The rms deviation from the target values for bond distance and angles are 0.014 \u00c5 and 1.75\u00b0 respectively. Refinement of the reduced form with TNT (110 solvent oxygens) or SHELXL-93 (including 130 solvent oxygen atoms) results in an R-factor of approximately 17% and the geometry of the model deviates from the target values by approximate rms values of 0.022 \u00c5 for the bond distances and 3.0\u00b0 for the bond angles.
\r\n\r\nThe x-ray crystal structure of the MoFe nitrogenasc protein from Azotobcacter vinelandii has been refined against data collected at the Stanford Synchrotron Radiation Laboratory (SSRL). The data extends to a maximum resolution of 2.2 \u00c5 and two packages were used in the restrained least squares refinement. Refinement of the model (including 625 solvent oxygens) with TNT or XPLOR yielded a crystallographic residual of less than 18% and a model with bond distances and angles deviate from the target values by rms values of 0.02 \u00c5 and 2.5\u00b0 respectively.
\r\n\r\nThe x-ray crystal structure of the Ru(2,2'-bppy)2(imd)His83 azurin from Pseudomonas aeruginosa has been solved and refined by the method of restrained least squares to a limiting resolution of 2.5 \u00c5. The labeled protein crystalizes in the monoclinic space group C 2 with a = 100.6 \u00c5, b = 35.4 \u00c5, c = 74.7 \u00c5, b = 106.5\u00b0 V = 255,069 \u00c53 and Z = 8. Data was collected at -161\u00b0C to a maximum resolution of 2.3 \u00c5 yielding a data set that is 82% complete containing 11,083 reflections. Refinement in TNT (including 150 solvent oxygen atoms) resulted in an R-factor of 17.3% with rms deviations in the model bond distances and angles from ideal values of 0.026 \u00c5 and 3.09\u00b0 respectively.
" }, { "name": "De Oliveira, Simone Loureiro", "degree": "PhD", "year": "1996", "title": "Model Predictive Control (MPC) for Constrained Nonlinear Systems", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-112031", "creators": [ { "name": { "family": "De Oliveira", "given": "Simone Loureiro" }, "id": "DeOliveira-Simone-Loureiro", "display_name": "De Oliveira, Simone Loureiro" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." }, { "name": { "family": "Wiggins", "given": "Stephen R." }, "id": "Wiggins-S-R", "role": "member", "display_name": "Wiggins, Stephen R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/MXYW-TB71", "abstract": "This thesis addresses the development of stabilizing model predictive control algorithms for nonlinear systems subject to input and state constraints and in the presence of parametric and/or structural uncertainty, disturbances and measurement noise.
\r\n\r\nOur basic model predictive control (MPC) scheme consists of a finite horizon MPC technique with the introduction of an additional state constraint which we have denoted contractive constraint. This is a Lyapunov-based approach in which a Lyapunov function chosen a priori is decreased, not continuously, but discretely; it is allowed to increase at other times (between prediction horizons). We will show \r\nin this work that the implementation of this additional constraint into the on-line optimization makes it possible to prove rather strong stability properties of the closed-loop system. In the nominal case and in the absence of disturbances, it is possible to show that the presence of the contractive constraint renders the closed-loop system exponentially stable. We will also examine how the stability properties weaken as structural and/or parametric model/plant mismatch, disturbances and measurement noise are considered.
\r\n\r\nAnother important aspect considered in this work is the computational efficiency and implement ability of the algorithms proposed. The MPC schemes previously proposed in the literature which are able to guarantee stability of the closed-loop system involve the solution of a nonlinear programming problem at each time step in order to find the optimal (or, at least, feasible) control sequence. Nonlinear programming is the general case in which both the objective and constraint functions may be non-linear, and is the most difficult of the smooth optimization problems.
\r\n\r\nDue to the difficulties inherent to solving nonlinear programming problems and since MPC requires the optimal (or feasible) solution to be computed on-line, it is important that an alternative implementation be found which guarantees that the problem can be solved in a finite number of steps. It is well-known that both linear and quadratic programming (QP) problems satisfy this requirement.
\r\n\r\nIf a standard quadratic objective function is used and the input/state constraints are linear in the decision variables, then the contractive constraint (which is originally a quadratic constraint) can be implemented in such a way that the optimization problem to be solved in the prediction step of the MPC algorithm is reduced to a QP. Having linear input/state constraints means that a linear approximation of the original nonlinear system has to be used in the prediction as well as in the computation of the contractive constraint. Thus, in order to make the algorithm more easily implementable we introduce the difficulty of having to handle the mismatch between the real nonlinear system and its linear approximation which is used for prediction. In other words, we now have a robust MPC control problem at hand. In this case, it is the contractive constraint which comes to the rescue and allows the MPC controller to stabilize the closed-loop system spite of the linear/nonlinear mismatch, for certain choices of the contractive parameter (the parameter which defines how much \"shrinkage\" of the states is required during one prediction horizon).
\r\n\r\nIn summary, this thesis is an application of contractive principles to model predictive control and it is dedicated to robust stability analysis, design and implementation of state and output feedback \"contractive\" MPC schemes.
\r\n" }, { "name": "Figl, Antonio", "degree": "PhD", "year": "1996", "title": "Structure-Function Analysis of the \u03b2 Subunit of Neuronal Nicotinic Acetylcholine Receptors", "advisor": "Lester, Henry A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11072019-170728389", "creators": [ { "name": { "family": "Figl", "given": "Antonio" }, "id": "Figl-Antonio", "display_name": "Figl, Antonio" } ], "advisors": [ { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "advisor", "display_name": "Lester, Henry A." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "role": "member", "display_name": "Lester, Henry A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e390-k051", "abstract": "Nicotinic receptors belong to the superfamily of ligand-gated ion channels. Since evidence was rapidly accumulating implicating the non-\u03b1 subunits in ligand-binding events, we decided to investigate eventual contributions of the neuronal \u03b2 subunit to these events by performing a series of increasingly detailed experiments on a series of chimeric \u03b2 subunits. In the first set of experiments, we constructed a variety of chimeric \u03b2 subunits consisting of NH2-terminal neuronal \u03b24 sequences and COOH-terminal \u03b22 sequences and expressed them with the \u03b13 subunit in Xenopus oocytes. The results showed that (a) two residues in the extracellular domain of chimeric \u03b24\u2022\u03b22 subunits (108\u03b22Phe\u2194\u03b24Val, 110\u03b22Ser\u2194\u03b24Thr) account for much of the relative cytisine sensitivity; and (b) four extracellular residues of chimeric \u03b24\u2022\u03b22 subunits (112\u03b22Ala\u2194\u03b24Val, 113\u03b22Val\u2194\u03b24Ile and 115\u03b22Ser\u2194\u03b24Arg, 116\u03b22Tyr\u2194\u03b24Ser) account for most of the relative tetramethylammonium sensitivity.
\r\n\r\nEncouraged by the above results, we continued our experiments with additional chimeras of the \u03b22 and \u03b24 neuronal nicotinic subunits to locate regions that contribute to differences between the acetylcholine dose-response relationships of \u03b13\u03b22 and \u03b13\u03b24 receptors. Substitutions within the first 120 residues convert the EC50 for ACh from one wild-type value to the other, suggesting that amino acids within the first 120 residues of \u03b22 and the corresponding region of \u03b24 contribute to an agonist binding site that bridges the \u03b1 and \u03b2 subunits in neuronal nicotinic receptors.
\r\n\r\nSince the EC50 phenotypes caused by the \u03b22 and \u03b24 subunits could be due to a difference in gating or binding properties, we attempted to unravel this question by performing voltage-jump relaxations for the series of neuronal nicotinic acetylcholine receptors we constructed previously. The chimeric \u03b24/\u03b22 subunits showed a transition in the concentration dependence of the relaxation rate constants in the region between residues 94 and 109, analogous to our previous observation with steady-state dose-response relationships. The data reinforce previous conclusions that the region between residues 94 and 109 on the \u03b2 subunit plays a role in binding agonist but also show that other regions of the receptor control gating kinetics subsequent to the binding step.
" }, { "name": "Forman, Jonathan Eric", "degree": "PhD", "year": "1996", "title": "Non-Covalent Interactions in Aqueous Media: Molecular Recognition Studies Through Circular Dichroism and Self-Assembly of Discrete Aggregates", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222020-175451626", "creators": [ { "name": { "family": "Forman", "given": "Jonathan Eric" }, "id": "Forman-Jonathan-Eric", "display_name": "Forman, Jonathan Eric" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ce8j-qk19", "abstract": "The application of circular dichroism (CD) spectroscopy to the study of molecular recognition phenomena in chiral water-soluble cyclophane hosts is described. The CD method produces results that complement and expand upon previous NMR studies. This includes allowing the measurement of larger binding constants by allowing studies to be carried out at lower concentrations.
\r\n\r\nUsing the excitonic chirality method, these studies have provided a means of assigning the absolute stereochemistry of the ethenoanthracene building blocks used in preparation of the hosts. This information, along with an x-ray structure of one of the cyclophane molecules, has provided important information concerning host structure. The x-ray structure and CD spectral changes observed on guest binding have also served to provide direct experimental evidence for binding conformations of the hosts.
\r\n\r\nThe chiral hosts have been shown to induce CD in achiral chromophoric guests. Analysis of this induced CD using INDO/S and coupled-oscillator calculations has provided valuable information concerning the conformations of the bound guest. These data complement information obtained in NMR studies (D values) and provide additional insights into the important factors that govern the binding event.
\r\n\r\nFinally, preliminary studies of self-assembling systems in aqueous media are reported. These studies employ etheno- and ethanoanthracene based structures designed to form aggregates with well defined order and discrete stoichiometries. These molecules are designed to aggregate through hydrophobic forces. The aggregate is kept from becoming a micelle using polar groups strategically placed to complement one another within the assembling structure.
" }, { "name": "Gerdy, James Joseph", "degree": "PhD", "year": "1996", "title": "Accurate Interatomic Potentials for Simulations", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-150813700", "creators": [ { "name": { "family": "Gerdy", "given": "James Joseph" }, "id": "Gerdy-James-Joseph", "display_name": "Gerdy, James Joseph" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/g2gs-kv14", "abstract": "This thesis develops a rational foundation for the application of long-range forces to atomistic simulations. This area has lagged behind the other components \r\nof simulations because of two factors. First, the nonbond forces are difficult to probe experimentally. There are only a few materials for which properties clearly \r\nand directly correlate with van der Waals forces (such as molecular crystals) and then some of these cases are not relevant to common modeling applications (e.g. the \r\nhydrogen van der Waals forces in H_(2(xtl)) to are different from those in hydrocarbons). Second, more than for valence force field terms, van der Waals forces are difficult to determine by calculation. The forces are weak and require a large number of basis functions per atom to treat properly.\r\n\r\nThis thesis contains a method which has optimized a level of ab initio calculation on small clusters in order to extract a van der Waals potential. The size of \r\nthe calculation is controlled by carefully optimizing the basis set. Moreover, unlike for previous calculations of this sort, it was recognized that the repulsive and attractive potentials (the monotonic potentials) which constitute the van der Waals potential can be calculated optimally with different basis sets, further accelerating the calculation for a given level of accuracy. Also the use of diffuse basis sets off of the atom centers is used here to make the basis sets more efficient. The method \r\nhas been optimized for the case of nitrogen because it is both a closed shell case and relatively common in simulations. What results is a computational method \r\nwhich produces pair potentials for use in force field simulations. This is called the combination of monotonic potentials (COMP) method.\r\n\r\nSubsequently, potentials have been calculated for the atoms H, He, C, N, 0, F, Ne, Si, P, S, Cl, and Ar. In order to test the accuracy, the potentials are \r\napplied to test cases of molecular crystals and compared to other commonly used potentials. Important issues that are addressed are standard combination rules and \r\nthe accuracy of using isotropic pair potentials. COMP potentials give a measure of accuracy of van der Waals potentials for any atom. This research has also yielded an\r\naccurate functional form, a variant of the Morse potential, which has not been used in simulations but provides very accurate fits to the ab initio data. The relationships between different functional forms are analyzed so that the designer of force fields can make a judicious choice of both ab initio calculations to determine potentials and the appropriate functions with which to fit them.\r\n" }, { "name": "Gupta, Vinay Kumar", "degree": "PhD", "year": "1996", "title": "Controlling molecular and microstructural alignment in anisotropic polymer systems", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12132007-085351", "creators": [ { "name": { "family": "Gupta", "given": "Vinay Kumar" }, "id": "Gupta-V-K", "display_name": "Gupta, Vinay Kumar" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xb3f-3a10", "abstract": "Molecular and microstructural orientation plays a key role in determining the useful mechanical, optical and electrical properties of a large class of polymeric materials. Realization of the technological promise of these materials requires rational control of the microstructure and understanding of the processing-structure-property relationships. Towards this end, we focus on the material properties and dynamical processes that affect molecular order of two complex polymeric systems (a) Ultra-thin Langmuir-Blodgett films of a hairy-rodlike polymer, and (b) Lamellar diblock copolymer melts of polystyrene and polyisoprene (PS-PI).\n\nWe accomplish our objective by improving and tying together existing analytic techniques into instruments extremely effective for measuring molecular orientation and order. For fundamental insights into the nature of alignment in ultra-thin (~ few nanometers thick) LB films, we integrate laser scanning microscopy (LSM) with polarization-modulation (PM) polarimetry. PM-LSM possesses high spatial resolution, sensitivity and speed, and allows us to image the anisotropy in films as thin as two molecular layers. To monitor the dynamics of flow alignment in diblock copolymers, in situ and in real time, we combine polarization-modulation polarimetry with rheometry. This rheo-optical technique enables us to monitor the evolution of microstructure by measuring the optical anisotropy, and correlate it with changes in macroscopic mechanical observables, such as stress and strain.\n\nUsing PM-LSM we have investigated the interplay of molecular weight, layer thickness and thermal annealing in controlling molecular order in rodlike polymer LB films. Upon investigating two different molecular weights of the polymer, we find lowering of molecular order in deposited films with increase in molecular weight. Furthermore, thermal annealing improves alignment only for films of shorter rodlike polymers (~ lower molecular weight). We believe that the underlying cause for these results is a difference in the structure of the deposited films for the longer polymer because of the relative changes in timescales for the macromolecular relaxation and the monolayer deformation during deposition. We also find that for both molecular weights, the substrate exerts an anchoring effect on the first two layers adjacent to it and suppresses improvement in alignment on annealing. This inability to improve alignment has important consequences for applications such as molecular electronics where monolayers or bilayers having a high degree of orientation are required.\n\nIn-situ measurement of flow birefringence during oscillatory shear alignment, clarifies the evolution of the lamellar orientation distribution for a diblock copolymer melt. Shearing results in \"parallel\" or \"perpendicular\" alignment i. e. layers normal to either the velocity gradient or the vorticity axis, respectively (Figure 1.1). Both states of alignment occur via an initial \"fast\" process followed by a \"slow\" one. The fast process is dominated by the depletion of the projection of the orientation distribution along either the perpendicular direction or the \"transverse\" direction (layers normal to the flow). This resulting biaxial distribution is then transformed into a well-aligned uniaxial one during the slow process. Surprisingly, at particular frequencies, the projection along the perpendicular direction can disappear faster than the projection along the transverse direction. In both the fast and the slow processes the time evolution of birefringence follows a highly non-linear scaling with strain; the scaling being different for the fast and slow processes. A systematic study of the effects of strain on shear alignment in block copolymers led to the discovery that strain affects not only the dynamics of alignment, but also the direction. This phenomenon expands the range of parameters that can be used to flip the direction of alignment. In relation to previous studies that examined the regimes of alignment only in terms of temperature and frequency, this phenomenon necessitates consideration of a third dimension - strain." }, { "name": "Hendrickson, Tamara Lynn", "degree": "PhD", "year": "1996", "title": "Insights into the Mechanism of Asparagine-Linked Glycosylation: Kinetic Studies with Substrates and Inhibitors", "advisor": "Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechTHESIS:12222020-184114663", "creators": [ { "name": { "family": "Hendrickson", "given": "Tamara Lynn" }, "id": "Hendrickson-Tamara-Lynn", "display_name": "Hendrickson, Tamara Lynn" } ], "advisors": [ { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5cca-3495", "abstract": "Investigations into the mechanism of action of oligosaccharyl transferase (OT), the enzyme that catalyzes the first committed step in the biosynthesis of all asparagine-linked glycoproteins, were conducted. Research focused on kinetic studies with small reactive molecules and tripeptide substrates and inhibitors; these experiments were designed to specifically probe the OT active site. Commercially available chemical modification agents were used to identify a reactive cysteine residue in or near the oligosaccharide binding site. Based on this observation, a novel biotinylated sufhydryl modification reagent, methyl N-biotinoyl(aminoethane)thiolsulfonate (BMTS), was developed. BMTS selectively modified the Wbp1p subunit of OT, thereby identifying this subunit as the site of the reactive cysteine and all or part of the oligosaccharide binding site.
\r\n\r\nThe role of the required divalent metal cofactor was examined through a series of parallel kinetic experiments on two substrates for OT: the asparagine-containing tripeptide Bz-Asn-Leu-Thr-NHMe and the corresponding thioasparagine tripeptide Bz-Asn(\u03b3S)-Leu-Thr-NHMe. These substrates were evaluated with OT which had been treated to remove metal and independently reconstituted with four different metal cations. The sizes and thiophilicities of the metal cations had a different, but direct impact on the kinetic behavior of each of the two peptides. These results place the metal cofactor in proximity to the peptide substrate during catalysis and suggest that it may play a direct mechanistic role. In addition, a detailed analysis of the glycopeptide product of the thioasparagine tripeptide suggests that OT plays a specific role in directing the regiochemistry of asparagine glycosylation.
\r\n\r\nThrough an iterative process, a new class of competitive inhibitors for OT was designed which exhibit nanomolar binding constants and are the first reported potent inhibitors for OT. The slow, tight binding inhibition observed with these peptides suggests that they may mimic the transition state of the glycosylation reaction. Nine irreversible peptidyl inactivators for OT were also evaluated; these affinity labels were designed to probe the peptide binding site of the enzyme. Based on the results with these inactivators, a proposal for the design of more potent affinity labels for OT is presented.
" }, { "name": "Herek, Jennifer Lynn", "degree": "PhD", "year": "1996", "title": "Femtochemistry and reactive intermediates : application to atmospheric and organic chemistry", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04082008-084916", "creators": [ { "name": { "family": "Herek", "given": "Jennifer Lynn" }, "id": "Herek-J-L", "display_name": "Herek, Jennifer Lynn" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qj6m-w225", "abstract": "The logical sequence of primary steps in a reaction mechanism is governed by the reactive intermediates which are postulated to ensure smooth transformations between stable species. Historically, such constructs were merely hypothetical as their (assumed) extreme reactivity and/or unstable nature precluded their observation. The introduction of femtosecond lasers to chemistry has allowed insight and understanding to many fundamental processes in reaction dynamics. This thesis presents applications of femtosecond spectroscopy to atmospheric and organic chemistry, specifically probing the reactive intermediates mediating various chemical transformations. Direct observation of these fleeting species can validate previously proposed mechanisms as well as offer new perspectives to their reaction dynamics.\r\n\r\nStudies of diradicals, the molecular species hypothesized to be archetypal of chemical bond transformations in many reactions in organic chemistry, have been made using femtosecond laser techniques combined with mass spectrometry in a molecular beam. Evolution of the diradical intermediate is monitored in real time throughout the course of the chemical reaction. These studies offer the first direct evidence of singlet 1,3- and 1,4-diradicals.\r\n\r\nHydrogen-atom transfer processes are fundamental to many reactions in organic chemistry. The dynamics of the motion may be localized, with little nuclear motion aside from the H-atom transfer between two \"anchors,\" or may be global, involving a multidimensional potential. Using methyl salicylate as a prototype system, direct studies of the nuclear motion in this important transformation are made with femtosecond resolution.\r\n\r\nMany reactive intermediates have been linked to stratospheric ozone depletion in recent years. In particular, catalytic cycles involving halogens are considered critical to establishing the overall mechanism for ozone depletion. Direct studies of the photochemically-activated dissociation of key species in atmospheric chemistry can offer insight to the global dynamics by providing important rate constants and branching ratios. Femtosecond reaction dynamics of OClO in a supersonic molecular beam are reported. The observations reveal the nuclear motions and couplings between potential energy surfaces relevant to the dissociation process. Comparisons with results of ab initio calculations are made.\r\n" }, { "name": "Hochemer, Ralf H.", "degree": "PhD", "year": "1996", "title": "Degradation of organic compounds by acoustic cavitation and pulsed-power discharges", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06262006-111213", "creators": [ { "name": { "family": "Hochemer", "given": "Ralf H." }, "id": "Hochemer-R-H", "display_name": "Hochemer, Ralf H." } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3tyz-e528", "abstract": "The exposure of organic chemical compounds to acoustically induced cavitation under various conditions in aqueous solution is studied. Emphasis is given to the degradation of undesired chemical compounds present at relatively low concentration.\n\nThe hydrolysis rate of p-nitrophenylacetate is enhanced in sonicated solution when compared to the reaction under ambient conditions. This rate enhancement is ascribed to the transient existence of supercritical water in sonicated aqueous solutions.\n\nThe degradation rate of 2,4,6-trinitrotoluene is shown to depend on the ultrasonic frequency and the nature of the background gas. Degradation products include nitrite, nitrate, carbon dioxide, and short-chain organic acids.\n\nUltrasonic irradiation of a mixture of nitro- and aminoaromatic compounds leads to competition of the substrates for reactive sites and rates of degradation scale with the electron density of the aromatic ring.\n\nThe near-field parallel-plate acoustical processor is investigated as an example of large-scale treatment a of dilute waste stream. Energy density and intensity have a pronounced effect on the overall degradation rate of p-nitrophenol. Most notably, the maximum reaction rate is found to be at an energy intensity of 1.2 W cm-2. Higher intensities decrease the rate due to decoupling of the reaction mixture from the vibrating surface.\n\nElectrical underwater discharges at relatively low electrical field strengths exhibit two distinct phases: the pre-breakdown, or initiation period, and the actual discharge itself. The length of the initiation period, the slope of the voltage transient, and the absolute and relative energy losses during initiation are investigated as a function of the electrical conductivity and temperature under various circuit parameters.\n\nThe temperature of the plasma-arc occurring during an electrical underwater discharge is estimated to be (9000 \u00b1 300) K." }, { "name": "Irion, Fredrick W.", "degree": "PhD", "year": "1996", "title": "Analyses of atmospheric CHF2Cl, heavy ozone, HDO and CH3D from ATMOS spectra", "advisor": "Yung, Yuk L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-115456", "creators": [ { "name": { "family": "Irion", "given": "Fredrick W." }, "id": "Irion-F-W", "display_name": "Irion, Fredrick W." } ], "advisors": [ { "name": { "family": "Yung", "given": "Yuk L." }, "id": "Yung-Y-L", "role": "advisor", "display_name": "Yung, Yuk L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/wn9a-7w35", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nMixing ratio measurements of tropospheric CHF2C1 and stratospheric heavy ozone ([...] and [...]), HDO and CH3D were derived from Atmospheric Trace Molecule Spectroscopy Experiment (ATMOS) spectra. The ATMOS instrument is a 0.01 cm-1 resolution, solar-absorption Fourier-transform spectrometer with a frequency response of 600-4800 cm-1 in the mid-infrared. It has recorded ground-based spectra over Table Mountain Facility (TMF), Wrightwood CA (34.4\u00b0N, 117.7\u00b0W, 2.2 km altitude) between 1985 to 1990, and space-based measurements during the four shuttle missions Spacelab 3 (April/May 1985), ATLAS-1 (March, 1992), ATLAS-2 (April, 1993) and ATLAS-3 (November, 1994).\n\nThe measured column burden of CHF2C1 over TMF showed an exponential increase rate of (6.7\u00b10.5)% yr-1 from October, 1985 to July, 1990. The current uncertainty in historical CHF2C1 emissions was found to be too large for CHF2C1 measurements to be used to infer adequately either its lifetime or the OH field. \n\nEnrichments of heavy ozone (with respect to [...]) were measured from both space and ground-based observations. Average enrichments between 26 to 2.6 mb inclusive to 41 km) were (15\u00b16)% for [...], (10\u00b17)% for [...], and (13\u00b15)% for [...] ([...] standard deviation). Enrichments increased slightly with altitude, but with no discernable latitudinal variability. From TMF, an average total column [...] enrichment of (17\u00b14)% ([\u2026] standard deviation) was determined, with no discernable seasonal variation. Possible biases in the spectral intensities that affect the determination of absolute enrichments are discussed, but any corrections to these intensities would not affect the observed lack of latitudinal and seasonal variability.\n\nFrom space-based measurements, stratospheric mixing ratios of [...] from 100 mb to 17mb ([...] to 28 km) and HDO from 100 mb to 10 mb ([...] to 32 km) were inferred. The average lifetime of [...]was found to be (1.19\u00b10.02) times that of [...], with an average of (1.0\u00b10.1) molecules of stratospheric HDO produced for each [...] destroyed ([...] combined precision and systematic error), indicating that the rate of stratospheric HDO production is approximately equal to the rate of [...] destruction.\n" }, { "name": "Jenkins, Yonchu", "degree": "PhD", "year": "1996", "title": "Dipyridophenazine Complexes of Ruthenium(II) as Luminescent Reporters of DNA", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11082019-094749072", "creators": [ { "name": { "family": "Jenkins", "given": "Yonchu" }, "id": "Jenkins-Yonchu", "display_name": "Jenkins, Yonchu" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/n4jx-hp63", "abstract": "The search for novel diagnostics for DNA detection has generated interest in the potential applications of polypyridyl complexes of ruthenium(II). Recently, it was reported that dipyridophenazine complexes of ruthenium(II) may serve as molecular light switches for DNA. These complexes, which bind DNA avidly through intercalation, show no luminescence in aqueous solutions. Upon intercalation into double-helical DNA and the concomitant protection of the phenazine ring from quenching by interaction with water, intense photoluminescence is apparent. The light switch effect as a function of nucleic acid sequence and conformation was examined for [Ru(phen)2dppz]2+ and [Ru(bpy)2dppz]2+. The emission properties of these complexes were found to be extremely sensitive to the nature of the intercalation environment with strong correlations between the luminescence parameters and the level of water protection afforded by the double helix. In order to impart sequence specificity to the light switch effect, various methods have been developed for appending a functionalized [Ru(phen)2dppz]2+ to the 5' terminus of oligonucleotides, both on the solid support and in solution. Assays for analyzing the structural integrity of the resulting conjugates are described. These ruthenated oligonucleotides can serve as enzyme substrates, enabling the construction of long metalated oligonucleotides not easily prepared using chemical synthesis. In order to evaluate their utility as useful DNA diagnostics, a series of ruthenated oligonucleotides were synthesized and their photophysical properties characterized. Biochemical analysis of oligonucleotide duplexes containing ruthenated strands showed no significant structural perturbation of the duplex as a result of the ruthenium modification. The overall results of this investigation suggest that an oligonucleotide functionalized with a dppz complex of ruthenium may be used to target single-stranded DNA in a sequence-specific fashion and that this derivative could be extremely valuable in the development of novel hybridization probes for both heterogeneous and homogeneous assays.
" }, { "name": "Johnson, Matthew Stanley", "degree": "PhD", "year": "1996", "title": "Spectroscopy of Reactive Molecules and Clusters", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202020-161109407", "creators": [ { "name": { "family": "Johnson", "given": "Matthew Stanley" }, "id": "Johnson-Matthew-Stanley", "display_name": "Johnson, Matthew Stanley" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ta23-4185", "abstract": "This thesis presents spectroscopic investigations of reactive molecules and clusters. The techniques of laser excited fluorescence, infrared predissociation spectroscopy, and photoelectron spectroscopy were employed to investigate systems relating to fundamental cluster chemistry, ion solvation, and atmospheric ozone depletion.
\r\n\r\nAn instrument was developed to investigate van der Waals complexes of refractory elements. A pulsed laser ablation cluster source harnessed the cooling power of a supersonic free jet to condense weakly bound neutral clusters. Laser excited fluorescence was used to characterize the products of the source, which included adducts of aluminum atoms with water molecules, hydrogen, and argon. The species Al(H\u2082O), AlAr and AlH were identified.
\r\n\r\nThe infrared predissociation spectra of positive and negative cluster ions were investigated using a tandem time-of-flight instrument. In this work the photofragment yield spectrum of mass-selected I\u207b(H\u2082O) and I\u207b(H\u2082O)\u2082 complexes was measured between 3170 and 3800 cm\u207b\u00b9. The dominant features in the I\u207b(H\u2082O) spectra were assigned as a hydrogen bonded OH stretch and a free OH stretch. Ab initio calculations were used to aid in spectral assignment and for geometrical information concerning I\u207b(H\u2082O). Absorptions in the iodide water dimer cluster are attributed to a symmetric and an antisymmetric bonded OH stretch, and a free OH stretch.
\r\n\r\nChlorine nitrate is a key reservoir of stratospheric chlorine, and as such its photolysis branching ratio is crucial to partitioning of species involved with stratospheric ozone depletion. The He(I) photoelectron spectrum of chlorine nitrate was measured and assigned in order to understand the photodissociation behavior of chlorine nitrate. The results include the ionization potential of the molecule (10.86 eV), and the assignment of the first ionization peak to a nonbonding chlorine atomic orbital.
" }, { "name": "Kelly, James J.", "degree": "PhD", "year": "1996", "title": "Binding site size limitations of imidazole-pyrrole polyamides for recognition in the minor groove of DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112014-150124711", "creators": [ { "name": { "family": "Kelly", "given": "James J." }, "id": "Kelly-J-J", "display_name": "Kelly, James J." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jc2t-pr07", "abstract": "The discovery that the three ring polyamide Im-Py-Py-Dp containing imidazole\r\n(Im) and pyrrole (Py) carboxamides binds the DNA sequence 5'-(A,T)G(A,T)C(A,T)-3'\r\nas an antiparallel dimer offers a new model for the design of ligands for specific\r\nrecognition of sequences in the minor groove containing both G,C and A,T base pairs. In\r\nChapter 2, experiments are described in which the sequential addition of five N-\r\nmethylpyrrolecarboxamides to the imidazole-pyrrole polyamide Im-Py-Py-Dp affords a\r\nseries of six homologous polyamides, Im-(Py)2-7-Dp, that differ in the size of their binding\r\nsite, apparent first order binding affinity, and sequence specificity. These results\r\ndemonstrate that DNA sequences up to nine base pairs in length can be specifically\r\nrecognized by imidazole-pyrrole polyamides containing three to seven rings by 2:1\r\npolyamide-DNA complex formation in the minor groove. Recognition of a nine base pair\r\nsite defines the new lower limit of the binding site size that can be recognized by\r\npolyamides containing exclusively imidazole and pyrrolecarboxamides. The results of this\r\nstudy should provide useful guidelines for the design of new polyamides that bind longer\r\nDNA sites with enhanced affinity and specificity.
\r\n\r\nIn Chapter 3 the design and synthesis of the hairpin polyamide Im-Py-Im-Py-\u03b3-Im-\r\nPy-Im-Py-Dp is described. Quantitative DNase I footprint titration experiments reveal\r\nthat Im-Py-Im-Py-\u03b3-Im-Py-Im-Py-Dp binds six base pair 5'-(A,T)GCGC(A,T)-3'\r\nsequences with 30-fold higher affinity than the unlinked polyamide Im-Py-Im-Py-Dp. The\r\nhairpin polyamide does not discriminate between A\u2022T and T\u2022A at the first and sixth\r\npositions of the binding site as three sites 5'-TGCGCT-3', 5'-TGCGCA-3', and 5 'AGCGCT-\r\n3' are bound with similar affinity. However, Im-Py-Im-Py-\u03b3-Im-Py-Im-PyDp\r\nis specific for and discriminates between G\u2022C and C\u2022G base pairs in the 5'-GCGC-3'\r\ncore as evidenced by lower affinities for the mismatched sites 5'-AACGCA-3', 5'-\r\nTGCGTT-3', 5'-TGCGGT-3', and 5'-ACCGCT-3'.
\r\n\r\nIn Chapter 4, experiments are described in which a kinetically stable hexa-aza\r\nSchiff base La3+ complex is covalently attached to a Tat(49-72) peptide which has been\r\nshown to bind the HIV-1 TAR RNA sequence. Although these metallo-peptides cleave\r\nTAR site-specifically in the hexanucleotide loop to afford products consistent with\r\nhydrolysis, a series of control experiments suggests that the observed cleavage is not\r\ncaused by a sequence-specifically bound Tat(49-72)-La(L)3+ peptide.
" }, { "name": "Lewis, John Edwin", "degree": "PhD", "year": "1996", "title": "Characterization and permeation studies on oriented single-crystal ferrierite membranes", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01042008-112721", "creators": [ { "name": { "family": "Lewis", "given": "John Edwin" }, "id": "Lewis-J-Ed", "display_name": "Lewis, John Edwin" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jcyz-xr37", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nSingle-crystals (up to 650 x 550 x 20 [...]) of highly silicious ferrierite (Si-FER, 1), suitable for single-crystal X-ray investigations, are synthesized under organothermal conditions. The structures of the as-synthesized (1a) and the calcined (1b) Si-FER are determined at room temperature. Both structures are refined in the orthorhombic space group Pnnm (No.58, standard setting) with a = 743.0(1), b = 1409.2(2), c = 1882.0(2)pm, V = 1970.5(4)[...], Z = 1,R = 0.041 (la) and a = 741.8(1), b = 1407.0(2), c = 1871.3(2) pm, V = 1953.1(5)[...], Z = 1, R = 0.037 (lb). The structure solution when combined with chemical analysis and [...] and [...] MAS NMR, give a unit cell content of [...] (x = 0 - 1, py = pyridine, ap = 1-amino-n-propane) and [...] for 1a and 1b, respectively. The structure of 1a shows only weak host-guest interactions between the [...] framework and the occluded, orientationally disordered pyridine molecules by means of relatively long organic-to-framework distances,d[...] [...] 354(2) pm. [...] MAS NMR spectra from the organic-containing Si-FER 1a and the organic-free form 1b are in good agreement with the crystallographic results in that they conform to the well-known linear relationship between the cosine expression of the T-O-T angles and the chemical shift of the respective tetrahedral sites (T-sites). A new modification of this relationship is presented here and offers an improved linear correlation between the X-ray and NMR data for 1a and 1b, as well as for other high-silica microporous materials. Application of this new correlation to denser SiO2 compounds is discussed.\r\n\r\nSelected individual crystals of the calcined Si-FER are mounted in a membrane configuration so that only the 10-membered ring channels (5.4 [...] x 5.4 [...] x 4.2 [...]) or the 8-membered ring channels (4.6 [...] x 3.7 [...] x 3.0 [...]) are accessible for gas molecule permeation. The first examples of transport exclusively through 8- or 10-membered ring channel systems are reported and obtained through crystal orientation in the membrane. A series of adsorption experiments are conducted in order to assist the selection of suitable probe molecules and evaluate the role of adsorption in the permeation process for the single-crystal membranes. Methane, n-butane, isobutane and nitrogen probe molecules are used to study intracrystalline sorption and transport effects for different crystal orientations, pressures and temperatures. Both pure gas selectivities and mixed gas separation factors are reported. A mixed gas separation factor of n-butane/isobutane = 116 for the 10-membered ring orientation of the crystal at 383 K and a transmembrane pressure difference of 1.01 x [...] Pa is found using this technique. In addition, molecular sieving is observed for the 8-membered ring orientation of the crystal since methane, but not butane, transport is observed for this crystal orientation.\r\n" }, { "name": "Marohn, John Aaron", "degree": "PhD", "year": "1996", "title": "I. Multiple-pulse radio-frequency gradient nuclear magnetic resonance imaging of solids ; II. Optical nuclear magnetic resonance analysis of epitaxial gallium arsenide structures", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02242011-083555306", "creators": [ { "name": { "family": "Marohn", "given": "John Aaron" }, "id": "Marohn-J-A", "display_name": "Marohn, John Aaron" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PDK5-7T44", "abstract": "This dissertation details two techniques for materials analysis by nuclear magnetic resonance.\r\nThe first is a general strategy for recording spin density maps from solids through improved nuclear\r\nmagnetic resonance imaging. The second involves ultrasensitive methods for detecting nuclear magnetic\r\nresonance optically and is applicable to semiconductors at low temperature.\r\nConventional liquids magnetic resonance imaging (MRJ) protocols fail in solids, where rapid\r\nlocal-field dephasing of nuclear magnetization precludes the frequency encoding of spatial information\r\nwith conventional magnetic field gradients. In our approach, a multiple-pulse line-narrowing sequence is\r\ndelivered with a solenoid coil to prolong a solid's effective transverse relaxation time. A radiofrequency\r\ngradient coil, delivering resonant pulses whose amplitude varies across the sample, is driven in concert\r\nwith the line-narrowing coil to encode spatial information. The practical implementation of this protocol\r\ndemanded the construction of an active Q-spoiling circuit to negate coupling of the two isoresonant coils.\r\nTwo-dimensional Fourier-zeugmatographic images of hexamethylbenzene have been obtained that exhibit\r\n300 \u00b5m x 300 \u00b5m planar resolution. This imaging protocol is one of the highest sensitivity methods for\r\nimaging solids by NMR (the other involves line narrowing and pulsed DC gradients).\r\nExtraordinary increases in detection sensitivity are required for NMR to study epitaxial\r\nsemiconductor devices. Optical pumping is one route to such increased sensitivity. Here, a transfer of\r\nangular momentum from polarized light to electrons (via selection rules), and electrons to nuclei (through\r\nhyperfine couplings), can result in > 10 % nuclear spin polarization in less than 5 seconds at 2 K. A total\r\nsensitivity gain of 10^5 follows by detecting this large polarization optically, through the inverse process,\r\nallowing collection of the NMR spectra for several GaAs-based epitaxial devices. Previous workers\r\nobserved these spectra to be either power-broadened at the rf levels required to induce optical response, or\r\ndistorted due to the presence of photocarriers during optical detection. An innovation of the Weitekamp\r\ngroup was to time-sequence and separately optimize the periods of optical pumping, NMR evolution, and\r\noptical detection. Although time sequencing in principle allows the collection of multiple-pulse high-resolution\r\nNMR spectra, it appeared inadequate when applied to a semiconductors heterojunction.\r\nIn conventional NMR, the entire dipole-allowed spectrum may be collected following a single\r\npulse. In time-sequenced optical NMR however, the desired interferogram must be built up pointwise by\r\nrepetitively incrementing an evolution time. Although sensitive, this experiment is time consuming and\r\nsensitive to drift. A new optical detection protocol has been developed which removes these problems and\r\nallows NMR spectra to be collected optically in real tillle. In this experiment, a circularly polarized\r\nreference nuclear hyperfine field is introduced during the precession of a signal field. The observed\r\nluminescence polarization is sensitive to the instantaneous vector sum of the fields, producing Larmor\r\nbeats. With the reference magnetization in equilibrium through the use of either continuous irradiation or\r\na pulsed spin-lock, the oscillation of luminescence polarization at the Larmor beat frequency is able to\r\nrecord the spectrum of the signal nucleus alone.\r\nA spectrometer has been constructed for implementing both time-sequenced and Larmer-beat\r\noptical detection of NMR. In order to implement rotation studies in a way compatible with optical\r\ndetection at 2K, variable-angle Helmholtz coils have been added to the apparatus so that the direction of\r\nthe static field can be varied. The results of preliminary rotation studies put a surprisingly low upper\r\nbound on the electric fields present at the most rapidly polarizable sites in a AlGaAs/GaAs heterojunction.\r\nThis can be understood in terms of a model where these sites are neutral donors at locations where the\r\nbuilt-in interfacial electric field has fallen off." }, { "name": "Martin, Scot Turnbull", "degree": "PhD", "year": "1996", "title": "Photocatalyzed Destruction of Chlorinated Hydrocarbons", "advisor": "Hoffmann, Michael R.; Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12092020-003246663", "creators": [ { "name": { "family": "Martin", "given": "Scot Turnbull" }, "id": "Martin-Scot-Turnbull Martin", "orcid": "0000-0002-8996-7554", "display_name": "Martin, Scot Turnbull" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/597h-8896", "abstract": "Semiconductor photocatalysis with a primary focus on TiO\u2082 as a durable photocatalyst has been applied as a method for water and air purification. In this thesis, the basic electronic and chemical processes underlying the quantum efficiencies of the TiO\u2082/UV process are investigated.
\r\n\r\nTime-resolved microwave conductivity experiments provide the recombination lifetimes and interfacial charge transfer rate constants of eight different TiO\u2082 catalysts. Their quantum efficiencies towards the photooxidation of chlorinated hydrocarbons vary from 0.04 to 0.44%. A direct correlation between (1) the quantum efficiencies and (2) the recombination lifetimes and the interfacial charge transfer rate constants is observed.
\r\n\r\nThe charge-carrier recombination rate in size-quantized particles ( 1-4 nm) is increased due to the mixing of states that relaxes the selections rules of an indirect bandgap semiconductor.
\r\n\r\nThe effects of protonation (i.e., pH 7-12) of amphoteric ZnO surface states on cross-sections for electron capture at the surface are studied by time-resolved radio frequency conductivity. Electrostatic repulsion due to a negatively-charged ZnO-surface leads to decreasing surf ace recombination rates with increasing pH.
\r\n\r\nVanadium doped into TiO\u2082 affects the quantum efficiency. Depending on the preparation method, vanadium plays three distinct roles. First, vanadium is present as surficial > VO\u2082\u207a and promotes charge-carrier recombination through electron-trapping\r\nfollowed by hole elimination. Second, V(IV) impurities in surficial V\u2082O\u2085 islands result in enhanced charge-carrier recombination through hole-trapping followed by electron elimination. Third, V(IV) is substitutional in the TiO\u2082 lattice in the form of a solid solution, V\u2093 Ti\u2081\u208b\u2093O\u2082. The V(IV) centers trap both electrons and holes and thus yield enhanced charge-carrier recombination.
\r\n\r\nThe addition of inorganic oxidants such as HSO\u2085\u207b, ClO\u2083\u207b, IO\u2084\u207b, and BrO\u2083\u207b increases the quantum efficiency. BrO\u2083\u207b acts by scavenging conduction-band electrons and reducing charge-carrier recombination. When ClO\u2083\u207b is present, however, competitive adsorption for the TiO\u2082 surface occurs among 4-CP, ClO\u2083\u207b, and O\u2082, and the heterogeneous photodegradation of 4-chlorophenol follows three parallel pathways. ClO\u2083\u207b favors a reaction pathway involving the thermal oxidation of the reactive intermediates.
" }, { "name": "Mislick, Kimberly Ann", "degree": "PhD", "year": "1996", "title": "The role of proteoglycans in the delivery of cationic-DNA complexes and enhanced delivery by folate receptor-mediated endocytosis", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182006-152253", "creators": [ { "name": { "family": "Mislick", "given": "Kimberly Ann" }, "id": "Mislick-K-A", "display_name": "Mislick, Kimberly Ann" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7yx4-gh95", "abstract": "Experiments were conducted to elucidate the mechanisms of polylysine-mediated transfection into mammalian cells in vitro. In the first chapter, the role of membrane-associated proteoglycans in transfection was investigated by testing transfection efficiency under a number of assay conditions. Cells were treated with sodium chlorate in order to desulfate glycosaminoglycan chains. Chlorate treatment inhibited expression of luciferase, the intracellular uptake of DNA, and binding of DNA to the cell surface. Expression, uptake, and binding of DNA was also inhibited by exogenous glycosaminoglycans and by glycosaminoglycan lyases. Similarly, each of the transfection steps was severely inhibited in CHO cell mutants, incapable of synthesizing proteoglycans. Transfection by certain cationic liposomes was also inhibited in the mutant cell line. The possible implications of these results for gene therapy of diseases affecting hematopoietic cells is described. In the second chapter, polylysine-mediated gene delivery via the folate receptor was developed. Gene delivery by folate receptor-mediated endocytosis was approximately 18 times higher than by nonspecific endocytosis of polylysine-DNA in the presence of chloroquine. A number of controls confirmed that the folate receptor was critical in the gene delivery mechanism. When chloroquine was removed from the media, transfection efficiency dropped approximately 30 fold, suggesting that gene delivery occurred via a lysosomal pathway. In the final chapter, transfection by folate receptor-mediated endocytosis was characterized by 2-photon laser scanning microscopy. KB cells were transfected with folate-polylysine-DNA complexes labeled with YOYO, a dimeric cyanine intercalator, and a single cell was examined over a two hour period. Although additional controls are required, preliminary evidence suggests that mitosis is not a strict requirement for delivery of DNA into the nucleus of cells." }, { "name": "Mizoguchi, Tadashi Jack", "degree": "PhD", "year": "1996", "title": "Probing the role of the active-site Cysteine of Azurin by site-directed mutagenesis", "advisor": "Gray, Harry B.; Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01162009-111204", "creators": [ { "name": { "family": "Mizoguchi", "given": "Tadashi Jack" }, "id": "Mizoguchi-T-J", "display_name": "Mizoguchi, Tadashi Jack" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4VTZ-PE72", "abstract": "The coordination chemistry and electron-transfer properties of a single-site mutant of the mononuclear copper electron-transfer protein azurin from Pseudomonas aeruginosa have been studied. The active-site cysteine at position 112 was replaced by an aspartate (Cys112Asp) to assess directly the importance of this ligand to the structure-function properties of azurin. Although the mutant protein retains a high-affinity copper-binding active site, the absorption and EPR spectra of Cu[superscript II]Cys112Asp azurin are quite distinct from those of the wild-type protein and indicate the presence of a normal (type 2) copper center. A Cu[superscript II/I] reduction potential of 180 mV vs. NHE (pH 7.0) was obtained through a redox titration experiment with cytochrome c[subscript 551]. The Co[superscript II] derivative of Cys112Asp azurin was prepared and found to be amenable to paramagnetic NMR spectroscopy. In conjunction with electronic absorption data, the NMR data were used to generate a computer model of the Co[superscript II] active-site structure in which the metal is coordinated by two histidines (His46 and His 117), a polypeptide backbone carbonyl oxygen (of Gly 45), and an out-of-plane, asymmetrically-bound bidentate aspartate (Asp 112) in an overall distorted square pyramidal geometry. The 2.4-\u00c5 resolution X-ray crystal structure of Cu[superscript II] Cys112Asp azurin is reported and confirms this ligand set and geometry. Ni[superscript II]-substituted Cys112Asp azurin was also made, but unlike Cu[superscript II] and Co[superscript II], the Ni[superscript II] ion is much less tightly bound by the protein. The electronic spectroscopy of Ni[superscript II] Cys112Asp azurin suggests the existence of some bonding interaction with the thioether sulfur atom of Met121. In contrast to Cys112-containing azurins, laser-induced intramolecular electron-transfer reactions from the reduced copper center of Asp 112-containing azurins to surface histidine-bound bis(bipyridy1)(imidazole) ruthenium(III) labels could not be observed. However, the kinetics of intermolecular protein-protein electron transfer between Cys112Asp and wild-type azurins were recorded by stopped-flow spectrophotometry. Analysis of the bimolecular kinetic data suggests that the Cys-to-Asp mutation has diminished significantly the electronic coupling between the copper and ruthenium centers in the intramolecular electron-transfer systems.\n" }, { "name": "Moore, Jeffrey Charles", "degree": "PhD", "year": "1996", "title": "Tailoring enzyme catalysts by directed evolution", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12222007-113626", "creators": [ { "name": { "family": "Moore", "given": "Jeffrey Charles" }, "id": "Moore-J-C", "display_name": "Moore, Jeffrey Charles" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/szy1-1e40", "abstract": "Directed evolution provides a nature-inspired methodology for the improvement of macromolecular properties. By imitating processes attributed to natural evolution, we have been able to improve an enzyme's activity against a desired substrate. Four rounds of random mutagenesis and screening have led to a p-nitrobenzyl (pNB) esterase with 16-fold improvement in catalytic turnover, 25-fold improvement in catalytic efficiency, and 30-fold improvement in total activity. An extensive library was screened during the fourth generation of random mutagenesis and screening which generated several clones more active than the third generation parent. These clones were recombined in a fifth generation using two techniques similar to that of recombination. A partial sampling of the resulting population contained individuals demonstrating activity two to four-fold higher than the most active variant from the fourth generation, making the total activity improvements greater than 100-fold. The mutations found to increase pNB esterase's activity in this directed evolution experiment were mapped onto a structural model. None of the effective amino acid substitutions lie in segments of the enzyme predicted to interact directly with the bound substrate. To predict in advance that these substitutions enhance pNB esterase activity would be practically impossible.\n\nSexual recombination provides a mechanism of information-sharing in nature, and an approximation of this method is available as DNA shuffling. The approximation was examined and compared to the natural method in terms of screening optimization. The natural method of pairwise sexual recombination appears optimal when additivity of mutational effects is assumed. In the absence of this assumption, the DNA shuffling procedure can be used to generate all the combinations of mutations present in a parent pool at the expense of requiring the screening of large numbers of clones. A compromise strategy is suggested which removes much of the additivity assumption and requires screening of substantially reduced numbers of clones.\n\nThe correlation between various enzyme properties were examined. Enzyme activities in varying concentrations of organic solvent are highly correlated, while no correlation was observed between enzyme activity and enzyme stability in oxidative environments. For the enzyme evolved, variants with increased stability were far more frequent than those with increased activity.\n" }, { "name": "Morris, Jeffrey Franklin", "degree": "PhD", "year": "1996", "title": "Suspensions: microstructure, diffusion, and inhomogeneous flow", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01102008-085702", "creators": [ { "name": { "family": "Morris", "given": "Jeffrey Franklin" }, "id": "Morris-J-F", "display_name": "Morris, Jeffrey Franklin" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/069F-Z696", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA theory of self-diffusivity in sheared suspensions valid for any particle volume fraction [phi], Peclet number Pe, and lengthscale of disturbance in [phi] is developed. The theory is applied to the determination of the full tensor self-diffusivity in a weakly- sheared (Pe << 1) suspension of hydrodynamically-interacting hard spheres and a strongly-sheared (Pe >> 1) suspension of hard spheres without hydrodynamic interactions, both at [phi] << 1.\r\n\r\nThe influence of weak Brownian motion alone and in conjunction with a repulsive interparticle force of hard-sphere type upon the pair-distribution function, g(r) where r is the separation vector of a pair of particles, is analyzed for a suspension of spheres at Pe >> 1 and [phi] << 1. At large Pe, the radial fluxes of pair probability due to advection and Brownian diffusion balance in a thin [...] boundary layer at contact, with a the sphere radius. The boundary-layer analyses demonstrate that Brownian diffusion renders g finite at contact in the absence of interparticle forces, and that within the boundary layer there is generally a large excess of pair probability along the compressional axes. By calculation of the bulk normal stress differences in the case with repulsive forces, it is shown how this asymmetry of the microstructure yields non-Newtonian constitutive behavior in the limit Pe[superscript -1] = 0.\r\n\r\nHydrodynamic resistance functions relating the particle and bulk motions to the bulk isotropic stress are developed. Application of these functions is demonstrated by calculations of the shear-induced correction to the osmotic pressure and the particle contribution to the pressure in a sheared lattice.\r\n\r\nPressure-driven flow in a channel at vanishing Reynolds number of a suspension of particles denser than the suspending fluid has been dynamically simulated by Stokesian Dynamics over ranges of the particle fraction, channel width, and a buoyancy parameter characterizing the relative strength of the buoyancy to shearing forces. The predictions of the flow by the suspension-balance model are in good agreement with simulation results.\r\n" }, { "name": "Musser, Siegfried M.", "degree": "PhD", "year": "1996", "title": "The Proton Translocation Mechanisms of the Cytochrome bo\u2083-Type Ubiquinol Oxidase Complex and the Mitochondrial Cytochrome c Oxidase Complex", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02042026-232356481", "creators": [ { "name": { "family": "Musser", "given": "Siegfried M." }, "id": "Musser-Siegfried-M", "orcid": "0000-0002-7793-2557", "display_name": "Musser, Siegfried M." } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nw3n-jd48", "abstract": "Every organism contains a respiratory chain that enables it to convert the energy\r\nobtained from food molecules into adenosine triphosphate (ATP), the universal energy\r\ncurrency which drives a multitude of life-giving biochemical reactions. A typical\r\nrespiratory chain contains a series of integral membrane protein complexes that produce a\r\ntransmembrane proton gradient as a result of sequential electron transfers through these\r\ncomplexes. The energy stored in this proton gradient, a biological battery, is utilized to\r\nsynthesize ATP. In the oxygenic respiratory process functioning in mitochondria,\r\ndioxygen is fully reduced to water by the cytochrome c oxidase (CcO) complex. This\r\nmolecular machine couples the highly exergonic reduction of dioxygen to the pumping of\r\nprotons against a transmembrane electrochemical gradient. Another structurally similar\r\nenzyme, the cytochrome bo3 complex from Escherichia coli, catalyzes the reduction of\r\ndioxygen to water using the same heme-copper dioxygen activating site and also\r\ncatalyzes the translocation of protons. However, whereas the electron donor for the CcO\r\ncomplex is the water-soluble one-electron carrier cytochrome c, two-electron-donating\r\nubiquinol molecules within the lipid bilayer input electrons into the cytochrome bo3\r\ncomplex. The dramatically different electron input mechanisms dictated by these\r\nelectron-donating substrates led to the hypothesis that the proton translocation\r\nmachineries for these two terminal oxidases are completely disparate. Based on the\r\navailable data, it is concluded that the cytochrome bo3 complex translocates protons via a\r\nquinone(quinol)-loop (Q(H2)-loop) mechanism. In a Q(H2)-loop proton translocation\r\nmechanism, proton uptake/release follows electron input to/output from two Q(H2)\r\nbinding sites and protein conformational cycling is not required. On the other hand, the\r\nmore complicated redox-linked proton pump of the CcO complex functions by forcing\r\nprotons through the protein matrix as a result of a series of conformational\r\nrearrangements and is successful only through careful control of both electron and proton\r\ntransfer reactions. This thesis focuses on deciphering the proton translocation capabilities\r\nof these two enzymes and contrasts the simplicity of a Q(H2)-loop mechanism with the\r\nmore evolutionarily advanced CcO proton pump." }, { "name": "Parks, Michelle E.", "degree": "PhD", "year": "1996", "title": "Sequence-specific recognition of DNA by pyrrole-imidazole hairpin polyamides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04282006-114140", "creators": [ { "name": { "family": "Parks", "given": "Michelle E." }, "id": "Parks-M-E", "display_name": "Parks, Michelle E." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4cd1-s277", "abstract": "Polyamides composed of pyrrole (Py) and imidazole (Im) amino acids bind as antiparallel, side-by side dimers in the minor groove of DNA to sequences containing both (A,T) and (G,C) base pairs. Initial polyamides based on the 2:1 model have demonstrated new, predictable specificities but only modest affinities. Chapter 2 describes the thermodynamic characterization of a series of covalently linked polyamides, revealing an increase in affinity (>300-fold) and specificity of the hairpin compared to the unlinked dimers. Chapter 3 reports the characterization of the corresponding cyclic polyamide, which results in a 40-fold increase in affinity, although specificity decreases.\n\nChapter 4 explores the generality of the 2:1 polyamide:DNA model by systematically varying the imidazole content and position within a series of eight three-ring polyamides. Of ten homodimeric and heterodimeric combinations of polyamides characterized, four bind as expected, indicating that the 2:1 model, while not completely general, is a valuable predictive tool. This work adds three new sequences to the targetable repertoire for polyamides, 5'-WGGWW-3', 5'-WGGCW-3', and 5'-WCGCW3'. Chapter 5 focuses on a series of linked hairpin analogs of the heterodimer AcImImPyDp/distamycin that recognize 5'-WGGWW-3' sequences. This study provides the first example of sequence-specific recognition of contiguous G\u2022C base pairs using the side-by-side polyamide:DNA model. In addition, footprinting experiments reveal that linker position does not significantly affect the affinity or specificity of hairpin polyamides. Chapter 6 describes the optimization of polyamide N- and C-terminal groups. Thermodynamic characterizations of a series of ten polyamides show that an unacetylated N-terminus and a C-terminal [beta]-alanine spacer are optimal for hairpin polyamides, providing important design guidelines.\n\nChapter 7 examines the simultaneous binding of an oligonucleotide in the major groove of DNA and a polyamide in the minor groove. Quantitative footprinting experiments indicate that the stability of a triple helix is not affected by simultaneous recognition in the minor groove, suggesting that oligonucleotide-polyamide conjugates could be designed for sequence-specific DNA recognition. Chapter 8 describes experiments designed to determine the DNA-binding orientation of a portion of a high mobility group protein. Although the synthetic peptides bind A,T-rich DNA, no specific cleavage was observed, precluding determination of binding orientation." }, { "name": "Rubin, Susan Felicia", "degree": "PhD", "year": "1996", "title": "Viscoelasticity and dynamics of alignment in side-group liquid crystalline polymers", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032008-082416", "creators": [ { "name": { "family": "Rubin", "given": "Susan Felicia" }, "id": "Rubin-S-F", "display_name": "Rubin, Susan Felicia" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Hubbell", "given": "Jeffrey A." }, "id": "Hubbell-J-A", "role": "member", "display_name": "Hubbell, Jeffrey A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/bdjk-n270", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nSide-group liquid-crystalline polymers (SG-LCPs) consist of a flexible polymeric backbone and rigid mesogens (molecules forming LC phases), attached laterally to the backbone via flexible spacers. Since the dynamics of the mesogen field and polymeric backbone are partially decoupled, uniformly-aligned SG-LCP materials show promise in a variety of applications such as non-linear optical materials, optical data storage media, and stress sensors, which require switching of the mesogen orientation. Recent work has shown that uniform alignment of SG-LCP materials can be accomplished using flow-fields. However, the mechanisms of alignment, which are essential for the development of effective and rational processing strategies for the SG-LCP materials, remain poorly understood. To address this need, we focus on the viscoelastic properties of nematic and smectic SG-LCPs and the dynamics of field-induced alignment of SG-LCPs.\r\n\r\nWe have investigated the dynamic mechanical response of SG-LCPs having methacrylate backbone, hexamethylene spacer, and phenyl benzoate mesogens as a function of molecular weight in the isotropic, nematic, and smectic phases [...], and have discovered a unique molecular-weight dependence of the sensitivity of the dynamic modulus to nematic order of the melt. Nematic order produced a profound change in the dynamics of the entangled SG-LPCs relative to the isotropic phase; however, this effect was absent in the unentangled SG-LCPs. In SGLCPs with smectic order, there was increase in the elastic character of the fluid with smectic ordering, but the incremental effect in a system that was entangled was relatively small. Oscillatory shear with large amplitude [...] induced macroscopic alignment in the nematic phase for all the SG-LCPs studied and could be used to alter the microstructure in the smectic liquid. Shearing the smectic phase produced a decrease in modulus, whereas shearing in the nematic phase followed by cooling into the smectic phase produced an increase in modulus.\r\n\r\nTo assess the effect of the coupling between the mesogen and the backbone on field- induced orientation of nematic SG-LCPs, we have compared magnetically aligned and flow-aligned nematic SG-LCPs. Magnetic forces act primarily on the mesogens, and the backbone conformation changes to accommodate the torques on its pendant mesogens. In contrast, oscillatory shear can couple to the relaxation modes of both the director field and backbone. We have discovered that while the flow-aligned material exhibits distinct low-frequency relaxation dynamics, the relaxation of magnetically- aligned monodomains is indistinguishable from that of polydomain nematic melts. This suggests that flow alignment and magnetic alignment produce qualitatively distinct changes in the fluid miscostructure. We have further compared the processes of shear- and magnetic-alignment by monitoring the evolution of director orientation in nematic SG-LCP melts, in-situ, through visible transmittance (related to the liquid-crystalline domain size) and visible birefringence (related to the molecular orientation)." }, { "name": "Russell, Lynn M.", "degree": "PhD", "year": "1996", "title": "The physics and chemistry of marine aerosols", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12202007-134328", "creators": [ { "name": { "family": "Russell", "given": "Lynn M." }, "id": "Russell-L-M", "orcid": "0000-0002-6108-2375", "display_name": "Russell, Lynn M." } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZRQC-R241", "abstract": "Understanding the physics and chemistry of the marine atmosphere requires both predicting the evolution of its gas and aerosol phases and making observations that reflect the processes in that evolution. This work presents a model of the most fundamental physical and chemical processes important in the marine atmosphere, and discusses the current uncertainties in our theoretical understanding of those processes. Backing up these predictions with observations requires improved instrumentation for field measurements of aerosol. One important advance in this instrumentation is described for accelerating the speed of size distribution measurements. Observations of aerosols in the marine boundary layer during the Atlantic Stratocumulus Transition Experiment (ASTEX) provide an illustration of the impact of cloud processing in marine stratus. More advanced measurements aboard aircraft were enabled by redesigning the design of the system for separating particles by differential mobility and counting them by condensational growth. With this instrumentation, observations made during the Monterey Area Ship Tracks (MAST) Experiment have illustrated the role of aerosol emissions of ships in forming tracks in clouds. High-resolution gas chromatography and mass spectrometry was used with samples extracted by supercritical fluid extraction in order to identify the role of combustion organics in forming ship tracks. The results illustrate the need both for more sophisticated models incorporating organic species in cloud activation and for more extensive boundary layer observations.\r\n" }, { "name": "Seidel, Peter Robert", "degree": "Masters", "year": "1996", "title": "Direct Decomposition of Nitric Oxide by Copper Containing ZSM-5", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03242025-182317095", "creators": [ { "name": { "family": "Seidel", "given": "Peter Robert" }, "id": "Seidel-Peter-Robert", "display_name": "Seidel, Peter Robert" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ab1s-x455", "abstract": "Currently there is an enormous demand for nitric oxide decomposition catalysts and hydrocarbon-based selective catalytic reduction catalysts to eliminate NO. The incorporation of copper atoms into the pores of ZSM-5\r\nhas endowed this solid with the catalytic ability for the direct decomposition of NO to N2 and O2. This report describes the synthesis, characterization, ion-exchange, and reactivity of several ZSM-5 samples prepared by various methods. ZSM-5 is prepared using TPA and also by template-free synthesis methods. Ion-exchange was performed using copper acetate and a copper ethylene complex. Reaction studies include determining rates and turnover frequencies for certain ZSM-5 samples. It was found that ion-exchange with copper ethylene almost doubled the copper weight percent and the reaction rate compared to samples exchanged with copper acetate, however, the turnover frequencies were similar.
" }, { "name": "Shnek, Deborah Rebecca", "degree": "PhD", "year": "1996", "title": "Targeting of Proteins and Protein Analogs to Metal-Chelating Lipid Vesicles", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032008-092017", "creators": [ { "name": { "family": "Shnek", "given": "Deborah Rebecca" }, "id": "Deborah Rebecca", "display_name": "Shnek, Deborah Rebecca" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "orcid": "0000-0002-0191-2154", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "orcid": "0000-0002-3361-6114", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ctnn-4057", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis investigation demonstrates that new metal-chelating lipids formed into mixed vesicles can bind to a variety histidine-rich ligands through metal coordination. Our results show the feasibility of metal-chelating lipids as a method for targeting histidine-rich compounds to lipid interfaces. Interesting metal chelating lipid materials for protein orientation studies, matching the surface distribution of surface residues, protein drug delivery, and for two-dimensional protein crystallization could be made with chelating-lipids. Engineered proteins containing a histidine \"tag\" or proteins with natural surface histidine residues are easily targeted to the interface using metal binding.\r\n\r\nBoth metal binding and histidine-rich ligand binding were investigated with mixed metal-chelating lipid vesicles. New metal-chelating lipids containing an iminodiacetate (IDA) chelating-moiety were formed into mixed vesicles and shown to bind transition metal ions through the lipid headgroup. Metal binding was characterized through calorimetry, freeze-etch microscopy, light scattering, ESR, and fluorescence studies. Fluorescently-labeled lipids containing iminodiacetate showed a large change in the fluorescence emission spectra upon metal binding, behavior which has proven useful for a vesicle-based metal sensor.\r\n\r\nMetal-loaded vesicles bound a model protein specifically through surface-accessible histidines, as shown using ESR studies. Equilibrium binding measurements showed at least an order of magnitude increase in binding affinity of the protein for the membrane when metal was present. The association constants determined through isothermal titration calorimetry for a model bivalent histidine compound binding to metal-chelating lipid bilayers were of the order of [...], while monovalent binding constants were of the order [...].\r\n\r\nLipid re-organization upon ligand binding was probed with model histidine compounds and histidine polymers using fluorescently-labeled metal-chelating lipid vesicles. The ability of lipids to form multivalent ligand-lipid complexes was investigated using the formation of lipid excimers, as demonstrated by fluorescence measurements of the E/M intensity ratio. Histidine content of model compounds determines the magnitude of the effect on the fluorescence emission spectra. Histidine polymers showed a larger increase of the E/M ratio than the smaller bivalent or monovalent compounds. Combining equilibrium binding results obtained with model complexes and results from fluorescence experiments, studies with metal-chelating vesicles support multivalent coordination and reorganization of the lipids by histidine-rich ligands." }, { "name": "Slutter, Claire Ellen", "degree": "PhD", "year": "1996", "title": "Overexpression and Characterization of the Copper A Domain from Cytochrome ba_3 of Thermus Thermophilus", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:06092017-092206826", "creators": [ { "name": { "family": "Slutter", "given": "Claire Ellen" }, "id": "Slutter-Claire-Ellen", "display_name": "Slutter, Claire Ellen" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ded1-5k24", "abstract": "Recently, the genes of cytochrome ba3 from Thermus thermophilus [Keightley, J.\r\nA. et al. (1995) J. Biol. Chem. 270 20345-20358], a homolog of the heme-copper oxidase\r\nfamily, have been cloned. We report here expression of a truncated gene, encoding the\r\ncopper A (Cu^ domain of cytochrome ba3, downstream from the T7 RNA polymerase\r\npromoter in Escherichia coli. The Cu^ domain is obtained in high yields as a watersoluble,\r\nthermostable, purple copper protein. The absorption spectrum of the Cu^ site, free\r\nof the heme interference in cytochrome ba3, is similar to the spectra of other soluble\r\nfragments from the aa3-type oxidase of Paracoccus denitrificans [Lappalainen, P. et al.\r\n(1993) J. Biol. Chem. 268 26416-26421] and the caa3-type oxidase of Bacillus subtilis\r\n[von Wachenfeldt, C. et al. (1994) FEBS Lett. 340 109-113]. There are intense bands at\r\n480 nm (3,100 M-1 cm-1) and 530 nm (3,200 M-1 cm-1), a band in the near-IR centered at 790 nm (1,900 M-1 cm-1) and a weaker band at 363 nm (1,300 M-1 cm-1). The secondary\r\nstructure prediction from the far-UV CD spectrum indicates that this domain is\r\npredominantly \u03b2-sheet, in agreement with the recent X-ray structure reported for the\r\ncomplete P. denitrificans cytochrome aa3 molecule [Iwata, S. et al. (1995) Nature 376\r\n660-669] and the engineered, purple CyoA protein [Wilmanns et al., Proc. Natl. Acad.\r\nSci. USA, in press]. Soluble Cu^ fragments from other terminal oxidases have been\r\nexpressed; however, the thermostability of the fragment described here (TM = 80 \u00b0C) and\r\nthe stable binding of copper over a broad pH range (pH 3-9) makes this protein uniquely\r\nsuitable for detailed physical-chemical study. Copper analysis by chemical assay, mass\r\nspectrometry, X-ray fluorescence, and EPR spin quantification all indicate that this protein\r\ncontains two copper ions bound in a mixed-valence state, consistent with the prediction\r\nthat the Cu^ site in cytochrome ba3 is a binuclear center.
\r\n\r\n\r\nFlash photolysis has been used to initiate electron transfer from excited tris(2,2'bipyridyl)\r\nruthenium(II) to the Cu^ site of the soluble Thermus domain. Luminescence\r\nquenching of the excited state of the ruthenium(II) complex was observed at low protein\r\nconcentrations (20-200 \u03bcM Cu^ domain), with second-order kinetics and rate constants of\r\n2.9 x 109 M-1s-1 and 1.3 x 109 M-1s-1 at low and high ionic strength, respectively, At\r\nhigh protein concentrations (>250 \u03bcM Cu^) and low ionic strength, the quenching rate\r\nsaturates due to ground-state complex formation; a first-order rate constant of 1.5 x 105 s-1 was estimated for ET in the complex.
" }, { "name": "Song, Xueyu", "degree": "PhD", "year": "1996", "title": "Quantum Effects in Electron Transfer Reactions and Solvation Dynamics", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02172022-225929135", "creators": [ { "name": { "family": "Song", "given": "Xueyu" }, "id": "Song-Xueyu", "orcid": "0000-0001-5142-4223", "display_name": "Song, Xueyu" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ejw2-cy95", "abstract": "This thesis focuses on the quantum effects of electron transfer reactions in solutions and solvation dynamics of pure solvent. A prototypical model system, the\r\nFe\u207a\u00b2 + Fe\u207a\u00b3 \u21cc Fe\u207a\u00b3 + Fe\u207a\u00b2 reaction in water, is treated using the spin-boson Hamiltonian model. The spectral density is related to the experimentally accessible data\r\non the dielectric dispersion of the solvent, using a dielectric continuum approximation. On this basis the quantum correction for the ferrous-ferric electron transfer rate is found to be a factor of 9.6, which is significantly smaller than the corresponding values calculated from molecular models which neglect the electronic and vibrational polarization of the solvent. Using an imaginary free energy method, a general formula for the rate valid in all orders of perturbation in electronic coupling is derived for a renormalized classical bath. It is found that the quantum degrees of freedom can be effectively eliminated from the model by renormalizing the electronic coupling matrix element to the first order approximation for the quantum modes. Furthermore, a similar result is obtained for the quantum bath with a better approximation scheme. In application it has been shown that the rate has a nonmonotonic behavior as a function of the coupling matrix element in the inverted region. In the solvent dynamics controlled regime a one-particle Green function method is used to calculate the electron transfer reaction rate with a spin-boson Hamiltonian. A quantum version of Zusman\u2019s result on solvent dynamical effect in electron transfer reactions is obtained for the symmetric case. It is shown that the quantum effect for most of the realistic systems is not significant at room temperature and it would become important for some fast dielectric relaxation solvents like water. In solvation dynamics studies a Gaussian field model is used to obtain the charge density correlation function of the solution in terms of charge density correlation function of the solvent. It then becomes possible to calculate the time-dependent solvation free energy without using the \"uniform dielectric approximation.\" It is found that the nonuniformity in the vicinity of the solute indeed retards the solvation relaxation." }, { "name": "Stockman, Paul Alan", "degree": "PhD", "year": "1996", "title": "Microwave and Far-Infrared Spectroscopy of Water-Containing, Hydrogen-Bonded Dimers: Vibrational, Rotational, and Tunneling Dynamics", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122012-111319894", "creators": [ { "name": { "family": "Stockman", "given": "Paul Alan" }, "id": "Stockman-Paul-Alan", "display_name": "Stockman, Paul Alan" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PYV0-B286", "abstract": "Microwave and far-infrared high-resolution spectroscopies have been used to investigate\r\nthe vibrational, rotational, and tunneling dynamics of water-containing, hydrogenbonded\r\ndimers, towards the goal of converting the recorded spectra into intermolecular\r\npotential energy surfaces (IPSs). Such intermolecular interactions are the basis for\r\nmuch of biological structure and function, as well as reaction and solution dynamics,\r\nand a comprehensive set of key IPSs can form the basis set for molecular modeling of\r\nthese complex phenomena. Specifically studied in this work are the following dimers\r\nand some of their isotopomers: N_2\u2022\u2022\u2022H_2O, OC\u2022\u2022\u2022H_2O, H_3N\u2022\u2022\u2022H_2O, CH_3OH\u2022\u2022\u2022H_2O.\r\nThese dimers constitute a series of increasing binding energy, dynamical complexity,\r\nand chemical and biological importance.
\r\n\r\nThe dimers of water with isoelectronic N_2 and CO are treated jointly because\r\nof their similar properties and level of study. The b-type K = 0 \u2192 1 rotational\r\nspectra for N_2\u2022\u2022\u2022H_2O and OC\u2022\u2022\u2022H_2O, as well as isotopomers containing HOD, D_2O,\r\nand ^(13)CO, were recorded between 325 and 661 GHz and measurements were also\r\nextended for the a-type spectra of the N_2\u2022\u2022\u2022H_2O and OC\u2022\u2022\u2022H_2O isotopomers. Each\r\nrotational transition was split by the effects of large-amplitude tunneling of the hydrogen\r\nand nitrogen nuclei, and the number of tunneling components corresponded\r\nwith that predicted from PI theory. After the effects of tunneling had been removed\r\nfrom the rotational constants, the structures of the two different complexes were fit\r\nto the rotational moments of inertia. These structures correspond to a nearly linear\r\nhydrogen bond and alignment of heavy atoms. The tunneling selection rules for\r\nOC\u2022\u2022\u2022H_2O were confirmed to be \"top-to-bottom, bottom-to-top,\" and the tunneling\r\nsplittings were obtained from the difference in the A_(eff) rotational constants. Using\r\ntwo- and three-term Fourier expansions, the one-dimensional tunneling coordinate\r\nwas fit to the tunneling splittings for OC\u2022\u2022\u2022H_2O and OC\u2022\u2022\u2022D_2O. Ab initio surfaces\r\nare used both to visualize the tunneling modes and as a basis for normal mode analyses. \r\nA reasonable and justified normal mode separation is presented, with the five\r\nintermolecular degrees of freedom separated into geared and anti-geared in-plane and\r\nout-of-plane motions of the the subunits as well as the intermolecular stretch. Finally,\r\npartial VRT spectra for both complexes recorded between 42 and 53 cm^(-1) are\r\npresented and preliminarily assigned to the in-plane geared motion.
\r\n\r\nMicrowave and far-infrared spectra of the H_3N\u2022\u2022\u2022H_2O dimer were recorded from\r\n36 to 86 GHz and 520 to 800 GHz. The a-type pure rotational microwave data extend\r\nthe previous m = 0,K = 0 A-symmetry manifold measurements of Herbine and Dyke\r\n[J. Chem. Phys. 83, 3768 (1980)] to higher frequency and also provide an additional\r\nset of microwave transitions in the mK = +1 E symmetry manifold. Two sets of five\r\nb-type rotation-tunneling bands one set shifted from the other by an approximately\r\nconstant 113 MHz, were observed in the far-infrared. The splitting into two sets arises\r\nfrom water tunneling, while the overall band structure is due to internal rotation of the\r\nammonia top. Non-linear least-squares fits to an internal rotor Hamiltonian provided\r\nrotational constants, and an estimation of V_3 = 10.5 \u00b15.0 cm^(-1) for the barrier height\r\nto internal rotation for the NH3 monomer. A non-linear equilibrium hydrogen bond is\r\nmost consistent with the vibrationally averaged rotational constants; with the angle\r\ncos^(-1) [\u3008\u03bb_z\u3009] determined from \u3008\u03bb_z\u3009, the projection of the ammonia's angular momentum\r\nonto the framework. The water tunneling splitting and observed selection rules place\r\nconstraints on the barrier height for proton exchange of the water as well as the most\r\nfeasible water tunneling path along the intermolecular potential energy surface. An\r\nestimated barrier of 700 cm^(-1) was derived for the water tunneling motion about its\r\nc axis.
\r\n\r\nFinally, microwave spectra of CH_3OH\u2022\u2022\u2022H-2O and CH_3OD\u2022\u2022\u2022D_2O were recorded\r\nbetween 20 and 60 GHz, along with data from our collaborators at the National Institute\r\nfor Science and Technology for CH_3OH\u2022\u2022\u2022H_2O, ^(13)CH_3OH\u2022\u2022\u2022H_2O, CH_3OH\u2022\u2022\u2022DOH,\r\nCD_3OH\u2022\u2022\u2022H_2O, and CH_3OD\u2022\u2022\u2022D_2O between 7 and 24 GHz. Because CH_3OH and\r\nH_2O are both capable of accepting and donating hydrogen bonds, there existed some\r\nquestion as to which donor-acceptor pairing of the molecules was the lowest energy\r\nform. This question is further emphasized by the ambiguity and variety present in\r\nprevious experimental and computational results. Transitions from the methyl torsional\r\nA state were assigned for the various isotopomers. The fit of the structure to\r\nthe rotational constants gave unambiguous confirmation that the only conformation\r\nobserved in the supersonically cooled molecular beams corresponded to a water-donor,\r\nmethanol-acceptor complex.
" }, { "name": "Suzuki, Sakae", "degree": "PhD", "year": "1996", "title": "Towards a More Quantitative Understanding of Intermolecular Interactions: Biologically Significant Intermolecular Clusters", "advisor": "Blake, Geoffrey A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282025-223101565", "creators": [ { "name": { "family": "Suzuki", "given": "Sakae" }, "id": "Suzuki-Sakae", "display_name": "Suzuki, Sakae" } ], "advisors": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "advisor", "display_name": "Blake, Geoffrey A." } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-G-A", "orcid": "0000-0003-0787-1610", "role": "member", "display_name": "Blake, Geoffrey A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z68g-sj24", "abstract": "Intermolecular potential energy surfaces (IPS's) of weakly bound clusters with potential\r\napplications to the interpretation of biological and other natural phenomena,\r\nnamely Ar-D2O, Ar-DOH, C6H6-H2O, C6H6-D2O, C6H6-DOH, and (D2O)3, were studied with fully rotationally resolved spectroscopy, ab intio calculations and diffision\r\nMonte Carlo simulations. These results contributed to the characterization of\r\nthe Ar-water, benzene-water and water trimer IPS's and reinforced the need to treat\r\ncomplete the complex dynamics of intermolecular forces.
\r\n\r\nThe Caltech tunable far-infrared spectrometer (TuFIR) was used to observe the\r\n\u03a3+000 \u2192 \u03a0111 transition at 19.32 cm-1 and the \u03a3+000 \u2192 \u03a3+111 transition at 20.65 cm-1 for\r\nAr-D2O, and the \u03a3+000 \u2192 \u03a0101 transition at 19.9 cm-1 for Ar-HDO. These transitions\r\nprobed previously unexplored regions of the Ar-water IPS and enabled the generation\r\nof an improved multi-dimensional IPS for this simplest model system of hydrophobic-polar\r\ninteractions.
\r\n\r\nThe Caltech direct absorption microwave spectrometer was used to record the\r\nsymmetric top rotational spectrum for the J=4 \u2192 5 to 9 \u2192 10 transitions in the\r\nm = 0 and m = \u00b11 manifold of C6H6-H2O, C6H6-D2O, and C6H6-DOH, to examine\r\nthe nature of \"aromatic-polar\" interactions. The rotational constants from the\r\nthree isotopomers demonstrated unambiguously that water is positioned above the\r\nbenzene plane in nearly free internal rotation with the hydrogen atoms pointing toward\r\nthe benzene \u03c0-electron cloud. A D0 of 1.9 kcal/mol was estimated based on\r\nthe spectra. Ab initio calculations supported the aromatic-\u03c0-H bond geometry and\r\npredicted a binding energy of De less than or equal to 1.78 kcal/mol. Diffusion Monte Carlo simulations\r\non the ab initio surface were performed to visualize the large amplitude motions in\r\nthis dimer. The TuFIR was also employed to measure a C6H6-D2O intermolecular\r\nvibrational band at 19.5 cm-1. The symmetric top pattern and l-type doubling in the\r\nexcited state revealed a strong coupling between the internal rotation and bending
\r\n\r\nFinally, a previously unpredicted c-type FIR band of (D2O)3 centered at 41.1 cm-1 \r\nwas observed, which prompted the replacement of a simple one-dimensional model\r\nwith a more realistic analysis of the (D2O)3 dynamics.
" }, { "name": "Takeuchi, Toshihiko", "degree": "PhD", "year": "1996", "title": "The Electronic Structure of Distorted Porphyins and Cobalt Schiff Base Derivatives as Novel Enzyme Inhibitors", "advisor": "Gray, Harry B.; Goddard, William A., III; Meade, Thomas J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-085123252", "creators": [ { "name": { "family": "Takeuchi", "given": "Toshihiko" }, "id": "Takeuchi-Toshihiko", "display_name": "Takeuchi, Toshihiko" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Meade", "given": "Thomas J." }, "id": "Meade-T-J", "role": "co-advisor", "display_name": "Meade, Thomas J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/py88-c390", "abstract": "Halogenated porphyrins, which are catalysts for the oxidation of alkanes, were studied by semiempirical AM 1 calculations. The calculations predicted the effects of halogenation of the porphyrin ring on UV-visible absorption spectra and electrochemical data. Predictions regarding the stability of catalysts were made, and have been experimentally verified. INDO/S semiempirical calculations were performed on a series of porphyrins to understand the effects of a highly disfavored distortion that is conserved in cytochromes c. The highest occupied molecular orbitals were destabilized, and the orbital energy of the metal and the lowest unoccupied orbitals change, causing a shift in the redox potential of the heme and a change in the electron transfer properties of cytochromes c.\r\n\r\nIn order to delineate the anti-enzymatic properties of Co(acacen) derivatives, which are potent inhibitors of the herpes virus, carbonic anhydrase (CA), thermolysin (TL), and thrombin (TH) were chosen as targets Inhibition of CA occurs upon incubation with the novel water-soluble Co(II)hydroxypropylacacen (Co(II)hpr) but not with [Co(III)hpr(NH_3)_2 ^+(OAc)^- . The difference in reactivity of the species is a consequence of the steric limitations imposed by the axial ligands bound to the Co(III) complex. [Co(III)acacen(NH_3)_2^+ irreversibly inhibits TL, and this inhibition was prevented by binding a strong reversible inhibitor to the active site of the enzyme before addition of the cobalt species, suggesting that cobalt-acacen derivatives can inhibit enzymes by binding to active site histidines. In an effort to develop more potent and selective enzyme inhibitors, active site-directed peptides were coupled via a peptide bond through a carboxylic acid, which is part of the acacen ligand framework. The peptide coupled derivatives rapidly and irreversibly inhibited TH, and the potency of inhibition was over an order of magnitude better than the uncoupled components.\r\n" }, { "name": "Terbrueggen, Robert Henry", "degree": "PhD", "year": "1996", "title": "Exploring the Direct and Indirect Readout of DNA with Phenanthrenequinone Diimine Complexes of Rhodium(III)", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152025-212928780", "creators": [ { "name": { "family": "Terbrueggen", "given": "Robert Henry" }, "id": "Terbrueggen-Robert-Henry", "display_name": "Terbrueggen, Robert Henry" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yv86-3710", "abstract": "Phenanthrenequinone diimine (phi) complexes of rhodium(III) have been\r\ndesigned and characterized in order to investigate the principles of direct and\r\nindirect readout of double helical DNA The metallointercalator l-Rh(MGP)2phi5+\r\n(MGP = 4-guanidylmethyl-1,10-phenanthroline) binds via intercalation in the\r\nmajor groove of DNA and upon irradiation promotes DNA strand scission. The\r\n\u039b-enantiomer, \u039b-1-Rh(MGP)2phi5+, binds at subnanomolar concentrations to the\r\n6 base pair sequence, 5'-CATATG-3', with enantiospecificity. An essential feature\r\nof this recognition is the sequence-specific unwinding of the DNA helix which\r\npermits direct contacts between guanidinium functionalities on the metal complex\r\nand guanine residues. Deazaguanine substitutions were used to establish direct\r\ncontacts between the N7 nitrogen atoms of guanine and the guanidinium moiety on\r\nthe metal complex. Through an assay developed to test for sequence-specific DNA\r\nunwinding, a 70 \u00b1 10 degrees unwinding of the sequence 5'-CATATG-3' upon\r\nbinding by \u039b-1-Rh(MGP)2phi5+ was established. Thus, the sequence-dependent\r\ntwistability of DNA plays an important role in determining the sequence specificity\r\nof the complex. The \u0394-enantiomer, \u0394-1-Rh(MGP)2phi5+, binds preferentially to\r\nthe 6 base pair sequence, 5'-CATCTG-3'. The hierarchy of recognition sites\r\ndetermined in photocleavage studies on oligonucleotides suggests that DNA\r\nrecognition by this complex also involves sequence specific contacts by the\r\nguanidinium functionalities. Photocleavage studies indicate additional similarities\r\nin the recognition of \u0394 and \u039b-1-Rh(MGP)2phi5+. Both enantiomers of 1-\r\nRh(MGP)2phi5+ display increased binding specificity relative to the parent\r\ncomplex, Rh(phen)2phi3+. The exchange rates of both enantiomers are also\r\ndecreased at least a 1000-fold relative to Rh(phen)2phi3+. Studies in which the\r\nlength of the linker arm between the core of the metal complex and the guanidinium\r\nmoiety was varied demonstrate that proper orientation of the guanidinium moiety is\r\nan essential feature of complex specificity. As the length of the linker arm\r\nincreases, the binding specificity of the complex decreases. DNA recognition\r\nstudies with Rh(APB)2phi5+ (APB= 4-(3-aminopropyl)-4'-2,2'-bipyridine) have\r\ndemonstrated that the amino moiety can also be used to alter the sequence\r\nspecificity of phi complexes of rhodium(III), although the sequence specificity of\r\nthis complex is reduced greatly as compared with \u0394- and \u039b-1-Rh(MGP)2phi5+.\r\nThis work therefore demonstrates that the guanidinium moiety may be used to\r\nenhance both the binding affinity and specificity of phi complexes of rhodium(III).\r\nIn mimicking DNA binding proteins, molecules which recognize their binding sites\r\nthrough direct and indirect readout of the DNA can be designed. Importantly, this\r\nstudy highlights a new structural element of DNA recognition, the sequence-dependent\r\ntwistability of the DNA helix. This sequence-dependent twistability may\r\nbe an essential feature of the recognition of sequences by DNA-binding proteins\r\nand may be powerfully exploited in future design." }, { "name": "Zhu, Mei", "degree": "Masters", "year": "1996", "title": "Selective hydroxylation of small alkanes by the particulate methane monooxygenase", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08212013-112742527", "creators": [ { "name": { "family": "Zhu", "given": "Mei" }, "id": "Zhu-M", "display_name": "Zhu, Mei" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qecc-y270", "abstract": "The particulate methane monooxygenase (pMMO) catalyzes the\r\noxidation of methane to methanol under ambient temperatures and\r\npressures. Other small alkanes and alkenes are also substrates of this\r\nenzyme. We measured and compared the initial rate constants of oxidation\r\nof small alkanes (C1 to C5) catalyzed by pMMO. Both primary and\r\nsecondary alcohols were formed from oxidation of n-butane and n-pentane.\r\nThe alcohols produced from alkane oxidation can be further oxidized,\r\nprobably by pMMO, to aldehydes and ketones. The apparent\r\nregioselectivity for n-butane and n-pentane is 100% 2-alcohols because the\r\nformation of primary alcohols is slower than further oxidation of these\r\nalcohols. The hydroxylation at the secondary carbons is highly\r\nstereoselective: (R)-alcohols are preferentially formed. The enantiomeric\r\nexcess increases slightly with decreasing reaction temperature. The steric\r\ncourse of hydroxylation on primary carbons was also studied by using\r\nisotopically substituted ethane: (S)- or (R)-CH_3-CHDT, and (S)- or (R)-CD_3-\r\nCHDT and the reactions were found to proceed with 100% retention of\r\nconfiguration. A primary isotopic effect of k_H/k_D=5.0 was observed in\r\nthese experiments." }, { "name": "Bart, John C.", "degree": "PhD", "year": "1995", "title": "Electrochemical investigations of ruthenium-substituted heteropolytungstate anions : catalytic studies of an inorganic oxometalloporphyrin analog", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122007-081836", "creators": [ { "name": { "family": "Bart", "given": "John C." }, "id": "Bart-J-C", "display_name": "Bart, John C." } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wdkr-zr39", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nRuthenium-substituted heteropolytungstate anions (Ru-HPAs), such as [...], are expected to be catalytically active for reactions such as the oxidation of alcohols. Since little is known about this compound, several studies were undertaken so as to better understand its chemical and electrochemical properties.\n\nLigand exchange of nitrogen bases like pyridine for the water molecule bound to the ruthenium center confirmed an earlier report that the polyoxotungstate cage acts as a weak [...]-electron acceptor. When this action is taken into account, the physical properties of the ruthenium-nitrogen base complexes and the rate constants for their formation are comparable to other [...] species such as [...].\n\nElectron transfer studies between [...] and [...] are complicated by the fact that the cage species does not act as a point charge, and thus rate constant calculations based on simple ionic strength equations are not accurate. Switching the oxidant to a neutral compound like dioxygen greatly simplifies the reaction conditions, so that the Marcus equation for outer sphere electron transfer can be used to precisely predict the electron transfer rate constant.\n\nRate constants for the catalytic oxidation of various alcohols by [...] have been measured. The magnitude of these rate constants was much smaller than initial expectations, but not unusually so compared to other oxoruthenium (V) catalysts which have been described in the literature since this project began. Work in which Ru-HPA was used to catalyze the oxidation of non-alcoholic substrates is also discussed. Lessons learned from this project are analyzed in the context of general catalysis of oxidation reactions and thoughts on the next generation of catalysts are presented.\n" }, { "name": "Bekiaris, Nikolaos", "degree": "PhD", "year": "1995", "title": "Multiple steady states in distillation", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122007-075846", "creators": [ { "name": { "family": "Bekiaris", "given": "Nikolaos" }, "id": "Bekiaris-N", "display_name": "Bekiaris, Nikolaos" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Wiggins", "given": "Stephen R." }, "id": "Wiggins-S-R", "role": "member", "display_name": "Wiggins, Stephen R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/S6MC-5V73", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nWe study multiple steady states in distillation. We first analyze the simplest case of ternary homogeneous azeotropic mixtures. We show that in the case of infinite reflux and an infinite number of trays ([...] case) one can construct bifurcation diagrams on physical grounds with the distillate flow as the bifurcation parameter. Multiple steady states exist when the distillate flow varies non-monotonically along the continuation path of the bifurcation diagram. We derive a necessary and sufficient condition for the existence of these multiple steady states based on the geometry of the distillation region boundaries. We also locate in the composition triangle the feed compositions that lead to these multiple steady states.\r\n\r\nWe further note that most of these results are independent of the thermodynamic model used. We show that the prediction of the existence of multiple steady states in the [...] case has relevant implications for columns operating at finite reflux and with a finite number of trays. Using numerically constructed bifurcation diagrams for specific examples, we show that these multiplicities tend to vanish for small columns and/or for low reflux flows. Nevertheless, the [...] multiplicities do exist for columns at realistic operating conditions. We comment on the effect of multiplicities on column design and operation for some specific examples. \r\n\r\nWe then extend the homogeneous mixture results to ternary heterogeneous mixtures. We study the [...] case in much more depth and detail by demonstrating how the [...] analysis can be applied to different column designs. More specifically, we show how the feasible distillate and bottom product paths can be located for tray or packed columns, with or without decanter and with different types of condenser and reboiler. We derive the fully detailed, necessary and sufficient condition for the existence of these multiple steady states based on the geometry of the product paths. Simulation results for finite columns show that the predictions carry over to the finite case.\r\n\r\nThe complete list of the [...] case predictions is presented. The implications of these multiplicities for column design, synthesis and simulation are demonstrated. More specifically, we show how the [...] predictions can be useful for the selection of the entrainer, the equipment and the separation scheme. We show that, in some cases, the column operation at an unstable steady state may have some advantages. The important issue of the effect of the thermodynamic phase equilibrium on the existence of multiplicities is discussed. Using the [...] analysis, we identify entire mixture classes for which multiplicities are inherent and robust. Mixtures with ambiguous VLE data are studied; we show that in some cases a slight VLE difference between models and/or experimental data may affect the existence of multiplicities while other, major VLE discrepancies do not. Finally, we identify the key issues and the pitfalls one should be cautious about when designing or computing the composition profile of an azeotropic distillation column with a commercial simulator.\r\n" }, { "name": "Benedicto, Alto D.", "degree": "PhD", "year": "1995", "title": "Rational Approaches to Regulating Polymer Properties in Ring-Opening Metathesis Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-131436", "creators": [ { "name": { "family": "Benedicto", "given": "Alto D." }, "id": "Benedicto-Alto-D", "display_name": "Benedicto, Alto D." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BC47-7W20", "abstract": "The molecular weight distribution of a living polymerization when chain-transfer agents are intentionally added were computed numerically. Results showed that traditional expressions for number-average degree of polymerization (X\u0305n) and polydispersity index (PDI) of chain-growth polymerization cannot be used. The well-known Mayo equation fails even when the system has achieved steady-state polymerization. Although the behavior of the system is complex, an analytical expression for X\u0305n was derived. Plots based on the analytical expression showed excellent agreement with that from numerical solutions. The implications of the calculations were discussed. The kinetics of living ring-opening metathesis polymerization (ROMP) of norbornene in the presence of neohexene catalyzed by Mo was investigated.
\r\n\r\nThe living ROMP of norbornene (n\u0332) and bicyclo[3.2.0]hept-2-ene (c\u0332) by Cl\u2082(PPh\u2083)\u2082Ru(=CHCHCPh\u2082) was demonstrated. The molecular weight varied linearly with conversion. Discrete propagating species showed that PPh\u2083 ligand dissociated during polymerization of c\u0332, and that CuCl (abstracts PPh\u2083) enhanced the rate of polymerization of n\u0332. The specific propagation rate constants (kn\u0332n\u0332 and kc\u0332c\u0332, respectively) of homopolymerization of n\u0332 and c\u0332 were measured, respectively. Block copolymers were easily prepared. From reactivity ratio studies, the ordering of the specific propagation rate constants are kn\u0332c\u0332 >> kkn\u0332n\u0332 > kc\u0332c\u0332 > kc\u0332n\u0332. The effect of styrene as chain-transfer agent on the molecular weight was examined.
\r\n\r\nThe hitherto unassigned (and unknown) microstructure of polymers prepared from 7-oxabicyclo[2.2.1]hept-2-ene derivatives have finally been unambiguously assigned. Polymers catalyzed by W(CH-t-Bu)(NAr)(OCMe(CF\u2083)\u2082)\u2082 have all cis double bonds and highly syndiotactic, while those from RuCl\u2083\u20223H\u20820 and [RuCl(\u03bc-Cl)(\u03bc\u00b3:\u03bc\u00b3-C\u2081\u2080H\u2081\u2086)]\u2082 {C\u2081\u2080H\u2081\u2086= 2,7-dimethyloctadienediyl} have high trans double bond content and highly isotactic.
\r\n\r\nStudies on the olefin isomerization catalyzed by Ru(H\u2082O)\u2086tos\u2082 revealed that the presence of hydroxyl functionality on the terminal olefin resulted in formation of 1:1 ratio of cis : trans double bonds on the isomerized internal olefin product, in contrast with near exclusive isomerization of double bond to trans when no hydroxyl group was present.
\r\n\r\nA numerical algorithm was developed for the evaluation of a chirality function for triangles on a plane, showing that such algorithm may be easily extended into the case of tetrahedron in 3-dimensional space.
\r\n" }, { "name": "Best, George C.", "degree": "PhD", "year": "1995", "title": "Sequence composition and mismatch effects on triple helix formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09062007-134504", "creators": [ { "name": { "family": "Best", "given": "George C." }, "id": "Best-G-C", "display_name": "Best, George C." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kj1w-5c31", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe association constants for the formation of sixteen triple helical complexes which vary at a single common position (Z\u2022XY where Z = A, G, [...], T and XY = AT, GC, CG, TA) were determined by quantitative affinity cleavage titration. The association constants ranged from 9.5 x [...] (A\u2022CG) to 5.6 x [...] (T\u2022AT) at 22 \u00b0C, pH 7.0, 10 mM bis-tris, 100 mM NaCl, 250 [...] spermine. For the sequences studied, T\u2022AT is more stable than T\u2022GC, T\u2022CG, or T\u2022TA by [...] 2.3 kcal mol[...]; [...]+GC is more stable than [...]\u2022AT, [...]\u2022CG, or [...]\u2022TA by [...] 1.4 kcal mol[...]; G\u2022TA is more stable than G\u2022AT, G\u2022CG, or G\u2022GC by [...] 0.8 kcal mol[...]. Under the conditions used in these experiments, none of the natural bases form triplets which offer means of recognizing the Watson-Crick CG base pair in a clearly energetically preferred manner.\n\nThe association constants for the formation of nine triple helical complexes of varying length and sequence composition were determined by quantitative DNase footprint titration. The association constants ranged from 2.0 x [...] to 3.1 x [...] at 22 \u00b0C, pH 7.0, 10 mM bis-tris, 100 mM NaCl, 250 [...]M spermine. The free energy of formation of the various triple helices was expressed as the linear combination of the free energy contributions of the various dinucleotide components of the oligonucleotide, and the value of each energetic contribution was determined. The 5'-TT-3' dinucleotide makes the greatest contribution to the stability of the triple helix, -1.2 kcal\u2022mol[...] dinucleotide[...], while the inclusion of a [...] dinucleotide requires the payment of an energetic penalty of 0.5 kcal\u2022mol[...] dinucleotide[...]." }, { "name": "Bierwagen, Erik Paul", "degree": "PhD", "year": "1995", "title": "Computational Studies of Ziegler-Natta Catalysis and Concurrent Resonance Computations", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-104050", "creators": [ { "name": { "family": "Bierwagen", "given": "Erik Paul" }, "id": "Bierwagen-Erik-Paul", "display_name": "Bierwagen, Erik Paul" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3w1m-hk72", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis discusses work on two different subjects. First, results from computational studies of Ziegler-Natta catalysts are presented. Quantum mechanical calculations of model Ziegler-Natta catalysts [...] are described, where X is either Cl or the cyclopentadienyl (Cp) ligand, M is a group three transition metal or group four transition metal cation, and R is a hydrogen or alkyl group. It is found that complexes based on group four cations have pyramidal structures (the R group is not in the [...] plane), whereas group three neutral complexes have planar structures. This difference in structure is considered in the context of syndiodirecting polymerization, leading to the conclusion that the group three metals are expected to show little, if any, syndiodirecting capabilities, while the group four cations, including thorium, are expected to show large syndiodirecting capabilities, in accord with experiments. Results from molecular mechanics simulations of zirconocene-based catalysts follow. These calculations are used to assess the steric demands of different ligand environments during propylene polymerization, to determine the relative importance of site and chain end control on the enantioface selectivity, both of which are found to be operative.\r\n\r\nThe second part of the thesis describes the development of concurrent algorithms for the computation of resonance matrix elements. The algorithms are described for two different models of concurrent computing: parallel and distributed. A general program design and architecture that facilitate the program development are described. The scaling of both algorithms with the number of processors is found to be nearly ideal." }, { "name": "Birnbaum, Eva Rachel", "degree": "PhD", "year": "1995", "title": "The mechanism of catalytic hydrocarbon oxidation by molecular oxygen and halogenated ruthenium and iron porphyrins", "advisor": "Bercaw, John E.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112007-142146", "creators": [ { "name": { "family": "Birnbaum", "given": "Eva Rachel" }, "id": "Birnbaum-E-R", "display_name": "Birnbaum, Eva Rachel" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/55r8-tt83", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nHighly halogenated ruthenium and iron porphyrins are shown to be active catalysts for alkene oxidation with dioxygen or iodosobenzene. The synthesis and characterization of [...]-octachloro-tetrakis(pentafluorophenyl)porphyrinato-ruthenium(II) carbonyl [RuTFPPCl[...](CO)] and [...]-octabromo-tetrakis(pentafluorophenyl)porphyrinato-iron(III) chloride [Fe(TIPPBr[...])Cl] are reported. Crystal structures of RuTFPPC1[...](CO) and the zinc and free ligand precursor complexes show extensive distortion of the halogenated porphyrin macrocycles due to steric interactions between the b-chlorine atoms and the pentafluorophenyl rings. [...]FNMR is developed as a method to characterize both paramagnetic and diamagnetic fluorinated porphyrins in solution. The anodically shifted reduction potentials and red shifted absorptions in the UV-Vis spectroscopy of the halogenated porphyrins are discussed in terms of steric and electronic effects on porphyrin frontier orbitals.\n\nBoth Fe(TFPPBr[...])Cl and RuTFPPCl[...](CO) catalyze the oxidation of cyclohexene with dioxygen and without added coreductant, with 73 and 296 turnovers, respectively, in 24 hours. Although both porphyrins will catalyze reactions with iodosobenzene, showing selectivity consistent with high-valent metal-oxo formation, overall activity with dioxygen is much higher. In accord with earlier work, cyclohexene oxidation by Fe(TFPPBr[...])Cl is consistent with a mechanism involving porphyrin-mediated decomposition of alkyl peroxides, which generates free radicals in solution. Catalysis with RuTFPPCl[...](CO) is shown to be of a photochemical nature, as irradiation with low energy light results in a dramatic increase in the reaction rate. A reaction mechanism involving olefin binding to the excited ruthenium porphyrin is suggested by laser photolysis experiments. This catalyst represents the first stable, effective metalloporphyrin catalyst for olefin oxidation with dioxygen and light.\n" }, { "name": "Burkett, Sandra Louise", "degree": "PhD", "year": "1995", "title": "Mechanisms of structure direction in zeolite synthesis", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-104907", "creators": [ { "name": { "family": "Burkett", "given": "Sandra Louise" }, "id": "Burkett-Sandra-Louise", "display_name": "Burkett, Sandra Louise" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/t6kk-w159", "abstract": "The mechanisms by which the geometries of organic structure-directing agents are translated into the product pore architectures in the synthesis of pure-silica and aluminosilicate zeolites are investigated by numerous spectroscopic techniques and variations in synthesis gel composition. For the tetrapropylammonium- and 1,6-hexanediamine-mediated syntheses of pure-silica ZSM-5 (Si-ZSM-5), 1H-29Si CP MAS NMR is performed between the protons of the organic species and the silicon atoms of the zeolite framework precursors in a deuterated synthesis medium to probe the interactions between the organic and inorganic components. The origin of structural specificity in the synthesis of pure-silica zeolites in the presence of structure-directing agents is attributed to the formation of favorable intermolecular van der Waals interactions within inorganic-organic composite species that form the key components in zeolite self-assembly. Investigation of the 1H-29Si CP MAS NMR profiles of silicate gels containing tetraalkylammonium cations that do not induce the formation of a crystalline zeolite product suggest the significance of hydrophobic hydration of the organic component in the formation of the inorganic-organic composite structures that is essential to the synthesis of pure-silica zeolites. For the syntheses of the hexagonal (EMT) and cubic (FAU) polymorphs of the aluminosilicate zeolite faujasite in the presence of 18-crown-6 and 15-crown-5, respectively, a combination of NMR and vibrational spectroscopic techniques and variations in the synthesis compositions are used to elucidate the structure-directing roles of the crown ethers. Sodium/crown ether complexes facilitate and direct the assembly of sodium-templated extended aluminosilicate structures via ion-dipole interactions to form the EMT and FAU products. Thus, for the synthesis of Si-ZSM-5 and the synthesis of EMT and FAU, two different mechanisms of structure direction and self-assembly via the formation of extended inorganic or inorganic-organic composite species are proposed." }, { "name": "Campbell, Sherrie A.", "degree": "PhD", "year": "1995", "title": "FT-ICR studies of the structures, energetics and reaction dynamics of biological molecules in the gas phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122005-160230", "creators": [ { "name": { "family": "Campbell", "given": "Sherrie A." }, "id": "Campbell-S-A", "display_name": "Campbell, Sherrie A." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z6t6-nz51", "abstract": "Fourier transform ion cyclotron resonance (FT-ICR) mass spectroscopy has been used to investigate the energetics and reaction dynamics of biological molecules in the gas phase. Experimental results aid in predicting gas phase protonation sites and molecular conformations of peptides and amino acids. Correlations of proton affinities with adiabatic lone-pair ionization energies indicate that amino acids lacking basic side chains protonate on the amine nitrogen, while more basic amino acids protonate on their side chain. These results have been similarly applied to small peptides, with protonation predicted on the N-terminus for peptides lacking basic amino acid residues.\n\nTwo novel experimental methods have been developed for measuring gas phase proton affinities, which utilize infrared multiphoton dissociation and collision induced dissociation techniques to cleave proton-bound dimers of reagent gases. The dimers fragment into two products with the more basic reagent retaining the proton. A simplified RRKM analysis is used to determine proton affinities from product ion abundances.\n\nIsotopic hydrogen exchange reactions of protonated glycine oligomers with a series of reagent bases have been performed, and the exchange mechanisms and energetics identified. Although it is not the sole determining factor, the extent and rates of H/D exchange increase with reagent basicity, with ND3 being the most efficient exchange gas studied. Exchange of the N-terminus hydrogens occurs via an onium ion mechanism in which an endothermic proton transfer is rendered energetically favorable by simultaneous solvation of the ammonium ion. Exchange of the C-terminus occurs via a salt bridge intermediate, in which the carboxylate and ammonium ion is stabilized by interactions with the nearby protonated N-terminus.\n\nFinally, the H/D exchange reactions of several peptides possessing basic residues with ND3 have been investigated. The results indicate that basic amino acids hinder exchange processes as protonation energetics and molecular folding become more important. Calculations using semiempirical AM1 and PM3 methods were performed to identify the gas phase configurations of the protonated peptides and determine if stable salt bridge structures are possible. Potential energy surfaces were also calculated for all exchange processes.\n" }, { "name": "Choi, Jong-Ho", "degree": "PhD", "year": "1995", "title": "Infrared spectroscopy of molecular ions and ion-solvent clusters", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechETD:etd-09252007-091111", "creators": [ { "name": { "family": "Choi", "given": "Jong-Ho" }, "id": "Choi-J-H", "display_name": "Choi, Jong-Ho" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "chair", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x6dv-j487", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nStudies to elucidate details of ion-molecule interactions at the molecular level are of extreme importance for understanding the solvation process and ion-molecule reactions in clusters and in the condensed phase. In the quest of this purpose, infrared predissociation spectroscopy has been applied to three ionic systems.\r\n\r\nInfrared spectra of mass-selected clusters NO[superscript +](H2O)n showed that the smaller clusters (n=1-3) were complexes of H2O ligands bound to a nitrosonium ion NO[superscript +] core. In the n = 4 cluster, we found evidence for the onset of an intracluster reaction that formed HONO. From an analysis of the spectrum, we concluded that the n = 5 cluster rearranged to form H3O[superscript +](H2O)3(HONO), i.e., an adduct of the reaction products. This study provides clear evidence for the intracluster rearrangement reaction NO[superscript +](H2O)n[...]H3O[superscript +](H2O)n-2(HONO) at n[...]4.\r\n\r\nInfrared spectroscopic results on NO2[superscript +](HOX)(X=H,D,[superscript 35]Cl,[superscript 37]Cl) clusters showed a remarkable similarity in the chemistry of protonated nitric acid and chlorine nitrate, and two types of isomers were observed. The structure of the ground-state isomer is an ionmolecule complex, NO2[superscript +](HOX), and the second most stable isomer is a covalently bound species, (OH)(OX)NO[superscript +]. We found evidence for an IR photon-induced isomerization reaction. These spectroscopic results were quite consistent with the predictions of ab initio theory, and may provide important clues to the heterogeneous reaction mechanism involved in the depletion of stratospheric ozone.\r\n\r\nThe first infrared spectroscopic observations of gas-phase hydrated chloride clusters, [...], led to crucial suggestions concerning the structures of halide-water systems. In [...], the water forms a nearly linear hydrogen bond with the chloride ion, and in [...] and [...], the water ligands hydrate the chloride ion asymmetrically, but do not form a hydrogen bond with each other. The observed results for n = 1 and 2 showed good agreement with correlated ab initio calculations. In the n = 4 cluster, the probed structure was the one in which one [...]-bonded water ligand forms a hydrogen bond to an adjacent water ligand. In [...], a liquid-phase-like broad spectrum was observed with several peaks still apparent." }, { "name": "Chung, Geun-Chang", "degree": "PhD", "year": "1995", "title": "Segmental dynamics of individual species in a miscible polymer blend", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182007-103953", "creators": [ { "name": { "family": "Chung", "given": "Geun-Chang" }, "id": "Chung-Geun-Chang", "display_name": "Chung, Geun-Chang" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/dp5v-gt76", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe segmental motion of each species in polyisoprene/poly(vinylethylene) (PI/PVE) miscible blends is studied at three different compositions using two-dimensional deuteron exchange NMR. The individual species exhibit widely different mean mobilities and broad mobility distributions near the glass transition of each blend. As PVE content increases, both the difference in mean mobilities between the two species and the width of mobility distribution for both components increase. Such enhancement of these two types of dynamic heterogeneity with PVE content appears to produce the anomalous broadening of the glass transition. The mean reorientational correlation times of each component can differ by two orders of magnitude under identical conditions. The mean correlation times and the monomeric friction coefficients can be described by a common temperature dependence, which differs for individual species. This difference can be described in terms of distinct effective glass transition temperatures, [...], for the two species. The separation between the two effective glass transition temperatures increases with PVE content, consistent with more pronounced thermorheological complexity of blends rich in PVE. The individual [...] also exhibit different compositional dependence from that of the calorimetric [...] of blend. This behavior can give rise to the complex compositional dependence of individual mobilities, apparent when mobilities are compared at the same [...], with respect to the calorimetric [...] of blend. Origins of these two types of dynamic heterogeneity are examined further by using a simple model that takes into account effect of random compositional variations. Although compositional variations can give rise to the observed width of mobility distribution and its compositional dependence, the observed difference in mean mobilities cannot be explained at the same time. This suggests that the observed dynamic heterogeneities can be explained only by including two distinct contributions: local compositional variations in the blend and intrinsic difference in chain mobilities. Distinct dynamic constraints between the two species can arise from their structural differences. In light of phenomenological models of cooperative local dynamics, distinct mobilities can arise from the difference in critical size of free volume or in cooperativity.\r\n" }, { "name": "Cohen, Scott B.", "degree": "PhD", "year": "1995", "title": "Mechanistic studies of the natural DNA-cleaving agents neocarzinostatin chromophore, calicheamicin [gamma]1, and dynemicin A", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182007-090157", "creators": [ { "name": { "family": "Cohen", "given": "Scott B." }, "id": "Cohen-S-B", "display_name": "Cohen, Scott B." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZJH6-AC74", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nExperiments establishing the intermediacy of the cumulene derived from neocarzinostatin chromophore are described. It is shown that [...]95% of DNA cleavage arises via the cumulene. The sequence specificity and efficiency of DNA cleavage by externally generated cumulene are identical to that by the cumulene formed in situ, supporting the proposal that the cumulene determines the sequence specificity of DNA cleavage. It is shown that DNA and a water-soluble cyclohexadiene derivative are equally effective in trapping of the biradical intermediate at concentrations of 5 mM and 1 M, respectively, supporting the idea that the biradical must be generated as a DNA-bound species to induce DNA cleavage.\r\n\r\nThe reaction of calicheamicin [...] with glutathione has been studied in the presence of DNA and is shown to produce all four products arising from S-S bond exchange. The calicheamicin-glutathione disulfide is formed as the major product of this reaction, and is shown to be 2-3 orders of magnitude less reactive toward glutathione than is calicheamicin [...]. The rate of DNA cleavage by calicheamicin [...] is essentially independent of the concentration of DNA, while the rate of DNA cleavage by the calicheamicin-glutathione disulfide is inversely proportional to the concentration of DNA. The data support the hypothesis that calicheamicin [...] undergoes thiol activation as a DNA-bound species, while the calicheamicin-glutathione disulfide is activated free in solution.\r\n\r\nBinding constants of dynemicin A and synthetic analogs to DNA show that the two E-ring hydroxyls of the anthraquinone contribute approximately 2.7 kcal/mol binding energy, and that neutralization of the negatively-charged carboxylate stabilizes the drug DNA binding complex by ~3 kcal/mol. Dynemicin A and the synthetic analogs display an inverse rate dependence on the concentration of DNA, supporting the proposal that these drugs must dissociate from DNA prior to chemical activation.\r\n" }, { "name": "Flatt, Brenton T.", "degree": "Masters", "year": "1995", "title": "Transition metal alkylidene complexes via the ring-opening of cyclopropenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10262007-082758", "creators": [ { "name": { "family": "Flatt", "given": "Brenton T." }, "id": "Flatt-B-T", "display_name": "Flatt, Brenton T." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9zd6-rr52", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe first chapter details the preparation and structural characterization of a rhenium (VII) oxo-vinylalkylidene complex and discusses its activity in olefin metathesis reactions. A substitution reaction affords the rhenium (V) oxo-trisalkoxide precursor, a species that \nsurprisingly adopts a facial arrangement of three very bulky alkoxide ligands in its crystal structure. This complex reacts with 3,3-diphenylcyclopropene in a non-coordinating solvent to yield a mixture of two rhenium alkylidene isomers. Over time one species \npredominates and is isolated. An X-ray diffraction study of the isolated complex and [...] NMR studies of the isomerization process are described. Reactivity studies indicate that the isolated product demonstrates very limited olefin metathesis activity. However, the addition of Lewis acid cocatalysts to the rhenium alkylidene complex generates a much more active catalyst system, in particular, for the metathesis of cis-2-pentene. No propagating alkylidene species are observed during the metathesis reaction.\n\nThe second chapter describes the synthesis and characterization of a dicyclopropene compound from which the preparation of ROMP diinitiators is reasoned to be possible. The starting material-1,4-di(1-phenylvinyl)benzene-is readily prepared via a Grignard reaction and subsequent dehydration. A series of three steps analogous to those of the 3,3 diphenylcyclopropene synthesis yield the desired roduct-1,4-di(1-phenylcycloprop-2-enyl)benzene. Alternate pathways to the product also are proposed and the investigations are detailed. In particular, a biphasic cyclopropanation reaction using either bromoform or chloroform as a carbene source affords the respective dicyclopropane intermediates. Ultimately the syntheses of bis(metal alkylidene) complexes from reactions of this dicyclo-propene with various transition metal precursors have implications for the formation of polymers which propagate in two directions and for the preparation of triblock copolymers.\n" }, { "name": "Fraley, Mark E.", "degree": "PhD", "year": "1995", "title": "Synthesis of (+)-dynemicin A and analogs of wide structural variability. Establishment of the absolute configuration of natural dynemicin A", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10022007-135120", "creators": [ { "name": { "family": "Fraley", "given": "Mark E." }, "id": "Fraley-M-E", "display_name": "Fraley, Mark E." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7a9e-t435", "abstract": "A highly convergent synthetic route to the potent natural antitumor agent (+)-dynemicin A (1) is described. Key features of the synthesis include: (1) the condensation of the potassium enolate of menthyl acetoacetate with trans-ethyl crotonate, providing the optically pure trans-disubstituted 1,3-cyclohexanedione 38; (2) the palladium-catalyzed coupling of the enol triflate 37 with t-butyl 2-borono-4-methoxycarbanilate to furnish 35, followed by the thermolysis of the latter to afford the quinolone 34; (3) the stereoselective acetylide addition of the (Z)-enediyne bridge to an acylquinolinium intermediate derived from quinoline 60, affording the addition product 61; (4) the acetylide-mediated closure of the (Z)-enediyne bridge of ketone 65 to produce 66; (5) the carboxylation and subsequent methylation of ketone 69, providing the vinylogous carbonic acid 70; (6) the oxidation of the phenol 73 to furnish the enone 74, as well as the reductive deprotection of 75 to afford the quinone imine 77; and (7) the Diels-Alder cycloaddition reaction of the quinone imine 77 with 1,4,7-tris(trimethylsiloxy)isobenzofuran, followed by the desilylation and oxidation of the resultant adduct to complete the synthesis of 1. The preparation of structurally diverse analogs of 1 by late-stage modification of the synthetic route is detailed. The absolute configuration of natural 1 is determined to be 2S, 3S, 4S, 7R, 8R, by the comparison of circular dichroism spectra of synthetic and authentic 1.\r\n" }, { "name": "France, Marcia Beth", "degree": "PhD", "year": "1995", "title": "Olefin metathesis with group VIII transition metal complexes : mechanism, reactivity, and catalyst development", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10122005-083645", "creators": [ { "name": { "family": "France", "given": "Marcia Beth" }, "id": "France-M-B", "display_name": "France, Marcia Beth" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/STRQ-Z291", "abstract": "Group VIII olefin metathesis catalysts are unusually functional group tolerant but are limited by their low reactivity and ill-defined nature. In order to address these concerns, mechanistic investigations of the Ru(H2O)6(tos)2-catalyzed ring-opening metathesis polymerization of norbornene and 7-oxanorbornene derivatives in aqueous media have been undertaken. Primarily through chain transfer studies and end group analysis, evidence supporting the intermediacy of ruthenium carbene species has been obtained. Furthermore, acyclic olefins have been shown to provide efficient molecular weight regulation during these polymerizations, allowing control of the polymer molecular weight and the identification of ring-opened units with well-defined functionalized end groups. The molecular weight regulation appears to occur by a standard chain-transfer mechanism.\r\n\r\nMethods of expanding the reactivity of group VIII metathesis catalysts to a wider variety of substrates have been developed. The polymerization of low-strain cyclic olefins such as cyclooctene was achieved with Ru(H2O)6(tos)2 in the presence of ethyl diazoacetate as an initiator. Such a finding indicates that the difficulties in polymerizing such monomers in the original system lies in the initiation and not in the propagation step. This result is an important indication that the development of more reactive group VIII systems is possible if the barrier to initiation can be overcome.\r\n\r\nIn addition, several iridium based systems for the polymerization of low-stain olefins are presented. Furthermore, [(COE)2IrCl]/AgO2CCF3 was found to be an active catalyst for the simultaneous isomerization/olefn metathesis of acyclic olefins, including methyl oleate. This transformation is essentially a single-step analogue of the two-step Shell Higher Olefins Process. The reaction conditions can also be varied to favor more selective metathesis without accompanying isomerization.\r\n\r\nFinally, a number of new, isolable ruthenium carbene complexes have been prepared by alkylidene transfer from diazo compounds. Several of these species are active catalysts for the ring-opening metathesis polymerization of norbornene, and one such system appears to be living. This route offers a facile entry into complexes with catalytic activity identical to that observed with ruthenium carbenes prepared from the less accessible 3,3-diphenylcyclopropene. This method appears to be a general route into ruthenium carbene complexes.\r\n" }, { "name": "Hajela, Sharad", "degree": "PhD", "year": "1995", "title": "Synthetic, structural, and mechanistic studies of homogeneous Ziegler-Natta catalysis", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052007-131102", "creators": [ { "name": { "family": "Hajela", "given": "Sharad" }, "id": "Hajela-S", "display_name": "Hajela, Sharad" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9nxq-m253", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe reaction of [...] with isobutene produces [...] along with isobutane, 2-methylpentane, isobutene, 2-methyl-l-pentene, propane and n-pentane. These products arise from a series of reactions involving olefin insertion, [...] and (faster) [...] elimination which proceeds until only the 2-methyl-l-alkenes [...] and the predominant organoscandium product [...] remain. A transient observed in the reaction sequence has been characterized as [...]. Slower [...] bond metathesis involving the methyl C-H bonds of [...] and the Sc-C bonds of the scandium alkyls accounts for the observation of saturated alkanes (2-methylalkanes [...], etc. ), normal alkanes [...] as well as a minor organoscandium product [...] in the product mixture. [...]-Ethyl migration is not observed for the closely related 2-ethyl-butyl derivative, [...], obtained from reaction of 2-ethyl-1-butene with [...].\n\nThe cyclopentylmethyl derivative, [...], slowly and cleanly decomposes in cyclohexane to give methylcyclopentane and a yellow crystalline precipitate. The [...] NMR spectrum of the yellow product is consistent with a compound containing one [...] and one [...], the latter arising via metallation of a [...] ligand (i.e. a \"tuck-in\" complex). The structure of the complex which crystallizes as the dimer, [...], when allowed to form slowly at room temperature is reported.\n\nReaction of the neutral ligand 1,4,7-trimethyl-1,4,7-triazacyclononane (Cn) with [...] in acetonitrile affords the novel trihalide complexes [...]. Subsequent alkylation with [...] in THF cleanly gives the corresponding trimethyl species [...]. Reactivity studies reveal that the metal carbon bonds of these 12 [...] complexes are remarkably unreactive toward insertion chemistry with typical unsaturated substrates such as olefins and acetylene. 2-butyne does, however, react with [...] by C-H activation to give a compound that is characterized as an equilibrium mixture of a major allenyl form with a minor propargyl component. In general, [...] is significantly more stable, but less reactive, than [...]. Activation of [...] with [...] or [...] results in partially characterized complexes which exhibit olefin polymerization chemistry. The crystal structure of [...] has been determined.\n\nWe have recently described the highly iso-specific Ziegler-Natta polymerization of [alpha]-olefins using the single component, [...] symmetric metallocene [...]. The steric bias exerted by the cyclopentadienyl substitution pattern allows for formation of only the desired racemic product upon metallation, with no detectable amount of the undesired meso isomer. A natural extension is the further development of methods for obtaining enantiomerically pure catalysts based on the [Bp] ligand system. Such single-component systems, in addition to serving as powerful mechanistic probes of Ziegler-Natta catalysis, would also be promising candidates for use in a variety of other catalytic asymmetric transformations. The most desirable ligand design would produce only one enantiomer upon coordination to the metal. Thus, not only would the wasteful and tedious separation of the meso isomer be avoided, but the subsequent resolution of the racemate would also be obviated. We have found that employment of chiral silyl-linkers is an effective design strategy for the synthesis of such enantiomerically pure complexes. Described herein are our efforts which have led to the synthesis of the ligand [...], designed to coordinate to give only one enantiomer, and BnBpY-H, the first example, as far as we are aware, of an enantiopure [...]-symmetric, group III metallocene which is competent for coordination polymerization of [alpha]-olefins.\n" }, { "name": "Han, Hogyu", "degree": "PhD", "year": "1995", "title": "Study of RNA structure by affinity cleaving", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052007-081104", "creators": [ { "name": { "family": "Han", "given": "Hogyu" }, "id": "Han-H", "display_name": "Han, Hogyu" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "member", "display_name": "Abelson, John N." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fwfk-4p70", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nChapter 1. Sequence-specific recognition of double helical RNA and RNA\u2022DNA by triple helix formation.\r\n\r\nThe stabilities of eight triple helical pyrimidine\u2022purine\u2022pyrimidine structures comprised of identical sequence but different RNA (R) or DNA (D) strand combinations were measured by quantitative affinity cleavage titration. The differences in equilibrium binding affinities reveal the importance of strand composition. For the sequences studied here, the stabilities of complexes containing a pyrimidine third strand D or R and purine\u2022pyrimidine double helical DD, DR, RD, and RR decrease in order: D + DD, R + DD, R + DR, D + DR > R + RD,R + RR >> D + RR,D + RD (pH 7.0, 25\u00b0C, 100 mM NaCl / 1mM spermine). These findings suggest that RNA and DNA oligonucleotides will be useful for targeting (i) double helical DNA and (ii) RNA\u2022DNA hybrids if the purine Watson-Crick strand is DNA. However, RNA, but not DNA, oligonucleotides will be useful for sequence-specific binding of (i) double helical RNA and (ii) RNA\u2022DNA hybrids if the purine Watson-Crick strand is RNA. This has implications for the design of artificial ligands targeted to specific sequences of double helical RNA and RNA\u2022DNA hybrids.\r\n\r\nChapter 2. Different conformational families of pyrimidine\u2022purine\u2022pyrimidine triple helices depending on backbone composition.\r\n\r\nDifferent helical conformations of DNA (D), RNA (R), and DNA\u2022RNA (DR) hybrid double and triple helices have been detected using affinity cleavage analysis. Synthetic methods were developed to attach EDTA\u2022Fe to a single nucleotide on RNA as well as DNA oligonucleotides. Cleavage patterns generated by a localized diffusible oxidant in the major groove on the pyrimidine strand of four purine\u2022pyrimidine double helices consisting of all DNA, all RNA, and the corresponding hybrids reveal that the relative cleavage intensity shifts to the 5' end of the purine strand increasingly in the order: DDIn Chapter 1, the recently developed aqueous ROMP was exploited in the synthesis of a polymer with pendant imide groups. The polymerization of exo-N-methyl-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboximide was accomplished in aqueous solution under mild conditions using the simple ruthenium(II) coordination complex RuIIH\u2082O\u2086tos\u2082 (tos=p-toluenesulfonate). The resultant high molecular weight polymer was isolated in high yield, exhibited a Tg of 225\u00b0C, and was thermally stable up to 402\u00b0C. Hydrogenation of the polymer yielded its saturated analog which exhibited a lower Tg (170\u00b0C) but a higher temperature of decomposition 430\u00b0C. Requirements for successful polymerization were investigated.
\r\n\r\nIn Chapter 2, the ROMP of a variety of 5-substituted cyclooctenes by the well-defined metathesis catalyst (PCy\u2083)\u2082(Cl)\u2082RuCHCHCPh\u2082 (1) was accomplished. The polymers were obtained in moderate to good yields. The structures of the polymers were investigated by IR, \u00b9H NMR, and \u00b9\u00b3C NMR spectroscopies. The molecular weight of one of the derivatives was controlled by varying the monomer to catalyst ratio and by the addition of a chain transfer agent to the polymerization solution. The thermal properties of the polymers are reported.
\r\n\r\nIn Chapter 3, the ring-opening metathesis polymerization (ROMP) of cyclooctadiene (COD) by three well-defined metathesis catalysts in the presence of a variety of chain transfer agents (CTAs) is described. Expressions for the theoretical molecular weight and functionality were derived for this type of ROMP system. Hydroxytelechelic polybutadienes (HTPBDs) synthesized contained one type of regiochemistry in the repeat unit (1,4) and one type of alcoholic endgroup. The molecular weight of the HTPBDs was controlled by the ratio of COD to CTA and number average functionalities that approached 2.0 were obtained at high CTA to catalyst ratios.
" }, { "name": "Hodge, Julia A.", "degree": "PhD", "year": "1995", "title": "Properties of distorted tetraphenylporphyrins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10092007-082429", "creators": [ { "name": { "family": "Hodge", "given": "Julia A." }, "id": "Hodge-J-A", "display_name": "Hodge, Julia A." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bwee-h202", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nX-ray crystallographic structure determinations reveal that tetrakis(pentafluorophenyl)-porphyrin derivatives substituted with bulky [beta]-substituents undergo a tetrahedral distortion that reduces the macrocyclic symmetry from [...] to [...]. The nickel complex of [2,3,7,8,12,13,17,18-octabromo-5,10,15,20-tetrakis(pentafluorophenyl)porphyrin], [...], has nitrogen atoms displaced \u00b10.192 [...] and meso-carbons \u00b10.211 [...] from the plane of the porphyrin. Despite large conformational changes, bond distances and angles are essentially conserved for all tetraphenylporphyrins. Electrochemical and UV-vis spectroelectrochemical experiments revealed a novel, ligand-centered two-electron (2e) oxidation for Zn and Mg derivatives. Values for the 1e potentials were calculated from [...], the constant for the disproportionation of the singly oxidized product into the doubly oxidized and the neutral species, [...], and the Nernst equation. The redox potentials are consistent with semiempirical AM1 calculations that indicate that [...] distortion destabilizes the HOMOs [...] preferentially over the [...] LUMOs whereas halogen substitution lowers the energy of both the HOMO and the LUMO approximately equally. Consistent with the meso-substituent influencing relative ordering, EPR spectra of [...], and [...], and [...] reveal [...] and [...] HOMOs, respectively. Furthermore, the [beta]-octaethyl and octamethyl tetrakis(pentafluorophenyl)porphyrins undergo a similar net 2e oxidation. Thus, the distortion observed in the neutral molecule appears to mirror an electronically favorable geometry for the doubly oxidized product. An understanding of the sterics and electronics that influence frontier orbital energy levels creates the possibility of tuning porphyrins for a variety of applications: light harvesting, electron transfer, and catalytic reactions involving 2e reductions.\n" }, { "name": "Johnson, Robert David", "degree": "PhD", "year": "1995", "title": "Multivalent Protein Binding to Metal-Complexing Materials: Applications to Synthetic Receptors and Affinity Chromatography", "advisor": "Arnold, Frances Hamilton", "url": "https://resolver.caltech.edu/CaltechETD:etd-10122007-091509", "creators": [ { "name": { "family": "Johnson", "given": "Robert David" }, "id": "Johnson-Robert-David", "display_name": "Johnson, Robert David" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" } ], "committee": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "chair", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "orcid": "0000-0001-9883-1600", "role": "member", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "member", "display_name": "Davis, Mark E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6kdk-t643", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\n\r\nThis investigation demonstrates that proteins have the capability to bind \r\nsimultaneously to multiple transition metals of metal-complexing materials. This finding \r\nhas important implications for the design of novel materials for protein recognition. Our \r\napproach to protein recognition, based on intermolecular metal-to-ligand interactions, \r\nmatches a protein's unique pattern of histidines with a complementary arrangement of \r\ntransition metal complexes.\r\n\r\n A model system is used to demonstrate the validity of this approach in the \r\nsimplest case by matching the distance between metal ions of rationally designed bis-metal [...] \"receptors\" to that between imidazoles of bis-imidazole \"targets.\" This \r\nsystem additionally demonstrates how other features of receptor design can influence \r\nbinding selectivity. A 2D NMR procedure is developed to measure directly protein \r\nsurface histidine binding to copper complexes, and subsequently demonstrates that the \r\nlocal environment of the histidine and the structure of the copper complex can modulate \r\nindividual copper-histidine interactions. Thus it may indeed be possible to design metal-containing receptors which are able to form simultaneous metal-ligand bonds with a \r\nspecific arrangement of protein metal-coordinating groups.\r\n\r\n There are two important obstacles preventing a similarly detailed description of \r\nprotein binding to metal-complexing surfaces: protein adsorption may involve binding to \r\none or more metal sites, and a detailed description of the geometry of surface metal sites \r\nwould be hopelessly complex. We can, however, apply the microscopic concept of \r\nsimultaneous metal-ligand interactions to interpret the macroscopic phenomena of \r\nprotein partitioning in immobilized metal affinity chromatography (IMAC). In this \r\ncontext, the ability of commercially available IMAC materials to support multiple \r\nprotein-surface interactions is shown to be dependent on three factors: the number of\r\nhistidines on the protein (as manipulated by site directed mutagenesis), the number of \r\ndeprotonated amino groups on the protein (pH control), and the density of binding sites \r\non the surface (copper loading). These results demonstrate that a realistic description of \r\nprotein binding in IMAC must consider a heterogeneous population of surface binding \r\nsites. In IMAC this is shown to be conveniently expressed by the Temkin isotherm, \r\nmaking it an instructive model to explore heterogeneity displayed by other \r\nchromatographic materials and by biological systems." }, { "name": "Kannan, Rangaramanujam Mudumbai", "degree": "PhD", "year": "1995", "title": "Flow-induced alignment in intrinsically anisotropic polymeric materials", "advisor": "Kornfield, Julia A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10112007-104204", "creators": [ { "name": { "family": "Kannan", "given": "Rangaramanujam Mudumbai" }, "id": "Kannan-R-M", "display_name": "Kannan, Rangaramanujam Mudumbai" } ], "advisors": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "advisor", "display_name": "Kornfield, Julia A." } ], "committee": [ { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "chair", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZDCX-2W89", "abstract": "To understand the processing behavior of complex polymeric materials, it is imperative that we understand the distinct underlying molecular and microstructural contributions to macroscopic mechanical response. We have developed rheo-optical methods to isolate the dynamics at such length scales, by combining conventional mechanical testing with polarimetry. The rheology and flow-induced alignment in side-group liquid-crystalline polymers (SG-LCPs) and lamellar diblock copolymers (BCPs) have been investigated using the rheo-optical apparatus.\r\n\r\nThe rheology of SG-LCPs arises from a combination of the polymeric nature of the backbone, the ordering tendency of the mesogens, and the coupling between the two introduced by the spacer. Contrary to previous studies, we find that the nematic order can significantly affects the macroscopic viscoelastic response in SG-LCP melts. In the nematic state, we have discovered that oscillatory shear is effective in inducing macroscopic orientation of the sample. Shear flow may prove to be an economical, efficient way to obtain macroscopically aligned SGLCPs, which have potential as optical data storage media and nonlinear optical materials. In contrast to magnetic field induced alignment, the mechanism of shear induced alignment appears to bedriven by the distortion of the polymer backbone.\r\n\r\nWe study the mechanisms of flow-induced alignment in a poly(ethylenepropylene)-poly(ethylethylene) lamellar diblock copolymer, which produce macroscopic alignment with lamellae normal along the shear gradient direction ('parallel' alignment), or along the vorticity direction ('perpendicular' alignment). We accomplish this by monitoring the evolution of the microstructure and viscoelasticity in situ during the alignment process. Our results suggest that 'parallel' alignment occurs due to irreversible 'rocking' of grains which tends to align the grains along the shear direction, whereas 'perpendicular' alignment occurs at conditions where the microscale deformation is nearly homogeneous." }, { "name": "Karp, Christoph D.", "degree": "Masters", "year": "1995", "title": "Photoelectrochemistry of Si/polymer and Si/metal/solution interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-10262007-085203", "creators": [ { "name": { "family": "Karp", "given": "Christoph D." }, "id": "Karp-C-D", "display_name": "Karp, Christoph D." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7enk-wj52", "abstract": "Part I of this thesis describes the formation of a silicon/polypyrrole junction utilizing a new method of polypyrrole polymerization which was developed in the Lewis Group by Dr. Michael Freund. This new method involves the chemical oxidation of pyrrole to form smooth, conducting polypyrrole films upon solvent evaporation. This polymerization process allows semiconductor/polymer junctions to be formed without exposing the silicon surface to harmful oxidative currents used in electrochemical polymerizations. The studies described herein demonstrate the formation of a stable, rectifying junction between silicon and chemically polymerized polypyrrole.\n\nPart II of this thesis describes work related to a recent hypothesis regarding the charge-transfer processes of metal-coated silicon electrodes in methanol solutions, proposed by Ming Tan of the Lewis Group. The silicon is modified by depositing thin metal lines onto the surface, which facilitate electron-transfer between the silicon and the solution and limit direct charge transfer through the silicon/solution interface. The design of these devices allows examination of the interaction of semiconductor/metal and semiconductor/liquid junction characteristics as a function of the size and distribution of metal lines.\n" }, { "name": "Kephart, Susan E.", "degree": "Masters", "year": "1995", "title": "Synthetic and mechanistic studies on a silicon-mediated aldol reaction", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-10312007-082516", "creators": [ { "name": { "family": "Kephart", "given": "Susan E." }, "id": "Kephart-S-E", "display_name": "Kephart, Susan E." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/t9y9-zk34", "abstract": "No abstract submitted.\n\n" }, { "name": "Khouw, Charles B.", "degree": "PhD", "year": "1995", "title": "Partial oxidation of hydrocarbons using titanium containing molecular sieves", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10122007-103304", "creators": [ { "name": { "family": "Khouw", "given": "Charles B." }, "id": "Khouw-C-B", "display_name": "Khouw, Charles B." } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9dyq-m742", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe objective of this work is to investigate the reaction mechanism of alkane activation on titanium containing, aluminum-free ZSM-5 (TS-1) and to elucidate the relationships between the physicochemical properties of the catalyst and its reactivity. Samples of TS-1 have been synthesized using different methods. The activities of these catalysts for the oxidation of alkanes, alkenes and phenol at temperatures below 100 [...] using aqueous [...] as oxidant are reported and compared to those from other titanium containing materials, e.g., anatase and an amorphous [...] coprecipitate.\r\n\r\nComparisons between the activities of TS-1 and [...] coprecipitate for alkane oxidation and alkene epoxidation using non-aqueous [...] indicate that the absence of water is crucial for the catalytic activity of silica-supported titanium oxide. Due to the hydrophobicity of TS-1, the concentration of water surrounding the titanium is maintained at low value so that aqueous [...] can be used as oxidant on this catalyst.\r\n\r\nIssues of mechanism of the alkane oxidation on TS-1 are investigated by analyzing the stereoselectivity pattern of cis- and trans-1,3-dimethylcyclopentane, the \"radical clock\" rearrangement of ethyl- and isopropylcyclopropane and the effect of oxidants on the catalytic activity of TS-1. The stereoselective reaction pattern of cis- and trans-1,3-dimethylcyclopentane indicates that radicals are formed during alkane oxyfunctionalization with TS-1. The presence of stereos crambling without any \"radical clock\"\r\nrearrangement during alkane oxidation on TS-1 reveals that the radicals formed may have a very short life-time or their movements are restricted such that no rearrangement can occur. A proposal for the mechanism of alkane oxidation on TS-1 is given and compared to a mechanism suggested for alkene epoxidation on TS-1 and the [...] coprecipitate. Alkyl hydroperoxides are active as oxidants for alkene epoxidation on the [...] coprecipitate but not for alkane oxidation reactions on both TS-1 and the [...] coprecipitate. A plausible explanation for the above results is provided.\r\n\r\nThe presence of alkali metal ions in the synthesis mixture of TS-1 completely eliminates the catalytic activity of this material. However, the catalytic activity can be restored by washing the solid with acid solution prior to catalytic testing. The washing removes [...] ions from silanol groups adjacent to the framework titanium active centers. Thus, it is postulated that a silanol group in the neighborhood of the titanium atom is a necessary feature for catalytic activity. The acid treatment may be useful in overcoming the problems of synthesizing TS-1 from reagents that contain alkali metal ions, e.g., TPAOH solutions. More importantly, this treatment opens the possibility of synthesizing other titanium containing silicate structures that require the presence of alkali metal ions in the synthesis mixture for their formation.\r\n\r\n" }, { "name": "Kiang, Ching-Hwa", "degree": "PhD", "year": "1995", "title": "Physics and chemistry of advanced nanoscale materials : experiment, simulation, and theory", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-10162007-105256", "creators": [ { "name": { "family": "Kiang", "given": "Ching-Hwa" }, "id": "Kiang-C", "display_name": "Kiang, Ching-Hwa" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4t4q-5805", "abstract": "This thesis discusses simulation and theory of lattice dynamics as well as experiments on novel forms of carbon.\n\nA new crystalline AgBr interaction potential was constructed by fitting literature experimental data. The shell model was successfully used to account for the polarizabilities of the ions. This approach overcame difficulties previous investigators faced in determining the AgBr potential.\n\nThe very useful shell model was generalized to allow, for the first time, its use in dynamical simulations. The rapid shell dynamics, simulating the electron polarization, were integrated out in a generalized Born-Oppenheimer-like approach. The effective Hamiltonians were derived for both quantum and classical descriptions of the shells.\n\nThe first crystallization and characterization of a metallofullerene were performed. Endohedral metallofullerenes were synthesized and characterized. Metals such as Sc, Y, and Er that formed stable compounds in fullerene cages were synthesized and products purified. The crystal structure of Sc2C84 was determined by transmission electron microscopy study.\n\nExperimental studies on fullerenes and related materials lead to the first example of a catalytically-grown, fullerene-like material. We discovered that single-layer carbon nanotubes can be produced by vaporizing cobalt and carbon with an electric arc in a helium atmosphere. Catalyst promoters such as sulfur, bismuth, and lead were found not only to enhance the yield of single-layer nanotubes but also to produce tubes in a diameter range not accessible with cobalt alone. Sulfur, bismuth, and tungsten were found to catalyze the formation of cobalt crystals encapsulated in graphitic polyhedra. Various carbon structures were also produced concurrently, e.g. multilayer nanotubes, strings of carbon nanocompartments, carbon nanofibers, and metal-filled nanomaterials. Nanotubes were observed to undergo real-time structural changes under electron beam heating.\n\nA growth model of single-layer nanotube was formulated based on the experimental results. The carbon ring is regarded as the nanotube precursor, and cobalt carbide is regarded as the catalytic species that efficiently supplies carbon clusters to the open end of tube. The catalyst promoter assists the reaction by keeping the growing end open.\n" }, { "name": "Kim, Kyoung-Hee", "degree": "PhD", "year": "1995", "title": "Crystallographic structure determination of neocarzinostatin, an antitumor protein-chromophore complex", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10162007-094617", "creators": [ { "name": { "family": "Kim", "given": "Kyoung-Hee" }, "id": "Kim-K", "display_name": "Kim, Kyoung-Hee" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6nef-8t49", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nCrystal structures of the protein-chromophore complex and the apoprotein form of the natural antitumor antibiotic neocarzinostatin (NCS) have been determined at 1.8 [...] resolution. NCS is composed of a labile chromophore component with DNA-cleaving activity and a protein component that binds and stabilizes the chromophore. The NCS protein consists of the large domain of a seven-stranded [beta] barrel and the small domain. The chromophore is bound noncovalently in a pocket between the two domains, primarily through van der Waals contacts with many nonpolar residues. [...] and [...] contact the two [pi] faces of the nine-membered enediyne ring through an edge of each benzene ring. [...] additionally contacts the aminosugar group through its [pi] face. The positioning of [...] represents the most significant difference between the holo- and apo-protein structures; in apo-NCS, [...] rotates to a more solvent-exposed position. The epoxide and C12 (the site of nucleophilic thiol addition during activation of the chromophore) are sequestered from the solvent, which likely contribute to the stability of the chromophore in holo-NCS. The amino group of the chromophore is oriented above C12 at a distance approximately the van der Waals diameter of a sulfur atom, supporting the idea that this group plays a role in the thiol activation mechanism. While the basic protein structure is conserved among at least five chromoprotein antibiotics, [...] is unique to NCS, perhaps accounting for the binding specificity of neocarzinostatin for its chromophore.\n\nWe have systematically investigated the effects of parameters in the molecular replacement methods on NCS using three different programs. The model with side chains of conserved residues and the maximum vector length or the integration radius of about half the diameter of the molecule, gave the best result. The low resolution limit of 15 [...] was needed for the rotation function calculation in both X-PLOR and AMoRe. The program MERLOT failed to give molecular replacement solutions in this case.\n" }, { "name": "Langen, Ralf", "degree": "PhD", "year": "1995", "title": "Electron transfer in proteins : theory and experiment", "advisor": "Gray, Harry B.; Richards, John H.; Warshel, Arieh", "url": "https://resolver.caltech.edu/CaltechETD:etd-03062006-091606", "creators": [ { "name": { "family": "Langen", "given": "Ralf" }, "id": "Langen-R", "display_name": "Langen, Ralf" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." }, { "name": { "family": "Warshel", "given": "Arieh" }, "id": "Warshel-A", "role": "advisor", "display_name": "Warshel, Arieh" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1sg4-x578", "abstract": "This thesis consists of two main parts and one appendix. The first part (Chapters 2 and 3) contains mainly experimental work on electron transfer in ruthenium-modified azurin mutants. The second part describes theoretical studies on the control of reduction potentials in cytochromes and feredoxins. The appendix presents calculations on the reaction mechanism for the GTP-hydrolysis in Ras p21.\n\nIn the experimental part electron tunneling through the beta-sheet in pseudomonas aeruginosa azurin is discussed. In agreement with theoretical consideration it is found that electron tunneling through a beta-strand is quite efficient. It is argued that the efficiency is due to the highly covalent nature of the bridge. Furthermore, the effects of the weakly coordinated M121 ligand and the strongly coordinated C112 ligand on the coupling are compared in Chapters 2 and 3. It is found that indeed the C112 ligand facilitates electron transfer, although the rate enhancement in the experiments does not appear to be much more than an order of magnitude.\n\nThe theoretical section (chapters 4-6) presents microscopical calculations of electrostatic effects found to be important for the control of reduction potentials. Chapter 4 analyzes the effect of the N521 mutation in cytochrome c. The calculations suggest that the change in reduction potential is due to an electrostatic effect and dominated by the loss of the N52 dipole, which compensates for the displacement of an internally bound water molecule. In chapter 5 it is concluded that the change in reduction potential for the M80H axial ligand replacement in cytochrome c is due to the effect of the ligand bonding rather than an electrostatic effect. The enormous variations in the reduction potentials of iron-sulfur clusters in several proteins are being investigated in chapter 6. The potentials mainly appear to be controlled by the number of hydrogen bonds. However, in some cases the effect of nearby water molecules need to be considered. The calculations presented in the appendix show that a previously proposed mechanism in Ras P21 does not appear energetically feasible (reprint 1). In reprint 2 an alternative mechanism is proposed." }, { "name": "Lee, Kelvin H.", "degree": "PhD", "year": "1995", "title": "The effects of the deregulated expression of the cloned transcription factor E2F-1 on Chinese hamster ovary cells", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-132158", "creators": [ { "name": { "family": "Lee", "given": "Kelvin H." }, "id": "Lee-K-H", "display_name": "Lee, Kelvin H." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9dwx-6f88", "abstract": "E2F-1 is one of a family of transcription factors known to be involved in cell cycle regulation at the G1/S phase transition. Several proteins intimately involved in DNA synthesis are regulated by the E2F-1 transcription factor family. It is believed that the presence of free E2F-1 in mammalian cells is required to activate transition of cells through the G1-S restriction point of the cell cycle. Stable clones from CHO K1 cells transfected with an expression vector for human E2F-1 were created. All of the clones expressed significantly higher amounts of E2F-1 than control cells as determined by Western analysis. Several clones were further studied by confocal microscopy and Southern analysis. Both of these studies also provide evidence for the expression of cloned E2F-1 in these CHO cells. CHO K1:E2F1 cells are able to proliferate in well-defined medium completely free from proteins or serum and flow cytometric analysis of CHO K1:E2F-1 cells indicates a prolonged S-phase compared to CHO cells grown by bFGF stimulation and by cyclin E overexpression. Two-dimensional gel electrophoresis (2DE) of CHO cellular proteins reveals increased expression of 236 spots indicating significant regulatory effects for cloned E2F-1 in CHO cells. These 2DE results also suggest new routes to identification of gene products regulated by a particular transcription factor. Expression of cloned E2F-1 is an important means for bypassing the serum requirement of mammalian cell culture. Metabolic engineering of cell cycle regulation bypasses exogenous growth factor requirements, addressing a priority objective in economical, reproducible, and safe biopharmaceutical manufacturing.\n" }, { "name": "Lim, Kian-Tat", "degree": "PhD", "year": "1995", "title": "Mega-molecular dynamics on highly parallel computers : methods and applications", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-10152007-143016", "creators": [ { "name": { "family": "Lim", "given": "Kian-Tat" }, "id": "Lim-K", "display_name": "Lim, Kian-Tat" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e3qc-t131", "abstract": "Large-scale systems of thousands and millions of atoms are of great interest in many areas of chemistry, biochemistry, and materials science. Atomic-level simulations of such systems can provide increased accuracy and especially enhanced insight and understanding when compared with either smaller-scale model calculations or grossly-averaged macroscopic models.\n\nMegamolecular simulations require large amounts of memory and computation, far more than can be provided by the typical scientific workstation. These resources can be most cost-effectively provided at this time by scalable massively parallel computers.\n\nThis thesis presents a large-scale, parallel, distributed-memory, general-purpose molecular dynamics code. The most time-consuming portion of the calculation, the computation of the nonbonded forces, is handled by the Cell Multipole Method, which was developed to overcome the speed and accuracy limitations of standard techniques for handling long-range power-law interactions in large molecular systems. Versions of the code for the KSR-1 and Intel Delta and Paragon parallel supercomputers are described, and performance, accuracy, and scalability results are given.\n\nThe applications section begins with a discussion of computational experiments leading to a prescription for choosing the value of the free timescale parameter in Nose-Hoover constant-volume, constant-temperature (NVT) canonical dynamics. This is followed by several applications of the above megamolecular dynamics codes to interesting chemical applications in the areas of argon cluster structure, polymer structure, surface tension of water drops, diffusion of gases through polymers, and viral structure.\n" }, { "name": "Lin, Jian", "degree": "PhD", "year": "1995", "title": "ATP modulation of the electron transfer between cytochrome c and cytochrome c oxidase", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10182007-085924", "creators": [ { "name": { "family": "Lin", "given": "Jian" }, "id": "Lin-J", "display_name": "Lin, Jian" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k5cg-8r54", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe mechanism by which ATP modulates the electron transfer activity of cytochrome [...] and cytochrome [...] oxidase (CcO) has been extensively investigated by the present thesis. The subunit location of magnesium ion of CcO has been identified as the subunit IV by chemical modification and amino acid sequence analysis. The pathway for the first electron input from cytochrome [...] to CcO has been studied by laser flash photolysis with native, type I, type II, [...]-depleted CcO. The first electron from cytochrome [...] inputs directly to either heme [...] or [...] with different rate. The electron input to [...] was finally deposited to heme [...] via fast electron transfer from [...] to heme [...]. The effect of 8-azido-ATP-modification on cytochrome [...] activity was examined by transient electron transfer, steady-state, and binding studies. The 8-azido-ATP-modification does significantly decrease the rate of electron transfer from heme [...] to heme [...], of CcO. The retardation effect of the 8-azido-ATP-modification on cytochrome [...] is largely due to the disruption of the cytochrome [...] docking surface for CcO, which results in different docking conformation assumed by modified cytochrome [...] to CcO. On the other hand, the effect of ATP binding to CcO on the electron input from cytochrome [...] to heme [...] has been extensively assayed by transient absorption experiments. 8-azido-ATP-modification of CcO has been shown to have similar effect on steady-state kinetics, binding affinity for cytochrome [...] and first electron input rate from cytochrome [...] as ATP non-covalent binding. The 8-azido-ATP-modification or ATP non-covalent binding to CcO decreases the electron transfer rate from cytochrome [...] to heme [...] to about 60% of that of native enzyme by the perturbation of the cytochrome [...] binding on CcO, which leads to a change of electronic coupling and/or branching of the electron input from cytochrome [...] to [...] (or heme [...]). The binding of ATP to CcO have been probed by ATP analog, TNP-ATP. The binding of TNP-ATP to CcO have been shown to have higher affinity than ATP itself. The higher binding affinity of TNP-ATP to CcO is due to a binding energy contributed by the interaction of TNP group with detergent. This high affinity TNP-ATP binding is relevant to the ATP effect as shown by steady-state kinetics, and binding studies. The ATP binding site at subunit IV of CcO is, thus, very close to lipid bilayer. The magnesium ion, located in subunit IV, is likely to provide the binding site for the ATP binding to CcO.\r\n" }, { "name": "Lobo, Raul Francisco", "degree": "PhD", "year": "1995", "title": "The Synthesis and Characterization of Novel High-Silica Zeolites", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06172005-085103", "creators": [ { "name": { "family": "Lobo", "given": "Raul Francisco" }, "id": "Lobo-Raul-Francisco", "display_name": "Lobo, Raul Francisco" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "orcid": "0000-0001-8294-1477", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/01DX-QC48", "abstract": "The synthesis and characterization of high-silica molecular sieves is reviewed using molecular recognition phenomena and structure-direction as the unifying themes. A comparative analysis between the synthesis conditions employed and the zeolite structures formed is carried out starting with the synthesis of clathradils or 0-dimensional zeolites, and extending to one-dimensional, multi-dimensional zeosils. The review finishes with the analysis of the combined effects of heteroatoms (Al, B and Zn) and organic structure-directing agents in zeolite product selectivity and thermodynamic stability.\r\n\r\nStructure-direction phenomena is further investigated using the synthesis and characterization of the pure-silica zeolite SSZ-24, prepared using the chiral molecule N(16)methylsparteinium hydroxide as the structure-directing agent. The material is characterized using X-ray powder diffraction (XRD), scanning electron microscopy (SEM), solid-state NMR spectroscopy, fourier transform IR spectroscopy (FTIR) and physical adsorption experiments. The B-substituted SSZ-24 prepared here is the first example where the isomorphous substitution of B for Si in the SSZ-24 framework is accomplished during synthesis using sodium borate as the source of B. The B can be easily substituted by Al. The Al-substituted SSZ-24 is an active catalyst for the cracking of alkanes and may be potentially useful in refinery and chemical processes.\r\n\r\nThe structure solutions and a detailed structural characterizations of the disordered zeolites SSZ-26 and SSZ-33 is presented. These two materials are the first synthetic zeolites with intersecting open 10- and 12-ring pore systems. SSZ-26 and SSZ-33 are expected to show a combination of reaction activity, selectivity and stability unique among known zeolites. SSZ-26 and SSZ-33 may be very useful for catalytic applications in the petrochemical and refining industries. The feasibility of synthesizing a zeolite whose pore structure has been designed a priori is demonstrated with the zeolite SSZ-26 and its structure-directing agent.\r\n\r\nThe synthesis of a new borosilicate, CIT-1, is described. The proposed structure of CIT-1 is confirmed by a Rietveld refinement of the synchrotron XRD pattern. CIT-1 is demonstrated to be an ordered polymorph of the SSZ-33 zeolites. The catalytic properties of CIT-1 are compared to the catalytic properties of known high-silica zeolites (ZSM-5 and zeolite beta) and CIT-1 is shown to be a very active catalyst for the cracking of n-butane. The synthesis of CIT-1 supports the idea that the chiral polymorph A of zeolite beta can be synthesized using the appropriate structure-directing agent.\r\n\r\nA combination of molecular modeling and 1H MAS NMR spectroscopy are used to characterize the interactions of structure-directing agents with the zeolite framework. The results indicate that to simulate correctly the energetic interaction and motional properties of structure-directing agents in zeolites, short-range and long-range forces, water molecules, silanol groups and defects need to be considered simultaneously.\r\n" }, { "name": "Longin, Teresa L.", "degree": "PhD", "year": "1995", "title": "Measurements of solvent effects on local barrier heights in scanning tunneling microscopy", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-085145", "creators": [ { "name": { "family": "Longin", "given": "Teresa L." }, "id": "Longin-T-L", "display_name": "Longin, Teresa L." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nyj2-gw70", "abstract": "Scanning tunneling microscopy (STM) has proven to be a powerful tool for obtaining atomic resolution images of surfaces and adsorbates on surfaces. In addition, the technique can be used to make highly localized electronic measurements of surfaces, adsorbates, and molecules in the tunnel gap. Such measurements, generally known as scanning tunneling spectroscopy (STS), can probe either the electronic density of states or the effective barrier height. Studying the effects of solvent on the effective barrier height is particularly interesting, since that is a direct measure of the bridging capacity of the solvent and has analogs in heterogeneous electron transfer and electron transfer in proteins and frozen glasses. Unfortunately, the effective barrier height as measured in STM experiments is very sensitive to contamination on the sample surface and on the tip, and it is difficult to differentiate between solvent effects and contamination effects. We attempted to measure effective barrier heights in air and in hexadecane using a solvent compatible STM and a sample whose surface is resistant to contamination. The cleanliness and order of the sample surface was determined before and after STM experiments using LEED and XPS, and estimates were made of the degree of contamination. Unfortunately, the barrier heights in air were much lower than expected (<1 eV) and indistinguishable from those measured in hexadecane.\n" }, { "name": "Marzluff, Elaine M.", "degree": "PhD", "year": "1995", "title": "Fundamental studies of the structures, energetics and collision dynamics of large molecules in the gas phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-112712", "creators": [ { "name": { "family": "Marzluff", "given": "Elaine M." }, "id": "Marzluff-Elaine-M", "display_name": "Marzluff, Elaine M." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ecqj-my65", "abstract": "The construction and application of an external source Fourier transform ion cyclotron resonance mass spectrometer equipped with a fast atom bombardment source for studies of biological molecules is described. The instrument features an octopole ion guide, Shulz-Phelps ionization gauge and 7-Tesla superconducting magnet and has been specifically designed for quantitative studies of biological molecules. The primary focus of the work described here has been the development of chemical and physical probes to examine the properties and structures of biomolecules in the gas phase.\r\n\r\nThe results of a complete study of the low energy dissociation pathways using off resonance collisional activation of deprotonated peptides is presented. The dissociation pathways are governed by the site of charge and yield partial C-terminus sequence information in favorable cases. Application of statistical RRKM calculations to these systems allows a qualitative understanding of the energetic changes associated with the observed dissociation processes. The bimolecular reactivity of these species was investigated. Several reactions taking advantage of the nucleophilicity of the deprotonated carboxylic group were observed. This is particularly noteworthy as there are few previously reported instances of bimolecular reactions (other than proton transfer) involving biological species in the gas phase.\r\n\r\nThe results of the above study identified a homologous system of deprotonated peptides which dissociate with similar activation parameters. This was used as a model system to investigate the effect of molecular size on the collisional activation process. Contrary to the common belief that it is inherently harder to activate large molecules and induce dissociation, it was discovered that molecules with many degrees of freedom dissociate more readily than molecules with fewer degrees of freedom. This is attributed to the ability of these molecules to easily deform and efficiently convert translational energy into internal excitation.\r\n\r\nThe mechanism of the collisional energy transfer was investigated using trajectory calculations with a molecular mechanics force field. The collisions appear to be impulsive in nature and energy transfer occurs on a timescale similar to a vibrational period. Large molecules have the ability to undergo several encounters with the collision gas in a single collision event, each encounter resulting in a significant amount of internal energy being transferred into internal modes.\r\n\r\nA master equation analysis was applied to the off resonance collisional activation process in an attempt to obtain a more quantitative understanding of the dissociation energetics of large molecules. This analysis takes into account all processes contributing to the change in ion internal energy. The primary result of this analysis was the observation that a significant fraction of the ions formed in the collisional activation process have a large internal energy and are slow to collisionally relax under conditions employed in our experiments. A more thorough knowledge of this energy distribution is required before an analysis such as this can be used." }, { "name": "Maurer, Barry James", "degree": "PhD", "year": "1995", "title": "Dihydrofolate reductase gene amplification in human cell lines VA2-B and hela BU25", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-10232007-082738", "creators": [ { "name": { "family": "Maurer", "given": "Barry James" }, "id": "Maurer-B-J", "display_name": "Maurer, Barry James" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pfsj-xf27", "abstract": "Mammalian gene amplification has been studied using as a model system the amplification of the endogenous Dihydrofolate Reductase (DHFR) gene in the human cell lines VA[subscript 2]-B and Hela BU25. Cell lines were stepwise-selected to high DHFR gene copy number using methotrexate, a DHFR enzyme inhibitor. Multiple cell lines and their derivatives were analyzed throughout the amplification process by karyotype, DHFR gene copy number, DHFR protein level, cell growth rate and, in some instances, by pulsed-field gel electrophoresis (PFGE).\r\n\r\nChromosomal fragmentation and rearrangements were observed in the initial stages of amplification in all cell lines examined. In subsequent stages, the formation of double minute chromosomes (DM) and Homogeneously and Abnormally Staining Regions (HSR/ASR) were observed in all cell lines except one. The order of appearance of DMs and HSRs varied among cell lines with HSRs becoming predominant at later stages under stable selection. In contrast to findings reported in other systems, DMs and HSRs were found to coexist within the same cell for extended periods of time in some cell lines.\r\n\r\nA novel class of mammalian extrachromosomal, submicroscopic DNA elements was discovered in some cell lines through the use of PFGE. The amplified DHFR genes in one cell line, Hela 10B3, were found to reside solely in this class of DNA element (\"amplisome\"). Amplisomes may represent the initial, or an obligatory, molecular intermediate in the mammalian gene amplification process, at least in some cases.\r\n" }, { "name": "McCurdy, Alison", "degree": "PhD", "year": "1995", "title": "Cation-pi and polarizability effects in biomimetic catalysis and the design of a photoactive donor-cyclophane-acceptor triad", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-094703", "creators": [ { "name": { "family": "McCurdy", "given": "Alison" }, "id": "McCurdy-A", "display_name": "McCurdy, Alison" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pgh6-6g40", "abstract": "The role of the cation-[pi] effect and polarizability in ground-state and transition-state stabilization by a cyclophane host P was explored. The family of guests that bind well to this host was expanded to include sulfonium salts and sulfoxides. The catalysis of the demethylation of aryldimethylsulfonium salts with thiocyanate by host P and the related host C was observed. This reaction is a model for the demethylation of S-adenosylmethionine (SAM), a cofactor of methyltransferase enzymes. The effect of aryl substituents on reaction rates was presented in linear Hammett plots for the uncatalyzed reaction in aqueous buffer, the host-catalyzed reaction, and the uncatalyzed reaction in acetonitrile. The data revealed that the cation-[pi] effect alone cannot be responsible for the biomimetic catalysis. Simple polarity effects were ruled out. To explain the catalysis data, the polarizability of the cyclophanes' cavities was invoked as the additional stabilizing factor. Sulfonium-aromatic interactions appear to be present in some methyltransferases, and the cation-[pi] effect and polarizability of the SAM binding site are possibly catalytic mechanisms found in Nature.\n\nAdditional work involved the synthesis and study of other cyclophane macrocycles to further explore the cation-[pi] effect. A host PHOS which uses phosphate groups as water-solubilizing groups was designed. This host should have superior solubility properties to host P. It also may be used to quantitatively assess the effect on cation binding affinities of negative charges on the macrocycle. The last synthetic step was unsuccessful. Small organic soluble cyclophanes O and S were synthesized to bind alkali metal cations. Although potassium-aromatic interactions have been invoked to explain selectivity in voltage-gated potassium channels, this kind of interaction was not detected in these cyclophanes.\n\nFinally, progress toward the synthesis of a photoactive donor-cyclophane-acceptor triad has been made. This triad is a model for a macrocycle-crosslinked conducting polymer-based sensor. A guest analyte would act as a conductivity switch by facilitating interchain hopping of charge carriers. A photoinduced electron donor ruthenium complex moiety and an acceptor quinone moiety will be linked to the host, fixed away from the binding cavity. The acceptor portion was successfully synthesized. However, while monodentate, bidentate, and tetradentate ligands for ruthenium have been synthesized, the formation of a stable ruthenium metal complex has been unsuccessful. Further work will be required to synthesize this triad.\n" }, { "name": "Mizoue, Laura S.", "degree": "PhD", "year": "1995", "title": "Investigations of cation-pi binding by cyclophane receptors in aqueous media", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10172007-133747", "creators": [ { "name": { "family": "Mizoue", "given": "Laura S." }, "id": "Mizoue-L-S", "display_name": "Mizoue, Laura S." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1dyc-q733", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe binding properties of two new cyclophane receptors in aqueous media were explored. Replacement of two benzene rings of the host P with furans or thiophenes was expected to enhance cation-[pi] interactions, but significant improvements in the binding of positively-charged guests were not observed. Ab initio calculations provided a rationalization for the experimental findings and a better understanding of the cation-[pi] interaction.\n\nThe binding in water of various guanidinium compounds to host P was also investigated. These molecules represented a new type of cationic guest for the receptor. Arginine was not measureably bound by P, but several alkylated guanidiniums were well bound, especially considering their high water solubility. Hexamethylguanidinium, a nonplanar molecule with [...] symmetry, was a particularly interesting guest which displayed enantioselective binding to P. In addition, some progess was achieved towards the synthesis of receptors that have either an amide or a carboxylate group attached to the rim of the cavity. The appended group is positioned such that it can form hydrogen bonds or electrostatic interactions with a bound guanidiniumn guest.\n\nFinally, exploratory work was carried out towards the synthesis of a cyclophane host that possesses a disulfide near the binding cavity. This receptor was designed to mimic the acetylcholine binding site of the nicotinic acetylcholine receptor. Although various disulfide containing macrocycles were synthesized, they were not sufficiently water soluble to permit studies of their binding properties.\n" }, { "name": "Nguyen, SonBinh TheBao", "degree": "PhD", "year": "1995", "title": "The designs, syntheses, and applications of well-defined, single component group VIII olefin metathesis catalysts", "advisor": "Grubbs, Robert H.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-09282005-160712", "creators": [ { "name": { "family": "Nguyen", "given": "SonBinh TheBao" }, "id": "Nguyen-S-T", "display_name": "Nguyen, SonBinh TheBao" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "co-chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "co-chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Carreira", "given": "Erick Moran" }, "id": "Carreira-E-M", "role": "member", "display_name": "Carreira, Erick Moran" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1BVB-S189", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis reports the synthesis and reactivity studies of a series of [...] complexes (X is an anionic ligand, L represents a neutral, two-electron donor ligand, M is either Ru or Os, and CHR represents a carbene moiety). These complexes are olefin metathesis catalysts and is remarkable in their stability toward a variety of functional groups, including protic species such as water and acid.\r\n\r\nChapter 2 describes the synthesis, stability, and mechanism of formation of the forementioned [...] catalysts from a strained 3,3-disubstituted cyclopropene. Their metathesis activities as functions of the anionic ligands and the metal center will be discussed together with the mechanism of cyclopropene-vinylcarbene rearrangement at Group VIII metal centers . In chapter 3 and chapter 4, the modification of the metathesis activity of these catalysts as functions of the ancillary phosphine ligands and the carbene substituents, respectively, will be presented. Chapter 5 describes the applications of this new catalyst system in the self metathesis and ethenolysis of oleic acid and its methyl ester. The acyclic diene metathesis polymerization and polyolefin depolymerization reactions catalyzed by these new catalysts are the subjects of chapter 6. Chapter 7 reports the results of resin-immobilization experiments and Chapter 8 is a collection of the author's personal impressions of the development in this area of chemistry over the last decade." }, { "name": "O'Connor, Stephen D.", "degree": "PhD", "year": "1995", "title": "Studying Material Properties on the Nanometer Scale: Instrumental Development and Applications", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01252005-092413", "creators": [ { "name": { "family": "O'Connor", "given": "Stephen D." }, "id": "O'Connor-Stephen-D", "display_name": "O'Connor, Stephen D." } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Fraser", "given": "Scott E." }, "id": "Fraser-S-E", "orcid": "0000-0002-5377-0223", "role": "member", "display_name": "Fraser, Scott E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/P0AA-7W43", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis thesis describes experimental work designed to understand and manipulate material properties on the nanometer scale. Two strategies have been explored: instrument development and experimental applications.\r\n\r\nSection I describes work associated with atomic force microscopy, including application studies of human hair morphology and the surface microstructure of a bulk metallic glass [...]. Also included in this section are two instrumental advances. First, a mathematical algorithm to extract intermolecular potentials from experimental data is described. Second, a simple, robust method for reducing mechanical noise in these experiments is presented.\r\n\r\nSection II outlines early experiments aimed at applying Near-field Scanning Optical microscopy to gas-phase chemical analysis. Standard instruments were constructed and tested. Preliminary work aimed at using the near-field effect to desorb ionized particles from surfaces was also completed.\r\n\r\nSection III describes the construction of temperature and vibration sensors based on material properties in silicon. Unprecedented resolution has been obtained with a simple, inexpensive device. The vibration sensors take advantage of Schottky barrier reshaping while the junction is excited with optically induced charge carriers. In a similar manner, the temperature sensors monitor changes in electron mobility." }, { "name": "Pehkonen, Simo Olavi", "degree": "PhD", "year": "1995", "title": "Redox chemistry of iron in multiphase atmosphere", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10182007-133403", "creators": [ { "name": { "family": "Pehkonen", "given": "Simo Olavi" }, "id": "Pehkonen-S-O", "display_name": "Pehkonen, Simo Olavi" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "chair", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Morgan", "given": "James J." }, "id": "Morgan-J-J", "role": "member", "display_name": "Morgan, James J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ezne-6339", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nIron redox chemistry was investigated in fog and stratus clouds in urban and remote locations in California, Delaware and New York. It was observed that iron(II) contributed from 20 to 70 % of the total iron in the samples and that iron(III) was bound mostly as oxalato complexes in most samples. The iron(II) oxidation state seemed to correlate best with organic compounds, i.e., carboxylic acids and TOC (total organic carbon), indicating the important role of organic compounds to the redox state of iron.\n\nThe applicability of a new spectrophotometric technique for measuring simultaneously iron(II) and iron(III) in atmospheric water samples real time in the field was studied. DPKBH (Di-2-pyridyl ketone benzoylhydrazone) forms complexes with both iron(II) and iron(III) with an absorption maximum at 375 nm for both iron(II)-DPKBH and iron(III)-DPKBH and an absorption maximum at 660 nm for iron(II)-DPKBH. The detection limit of this method is 4 nM of iron with chloroform-water extraction and 0.1 [...] without the extraction. DPKBH forms bis complexes with iron and binds via the oxygen and two nitrogen atoms of the enol form of DPKBH as indicated by a FTIR study of the iron(III)-DPKBH complex.\n\nIn addition to field observations, complementary laboratory photoreduction experiments were carried out with a variety of iron oxides and a variety of important atmospheric organic compounds such as oxalate, formate, acetate and formaldehyde. Photoreduction of [...] with formate yielded the highest rates of photoreduction. Stability of the iron oxide and the strength of Fe-O bonds in the lattice played a more important role in the rate of iron photoreduction than the reactive surface area. Hydrogen peroxide was produced in the case of oxalate as the electron donor. Additional iron photoreduction experiments were carried out with halogenated acetic acids (the end products of tropospheric HCFC degradation) as electron donors and it was observed that monohalo acetic acids reduce iron oxides faster and get photooxidized faster compared to acetic acid.\n" }, { "name": "Pustilnik, Michael Morris", "degree": "PhD", "year": "1995", "title": "The construction and application of metal complexes for DNA strand scission", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10182007-103625", "creators": [ { "name": { "family": "Pustilnik", "given": "Michael Morris" }, "id": "Pustilnik-M-M", "display_name": "Pustilnik, Michael Morris" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h206-6d32", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nSubstitutionally inert transition metal complexes have been constructed which bind to DNA and deliver additional labile metal ions to promote cleavage of the phosphodiester backbone. Both oxidative and hydrolytic DNA cleavage have been explored through the use of different chelates and reactive metal ions.\n\nTo explore oxidative chemistry, two complexes, [...] and [...], have been synthesized by tethering two bis(2-picolyl)amine or bis(2-ethylpyridyl)amine chelates to the [...] moiety. Both complexes promote site-selective oxidative DNA cleavage in the presence of CuSO4 and a thiol, with the site-selectivity being governed by the [...] core. Copper-ligand binding affinity, complex-DNA binding mode, and the [...]/[...] redox potential all appear to sensitively influence the cleavage efficiency. Product analysis of the DNA cleavage reaction is consistent with hydrogen abstraction from C1', C3', and C4' of the deoxyribose ring. The [...] core therefore serves as a vehicle to deliver oxidative reactions to DNA. These complexes may be valuable for the design of drugs that cleave DNA in vivo.\n\nThe complexes [...], [...], [...], and [...] have also been prepared so as to explore the delivery of secondary metal ions and functionalities to promote DNA hydrolysis. The complexes each have two tethered bis(2-picolyl)amine chelating groups; the latter three complexes also have two 2-dimethylaminoethyl or 3-dimethylaminopropyl groups designed for general acid assistance. DNA hydrolysis has not been established, but [...] promotes efficient DNA cleavage in the presence of [...]. Product analysis of DNA oligonucleotide cleavage by [...] is consistent with a [...] mediated reaction which is remarkably enhanced compared to those of ruthenium complexes lacking the tethered chelates; this reactivity may indicate that [...] promotes abasic site cleavage. [...], which does not sensitize [...] formation, promotes still more efficient DNA cleavage. The mechanism is yet to be established.\n" }, { "name": "Sardesai, Niranjan Y.", "degree": "PhD", "year": "1995", "title": "Rhodium intercalators as novel peptide delivery systems to the major groove of DNA : towards the design of artificial repressors", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222007-132632", "creators": [ { "name": { "family": "Sardesai", "given": "Niranjan Y." }, "id": "Sardesai-N-Y", "display_name": "Sardesai, Niranjan Y." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0v7r-fp28", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nPhenanthrenequinone diimine (phi) complexes of rhodium(III) bearing tethered peptides have been designed to serve as metallointercalating anchors to deliver peptide side chain functionalities for DNA recognition in the major groove. Metal-peptide \ncomplexes containing 11-15 amino acid residues were prepared using two complementary synthetic strategies: by direct coupling of a pendant carboxylate on the coordinatively saturated rhodium complex, [...] (phen'=5-amidoglutaryl-1, 10-phenanthroline), to the N-terminus of a resin-bound peptide in a manner analogous to the chain-elongation step in solid phase peptide synthesis; or by coupling phen' containing the pendant carboxylate to the resin-bound peptide, followed by coordination of [...] to the bidentate chelator attached to the peptide. With coordination complexes which are stable to peptide deprotection and cleavage conditions from the resin, the solid phase synthetic strategies prove convenient to apply. The metal-peptide complexes have been characterized by amino acid analysis, electronic spectroscopy, circular dichroism and mass spectrometry, where a novel pattern of peptide fragmentation facilitates the detailed sequence analysis of the appended peptide. All the metal-peptide complexes bind and, with photoactivation, cleave DNA with evidence of major groove chemistry. Significantly, the DNA site-specificity is seen to depend on the peptide side-chain functional groups. In one series, a single glutamate at position 10 is found to be essential in directing DNA site-recognition to the sequence 5'-CCA-3'. Methylation of the glutamate side chain or single ElOQ, E1OD, E1OA mutations abolish this selectivity. The glutamate is essential to maintain [...]-helicity in the peptide and make base specific contacts, thereby providing a glutamate switch for site-specific DNA recognition. A second series, based on the recognition helix of the phage 434 repressor, reproduces operator binding. Photocleavage and MPE-Fe footprint analysis indicates that these metal-peptide complexes bind to the 5'-ACAA-3' operator sequences as monomers at\n10 nM concentration and differentiate between operator site variants. These studies represent a new strategy to create an array of metal-peptide complexes with differing sequence specificity for DNA and suggest a route to the construction of small molecules that function as artificial repressors.\n" }, { "name": "Shields, Thomas P.", "degree": "PhD", "year": "1995", "title": "DNA recognition by the enantiomers of Rh(en)2phi3+ : recognition through hydrogen bonding and van der Waals contacts", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222007-131939", "creators": [ { "name": { "family": "Shields", "given": "Thomas P." }, "id": "Shields-T-P", "display_name": "Shields, Thomas P." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tx6p-mg53", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe enantiomers of Rh(en)2phi[...] (en = ethylene diamine, phi = 9,10-phenanthrene quinone diimine) have been prepared in order to explore systematically the contributions of hydrogen bonding and van der Waals contacts to sequence selective DNA binding. Both enantiomers bind strongly to DNA via intercalation of the aromatic phi ligand, and produce direct strand scission upon irradiation with near-UV light. The cleavage mechanism is consistent with the direct abstraction of the C3'-H atom from the major groove of DNA by a bound, photoexcited Rh(phi)[...] species. Elements of the sequence specificity of [...] and [...] were established by comparing recognition characteristics to those of several [...] complexes containing ancillary saturated amines and a thioether, and by cleavage of oligonucleotide targets containing [...], 7-deazaguanine and deoxyuracil substitutions. Both enantiomers display a strong sensitivity to the inclusion or removal of a single methyl group in the major groove of [...] displays relatively high selectivity in targeting [...] steps and this selectivity is the result of hydrogen bonding between the axial amines of the metal complex and the [...] position of guanine residues. In contrast, [...] is less selective; besides binding to [...] steps, the A-enantiomer also recognizes [...] steps through a positive van der Waals contact between the ancillary methylene groups and the 5-methyl group of thymine. The structural basis for these enantioselective elements of recognition have also been investigated via [...] methods. Both [...] bind to d(GTGCAC)[...] by classical intercalation, and 2D-NOESY studies of the [...] complex demonstrate specific intercalation at the central [...] site. Molecular models show that deep intercalation of the phi ligand ideally locates the ancillary ethylene diamine ligands for the proposed hydrogen bonding and van der Waals contacts. While illustrating the importance of hydrogen bonding and van der Waals contacts in achieving site specificity, the current work also suggests a modular approach to the design of molecules capable of recognizing larger DNA sequences." }, { "name": "Shreve, Gary A.", "degree": "PhD", "year": "1995", "title": "Electron transfer at n-silicon-methanol junctions", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222007-110727", "creators": [ { "name": { "family": "Shreve", "given": "Gary A." }, "id": "Shreve-G-A", "display_name": "Shreve, Gary A." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0c04-3j56", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nOne of the first semiconductor systems limited by electron transfer has been explored. Rate constants for electron transfer from n-Si to methyl viologen dichloride [...] and benzyl viologen dichloride [...] in LiC1 methanol solutions have been measured for the first time. The driving force dependence of ket for electron transfer to MVC12 from n-Si has been determined. Best fit to the data gave a reorganization energy of 0.9 eV and a maximum rate constant (ket,max) for this system of [...] . To our knowledge this is the first experimentally determined value for the maximum rate constant predicted by Marcus theory at a semiconductor/liquid interface. This allowed an upper limit of [...] nO greater than [...] to be determined for this system.\n\nThis work describes a search for active corrosion of Si in contact with [...] and [...] solutions through the use of very sensitive electrochemical, chemical, and physical methods. For [...] solutions, an upper limit on the active corrosion rate of [...] has been established through direct experimental measurements; thus, a 400 im thick Si photoelectrode in contact with the [...] electrolyte would require over 1500 years to corrode completely at room temperature. An alternative explanation for scanning electrochemical microscopy data published previously claiming [...] is presented, based on the documented existence of an inversion layer at the Si/liquid contact, and shown to be consistent with the available data.\n\nKey differences between the conventional and \"irreversible\" models of semiconductor photoelectrochemistry are identified and discussed within the framework of experimental observations. Conceptual differences between these two models appear to lie in the treatment of interfacial charge transfer processes for photogenerated charge carriers. It is shown analytically that the two models predict differences in the behavior of the available free energy produced by a photoelectrochemical cell at a fixed incident light intensity and are compared to experimental results for semiconductor/liquid junctions.\n" }, { "name": "Singleton, Scott F.", "degree": "PhD", "year": "1995", "title": "The thermodynamics of oligonucleotide-directed triple helix formation at single DNA sites", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10242007-090557", "creators": [ { "name": { "family": "Singleton", "given": "Scott F." }, "id": "Singleton-S-F", "display_name": "Singleton, Scott F." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/382c-fz95", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe local triple-helical complexes formed upon binding of pyrimidine oligonucleotides to double-helical DNA offer a versatile structural motif for designing sequence specific duplex DNA-binding molecules. The experimental determination of oligonucleotide association constants as a function of solution conditions is necessary to characterize the noncovalent forces which contribute to the affinity and specificity of DNA recognition by triple helix formation. Such information will be important for the rational application of oligonucleotide-directed triple helix formation to such tasks as the manipulation of large DNAs, and the artificial modulation of biological events. We are interested in controlling the relative amount of a local triple-helical complex formed at equilibrium under conditions which approximate those found within cells. Thus, we chose to measure equilibrium constants for the formation of triple-helical complexes at single sites within larger duplex DNAs in mixed valence salt solutions near neutral pH.\n\nConcepts borrowed from existing footprint titration methods were combined with the powerful affinity cleaving strategy in the development of the affinity cleavage titration method for the measurement of single-site DNA-binding isotherms (Chapters One and Two). The amount of site-specific cleavage of a radiolabeled plasmid DNA fragment produced by a 15mer oligonucleotide-EDTA[...]Fe is measured over an oligonucleotide concentration range covering four orders of magnitude, allowing a binding curve to be constructed. Curve-fitting a Langmuir titration isotherm to the data points affords an equilibrium binding constant, [...], that is identical within experimental uncertainty to those obtained from quantitative DNase I footprint titrations of the same oligonucleotide with and without EDTA[...]In. Further affinity cleavage titrations demonstrate that the energetic stabilization of this local triple-helical structure depends on the length of the oligonucleotide, the presence of base triplet mismatches, and the solution conditions, including the pH, the concentration and valence of cations, and the temperature.\n\nDecreasing the length of the oligonucleotide from 15 to 11 nts reduces the stability of the corresponding triplexes by ~0.3 kcal/mol per nucleotide removed (Chapter Two). Single internal base triplet mismatches result in a destabilization of the local triple-helical structure by ~ 3 kcal/mol. The equilibrium association constants for the 15mer increased by 10-fold as the pH was decreased from pH 7.6 to pH 5.8, indicating that the corresponding triple-helical complex was stabilized by 1.4 kcal[...]mol[superscript -1] at the lower pH (Chapter Three). Equilibrium association constants for the 15mer in the presence of various concentrations of KCl,MgCl[subscript 2], and spermine tetrahydrochloride (SpmCl[subscript 4]) are reported in Chapter Four. Varying the K[...] concentration by a factor of 28 in the presence NaCl, MgCl[subscript 2], and SpmCl[subscript 4] resulted in an overall 100-fold decrease in the binding affinity from the lowest to the highest concentration. In contrast, measured binding constants increased 500-fold as the Spm[superscript 4+] concentration was increased 10-fold. \n\nThere was a modest effect on the binding constant (a 3-fold decrease) upon increasing the Mg[superscript 2+] concentration by a factor of 100. The influence of temperature on the energetics of oligonucleotide-directed triple helix formation in mixed valence salt solutions at pH 7.0 are reported in Chapter Five. In three solutions differing in their salt compositions, the equilibrium association constants decreased at least 100-fold (from >10[superscript 7]M[superscript -1] to ~ 10[superscript 5]M[superscript -1]) as the temperature was increased from 8\u00b0C to 37\u00b0C. Least squares analysis of van't Hoff plots (lnK versus 1/T) of the data revealed that in each solution the triplex is enthalpically stabilized by ~ 2 kcal per mole of base triplets.\n\nThis value for the enthalpic contribution to triplex stability, which reflects contributions from both T[...]AT and C+GC base triplets, is identical within experimental error to that measured previously using differential scanning calorimetry for the 15mer binding to 15 by within a 21-bp duplex. We collaborated with Professor Kenneth J. Breslauer of Rutgers University to make the calorimetric measurement, and the complete thermodynamic characterization of the stability and the melting behavior of the triplex are described in Chapter Six.\n\nTaken together, the equilibrium association constants, the thermal denaturation data, and the calorimetric data reported here provide a quantitative measure of the influence of third strand length, base triplet mismatches, pH, salt, and temperature on the stability and the melting behavior of a DNA triplex. Such information should prove useful in designing triplex-forming oligonucleotides and in defining solution conditions for the effective use of triple-helical structure formation as a tool for modulating biochemical events." }, { "name": "Tan, Ming X.", "degree": "PhD", "year": "1995", "title": "Photoelectrochemistry of GaAs and Si liquid junctions", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072015-150517492", "creators": [ { "name": { "family": "Tan", "given": "Ming X." }, "id": "Tan-M-X", "display_name": "Tan, Ming X." } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/406d-qa79", "abstract": "A quantitative study has been performed on the stability of GaAs surfaces in a\r\n0.10 M K2Se-0.01 M K2Se2 aqueous solution. In this electrolyte, n-type GaAs electrodes\r\ndisplayed significant photocorrosion in competition with faradaic charge transfer to Se2-.\r\nChemisorption of group VIIIB metal ions onto the GaAs surfaces yielded improved\r\ncurrent-voltage behavior of the GaAs photoanodes, and also resulted in a significant\r\nreduction in photocorrosion. This behavior implies that the chemisorbed metal ions act to\r\nincrease the rate of hole transfer to the Se2- species. Related experiments on n-GaAs, pGaAs,\r\nand Sn-doped In2O3 electrodes in Te2-/- aqueous solutions have also been\r\nperformed.
\r\n\r\nThe majority carrier (electrons) transfer rate constant at a highly doped\r\nn+-Si/Co(Cp)2Cl-methanol junction has been measured directly using the\r\nchronoamperometry electrochemical technique. The reduction reaction rate of Co(Cp)2+\r\nwas 0.03 cm-s-1 at the Si electrode, and was more than 100 times slower than at a hanging\r\nmercury electrode. The slower rate was attributed to the smaller optical and static dielectric\r\nconstants, and the lower density of electrons of the semiconductor. The experimental\r\nresults were compared to the Marcus theory of charge transfer.
\r\n\r\nThe unique properties of high purity Si/liquid junctions have been investigated\r\nunder illumination conditions in which the photogenerated carrier concentration exceeds the\r\ndopant concentration. Under these high injection conditions, negligible electric fields exist\r\nat the semiconductor/liquid interface, and carrier motion is driven by diffusion. Studies of\r\nthe current-voltage properties of the Si in methanol solutions containing various redox\r\ncouples suggested that high efficiency photoelectrochemical cells could be established\r\nthrough selective collection of carriers at the semiconductor/liquid junction. The quasi-Fermi\r\nlevels of electrons and holes were measured directly against the solution potential.\r\nSteady-state and transient photovoltage measurements, and theoretical modeliug of the\r\ncarrier transport, generation, and recombination dynamics indicated that the quasi-Fermi\r\nlevels were flat across the semiconductor sample. The recombination velocities at the\r\nSi/liquid junctions have also been measured, and were shown to vary with the solution\r\npotential following the Shockley-Read-Hall theory on recombination.
\r\n\r\n" }, { "name": "Wang, Neng E.", "degree": "Masters", "year": "1995", "title": "Studies in dynamics", "advisor": "Marcus, Rudolph A.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-10292007-104923", "creators": [ { "name": { "family": "Wang", "given": "Neng E." }, "id": "Wang-Neng-E", "display_name": "Wang, Neng E." } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Wang", "given": "Zhen-Gang" }, "id": "Wang-Zhen-Gang", "role": "member", "display_name": "Wang, Zhen-Gang" } ], "option_major": [ "chemistry" ], "doi": "10.7907/j1ch-3v41", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn this thesis, three parts of my work are reported. The first part of the work was done with Prof. Rudy Marcus, the second and third parts of the work were done with Prof. Bill Goddard. Here I would like to summarize the results from each part briefly.\r\n\r\nIn the first part, we propose doing Scanning Tunneling Microscopy(STM) current calculations with a new model in the spheroidal coordinate system. The tip is modeled as a hyperboloid. The electrostatic potential part of this model is solved exactly. The free electron model of the whole system is also solved exactly.\r\n\r\nIn the second part, we found that the Nose Canonical Molecular Dynamics, the most commonly used CMD method, leads to the wrong heat capacity for the system and hence is inconsistent with the thermodynamics. To solve this problem, we propose Two Nose variable Dynamics by changing the dimensionality of the Nose variable s and its conjugate [...] from one- to two-dimension.\r\n\r\nIn the third part, The exact expression for the quantum statistical partition function in the canonical ensemble is given. The physical interpretation of each term for N-particle system is discussed. The new formula is applied to the weakly degenerate quantum ideal case. By analyzing each term in the expansion, it is possible that this canonical partition function can be applied to cases where both quantum correlation effects and particle interactions are important.\r\n" }, { "name": "Wang, Youqi", "degree": "PhD", "year": "1995", "title": "Electron energy loss spectroscopic study of small molecules on transition metal surfaces", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-10122007-112248", "creators": [ { "name": { "family": "Wang", "given": "Youqi" }, "id": "Wang-Youqi", "display_name": "Wang, Youqi" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Goodstein", "given": "David L." }, "id": "Goodstein-D-L", "role": "member", "display_name": "Goodstein, David L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Thorne", "given": "Kip S." }, "id": "Thorne-K-S", "role": "member", "display_name": "Thorne, Kip S." }, { "name": { "family": "Frautschi", "given": "Steven C." }, "id": "Frautschi-S-C", "role": "member", "display_name": "Frautschi, Steven C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h31m-na55", "abstract": "The scheme of ultrahigh-resolution electron energy loss spectroscopy (UNREELS) is described in detail with graphical examples of the real data processing. On the basis of modern digital information processing techniques, this method promises to yield EEL spectra with the ultimate resolution and superior signal to noise ratio.\r\n\r\nThe interaction of ammonia with clean and chemically modified Ru(001) surfaces were studied by using HREELS, TPD, and LEED techniques under UHV condition. Ammonia is found to interact with the surface chiefly through its lone-pair electrons, evidenced by the blue-shift of ammonia symmetric deformation mode and the increase of thermal desorption temperature of ammonia on both oxygen and nitrogen modified surfaces. No detectable dissociation of ammonia is found under the specified conditions.\r\n\r\nThe reactions of gas-phase atomic hydrogen with oxygen and carbon monoxide pre-adsorbed on Ru(001) surface at low temperature were studied via HREELS technique. The experimental results can be understood via an Eley-Rideal-like mechanism.\r\n\r\nThe decomposition mechanism of methylamine on Ru(001) surface was investigated by HREELS and TPD techniques. The cyanide adspecies was found to be side-on bonded on the ruthenium surface and its bond order is reduced from three to two.\r\n" }, { "name": "Zheng, Zhi Qiang (Alex)", "degree": "PhD", "year": "1995", "title": "Robust control of systems subject to constraints", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-10232007-141113", "creators": [ { "name": { "family": "Zheng", "given": "Zhi Qiang (Alex)" }, "id": "Zheng-Z-Q-A", "display_name": "Zheng, Zhi Qiang (Alex)" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/q8vt-s855", "abstract": "Most practical control problems are dominated by constraints. Although a rich theory has been developed for the robust control of linear systems, very little is known about the robust control of linear systems with constraints. Over the years various model-based algorithms (given a generic term Model Predictive Control) have been used in industry to control complex multivariable systems with operating constraints. The design and tuning of these controllers is difficult for two reasons:\n\n1. Process models are always inaccurate which implies that the controllers must be robust.\n\n2. Even in the simplest case where process models are linear, the overall systems are nonlinear because of the constraints.\n\nDespite Model Predictive Control's considerable practical importance, there is very little theory to guide the design and tuning of these controllers for stability and robustness. It is the goal of this thesis to develop such a theory. Specifically, a general framework based on Model Predictive Control is developed to synthesize controllers for discrete-time linear systems subject to constraints with robust stability and performance guarantees." }, { "name": "Beal, Peter A.", "degree": "PhD", "year": "1994", "title": "Recognition of double helical DNA by purine oligonucleotides via triple helix formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04252013-080541344", "creators": [ { "name": { "family": "Beal", "given": "Peter A." }, "id": "Beal-Peter-A", "orcid": "0000-0003-4855-7185", "display_name": "Beal, Peter A." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5bbg-zs22", "abstract": "Oligonucleotide-directed triple helix formation is one of the most\r\nversatile methods for the sequence specific recognition of double helical\r\nDNA. Chapter 2 describes affinity cleaving experiments carried out to assess\r\nthe recognition potential for purine-rich oligonucleotides via the formation\r\nof triple helices. Purine-rich oligodeoxyribonucleotides were shown to bind\r\nspecifically to purine tracts of double helical DNA in the major groove\r\nantiparallel to the purine strand of the duplex. Specificity was derived from\r\nthe formation of reverse Hoogsteen G\u2022GC, A\u2022AT and T\u2022AT triplets and\r\nbinding was limited to mostly purine tracts. This triple helical structure was\r\nstabilized by multivalent cations, destabilized by high concentrations of\r\nmonovalent cations and was insensitive to pH. A single mismatched base\r\ntriplet was shown to destabilize a 15 mer triple helix by 1.0 kcal/mole at 25\u00b0C.\r\nIn addition, stability appeared to be correlated to the number of G\u2022GC triplets\r\nformed in the triple helix. This structure provides an additional framework\r\nas a basis for the design of new sequence specific DNA binding molecules.
\r\n\r\nIn work described in Chapter 3, the triplet specificities and required\r\nstrand orientations of two classes of DNA triple helices were combined to\r\ntarget double helical sequences containing all four base pairs by alternate\r\nstrand triple helix formation. This allowed for the use of oligonucleotides\r\ncontaining only natural 3'-5' phosphodiester linkages to simultaneously bind\r\nboth strands of double helical DNA in the major groove. The stabilities and\r\nstructures of these alternate strand triple helices depended on whether the\r\nbinding site sequence was 5'-(purine)_m (pyrimidine)_n-3' or 5'-\r\n(pyrimidine)_m (purine)_n-3'.
\r\n\r\nIn Chapter 4, the ability of oligonucleotide-cerium(III) chelates to direct\r\nthe transesterfication of RNA was investigated. Procedures were developed\r\nfor the modification of DNA and RNA oligonucleotides with a hexadentate\r\nSchiff-base macrocyclic cerium(III) complex. In addition, oligoribonucleotides\r\nmodified by covalent attachment of the metal complex through two different\r\nlinker structures were prepared. The ability of these structures to direct\r\ntransesterification to specific RNA phosphodiesters was assessed by gel\r\nelectrophoresis. No reproducible cleavage of the RNA strand consistent with\r\ntransesterification could be detected in any of these experiments.
" }, { "name": "Casimiro, Danilo Riguera", "degree": "PhD", "year": "1994", "title": "Electron transfer in ruthenium-modified recombinant cytochromes and myoglobins", "advisor": "Winkler, Jay Richmond", "url": "https://resolver.caltech.edu/CaltechTHESIS:06152010-102901683", "creators": [ { "name": { "family": "Casimiro", "given": "Danilo Riguera" }, "id": "Casimiro-D-R", "display_name": "Casimiro, Danilo Riguera" } ], "advisors": [ { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "advisor", "display_name": "Winkler, Jay Richmond" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jh62-an41", "abstract": " The aim of the work described in Chapters 2-4 is to elucidate the role of the protein matrix in determining the distant electronic couplings for intramolecular electron- transfer (ET) reactions. The study focuses on two paradigmatic proteins - myoglobin, a non-ET molecule, and cytochrome c, a mitochondrial electron carrier. Site-directed mutants of human myoglobin were constructed each having a single surface histidine for ruthenium labeling. These histidines are at various distances from the heme center (9.5, His70; 12.7, His48; 15.5 \u00c5, His83). Each mutant was derivatized with a pentaammineruthenium complex and the heme was substituted with a photoexcitable zinc mesoporphyrin. The rates of photoinduced and back ET between the histidine-bound Ru complex and the porphyrin were measured via a laser flash technique. The experimentally derived electronic couplings were found to decay exponentially with the intersite separation.\r\n Three site-directed mutants (Glu66His, Glu66His/Tyr67Phe, and Leu58His) of yeast iso-1-cytochrome c were constructed in order to examine whether intervening aromatic side chains affect the rates of intramolecular ET to a significant extent. The crystal structure of the wild-type protein indicates that the ET pathways involve aromatic side chains - a bridging tryptophan at position 59 (in the case of His58) or a tyrosine at 67 (for His66). Incorporation of the Tyr67Phe mutation in the His66 mutant modifies the ET path in a well defined manner. The rates of intramolecular ET from the ferroheme to ruthenium polypyridine complexes bound to the surface histidines were measured using a laser flash-quench technique. Comparison of the experimentally derived donor-acceptor couplings with those of other previously studied cytochromes does not indicate any significant rate enhancement in the presence of bridging aromatic side chains. Furthermore, the rates correlate reasonably well with the predictions of a \u03c3-tunneling pathway model.\r\n The electronic couplings in these myoglobins and cytochromes were analyzed in the context of current theoretical models. The data on cytochrome c strongly support the presence of specific routes for ET to and from the heme. In contrast, myoglobin provides a homogeneous barrier for ET. A comprehensive analysis of the data on both proteins, however, suggests that the apparent square-barrier nature of the polypeptide matrix of myoglobin is symptomatic of the presence of several competing pathways that effectively cause the electronic couplings to scale with direct intersite separations. These results suggest that more complex factors such as stereoelectronic effects and multiple pathways can contribute significantly to the coupling through a structurally heterogeneous medium such as that of a protein.\r\n In Chapter 5, we have extended the use of a substitution-inert ruthenium polypyridine complex in introducing stabilizing intramolecular crosslinks in a protein. We found a dramatic increase in thermal stability of a yeast iso- 1 -cytochrome c mutant upon crosslinking two adjacent histidines (His39 and His58) on opposite strands of a p- sheet with bis(2,2'-bipyridine)ruthenium complex. The melting point of the Ru-modified cytochrome (72.8 \u00b0C) is 23.2 \u00b0C higher than that of the unmodified protein. Comparison with another Ru-modified di-histidine mutant suggests that the extent of the effect is largely dependent on the size of the loop generated by the crosslink. The technique should be readily applicable to stabilizing proteins with \u03b2-sheets.\r\n Chapter 6 describes a novel strategy for the expression and purification of a recombinant, nonfunctional axial-ligand mutant of iso-1-cytochrome c (Met80\u2014>Ala) in S. cerevisiae. It involves coexpressing in the same plasmid(YEp213) the nonfunctional gene with a functional gene copy for complementation on a nonfermentable carbon medium. The functional gene encodes a product with an engineered metal-chelating site (His39 and His58) that enables efficient separation of the two isoforms by immobilized metal-affinity chromatography. The purified Met80\u2014>Ala protein, which possesses a binding site for dioxygen and other exogenous ligands, was produced in quantities sufficient for extensive biophysical characterization. Absorption spectra of several derivatives of this mutant show striking similarities to those of the corresponding derivatives of horseradish peroxidase, myoglobin, and cytochrome P-450. The new method greatly expands the possible structural changes that can be incorporated into this paradigmatic protein.\r\n" }, { "name": "Chen, Ruizhen", "degree": "PhD", "year": "1994", "title": "Metabolic and energetic studies of recombinant Escherichia coli strains : applications of NMR techniques", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10282005-134201", "creators": [ { "name": { "family": "Chen", "given": "Ruizhen" }, "id": "Chen-R", "display_name": "Chen, Ruizhen" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Ross", "given": "Brian" }, "id": "Ross-Brian", "role": "member", "display_name": "Ross, Brian" }, { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "member", "display_name": "Davis, Mark E." }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/PEEN-4S74", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis work concerns applications of NMR techniques in metabolic engineering studies. As demonstrated here, NMR is a valuable tool in analyzing intracellular metabolic and energetic states. When combined with growth and fermentation studies, it greatly enhances the understanding of cellular responses to particular genetic modifications.\r\n\r\nA novel on-line NMR system has been developed in this work which extends the capacities of in vivo NMR to growing cell cultures. This new approach eliminates possible artifacts and time limitations associated with conventional NMR methods. Furthermore, experiments can be conducted under well-defined conditions. New types of physiological states and experimental regimes are accessible with this on-line system.\r\n\r\nSteady-state levels of ATP and [...] have been measured using the on-line NMR system for strains with and without Vitreoscilla hemoglobin (VHb) (GRO21 and MG1655, respectively) during their growth under oxygen-limited conditions. GRO21 has similar levels of ATP and [...] while exhibiting a higher specific growth rate, indicating that the net ATP accumulation rate is enhanced. Studies on ATP synthase (ATPase) kinetics show that the presence of VHb accelerates ATP synthesis rate catalyzed by ATPase by 30%.\r\n\r\nSwitching from the phosphotransferase system (PTS) to the galactose-proton symport system for glucose uptake brings about many changes in cell energetics and metabolism. The extra energy cost in the non-PTS glucose uptake has a greater effect on the specific growth rates in anaerobic conditions than in aerobic conditions. Fermentation patterns are significantly different in the non-PTS strain, compared to the PTS strain. The non-PTS strain has a much lower NTP and [...] and higher NDP; NAD(H) is also considerably reduced. Different levels of glycolytic intermediates have also been observed in these two strains.\r\n\r\nThe non-PTS strain carrying a phenylalanine overproduction plasmid exhibits much lower energy level (NTP and ApH), lower sugar phosphate (S-P) total concentration, NAD(H) and PEP concentrations than its PTS counterpart. The compositions of S-P are significantly different between the two strains. Phenylalanine production is not increased in the non-PTS strain and a larger portion of carbon is oxidized to CO2." }, { "name": "Condroski, Kevin Ronald", "degree": "PhD", "year": "1994", "title": "Synthesis of (\u00b1)-7,8-Epoxy-4-basmen-6-one by a Transannular Cyclization Strategy", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292013-162401827", "creators": [ { "name": { "family": "Condroski", "given": "Kevin Ronald" }, "id": "Condroski-Kevin-Ronald", "display_name": "Condroski, Kevin Ronald" } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/svsh-y716", "abstract": "The first synthesis of the cembranoid natural product (\u00b1)-7,8-epoxy-4-basmen-6-one (1) is described. Key steps of the synthetic route include the cationic cyclization of the acid chloride from 15 to provide the macrocycle 16, and the photochemical transannular radical cyclization of the ester 41 to form the tricyclic product 50. Product 50 was transformed into 1 in ten steps. Transition-state molecular modeling studies were found to provide accurate predictions of the structural and stereochemical outcomes of cyclization reactions explored experimentally in the development of the synthetic route to 1. These investigations should prove valuable in the development of transannular cyclization as a strategy for synthetic simplification." }, { "name": "Coughlin, Edward Bryan, III", "degree": "PhD", "year": "1994", "title": "Iso-Specific Ziegler-Natta Polymerization of \u03b1-Olefins with a Single-Component Organoyttrium Catalyst", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05012013-111738760", "creators": [ { "name": { "family": "Coughlin", "given": "Edward Bryan, III" }, "id": "Coughlin-Edward-Bryan-III", "display_name": "Coughlin, Edward Bryan, III" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/djm5-zt75", "abstract": "The synthesis of a sterically tailored ligand array\r\n(M)_2((C_5H_2-2-Si(CH_3)_3-4-C(CH_3)_3)S_2i(CH_3)_2](\"M_2Bp\") (M = Li, 16; K, 19) is\r\ndescribed. Transmetallation of Li_2Bp with YCl_3(THF)_3 affords exclusively the\r\nC_2 symmetric product rac-[BpY(\u00b5_2-Cl)_2Li(THF)_2], 20. A X-ray crystal structure\r\nof 20 has been determined; triclinic, P1, a= 13.110 (8), b = 17.163 (15), c = 20.623\r\n(14) \u00c5, \u03b1 = 104.02 (7), \u03b2 = 99.38 (5), \u03b3 = 100.24 (6)\u00b0 , Z = 4, R = 0.056.\r\nTransmetallation of K_2Bp with YCl_3(THF)_3 affords the halide free complex\r\nrac-BpYCl, 23. The corresponding rac-BpLaCl, 28, is prepared in an anlogous\r\nmanner. In all cases the achiral meso isomer is not obtained since only for\r\nthe racemic isomers are the unfavorable steric interactions between the\r\nSi(CH3)_3 groups in the narrow portion of the [Cp-M'-Cp] wedge avoided.\r\nAlkylation of 20 or 23 with LiCH(Si(CH_3)_3)_2 affords rac-BpYCH(Si(CH_3)_3)_2, 26\r\nin good yield. Alkylation of 28 with LiCH(Si(CH_3)_3)_2 affords\r\nrac-BpLaCH(Si(CH_3)_3)_2 29. Hydrogenation of 26 cleanly affords the bridging\r\nhydride species [BpY(\u00b5_2-H)]_2, 27, as the homochiral (R,R) and (S,S) dimeric\r\npairs. 26 is an efficient initiator for the polymerization of ethylene to high\r\nmolecular weight linear polyethylene. 27 catalyzes the polymerization of\r\npropylene (25% v/v in methylcyclohexane) and neat samples of 1-butene,\r\n1-pentene, 1-hexene to moderately high molecular weight polymers:\r\npolypropylene (M_n = 4,200, PDI 2.32, T_m 157 \u00b0C); poly-1-butene (M_n = 8,500, PDI\r\n3.44, T_m 105 \u00b0C); poly-1-pentene (M_n = 20,000, PDI 1.99, T_m 73 \u00b0C);\r\npoly-1-hexene (M_n = 24,000, PDI 1.75, T_m < 25 \u00b0C). ^(13)C NMR spectra at the\r\npentad analysis level indicates that the degree of isotacticity is 99% mmmm\r\nfor all polymer samples. 27 is the first single component iso-specific \u03b1-olefin\r\npolymerization catalyst. The presumed origins of the high isospecificity are\r\npresented." }, { "name": "Finney, Nathaniel S.", "degree": "PhD", "year": "1994", "title": "Structural and mechanistic study of monoalkyl diazenes. Synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302013-092335648", "creators": [ { "name": { "family": "Finney", "given": "Nathaniel S." }, "id": "Finney-N-S", "display_name": "Finney, Nathaniel S." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pjpf-6x38", "abstract": "Methodology for the preparation of allenes from propargylic hydrazine precursors\r\nunder mild conditions is described. Oxidation of the propargylic hydrazines, which can\r\nbe readily prepared from propargylic alcohols, with either of two azo oxidants, diethyl\r\nazodicarboxylate (DEAD) or 4-methyl 1,2-triazoline-3,5-dione (MTAD), effects\r\nconversion to the allenes, presumably via sigmatropic rearrangement of a monoalkyl\r\ndiazene intermediate. This rearrangement is demonstrated to proceed with essentially\r\ncomplete stereospecificity. The application of this methodology to the preparation of\r\nother allenes, including two that are notable for their reactivity and thermal instability, is\r\nalso described.
\r\n\r\nThe structural and mechanistic study of a monoalkyl diazene intermediate in the\r\noxidative transformation of propargylic hydrazines to allenes is described. The use of\r\nlong-range heteronuclear NMR coupling constants for assigning monoalkyl diazene\r\nstereochemistry (E vs Z) is also discussed. Evidence is presented that all known\r\nmonoalkyl diazenes are the E isomers, and the erroneous assignment of stereochemistry\r\nin the previous report of the preparation of (Z)-phenyldiazene is discussed.
\r\n\r\nThe synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene are\r\ndescribed. This molecule has been recognized as an interesting synthetic target for over\r\n40 years and represents the intersection of two sets of extensively studied molecules: nonbenzenoid\r\naromatic compounds and molecules containing sterically compressed \u03c0-systems.The formation of 1,5-dehydronaphthalene from 1 ,6-didehydro[10]annulene is\r\nbelieved to be the prototype for cycloaromatizations that produce 1,4-dehydroaromatic\r\nspecies with the radical centers disposed anti about the newly formed single bond. The\r\naromaticity of this annulene and the facility of its cycloaromatization are also analyzed.
\r\n" }, { "name": "Fisher, Stewart L.", "degree": "PhD", "year": "1994", "title": "Unnatural amino acids in the synthesis and semisynthesis of metalloprotein motifs", "advisor": "Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechTHESIS:05012013-144202651", "creators": [ { "name": { "family": "Fisher", "given": "Stewart L." }, "id": "Fisher-S-L", "display_name": "Fisher, Stewart L." } ], "advisors": [ { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/aww9-zr55", "abstract": "The design, synthesis, and characterization of two novel metalloprotein motifs is\r\npresented. The first project involved the design and construction of a protein motif which\r\nwas programmed to form a tetradentate metal complex upon the addition of metal cations.\r\nThe overall structure of the motif was based on a \u03b2\u03b2 super-secondary structure consisting of\r\na flexible peptide sequence flanked by metal binding regions located at the carboxy and\r\namino termini. The metal binding region near the amino terminus was constructed from a\r\nreverse turn motif with two metal ligating residues, (2R, 3R)-\u03b2-methyl-cysteine and\r\nhistidine. Selection of the peptide sequence for this region was based on the\r\nconformational analysis of a series of tetrapeptides designed to form reverse turns in\r\nsolution.
\r\n\r\nThe stereospecific syntheses of a series of novel bipyridyl- and phenanthrolylsubstituted\r\namino acids was carried out to provide ligands for the carboxy terminus metal\r\nbinding region. These residues were incorporated into peptide sequences using solid phase\r\npeptide synthesis protocols, and metal binding studies indicated that the metal binding\r\nproperties of these ligands was dictated by the specific regioisomer of the heteroaromatic\r\nring and the peptide primary sequence.
\r\n\r\nFinally, a peptide containing optimized components for the metal binding regions\r\nwas prepared to test the ability of the compound to form the desired intramolecular\r\npeptide:metal cation complexes. Metal binding studies demonstrated that the peptide\r\nformed monomeric complexes with very high metal cation binding affinities and that the\r\ntwo metal binding regions act cooperatively in the metal binding process. The use of these\r\nsystems in the design of proteins capable of regulating naturally occurring proteins is\r\ndiscussed.
\r\n\r\nThe second project involved the semisynthesis of two horse heart cytochrome c\r\nmutants incorporating the bipyridyl-amino acids at position 72 of the protein sequence.\r\nStructural studies on the proteins indicated that the bipyridyl amino acids had a neglible effect on the protein structure. One of the mutants was modified with Ru(bpy)_2^(+2) to form\r\na redox-active protein, and the modified protein was found to have enhanced electron\r\ntransfer properties between the heme and the introduced metal site.
\r\n" }, { "name": "Ghosh, Shubhro", "degree": "PhD", "year": "1994", "title": "The role of various geometrical structures in scalar advection-diffusion", "advisor": "Wiggins, Stephen R.; Leonard, Anthony", "url": "https://resolver.caltech.edu/CaltechETD:etd-10192005-143443", "creators": [ { "name": { "family": "Ghosh", "given": "Shubhro" }, "id": "Ghosh-Shubhro", "display_name": "Ghosh, Shubhro" } ], "advisors": [ { "name": { "family": "Wiggins", "given": "Stephen R." }, "id": "Wiggins-S-R", "role": "advisor", "display_name": "Wiggins, Stephen R." }, { "name": { "family": "Leonard", "given": "Anthony" }, "id": "Leonard-A", "role": "co-advisor", "display_name": "Leonard, Anthony" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/SZMP-XC12", "abstract": "This thesis is divided in two parts: in Part I, using a time-periodic perturbation of a two-dimensional steady separation bubble on a plane no-slip boundary to generate chaotic particle trajectories in a localized region of an unbounded boundary-layer flow, we study the impact of various geometrical structures that arise naturally in chaotic advection fields on the transport of a passive scalar from a local \"hot spot\" on the no-slip boundary. We consider here the full advection-diffusion problem, though attention is restricted to the case of small scalar diffusion, or large Peclet number. In this regime, a certain one-dimensional unstable manifold is shown to be the dominant organizing structure in the distribution of the passive scalar. In general, it is found that the chaotic structures in the flow strongly influence the scalar distribution while, in contrast, the flux of passive scalar from the localized active no-slip surface is, to dominant order, independent of the overlying chaotic advection. Increasing the intensity of the chaotic advection by perturbing the velocity field further away from integrability results in more non-uniform scalar distributions, unlike the case in bounded flows where the chaotic advection leads to rapid homogenization of diffusive tracer. In the region of chaotic particle motion the scalar distribution attains an asymptotic state which is time-periodic, with the period same as that of the time-dependent advection field. Some of these results are understood by using the shadowing property from dynamical systems theory. The shadowing property allows us to relate the advection-diffusion solution at large Peclet numbers to a fictitious zero-diffusivity or frozen-field solution - the so-called stirring solution - corresponding to infinitely large Peclet number. The zero-diffusivity solution is an unphysical quantity, but it is found to be a powerful heuristic tool in understanding the role of small scalar diffusion. A novel feature in this problem is that the chaotic advection field is adjacent to a no-slip boundary. The interaction between the necessarily non-hyperbolic particle dynamics in a thin near-wall region with the strongly hyperbolic dynamics in the overlying chaotic advection field is found to have important consequences on the scalar distribution: that this is indeed the case is shown using shadowing. Comparisons are made throughout with the flux and the distributions of the passive scalar for the advection-diffusion problem corresponding to the steady, unperturbed, integrable advection field.\r\n\r\nIn Part II, the transport of a passive scalar from a no-slip boundary into a two-dimensional steady boundary-layer flow is studied in the vicinity of a laminar separation point, where the dividing streamline - which is also a one-dimensional unstable manifold - is assumed to be normal to the boundary locally near the separation point. The novelty of the ensuing convection-diffusion process derives from the convective transport normal to the active boundary resulting from convection along the dividing streamline, and because of which the standard thermal boundary-layer approximations become invalid near the separation point. Using only the topology of the laminar, incompressible separated flow, a local solution of the Navier-Stokes equations is constructed in the form of a Taylor-series expansion from the separation point. The representation is universal, without regard to the outer inviscid flow and it is used in obtaining an asymptotically exact solution for the steady scalar distribution near the separation point at large Peclet number, using matched asymptotic expansions. The method demonstrates the application of local solutions of the Navier-Stokes equations in seeking asymptotic solutions to convection-diffusion problems. Verification of the asymptotic result is obtained from numerical computations based on the Wiener bundle solution - which is particularly well-suited to the large-Peclet-number transport problem.\r\n" }, { "name": "Gin, David Y.", "degree": "PhD", "year": "1994", "title": "A Convergent Synthetic Route to the Tunicamycin Antiobiotics. Synthesis of (+)-Tunicamycin V", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072013-095813413", "creators": [ { "name": { "family": "Gin", "given": "David Y." }, "id": "Gin-D-Y", "display_name": "Gin, David Y." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p6qx-ng34", "abstract": "A concise synthetic route to the tunicamycin antibiotics is described, illustrated by\r\nthe preparation of (+)-tunicamycin-V (1-V). Key features of the synthesis include: (1) the\r\ndevelopment and application of a silicon-mediated reductive coupling of aldehydes and\r\nallylic alcohols to construct the undecose core of the natural product; and (2) the\r\ndevelopment of an efficient procedure for the synthesis of the trehalose glycosidic bond\r\nwithin the antibiotic. These innovations allow for the coupling of a uridine-derived aldehyde\r\nfragment with a preformed trehalose-linked disaccharide allylic alcohol to form the\r\ncarbohydrate core (1) of the natural product in a highly convergent manner. The resultant\r\namino polyol is a versatile intermediate for the synthesis of any of the homologous\r\ntunicamycin antibiotics." }, { "name": "Jacobs, Simon Joshua", "degree": "PhD", "year": "1994", "title": "One-dimensional models for organic magnetic materials", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072013-105023604", "creators": [ { "name": { "family": "Jacobs", "given": "Simon Joshua" }, "id": "Jacobs-S-J", "display_name": "Jacobs, Simon Joshua" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/270t-0719", "abstract": "In the preparation of small organic paramagnets, these structures may\r\nconceptually be divided into spin-containing units (SCs) and ferromagnetic coupling\r\nunits (FCs). The synthesis and direct observation of a series of hydrocarbon tetraradicals\r\ndesigned to test the ferromagnetic coupling ability of m-phenylene, 1,3-cyclobutane, 1,3-\r\ncyclopentane, and 2,4-adamantane (a chair 1,3-cyclohexane) using Berson TMMs and\r\ncyclobutanediyls as SCs are described. While 1,3-cyclobutane and m-phenylene are good\r\nferromagnetic coupling units under these conditions, the ferromagnetic coupling ability of\r\n1,3-cyclopentane is poor, and 1,3-cyclohexane is apparently an antiferromagnetic\r\ncoupling unit. In addition, this is the first report of ferromagnetic coupling between the\r\nspins of localized biradical SCs.
\r\n\r\nThe poor coupling of 1,3-cyclopentane has enabled a study of the variable\r\ntemperature behavior of a 1,3-cyclopentane FC-based tetraradical in its triplet state.\r\nThrough fitting the observed data to the usual Boltzman statistics, we have been able to\r\ndetermine the separation of the ground quintet and excited triplet states. From this data,\r\nwe have inferred the singlet-triplet gap in 1,3-cyclopentanediyl to be 900 cal/mol, in\r\nremarkable agreement with theoretical predictions of this number.
\r\n\r\nThe ability to simulate EPR spectra has been crucial to the assignments made\r\nhere. A powder EPR simulation package is described that uses the Zeeman and dipolar\r\nterms to calculate powder EPR spectra for triplet and quintet states.
\r\n\r\nMethods for characterizing paramagnetic samples by SQUID magnetometry have\r\nbeen developed, including robust routines for data fitting and analysis. A precursor to a\r\npotentially magnetic polymer was prepared by ring-opening metathesis polymerization\r\n(ROMP), and doped samples of this polymer were studied by magnetometry. While the\r\npresent results are not positive, calculations have suggested modifications in this structure\r\nwhich should lead to the desired behavior.
\r\n\r\nSource listings for all computer programs are given in the appendix.
\r\n" }, { "name": "Johnson, Dale Fredrick", "degree": "PhD", "year": "1994", "title": "Mechanistic and kinetic studies of the surface chemistry of iridium and ruthenium", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032013-115316910", "creators": [ { "name": { "family": "Johnson", "given": "Dale Fredrick" }, "id": "Johnson-D-F", "display_name": "Johnson, Dale Fredrick" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0myw-fk78", "abstract": "Quantitative investigations of the mechanisms and the kinetics of the\r\nsurface-catalyzed activation of C-H, N-H, C-C, and C-N bonds on the close-packed\r\nsurfaces of Ir(111) and Ru(001) have been performed. The interaction\r\nof CH_3NH_2 with Ru(001) was investigated in ultrahigh vacuum with the\r\ntechniques of high-resolution electron energy loss spectroscopy and thermal\r\ndesorption mass spectrometry. Activation of the central C-N bond is\r\nobserved, but it is less favored than the competing channel of complete\r\ndehydrogenation, by a ratio between 2:1 to 3:1. The decomposition\r\nmechanism has been characterized with several surface intermediates and\r\ngas-phase products identified. A pronounced preference for the activation of\r\nC-H over N-H and C-N bonds has been established. Additionally, the kinetics\r\nof the initial dissociation of short chain alkanes on Ir(111) has been\r\nexamined, and the rate parameters of the activation of C-C bonds and\r\nprimary, secondary, and tertiary C-H bonds have been determined. The\r\nformation of primary alkyl products is favored, over most of the experimental\r\ntemperature range, despite the thermodynamic preference for the activation\r\nof individual secondary and tertiary C-H bonds in comparison to individual\r\nprimary C-H bonds. At higher surface temperatures, the activation of C-C\r\nbonds occurs at competitive rates to the C-H reaction channel. The measured\r\ndeuterium kinetic isotope effect implicates substantial deformation of the\r\nterminal methyl group in the transition state of C-C bond cleavage. Finally,\r\nthe surface structure sensitivity of C-H bond cleavage has been quantified for\r\nsmooth (111) and corrugated (110) surfaces of iridium and platinum, as well\r\nas for step edge defect sites on Ir(111).\r\n" }, { "name": "Kearney, Patrick C.", "degree": "PhD", "year": "1994", "title": "Studies of Organic Molecule Recognition by Synthetic Cyclophane Receptors in Aqueous Media", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032013-113036356", "creators": [ { "name": { "family": "Kearney", "given": "Patrick C." }, "id": "Kearney-P-C", "display_name": "Kearney, Patrick C." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d6bz-fq48", "abstract": "The behaviors of six new cyclophane receptors for organic guest molecules in\r\naqueous media are reported. These new hosts are modifications of more basic\r\nparent structures, and the main goal of their examination has been to determine\r\nhow the modifications affect host selectivity for cationic guests. In particular, we\r\nhave been interested in determining how additional non-covalent binding\r\ninteractions can complement the cation-\u03c0 interactions active in the parent\r\nsystems. Three types of modifications were made to these systems. Firstly,\r\nneutral methoxy and bromine substituents were added to produce four of the six\r\nnew macrocycles. Secondly, two additional aromatic rings (relative to the parent\r\nhost) capable of making cation-\u03c0 interactions with charged guest species were\r\nappended. Thirdly, a negatively charged carboxyl group was attached to\r\nproduce a cavity in which electrostatic interactions should enhance cationic guest\r\nbinding. ^1H-NMR and circular dichroic techniques were employed to determine\r\nthe binding affinities of a wide variety of organic guests for the parent and\r\nmodified structures in aqueous media.
\r\n\r\nBromination of the parent host greatly enhances its binding in a general\r\nfashion, primarily as the result of hydrophobic interactions. The addition of\r\nmethoxy groups does not enhance binding, apparently as a result of a collapse of\r\nthe hosts into a conformation that is not suitable for binding. The appendage of\r\nextra aromatic rings enhances the binding of positively charged guests, most\r\nlikely in response to more complete encapsulation of guest species. The addition\r\nof a negatively charged carboxylate enhances the binding to only selective\r\ngroups of cationic guests. AM1 calculations of the electrostatic potentials of\r\nseveral guests molecules suggests that the enhancements seen with the modified\r\nreceptor compared to the parent are most likely the result of close contact\r\nbetween regions of highest potential on the guest and the appended carboxylate.
" }, { "name": "Kelson, Eric P.", "degree": "PhD", "year": "1994", "title": "The electrocatalytic and stoichiometric oxidation chemistry of binuclear ruthenium complexes incorporating the anionic tripod ligand {(\u03b75-C5H5)Co[P(OCH3)2(=O)]3}-\r ", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032013-095024526", "creators": [ { "name": { "family": "Kelson", "given": "Eric P." }, "id": "Kelson-E-P", "display_name": "Kelson, Eric P." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xmwk-dk48", "abstract": "The anionic tripod ligand NaLoMe (L_(oMe) - = [(\u03b7^5-C_5H_5)Co{P(O)(OCH_3)_2}_3]^-) reacts\r\nwith RuO_4 in a biphasic reaction mixture of 1% H_2SO_4 and CCI_4 to afford [(L_(oMe) (HO)Ru^(IV)\r\n(\u00b5-O)_2Ru ^(IV)(OH)(L_(oMe)] (1), which is treated with aqueous CF_3S0_3H to generate\r\n[(L_(oMe)(H_2O)Ru^(IV) (\u00b5-O)_2R^(IV) (OH_2)(L_(oMe)][CF_3SO_3]_2 ([H_21][CF_3SO_3]_2). \r\nAddition of iodosobenzene to an acetonitrile solution of this salt yields [(L_(oMe)(O)Ru^v(\u00b5-0)2Ru^v-(O)(_(LoMe)] (2). The dimer 1 can be reduced chemically or electrochemically to the Ru^(III)- Ru^(III)\r\ndimers [(L_(oMe)(H_20)Ru^(III) (\u00b5-OH)_2Ru^(III) (OH_2)(L_(oMe)) ]^2+ and [(L_(oMe)) ^(III) (\u00b5-0Hh(\u00b5-0H2)Ru^(III) (L_(oMe)]^2+ which interconvert in aqueous media. Two electron processes dominate both the bulk chemistry and the electrochemistry of 1. Among these processes are the quasi-reversible\r\nRu^(IV) - Ru^(IV)/Ru^(III)- Ru^(III) and Ru^(III)- Ru^(III)/ Ru^(II)- Ru^(II) reductions and a largely irreversible\r\nRu^(V) - Ru^(V)/ Ru^(IV) - Ru^(IV)/oxidation. The dioxo dimer 2 oxidizes alcohols and aldehydes in organic\r\nmedia to afford 1 and the corresponding aldehydes and acids. Analogously, the Ru^(V) - Ru^(V)/ Ru^(IV)- Ru^(IV)\r\nredox wave mediates the electrooxidation of alcohols and aldehydes in aqueous buffer. In\r\nthis system, substrates can be oxidized completely to CO_2. The kinetic behavior of these\r\noxidations was examined by UV-vis and chronoamperometry, respectively, and the chemistry\r\nis typical of metal-oxo complexes, indicating that electronic coupling between two metal centers\r\ndoes not dramatically affect the metal-oxo chemistry. Dimer [H_21]^(2+) also reacts with\r\nalcohols, aldehydes, and triphenylphosphine in CH_3CN to afford Ru^(III)- Ru^(III) products\r\nincluding [(L_(oMe))CH_3CN) Ru^(III) (\u00b5-OH)_2 Ru^(III) (NCCH_3)( L_(oMe))][CF_3SO_3]2 (characterized by X-ray\r\ncrystallography) and the corresponding organic products. Reaction of 1 with formaldehyde\r\nin aqueous buffer quantitatively affords the triply bridged dimer [(L_(oMe)Ru^(III) (\u00b5-OH)2-\r\n(\u00b5-HCOO) Ru^(III) (L_(oMe)][CF_3SO_3] (characterized by X-ray crystallography). This reaction\r\nevidently proceeds by two parallel inner-sphere pathways, one of which is autocatalytic.\r\nNeither pathway exhibits a primary isotope effect suggesting the rate determining process\r\ncould be the formation of an intermediate, perhaps a Ru^(IV) - Ru^(IV) formate adduct. The Ru^(III)- Ru^(III)formate adduct is easily oxidized to the Ru^(IV) - Ru^(IV) analog \r\n[(L_(oMe)Ru^(IV)(\u00b5-OH)_2-(\u00b5-HCOO) Ru^(IV) (L_(oMe)][CF_3SO_3], which, after isolation, reacts slowly with aqueous formaldehyde to\r\ngenerate free formate and the Ru^(III)- Ru^(III) formate adduct. These dimers function as catalysts for\r\nthe electrooxidation of formaldehyde at low anodic potentials (+0.0 V versus SCE in aqueous\r\nbuffer, pH 8.5) and enhance the activity of Nafion treated palladium/carbon heterogeneous\r\nfuel cell catalysts.\r\n\r\n" }, { "name": "Kim, Soojin", "degree": "PhD", "year": "1994", "title": "Chemical vapor deposition of permselective oxide membranes for hydrogen separation", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12032007-142610", "creators": [ { "name": { "family": "Kim", "given": "Soojin" }, "id": "Kim-S", "display_name": "Kim, Soojin" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/cme7-m131", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nMembranes have recently emerged as energy-efficient means of gas separation. Oxide membranes that are effective for hydrogen separation at elevated temperatures (400-800\u00b0C) were developed. The membranes have high [...] selectivities along with permeances that are comparable to those of conventional polymeric membranes operating at ambient temperature.\n\nHydrogen-permselective membranes were synthesized by chemical vapor deposition of [...], [...], [...], and [...] layers within the pores of Vycor tubes. The deposition was carried out by continuous flow of [...], etc., and water in either the one-sided or the two-sided (opposing-reactants) geometry at 100-800\u00b0C. Permselective [...] layers could be formed in both geometries, while deposition of [...] and [...] layers was achieved only in the two-sided geometry. The permeation coefficients at 450\u00b0C were 0.3 and 0.1 [...] for [...] membranes produced in the one-sided geometry and two-sided geometries, respectively. The [...] permeation ratios were 500-5000. The [...] and [...] membranes had somewhat lower permeation coefficients and [...] ratios.\n\nThe [...] membranes prepared in the opposing-reactants geometry were characterized by scanning electron microscopy, electron microprobe analysis, and transmission electron microscopy. Examining tube cross section containing [...] deposit revealed that the membrane consisted of a thin region (approximately 1 [...] thick) of totally plugged pores and a broad region (100 [...]) of partially filled pores. The spatial density distribution of [...] in the tube cross section showed an asymmetric profile located close to the side of chloride flow indicating heterogeneous mechanism of the deposition reaction. The [...] permeance of the membranes decreased by 50-75%, and the selectivity diminished upon prolonged hydrothermal treatment.\n\nA mechanism of the deposition process is suggested involving heterogeneous reactions of gaseous chloride and surface hydroxyl groups and of water vapor with surface chloride groups on the growing deposit layer. The mechanism and kinetics of [...] deposition were investigated by thermogravimetric analysis. The reactions were decoupled by alternating reactions of [...] and [...] with the surface of Vycor glass. The results are interpreted by postulating two types of silanol groups Si-OH on the Vycor surface, paired and isolated. Reaction of [...] with paired silanols proceeds by competing steps which control the total extent of silylation. Upon reaction with [...], all surface Si-Cl groups are hydrolyzed regenerating Si-OH. Simultaneous silanol-silanol and silanol-surface chloride condensations eliminate [...] or HCl to form new Si-O-Si bridges with final product silica. A kinetic model incorporating the silylation, hydrolysis and condensation steps describes well the TGA data.\n\nThe reaction of the chlorosilanes with surface hydroxyls occurs very rapidly at temperatures above [...] and causes significant axial concentration gradients in the one-sided deposition, resulting in nonuniform deposit layer along the length of the tube. A new technique that eliminated the axial concentration gradients was used to deposit thin [...] layers on the surface of porous Vycor glass. Alternating vapor phase reaction with SiC14 and H2O was used to prepare membranes having [...] permeance of 0.3-0.4 [...] and [...] selectivity of 500-1000 at [...] 600\u00b0C. The [...] dosage at each silylation cycle, the concentration of initial surface -OH groups, and the reaction temperature influence significantly the deposit layer thickness. The membranes were stable to long hydrothermal treatments with the [...] permeance decreasing by about 20% and the selectivity increasing to more than 2000. The membrane properties after hydrothermal treatment are superior to those of membranes prepared by one-sided (steady flow) deposition due to thinner and more uniform deposit layers. A simple model incorporating diffusion and surface reaction was used to study the effect of various parameters on the formation of the deposit layer." }, { "name": "Larson, Wayne E.", "degree": "PhD", "year": "1994", "title": "Synthesis, structure, and photophysics of polypyridophenazine transition-metal complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082013-114702641", "creators": [ { "name": { "family": "Larson", "given": "Wayne E." }, "id": "Larson-W-E", "display_name": "Larson, Wayne E." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9vpr-ha57", "abstract": "The condensation of phenanthroline-5,6-dione (phendione) with polyamines is a\r\nversatile synthetic route to a wide variety of chelating ligands. Condensation with 2,3-\r\nnapthalene diamine gives benzo[i]dipyrido[3,2-a:2',3'-c]phenazine (bdppz) a ligand\r\ncontaining weakly-coupled orbitals of benzophenazine (bpz) and 2,2' -bipyridinde(bpy)\r\ncharacter. The bpy character gives Re and Ru complexes excited-state redox properties;\r\nintramolecular electron transfer (ET) takes place to the bpz portion of the ligand. The\r\ncharge-separated state so produced has an extraordinarily-long 50 \u00b5s lifetime. The slow\r\nrate of charge recombination arises from a combination of extremely weak coupling\r\nbetween the metal center and the bpz acceptor orbital and Marcus \"inverted region\"\r\nbehavior. Molecular orbital calculations show that only 3% the electron density in the\r\nlowest unoccupied molecular orbital lies on the bpy atoms of bdppz, effectively trapping\r\nthe transferred electron on the bpz portion. The rate of charge recombination decreases\r\nwith increasing driving force, showing that these rates lie in the inverted region.\r\nComparison of forward and back ET rates shows that donor-acceptor coupling is four\r\norders of magnitude greater for photoinduced electron transfer than it is for thermal\r\ncharge recombination.
\r\n\r\nCondensation of phendione with itself or tetramines gives a series of binucleating\r\ntetrapyridophenazine ligands of incrementally-varying coordination-site separation.\r\nWhen a photoredox-active metal center is attached, excited-state energy and electron\r\ntransfer to an acceptor metal center at the other coordination site can be studied as a\r\nfunction of distance. A variety of monometallic and homo- and heterodimetallic\r\ntetrapyridophenazine complexes has been synthesized. Electro- and magnetochemistry\r\nshow that no ground-state interaction exists between the metals in bimetallic complexes.\r\nExcited-state energy and electron transfer, however, takes place at rates which are\r\ninvariant with increasing donor-acceptor separation, indicating that a very efficient coupling mechanism is at work. Theory and experiment have suggested that such behavior might exist in extended \u03c0-systems like those presented by these ligands.
\r\n\r\nCondensation of three equivalents of 4,5-dimethyl-1,2-phenylenediamine with\r\nhexaketocyclohexane gives the trinucleating ligand hexaazahexamethyltrinapthalene\r\n(hhtn). Attaching two photredox-active metal centers and a third catalytic center to hhtn\r\nprovides means by which multielectron photocatalyzed reactions might be carried out.\r\nThe coordination properties of hhtn have been examined; X-ray crystallographic\r\nstructure determination shows that the ligand's constricted coordination pocket leads to\r\ndistorted geometries in its mono- and dimetallic derivatives.
\r\n" }, { "name": "Lee, Inho", "degree": "PhD", "year": "1994", "title": "Distinct intron DNA structures in simian virus 40 T-antigen and adenovirus 2 E1A genes", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222013-114326444", "creators": [ { "name": { "family": "Lee", "given": "Inho" }, "id": "Lee-I", "display_name": "Lee, Inho" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zhde-t378", "abstract": "Distinct structures delineating the introns of Simian Virus 40 T-antigen and Adenovirus 2 E1A genes have been discovered. The structures, which are centered around the branch points of the genes inserted in supercoiled double-stranded plasmids, are specifically targeted through photoactivated strand cleavage by the metal complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III). The DNA sites that are recognized lack sequence homology but are similar in demarcating functionally important sites on the RNA level. The single-stranded DNA fragments corresponding to the coding strands of the genes were also found to fold into a structure apparently identical to that in the supercoiled genes based on the recognition by the metal complex. Further investigation of different single-stranded\r\nDNA fragments with other structural probes, such as another metal complex bis(1,10-phenanthroline)(phenanthrenequinone diimine)rhodium(III), AMT (4'aminomethyl-4,5',8 trimethylpsoralen), restriction enzyme Mse I, and mung bean\r\nnuclease, showed that the structures require the sequ ences at both ends of the intron plus the flanking sequences but not the middle of the intron. The two ends form\r\nindependent helices which interact with each other to form the global tertiary structures. Both of the intron structures share similarities to the structure of the\r\nHolliday junction, which is also known to be specifically targeted by the former metal complex. These structures may have arisen from early RNA intron structures and may have been used to facilitate the evolution of genes through exon shuffling by acting as target sites for recombinase enzymes.
\r\n" }, { "name": "McCleskey, T. Mark", "degree": "PhD", "year": "1994", "title": "Design and applications of luminescent inorganic complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202005-153301", "creators": [ { "name": { "family": "McCleskey", "given": "T. Mark" }, "id": "McCleskey-T-M", "display_name": "McCleskey, T. Mark" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kqh2-zq63", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nA series of Au(I) phosphine complexes were designed and synthesized to investigate the possibility of room temperature phosphorescence in solution from three different types of transitions: metal-to-ligand-charge-transfer in four coordinate monomers, [...] in Au(I) dimers, and [...] in two and three coordinate monomers. Solution emission was only observed from the three coordinate Au(I) complexes. The complex [...] (dcpe = 1,2-bis-dicyclohexylphosphinoethane) has two isolated AuP3 units and emits at 508 nm in acetonitrile solution with a lifetime of 21 [...] and a quantum yield of 0.8 (366 nm excitation). The emission has been assigned as a [...] transition with the corresponding absorption band at 370 nm. The excited state is a powerful reductant capable of reducing aryl halides.\n\nElectron transfer (ET) rates were studied from the excited [...] to a series of substituted pyridiniums (py+). The low excited state reduction potential (Au(II)/Au(I)) of -2.3 V made it possible to study ET rates at driving forces as high as 2.1 eV. High driving force, bimolecular ET rates were also studied with [Ir(cod)(pz)]2 (IR2; cod = cyclooctadiene, pz = pyrazole). The forward ET rates from Ir2 to py+ increase to the diffusion limit and remain diffusion limited at driving forces as high as 1.60 eV. The recombination ET rates from py to Ir2+ show inverted behavior (rates decrease as the driving force increases) at driving forces > 0.85 eV, representing the first observation of inverted behavior for a bimolecular system. The discrepancy between the forward ET and recombination ET rates is explained by ET to low lying excited states.\n\nOn the basis of the emission observed from three coordinate Au(I) complexes, Au(I) was used as a probe for the coordination environment of the active site in Pseudomonas auruginosa azurin. The active site consists a copper center strongly bound to two histidines and a cysteine in a trigonal plane with a disputed axial interaction to [...] away. The Au(I)-WT-azurin is stable and emits at 580 nm, indicating that there is little or no interaction with the Metl2l." }, { "name": "Mrksich, Milan", "degree": "PhD", "year": "1994", "title": "Design of peptides for sequence-specific recognition of the minor groove of DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09212005-075404", "creators": [ { "name": { "family": "Mrksich", "given": "Milan" }, "id": "Mrksich-M", "display_name": "Mrksich, Milan" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7CWH-FH04", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nDistamycin A and netropsin are natural products which bind in the minor groove of DNA at four and five A,T base pair sites, respectively. While the peptides pyridine-2-carboxamide-netropsin (2-PyN) and 1-methylimidazole-2-carboxamide-netropsin (2-ImN) were designed to bind [...] sequences in a single orientation, they bind 5'-TGTCA-3' with no orientation preference. Direct characterization of the [...] complex by NMR reveals that the peptide binds in the minor groove as a side-by-side dimer.\n\nCovalent peptide dimers wherein the nitrogens of the central pyrroles of 2-PyN are connected with propyl, butyl, pentyl and hexyl linkers bind the 5'-TGTCA-3' site with affinities ten-fold greater than that of the non-linked peptides. The ratio of binding affinities of 2-PyN for 5'-TGTCA-3' and 5'-TTTTT-3' sites have been altered from 1:1 to 20:1.\n\nFootprinting and affinity cleaving experiments demonstrate that the two peptides distamycin and 2-ImN simultaneously bind the five-base pair sequence 5'-TGTTA-3' as a side-by-side heterodimer in the minor groove. The specific affinity for this site was enhanced with the design and synthesis of a covalent peptide heterodimer.\n\nFour hexapeptides were synthesized wherein the terminal amine and carboxyl groups of distamycin and 2-ImN, respectively, are connected with amino acids. 2-ImN-GABA-P3 binds the 5'-TGTTA-3' site with similar binding affinity as the first generation covalent peptide dimer. The general and efficient synthetic methodology for preparation of GABA linked peptides may allow the design of a new class of hairpin peptide-turn-peptides for specific recognition of many different sequences in the minor groove of DNA.\n\nFootprinting and affinity cleaving experiments demonstrate that the designed peptide ImPImP specifically binds the designated six-base-pair sites 5'-AGCGCT-3' and 5'-TGCGCA-3' in two equal orientations, consistent with a side-by-side antiparallel arrangement of peptides in the minor groove. This example underscores the utility of 2:1 peptide-DNA models for the design of ligands for sequence-specific recognition of designated DNA sites. Binding of this designed peptide to a pure four base pair GC-core sequence represents an absolute reversal of the specificity of the natural products distamycin and netropsin.\n" }, { "name": "Muller, Richard P.", "degree": "PhD", "year": "1994", "title": "Development and implementation of ab initio methods for application to large molecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-080702117", "creators": [ { "name": { "family": "Muller", "given": "Richard P." }, "id": "Muller-R-P", "display_name": "Muller, Richard P." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gtra-9x03", "abstract": "This thesis describes new methods for extending ab initio electronic structure theory calculations to larger molecules\u2014those requiring more than ~200 basis functions. These molecules are difficult to describe with standard methods in electronic structure theory because they require large amounts of CPU time, disk storage space, and physical memory. The work presented in this thesis develops the PS-GVB program that uses pseudospectral operator construction\u2014a faster method of constructing two electron operators\u2014to calculate the electronic structure of real chemical systems; and it outlines the procedure for using these operators to calculate the electronic structure of molecules with a variety of compositions, geometries, and wave functions. This thesis extends PS-GVB to metallic elements, which present particular problems for the pseudospectral method because the nature of the chemical bonding is qualitatively different between metallic elements than between non-metallic main group elements. This thesis also generalizes the Direct Inversion in the Iterative Subspace method to wave functions with arbitrary numbers of core, open-shell, and GVB natural orbitals. These wave functions are necessary to describe physical properties of chemical systems. Finally, this thesis applies these methods to study porphyrin excited states. Porphyrins appear in a variety of biological applications including the photosynthetic reaction center and the heme group, as well as applications in chemical catalysis. Semi-empirical electronic structure calculations have suggested that the porphyrin excited states are composed of coupled single excitations from the ground state. The combination of the large size of the porphyrins and the multi-configurational nature of the excited states have prevented ab initio calculations with quality basis sets on these states. Two different approaches are used: (i) Frozen Core-Four Orbital Excited States, which takes advantage of the planar geometry of many porphyrin rings to separate the \u03c3 and \u03c0orbitals of the molecules; and (ii) Self-Consistent-Four Orbital Excited States, which calculates explicitly the multi-configurational excited state energies and optimum orbitals. Both methods yield excellent agreement with experimental results suggesting that they may be used to analyze a wide variety of different porphyrin spectra.\r\n" }, { "name": "Nelson, Christine Marie", "degree": "PhD", "year": "1994", "title": "Photodissociation and reaction dynamics of chlorine-containing species important in stratospheric ozone chemistry", "advisor": "Okumura, Mitchio", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092013-083114535", "creators": [ { "name": { "family": "Nelson", "given": "Christine Marie" }, "id": "Nelson-C-M", "display_name": "Nelson, Christine Marie" } ], "advisors": [ { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "role": "advisor", "display_name": "Okumura, Mitchio" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0702-4f92", "abstract": "Chlorine oxide species have received considerable attention in recent years due to\r\ntheir central role in the balance of stratospheric ozone. Many questions pertaining to the\r\nbehavior of such species still remain unanswered and plague the ability of researchers to\r\ndevelop accurate chemical models of the stratosphere. Presented in this thesis are three\r\nexperiments that study various properties of some specific chlorine oxide species.
\r\n\r\nIn the first chapter, the reaction between ClONO_2 and protonated water clusters is\r\ninvestigated to elucidate a possible reaction mechanism for the heterogeneous reaction of\r\nchlorine nitrate on ice. The ionic products were various forms of protonated nitric acid,\r\nNO_2 +(H_20)_m, m = 0, 1, 2. These products are analogous to products previously reported\r\nin the literature for the neutral reaction occurring on ice surfaces. Our results support the\r\nhypothesis that the heterogeneous reaction is acid-catalyzed.
\r\n\r\nIn the second chapter, the photochemistry of ClONO_2 was investigated at two\r\nwavelengths, 193 and 248 nm, using the technique of photofragmentation translational\r\nspectroscopy. At both wavelengths, the predominant dissociation pathways were Cl +\r\nNO_3 and ClO + NO_2. Channel assignments were confirmed by momentum matching the\r\ncounterfragments from each channel. A one-dimensional stratospheric model using the\r\nnew 248 nm branching ratio determined how our results would affect the predicted Cl_x\r\nand NO_x partitioning in the stratosphere.
\r\n\r\nChapter three explores the photodissociation dynamics of Cl_2O at 193, 248 and\r\n308 nm. At 193 nm, we found evidence for the concerted reaction channel, Cl_2 + O. The\r\nClO + Cl channel was also accessed, however, the majority of the ClO fragments were\r\nformed with sufficient internal energies for spontaneous secondary dissociation to occur.\r\nAt 248 and 308 nm, we only observed only the ClO + Cl channel. . Some of the ClO\r\nformed at 248 nm was formed internally hot and spontaneously dissociated. Bimodal\r\ntranslational energy distributions of the ClO and Cl products indicate two pathways\r\nleading to the same product exist.
\r\n\r\nAppendix A, B and C discuss the details of data analysis techniques used in\r\nChapters 1 and 2. The development of a molecular beam source of ClO dimer is\r\npresented in Appendix D.
" }, { "name": "Oakley, Martha G.", "degree": "PhD", "year": "1994", "title": "Design, synthesis and characterization of sequence-specific DNA-cleaving metalloproteins", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132013-153337171", "creators": [ { "name": { "family": "Oakley", "given": "Martha G." }, "id": "Oakley-M-G", "display_name": "Oakley, Martha G." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/35m1-1m12", "abstract": "This thesis describes research pursued in two areas, both involving the\r\ndesign and synthesis of sequence specific DNA-cleaving proteins. The first\r\ninvolves the use of sequence-specific DNA-cleaving metalloproteins to probe\r\nthe structure of a protein-DNA complex, and the second seeks to develop\r\ncleaving moieties capable of DNA cleavage through the generation of a non-diffusible\r\noxidant under physiological conditions.
\r\n\r\nChapter One provides a brief review of the literature concerning\r\nsequence-specific DNA-binding proteins. Chapter Two summarizes the\r\nresults of affinity cleaving experiments using leucine zipper-basic region\r\n(bZip) DNA-binding proteins. Specifically, the NH_2-terminal locations of a\r\ndimer containing the DNA binding domain of the yeast transcriptional\r\nactivator GCN4 were mapped on the binding sites 5'-CTGACTAAT-3' and 5'ATGACTCTT-\r\n3' using affinity cleaving. Analysis of the DNA cleavage\r\npatterns from Fe\u2022EDTA-GCN4(222-281) and (226-281) dimers reveals that the\r\nNH_2-termini are in the major groove nine to ten base pairs apart and\r\nsymmetrically displaced four to five base pairs from the central C of the\r\nrecognition site. These data are consistent with structural models put\r\nforward for this class of DNA binding proteins. The results of these\r\nexperiments are evaluated in light of the recently published crystal structure\r\nfor the GCN4-DNA complex. Preliminary investigations of affinity cleaving\r\nproteins based on the DNA-binding domains of the bZip proteins Jun and Fos\r\nare also described.
\r\n\r\nChapter Three describes experiments demonstrating the simultaneous\r\nbinding of GCN4(226-281) and 1-Methylimidazole-2-carboxamide-netropsin\r\n(2-ImN), a designed synthetic peptide which binds in the minor groove of\r\nDNA at 5'-TGACT-3' sites as an antiparallel, side-by-side dimer. Through the\r\nuse of Fe\u2022EDTA-GCN4(226-281) as a sequence-specific footprinting agent, it is\r\nshown that the dimeric protein GCN4(226-281) and the dimeric peptide 2-\r\nImN can simultaneously occupy their common binding site in the major and\r\nminor grooves of DNA, respectively. The association constants for 2-ImN in\r\nthe presence and in the absence of Fe\u2022EDTA-GCN4(226-281) are found to be\r\nsimilar, suggesting that the binding of the two dimers is not cooperative.
\r\n\r\nChapter Four describes the synthesis and characterization of PBA-\u03b2-OH-His-\r\nHin(139-190), a hybrid protein containing the DNA-binding domain of\r\nHin recombinase and the putative iron-binding and oxygen-activating\r\ndomain of the antitumor antibiotic bleomycin. This 54-residue protein,\r\ncomprising residues 139-190 of Hin recombinase with the dipeptide\r\npyrimidoblamic acid-\u03b2-hydroxy-L-histidine (PBA-\u03b2-OH-His) at the NH2\r\nterminus, was synthesized by solid phase methods. PBA-\u03b2-OH-His-Hin(139-\r\n190) binds specifically to DNA at four distinct Hin binding sites with affinities\r\ncomparable to those of the unmodified Hin(139-190). In the presence of\r\ndithiothreitol (DTT), Fe\u2022PB-\u03b2-OH-His-Hin(139-190) cleaves DNA with\r\nspecificity remarkably similar to that of Fe\u2022EDTA-Hin(139-190), although\r\nwith lower efficiency. Analysis of the cleavage pattern suggests that DNA\r\ncleavage is mediated through a diffusible species, in contrast with cleavage by\r\nbleomycin, which occurs through a non-diffusible oxidant.
\r\n" }, { "name": "Oh, Kyoung Joon", "degree": "PhD", "year": "1994", "title": "Exploration of New Drug Delivery Pathways: I. Mechanism of Folate Uptake in Cultured Human Cells. II. Role of Nuclear Localization Signal Peptides in the Delivery of Oligonucleotide into Reconstituted Nuclei", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132013-115254310", "creators": [ { "name": { "family": "Oh", "given": "Kyoung Joon" }, "id": "Oh-Kyoung-Joon", "orcid": "0000-0002-4729-9674", "display_name": "Oh, Kyoung Joon" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Strauss", "given": "James H." }, "id": "Strauss-J-H", "role": "member", "display_name": "Strauss, James H." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p6kk-r616", "abstract": "The roles of the folate receptor and an anion carrier in the uptake of 5-\r\nmethyltetrahydrofolate (5-MeH_4folate) were studied in cultured human (KB)\r\ncells using radioactive 5-MeH_4folate. Binding of the 5-MeH_4folate was inhibited\r\nby folic acid, but not by probenecid, an anion carrier inhibitor. The\r\ninternalization of 5-MeH_4folate was inhibited by low temperature, folic acid,\r\nprobenecid and methotrexate. Prolonged incubation of cells in the presence of\r\nhigh concentrations of probenecid appeared to inhibit endocytosis of folatereceptors\r\nas well as the anion carrier. The V_(max) and K_M values for the carrier\r\nwere 8.65 \u00b1 0.55 pmol/min/mg cell protein and 3.74 \u00b1 0.54\u00b5M, respectively. The\r\ntransport of 5-MeH4folate was competitively inhibited by folic acid, probenecid\r\nand methotrexate. The carrier dissociation constants for folic acid, probenecid\r\nand methotreate were 641 \u00b5M, 2.23 mM and 13.8 \u00b5M, respectively. Kinetic\r\nanalysis suggests that 5-MeH_4folate at physiological concentration is transported\r\nthrough an anion carrier with the characteristics of the reduced-folate carrier\r\nafter 5-MeH_4folate is endocytosed by folate receptors in KB cells. Our data with\r\nKB cells suggest that folate receptors and probenecid-sensitive carriers work in\r\ntandem to transport 5-MeH_4folate to the cytoplasm of cells, based upon the\r\nassumption that 1 mM probenecid does not interfere with the acidification of the\r\nvesicle where the folate receptors are endocytosed.
\r\n\r\nOligodeoxynucleotides designed to hybridize to specific mRNA sequences\r\n(antisense oligonucleotides) or double stranded DNA sequences have been used\r\nto inhibit the synthesis of a number of cellular and viral proteins (Crooke, S. T.\r\n(1993) FASEB J. 7, 533-539; Carter, G. and Lemoine, N. R. (1993) Br. J. Cacer 67,\r\n869-876; Stein, C. A. and cohen, J. S. (1988) Cancer Res. 48, 2659-2668).\r\nHowever, the distribution of the delivered oligonucleotides in the cell, i.e., in the cytoplasm or in the nucleus has not been clearly defined. We studied the kinetics\r\nof oligonucleotide transport into the cell nucleus using reconstituted cell nuclei\r\nas a model system. We present evidences here that oligonucleotides can freely\r\ndiffuse into reconstituted nuclei. Our results are consistent with the reports by\r\nLeonetti et al. (Proc. Natl. Acad. Sci. USA, Vol. 88, pp. 2702-2706, April 1991),\r\nwhich were published while we were carrying this research independently. We\r\nalso investigated whether a synthetic nuclear localization signal (NLS) peptide of\r\nSV40 T antigen could be used for the nuclear targeting of oligonucleotides. We\r\nsynthesized a nuclear localization signal peptide-conjugated oligonucleotide to\r\nsee if a nuclear localization signal peptide can enhance the uptake of\r\noligonucleotides into reconstituted nuclei of Xenopus. Uptake of the NLS\r\npeptide-conjugated oligonucleotide was comparable to the control\r\noligonucleotide at similar concentrations, suggesting that the NLS signal peptide\r\ndoes not significantly enhance the nuclear accumulation of oligonucleotides.\r\nThis result is probably due to the small size of the oligonucleotide.
\r\n" }, { "name": "Perry, Jason Kendrick", "degree": "PhD", "year": "1994", "title": "Alkane activation by first, second, and third row transition metal ions : organometallic chemistry in the gas plate", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-152204878", "creators": [ { "name": { "family": "Perry", "given": "Jason Kendrick" }, "id": "Perry-J-K", "display_name": "Perry, Jason Kendrick" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cs1d-8f56", "abstract": "Reactions of the atomic transition metal cations, Co^+, Rh^+, and Ir^+, with H_2, CH_4, and C_2H_6 in the gas phase are considered using high level ab initio techniques. The nature of complexation and oxidative addition, in particular, are discussed. We find that the third row metal, Ir^+, is significantly more reactive toward these small molecules in comparison to the first and second row metals. Ir^+ is capable of inserting into the H\u2014H bond and leads to the facile dehydrogenation of CH_4 to form IrCH^+_2. Co^+ and Rh^+ form only molecular complexes with these molecules. All three metals exothermically dehydrogenate ethane but Co^+ has a barrier which prevents the reaction from being observed at room temperature. The mechanisms for dehydrogenation are distinctly different for each metal. For Co^+, the initial C\u2014H insertion to form Co(H)(C_2 H_5)^+ is rate limiting. This is followed by a multi-center elimination of H_2. For Rh^+, the concerted insertion into two C\u2014H bonds to form Rh(H)_2(C_2H_4)+ is seen without the intermediacy of Rh(H)(C_2H_5)^+. Reductive elimination ofH_2 follows. For Ir^+, a number of reaction pathways are viable with the most favorable being a stepwise oxidative addition/\u03b2-H shift mechanism. Much of the difference in the chemistry of these metals stems from two principal factors: the atomic state splittings and the orbital sizes. For Co^+ and Ir^+, both the s^1d^7 and d^8 valence electron configurations are accessible, providing the flexibility needed to adapt to the changing ligation of the reaction profile. For Rh^+, the s^1d^7 state is high in energy, limiting the efficiency of this metal in these reactions. In addition, the s and d orbitals have dramatically different sizes for Co^+, which diminishes the effectiveness of sd hybridization and leads to weaker bonds, particularly in highly ligated complexes. The s and d orbitals of Rh^+ and Ir^+ are more similar in size, providing strong sd hybrid bonds. These two factors compromise the reactivity of Co^+ and Rh^+, leaving only Ir^+ near the ideal." }, { "name": "Pizarro, Pedro Jos\u00e9", "degree": "PhD", "year": "1994", "title": "Trapped ion magnetic resonance: concepts and designs", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102013-144219320", "creators": [ { "name": { "family": "Pizarro", "given": "Pedro Jos\u00e9" }, "id": "Pizarro-P-J", "display_name": "Pizarro, Pedro Jos\u00e9" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/eeq1-kw72", "abstract": "A novel spectroscopy of trapped ions is proposed which will bring single-ion\r\ndetection sensitivity to the observation of magnetic resonance spectra. The approaches\r\ndeveloped here are aimed at resolving one of the fundamental problems of molecular\r\nspectroscopy, the apparent incompatibility in existing techniques between high information\r\ncontent (and therefore good species discrimination) and high sensitivity. Methods for\r\nstudying both electron spin resonance (ESR) and nuclear magnetic resonance (NMR) are\r\ndesigned. They assume established methods for trapping ions in high magnetic field and\r\nobserving the trapping frequencies with high resolution (<1 Hz) and sensitivity (single ion)\r\nby electrical means. The introduction of a magnetic bottle field gradient couples the spin\r\nand spatial motions together and leads to a small spin-dependent force on the ion, which\r\nhas been exploited by Dehmelt to observe directly the perturbation of the ground-state\r\nelectron's axial frequency by its spin magnetic moment.
\r\n\r\nA series of fundamental innovations is described m order to extend magnetic\r\nresonance to the higher masses of molecular ions (100 amu = 2x 10^5 electron masses) and smaller magnetic moments (nuclear moments = 10^(-3) of the electron moment). First, it is\r\ndemonstrated how time-domain trapping frequency observations before and after magnetic\r\nresonance can be used to make cooling of the particle to its ground state unnecessary.\r\nSecond, adiabatic cycling of the magnetic bottle off between detection periods is shown to\r\nbe practical and to allow high-resolution magnetic resonance to be encoded pointwise as\r\nthe presence or absence of trapping frequency shifts. Third, methods of inducing spindependent\r\nwork on the ion orbits with magnetic field gradients and Larmor frequency\r\nirradiation are proposed which greatly amplify the attainable shifts in trapping frequency.
\r\n\r\nThe dissertation explores the basic concepts behind ion trapping, adopting a\r\nvariety of classical, semiclassical, numerical, and quantum mechanical approaches to\r\nderive spin-dependent effects, design experimental sequences, and corroborate results\r\nfrom one approach with those from another. The first proposal presented builds on\r\nDehmelt's experiment by combining a \"before and after\" detection sequence with novel\r\nsignal processing to reveal ESR spectra. A more powerful technique for ESR is then\r\ndesigned which uses axially synchronized spin transitions to perform spin-dependent work\r\nin the presence of a magnetic bottle, which also converts axial amplitude changes into\r\ncyclotron frequency shifts. A third use of the magnetic bottle is to selectively trap ions\r\nwith small initial kinetic energy. A dechirping algorithm corrects for undesired frequency\r\nshifts associated with damping by the measurement process.
\r\n\r\nThe most general approach presented is spin-locked internally resonant ion\r\ncyclotron excitation, a true continuous Stern-Gerlach effect. A magnetic field gradient\r\nmodulated at both the Larmor and cyclotron frequencies is devised which leads to\r\ncyclotron acceleration proportional to the transverse magnetic moment of a coherent state\r\nof the particle and radiation field. A preferred method of using this to observe NMR as an\r\naxial frequency shift is described in detail. In the course of this derivation, a new quantum\r\nmechanical description of ion cyclotron resonance is presented which is easily combined\r\nwith spin degrees of freedom to provide a full description of the proposals.
\r\n\r\nPractical, technical, and experimental issues surrounding the feasibility of the\r\nproposals are addressed throughout the dissertation. Numerical ion trajectory simulations\r\nand analytical models are used to predict the effectiveness of the new designs as well as\r\ntheir sensitivity and resolution. These checks on the methods proposed provide\r\nconvincing evidence of their promise in extending the wealth of magnetic resonance\r\ninformation to the study of collisionless ions via single-ion spectroscopy.
\r\n" }, { "name": "Pritchard, Howard P.", "degree": "PhD", "year": "1994", "title": "Application of the Schwinger multichannel method to multichannel studies of electronically inelastic electron-molecule collisions", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132013-112837527", "creators": [ { "name": { "family": "Pritchard", "given": "Howard P." }, "id": "Pritchard-H-P", "display_name": "Pritchard, Howard P." } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tptz-6s51", "abstract": "We have applied the Schwinger Multichannel Method(SMC) to the study of\r\nelectronically inelastic, low energy electron-molecule collisions. The focus of these\r\nstudies has been the assessment of the importance of multichannel coupling to the\r\ndynamics of these excitation processes. It has transpired that the promising quality\r\nof results realized in early SMC work on such inelastic scattering processes has been\r\nfar more difficult to obtain in these more sophisticated studies.
\r\n\r\nWe have attempted to understand the sources of instability of the SMC method\r\nwhich are evident in these multichannel studies. Particular instances of such instability\r\nhave been considered in detail, which indicate that linear dependence, failure\r\nof the separable potential approximation, and difficulties in converging matrix\r\nelements involving recorrelation or Q-space terms all conspire to complicate application\r\nof the SMC method to these studies. A method involving singular value\r\ndecomposition(SVD) has been developed to, if not resolve these problems, at least\r\nmitigate their deleterious effects on the computation of electronically inelastic cross\r\nsections.
\r\n\r\nIn conjunction with this SVD procedure, the SMC method has been applied to\r\nthe study of the H_2 , H_2O, and N_2 molecules. Rydberg excitations of the first two\r\nmolecules were found to be most sensitive to multichannel coupling near threshold.\r\nThe (3\u03c3_g \u2192 1\u03c0_g ) and (1\u03c0_u \u2192 1\u03c0_g) valence excitations of the N_2 molecule were\r\nfound to be strongly influenced by the choice of channel coupling scheme at all\r\ncollision energies considered in these studies.
\r\n\r\n" }, { "name": "Quan, Roger Weihong", "degree": "PhD", "year": "1994", "title": "Oxo, imido, and borollide complexes of tantalum and zirconium", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07052012-161238837", "creators": [ { "name": { "family": "Quan", "given": "Roger Weihong" }, "id": "Quan-R-W", "display_name": "Quan, Roger Weihong" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0351-pe35", "abstract": "The preparation of reactive oxo, imido, and borollide complexes on tantalum and zirconium will be described. Metathesis of Cp*2Ta(=O)Cl with AgPF6 afforded [Cp*2TaF2HPF6], which presumably formed from P-F activation of PF6-. When AgS03CF3 was used, [Cp*2Ta(=O)][S03CF3] was isolated; however, it was unreactive toward styrene, methane, or benzene. Exposure to water resulted in the 1,2-addition product, [Cp*2Ta(OH)2][S03CF3]. Finally, treating Cp*2Ta(=O)H with [Ph3C][B(C6F5)4] afforded [Cp*2Ta(=O)][B(C6F5)4]. Even with this non-coordinating counterion, the complex was found to be surprisingly unreactive. To prepare an imido complex, treating Cp*TaCl4 with four equivalents of lithium anilide affords Cp*Ta(=NPh)(NHPh)2. This complex reacts readily with substituted anilines to generate Cp*Ta(=NPh')(NHPh')2 and with alcohols such as pinacol to afford Cp*Ta(OCMe2CMe2O)2, products whereby both the imido and amido groups are exchanged. Exposing Cp*Ta(=NPh)(NHPh)2 to C02 resulted in the isolation of Cp*Ta(OCONPh)(\u03b74-OCONHPh)2 with both the formal [2+2] addition of C02 across the imido group and insertion of C02 into the amido group. Finally, bis-imido complexes were prepared by treating Cp*Ta(=NPh)(NHPh)2 to one equivalent of HCl to yield Cp*Ta(=NPh)2 or by treating Cp*TaCl4 with four equivalents of lithium 2,6-diisopropylanilide to yield Cp*Ta(=NPh\")2. The borollide ligand, (C4H4BNiPr2)2-, ligand is introduced by treating Cp*ZrCl3 with one equivalent of Li2(C4H4BNiPr2)\u2022THF to generate Cp*(C4H4BNiPr2)ZrCl\u2022LiCl. This complex contains a \u03b75- coordinated borollide ligand, as shown by an X-ray crystal structure analysis. Alkylation and arylation with trimethylsilylmethyllithium, benzylpotassium or phenyllithium yielded Cp*(C4H4BNiPr2)ZrR complexes. These catalysts polymerizes ethylene, but only oligomerizes \u03b1-olefins. In addition, Cp*(C4H4BNiPr2)ZrCl\u2022LiCl has been found to exhibit the formal heterolytic cleavage of HCl and CH3I, affording Cp*(C4H4BNHiPr2)ZrCl2 and Cp*(C4H4BNiPr2)ZrCl(I), respectively. Finally, treatment of Cp*(C4H4BNiPr2)ZrCl\u2022LiCl with LiNHtBu generated the zwitterionic complex, Cp*(C4H4BNHiPr2)Zr=NtBu.\r\n\r\n" }, { "name": "Ramamoorthi, Roopa", "degree": "PhD", "year": "1994", "title": "Genetics and Regulation of Pyrroloquinoline Quinone (PQQ) Biosynthesis in the Methylotrophic Bacterium Methylobacterium extorquens AM1", "advisor": "Lidstrom, Mary E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12072007-081526", "creators": [ { "name": { "family": "Ramamoorthi", "given": "Roopa" }, "id": "Ramamoorthi-Roopa", "display_name": "Ramamoorthi, Roopa" } ], "advisors": [ { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "advisor", "display_name": "Lidstrom, Mary E." } ], "committee": [ { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "chair", "display_name": "Lidstrom, Mary E." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/cnm0-mm56", "abstract": "Pyrroloquinoline quinone (PQQ) has potential applications in the treatment of Alzheimers disease and jaundice. PQQ is produced and secreted in large amounts by methylotrophic bacteria, and they have potential for commercial PQQ production.
\r\n\r\nPQQ is the prosthetic group in methanol dehydrogenase of the facultative methylotroph, Methylobacterium extorquens AM1. Previous work had shown that seven genes were required for PQQ production in M.extorquens AM1. Dr. Christina Morris in our lab had sequenced the first two genes, pqqD and pqqG. pqqD encoded a twenty-nine amino acid peptide containing tyrosine and glutamate separated by three amino acids. Tyrosine and glutamate had been shown to be the precursors of PQQ, and this peptide is believed to be the precursor of PQQ biosynthesis in vivo.
\r\n\r\nThis thesis was initiated by mapping the transcriptional start site in front of pqqD. A high abundance 240 base pair transcript containing pqqD and a low abundance 1300 base pair transcript containing both pqqD and the next gene pqqG were detected using RNA-DNA blots. This was supported by data with Tn5lac insertions.
\r\n\r\nStudies were carried out to understand the regulation of PQQ biosynthesis in more detail. It was found that the products of the regulatory genes moxM, moxD and moxB were required for induction of pqqD on methanol plus methylamine compared to succinate, while the products of the regulatory genes moxQ and moxE were not required. The products of moxM and moxD were also required for high level transcription of pqqD. Measurements of PQQ in the culture supernatants of wild-type and mutants indicated that transcription of pqqD was not the rate limiting step in PQQ biosynthesis, and in addition that regulation of PQQ biosynthesis occurs at more than one step in the process.
\r\n\r\nUsing functional complementation it was found that pqqE of M.extorquens AM1 was equivalent to pqqF of K.pneumoniae. The middle portion of pqqE was sequenced and by aligning PqqE with PqqF of K.pneumoniae, the direction of transcription and size of pqqE was determined. PqqF shows similarity to proteases and this strongly suggests that a protease is involved in PQQ biosynthesis.
" }, { "name": "Richmond, Todd Alan", "degree": "PhD", "year": "1994", "title": "Structural requirements for catalysis: studies on RTEM-1 \u03b2-lactamase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172013-094843923", "creators": [ { "name": { "family": "Richmond", "given": "Todd Alan" }, "id": "Richmond-T-A", "display_name": "Richmond, Todd Alan" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bmqt-cf02", "abstract": "\u03b2-lactamases are a group of enzymes that confer resistance to penam and\r\ncephem antibiotics by hydrolysis of the \u03b2-lactam ring, thereby inactivating the antibiotic.\r\nCrystallographic and computer modeling studies of RTEM-1 \u03b2-lactamase have indicated\r\nthat Asp 132, a strictly conserved residue among the class A \u03b2-lactamases, appears to be\r\ninvolved in substrate binding, catalysis, or both. To study the contribution of residue 132\r\nto \u03b2-lactamase function, site saturation mutagenesis was used to generate mutants coding\r\nfor all 20 amino acids at position 132. Phenotypic screening of all mutants indicated that\r\nposition 132 is very sensitive to amino acid changes, with only N132C, N132D, N132E,\r\nand N132Q showing any appreciable activity. Kinetic analysis of three of these mutants\r\nshowed increases in K_M, along with substantial decreases in k_(cat). Efforts to trap a stable\r\nacyl-enzyme intermediate were unsuccessfuL These results indicate that residue 132 is\r\ninvolved in substrate binding, as well as catalysis, and supports the involvement of this\r\nresidue in acylation as suggested by Strynadka et al.
\r\n\r\nCrystallographic and computer modeling studies of RTEM-1 \u03b2-lactamase have\r\nindicated that Lys 73 and Glu 166, two strictly conserved residues among the class A \u03b2-lactamases,\r\nappear to be involved in substrate binding, catalysis, or both. To study the\r\ncontribution of these residues to \u03b2-lactamase function, site saturation mutagenesis was used\r\nto generate mutants coding for all 20 amino acids at positions 73 and 166. Then all 400\r\npossible combinations of mutants were created by combinatorial mutagenesis. The colonies\r\nharboring the mutants were screened for growth in the presence of ampicillin. The\r\ncompetent colonys' DNA were sequenced, and kinetic parameters investigated. It was\r\nfound that lysine is essential at position 73, and that position 166 only tolerated fairly\r\nconservative changes (Aspartic acid, Histidine, and Tyrosine). These functional mutants\r\nexhibited decreased kcat's, but K_M was close to wild-type levels. The results of the\r\ncombinatorial mutagenesis experiments indicate that Lysis absolutely required for activity\r\nat position 73; no mutation at residue 166 can compensate for loss of the long side chain\r\namine. The active mutants found--K73K/E166D, K73KIE166H, and K73KIE166Y were\r\nstudied by kinetic analysis. These results reaffirmed the function of residue 166 as\r\nimportant in catalysis, specifically deacylation.
\r\n\r\nThe identity of the residue responsible for enhancing the active site serine (Ser 70) in\r\nRTEM-1 \u03b2-lactamase has been disputed for some time. Recently, analysis of a crystal\r\nstructure of RTEM-1 \u03b2-lactamase with covalently bound intermediate was published, and it\r\nwas suggested that Lys 73, a strictly conserved residue among the class A \u03b2-lactamases,\r\nwas acting as a general base, activating Ser 70. For this to be possible, the pK_a of Lys 73\r\nwould have to be depressed significantly. In an attempt to assay the pK_a of Lys 73, the\r\nmutation K73C was made. This mutant protein can be reacted with 2-bromoethylamine,\r\nand activity is restored to near wild type levels. ^(15)N-2-bromoethylamine hydrobromide and\r\n^(13)C-2-bromoethylamine hydrobromide were synthesized. Reacting these compounds with\r\nthe K73C mutant gives stable isotopic enrichment at residue 73 in the form of\r\naminoethylcysteine, a lysine homologue. The pK_a of an amine can be determined by NMR\r\ntitration, following the change in chemical shift of either the ^(15)N-amine nuclei or adjacent\r\nBe nuclei as pH is changed. Unfortunately, low protein solubility, along with probable\r\nlabel scrambling in the Be experiment, did not permit direct observation of either the ^(15)N\r\nor ^(13)C signals. Indirect detection experiments were used to observe the protons bonded\r\ndirectly to the ^(13)C atoms. Two NMR signals were seen, and their chemical shift change\r\nwith pH variation was noted. The peak which was determined to correspond to the\r\naminoethylcysteine residue shifted from 3.2 ppm down to 2.8 ppm over a pH range of 6.6\r\nto 12.5. The pK_a of the amine at position 73 was determined to be ~10. This indicates that\r\nresidue 73 does not function as a general base in the acylation step of the reaction.\r\nHowever the experimental measurement takes place in the absence of substrate. Since the\r\nenzyme undergoes conformational changes upon substrate binding, the measured pK_a of\r\nthe free enzyme may not correspond to the pK_a of the enzyme substrate complex.
" }, { "name": "Ross, Scott Alan", "degree": "PhD", "year": "1994", "title": "Insights into the Mechanism of Human Erythrocyte Hexose Transport: a Transferred NOE Study of Glucose Binding to GLUT1", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172013-114618257", "creators": [ { "name": { "family": "Ross", "given": "Scott Alan" }, "id": "Ross-Scott-Alan", "display_name": "Ross, Scott Alan" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nb45-1b79", "abstract": "This study examines binding of \u03b1- and \u03b2-D-glucose in their equilibrium mixture to the glucose transporter (GLUT1) in human erythrocyte membrane preparations by an ^1H NMR method, the transferred NOE (TRNOE). This method is shown theoretically and experimentally to be a sensitive probe of weak ligand-macromolecule interactions. The TRNOEs observed are shown to arise solely from glucose binding to GLUT1. Sites at both membrane faces contribute to the TRNOEs. Binding curves obtained are consistent with a homogeneous class of sugar sites, with an apparent KD which varies (from ~30 mM to ~70 mM for both anomers) depending on the membrane preparation examined. Preparations with a higher proportion of the cytoplasmic membrane face exposed to bulk solution yield higher apparent KKDs. The glucose transport inhibitor cytochalasin B essentially eliminates the TRNOE. Nonlinearity was found in the dependence on sugar concentration of the apparent inhibition constant for cytochalasin B reversal of the TRNOE observed in the \u03b1 anomer (and probably the \u03b2 anomer); such nonlinearity implies the existence of ternary complexes of sugar, inhibitor and transporter. The inhibition results furthermore imply the presence of a class of relatively high-affinity (KD < 2mM) sugar sites specific for the \u03b1 anomer which do not contribute to NMR-observable binding. The presence of two classes of sugar-sensitive cytochalasin B sites is also indicated. These results are compared with predictions of the alternating conformer model of glucose transport. Variation of apparent KD in the NMR-observable sites, the formation of ternary complexes and the presence of an anomer-specific site are shown to be inconsistent with this model. An alternate model is developed which reconciles these results with the known transport behavior of GLUT1. In this model, the transporter possesses (at minimum) three classes of sugar sites: (i) transport sites, which are alternately exposed to the cytoplasmic or the extracellular compartment, but never to both simultaneously, (ii) a class of sites (probably relatively low-affinity) which are confined to one compartment, and (iii) the high-affinity \u03b1 anomer-specific sites, which are confined to the cytoplasmic compartment.\r\n" }, { "name": "Singleton, Jennifer Wales", "degree": "Masters", "year": "1994", "title": "Affinity Cleavage of Double-Stranded DNA Directed by a RecA Nucleoprotein Filament Containing an Oligonucleotide-EDTA\u2022Fe(II)", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09142018-083120243", "creators": [ { "name": { "family": "Singleton", "given": "Jennifer Wales" }, "id": "Singleton-Jennifer-Wales", "display_name": "Singleton, Jennifer Wales" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x3y9-dk45", "abstract": "Escherichia coli RecA protein promotes strand exchange between two homologous DNAs by polymerizing on single-stranded DNA to form nucleoprotein filaments which then bind to a homologous sequence of duplex DNA. Joint formation between the RecA protein and three strands of DNA is followed by strand exchange in which the original single strand is inserted into the duplex while the homologous duplex strand is displaced out. The structures of the strand exchange intermediates formed by the RecA protein have not been elucidated. We review studies aimed at determining such structures and we report the use of affinity cleaving techniques to probe the structure of the joint molecule formed between a RecA-oligonucleotide filament and duplex DNA by incorporating a thymidine-EDTA\u2022Fe (T*) into the oligonucleotide of the filament. In our study, we find that the nucleoprotein filament binds antiparallel to the complementary strand within the homologous sequence of DNA and that it is associated more strongly with the complementary strand than with the homologous strand of the duplex.
\r\n" }, { "name": "Stroud, Carrie Kim", "degree": "Masters", "year": "1994", "title": "Collinear Reaction Dynamics and Hydrodynamic Analysis of the Vibrationally Excited Cl + HCl \u2192 ClH + Cl, Cl + DCl \u2192 ClD + Cl and Cl + TCl \u2192 ClT + Cl Reactions on Two Leps Surfaces", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062018-160235948", "creators": [ { "name": { "family": "Stroud", "given": "Carrie Kim" }, "id": "Stroud-Carrie-Kim", "display_name": "Stroud, Carrie Kim" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/aqts-fq51", "abstract": "Quantum dynamical calculations for the collinear Cl + HCl \u2192 ClH + Cl, Cl + DCl \u2192 ClD + Cl, and Cl + TCl \u2192 ClT + Cl reactions on low and high barrier potential energy surfaces are presented and discussed within the framework of the hyperspherical coordinate representation. Vibrational excitation of the reagent diatomic is found to decrease the reaction rate for the low barrier surface and increase the reaction rate for the high barrier surface. Quantum mechanical streamline calculations and tunneling fractions are used for analysis, and discussion of the results is made in terms of the topology of the potential surface, in which the skew angle and barrier height of the system play a leading role in explaining the dynamics of the reaction.
" }, { "name": "Sun, James Te", "degree": "Masters", "year": "1994", "title": "Chemical Sensing with Surface Acoustic Wave Devices", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172025-153654379", "creators": [ { "name": { "family": "Sun", "given": "James Te" }, "id": "Sun-James-Te", "display_name": "Sun, James Te" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fm93-5h73", "abstract": "There is much current interest in developing new techniques for\r\nthe continuous monitoring of chemical environments. However, as there\r\nare many applications where the excessive size and power demands of\r\nconventional sensors have precluded their use, interest in microsensors\r\nsuch as the surface acoustic wave (SAW) device has been spurred by\r\ntheir small size, ruggedness, sensitivity, and low power consumption.\r\nIn this work, 158 MHz SAW oscillators coated with organic polymers\r\nand inorganic crystallites were tested as model systems for vapor\r\nsensors that can monitor the level of humidity and carbon dioxide in a\r\ncontinuous stream of nitrogen. All coatings exhibited responses to water\r\nvapor on the order of kilohertz, while the responses to carbon dioxide\r\nwere significantly (generally one order of magnitude) smaller.\r\nInterferences by the presence of both water and CO2 on the SAW device\r\nsensitivity were observed with poly-(ethylenimine) (PEI) coatings as\r\nevidenced by the large extent of hysteresis. P El coatings were also\r\nfound to exhibit anomalous directions in frequency shifts when exposed\r\nto pulses of humidified CO2, as did poly-(4-vinylpyridine) (PVP)\r\ncoatings for lower humidity levels. ZSM-5 coatings, however, showed\r\nno evidence of such interference between water and CO2." }, { "name": "Tsapatsis, Michael", "degree": "PhD", "year": "1994", "title": "Composite inorganic membranes for gas separations : chemical vapor deposition of hydrogen permselective oxide membranes and preparation of supported zeolite NaA films", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11102005-083452", "creators": [ { "name": { "family": "Tsapatsis", "given": "Michael" }, "id": "Tsapatsis-M", "display_name": "Tsapatsis, Michael" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RZP1-G920", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nHydrogen-perselective membranes were synthesized by chemical vapor deposition of SiO2, TiO2, Al2O3, and B2O3 layers within the pores of Vycor tubes. The deposition involved reaction of SiCl4, etc., with water at 100-800 [degrees]C depending on the chloride and the reaction geometry. The reactants were passed either through the bore of the support tube (one sided geometry) or separately through the bore and the outside surface of the support tube (opposing reactants geometry). Permselective SiO2 and B2O3 layers could be formed in either the one-sided or the two-sided (opposing reactants) geometry, while deposition of TiO2 and Al2O3 layers was achieved only in the two-sided geometry. The permeances at 450 [degrees]C were 0.3 and 0.1 [...]-min-atm for SiO2 membranes produced in the one-sided geometry and two-sided geometries respectively. The H2:N2 permeance ratios were 500-5000. The TiO2 and Al2O3 membranes had somewhat lower permeance and H2:N2 ratios. Annealing at high temperatures causes densification of the deposited material as evidenced by increased activation energy for H2 permeation and correspondingly reduced permeance. The presence of H2O vapor accelerates the densification process. The densified membranes had a H2 permeance as high as 0.1 [...](STP)/min-atm-[...] at 500 [degrees]C and a H2/N2 permeance ratio above 500.\n\nSilica, titania and alumina layers deposited in an opposing reactants geometry were characterized by scanning electron microscopy (SEM) and electron microprobe analysis (EPMA). The layers are asymmetric, having a long tail towards the side of the chloride flow and a sharp boundary at the other side. The deposit thickness is several tenths of microns while the totally plugged region is of order of one micron. Silica deposit layers prepared in the one-sided geometry were examined by transmission electron microscopy (TEM), SEM, and EPMA. When the deposit was confined inside the pores of the Vycor substrate, the membranes were mechanically stable, but when it extended substantially outside of the porous matrix, the stresses induced by thermal cycling led to crack formation and propagation. Electron microscopy revealed that the SiO2 deposit density is maximum in a region about 0.5 \u00b5m thick adjacent to the bore surface and gradually declines to zero within a depth of about 10 \u00b5m from the surface. The thin region of maximum deposit density is responsible for permselectivity, for it essentially blocks the permeation of nitrogen and larger molecules while allowing substantial permeation of hydrogen. This region contains about 10% by volume trapped voids and as a result has relatively high permeability as suggested by percolation theory.\n\nA mathematical model is developed for SiO2 deposition in porous Vycor using SiCl4 hydrolysis. The model describes reaction, diffusion and evolution of the pore structure due to accumulation of the solid product. The deposition reaction is described by transient heterogeneous kinetics in terms of the concentrations of silanol and chloride groups in the product layer as well as the concentrations of the gaseous reactants. Pore structure evolution was modeled by incorporating results of percolation theory in a continuum model. The model is capable of generating deposit profiles in good agreement with the experiment. It is shown that for typical deposition conditions the pseudosteady state approximation for surface species could lead to erroneous predictions. Pore connectivity interruption at a nonzero void fraction leads to thinner deposits and shorter deposition times for pore plugging compared to the corresponding ones for an infinitely connected medium.\n\nThe growth of zeolite NaA films on various inorganic substrates from a clear solution with composition 10 Na2O - 0.2 Al2O3 - 1SiO2 - 200 H2O was followed by XRD, SEM and TEM. Deposition geometries and conditions are identified for the development of uniform polycrystalline thin (<5\u00b5m) films consisting of intergrown crystals of zeolite NaA on porous and nonporous Al2O3 disks. The films exhibit high crystallinity good adhesion to the substrate and thermal stability. The deposition technique demonstrates potential for developing molecular sieve membranes." }, { "name": "Wan, Kam To", "degree": "PhD", "year": "1994", "title": "The Design and Synthesis of a True, Heterogeneous, Asymmetric Catalyst", "advisor": "Davis, Mark E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152013-113928711", "creators": [ { "name": { "family": "Wan", "given": "Kam To" }, "id": "Wan-Kam-To", "display_name": "Wan, Kam To" } ], "advisors": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "advisor", "display_name": "Davis, Mark E." } ], "committee": [ { "name": { "family": "Davis", "given": "Mark E." }, "id": "Davis-M-E", "role": "chair", "display_name": "Davis, Mark E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6m3g-3y70", "abstract": "This work describes the design and synthesis of a true, heterogeneous,\r\nasymmetric catalyst. The catalyst consists of a thin film that resides on a high-surface-\r\narea hydrophilic solid and is composed of a chiral, hydrophilic\r\norganometallic complex dissolved in ethylene glycol. Reactions of prochiral\r\norganic reactants take place predominantly at the ethylene glycol-bulk organic\r\ninterface.
\r\n\r\nThe synthesis of this new heterogeneous catalyst is accomplished in a\r\nseries of designed steps. A novel, water-soluble, tetrasulfonated 2,2'-bis\r\n(diphenylphosphino)-1,1'-binaphthyl (BINAP-4S0_3Na) is synthesized by\r\ndirect sulfonation of 2,2'-bis(diphenylphosphino)-1,1'-binaphthyl (BINAP).\r\nThe rhodium (I) complex of BINAP-4SO_3Na is prepared and is shown to be\r\nthe first homogeneous catalyst to perform asymmetric reductions of prochiral\r\n2-acetamidoacrylic acids in neat water with enantioselectivities as high as\r\nthose obtained in non-aqueous solvents. The ruthenium (II) complex,\r\n[Ru(BINAP-4SO_3Na)(benzene)Cl]Cl is also synthesized and exhibits a broader\r\nsubstrate specificity as well as higher enantioselectivities for the homogeneous\r\nasymmetric reduction of prochiral 2-acylamino acid precursors in water.\r\nAquation of the ruthenium-chloro bond in water is found to be detrimental to\r\nthe enantioselectivity with some substrates. Replacement of water by ethylene\r\nglycol results in the same high e.e's as those found in neat methanol. The\r\nruthenium complex is impregnated onto a controlled pore-size glass CPG-240 by the incipient wetness technique. Anhydrous ethylene glycol is used as the\r\nimmobilizing agent in this heterogeneous catalyst, and a non-polar 1:1\r\nmixture of chloroform and cyclohexane is employed as the organic phase.
\r\n\r\nAsymmetric reduction of 2-(6'-methoxy-2'-naphthyl)acrylic acid to the\r\nnon-steroidal anti-inflammatory agent, naproxen, is accomplished with this\r\nheterogeneous catalyst at a third of the rate observed in homogeneous\r\nsolution with an e.e. of 96% at a reaction temperature of 3\u00b0C and 1,400 psig of\r\nhydrogen. No leaching of the ruthenium complex into the bulk organic phase\r\nis found at a detection limit of 32 ppb. Recycling of the catalyst is possible\r\nwithout any loss in enantioselectivity. Long-term stability of this new\r\nheterogeneous catalyst is proven by a self-assembly test. That is, under the\r\nreaction conditions, the individual components of the present catalytic system\r\nself-assemble into the supported-catalyst configuration.
\r\n\r\nThe strategies outlined here for the design and synthesis of this new\r\nheterogeneous catalyst are general, and can hopefully be applied to the\r\ndevelopment of other heterogeneous, asymmetric catalysts.
\r\n" }, { "name": "Willberg, Dean Michael", "degree": "PhD", "year": "1994", "title": "Picosecond spectroscopy of van der Waals clusters", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-110156", "creators": [ { "name": { "family": "Willberg", "given": "Dean Michael" }, "id": "Willberg-D-M", "display_name": "Willberg, Dean Michael" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/605h-j578", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis thesis presents pump/probe picosecond spectroscopic investigations of the dynamics of van der Waals clusters. The first phase of these investigations was the construction of a laboratory specifically designed for van der Waals cluster research consisting of a molecular beam apparatus and a two-color picosecond laser system. It is possible to perform both time resolved laser induced fluorescence (LE), and multi-photon ionization (MPI) experiments in this laboratory. A description of the construction and operation of the laboratory, focusing on the laser system, is presented. A full account of the real-time studies of the vibrational predissociation of [...] clusters where [...] is given. The first set of experiments described is the measurement of the rates of vibrational predissociation for [...] clusters. The results for [...] are compared with a number of theoretical models of vibrational predissociation, specifically focusing on the dependence of the rates on the initially prepared vibrational state of the cluster. The results for the [...] cluster are described in terms of the competition between two relaxation channels: vibrational predissociation of the van der Waals cluster, and electronic predissociation of the [...] moiety. The second set of experiments are the analogous measurements of the rates of vibrational predissociation of [...] clusters. These results are compared with the [...] results, as well as with lifetime estimates available from high resolution spectroscopy. The final chapter in this series describes our investigation of vibrational predissociation and intramolecular vibrational energy relaxation in [...] clusters. The dynamics of these larger clusters are inherently more complicated than when n = 1, however, a quantitative model for the fragmentation of n = 2 clusters is presented. This thesis also presents a preliminary description of an ongoing MPI experiment on the dynamics of t-stilbene clusters." }, { "name": "Wu, Zhe", "degree": "PhD", "year": "1994", "title": "Transition metal carbenes : controlled ring-opening metathesis polymerizations and metathetical reactions with acyclic olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08162006-082323", "creators": [ { "name": { "family": "Wu", "given": "Zhe" }, "id": "Wu-Z", "display_name": "Wu, Zhe" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xx2p-3468", "abstract": "Although strained cyclic olefins undergo facile ring-opening metathesis polymerization (ROMP) catalyzed by transition metal alkylidene or carbene complexes, there are few examples of living ROMP systems because the rate of the polymerization is much faster than that of the initiation. The phosphines reversibly bind to both the initial and the propagating tungsten or molybdenum alkylidene complexes, thus altering the rates of both initiation and the propagation. Due to the steric bulk difference of the propagating species and the initiating complexes, phosphines bind more strongly to the propagating alkylidene than to the initial alkylidene, which reduces the rate of propagation much more than that of the initiation and results in a living system. The kinetics and mechanism for both initiation and propagation have been studied. By using this living system, linear and near monodispersed polybutadiene and polyethylene can be synthesized. Block copolymers of both practical and theoretical interests can be prepared.\n\nMetathesis of functionalized olefins using a molybdenum alkylidene complex was conducted. The metathesis of functionalized olefins is controlled by a fine balance between the coordination of olefins and that of the heteroatoms. The formation of chelated alkylidene complexes during the metathesis of alkyl-3-alkenoate slows down the rate of productive metathesis. The formation of a stable chelated metallacyclobutane complex during the metathesis of N,N-dimethyl alkenamide prevent its productive metathesis.\n\nReactions of the late transition metal ruthenium carbene complexes with strained acyclic olefins and functionalized olefins are explored. Several [alpha]-hetero substituted carbene complexes and active ruthenium carbenes are synthesized through the metathesis of functionalized olefins and strained acyclic olefins, respectively. The mechanism for the rearrangement of alkoxy substituted ruthenium carbenes is determined by deuterium and 13C labeling studies.\n\nPerfect rubber (cis-1,4-polyisoprene) is synthesized by ROMP of 1-methylcyclobutene using a molybdenum alkylidene complex. New living polymerization systems of both bicyclo[3.2.0]heptene and bicyclo[4.2.0]octene are discovered using a ruthenium carbene complex. Narrow dispersed and regioselective alternating copolymers are synthesized through the ROMP of 3-methylcyclobutene and 3,3-dimethylcyclobutene." }, { "name": "Wuttke, Deborah Sharon", "degree": "PhD", "year": "1994", "title": "Preparation, characterization and intramolecular electron-transfer studies of ruthenium-modified cytochromes c", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152013-095643991", "creators": [ { "name": { "family": "Wuttke", "given": "Deborah Sharon" }, "id": "Wuttke-D-S", "display_name": "Wuttke, Deborah Sharon" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/908p-0x37", "abstract": "Redox-active ruthenium complexes have been covalently attached to the surface\r\nof a series of natural, semisynthetic and recombinant cytochromes c. The protein\r\nderivatives were characterized by a variety of spectroscopic techniques. Distant Fe^(2+) -\r\nRu^(3+) electronic couplings were extracted from intramolecular electron-transfer rates in\r\nRu(bpy)_2(im)HisX (where X= 33, 39, 62, and 72) derivatives of cyt c. The couplings\r\nincrease according to 62 (0.0060) < 72 (0.057) < 33 (0.097) < 39 (0.11 cm^(-1)); however,\r\nthis order is incongruent with histidine to heme edge-edge distances [62 (14.8) > 39\r\n(12.3) > 33 (11.1) > =72 (8.4 \u00c5)]. These results suggest the chemical nature of the\r\nintervening medium needs to be considered for a more precise evaluation of couplings.\r\nThe rates (and couplings) correlate with the lengths of a-tunneling pathways comprised\r\nof covalent bonds, hydrogen bonds and through-space jumps from the histidines to the\r\nheme group. Space jumps greatly decrease couplings: one from Pro71 to Met80 extends\r\nthe \u03c3-tunneling length of the His72 pathway by roughly 10 covalent bond units.\r\nExperimental couplings also correlate well with those calculated using extended Hiickel\r\ntheory to evaluate the contribution of the intervening protein medium.
\r\n\r\nTwo horse heart cyt c variants incorporating the unnatural amino acids (S)-2-\r\namino-3-(2,2'-bipyrid-6-yl)-propanoic acid (6Bpa) and (S)-2-amino-3-(2,2'-bipyrid-4-yl)propanoic\r\nacid ( 4Bpa) at position 72 have been prepared using semisynthetic protocols.\r\nNegligible perturbation of the protein structure results from this introduction of unnatural\r\namino acids. Redox-active Ru(2,2'-bipyridine)_2^(2+) binds to 4Bpa72 cyt c but not to the\r\n6Bpa protein. Enhanced ET rates were observed in the Ru(bpy)_2^(2+)-modified 4Bpa72 cyt\r\nc relative to the analogous His72 derivative. The rapid (< 60 nanosecond)\r\nphotogeneration of ferrous Ru-modified 4Bpa72 cyt c in the conformationally altered\r\nalkaline state demonstrates that laser-induced ET can be employed to study\r\nsubmicrosecond protein-folding events.
\r\n" }, { "name": "Balazs, Gabriel Bryan", "degree": "PhD", "year": "1993", "title": "Mechanistic and electrochemical studies of the reduction of carbon dioxide as catalyzed by Ni(I)CYCLAM+", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042012-160347510", "creators": [ { "name": { "family": "Balazs", "given": "Gabriel Bryan" }, "id": "Balazs-G-B", "display_name": "Balazs, Gabriel Bryan" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RJF2-WD05", "abstract": "A detailed electrochemical investigation of Ni(cyclam)^(2+) and its derivatives is described, especially with regard to the aqueous electrocatalytic reduction of CO_2 at mercury. Detailed chronocoulometric studies which quantify the extent of the adsorption of the active catalytic species Ni(cyclam)^+_(ads) are discussed. Ni(cyclam)^(2+) is only weakly adsorbed at mercury and in quantities substantially less than a monolayer. In contrast, Ni(cyclam)+ is adsorbed over a wide potential range and the adsorption process occurs in two potential dependent stages. An analysis of the kinetics of the adsorption process is discussed.
\r\n\r\nIn the presence of CO, Ni(cyclam)^(2+) is electrochemically reduced to Ni(cyclam)^+-CO and Ni(cyclam)^0-CO. This latter species is insoluble and precipitates on the electrode surface. Both of these species are chemically unstable and slowly react to form Ni(cyclam)^(2+) in the presence of oxidizing agents.
\r\n\r\nNi(cyclam)^+_(ads) catalyzes the reduction of CO_2 to exclusively CO. In unbuffered solutions, the OH- ion produced as a result of the reduction of CO_2 can decrease the flux of CO_2 molecules to the electrode surface by direct reaction with CO_2 to form HCO-^_3 or CO^(2-)_3,both of which are catalytically inactive towards reduction by Ni(cyclam)^+_(ads). In both buffered and unbuffered solutions, the precipitate Ni(cyclam)^0-CO which is formed on the electrode surface under all conditions where CO_2 is reduced causes a slow passivation of the electrode surface towards further catalytic reduction of CO_2.
\r\n\r\nThe binding of CO_2 and CO to Ni(cyclam)^(2+), Ni(cyclam)^+, and Ni(cyclam)^+_(ads) is discussed. The active catalyst, Ni(cyclam) )^+_(ads), is able to coordinate CO_2, but not the product of the reduction, CO. Both Ni(cyclam)^(2+) and Ni(cyclam)+ are unable to coordinate CO_2 and thus solution species are not important in the catalytic cycle. A comparison of these results with previous studies is given and an overall mechanism for the electrocatalytic reduction of CO_2 is proposed. This mechanism contains several important modifications from earlier studies.
" }, { "name": "Barrans, Richard E., Jr.", "degree": "PhD", "year": "1993", "title": "Investigations in molecular recognition: statistical tools and experimental studies", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12062012-140020355", "creators": [ { "name": { "family": "Barrans", "given": "Richard E., Jr." }, "id": "Barrans-R-E-Jr.", "display_name": "Barrans, Richard E., Jr." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/42WC-0V58", "abstract": "The free energies of formation of intermolecular complexes in solution are often\r\nestimated by fitting a nonlinear model to an NMR titration experiment. A regression\r\nprocedure that assigns weights to each observation on the basis of expected measurement\r\nerrors has been developed, and yields better parameter estimates than\r\nother methods in common use. Procedures for critically evaluating the fit of the\r\nmodel to the experimental data and for assigning confidence limits to the fitted parameters\r\nhave also been developed. These employ Monte Carlo simulations of the\r\nNMR titration experiment to obtain probability distributions that are not available\r\nby theoretical means.
\r\n\r\nAspects of the complexation behavior of a family of water-soluble macrocyclic\r\ncyclophanes are also described. Significant heat capacity effects, which are interpreted\r\nin terms of hydrophobic hydration, are seen in variable-temperature studies.\r\nThe alkylation reactions of pyridine-based compounds are accelerated by complexation\r\nwith these cyclophanes; an interpretation based on the dynamic properties of\r\nthe alkylation reaction, the solvent, and the cyclophane is offered. In addition, accounts\r\nof efforts to make axially-substituted cyclophanes, to synthesize cyclophanes\r\nincorporating a diphosphine ligand, to append additional water-solubilizing groups\r\nto the cyclophanes, and to employ small cyclophanes as complexants for alkali metal\r\ncations are given.
" }, { "name": "Baselt, David Randall", "degree": "PhD", "year": "1993", "title": "The Tip-Sample Interaction in Atomic Force Microscopy and its Implications for Biological Applications", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03222005-105400", "creators": [ { "name": { "family": "Baselt", "given": "David Randall" }, "id": "Baselt-David-Randall", "display_name": "Baselt, David Randall" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Revel", "given": "Jean-Paul" }, "id": "Revel-J-P", "role": "member", "display_name": "Revel, Jean-Paul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5ZMM-7Q64", "abstract": "This thesis describes the construction of an atomic force microscope and its application to the study of tip-sample interactions, primarily through the use of friction and hardness (elasticity) imaging.\r\n\r\nPart one describes the atomic force microscope, which consists of a scanned-cantilever stage (chapter 2); a versatile digital signal processor-based control system with self-optimizing feedback, lock-in amplifier emulation (for hardness imaging), and macro programmability (chapter 3); and image processing software (chapter 4).\r\n\r\nPart two describes a number of results that have helped to characterize the tip-sample interaction and the contact imaging modes used for its study. Meniscus forces act laterally as well as normally, and that they vary with position (chapter 5). Friction measurements couple with scanner position quid feedback, and the meniscus effects friction images (chapter 6). Sliding of the tip over the sample surface introduces slope-dependence into hardness measurements (chapter 7). Dull tips can create prominent topography artifacts even on very flat surfaces (chapter 8).\r\n\r\nIn an investigation of collagen fibrils, AFM has revealed die characteristic 65 nm banding pattern, a second, minor banding pattern, and microfibrils that run along the fibril axis. The distribution of proteoglycans along the fibrils creates a characteristic pattern in friction images. Although imaging in water reduces interaction forces, water can also make biological samples more sensitive to force. However, for robust biological samples imaged in air, tip shape presents a greater obstacle than tip-sample interaction forces to obtaining high-resolution images. Tip contamination increases tip-sample friction and can occasionally improve resolution (chapter 9).\r\n\r\nFor a separate project I have designed a general-purpose nearfield scanning optical microscope (chapter 10)." }, { "name": "Braatz, Richard Dean", "degree": "PhD", "year": "1993", "title": "Robust Loopshaping for Process Control", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-08222007-105213", "creators": [ { "name": { "family": "Braatz", "given": "Richard Dean" }, "id": "Braatz-Richard-Dean", "orcid": "0000-0003-4304-3484", "display_name": "Braatz, Richard Dean" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "orcid": "0000-0002-1828-2486", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Murray", "given": "Richard M." }, "id": "Murray-R-M", "orcid": "0000-0002-5785-7481", "role": "member", "display_name": "Murray, Richard M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/vqmv-kw76", "abstract": "Strong trends in chemical engineering and plant operation have made the control of processes increasingly difficult and have driven the process industry's demand for improved control techniques. Improved control leads to savings in resources, smaller downtimes, improved safety, and reduced pollution.
\r\n\r\nThough the need for improved process control is clear, advanced control methodologies have had only limited acceptance and application in industrial practice. The reason for this gap between control theory and practice is that existing control methodologies do not adequately address all of the following control system requirements and problems associated with control design:\r\n
A framework is presented to address these control requirements/problems in a general, unified manner. The approach will be demonstrated on adhesive coating processes and distillation columns.
" }, { "name": "Burns, Elizabeth G.", "degree": "PhD", "year": "1993", "title": "Functional polymers via ring-opening metathesis polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132012-090744842", "creators": [ { "name": { "family": "Burns", "given": "Elizabeth G." }, "id": "Burns-E-G", "display_name": "Burns, Elizabeth G." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a1m4-4k34", "abstract": "The first chapter describes the use of ring-opening metathesis polymerization (ROMP) for the synthesis of poly(sulfones) from functionalized 7-oxanorbomenes. Tungsten and molybdenum alkylidenes as well as ruthenium salts were used to generate polymers with varied backbone geometric- and stereo-isomerism. These poly(sulfones) exhibit clean mass loss under both oxidative and inert atmospheres. Thermal gravimetric analysis was used to investigate these poly(sulfones), as well as other 7-oxanorbornene polymers. Comparison of ether, amide and acid\r\nderivitized polymers indicates that clean thermolysis is observed when the polymer contains the following features: an oxygen of the tetrahydrofuran ring, a second ring fused to the tetrahydrofuran ring, a high proportion of trans-to-cis bonds, an atactic backbone, and the sulfone group. Product studies indicate that the mechanism of decomposition under an argon atmosphere involves initial loss of sulfur dioxide. Based on comparison of thermal analysis data of olefinic and saturated polymers, oxidative attack at the olefin backbone is postulated as the first step in degradation under ambient atmosphere.
\r\n\r\nIn the second chapter of this thesis, the use of living poly(exodicyclopentadiene) and living poly(norbornene) in reactions with a telechelic dialdehyde to form triblock co-polymers by coupling of reactive end groups is detailed. A reagent-specific degradation reaction prevented the isolation of triblock co-polymers from excess homopolymer, although gel-permeation chromatographs indicate that the coupling takes place with good efficiency. The successful use of poly(styrene-co-vinylbenzaldehyde) as a scavenging\r\nreagent for ROMP polymers is also reported.
\r\n\r\nSeveral small projects are discussed in the third chapter. The most important topic is the ionophoric behavior of ROMP poly( ethers). Monomers and polymers containing amines, thiophenes and methanesulfonyl groups are also discussed. The methanesulfonylderivitized ROMP polymer exhibits clean, uncatalyzed, elimination of methanesulfonic acid at 220 \u00b0C, which has implications for precursor polymers currently under study.
\r\n" }, { "name": "Coley, Terry Ronald", "degree": "PhD", "year": "1993", "title": "Prediction of scanning tunneling microscope images by computational quantum chemistry: chemical models and software design", "advisor": "Goddard, William A., III; Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-102157942", "creators": [ { "name": { "family": "Coley", "given": "Terry Ronald" }, "id": "Coley-T-R", "display_name": "Coley, Terry Ronald" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "co-advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jey5-ex12", "abstract": "We have created chemical models for predicting and interpreting STM images of several specific systems. Detailed studies are made of transition metal dichalcogenides (MoS_2 and MoTe_2), Xe on Ni (110), C_3H_4 on Ni (110) and n-butyl benzene on a graphite model (C_(42)O_6H_(12). In the case of MoS_2 we study the ambiguity in the STM images regarding the assignment of peaks to the subsurface metal or the surface chalcogenide. In the Ni models we study STM imaging mechanisms for cases where the adsorbate states lie far above and below the metal Fermi level. The large n-butyl on graphite system models a system where adsorbate states can play a direct role in the imaging. Results from the cluster studies are related to various STM imaging modes, including constant current mode, constant height mode, and barrier height imaging.\t\r\nTwo new procedures are developed to aid in computational prediction of STM images. First, we implement an algorithm for computing Bardeen-type tunneling matrix elements from ab initio wave functions in Gaussian basis sets. Second, we show how to obtain state densities as a function of energy for bulk substrate/adsorbate systems using only Fock matrix elements from cluster calculations. Initial results are presented for a linear chain of Ni atoms with a perturbing Xe atom.\r\nA software environment for computational chemistry developed in the course of performing these calculations is presented. Tools for creating computational servers to perform chemistry calculations are described. Embedded in each chemistry server is a public domain control language created by J. Ousterhout at the University of California, Berkeley. This allows the development of a variety of clients for controlling the servers using a common language. Clients can be simple text \"scripts\" that organize a calculation, graphical interfaces, or control streams from other programs. All software entities are designed in an object oriented fashion discussed in the text.\r\n" }, { "name": "Cotter, W. Donald", "degree": "PhD", "year": "1993", "title": "Organoscandium complexes as mechanistic probes in the Ziegler-Natta polymerization of \u03b1-olefins and dienes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11282012-135537271", "creators": [ { "name": { "family": "Cotter", "given": "W. Donald" }, "id": "Cotter-W-D", "display_name": "Cotter, W. Donald" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9wx4-9x03", "abstract": "Measurement of the molecular-weight distributions of alkanes prepared by treatment\r\nof permethylscandocene alkyl complexes at -78\u00b0C reveals that under the reaction conditions the\r\nreaction may be described as \"living.\"
\r\n\r\nThe stoichiometric insertion of 2-butyne across the scandium-carbon \u03c3-bond in Cp*_2ScCH_3\r\nproceeds without a visible kinetic deuterium isotope effect, either for substitution at the alkyne\r\nmethyl groups or at the scandium-methyl group. The first result reveals that steric isotope\r\neffects are not important in this reaction, which models the propagation step in Ziegler-Natta\r\npolymerization. The second result suggests that an \u03b1-agostic interaction is likely not present in\r\nthe transition state for 2-butyne insertion.
\r\n\r\nThe polymerization of conjugated dienes with organoscandium complexes of the type {[(\u03b7^5-\r\nC_5Me_4)SiMe_2NCMe_3]ScR}_2 (R = n-propyl, n-butyl) leads to polymers with very narrow\r\nmolecular-weight distributions and microstructures rich in 1,2-repeat units and an unusual\r\ncyclic repeat unit derived from two sequential 1,2-insertions. The 1,4-repeat unit characteristic\r\nof rubber account for about 40 mass-% of the products. Allyl complexes are readily prepared\r\nfrom treatment of alkylscandium complexes with conjugated dienes, or from treatment of the\r\nscandium hydride complex {[(\u03b7^5-C_5Me_4)SiMe_2NCMe_3]ScH(PMe_3)}_2 with allenes. This hydride\r\ncomplex, however, reacts with butadiene to form an ethylene-bridged complex and ethane.
\r\n\r\nBoth the hydride complex {[(\u03b7^5-C_5Me_4)SiMe_2NCMe_3]ScR}_2 and the alkyl complex {[(\u03b7^5-\r\nC_5Me_4)SiMe_2NCMe_3]Sc(CH_2CH_2CH_3)]_2 catalyze the cyclopolymerization of 1,5-hexadiene.\r\nAlthough polymers with narrow molecular weight distributions (1.1-1.2) can be obtained, the\r\npolydispersity index is very sensitive to the presence of trimethylphosphine and, to a lesser\r\nextent, to the nature of the initiating group. Chain-transfer processes could not be studied\r\ndirectly due to deleterious reactivity with scandium-hydride trapping reagents.\r\nCyclopolymerization is not accompanied by a measurable a deuterium isotope effect on the\r\ncyclization step, which suggests that trans-fused [5,4]-bicyclic transition states are allowed for\r\nthis step.
\r\n\r\nVariable-temperature NMR spectroscopy was used to examine the dynamic solution behavior\r\nof several ansa-(cyclopentadienyl)amidoscandium alkyl complexes. On the basis of these\r\nstudies, it is proposed that the primary equilibrium when trimethylphosphine is present is\r\nbetween a phosphine-bound scandium alkyl and a free, 12-electron monomeric scandium alkyl.
" }, { "name": "Dawn, Douglas David", "degree": "Masters", "year": "1993", "title": "Saving Stratospheric Ozone: Putting the Problem in Perspective and Evaluating Hydrohalocarbons and their Mixtures as Potential Solutions", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132026-170425336", "creators": [ { "name": { "family": "Dawn", "given": "Douglas David" }, "id": "Dawn-Douglas-David", "display_name": "Dawn, Douglas David" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k64d-7m04", "abstract": "Stratospheric ozone depletion by halocarbon gases is reviewed. Some\r\ninsight is offered to explain the technical and political difficulties currently\r\nfacing industrial producers and end use consumers. Industry estimates that\r\n40% of the ozone destruction caused by halocarbons from the United States\r\nis a result of air conditioning and refrigeration.
\r\n\r\nA partial solution employing mixtures of gases relatively harmless to the\r\nozone layer is investigated to replace refrigerant fluids currently in use.\r\nComputer subroutines developed at the National Institute of Standards and\r\nTechnology for modeling mixtures using a semi-empirical equation of state\r\nare utilized to generate results. Superior properties are predicted for an\r\napplication defined within the temperature range of human comfort.\r\nBenefits and shortcomings are discussed that are both specifically applicable\r\nto this approach and generally applicable to the development of\r\nreplacements.
" }, { "name": "Dragovich, Peter S.", "degree": "PhD", "year": "1993", "title": "Synthesis and study of chemically activated biradical precursors", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11142012-144010600", "creators": [ { "name": { "family": "Dragovich", "given": "Peter S." }, "id": "Dragovich-P-S", "display_name": "Dragovich, Peter S." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p2kc-rn13", "abstract": "The design, synthesis and study of molecules which produce 1,4-biradical intermediates upon thermal or chemical activation is described. The preparation and cyclization behavior of (Z)-1,2,4-heptatrien-6-yne and compounds that contain the (Z)-allene-ene-yne functional group or that form it in a serial reaction sequence are discussed. Evidence is presented that supports the thermal transformation of the (Z)-allene-ene-yne functional group to an \u03b1,3-dehydrotoluene intermediate that is best described as a singlet \u03c3,\u03c0-biradical with substantial polar character. The partitioning between polar and free radical reaction pathways in these systems is shown to be influenced by biradical substitution and by the reaction medium in which the intermediate is generated. These results are discussed with reference to electrocyclization reactions occurring within the enediyne family of natural antitumor agents.
\r\n\r\nThe design, synthesis and reactivity of a system that produces a strained (Z)-enediyne moiety via the reductive activation of an anthraquinone-diacetylene conjugate in\r\nwater with a flavin-based enzymatic system is described. The (Z)-enediyne thus produced is shown to undergo thermal rearrangement to form a naphthofuran product via a 1,4-dehydrobenzene biradical intermediate.
\r\n\r\nThe preparation of a molecule which forms a substituted 1,6-didehydro[10]annulene intermediate by nucleophilic addition of thiol is described. This intermediate is\r\nnot observed, but rearranges to form two isomeric 1,5-dehydronaphthalene biradicals as evidenced by the isolation of the corresponding aromatized products.
\r\n" }, { "name": "Driscoll, Robert James", "degree": "PhD", "year": "1993", "title": "Scanning Tunneling Microscopy and Spectroscopy: I. Semimetals and Semiconductors. II. Atom-Resolved Imaging of DNA", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11292012-090633873", "creators": [ { "name": { "family": "Driscoll", "given": "Robert James" }, "id": "Driscoll-Robert-James", "display_name": "Driscoll, Robert James" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" }, { "name": { "family": "Revel", "given": "Jean-Paul" }, "id": "Revel-J-P", "role": "member", "display_name": "Revel, Jean-Paul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fp55-ng98", "abstract": "The topographic and electronic structure of semiconductor and semimetal surfaces were investigated using scanning tunneling microscopy (STM) and scanning tunneling spectroscopy (STS), respectively. The longrange morphology and atomic-scale characteristics of cleaved materials such as highly oriented pyrolitic graphite (HOPG), boronated pyrolitic graphite (BPG), titanium disulfide, and gallium arsenide (GaAs) were revealed by STM performed under ultrahigh vacuum (UHV) conditions.
\r\n\r\nAtomic resolution constant-current and current-imaging data, as well as barrier height information obtained from tunneling gap modulation, are presented. Both point and line defects were observed on these surfaces; the origin and role of native and adsorbed surface defects are discussed. Visual evidence of coulombic screening caused by adsorption of charged species on n-type GaAs(110) is provided. The atomic corrugation of the GaAs surface was measured to be as little as 0.03 \u00c5 peak-to-valley, attesting to the stability of the microscope design. The BPG sample used in these studies consisted of up to 0.5% boron; boron is the only known substitutional impurity of graphite. Boron substituent atoms appeared as small protrusions approximately 3 \u00c5 in diameter, with an atom density consistent with the assumed concentration.The BPG surface exhibited frequent line defects, including large-angle grain\r\nboundaries, and monolayer-depth etch pits. Images of BPG in air using graphite tips showed similar results; the validity of the popular \"sliding-planes\" mechanism for graphite imaging is evaluated.
\r\n\r\nThe effects of anisotropic stress on the morphology and reconstruction of a thermally annealed Si(111) wafer were explored. The height and orientation of step bunches, as well as terrace widths, on the (7x7) surface were determined. Electromigration effects were also observed; although the overall surface slope was conserved, the step bunches were \"smeared out\" by reversal of the current direction during heating. Line fault defects at step\r\nkinks were observed; a theory for the origin and structure of these features based on stress relief is proposed. Current imaging tunneling spectroscopy (CITS) and localized STS revealed differences between the adatom sites of the\r\n(7x7) surface. Atom-resolved barrier height images were also obtained;comparison to constant-current images may in fact provide a means of differentiating between defects and adsorbed species on the surface. The local effective barrier height was seen to depend strongly on the \"cleanliness\" of the STM tip. The barrier height increased dramatically following voltage pulsing on the order of ten volts. The large height of the step bunches also provided a good test to evaluate the sharpness of the STM tip; examples of \"tip changes\" affecting image resolution and \"multiple-tipping\" are provided. Silicon samples annealed at temperatures below 1000\u00b0C revealed substantial\r\nsilicon carbide (SiC) contamination which effected step pinning. No SiC islands were observed on samples annealed above 1250\u00b0C.
\r\n\r\nIn addition, atom-resolved STM images of duplex DNA supported on a HOPG surface were obtained in UHV. These images revealed double-helical structure, major and minor groove alternation, base pairs, and atomic-scale substructure. Comparison of the DNA dimensions derived from the STM data were in agreement with those from x-ray crystallography for \"random-sequence\" A-form DNA. Cross sectional profiles of the experimental STM data showed excellent correlation with the atomic contours of the van der Waals surface of A-DNA. Barrier height cross-sections showed general correlation with the atomic-scale topography over the phosphate-sugar backbone but distinct anticorrelation (complementarity) over the base pair region. The problems of aggregation and deposition coverage are discussed in the context of possible future applications of STM to DNA sequencing. The use of alternate techniques of DNA deposition, including electrospray\r\nionization, for increased experimental reproducibility are described. The limitations of HOPG as a substrate for biomolecular adsorbates in STM experiments are evaluated.
\r\n" }, { "name": "Evans, John Spencer", "degree": "PhD", "year": "1993", "title": "NMR and Computational Studies on the Conformational Folding of the Biomineralization Template, Posphophoryn", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-152426877", "creators": [ { "name": { "family": "Evans", "given": "John Spencer" }, "id": "Evans-John-Spencer", "orcid": "0000-0002-9565-7296", "display_name": "Evans, John Spencer" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ky1z-w552", "abstract": "Bovine Dentine Phosphophoryn (BDPP) is a member of the \"Asp-rich\" superfamily of template macromolecules known as polyelectrolyte mineral matrix proteins (PMMPs). Using 1-D and 2-D NMR multinuclear spectroscopy, protein sequencing, solid-phase peptide synthesis, and molecular modeling, we investigated the capacity of BDPP to fold in solution under certain conditions. It is believed that the folding properties of a template macromolcule are important in the formation of n inorganic mineral phase. In this report, we have established the following regarding BDPP structure:\r\n\r\nI. BDPP sequence organization can be conceptualized as three types of domains: polyelectrolyte calcium binding domains (PCBD), hinge \r\ndomains (HD), and the hydrophobic domains (HC). The PCBD regions can be further subdivided into (Asp)_n, (PSer)_n, and (PSerAsp)_n-containing\r\nhomopolymer and heteropolymer sequence stretches. The HD contain predominantly neutral or uncharged amino acids such as Ser, Gly, and \r\nPro. These HD domain sequences are flanked on either side by PCBD regions.\r\n\r\nII. BDPP contains a number of Lys sidechains (44/1000 residues) which are believed to form ion pairs with either Asp, Glu, or PSer residues \r\nin the protein. The function of this salt-bridging is not understood at this time, but it may be responsible for maintaining the protein template molecule in a conformation that retains a high negative charge density.\r\n\r\nIII. At low pH, or in the presence of divalent cations, BDPP assumes a global conformation that is condensed in particle size. At neutral pH \r\nunder conditions of low ionic strength and in the absence of divalent cations, this global conformation converts to an extended form. The \r\nfolding transition between these two conformers is mediated by conformational change in the BD regions which are flanked by specific \r\nPCBD sequence regions.\r\n\r\nIV. The PCBD regions possess some degree of tertiary and secondary structural organization in the absence of divalent cations at low ionic \r\nstrength. This folding permits the surface charge density of these regions to remain high, relative to that of a random coil conformer.\r\n\r\nV. BDPP exhibits a selectivity in terms of divalent cation binding sites. Under conditions of low ionic strength and divalent cation depletion, the addition of Cd (II) to BDPP leads to binding at various PCBD sequence stretches, according to the following order:\r\n(PSer)_n > (PserAsp)_n > (Asp)_n\r\n\r\nVI. Modeling studies conducted on PCBD sequence peptides [(Asp)_(20), (PSer)_(20), and (PSerAsp)_(10)] indicate that there is a sequence preference for certain conformers in the presence of Na^+, i.e., (Asp)_(20) forms \"supercoils\", (PSer)_(20) forms \"hairpins\", and (PSerAsp)_(10) forms \"spirals\" or \"distorted\" hairpins. Each of these conformers features some degree of sidechain folding and/or peptide backbone secondary structure, in support of Mann's hypothesis, as well as the experimental data obtained for BDPP.\r\n\r\nVII. A peptide mimetic which represents a PCBD-Hinge-PCBD motif of rat \u03b1-phosphophoryn, was constructed using FMOC solid-phase peptide \r\nsynthesis. Using 2-D NMR spectroscopy and monitoring \u03b1-CH and sidechain \u03b2-CH_2 proton chemical shifts, we can demonstrate that this \r\npeptide mimetic folds or collapses under conditions of low pH and divalent cation addition, in a manner similar to that observed for intact \r\nBDPP.\r\n" }, { "name": "Forstner, Hali Janine Lala", "degree": "Masters", "year": "1993", "title": "Molecular Speciation of Secondary Organic Aerosol from Various Anthropogenic Hydrocarbons", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06272025-191230924", "creators": [ { "name": { "family": "Forstner", "given": "Hali Janine Lala" }, "id": "Forstner-Hali-Janine-Lala", "display_name": "Forstner, Hali Janine Lala" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1dqr-8g94", "abstract": "Gas-to-particle conversion is a ubiquitous process in the\r\natmosphere, understanding its detailed chemistry and physics\r\nwill allow one to predict the effects of primary gaseous and\r\nparticulate emissions on airborne particulate matter composition and size. This research proposes to determine the mechanisms of secondary organic aerosol formation in the\r\natmosphere for a number of important anthropogenic\r\nhydrocarbons. A 6 m3 outdoor smog chamber will be used to\r\ngenerate organic aerosols for molecular speciation analysis by gas chromatography/mass spectrometry. Gas-phase photooxidation mechanisms of the parent hydrocarbon will be\r\nformulated based on the results from this analysis." }, { "name": "Fujiwara, Mitsuko", "degree": "PhD", "year": "1993", "title": "Characterization of pH-Dependent Poly(Acrylic Acid)-Vesicle Interaction and its Application in Cellular Drug Delivery", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11262012-114541543", "creators": [ { "name": { "family": "Fujiwara", "given": "Mitsuko" }, "id": "Fujiwara-Mitsuko", "display_name": "Fujiwara, Mitsuko" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Revel", "given": "Jean-Paul" }, "id": "Revel-J-P", "role": "member", "display_name": "Revel, Jean-Paul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ky3h-q886", "abstract": "Polymers can be used to control drug targeting and drug release from phospholipid vesicles through changes in pH. Understanding the effect of polymers on vesicle properties is important in obtaining a better control over drug delivery using phospholipid vesicles. The pH-dependent interaction of poly(acrylic acid) (PAA) with phosphatidylcholine (PC) vesicles (bilayers) and monolayers was investigated to elucidate the mechanism of P AA-induced vesicle destabilization. PAA induced aggregation of vesicles below pH 4.6 and lipid intermixing of vesicles below pH 4.1. Mixing of aqueous contents was not observed, indicating that the process is not a true membrane fusion. An increase in the membrane permeability accompanied lipid intermixing of vesicles. Both the hydrocarbon chain and phospholipid headgroup packing was more disordered from\r\npolymer association as evidenced by the increase in the CH_2 asymmetric stretching peakwidth and peak position and by the increase in the binding of potential-sensitive dye to\r\nthe vesicle surface, respectively. Polymer binding to vesicles at pH 3.8 showed a negative cooperativity with a K_b of 1.5 x 10^6 M^(-1).The driving force for PAA adsorption on vesicles is the formation of hydrogen-bonds between the protonated carboxyl groups of the polymer and the phospholipid molecule. The polymer mobility was restricted upon complexation with vesicles as evidenced by the anisotropy measurements of polymerassociated fluorophore. The polymer-associated vesicles exhibited fused vesicles and tubular structures in freeze-fracture images. Formation of nonbihyer phases or phase separation was not detected in freeze-fracture images or ^(31)P-NMR powder spectra of PC vesicles. PAA induced expansion of PC monolayers at low pH, and the extent of expansion was dependent on the monolayer surface pressure and on the pH of the subphase. Polymer-induced expansion became more difficult at increasing monolayer packing density and increasing pH. Therefore PAA-induced destabilization of vesicles is believed to be initiated by partial penetration of PAA on vesicle surface. The stress on the membrane created by PAA association presumably resulted in the rupture of bilayer and lipid intermixing of vesicles.
\r\n" }, { "name": "Gin, Douglas L.", "degree": "PhD", "year": "1993", "title": "A new route to poly(p-phenylene): stereoregular precursors via transition-metal-catalyzed polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112012-102613746", "creators": [ { "name": { "family": "Gin", "given": "Douglas L." }, "id": "Gin-D-L", "display_name": "Gin, Douglas L." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kxta-zd48", "abstract": "Poly(p-phenylene)(PPP) is an insoluble rigid-rod polymer that possesses remarkable thermal stability, chemical resistance, and electrical conductivity when doped. The structural properties that make PPP such an attractive engineering material also make it very difficult to synthesize and process. Although many direct and precursor routes to PPP have been developed they have generally afforded low molecular weight material containing a substantial amount of structural defects that are detrimental to the properties of the final product. We have developed a new precursor route to PPP which offers processability as well as a high molecular weight, high quality polymer.
\r\n\r\n1,4-Linked, stereoregular precursors to PPP were synthesized by transition-metal\u00ad catalyzed polymerization of heteroatom-functionalized 1,3-cyclohexadienes. cis-5,6- Bis(trimethylsiloxy)-1,3-cyclohexadiene (TMS-CHD),a derivative of a microbial oxidation product of benzene, is polymerized stereospecifically by bis[(\u03b7 ^(3-)allyl)trifluoroacetatonickel(II)] with yields up to 96%. Not only does this polymerization system afford a highly 1,4-linked, stereoregular polymer, but it also has the potential for molecular weight control. The resulting polymer, [1,4-poly(TMS-CHD)], is a soluble, processable, semicrystalline material. Although 1,4-poly(TMS-CHD) cannot be pyrolyzed to yield PPP directly, the trimethylsilyl ethers on the polymer can be transformed to better leaving groups such as acetates to give the corresponding stereoregular acetoxy polymer (100% acetylation; 93% overall yield). Due to the low thermal stability of the stereroregular backbone, aromatization of this acetoxy polymer to PPP requires Lewis or Br\u00f8nsted acid catalysts. Acids lower the onset temperature of the acid elimination process to a temperature regime well below that at which depolymerization can occur. The high quality PPP produced by the acid-catalyzed aromatization of the stereoregular acetoxy polymer exhibits properties comparable to those of PPP samples in the literature. However, it is completely amorphous whereas PPP samples made by other routes are almost always semicrystalline. Since the physical and chemical properties of PPP and many other conjugated polymers depend highly on sample morphology, processing techniques for this material will have to be developed before its optimum properties can be realized.
\r\n" }, { "name": "Graham, Kenneth Scott", "degree": "PhD", "year": "1993", "title": "Design and chemical synthesis of a sequence-specific DNA-cleaving metalloprotein: NI (II) GGH-\u03b3\u03b4(141-183)", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12182012-094906629", "creators": [ { "name": { "family": "Graham", "given": "Kenneth Scott" }, "id": "Graham-K-S", "display_name": "Graham, Kenneth Scott" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7xmm-gb60", "abstract": "Chapter I: Affinity-Cleaving Studies Examining the Orientation and Specificity of the DNA-Binding Domain from y\u03b4 Resolvase
\r\n\r\nThe DNA binding domain of gd resolvase, residues 141-183, is thought to bind DNA by the helix-turn-helix motif based on sequence similarities with other known DNA binding proteins. Incorporation of the DNA cleaving moiety, EDTA\u2022Fe at the amino and carboxy termini of y\u03b4 (141-183),\r\nallows the positions of these residue relative to the DNA bases at three resolvase binding sites, each consisting of inverted copies of an imperfectly conserved nine base pair consensus sequence, to be mapped by highresolution gel electrophoresis. Cleavage data for EDTA-y\u03b4(141-183) reveal\r\nthat the NH^2 terminus of the DNA binding domain of y\u03b4 resolvase is bound proximal to the minor groove of DNA near the center of the resolvase binding sites. Cleavage by EDTA\u2022Fe attached to a lysine side chain at (Asn^183_Lys^183) at the COOH terminus of y\u03b4 (141-183) reveals that the putative recognition helix is in the adjacent major groove on the same face of the helix, oriented towards the center of the inverted repeats. Subsequent studies utilized affinity cleavage to analyze the effects of changes in amino acid composition of the recognition helix on the binding characteristics of y\u03b4 (141-183).In a systematic helix-switch experiment, the DNA contact residues of the putative recognition helix were exchanged for the DNA contact residues from another putative helix-turn-helix protein, Hin recombinase. Substitution of the amino acid in the putative recognition\r\nhelix of y\u03b4 resolvase resulted in five proteins that showed no DNA binding specificity, six proteins that showed no significant alterations in DNA binding specificity, and four proteins that showed altered DNA binding specificity.
\r\n\r\nChapter II: Design of a Sequence-Specific DNA-Cleavage Metalloprotein Ni(II) GGH- y\u03b4 (141-183)
\r\n\r\nA forty-six residue chymeric protein that combines the cuperic binding domain of serum albumin, GGH, with the DNA binding domain of y\u03b4 resolvase (residues 141-183), was synthesized. This protein, in the presence of Ni(II) and monoperoxyphthalic acid, cleaves DNA sequence specifically at one nucleotide adjacent to each of the six y\u03b4 resolvase binding sites contained within res. Cleavage occurs at the center of each of the dimeric binding sites, indicating that the position of the Ni(II)GGH is proximal to the minor groove. The characteristics of the DNA products created by Ni(GGH- y\u03b4 141-183) cleavage of DNA indicates that cleavage is produced by some time of non-diffusible oxidizing species. ESR studies indicate that cleavage is not mediated by Ni(III)\u2022GGH. Mechanistic studies indicate that DNA cleavage likely results from abstraction of the hydrogen atom at the C4' position of the deoxyribose backbone by some high valent, nickel-oxo species. Protocols for the synthesis of deuterated thymidines are included.
\r\n" }, { "name": "Hoffman, Amy Jo", "degree": "PhD", "year": "1993", "title": "Photocatalytic reactions on quantum-sized semiconductor colloids : photoinitiated polymerization of vinylic monomers, formation of hydrogen peroxide and organic peroxides, oxidation of carboxylic acids, and synthesis of humic-like material", "advisor": "Hoffmann, Michael R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09272005-134829", "creators": [ { "name": { "family": "Hoffman", "given": "Amy Jo" }, "id": "Hoffman-A-J", "display_name": "Hoffman, Amy Jo" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "advisor", "display_name": "Hoffmann, Michael R." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "co-chair", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qxc8-7431", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nUltrasmall semiconductor particles (diameters 1-10 nm) of CdS, ZnO, and TiO2 have been synthesized. These particles exhibit the quantum-size effect, which is characterized by a shift of the absorption onset (i.e., bandgap energy) from the visible region for the bulk material to the UV for ultrasmall diameters. The ability of these colloids to photocatalyze various chemical transformations was investigated.\n\nSemiconductors were found to be efficient photoinitiators of polymerization of vinylic monomers. Q-sized colloids demonstrated significantly higher rates of photopolymerization than their bulk-sized counterparts. The semiconductor photoinitiation efficiencies were correlated to the reduction potentials of the conduction band electrons. The rates of polymerization were found to depend upon the solvent nature, the monomer and initiator concentrations, and the incident light intensity. The polymerization reaction proceeds via a mechanism involving anionic initiation by conduction band electrons. The valence band holes, which are formed upon illumination, are scavenged by the solvent. The observed rate of polymerization increased proportionally to the square root of the incident light intensity; this functional dependence arises from the second-order termination reactions of the free-radical intermediates.\n\nAqueous, oxygenated suspensions of quantum-sized ZnO particles with added hole scavengers produced steady-state H2O2 concentrations as high as 2 mM upon bandgap illumination. Isotopic labeling experiments demonstrated that H2O2 was produced via the reduction of adsorbed oxygen by conduction band electrons. The quantum yields followed an inverse square-root dependency on absorbed light intensity. Quantum yields as high as 30% were obtained. The quantum yield of H2O2 production increased as the Q-sized particle diameter decreased.\n\nQ-sized ZnO particles also photocatalyzed the oxidation of acetate, formate, and glyoxylate. The observed product distributions were discussed regarding direct oxidation by the valence band holes or indirect oxidation by surface-bound hydroxyl radical intermediates. In illuminated semiconductor suspensions, radical intermediates react with the semiconductor surface, forming trapped species which are further oxidized either by semiconductor holes or by self-injection of a second electron into the conduction band.\n\nIn the final investigation of semiconductor photocatalyzed reactions, humic-like substances were formed in illuminated aqueous Q-sized suspensions containing catechol or gallic acid. Their formation was attributed to polymerization-type reactions initiated by [...] radicals.\n" }, { "name": "Jones, Daniel Hall", "degree": "PhD", "year": "1993", "title": "Quantum-mechanical chemical exchange. Stochastic averaging in magnetic resonance", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12172012-092540697", "creators": [ { "name": { "family": "Jones", "given": "Daniel Hall" }, "id": "Jones-D-H", "display_name": "Jones, Daniel Hall" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "role": "member", "display_name": "Labinger, Jay A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nr9w-1k51", "abstract": "I. Quantum-Mechanical Chemical Exchange
\r\n\r\nA quantum-mechanical treatment of both spin and space degrees of freedom is derived which accounts for both tunnelling splittings and lineshape behavior in the observed NMR of exchanging proton pairs. In this self-consistent treatment, the chemical exchange rate is expressed in terms of a correlation function of the operator which couples space and spin. A master equation formulation of the correlation function is presented which can be solved for any model of discrete rovibrational states. In contrast to previous descriptions of intramolecular chemical exchange, which either use transition state theory and the notion of molecular tunnelling or ad hoc ideas of incoherent tunnelling, the present treatment places chemical exchange among the class of transport and relaxation rates described by the quantum-statistical fluctuation-dissipation theorem. Results from simple models of the tunnelling system are analyzed in order to relate the observed NMR lineshape of certain transition metal hydrides to the underlying Born-Oppenheimer potential for the quantized nuclear motion.
\r\n\r\nII. Stochastic Averaging in Magnetic Resonance
\r\n \r\nAs a result of the typical smallness of spin Hamiltonian parameters relative to the rates of relaxation of spatial degrees of freedom, many magnetic resonance spectra are\r\nunderstood to be stochastic averages over thermally accessible molecular configurations or spatial (e.g., rovibrational) eigenstates. The temperature dependence of the average spin parameters is widely used to provide information on the potential energy functions which determine molecular conformation. It is universal practice in computing these averages that the energies (or free energies) multiplying \u03b2(=1/kT) in the Boltzmann probability factors are the spatial contributions only. It is argued that any such averaging procedure is inconsistent with statistical mechanics and an alternative procedure is\r\npresented for calculating the stochastically-averaged spin Hamiltonian. The experimental conditions and possible test systems for validating the traditional or alternative forms of the stochastic average are discussed.
\r\n" }, { "name": "Kim, Jongsun", "degree": "PhD", "year": "1993", "title": "Crystallographic structures and functional implications of nitrogenase molybdenum-iron proteins from Azotobacter vinelandii and Clostridium pasteurianum", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182007-093920", "creators": [ { "name": { "family": "Kim", "given": "Jongsun" }, "id": "Kim-J", "display_name": "Kim, Jongsun" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bnbs-6507", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThree-dimensional structures of the nitrogenase molybdenum-iron (MoFe-) proteins from Azotobacter vinelandii and Clostridium pasteurianum have been determined by X-ray crystallography. The structure of MoFe-protein from A. vinelandii (Av1) was determined at 2.7[...] by the method of multiple isomorphous replacement (MIR) and noncrystallographic symmetry (NCS) averaging both within and between crystal forms. The Av1 model has been refined to a crystallographic R factor of 19% with good geometry. The root mean square (rms) deviation of bond lengths and bond angles are 0.016[...] and 3.3\u00b0, respectively. The structure of MoFe-protein from C. pasteurianum (Cp1) was determined at 3.0[...] by a combination of molecular replacement, single isomorphous replacement (SIR) and NCS averaging both within and between crystal forms. The Cp1 model has been refined to a crystallographic R factor of 18% with good geometry. The rms deviation of and lengths and bond angles are 0.018[...] and 3.9\u00b0, respectively.\n\nThe MoFe-protein, which is an [alpha]2[beta]2 tetramer with a total molecular weight of ~240kD, contains two types of metal centers: the FeMo-cofactor and the P-cluster pair. The FeMo-cofactor is believed to represent the site of substrate reduction and the P-cluster pair may function in electron transfer between iron (Fe-) protein and the FeMo-cofactor. The FeMo-cofactor contains two clusters of composition 4Fe:3S and lMo:3Fe:3S that are bridged by three non-protein ligands. Two of the bridging ligands are assigned as sulfurs, while the chemical identity of the \"Y\" ligand is still ambiguous, but it could be sulfur. The Fe-Fe distance between bridged iron sites average ~2.5[...], suggesting that there may be some iron-iron bonding interactions, which could contribute the fourth coordination for the bridging irons. Ignoring the partial iron-iron bonding interactions between bridged irons, six of the seven Fe atoms in the FeMo-cofactor have trigonal coordination geometry, are coordinatively unsaturated, and are potential sites for N2 activation. The N2 binding site in FeMo-cofactor may be relevant to the H2 binding site in the H-cluster of Fe-hydrogenases and the O2 binding site in the Mn-center of PSII. Homocitrate, an essential component of FeMo-cofactor, is coordinated through a hydroxyl and carboxyl oxygen to the molybdenum site. The FeMo-cofactor is attached to the [alpha] subunit through two protein ligands, Cys [alpha]275 and His [alpha]442. The P-cluster pair consists of two 4Fe:4S clusters that are bridged by two cysteine thiol ligands and a disulfide bond between two of the cluster sulfurs. The P-cluster pair is attached at the interface between the [alpha] and [beta] subunits through seven protein ligands: Cys [alpha]62, Cys [alpha]88, Cys [alpha]154, Cys [beta]70, Cys [beta]95, Cys [beta]153, and Ser [beta]188. The structure of the P-cluster pair indicates that the P-cluster pair can act as a two-electron redox group, involving cleavage and reformation of the [mu]3-disulfide bridge coupled to the transfer of electrons into the FeMo-cofactor. This disulfide bond may also provide a site for H2 evolution.\n\nThe [alpha] and [beta] subunits in the [alpha]2[beta]2 MoFe-protein tetramer exhibit similar polypeptide folds consisting of three domains of [alpha]/[beta] type with some extra helices. The [alpha] and [beta] subunits of MoFe-protein are related by an approximate two-fold axis which passes through the center of the P-cluster pair, and there are two wide and shallow clefts around the P-cluster pair which may provide the binding site for the dimeric Fe-protein. Docking studies between the Fe-protein and MoFe-protein suggest a possible interaction mode between the two proteins that involves the surface of the MoFe-protein near the approximate two-fold axis passing through the P-cluster pair, and the surface of the Fe-protein near the 4Fe:4S cluster. The overall dimensions of the [alpha]2[beta]2 MoFe-protein teamer are ~70[...] x 80[...] x 110[...]. The two [alpha][beta] subunit pairs are related by a two-fold NCS axis. Even though the [alpha] and [beta] subunits in an [alpha][beta] subunit pair are also approximately related by a two-fold rotation, the MoFe-protein does not exhibit 222 symmetry. The MoFe-protein tetramer interface is stabilized by packing of helices primarily provided by two [beta] subunits, with some contribution from the [alpha] subunit, and further stabilized by divalent cation binding.\n\nThe FeMo-cofactor is buried at least 10[...] below the protein surface. No permanent channels between the protein surface and the FeMo-cofactor are present, however, there are two potential clefts which could be utilized for substrate entry/product release and/or H3O+ transport. The protein environment of the FeMo-cofactor indicates that there are multiple potential transfer pathways. The P-cluster pair is also buried about 12[...] below the protein surface and the environment of the P-cluster pair is primarily provided by hydrophobic residues. The edge-edge distance of the FeMo-cofactor to the P-cluster pair is about 14[...]. Four helices are oriented in parallel between the two metal centers and could play a role in electron transfer. In particular, the helices [alpha]63-74 and [alpha]88-92 provide the most direct structural connection between a P-cluster pair and FeMo-cofactor.\n\nThe structure of Cp1, including the two types of metal centers associated with the protein, are similar to that of Av1. Unique features of the Cp1 structure arise from the presence of a ~50 residue insertion in the [alpha] subunit and a ~50 residue deletion in the [beta] subunit. As a consequence, the FeMo-cofactor is more buried in Cp1 than in Av1, since the insertion is located on the surface above the FeMo-cofactor. The location of this insertion near the putative Fe-protein binding site provides a structural basis for the observation that the nitrogenase proteins from C. pasteurianum have low activity with complementary nitrogenase proteins isolated from other organisms.\n" }, { "name": "Kuo, Elaine Y.", "degree": "PhD", "year": "1993", "title": "I. Thermal cyclization of (Z)-1,2,4-heptatrien-6-yne. II. Studies directed toward the synthesis of neocarzinostatin chromophore", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-092055513", "creators": [ { "name": { "family": "Kuo", "given": "Elaine Y." }, "id": "Kuo-E-Y", "display_name": "Kuo, Elaine Y." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x7qa-8x77", "abstract": "The possibility that the hydrocarbon (Z)-1,2,4-heptatrien-6-yne might undergo a\r\nthermal cyclization to the biradical \u03b1,3-dehydroluene was considered. A methodology\r\nfor the synthesis of (Z)-1,2,4-heptatrien-6-yne was developed wherein propargyl\r\nhydrazines, obtained from the corresponding propargyl alcohols, were oxidized to allenes\r\nwith diethyl azodicarboxylate in good yields. The formation of products consistent with\r\nthe intermediacy of the biradical \u03b1,3-dehydrotoluene is discussed.
\r\n\r\nIn studies directed toward the total synthesis of neocarzinostatin chromophore, the\r\nattempted formation of the cyclononadiyne core of the molecule via the intramolecular\r\ninsertion of an alkylidene carbene into an acetylenic carbon-hydrogen bond was\r\ninvestigated. The alkylidene carbene was generated from the appropriately\r\nfunctionalized cyclopentanone precursor with the reagent dimethyl\r\ndiazomethylphosphonate (DAMP). While the identification of the reaction products was\r\nconsistent with the formation of the desired carbene, the formation of the desired\r\ninsertion product was not observed. In conjunction with studies seeking to synthesize\r\nneocarzinostatin chromophore via an intramolecular acetylide addition, the synthesis of\r\nan epoxy carbonate fragment to be used in the convergent synthesis of a suitable\r\ncyclization precursor is described, as well as initial efforts concerning glycosylation with\r\na suitably protected N-methyl D-fucosamine derivative.
\r\n\r\n\r\n\r\n" }, { "name": "Lovalenti, Philip Michael", "degree": "PhD", "year": "1993", "title": "Inertial effects on particle dynamics", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08302007-112722", "creators": [ { "name": { "family": "Lovalenti", "given": "Philip Michael" }, "id": "Lovalenti-P-M", "display_name": "Lovalenti, Philip Michael" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/q7ya-ex37", "abstract": "While the theory of suspension flows and particle dynamics is well understood under Stokes flow conditions when viscous forces dominate, little is known at finite Reynolds number when the inertial forces of the suspending fluid are important. In the present study, expressions are derived that allow for dynamic calculations of particle, drop, and bubble motion at finite Reynolds number. The results show a significant change in the temporal behavior of the force/velocity relationship from that derived from the unsteady Stokes equations, particularly as a body approaches its steady state. At finite Reynolds number, when the convective inertial effects are included, the hydrodynamic force on a body has much weaker history dependence on the past motion of the body and it reaches its steady state faster than what would be predicted if only the unsteady inertial effects are accounted for. When compared with numerical solutions of the Navier-Stokes equations, the analytical force expressions perform well up to a Reynolds number of 0.5.\n\nA common theme to the derivations is the use of the reciprocal theorem which provides for an efficient and elegant means for computing inertial effects in suspension mechanics. Connections with past approaches are made in light of these new applications of the reciprocal theorem." }, { "name": "Male, Roxanne", "degree": "PhD", "year": "1993", "title": "Development of an Effective Drug Delivery System Using Loaded Platelets", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01022013-133723062", "creators": [ { "name": { "family": "Male", "given": "Roxanne" }, "id": "Male-Roxanne", "display_name": "Male, Roxanne" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1q2y-nz07", "abstract": "Liposomes have been used to deliver diagnostic and therapeutic drugs\r\nwith moderate success. Current applications include targeting to tumors\r\n(1), where the vasculature is leaky and allows liposome penetration, and\r\nKupffer cells in the liver (2). Reticuloendothelial system (RES) uptake and\r\nlack of targeting specificity of the liposomes have been the major problems\r\nencountered. Several groups including Allen et al. (3) and Liu et al. (4)\r\nhave increased the circulation times by attaching polyethylene glycol (PEG)\r\nor the ganglioside GM_1 to the liposome surface; the circulation half-lives\r\nfor disteroylphosphatidylcholine (DSPC):cholesterol:PEG and GM_1\r\nliposomes are 20.0 \u00b1 3.5 and 16.4 \u00b1 3.1 hours, respectively as compared to\r\n6.7 \u00b1 4.5 hours for DSPC:cholesterol (2:1 mole ratio) liposomes (3). In\r\naddition, some attempts have been made to target specific areas by the\r\naddition of ligands, such as human gamma globulin or aminomannose;\r\nhowever this increased targeting has been largely limited to increased\r\nKupffer cell and RES uptake (5,6). Addition of antibodies to the liposomes\r\nincreases targeting specificity, but has met with limited success since the\r\nliposomes are still prone to RES uptake (7).
\r\n\r\nReconstituted Sendai virus envelopes (RSVE) are essentially liposomes\r\nwith binding and fusogenic glycoproteins on their surface. These vesicles\r\nhave been used as vehicles for delivering molecules into cells in vitro\r\nand for the transfer of membrane proteins into the cells' plasma\r\nmembranes. Similar to intact viruses, RSVE attach preferentially to cells\r\nhaving the appropriate receptors, usually gangliosides, and fuse with the\r\ncellular membranes, thus emptying their contents into the cell cytoplasm.\r\nThis also results in the implantation of the viral envelope components\r\ninto the recipient cell plasma membrane.
\r\n\r\nWe have studied the in vitro interactions of small unilamellar\r\nvesicles (SUV) and reconstituted Sendai virus (RSVE) with platelets with\r\nthe objective of developing new drug delivery systems. Specifically, we\r\nhave examined the kinetics and mechanisms of uptake of SUV, with and\r\nwithout covalently attached proteins, and RSVE. Liposomes that have\r\nbeen studied include: DSPC:cholesterol (2:1 mole ratio) liposomes\r\n(control) (8) and aminomannose (Am), human gamma globulin (HgG)\r\nand transferrin (Tf) labeled control liposomes (9). From our data we\r\nconclude that the mechanisms and kinetics of uptake and subsequent\r\nspecific localization of the lipid and aqueous components of the liposomes\r\nwithin the cells are dependent on the type of liposome used.
\r\n\r\nPlatelets have the unique ability to target to specific areas in vivo\r\nincluding areas of infection and inflammation, tumors and clots.\r\nTherefore we hoped to combine this in vivo targeting ability with the\r\nplatelets' ability to take up liposomes and RSVE in vitro to create new\r\ndrug delivery systems to deliver diagnostic and therapeutic reagents.\r\nHaving a variety of systems from which to choose should offer the ability\r\nto optimize drug delivery parameters.
\r\n\r\nIn vitro functional assays, including microaggregation, serotonin\r\nrelease and membrane integrity, conclude that platelet function is not\r\ninhibited by liposome uptake (8, 9). However, uptake of intact and\r\nreconstituted Sendai virus particles induce platelet aggregation and\r\nsecretion. In vivo organ distribution studies in Sprague-Dawley rats\r\nindicate that circulation times and RES uptake of liposome-loaded rat\r\nplatelets are identical to control rat platelets (10).
\r\n" }, { "name": "Mathiowetz, Alan Martin", "degree": "PhD", "year": "1993", "title": "Dynamic and Stochastic Protein Simulations: from Peptides to Viruses", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-110407804", "creators": [ { "name": { "family": "Mathiowetz", "given": "Alan Martin" }, "id": "Mathiowetz-Alan-Martin", "display_name": "Mathiowetz, Alan Martin" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pe34-yy14", "abstract": "In order to increase the efficiency of protein simulations, both deterministic and stochastic methods can be formulated in terms of the most important degrees of freedom in polypeptide and protein systems: the torsions. Two such methods are presented here. The first is Newton-Euler Inverse Mass Operator (NEIMO) Dynamics, an internal-coordinate molecular dynamics method originally designed to study the dynamics of general multibody systems. The second is the Probability Grid Monte Carlo (PGMC) method, developed for searching the conformational space of polypeptides using a weighted sampling of the most favorable dihedral angles.
\r\n\r\nThe first use of the NEIMO Dynamics method for studying molecular systems is reported here. The method is used to study the dynamics of a wide range of peptide and protein systems. These range from the pentapeptide Met-enkephalin to the crystallographic asymmetric unit of the tomato bushy stunt virus (TBSV), an assembly of three chains totaling 893 residues. Bond lengths and angles do not vary during the dynamics simulations; this enables timesteps larger than 10 femtoseconds to be used for small peptides, a substantial improvement over Cartesian coordinate molecular dynamics. Timesteps of 10 fs do not work well for NEIMO simulations of large proteins because of unacceptably large energy fluctuations. However, timesteps of 2-5 fs give acceptable results, even for very large systems. The NEIMO method is applied to TBSV coat proteins, in an investigation of the effect of Ca2+ ions on the coat stability.
\r\n\r\nThe PGMC method provides efficient conformational searches for polypeptide systems by assigning probabilities to different discrete values of the \u03c6, \u03c8, and \u03c7 dihedral angles. These probabilities were derived by investigation of the protein structures in the Brookhaven Protein Database. The PGMC method is applied successfully to several important problems in protein modeling: studies of the low-energy conformations of a peptide, prediction of the all-atom conformation of a protein from its C\u03b1 coordinates alone, and the prediction of antibody loop conformations. The success of the C\u03b1, modeling is further extended by its application to structures with coordinates constrained to a lattice, through the use of a simple C\u03b1 Forcefield.
\r\n" }, { "name": "Miller, Ann Elizabeth", "degree": "PhD", "year": "1993", "title": "Ab initio calculations in heterogeneous and homogeneous catalysis : I. Methanol to gasoline with ZSM-5. II. Carbonyl ligand effects on metal-metal bonds", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-09042007-152645", "creators": [ { "name": { "family": "Miller", "given": "Ann Elizabeth" }, "id": "Miller-Ann-Elizabeth", "display_name": "Miller, Ann Elizabeth" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WRBP-E952", "abstract": "This thesis is composed of two studies in catalysis. The first is an exploration, using computational techniques, of the mechanism for the first carbon-carbon bond formation in the Methanol to Gasoline (MTG) reaction. The second is a study of the factors important to the understanding of ligand effects on metal-metal bonds, and in particular, to metal clusters.\r\n\r\nThree possibilities were considered as ways to activate a carbon in the MTG process prior to formation of C2 or higher hydrocarbons. These were a free radical mechanism, a surface ylide mechanism, and a possible defect site which might lead to steric crowding of CH2 groups.\r\n\r\nAlthough the free radical mechanism was found to be thermodynamically within the parameters of the MTG process, it contained a high transition state. Consideration of the molecules available prior to hydrocarbon build-up and their specific electronic structure, led to the view that the available carbon atoms (methanol, dimethyl ether, etc.) were unlikely to be activated by a free radical intermediate. \r\n\r\nThe surface-stabilized ylide which has been proposed as an intermediate by many was studied to determine if in fact the ylide was stabilized. The total energy of the ylide was compared to that of the naked site on the zeolite and free methylene. Free methylene ranged, depending on the geometry of the ylide, between 50 and 80 kcal more stable. These numbers are qualitatively correct, but more electron correlation would have to be incorporated in the calculation to get an accurate value for the destabilization.\r\n\r\nStarting from a defect site, two CH2 groups were each attached to two oxygen atoms. It was thought that two CH2 groups would take up considerably more space than either the original Al atom or the four hydrogens. Molecular Mechanics calculations showed the zeolite to be sufficiently flexible to prevent crowding of the CH2's.\r\n\r\nThe second study involved determining the effects of colinear carbonyl ligands on osmium-osmium bonds. Calculations at the Dissociation Consistent Cl level showed that the ligands were weakening the metal-metal [pi]-bonds through back-donation.\r\n" }, { "name": "Murthy, Srihari", "degree": "PhD", "year": "1993", "title": "The Gas-Phase Ion Chemistry of Substituted Silanes", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042013-113332582", "creators": [ { "name": { "family": "Murthy", "given": "Srihari" }, "id": "Murthy-Srihari", "display_name": "Murthy, Srihari" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8gv5-xy57", "abstract": "Ion-molecule reactions in the chlorosilanes, SiHnCl4-n (n = 0-3), and in phenylsilane have been studied by the technique of Fourier transform ion cyclotron resonance spectrometry.
\r\n\r\nIn Chapter 1, the motivations for studying the gas-phase ion chemistry of substituted silanes as well as brief descriptions of the gas phase ion chemistry of the chlorosilanes and of phenylsilane are presented.
\r\n\r\nChapter 2 deals with the gas-phase ion chemistry of the chlorosilanes, SiHnCl4-n (n = 0-2). Reactions of the chlorosilyl ions with neutral chlorosilanes and with silane as well as the reactions of the silyl ion with neutral chlorosilanes are presented. The chlorosilyl ions participate in H\u02c9, Cl\u02c9 transfer reactions and disproportionation reactions. The mechanisms of these reactions are discussed. The Cl\u02c9 affinities of the chlorosilyl ions, SiHnCl3-n+ (n = 0-2), lie within a range of 1.2 kcal mol-1 and decrease in the order SiH2Cl+ > SiHCl2+ \u2248 SiCl3+. The heats of formation of the chlorosilyl ions are determined.
\r\n\r\nChapter 3 deals with the gas-phase ion chemistry of monochlorosilane. The difference in the H\u02c9 affinities of the ions SiH2Cl+ and SiHCl2+ is determined to be 1.5 \u00b1 0.3 kcal mo-1. The H\u02c9 affinities of the chlorosilyl ions, SiHnCl3-n+ (n = 0-2), lie within a range of 1.8 kcal mol-1 and decrease in the order SiHCl2+ \u2248 SiCl3+ > SiHCl2+. Protonated SiH3Cl is generated by proton transfer from CH5c and is observed to react with SiH3Cl to yield (SiH3)2Cl+.
\r\n\r\nChapter 4 deals with the gas-phase ion chemistry of phenylsilane. In analogy with toluene, two (parent \u2013 H)+ cations are produced by the electron impact ionization of phenylsilane. These cations are identified to be the phenylsilyl and the silacycloheptatrienyl cations.
\r\n\r\nChapter 5 explores the gas-phase ion chemistry of phenylsilane in great detail. Reactions of the parent and fragment ions (created by electron impact ionization) with neutral phenylsilane and with C6D6 are presented. Two structural isomers are identified for the C6H8Si+ cation and three structural isomers are identified for the C6H6Si+ cation. The H\u02c9 affinity of the phenylsilyl cation is also presented.
\r\n" }, { "name": "Park, Changmoon", "degree": "PhD", "year": "1993", "title": "Protein design and simulation. Part I. Protein design. Part II. Protein simulation", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112009-114142428", "creators": [ { "name": { "family": "Park", "given": "Changmoon" }, "id": "Park-C", "display_name": "Park, Changmoon" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sv6x-9s75", "abstract": "Since specific DNA binding proteins play many important roles in the regulation of cellular reactions including replication, transcription, and translation by the specific interactions of DNA binding proteins with DNA, the design and synthesis of sequence-specific DNA binding proteins is of great interest in modern chemistry and biology.\r\n\r\nChapter 1 introduces a strategy by which to design new protein structures recognizing new sequences of DNA. The results of experiments using new protein show that there is cooperation between the monomers in binding to DNA and each monomer recognizes the half-site of the dimer binding site.\r\n\r\nChapter 2 describes the advantage of palindromic sites and dimerization in DNA recognition according to the experimental results. The results also show that each monomer in a dimer recognizes one half-site of the dimer binding site irrespective of the relative orientation monomer in the dimer and the dimer binding site depends on the relative orientation of the two monomer in the dimer.\r\n\r\nChapter 3 shows that the monomer of DNA binding region of the v-Jun leucine zipper protein recognizes the dimer binding site. Our results support the possibility that two monomers of v-Jun might bind sequentially to the dimer site with dimerization of v-Jun occurring while bound.\r\n\r\nChapter 4 describes the design of a new protein recognizing a new 16 by site in DNA. Our results show that there is cooperation between monomers and all three monomers in the new peptide recognize unique half-sites in the proposed trimeric binding site.\r\n\r\nChapter 5 describes quantum mechanical calculations on the active site of cytochrome P-450cam to improve force constants for the molecular simulations of cytochrome P-450cam. Our results show that the size of iron ion is a function of its spin and oxidation state and plays a key role in the process of oxygenation.\r\n" }, { "name": "Phung, Thanh Ngoc", "degree": "PhD", "year": "1993", "title": "Behavior of concentrated colloidal suspensions by Stokesian dynamics simulation", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02052008-140111", "creators": [ { "name": { "family": "Phung", "given": "Thanh Ngoc" }, "id": "Phung-T-N", "display_name": "Phung, Thanh Ngoc" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZA49-9N69", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe Stokesian dynamics simulation method is applied to study the behavior of concentrated suspensions of hydrodynamically interacting colloidal particles in a shear flow. The aim of this study is the prediction of suspension macroscopic properties from the microstructure - the temporal and spatial distribution of suspended particles. The macroscopic properties includes the shear viscosity, normal stress differences, short- and long-time self-diffusivities. Suspension macroscopic properties and the microstructure are modeled as functions of two parameters: particle volume fraction, [...], and the Peclet number, Pe, which measures the relative importance of the imposed shear and Brownian forces. Stokesian dynamics accurately accounts for both the hydrodynamic and Brownian forces of a colloidal dispersion. The method, which is very general and computationally efficient, imposes no restriction on the particle displacements and allows simulation of flowing suspension with particle volume fractions from infinite dilution to dense packing and a continuous range of the Peclet number from pure Brownian motion (Pe 0) to pure hydrodynamics (Pe \u2014> [...]).\r\n\r\nThe method is first employed for the pure Brownian suspensions (Pe=0) at a volume fraction [...]=0.45. The accuracy of Stokesian dynamics is demonstrated by an excellent comparison of the radial pair-distribution function obtained from dynamic simulation which captures the same isotropic hard-sphere distribution computed by the random Monte-Carlo method. The simulation method is then applied to study the dynamics of sheared SCC, BCC, and FCC periodic lattices of non-colloidal spheres (Pe [...]) with particle volume fraction ranging from dilution to maximum close packing. Results of the resistivity and the shear viscosity of sheared periodic lattices are successfully determined as a function of the volume fraction.\r\n\r\nThe Stokesian dynamics simulation method is finally applied to the dynamic simulation of unbounded concentrated suspensions of force- and torque-free colloidal particles. The particle volume fractions are varied from 0.316 to 0.6 and the Peclet numbers are ranged from the strong Brownian limit (Pe=0.01) to the hydrodynamic dominated \r\nregime (Pe=[...]). Comparisons of simulation results for the steady shear viscosities, self-diffusivities, and the structure factors with experiments are remarkably good. For the first time, the flow of particles are probed with detail to illustrate the shearing deformation to suspension microstructure. This information provides a physical understanding of the fundamental mechanisms causing interesting shear thinning and shear thickening behavior and its important relation to the shear-induced microstructure. The simulation results reveal three distinct behaviors of hard-sphere suspensions in the regions of strong Brownian motion, balance of Brownian and hydrodynamic interactions, and hydrodynamic domination.\r\n\r\nIn the region of strong Brownian motion with small Peclet numbers (Pe < 1), the suspension shear thins due to a decrease of Brownian contribution to particle stress. The isotropic microstructure is slightly deformed, but the particles are very well dispersed. More importantly, simulation results do not reveal ordered microstructure in the shear thinning region. For the special plateau region with Pe [...] 10, the suspension no longer shear thins and the shear viscosity is minimized. The balance of hydrodynamic and Brownian forces induce a strongly ordered flowing suspension with hexagonally packed strings of particles flowing with the bulk flow. The string formation is due to the Brownian forces which act as short-range springlike repulsive and random forces to counter the shearing deformation to the suspension by the imposed shear; the string formation does not relate to the shear thinning. In the region of hydrodynamic domination (Pe > [...]), the suspension shear thickens due to formation of large, elongated clusters of particles. In this region, the hydrodynamics contribute all particle stress as the direct Brownian contribution has essentially vanished, but weak Brownian forces are seen to perturb and induce a local anisotropic microstructure. The complete relation of the steady shear viscosity to particle volume fraction and the Peclet number for concentrated hard-sphere suspensions is also given.\r\n" }, { "name": "Potter, Earl Douglas", "degree": "PhD", "year": "1993", "title": "Ultrafast control and dynamics of chemical reactions", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-113817", "creators": [ { "name": { "family": "Potter", "given": "Earl Douglas" }, "id": "Potter-E-D", "display_name": "Potter, Earl Douglas" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k9hx-hh19", "abstract": "This thesis presents four distinct applications of ultrafast laser spectroscopy. Unimolecular photodissociation was one of the early applications of this technique and proved to be invaluable in furthering the understanding of unimolecular dissociation mechanisms. As such, the photodissociation of ketene represents one of the two systems where micro-canonical, state-to-state reaction rates, have been measured. Clocking of bimolecular reactions, while still in its infancy, provides a means of measuring the rate at which an elementary reaction actually occurs--isolated from other molecules. The rate at which the bimolecular reaction of bromine atoms with molecular iodine to form iodine monobromide has been measured at two collision energies. An area where ultrafast techniques are just now seeing application, is control of chemical reactions. This thesis illustrates an initial study, albeit limited, of how ultrashort light pulses can be used to \"control\" the outcome of a chemical reaction. The experiments here show how the natural wave-packet motion of the initially prepared B state iodine can be used to \"control\" whether or not xenon iodide is formed even when the necessary photons are available. Finally, cluster science is becoming a mature field within physical chemistry, but one of the goals of such work has been to make a connection between gas-phase studies and condensed-phase work. Small clusters, those not large enough to bridge this gap, have proven sufficiently interesting to monopolize the efforts of many groups. Again in a limited way, we have begun to study large clusters in the hope that these systems will truly show characteristics that are somehow intermediate to the gas-phase and condensed-phase characteristics. A dissociating iodine molecule surrounded by many argon atoms encounters an environment that significantly alters the time scales and overall mechanism for separation of the two iodine atoms.\n\nWork done under the direction of Professor Ahmed H. Zewail.\n" }, { "name": "Pylkki, Russell John", "degree": "PhD", "year": "1993", "title": "Probing Chemical Dynamics Near Electrode Surfaces with U1tramicroelectrodes", "advisor": "Anson, Fred C.; Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:01022013-155536079", "creators": [ { "name": { "family": "Pylkki", "given": "Russell John" }, "id": "Pylkki-Russell-John", "display_name": "Pylkki, Russell John" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pycn-4626", "abstract": "This thesis describes work carried out to observe the dynamics of diffusion layer\r\ngrowth near electrode surfaces. For the first time, these processes are observed within\r\n1 \u00b5m of an electrode. This is accomplished by positioning an ultramicroelectrode near an electrode surface with a scanning tunneling microscope. A bipotentiostat is integrated with the scanning tunneling microscope to allow potential control of the sample cell, permitting independent control of both the electrode substrate and the ultramicroelectrode tip potentials.
\r\n\r\nThe response of the diffusion layer to potentiostatic and galvanostatic stimulus of\r\nthe substrate is described. The responses to the stimulus in the absence of coupled\r\nchemical reactions are shown to agree well with theory. The observed effects of a coupled\r\nchemical reaction are also reported and compared to the responses generated from a\r\nsimulation program. Good agreement of the experimental data to the simulated data is\r\nshown, which demonstrates the ability of the instrument to study homogeneous kinetics.
" }, { "name": "Rock, Michael M., Jr.", "degree": "PhD", "year": "1993", "title": "The design and synthesis of electroactive and magnetic polymers", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01082013-155858039", "creators": [ { "name": { "family": "Rock", "given": "Michael M., Jr." }, "id": "Rock-M-M-Jr.", "display_name": "Rock, Michael M., Jr." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w5nj-m257", "abstract": "Ring-opening metathesis polymerization (ROMP) remains a\r\nvaluable tool in polymer synthesis because it affords structurally well-defined,\r\nfunctionalized materials with highly unsaturated polymer\r\nbackbones. The power and flexibility of organic and polymer chemistry are\r\nused here to create fully conjugated, electroactive organic polymers.
\r\n\r\nA series of electroactive poly(norbornadienebenzoquinone-imine)\r\nand poly(norbornadienebenzoquinone) polymers have been synthesized\r\nby the ring-opening metathesis polymerization (ROMP) of functionalized\r\nbicyclo[2.2.1]hepta-2,5-dienes using alkylidene metathesis catalysts.\r\nIncorporation of these quinone and imine redox units into organic\r\nnorbornadiene polymers generates highly reactive and conductive\r\nmaterials capable of charge storage and electrochromism.
\r\n\r\nIn a second effort, we describe an improved precursor polymer\r\nroute to polyparaphenylene (PPP) based upon the ring-opening metathesis\r\npolymerization (ROMP) chemistry of cis-di(3,4-\r\ndihydroxymethyl)cyclobutene dicarbonate. These precursor\r\npolybutenamers undergo a final conversion, under mild reaction\r\nconditions, to insoluble polyparaphenylene (PPP) without destroying or\r\ndisturbing the existing polymer structure. These polybutenamers, in\r\naddition to their success in PPP conversion, are of great interest because\r\nthey incorporate high degrees of acid, oxygen, and hetereoatom\r\nfunctionality into a soluble 1,4-poly(butadiene) structure.
\r\n\r\nFinally, organic magnets offer new insights into the nature of\r\nmagnetism and lead to the development of materials with unique optical,\r\nelectrical, and magnetic properties. To test the claims and postulates of the\r\nTopological Coupling Model, an organic-based ferromagnetic polymer was\r\ndesigned around the ring-opening metathesis polymerization (ROMP) of\r\n3-diphenylmethylenecyclobutene. Doping, the generation of charged\r\nspecies along the polymer, generates a radical spin (1/2) on every\r\nmonomer unit in the polymer chain, resulting in a fully conjugated\r\npolybutenamer polymer with active spin centers every five (5) carbons\r\napart. Oxidative doping of this material evokes ferromagnetic couplings\r\namong unpaired spins in the material.
\r\n\r\n" }, { "name": "Ryba, Gail Naomi", "degree": "PhD", "year": "1993", "title": "Time-resolved photoluminescence studies of metal ion treated n-GaAs in electrolytes", "advisor": "Winkler, Jay Richmond", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-103203745", "creators": [ { "name": { "family": "Ryba", "given": "Gail Naomi" }, "id": "Ryba-Gail-Naomi", "display_name": "Ryba, Gail Naomi" } ], "advisors": [ { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-J-R", "role": "advisor", "display_name": "Winkler, Jay Richmond" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mzj0-sz79", "abstract": "Using the technique of time-correlated photon counting, the time-resolved\r\nphotoluminescence response of n-type gallium arsenide (n-GaAs) in contact with aqueous\r\nKOH \u2013 Se^2- - Se2^(2-) electrolytes was monitored before and after exposure to aqueous\r\n0.010 M solutions of ruthenium, cobalt and osmium ions. Cobalt ions caused the rate of\r\ncarrier loss from the GaAs to increase relative to that for untreated samples, as evidenced\r\nby faster decays. It was inferred that hole and/or electron transfer to the selenide redox\r\nspecies was catalyzed by the cobalt ions.
\r\n\r\nA model incorporating ambipolar diffusion, bulk trapping, radiative bimolecular\r\nrecombination, surface trapping and surface charge transfer and employing a finite-difference\r\nalgorithm was applied to the photoluminescence decays. Under high intensity\r\nillumination, the photoluminescence decays from the gallium arsenide samples with\r\naluminum gallium arsenide overlayers could be fit using the expression for bimolecular\r\nkinetics, indicating that radiative recombination dominated the decays in these samples.
\r\n\r\nFor the samples immersed in aqueous KOH \u2013 Se^(2-) \u2013 Se_2^(2-) solutions, with and\r\nwithout chemisorbed metal ions, a time-dependent increase in the GaAs photoluminescence\r\nindicated that changes occurred at the surface during the course of the experiment Prior to\r\nmetal ion treatment, the lifetime in KOH - Se^(2-) \u2013 Se_2^(2-) solutions stabilized at about 3.7 ns, which could be fit with an effective surface hole capture rate constant of 5.1x10^3 cm/sec.\r\nAfter cobalt ion treatment photoluminescence decays with 1/e lifetimes on the order of 0.6\r\nns were measured and, if it is assumed that surface hole capture dominated the decay,\r\ncorrespond to a surface hole capture rate constant of 1.7x10^5 cm/sec. The 1/e lifetimes for\r\nruthenium and osmium treated surfaces were never observed to be less than 1.5 ns and\r\nquickly returned to the 3.7 ns lifetimes observed prior to metal ion treatment It is inferred that the cobalt treated surface is more chemically inert under illumination than either ruthenium or osmium treated surfaces.
\r\n\r\nPreliminary measurements for GaAs immersed in acetonitrile with and without\r\ndimethylferrocene and dimethylferrocenium indicated that the rates of carrier loss at the\r\nsurface are much higher than they are for the aqueous selenide redox species, even in the\r\nabsence of the redox species. However, small increases in rate of loss were discernible\r\nafter addition of redox couple to the acetonitrile, and further work is warranted.
\r\n" }, { "name": "Sitlani, Ayesha", "degree": "PhD", "year": "1993", "title": "Sequence specific recognition and photocleavage of DNA by phenanthrenequinone diimine complexes of rhodium(III)", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-100729852", "creators": [ { "name": { "family": "Sitlani", "given": "Ayesha" }, "id": "Sitlani-A", "display_name": "Sitlani, Ayesha" } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/phhk-4s21", "abstract": "Sequence-specific recognition and photocleavage of DNA by a series of 9,10- phenanthrenequinone diimine (phi) complexes of rhodium(III) was studied. [Rh(phi)]^(3+) complexes bind to DNA via intercalation of their phi ligand and upon photoactivation promote strand scission. The DNA degradation products formed are consistent with photoreaction of [Rh(phi)]^(3+) intercalated in the major groove of DNA, via abstraction of the C3'-H atom of the deoxyribose. For the complex [Rh(phen)2phi]^(3+) and its derivatives [Rh(X)2phi]^(3+), the primary products are 5' and 3' phosphate termini and nucleic acid bases. For the complex [Rh(phi)2bpy]^(3+) and its derivatives [Rh(phi)2X]^(3+), additional products, dependent on dioxygen concentrations, are characterized as base propenoic\r\nacids and 3'-phosphoglycaldehyde termini. The partitioning between the oxygen dependent and oxygen independent pathways correlates best with how the shapes of these\r\ncomplexes limit access of dioxygen to the C3' deoxyribose position. The shapes of [Rh(phi)]^(3+) complexes also govern their sequence-specific DNA recognition. The more\r\nsterically bulky complexes with methyl or phenyl groups on their ancillary ligands cleave at a subset of sequences recognized by their parent molecules. The \u2206 and \u039b isomers of\r\n[Rh(5,5'-dimethylbpy)2phi]^(3+) cleave specifically at sites that are defined by the consensus sequences 5'-C-T-pu/py-G-3' and 5'-A-C/G-T-C/G-3', respectively. This\r\nsequence-specificity may be understood on the basis of negative steric clashes and positive van der Waals interactions between methyl groups on the metal complex and\r\nthymine methyl groups in the DNA major groove. The complex [Rh(4,4'diphenylbpy) 2phi]^(3+) recognizes the self-complementary eight base-pair sequence 5'CTCTAGAG-\r\n3', both due to its bulky shape and its ability to cooperatively associate through non-covalent dimerization on the DNA helix. [Rh(4,4'-diphenylbpy)2phi]^(3+) is\r\nshown to inhibit sequence-specific cleavage by the restriction enzyme Xbal. It is likely that, like [Rh(phi)]^(3+) complexes, DNA binding proteins exploit shape selection to achieve high levels of sequence-specificity.
\r\n" }, { "name": "Todd, Robert J.", "degree": "PhD", "year": "1993", "title": "Designing protein separations based on metal-affinity interactions", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11292007-090410", "creators": [ { "name": { "family": "Todd", "given": "Robert J." }, "id": "Todd-R-J", "display_name": "Todd, Robert J." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/aph0-0p32", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nImmobilized metal-affinity chromatography (IMAC) provides a technique to separate proteins based on their histidine multiplicity and microenvironment. A set of S. cerevisiae iso-l-cytochrome c variants which differed only in their histidine content and placement was used to study equilibrium binding and chromatographic retention on matrices of immobilized Cu(II) (TSK macroporous support). The structural integrity of the variants was verified by UV-visible absorbance and [...] NMR spectroscopy. Equilibrium binding studies indicate that a surface histidine is required in iso-l-cytochrome for interaction with a Cu(II)IDA (iminodiacetic acid) matrix. The apparent binding affinity of variants depends on the accessibility of the histidine side chains and on the total number of surface histidines. The overall equilibrium binding behavior is consistent with a model in which bound protein covers multiple copper sites on the matrix surface. Chromatographic studies on a Cu(II)IDA TSK column showed that a surface histidine is required for significant protein retention. It was also shown that proteins can be separated based on the microenvironment (accessibility or [...]) of a single surface accessible histidine or on the multiplicity of surface histidines and the order of retention in all cases correlated with the initial slope of the equilibrium binding isotherm. The effect of proton and imidazole competition on retention was also studied, and it was seen that simple equilibrium models, describing the interaction of a single-histidine protein with independent copper binding sites, are insufficient to account for the strong competitive behavior that is observed experimentally. The ability of IMAC to discriminate between proteins based on their histidine multiplicity and microenvironment provides a powerful dimension in protein separations.\n\nThe concept of engineering di-histidine metal-chelating sites into proteins for applications in purification and protein stabilization was investigated. A His-[...]-His site was engineered into the N-terminal [...]-helix of iso-l-cytochrome c at positions 4 and 8. A di-histidine site was also engineered across a small section of [...]-sheet structure at positions 39 and 58. Cu(II)IDA titrations of [...] NMR spectra show selective paramagnetic broadening of the C2 resonances of the chelating histidines. The His-[...]-His site at positions 4 an 8 binds Cu(II)IDA-PEG in solution 24 times stronger than a single histidine site and both metal-chelating variants have increased retention in a Cu(II) IMAC column relative to a non-chelating control protein. The engineered metal-chelating sites were also shown to stabilize the folded form of iso-1-cytochrome c in the presence of Cu(II)IDA by as much as 2.5 kcal/mol." }, { "name": "Youngquist, Michael George", "degree": "PhD", "year": "1993", "title": "Atomic-Scale Imaging and Spectroscopy Using Scanning Tunneling Microscopy", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01112013-110414331", "creators": [ { "name": { "family": "Youngquist", "given": "Michael George" }, "id": "Youngquist-Michael-George", "display_name": "Youngquist, Michael George" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Kaiser", "given": "William J." }, "id": "Kaiser-William-J", "role": "member", "display_name": "Kaiser, William J." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0d6k-be86", "abstract": "Advances in scanning tunneling microscopy (STM) instrumentation\r\nand applications are presented. An ultrahigh vacuum (UHV) scanning\r\ntunneling microscope incorporating computer-controlled two-dimensional\r\nsample translation and in vacuo tip and sample transfer was developed. Its\r\nperformance is documented through large-area and atomic-resolution\r\nimaging of highly stepped Si(111) 7x7 reconstructed surfaces and physisorbed\r\nclusters on graphite. An STM with automated approach and intra-Dew\u00e4r\r\nspring suspension was developed for operation in cryogenic liquids. A high\r\nperformance digital signal processor (DSP) based control system was\r\nconstructed, and software with advanced spectroscopic imaging and data\r\nprocessing capabilities was developed.
\r\n\r\nThe feasibility of individual-molecule vibrational spectroscopy via\r\nSTM-detected inelastic electron tunneling is assessed. In preliminary\r\nexperiments, a low-temperature STM was used for energy gap and phonon\r\nspectroscopy of superconducting Pb films. The first STM observation of\r\nphonon density of states effects in a superconductor is reported.
\r\n\r\nA systematic UHV STM imaging and spectroscopy study of 2H-MoS_2\r\nwas conducted. Atom-resolved images from three distinct imaging modes\r\nare presented. Occasional appearance of negative differential resistance\r\n(NOR) in I vs. V measurements is traced to changing tip electronic structure\r\nrather than localized surface states. Other potential NOR mechanisms are\r\ndiscussed including electron trap charging and resonant tunneling through a\r\ndouble-barrier quantum well structure arising from layer separation in the\r\nMoS_2 crystal.
\r\n\r\nDNA was imaged at atomic resolution with a UHV STM. Images show\r\ndouble-helical structure, base pairs, and atomic-scale substructure.\r\nExperimental STM profiles have atom-for-atom correlation with the A-DNA\r\nvan der Waals surface. This work demonstrates the potential of the STM for\r\ncharacterization of large biomolecular structures.
\r\n\r\nImpurity-pinned steps on silicon and gold surfaces were imaged by\r\nSTM. Pinned gold steps have short linear coherence lengths and form step\r\nloops at impurities by an Orowan-type bypassing mechanism. Step loops\r\nwere not observed at Si(111) pinning sites; step contours seem to be correlated\r\nwith the degree of order in the Si surface reconstruction.
" }, { "name": "Zhu, Xiaotian", "degree": "PhD", "year": "1993", "title": "Structure-function studies of fibroblast growth factors (FGFS)", "advisor": "Rees, Douglas C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-134402009", "creators": [ { "name": { "family": "Zhu", "given": "Xiaotian" }, "id": "Zhu-Xiaot", "display_name": "Zhu, Xiaotian" } ], "advisors": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "advisor", "display_name": "Rees, Douglas C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d0f2-e676", "abstract": "The fibroblast growth factor (FGF) family exhibits mitogenic, chemotactic and\r\nangiogenic activity in a variety of cell types. The first three-dimensional structures of\r\ntwo members of the FGF family, bovine acidic FGF (aFGF) and human basic FGF\r\n(bFGF), have been crystallographically determined by multiple isomorphous\r\nreplacement (MIR), and refined to 2.7 \u00c5 and 1.9 \u00c5 respectively. The structures of\r\nboth aFGF and bFGF consist of twelve antiparallel \u03b2 strands which are arranged in a\r\nfolding pattern with approximate three-fold internal symmetry. A striking feature of\r\nthe FGF structures is the overall similarity to the structures of soybean trypsin\r\ninhibitor and interleukins-1\u03b1 and 1\u03b2, in spite of the low sequence homology between\r\nthese proteins.
\r\n\r\nFGF stimulates cellular proliferation and differentiation through the interactions\r\nwith both the cell surface FGF receptor and heparin. In the FGF structures, the two\r\nputative receptor binding sites are located on different sides of FGF. Also, a region\r\nrich in positively charged amino acids that is likely involved in heparin binding has\r\nbeen found in the FGF structures. It is further shown that the putative heparin and\r\nreceptor binding regions occupy distinct locations on the protein surface.
\r\n\r\nBecause heparin is required for FGF binding to its receptor, the interactions\r\nbetween FGF and sucrose octasulfate, a heparin analog, have been studied. The\r\ncrystal structure of the complex between aFGF and sucrose octasulfate has been\r\ndetermined to 2.7 \u00c5 resolution by a combination of MIR and molecular replacement\r\nmethods. Sucrose octasulfate binds to the aFGF positive patch mentioned above as a\r\npotential heparin binding site. Based on the structure of aFGF and sucrose octasulfate complex, a possible FGF receptor binding mechanism in the presence of heparin is\r\nproposed.
\r\n\r\nOther crystallographic studies of FGF include the structural determination of the\r\ntwo FGF mutants; the complex of aFGF and 1,3,6-naphthalene trisulfonate, a close\r\nanalog of the FGF inhibitor suramin; and the bFGF-copper complex.
\r\n" }, { "name": "Baker, Shenda Mary", "degree": "PhD", "year": "1992", "title": "Scanning Tunneling Microscopy and Spectroscopy of Silicon and Carbon Surfaces", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09012011-151648229", "creators": [ { "name": { "family": "Baker", "given": "Shenda Mary" }, "id": "Baker-Shenda-Mary", "orcid": "0000-0002-9985-473X", "display_name": "Baker, Shenda Mary" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "orcid": "0000-0002-4571-6884", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5JGQ-4X60", "abstract": "Scanning Tunneling Microscopy (STM) investigations and additional surface analyses were performed on carbon and silicon surfaces. A number of anomalies have been observed on highly oriented pyrolytic graphite (HOPG), including large corrugations, distorted images, large range of tip motion and the absence of defects. A mechanism involving direct contact between tip and sample or contact through a contamination layer to provide an additional conduction pathway is proposed. This model of point-contact imaging provides an explanation for added stability of the STM system, a mechanism for producing multiple tips or sliding graphite planes and an explanation for the observed anomalies. These observations indicate that the use of HOPG for testing and calibration of STM instrumentation may be misleading. Designs for the atmospheric STM used in this study are also presented.
\r\n\r\nThe conditions necessary for preparing a dean silicon(111) (7x7) surface are discussed. The design and analysis of heaters necessary to prepare the silicon reconstructed surface at ultrahigh vacuum (UHV) are described. Results from both radiatively and resistively heated samples are shown in addition to a comparision of topographic and barrier height images of the boron (\u221a3 x\u221a3) reconstructed surfaces. A spectroscopic distinction between sites of boron, silicon or contaminants is demonstrated.
\r\n\r\nA synthetic boron-doped diamond was examined by a number of analytical techniques in order to determine its composition and surface morphology. Current-voltage spectroscopy taken with the STM indicates that the diamond Fermi level can be pinned in atmospheric conditions. In ultrahigh vacuum, band bending is observed, but the strength of the electric field experienced by the diamond semiconductor is less than expected; introduction of surface charges is shown to account for the field screening.
\r\n\r\nPresentation of an STM study of a protein-antibody complex on a gold surface illustrates the requirements for and difficulties of imaging large biomolecules. A flat, conducting substrate and sample stability on the surface\r\nare shown and discussed. Molecular manipulation by the STM tip is also presented. Although routine imaging of large adsorbates on surfaces is not yet possible, this study presents the obstacles and the potential afforded by the STM in attaining this goal.
\r\n" }, { "name": "Bauer, John Edward", "degree": "PhD", "year": "1992", "title": "Hydrodynamic interactions in polymer dynamics", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202007-145157", "creators": [ { "name": { "family": "Bauer", "given": "John Edward" }, "id": "Bauer-John-Edward", "display_name": "Bauer, John Edward" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/W1HN-XC85", "abstract": "A modification to the traditional bead-spring model of polymers is proposed, which properly accounts for the full hydrodynamic interactions between the beads. The new model uses the Stokesian dynamics simulation technique to calculate far-field, many-body effects as well as near-field lubrication and excluded-volume effects. No preaveraging of the interactions is required. In addition to the xF, \"spring\" contribution to the stress, the Stokesian dynamics model calculates hydrodynamic and direct Brownian contributions to the stress.
\r\n\r\nOrientations and stresses obtained from the Stokesian dynamics dumbbell were compared to predictions of the Rouse dumbbell (no hydrodynamic interaction) and the Zimm dumbbell (Rotne-Prager hydrodynamic interaction). Infinite-dilution behaviors were examined in steady, simple shear and oscillatory shear flows. In steady shear the Stokesian dynamics model provides no improvement over the Zimm model. Both give qualitatively similar results for shear and normal stresses. The hydrodynamic stress is constant and equal to the Einstein viscosity contribution from each bead. The Brownian stress is negligible. The analysis reveals how hydrodynamic interaction causes shear thinning. The interaction between the beads tilts the dumbbell towards the shear axis, reducing the xF contribution to the shear stress. The oscillatory-shear results are similar to the steady-shear results, except that the hydrodynamic stress results in a non-zero high-frequency viscosity. Hydrodynamic and Brownian stresses will provide greater contributions to the rheology of multibead chains, in which many-body effects are more important. This is true of both steady shear and oscillatory shear.
\r\n\r\nSimulations of non-dilute suspensions of Stokesian dynamics dumbbells were compared with results for suspensions of spheres at the same volume fractions. The xF stress reaches a maximum at a bead volume fraction of 0.15, above which hydrodynamic forces dominate the solution rheology. The interparticle forces have little effect on the magnitudes of the hydrodynamic and Brownian stresses. The interparticle forces become very dependent upon initial configuration at high volume fractions. It is hypothesized that there exists a critical volume fraction, above which the polymer distribution function will always be dependent upon the initial configuration and the shear history.
" }, { "name": "Chan, Chak Keung", "degree": "PhD", "year": "1992", "title": "Studies of Levitated Single Droplets", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07232007-131610", "creators": [ { "name": { "family": "Chan", "given": "Chak Keung" }, "id": "Chan-Chak-Keung", "orcid": "0000-0001-9687-8771", "display_name": "Chan, Chak Keung" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7q3j-q875", "abstract": "The electrodynamic balance is a very unique and versatile device to study single particles. In-situ measurements of particles in a well characterized and controlled environment are possible. Supersaturated solutions can also be studied. In this research, its applications in studying light scattering, water activities and evaporation kinetics of single droplets are demonstrated. In particular, we studied the elastic and Raman scattering of an evaporating NaNO3 droplet. Different types of size dependent optical resonance structures were identified. The strongest Raman signal received was due to internal resonance of the excitation beam, giving similar enhancements to all Raman emissions. The intensity ratio of Raman nitrate to Raman water peaks can be used as a probe to semi-quantitatively characterize the droplet compositions.\r\n\r\nWater activities of mixed NH4NO3/(NH4)2SO4 aqueous solutions were also studied using the Spherical Void Electrodynamic Levitator. The compositional water activity data were used to evaluate the performance of three commonly used mixed electrolyte models: the Zdanovskii-Strokes-Robinson model, the Kusik and Meissner model, and the Pitzer model. They all predict droplet concentrations in mass fractions to a few percents error within the range where water activity data of single electrolytes are available. Evaporation of a few ceramic precursor solution droplets were investigated. While some precursor solutions crystallized, some others formed gels. Gel formation hindered further evaporation of water and the droplets exhibited a sharp decrease in evaporation rates. An approach to study rapid evaporation of droplets in the time scales of a few seconds was also demonstrated." }, { "name": "Choi, Moon Kyu", "degree": "PhD", "year": "1992", "title": "Particle Shape Effects on Gas-Solid Reactions", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07232007-152302", "creators": [ { "name": { "family": "Choi", "given": "Moon Kyu" }, "id": "Choi-Moon-Kyu", "display_name": "Choi, Moon Kyu" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/kg6r-ft80", "abstract": "A theoretical study of the reaction of nonspherical particles is carried out in the shrinking core regime to determine the effect of particle shape on total reaction rate, particle temperature, and to characterize the evolution of shape with consumption of particle. This problem involves the solution of the external diffusion and heat conduction equations with the reaction entering as a boundary condition over the particle surface. Firstly, the problem is treated isothermally by a domain perturbation technique to give analytical results for a slightly nonspherical particle and by the boundary integral technique for spheroids of arbitrary aspect ratio. Secondly, the nonisothermal problem is solved to give the pseudosteady and dynamic behaviors of nonspherical particles taking char combustion as an example. For the dynamic problem the diffusion and heat conduction in the gas phase are assumed to be at pseudosteady state with respect to the evolving particle temperature and particle size and shape. Lastly, the effect of surface roughness on the gas-solid reaction is similarly examined by representing the particle surface as a series in Legendre polynomials superimposed on an underlying spherical surface.
\r\n\r\nFor nonspherical particles of equal volume but varying shape reacting under isothermal or nonisothermal conditions, the total reaction rate increases with the aspect ratio and is approximately equal to that of the sphere of equal surface area, and the local reaction rate increases with the distance from the particle center. The pseudosteady particle temperature under nonisothermal conditions is essentially the same for various spheroidal particles of equal volume. The particle temperature approaches quickly and remains close to its pseudosteady trajectory with conversion. During reaction a particle becomes more and more nonspherical. As for the effect of roughness, from the method of domain perturbation the nth mode decreases if the Damkohler number Q > Qcr = n+1/n-2, and vice versa. For highly irregular particles, too, this criterion applies overall, but they do not have sharp critical values of Q showing mixed behavior in a certain range around Qcr.
" }, { "name": "Chow, Christine S.", "degree": "PhD", "year": "1992", "title": "Transition Metal Complexes as Probes for Higher-Order Structure in RNA", "advisor": "Barton, Jacqueline K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10142011-105722078", "creators": [ { "name": { "family": "Chow", "given": "Christine S." }, "id": "Chow-Christine-S", "display_name": "Chow, Christine S." } ], "advisors": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "advisor", "display_name": "Barton, Jacqueline K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/npv2-kv27", "abstract": "A series of transition metal complexes were employed to examine higher-order structure in ribonucleic acids. Our results indicate that the complexes Ru(phen)_3^(2+), Ru(TMP)_3^(2+), Rh(TMP)_3^(3+), Rh(phen)_2phi^(3+), Rh(phi)_2bpy^(3+), and Rh(DIP)_3^(3+) (phen = 1,10-phenanthroline; TMP = 3,4,7,8,-tetramethy1-1,10-phenanthroline; phi = 9,10- phenanthrenequinone diimine; bpy = bipyridyl; DIP = 4,7-dipheny1-1,10-phenanthroline) have different affinities for tRNA and bind RNA by several different modes of interaction, as shown through a variety of biophysical analyses. These differences in binding have been attributed to the different shapes of the metal complexes. Photolysis of the metal complexes promotes cleavage of native, structured RNA at diverse and novel sites with comparable efficiency and analogous product formation as found with cleavage of double-stranded DNA. As on DNA, RNA strand scission promoted by the complexes of rhodium(III) occurs through an oxidative pathway with the sugar moiety as the target. Reactions with the complexes of ruthenium(II) are consistent with mediation by singlet oxygen with the nucleic acid base as the target. The site selectivity associated with cleavage appears to be based upon the different binding properties and therefore the molecular shapes of the complexes. Ru(TMP)_3^(3+) cleaves at a subset of solvent accessible sites cleaved by Ru(phen)_3^(2+). Different sites of cleavage on tRNA are apparent with the rhodium complexes, Rh(phen)_2phi^(3+), Rh(phi)_2bpy^(3+), and Rh(DIP)_3^(3+), while Rh(TMP)_3^(3+) does not promote strand scission of RNA. In particular, Rh(phen)_2phi^(3+) targets sites of triple-base interaction, D-T\u03a8C loop interactions, and helix-loop junctions in tRNA, where the major groove is open and accessible. Rh(DIP)_3^(3+) targets RNA loop structures and G-U mismatches that occur within an RNA double-helix. These shape-selective probes, which promote strand scission of tRNA at unique sites, have also been applied to probe mutant tRNAs and to delineate the structure of 5S rRNA. This study demonstrates that small molecules can recognize distinct structures along an RNA strand and suggests that these structures may be utilized for specific recognition by proteins." }, { "name": "Cong, Peijun", "degree": "PhD", "year": "1992", "title": "Femtosecond photodissociation dynamics of alkali halides", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-154309", "creators": [ { "name": { "family": "Cong", "given": "Peijun" }, "id": "Cong-P", "display_name": "Cong, Peijun" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w8dq-ee77", "abstract": "Femtosecond transition-state spectroscopy (I. S) is a time-resolved spectroscopic technique by which the real time dynamics of the transition state of a chemical reaction can be studied with femtosecond resolution. This technique has been applied to study a number of chemical reactions. This thesis presents one such system, the photodissociation of alkali halides, and that of NaI in particular.\n\nUpon excitation to the covalent state, the alkali halide molecule will encounter a curve crossing during its way to dissociation. This curve-crossing phenomenon manifests itself in the dynamics of the photodissociation process. Experimentally, wave-packet trapping and leaking that are due to the curve crossing are observed. Taking full advantage of the femtosecond resolution offered by the FTS technique, the wave-packet dephasing dynamics is separated from the population decay. The Landau-Zener coupling-matrix element is also obtained from the time-resolved data, which is in close agreement with previous literature values. Furthermore, the combination of the temporal resolution and the spectral resolution of the FTS methodology allows the wave-packet motion to be monitored at a specific internuclear separation, which covers a wide range of distances. This feature of the FTS technique makes the mapping of reaction trajectories possible. A classical mechanics-based inversion procedure is then developed to obtain the relevant potential- energy curves involved in the photodissociation reaction from the results of such trajectory mapping experiments. The potentials inverted this way are tested by quantum dynamical simulation and compared with those obtained by other workers from different techniques. The long-time behavior of the wave-packet motion after many oscillations is also discussed." }, { "name": "Di Simone, Christopher", "degree": "PhD", "year": "1992", "title": "The Membrane Fusion Activities of Native and Reconstituted Mumps and Sendai Viruses", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-085913260", "creators": [ { "name": { "family": "Di Simone", "given": "Christopher" }, "id": "Di-Simone-Christopher", "display_name": "Di Simone, Christopher" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Strauss", "given": "James H." }, "id": "Strauss-J-H", "role": "member", "display_name": "Strauss, James H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rr73-5d56", "abstract": "The structure and activities of whole and reconstituted Sendai and mumps viruses were examined using a number of physical and biological techniques: electron microscopy, photon correlation spectroscopy, perturbed angular\r\ncorrelation spectroscopy, gel electrophoresis, hemagglutination assays, plaque assays, fluorescence microscopy and fluorescent assays of membrane fusion. The fluorescent probe octadecyl rhodamine (RIB) was found to have a proximal transfer behavior which reduced usage of the probe as a membrane fusion indicator to short time periods. Simple bireactant and mass action kinetic models were sufficent to fit the data provided by the fluorescent assays on viral fusion with cell membranes. The\r\nreconstitution of mumps virus was optimized by using the detergent Triton X-IOO. Reconstituted virus envelopes which were the same size as whole virus and which were active in binding and fusing to cells were produced. The reconstituted Sendai and mumps virus accumulated in the reticuloendothelial system when injected into mice and hamsters, respectively. The kinetics of the membrane fusion activity of mumps with ghost erythrocytes and CV-I cells was measured and analysed. A general rate of reaction of 3 (\u00b11) x 10^9 M^-l sec^-1 was found. The membrane fusion activity of reconstituted Sendai with HL60, U937, Cos, H9\r\nand PBL cell lines was also measured and analyzed. The fusion activity was utilized to deliver plasmids for transfection to the interiors of the HL60 and Cos cells. Luciferase expression was found in the Cos cells but not in the HL60 cells. Loading of plasm ids into the vesicle interiors was enhanced by a factor of ten by complexing the DNA with the positive proteins polylysine, lysozyme and protamine.\r\n" }, { "name": "Donnelly, Robert Edward", "degree": "PhD", "year": "1992", "title": "Modeling and visualizing surfaces", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212009-105855010", "creators": [ { "name": { "family": "Donnelly", "given": "Robert Edward" }, "id": "Donnelly-R-E", "display_name": "Donnelly, Robert Edward" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1d15-vv30", "abstract": "\"Modeling and Visualizing Surfaces\" denotes several developments aimed at increasing our ability to model and understand molecular surfaces. The Generalized London Potential is a new method of modeling potential energy surfaces of reactions. The London Equation assumptions of zero overlap and no three-body interactions are discarded and a more general potential is derived via valence bond theory and careful substitution of two-body terms into three-body energy expressions. Three-body corrections for dispersion energy are also introduced. Using the lowest order forms of overlap and dispersion corrections, a much improved potential energy surface is found for H_3. Input is limited to H_2 potentials and information only about the H_3 saddle point region, the latter determining the two or three parameters used. The predicted surface is shown to be stable with respect to varied input. A straightforward method of extending the method to make use of additional input is discussed. The method is applied to hydrogen abstraction from terminal carbons. The development of a stable model of exchange reactions will greatly increase the complexity of systems which can be studied with the increasingly accurate force fields of molecular modeling techniques by providing the means of handling reactive dynamics at polymer and crystalline surfaces. This introduces the second major theme of modeling and visualizing molecular surfaces.\r\n\r\nCommon to most definitions of a molecule's surface and, in fact, many calculations involving local spherical symmetry is the use of spherical meshes. A method of systematically creating spherical meshes of various sizes is presented. Degrees of freedom built into the mesh design can be optimized for a variety of problems. The meshes are used in calculating molecular surfaces and determining surface area. They are separately optimized for the integration of spherical harmonics and provide lower error for integration of higher angular momentum functions than previous quadratures. Finally, methods of visualizing molecular surfaces that allow real-time manipulation of complex molecules and yield a better understanding of surface properties are presented.\r\n" }, { "name": "Fiala, Brenda L.", "degree": "Masters", "year": "1992", "title": "Ortho-chain-bridged polyacetylene via the ring-opening metathesis polymerization", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032011-105315204", "creators": [ { "name": { "family": "Fiala", "given": "Brenda L." }, "id": "Fiala-B-L", "display_name": "Fiala, Brenda L." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m5rd-gg62", "abstract": "Chain-bridged poly(acetylene) polymers have previously been\r\nsynthesized with meta- and para- linkages to the substituents. In this paper, two ortho-chain-bridged poly(cyclooctatetraene) polymers demonstrate the effects of an enforced cis linkage approximately every fourth carbon-carbon double bond in a poly(acetylene)-like polymer.\r\n" }, { "name": "Giorgi, Maria Rebecca", "degree": "PhD", "year": "1992", "title": "Experimental and theoretical studies of the hydrogen exchange reaction", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:09082011-073645691", "creators": [ { "name": { "family": "Giorgi", "given": "Maria Rebecca" }, "id": "Giorgi-M-R", "display_name": "Giorgi, Maria Rebecca" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m4a8-mm29", "abstract": "This thesis consists of experimental and theoretical efforts to better understand the hydrogen exchange reaction. Colinear quantum mechanical calculations were conducted on the isotopic H + H_2 reaction, using the method of hyperspherical coordinates. Reaction probabilities and rate constants have been obtained for thirteen isotopic hydrogenic systems, and the results compared to those of conventional transition state theory and transition state theory with quantum corrections. The validity of the conservation of vibrational energy (CVE) and the vibrationally adiabatic (VA) approximations were tested. It was found that the VA approximation gives fairly accurate rate constants, although it is inadequate at predicting low temperature isotope effects. On the other hand, conventional transition state theory predicts isotope effects accurately, except in the cases where tunnelling is a major effect, such as the H_3 system.
\r\n\r\nThe second part of the thesis illustrates the technique of vacuum ultraviolet laser induced fluorescence for the state-specific detection of molecular hydrogen. Preliminary investigations of the potential application of the LIF technique to the detection of products of the hydrogen exchange reaction are described.
\r\n" }, { "name": "Gorman, Christopher B.", "degree": "PhD", "year": "1992", "title": "Highly conjugated, substituted polyacetylenes via the ring-opening metathesis polymerization of monosubstituted cyclooctatetraenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312011-085045975", "creators": [ { "name": { "family": "Gorman", "given": "Christopher B." }, "id": "Gorman-C-B", "display_name": "Gorman, Christopher B." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2y3b-8q23", "abstract": "A number of monosubstituted cyclooctatetraenes were polymerized via ring-opening metathesis polymerization, producing derivatives of polyacetylene that were highly conjugated. Most of these polymers were soluble in the nascent, high-cis form, and some remained soluble upon isomerization to the trans form. The polymers had a high molecular weight (as determined by gel permeation\r\nchromatography) and were composed of polyacetylene backbones (as determined by Raman spectroscopy).\r\n\r\nNot all of the polymers were completely soluble after isomerization to the trans form. Observations relating the steric bulk of the side group with solubility\r\nbehavior indicate a tradeoff between solubility and conjugation. Structural variation permitted the synthesis of very highly conjugated, yet soluble polyacetylenes. For example, trans-poly-s-butyICOT, had a low-energy optical\r\nabsorption (560 nm in tetrahydrofuran, 586 nm in CS_2) corresponding to extended conjugation. The polymer was formed as an amorphous film, yet it had a conductivity after iodine doping of 0.03 S/cm. THG measurements at 1064 nm gave I \u03c7 (3) I = 2 \u00b1 1 x 10^(-11) esu for polytrimethylsilylCOT. Activation parameters for cis/trans isomerization of trans-poly-s-butyICOT in solution were\r\nobtained. NMR spectroscopy revealed that two isomers exist in the so-called \"trans\" form, suggesting the existence of cis/trans and trans/trans diads in the polymer. The trisubstituted olefin at which the side-group is attached can isomerize between the cis and the trans forms with a very low barrier (\u0394G\u2021 =18.9\u00b1 0.4 kcal/mol was measured at 50\u00b0C by magnetization transfer in benzene).\r\n\r\nBoth semi-empirical (AM1) and empirical (MM2) calculations on model compounds were used to provide a model relating side group sterics with twisting in the polymer main chain. Molecular dynamics was used to probe the magnitude of motion in the polymer main chain. AMI heat-of-formation\r\ncalculations were used to explore the cis/trans preference of a trisubstituted double bond in a polyene chain.\r\n\r\nPolyacetylenes bearing chiral side groups were synthesized and explored. Strong Cotton effects were observed for the backbone \u03c0 \u2192 \u03c0* transition. The data suggest that the side group geometrically perturbs the main chain, possibly\r\ntwisting it in predominantly one screw sense.\r\n" }, { "name": "Guo, Yuejin", "degree": "PhD", "year": "1992", "title": "I. Molecular simulations of buckyball fullerenes. II. Quantum chemistry studies on high-T_c superconductors.", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282009-111805575", "creators": [ { "name": { "family": "Guo", "given": "Yuejin" }, "id": "Guo-Y", "display_name": "Guo, Yuejin" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jvvc-ry41", "abstract": "Part I. In order to interpret and predict the unusual chemical and physical properties of the C_(60) and related fullerenes, fullerites, and molecular/solid state derivatives, we started with the graphite force field (GraFF) developed for sp^2 carbon centers (based on fitting experimental lattice parameters, elastic constants, phonon frequencies for graphite and alkali-intercalated graphite), and successfully predicted vibrational frequencies, fullerite and alkali-doped fullerite crystal structure, density, heat of sublimation, and compressibility, etc., for C_(60), C_(70) and their derivatives. We also developed a highly accurate force field for C_(60) in excellent agreement with all 14 experimental frequencies within abs error 3.0 cm^(-1).\r\n\r\nPart II. We have applied ab initio electronic methods (GVB and CI) to various clusters representing La_2CUO_4, Nd_2CuO_4, YBa_2Cu_3O_7, and Bi and Tl containing high-Tc materials to study their basic electronic structure and magnetic interaction. Particularly, we develop the GVB superexchange CI (GVB - X - CI) method to study the superexchange coupling interaction. Using this method, we can calculate the J_(dd) from the first principle at about the same accuracy as experiment.\r\n\r\nOur results indicate that the superconductivity in Cu-0 plane of these cuprates arise from a essentially magnetically induced interaction, that is, (i) all Cu have a Cu^(II) d^9 oxidation state with one unpaired spin that is coupled antiferromagnetically to the spins of adjacent Cu^(II) sites; (ii) reduction below the cupric Cu^(II) state leads to Cu^I d^(10) sites with a highly mobile Cu(3d) electron, and these extra electrons hop from site to site (while the oxygen remains in the O^(2-) state). The hopping of these extra electrons causes the flipping of the local spin moment of the antiferromagnetic background; (iii) oxidation beyond the cupric Cu^(II) state leads not to Cu^(III) but rather to oxidized oxygen atoms with an highly mobile Op hole, which is ferromagnetically coupled to the adjacent Cu^(II) d electrons despite the fact that this is opposed by the direct dd exchange. This coupling induces an attractive interaction between conduction electrons that is responsible for the superconductivity\r\n" }, { "name": "Haney, Susan Elaine", "degree": "Masters", "year": "1992", "title": "Investigation of low-valent ruthenium aquo complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032011-090148072", "creators": [ { "name": { "family": "Haney", "given": "Susan Elaine" }, "id": "Haney-S-E", "display_name": "Haney, Susan Elaine" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bd27-j183", "abstract": "The work presented in this thesis investigates the synthesis of low oxidation state coordination complexes of ruthenium incorporating the anionic ligand, [CpCo(P(O)(OMe)_2)_3]-,(L_(OMe)). Several routes to RuL_(OMe)(H_2O)_3^+ are outlined. These routes produced two major products, possibly related by acid-base chemistry.
\r\n\r\nA new dimeric ruthenium aquo species with the proposed structure [Ru(III)L_(OMe)(H_2O)(\u00b5-OH)_2OTs_2 was isolated. This complex does not provide a straightforward route to the target monomeric oxo compounds, but could conceivably provide a entry into synthesis of ruthenium dimers containing arnines and other ligands.
\r\n\r\nFinally, a new route to [Ru(IV)(H_20)(\u00b5-O)]_2OTf_2 was discovered which is more convenient and is higher yielding than the previously published procedure.
" }, { "name": "Johnson, Lynda K.", "degree": "PhD", "year": "1992", "title": "Methods for the Synthesis of Tungsten Alkylidenes: Ring-Opening of Cyclopropenes and Alkylidene Transfer from Phosphoranes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-105236506", "creators": [ { "name": { "family": "Johnson", "given": "Lynda K." }, "id": "Johnson-Lynda-K", "display_name": "Johnson, Lynda K." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/scx7-0w89", "abstract": "In the research reported in this thesis, two methods for synthesizing alkylidene complexes were investigated: (1) ring-opening of cyclopropenes to give vinyl alkylidene complexes and (2) alkylidene transfer from phosphorus ylides to metal centers. Tungsten(IV) imido precursors of the form WX_2(NAr)L_n (X = Cl or OR; Ar = Ph, 2,6-C_6H_3-Me_2, 2,6-C_6H_3-(i-PR)_2, L_n = PR3, P(OR)_3 or ether donor ligands) were used throughout the investigation.
\r\n\r\nA brief overview of the syntheses and uses of high-valent alkylidene complexes is given in Chapter 1. The reactions of WCl_2(NAr)(PX_3)_3 (X = R or OR) precursors with 3,3-diphenylcyclopropene and 4,8-dioxaspiro[2.5]oct-1-ene are reported in Chapter 2. \u03b7^2-Cyclopropene complexes [W(\u03b72-cyclopropene)Cl_2(NAr)(PX_3)_2] were synthesized from precursors containing the smaller imido ligands; increasing the steric bulk of the imido ligand favored the ring-opening of the cyclopropenes to yield the vinyl alkylidene compounds [W(=CH-CH=CR'_2)Cl_2(NAr)(PX_3)_2]. Conversion of thermally stable \u03b7^2-cyclopropene complexes to give the corresponding vinyl alkylidene compounds was observed upon photolysis or addition of catalytic amounts of H_gCl_2.
\r\n\r\n\r\nThe transfer of alkylidenes from Ph_3P=CHAr' and Ph_3P=CH-CH=CMe_2 to WCI_2(NPh)(PMePh_2)_3 to give W(=CHR')CI_2(NPh)(PMePh_2)_2 is reported in the first half of Chapter 3, and the effects of varying the solvent, the ylides, and the tungsten precursors are discussed. The remainder of Chapter 3 deals with the in situ reduction and trapping of WCl_2(NAr)[OCMe(CF3_ 3) _ 2] _ 2(THF) precursors by Ph_3P=CHAr' to give W(=CHAr')(NAr)[OCMe(CF_3)_2]_2(PPh_3). The use of the chelating o-methoxybenzylidene was especially effective here, as coordination by the o-methoxy group greatly aided the transfer reaction and, in addition, stabilized the resulting product.
\r\n\r\nChapter 4 documents initial studies involving the reactions of WCI_2(NAr)(PX_3) _3 precursors with exo-5,6-dimethoxymethyl-7-oxanorbornene. For reactions involving tungsten precursors with the smaller imido ligands, fonnation of \u03b72-olefin complexes W[\u03b7_2-(7-oxanorbomene]Cl2(NAr)(PX3h was observed. Oxygen abstraction to give 5,6- dimethoxymethylcyclohexadiene occurred upon reaction of this olefin with WCl_2[N-2,6-C_6H_3-(i-Pr) _2] [P(OMe) _3] _3.
\r\n" }, { "name": "Kim, Yong Pyo", "degree": "PhD", "year": "1992", "title": "Simulation of multicomponent aerosol dynamics", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08062007-150332", "creators": [ { "name": { "family": "Kim", "given": "Yong Pyo" }, "id": "Kim-Y-P", "display_name": "Kim, Yong Pyo" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Okuyama", "given": "Kikuo" }, "id": "Okuyama-K", "role": "member", "display_name": "Okuyama, Kikuo" } ], "option_major": [ "chemeng" ], "doi": "10.7907/SE1X-K706", "abstract": "Chemical composition and, therefore, several physical properties, such as refractive index or density, of an aerosol system may be distributed in one particle size. The effect of these particles of the same size but different properties, so-called mixed particles, on aerosol dynamics can be important. Several aspects of the number-property distribution; effect on aerosol dynamics and importance, definition, state of the art of the measurement technique, available data, and numerical schemes are discussed and further research directions are discussed.\r\n\r\nThe moving sectional method is extended to simulate multicomponent aerosol dynamics resulting from condensation/evaporation processes. This method uses a Lagrangian approach in which section boundaries and component masses in a section vary according to the characteristics of condensation/evaporation rates while conserving number concentration in a section throughout the simulation. Simulation of model problems for which new analytical solutions have been obtained shows excellent agreement with the analytical solutions. Limitations and applicability of the sectional method are discussed.\r\n\r\nA technique for direct numerical solution of the multicomponent aerosol general dynamic equation is developed and tested. The method obtains the aerosol size-composition distribution without the need to make any a priori assumptions about the nature of the distribution. Numerical solutions are compared with analytical solutions for model problems of pure condensation/evaporation, pure coagulation, and simultaneous condensation and coagulation. The advantages, applicability, and the limitations of the approach are discussed.\r\n\r\nAn analysis of the tandem differential mobility analyzer (TDMA) is proposed in which the conditioner between the two DMAs is simulated by the multicomponent aerosol general dynamic equation (GDE). The use of the TDMA to separate an externally mixed aerosol is illustrated by simulating the data of Liu et al. (1978).\r\n\r\nNumerical issues in grid-based photochemical air quality models are reviewed. Numerical schemes for advection and chemical kinetics in gas-phase and for dynamics in aerosol-phase are compared.\r\n\r\nFinally, a numerical code is developed based on direct numerical solution of the multicomponent aerosol general dynamic equation." }, { "name": "Kumar, Amit", "degree": "PhD", "year": "1992", "title": "Charge transfer studies of semiconductor interfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:08252011-134056337", "creators": [ { "name": { "family": "Kumar", "given": "Amit" }, "id": "Kumar-A", "display_name": "Kumar, Amit" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3s37-cw77", "abstract": "For all semiconductors (n-Si, p-Si, n-GaAs, n-InP, a-Si:H), the spectral response of liquids junctions, in the short wavelength region (200-600 nm), showed higher quantum\r\nyields than metal junctions. This general trend was independent of redox species, solvent, supporting electrolyte, and metal overlayer. This technique was also used to distinguish between Schottky barrier behavior from electrocatalytic behavior of metal overlayers.\r\n\r\nStudies of n-Si photoelectrodes in aqueous and non-aqueous electrolytes have been conducted. For all n-Si/CH_3OH-dimethylferrocne^(+/O)(Me_2Fc^(+/O)) cells, the forward bias\r\ndark currents,the open circuit voltage (V_(oc)), and temperature dependence of V_(oc) were independent redox species concentrations. All n-Si photoanodes (naked and coated with discontinuous metal overlayers) were found to be unstable in aqueous electrolytes.\r\n\r\nNovel metal/insulator/semiconductor devices have been fabricated through the anodic growth of the insulator layer in a methanol based electrolyte. These devices do not\r\nsuffer from Fermi level pining restrictions, and some exhibit electronic properties limited by minority carrier transport.\r\n\r\nA theoretical framework has been formulated to describe the behavior of photoelectrolysis cells, and experiments at n-SrTiO3/5.0 M KOH(aq)/Pt junctions have been conducted. The data exhibits a photocurrent threshold in the short circuit electrolysis current at 0.02-0.03 mW/cm^2 of 325 nm illumination, which is consistent with the theoretical framework.\r\n\r\nThe behavior of Si/CH_3OH-Me_2Fc^(+/O) junctions has been investigated under high injection conditions. With a structure having n+ diffused back contacts, V_(oc)s of 626+5 mV were obtained at short circuit photocurrent densities of 20 mA/cm^2. The diode quality factor and reverse saturation current were 1.8+0.1 and (2.6+1.5)x 10^(-8) A/cm^2, respectively. These data are consistent with recombination dominated by the base and back contact regions, and not at the Si/CH_3OH interface.\r\n" }, { "name": "Kurur, Narayanan Damodaran", "degree": "PhD", "year": "1992", "title": "I. Quantum-mechanical chemical exchange. II. NMR of semiconductors", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09022011-090934651", "creators": [ { "name": { "family": "Kurur", "given": "Narayanan Damodaran" }, "id": "Kurur-N-D", "display_name": "Kurur, Narayanan Damodaran" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0TQK-G720", "abstract": "Part I. Quantum-Mechanical Chemical Exchange:
\r\n\r\nThe requirement that the total wavefunction of a system be antisymmetric to the exchange of identical fermions manifests itself as a scalar coupling between the spin angular momenta. In a class of transition metal trihydrides, this effect is observed as multiplet structure in the liquid state NMR spectrum due to proton tunnelling. Numerical fits to the temperature dependence of these couplings are described as the ensemble averaged tunnel splitting over thermally occupied rovibrational states. The accepted concept of stochastic average of the coupling is questioned on theoretical grounds and an alternative prescription given which differs significantly in its numerical predictions. It is also shown how the fluctuations of the tunnel splitting due to dissipative coupling to the lattice contribute to the chemical rate processes that incoherently exchange nuclei between different sites and the coherent exchange effect. A master equation procedure for evaluating such rates numerically is presented.
\r\n\r\nPart II. NMR of Semiconductors:
\r\n\r\nNMR is an inherently low-sensitive technique. Moreover, unless special procedures are employed the structural information obtainable from an NMR line in the solid-state is also limited. Both these problems are addressed here. A method is proposed for the high resolution solid-state NMR of nuclei around paramagnetic defects which uses multiple pulse techniques to selectively average spin couplings and extract structural information. It is shown by numerical simulations how the method could resolve a long-standing controversy on the assignment of hyperfine tensors to silicon sites around a phosphorous dopant. Experimental results on a novel time-domain optical nuclear magnetic resonance method are obtained on gallium arsenide. Comparison with an earlier continuous-wave variant of the technique show improved absolute sensitivity and relative sensitivity to low-abundance sites near an optically relevant defect.
\r\n" }, { "name": "Li, Zhuyin", "degree": "PhD", "year": "1992", "title": "Proton pumping in cytochrome c oxidase: the possible role of Cu_A in redox linkage", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262011-094449362", "creators": [ { "name": { "family": "Li", "given": "Zhuyin" }, "id": "Li-Zhuyin", "display_name": "Li, Zhuyin" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/eecg-cn69", "abstract": "Cytochrome c oxidase is the terminal enzyme of cellular\r\nrespiration. It catalyzes the reduction of dioxygen to water by ferrocytochrome c. In addition, cytochrome c oxidase is an electrogenic proton pump capable of transporting up to four protons against the proton electrochemical gradient.
\r\n\r\nAn extensive and accurate analysis of the Cu, Fe, Zn and Mg contents in bovine heart cytochrome c oxidase was carried out by direct current plasma atomic emission spectrophotometer. The results confirmed a stoichiometry of 5Cu/4Fe/2Zn/2Mg per dimer. Seven enzyme preparations treated by different methods were analyzed to examine the nature of Cu_X. The results obtained suggested that Cux may reside in subunit III and plays a structural role in enzyme\r\ndimerization.
\r\n\r\npHMB-modification of cytochrome c oxidase and heat-treatment of the oxidase have previously been shown to have a profound effect on the dioxygen reduction and proton pumping activities of the enzyme. The intrinsic reduction potentials and the midpoint reduction potential of the \"Cu_A\" site in both of these modified oxidases have been\r\nmeasured under various conditions in order to clarify the\r\nintramolecular electron transfer pathways in these systems. The study reveals that the Cu_A intrinsic reduction potential decreases by almost 150 mV upon pHMB modification, whereas it increases by 100 mV upon heat treatment. In addition, the redox interactions between Cu_A\r\nand the remaining metal centers are perturbed upon Cu_A modification.
\r\n\r\nDCCD-modification and subunit III-depletion of cytochrome c oxidase decreased the observed H+/e- stoichiometry in proton pumping to 0.5 during enzyme turnover under coupled conditions. The effects of these treatments on the optical and EPR spectra, and\r\nthe reduction potentials of Cu_A. have been examined. DCCD-modification distorts the Cu_A ligand structure, while subunit III-depletion destabilizes the Cu_A structure leading ultimately to the displacement of one of the cysteine ligands. The intrinsic reduction potential of Cu_A is not significantly altered in the two modified\r\noxidases. However, the redox interaction between Cu_A and\r\ncytochrome a becomes dramatically different: in the absence of subunit III, this redox interaction is essentially eliminated, whereas in the DCCD-modified enzyme, it becomes highly anticooperative. The results of this study implicate Cu_A as a component of the proton pumping machinery of the enzyme, and suggest that subunit III plays\r\nan important allosteric role in communicating the redox changes at the Cu_A site to the proton translocating element(s) of the proton pumping machinery during turnover.
\r\n\r\nThe strong magnetic interaction between Fe_(a3) and Cu_B in the resting form of cytochrome c oxidase is thought to be mediated by a bridging ligand. The identity of this bridging ligand has been proposed to be an imidazole from a histidine residue, cysteine thiolate sulphur, an oxygen from hydroxide or \u03bc-oxo anions. However, recent EXAFS\r\nexperiments on a sample of oxidase isolated and purified in Cl^--free buffer solutions revealed no (S, Cl) scattering in Fe EXAFS of the resting oxidase, thus suggesting Cl^-. To confirm this finding, we have dialyzed samples of reduced oxidase against Cl^--free buffer in the\r\npresence of chelex resin, and have examined the spectroscopic and ligand-binding properties of the reoxidized enzyme. The dialyzed/oxygenated oxidase exhibits rapid and homogeneous binding kinetics. Upon re-addition of Cl^- to the dialyzed/oxygenated oxidase, the CN^-binding slows down and becomes heterogeneous. The anions F^-, Cl^-and Br^- all exhibit notable effects on the Soret absorption of the dialyzed/oxygenated oxidase. Similarly the EPR spectra of CI^- or Br^-substituted oxidase are similar to native oxidase. Both F^--substituted oxidase and dialyzed / oxygenated oxidase exhibit complex EPR spectra. On the basis of these experiments, we conclude that the bridging ligand must be Cl^- in resting cytochrome c oxidase.
\r\n" }, { "name": "Licari, Peter", "degree": "PhD", "year": "1992", "title": "An engineering analysis of the insect cell - baculovirus expression system", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08072007-103816", "creators": [ { "name": { "family": "Licari", "given": "Peter" }, "id": "Licari-P", "display_name": "Licari, Peter" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/k2av-2h76", "abstract": "Baculovirus expression vectors are routinely used for the expression of heterologous proteins, affording the user relatively high product yields and a variety of post-translational modifications. The insect cell-baculovirus system utilizing the Autographa californica multicapsid nuclear polyhedrosis virus has been studied here with regard to product yield and product quality. Product yield was demonstrated to be affected by both the time of infection and the multiplicity of infection. Through experimental results and population modeling of infected cultures, the product yield was maximized by infecting in the early-exponential growth phase with a low multiplicity of infection.
\r\n\r\nThe importance of intracellular protein degradation on cloned protein yield and product quality in this system was also studied. Intracellular degradation was observed throughout the infection; however, when compared to the synthesis rate, degradation was found to have an insignificant effect on system productivity. A population of discrete [beta]-galactosidase fragments was observed in protein-radiolabelling experiments. The synthesis rate of these fragments compared to the degradation rate of the complete [beta]-galactosidase molecule suggested that they are probably not a result of intracellular protein degradation. Although proteolytic origin cannot be excluded, transcript hybridization analysis suggests that premature transcript termination may be the cause. It is believed that after premature transcription termination, the transcript is translated to yield the fragmented polypeptides. Other evidence using different recombinant viruses, all expressing related forms of [beta]-galactosidase, are consistent with the hypothesis of premature transcription termination. Although the synthesis of [beta]-galactosidase was most thoroughly studied, transcript heterogeneity and protein heterogeneity were observed for a variety of recombinant viruses with the heterologous gene under the control of the polyhedrin promoter
.\r\n\r\nWhen expressing a heterologous glycoprotein, the insect cell-baculovirus expression system produces a heterogeneous population of glycoforms different from those of authentic mammalian hosts. Four different cell lines that can be used as hosts for baculovirus expression were analyzed for the existence of endogenous exoglycosidases. Cells derived from Spodoptera frugiperda, Trichoplusia ni, Bombyx mori, and Malacosoma disstria contained N-acetyl-[beta]-glucosaminidase, -acetyl-[beta]-galactosaminidase, [beta]-galactosidase, and sialidase activities. These endogenous activities were also observed in the medium from uninfected and wild-type baculovirus-infected cultures. Lectin analysis of insect cell glycoproteins indicates that oligosaccharides formed in these hosts are susceptible to the exoglycosidase activities identified.
\r\n\r\nOn the basis of reports that insect cells lack terminal glycosyltransferases, mammalian [beta]1,4-galactosyltransferase and [alpha]2,6-sialyltransferase were cloned into baculovirus expression vectors. The degree of altered glycosylation resulting from the expression of these enzymes in insect cells, alone or together, will require more sensitive carbohydrate analysis than that provided by lectins.
\r\n" }, { "name": "Luebke, Kevin J.", "degree": "PhD", "year": "1992", "title": "Sequence specific nonenzymatic ligation of single- and double-stranded DNA by triple helix formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09072011-081106540", "creators": [ { "name": { "family": "Luebke", "given": "Kevin J." }, "id": "Luebke-K-J", "display_name": "Luebke, Kevin J." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/60d2-7x44", "abstract": "Phosphodiesters link the units of chemical information within nucleic acids. The formation of a phosphodiester linkage by condensation of phosphate and hydroxyl termini of DNA requires activation of the phosphate toward\r\nnucleophilic displacement and proper placement of the\r\nhydroxyl for nucleophilic attack on the activated phosphate in competition with water. Sequence information is\r\ntransferred when a nucleic acid template promotes this condensation reaction by the sequence specific formation of a complex in which condensing functionalities are juxtaposed. This thesis describes investigations of the sequence specific formation of phosphodiester linkages by the assembly of triple-helical complexes. In the first part of Chapter I, sequence specific recognition of double\r\nstranded DNA by triple helix formation is reviewed. Structural features of nucleic acid triple helices, the sequence specificity of their formation, and functions\r\nassociated with them are considered in this review. In the second part of Chapter I, literature regarding template-directed formation of phosphodiesters in aqueous solution is reviewed.\r\n\r\nChapter 2 describes investigations of the sequence specific formation of a phosphodiester linkage between pyrimidine oligodeoxyribonucleotides using a double-stranded DNA template to juxtapose their termini in a triple helix. Several approaches to activation of the condensing phosphate were explored. The most effective of these was activation in situ with the condensing agent N\r\n-cyanoimidazole with which condensation yields greater than 80% could be obtained. The reaction was directed by the double stranded template and could be shown to form a 3',5' phosphodiester linkage between the two\r\noligodeoxyribonucleotides. A single mismatch in one of the condensing oligodeoxyribonucleotides at the condensing\r\nterminus resulted in at least a 25 to 60 fold decrease in the rate of the reaction. The relevance of this reaction to the detection of sequences, nucleic acid catalysts, and the evolution of template-directed information transfer is discussed.\r\n\r\nChapter 3 describes the nonenzymatic sequence specific ligation of blunt-ended duplex DNA by triple helix formation. Using a pyrimidine oligodeoxyribonucleotide as a template and N-cyanoimidazole as a condensing agent, a double-stranded plasmid with homopurine tracts at\r\none 3' terminus and one 5' terminus could be covalently circularized In yields exceeding 50%. Ligation on both strands was demonstrated in some of the circularized product. Ligation of duplexes with homopurine tracts at\r\ntheir 3' termini was directed by a pyrimidine\r\noligodeoxyribonucleotide of two segments joined 3' to 3' through an abasic linker, creating a duplex of the sequence type 5'-(purine)_m(pyrimidine)_n-3'. The linkages formed in the ligation reaction were demonstrated to be substrates for a restriction endonuclease, identifying them as phosphodiesters. The sequence specificity of these reactions is not accessible by enzymatic ligation of\r\ndouble-stranded DNA.\r\n" }, { "name": "Lunt, Sharon Ruth", "degree": "PhD", "year": "1992", "title": "Electrochemical, photoluminescence, and surface studies of the passivation of surface recombination processes on chemically treated gallium arsenide surfaces", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:09012011-141930677", "creators": [ { "name": { "family": "Lunt", "given": "Sharon Ruth" }, "id": "Lunt-S-R", "display_name": "Lunt, Sharon Ruth" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x6vc-m765", "abstract": "This thesis describes work that has been done to study the chemical properties of GaAs surfaces relating to recombination processes. A variety of electrochemical, photoluminescence, and surface techniques have been used to study the mechanism an chemistry of the reduction of surface recombination in GaAs exposed to transition metal ions and complexes, and GaAs exposed to sulfur-containing molecules.
\r\n\r\nElectrochemical studies done on polycrystalline n-GaAs/liquid junctions treated with a variety of transition metal ions to study the mechanism of the observed improvement in I-V properties of GaAs(M3^(+))/Se^(-/2-)-KOH photoelectrochemical cells showed that the primary route is electrocatalysis. X-ray photoelectron spectroscopy (XPS) and extended x-ray adsorption fine structure (EXAFS) studies were performed on single crystal GaAs with Co, Ru and Cr ammines in order to determine the surface binding chemistry of the transition metals.
\r\n\r\nSteady state and time resolved and photoluminescence studies were done on GaAs surfaces exposed to sodium sulfide and a variety of organic thiols, alcohols and ammines. Unlike the transition metal ions, these types of complexes are shown to affect the cross section of surface recombination sites as determined by photoluminescence experiments. XPS studies were also done to correlate the observed changes in photoluminescence yield and lifetime with changes in surface chemistry.
\r\n\r\nFinally, some work has been done on an entirely different semiconductor system in order to explore the surface reactivity of a semiconductor surface at a more fundamental level. Several different types of metal dichalcogenides were exposed to strong Lewis acid complexes, and the surface chemistry was followed by XPS. These studies showed that there is a marked difference in the reactivity of metal dichalcogenide surfaces, which can be predicted from the known electronic structure of the conduction bands.
\r\n" }, { "name": "McGrath, Dominic V.", "degree": "PhD", "year": "1992", "title": "The organometallic chemistry of aqueous ruthenium(II) with functionalized olefins: complex formation, isomerization, and metathesis chain transfer", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312011-153706837", "creators": [ { "name": { "family": "McGrath", "given": "Dominic V." }, "id": "McGrath-D-V", "display_name": "McGrath, Dominic V." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cdnv-xe78", "abstract": "The chemistry of aqueous Ru^(II)(H_2O)_6(tos)_2(tos = p-toluene sulfonate)(1) with functionalized olefins has been investigated. Complexes of the type (H_2O)_5Ru^(II)(olefin)(tos)_2 are formed from 1 and monoolefins. Dienes such as diallyl ether and 1,5-hexadiene displace two aquo ligands from 1 to form chelate complexes of the type (H_2O)_4Ru^(II)(olefin)_2(tos)_2. Chelation of oxygen containing functionalities such as alcohols, ethers, and sulfonates has also been observed when the functional group is a specified distance from the olefin. Thus, 3-buten-\r\n1-o1, 3-butenyl methyl ether, and 2-propenesulfonate anion form chelate complexes Ru^(II)(H_2O)_4(\u03b7^1(O): \u03b7^2(C,C')-HOCH_2CH_2CH=CH_2)(tos)_2, Ru^(II)(H_2O)4-( \u03b7^1(O): \u03b7^2(C,C')-CH_3OCH_2CH_2CH=CH_2)(tos)_2, and Ru^(II)(H_2O)_4(\u03b7^1(O): \u03b7^2(C,C')OSO_2CH_2CH=CH_2)(tos), but allyl ethyl ether forms only the olefin complex Ru^(II)(H_2O)_5(\u03b7^2(C,C')-CH_2=CHCH_2OCH_2CH_3)(tos)_2. Carboxylic acid functionalities react irreversibly with 1 to form carboxylate complexes. 3-Pentenoic acid reacts with 1 yielding the bis(olefin)-bis(carboxylate) complex Ru(H_2O)_2(\u03b7^1(O), \u03b7^2-(C,C\u2019)-OCOCH_2CH=CHCH_3)_2 which has been structurally characterized.\r\n\r\nOlefin isomerization of allylic ethers and alcohols is catalyzed by 1 under mild conditions in aqueous solution to yield the corresponding carbonyl compounds. Non-allylic olefins are also isomerized, although homoallylic alcohols\r\nexhibit stability towards isomerization. An exclusive 1,3-hydrogen shift is observed in the 1-catalyzed isomerization of allyl-1,1-d_2 alcohol to propionaldehyde-1,3-d_2 and allyl-1,1-d_2 methyl ether to 1-propenyl-1,3-d_2 methyl ether. The presence of crossover products from the isomerizations of mixtures of (a) allyl-3-^(13)C alcohol and allyl-1,1-d_2 alcohol and (b) allyl-1,1-d_2 methyl ether and allyl ethyl ether demonstrates that the isomerization of both ethers and alcohols occurs via intermolecular hydrogen shifts. A modified metal hydride addition-elimination mechanism involving exclusive Markovnikov addition to the double bond directed by the oxygen functionality of the substrate has been proposed.\r\n\r\nThe acyclic terminal olefins 3-buten-1-ol and methyl acrylate are effective chain transfer agents in the ROMP the 7-oxanorbornene derivative 5,6-exobis(methoxymethyl)-7-oxabicyclo[2.2.1]hept-2-ene by 1, providing the first\r\nexample of acyclic olefin metathesis in this system. Oligomer samples with M_n as low as 2K have been prepared. End groups corresponding to the alkylidene moieties of the chain transfer agents have been identified in the ^1H and ^(13)C NMR of the oligomer mixtures. Connectivity has been established between these end groups and the polymer chain through two-dimensional ^1H NMR. Ring-opened monomer units end capped by the chain transfer agent have been identified by mass spectrometry techniques." }, { "name": "Povsic, Thomas J.", "degree": "PhD", "year": "1992", "title": "Oligonucleotide directed sequence specific recognition and alkylation of double helical DNA by triple helix formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09222011-113738481", "creators": [ { "name": { "family": "Povsic", "given": "Thomas J." }, "id": "Povsic-T-J", "display_name": "Povsic, Thomas J." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/krbx-2z47", "abstract": "Chapter II:\r\nFootprinting of Oligonucleotides on Double Helical\r\nDNA using MPE\u2022Fe(II), DNase I, and Dimethyl Sulfate
\r\n\r\nPyrimidine oligonucleotides can, when equipped with the thymidine-EDTA\u2022 Fe(II) analogue (T*), recognize and subsequently cleave double helical DNA at binding sites>15 base pairs in size. If binding affinities of unmodified\r\noligonucleotides are to be determined under conditions relevant to those in vivo, alternate methods of detecting oligonucleotide-directed triple helix formation are required. The footprinting of short (up to 15 base pairs) triple helical regions on restriction fragment size DNA has been undertaken. Techniques for the determination of oligonucleo tide binding to double helical DNA using MPE\u2022Fe(II), DNase I, and dimethyl sulfate have been\r\ndeveloped. MPE\u2022Fe(II) allows for the determination of binding site size, and has shown that oligonucleo tide binding to DNA is cation concentration, solvent, and oligonucleotide length dependent. DNase I footprinting was\r\nconducted under conditions optimal for DNase I activity (10 mM in each Mg^(+2) and Ca^(+2)), demonstrating that oligonucleotide-directed triplexes are capable of interfering with protein activity at the oligonucleotide binding site under physiological conditions, and that divalent cations can stabilize triple helix formation. Footprinting using dimethyl sulfate reveals that a single guanine 3' to the binding site becomes hyperreactive to methylation upon triplex formation. This suggests that the triplex-duplex junction involves a change in DNA conformation which is largely limited to a single base pair.
\r\n\r\nDMS footprinting reveals that the oligonucleotide CT-15 (T_5(CT)_5) does not bind the terminal 2 base pairs of the binding site in plasmid PDMAG10. DMS footprinting can be used to analyze the binding of oligonucleotides to DNA\r\nunder conditions not amenable to MPE\u2022Fe(II) or DNase I activity, and to assay the kinetics of oligonucleotide binding. DMS and DNase I footprinting techniques were used to assay for the effect of oligonucleotide concentration\r\nand base composition on binding affinity.
\r\n\r\nChapter III:\r\nOligonucleotide-Directed Triple Helix Formation using\r\nOligonucleotides with Increased Binding Affinities
\r\n\r\nThe specificity offered by the triple helix motif might provide a method for the artificial repression of gene expression and viral diseases. Changes in\r\noligonucleotide structure could be used to control oligonucleotide affinity under in vivo conditions, where temporal and spatial intracellular pH (7.0-7.4) and ionic strength are strictly regulated and cannot be altered. Substitution at position 5 of pyrimidines alters the hydrophobic driving force, base stacking, and the electronic complementarity of the Hoogsteen base pairing for triple helix formation. Incorporation of 5-substituted pyrimidines offers a method of modulating binding affinity without changing the hydrogen bonding pattern and sequence specificities of pyrimidine oligonucleotides. Replacement of 2'd eoxycytidine with 5-methyl-2'-deoxycytidine increases the oligonucleotide affinity and extends the pH range for binding. Substitution of 5-bromo-2'deoxyuridine\r\nfor thymidine increases binding affinity. Oligonucleotides constructed with 2'-deoxyuridine show lower binding affinities. Pyrimidine oligonucleotides constructed from 5-iodo-2'-deoxyuridines and 5-ethynyl-2'deoxyuridines display increased binding affinities relative to thymidine, but decreased relative to 5-bromouridine containing Oligonucleotides. Substitution by ethyl, pentyl, pentynyl, 2-phenyl-ethynyl, or fluoro at the 5 position of 2'deoxyuridine or bromo at the 5 position of 2'-deoxycytidine residues results in oligonucleotides with decreased binding affinities for double helical DNA.
\r\n\r\nChapter IV:\r\nEfficient, Base-Specific Alkylation of DNA\r\nusing N-Bromoacetyloligonucleotides
\r\n\r\nThe attachment of a non-specific diffusible cleaving functionality to a DNA binding molecule allows for the elucidation of the structural principles for DNA recognition, a technique termed affinity cleaving. Once these principles have been determined, it becomes possible to design and attach structural domains designed to carry out a desired DNA modification. The development of a thymidine derivative capable of efficient and base specific\r\nDNA modification is reported. N-bromoacetyloligonucleotides are capable of near quantitative double strand modification of double helical DNA at a single guanine position in a manner which produces ends which are ligatable with\r\ncompatible ends produced by conventional restriction enzyme digestion. The products thus produced are capable of transforming bacterial cell lines. \r\nN-bromoacetyloligonucleotides modify double helical DNA with specificities great enough to produce efficient (>90%) chemical cleavage at a single site within a yeast chromosome 340 kbp in size.
\r\n\r\nThe acceleration obtained by tethering a reactive moiety to a DNA binding unit has been estimated. The rate of alkylation of DNA by N-bromoacetyloligonucleotides\r\nand bromoacetamide has been measured. Comparison of these ra tes indicates that an effective molarity of 2-3 M is obtained upon tethering the bromoacetyl moiety to an oligonucleotide to effect triple helix mediated DNA alkylation.
\r\n\r\nThe utility of the bromoacetyl moiety as a reporter group is shown in studies concerning the effect of oligonucleotide length on binding affinity and\r\nthe cooperative interaction between oligonucleotides binding abutting sites is reported.
\r\n\r\n" }, { "name": "Rico, Rudolph J.", "degree": "Masters", "year": "1992", "title": "Quantum-mechanical studies of vanadium oxides", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10042011-094257165", "creators": [ { "name": { "family": "Rico", "given": "Rudolph J." }, "id": "Rico-R-J", "display_name": "Rico, Rudolph J." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2set-6e48", "abstract": "A variety of V-O systems were examined in order to model the catalytic site for VPO-catalyzed conversion of butane to maleic anhydride. All V-O systems examined could be described as a V-O triple bond, with a covalent \u03c3-bond and two \u03c0-bonds, and a bond length of approximately 1.56-1.60 \u00c5. The nature of the \u03c0-bonds varied. In VOCl_4^(3-) and VOCl_(2-), the \u03c0-bonds were both described as donor-acceptors. All other systems displayed one covalent bond and one donor-acceptor bond. Resonance between the two \u03c0-bonds was displayed for four-chloride C_(4v) VOCl_4^(2-/-). Optimized C_(2v) geometries for VOCl_4^(2-/-) appear to be the result of this resonance, in which the wavefunction and geometry represent one resonance state of the overall C_(4v) system, in which one \u03c0 -bond is highly covalent, and the other highly donor-acceptor. The C_(4v) system is lower in energy than the C_(2v) system at all levels of theory (HF, CASSCF, MRCI) except GVB(3/6)-PP. VOCl_2^(0/+) calculations show strong similarities to C_(2v) VOCl_4^(2-/-) in both V-O bond description and geometry, suggesting that these systems\r\ncan be described as C_(2v) VOCl_4^(2-/-) systems without the axial chlorides. VO+ and VOCl_3 results, for which experimental data exists, support the descriptions of geometry and bonding given. V(V) systems display a strong degree of covalent character to the chlorides (as does VO_3 to the bound oxygen molecule), but this effect decreases\r\nsignificantly as the V(3d\u03b4 )-orbitals are occupied. Snap bond calculations indicate that the V(V)-O bond is approximately 28 kcal/mol weaker than the V(lV)-O bond - this may be due to the increased V-C1 interaction in the products of the V(V) bondbreaking.\r\n" }, { "name": "Rodgers, Mary Theresa", "degree": "PhD", "year": "1992", "title": "A theoretical and experimental investigation of the H_3 system", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:09122011-095236680", "creators": [ { "name": { "family": "Rodgers", "given": "Mary Theresa" }, "id": "Rodgers-M-T", "display_name": "Rodgers, Mary Theresa" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ey99-a620", "abstract": "The H_3 system is the simplest triatomic neutral molecular species. It possesses only three electrons and three protons. As a result of its simplicity, the H_3 system has received a great deal of attention in ab initio quantum mechanical as well as experimental studies.
\r\n\r\nThis dissertation consists of two parts. The first part is a theoretical investigation of the H_3 molecular system. Results of the ab initio quantum mechanical calculations for the lowest three electronic potential energy surfaces are given, as well as electronically nonadiabatic coupling elements between these states. The calculated nonadiabatic coupling elements compare well in some regions of configuration space with previous calculations performed on this system. Discrepancies in other regions can be attributed to the method of calculation. In our study these coupling elements were calculated by an ab initio method whereas analytic continuation was used in previous work. Calculation of the nonadiabatic coupling surfaces represents notable progress and will improve the fidelity of dynamics calculations of the H_3 system. All 3-D quantum mechanical theoretical investigations to date invoke the Born-Oppenheimer approximation and neglect nonadiabatic coupling of the nearby states. Although this is justified in many cases, the H_3 system exhibits a conical intersection near which this approximation breaks down. To obtain theoretical estimates of predissociative lifetimes of excited states of the H_3 system, accurate bound state wavefunctions and energies of the excited states of H_3 and accurate differential and integral cross sections in quantum mechanical scattering studies of the H + H_2 system above 2.75 eV, these nonadiabatic terms must be included.
\r\n\r\nThe second part of this dissertation involves the development and characterization of an intense source of trihydrogen molecules. The ultimate goal of this work is to fully characterize the metastable H_3 molecules formed in this beam and to create a source of monoenergetic trihydrogen molecules whose translational energy would be continuously tunable from ~1-12 eV. Once developed, it could be utilized in crossed beam experiments and would enable many reactions to be studied that might not otherwise take place due to low reaction probability. The H_3 molecule in its 2p^2_zA^\u02dd_2 electronic state is 5.85 eV higher and the 2p^2_x,_yE' repulsive ground state is 2.65 eV higher in energy than H + H_2 .^(17-20) Therefore, upon a vertical transition to the ground state, the 2p^2_zA^\u02dd_2 state of H_3 will liberate about 3 eV of electronic energy with the remaining energy being channeled into vibration and rotation of the H + H_2 dissociated system. In a collision with another molecule, this energy could become available for reaction along with some fraction of the translational energy of these molecules (1-12 eV). This species can be expected to exhibit unusual dynamics, in that it may undergo novel chemical reactions as well as unique partitioning of the available energy into electronic, vibrational, rotational and translational energy of the products.
\r\n" }, { "name": "Shannon, Karen Lynn", "degree": "PhD", "year": "1992", "title": "Conformational and mechanistic studies of asparagine-linked glycosylation", "advisor": "Imperiali, Barbara", "url": "https://resolver.caltech.edu/CaltechTHESIS:09082011-144447003", "creators": [ { "name": { "family": "Shannon", "given": "Karen Lynn" }, "id": "Shannon-K-L", "display_name": "Shannon, Karen Lynn" } ], "advisors": [ { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "advisor", "display_name": "Imperiali, Barbara" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/j6dq-0n18", "abstract": "In asparagine-linked glycosylation, a complex carbohydrate is transferred by oligosaccharyl transferase to an asparagine in the consensus triad -Asn-Xaa-Thr/Ser-. The mechanism of this transfer is not fully understood but appears to involve nucleophilic attack by the carboxyamido group of asparagine at the anomeric carbon of the sugar with concomittant displacement of dolichol pyrophosphate. Central to understanding the mechanism of N-glycosylation is ascertaining how the reactivity of a relatively poor nucleophile, the carboxyamido group, can be enhanced.
\r\n\r\nTo increase the amide-nitrogen nucleophilicity, the amide\r\nresonance interaction must be disrupted. The necessity for a\r\nhydroxy amino acid two residues from the asparagine suggests\r\nthat this residue may participate in a hydrogen bonding\r\ninteraction. If the hydroxyl group is hydrogen bonded to the\r\namide oxygen of the asparaginyl side chain, this interaction would increase the pKa of the amide protons through disruption of the amide resonance. Further, a general base could then abstract a proton, thereby increasing the nucleophility of the amide nitrogen.
\r\n\r\nIf such a hydrogen bonding array is crucial to the\r\nmechanism of the transfer, the conformation of the peptidyl\r\nsubstrate must allow for the asparagine and threonine side chains to be in close proximity. If such a hydrogen bonding array is crucial to the mechanism of the transfer, the conformation of the peptidyl substrate must allow for the asparagine and threonine side chains to be in close proximity. If such a hydrogen bonding array is crucial to the mechanism of the transfer, the conformation of the peptidyl substrate must allow for the asparagine and threonine side chains to be in close proximity.
\r\n\r\nA series of tripeptides that satisfy the -Asn-Xaa-Thr/Ser-primary sequence requirement were synthesized and examined as potential acceptors in an oligosaccharyl transferase assay. It was demonstrated that the dominant solution conformation of substrates in glycosylation were Asx-tums. This conformation is stabilized by an interaction between the asparaginyl carboxyamido oxygen and the backbone amide proton of the hydroxy amino acid residue. The Asx-tum is a common structural motif in peptides and, in this case, brings the carboxyamido and hydroxyl groups within hydrogen bonding distance. Using constrained peptidyl analogs, the Asx-tum was demonstrated to be the bioactive conformation in N-glycosylation.
\r\n\r\nFurther, peptidyl analogs were used to probe the mechanism of glycosylation. A mechanism which is consistent with both the conformational and kinetic data obtained in these studies is proposed.
\r\n\r\n" }, { "name": "Shi, Frank Guojun", "degree": "PhD", "year": "1992", "title": "Kinetics of Nucleation and Crystallization", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08142007-132348", "creators": [ { "name": { "family": "Shi", "given": "Frank Guojun" }, "id": "Shi-Frank-Guojun", "display_name": "Shi, Frank Guojun" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Zhao", "given": "Bin" }, "id": "Zhao-Bin", "role": "member", "display_name": "Zhao, Bin" }, { "name": { "family": "Wagner", "given": "Paul E." }, "id": "Wagner-P-E", "role": "member", "display_name": "Wagner, Paul E." }, { "name": { "family": "Johnson", "given": "William Lewis" }, "id": "Johnson-W-L", "role": "member", "display_name": "Johnson, William Lewis" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2xd8-8y76", "abstract": "A link between nucleation models and experimental kinetic measurements has been established as a result of the present studies of the general transient kinetics of nucleation in the barrier region and beyond. Based on the new results on the transient kinetics of nucleation, a theoretical basis for measuring directly the nucleation energy barrier and its temperature dependency is developed, an approach for determining the interfacial atomic transfer mechanism in the nucleation process is presented and some new experimental strategies for conducting nucleation and crystallization kinetic measurements are outlined. A new mathematical approach developed for solving the nucleation kinetic equation in the barrier region and beyond is described. The results are also presented for the nucleation kinetics in some spatially inhomogeneous systems where there are mechanisms for subcritical clusters loss from the system. In addition, a chemical-nucleation model developed for the cluster formation in a chemically reacting system is outlined." }, { "name": "Shin, Jumi Anne", "degree": "PhD", "year": "1992", "title": "Characterization of the DNA Binding Domains of Helix-Turn-Helix Proteins by Affinity Cleaving", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09092011-135058263", "creators": [ { "name": { "family": "Shin", "given": "Jumi Anne" }, "id": "Shin-Jumi-Anne", "orcid": "0000-0001-9939-2072", "display_name": "Shin, Jumi Anne" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dervan", "given": "Peter B." }, "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A." }, "role": "member", "display_name": "Goddard, William A." }, { "name": { "family": "Rees", "given": "Douglas C." }, "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gmk8-2d12", "abstract": "Protein recognition of specific DNA binding sites is critical for cellular processes; transcription, replication, and restriction are but a few of the biological activities regulated by DNA binding proteins. Although DNA can exist in any number of sequences and conformations, proteins have the exquisite capability of recognizing specific nucleotide sequences in an entire genome. Chapter One is a review that concentrates on sequence-specific DNA binding proteins primarily capable of regulating gene expression and also able to serve structural and catalytic roles in biological processes. The helix-turn-helix repressor proteins from phages \u03bb and 434 and lac and trp repressors, leucine zipper proteins, zinc-finger proteins, the homeodomain, basic helixloop-helix proteins, arc and mnt repressors, and double helix-turn-helix proteins are discussed.
\r\n\r\nAffinity cleaving studies on mutants of the DNA binding domain of Hin recombinase, Hin(139-190), are discussed in Chapter Two. Arg140 has been previously found to be extremely important for sequence-specific binding of Hin(139-190) to the hixL operator. Mutants in which Arg140 of Hin(139-190) is replaced with Lys, Ala, \u03b2-Ala, Glu, Gly, and GIn were studied; a mutant in which Arg142 is replaced by Lys is also discussed. The binding affinities and sequence specificities of these mutants are very different from that of Hin(139- 190). Also Hin(139-184), in which the six carboxyl terminal residues are removed, was studied by affinity cleaving and shown to have a similar sequence specificity, albeit reduced binding affinity, compared to Hin(139-190). In Chapter Three, a procedure for quantitating thermodynamic parameters using the affinity cleaving technique is discussed. In this procedure, affinity cleaving reactions are run over a wide range of protein concentrations. A binding isotherm is generated and fit, using a least-squares program, and reproducible values for binding constants can be obtained. Binding constants were quantitated for Hin(39-190), two of the mutant proteins, and Hin(139-184). This methodology was developed in order to obtain thermodynamic parameters of complexation between these synthesized proteins and their DNA binding sites. Binding constants were measured only for the hixL IRL and IRR sites for each protein, although in some cases, strong binding was also exhibited at the secondary and even tertiary sites. This method can resolve binding curves for individual sites in a cooperative system. Typical binding constants ranged between 105 M-1 and 107 M-1 at 20mM NaCI for the hixL site.
\r\n\r\nAffinity cleaving studies were performed on the DNA binding domain of lac repressor in Chapter Four. Based upon sequence homology analysis between the binding domains of lac and cro repressors, the DNA binding interaction between the lac repressor and operator was assigned as a helix-turn-helix motif. NMR studies on the DNA binding domain of lac repressor have shown that the recognition helix of lac binds the major groove of DNA in an orientation opposite that of cro. Affinity cleaving studies on the lac repressor DNA binding domain support the NMR results and establish the orientation of the recognition helix of the lac repressor.
\r\n\r\nIn Chapter Five are discussed affinity cleaving studies on the engrailed homeodomain, for which a high-resolution cocrystal structure was recently published. Until now, affinity cleaving has been performed on proteins for which no high-resolution structural data exist. Because the engrailed homeodomain contains sequence elements very similar to Hin(139-190), it was chosen for affinity cleaving studies in order to compare and to interpret structural data obtained by affinity cleaving with a protein of known structure.
" }, { "name": "Stewart, Edward G", "degree": "PhD", "year": "1992", "title": "I. The synthesis and spectroscopy of a series of 1,3-diaryl-1,3-cyclopentadiyls and 1,4-diarylbicyclo[2.1.0]pentanes. II. Progress toward the synthesis of non-Kekul\u00e9 naphthalene, a series of tetramethyleneethanes, and bi(cyclobutadienyl)", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08302011-090100151", "creators": [ { "name": { "family": "Stewart", "given": "Edward G" }, "id": "Stewart-E-G", "display_name": "Stewart, Edward G" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/42ek-vh68", "abstract": "1,4-Diarylbicyco[2.1.0]pentanes 6-XY were prepared from the corresponding diazenes by thermolysis. Variable temperature NMR reveals that para substituents have only small effects on the free energies of activation at coalescence in the bridge-flip reaction. The effects correlate with the Hammett parameters derived from the thermolysis of para-substituted dibenzyl mercurials, \u03c3j\u02d9. The reduced magnitude of substituent effects observed in these compounds was attributed to the incomplete formation of radical character at the transition state and to its cumyl radical nature.\r\n\r\n1,3-Diaryl-I,3-cyclopentadiyls 7-XY prepared by low-temperature photolysis of the same diazenes have triplet grounds states. The zfs parameter |E/hc| is constant for the series, indicating para substituents cause no substantial change in molecular symmetry. The zfs parameter |D/hc| correlates extremely well with the general Hammett parameter for para groups, \u03c3p\u02d9, which allows the separation of observed |D/hc| values for bromine-containing\r\nmembers of the series into contributions from spin-orbit coupling and from inductive and resonance effects of the substituents. Spin-orbit coupling effects of the\r\nbromines on ID/hcI are small relative to the system's hyperfine couplings and estimated spin-orbit effects based on interactions without heavy atoms.\r\n\r\nPhenylsulfonyl-containing members of this series undergo significant unimolecular decay at 77 K. The relative decay rates correlate well with a decrease in the exchange\r\nenergy (as implied by smaller |D/hc| values), which decreases the singlet-triplet gap.\r\n\r\nLinear free-energy relationships for these systems depend on both substituents present. A sum of the two individual substituent constants was used because each radical\r\nunit contributes equally to the observed properties. This is the first reported correlation of biradical properties with para-substituent effects determined in other systems.\r\n\r\nSignificant progress toward the syntheses of non-Kekul\u00e9 naphthalene, a series of tetramethyleneethanes, and bi(cyc1obutadienyl) was made. The reactivity of precursors to these compounds has been explored, and routes for future efforts have been charted.\r\n" }, { "name": "Sun, Yun", "degree": "PhD", "year": "1992", "title": "NMR Studies of Protein-DNA Interactions: Determinations of DNA Structures Recognized by Bin Recombinase and Studies of Their Roles in Protein Binding Interactions", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132011-160134197", "creators": [ { "name": { "family": "Sun", "given": "Yun" }, "id": "Sun-Yun", "display_name": "Sun, Yun" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "member", "display_name": "Rees, Douglas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/em1y-p761", "abstract": "The solution structures of two DNA oligomers were determined by the 2-D NMR method. These 14-base-pair DNA molecules contain the recognition sites for Hin recombinase. In spite of the differences in their sequences, the two structures are remarkably similar. The refined DNA structures possess a significant bend (25-32\u00b0) in the middle of the helices. As a result of the bending, the nearby major groove is compressed at almost exactly the position where the recombinase binds. The DNA molecules were also found to have a deepened and narrowed minor groove near the continuous dA tracts, where the minor groove contact happens between the N-terminal residues of the recombinase binding domain and the DNA molecules. Such pre-existing unique features of the free DNA molecules are likely to contribute to the specific interaction of the protein and the DNA tracts. Structure determinations by the NMR method were preceded with the use of complete relaxation matrix analysis and restrained molecular dynamics. A data processing system were developed which allowed us to simulate the NMR spectra and quantifying intensities from an overlapped data set. A complete system for high-resolution structure determinations in solution were set up and evaluated.
\r\n\r\nThe conformation of the Hin 52mer peptide-the binding domain of the Hin recombinase-and its binding interactions with the DNA oligomers are studied by NMR, circular dichroism and chromatographic methods. The conclusion is that the peptide does not have a unique and stable conformation alone as a single monomer in solution. The Hin peptide can be prevented from being aggregated by adjusting to acidic conditions, and it can be folded to a stable tertiary structure in an artificial environment with small amounts of trifluoroethanol. The Hin 52mer peptide conformation is greatly stabilized or induced by the presence of the DNA bearing specific binding sequences. The DNA binding activities of the peptide may be assayed by a chromatographic method. The behavior of the peptide in the binding complex and the characteristic structural features of the DNA molecules suggest the active role of the DNA in protein-DNA interactions providing complementary interactions with the peptide and stabilizing the peptide conformation upon its binding.
\r\n" }, { "name": "Uffelman, Erich Stuart", "degree": "PhD", "year": "1992", "title": "Macrocylic tetraamido-N ligands that stabilize high valent complexes of chromium, manganese, iron, cobalt, nickel, and copper", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06012005-153821", "creators": [ { "name": { "family": "Uffelman", "given": "Erich Stuart" }, "id": "Uffelman-E-S", "display_name": "Uffelman, Erich Stuart" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1byt-rm91", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nHigh valent middle and later transition metal centers tend to oxidatively degrade their ligands. A series of ligand structural features that prevent discovered decomposition routes is presented. The result of the iterative design, synthesis, and testing process described are the macrocyclic tetraamides H4MAC* and H4DEMAMPA-DCB. H4MAC* and H4DEMAMPA-DCB are the parent acids of the macrocyclic tetraamido-N ligands [...] and [...], which are shown to stabilize high valent middle and later transition metal complexes unavailable in other systems. The crystal structures of H4MAC* and a copper complex of one of its synthetic precursors reveal intramolecular and intermolecular hydrogen-bonding patterns which are relevant to recent developments in the ordering effects of hydrogen-bonding on solution and solid state structures. The synthetic value of these ordering effects is discussed.\n\nTwo chromium(V) oxo complexes, [...] and [...], have been synthesized and characterized by X-ray crystallography and IR and EPR spectroscopies. Because exchange of the oxo ligand with water is slow, the easily synthesized, stable, crystalline [...]O-labeled diperoxide [...], was prepared and used to conveniently synthesize [...]O-labeled oxo complexes in high yields. The bonding of the two unique oxidation resistant macrocyclic tetraamides to chromium is compared. The structural and EPR properties are consistent with a chromium centered radical in each case and suggest that a chromium(V) oxidation state assignment is equally appropriate whether the ancillary ligand is the innocent [...] or the potentially noninnocent [...]. Both oxo complexes contain nonplanar amide groups. The distortions in [...] are more marked, and it is a unique species in containing four distinctly nonplanar amides.\n\nThe synthesis and characterization of the first water-stable Mn(V) monooxo complex is described. [...] has been isolated as a green crystalline material and characterization includes [...] NMR, IR, resonance Raman, and an X-ray crystal structure determination. The first definitive assignment of a [...] IR stretch [...] is made.\n\nThe first mononuclear five-coordinate Fe(IV) complex to be isolated as a crystalline compound and structurally characterized, [...], is described. The species has a square pyramidal structure. Cyclic voltammetry of [...] shows a reversible [...] couple at [...] vs. [...] with [...] (0.1 M) as supporting electrolyte. The Mossbauer spectrum of [...] obtained at 150 K has [...] and an isomer shift, [...], lending film support to the iron(IV) oxidation state assignment. Data on [...] are provided for comparison.\n\nThe synthesis and characterization of the first macrocyclic square planar Co(III) complex is described. [...] has been isolated as a red crystalline material and characterization includes a [...] spectrum of the lithium salt and an X-ray crystal structure determination of the [...] salt. The cobalt complex contains one significantly nonplanar amido-N ligand where the source of the nonplanarity appears to be a simple mismatch between the geometrical features of the macrocycle and the structural requirements of the square planar metal center, a unique case of amide nonplanarity in inorganic chemistry.\n\nThe first crystallographically characterized neutral square planar complex of cobalt in an oxidation state higher than [...], [...], is reported. Structural data for this new class of compounds indicate that the macrocycle in [...] is noninnocent; however, EPR data in toluene at 5.9 K [...] show that the metal center is the primary residence site of the unpaired electron. [...] is a stable, yet potent, oxidant which is soluble in benzene and slightly soluble in pentane. The [...] couple is reversible and found at 0.550 V vs. [...] in [...]. [...] slowly oxidizes water, yielding [...], which may also be prepared by the reaction of [...] with [...]. Both the redox and the acid/base chemistries of [...] are reversible. Electrochemical and EPR data are also presented for other derivatives.\n\nThe first square planar nickel(III) complex with an innocent ligand to be structurally characterized, [...], is described: All four Ni(III)N bond distances are significantly shorter [...] than any known Ni(III)-N bond distance. The average Ni-N distance in [...] is [...] and the shortest of the four is 1.825(4). [...] EPR and UV-vis evidence are presented which indicate that the four-coordinate structure found for the solid state form is also present in solutions of non-coordinating solvents, and in noncoordinating glasses at 4 K. In [...], five-coordinate species can be produced at [...] with cyanide ion [...] = [...], and at 77 K with pyridine, 2,6-lutidine, and [...], but not with [...], [...], THF (neat), [...] (neat), MeCN (neat), [...] (neat), or acetone (neat) which do not coordinate. The EPR spectra of the four coordinate complex in glasses of [...]/toluene or [...] are of significance to nickel bioinorganic chemistry since [...], the opposite to the usually accepted EPR signature for square planar nickel(III). The Ni(III/II) couple of [...] is reversible and occurs at -0.58 V vs. [...] supporting electrolyte, 0.13 V vs. NHE showing that an abiological square planar ligand complement consisting of four deprotonated amides can produce a marked stabilization of four-coordinate nickel(III). Data on [...] are provided for comparison.\n\nThe synthesis of copper(III) complexes with reversible cathodic and anodic waves is described. The low values for the Cu(III/II) couples (-0.815 V vs. [...]) and the high potentials for the [...] couples (ca. +0.830 V vs. [...]) are presented.\n\nThe Dunitz amide nonplanarity analysis is applied to the crystal structures presented to illustrate the unique bonding that occurs in some of the macrocyclic compounds.\n" }, { "name": "Wang, Wen-Ching", "degree": "PhD", "year": "1992", "title": "Expression, structural and functional studies of fasciclin I", "advisor": "Bjorkman, Pamela J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152011-080428062", "creators": [ { "name": { "family": "Wang", "given": "Wen-Ching" }, "id": "Wang-Wen-Ching", "display_name": "Wang, Wen-Ching" } ], "advisors": [ { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "advisor", "display_name": "Bjorkman, Pamela J." } ], "committee": [ { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "orcid": "0000-0003-4073-1185", "role": "chair", "display_name": "Rees, Douglas C." }, { "name": { "family": "Bjorkman", "given": "Pamela J." }, "id": "Bjorkman-P-J", "orcid": "0000-0002-2277-3990", "role": "member", "display_name": "Bjorkman, Pamela J." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Zinn", "given": "Kai George" }, "id": "Zinn-K-G", "orcid": "0000-0002-6706-5605", "role": "member", "display_name": "Zinn, Kai George" }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ykbt-jt41", "abstract": "Fasciclin I is a cell surface glycoprotein thought to be involved in growth cone guidance in the embryonic insect nervous system. It is expressed on the cell surfaces of all\r\nperipheral nervous system (PNS) axons, a subset of central nervous system (CNS) axons and on some nonneuronal cells. Fly embryos bearing mutations eliminating expression of\r\nboth fasciclin I and the Abelson tyrosine kinase exhibit a severe phenotype in which many axon pathways fail to form. Fasciclin I mediates homophilic adhesion in transfected tissue culture cells, suggesting that it may affect growth cone guidance through homophilic interactions. To facilitate structure-function studies of fasciclin I, we have generated mammalian (CHO) cell lines expressing fasciclin I at a high level. The expressed fasciclin I\r\nprotein was released from the cell surface in a soluble form by phospholipase C treatment. Milligram quantities of soluble expressed fasciclin I were purified on an immunoaffinity column. Large single crystals were obtained that diffracted to ~5 \u00c5 resolution which is\r\ninsufficient for a structure determination to atomic resolution by x-ray crystallography. In an effort to produce a form of fasciclin I more amenable to crystallization, we also generated CHO and Drosophila cell (S2) lines that produce a truncated form of fasciclin I.\r\nThe soluble fasciclin I expressed in S2 cells contains significantly less carbohydrate (~15 kDa) as compared to the molecules expressed in CHO cells. Therefore, S2-derived\r\nfasciclin I may be more suitable for crystallization. Biochemical characterization of the expressed fasciclin I indicates that fasciclin I exists as a monomer in solution, an observation consistent with homophilic interaction properties only if the interaction is of low affinity. Electron micrographs of fasciclin I suggest that it has a compact rectangular shape with no obvious flexible linker regions, in contrast to what has been seen in electron\r\nmicroscopic studies of other adhesion molecules. Circular dichroism analysis suggests that fasciclin I contains significant amounts of \u03b1-helical structure, which together with the electron microscopic results, suggests that its structure is substantially different from the \u03b2-sheet structures predicted for adhesion molecules that are members of the immunoglobulin superfamily and/or contain fibronectin III repeats. Future structural and functional studies of fasciclin I will ultimately increase our understanding of neuronal cell surface recognition\r\nand axon guidance.\r\n" }, { "name": "Widdowson, Katherine", "degree": "PhD", "year": "1992", "title": "Silicon-Directed Carbon-Carbon Bond Forming Reactions", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09282011-115011728", "creators": [ { "name": { "family": "Widdowson", "given": "Katherine" }, "id": "Widdowson-Katherine", "display_name": "Widdowson, Katherine" } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z89M-4K49", "abstract": "It is shown that O-silyl ketene N,O-acetals react with aldehydes, without catalysis, to form aldol-type products with high diastereoselectivity. For example, the prolinolderived O-silyl ketene N,O-acetal 7 reacts with benzaldehyde to form the anti aldol product 9 with > 98% diastereoselectivity. Mechanistic studies are presented which support a scheme involving formation of trigonal bipyrarnid (tbp) G, pseudorotation to form tbp Tboat, and rate-determining C-C bond formation to produce 9.
\r\n\r\n[Formula. See abstract in scanned thesis for details]
\r\n\r\nIt is shown that aldehydes react with pyridine, benzeneselenol, dichlorodimethylsilane, and an allylic alcohol to form O-allyloxy dimethylsilyl hemiselenoacetals in high yield. These derivatives undergo efficient free radical-mediated cyclization upon treatment with BU3SnH, as exemplified by the transformation of 7\u21928. Together these steps provide an efficient method for carbon-carbon bond formation between the carbonyl carbon of an aldehyde and the terminus of an allylic alcohol.
\r\n\r\n[Formula. See abstract in scanned thesis for details]
\r\n\r\n2,3-Epoxy alcohols are transformed to C2-inverted cyclic carbonates upon treatment with cesium carbonate under an atmosphere of carbon dioxide (e.g., 5\u21926).The reaction is completely stereospecific, within experimental error, and forms only 5-membered ring cyclic carbonates.
\r\n\r\n[Formula. See abstract in scanned thesis for details]
" }, { "name": "Wu, Yi-Shuen Mark", "degree": "PhD", "year": "1992", "title": "Quantum three-body reaction dynamics including the geometric phase effect.", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152011-095849979", "creators": [ { "name": { "family": "Wu", "given": "Yi-Shuen Mark" }, "id": "Wu-Y-M", "display_name": "Wu, Yi-Shuen Mark" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PPME-QC88", "abstract": "Accurate quantum mechanical reactive scattering calculations within the framework of symmetrized hyper spherical coordinate techniques are presented for several processes involving collisions of an electron with a hygrogen atom and an atom with a diatomic molecule in three-dimensional space, and the collinear collision of an atom with a diatomic molecule. In addition to the interest of the processes themselves, the results are compared with previous experimental and theoretical results in such a way as to provide tests of the general usefulness of the methods used.
\r\n\r\n\r\nThe general theory for the calculation of accurate differential cross sections in the reactive collision of an atom with a diatomic molecule including the geometric phase effect in three-dimensional space is described. This methodology has permitted, for the first time, the calculation of integral and differential cross sections over a significantly larger range of collision energies (up to 2.6 eV total energy) than previously possible for the system H + H_2.
\r\n\r\nWe present numerical solutions of the quantum mechanical streamlines of probability current density for collinear atom-diatom reactions. It is used to study the barrier height dependence of dynamics on the C1 + HC1 reaction.
\r\n" }, { "name": "Wyslouzil, Barbara Ellen", "degree": "PhD", "year": "1992", "title": "Aspects of homogeneous nucleation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08172007-132240", "creators": [ { "name": { "family": "Wyslouzil", "given": "Barbara Ellen" }, "id": "Wyslouzil-B-E", "display_name": "Wyslouzil, Barbara Ellen" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Okuyama", "given": "Kikuo" }, "id": "Okuyama-K", "role": "member", "display_name": "Okuyama, Kikuo" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5M1F-WC03", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nExperimental investigations of vapor phase binary nucleation were carried out for both the methanesulfonic acid-water and the sulfuric acid-water systems. A rapid mixing device produced acid-water aerosols under isothermal conditions and at relative acidities (Ra), 0.04 < Ra < 0.65, relative humidities (Rh), 0.01 < Rh < 0.65, and temperatures, T = 20, 25 and 30\u00b0C. The number concentration of the aerosol at the exit of the nucleation and growth tube is extremely sensitive to the binary nucleation rate. Thus at low particle concentrations, when condensation did not significantly change the saturation levels the binary nucleation rates were estimated from the number concentration data as a function of Ra, Rh and temperature. Particle size distributions were also measured and found to vary with the amount of acid and water present. An integral model considering both nucleation and growth simulated the experimental system and predicted the total number of particles, the total mass in the aerosol phase, and the mass average diameter at the exit of the nucleation and growth tube. The simulations reproduced the experimental results quite well for the methansulfonic acid-water binary, if the nucleation rate was adjusted by a temperature dependent correction factor which ranged from [...] to [...]. Further analysis showed that the ratio of experimental to theoretical nucleation rates for both acid-water systems was a strong function of the predicted number of acid molecules in the critical nucleus.\r\n\r\nClassical homogeneous nucleation theory was extended to nonisothermal conditions by simultaneously solving cluster mass and energy balances. In vapor phase nucleation, the steady state nucleation rate was lower than the corresponding isothermal rate and this discrepancy increased as the pressure of the background gas decreased. After the initial temperature transients decayed, subcritical clusters were found to have temperatures elevated with respect to that of the background gas." }, { "name": "Yang, Maximillian Y.", "degree": "Masters", "year": "1992", "title": "Progress on the synthesis of 1,2,3,5,9-cyclodecapentaen-7-yne and supporting studies", "advisor": "Myers, Andrew G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10042011-102102178", "creators": [ { "name": { "family": "Yang", "given": "Maximillian Y." }, "id": "Yang-M-Y", "display_name": "Yang, Maximillian Y." } ], "advisors": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "advisor", "display_name": "Myers, Andrew G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bfhp-k953", "abstract": "Progress on the synthesis of 1,2,3,5,9-cyclodecapentaen-7-yne (1), a compound structurally related to both (Z)-1,2,4-heptatrien-6-yne and the activated\r\ncore of neocarzinostatin chromophore, is reported. The novel compound 1 is of theoretical interest as an example of a monocyclic 10-membered ring that fulfills the aromaticity requirements of H\u00fcckel's rule. The alcohol 24, envisioned to serve as a possible precursor to 1, has been synthesized.
\r\n\r\nIn related, collaborative studies, 1-bromo-4-trimethylsilylnaphthalene, 1-bromo-5-trimethylsilylnaphthalene, 2-bromo-7-trimethylsilylnaphthalene, 1-chloro-\r\n4-trimethylsilylnaphthalene, 1-chloro-5-trimethylsilylnaphthalene, and 2-chloro-7-\r\ntrimethylsilylnaphthalene have been synthesized. These compounds will be used in gas-phase studies as precursors to the corresponding naphthalene biradicals. These studies will determine the heat of formation of each corresponding \r\nnaphthalene biradical.
\r\n" }, { "name": "Yoon, Hye-Joo", "degree": "PhD", "year": "1992", "title": "The Saccharomyces cerevisiae CDC7 protein kinase, a potential link between START and the initiation of DNA replication", "advisor": "Campbell, Judith L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152011-110250530", "creators": [ { "name": { "family": "Yoon", "given": "Hye-Joo" }, "id": "Yoon-H", "display_name": "Yoon, Hye-Joo" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "advisor", "display_name": "Campbell, Judith L." } ], "committee": [ { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "member", "display_name": "Abelson, John N." }, { "name": { "family": "Dunphy", "given": "William G." }, "id": "Dunphy-W-G", "role": "member", "display_name": "Dunphy, William G." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mapz-nx18", "abstract": "Two major controls of the eukaryotic cell cycle exist in the G1/S and G2/M transitions. In an attempt to understand the molecular basis of the G1/S regulatory pathway, biochemical characterization of the Saccharomyces cerevisiae CDC7 protein has been carried out. The temperature sensitive cdc7 mutation arrests yeast cells at the G1/S phase boundary, after the completion of START and prior to the initiation of DNA synthesis. START is defined as the point of commitment to DNA replication in yeast. The open reading frame encoding CDC7 protein contains the 11 catalytic domains characteristic of protein kinases. That CDC7 protein indeed has protein kinase activity was demonstrated by incubating CDC7 immune complexes with histone H1. Kinase activity was elevated more than 10-fold in strains carrying the wild-type CDC7-overproducing plasmid. Overproduction of thermolabile cdc7 protein gave rise to overproduction of thermolabile kinase. In vivo _(32)P-labeling of yeast cells revealed that CDC7 protein itself was a phosphoprotein. In addition, indirect immunofluorescence and biochemical fractionation studies showed CDC7 was located mainly in yeast nuclei.
\r\n\r\nThe cell cycle-specific roles of CDC7 at the G1/S border were explored by following the phosphorylation state and kinase activity of CDC7 protein throughout the cell cycle. CDC7 was not active as a histone H1 kinase, nor was it phosphorylated in cells arrested by a cdc28 mutation. Furthermore, phosphorylation of CDC7 protein was required for its activity. CDC28 encodes the budding yeast homolog of the highly conserved p34^(cdc2)/MPF kinase subunit and its function is crucial to passage through START. The possibility that CDC7 is a substrate of the CDC28 kinase was tested using CDC28 immune complexes and bacterially produced, inactive CDC7 kinase. The CDC28 kinase specifically phosphorylated the CDC7 protein. which in tum led to activation of the CDC7 kinase. CDC28 and CDC7 could interact in vivo as well since CDC7 hyperexpression suppressed the inviability of a cdc28 mutation at 33\u00b0C but not at 36\u00b0C. Finally, possible mechanisms of action of CDC7 protein kinase in the initiation of DNA synthesis were examined by searching for endogenous substrates among yeast replication proteins. The 34 kDa subunit of yeast replication protein-A (RP-A) is a substrate of both CDC7 and CDC28 kinases.
\r\n\r\nIn conclusion, the biochemical evidence indicates that there is a phosphorylation cascade operating between START and the initiation of DNA replication involving yeast CDC28, CDC7, and RP-A.
\r\n" }, { "name": "Blauch, David N.", "degree": "PhD", "year": "1991", "title": "Part I. Improvements in the rotation-rate step experiment for the evaluation of diffusion coefficients at rotating disk electrodes. Part II. Ion-pairing and electric field effects on electron hopping in the Nafion-tris(2,2'-bipyridine)osmium(3+/2+) system", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06152007-081035", "creators": [ { "name": { "family": "Blauch", "given": "David N." }, "id": "Blauch-D-N", "display_name": "Blauch, David N." } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8683-j681", "abstract": "Part I: An improved description of the current transient produced by an abrupt change in the rate of rotation of a rotating disk electrode has been obtained by the method of orthogonal collocation. The procedure provides a formula that accurately describes the expected current transient for at least 90% of its duration. If the final rotation rate is chosen to be ca. 58% of the initial rotation rate, the resulting current transient exhibits simple exponential decay, thereby facilitating data analysis. A simple offset in the time scale of the experiment proves effective in compensating for the effects of both hydrodynamic relaxation and imperfections in the response of the electrode rotator.\n\nPart II: The high ionic content and low dielectric constant that prevail in the interior of many redox polymers are expected to promote ionic association between the polyelectrolyte and counterions. The present study is an attempt to evaluate the influence of ion-pairing interactions on charge propagation within polyelectrolyte films. The system under investigation consists of the Os(bpy)3(3+/2+) redox couple incorporated into Nafion, where ion-pairing between the osmium complex and pendant sulfonate groups is argued to be responsible for the irreversible retention of the complex within the film. The apparent diffusion coefficient characterizing the dynamics of electron propagation through the redox polymer exhibits a remarkably sudden increase as the film approaches electrostatic saturation with the Os(bpy)3(3+) complex. Existing models, even those taking into account the presence of electric fields within the film, do not account satisfactorily for the observed behavior of the apparent diffusion coefficients. The introduction of ion-pairing into the model for charge transport leads to predictions that are consistent with the observed behavior. Key ingredients in the successful model are the assumptions that the predominant forms of the Os(bpy)3(3+/2+) complex incorporated in Nafion are neutral aggregates resulting from the formation of triple or double ion-pairs and that the triply ion-paired Os(bpy)3(3+) species dissociates into a singly charged species containing the same number of sulfonate groups as the predominant form of the Os(bpy)3(2+) complex, thereby providing a low-energy pathway for electron self-exchange. The dissociation of the triply ion-paired Os(bpy)3(3+) complex provides a natural explanation for the steep increase in the apparent diffusion coefficient, i.e., the rate of electron propagation, as the concentration of the osmium complex comes close to saturation, because as saturation is approached the ion-pairing equilibrium shifts to favor the formation of the doubly ion-paired form of Os(bpy)3(3+) that is the best partner for accepting an electron from the doubly ion-paired Os(bpy)3(2+) complex. The inevitable presence of electric fields within the polyelectrolyte films also affects the observed behavior, especially as the concentration of the incorporated cation is increased." }, { "name": "Bonnecaze, Roger Temor", "degree": "PhD", "year": "1991", "title": "Macroscopic properties of electrically interacting suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07092007-143213", "creators": [ { "name": { "family": "Bonnecaze", "given": "Roger Temor" }, "id": "Bonnecaze-R-T", "display_name": "Bonnecaze, Roger Temor" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/bshd-xb74", "abstract": "Several bulk or macroscopic properties of electrically interacting suspensions -or at least electrically interacting by mathematical analogy- are studied using simulation methods. These bulk properties include the effective conductivity, percolation transitions, effective reaction rates, and the effective viscosity of an electrorheological fluid. In order to compute these properties, the detailed potential field in the suspension is not required, but rather only the linear relationship between the charge and dipole moments of the particles to their potentials and the applied electric field is needed. A method is developed to compute this relationship accurately and efficiently for arbitrary particle configuration and shape. The method includes both the many-body far-field and near-field particle interactions and properly accounts for the long-ranged interactions common to electrostatic problems.\n\nThe method is applied as part of a simulation to determine the effective conductivity of spherical particles. The simulation accurately reproduces the known values of the conductivity for cubic lattices of spheres for any volume fraction and particle-matrix conductivity ratio providing confidence in the method. It is then applied to determine the conductivity of mono-disperse, random hard-sphere suspensions for a variety of conductivity ratios of up to sixty volume percent particles. This is the first rigorous theoretical determination of the effective conductivity at such large volume fractions. The method is also used to study the percolation behavior of highly conducting spherical particles in close contact. It is found that such a system does exhibit a percolation transition, but only when the near-field effects are extremely large compared to the far-field interactions. This indicates that such a condition is a necessity for modeling a suspension as a percolating system.\n\nThe diffusion-limited reaction rate of a highly mobile reactant with spherical traps is also computed using the simulation method. Here the average \"charge\" on the particle is the effective consumption of the reactant by the spherical particle. The results are quite good up to a volume fraction of 30%, but then unphysically deviate from the expected increasing reaction rate with volume fraction and show a maximum rate at forty volume percent. The deviation is explained and serves as an example of the limitations of the method developed earlier. Using the effective conductivity results, however, a self-consistent Brinkman medium-like theory is developed that predicts the effective reaction rate quite accurately.\n\nThe method is finally applied to the dynamic simulation of electrorheological (ER) fluids -suspensions of dielectric particles with electric field tunable effective viscosities. Using the method developed in earlier chapters, the electrostatic interparticle forces in the ER suspension can be determined accurately and efficiently for arbitrary particle configurations, especially in capturing the strong near-field interactions. Coupled with Stokesian dynamics to account for the hydrodynamic interactions among the particles, the dynamics of the microstructure and its rheology can be determined. Dynamic simulations of an unbounded monolayer for a variety of electric field strengths and shear rates reproduce qualitatively and quantitatively experimental behavior. From the correlation of the dynamics and rheology, a theory for the dynamic yield stress observed in the suspensions is proposed and then successfully tested with the dynamic simulation. From the theory a simple model of the dynamic yield stress is created to predict its dependence on the volume fraction and the particle to fluid dielectric constant. The power of simulations to provide insight into the physics of multiphase materials and then to allow the testing of theories is particularly well illustrated with the study on ER fluids." }, { "name": "Bowers, Clifford Russell", "degree": "PhD", "year": "1991", "title": "Parahydrogen and Synthesis Allow Dramatically Enhanced Nuclear Alignment", "advisor": "Weitekamp, Daniel P.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04172006-141634", "creators": [ { "name": { "family": "Bowers", "given": "Clifford Russell" }, "id": "Bowers-Clifford-Russell", "orcid": "0000-0001-6155-5163", "display_name": "Bowers, Clifford Russell" } ], "advisors": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "advisor", "display_name": "Weitekamp, Daniel P." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Chan", "given": "David C." }, "id": "Chan-D-C", "role": "member", "display_name": "Chan, David C." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R5TV-Z220", "abstract": "The PASADENA effect is a method for transient high-sensitivity proton spin-labelling by molecular addition of dihydrogen. When the parahydrogen mole fraction differs from the high-temperature limit of 1/4, this population difference constitutes a form of spin order which can be converted to magnetization observable by NMR. Large NMR signals are observed, if subsequent to the hydrogen addition, the two protons experience magnetic inequivalence and spin-spin coupling and if observation is made before spin-lattice relaxation restores the equilibrium spin order. The analogous effect for D2 is also possible.
\r\n\r\nThe kinetic mechanisms of the homogeneous hydrogenation catalysts which permit the realization of the PASADENA effect have been the target of the experimental applications. The enhancement of the NMR transitions has facilitated the determination of true molecular rate constants. Ordinarily, the activity of a catalyst is assessed by dividing the observed rate by the total catalyst concentration. However, the question as to whether most of the catalytic rate is due to a tiny fraction of active species or a large fraction with a relatively low molecular rate is not clearly addressed by such an analysis. This ambiguity is entirely avoided in the PASADENA studies, since only active catalyst molecules can contribute to the enhanced signals from which all kinetic inferences are made.
\r\n\r\nThe sensitivity enhancement has also led to the identification of a novel intermediate in the mechanism for the Rh(DIPHOS)+ catalyzed hydrogenation of styrene. The rate of conversion of this species into product and starting material has been studied using two-dimensional NMR. The dramatically improved sensitivity should make it possible to observe key catalytic intermediates which do not build up in sufficient quantity to allow detection by conventional NMR arising from Curie-Law magnetization.
\r\n\r\nThe study of surface sites which bind pairwise with H2 is also a potentially fruitful area for future experimental work. The ambient temperature NMR spectroscopy of surfaces is not often feasible due to sensitivity limitations. Simulations have been performed using typical shift and coupling parameters in an effort to characterize the enhanced lineshapes which can be expected.
\r\n\r\nThe inverse of the PASADENA effect has also been proposed, whereby the spin order of a molecule containing hydrogen is probed by measuring the branching ratio to ortho and para dihydrogen. This RAYMOND phenomenon (radiowave application yields modulated ortho number desorbed) has the potential for measuring precursor NMR with extraordinary sensitivity, since it finesses the need for detection of radiowaves.
" }, { "name": "Braatz, Richard Dean", "degree": "Masters", "year": "1991", "title": "\u03bc-Sensitivities as an Aid for Robust Identification", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechTHESIS:06272025-182529568", "creators": [ { "name": { "family": "Braatz", "given": "Richard Dean" }, "id": "Braatz-Richard-Dean", "orcid": "0000-0003-4304-3484", "display_name": "Braatz, Richard Dean" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4ckj-5r83", "abstract": "Identification for a model for robust control design is more complicated than for the standard linear system transfer function model-the structure of the uncertainty as well as bounds on its size must be determined. It is especially unclear as to which parts of the system should be better modeled to improve robust performance. This paper addresses this question through some new tools, the \u03bc-sensitivities." }, { "name": "Braunstein, Matthew", "degree": "PhD", "year": "1991", "title": "Photoionization dynamics and ion state distributions in single-photon and resonance enhanced multiphoton ionization of molecules", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechETD:etd-06182007-133055", "creators": [ { "name": { "family": "Braunstein", "given": "Matthew" }, "id": "Braunstein-M", "display_name": "Braunstein, Matthew" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ct0v-g194", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThis thesis presents results of theoretical studies of single-photon ionization and resonance enhanced multiphoton ionization (REMPI) of several small molecules. These studies parallel several recent experiments which use tunable sources of radiation to photoionize molecules and measure the resulting electronic, vibrational, and rotational population of ions via photoelectron spectroscopy. The objective of this thesis is to examine the underlying dynamics between the ion and the ejected electron and to understand how these interactions affect photoion state distributions. In particular, this work focuses on the presence and influence of localized quasi-bound states of the photoelectron called \"shape resonances\" which significantly influence these ion distributions. A key feature of these studies is the use of accurate Hartree-Fock photoelectron wave functions determined from the Schwinger variational method. This method provides a photoelectron wave function determined in the static-exchange and non-central field of the molecular ion. Use of such photoelectron wave functions is crucial in an accurate determination of transition moments and ion state populations.\n\nThe first part of the thesis examines shape resonances in the photoionization of O2. Studies reported here include investigations of branching ratios of electronic multiplet states in the [...] and [...] photoionization of O2 and a comparison of photoionization of the singlet states, a [...] and [...], with that of the ground state of O2. These studies show that the electronic exchange interaction between the ion core and the photoelectron in shape resonant energy regions profoundly affects the electronic state distributions of the molecular ion. We also report vibrational branching ratios in the single-photon ionization of O2, and in REMPI of O2 via the [...] Rydberg state. In these studies, we find that a shape resonance causes a dependence of the electronic transition moment on the molecular geometry leading to non-Franck-Condon ion vibrational distributions and a dependence of the rotational branch intensity on the ion vibrational state.\n\nThe second part of this thesis examines shape resonances in other molecules, focusing on the more general aspects of the photoionization dynamics. Here we present studies of the vibrational state distributions in the [...] photoionization of the polyatomic N2O, where a shape resonance causes non-Franck-Condon vibrational state distributions, the degree of which depends on the nuclear displacements involved and whether the shape resonance is localized on a particular bond. We also study the photoionization dynamics of the valence shell of Cl2, where a shape resonance is also seen. In contrast to what has been seen in other molecules, this shape resonance is not oriented along the molecular axis, but perpendicular to it. The shape resonance therefore is less sensitive to vibrational motion and does not influence vibrational distributions. Finally, we present studies of the K-shell ionization of CO. Studies in this energy region have assumed a new importance with the development of tunable X-ray synchrotron soures. Here, electronic relaxation in the production of a K-shell hole is seen to significantly influence the photoionization cross section in shape resonant energy regions. The mathematical framework is given to separate and analyze the effects of electronic relaxation in the photoionization cross section and calculate K-shell satellite spectra from first principles.\n\nThe results of examination of all these photoionization processes are discussed in the context of recent experiments." }, { "name": "Brewer, John C.", "degree": "PhD", "year": "1991", "title": "Syntheses, characterizations and reactivity of trans-dioxorhenium(V) and -(VI) complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142007-144656", "creators": [ { "name": { "family": "Brewer", "given": "John C." }, "id": "Brewer-J-C", "display_name": "Brewer, John C." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9r7z-ax43", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe synthesis, electronic structure and reactivity of trans-dioxorhenium(V) and -(VI) complexes have been examined in detail. An improved general synthesis of trans-[ReO2(L)4]X complexes is presented. The amine complex [ReO2(en)2]I can be made in 90% yield from ReO2(PPh3)2I and ethylenediamine in less than 15 minutes at room temperature. Refluxing methanol suspensions of ReO2(PPh3)2I with 12-50 equivalents of electron-rich pyridines results in the formation of [ReO2L4]I compounds in 50 to 85% yield.\r\n\r\nSystematic substituent studies reveal the influence of ancillary ligands on the physical properties of trans-[ReO2(L)4][PF6] compounds. The Re(VI)/Re(V) redox couple is a linear function of pyridine ligand [...] (ReVI/Re/V) = (0.96 + [...]) V vs. Fc+/Fc. The dxy/dxz,dyz energy gap is also a linear function of pyridine [...]; increasing the pyridine basicity lowers the energy of the dxy [...] dxz,dyz transition and the energy of the [...] excited state. The excited-state properties of trans-[ReO2(L)4][PF6] pyridine complexes follow a trend consistent with the energy-gap law.\r\n\r\nStrongly basic 4-dialkylaminopyridine ligands stabilize d(1) trans-dioxorhenium(VI) complexes. Analysis of the X-ray structure of trans-[...] shows that there is considerable shortening (0.04 A) in the Re-N bond lengths relative to Re(V) analogues, but the Re-oxo bond lengths are virtually the same in both oxidation states. The EPR spectrum of the d(1) ion trans-[...] (dmap = 4-dimethylaminopyridine) has been measured in a 50% DMSO/H2O glass at 7 K. Analysis of the spectrum gives g[...] = 1.91, A[...] = 0.031 cm(-1), g|| = 1.83, A|| = 0.060 cm(-1), and Qz = 0.0075 cm(-1). Because of the large quadrupole coupling, the forbidden ([...] = \u00b11, \u00b12) transitions are quite intense and some are stronger than the allowed ([...] = 0) transitions. Comparison of Qz values and dxy [...] dxz,dyz transition energies for trans-[reO2(dmap)4](2+) and related monooxo and mononitrido complexes confirms that the ligand-field splitting associated with the multiply bonded units increases in the order ReO(4+) < ReN(3+) < ReO2(2+).\r\n" }, { "name": "Chang, Thomas Kyu-Young", "degree": "PhD", "year": "1991", "title": "Gene synthesis, expression, and mutagenesis of azurin", "advisor": "Richards, John H.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142007-132218", "creators": [ { "name": { "family": "Chang", "given": "Thomas Kyu-Young" }, "id": "Chang-T-K", "display_name": "Chang, Thomas Kyu-Young" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Barton", "given": "Jacqueline K." }, "id": "Barton-J-K", "role": "chair", "display_name": "Barton, Jacqueline K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/795e-hp65", "abstract": "A synthetic gene for the blue copper protein Pseudomonas aeruginosa azurin has been constructed using a novel, stepwise method. This method is designed to synthesize a gene of any size reliably by building only controlled amounts of the gene in each step. Another advantage of this method is that the intermediate plasmids, which are typically present in picomolar amounts, can be amplified through plasmid preparation for editing. Using this approach, the azurin gene was synthesized in five steps.\n\nBoth the synthetic genes for azurin and Populus nigra, var italica plastocyanin have been expressed in E. coli. These expressions have been achieved by using a synthetic Shine-Dalgano sequence and the signal sequence for azurin, which directs the transport of the expressed proteins to the periplasmic space of E. coli. The membrane translocation not only facilitates the purification of azurin and plastocyanin but also seems to be required for the proper folding of these proteins. In contrast to these successful expressions, earlier efforts to express plastocyanin in the cytoplasm of E. coli, either directly or as a fusion protein, have been unsuccessful at yielding folded plastocyanin.\n\nSite-saturation cassette mutagenesis was performed in azurin at Methionine 121, one of the four ligands to the copper. Variants that contain each of the other nineteen amino acids as well as the amber stop codon have been identified. Surprisingly, all the variants are stable, as judged by Western blot. Furthermore, all mutants that have been isolated at this position (Asn, Asp, Gly, His, Ile, Leu, Val) have the characteristic blue absorption near 600 nm. Despite such similarity with the wild-type azurin, these mutants seem to have a more flexible copper center. They can lose or incorporate copper at a faster rate than the wild-type protein.\n\nThese results, along with those from EPR experiments, suggest that while Methionine 121 is important in giving stability to the copper center and in tuning the redox potential, its contribution to azurin's spectroscopic properties is small when copper is coordinated to the site. Its spectroscopic contribution apparently becomes more significant when nickel or cobalt resides in the copper site, for the electronic spectra of these derivatives differ markedly from that of azurin with copper. It is likely that the copper centers of the mutants are flexible enough to accommodate the preferred geometries of nickel and cobalt, whereas it is more rigid in the wild-type. Finally, several mutants of azurin are proposed that are designed to probe systematically specific aspects of the biological electron transfer mechanism." }, { "name": "Claeys, Ivan Lode Andre Maria", "degree": "PhD", "year": "1991", "title": "Hydrodynamic Transport Properties of Suspensions of Non-Brownian Prolate Spheroids", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01282005-165455", "creators": [ { "name": { "family": "Claeys", "given": "Ivan Lode Andre Maria" }, "id": "Claeys-Ivan-Lode-Andre-Maria", "display_name": "Claeys, Ivan Lode Andre Maria" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Kornfield", "given": "Julia A." }, "id": "Kornfield-J-A", "orcid": "0000-0001-6746-8634", "role": "member", "display_name": "Kornfield, Julia A." }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DYJ3-4223", "abstract": "The methodology of \"Stokesian dynamics,\" an efficient and accurate simulation technique for suspensions of spheres, is extended to non-spherical particles. The model system consists of rigid, non-Brownian prolate spheroids suspended in an incompressible Newtonian fluid at zero Reynolds number. The method is applied to calculate the hydrodynamic transport properties of unbounded dispersions of ellipsoids. Both \"random\" configurations and very orderly arrangements of particles are considered in order to probe the relation between the microstructure of the suspension and its macroscopically observable properties.
\r\n\r\nThe simulation method is based on a microstructurally detailed description of the two-phase system and explicitly takes into account hydrodynamic interactions between the particles. Non-local singularity solutions for ellipsoids in Stokes flow are combined with Faxen laws using pair-wise additivity of velocities to construct a far-field approximation to the mobility tensor. The convergence problems associated with the long-ranged nature of viscous interactions at zero Reynolds number are handled using O'Brien's renormalization procedure. The Ewald summation technique is applied to accelerate the evaluation of the lattice sums generated by the periodic boundary conditions. Lubrication stresses between almost touching spheroids are added in a pair-wise manner to the mobility inverse. All the two-body resistance functions which diverge as the surface separation vanishes are computed to O(\u03b50), with \u03b5 the gap width, so that the singular behavior of the lubrication interactions is captured correctly for arbitrary relative orientations and relative motions of the particles.
\r\n\r\nThe method is first illustrated for a finite number of particles in an unbounded fluid domain, and shown to be accurate and efficient. It is then applied to crystalline geometries of spheroids over the full concentration range from 0 to closest packing (74% by volume). The dependence of the hydrodynamic transport properties (sedimentation rate, diffusion coefficient, stress/rate-of-strain relation, permeability and hindered diffusivity) on the density of the dispersion, the aspect ratio of the particles and the lattice type is investigated. Equilibrium structures of hard ellipsoids generated by a Monte Carlo procedure are also considered. The high frequency limit of the hydrodynamic transport properties is computed and compared to the results for crystalline configurations, and to available experimental measurements. A discontinuous jump in some suspension properties is observed at the isotropic to nematic transition.
\r\n\r\nAs a prelude to dynamic simulations, the compatibility of unit cells with pure straining flows is examined. It is demonstrated that no self-reproducing lattices exist in axisymmetric extensional flows, but a set of compatible basis vectors is derived. Planar straining fields on the other hand possess an infinite number of strain-periodic lattices.
" }, { "name": "Cuccaro, Steven Andrew", "degree": "PhD", "year": "1991", "title": "Ab initio three-dimensional atom-diatom reaction cross sections using hyperspherical coordinates and variational surface functions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-06192007-074253", "creators": [ { "name": { "family": "Cuccaro", "given": "Steven Andrew" }, "id": "Cuccaro-S-A", "display_name": "Cuccaro, Steven Andrew" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n1ec-7f47", "abstract": "This thesis discusses the development of a symmetrized hyperspherical coordinate technique for the calculation of accurated differential cross sections in the reactive collision of an atom with a diatomic molecule in three-dimensional space. The hyperspherical methodology has the advantage that all regions of configuration space are treated equivalently; this allows the reduction of the reactive scattering problem to an equivalent inelastic scattering problem, which is both computationally simpler and more straightforward conceptually.\n\nThe hyperspherical methodology is discussed in detail, including the expansion of the scattering wavefunction in terms of a basis of local hyperspherical surface functions and the calculation of this basis set. The methods are applied to the H + H2 system (using the LSTH potential energy surface) and used to calculate scattering matrices and partial wave cross sections for this reaction up to a total energy of 1.6 eV. The results presented here include the geometric phase effect due to the conical intersection of the H3 system, along with a set of results which do not include this effect for comparison with the previous work in the field." }, { "name": "Dantus, Marcos", "degree": "PhD", "year": "1991", "title": "Femtosecond transition-state spectroscopy of chemical reactions", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06202007-112232", "creators": [ { "name": { "family": "Dantus", "given": "Marcos" }, "id": "Dantus-M", "display_name": "Dantus, Marcos" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6aam-8f30", "abstract": "The field of molecular dynamics emerged in the beginning of this century with the goal of understanding chemical reactions at the molecular level. The main interest was to study elementary processes such as bond rupture and bond formation as they occur on isolated molecules. Progress in that field has been directly related to technological advances. The development of the cross molecular beam techniques, for example, allowed the first observations of single molecule reactive collisions. Since the early experiments, it was recognized that the elementary steps in chemistry occurred on the time scale of a single vibration, many thought they might be unmeasurably fast. This thesis presents the first real-time observations of elementary chemical processes occurring on dissociative and bound potentials with a time resolution of 10(-14) s.\r\n\r\nThe technique for achieving real-time monitoring of chemical reactions is Femtosecond Transition-State Spectroscopy (FTS). In essence, it involves two femtosecond (10(-15) s) laser pulses; one to initiate the reaction and the second to probe the progress at subsequent times. In addition to the time delay between the two pulses, the experiments include different wavelengths for the pump and probe pulses. The collection of data scans as a function of time delay for each combination of pump and probe wavelengths provides sufficient information about the dynamics to allow inversion to the potential energy surface of the reaction. The potential energy surface then contains all information about the reaction.\r\n\r\nThe FTS technique has been applied with success to several systems. For repulsive states, such as the dissociation reaction of ICN, it has yielded a direct clocking of the bond rupture process and the real-time observation of transition states. For bound and quasi-bound states, the technique has allowed the real-time observation of wave packet oscillation in alkali-halides, halogens and inter-halogens. The technique has been applied to more than one dimensional systems such as HgI2. In addition to the scalar quantities, FTS has also been successful in the measurement of vectorial quantities such as the angular momentum and torque during dissociation reactions. Of all these, and many other measurements under different conditions, only a few representative examples are discussed here. The technique is now well established and it has become an important tool for the study of molecular dynamics on bound and repulsive potential energy surfaces." }, { "name": "Deem, Michael William", "degree": "Senior Thesis", "year": "1991", "title": "Numerical Investigation of Some Aspects of Fourier Transform Ion Cyclotron Resonance Spectroscopy", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112026-221909043", "creators": [ { "name": { "family": "Deem", "given": "Michael William" }, "id": "Deem-Michael-William", "orcid": "0000-0002-4298-3450", "display_name": "Deem, Michael William" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8ccb-sv98", "abstract": "Chapter 1
\r\n\r\nA detailed kinematic analysis is presented comparing the use of quadrupole and\r\noctopole ion guides in conjunction with external ion source Fourier transform ion\r\ncyclotron resonance spectrometers. Methods to determine simply the electric fields\r\nfor ideal and real quadrupoles and octopoles are presented, with emphasis on the\r\nimportance of the effective potential in analyzing the design of an ion guide.\r\nTrajectory calculations are presented for a wide range of ion guide operating\r\nparameters and initial ion energies, along with an evaluation of the range of injected\r\nmasses. Radial and axial ion energies together with a projection of the off-axis\r\nexcursions of the ion motion on the plane perpendicular to the axis of the ICR cell are\r\ngraphically illustrated. The real octopole exhibits more nearly ideal behavior than does\r\na real quadrupole. It does not suffer from the anti-magnetic mirror effect, has uniform\r\nmass cutoffs, and has a four times greater maximum mass cutoff for given operating\r\nparameters than does a quadrupole.
\r\n\r\nChapter 2
\r\n\r\nA detailed analysis of ion motion in a cubic FT-ICR cell reveals dephasing effects of\r\nthe z-axis (magnetic field direction) oscillations that limit the maximum resolution that\r\ncan be achieved. With typical ranges of operating conditions using a 1 inch cubic cell\r\nin a 7 Tesla field, unit mass resolution is lost in the range between 103 and 104 amu,\r\nand peaks may be up to 20 amu in width at the upper end of this range. The finite\r\ntransient length is due to the coupling between the effective radial force on the ion\r\nand the z-axis motion and to a lesser extent, on the instantaneous center of the\r\ncyclotron orbit. Operating conditions that minimize the amplitude of the z-axis\r\noscillations and cell designs that incorporate more homogeneous electric fields serve\r\nto increase the coherence time and provide higher ultimate resolution\"
\r\n\r\nChapter 3
\r\n\r\nWe report here a detailed numerical study of space charge effects on ion trajectories\r\nin a typical FT-ICR experiment. In particular, we focus on ions with high mass to\r\ncharge ratios, 3000 amu/|e-| \u2264 m/z \u2264 10000 amu/|e-|, which are particularly relevant\r\nto experimental studies of clusters, polymers, or biomolecules. We assume excitation\r\nand trapping voltages of 1 V in the one inch cubic cell and a magnetic field of 7 T.\r\nWe find essentially no discernable effect on the dephasing time, mass resolution, or\r\nmass shifts for ion densities below about 7 x 104 |e-|/cm3. That is, the natural\r\ninhomogeneous broadening due to the excitation fields[1] is far more deleterious to\r\nFT-ICR performance than are space charge effects.
\r\n\r\nChapter 4
\r\n\r\nA numerical study of the application of magnetic excitation to FT-ICR is presented. It\r\nis concluded that magnetic excitation, which would permit nonstandard cell designs,\r\nmight be practical for excitation to small final cyclotron radii. For greater degrees of\r\nexcitation, this technique results in excessive magnetron motion and consequent loss\r\nof phase coherence and loss of signal. Unlike conventional rf excitation, the time\r\nrequired for magnetic excitation to a given final radius scales linearly with the mass to\r\ncharge ratio. The technique is thus most applicable to low mass to charge ratio\r\nspecies.
\r\n\r\nChapter 5
\r\n\r\nWe present here computational results for the collision cross section and rate constant\r\nfor proton transfer reactions of a multiply-charged, linear, gas-phase protein. The\r\nprotein is intended to resemble cytochrome c, with a length of 400 \u00c5, a mass of\r\n12 400 amu. The model protein is studied with proton charges of between 9 and 15\r\n|e-|. The computational reactant is intended to model dimethyl amine, with a mass of\r\n45 amu, a polarizability of 5.0 \u00c53 (dimethyl amine has a polarizability estimated by the\r\nLe Fevre method of 5.86 \u00c53[1]), and a dipole moment of 1.03 Debye[2]. Results\r\nfor low linear charge densities on the protein are interpretable in terms of a geometric\r\nmodel that accounts for the overlap of adjacent spheres of capture of each charge on\r\nthe protein.
" }, { "name": "Doyle, Francis Joseph, III", "degree": "PhD", "year": "1991", "title": "Robustness properties of nonlinear process control and implications for the design and control of a packed bed reactor", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-07112007-084012", "creators": [ { "name": { "family": "Doyle", "given": "Francis Joseph, III" }, "id": "Doyle-Francis-Joseph-III", "display_name": "Doyle, Francis Joseph, III" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Burdick", "given": "Joel Wakeman" }, "id": "Burdick-J-W", "role": "member", "display_name": "Burdick, Joel Wakeman" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3n52-hk32", "abstract": "The robustness properties of nonlinear process control are studied with particular emphasis on applications to the design and control of a catalytic fixed bed reactor.\r\n\r\nAnalysis tools are developed to determine the stability and performance of nonlinear dynamical systems. The results are based upon new extensions of the structured singular value to a class of nonlinear and time-varying systems. Conic sectors are utilized in approximating the static nonlinearities present and an algorithm is developed for optimal conic sector calculation.\r\n\r\nThe synthesis tools of differential geometry are studied with respect to their closed loop robust performance properties. New results in approximate linearization are contrasted with exact linearization and linear control. It is shown that the approximate linearization technique is superior with respect to disturbance handling, optimization of the resultant transformations, and range of applicability.\r\n\r\nNonlinear approaches for the control of a packed bed reactor are investigated. In particular, the differential geometric technique of input-output linearization is found to yield superior closed-loop performance over regions of open-loop parametric sensitivity. The synthesis of a linearizing controller for this nonlinear distributed parameter system involves a two-tier approach. In the first stage, a low order nonlinear model is developed for the reactor. This is accomplished by treating the active transport mechanisms in the bed as a nonlinear wave which propagates through the bed in response to changes in the operating conditions. The resultant lumped parameter model facilitates the design of the input-output linearizing controller in the second tier of this scheme. The implementational hurdles for this approach are identified and comparisons are drawn on the strengths of this approach over robust linear control for the reactor.\r\n\r\nPractical guidelines are developed for the design of packed bed reactors. The criteria result from requirements on the radial temperature profile, temperature sensitivity, and acceptable pressure drop. The stabilizing effects of feedback control for industrial fixed bed catalytic reactors are addressed. Simulations support the result that violation of the proposed criteria leads to unacceptable closed-loop performance.\r\n\r\nIn conclusion, general guidelines are constructed from a series of case studies on the proper selection of linear versus \"linearizing\" control. The relative performance is measured by the region of attraction, magnitude of manipulated variable action, and sensitivity to input disturbances. The work represents the first objective evaluation of the strengths and limitations of input-output linearization compared to linear control." }, { "name": "Farid, Ramy Samir", "degree": "PhD", "year": "1991", "title": "Electron transfer in rigid and semi-rigid iridium d8-d8 donor-spacer-acceptor complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06212007-154303", "creators": [ { "name": { "family": "Farid", "given": "Ramy Samir" }, "id": "Farid-R-S", "display_name": "Farid, Ramy Samir" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gvqg-9695", "abstract": "A series of rigid and semi-rigid donor-spacer-acceptor complexes, [Ir(\u00b5-pz*)(CO)(Ph2P-O-C6H4-(CH2)n-py[superscript +]-R)]2(pz* = 3,5-dimethylpyrazolyl; C6H4 = phenylene; py[superscript +] = pyridinium; R = H, 4-tert-butyl, and 4-amide; and n = 0,1,2, and 3, has been synthesized for the purpose of studying photoinduced electron-transfer (ET) reactions. The spacers separating the iridium center (electron donor, Ir2) and pyridinium cation (electron acceptor, py[superscript +]) are based on terminal phosphinite ligands, consisting of a phenylene group and a number of methylene groups ranging from 0 to 3. Three distinct ET reactions can be studied in each complex: singles excited-state electron transfer ([superscript 1]ET), triplet excited-state electron transfer ([superscript 3]ET), and thermal back electron transfer (ET[superscript b]).\n\nAtomic positions, obtained from the X-ray crystal structure of [Ir(\u00b5-pz*)(CO)(Ph2P-O-C6H4-CH3]2 were used as a basis for molecular mechanics calculations, furnishing solution structures for the series of Ir2-py[superscript +] donor-acceptor complexes. These results revealed that the spacers in complexes where n = 0 and n =1 are rigid, and that in complexes where n = 2 and n = 3, the spacers are semi-rigid, taking on either folded or stretched conformations in fluid solution.\n\nSteady-state and time-resolved emission and absorption experiments were employed to determine [superscript 1]ET, [superscript 3]ET, and ET[superscript b] rates in these complexes. The [superscript 1]ET and [superscript 3]ET rates for the n = 2 and n = 3 complexes exhibit Gaussian free-energy dependence, in excellent agreement with classical ET theory (n = 2: [lambda] = 1.10 eV, H[subscript DA] = 26 cm[superscript -1]; n = 3: [lambda] = 1.05 eV and H[subscript DA] = 7 cm[superscript -1]). However, the [superscript 1]ET and [superscript 3]ET rates in n = 0 and n = 1 complexes exhibit dramatically different behavior: the [superscript 3]ET rates in these rigid complexes are on the order of 10,000 times slower than the corresponding [superscript 1]ET rates. H[subscript DA]s for the ET[superscript b] reactions (n = 1,2) are similar to those of the corresponding [superscript 1]ET reactions. These results are discussed in terms of the solution structure parameters obtained for the series of donor-acceptor complexes. Evidence that through-bond and through-space couplings play different roles in singles and triplet electron transfer is presented for the first time." }, { "name": "Ginsburg, Eric Jay", "degree": "PhD", "year": "1991", "title": "Soluble polyacetylenes by the ring-opening methathesis polymerization of substituted cyclooctatetraenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06212007-094300", "creators": [ { "name": { "family": "Ginsburg", "given": "Eric Jay" }, "id": "Ginsburg-E-J", "display_name": "Ginsburg, Eric Jay" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wqt5-ka47", "abstract": "Ring-opening metathesis polymerization has been applied to the synthesis of substituted polyacetylenes. The set of Me3M-substituted cyclooctatetraenes, where M = C, Si, Ge and Sn, have been polymerized using a well-defined tungsten alkylidene as an active metathesis catalyst. The resulting high molecular weight polyacetylenes have a substituent located at every eighth carbon atom, on the average. This substitution pattern allows substantial electronic delocalization along the main chain, in contrast to more highly substituted polyacetylenes which have been studied in the past.\n\nThe properties of the four polymers depend on the size of the side chain. As the substituent is varied from t-Bu to Me3Si to Me3Ge or Me3Sn, the absorption maximum of the polymer decreases in energy. Also, whereas poly(t-butylcyclooctatetraene) and poly(trimethylsilylcyclooctatetraene) are soluble in organic solvents, including benzene, methylene chloride, and tetrahydrofuran, the trimethylgermyl- and trimethylstannyl-substituted polymers are not totally soluble.\n\nAs synthesized, the polymers contain a high percentage of cis double bonds. They may be isomerized to a form containing mostly trans double bonds either photochemically or thermally. The trans isomers absorb at lower energy than do the cis isomers, indicating that the trans polymers can assume a more conjugated conformation. A set of visible absorption spectra obtained over the course of a photochemical isomerization contain an isosbestic point, which indicates that a number of double bonds are isomerizing simultaneously, i.e., the isomerization does not proceed a bond at a time.\n\nMolecular mechanics calculations have been used to explore the effect of the steric requirements of the side chain on the conformation of the polyene backbone. It is observed that those polyenes which are soluble are calculated to be significantly twisted because of nonbonded interactions between the substituent and the protons on adjacent carbon atoms. Substituted polyenes calculated to have a more planar conformation are found to be insoluble in the trans form.\n\ntrans-Poly(trimethylsilylcyclooctatetraene) films are greenish gold and appear metallic. After iodine doping, they have an electrical conductivity of ~ 10(-1) [omega](-1) cm(-1). The doped polymer has been used to investigate the properties of conducting polymer/silicon Schottky-type solar cells in a collaborative effort with Drs. Michael Sailor and Nathan Lewis. It was found that the polymer/semiconductor interface is not subject to Fermi-level pinning, and that the efficiency of the device is limited by the properties of the silicon, not those of the interface, in contrast to devices made with conventional metals on silicon. The third-order nonlinear optical coefficient of the undoped polymer has been measured by Dr. Joseph Perry and was found to be 2\u00b11 x 10(-11) esu.\n\nPreliminary investigations of the polymers by scanning tunneling microscopy have been initiated in collaboration with Drs. Reginald Penner and Lewis. Some images which may represent individual polymer strands have been obtained, although interpretation of the data is complicated by the appearance of defects in the underlying graphite substrate." }, { "name": "Hart, Roger A.", "degree": "PhD", "year": "1991", "title": "Characterization of Vitreoscilla hemoglobin inclusion bodies produced in Escherichia coli", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06272007-152616", "creators": [ { "name": { "family": "Hart", "given": "Roger A." }, "id": "Hart-Roger-A", "display_name": "Hart, Roger A." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7504-m295", "abstract": "The process of inclusion body (IB) formation in the gram-negative bacterium Escherichia coli (E. coli) was investigated. The homodimeric hemeprotein Vitreoscilla hemoglobin (VHb) from the gram-negative bacterium Vitreoscilla was taken as the model protein.\r\n\r\nExpression of VHb under control of its native promoter from a pUC19-derived plasmid in strain JM101 lead to high-level accumulation of VHb in both soluble and insoluble forms. The soluble form was purified by sequential two-phase extraction techniques and used as a basis for analyzing the insoluble form. The amino acid content and N-terminal sequence of purified soluble VHb is consistent with that of VHb purified from Vitreoscilla. Soluble and insoluble VHb exhibit identical migration properties during denaturing two-dimensional electrophoresis.\r\n\r\nThe protein composition of VHb inclusion bodies was analyzed by one-dimensional and two-dimensional electrophoresis techniques. Results indicate the presence of two types of cytoplasmic aggregates of differing morphology in single bacterial cells. These aggregates also differ in their relative content of VHb, pre-[beta]-lactamase, and the cytoplasmic protein elongation factor Tu and are separable by differential centrifugation.\r\n\r\nConformational properties of soluble and insoluble VHb were studied by electron paramagnetic resonance spectroscopy. Purified soluble VHb exhibits three high-spin resonances in the vicinity of g 6 from two heme centers. One center is axial (g 6.00). The other is rhombic (g 5.50 and 6.39). Inclusion body isolates containing insoluble VHb exhibit a single resonance (g 5.98) which is also present in control cell debris. Iron quantitation demonstrates that inclusion body VHb uniformly lacks heme. Titration of IB fractions with monomeric ferrous heme followed by difference absorption spectroscopy suggests that some inclusion body VHb is competent for heme binding.\r\n\r\nA series of perturbation-response experiments was conducted to determine what cellular processes influence VHb IB formation. Results show that VHb inclusion body formation is highly influenced by the expression plasmid construction and the heme biosynthetic capacity. The level of induction and accumulation appear less important than the general metabolic state of the culture. Temperature and chaperone protein levels have little effect. Efforts to reduce inclusion body formation through genetic amplification of ALA synthase and ALA dehydratase levels were unsuccessful, presumably due to regulation. Results suggest a heme biosynthetic limitation is involved in VHb in vivo insolubilization." }, { "name": "Hollenbaugh, Diane", "degree": "PhD", "year": "1991", "title": "Specificity determinants of the class A [beta]-lactamase RTEM-1", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06192007-142753", "creators": [ { "name": { "family": "Hollenbaugh", "given": "Diane" }, "id": "Hollenbaugh-D", "display_name": "Hollenbaugh, Diane" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0qza-et62", "abstract": "Factors determining the substrate specificity of RTEM-1 [beta]-lactamase have been studied with the use of cassette mutagenesis. Three studies were performed to elucidate these factors. First, two chimeric proteins were created, substituting the active site helix of RTEM-1, residues 71-82, with the corresponding sequence from PBP5 of E. coli. In Chimera2, the potential disulfide bond between Cys77 and Cys123 was preserved, whereas it was removed in Chimera1 by a C77S mutation. The expression of either chimera produced no observable phenotypic effects. Both chimeras were present in E. coli only at reduced temperatures (25\u00b0C). Chimera2 was more stable to periplasmic proteases than Chimera1, suggesting that the disulfide bond was formed, increasing the stability. The formation of the disulfide was verified by an SDS-PAGE mobility shift assay. The behavior of Chimera2 and RTEM-1 on ion-exchange and chromatofocusing columns and the circular dichroism (CD) spectra of the two enzymes suggested a significant structural difference. Chimera2 was much more sensitive to thermal denaturation than RTEM-1, as monitored by CD. Chimera2 displayed no detectable activity as a [beta]-lactamase against benzylpenicillin or as a depsipeptidase against diacetyl-Lys-D-Ala-D-lactate in assays with detection limits of 3 x 10(-3) sec(-1) and 3 x 10(-3) sec(-1), respectively. Radiolabelled acyl-enzyme could not be detected following incubation of Chimera2 with [[superscript 14] C]-benzylpenicillin.\n\nIn the second study, residues 233, 234, 235 and 237 of RTEM-1 [beta]-lactamase were substituted with residues believed to be important in the differing substrate specificities of the penicillin-recognizing enzymes. Mutants were generated to yield all possible combinations of the substitutions D233H, K234H, K234N, K234Q, S235T and A237N, resulting in thirty-two sequences, including the wild-type sequence. Results of phenotypic screening were as follows: 1) Mutants with a substitution at Lys234 were phenotypically inactive against all antibiotics tested. 2) The substitution D233H destabilized the enzyme as seen by differences in the conferred resistance at 30\u00b0C vs. 37\u00b0C. 3) The substitution S235T led to increased resistance to cephalothin compared to RTEM-1. Molecular modeling studies suggest that the instability imparted by the D233H substitution may be due to the accommodation of the five-membered ring of histidine and the loss of a favorable contact between Asp233 and Arg222. These studies also suggest that the incorporation of the methyl group in the S235T mutants into the packed space within the structure alters the orientation of the hydroxyl group. This hydroxyl group is hydrogen-bonded to the ammonium group of the conserved Lys234, which has been shown previously to be necessary in the binding of the substrate.\n\nIn the third study of RTEM-1 substrate specificity, residues 237, 238 and 240, were simultaneously randomized, and mutants were screened for the ability to confer resistance to the antibiotic cefotaxime. The three residues were chosen for study based on the sequences of the naturally occurring extended-spectrum [beta]-lactamases, which are active against the third generation cephems. Sixty-eight different mutant enzymes were found to possess extended activity. In general, small amino acids were found at position 237 (Ser, Gly, Ala, Thr), a range of residues were found at position 238 (Ala, Asn, Arg, Ser, Thr, Asp, Gly), and a positively charged residue (Lys, Arg, His) was commonly found at position 240. Glycine was found at position 238 if and only if proline was present in position 240. All of the mutants conferred a reduced level of resistance to ampicillin and benzylpenicillin compared to the wild-type RTEM-1. The majority of the mutants conferred increased resistance to cephalothin and cloxacillin. The values of kcat and KM, were determined for three of the mutants, ASK, ASE and AAK. The values of kcat on the substrate benzylpenicillin were only slightly reduced from the values obtained for the wild-type RTEM-1 enzyme. The values of KM for both benzylpenicillin and cefotaxime were reduced substantially, with the value of KM on cefotaxime for the most active mutant, ASK, reduced to 120\u00b5M, compared with Ki of > 3 mM for the wild-type RTEM-1. With a consideration of the structural differences between benzylpenicillin and cefotaxime and the results of molecular modeling studies, the results suggest that the effect of these mutations on the substrate specificity of the enzyme is not a simple enzyme-substrate contact as was previously proposed but instead suggest that the substitutions allow a conformational change not accessible to the wild-type enzyme.\n" }, { "name": "Horrell, Robin Scott", "degree": "PhD", "year": "1991", "title": "Aspects of atmospheric transport and dispersion within an air basin", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07092007-080911", "creators": [ { "name": { "family": "Horrell", "given": "Robin Scott" }, "id": "Horrell-R-S", "display_name": "Horrell, Robin Scott" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/070p-1483", "abstract": "Atmospheric transport and dispersion and their relationship to observed pollution levels are analyzed using three methods. Two traditional methods, (1) dimensional analysis and (2) atmospheric sulfur hexafluoride tracer experiments are applied to new problems; the third, (3) neural computation is a new method of looking at incomplete ozone data reconstruction, and short term ozone forecasting.\n\nA comprehensive dimensional analysis of buoyantly driven slope wind is presented to unify the subject. The functional relationship between thickness, velocity, Reynolds, Froude, Rossby and Richardson numbers of the buoyant layer and the characteristic slope parameters is established. A detailed study of the velocity and temperature profiles is done using the Von Karman-Pohlhausen (KP) integral technique. Generated profiles are in agreement with field measurements. The technique is extended to handle transient slope flows using a combination of the KP method and the method of characteristics.\n\nThe transport and dispersion of airborn emissions from Los Angeles are studied using tracer during the Southern California Air Quality Study of 1987. Emphasis is placed on emissions generated during the morning land breeze/sea breeze transition periods. Analysis of tracer transport patterns indicates emission transport from downtown Los Angeles was by two routes, and the relative importance of each route was determined by a diurnally occurring divergence zone. This zone, resulting from geography and pressure gradients, was shown to migrate east to west in the air space above Los Angeles. The zone routes a majority of morning emissions northwest of Los Angeles, contrary to the commonly held belief that morning emissions were routed east. Results were verified using surface wind trajectories constructed from telemetry data.\n\nArtificial neural computing strategies are applied to two air quality data sets for the purpose of ozone data reconstruction and forecasting at Newhall, California. The Madaline III algorithm is used to reconstruct data at a single site. The reconstruction is done to add missing data. This method is advantageous when peaks in the data are missing, and traditional interpolation methods inapplicable. Williams and Zipser's recurrent algorithm is used to make short-term ozone forecasts at a single location based on past history of ozone observations at that site. The results are systematically better than regression methods." }, { "name": "Huang, David Da-Teh", "degree": "PhD", "year": "1991", "title": "Aerosol coagulation and nucleation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06222005-162441", "creators": [ { "name": { "family": "Huang", "given": "David Da-Teh" }, "id": "Huang-D-D", "display_name": "Huang, David Da-Teh" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Okuyama", "given": "Kikuo" }, "id": "Okuyama-K", "role": "member", "display_name": "Okuyama, Kikuo" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/G2RC-S602", "abstract": "For aerosol Brownian coagulation in the transition regime of Knudsen number in the presence of an interparticle potential, the Fokker-Planck equation is solved by using the Grad's 13-moment method. The mass and energy accommodation coefficients that are used to describe the results of collisional processes are appropriately defined and interfaced with the Fokker-Planck moment equations. Analytical and numerical solutions of the number and energy flux profiles for the potential-free, power-law potential, van der Waals potential, and Coulombic potential situations are obtained. The results are in good agreement with those predicted by the flux-matching method of Fuchs. The present fundamental approach, therefore, provides theoretical support of the coagulation coefficient expression obtained by the empirical flux-matching method.\n \nFor coagulation between ultrafine particles, we solved the BGK equation for large but finite Knudsen number situations by taking into account the van der Waals potential and/or the Coulombic/image potential. We present closed form best-fit equations for data calculated from the theory. The conditions where either Coulombic, image, or van der Waals forces predominate are determined.\n\nA new expression of the image potential between a charged particle and an uncharged particle is obtained. We calculate the coagulation rate between the particles and are able to determine the enhancement of coagulation rate due to the interparticle potential in all size regimes.\n\nAn aerosol coagulation process is applied to the formation of aerosol particles in the semiconductor thin film preparation. In the CVD reactor, we consider simultaneous aerosol coagulation, diffusion, and generation of aerosol monomers by chemical reaction. The mass and number concentration of monomers and particles are computed as functions of temperature, pressure, input vapor concentration, and position in the reactor. The thin film growth rate can be subsequently evaluated. It is found that under certain circumstances, aerosol particle generation may significantly suppress the film growth due to monomers.\n\nThe formulation of the homogeneous nucleation free energy change of aerosol clusters is reexamined. It is shown that the inclusion of the cluster translational and rotational motion in the cluster formation free energy change is appropriate. The classical and statistical thermodynamics are shown to be consistent.\n\nThe cell model of liquids of statistical mechanics is employed to reevaluate the free energy change of cluster formation in aerosol nucleation. We provide a new molecular level theory that is applicable in the larger cluster size range where liquid-like properties begin to emerge and a cluster surface is present. The microcluster surface tension can be appropriately defined. The cluster rotational contribution to the free energy change, though it must be accounted for, is shown to be insignificant for liquid-like clusters.\n" }, { "name": "Irikura, Karl Kensuke Mason", "degree": "PhD", "year": "1991", "title": "Gas-Phase Chemistry of Organotransition Metal Ions", "advisor": "Goddard, William A., III; Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06202007-111048", "creators": [ { "name": { "family": "Irikura", "given": "Karl Kensuke Mason" }, "id": "Irikura-Karl-Kensuke-Mason", "display_name": "Irikura, Karl Kensuke Mason" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "co-advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/REZ3-DD85", "abstract": "The gas-phase chemistry of many transition metal ions has been investigated by Fourier transform ion cyclotron resonance spectrometry (FTICR). Emphasis is on organometallic chemistry, including an application to geochronology, but inorganic and bio-inorganic systems have also been investigated. Quantum chemical calculations have been performed to address problems in interstellar chemistry and also traditional physical organic chemistry.
\r\n\r\nChapter I is concerned with the chemistry of ions OsOn+(n=0-4) with several small molecules, including methane. A wide variety of reactions are observed, including many that are archetypes for fundamental mechanistic processes in organometallic chemistry. In Chapter II, the differences in the gas-phase chemistry of Os+ and Re+ are applied to analytical problems associated with the 187RE-187 dating method, which is important in geology.
\r\n\r\nChapter III is a survey of the reactivity of third-row transition metal ions, with emphasis on the unusual reactions involving methane. Fundamental concepts that have proven useful in the interpretation of chemistry in the first and second transition series are also applicable in the third row.
\r\n\r\nChapter IV describes the gas-phase synthesis of positive and negative metalloporphyrin ions by reactions of metal-containing ions with porphine vapor. Chapter V presents some possibilities for transition metal catalysis in interstellar clouds. A very low value is calculated for the rate of radiative association of Fe+ and hydrogen atoms, suggesting that transition metal chemistry is not important in these systems.
\r\n\r\nChapter VI involves scaling the results of ab initio calculations in order to predict accurate singlet-triplet energy gaps in many substituted carbenes. Observed trends are rationalized using a synergistic bonding model. A simple relationship based upon electronegativity is presented to permit carbene singlet-triplet gaps to be computed using minimal resources, such as a hand calculator.
\r\n\r\nChapter VII deals with five different experimental issues that have arisen during FTICR studies of reactive transition metal ions. Difficulties, helpful techniques, and data analysis are discussed.
" }, { "name": "Jacobs, Bradley Anson", "degree": "PhD", "year": "1991", "title": "Preparation, characterization, and intramolecular electron transfer in pentaammineruthenium-modified derivatives of cytochrome b5 and azurin", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06292007-133449", "creators": [ { "name": { "family": "Jacobs", "given": "Bradley Anson" }, "id": "Jacobs-B-A", "display_name": "Jacobs, Bradley Anson" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cgbx-aq84", "abstract": "Wild-type, mutant, and deuteroporphyrin-substituted bovine cytochrome b5 have been modified with pentaammineruthenium (a5Ru) for intramolecular electron-transfer (ET) studies. The reactivity of the three surface histidines of the wild-type trypsinsolubilized protein (WT-b5) with [a5Ru(OH2)]2+ increases in the order His-15 < His-80 < His-26. Intramolecular ET rates from Fe(II) to Ru(IlI) have been measured by flash photolysis for a5Ru(His-26)-modified WT-b5, Ru(H26)WT-b5; mutant (asn-57 to Asp, Gln-13 to Glu, Glu-11 to Gln, His-15 to Asn, His-80 to Asn) lipase-solubilized cyt b5, Ru(H26)LM-b5; and deuteroporphyrin-substituted WT-b5, Ru(H26)DP-b5. The observed rates display a weak concentration dependence (0.5 - 3 \u00b5M protein, \u00b5 = 0.5 M sodium phosphate, ph 7.0 25\u00b0C): kET = 1.4(1)s[superscript-1], Ru(H26)WT-b5; 5.9(5) s[superscript-1], Ru(H26)LM-b5; and 0.2(1)s[superscript-1], Ru(H26)DP-b5. The rates do not directly correspond to differences in driving force (-0.08, -0.10, -0.13 eV) or edge-to-edge, donor-acceptor separation (12.1, 12, 12.9 A). Evaluation of the donor-acceptor electronic coupling (HAB) in terms of specific through-bond and through-space interactions in the intervening medium for Ru(H26)WT-b5 and Ru(H26)LM-b5 revealed a probable ET pathway consisting of eight covalent bonds from C[gamma] of His-26 to the end of the Leu-25 side chain, then a through-space jump (R = 3.8, 3.7 A) to the heme 2-vinyl. Ru(H26)DP-b5 lacks the 2-vinyl, requiring a longer jump (R = 4.5 A) to the heme 3-methyl. Because HAB is predicted to decay rapidly with R, the calculated rate constants (assuming [lambda] = 1.2 eV reflect the differences in R for the three derivatives: Ru(H26)WT-b5, 1.9 s[superscript-1]; Ru(H26)LM-b5, 4.4 s[superscript-1]; Ru(H26)DP-b5, 0.16 s[superscript-1]. The close agreement of calculated and observed rate constants indicates that the electronic coupling in this system is reasonably described by the (His-26)(Leu-25)(through-space jump to heme) pathway. The ET rate in a mutant (His-26 to Arg), trypsin-solubilized cyt b5 modified with a5Ru3+ at His-80 was also measured. As expected from the long donor-acceptor separation (21 A) and poor electronic coupling predicted by pathway analysis, kET was within experimental error of 0 s[superscript-1].\n\nAzurin from Alcaligenes denitrificans was singly modified at His-83 with asRu3+; the other surface histidine (32) was not successfully modified. The intramolecular ET rate from Ru(II) to Cu(II) for Ru(H83)Az was measured (1.0(3) s[superscript-1]) and was found to be comparable to that reported for the analogous ruthenium-modified P. a. azurin. These rates are slower than would be expected for a similar distance in cytochrome c. The application of a pathway theoretical model to both the P. a. and A. d. azurin systems showed no evidence that the \u00df-sheet secondary structure of azurin precludes effective electronic coupling. This suggests that weak electronic coupling to the copper site itself is responsible for the low kET's in azurin.\n" }, { "name": "Koh, Christopher James", "degree": "PhD", "year": "1991", "title": "Experimental and theoretical studies on two-phase flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-06062005-103146", "creators": [ { "name": { "family": "Koh", "given": "Christopher James" }, "id": "Koh-C-J", "display_name": "Koh, Christopher James" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RYPY-W035", "abstract": "This thesis, comprised of two parts, deals with the flow of suspensions. Part I concerns specifically with the stability of a single drop translating through a quiescent, unbounded suspending fluid at low Reynolds number. The evolution of the shape of an initially nonspherical drop as it translates is studied numerically and experimentally. For finite capillary numbers, it is shown that the drop reverts to a sphere provided that the initial deformation is small enough. However, beyond certain critical initial deformation, the drop deforms continuously. For initially prolate shapes, the drop elongates with the formation of a tail; for initially oblate shapes, the drop flattens with the formation of a cavity at its rear. Experiments extend the numerical results. It is found that initially unstable prolate drops break up into multiple droplets, while initially unstable oblate drops deform in double-emulsion drops.\n\nPart II of this thesis considers the flow of high concentration solid suspensions through a rectangular channel. By adapting the well-known Laser Doppler Anemometry, an experimental technique is developed to measure the velocity as well as particle volume fraction of the suspension. A crucial element in these experiments is the reduction of the optical turbidity of the suspension. To accomplish this goal, a systematic method based on refractive-index-matching of the two phases is employed. Experimental results show that the velocity profile is blunted while the concentration profile has a maximum near the center. The qualitative features of the experimental data compare reasonably well with theoretical predictions based on the shear-induced particle migration theory.\n" }, { "name": "Koh, Jong Sung", "degree": "PhD", "year": "1991", "title": "Design of novel bases for recognition of GC base pairs by oligonucleotide-directed triple helix formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11292005-133156", "creators": [ { "name": { "family": "Koh", "given": "Jong Sung" }, "id": "Koh-J-S", "display_name": "Koh, Jong Sung" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "role": "member", "display_name": "Imperiali, Barbara" }, { "name": { "family": "Rees", "given": "Douglas C." }, "id": "Rees-D-C", "role": "member", "display_name": "Rees, Douglas C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9655-mf61", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nPart I: Triple Helix Formation by Oligonucleotide Analogs on Double-Stranded DNA\n\nChapter 1: Design of Novel Bases for pH-Independent Recognition of GC Base Pairs by Triple Helix Formation\n\nThe ability to design synthetic molecules that bind sequence-specifically to unique sites on human DNA could have major applications in the treatment of genetic, neoplastic, and viral diseases. One powerful approach to sequence-specific binding of double helical DNA is oligonucleotide-directed triple helix formation. Specificity arises from the base triplets ([...] and C+GC) formed by Hoogsteen base pairing of the second pyrimidine strand with the purine strand of the double helix. Because protonation of the N3 is required for cytosine, triple helix formation at rich sequences is limited to a narrow pH range. The novel base 3-methyl-5-amino-7H-pyrazolo(4, 3-d)pyrimidine-7-one (P1) specifically recognizes GC base pairs as selectively and strongly as C+, but with greater affinity and over an extended pH range. Such selectivities allow binding at a 15 base pair site in pDMAG10 DNA (pH 7.8) containing [...] and at a 16 base pair site in pHIV-CAT DNA (pH 7.4, 37[degrees]C) containing [...].\n\nChapter 2: Extension of Triple Helix Formation. Design of Novel Bases for Recognition of CG Base Pairs\n\nOligonucleotide recognition offers a powerful chemical approach for the sequence-specific binding of double-helical DNA. Because pyrimidine oligonucleotides limit triple helix formation to homopurine tracts containing AT and GC base pairs, it is desirable to study whether oligonucleotides can be designed to bind to all four base pairs. A general solution would allow targeting of oligonucleotides to any sequence. The novel base 3-methyl-5-amino-7H-pyrazolo(4, 3-d)pyrimidine-7-one (P1) and cytosine (C) moderately recognize CG base pairs. Such specificities allow binding at an 18 base pair site in SV 40 (pH 7.0, 37[degrees]C) DNA containing all four base pairs.\n\nPart II: Design of DNA Cleaving Groups\n\nChapter 3: Design of New DNA Cleaving Fuctional Groups and Studies of Their DNA Cleaving Mechanisms\n\nThe utility of the DNA cleaving molecules is enormous, ranging from the creation of synthetic restriction enzymes for use by molecular biologists to the development of chemotherapeutic agents which may be effective against a variety of neoplastic diseases. We synthesized three compounds: 12 (P3-Ga-His), 19 (P3-Ga-PYML), and 23 (P3-Ga-Phe). Compound 12 shows sequence-specific cleavage in the presence of Cu(II) and dioxygen, while compound 19 shows sequence-specific cleavage in the presence of dithiothreitol and dioxygen. Interestingly, compound 23 shows strong cleavage at a single site in 167 base pair fragment (EcoRI/RsaI) from plasmid pBR322 in the presence of UV light and [beta]-carbonato(trien)cobalt(III)perchlorate complex. The end product analysis of the cleaved oligonucleotide shows 5'-phosphate, 3'-phosphate, and an unknown 3'-product.\n" }, { "name": "Kosinski, Michael J.", "degree": "PhD", "year": "1991", "title": "Degradation kinetics of an abnormal beta-galactosidase in Escherichia coli", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06222007-141447", "creators": [ { "name": { "family": "Kosinski", "given": "Michael J." }, "id": "Kosinski-M-J", "display_name": "Kosinski, Michael J." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pcv7-rb38", "abstract": "Many recombinant proteins expressed in Escherichia coli are identified by the cell as abnormal and are degraded rapidly. As a model protein, we employed an unstable fragment of E. coil beta-galactosidase, the CSH11 mutant, coded by a single copy in the chromosome. This experimental system enabled identification of the process and cellular variables having the greatest impact on the degradation rate of abnormal proteins.\n\nThe in vivo degradation rates were measured using pulse-chase radioactive labeling techniques, and intracellular concentrations were determined using [alpha]-complementation assays. The degradation of the CSH11 fragment was sensitive to the culture temperature and approximately followed Arrhenius behavior, but the apparent degradative rate constant for its 90 kDa degradative intermediate increased by an order of magnitude between 37 and 40\u00b0C. The apparent rate constants for both beta-galactosidase fragments inexplicably decreased with increasing induction level. There was no aggregation of the fragments to account for this decrease in rate constants.\n\nCellular protease levels were determined using an in vitro assay of cell extracts. The ATP-independent proteases were not induced when the abnormal beta-galactosidase was expressed, and their level decreased by 20% from 37\u00b0 to 42\u00b0C. Expression of the abnormal protein caused a doubling in the ATP-dependent proteolytic activity. This ATP-dependent activity also increased 2.5-fold from 30\u00b0 to 42\u00b0C with induction of the abnormal protein.\n\nStress (heat shock-like) responses were detected by radioactive pulse- labeling of cellular proteins and analysis by one- and two-dimensional PAGE. There was no response to induction of the abnormal beta-galactosidase at 30\u00b0C, even though the concentration of abnormal protein was approximately the same as at 37\u00b0C where a stress response was observed. Determined with the protease assay, ATP-dependent proteolytic activity was associated with the stress proteins independent of protease La.\n\nProteolytic susceptibility to [alpha]-chymotrypsin correlated well with the thermal stability of the affinity purified, beta-galactosidase fragments. Thermal instability of the 90 kDa intermediate is the likely cause of the significant increase in its in vivo degradation rate between 37\u00b0 and 40\u00b0C.\n" }, { "name": "Labgold, Marc Robert", "degree": "PhD", "year": "1991", "title": "Novel Biological Catalysts: Mutagenesis of RTEM \u03b2-Lactamase to Alter Substrate and Catalytic Specificity", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07092007-104132", "creators": [ { "name": { "family": "Labgold", "given": "Marc Robert" }, "id": "Labgold-Marc-Robert", "display_name": "Labgold, Marc Robert" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m8m6-yc79", "abstract": "I have used the techniques of site-directed mutagenesis to study the structural requirements for substrate specificity in RTEM-1 \u03b2-lactamase and the evolutionary relationship between the \u03b2-lactamases and the D,D carboxypeptidases. The D-Ala-D-Ala carboxypeptidases/transpeptidases (penicillin-binding proteins, PBPs) share considerable structural homology with class A \u03b2-lactamases. Both enzymes recognize the \u03b2-lactam antibiotics as substrates; however, the \u03b2-lactamases have no observable D,D-carboxypeptidase activity.
\r\n\r\nTo investigate the possibility of incorporating D,D-carboxypeptidase activity into [\u03b2-lactamase a chimeric protein was prepared by replacing a 28 amino acid sequence of \u03b2-lactamase with the corresponding sequence from PBP-5 of E. coli. The resulting chimera was capable of hydrolyzing the D-Ala-D-Ala dipeptide; however, it was determined that a secondary mutation had occurred which inserted a glutamic acid residue between residues 59 and 60.
\r\n\r\nIn Chapter 2, I have performed site-directed mutagenesis on the gene encoding the RTEM-1 PBP-5 chimera to delete the additional residue. The resulting chimera was not thermally stable at 37\u00b0C, but is stabilized by interaction with \u03b2-lactam compounds such as ampicillin. Despite the finding that the \u03b2-lactamase activity was reduced by five orders of magnitude, the chimera displays approximately one percent of the D,D carboxypeptidase activity exhibited by wild-type PBP-5.
\r\n\r\nIn Chapter 3, to further investigate the proposed evolutionary relationship between the PBPs and \u03b2-lactamase, I have designed a series of chimeras between the R61 carboxypeptidase/transpeptidase of Streptomyces and RTEM-1 \u03b2-lactamase. The design of the chimeras involved building a chimeric substrate binding cavity within the RTEM framework. One chimera (Asp131Asn, Asnl32Phe) was thermally stable and exhibited altered cell morphology in E. coli harboring the chimeric gene.
\r\n\r\nIn Chapter 4, I describe the detailed kinetic analysis of the Asn l32Phe, single-mutant chimera, and the Asp 13 lAsn/Asn l32Phe, double-mutant chimera. The double mutant shows tremendously altered catalytic activity, degrading benzyl penicillin to phenylacetyiglycine and producing the corresponding transpeptidase product, phenylacetyiglycylglycine, when reacted in the presence of glycine. The single mutant, Asnl32Phe, shows no such activity. Furthermore, I have shown that while the Asnl32Phe mutation blocks deacylation in the chimeric proteins, when produced in conjunction with the Aspl3lAsn mutation, the resulting chimera is capable of carboxypeptidase/transpeptidase activity.
\r\n\r\nFinally, in Appendix I, the description of the site-saturation of RTEM-1 residue 237 is included. Two mutants, Ala237Thr and Ala237Asn, exhibited enhanced preference for cephem over penam antibiotics. The phenotypic screening of all 19 mutants is described.
" }, { "name": "Laroche, Lionel", "degree": "PhD", "year": "1991", "title": "Homogeneous Azeotropic Distillation: Entrainer Selection", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-11162005-143300", "creators": [ { "name": { "family": "Laroche", "given": "Lionel" }, "id": "Laroche-Lionel", "display_name": "Laroche, Lionel" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/V760-0555", "abstract": "We examine the simplest homogeneous azeotropic distillation sequence of industrial relevance, where we add an entrainer to a binary azeotrope in order to recover both azeotropic constituents as pure products. Despite its apparent simplicity, such distillation columns can exhibit an unusual behavior not observed in zeotropic distillation:
\r\n\r\n- For some mixtures, separation as a function of reflux goes through a maximum. At infinite reflux, no separation is achieved.
\r\n\r\n- In some cases, achieving the same specifications with a larger number of trays requires a larger reflux.
\r\n\r\n- In some cases the only feasible separation yields the intermediate component as a pure distillate while the bottom product contains the light and heavy components.
\r\n\r\n- In some cases the only feasible separation yields the intermediate component as a pure bottom product while the distillate contains the light and Hay components.
While these unusual features can be regarded as curiosities, they are essential for proper entrainer selection and design. When designing a homogeneous azeotropic sequence which separates a binary azeotrope into two pure products, we must first choose the entrainer. Currently available entrainer selection criteria, are inadequate: They contradict one another and often lead to incorrect conclusions. Indeed, for a minimum boiling azeotrope, the existing entrainer selection rules state that, one should use a high boiling component that introduces no additional azeotrope (Benedict & Rubin 1945), an intermediate boiling component that introduces no additional azeotrope (Hoffman 1964), a component which introduces no distillation boundary between the azeotropic constituents (Doherty & Caldarola 1985), and either a low boiling component that introduces no additional azeotrope or a component that introduces new minimum boiling azeotropes (Stichlmair, Fair & Bravo 1989). By taking advantage of the curious aforementioned features, we have been able to understand when these criteria, are correct, or incorrect.
\r\n\r\nIn the case of homogeneous azeotropic distillation, separability at finite reflex and at infinite reflux are not equivalent and must be examined separately. By analyzing in detail the profiles of columns operated at infinite reflux, we have:
\r\n\r\n- shown that a binary azeotrope can be separated with only one distillation column. We present a necessary and sufficient condition that identifies such situations;
\r\n\r\n- found a necessary and sufficient condition for separability in a two-column sequence. When separation is feasible, this condition indicates the flowsheet of the corresponding separation sequence;
\r\n\r\n- shown that separation is very often feasible in a three-column separation if the two azeotropic constituents are located in adjacent distillation regions.
Then, we examine two situations where separation is feasible at finite reflux but not at infinite reflex.
\r\n\r\nFinally, we present practical solutions (in the case of entrainers that add no azeotropes to two problems of industrial relevance: Given a binary azeotrope that we want to separate into pure components, and a set of candidate entrainers, how do we determine which one is the best? Also, for each of these entrainers, what is the flowsheet of the feasible separation sequence(s)? We obtain these solutions by analyzing in detail the mechanisms by which heavy, intermediate and light entrainers make separation feasible, using the new notions of equivolatility curves, of isovolatility curves and of local volatility order. We show that the second question finds an easy solution from the volatility order diagram.
\r\n\r\nThis analysis shows that a good entrainer is a component that \"breaks\" the azeotrope easily (i.e., even when its concentration is small) and yields high relative volatilities between the two azeotropic consituents. Because these attributes can be easily identified in an entrainer from the equivolatility curve diagram of the ternary mixture azeotropic component #1 - azeotropic component #2 - entrainer, we can easily compare entrainers by examining the corresponding equivolatility curve diagrams. We also demonstrate the validity and limits of this method with numerous examples.
\r\n" }, { "name": "Lee, Jay Hyung", "degree": "PhD", "year": "1991", "title": "Robust Inferential Control: A Methodology for Control Structure Selection and Inferential Control System Design in the Presence of Model/Plant Mismatch", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-11162005-134952", "creators": [ { "name": { "family": "Lee", "given": "Jay Hyung" }, "id": "Lee-Jay-Hyung", "display_name": "Lee, Jay Hyung" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/3dp3-ba80", "abstract": "Two major tasks that are required to obtain a control system utilizing secondary measurements are measurement selection and inferential control system design. The first involves choosing an appropriate subset of the available measurements and the second involves designing a feedback controller based on the chosen measurements. The important issues to be addressed are not only the theoretical performance of the closed-loop system, but also the effects arising from the factors prevalent in practical environments such as model/plant mismatch, constraints, and failures of actuators and sensors.
\r\n\r\nGeneral measurement selection methodology is developed accounting for all the factors that can affect the measurement selection in signifcant ways. These factors include model uncertainty, signal-to-noise ratios, and measurement dynamics. The underlying philosophy is to reduce the number of candidates to a sufficiently low level before going onto detailed analysis by eliminating those candidates for which there does not exist a linear time-invariant controller meeting the required level of robust performance. Based on this philosophy and using the Structured Singular Value theory as a vehicle, a number of numerically efficient screening tools are developed. Conditions are derived under which some of the new criteria reduce to previously published measurement selection criteria. The proposed tools are applied to the measurement selection problems in a multi-component distillation column and a high-purity distillation column.
\r\n\r\nTwo different approaches are considered for inferential control system design: an output estimation based design approach and a state estimation based design approach. The former approach involves independent design of an output estimator and a feedback controller while the latter involves direct one step design although the design can be actually separated into those of a state estimator and of a feedback regulator using the separation principle argument.
\r\n\r\nFor the former approach, design of the output estimator was examined for two different cases: the case where a full dynamic model is available and the case where only the time records of the primary and secondary measurements are available either from simulations or from process measurements. For the former case, multi-rate Kalman filter design and \u03bc-Synthesis design are discussed. For the latter case, the estimator design problem is formulated as a regression problem and various regression techniques are evaluated in terms of their suitability to the output estimator design problem. For design of the feedback controller, traditional techniques such as LQG, IMC, and MPC were combined into a control technique that has nice algorithmic properties as well as many operational merits such as straightforward constraint handling and simple, intuitive on-line tuning. A heavy-oil fractionator was used as an example application.
\r\n\r\nFor the latter approach, general state estimation techniques (e.g., multi-rate Kalman filtering) used in LQG and finite receding horizon control used in traditional MPC were integrated into a control technique that can incorporate general disturbances and multi-rate sampled measurements and has desirable operational characteristics. The concept of classical IMC was extended to equip the control system with on-line tuning parameters that have direct connections with the speed of the closed-loop responses. Application to a high purity distillation column demonstrates the effectiveness of the control technique in terms of closed-loop performance and operational flexibility.
" }, { "name": "Long, David M.", "degree": "PhD", "year": "1991", "title": "Structure and mechanism of RTEM-1 [beta]-lactamase : the role of lysine 234", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06272007-133916", "creators": [ { "name": { "family": "Long", "given": "David M." }, "id": "Long-D-M", "display_name": "Long, David M." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p6e6-vp61", "abstract": "Site-saturation mutagenesis has been used to substitute lysine 234 in RTEM-1 [beta]-lactamase with 18 natural amino acids. Lysine 234 is conserved among the class A [beta]-lactamases and has been implicated in x-ray diffraction and molecular modeling studies as a cationic residue that binds the C3 carboxylate common to most [beta]-lactamase substrates (Hertzberg and Moult (1987) Science, 236, 694.; Meows et al. (1990) PROTEINS: Structure, Function, and Genetics, 7, 156.; Chapter 2 of this Thesis).\n\nThe 234 mutant proteins have significantly reduced activity towards hydrolysis of penicillin, ampicillin, and cephalosporin C and do not have observable phenotypic activity towards hydrolysis of cephalothin. With the exception of K234R, the phenotypic activities are essentially indistinguishable. The high phenotypic resistance of the K234R mutant shows that a positively charged guanidinium group can effectively substitute for the wild-type ammonium group of lysine 234. The uniformly reduced phenotypic activities of all other mutants indicate that the mutant amino acids do not interfere with or participate directly in the enzymatic reaction mechanism. Behavior of the mutants on anion exchange columns and analysis by circular dichroism spectroscopy show that the secondary and tertiary structures characteristic of the wild-type enzyme are not significantly disrupted by mutation.\n\nFour mutants were purified to homogeneity and the steady-state kinetic parameters for hydrolysis of benzylpenicillin were measured for each. The kinetics show that substituting lysine 234 with glutamate, glutamine, or valine causes a decrease in the apparent equilibrium-binding constant for benzylpenicillin of about three orders of magnitude. In contrast, the binding constant for the K234R mutant, which preserves the positive charge at position 234, is reduced by only one order of magnitude. These results indicate that lysine 234 is responsible for stabilizing the RTEM-1/benzylpenicillin complexes by approximately 4.5 kcal mol(-1), consistent with the formation of an intermolecular charged hydrogen bond.\n\nThe mutations have much less pronounced effects on the ability of the enzyme to catalyze the hydrolysis of benzylpenicillin under saturating substrate concentrations. K234R and K234E have the wild-type kcat, while K234Q and K234V have kcats reduced by one and two orders of magnitude, respectively.\n\nAnalysis of the kinetic results shows that lysine 234 performs a uniform binding function in catalysis by RTEM-1 lactamase (Albery and Knowles (1976) Biochemistry, 15, 5631). This contrasts with the differential binding role that has been determined for lysine 234 in catalysis by [beta]-lactamase from Bacillus licheniformis (BL) (Ellerby et al. (1990), Biochemistry, 29, 5797). The results indicate that RTEM-1 utilizes the binding capabilities of lysine 234 to increase the catalytic rate under low substrate concentrations, while BL utilizes it to increase the rate under conditions of high substrate concentration.\n\nIn Chapter 2, molecular modeling of the RTEM-1 [beta]-lactamase active site is described. The models were based on the published [alpha]-carbon trace of [beta]-lactamase from Staphylococcus aureus PC1 (Hertzberg and Moult, ibid.) and were built in the absence of an experimentally determined high-resolution x-ray structure of a class A [beta]-lactamase. The experiments were designed to yield structures useful for rationalizing the results of mutagenesis experiments and for formulating mechanistic ideas testable by experiment. The model structures are shown to compare favorably with the high-resolution structure of a class A [beta]-lactamase published after the modeling was completed. Two working mechanisms for catalysis by RTEM-1 are proposed, based on the modeling, mutagenesis results, and on precedent.\n\nChapter four describes the development of methods for measuring enzymatic reaction rates with circular dichroism spectroscopy (CD). Application of the methods to two enzymes, [beta]-lactamase and ribulose-1,5-bisphosphate carboxylase/oxygenase, is described. The general utility of the methods is addressed." }, { "name": "Mack, David Phillip", "degree": "PhD", "year": "1991", "title": "Design and chemical synthesis of sequence specific DNA cleaving metalloproteins", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06282007-112041", "creators": [ { "name": { "family": "Mack", "given": "David Phillip" }, "id": "Mack-D-P", "display_name": "Mack, David Phillip" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x5gq-8t63", "abstract": "Part I: Affinity Cleaving Studies of the DNA Binding Domain of Hin Recombinase.\n\nPrevious studies have shown that attachment of ethylenediaminetetraacetic acid (EDTA) to the NH2 terminus of the DNA binding domain of Hin recombinase creates an affinity cleaving molecule. The DNA cleavage pattern produced by this molecule has allowed a model for the DNA binding domain to be put forward which includes the NH2 terminus binding in the minor groove and a helix-turn-helix structure binding in the major groove. In this work the affinity cleaving methodology has been extended by placing the EDTA on a lysine side chain. Differential protection of the [alpha]- and [epsilon]- amino groups of lysine has allowed EDTA to be attached at the COOH terminus and at an internal position of the protein. Using these techniques EDTA has been attached at the COOH and NH2 terminus of the recognition helix of the DNA binding domain of Hin recombinase. Affinity cleaving studies with these molecules allows the orientation of the recognition helix on the DNA to be determined, as well as refine our model of the protein-DNA complex. The techniques developed are general and offer a powerful tool for examining the nature of protein-DNA complexes in the absence of crystallographic or NMR data.\n\nPart II: Design of a DNA Cleaving Protein Consisting of Only Natural Amino Acids.\n\nAttachment of the metal binding tripeptide, Gly-Gly-His, to the amino terminus of the DNA binding domain of Hin recombinase (residues 139-190) creates a new 55 residue protein containing only naturally occurring [alpha]-amino acids, GGH(Hin 139-190), with two structural domains each with distinct functions, sequence-specific recognition and cleavage of double helical DNA. This protein has been shown by footprinting to be competent to bind at four Hin sites, each 13 base pairs in length. In the presence of Cu(II), hydrogen peroxide and sodium ascorbate strong cleavage of the DNA occurs at one of the four sites by oxidative degradation of the deoxyribose backbone. Further, in the presence of Ni(II) and an oxygen atom source (eg. monoperoxyphthalic acid), the sequence specificity and efficiency of the DNA cleavage are remarkably altered. The nickel-mediated cleavage occurs at all four binding sites, is more rapid and efficient, and requires only one equivalent of an oxygen atom donor. At the hixL site, cleavage occurs predominantly at a single deoxyribose position on one strand of each binding site. Studies show that modification of the ligand system, Gly-Gly-His, can have tremendous effects on the intensity and position of DNA cleavage, and further, that for DNA cleavage mediated by the Ni(II)-protein a free amino terminus is required. Mechanistic studies indicate that the DNA cleavage by Ni(II)\u2022GGH(Hin 139-190) likely results from abstraction of the C-4' hydrogen atom from the deoxyribose backbone by a high valent nickel-oxo species to produce a base labile modification. The tripeptide Gly-Gly-His thus is a metal specific structural domain with the function of substrate directed oxidation." }, { "name": "Nelson, Janet Elizabeth", "degree": "PhD", "year": "1991", "title": "Synthetic, Structural, and Mechanistic Studies in Early Transition Metal and Actinide Chemistry", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07192007-074200", "creators": [ { "name": { "family": "Nelson", "given": "Janet Elizabeth" }, "id": "Nelson-Janet-Elizabeth", "display_name": "Nelson, Janet Elizabeth" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Labinger", "given": "Jay A." }, "id": "Labinger-J-A", "orcid": "0000-0002-1942-9232", "role": "member", "display_name": "Labinger, Jay A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qwqn-0x07", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA series of permethyltantalocene thioaldehyde hydride complexes is prepared by treatment of Cp*2Ta([eta superscript 2]-C6H4)H with thiols. The X-ray structure of Cp*2Ta([eta superscript 2]-S=CHCH2Ph)H is reported. These permethyltantalocene thioaldehyde hydride complexes are shown to be in rapid equilibrium with a 16 electron thiolate species through a beta-H elimination/migration process. Upon heating, the permethyltantalocene thioaldehyde hydride complexes undergo an a-alkyl migration to the thermodynamically favored tautomer, the permethyltantalocene sulfido alkyl, Cp*2Ta(=S)CH2R. Derivatives of the permethyltantalocene phenethylthioaldehyde hydride have been prepared from the erythro- and threo-phenethyl-d2 mercaptan to elucidate the mechanism of this migration. The migration has been found to proceed primarily with retention of stereochemistry at carbon for the migrating alkyl.\r\n\r\nIn contrast to the extremely specific regioselectivity and stereoselectivity normally demonstrated by Schwartz's reagent (Cp2ZrHCl), hydrozirconation of styrene shows two unusual behaviors. First, treatment of Cp2ZrHCl with styrene leads to a mixture of terminal (85%) and internal (15%) insertion products. The benzylic insertion product is stable, and does not undergo migration to a terminal organozirconium product, even when heated. Second, attempts to prepare stereospecifically labeled deutero organozirconium derivatives result in scrambling of the 6 positions of both isomers, yielding a statistical distribution of isotopomers. The features of this scrambling process are described and a mechanism involving an organozirconium alkyl hydride species is proposed.\r\n\r\n[K(THF)2]2[U(NHAr)5] [...] THF, (Ar = 2,6-diisopropylphenyl) is prepared by treatment of Ul3(THF)4 with five equivalents of potassium 2,6-diisopropylanilide (KNHAr) in THF. Electronic absorption spectra reveal internal f-f transitions characteristic of trivalent uranium. A single crystal X-ray study revealed that the dianion is a monomer containing a trigonal bipyramidal five-coordinate uranium center. The potassium cations each interact in an [eta]6 and [eta]4 fashion with two arene rings of the arylamido ligands, and two THF molecules. Crystal data (at -70[degrees] C): Monoclinic space group P2[1]/C, with a = [...], and Z = 4." }, { "name": "Pandis, Spyros N.", "degree": "PhD", "year": "1991", "title": "Studies of physicochemical processes in atmospheric particles and acid deposition", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05062004-154106", "creators": [ { "name": { "family": "Pandis", "given": "Spyros N." }, "id": "Pandis-S-N", "orcid": "0000-0001-8085-9795", "display_name": "Pandis, Spyros N." } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z6AN-AJ83", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAtmospheric particles, or particulate matter, can be solid or liquid with diameters varying from around 0.002[micrometers] to roughly 100[micrometers]. Atmospheric aerosol sources can be classified as primary or secondary, with the primary aerosol being directly emitted from the corresponding sources and the secondary particles being formed in the atmosphere, for example, from gas-phase chemical reactions that produce condensable vapors. At the same time aerosol particles are ultimately connected with the formation of water droplets and equivalently with the formation of clouds and fogs in the atmosphere.\r\n\r\nThe first part of this thesis concerns the mathematical modeling of wet and dry acid deposition and of the relevant physicochemical processes. Acid deposition consists of the delivery of acidic substances, principally sulfuric and nitric acid, from the atmosphere to the earth's surface. Upon emission to the atmosphere, SO2 and NOx, are photochemically oxidized, yielding sulfuric and nitric acid vapors. Sulfuric acid is rapidly incorporated into aerosol particles, while nitric acid may be scavenged by particles or droplets or remain in the gas phase. Even in the absence of an aqueous phase (no clouds or fog), the acidic gases and dry particles can be transported to and deposited at ground level; this process is called dry deposition. When an aqueous phase is present (inside a cloud or a fog), gas-phase species like SO2, HNO3, NH3 and aerosol particles are scavenged by water droplets resulting in a solution that can be significantly acidic. Additional cloudwater or fogwater acidity beyond that attained purely from scavenging of gases and particles results from aqueous-phase chemistry, most notably oxidation of dissolved SO2 to sulfuric acid. These acidic droplets can reach the earth's surface either as precipitation or as impacted cloud and fogwater, in the processes termed wet deposition. If they are not rained or deposited out the aqueous droplets can evaporate leaving as residue new aerosol particles that may themselves undergo dry deposition to the earth's surface. The effects of acid deposition include soil and lake acidification, forest decline and deterioration of cultural monuments.\r\n\r\nMathematical models are a major tool in our effort to understand and ultimately control acid deposition. The development of such a mathematical model represents a major challenge as it requires the ability to describe the entire range of atmospheric physicochemical phenomena.\r\n\r\nAs a first step in the modeling, a comprehensive chemical mechanism for aqueous-phase atmospheric chemistry was developed and its detailed sensitivity analysis was performed. The main aqueous-phase reaction pathways for the system are the oxidation of S(IV) to S(VI) by H2O2, OH, HO2, O2 (catalysed by Fe3+ and Mn2+), O3, and [...]. The dominant pathway for HNO3(aq) acidity is scavenging of nitric acid from the gas phase. HCOOH is produced because of the reaction of HCHO(aq) with OH(aq). The gas-phase concentrations of SO2, H2O2, HO2, OH, O3, HCHO, NH3, HNO3, and HCl are of primary importance. Increase of the liquid water content of the cloud results in a decrease of the sulfate concentration, but an increase of the total sulfate amount in the aqueous-phase. On the basis of the sensitivity analysis, a condensed mechanism was derived.\r\n\r\nThe next step was the development of a model that actually predicts the amount of liquid water in the atmosphere solving the energy balance. This Lagrangian model combines for the first time a detailed description of gas and aqueous-phase atmospheric chemistry with a treatment of the dynamics of radiation fog, that is the fog that is created due to the radiative cooling of the earth's surface to the space during the night. The model was evaluated against a well documented radiation fog episode in Bakersfield in the San Joaquin Valley of California over the period January 4-5, 1985. This application showed that the model predictions for temperature profile, fog development, liquid water content, gas-phase concentrations of SO2, HNO3, and NH3, pH, aqueous-phase concentrations of [...], [...], and [...], and finally deposition rates of the above ions match well the observed values. The fog was found to lead to a drastic increase of deposition rates over those in its absence for the major ionic species, with most notable being the increase of sulfate deposition. Several important differences were found to exist between the characteristics of a radiation fog and a representative cloud environment. Radiation fogs typically develop under stable conditions (very low wind speed) resulting in weak mixing and significant vertical gaseous species concentration gradients. Because of the proximity of the fog to ground-level sources of pollutants like SO2 and NOx, the corresponding gas-phase concentrations can reach much higher levels that in a cloud. In such a case, pathways for aqueous-phase sulfate production that are of secondary importance in a cloud environment may become significant in a fog.\r\n\r\nThe next level of treatment beyond assuming that all the water droplets have the size and chemical composition is to explicitly model the size-composition distribution of droplets as a result of nucleation on aerosol particles. A third model was developed to study the distribution of acidity and solute concentration among the various droplet sizes in a fog or a cloud. The major finding of this study was that significant solute concentration differences can occur in aqueous droplets inside a fog or a cloud. For the fog simulated, during the period of dense fog, the solute concentration in droplets larger than 10[micrometers] diameter increased with size, in such a way that droplets of diameter 20[micrometers] attain a solute concentration that is a factor of 3.6 larger than that in the 10[micrometer] droplets. Chemical processes tend to decrease the total solute mass concentration differences among the various droplet sizes. Low cooling rates of the system also tend to decrease these concentration differences while high cooling rates have exactly the opposite effect. The mass/size distribution of the condensation nuclei influences quantitatively, but not qualitatively, the above concentration differences.\r\n\r\nThe effects of equilibration processes on wet and dry deposition were then investigated and furthermore the accuracy of the currently used modelling approaches of these phenomena was examined. Atmospheric equilibration processes between two phases with different deposition velocities have the potential to affect significantly the amount of total material deposited on the ground. The magnitude of the effects of the equilibration processes depends primarily on the ratio of the deposition velocities of the two phases, on the production/emission rate of the gas-phase species, and on the initial distribution of species between the two phases.\r\n\r\nAt this point all the tools were available for the detailed investigation of the cyclical relationship between the aerosol and aqueous droplets; a polluted atmosphere with high aerosol concentration assists the formation of the aqueous phase which itself appears to enhance smog production, visibility reduction and aerosol sulfate levels after its dissipation. A model including descriptions of aerosol and droplet microphysics, gas and aqueous-phase chemistry and deposition was used to study the transformation of aerosol to fog droplets and back to aerosol in an urban environment. Fogs in polluted environments have the potential to increase aerosol sulfate concentrations, but at the same time to cause reductions in the aerosol concentration of nitrate, chloride, ammonium and sodium as well as in the total aerosol mass concentration. The sulfate produced during fog episodes favors the aerosol particles that have access to most of the fog liquid water which are usually the large particles. Aerosol scavenging efficiencies of around 80% were calculated for urban fogs. Sampling and subsequent mixing of fog droplets of different sizes may result in measured concentrations that are not fully representative of the fogwater chemical composition and can introduce errors in the reported values of the ionic species deposition velocities. Differences in the major ionic species deposition velocities can be explained by their distribution over the aerosol size spectrum and can be correlated with the species average diameter.\r\n\r\nThe second part of this work was focused on the experimental study of the mechanisms of formation of secondary aerosol particles due to the atmospheric photooxidation of hydrocarbons. In this smog chamber the aerosol forming potential of natural hydrocarbons was investigated. Natural hydrocarbons like the monoterpenes C10H16 and isoprene C5H8 are emitted by various trees and plants in significant quantities. Isoprene and [Beta]-pinene, at concentration levels ranging from a few ppb to a few ppm were reacted photoehemically with NOx, in the Caltech outdoor smog chamber facility. Aerosol formation from the isoprene photooxidation was found to be negligible even under extreme ambient conditions due to the relatively high vapor pressure of its condensable products. Aerosol carbon yield from the [Beta]-pinene photooxidation is as high as 8% and depends strongly on the initial HC/NOx ratio. The average vapor pressure of the [Beta]-pinene aerosol is estimated to be 37 [plus or minus] 24 ppt at 31?c. Monoterpene photooxidation can be a significant source of secondary aerosol in rural environments and in urban areas with extended natural vegetation." }, { "name": "Peng, Lawrence Weiman", "degree": "PhD", "year": "1991", "title": "Reactions in small clusters studied by time-resolved laser spectroscopy", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-130407", "creators": [ { "name": { "family": "Peng", "given": "Lawrence Weiman" }, "id": "Peng-L-W", "display_name": "Peng, Lawrence Weiman" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3cw7-7w07", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nMolecular solute/solvent clusters are an ideal medium for studying solvent effects from the van der Waals complex to the solution bulk limit. Such clusters are conveniently produced using molecular beams. Thus, a new apparatus for making time-resolved measurements of large neutral clusters was constructed and is described in detail herein. The apparatus consists of a molecular beam interrogated by two picosecond lasers. Detection is by laser-induced fluorescence and resonance-enhanced multiphoton ionization. The laser and molecular beam combination permits the study of the role of solvation on the solute's excited electronic-state dynamics for a specific cluster size.\n\nPicosecond time-resolved laser spectroscopy is applied to neutral solute/solvent clusters to study the effect of solvation on charge-transfer reactions in real-time. p(Dimethylamino)benzonitrile (4-DMABN) and [...]-naphthol ([...]-NpOH) are used as model systems since the charge-transfer is solvent dependent. The S[...] excited state dynamics of gas-phase 4-DMABN has been studied both in a supersonic jet expansion and in a thermalized vapor. The jet studies show that 1:1 complexes with water, ammonia, methanol, and acetonitrile do not undergo charge-transfer. At higher jet temperatures, emission is observed from 4-DMABN self-complexes. Charge-transfer fluorescence from 4-DMABN self-complexes is observed in a thermalized vapor. Studies have been done on the S[...] excited state dynamics of gas phase [...]-NpOH clustered with ammonia, piperidine and water. The measurements reveal cluster-size dependent dynamics for [...]-NpOH clustered with ammonia and piperidine, but not with water. The fast-time dynamics in the ammonia and piperidine clusters indicates the occurrence of proton-transfer reactions in these solute/solvent clusters. The cluster size, solvent dependence and the timescale for the reactions serve to emphasize the importance of the local solvent environment.\n" }, { "name": "Shapiro, Pamela Joy", "degree": "PhD", "year": "1991", "title": "Part I. Scandium Hydride and Alkyl Complexes with a Linked Monocyclopentadienyl-Amido Ligand-Framework: Single Component Catalysts for the Polymerization of \u03b1-Olefins. Part II. Hydrazido(1-) and 2,2-Dimethylhydrazido(1-) Derivatives of Permethylscandocene. Preparation and Structural Characterization of their Products from Reactions with Acetonitrile", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-173308161", "creators": [ { "name": { "family": "Shapiro", "given": "Pamela Joy" }, "id": "Shapiro-Pamela-Joy", "display_name": "Shapiro, Pamela Joy" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hmc3-gy25", "abstract": "Various monocyclopentadienyl scandium amido derivatives with the general formulas {(\u03b75-C5Me4)SiMe2(\u03b71-NCMe3}ScR, (Cp*SiNR)ScR, and {(\u03b75-C5H3CMe3)SiMe2(\u03b71-NCMe3}ScR, (tBuCpSiNR)ScR, have been prepared. [(Cp*SiNR)(PMe3)ScH]2 is prepared from the hydrogenation of (Cp*SiNR)ScCH(SiMe3)2 in the presence of PMe3. The scandium hydride effects the multiple insertion of \u03b1-olefins in a controlled fashion to form low molecular weight polymers. \u03b2-H elimination appears to be a principal chain-transfer pathway in this catalyst system. The stoichiometric reaction between [(Cp*SINR)(PMe3)ScH]2 and two equivalents of ethylene produces the ethylene bridged dimer [(Cp*SiNR)(PMe3)Sc]2(\u00b5, \u03b72, \u03b72-C2H4) and an equivalent of ethane. The stoichiometric reaction between the scandium hydride and either propene or butene affords the PMe3-free, alkyl-bridged scandium dimers [(Cp*SiNR)Sc]2(\u00b5-CH2CH2CH3)2 and [(Cp*SiNR)Sc]2(\u00b5-CH2CH2CH2CH3)2. The absence of coordinating phosphine makes these complexes more active olefin polymerization catalysts. The complexes (Cp*SiNR)(PMe3)ScCH2CH(CH)3CH2CH3 and (Cp*SiNR)(PMe3)ScCH(C6H5)CH2CH2CH2(C6H5) have also been prepared and spectroscopically characterized.
\r\n\r\nKinetic analysis of the rate dependence of 1-pentene polymerization by [(Cp*SiNR)(PMe3)ScH]2 on added PMe3 reveals a phosphine dissociation pre-equilibrium to form a PMe3-free active intermediate. The monomeric nature of this intermediate is revealed by the kinetic analysis of 1-pentene polymerization by [(Cp*SiNR)Sc]2(\u00b5-CH2CH2CH3)2 as a function of scandium concentration.
\r\n\r\n(Cp*SiNR)ScR was found to be >99% head-to-tail regioselectfve in the polymerization of propene. Preliminary 13C NMR data indicate lower regioselectivity in propene polymerization by (tBuCpSiNR)ScR. A slight syndiotactic preference is observed in the stereochemistry of the polypropene produced with [(Cp*SiNR)Sc]2(\u00b5-CH2CH2CH3)2. By contrast, [(tBuCpSiNR)ScMe]x displays no stereocontrol, producing an atactic polymer.
\r\n\r\nA rare example of an unsubstituted hydrazido(1-) complex, Cp*2ScNHNH2 (Cp* = (\u03b75-C5Me5)), prepared by reaction of one equivalent of anhydrous hydrazine with Cp*2ScCH3, reacts with acetonitrile to form [chemical formula; see abstract in scanned thesis for details]. The crystal structure of [chemical formula; see abstract in scanned thesis for details] reveals a five-membered, nearly planar [chemical formula; see abstract in scanned thesis for details] ring. The results of a labeling study using 15N=CCH3 are consistent with a mechanism involving insertion of acetonitrile into the Sc-N bond of Cp*2ScNHNH2, followed by tautomerization to form [chemical formula; see abstract in scanned thesis for details]. The closely related compounds Cp*2ScNHNMe2 and [chemical formula; see abstract in scanned thesis for details] have also been prepared, and the structure of the latter compound has been determined.
" }, { "name": "Smith, Paul Andrew", "degree": "Masters", "year": "1991", "title": "A Reexamination of Tryptophan Fluorescence in Cytochrome c Oxidase", "advisor": "Khundkar, Lutfur R.; Perry, Joseph W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192011-145437221", "creators": [ { "name": { "family": "Smith", "given": "Paul Andrew" }, "id": "Smith-P-A", "display_name": "Smith, Paul Andrew" } ], "advisors": [ { "name": { "family": "Khundkar", "given": "Lutfur R." }, "id": "Khundkar", "role": "advisor", "display_name": "Khundkar, Lutfur R." }, { "name": { "family": "Perry", "given": "Joseph W." }, "id": "Perry-J-W", "role": "advisor", "display_name": "Perry, Joseph W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5tq9-2s50", "abstract": "Cytochrome c oxidase links reduction of oxygen with the pumping of protons across the inner mitochondrial membrane. Recently it has been shown that only two of the four electron transfers to the oxygen binding site are coupled with proton translocation. The discovery implies that there is a conformational switch between pumping and non-conformational changes. Gating conformational transitions occur in each cycle of the pump when electrons and protons are alternatively accessible to either the inside or outside of the membrane. Such transitions are linked to the redox state of the coupling site. The unloaded/loaded transition, on the other hand, depends on the intermediate at the oxygen binding site and is not part of the pumping cycle.\r\n\r\nA 16 nm red-shift in the tryptophan emission maximum of cytochrome oxidase upon reduction of the enzyme with dithionite was reported earlier [Copeland, R.A., Smith, P.A., and Chan, S.I. (1987) Biochemistry 26, 7311]. As such redox-linked change could be an important probe of pumping transitions, the fluorescence change of cytochrome oxidase upon reduction with ascorbate and cytochrome c was measured. The absence of a shift led to the reevalution of the earlier experiments for inner filter effects. The earlier experiments were reproduced with proper optical controls, and a method for reconstructing absorbance aftifacts from the reported fluourescence spectra was devised. Tryptophan fluourescence lifetimes were also measured. All the data support the conclusion that the earlier reports of a redox-linked fluourescence change were artifacts and that the other transient changes in fluorescence which have been measured cannot be associated with either the unloaded/loaded transition or a gating transition." }, { "name": "Tufts, Bruce John", "degree": "PhD", "year": "1991", "title": "Electrochemical and surface chemical studies of n-GaAs photoanodes", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112011-141342746", "creators": [ { "name": { "family": "Tufts", "given": "Bruce John" }, "id": "Tufts-B-J", "display_name": "Tufts, Bruce John" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1zzp-t398", "abstract": "The electrochemical response of n-type gallium arsenide (n-GaAs) pbotoanodes\r\nwas monitored while in contact with aqueous basic selenide electrolytes before and after\r\nexposme to separate aqueous 0.010 M solutions of transition metal ions. Representative\r\nmembers of the transition metal complexes included RuCl_3\u2022xH_2O, RhCl_3\u2022xH_2O,\r\nIrCl_3\u2022xH_2), OsCl_3\u2022xH_2O, [Co(lll)(NH_3)_6](Br)_3, [Ru(III)(NH_3)_5(Cl)](Cl)_2, and\r\n[Ru(II)(NH_3)_5(OH_2)](Cl)_2. Several members of this group were shown to yield improved\r\ncurrent-voltage (I-V) characteristics at the n-GaAs/KOH \u2013 Se^(-/2-)(aq) junction. A\r\ncomparison of the current-voltage properties for p-type and n^+-type GaAs electrodes in the\r\n~ as well as for 10% Sn-doped In_2O_3 electrodes, demonstrated that the source of the\r\nimproved I-V response following metal ion exposure was a large decrease in the\r\noverpotentials, at a given current density, required for selenide oxidation.\r\n\r\nAn extensive surface analytic study revealed that Co(III) ammine complexes became\r\nadsorbed on GaAs surfaces from solutions of pH > 9 by a redox reaction involving\r\nsacrificial oxidation of the GaAs substrate. The product in all cases was an amorphous\r\nCo(OH)_2 surface layer. The stoichiometry of the redox reaction involves one equivalent of\r\nGaAs per six equivalent Co(III) species. Following immersion into the KOH \u2013 Se^(-/2)(aq)\r\nelectrolyte, the Co(OH)_2 surface layer was converted to a CoSe_2-like phase that is believed\r\nto be the active electrocatalyst responsible for the reduced overpotential dependence\r\nfollowing Co(III) ammine treatment.\r\nFinally, the surface composition of n-GaAs electrodes that had been specifically\r\netched to produce either a clean, a metallic arsenic covered, or a uniformly oxidized surface\r\nwere probed by high resolution XPS and were correlated with the n-GaAs I-V properties in\r\naqueous and non-aqueous electrolytes.\r\n" }, { "name": "Whinnery, Leroy L.", "degree": "PhD", "year": "1991", "title": "Synthesis, characterization and reactivity of some permethyltantalocene alkylidenes and unusually stable metallaoxetanes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112011-130949006", "creators": [ { "name": { "family": "Whinnery", "given": "Leroy L." }, "id": "Whinnery-L-L", "display_name": "Whinnery, Leroy L." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s4x8-zb56", "abstract": "Several tantalaoxetanes have been prepared and the X-ray crystal structure of O-exo-Cp_2*Ta(OCHPhCH_2)CH_3 is reported (Cp* = \u03b7^5-C_5Me_5). The kinetic products of the reactions of Cp_2*Ta(=CH_2)CH_3 with paraformaldehyde or benzaldehyde are O-endo-Cp_2*Ta(CH_2CH_20)CH_3 and O-endo-Cp_2*Ta(CH_2CHPhO)CH_3, respectively. These tantalaoxetanes undergo an acid and base-catalyzed isomerization to O-exo-Cp_2*Ta(OCH_2CH_2)CH_3 and O-exo-CP_2*Ta(OCHPhCH_2)CH_3 followed by thermal decomposition to Cp_2*Ta(=O)CH_3 and the appropriate olefin. Cp_2*Ta(=CH_2)H deoxygenates epoxides to form Cp_2*Ta(=O)CH_3 and olefin. No intermediates are observed in this deoxygenation under conditions where the appropriate tantalaoxetanes are stable and would have been spectroscopically observed. Stereolabeled epoxides were deoxygenated to probe the mechanism for the possible intermediacy of a 1,4-biradical. Retention of stereochemistry of the resulting olefin was observed and is indicative of a concerted mechanism. These results and their implications for the mechanism of olefin epoxidation are discussed.\r\n\r\nTreatment of Cp*_2 TaCI_2 with a variety of substituted benzyl potassium reagents affords an equilibrium mixture of CP*_2 Ta(=CHC_6H_5)H, 1, and Cp*_2 Ta(o-CH_2C_6H_4)H, 2, which interconvert presumably via the unstable 16 electron intermediate [Cp*_2Ta(CH_2C_6H_5)]. Several derivatives substituted at the phenyl ring have been prepared to explore the effect of both sterics and electronics on the a-hydrogen migration equilibrium. Trapping of the benzyl intermediate by methylenetrialkylphosphoranes results in methylene transfer to give Cp*_2 Ta(=CH_2)CH_2C_6H_5. The substituted benzyl derivatives have provided a system to determine the influence of phenyl sUbstituents on migratory aptitude of the benzyl group.\r\n" }, { "name": "Axe, Douglas D.", "degree": "PhD", "year": "1990", "title": "Kinetics of RNA Polymerase \u03b2 Subunit Synthesis and Acid End Product Transport in Escherichia coli", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02222007-113422", "creators": [ { "name": { "family": "Axe", "given": "Douglas D." }, "id": "Axe-Douglas-D", "display_name": "Axe, Douglas D." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Emr", "given": "Scott D." }, "id": "Emr-S-D", "role": "member", "display_name": "Emr, Scott D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ejy5-sm51", "abstract": "An approach to modeling the regulation of synthesis of crucial bacterial proteins has been developed. The unique features of this approach are that it focuses on maintenance of a steady state rather than on transitions between steady states, and that stochastic fluctuations in the number of transcripts per cell are treated as the perturbation. It has been used to investigate various models of translational regulation of RNA polymerase \u03b2 subunit synthesis. The simplest autogenous regulatory mechanism, binding of a single RNA polymerase molecule to the rpoBC mRNA, appears to provide inadequate control. A more sophisticated mechanism, sequential binding of multiple polymerase molecules in a cooperative manner, was shown to dramatically improve the control characteristics.
\r\n\r\nThe interaction between RNA polymerase and rpoBC mRNA was examined experimentally. RNA polymerase was incubated with RNA that is identical to a small portion of the native rpoBC message. Gel mobility-shift assays were performed to detect complexes. The relative amount of RNA in different complexes was determined by radiolabeling the transcript. Data obtained in this way indicate that cooperative binding is occuring.
\r\n\r\n\u00b3\u00b9P NMR studies of intact E. coli cells suggested a difference in membrane function between a plasmid-containing strain and the plasmid-free host. Similar \u00b3\u00b9P NMR experiments were complemented with \u00b9\u00b3C NMR experiments to examine the transport of lactate and acetate through the cytoplasmic membrane during anaerobic glycolysis. Methods were developed to measure cytoplasmic and extracytoplasmic solution volumes and intra- and extracellular acid concentrations using \u00b9\u00b3C NMR. The results demonstrated significant differences in the transport of the two acids. Acetate was determined to permeate the membrane at comparable rates in the dissociated and undissociated forms. The mode of lactate transport in cells that are actively glycolyzing was found to be different from that of cells that have exhausted their supply of glucose. Lactate thus appears to be transported by a system that is sensitive to some indicator of glycolytic activity. It also appears to diffuse across the membrane in both forms.
\r\n\r\nA kinetic approach was used to deduce constraints on the unidirectional fluxes for a general protein-mediated, ATP-independent transport process. The conclusion was that under certain circumstances, the Ussing-Teorell flux ratio equation applies to protein-mediated transport. From the analysis, an expression was derived for the driving force of such a transport process, and the relationship between this and the net flux is discussed.
" }, { "name": "Barner, Claudia Jane", "degree": "PhD", "year": "1990", "title": "Part I. Coordination Chemistry of High-Valent Osmium Polyanionic Chelating Ligand Complexes with Imine, Imido and Nitrido Ligands. Part II. Asymmetric Hydrogenation Using a Resolved Chiral Scandium Hydride Complex", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06112007-095040", "creators": [ { "name": { "family": "Barner", "given": "Claudia Jane" }, "id": "Barner-Claudia-Jane", "display_name": "Barner, Claudia Jane" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tj33-3482", "abstract": "Part I: The chemistry of high-valent osmium polyanionic chelating ligand complexes with imine, imido and nitrido ligands is explored. The synthesis and x-ray diffraction study of Os(\u03b7\u2074-HBA-B)(NC\u2086H\u2085NHC\u2086H\u2084) is reported. A neutral, octahedral Os(VIII) intermediate complex is postulated. The synthesis and x-ray diffraction study of [OsN(\u03b7\u2074-HBA-B)]- is reported. The mechanism of formation is discussed. These complexes represent two of the first examples of non-planar amide ligands in transition metal chemistry. The synthesis of a five-coordinate imido complex, Os(N-C\u2081\u2080 H\u2081\u2086), is reported. The formation of the first osmium-osmium quadruply-bonded complex, [Os(\u03b7\u2074-HBA-B)]\u2082, is reported. Reactions with the nitrido complex, [OsN(\u03b7\u2074-HBA-B)]\u207b,and the methylimido complex, OsNMe(\u03b7\u2074-HBA-B), are also reported.
\r\n\r\nPart II: The asymmetric hydrogenation of the prochiral substrate, methylene indane, is induced by the resolved chiral scandium complex, Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)(\u03b7\u2075-(C\u2085H\u2083(1R,2R,5S)-menthyl)ScH, in substoichiometric quantities. Methylene indane is hydrogenated to produce methylindane with an enantiomeric excess of 34% and a maximum turnover of four.
" }, { "name": "Campo, Peter John", "degree": "PhD", "year": "1990", "title": "Studies in Robust Control of Systems Subject to Constraints", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252002-161632", "creators": [ { "name": { "family": "Campo", "given": "Peter John" }, "id": "Campo-Peter-John", "display_name": "Campo, Peter John" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "orcid": "0000-0002-1828-2486", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4w3h-b335", "abstract": "Two approaches to control system design for constrained systems are studied. The first involves theoretical investigations of constrained model predictive control algorithms. The second involves extensions of robust linear control theory to handle the nonlinear control schemes commonly used in practice for constrained systems.
\r\n\r\nA novel model predictive control algorithm, with attractive functional and numerical characteristics is developed. This algorithm minimizes peak excursions in the controlled outputs and is particularly suited to regulatory control problems common in continuous process systems.
\r\n\r\nModel predictive control concepts are extended to uncertain linear systems. An on-line optimizing control scheme (RMPC) is developed which has as its objective the minimization of worst-case tracking error for an entire family of linear plants. For model uncertainty descriptions which provide plant impulse response coefficients as affine functions of uncertain parameters, it is shown that the required minimax optimization problem can be recast as a single linear program.
\r\n\r\nThe discrete time optimal averaging level control problem is formulated and solved. A finite horizon approximation to the problem is introduced and analytical solutions are obtained in important special cases. A model predictive control formulation is introduced which provides optimal flow filtering and integral action. Analysis tools are provided to characterize the trade-off between flow filtering and rapid integral action.
\r\n\r\nA complete theory is developed for the multivariable anti-windup, bumpless transfer (AWBT) problem. The theoretical framework allows the consideration of any linear time invariant (LTI) control system subject to plant input limitations and substitutions. A general AWBT compensation scheme, applicable to multivariable controllers of arbitrary structure and order, is developed. Conditions are derived under which this general AWBT method reduces to any one of several well-known heuristics for AWBT (e.g., PI anti-reset windup and IMC). The design issues which affect AWBT performance are identified and quantitative analysis methods are developed. Sufficient conditions for nonlinear stability of the AWBT compensated system are provided. These results are a generalization of, and are less conservative than, those available in the AWBT literature. The definition of AWBT performance objectives which are independent of controller structure allows the formulation of a general AWBT synthesis problem. This formal synthesiproblem addresses each of the identified performance objectives in a quantitative manner. The synthesis problem is shown to be a special case of a constrained structure controller synthesis (CSCS) problem. A solution method via reduction to static output feedback is presented and the engineering trade-offs available in the AWBT design are discussed.
" }, { "name": "Geffroy Aguilar, Enrique", "degree": "PhD", "year": "1990", "title": "Birefringence of Polymer Solutions in Time Dependent Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02232007-154744", "creators": [ { "name": { "family": "Geffroy Aguilar", "given": "Enrique" }, "id": "Geffroy-Aguilar-Enrique", "display_name": "Geffroy Aguilar, Enrique" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "member", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/gpt7-3556", "abstract": "This is a study of changes of conformation of macromolecules in polymeric solutions which are subjected to time-dependent extensional flows generated by a two-roll mill flow device. The flows produced by the two-roll mill are linear, and two-dimensional. It has a stagnation point at the center of the flow field where the magnitudes of the strain-rates are greater than the vorticity. This study of conformational changes is based on data around the vicinity of the stagnation point, I for steady state flows, and several transient flow histories such as startup, cessation, and double-step flows. We also present an analytical solution for the creeping flow generated by an infinitely long two-roll mill embedded in an unbounded fluid. This solution is used as a benchmark to compare the behavior of the polymer solutions when subjected to flows with different values for the ratio of rate-of-strain to vorticity.
\r\n\r\nThe conformational changes are determined experimentally using the Two-color Flow-Birefringence which provides an instantaneous and point-wise measure of the anisotropy of the fluid, together with the relative orientation of the anisotropy with respect to the principal axes of the flow field. Based on relaxation of the fluid anisotropy the characteristic time-scales of the polymer have been evaluated as a function of the flow field properties and the degree of conformational change of the macromolecules. Data for two polymeric solution is presented. The first polymer system is the so-called test-fluid M1. This polymeric solution is shown to degrade significantly, even for small values of the velocity gradient, as measured by the changes in the macroscopic relaxation time-scales. The second solution is a concentrated polystyrene solution that presents overshoots and undershoots of the polymer conformation dependent of the ratio of vorticity to rate-of-strain. When subjected to large deformations, this polystyrene solution shows not only the possibility of a reduced number of entanglements, but also a significant deformation of the macromolecule segments associated to a shorter relaxation time-scale for the dynamics of concentrated solutions, which corresponds to that predicted by the intermediate relaxation time-scale of Doi-Edwards model.
" }, { "name": "Goodrich, Raymond Paul, Jr.", "degree": "PhD", "year": "1990", "title": "Modification of Membrane Surfaces with Carbohydrates: An Approach for Stabilization During Freezing and Drying", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-091301", "creators": [ { "name": { "family": "Goodrich", "given": "Raymond Paul, Jr." }, "id": "Goodrich-Raymond-Paul-Jr", "orcid": "0000-0002-5945-4571", "display_name": "Goodrich, Raymond Paul, Jr." } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Revel", "given": "Jean-Paul" }, "id": "Revel-J-P", "role": "member", "display_name": "Revel, Jean-Paul" }, { "name": { "family": "Imperiali", "given": "Barbara" }, "id": "Imperiali-B", "orcid": "0000-0002-5749-7869", "role": "member", "display_name": "Imperiali, Barbara" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ff9e-th51", "abstract": "A new class of molecules possessing amphipathic character was prepared. These compounds possessed a hydrophobic region capable of intercalation into a lipid bilayer, a hydrophilic linker group capable of extending beyond the surface of a membrane, and a carbohydrate attached at the end of this linker group. These features of this class of compounds permitted their direct incorporation into vesicle formulations and hence the direct examination of interactions occuring in the dry state between carbohydrates and lipid groups in such vesicle membrane systems.
\r\n\r\nSamples of treated vesicle preparations were subjected to freezing and thawing as well as to direct dehydration via lyophilization. Under these conditions, the stability and integrity of the membrane was examined via several spectroscopic techniques.
\r\n\r\nThrough these studies of systems in which a carbohydrate is directly bound to a membrane surface, it was possible to determine a defined ratio, independent of solution and concentration effects, at which carbohydrates can afford protection to dehydrated membranes. In addition, the interactions responsible for conferring the protection were determined. It was found that direct intercalation of the carbohydrates into a membrane interface preserves the membrane structure and organization that is normally observed in the presence of water. This behavior prevents the phase transitions, lipid phase separations, and fusion phenomena that normally compromise dehydrated membrane systems. This phenomena is directly related to the amount of carbohydrate that is present and the structure of the carbohydrate that is used. These results indicate that the partitioning behavior of the carbohydrates at the interface is of prime importance in determining the effectiveness in this regard.
" }, { "name": "Griffin, John Hampton", "degree": "PhD", "year": "1990", "title": "Structure-, stereochemistry-, and metal-regulated DNA binding/cleaving molecules", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302014-102529450", "creators": [ { "name": { "family": "Griffin", "given": "John Hampton" }, "id": "Griffin-J-H", "display_name": "Griffin, John Hampton" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fnf1-yc64", "abstract": "In the cell, the binding of proteins to specific sequences of double helical DNA is\r\nessential for controlling the processes of protein synthesis (at the level of DNA\r\ntranscription) and cell proliferation (at the level of DNA replication). In the laboratory, the\r\nsequence-specific DNA binding/cleaving properties of restriction endonuclease enzymes\r\n(secreted by microorganisms to protect them from foreign DNA molecules) have helped to\r\nfuel a revolution in molecular biology. The strength and specificity of a protein:DNA\r\ninteraction depend upon structural features inherent to the protein and DNA sequences, but\r\nit is now appreciated that these features (and therefore protein:DNA complexation) may be\r\naltered (regulated) by other protein:DNA complexes, or by environmental factors such as\r\ntemperature or the presence of specific organic molecules or inorganic ions. It is also now\r\nappreciated that molecules much smaller than proteins (including antibiotics of molecular\r\nweight less than 2000 and oligonucleotides) can bind to double-helical DNA in sequence-specific\r\nfashion. Elucidation of structural motifs and microscopic interactions responsible for the\r\nspecific molecular recognition of DNA leads to greater understanding of natural processes\r\nand provides a basis for the design of novel sequence-specific DNA binding molecules.\r\nThis thesis describes the synthesis and DNA binding/cleaving characteristics of molecules\r\ndesigned to probe structural, stereochemical, and environmental factors that regulate\r\nsequence-specific DNA recognition.
\r\n\r\nChapter One introduces the DNA minor groove binding antibiotics Netropsin and\r\nDistamycin A, which are di- and tri(N-methylpyrrolecarboxamide) peptides, respectively.\r\nThe method of DNA affinity cleaving, which has been employed to determine DNA\r\nbinding properties of designed synthetic molecules is described. The design and synthesis\r\nof a series of Netropsin dimers linked in tail-to-tail fashion (by oxalic, malonic, succinic, or\r\nfumaric acid), or in head-to-tail fashion (by glycine, \u03b2-alanine, and \u03b3-aminobutanoic acid\r\n(Gaba)) are presented. These Bis(Netropsin)s were appended with the iron-chelating\r\nfunctionality EDTA in order to make use of the technique of DNA affinity cleaving.\r\nBis(Netropsin)-EDTA compounds are analogs of penta(N-methylpyrrolecarboxamide)-EDTA\r\n(P5E), which may be considered a head-to-tail Netropsin dimer linked by Nmethylpyrrolecarboxamide.\r\nLow- and high-resolution analysis of pBR322 DNA affinity\r\ncleaving by the iron complexes of these molecules indicated that small changes in the length\r\nand nature of the linker had significant effects on DNA binding/cleaving efficiency (a\r\nmeasure of DNA binding affinity). DNA binding/cleaving efficiency was found to\r\ndecrease with changes in the linker in the order \u03b2-alanine > succinamide > fumaramide >\r\nN-methylpyrrolecarboxamide > malonamide >glycine, \u03b3-aminobutanamide > oxalamide.\r\nIn general, the Bis(Netropsin)-EDTA:Fe compounds retained the specificity for seven\r\ncontiguous A:T base pairs characteristic of P5E:Fe binding. However, Bis(Netropsin)Oxalamide-\r\nEDTA:Fe exhibited decreased specificity for A:T base pairs, and\r\nBis(Netropsin)-Gaba-EDT A:Fe exhibited some DNA binding sites of less than seven base\r\npairs. Bis(Netropsin)s linked with diacids have C2-symmmetrical DNA binding subunits\r\nand exhibited little DNA binding orientation preference. Bis(Netropsin)s linked with amino\r\nacids lack C2-symmetrical DNA binding subunits and exhibited higher orientation\r\npreferences. A model for the high DNA binding orientation preferences observed with\r\nhead-to-tail DNA minor groove binding molecules is presented.
\r\n\r\nChapter Two describes the design, synthesis, and DNA binding properties of a\r\nseries of chiral molecules: Bis(Netropsin)-EDTA compounds with linkers derived from\r\n(R,R)-, (S,S)-, and (RS,SR)-tartaric acids, (R,R)-, (S,S)-, and (RS,SR)-tartaric acid\r\nacetonides, (R)- and (S)-malic acids, N ,N-dimethylaminoaspartic acid, and (R)- and (S)-alanine,\r\nas well as three constitutional isomers in which an N-methylpyrrolecarboxamide\r\n(P1) subunit and a tri(N-methylpyrrolecarboxamide)-EDTA (P3-EDTA) subunit were\r\nlinked by succinic acid, (R ,R)-, and (S ,S)-tartaric acids. DNA binding/cleaving\r\nefficiencies among this series of molecules and the Bis(Netropsin)s described in Chapter\r\nOne were found to decrease with changes in the linker in the order \u03b2-alanine > succinamide\r\n> P1-succinamide-P3 > fumaramide > (S)-malicamide > N-methylpyrrolecarboxamide >\r\n(R)-malicamide > malonamide > N ,N-dimethylaminoaspanamide > glycine = Gaba =\r\n(S,S)-tartaramide = P1-(S,S)-tanaramide-P3 > oxalamide > (RS,SR)-tartaramide = P1-\r\n(R,R)-tanaramide-P3 > (R,R)-tartaramide (no sequence-specific DNA binding was\r\ndetected for Bis(Netropsin)s linked by (R)- or (S)-alanine or by tartaric acid acetonides).\r\nThe chiral molecules retained DNA binding specificity for seven contiguous A:T base pairs.\r\nFrom the DNA affinity cleaving data it could be determined that: 1) Addition of one or two\r\nsubstituents to the linker of Bis(Netropsin)-Succinamide resulted in stepwise decreases in\r\nDNA binding affinity; 2) molecules with single hydroxyl substituents bound DNA more\r\nstrongly than molecules with single dimethylamino substituents; 3) hydroxyl-substituted\r\nmolecules of (S) configuration bound more strongly to DNA than molecules of (R)\r\nconfiguration. This stereochemical regulation of DNA binding is proposed to arise from\r\nthe inherent right-handed twist of (S)-enantiomeric Bis(Netropsin)s versus the inherent lefthanded\r\ntwist of (R)-enantiomeric Bis(Netropsin)s, which makes the (S)-enantiomers more\r\ncomplementary to the right-handed twist of B form DNA.
\r\n\r\nChapter Three describes the design and synthesis of molecules for the study of\r\nmetalloregulated DNA binding phenomena. Among a series of Bis(Netropsin)-EDTA\r\ncompounds linked by homologous tethers bearing four, five, or six oxygen atoms, the\r\nBis(Netropsin) linked by a pentaether tether exhibited strongly enhanced DNA\r\nbinding/cleaving in the presence of strontium or barium cations. The observed\r\nmetallospecificity was consistent with the known affinities of metal cations for the cyclic\r\nhexaether 18-crown-6 in water. High-resolution DNA affinity cleaving analysis indicated\r\nthat DNA binding by this molecule in the presence of strontium or barium was not only\r\nstronger but of different sequence-specificity than the (weak) binding observed in the\r\nabsence of metal cations. The metalloregulated binding sites were consistent with A:T\r\nbinding by the Netropsin subunits and G:C binding by a strontium or barium:pentaether\r\ncomplex. A model for the observed positive metalloregulation and novel sequence-specificity\r\nis presented. The effects of 44 different cations on DNA affinity cleaving by\r\nP5E:Fe were examined. A series of Bis(Netropsin)-EDTA compounds linked by tethers\r\nbearing two, three, four, or five amino groups was also synthesized. These molecules\r\nexhibited strong and specific binding to A:T rich regions of DNA. It was found that the\r\niron complexes of these molecules bound and cleaved DNA most efficiently at pH 6.0-6.5,\r\nwhile P5E:Fe bound and cleaved most efficiently at pH 7.5-8.0. Incubating the\r\nBis(Netropsin) Polyamine-EDTA:Fe molecules with K2PdCl4 abolished their DNA\r\nbinding/cleaving activity. It is proposed that the observed negative metalloregulation arises\r\nfrom kinetically inert Bis(Netropsin) Polyamine:Pd(II) complexes or aggregates, which are\r\nsterically unsuitable for DNA complexation. Finally, attempts to produce a synthetic\r\nmetalloregulated DNA binding protein are described. For this study, five derivatives of a\r\nsynthetic 52 amino acid residue DNA binding/cleaving protein were produced. The\r\nsynthetic mutant proteins carried a novel pentaether ionophoric amino acid residue at\r\ndifferent positions within the primary sequence. The proteins did not exhibit significant\r\nDNA binding/cleaving activity, but they served to illustrate the potential for introducing\r\nnovel amino acid residues within DNA binding protein sequences, and for the development\r\nof the tricyclohexyl ester of EDTA as a superior reagent for the introduction of EDT A into\r\nsynthetic proteins.
\r\n\r\nChapter Four describes the discovery and characterization of a new DNA\r\nbinding/cleaving agent, [SalenMn(III)]OAc. This metal complex produces single- and\r\ndouble-strand cleavage of DNA, with specificity for A:T rich regions, in the presence of\r\noxygen atom donors such as iodosyl benzene, hydrogen peroxide, or peracids. Maximal\r\ncleavage by [SalenMn(III)]OAc was produced at pH 6-7. A comparison of DNA singleand\r\ndouble-strand cleavage by [SalenMn(III)]+ and other small molecules\r\n(Methidiumpropyl-EDTA:Fe, Distamycin-EDTA:Fe, Neocarzinostatin, Bleomycin:Fe) is\r\npresented. It was found that DNA cleavage by [SalenMn(III)]+ did not require the\r\npresence of dioxygen, and that base treatment of DNA subsequent to cleavage by\r\n[SalenMn(III)]+ afforded greater cleavage and alterations in the cleavage patterns. Analysis\r\nof DNA products formed upon DNA cleavage by [SalenMn(III)] indicated that cleavage\r\nwas due to oxidation of the sugar-phosphate backbone of DNA. Several mechanisms\r\nconsistent with the observed products and reaction requirements are discussed.
\r\n\r\nChapter Five describes progress on some additional studies. In one study, the\r\nDNA binding/cleaving specificities of Distamycin-EDTA derivatives bearing pyrrole N-isopropyl\r\nsubstituents were found to be the same as those of derivatives bearing pyrrole N-methyl\r\nsubstituents. In a second study, the design of and synthetic progress towards a\r\nseries of nucleopeptide activators of transcription are presented. Five synthetic plasmids\r\ndesigned to test for activation of in vitro run-off transcription by DNA triple helix-forming\r\noligonucleotides or nucleopeptides are described.
\r\n\r\nChapter Six contains the experimental documentation of the thesis work.
" }, { "name": "Griffin, Linda Chu-Li", "degree": "PhD", "year": "1990", "title": "Oligonucleotide-Directed Cleavage of Single- and Double-Stranded DNA by Double and Triple Helix Formation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-095616", "creators": [ { "name": { "family": "Griffin", "given": "Linda Chu-Li" }, "id": "Griffin-Linda-Chu-Li", "display_name": "Griffin, Linda Chu-Li" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vsda-zz91", "abstract": "Part I
\r\n\r\nOligonucleotide-Directed Cleavage of Single-Stranded DNA by Double Helix Formation
\r\n\r\nChapter 1: Sequence-Specific Cleavage of Single-Stranded DNA with Oligonucleotide-EDTA\u2022Fe(II): Study of Reaction Conditions
\r\n\r\nThe machine synthesis of a DNA hybridization probe 19-nucleotides in length, equipped with the metal chelator EDTA 1 has the sequence 5'-GCAAGGCGAT*TAAGTTGGG-3', which is complementary to a 19-nucleotide sequence in M13mp7 (+) strand phage DNA. In the presence of Fe(II), O\u2082, and dithiothreitol, oligonucleotide 1 affords specific cleavage (0\u00b0C, pH 7.4, 20 hours) at its complementary sequence in the 7214 base M13mp7 (+) strand. Cleavage occurs over a range of 17 nucleotides at the site of hybridization of 1. No other cleavage sites are observed in the 7214 base strand. Optimum cleavage conditions occur at concentrations of 0.25-1 \u00b5M T* oligonucleotide, 20 \u00b5M Fe(II), and 50-1000 mM NaCl. Optimum pH is 7.4 (25 mM tris-acetate buffer). The optimum cleavage time is between 16-24 hours at 0\u00b0C. The melting temperature (T\u2098) for T* oligonucleotide 1 and its 19-nucleotide complement under reaction conditions is 54.5\u00b0C, 3.5\u00b0C lower than the same duplex without T* (T\u2098=58\u00b0C).
\r\n\r\nPart II
\r\n\r\nOligonucleotide-Directed Cleavage of Double-Stranded DNA by Triple Helix Formation
\r\n\r\nChapter 2: Recognition of Thymine\u2022Adenine Base Pairs by Guanine in a Pyrimidine Triple Helix Motif
\r\n\r\nOligonucleotide recognition offers a powerful chemical approach for the sequence-specific binding of double helical DNA. In the pyrimidine-Hoogsteen model, a binding site size of >15 homopurine base pairs affords >30 discrete sequence-specific hydrogen bonds to duplex DNA. Because pyrimidine oligonucleotides limit triple helix formation to homopurine tracts, it is desirable to determine whether oligonucleotides can be used to bind all four base pairs of DNA. A general solution would allow targeting of oligonucleotides (or their analogs) to any given sequence in the human genome. A study of 20 base triplets reveals that the triple-helix can be extended from homopurine to mixed sequences. Guanine contained within a pyrimidine oligonucleotide specifically recognizes thymine\u2022adenine base pairs in duplex DNA. Such specificity allows binding at mixed sites in SV40 and HIV DNA.
\r\n\r\nChapter 3: Recognition of All Four Base Pairs of Duplex DNA by Triple Helix Formation \u2022 Design of Pyrimidine Specific Bases
\r\n\r\nOligonucleotide recognition offers a powerful chemical approach for the sequence-specific binding of double helical DNA. In the pyrimidine-Hoogsteen model, a binding site size of >15 homopurine base pairs affords >30 discrete sequence-specific hydrogen bonds to duplex DNA. Because pyrimidine oligonucleotides limit triple helix formation to homopurine tracts, it is desirable to determine whether oligonucleotides can be used to bind all four base pairs of DNA. A general solution would allow targeting of oligonucleotides (or their analogs) to any given sequence in the human genome. The novel base 4-(3-benzamido)phenylimidazole specifically recognizes pyrimidine\u2022purine base pairs over purine\u2022pyrimidine base pairs. Such specificity allows binding at an 18 base pairs site in SV40 DNA (pH 7.4, 40\u00b0C) containing all four base pairs.
" }, { "name": "Guske, Christopher James", "degree": "PhD", "year": "1990", "title": "Metabolic modeling of growth and poly-[beta]-hydroxybutyrate (PHB) production in Alcaligenes eutrophus H16", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-110221", "creators": [ { "name": { "family": "Guske", "given": "Christopher James" }, "id": "Guske-C-J", "display_name": "Guske, Christopher James" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/J4NT-HG32", "abstract": "A physiologically based metabolic model for growth and poly-[beta]-hydroxybutyrate (PHB) production in Alcaligenes eutrophus H16 has been formulated. The model is based upon A. eutrophus' five major heterotrophic metabolic pathways: an overall biosynthesis pathway, respiration, glycolysis, the citric acid cycle, and PHB polymerization. Beginning with microscopic intracellular balances, intracellular phenomena such as pathway flux activities and intracellular balances on acetyl-CoA, ATP and NADH are related to the macroscopic time evolutions of fructose concentration, cell dry weight concentration, PHB concentration, carbon dioxide evolution rate, and oxygen consumption rate.\n\nUsing the derived model framework, Alcaligenes eutrophus H16's metabolic responses to different medium fructose, ammonium and oxygen concentrations as well as nutrient limitations and exhaustions were determined in a well-controlled, fully monitored bioreactor. Ammonium exhaustion led to the highest observed PHB synthesis rates, while the PHB polymerization rates correlated with the severity of ammonium and oxygen limitations. Surprisingly, fructose limitation led to an increase in intracellular PHB levels. Glycolysis, citric acid cycle and repiration activities were very sensitive to short-term fluctuations during fructose-limited feeding, while biosynthesis and PHB polymerization responses were sluggish. Fructose exhaustion PHB depolymerization occurred at a small absolute rate relative to polymerization during periods of fructose sufficiency. High intracellular PHB levels appeared to inhibit cell growth.\n\nUsing in vitro kinetic study data, model metabolic pathway responses were compared with the regulatory properties of the key regulatory enzymes. Glucose-6-phosphate NADH-regulation appears weaker than that exerted on isocitrate dehydrogenase as evidenced by increased ammonium-limited glycolysis activity and presumed elevated NADH levels. Increased NADH levels sharply correlated with increased PHB polymerization activity. Along this line, culture fluorescence was used as a sensitive indicator of NAD(P)H level changes. Culture fluorescence was a good indicator of metabolic shifts, particularly at the onset of increased PHB polymerization. Increases in specific culture fluorescence correlated strongly with intracellular PHB levels.\n\nFrom the pathway-associated intracellular balances, average metabolic parameters for the ATP yield coefficient, Ymax/ATP, the oxidative phosphorylation ratio, P/O, and the ATP maintenance coefficient, mATp,e, were determined of 0.34 C-mol biomass/mol ATP, 2.9 mol ATP/mol H2O, and 9.8 mmol ATP/((g biomass)(hr)), respectively, which agree favorably with other work. Use of the constant metabolic parameters and the closed intracellular balances predicted balanced growth conditions well but deviated under ammonium limitation conditions. Also, the metabolic parameters seemed to shift to lower values as during the growth/PHB storage phase transition.\n\nIncorporation of kinetic expressions for biosynthesis and PHB polymerization activities mimicked balanced growth conditions very well while deviating from ammonium limitation and ammonium exhaustion conditions.\n" }, { "name": "Hanson, James Edward", "degree": "PhD", "year": "1990", "title": "I. Matrix Isolation of 1,1-Diazenes. II. Distance, Temperature, and Dynamic Solvent Effects on Electron Transfer Reactions", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-131625", "creators": [ { "name": { "family": "Hanson", "given": "James Edward" }, "id": "Hanson-James-Edward", "orcid": "0000-0001-7899-2802", "display_name": "Hanson, James Edward" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1F5A-AC10", "abstract": "Part I: Investigations of the reactive intermediates known as 1, 1-diazenes or aminonitrenes are reported. These unstable species were generated by UV photolysis of appropriately substituted carbamoyl azides under matrix isolation conditions. Four systems were investigated: three cyclic dialkyl 1,1-diazenes (1,1-tetramethylenediazene 1, 1, 1-trimethylenediazene 2, and 3,4-dehydro-1, 1-tetramethylenediazene 15) and the first diaryl 1,1-diazene, 1,1-diphenyldiazene 22. 1,1-Diazene 1 could be generated by broad band UV photolysis (200-400 nm) of the carbamoyl azide, but 2 and 22 required narrow band photolysis (290-310 nm) and gave poorer yields. 1, 1-Diazene 15 could not be isolated even at 10 K. The chemical and spectroscopic properties of the 1, 1-diazenes were investigated in some detail, and the results were analyzed with regard to the stability of the various 1,1-diazenes and the different reactive pathways available to 1,1-diazenes with different substituents.
\r\n\r\nPart II: The dependence of intramolecular electron transfer rates for porphyrin-quinone compounds on distance and temperature was studied. It was found that the rates depend exponentially on the edge-to-edge donor acceptor distance Re as
\r\n\r\nkET = ko exp [-\u03b1 Re]
\r\n\r\nwith \u03b1 values of 1.10 to 1.25 in different solvents. The temperature dependence studies revealed that the electron transfer rates are not activated in a classical sense, but instead depend on the dynamic relaxation properties of the solvent. In 2-methyltetrahydrofuran, the rates are nearly independent of temperature at high\r\ntemperatures (200-300 K), then begin to decrease with decreasing temperature. In toluene, the rates increase with decreasing temperature, while in deuterated toluene the rates initially increase with decreasing temperature, then go through a maximum around 215 K, and finally decrease. Apart from the unusual solvent isotope effect in the toluene and toluene-8 data, this appears to be the first observation of the rate turnover with solvent \"friction\" predicted by Kramers. The results were analyzed in terms of theoretical predictions of the dependence of electron transfer rates on the longitudinal relaxation time of the solvent \u03c4L using the equation
\r\n\r\nkET = kNA / 1.00 + (\u03b1 / KNA\u03c4L) + \u03b3kNA\u03c4L
\r\n\r\nwhere kNA is a maximum rate and \u03b1 and \u03b3 are fitted parameters. This equation gave reasonable fits to the data for all three solvents.
" }, { "name": "Hardy, Winters Reef", "degree": "PhD", "year": "1990", "title": "The characterization and processing of the nonstructural proteins of Sindbis virus", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06082007-084319", "creators": [ { "name": { "family": "Hardy", "given": "Winters Reef" }, "id": "Hardy-W-R", "display_name": "Hardy, Winters Reef" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Emr", "given": "Scott D." }, "id": "Emr-S-D", "role": "member", "display_name": "Emr, Scott D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gk9d-5371", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nSHORT ABSTRACT:\n\nThe nonstructural proteins of Sindbis virus, the type alphavirus of the family Togaviridae, are produced by proteolytic cleavage of two polyprotein precursors. One precursor (P123) is 1,896 amino acids in length and contains the sequences of nsP1, nsP2, and nsP3, while the second (P1234) of 2,513 amino acids is produced by readthrough of an opal termination codon and contains a fourth nonstructural protein, nsP4.\n\nIn order to study the kinetics of processing of these polyproteins, monospecific antisera were produced in rabbits to fusion protein antigens containing the N-terminal two-thirds of the trpE protein of E. coli fused to a large part of the sequence within each of the nonstructural proteins of Sindbis virus. Using these antisera the following details of processing were elucidated: i) most nonstructural proteins arise from the processing of the completed precursor P123 and its cleavage product, P12; ii) in the P123 precursor, the primary cleavage occurs in trans, between nsP2 and nsP3 to generate P12 and nsP3 with a half-life of [...]19 min. in vivo, followed by processing of P12 to produce nsP1 and nsP2, either intramolecularly or in trans, at a rate which exceeds that of the first cleavage; iii) processing of the 3-4 site is complex; and iv) nsP3 was found to be phosphorylated during posttranslational modification.\n\nIn vitro, processing could be inhibited with antibodies to nsP2, but not with antisera to the other three nonstructural proteins, suggesting that the nonstructural proteinase is in nsP2. Deletion-mapping studies were performed which further localized the proteinase to a region of approximately 334 amino acids at the C terminus of nsP2. From a comparison of the deduced sequences of several alphaviruses in this part of nsP2 with the sequences of cellular proteinases, a hypothesis was presented that the proteinase is a thiol protease related to papain. Finally, the examination of several temperature-sensitive mutants of Sindbis virus has confirmed the importance of this region as only mutants that possessed a mutation in the C-terminal domain of nsP2 produced aberrant processing patterns at the nonpermissive temperature.\n" }, { "name": "Harvey, Erica Lyn", "degree": "PhD", "year": "1990", "title": "Photochemical hydrogen atom transfer reactions of binuclear platinum complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06112007-134908", "creators": [ { "name": { "family": "Harvey", "given": "Erica Lyn" }, "id": "Harvey-E-L", "display_name": "Harvey, Erica Lyn" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2HE2-C733", "abstract": "This thesis focuses on hydrogen atom (H-atom) transfer reactions of the lowest electronic excited state of the d8 dimer [Pt2(P2O5H2)4]4- (the ground state is abbreviated Pt2]; the lowest excited state is a long-lived triplet, abbreviated 3Pt2*). Factors that influence initial rates of reaction of the excited state with alcohol and hydrocarbon H-atom donors are examined in Chapter 2. Observation of a large kinetic deuterium isotope effect (kH/kD=4) for phosphorescence quenching by [alpha]-secphenethyl alcohol verifies the importance of bond strength in determining reaction rates. A plot of H-atom abstraction rates versus C-H bond strengths reveals that bond strength is not the sole determinant of abstraction rate, however. Faster rates are observed when an [alpha]-hydroxy functionality is present, and the size of the substrate also influences abstraction rates. Chapter 3 features characterization of a diplatinum dihydride complex (Pt2H2) that acts as a key intermediate in H-atom transfer reactions. 3Pt2* reacts with hydrogen-atom donors to give a complex characterized by strong absorption at 314 nm; NMR (1H and 31P) and IR spectroscopic studies show that the complex is an axial dihydride (Pt2H2). Reactions of Pt2H2 include photochemical release of H2, rapid thermal reduction of O2, and thermal reduction of HCl to H2. Chapter 4 describes synthesis and characterization of a derivative of Pt2 modified by substitution of electron-withdrawing BF2+ groups for ligand H+. The new compound exhibits photophysical properties (phosphorescence lifetime, quantum yield, absorption and emission maxima) virtually identical with those of 3Pt2*, but dramatically shifted ground-state electrochemical properties (peak potential for oxidation shifted +750 mV). Comparisons of thermal reactivity (preparation of axial dihalide and dihydride complexes) and photochemical reactivity (reductive quenching and H-atom transfer quenching) of the two platinum dimers, detailed in Chapter 5, provide further insight into the factors influencing H-atom transfer in binuclear d8-d8 compounds." }, { "name": "Heben, Michael Joseph", "degree": "PhD", "year": "1990", "title": "Scanning tunneling microscopy in electrochemical environments", "advisor": "Lewis, Nathan Saul", "url": "https://resolver.caltech.edu/CaltechETD:etd-06122007-104233", "creators": [ { "name": { "family": "Heben", "given": "Michael Joseph" }, "id": "Heben-M-J", "display_name": "Heben, Michael Joseph" } ], "advisors": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "advisor", "display_name": "Lewis, Nathan Saul" } ], "committee": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "role": "chair", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8myg-1s98", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nScanning tunneling microscopy (STM) has been demonstrated to be an important analytical tool for the in situ characterization of electrode surfaces. However, in an electrochemical environment, the tip/sample bias necessary for electron tunneling can also drive heterogeneous charge transfer reactions between the solution-contacted portions of the tip and sample. This faradaic current acts in parallel to the normally measured tunneling current and the measured sum may not exhibit the expected exponential dependence on tip/sample separation. As a result, the interpretation of STM-derived data is not straightforward. The faradaic current component can be selectively reduced by coating the shaft and apex of the STM tip with insulating layers. Two tip-insulating procedures were developed, employing thin layers of either glass or polymer, that effectively reduce tip/sample faradaic currents even in the presence of redox active ions. The amount of exposed metal remaining after insulation was characterized with cyclic voltammetry. Using these insulated STM tips in an instrument constructed specifically for electrochemical investigations, atomic resolution images of highly ordered pyrolytic graphite were obtained in deionized water and in aqueous 0.1 [...] NaCl solutions at tip biases of \u00b1 1.5 V, and in aqueous solutions simultaneously containing 0.1 [...], 0.1 [...] and 1.0 [...] NaCl at biases of \u00b1 0.8 V. Images of MoS2 were obtained in 0.5 [...] NaClO4 at tip potentials as large as + 0.5 V. The distance dependence of the tip/sample faradaic current was investigated for the two different kinds of coated tips. A reduction in the faradaic current at tip/sample spacings less than ca 0.3 [mu]m was observed for polymer-coated tips. No such reduction was observed for glass-coated tips. Thin-layer current enhancements were observed for these tips when the amount of exposed metal area was relatively large (ca > 50 nm2). The tip insulation techniques were also used to produce, with minor modifications, conical and hemispherical ultramicroelectrodes. These were characterized with cyclic voltammetry and chronoamperometry and were applied to the measurement of the heterogeneous rate constant for Ru[...] reduction." }, { "name": "Kaisaki, David A.", "degree": "PhD", "year": "1990", "title": "Part I. 3,4-diazabenzvalene, the azoalkane precursor to tetrahedrane. Part II. Magnetic properties of polaronic polymers", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142007-110031", "creators": [ { "name": { "family": "Kaisaki", "given": "David A." }, "id": "Kaisaki-D-A", "display_name": "Kaisaki, David A." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4xjm-q168", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe synthesis and reactivity of 3,4-diazabenzvalene (9) are described. This strained diazene thermally decomposes to yield cyclobutadiene dimer with a unimolecular rate at constant -60\u00b0C of 5.24 x 10(-4) sec(-1). This corresponds to a half-life for 9 of 22 min. at -60\u00b0C. The high thermal reactivity of 9 is postulated to be due to a six-electron, concerted [...] + [...] + [...] N2 extrusion mechanism as opposed to the one-bond diazenyl biradical mechanism observed in the similar molecule, 48. Low temperature (-100 to -150\u00b0C) 1H NMR spectroscopy of -196\u00b0C photolysis products of 9 in a variety of solvents showed the formation of cyclobutadiene dimer and pyridazine. Attempts at the 10 K FT-IR matrix isolation photolysis studies on 9 failed due to our inability to sublime the cooled, unstable diazene onto the matrix window. No evidence of tetrahedrane formation upon photolysis or thermolysis at any temperature was observed.\n\nThe magnetic behavior of AsF5- and I2-doped poly(metaphenyleneoctatetraene) (PMPOT) derivatives is also investigated. A synthetic scheme for O-alkyl substituted PMPOT derivatives is developed using the Wittig reaction as the polymerization method. O-alkyl substitution provides an increase in solubility and degree of polymerization relative to the unsubstituted, intractable, parent polymer PMPOT. The O-octadecyl-substituted PMPOT derivative, PMPOT-18, is completely soluble in chloroform or toluene and has a degree of polymerization of 22.\n\nOxidative doping of PMPOT-18 and PMPOT-6 (O-hexyl-substituted) with AsF5 or I2 produces small concentrations (0.2-4 spins/100 monomers) of polarons (partially delocalized radical cations). Fitting the Brillouin function to the magnetization behavior of these polaronic materials provides a method of obtaining the spin state without the need of an estimate of the concentration of polarons present. A spin state of S = 2.2 for AsF5-doped PMOT-18 was found at 1.95 K, while I2-doped PMPOT-6 and PMPOT-18 fit to a Brillouin function with S = 1.2 - 1.3. This is consistent with a net ferromagnetic coupling between 2-4 polarons. Temperature-dependent magnetic susceptibility measurements indicate the presence of both antiferro- and ferromagnetic interactions at temperatures below ca. 50 K. This is interpreted in terms of a model in which doping produces clusters of polarons that interact ferromagnetically. There is also a weaker, antiferromagnetic interaction between clusters that is apparent at low temperatures." }, { "name": "Kang, Hway-Chuan", "degree": "PhD", "year": "1990", "title": "Model studies of adsorbate ordering, adsorption and reaction using Monte-Carlo simulations", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-05152007-125719", "creators": [ { "name": { "family": "Kang", "given": "Hway-Chuan" }, "id": "Kang-Hway-Chuan", "display_name": "Kang, Hway-Chuan" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/b1hf-xj64", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe application of Monte-Carlo simulations to study thermally excited time-dependent phenomena is examined. The diffusion coefficient and the exponent for domain growth for a square lattice gas experiencing equal and repulsive nearest-neighbor and next-nearest-neighbor interactions are calculated for three different dynamics: Kawasaki; Metropolis and energy-barrier. All three dynamics satisfy detailed balance, but the diffusion coefficient is found to show a different temperature dependence for each. The growth exponents for Kawasaki and energy-barrier dynamics are in close agreement, and larger than that for Metropolis dynamics. This difference arises because the domain sizes reached were not sufficiently large.\r\n\r\nIn further Monte-Carlo simulations of the same lattice gas model using dynamics which allow precursor-mediated migration, the growth exponent of fourfold degenerate ordered (2x1) domains on a square lattice is found to be 1/2. If the growth law is written as [...], A is found to be proportional to [...], where D is the diffusion coefficient of the adsorbed particle. Kawasaki dynamics simulations at zero temperature are performed for the growth of [...] domains on a triangular lattice. The results show that the low temperature behavior is markedly dependent upon the details of the lateral interactions and the range of the particle hops. This latter result demonstrates the strong influence of a precursor state on growth kinetics.\r\n\r\nMonte-Carlo analysis of molecular beam reflectivity measurements of the probability of molecular adsorption of ethane on the Ir(110)-(1x2) surface shows that a precursor state can also be rather important in adsorption. We show that the experimental data can be explained by adsorption occurring in two channels: direct and precursor-mediated. In this case the precursor is an ethane molecule trapped in a second layer on top of the first layer of molecularly adsorbed ethane. From the simulations we were also able to calculate the energy barriers for diffusion and desorption of an ethane molecule in the precursor state.\r\n\r\nMonte-Carlo simulations of a Langmuir-Hinshelwood reaction between two interacting species were also performed. The parametrization of the reaction rate coefficient that is implicit in an Arrhenius plot is examined. It is shown that the effective energy barrier and preexponential factor obtained from an Arrhenius plot show strong compensation when the overlayer configuration is strongly temperature dependent. This can explain the anomalously high reaction or desorption preexponential factors observed for some adsorbed systems.\r\n\r\nIt is also shown that a Langmuir-Hinshelwood reaction occurring between two species, even when they are non-interacting, can lead to configurational effects. Compact 'islands' consisting solely of either species A or species B are observed in simulations. An order parameter which allows an analogy between the reacting system and magnetic systems to be drawn is defined. The reactivity of the catalyst surface is inversely proportional to the 'island' size." }, { "name": "Khosla, Chaitan", "degree": "PhD", "year": "1990", "title": "Vitreoscilla hemoglobin: gene structure and regulation functions, and applications to aerobic bioprocesses", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04212004-154615", "creators": [ { "name": { "family": "Khosla", "given": "Chaitan" }, "id": "Khosla-C", "display_name": "Khosla, Chaitan" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/CQTP-5511", "abstract": "Vitreoscilla sp. is a Gram-negative obligately aerobic bacterium, which is capable of synthesizing a soluble, homodimeric hemoglobin-like molecule (VHb) in response to hypoxic environments. Although the mechanism of action of VHb is not understood, it has been hypothesized that the heme-protein enables the bacterium to survive in oxygen-limited environments. The functional role of this bacterial globin has been studied with the aim of exploiting such a naturally evolved strategy to improve oxygen-limited bioprocesses. Furthermore, the regulation of expression of the VHb gene in response to changes in environmental conditions has also been investigated. This has provided insights into mechanisms of microaerobic gene regulation, and has enabled the development of oxygen-dependent expression systems for high-level synthesis of recombinant proteins.\n\nThe gene encoding the VHb polypeptide was isolated from a Vitreoscilla genomic library. The nucleotide sequence of the gene and its flanking regions was determined and analyzed. Synthesis of active VHb was shown to occur in E. coli from the natural expression signals of the VHb gene.\n\nStudies in fed-batch fermentations demonstrated that under oxygen limitation, the presence of the VHb gene on a multicopy plasmid enhanced the growth and respiratory characteristics of a recombinant E. coli host as compared to equivalent plasmid-carrying and plasmid-free cells. These results illustrated the possibility of studying the mechanism of VHb action in E. coli as a surrogate host, and were also indicative of the potential applicability of such a genetic strategy in organisms other than Vitreoscilla. Furthermore, it was observed that VHb expression is under oxygen-dependent control in E. coli, suggesting that the mechanism of regulation of the gene in Vitreoscilla is also functional in E. coli.\n\nBiochemical studies revealed that a considerable fraction, but not all, of the intracellular VHb is localized in the periplasm of E. coli and Vitreoscilla. The activity of the two fractions was identical, as judged by visible spectroscopy. Genetic evidence for the role of the N-terminal domain of the VHb polypeptide in protein translocation was also obtained; however no cleavage was detected at this end as a result of translocation. Based on available biochemical and biophysical data, it was suggested on theoretical grounds that periplasmic VHb is capable of supporting an additional oxygen flux to the respiratory chain, which may be physiologically significant (the facilitated diffusion hypothesis).\n\nIn E. coli strains containing VHb integrated into the chromosome in single copy, the presence of VHb improved cellular energetics under oxygen-limiting, but not oxygen-excess conditions. Indirect evidence was obtained, suggesting that the net effect of VHb in E. coli is to improve the efficiency, rather than the kinetics of oxygen-limited aerobic metabolism. Although the facilitated diffusion hypothesis could not be confirmed or ruled out, an alternative hypothesis (the intracellular redox effector hypothesis) was also proposed. This implies that oxygenated VHb influences the activity of a key redox-sensitive cell function, which is affected under hypoxic conditions.\n\nGenetic studies demonstrated the presence of an oxygen-responsive element (ORE) upstream of the VHb gene. Gene expression is maximal under microaerobic conditions, and is also influenced by catabolite repression. Mechanisms responsible for oxygen-dependent regulation act at the level of transcription initiation from two overlapping promoters within the region upstream of the VHb gene.\n\nProtocols were developed for the use of ORE-based expression systems for regulated, high level synthesis of recombinant proteins in high cell density fermentations. A 30-fold modulation of promoter activity could be achieved in these experiments. By simply decreasing the air supply to cells carrying a VHb-lacZ fusion, [Beta]-galactosidase was expressed to a level of about 10% of total cellular protein in a culture containing 20 g dry cell weight/L." }, { "name": "Kibbe, Warren Alden", "degree": "PhD", "year": "1990", "title": "A Detailed Analysis of Transcriptional Regulators Affecting the Saccharomyces cerevisiae Heat-shock Gene SSA1", "advisor": "Parker, Carl Stevens", "url": "https://resolver.caltech.edu/CaltechTHESIS:07242014-161229419", "creators": [ { "name": { "family": "Kibbe", "given": "Warren Alden" }, "id": "Kibbe-W-A", "display_name": "Kibbe, Warren Alden" } ], "advisors": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "advisor", "display_name": "Parker, Carl Stevens" } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "member", "display_name": "Davidson, Eric H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fraq-3065", "abstract": "The yeast Saccharomyces cerevisiae contains a family of hsp70 related genes. One member of this family, SSA1, encodes a 70kD heat-shock protein which in addition to its heat inducible expression has a significant basal level of expression. The first 500 bp upstream of the SSA1 start point of transcription was examined by DNAse I protection analysis. The results reveal the presence of at least 14 factor binding sites throughout the upstream promoter region. The function of these binding sites has been examined using a series of 5' promoter deletions fused to the recorder gene lacZ in a centromere-containing yeast shuttle vector. The following sites have been identified in the promoter and their activity in yeast determined individually with a centromere-based recorder plasmid containing a truncated CYC1 /lacZ fusion: a heat-shock element or HSE which is sufficient to convey heat-shock response on the recorder plasmid; a homology to the SV40 'core' sequence which can repress the GCN4 recognition element (GCRE) and the yAP1 recognition element (ARE), and has been designated a upstream repression element or URE; a 'G'-rich region named G-box which can also convey heatshock response on the recorder plasmid; and a purine-pyrimidine alternating sequence name GT-box which is an activator of transcription. A series of fusion constructs were made to identify a putative silencer-like element upstream of SSA1. This element is position dependent and has been localized to a region containing both an ABF1 binding site and a RAP1 binding site. Five site-specific DNA-binding factors are identified and their purification is presented: the heat-shock transcription factor or HSTF, which recognizes the HSE; the G-box binding factor or GBF; the URE recognition factor or URF; the GT-box binding factor; and the GC-box binding factor or yeast Sp1.
" }, { "name": "Kramar, John Adam", "degree": "PhD", "year": "1990", "title": "Scanning Tunneling Microscopy and Spectroscopy of Molybdenum Disulfide", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06132007-103520", "creators": [ { "name": { "family": "Kramar", "given": "John Adam" }, "id": "Kramar-John-Adam", "orcid": "0000-0001-6038-637X", "display_name": "Kramar, John Adam" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q36A-AW73", "abstract": "Scanning tunneling microscopy (STM) is a recently developed surface analysis technique that is capable of atomic resolution imaging in real space. In STM, a sharp electrically conducting tip is brought near the sample and a tunneling current is established between the two. For topographical imaging, the tip is then raster-scanned over the surface while a feedback control system maintains constant current by adjusting the position of the tip in the surface normal. The trajectory that the tip follows is displayed as the surface topography. The unique geometry of the STM has also allowed the electronic nature of surfaces to be probed with unprecedented spatial resolution. This can be implemented, for example, by posing the probe tip over a specific surface location and examining the current-versus-voltage characteristics.\r\n\r\nCareful consideration must be given in the design of an STM system. The crucial elements of vibration isolation and microscope rigidity must be optimized within the constraints of allowing coarse positioning of the tip and sample and permitting high-resolution scanning. A stable feedback control system must also be designed with flexibility to allow for different operating conditions.\r\n\r\nWe have built an ultrahigh vacuum (UHV) STM that is similar to the familiar pocket STM design. The UHV system includes a separate sample preparation chamber and vacuum-transfer load lock to facilitate in studies of clean, carefully prepared surfaces. The instrument is interfaced with a microprocessor for control of scanning, data acquisition, and coarse tip-sample approach and positioning. A high-resolution graphics monitor is also included for displaying the topographic images and the current-voltage spectra during acquisition and for reviewing previously stored images.\r\n\r\nStudies of the basal cleavage plane of MoS2 have been performed with this instrument. Large area images up to 360 x 360 nm reveal a high degree of variability in surface morphology, ranging from atomically smooth planes, to islands or mounds ranging from 1 to 10 nm in diameter, to areas of complete surface roughness. Many unusual imaging phenomena were also observed in these scans, including bias-dependent images and surface modifications that were due to tip-sample interactions.\r\n\r\nAtomic-resolution images revealing the trigonal symmetry of the surface plane were obtained in both the constant-current and current-imaging modes on the smooth areas of the surface. Two distinct sites can be seen, corresponding to the known molybdenum and sulfur atomic positions.\r\n\r\nA simple description of the distance dependence of tunneling between the STM tip and an ideal semiconductor surface (no surface Fermi level pinning) is presented, based on conventional metal-insulator-semiconductor (MIS) theories. The current conduction mechanism involves thermionic emission over the semiconductor diffusion-potential barrier, which is a decreasing function of the tip-sample separation, followed by tunneling through the vacuum gap. The competition between the decreased vacuum-tunneling probability and the increased carrier population at the semiconductor surface for increasing separation gives rise to a predicted peak in the I-s curves at small separations, and a lowering of the apparent tunneling barrier height out to separations of more than 1 nm. The normally rectified current-voltage characteristics are also found to be a function of the tip-sample spacing, showing a weakening and then a reversal of rectification as the separation is increased. These predicted effects are substantiated by means of a detailed numerical calculation for the passivated n-type Si(111) surface.\r\n\r\nThe current-voltage spectroscopy of MoS2, which is expected to behave as an ideal semiconductor, was examined. The surface-averaged spectra show a high degree of variability, with different data sets showing rectification in opposite polarities for the same physical tip and sample. The results are shown to be qualitatively different from known mechanisms for rectification in STM, including tip-curvature-induced field gradient effects and effects that are due to the separation dependence of rectification in ideal MIS structures. The results are best explained as doping inhomogeneities in our mineralogical samples.\r\n" }, { "name": "Li, Peter Mark", "degree": "PhD", "year": "1990", "title": "The role of CuA in the cytochrome c oxidase proton pump", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06202007-085253", "creators": [ { "name": { "family": "Li", "given": "Peter Mark" }, "id": "Li-P-M", "display_name": "Li, Peter Mark" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nahx-1j91", "abstract": "Cytochrome c oxidase plays a central role in energy transduction in most aerobic organisms. It catalyzes the transfer of electrons from ferrocytochrome c on the cytosolic side of the inner mitochondrial membrane, to dioxygen. The protons consumed during this reaction are derived exclusively from the matrix space, resulting in a charge separation that contributes to the transmembrane electrochemical gradient. In addition to the dioxygen reduction activity, cytochrome oxidase is also a proton pump that can pump up to four protons from the matrix side of the inner membrane to the cytosolic side for every molecule of dioxygen reduced. This thesis investigated the role of the structure and function of CuA in the proton pumping function of the enzyme.\n\nThe structure of the CuA site was studied using Extended X-ray Absorption Fine Structure (EXAFS). Using the p-(hydroxymercuri)benzoate (pHMB)-modified enzyme and a CuA-depleted form of the enzyme, we assigned the ligand structures for CuA and CuB in the resting form of the enzyme. The best fit model for the coordination environment at CuA was found to be 2 (N,O) ligands at 1.99A (presumably from histidine) and 2 (S,CI) ligands at 2.3A (presumably from cysteine). The EXAFS curve fitting techniques were further refined to investigate the copper sites in both the resting and fully reduced forms of the enzymes. These results indicated that the resting form of the enzyme contains a \"long\" 2.6A Cu-(S,Cl) in addition to the 2.3A Cu-(s,Cl) interactions previously reported. Using the curve-fitting results from the CuA-modified and CuA-depleted enzymes, we were able to assign this interaction to one of the two Cu-(S,CI) interactions at the CuA site. The curve-fitting results for the reduced enzyme showed no \"long\" interaction and indicated an average of one less sulfur per two coppers, suggesting that a a ligand rearrangement occurs upon reduction of CuA.\n\nThe role of CuA in proton pumping was assessed by reconstituting the pHMB-modified enzyme into artificial phospholipid vesicles, and measuring its proton pumping activity. We found that this form of the enzyme, which contains a perturbed CuA site, exhibits a rapid proton leak. This leak is not associated with pHMB modification of the protein surface sulfhydryl groups, but appears to be specifically correlated with the modification of the CuA site. We also developed a method for specifically perturbing the CuA site using gentle heating at 43\u00b0C. It was found that heat treatment causes a specific modification of the CuA site. We showed that the products of this reaction are native CuA, a type 2 Cu, and novel \"blue copper\" species. Furthermore, reduction of the enzyme as well as ligand binding to the binuclear center were found to protect the CuA site from heat-induced modifications. When the heat-treated enzyme was reconstituted into vesicles, it displayed proton pumping behavior similar to the pHMB-modified enzyme, again pointing to a role for CuA in the proton pumping machinery of the enzyme. These results also suggest that the CuA site is different in the oxidized and reduced forms of the enzyme, and that a strong allosteric interaction exists between the CuA site and the binuclear center.\n\nBased on indications that there is a strong interaction between the binuclear center and CuA, we probed the protein matrix for a conformational change that could be caused by ligand binding to the binuclear center. Using the flow-flash technique, we identified a transient conformational change that appears to be associated specifically with dioxygen binding and reduction. This conformational change occurs rapidly enough to be involved in the turnover of the enzyme, and can be influenced by the redox state of cytochrome a and CuA. We conclude this thesis with a model for the turnover cycle of the enzyme, which utilizes CuA as the site of redox linkage, and a conformational switch which engages the pumping cycle.\n" }, { "name": "Mendel, David", "degree": "PhD", "year": "1990", "title": "Chemical and Enzymatic Footprinting of Quinoxaline Antibiotics on DNA", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-085143", "creators": [ { "name": { "family": "Mendel", "given": "David" }, "id": "Mendel-David", "display_name": "Mendel, David" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1kmd-qq48", "abstract": "A key element of antitumor drug design is an understanding of how naturally occurring antitumor antibiotics recognize and bind to DNA, the major means by which many of these agents act. Once such an understanding is attained, the salient elements of recognition may be extracted and then extended to create more powerful and more specific antitumor (chemotherapeutic) agents. In an effort to understand G\u2022C recognition, we studied the binding interactions between DNA and the antitumor antibiotics triostin A and echinomycin.
\r\n\r\nRecent studies by the Rich group at MIT and by the Patel group at Columbia have shown that the naturally occurring antitumor antibiotics triostin A and echinomycin bind four base pairs of DNA and can induce the formation of Hoogsteen base pairs at the first and fourth base pair positions of their binding sites on small oligonucleotides. The central aim of the thesis work described below was to establish whether this novel base-pairing occurs at echinomycin and triostin A binding sites on native DNA and if so, whether this represents a new recognition motif on which to base anticancer drug design.
\r\n\r\nWe find that purines occupying the first and/or fourth base pair positions of echinomycin and triostin A binding sites become hyperreactive to diethyl pyrocarbonate (DEP) in the presence of drug. This finding raised the issue as to whether DEP detects Hoogsteen base-pairing at echinomycin binding sites in solution. We analyzed the products of DEP-purine reaction formed in the presence of echinomycin and ethidium bromide at six different echinomycin binding sites. Two different DEP-purine adducts were identified: 5-carbethoxyamino-4,6-diaminopyrimidine and 5-carbethoxyamino-2,4-diamino-6-hydroxypyrimidine. These products correspond to reaction of DEP at the N7 positions of adenosine and guanosine residues, respectively. The identity of these compounds strongly suggests that DEP responds to local helix unwinding caused by antibiotic intercalation into DNA and not to a Watson-Crick to Hoogsteen base-pairing transition caused by echinomycin binding to DNA. Nonetheless, DEP is a sensitive and precise probe of echinomycin and triostin A binding to DNA, and we describe this chemical footprinting reagent as the preferred means by which to identify echinomycin and triostin A binding sites on DNA. We also note three new types of echinomycin binding sites (5'-3') GGGG, TCAT, and TCAC not previously identified.
\r\n\r\nWe find that another chemical footprinting reagent, dimethyl sulfate (DMS), demonstrated that isolated C.G Hoogsteen base pairs may exist at echinomycin binding sites within a DNA duplex under acidic conditions. If this is indeed the case, it would be the first example of isolated Hoogsteen base pairs to exist within a DNA fragment in solution. However, at neutral pH, echinomycin and triostin A appear to bind DNA via simple bisintercalation and probably do not form stable Hoogsteen base pairs at their binding sites. Therefore, we conclude that the induction or recognition of Hoogsteen base pairs at drug binding sites does not yet constitute a practical approach to the design of sequence specific DNA binding agents.
\r\n\r\nIn addition, using a series of plasmid DNAs and a battery of enzymatic and chemical probes of DNA structure, we find that echinomycin binding to DNA apparently alters the helix structure of sequences adjacent and distal to its binding sites. Echinomycin can thus be considered an allosteric effector of DNA structure.
" }, { "name": "Montgomery, Donald David", "degree": "PhD", "year": "1990", "title": "Part I. Influence of membrane morphology on ion-exchange and charge propagation in composite polyelectrolyte electrode coatings. Part II. Dynamic surface tension measurements of polarization relaxation at mercury pool electrodes by the method of Wilhelmy.", "advisor": "Borup, Richard", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252014-125443654", "creators": [ { "name": { "family": "Montgomery", "given": "Donald David" }, "id": "Montgomery-D-D", "display_name": "Montgomery, Donald David" } ], "advisors": [ { "name": { "family": "Borup", "given": "Richard" }, "id": "Borup-R", "role": "advisor", "display_name": "Borup, Richard" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cgnm-tz37", "abstract": "Part I. Novel composite polyelectrolyte materials were developed that exhibit desirable charge propagation and ion-retention properties. The morphology of electrode coatings cast from these materials was shown to be more important for its electrochemical behavior than its chemical composition.
\r\n\r\nPart II. The Wilhelmy plate technique for measuring dynamic surface tension was extended to electrified liquid-liquid interphases. The dynamical response of the aqueous NaF-mercury electrified interphase was examined by concomitant measurement of surface tension, current, and applied electrostatic potential. Observations of the surface tension response to linear sweep voltammetry and to step function perturbations in the applied electrostatic potential (e.g., chronotensiometry) provided strong evidence that relaxation processes proceed for time-periods that are at least an order of magnitude longer than the time periods necessary to establish diffusion equilibrium. The dynamical response of the surface tension is analyzed within the context of non-equilibrium thermodynamics and a kinetic model that requires three simultaneous first order processes.
\r\n" }, { "name": "Mullins, Charles Buddie", "degree": "PhD", "year": "1990", "title": "Molecular Beam Investigations of Surface Chemical Reactions and Dynamics", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-03122007-135158", "creators": [ { "name": { "family": "Mullins", "given": "Charles Buddie" }, "id": "Mullins-Charles-Buddie", "orcid": "0000-0003-1030-4801", "display_name": "Mullins, Charles Buddie" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/64s4-0182", "abstract": "Experimental results from molecular beam investigations of trapping and dissociative chemisorption phenomena for several gas-surface systems are presented. The dissociative chemisorption of oxygen on Ir(110)-(1x2) in the limit of zero coverage So was studied as a function of incident kinetic energy Ei, incident angle \u03b8i and surface temperature Ts. Results from this investigation indicate that two mechanisms account for the initial chemisorption. At low incident kinetic energy (less than 4 kcal/mol) chemisorption mediated by trapping is primarily responsible for the dissociative adsorption while at high energies a direct mechanism can account for the results. In both energy ranges the initial dissociative chemisorption probability is insensitive to incident angle.
\r\n\r\nThe trapping of molecular ethane as well as the dissociative chemisorption of ethane on the clean Ir(110)-(1x2) surface has also been investigated. The initial trapping probability \u03b6o is found to decrease with incident kinetic energy from a value of ~0.98 at 1 kcal/mol to ~0.1 at 16 kcal/mol. These data scale with Eicos0.5\u03b8i. The initial dissociative chemisorption of ethane on Ir(110)-(1x2) occurs via a trapping-mediated mechanism at low Ei and a direct mechanism at high kinetic energies. In the trapping-mediated regime So decreases rapidly with increasing Ts. These data quantitatively support a kinetic model consistent with a trapping-mediated chemisorption mechanism. The difference in the activation energies for desorption and chemisorption from the physically adsorbed, trapped state Ed-Ec is 2.2\u00b10.2 kcal/mol. Chemisorption at high kinetic energies, in the direct regime, is independent of surface temperature.
\r\n\r\nAdditionally, the trapping probability of Ar on Pt(111) has been measured as a function of incident kinetic energy, and angle for Ts = 80, 190 and 273 K. The trapping probability decreases with increasing Ei in a manner that depends on both \u03b8i and Ts. The angular scaling law governing the trapping is a function of Ts such that \u03b6o scales with Eicos1.5\u03b8i at 80 K, Eicos1.0\u03b8i at 190 K and Eicos0.5\u03b8i at 273 K. These results suggest that parallel momentum dissipation becomes increasingly more important to the trapping dynamics as the surface temperature is increased.
\r\n" }, { "name": "Ng, Ricky Chiu-Yin", "degree": "PhD", "year": "1990", "title": "Semi-dilute polymer solutions in strong flows. Part I: Birefringence and flow modification in extensional flows. Part II: Chaotic mixing in time-periodic flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-05172007-154209", "creators": [ { "name": { "family": "Ng", "given": "Ricky Chiu-Yin" }, "id": "Ng-R-C", "display_name": "Ng, Ricky Chiu-Yin" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "member", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Wiggins", "given": "Stephen R." }, "id": "Wiggins-S-R", "role": "member", "display_name": "Wiggins, Stephen R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/z6wv-9136", "abstract": "Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe non-Newtonian effects of semi-dilute polymer solutions in laminar two-dimensional steady and time-periodic strong flows are examined separately in two parts of this thesis. Strong flows are flows that can induce large deformation of the polymer molecules. The first part of this thesis is the study of flow-induced stretching of macromolecules in semi-dilute solutions and the subsequent modification to extensional flows in a two-roll and a four-roll mill. Experimental results are presented for flow birefringence, which provides a measure of the degree of polymer extension. In addition, we report on velocity gradient measurements via the technique of homodyne light scattering for solutions of various polymer concentrations in the dilute to semi-dilute regime. Model predictions are also discussed using an interacting dumbbell model. In the second part of the thesis, we examine fluid mixing and transport in two-dimensional time-periodic Stokes flows produced in a blinking two-roll mill (BTRM) for both Newtonian and polymer solutions. Here, we report experimental data obtained by the technique of flow visualization using dye tracer, as well as quantitative measurements using a digital imaging technique.\n\nThe flow birefringence results for 100, 1500, and 4500 ppm polystyrene in viscous solvents indicate that increasing concentration will inhibit stretching of polymer molecules due to strong intermolecular interactions. The birefringence data for all three solutions correlate with the eigenvalue of the velocity gradient tensor for different extensional flows in the 2-roll and the 4-roll mill. Inception and cessation of steady extensional flows show distinctive overshoots in birefringence for the semi-dilute (1500 and 4500 ppm) solutions. Complementary velocity gradient measurements show a significant inhibition of large strain rates when a sufficient amount of extended polymer is present (the dilute 100 ppm solution shows no flow effect). The onset of polymer-induced changes in the flow (flow modification) occurs at a critical effective volume concentration, [...] ~ 175, based upon the volume of spheres that circumscribe the extended polymer chain, for both semi-dilute solutions. The magnitude of flow modification is larger in the less concentrated 1500 ppm solution due to the competing effects of increasing concentration and the inhibition of polymer extension which tends to lower the effective volume concentration, [...]. The correlation of the magnitude of flow modification with [...] is revealed by the local (pointwise) velocity gradient measurements for different concentration polymer solutions.\n\nVarious molecular models for non-dilute polymer solutions are discussed. The best comparison with the present flow birefringence data is obtained from the predictions of an interacting nonlinear elastic dumbbell (FENE-IDB) model. The FENE-IDB model predictions show a smooth transition of dilute solution behavior to semi-dilute solution behavior. In dilute solutions, the birefringence normalized with polymer concentration (or specific birefringence) is independent of concentration, c. However, the specific birefringence is proportional to c(-1) when plotted versus the dimensionless eigenvalue of the velocity gradient tensor, [...], for semi-dilute solutions. We also noted that the relaxation time of polymer, [...], is dependent on c for semi-dilute solutions.\n\nStudies of mixing and fluid transport properties in time-periodic laminar BTRM flows are first performed for Newtonian solutions. Fluid mixing is shown to be either regular or chaotic depending on the characteristic period of oscillation, \u00b5. Chaotic (efficient) mixing is achieved globally in the flow device when \u00b5 >= 0.5. The results in the mixing study can be compared qualitatively with dynamical systems theory predictions of chaos in time-periodic vortex-pair flows. The effect of polymer (a 1500 ppm solution of polystyrene in viscous solvent) on chaotic mixing and fluid transport in the BTRM flows is an O(1) decrease in both the area of mixing and the rate of fluid transport between different regions of the flow when compared with the corresponding Newtonian data. The onset of the polymer effect on the flow occurs at a critical Deborah number of (De)c ~ 2. This high De effect may be related to polymer-induced changes to both the weak and strong flow regions in the BTRM since the time-periodic flow is alternatively strong and mostly weak in the Lagrangian frame of reference." }, { "name": "Nguyen, Hung Viet", "degree": "PhD", "year": "1990", "title": "Powder production in aerosol reactors : particle structure and reactor optimization", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03122007-105616", "creators": [ { "name": { "family": "Nguyen", "given": "Hung Viet" }, "id": "Nguyen-H-V", "display_name": "Nguyen, Hung Viet" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" } ], "option_major": [ "chemeng" ], "doi": "10.7907/qk6a-e067", "abstract": "Powders consisting of dense, nonagglomerated, roughly spherical particles with a controlled size distribution are thought to be ideal for engineering applications of ceramic materials. The production of such powders in aerosol reactors is difficult due to the extreme difficulty of controlling particle formation by homogeneous nucleation of condensible vapors produced by gas phase chemical reactions. To generate the quality of powders necessary for engineering applications, one needs to understand the processes governing particle formation and growth in aerosol reactors.\n\nHomogeneous and heterogeneous nucleation were studied in a laminar flow aerosol generator using dibutylphthalate vapor. Seed particles were found to suppress homogeneous nucleation to an extent depending on their concentration. With additional insights on nucleation and nucleation suppression, aerosol physics was applied to an effort to generate dense, spherical silicon particles in a single stage multi-zone externally heated aerosol reactor. Subsequent experiments revealed that the dense silicon particles generated resulted from the sintering of aggregates formed by coagulation of like-sized particles. While the production of dense particles by sintering of low density agglomerates are feasible for low melting materials, it is not practical for refractory materials due to the high sintering temperatures required for complete coalescence in the available residence time. To produce ideal refractory powder materials, growth must be limited to vapor and small cluster deposition. An optimization technique was applied to the highly nonlinear aerosol reactor system to directly derive optimal temperature profiles that maximizes seed growth while minimizing the amount of fine particles formed. " }, { "name": "Novick, Steven Louis", "degree": "PhD", "year": "1990", "title": "Chemical Studies of Viral Entry Mechanisms: I. Hydrophobic Protein-Lipid Interactions During Sendai Virus Membrane Fusion. II. Kinetics of Bacteriophage \u03bb DNA Injection", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252014-124055207", "creators": [ { "name": { "family": "Novick", "given": "Steven Louis" }, "id": "Novick-Steven-Louis", "display_name": "Novick, Steven Louis" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Strauss", "given": "James H." }, "id": "Strauss-J-H", "role": "member", "display_name": "Strauss, James H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/k40w-2z72", "abstract": "Viruses possess very specific methods of targeting and entering cells. These methods would be extremely useful if they could also be applied to drug delivery, but little is known about the molecular mechanisms of the viral entry process. In order to gain further insight into mechanisms of viral entry, chemical and spectroscopic studies in two systems were conducted, examining hydrophobic protein-lipid interactions during Sendai virus membrane fusion, and the kinetics of bacteriophage \u03bb DNA injection.
\r\n\r\nSendai virus glycoprotein interactions with target membranes during the early stages of fusion were examined using time-resolved hydrophobic photoaffinity labeling with the lipid-soluble carbene generator3-(trifluoromethyl)-3-(m-^(125\r\n)I] iodophenyl)diazirine (TID). The probe was incorporated in target membranes prior to virus addition and photolysis. During Sendai virus fusion with liposomes composed of cardiolipin (CL) or phosphatidylserine (PS), the viral fusion (F) protein is preferentially labeled at early time points, supporting the hypothesis that hydrophobic interaction of the fusion peptide at the N-terminus of the F_1 subunit with the target membrane is an initiating event in fusion. Correlation of the hydrophobic interactions with independently monitored fusion kinetics further supports this conclusion. Separation of proteins after labeling shows that the F_1 subunit, containing the putative hydrophobic fusion sequence, is exclusively labeled, and that the F_2 subunit does not participate in fusion. Labeling shows temperature and pH dependence consistent with a need for protein conformational mobility and fusion at neutral pH. Higher amounts of labeling during fusion with CL vesicles than during virus-PS vesicle fusion reflects membrane packing regulation of peptide insertion into target membranes. Labeling of the viral hemagglutinin/neuraminidase (HN) at low pH indicates that HN-mediated fusion is triggered by hydrophobic interactions, after titration of acidic amino acids. HN labeling under nonfusogenic conditions reveals that viral binding may involve hydrophobic as well as electrostatic interactions. Controls for diffusional labeling exclude a major contribution from this source. Labeling during reconstituted Sendai virus envelope-liposome fusion shows that functional reconstitution involves protein retention of the ability to undergo hydrophobic interactions.
\r\n\r\nExamination of Sendai virus fusion with erythrocyte membranes indicates that hydrophobic interactions also trigger fusion between biological membranes, and that HN binding may involve hydrophobic interactions as well. Labeling of the erythrocyte membranes revealed close membrane association of spectrin, which may play a role in regulating membrane fusion. The data show that hydrophobic fusion protein interaction with both artificial and biological membranes is a triggering event in fusion. Correlation of these results with earlier studies of membrane hydration and fusion kinetics provides a more detailed view of the mechanism of fusion.
\r\n\r\nThe kinetics of DNA injection by bacteriophage \u03bb. into liposomes bearing reconstituted receptors were measured using fluorescence spectroscopy. LamB, the bacteriophage receptor, was extracted from bacteria and reconstituted into liposomes by detergent removal dialysis. The DNA binding fluorophore ethidium bromide was encapsulated in the liposomes during dialysis. Enhanced fluorescence of ethidium bromide upon binding to injected DNA was monitored, and showed that injection is a rapid, one-step process. The bimolecular rate law, determined by the method of initial rates, revealed that injection occurs several times faster than indicated by earlier studies employing indirect assays.
\r\n\r\nIt is hoped that these studies will increase the understanding of the mechanisms of virus entry into cells, and to facilitate the development of virus-mimetic drug delivery strategies.
\r\n" }, { "name": "Proteau, Philip Jerome", "degree": "Masters", "year": "1990", "title": "Neocarzinostatin chromophore: structural, mechanistic, and synthetic studies", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08122014-131021849", "creators": [ { "name": { "family": "Proteau", "given": "Philip Jerome" }, "id": "Proteau-Philip-Jerome", "display_name": "Proteau, Philip Jerome" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tmh7-8559", "abstract": "Neocarzinostatin chromophore 1 is the active component of the antitumor antibiotic\r\nneocarzinostatin (NCS). The chromophore reacts with thiols to form a highly strained\r\ncumulene-enyne species which rapidly rearranges to a biradical intermediate which can\r\nabstract hydrogen atoms from DNA, leading to strand cleavage. DNA damage is the\r\nproposed source of biological activity for NCS. The structure of the methyl thioglycolate\r\nmonoadduct 2 of NCS chromophore, including the absolute stereochemistry, was\r\ndetermined by NMR studies. The presence of the cumulene-enyne intermediate and the\r\nrearrangement to a biradical were supported by data from low temperature NMR\r\ninvestigations. Also included are synthetic approaches to NCS chromophore model\r\ncompounds based on intramolecular addition of an acetylide to an aldehyde." }, { "name": "Semmes, David Haynes", "degree": "PhD", "year": "1990", "title": "Picosecond studies of the vibrational predissociation of van der Waals complexes", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-144110", "creators": [ { "name": { "family": "Semmes", "given": "David Haynes" }, "id": "Semmes-D-H", "display_name": "Semmes, David Haynes" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NTP7-RS50", "abstract": "The vibrational predissociation of several van der Waals complexes of aromatic molecules with rare gas atoms, isolated in a free-jet molecular beam expansion, has been studied using time-resolved spectroscopy. Direct measurements have been made, on a picosecond time scale, of the fluorescence intensity from the initially excited single vibrational level and from the various final vibrational states formed in the dissociation of the complexes. The time-resolved data is analyzed with the aid of different kinetic models and can distinguish between parallel decay paths, sequential paths with intramolecular vibrational redistribution (IVR) preceding vibrational predissociation, and sequential paths with reversible IVR preceding vibrational predissociation. The contribution of the van der Waals modes to the total vibrational state density induces dissipative IVR in the complexes at much lower energies than in the bare aromatic molecule. The measured predissociation rates are compared with rates calculated according to the statistical RRKM theory of unimolecular reactions. Some of the experimental results show mode-selective behavior, while other results suggest statistical behavior." }, { "name": "Sun, Yongkui", "degree": "PhD", "year": "1990", "title": "Kinetic investigations of heterogeneously catalyzed reactions on the Ru(001) and Pt(110)-(1x2) surfaces", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292014-090847834", "creators": [ { "name": { "family": "Sun", "given": "Yongkui" }, "id": "Sun-Yongkui", "display_name": "Sun, Yongkui" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s955-n828", "abstract": "The initial probabilities of activated, dissociative chemisorption of methane and\r\nethane on Pt(110)-(1 x 2) have been measured. The surface temperature was varied\r\nfrom 450 to 900 K with the reactant gas temperature constant at 300 K. Under these\r\nconditions, we probe the kinetics of dissociation via trapping-mediated (as opposed\r\nto 'direct') mechanism. It was found that the probabilities of dissociation of both\r\nmethane and ethane were strong functions of the surface temperature with an apparent\r\nactivation energies of 14.4 kcal/mol for methane and 2.8 kcal/mol for ethane,\r\nwhich implys that the methane and ethane molecules have fully accommodated to\r\nthe surface temperature. Kinetic isotope effects were observed for both reactions,\r\nindicating that the C-H bond cleavage was involved in the rate-limiting step. A\r\nmechanistic model based on the trapping-mediated mechanism is used to explain\r\nthe observed kinetic behavior. The activation energies for C-H bond dissociation\r\nof the thermally accommodated methane and ethane on the surface extracted from\r\nthe model are 18.4 and 10.3 kcal/mol, respectively.
\r\n\r\nThe studies of the catalytic decomposition of formic acid on the Ru(001) surface\r\nwith thermal desorption mass spectrometry following the adsorption of DCOOH and\r\nHCOOH on the surface at 130 and 310 K are described. Formic acid (DCOOH)\r\nchemisorbs dissociatively on the surface via both the cleavage of its O-H bond to\r\nform a formate and a hydrogen adatom, and the cleavage of its C-O bond to form\r\na carbon monoxide, a deuterium adatom and an hydroxyl (OH). The former is the\r\npredominant reaction. The rate of desorption of carbon dioxide is a direct measure\r\nof the kinetics of decomposition of the surface formate. It is characterized by a\r\nkinetic isotope effect, an increasingly narrow FWHM, and an upward shift in peak\r\ntemperature with \u019f_T, the coverage of the dissociatively adsorbed formic acid. The\r\nFWHM and the peak temperature change from 18 K and 326 K at \u019f_T = 0.04 to\r\n8 K and 395 K at \u019f_T = 0.89. The increase in the apparent activation energy of the\r\nC-D bond cleavage is largely a result of self-poisoning by the formate, the presence\r\nof which on the surface alters the electronic properties of the surface such that the\r\nactivation energy of the decomposition of formate is increased. The variation of the\r\nactivation energy for carbon dioxide formation with \u019f_T accounts for the observed\r\nsharp carbon dioxide peak. The coverage of surface formate can be adjusted over\r\na relatively wide range so that the activation energy for C-D bond cleavage in the\r\ncase of DCOOH can be adjusted to be below, approximately equal to, or well above\r\nthe activation energy for the recombinative desorption of the deuterium adatoms.\r\nAccordingly, the desorption of deuterium was observed to be governed completely by\r\nthe desorption kinetics of the deuterium adatoms at low \u019f_T, jointly by the kinetics\r\nof deuterium desorption and C-D bond cleavage at intermediate \u019f_T, and solely by\r\nthe kinetics of C-D bond cleavage at high \u019f_T. The overall branching ratio of the\r\nformate to carbon dioxide and carbon monoxide is approximately unity, regardless\r\nthe initial coverage \u019f_T, even though the activation energy for the production of\r\ncarbon dioxide varies with \u019f_T. The desorption of water, which implies C-O bond\r\ncleavage of the formate, appears at approximately the same temperature as that of\r\ncarbon dioxide. These observations suggest that the cleavage of the C-D bond and\r\nthat of the C-O bond of two surface formates are coupled, possibly via the formation\r\nof a short-lived surface complex that is the precursor to to the decomposition.
\r\n\r\nThe measurement of steady-state rate is demonstrated here to be valuable in\r\ndetermining kinetics associated with short-lived, molecularly adsorbed precursor to\r\nfurther reactions on the surface, by determining the kinetic parameters of the molecular\r\nprecursor of formaldehyde to its dissociation on the Pt(110)-(1 x 2) surface.
\r\n\r\nOverlayers of nitrogen adatoms on Ru(001) have been characterized both by\r\nthermal desorption mass spectrometry and low-energy electron diffraction, as well as\r\nchemically via the postadsorption and desorption of ammonia and carbon monoxide.
\r\n\r\nThe nitrogen-adatom overlayer was prepared by decomposing ammonia thermally\r\non the surface at a pressure of 2.8 x 10^(-6) Torr and a temperature of 480 K. The\r\nsaturated overlayer prepared under these conditions has associated with it a (\u221a247/10 x \u221a247/10)R22.7\u00b0 LEED pattern, has two peaks in its thermal desorption spectrum, and\r\nhas a fractional surface coverage of 0.40. Annealing the overlayer to approximately\r\n535 K results in a rather sharp (\u221a3 x \u221a3)R30\u00b0 LEED pattern with an associated\r\nfractional surface coverage of one-third. Annealing the overlayer further to 620\r\nK results in the disappearance of the low-temperature thermal desorption peak\r\nand the appearance of a rather fuzzy p(2x2) LEED pattern with an associated\r\nfractional surface coverage of approximately one-fourth. In the low coverage limit,\r\nthe presence of the (\u221a3 x \u221a3)R30\u00b0 N overlayer alters the surface in such a way that\r\nthe binding energy of ammonia is increased by 20% relative to the clean surface,\r\nwhereas that of carbon monoxide is reduced by 15%.
\r\n\r\nA general methodology for the indirect relative determination of the absolute\r\nfractional surface coverages has been developed and was utilized to determine the\r\nsaturation fractional coverage of hydrogen on Ru(001). Formaldehyde was employed\r\nas a bridge to lead us from the known reference point of the saturation fractional\r\ncoverage of carbon monoxide to unknown reference point of the fractional coverage\r\nof hydrogen on Ru(001), which is then used to determine accurately the saturation\r\nfractional coverage of hydrogen. We find that \u019fSAT/H = 1.02 (\u00b10.05), i.e., the surface\r\nstoichiometry is Ru : H = 1 : 1. The relative nature of the method, which cancels\r\nsystematic errors, together with the utilization of a glass envelope around the mass\r\nspectrometer, which reduces spurious contributions in the thermal desorption spectra,\r\nresults in high accuracy in the determination of absolute fractional coverages.
\r\n" }, { "name": "Sweeney, Robert Joseph", "degree": "PhD", "year": "1990", "title": "Hydrogen-Atom Transfer Photochemistry of Tetrakis(\u00b5-pyrophosphito)diplatinate(II)", "advisor": "Gray, Harry B.; Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162014-152027500", "creators": [ { "name": { "family": "Sweeney", "given": "Robert Joseph" }, "id": "Sweeney-Robert-Joseph", "display_name": "Sweeney, Robert Joseph" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "co-advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/039n-6p75", "abstract": "In many senses, the hydrogen-atom transfer reactions\r\nobserved with the triplet excited state of pyrophosphito-bridged\r\nplatinum(II) dimers resemble the reactions of organic ketone n\u03c0*\r\nstates. The first two chapters describe our attempts to understand\r\nthe reactivity differences between these two chromophores.\r\nReactivity of the metal dimers is strongly regulated by the detailed\r\nnature of the ligands that ring the axial site, the hydrogen-abstraction\r\ncenter. A hydrogen-bonded network linking the ligands\r\nfacilitates H-atom transfer quenching with alcohols through the\r\nformation of a hydrogen-bonded complex between the alcohol and a\r\ndimer. For substrates of equal C-H bond strength that lack a hydroxyl\r\ngroup (e.g., benzyl hydrocarbons), the quenching rate is several\r\norders of magnitude slower.
\r\n\r\nThe shape and size of the axial site, as determined by the\r\nligands, also discriminate among quenchers by their steric\r\ncharacteristics. Very small quenchers quench slowly because of high\r\nentropies of activation, while very large ones have large enthalpic\r\nbarriers. The two effects find a balance with quenchers of \"just the\r\nright size.\"
\r\n\r\nThe third chapter discusses the design of a mass\r\nspectrometer that uses positron annihilation to ionize neutral\r\nmolecules. The mass spectrometer creates positron-molecule\r\nadducts whose annihilation produces fragmentation products that\r\nmay yield information on the bonding of positrons in such complexes.
" }, { "name": "Toth, James E.", "degree": "PhD", "year": "1990", "title": "Electrocatalytic activity of transition metal substituted heteropolytungstates", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162014-142404383", "creators": [ { "name": { "family": "Toth", "given": "James E." }, "id": "Toth-J-E", "display_name": "Toth, James E." } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qg82-8y71", "abstract": "The electrochemical and electrocatalytic behavior of a series of\r\nheteropolytungstate anions in which a tungsten atom in the well known\r\nKeggin structure has been replaced by an iron atom is described. All\r\nof the iron substituted ions exhibit a one electron reversible couple\r\nassociated with the Fe3+ center and a pair of two electron waves\r\nattributed to electron addition and removal from the tungsten oxo\r\nframework. The pH and ionic strength effects upon the various\r\nelectrochemical processes are discussed and interpreted in terms of a\r\ncompetition between protonation and ion pairing of the highly\r\nnegatively charged ions.
\r\n\r\nThe anions are efficient catalysts for the electroreduction of\r\nhydrogen peroxide. A catalytic mechanism involving a formally Fe(IV)\r\nintermediate is proposed. Pulse radiolysis experiments were employed\r\nto detect the intermediate and evaluate the rate constants for the\r\nreactions in which it is formed and decomposed. A chain mechanism for\r\nthe catalytic decomposition of hydrogen peroxide in which the Fe\r\ncenter shuttles between the +2, +3, and +4 oxidation states is\r\nproposed to explain the non-integral stoichiometry observed for the\r\niron substituted polytungstate catalyzed electroreduction of hydrogen\r\nperoxide.
\r\n\r\nThe anions are also efficient electrocatalyst for the\r\nelectrochemical conversion of nitric oxide to ammonia. The catalyzed\r\nreduction does not produce hydroxylamine as an intermediate and\r\nappears to depend upon the ability of the multiply reduced\r\nheteropolytungstates to deliver several electrons to the bound NO\r\ngroup in a concerted step. A valuable feature of the\r\nheteropolytungstates is the ease at which the formal potentials of the\r\nseveral redox couples they exhibit may be shifted by changing the\r\nidentity of the central heteroatom. Exploitation of this feature\r\nprovided diagnostic information that was decisive in establishing the\r\nmechanism of electrocatalytic reduction.
\r\n\r\nThe iron substituted heteropolytungstates are not degraded by\r\nrepeated cycling between their oxidized and reduced states. They also\r\nshow superior activity compared to their unsubstituted analogues,\r\nindicating that the Fe center acts as a binding site that facilitates\r\ninner-sphere electron transfer processes. The basic electrochemistry\r\nof several other transition metal substituted Keggin ions is also\r\ndescribed.
" }, { "name": "Webb, Christopher John", "degree": "PhD", "year": "1990", "title": "Robust Control Strategies for a Fixed Bed Chemical Reactor", "advisor": "Morari, Manfred; Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11132007-110352", "creators": [ { "name": { "family": "Webb", "given": "Christopher John" }, "id": "Webb-Christopher-John", "display_name": "Webb, Christopher John" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/h2d4-tq78", "abstract": "This thesis addresses the practical application of robust control design to an experimental fixed bed reactor. Controllers are designed using robust control theory, specifically, Structured Singular Value analysis and Internal Model Control theory. These controllers are guaranteed to be stable and have good performance even when there is plant-model mismatch. To understand the sources of model mismatch and how model mismatch affects a fixed bed reactor's control design, an experimental methanation reactor was constructed.
\r\n\r\nThe reactor is non-adiabatic with a constant wall temperature. A series of thermo couples located inside an axial thermowell are used to measure bed temperatures, and a gas chromatograph is used to measure gas concentrations. The pilot plant includes a feed-effluent heat exchanger and a product recycle line for positive feedback of both mass and energy.
\r\n\r\nA mathematical model of the reactor is developed from first principles. This dynamic model is a three dimensional heterogenous model. It consists of four non-linear coupled partial differential equations. Finite difference methods are used to approximate these equations with a series of ordinary differential equations. The temperature profiles simulated using the model compare favorably with the profiles obtained from the experimental reactor.
\r\n\r\nTwo control configurations are studied: the control of the hot spot temperature using the flow rate of an inert gas, and the control of the outlet concentration and temperature by manipulating the recycle flow rate and power supplied to an inlet heater. For both of these experiments, the control objective is to maintain stability and acceptable performance for a variety of operating conditions. Bounds of the amount of model uncertainty are explicitly incorporated in the controller design.
\r\n\r\nA new methodology for computing frequency domain uncertainty bounds for single-input single-output systems is presented. This new methodology uses spectral analysis to identify a series of non-parametric frequency domain models and a \"regions-mapping\" technique to bound the frequency by frequency description of these models in the complex plane. The methodology is compared to existing non-parametric techniques and shown to be superior for identifying the uncertainty bound associated with a nonlinear system. This methodology is then applied to the hot spot temperature identification problem of the fixed bed reactor. A robust controller with a single adjustable parameter is designed for the reactor using Internal Model Control (IMC) theory. The computed uncertainty bounds are experimentally validated using the IMC controller.
\r\n\r\nA simple procedure is presented for designing a robust controller when one or more of the control variables must be inferred from other process measurements. As part of this procedure, a robust measurement selection scheme determines which process measurements should be used for inference. The measurement selection scheme is based on Structured Singular Value analysis. This procedure is successfully applied to the outlet concentration control for the experimental methanation reactor.
" }, { "name": "Wheeler, David Roger", "degree": "PhD", "year": "1990", "title": "Mechanism and applications of the photochemistry of Bis(\u03b7^5-cyclopentadienyl)titanacyclobutanes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182015-140227559", "creators": [ { "name": { "family": "Wheeler", "given": "David Roger" }, "id": "Wheeler-D-R", "display_name": "Wheeler, David Roger" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6cmf-kz46", "abstract": "The photochemically induced reductive elimination of cyclopropanes\r\nfrom bis(\u03b75-cyclopentadienyl)titanacyclobutanes has been examined.\r\nStereochemical labelling studies indicate that the cyclopropane is initially\r\nformed in a 6\u00b11:1, ratio favoring retention of stereochemistry. The starting\r\ntitanacyclobutane is isomerized during the course of the reaction. The\r\nisomerization of the starting material results from metal-carbon bond\r\nhomolysis to yield a 1,4-biradical, which can either close to give the starting\r\nmaterial or generate cyclopropane. The 1,4-biradical can be observed\r\nthrough a cyclopropyl carbinyl rearrangement employing 2-bis(\u03b75-\r\ncyclopentadienyl)titana-5,5-dimethylbicyclo[2.1.0]pentane, to give the\r\ntitanium alkylidene, 1-bis(\u03b75-cyclopentadienyl)titana-3,3-dimethyl-1,4-\r\npentadiene, which can be observed directly by NMR at low temperature.
\r\n\r\nThe oxidation of titanacyclobutanes by chemical and electrochemical\r\nmethods also yields cyclopropanes. Reduction of the metal center does not\r\nyield cyclopropanes. Depending on the oxidant, stereochemically labelled\r\ntitanacyclobutanes yield cyclopropanes that are between 7:1 and 100:1\r\nretention:isomerization. The fragmentation reaction resembles the\r\nphotochemically induced reductive elimination. Both result from formal\r\noxidation of a metal-carbon bond, which then results in very rapid\r\nformation of cyclopropane.
\r\n\r\nThe titanocene generated photochemically reacts with a variety of\r\nsubstrates even at low temperature. Titanocene can be generated in a glass\r\nat 77 K. The titanocene can be trapped in noncoordinating solvents in high\r\nyield with bulky internal acetylenes to give monoacetylene adducts of\r\ntitanocene. Less bulky acetylenes give the titanacyclopentadienes. The\r\ntitanocene can be trapped with olefins to give less stable adducts, which\r\nappear by NMR analysis to be intermediate in structure between a\r\ntitanacyclopropane and an \u03b72 olefin adduct of titanocene. Reaction of\r\ntitanocene with butadiene gives a stable product, which appears to be the s-trans\r\nbutadiene adduct of titanocene. It does not isomerize on heating.\r\nTitanocene reacts with epoxides to give titanocene-\u00b5-oxo polymer and olefin.\r\nStereochemically labelled epoxides and episulfides yield isomerized olefin\r\nupon deoxygenation by titanocene. The observations are rationalized as a\r\nresult of a 1,4-biradical formed by stepwise insertion of titanocene into a\r\ncarbon-oxygen bond.
" }, { "name": "Wolfenbarger, J. Kenneth", "degree": "PhD", "year": "1990", "title": "Aerosol Data Inversion: Optimal Solutions and Information Content", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11092007-094509", "creators": [ { "name": { "family": "Wolfenbarger", "given": "J. Kenneth" }, "id": "Wolfenbarger-J-Kenneth", "display_name": "Wolfenbarger, J. Kenneth" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/efdm-c587", "abstract": "The determination of an aerosol size distribution is presently difficult because current aerosol instruments cannot perfectly discriminate aerosols based on size and because a only limited number of data can be obtained. As a result, for a given set of data the relationship between the unknown distribution and the data is a finite Fredholm integral equation. If the size distribution is desired, then one should answer the following
\r\n\u2022 What measurements should be taken?
\r\n\u2022 How should the measurements be used to determine a size distribution?
In this thesis, we shed some light on the answers to these questions by finding optimal solutions to the Fredholm integral equation, and by characterizing the size of the solution set.
\r\n\r\nThe questions of existence and uniqueness of solutions subject to linear inequality constraints are examined. Optimal solutions based on regularization are developed, and numerical methods for finding these solutions are described. Numerical experiments are presented that demonstrate the importance of
\r\n\u2022 describing dependent error sources.
\r\n\u2022 considering the magnitude of the errors in the data when there are few data.
\r\n\u2022 using generalized cross validation when there are many data and the magnitude of the errors is unknown.
An analysis that uses some simple information concepts is presented for examining the size of the solution set. An example is presented that demonstrates the effect of dependent errors on the information provided by the data, and some illustrative experiment design studies are presented.
\r\n" }, { "name": "Wysong, Ernest Byron", "degree": "PhD", "year": "1990", "title": "Investigations of group IVA transition metal mediated carbon-carbon bond forming reactions", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182015-144109882", "creators": [ { "name": { "family": "Wysong", "given": "Ernest Byron" }, "id": "Wysong-E-B", "display_name": "Wysong, Ernest Byron" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/65sq-fy18", "abstract": "Zirconocene aldehyde and ketone complexes were synthesized in high yield by treatment of zirconocene acyl complexes with trimethylaluminum or diisobutylaluminum hydride. These complexes, which are activated by dialkylaluminum chloride ligands, inserted unsaturated substrates such as alkynes, allenes, ethylene, nitriles, ketenes, aldehydes, ketones, lactones, and acid chlorides with moderate to high conversion. Insertion of aldehyde substrates yielded zirconocene diolate complexes with up to 20:1 (anti:syn) diastereoselectivity. The zirconocene diolates were hydrolyzed to afford unsymmetrical 1,2-diols in 40-80% isolated yield. Unsymmetrical ketones gave similar insertion yields with little or no diastereoselectivity. A high yielding one-pot method was developed that coupled carbonyl substrates with zirconocene aldehyde complexes that were derived from olefins by hydrozirconation and carbonylation. The zirconocene aldehyde complexes also inserted carbon monoxide and gave acyloins in 50% yield after hydrolysis.
\r\n\r\nThe insertion reaction of aryl epoxides with the trimethylphoshine adduct of titanocene methylidene was examined. The resulting oxytitanacyclopentanes were carbonylated and oxidatively cleaved with dioxygen to afford y-lactones in moderate yields. Due to the instability and difficult isolation of titanocene methylidene trimethylphoshine adducts, a one-pot method involving the addition of catalytic amounts of\r\ntrimethylphosphine to \u03b2,\u03b2-dimethyltitanacyclobutane was developed. A series of disubstituted aryl epoxides were examined which gave mixtures of diastereomeric insertion products. Based on these results, as well as earlier Hammett studies and labeling experiments, a biradical transition state intermediate is proposed. The method is limited to aryl substituted\r\nepoxide substrates with aliphatic examples showing no insertion reactivity.
\r\n\r\nThe third study involved the use of magnesium chloride supported\r\ntitanium catalysts for the Lewis acid catalyzed silyl group transfer\r\ncondensation of enol silanes with aldehydes. The reaction resulted in\r\nsilylated aldol products with as many as 140 catalytic turnovers before\r\ncatalyst inactivation. Low diastereoselectivities favoring the anti-isomer\r\nwere consistent with an open transition state involving a titanium atom\r\nbound to the catalyst surface. The catalysts were also used for the aldol\r\ngroup transfer polymerization of t-butyldimethylsilyloxy-1-ethene resulting in polymers with molecular weights of 5000-31,000 and molar mass\r\ndispersities of 1.5-2.8. Attempts to polymerize methylmethacrylate using\r\nGTP proved unsuccessful with these catalysts.
\r\n" }, { "name": "Yin, Fangdong", "degree": "PhD", "year": "1990", "title": "Atmospheric photooxidation of organosulphur compounds", "advisor": "Seinfeld, John H.; Grosjean, Daniel; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11192007-092214", "creators": [ { "name": { "family": "Yin", "given": "Fangdong" }, "id": "Yin-F", "display_name": "Yin, Fangdong" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "co-advisor", "display_name": "Grosjean, Daniel" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "member", "display_name": "Grosjean, Daniel" }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9gn5-p598", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\n\nThe atmospheric chemistry of organosulfur compounds is of fundamental importance to understanding the biogeochemical sulfur cycle as well as environmental issues such as acid precipitation and sulfur aerosol formation in the atmosphere. The research goal of the present work is to elucidate the atmospheric reaction mechanisms of conversion of organosulfur compounds to sulfur-containing aerosols.\n\nBased on the fundamental chemistry and the available kinetic and mechanistic information from experimental studies, detailed chemical reaction mechanisms have been developed for the atmospheric photooxidation of dimethyl sulfide, [...], dimethyl disulfide, [...], methanethiol, [...], and diethyl sulfide, [...]. Predictions of the developed mechanisms by computer simulation are compared with available data on laboratory photooxidation of organosulfur compounds to identify critical uncertainties in chemical pathways and reaction rate constants. Further experimental studies have been designed based on the findings from computer modeling work. Using the outdoor smog chamber reactor, the dynamic behavior of various chemical species and particle nucleation and growth have been investigated in detail under well-defined atmospheric conditions for systems [...] and [...]. Through analysis of the experimental data from outdoor smog chamber experiments by computer simulation, the mechanisms developed for photooxidation of [...] and [...] have been evaluated and reformulated. The key problems regarding the initial reactions, secondary reactions of RSOX radicals and [...] radicals, and the major chemical pathways for the formation of [...] and [...] compounds have been elucidated and the discrepancies of the experimental results between different investigators have been resolved. Critical uncertatinties regarding chemical path- ways and reaction rate constants have been identified and further detailed kinetic experimental studies have been recommended.\n" }, { "name": "Zewert, Thomas Edward", "degree": "PhD", "year": "1990", "title": "Electron transfer in chemically and genetically modified myoglobins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182015-162901623", "creators": [ { "name": { "family": "Zewert", "given": "Thomas Edward" }, "id": "Zewert-T-E", "display_name": "Zewert, Thomas Edward" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wwr5-pe34", "abstract": "The temperature dependences of the reduction potentials (Eo') of wildtype human myoglobin (Mb) and three site-directed mutants have been measured by using thin-layer spectroelectrochemistry. Residue Val68, which is in van der Waals contact with the heme in Mb, has been replaced by Glu, Asp, and Asn. At pH 7.0, reduction of the heme iron (III) in the former two proteins is accompanied by uptake of a proton by the protein. The changes in Eo', and the standard entropy (\u0394So') and enthalpy (\u0394Ho') of reduction in the mutant proteins were determined relative to values for wild-type; the change in Eo' at 25\u00b0C was about -200 millivolts for the Glu and Asp mutants, and about -80 millivolts for the Asn mutant. Reduction of Fe(III) to Fe(II) in the Glu and Asp mutants is accompanied by uptake of a proton. These studies demonstrate that Mb can tolerate substitution of a buried hydrophobic group by potentially charged and polar residues, and that such amino acid replacements can lead to substantial changes in the redox thermodynamics of the protein.
\r\n\r\nThrough analysis of the temperature dependence and shapes of NMR dispersion signals, it is determined that a water molecule is bound to the sixth coordination site of the ferric heme in the Val68Asp and in the Val68Asn recombinant proteins while the carboxyl group of the sidechain of Glu68 occupies this position in Val68Glu. The relative rhombic distortions in the ESR spectra of these mutant proteins combined with H217O and spin interconversion experiments performed on them confirm the conclusions of the NMRD study.
\r\n\r\nThe rates of intramolecular electron transfer (ET) of (NH3)5Ru-His48 (Val68Asp, His81GIn, Cys110AIa)Mb and (NH3)5Ru-His48\r\n(Val68GIu,His81GIn,Cys110Ala)Mb were measured to be .85(3)s-1 and .30(2)s-1, respectively. This data supports the hypothesis that entropy of 111 reduction and reorganization energy of ET are inversely related. The rates of forward and reverse ET for (NH3)5 Ru-His48 (Val68GIu, His81 GIn, Cys110AIa)ZnMb -7.2(5)\u2022104s-1and 1.4(2)\u2022105s-1, respectively- demonstrate that the placement of a highly polar residue nearby does not significantly change the reorganization energy of the photoactive Zn porphyrin.
\r\n\r\nThe distal histidine imidazoles of (NH3)4isnRu-His48 SWMb and\r\n(NH3)5Ru-His48 SWMb were cyanated with BrCN. The intramolecular ET rates of these BrCN-modified Mb derivatives are 5.5(6)s-1 and 3.2(5)s-1, respectively. These respective rates are 20 and 10 times faster than those of their noncyanated counterparts after the differences in ET rate from driving force are scaled according to the Marcus equation. This increase in ET rate of the cyanated Mb derivatives is attributed to lower reorganization energy since the cyanated Mb heme is pentacoordinate in both oxidation states; whereas, the native Mb heme loses a water molecule upon reduction so that it changes from six to five coordinate. The reorganization energy from Fe-OH2 dissociation is estimated to be .2eV. This conclusion is used to reconcile data from previous experiments in our lab. ET in photoactive porphyrin-substituted myoglobins proceed faster than predicted by Marcus Theory when it is assumed that the only difference in ET parameters between photoactive porphyrins and native heme systems is driving force. However, the data can be consistently fit to Marcus Theory if one corrects for the smaller reorganization in the photoactive porphyrin systems since they do not undergo a coordination change upon ET.
\r\n\r\nFinally, the intramolecular ET rate of (NH3)4isnRu-His48 SWMb was measured to be 3.0(4)s-1. This rate is within experimental error of that for\r\n(NH3)4pyrRu-His48 SWMb even though the former has 80mV more driving force. One likely possibility for this observation is that the tetraamminepyridineruthenium group undergoes less reorganization upon ET than the tetraammineisonicotinamideruthenium group. Moreover, analysis of the (NH3)4isnRu-His48 SWMb experimental system gives a likely explanation of why ET was not observed previously in (NH3)4isnRu-Cytochrome C.
\r\n" }, { "name": "Brown, Thomas Kingsley", "degree": "Masters", "year": "1989", "title": "Structure and function of neuronal postsynaptic densities of the central nervous system", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-152248735", "creators": [ { "name": { "family": "Brown", "given": "Thomas Kingsley" }, "id": "Brown-T-K", "display_name": "Brown, Thomas Kingsley" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qzpb-d552", "abstract": "No abstract." }, { "name": "Bunel, Emilio Enrique", "degree": "PhD", "year": "1989", "title": "Synthetic and Mechanistic Studies of Organoscandium Compounds. Dimerization and Branching of Alkenes Catalyzed by Scandocene Hydrides", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05242007-075254", "creators": [ { "name": { "family": "Bunel", "given": "Emilio Enrique" }, "id": "Bunel-Emilio-Enrique", "display_name": "Bunel, Emilio Enrique" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3HDJ-ST65", "abstract": "Mixed-ring scandocene alkyl and hydride derivatives of structure Cp*CpSc(CH\u2083)(PMe\u2083), Cp*CpSc(\u03b7\u00b9-\u03b7\u2075-C\u2085H\u2084(Cp*Sc(H), Cp*(\u03b7\u2075-1,3,4-C\u2085Me\u2083H\u2082)Sc(CH\u2083)(PMe\u2083), and Cp*(\u03b7\u2075-1,3,4-C\u2085Me\u2083H\u2082)Sc(H)(PMe\u2083) were prepared (Cp* = \u03b7\u2075-C\u2085Me\u2085, Cp = \u03b7\u2075-C\u2085H\u2085. Dimethylsilicon bridged scandocene alkyl and hydride derivatives Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)\u2082ScCH(SiMe\u2083)\u2082, Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)\u2082Sc(H)(PMe\u2083), meso-Me\u2082Si(\u03b7\u2075-t-butylC\u2085H\u2083)\u2082ScCH\u2082SiMe\u2083, and (meso-Me\u2082Si(\u03b7\u2075-t-butylC\u2085H\u2083)\u2082Sc(H))\u2082 were also prepared. The activation energy for phosphine dissociation in Cp*CpSc(CH\u2083)(PMe\u2083) and Cp*(\u03b7\u2075-1,3,4-C\u2085Me\u2083H\u2082)Sc(H)(PMe\u2083) were measured. The crystal structures of Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)\u2082ScCH(SiMe\u2083)\u2082 and Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)\u2082Sc(H)(PMe\u2083) were determined.
\r\n\r\nThe hydride derivatives, Me\u2082Si(\u03b7\u2075-C\u2085Me\u2084)\u2082Sc(H)(PMe\u2083) and (meso-Me\u2082Si(\u03b7\u2075-t-butylC\u2085H\u2083)\u2082Sc(H))\u2082 catalyze the following carbon-carbon bond forming reactions: (1) The catalytic dimerization of \u03b1-olefins to head-to-tail dimers, (2) The catalytic cyclization of \u03b1, \u03c9-diolefins to methylenecycloalkanes with ring sizes between 5 and 9 carbon atoms, (3) The catalytic formation of six-membered ring nitrogen and sulfur heterocycles by catalytic cyclization of bisallyl amines and bisallyl sulfides respectively and (4) The catalytic formation of the spiro hydrocarbons 2-methylene spiro[4.4] nonane and 2-methylene dispiro [4.1.4.2] tridecane by catalytic cyclization of 5-methylene-1,8-nonadiene and 5,8-dimethylene-1,11-dodecadiene.
\r\n\r\n(meso-Me\u2082Si(\u03b7\u2075-t-butylC\u2085H\u2083)\u2082Sc(H))\u2082 catalyzes the ring opening reaction of methylenecyclopropane to butadiene and methylenecyclobutane to 1,4-pentadiene. Labelling experiments show that intramolecular olefin insertion in \u03c9-alkenyl scandium complexes and \u03b2-alkyl elimination in cycloalkylmethyl scandium complexes is reversible when rings containing 3 or 4 carbon atoms are involved. The hydride derivative (meso-Me\u2082Si(\u03b7\u2075-t-butylC\u2085H\u2083)\u2082Sc(H))\u2082 also catalyzes the isomerization of 1,4-pentadiene to isoprene and 2-methyl-1,4-pentadiene to 2,3-dimethylbutadiene and the isomerization of 3-methyl-1,4-pentadiene to 1,5-hexadiene, which is then cyclized to methylenecyclopentane.
" }, { "name": "Colberg, Richard Dale", "degree": "PhD", "year": "1989", "title": "Area, Cost and Resilience Targets for Heat Exchanger Networks", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-02062007-104756", "creators": [ { "name": { "family": "Colberg", "given": "Richard Dale" }, "id": "Colberg-Richard-Dale", "display_name": "Colberg, Richard Dale" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/pndd-bc72", "abstract": "This thesis presents improved area and capital cost targets for synthesis of heat exchanger networks (HEN) for fixed operating conditions, and a new resilience target for synthesis of HENs for changing, uncertain operating conditions. In addition, methods are presented to predict, before synthesis, the trade-off between cost and resilience.
\r\n\r\nA pair of \"transshipment\" nonlinear programs (NLP) is formulated to calculate the area and capital cost targets for HEN synthesis with unequal heat transfer coefficients and different capital cost laws (for different materials of construction, pressure ratings, etc.) when there are constraints on the number of matches, forbidden matches, and required matches with specified areas (for revamp synthesis). With these NLPs, the trade-off between area and number of units can be evaluated before synthesis. In addition to the targets themselves, solution of the NLPs yields \"ideal\" temperature profiles (much like the composite curves) for a HEN achieving the targets, and a selection of stream matches and their heat loads which provide an excellent starting point for synthesis of HENs achieving (within a few percent) the area and capital cost targets.
\r\n\r\nFor changing or uncertain operating conditions, a Class 1 resilience target is presented which predicts, given the nominal operating conditions, the largest uncertainty range for which a \"practical\" HEN (with few more units and stream splits than that required for nominal conditions) can be synthesized. This resilience target also predicts whether trade-offs (in utilities, number of units, or size of uncertainty range) must be made to achieve resilience, and the operating condition and constraint most likely to limit resilience.
\r\n\r\nA nonlinear program is formulated to calculate the Class 1 HEN resilience target. Trade-offs with minimum approach temperature, utility consumption, and nominal network area are presented. The use of the Class 1 resilience target as a synthesis tool is discussed.
\r\n\r\nFinally, a simple procedure to predict the trade-off between cost and resilience is introduced so that a process engineer can design for an economically \"optimal\" amount of resilience.
" }, { "name": "Coms, Frank D.", "degree": "PhD", "year": "1989", "title": "Synthesis, Spectroscopy and Reactivity of Phenyl-Substituted 1,3-Biradicals", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302007-152726", "creators": [ { "name": { "family": "Coms", "given": "Frank D." }, "id": "Coms-Frank-D", "display_name": "Coms, Frank D." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1xkp-ft85", "abstract": "Irradiation of frozen MTHF solutions of 1,4-diphenyl- and l-methy-4-phenyl-2,3-diazabicyclo[2.l.l]hex-2-enes(14 and 15) at cryogenic temperatures produces the corresponding triplet 1,3-diphenyl- and l-methyl-3-phenylcyclobutanediyls (24-Ph and 24-MP) as monitored by EPR spectroscopy. The spectra of 24-Ph and 24-MP exhibit zero-field splitting (zfs) parameters of |D/hc| = 0.060 cm\u207b\u00b9, |E/hc| = 0.001 cm\u207b\u00b9 and |D/hc| = 0.0082 cm\u207b\u00b9, |E/hc| = 0.003 cm-1, respectively. The triplet EPR spectra provide valuable information concerning biradical geometry and spin distribution. The trends in the observed D values can be quantitatively modeled using a relatively simple scheme for zfs calculations. Analysis of the hyperfine splitting pattern observed in the \u0394m\u209b = 2 transition of \u00b324-Ph reveals that the four-membered ring is planar.
\r\n\r\nUpon warming biradicals \u00b324-Ph and \u00b324-MP to 20-50 K, nonexponential decay to the corresponding bicyclobutanes commence. The decay kinetics of \u00b324-Ph were quantitatively studied from 27 to 54 K with the explicit inclusion of matrix-site effects. The kinetics analysis revealed that the variation of the decay rates with temperature follows the Arrhenius law, producing activation parameters of log A = 7.8, E\u2090\u00b0 = 2.29 kcal/mol. These activation parameters are compared with those of other cyclobutanediyls.
\r\n\r\nPhotolysis of matrix-isolated 1,4-diphenyl-2,3-diazabicyclo[2.2.1]-hept-2-ene (21) in the cavity of an EPR spectrometer at 3.8 and 77 K produces the triplet spectrum of 1,3-diphenylcyclopentanediyl 20. The zfs parameters of the spectrum are |D/hc| = 0.045 cm\u207b\u00b9, |E/hc| = 0.001 cm\u207b\u00b9. The observed zfs parameters and hyperfine splitting pattern are completely in line with expectation and are consistent with a planar cyclopentanediyl geometry. Biradical \u00b320 is considerably more persistent than its four-membered ring analog \u00b324-Ph.
\r\n\r\n1,4-Diphenylbicyclo[2.l.0]pentane (22), the closed-shell isomer of 20, possesses a very weak C1-C4 bond. This weak bond is manifested in the low activation barrier for a degenerate bridge-flip process. Through a combination of \u00b9H NMR complete lineshape analysis and magnetization transfer studies, the activation parameters for this process are determined to be \u0394H\u2021 = 12.2 kcal/mol, \u0394S\u2021 = -16.4 eu. At room temperature, bicyclopentane 22 reacts rapidly to form 2,3-dioxa-1,4-diphenylbicyclo[2.2.l]heptane(23). Using the activation parameters for the bridge-flip reaction along with other data results in the development of a detailed model of the kinetic and thermodynamic relationships among \u00b920, \u00b320, and 22.
" }, { "name": "Dearden, David Vernell", "degree": "PhD", "year": "1989", "title": "Experimental Probes of Gas Phase Ions and Molecules: I. Product Kinetic Energy Release Measurements as a Probe of Reaction Thermochemistry, Dynamics, and Chemical Structure in Systems Containing Transition Metal Ions. II. Photoelectron and Optical Studies of Organic Transient Species", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082007-130036", "creators": [ { "name": { "family": "Dearden", "given": "David Vernell" }, "id": "Dearden-David-Vernell", "display_name": "Dearden, David Vernell" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6tyj-gy42", "abstract": "The release of kinetic energy in the decomposition of a metastable ion is a reflection of both the overall energetics and the potential energy surface on which the process takes place. Chapter 1 applies measurements of the kinetic energy release distributions (KERDs) for decomposition of metastable Mn(CO)\u2093\u207a to the dynamics and energetics of exchange processes for the CO ligands. All the dissociations can be described by statistical phase space theory, in agreement with efficient CO exchange rates indicating that conservation of electronic spin is not important to the dynamics. A general method is presented and used whereby Mn\u207a-CO bond energies are obtained from the KERDs. Chapter 2 deals with reactions of Fe\u207a and Co\u207a with alkanes to eliminate methane, which have KERDs narrower than predicted by statistical theory. Restriction of the angular momentum (or, equivalently, the impact parameter) to values less than those anticipated by simple ion-molecule collision theory can account for the narrowed distributions. The restrictions result from barriers in the effective potential energy surfaces and from limitations in our measurement techniques. In Chapter 3, KERDs are used to demonstrate the existence of cobaltacyclobutane\u207a, (hydrido)(cyclopropyl)Co\u207a and Co(propene)\u207a structures which do not interconvert on the \u00b5s time scale in the gas phase. Chapter 4 deals with the dehydrogenations of cyclic alkanes by Fe\u207a and Co\u207a, and shows that, contrary to previous assumptions, statistical energy partitioning occurs in these processes.
\r\n\r\nChapters 5 and 6 deal with studies of transient organic species. Chapter 5 presents preliminary work on charge-reversed, resonance enhanced multiphoton ionization (CRREMPI), a potentially powerful new method which exploits the special characteristics of the ion cyclotron resonance spectrometer to obtain optical spectra of a wide variety of transient species. In Chapter 6 photoelectron spectroscopy is used to observe the rearrangements of primary alkyl radicals, produced by flash vacuum pyrolysis of nitrites, to the thermodynamically more stable secondary isomers. Decomposition processes are also observed.
" }, { "name": "El-Kareh, Ardith W.", "degree": "PhD", "year": "1989", "title": "I. On a New Constitutive Equation for Non-Newtonian Fluids. II. Brownian Motion with Fluid-Fluid Interfaces", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092007-131907", "creators": [ { "name": { "family": "El-Kareh", "given": "Ardith W." }, "id": "El-Kareh-Ardith-W", "display_name": "El-Kareh, Ardith W." } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Brenner", "given": "Howard" }, "id": "Brenner-H", "role": "member", "display_name": "Brenner, Howard" }, { "name": { "family": "Luxemburg", "given": "W. A. J." }, "id": "Luxemburg-W-A-J", "role": "member", "display_name": "Luxemburg, W. A. J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/xd3m-5r94", "abstract": "This thesis is a small contribution to the ambitious goal of understanding some of the more complex flows that are found in nature, namely, flows of fluids with a microstructure. There is a great diversity of such flows: suspensions, emulsions, polymeric solutions, . . ., each exhibiting phenomena not found in the flow of homogeneous Newtonian fluids. A bit of this diversity has been incorporated in this thesis: The first part of it is on some aspects of non-Newtonian fluid flow, and in the second part Brownian motion involving interfaces between Newtonian fluids is studied.
\r\n\r\nGiven the large amount of effort devoted recently to the numerical simulation of non-Newtonian fluid flow, the absence of mathematical proofs that any of the standard computational methods for solving the equations will converge except for nearly Newtonian flows seems somewhat disturbing. While there is evidence that investigators may have overcome the so-called \"high Weissenberg-number problem,\" at least in specific cases, confidence in the numerical solutions would undoubtedly be increased by a rigorous mathematical foundation for the numerical algorithm. The first, and in many cases nontrivial, step towards this is to prove that a solution actually exists. In the first part of this thesis, a proof of existence without restriction on the parameters is given for a particular modified finitely extendible nonlinear elastic dumbbell model. A physical basis for the modifications is given.
\r\n\r\nFor numerical computation, the issue of stability of a flow is also an important one, as the small errors introduced by discretization are essentially perturbations in the flow, which, if they grow too fast, can make convergence impossible. An energy method calculation is given here for the same FENE dumbbell model considered in the existence proof (except for the modifications) to show that for any flow in a bounded domain, at small enough Reynolds number and high enough Deborah number, all disturbances will remain bounded. While the estimate found for the highest Reynolds number and lowest Deborah number for guaranteed stability may be very conservative, the result is nevertheless useful in that it shows that if there is an instability, it must occur at a critical Reynolds or Deborah number.
\r\n\r\nWhile the Brownian motion of a rigid particle has received much attention in the literature, and the Stokes-Einstein diffusivity of a rigid particle is a result almost as well-known as the Stokes drag law, the Brownian motion of systems that are more complex hydrodynamically has only recently begun to be investigated. Most recent work on such systems has been for systems with rigid boundaries, e.g., suspensions of rigid spheres. In this thesis, the case of deformable fluid-fluid interfaces is considered. Since the understanding of the behavior of clusters or suspensions of particles can only follow an understanding of the behavior of a single particle, the two cases considered here are a drop in an infinite fluid, and an isolated particle in the presence of an approximately planar interface. Expressions for statistical quantities, such as the velocity autocorrelation, of the particle and drop motion are derived. In the case of the interface, the nature of its effect on the particle's behavior, beyond the obvious fact that it changes the particle's mobility, is explored. Similarly, the surface-tension dependence of the drop's motion is investigated.
\r\n\r\nFinally, in a slight digression, the problem of high-frequency oscillatory Stokes flow around two spheres, with specified velocity at their surfaces, is reduced to an infinite system of algebraic equations for the (frequency-dependent) coefficients in a spherical harmonic expansion of the solution. This is expected to be useful for computations of such flows where better accuracy than an approximate solution obtained by the method of reflections is desired.
" }, { "name": "Fox, Lucius Seiberling", "degree": "PhD", "year": "1989", "title": "Intramolecular Electron Transfer in an Iridium d\u2078-d\u2078 Donor-Acceptor System", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072007-081509", "creators": [ { "name": { "family": "Fox", "given": "Lucius Seiberling" }, "id": "Fox-Lucius-Seiberling", "display_name": "Fox, Lucius Seiberling" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hapm-b986", "abstract": "A series of donor-acceptor complexes, [Ir\u2082(\u00b5-Pz*)\u2082(CO)\u2082(Ph\u2082POCH\u2082CH\u2082-Py\u207a-R)\u2082](Ph\u2084B)\u2082 (Py\u207a-R = 2,4,6-trimethylpyridinium, 4-methylpyridinium, pyridinium, and 4-phenylpyridinium; Pz* = 3,5-dimethylpyrazole), have been synthesized for studying the rate of photoinduced electron transfer from the metal localized (d\u03c3*p\u03c3) excited states of d\u2078-d\u2078 chromophores. The pyridinium electron acceptors are covalently attached to the iridium metal centers (donor) via a three atom hydrocarbon linker bound to the terminal phosphine ligands. The x-ray crystallographic structure of [Ir\u2082(\u00b5-Pz*)\u2082(CO)\u2082(Ph\u2082POCH\u2082CH\u2082-Py\u207a)\u2082](Ph\u2084B)\u2082 reveals a metal-metal distance of 3.219(1) \u00c5 and a solid state donor-acceptor separation of 5.34(1) \u00c5. Additional donor-acceptor separations and orientations are available to the compounds in fluid solution through rotations about the Ir-P and linker group C-O, C- N, and C-C bonds. Steady state emission spectra show that the fluoresence and phosphoresence quantum yields in these compounds are substantially reduced relative to a appropriate model complex. To date the excited state reactivity of d\u2078-d\u2078 metal dimers has been exclusively attributed to their \u00b3(d\u03c3*p\u03c3) states. These findings represent the first evidence for reactivity from a shorter lived \u00b9(d\u03c3*p\u03c3) state.
\r\n\r\nPicosecond and nanosecond laser flash-photolysis techniques were employed to measure the rates of photoinduced electron transfer and charge recombination in these systems. Values of kET, obtained from these studies, vary between 10\u2076 sec\u207b\u00b9 and 10\u00b9\u00b2 sec\u207b\u00b9 as a function of reaction exoergicity (\u0394G\u1d52' = -0.8 eV to 1.92 eV). Clear evidence for the inverted behavior predicted by classical and semiclassical electron transfer models is seen at high driving force. Rate constants for reactions involving the \u00b9(d\u03c3*p\u03c3) and \u00b3(d\u03c3*p\u03c3) excited states, as well as the rates of charge recombination are characterized by very similar values of \u03bb and Hab. Our data are adequately modeled by the classical theory of electron transfer proposed by Marcus (\u03bb = 1.0 eV, Hab = 35 cm\u207b\u00b9) or by a semiclassical model for kET where nuclear tunneling involves a low frequency metal-ligand mode (\u03bb = 1.0 eV, Hab = 35 cm\u207b\u00b9, \u03c9 = 100 cm\u207b\u00b9). These findings are explored with regard to utilizing the donor-acceptor complexes as molecular photochemical energy storage systems.
" }, { "name": "Fuhry, Mary Ann M.", "degree": "Masters", "year": "1989", "title": "Progress on the synthesis of a model system for neocarzinostatin chromophore", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-111308897", "creators": [ { "name": { "family": "Fuhry", "given": "Mary Ann M." }, "id": "Fuhry-M-A-M", "display_name": "Fuhry, Mary Ann M." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tj6s-2x96", "abstract": "No abstract." }, { "name": "Galazzo, Jorge Luis", "degree": "PhD", "year": "1989", "title": "Effects of Cell Entrapment in Ca-Alginate on the Metabolism of Yeast Saccharomyces cerevisiae", "advisor": "Fox, Geoffrey C.; Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02022007-144010", "creators": [ { "name": { "family": "Galazzo", "given": "Jorge Luis" }, "id": "Galazzo-Jorge-Luis", "display_name": "Galazzo, Jorge Luis" } ], "advisors": [ { "name": { "family": "Fox", "given": "Geoffrey C." }, "id": "Fox-G-C", "role": "advisor", "display_name": "Fox, Geoffrey C." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "co-advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." }, { "name": { "family": "Fox", "given": "Geoffrey C." }, "id": "Fox-G-C", "role": "member", "display_name": "Fox, Geoffrey C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/gq59-ka36", "abstract": "Saccharomyces cerevisiae cells grown in suspension have been immobilized in calcium-alginate beads. Fermentation rates and intracellular composition have been determined under nongrowing conditions in these Ca-alginate entrapped cells and for identical cells in suspension. Glucose uptake and ethanol and glycerol production are approximately two times faster in immobilized cells than in suspended cells. Intermediate metabolite levels such as fructose-1,6-diphosphate, glucose-6-phosphate and 3-phosphoglycerate have been determined by phosphorus-31 nuclear magnetic resonance (NMR) spectroscopy under glucose fermenting conditions. Results show a different sugar phosphate composition in immobilized cells. Also, at steady-state glucose fermentation, the intracellular pH of entrapped cells is lower as indicated by the chemical shift of the intracellular inorganic phosphorus resonance. Carbon-13 NMR shows an increase in polysaccharide production in immobilized cells.
\r\n\r\nS. cerevisiae cells grown within a Ca-alginate matrix have a specific growth rate 40% lower that the growth rate of similar cells cultivated in suspension. Alginate-grown cells have been used to compare glucose fermentation under nongrowing conditions in suspended and Ca-entrapped cells. Fermentation rate is higher in immobilized cells than in suspended cells. The observed differences in intracellular components between suspended and immobilized cells are qualitatively similar to the differences observed for cells grown in suspension. Ethanol production rate is 2.7 times faster in immobilized alginate-grown cells than in suspended suspension-grown cells.
\r\n\r\nThese results suggest that cell immobilization is affecting cell metabolism at different levels. Catabolic regulation is altered as indicated in the nongrowing condition experiments. Also, anabolic regulation is altered as suggested by the changes in growth rate observed in cells growing within the immobilization matrix. The combination of these experimental determinations with knowledge of the metabolic pathways involved in S. cerevisiae allows the development of a quantitative in vivo description of most key pathway enzymes involved in yeast glucose catabolism. The evaluation of flux-control coefficients for all these steps indicates that alginate entrapment of suspension-grown cells increases the glucose uptake rate and shifts the step most influencing ethanol production from glucose uptake to phosphofructokinase. In alginate-grown cells, glucose uptake is limiting ethanol production in both suspended and immobilized cells. There is a 5% decrease in the glucose uptake flux-control coefficient of immobilized cells due to an increment in the glucose uptake rate. This increment increases ethanol production by approximately 100%.
\r\n\r\nAn analysis of the anticipated effects of genetic manipulation to improve the ethanol production rate in yeast S. cerevisiae using the framework of the metabolic control theory indicates that in suspended suspension-grown cells the highest improvement is obtained by increasing the activity of glucose transport, whereas in immobilized suspension-grown cells the greatest enhancement is obtained by incrementing the maximum activity of phosphofructokinase. This indicates that the metabolic engineering strategy to be used in order to enhance any properties in the cell will depend not only on the specific microorganism, but also on the environmental conditions in which it is placed. In conditions where several steps share the flux control in a pathway, a substantial enhancement in pathway rate will be possible only if the activities of all those steps are increased simultaneously.
" }, { "name": "Handel, Tracy Marie", "degree": "PhD", "year": "1989", "title": "Disulphide Polymerizeable Phosphatidylcholines: Characterization of Membrane Physical Properties and Investigations of in vivo Behavior", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06082007-081855", "creators": [ { "name": { "family": "Handel", "given": "Tracy Marie" }, "id": "Handel-Tracy-Marie", "orcid": "0000-0002-2558-6138", "display_name": "Handel, Tracy Marie" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x0z5-ef38", "abstract": "In the past ten years, polymerizeable amphiphiles have been recognized as an important class of synthetic phospholipids due to their ability to modify the mechanical and chemical stability of membranes. The motivation behind studies of polymerizeable phospholipids is based on the potential importance of stable membranes in a wide variety of applications including reactivity control, encapsulation technologies and drug delivery. However, compared to nonpolymerizeable lipids, there is a relative paucity of information correlating membrane physical properties with the structure of the polymeric lipid. The present investigation involves the synthesis of a series of disulfide polymerizeable phosphatidylcholines, the characterization of the physical properties of membranes formed from these lipids, and an investigation of the biodistributions, vascular clearance rates and degradation rates of these liposomes in vivo.
\r\n\r\nThe structures of the lipids under investigation are analogous to saturated phosphayitdylcholines but with a thiol either alpha to the carbonyl of the acyl chain (\u03b1-THIOL) or at the chain terminus (\u03c9-THIOL). It is found that the presence and position of the polymerizeable moiety drastically alters the physical characteristics of the membranes. A variety of physical techniques have been utilized to understand both the bulk properties of the lipids such as morphology and permeability, as well as the molecular details of the lipid conformation and dynamics. On the basis of such studies including Raman, FT-IR and DSC, it appears that the presence of the polymerizeable group at the interfacial region (\u03b1-THIOLS) causes a reduction in the lipid packing and an increase in chain disorder compared to nonpolymerizeable analogs. For the monomeric form of the \u03b1-THIOLS, the decreased interlipid interaction may be ascribed to the presence of an additional hydrophilic pendant group at the interface that interferes with tight crystalline packing, most likely by a combination of steric and hydration effects. In contrast to the general expectations for polymerized versus nonpolymerized phospholipids, upon polymerization, the membrane disorder is augmented even further. We believe this to be a consequence of the conformational restrictions of polymerization which inhibit the ability of the polymeric lipids to adopt a highly ordered and uniform packing state. Instead it is suspected that the reduced conformational freedom of polymerized lipids promotes the formation of surface defects between unlinked polymer chains. As a morphological consequence, the polymeric \u03b1-THIOLS tend to form smaller and largely unilamellar vesicles on dispersion in water. Furthermore because of the disorder in the hydrocarbon chain region, they are quite permeable to entrapped solutes and when administered in vivo, are cleared rapidly from the circulatory system. The latter effect is likely the result of facilitated absorption of opsonizing proteins into the disordered membrane surface which subsequently accelerates vascular clearance and uptake by the cells of the reticuloendothelial system (RES).
\r\n\r\nOn the basis \u00b3\u00b9P NMR relaxation measurements, it was observed that the motion of the headgroups in polymeric \u03b1-THIOLS was reduced relative to nonpolymerizeable analogs. Furthermore a reduced chemical shift anisotropy of polymeric \u03b1-THIOLS in the liquid-crystalline state relative to nonpolymerizeable lipids was observed and suggests an alteration in the average orientation of the headgroup for the polymer. Because the headgroup of phosphatidylcholines is zwitterionic, changes in the average orientation can have marked effects on the electrostatic properties of the membrane surface, which in turn can affect membrane morphology and interactions with cell-surfaces and proteins.
\r\n\r\nFor \u03c9-THIOLS, a distinctly different behavior was observed compared to the \u03b1-THIOLS. For the monomers and especially the polymers, results from vibrational spectroscopy and DSC suggest that the membrane conformational order and rigidity is increased relative to nonpolymerizeable phosphatidylcholine analogues. However, in contrast to the \u03b1-THIOLS that form normal self-sealed liposomal structures in both the monomeric and polymeric state, polymerization induces the transformation of \u03c9-THIOLS into bilayer fragments lacking an internal aqueous compartment. The most likely explanation for this was derived from \u00b9\u00b3C NMR relaxation experiments, which indicated that the mobility at the bilayer midplane of polymeric \u03c9-THIOLS is as restricted as the interfacial region. This contrasts to nonpolymerizeable phospholipids and \u03b1-THIOLS, which have the bilayer interior as the most fluid portion of the membrane. The rigidity at the midplane may prohibit the ability of the polymeric \u03c9-THIOLS to form curved or continuous multilamellar sheets or to respond to transient defects in the membrane without fragmentation.
\r\n\r\nAn interesting and unexpected result concerning the \u03c9-THIOLS was retention of a phase transition after polymerization. For most polymeric lipids that have the polymerizeable moiety at the chain terminus, polymerization has resulted in the disappearance of the transition due to crosslinking of the hydrocarbon chains. The presence of the transition in polymerized \u03c9-THIOLS may be evidence for the fact that polymerization results in a predominance of intra- rather than inter-leaflet coupled chains.
" }, { "name": "Harshman, Keith Duncan", "degree": "PhD", "year": "1989", "title": "Isolation and Characterization of Factors that Interact with Eukaryotic Transcriptional Enhancers", "advisor": "Parker, Carl Stevens", "url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-152402", "creators": [ { "name": { "family": "Harshman", "given": "Keith Duncan" }, "id": "Harshman-Keith-Duncan", "display_name": "Harshman, Keith Duncan" } ], "advisors": [ { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "advisor", "display_name": "Parker, Carl Stevens" } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5cem-2h95", "abstract": "The regulatory region controlling the transcription of the SV40 early genes provides a useful system in which to study the mechanisms of eukaryotic gene expression. The enhancer element of this region is composed of sequence motifs that can function independently or in combination to potentiate transcription in a wide range of cellular contexts. This thesis describes the purification and characterization of two proteins that specifically bind separate motifs.
\r\n\r\nAn enhancer binding protein was identified in bovine thymus extracts and purified to homogeneity. This factor, designated EP2, was shown by chemical and enzymatic footprinting techniques to bind the core as well as two pseudo-core sequences. In a DNase I footprinting experiment, EP2 was unable to bind to a mutated core sequence that is incapable of activating transcription in vivo. EP-2 was shown to consist of a group of polypeptides, ranging in molecular weight from 34 kd to 43 kd, each of which has the ability to bind to the core and two pseudo-core sequences.
\r\n\r\nIt was shown that the sequence bound by the mammalian transcription factor AP-1 -- the AP-1 recognition element (ARE) -- was capable of activating transcription in yeast. The ARE is very similar in sequence to the GCN4 recognition element (GCRE), yet the ARE was shown to activate transcription in a gcn4 yeast strain. A protein present in yeast extracts, designated yAP-l, was shown to bind to the ARE and was purified to near homogeneity based on this ability. yAP-1 and AP-1 display remarkably similar biochemical and DNA binding characteristics. It was shown in vitro that yAP-1 can discriminate between the ARE and the GCRE, while GCN4 exhibits approximately equal affinities for the two elements.
\r\n\r\nThe structural gene encoding yAP-1 was isolated and characterized. The DNA binding domain of the protein was localized to a sequence of 93 amino-acids in the amino-terminus. This sequence was shown to have significant homology with domains in cJUN and GCN4, which have been ascribed the ability to bind DNA. The YAP1 gene was shown to be non-essential by gene disruption. DNA-affinity blot experiments performed using extracts from YAP1 and yap1 strains suggest the existence of a family of yeast genes encoding proteins that recognize the ARE.
" }, { "name": "Healey, William Joseph", "degree": "PhD", "year": "1989", "title": "The Structural Basis of Enzyme Catalysis: Mutagenesis of \u03b2-lactamase at Ala 172, Glu 166, and Ala 237", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05212007-133513", "creators": [ { "name": { "family": "Healey", "given": "William Joseph" }, "id": "Healey-William-Joseph", "display_name": "Healey, William Joseph" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/t2g7-x074", "abstract": "RTEM-1 \u03b2-lactamase is one of a group of enzymes that confer resistance to penam and cephem antibiotics by hydrolizing the \u03b2-lactam bond. In order to elucidate the structural basis for its catalytics, site saturation mutagenesis was performed on alanine 172, glutamate 166, and alanine 237. Site saturation is the replacement of any codon with a mixture of codons to produce all possible mutations at a single location.
\r\n\r\nAlanine 172 was found to have no effect on penam hydrolysis, but seven mutants -- Arg, Asp, Glu, Gln, Ile, Leu, and Lys -- were inactive on cephalothin. Although no specific structural role is hypothesized for this residue, some mutations (including those that change the charge) are able to affect activity. This altered activity is most likely due to propagated structural changes.
\r\n\r\nGlutamate 166 was chosen for mutagenesis because of its probable role as a general base in the deacylation step of the catalytic mechanism. Only three mutants (Asp, His, and Tyr) exhibited low activity. The KM was measured for several mutants and found to be the same as wild-type (20 \u00b5M), indicating that mutations at this site do not affect substrate binding. Two mutants, Lys and Arg, yielded proteins that were unstable at 37\u00b0C, possibly because of an unfavorable interaction with lysine 73. A double mutant was constructed to replace Lys 73 with Glu while keeping Lys at 166; full cellular stability was restored.
\r\n\r\nFinally, the series of mutants at alanine 237 was produced; this residue is important to catalysis since it makes up part of the oxyanion hole that stabilizes a catalytic intermediate. Of all mutants at this site, only proline was inactive. Two mutants showed increased activity on cephems, asparagine (which had 380% of wild-type activity) and threonine (150%), revealing that this site is involved in substrate specificity.
" }, { "name": "Kanes, Katherine J.", "degree": "PhD", "year": "1989", "title": "Band 3 Structure and Function: \u00b3\u2075Cl NMR and Topographical Investigations", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05302007-081241", "creators": [ { "name": { "family": "Kanes", "given": "Katherine J." }, "id": "Kanes-Katherine-J", "display_name": "Kanes, Katherine J." } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Strauss", "given": "James H." }, "id": "Strauss-J-H", "role": "member", "display_name": "Strauss, James H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/21yt-cg83", "abstract": "Band 3 is the anion exchange protein in red blood cells. It is the most abundant protein in the erythrocyte membrane and is the most heavily used ion transport protein in vertebrates. Physiologically, it transports Cl\u207b into or out of the red blood cell and then transports HCO\u2083\u208b in the opposite direction so that electroneutrality is maintained on both sides of the membrane.
\r\n\r\nThe anion exchange mechanism of band 3 is unique among the ion transport proteins. It transports anions by a 'ping-pong' mechanism, meaning it is a gated protein which effects the one-for-one exchange of anions across the membrane. It is also unusual because it transports a wide variety of anions in a very efficient manner (up to 200 sec\u207b\u00b9). An arginine has been implicated in the binding and transport of chloride across the red blood cell membrane. The primary goal of this work was to determine the location of that arginine. A second goal was to investigate divalent anion binding to the active site.
\r\n\r\n\u00b3\u2075Cl NMR was used to investigate the competition of chloride with divalent anions at the chloride binding site of band 3. These studies were performed to determine if divalent anions compete with chloride for binding at the active site. These investigations indicate that molybdate, sulfate, and sulfate's analogue selenate interfere with chloride's binding to the transport site. Hydrogen phosphate and its analogue hydrogen arsenate also appear to compete with chloride for binding at the transport site. However, it appears that chloride binding is only fractionally inhibited by these two dianions. This is demonstrated by the inability of hydrogen phosphate and hydrogen arsenate to saturate the transport site and completely inhibit transport site linebroadening. pH profiles of chloride competition with divalent anions were also obtained. It appears that these large, inorganic, hydrated, approximately spherical molecules can reach the transport site in the band 3 channel but not as effectively as chloride.
\r\n\r\nThe goal of the biochemical studies was to determine the location of the band 3 arginine anion binding site. The complete sequence of human band 3 is was not known until very recently, but it has been available for chickens and mice since 1986. On the basis of these sequences, Vogelaar and Chan have modeled transmembrane helices to determine the number of times the protein traverses the membrane\u00b9. In order to insure that an arginine preferentially labeled by \u00b9\u2074C-phenylglyoxal was indeed at a transmembrane peptide and to verify the model, many of the transmembrane sequences have been isolated. This was accomplished by modification of a technique developed to separate hydrophobic synthetic peptides\u00b2. The band 3 transmembrane helices are tightly associated and very similar in hydrophobicity. Of a probable total of 14 transmembrane helices, the N-termini and/or C-termini have been determined for 6 of them. Because x-ray crystallography has been difficult to achieve for membrane systems (rhodopsin and the reaction center are two that that have been crystallized), this method provides a simple and relatively inexpensive method of studying membrane protein topography.
\r\n\r\nFinally, \u00b9\u2074C-phenylglyoxal has shown the location of at least one arginine in band 3 when labeled by the method of Zaki\u00b3. (By this method, two to three arginines are labeled per band 3 monomer.) The location of the second arginine has been restricted to two possible other transmembrane peptides (modeled helices 10 and 14). The active site arginine is probably at position R748 in the mouse erythrocyte band 3 sequence.
\r\n\r\n1. Vogelaar, N.S. (1989) Doctoral Thesis California Institute of Technology.
\r\n\r\n2. Tomich, J.M., Carson, L.W., Kanes, K.J., Vogelaar, N.S., Emerling, M.R., and Richards, J.H. (1988) Anal. Biochem. 174, 197-203.
\r\n\r\n3. Zaki, L. (1984) FEBS Lett. 189, 234-240.
" }, { "name": "Karas, Jennifer Lynn", "degree": "PhD", "year": "1989", "title": "Long-Range Electron Transfer in Ruthenium-Labelled Myoglobin", "advisor": "Chan, Sunney I.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06082007-092426", "creators": [ { "name": { "family": "Karas", "given": "Jennifer Lynn" }, "id": "Karas-Jennifer-Lynn", "display_name": "Karas, Jennifer Lynn" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pc6d-xe62", "abstract": "The driving force dependence of electron-transfer (ET) reactions has been investigated in protein derivatives of the type trans-Ru(NH\u2083)\u2084L-myoglobin (L=NH\u2083, pyridine, isonicotinamide). In these species, the labelling sites of the ruthenium moiety were determined by proton NMR spectroscopy. ET rates have been measured from the iron(II)-heme in myoglobin to both a\u2085Ru (a=NH\u2083) and a\u2084pyRu (py=pyridine) acceptors bound to histidine 48 (kET=0.04 and 2.5 s\u207b\u00b9; \u0394E\u00b0=0.02 and 0.275, respectively). These kinetic results demonstrate for the ruthenium-labelled Mb system that long-range ET is reversible and that the dependence of the ET rates on reaction free energy closely follows Marcus theory. ET rates were also determined for high driving-force systems that were prepared by substitution of palladium and zinc(mesoporphyrin IX), (PdP, ZnP) into the a\u2084LRu(His-48) derivatives of Mb. ET from the excited state MbMP* (M=Pd or Zn) to the ruthenium acceptor was measured by transient spectroscopy. Reverse ET rates from the surface RuII to the ZnP radical cation, (RuII\u2192ZnP\u207a) were also determined. The ET rates range from 0.04 s\u207b\u00b9 for FeII\u2192RuIII ET in a\u2085Ru(His-48)MbFe (\u0394E\u00b0=0.02 V), to 3x10\u2075 s\u207b\u00b9 for ZnP*\u2192RuIII in a\u2084isnRu(His48)MbZn (\u0394E\u00b0=1.2 V). The driving force dependence of the ET rates in the ruthenium-labelled Fe, Zn and Pd(His-48)Mb derivatives has provided information on the reorganization energy. Using Marcus theory, a reorganization energy of 1.5(2) eV has been estimated.
" }, { "name": "Klavetter, Floyd L.", "degree": "PhD", "year": "1989", "title": "Polyacetylene and Novel Conjugated Derivatives through the Metathesis Polymerization of 1,3,5,7-Cyclooctatetraenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-110626", "creators": [ { "name": { "family": "Klavetter", "given": "Floyd L." }, "id": "Klavetter-Floyd-L", "display_name": "Klavetter, Floyd L." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wqc2-mk42", "abstract": "A Diels-Alder adduct of cyclooctatetraene and benzyne has been polymerized through ring-opening metathesis by titanium methylidene sources to produce a soluble polyacetylene precursor. The polymerization proceeds through first order kinetics and linear increase in molecular weight, providing a route into conjugated polyene segments of various and controlled length.
\r\n\r\nA versatile and convenient route to polyacetylene has been developed through the condensed phase metathesis polymerization of cyclooctatetraene. Dissolution of catalyst in \"neat\" cyclooctatetraene provides a means of transforming the liquid into a highly lustrous film at ambient temperature and pressure. These films have physical and spectral properties very similar to films prepared by the Shirakawa methodology. Iodine-doped films exhibit conductivities greater than 300 \u03a9\u207b\u00b9/cm. New processing modes and novel morphologies for polyacetylene have been discovered. Novel polyacetylene derivatives have been prepared to demonstrate the versatility of the method. Both electron-releasing and electron-withdrawing groups have been attached to carbons in the \u03c0-conjugated system. These organic materials have been used in the fabrication of solid state devices.
\r\n\r\nThe mechanism of metathesis polymerization with a well-defined tungsten carbene catalyst has been explored, using cyclooctatetraene and its soluble analogue 1,5-cyclooctadiene as monomers. A new phenomenon referred to as \"cycloextrusion\" has been discovered, and its influence upon the statistical distribution of isomers and the cis-trans polymer stereochemistry delineated. Cycloextrusion is a dilute solution phenomenon, limited to cycloolefins containing an unhindered diene moeity in the ring. The thermodynamics and kinetics of the catalyst in the presence of a reversibly binding ligand have been intensively researched. Tetrahydrofuran serves as the reversibly binding ligand which deactivates the catalyst to an extent dependent upon concentration of tetrahydrofuran present. The metathesis of cyclooctadiene with this tungsten carbene can thus be sufficiently retarded to show that the polymerization kinetics involves a catalyst-monomer bound complex, followed by regeneration of catalyst.
\r\n\r\nLinear copolymers are prepared in both random and block form from the metathesis polymerization of 1,5-cyclooctadiene/cyclooctatetraene and norbornene/cyclooctatetraene solutions, respectively. The average conjugation length in the random copolymers can be varied systematically by varying the mole fraction of cyclooctatetraene in the copolymerization solution. Raman spectroscopy, UV-Vis, NMR, electrical conductivity, and non-linear optical measurements all indicate a progression of conjugation length in the copolymer with increasing mole fraction cyclooctatetraene.
" }, { "name": "Kormann, Claudius", "degree": "PhD", "year": "1989", "title": "Synthesis and Characterization of Quantum Size Metal Oxide Colloidal Particles. Photocatalytic Peroxide Formation on ZnO and TiO\u2082", "advisor": "Hoffmann, Michael R.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05182007-110357", "creators": [ { "name": { "family": "Kormann", "given": "Claudius" }, "id": "Kormann-Claudius", "display_name": "Kormann, Claudius" } ], "advisors": [ { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "advisor", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Morgan", "given": "James J." }, "id": "Morgan-J-J", "role": "member", "display_name": "Morgan, James J." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bya7-6g55", "abstract": "The syntheses of transparent colloidal solutions of extremely small ZnO (d < 5nm) and TiO\u2082 (d < 3 nm) particles in water, alcohol, and acetonitrile are presented. Quantum size effects are observed during particle growth and at final stages of synthesis. They are qualitatively and quantitatively (TiO\u2082) interpreted by using a simple molecular orbital (MO) picture and a quantum mechanical model developed by Brus. The optical absorption and fluorescence properties as well as the surface acid-base properties are characterized in detail. The two materials are shown to be active photocatalysts in the formation and degradation of H\u2082O\u2082 and organic peroxides and in the degradation of chlorinated hydrocarbons. Quantum yields and steady state concentrations are given as function of various reaction parameters such as the oxygen concentration, the nature and concentration of electron donor, pH, and charge of the electron donor. Rates of reaction are correlated with surface speciation as calculated by the SURFEQL computer code. Transparent colloidal solutions of Fe\u2082O\u2083 (hematite) have also been prepared, however only negligible photocatalytic activity is found when compared to ZnO and TiO\u2082. Evidence is presented for OH\u2022 radical activity when aqueous TiO\u2082 suspensions are illuminated at high pH.
" }, { "name": "Kreidenweis-Dandy, Sonia Maria", "degree": "PhD", "year": "1989", "title": "Experimental and Theoretical Studies of Binary Nucleation and Condensation", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02132007-092817", "creators": [ { "name": { "family": "Kreidenweis-Dandy", "given": "Sonia Maria" }, "id": "Kreidenweis-Dandy-Sonia-Maria", "display_name": "Kreidenweis-Dandy, Sonia Maria" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "member", "display_name": "Grosjean, Daniel" }, { "name": { "family": "Okuyama", "given": "Kikuo" }, "id": "Okuyama-K", "role": "member", "display_name": "Okuyama, Kikuo" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pmy6-3d94", "abstract": "Many gas-to-particle conversion processes occurring in the atmosphere (and in technological applications) involve more than one gaseous species. An understanding of how gas-to-particle conversion occurs in multicomponent systems is necessary to predict the evolution of atmospheric aerosols. Of particular interest is the validity of binary nucleation theory in describing particle formation from two interacting vapors.
\r\n\r\nChapter II presents a modeling study of heat and mass transfer to aqueous droplets dried under various conditions, and discusses the applicability of common assumptions in describing such processes. A method for the separation, into droplets containing different solutes, of an aerosol composed of two types of aqueous droplets is proposed.
\r\n\r\nNext, in Chapter III, an experimental study of binary nucleation theory using two similar organics (dibutylphthalate and dioctylphthalate) is presented, and compared with the predictions of an integral model that describes particle formation using binary nucleation theory. It was found that the number concentrations of particles formed in the presence of both vapors was higher than could be attributed to single-component nucleation of either organic, suggesting that binary nucleation was the mechanism for particle formation. Model predictions using the theoretical binary nucleation rates, modified by suitable (species-dependent) enhancement factors, were able to represent the data well.
\r\n\r\nAttention was next focused on an environmentally-important organosulfur compound, dimethylsulfide, and its oxidation under atmospheric-type conditions. In particular, the aerosol-forming ability of the two major sulfur containing products, methanesulfonic acid and sulfuric acid, was investigated theoretically. Binary nucleation and multicomponent condensation theories were used to predict particle formation and growth in the chemically reacting system at 36% relative humidity, and model predictions were compared with published experimental smog chamber measurements of dimethylsulfide photooxidation. It was found that the experimental results could be well represented by a model that allowed for binary nucleation of aqueous sulfuric acid droplets, and ternary growth of these droplets by condensation of water, methanesulfonic acid, and sulfuric acid vapors. This investigation is presented in Chapter IV.
\r\n\r\nThe calculations presented in Chapter IV are some of the first estimates of particle formation in the methanesulfonic acid/water binary vapor system. In order to assess the validity of binary nucleation theory in describing this particle formation, an experimental program was initiated for the investigation of binary nucleation phenomena in this system. A continuous-flow, mixing-type device was proposed that would yield information not only on the critical saturation ratios required for observable particle formation, but the actual variation of nucleation rate with the gas-phase concentration of each species. The experimental apparatus that was constructed and used for this purpose and a summary and analysis of the experimental results are found in Chapter V. Particle formation was observed at moderate relative humidities and undersaturated acid vapor concentrations, demonstrating that methanesulfonic acid is able to undergo binary nucleation with water vapor. The adequacy of classical binary nucleation theory in predicting the nucleation rates is discussed in detail. The second major goal of the experimental program that was realized was the demonstration of the usefulness of this device in the investigation of binary nucleation phenomena, particularly for corrosive materials, which are difficult to work with in conventional systems.
\r\n\r\nBecause of its successful application to the methanesulfonic acid/water vapor system, this device shows great promise for future applications in the study of binary nucleation phenomena. Suggestions for the modification and improvement of the apparatus that emerged from laboratory experience and from the data analysis are presented in Chapter VI.
" }, { "name": "Ma, Doreen", "degree": "PhD", "year": "1989", "title": "Regulatory Elements in ColE1 DNA Replication in Escherichia coli. Mutants of Saccharomyces cerevisiae DNA Polymerase I Resistant to Nucleotide Analogs: dNTP Binding Site Definition", "advisor": "Campbell, Judith L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05222007-091103", "creators": [ { "name": { "family": "Ma", "given": "Doreen" }, "id": "Ma-Doreen", "display_name": "Ma, Doreen" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "advisor", "display_name": "Campbell, Judith L." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5b4k-wx16", "abstract": "Control of Co1E1-type plasmid DNA replication in Escherichia coli was investigated. The initiation of DNA replication in Co1E 1-type plasmids is regulated by two trans-acting negative control elements: RNA I and the rop protein. RNA I is a transcript 108 nucleotides long made off the L-strand (lagging strand) of the plasmid and is complementary to the 5' portion of the preprimer, RNA II. The direct base-pairing interaction between the two RNA species precludes the formation of an RNA II:template DNA hybrid, which is processed by RNase H at the origin of replication to create the 3'-OH end of the mature primer. Another trans-acting regulatory element is a 63 amino acid plasmid-encoded protein, the rop gene product. By providing the rop gene product in trans on a compatible plasmid, suppression of the runaway replication phenotype of pJN75 was observed. Utilizing this property of the regulatory mechanism, we proceeded to select pJN75 derivatives that are insensitive to rop-mediated suppression. These mutant plasmids were designated pJN75nsr for non-suppressible by rop. Sequence analyses of 7 nsr, showed disruptions of base-pairing within the stem of loop structure III of RNA II and loop structure III' of RNA I, implying that rop mediates its action via the region comprising loop structures III and III'. We were also interested in the presence of a dnaA protein binding site about 90bp downstream of the ori-pBR322. We investigated the role of dnaA protein in Co1E1-type DNA replication by purifying the dnaA protein to homogeneity from an overproducing strain and examining its effect on various mutant DNA templates in an in vitro E. coli DNA replication extract developed in the Campbell lab. We found that the combination of dnaA protein binding at the dnaA consensus sequence can substitute for the lack of primosome assembly site (pas) on the H-strand (leading strand), which is postulated to be the point of transition between DNA polymerase I and polymerase III-dependent DNA synthesis. In the absence of the H-strand pas, dnaA protein may direct other essential proteins to form a replication complex at the dnaA site, functionally acting as proteins i, n, n' and n\" at pas.
\r\n\r\nIn an effort to identify and characterize the nucleotide and/or pyrophosphate binding site(s) of yeast DNA polymerise I, we have attempted to isolate pol1 mutants that are resistant to nucleotide/pyrophosphate analogs. We successfully constructed a Saccharomyces cerevisiae strain that depends on exogenous thymidine for survival and also contains a temperature-sensitive DNA polymerase I allele (pol1-17). Using this strain, 167-poll-17, we screened for pol1 mutants that are resistant to nucleotide/pyrophosphate analogs, e.g., AraT or PAA, which are normally impermeable to the cell wall of yeast. Our strategy was to introduce a plasmid containing a mutagenized pol1 gene into 167-poll-17, which contains a ts DNA polymerase. By screening for survivors at 37\u00b0C (non-permissive temperature of pol1-17 allele) on plates containing 1 mM AraT and 40 mM PAA, we hoped to isolate DNA polymerase I mutants on the transformed plasmid. To our disappointment, we were unable to isolate such DNA pol I mutants. We offer two explanations for the failure of our strategy: 1) the presence of another essential polymerase, CDC2 gene product and 2) perturbation of pyrimidine nucleotide pool. Finally, we propose to conduct site-directed mutagenesis of DNA polymerase I at putative dNTP/PPi binding domains and to analyze the mutant polymerases in vitro for resistance to dNTP/PPi analogs. Site-directed mutagenesis experiments are now in progress, and we are hopeful that these mutants will provide structural and functional information regarding the nucleotide/pyrophosphate binding site(s) of yeast DNA polymerase I.
" }, { "name": "McQueen, Anne T.", "degree": "PhD", "year": "1989", "title": "Ammonium Ion Effects on Hybridoma Cell Physiology", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02122007-131458", "creators": [ { "name": { "family": "McQueen", "given": "Anne T." }, "id": "McQueen-Anne-T", "display_name": "McQueen, Anne T." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Attardi", "given": "Giuseppe" }, "id": "Attardi-G", "role": "member", "display_name": "Attardi, Giuseppe" }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." } ], "option_major": [ "chemeng" ], "doi": "10.7907/a159-dy39", "abstract": "Ammonium ion is an important inhibitor of mammalian cell growth. Measurements of changes in hybridoma intracellular pH upon NH4Cl addition (using a flow cytometric assay in which cells are stained with a pH-sensitive fluorescent dye) indicate that NH+4 causes a steady-state cytoplasmic acidification. There is a correlation between NH4Cl effects on growth and on intracellular pH, and these effects are independent of the external pH value, suggesting that NH+4, not NH3 (produced by the dissociation of NH+4 at higher external pH values), is the species responsible for growth inhibition.
\r\n\r\nAmmonium ion has similar effects on batch growth in flasks in an incubator and in a bioreactor at controlled pH and dissolved oxygen concentration. Both decreases in the external pH value and increases in the NH4Cl concentration inhibit glucose consumption in batch growth. This is hypothesized to be due to intracellular pH decreases. However, cell growth is not dependent on glucose consumption. Changes in the external pH value and in the NH4Cl concentration, which result in growth inhibition, have no effect on the specific antibody production rate.
\r\n\r\nA mechanism is proposed and a mathematical model is developed to explain the intracellular pH decreases caused by NH+4. This model incorporates a detailed description of the behavior of the Na+/H+-exchanger, which is assumed to be the main pHi controller of the cell. The model is able to reproduce the salient features of the experimental results.
" }, { "name": "Morgan, Joel Edgar", "degree": "PhD", "year": "1989", "title": "Electron Transfer in Cytochrome c Oxidase: The Rate of Electron Equillibration Between Cytochrome a and Copper A", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042013-091916969", "creators": [ { "name": { "family": "Morgan", "given": "Joel Edgar" }, "id": "Morgan-Joel-Edgar", "display_name": "Morgan, Joel Edgar" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "chair", "display_name": "Hopfield, John J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lester", "given": "Henry A." }, "id": "Lester-H-A", "orcid": "0000-0002-5470-5255", "role": "member", "display_name": "Lester, Henry A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/88fd-2939", "abstract": "Intramolecular electron transfer in partially reduced cytochrome c oxidase has been studied by means of perturbed equilibrium techniques. We have prepared a three electron reduced, CO inhibited form of the enzyme in which cytochrome a and copper A are partially reduced an in intramolecular redox equilibrium. When these samples were photolyzed using a nitrogen laser (0.6 \u00b5s, 1.0 mJ pulses) changes in absorbance at 598 nm and 830 nm were observed which are consistent with a fast electron from cytochrome a to copper A. The absorbance changes at 598 nm have an apparent rate of 17,200 \u00b1 1,700 s-1 (1\u03c3), at pH 7.0 and 25.5 \u00b0C. These changes were not observed in either the CO mixed valence or CO inhibited fully reduced forms of the enzyme. The rate is fastest at about pH 8.0, and falls off in either direction, and there is a small, but clear temperature dependence. The process was also observed in the cytochrome c -- cytochrome c oxidase high affinity complex.
\r\n\r\nThis rate is far faster than any rate measured or inferred previously for the cytochrome a -- copper A electron equilibration, but the interpretation of these results is hampered by the fact that the relaxation could only be followed during the time before CO became rebound to the oxygen binding site. The meaning of our our measured rate is discussed, along with other reported rates for this process. In addition, a temperature-jump experiment on the same system is discussed.
\r\n\r\nWe have also prepared a partially reduced, cyanide inhibited form of the enzyme in which cytochrome a, copper A and copper B are partially reduced and in redox equilibrium. Warming these samples produced absorbance changes at 605 nm which indicate that cytochrome a was becoming more oxidized, but there were no parallel changes in absorbance at 830 nm as would be expected if copper A was becoming reduced. We concluded that electrons were being redistributed from cytochrome a to copper B. The kinetics of the absorbance changes at 605 nm were investigated by temperature-jump methods. Although a rate could not be resolved, we concluded that the process must occur with an (apparent) rate larger than 10,000 s-1.
\r\n\r\nDuring the course of the temperature-jump experiments, we also found that non-redox related, temperature dependent absorbance changes in fully reduced CO inhibited cytochrome c oxidase, and in the cyanide mixed valence enzyme, took place with an (apparent) rate faster that 30,000 s-1.
" }, { "name": "Nam, Suk Woo", "degree": "PhD", "year": "1989", "title": "Oxidative Chemisorption of SO\u2082 on \u03b3-Al\u2082O\u2083 and Deposition of H\u2082-Permselective SiO\u2082 Films", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06282013-092232283", "creators": [ { "name": { "family": "Nam", "given": "Suk Woo" }, "id": "Nam-Suk-Woo", "orcid": "0000-0002-4884-8137", "display_name": "Nam, Suk Woo" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/8c25-cf68", "abstract": "The interaction of SO\u2082 with \u03b3-Al\u2082O\u2083 and the deposition of H\u2082 permselective SiO\u2082 films have been investigated. The adsorption and oxidative adsorption of SO\u2082 on \u03b3-Al\u2082O\u2083 have been examined at temperatures 500-700\u00b0C by Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). At temperatures above 500\u00b0C most of SO\u2082 adsorbed on the strong sites on alumina. The adsorbed SO\u2082 species was characterized by an IR band at 1065 cm\u207b\u00b9. The equilibrium coverage and initial rate of adsorption decreased with temperature suggesting a two-step adsorption. When \u03b3-Al\u2082O\u2083 was contacted with a mixture of SO\u2082 and O\u2082, adsorption of SO\u2082 and oxidation of the adsorbed SO\u2082 to a surface sulfate characterized by broad IR bands at 1070 cm\u207b\u00b9, 1390 cm\u207b\u00b9 took place. The results of a series of TGA experiments under different atmospheres strongly suggest that surface SO\u2082 and surface sulfate involve the same active sites such that SO\u2082 adsorption is inhibited by already formed sulfate. The results also indicate a broad range of site strengths.
\r\n\r\nThe desorption of adsorbed SO\u2082 and the reductive desorption of oxidatively adsorbed SO\u2082 have been investigated by microreactor experiments and thermogravimetric analysis (TGA). Temperature programmed reduction (TPR) of adsorbed SO\u2082 showed that SO\u2082 was desorbed without significant reaction with H\u2082 when H\u2082 concentration was low while considerable reaction occurred when 100% H\u2082 was used. SO\u2082 adsorbed on the strong sites on alumina was reduced to sulfur and H\u2082S. The isothermal reduction experiments of oxidatively adsorbed SO\u2082 reveal that the rate of reduction is very slow below 550\u00b0C even with 100% H\u2082. The reduction product is mainly composed of SO\u2082. TPR experiments of oxidatively adsorbed SO\u2082 showed that H\u2082S arose from a sulfate strongly chemisorbed on the surface.
\r\n\r\nFilms of amorphous SiO\u2082 were deposited within the walls of porous Vycor tubes by SiH\u2084 oxidation in an opposing reactants geometry : SiH\u2084 was passed inside the tube while O\u2082 was passed outside the tube. The two reactants diffused opposite to each other and reacted within a narrow front inside the tube wall to form a thin SiO\u2082 film. Once the pores were plugged the reactants could not reach each other and the reaction stopped. At 450\u00b0C and 0.1 and 0.33 atm of SiH\u2084 and O\u2082, the reaction was complete within 15 minutes. The thickness of the SiO\u2082 film was estimated to be about 0.1 \u00b5m. Measurements of H\u2082 and N\u2082 permeation rates showed that the SiO\u2082 film was highly selective to H\u2082 permeation. The H\u2082:N\u2082 flux at 450\u00b0C varied between 2000-3000.
\r\n\r\nThin SiO\u2082 films were heat treated in different gas mixtures to determine their stability in functioning as high-temperature hydrogen-permselective membranes. The films were heat-treated at 450-700\u00b0C in dry N\u2082, dry O\u2082, N\u2082-H\u2082O, and O\u2082-H\u2082O mixtures. The permeation rates of H\u2082 and N\u2082 changed depending on the original conditions of film formation as well as on the heat treatment. Heating in dry N\u2082 slowly reduced the permeation rates of both H\u2082 and N\u2082. Heating in a N\u2082-H\u2082O atmosphere led to a steeper decline of H\u2082 permeability. But the permeation rate of N\u2082 increased or decreased according to whether the film deposition had been carried out in the absence or presence of H\u2082O vapor, respectively. Thermal treatment in O\u2082 caused rapid decline of the permeation rates of H\u2082 and N\u2082 in films that were deposited under dry conditions. The decline was moderate in films deposited under wet conditions.
" }, { "name": "Naylor, Adel Marie", "degree": "PhD", "year": "1989", "title": "Insights on Enzymes and Polymers from Molecular Dynamics Simulations: Applications to Dihydrofolate Reductase Complexes and Starburst Dendrimers", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-134341582", "creators": [ { "name": { "family": "Naylor", "given": "Adel Marie" }, "id": "Naylor-Adel-Marie", "display_name": "Naylor, Adel Marie" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "chair", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0789-jw44", "abstract": "Examples are given for the role of simulation and theory in designing artificial biomimetic and biocatalytic systems. Simulations on the \u03b2-alanine starburst dendrimer polymers indicate that, for the higher generation systems: (1) ~50% of the surface area is internal, and (ii) ~50% of the spheroidal volume is solvent- filled. These studies suggest a design for encapsulating and delivering dopamine to the kidney for cardiovascular therapies. Investigations of the penta-erythritol based polyether starburst dendrimers show that: (i) the later generations lack any internal surface area or volume and (ii) the dense-packed limit for these polymers to be the third generation, consistent with experiment. For Dihydrofolate Reductase (DHFR), the modeling and simulations: (i) explain the high degree of kinetic similarity between two dissimilar forms of DHFR; (ii) indicate why site specific mutation (Phe-31\u2192Tyr-31, Leu-54\u2192Ile-54, or Leu-54\u2192Gly-54) causes a significant change in the catalytic rate; and (iii) suggest modifications to engineer E. coli Chicken hybrid proteins capable of reducing folate.
" }, { "name": "Novak, Bruce Michael", "degree": "PhD", "year": "1989", "title": "Aqueous Ring-Opening Metathesis Polymerizations", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-082941390", "creators": [ { "name": { "family": "Novak", "given": "Bruce Michael" }, "id": "Novak-Bruce-Michael", "display_name": "Novak, Bruce Michael" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nt5n-ap60", "abstract": "Past workers in this group as well as in others have made considerable progress in the understanding and development of the ring-opening metathesis polymerization (ROMP) technique. Through these efforts, ROMP chemistry has become something of an organometallic success story. Extensive work was devoted to trying to identify the catalytically active species in classical reaction mixtures of early metal halides and alkyl aluminum compounds. Through this work, a mechanism involving the interconversion of metal carbenes and metallacyclobutanes was proposed. This preliminary work finally led to the isolation and characterization of stable metal carbene and metallacyclobutane complexes. As anticipated, these well-characterized complexes were shown to be active catalysts. In a select number of cases, these catalysts have been shown to catalyze the living polymerization of strained rings such as norbornene. The synthetic control offered by these living systems places them in a unique category of metal catalyzed reactions. To take full advantage of these new catalysts, two approaches should be explored. The first takes advantage of the unusual fact that all of the unsaturation present in the monomer is conserved in the polymer product. This makes ROMP techniques ideal for the synthesis of highly unsaturated, and fully conjugated polymers, which find uses in a variety of applications. This area is currently under intense investigation. The second aspect, which should lend itself to fruitful investigations, is expanding the utility of these catalysts through the living polymerization of monomers containing interesting functional groups. Polymer properties can be dramatically altered by the incorporation of functional groups. It is this latter aspect which will be addressed in this work.
\r\n\r\nAfter a general introduction to both the ring-opening metathesis reaction (Chapter 1) and the polymerization of fuctionalized monomers by transition metal catalysts (Chapter 2), the limits of the existing living ROMP catalysts with functionalized monomers are examined in Chapter 3. Because of the stringent limitations of these early metal catalysts, efforts were focused on catalysts based on ruthenium complexes. Although not living, and displaying unusually long induction periods, these catalysts show high promise for future investigations directed at the development of catalysts for the living polymerization of functionalized monomers. In an attempt to develop useful catalysts based on these ruthenium complexes, efforts to increase their initiation rates are presented in Chapter 4. This work eventually led to the discovery that these catalysts are highly active in aqueous solution, providing the opportunity to develop aqueous emulsion ROMP systems. Recycling the aqueous catalysts led to the discovery that the ruthenium complexes become more activated with use. Investigations of these recycled solutions uncovered new ruthenium-olefin complexes, which are implicated in the activation process. Although our original goal of developing living ROMP catalysts for the polymerization of fuctionalized monomers is yet to be realized, it is hoped that this work provides a foundation from which future investigations can be launched.
\r\n\r\nIn the last chapter, the ionophoric properties of the poly(7-oxanobornene) materials is briefly discussed. Their limited use as acyclic host polymers led to investigations into the fabrication of ion-permeable membranes fashioned from these materials.
" }, { "name": "Novak, Julia Anne", "degree": "Masters", "year": "1989", "title": "The quintet state of a partially localized, hydrocarbon tetraradical: cyclobutane as a general ferromagnetic coupling unit", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-085334137", "creators": [ { "name": { "family": "Novak", "given": "Julia Anne" }, "id": "Novak-J-A", "display_name": "Novak, Julia Anne" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9az5-6648", "abstract": "The partially localized tetraradical 22 has been generated at temperatures of 77 K and below in 2-methyltetrahydrofuran and poly(methylmethacrylate) \r\nmatrices, and directly observed by EPR spectroscopy. The evolution of the EPR spectrum resulting from prolonged photolysis of the bisdiazene precursor 20 indicates a two-photon process, wherein a triplet spectrum (assigned unambiguously to the monoazobiradical) gradually gives way to a quintet spectrum, ascribed to the target tetraradical. The observed quintet state is tentatively identified as the ground state of the tetraradical, based on design considerations, the fact that the quintet spectrum is intense at temperatures as low as 3.8 K, and preliminary Curie Law studies. The thermal stability of 22 (indefinitely stable in the dark at 77 K) is an unexpected \r\nattribute of this molecule; no other cyclobutanediyl studied thus far has exhibited similar sturdiness at temperatures above ca. 60 K. Two synthetic routes to the prerequisite bisfulvene 15 are discussed." }, { "name": "Park, Joon Won", "degree": "PhD", "year": "1989", "title": "Reactivity of Titanocene Methylidene with Metal Halides, Alkene Sulfides, and Alkene Oxides", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062013-085651174", "creators": [ { "name": { "family": "Park", "given": "Joon Won" }, "id": "Park-Joon-Won", "display_name": "Park, Joon Won" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0ds2-5h68", "abstract": "Titanocene metallacyclobutanes show a wide variety of reactivites with organic and inorganic reagents. Their reactions include methylene transfer to organic carbonyls, formation of enolates, electron transfer from activated alkyl chlorides, olefin metathesis, ring opening polymerization. Recently, preparations of heterobinuclear \u00b5-methylene complexes were reported. In this thesis, mechanistic, synthetic, and structural studies of the heterobinuclear \u00b5-methylene complexes will be described. Also, the reaction of titanocene methylidene trimethylphosphine complex with alkene sulfide and styrene sulfide will be presented.
\r\n\r\nHeterobinuclear \u00b5-methylene-\u00b5-methyl complexes Cp\u2082Ti(\u00b5-CH\u2082)(\u00b5-CH\u2083)M(1,5-COD) have been prepared (M = Rh, Ir). X-ray crystallography showed that the methyl group of the complex was bonded to the rhodium and bridges to the titanium through an agostic bond. The \u00b9H, \u00b9\u00b3CNMR, IR spectra along with partial deuteration studies supported the structure in both solution and solid state. Activation of the agostic bond is demonstrated by the equilibration of the \u00b5-CH\u2083 and \u00b5-CH\u2082 groups. A nonlinear Arrhenius plot, an unusually large kinetic isotope effect (24(5)), and a large negative activation entropy (-64(3)eu) can be explained by the quantum-mechanical tunneling. Calculated rate constants with Bell-type barrier fitted well with the observed one. This equilibration was best explained by a 4e-4c mechanism (or \u03c3 bond metathesis) with the character of quantum-mechanical tunneling.
\r\n\r\nHeterobinuclear \u00b5-methylene-\u00b5-phenyl complexes were synthesized. Structural study of Cp\u2082Ti(\u00b5-CH\u2082)(\u00b5-p-Me\u2082NC\u2086H\u2084)Rh(l,5-COD) showed that the two metal atoms are bridged by the methylene carbon and the ipso carbon of the p-N,N-dimethylarninophenyl group. The analogous structure of Cp\u2082Ti(\u00b5-CHp\u2082)(\u00b5-o-MeOC\u2086H\u2084)Rh(1,5-COD) has been verified by the differential NOE. The aromaticity of the phenyl group observed by \u00b9H NMR, was confirmed by the comparison of the C-C bond lengths in the crystallographic structure. The unusual downfield shifts of the ipso carbon in the \u00b9\u00b3C NMR are assumed to be an indication of the interaction between the ipso carbon and electron-deficient titanium.
\r\n\r\nTitanium-platinum heterobinuclear \u00b5-methylene complexes Cp\u2082Ti(\u00b5-CH\u2082)(\u00b5-X)Pt(Me)(PMe\u2082Ph) have been prepared (X = Cl, Me). Structural studies indicate the following:(1) the Ti-CH\u2082 bond possesses residual double bond character, (2) there is a dative Pt \u2192 Ti interaction which may be regarded as a \u03c0 back donation from the platinum atom to the \"Ti=CH\u2082\" group, and (3) the \u00b5-CH\u2083 group is bound to the titanium atom through a three-center, two-electron agostic bond.
\r\n\r\nTitanocene (\u03b7\u00b2-thioformaldehyde)\u2022PMe\u2083 was prepared from Cp\u2082Ti=CH\u2082\u2022PMe\u2083 and sulfur-containing organic compounds (e.g. alkene sulfide, triphenylphosphine sulfide) including elemental sulfur. Mechanistic studies utilizing trans-styrene sulfide-d\u2081 suggested the stepwise reaction to explain equimolar mixture of trans- and cis-styrene-d\u2081 as by-products. The product reacted with methyl iodide to produce cationic titanocene (\u03b7\u00b2-thiomethoxymethyl) complex. Complexes having less coordinating anion like BF\u2084 or BPh\u2084 could be obtained through metathesis. Together with structural analyses, the further reactivities of the complexes have been explored.
\r\n\r\nThe complex [chemical formula; see thesis file (PDF) abstract for details] was prepared from the compound Cp\u2082Ti=CH\u2082-PMe\u2083 and styrene oxide. The product was characterized with \u00b9H-\u00b9H correlated 2-dimensional NMR, selective decoupling of \u00b9H NMR, and differential NOE. Stereospecificity of deuterium in the product was lost when trans-styrene oxide-d\u2081 was allowed to react. Relative rates of the reaction were measured with varying substituents on the phenyl ring. Better linearity (r = -0.98, \u03c1\u207a = -0.79) was observed with \u03c3p\u207a than \u03c3(r = -0.87, \u03c1 = -1.26). The small magnitude of \u03c1\u207a value and stereospecificity loss during the formation of product were best explained by the generation of biradicals, but partial generation of charge cannot be excluded. Carbonylation of the product followed by exposure to iodine yields the corresponding \u03b2-phenyl \u03b3-lactone.
" }, { "name": "Patrick, Valerie", "degree": "PhD", "year": "1989", "title": "Synthesis, Characterization, and Kinetics of Mixed Copper-Aluminum and Iron-Aluminum Oxides for High-Temperature Desulfurization", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212007-133209", "creators": [ { "name": { "family": "Patrick", "given": "Valerie" }, "id": "Patrick-Valerie", "display_name": "Patrick, Valerie" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Fultz", "given": "Brent T." }, "id": "Fultz-B-T", "orcid": "0000-0002-6364-8782", "role": "member", "display_name": "Fultz, Brent T." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2TRJ-1P91", "abstract": "Hot-gas desulfurization is an important step for optimizing the process economics of new schemes for power generation from coal. Mixed oxides such as CuO\u2022Al\u2082O\u2083 and Fe\u2082O\u2083\u2022Al\u2082O\u2083 are attractive as high-temperature, regenerable, desulfurization sorbents because they exhibit higher performance than CuO and Fe\u2082O\u2083.
\r\n\r\nMixed copper-aluminum and iron-aluminum oxides were prepared in porous form by the citrate process under various calcination conditions for subsequent reduction and sulfidation studies. The oxide samples were characterized by several techniques to determine chemical structure and texture. For the mixed copper-aluminum oxides, atomic absorption spectroscopy (AAS) provided the fractions of copper, soluble and insoluble, in hot nitric acid which closely corresponded to CuO and CuAl\u2082O\u2084, respectively; x-ray diffraction (XRD) provided complementary information about the content of the pure and compound oxides; and a combination of x-ray line broadening, scanning electron microscopy (SEM), and transmission electron microscopy (TEM) provided an estimate of the size of crystallites or phase domains. For the mixed iron-aluminum oxides, XRD identified crystalline phases, SEM revealed the changing surface texture with iron composition, and BET surface area measurements indicated the content of free alumina.
\r\n\r\nTemperature-programmed reduction (TPR) of mixed oxides was more complex than TPR of the pure, reducible oxides. The compound oxide, CuAl\u2082O\u2084, and part of CuO closely associated with Al\u2082O\u2083 were reduced much more slowly than bulk CuO. Similarly, the compound oxide, FeAl\u2082O\u2084, a solid solution between Fe\u2083O\u2084 and FeAl\u2082O\u2084, and Fe\u2083O\u2084 in close association with alumina were reduced much more slowly than bulk Fe\u2083O\u2084. While oxides of +1 oxidation state, Cu[2]O and CuAlO[2], were identified as reduction intermediates for TPR of CuAl\u2082O\u2084, no oxides of +1 oxidation state were identified for reduction of iron-aluminum oxides.
\r\n\r\nMixed copper-aluminum oxides were studied more extensively than mixed iron-aluminum oxides. The interaction between CuO and Al\u2082O\u2083 seen in TPR studies was further examined by XRD, diffuse reflectance spectroscopy, and laser Raman spectroscopy. Pronounced sintering of CuAl\u2082O\u2084 was observed to commence at temperatures in excess of 700\u00b0C, and the dispersion of copper on reduction of CuAl\u2082O\u2084 was poorer than that obtained by reduction of mixed oxide, CuO and Al\u2082O\u2083.
\r\n\r\nIn studies using a thermogravimetric analyzer, sulfidation of reduced sorbents produced high-temperature digenite (Cu\u2089\u208a\u2093S\u2085) in the case of copper aluminum samples, and high-temperature pyrrhotite (Fe\u2081\u208b\u2093S) in the case of iron-aluminum samples as the major crystalline products. Both CuAl\u2082O\u2084 and FeAl\u2082O\u2084 were found to be resistant to sulfidation as compared to the pure oxides, CuO and Fe\u2082O\u2083, and to mixed oxides, CuO-Al\u2082O\u2083 and Fe\u2082O\u2083-Al\u2082O\u2083. Formation of copper sulfate during air regeneration of sulfided Cu-Al-O samples was increased in the presence of free alumina.
" }, { "name": "Pranata, Julianto", "degree": "PhD", "year": "1989", "title": "Theoretical Studies of Novel Organic Systems: Biradicals, Polyradicals, and Conducting Polymers", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232013-142740600", "creators": [ { "name": { "family": "Pranata", "given": "Julianto" }, "id": "Pranata-Julianto", "display_name": "Pranata, Julianto" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x0ka-7s95", "abstract": "Chapter 1
\r\n\r\nCyclobutanediyl has been studied in both its singlet and triplet states by ab initio electronic structure theory. The triplet, which is the ground state of the molecule, exists in both C2h and C2v forms, which interconvert via a Cs transition state. For the singlet, only a C2h form is found. It passes, via a Cs transition state, onto the C2v surface on which bicyclobutane is the only minimum. The ring-flipping (inversion) process in bicyclobutane includes the singlet biradical as an intermediate, and involves a novel, nonleast motion pathway. Semiclassical periodic orbit theory indicates that the various minima on both the singlet and triplet surfaces can interconvert via quantum mechanical tunneling.
\r\n\r\nChapter 2
\r\n\r\nThe dimethylenepolycyclobutadienes (n) are the non-Kekul\u00e9 analogues of the classical acenes. Application of a variety of theoretical methods reveals several novel features of such structures. Most interesting is the emergence of a parity rule. When n is even, n is predicted to be a singlet, with n disjoint NBMOs. When n is odd, theory predicts a triplet ground state with (n+1) NBMOs that are not fully disjoint.
\r\n\r\nChapter 3
\r\n\r\nBi(cyclobutadienyl) (2), the cyclobutadiene analogue of biphenyl, and its homologues tri- (3) and tetra(cyclobutadienyl) (4) have been studied using electronic structure theory. Ab initio calculations on 2 reveal that the central bond is a true double bond, and that the structure is best thought of as two allyl radicals plus an ethylene. The singlet and triplet states are essentially degenerate. Trimer 3 is two allyls plus a dimethylenecyclobutanediyl, while 4 is two coplanar bi(cyclobutadienyl) units connected by a single bond. For both 3 and 4, the quintet, triplet, and singlet states are essentially degenerate, indicating that they are tetraradicals. The infinite polymer, polycyclobutadiene, has been studied by HMO, EHCO, and VEH methods. Several geometries based on the structures of 3 and 4 have been studied, and the band structures are quite intriguing. A novel crossing between the valence and conduction bands produces a small band gap and a high density of states at the Fermi level.
\r\n\r\nChapter 4
\r\n\r\nAt the level of H\u00fcckel theory, polyfulvene has a HOCO-LUCO degeneracy much like that seen in polyacetylene. Higher levels of theory remove the degeneracy, but the band gap (Eg) is predicted to be significantly smaller than analogous structures such as polythiophene and polypyrrole at the fulvenoid geometry. An alternative geometry, which we have termed quinoid, is also conceivable for polyfulvene, and it is predicted to have a much larger Eg. The effects of benzannelation to produce analogues of polyisothianaphthene have been evaluated. We propose a new model for such structures based on conventional orbital mixing arguments. Several of the proposed structures have quite interesting properties, which suggest that they are excellent candidates for conducting polymers.
\r\n\r\nChapter 5
\r\n\r\nTheoretical studies of polydimethylenecyclobutene and polydiisopropylidene-cyclobutene reveal that, because of steric crowding, they cannot achieve a planar, fully conjugated structure in either their undoped or doped states. Rather, the structure consists of essentially orthogonal hexatriene units. Such a structure is incompatible with conventional conduction mechanisms involving polarons and bipolarons.
" }, { "name": "Przybycien, Todd Michael", "degree": "PhD", "year": "1989", "title": "Structure, Function and Aggregation Kinetics in Salt-Induced Protein Precipitation", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02202007-153541", "creators": [ { "name": { "family": "Przybycien", "given": "Todd Michael" }, "id": "Przybycien-Todd-Michael", "display_name": "Przybycien, Todd Michael" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2atq-2y42", "abstract": "Salt-induced precipitation is a biological separation technique that exposes proteins to unnatural environments. Macromolecular-scale issues of activity, structure, and aggregation have been addressed as a function of governing parameters.
\r\n\r\nThe effects of salt type and concentration on protein solubility and recoverable activity were studied using \u03b1-chymotrypsin (\u03b1CT) as a model protein and five salts spanning the lyotropic series. Unaccounted for salt-protein interactions and changes in protein physical properties were the likely source of discrepencies between the experimental and theoretical solubility behavior. Active protein recovery was a function of salt type, but not concentration. A salting-out performance parameter was identified; an optimum salt may exist for a particular protein.
\r\n\r\n\u03b1CT precipitates from the solubility-activity study were examined for perturbations in secondary structure via Raman spectroscopy and in active site tertiary structure via electron paramagnetic resonance spectroscopy. NaBr, KBr, and KSCN-induced precipitates had increased \u03b2-sheet and decreased \u03b1-helix contents; these changes were correlated with active protein yields. Spectra of spin-labelled precipitates indicated that the active site remains intact. Molecular modelling was used to estimate changes in the dipole moment and hydrophobic surface area for the altered precipitates. A general mechanism for the precipitation of globular proteins was proposed.
\r\n\r\nThe generality of secondary structure changes was explored for twelve different proteins via Raman spectroscopy. KSCN-induced precipitates exhibited increased \u03b2-sheet and decreased \u03b1-helix contents; structural changes for Na\u2082SO\u2084-induced precipitates were less significant. The \u03b2-sheet increase may occur at the expense of \u03b1-helix segments. \u03b2-sheet increases were correlated with the fraction of charged residues and the surface area of the native protein. \u03b1-helix decreases were correlated with the dipole moment and helical content of the native protein.
\r\n\r\nThe effects of temperature, protein concentration, salt type, and salt concentration on \u03b1CT aggregation kinetics were studied. Stopped-flow turbidimetry indicated that temperature and salt concentration effects are exerted through changes in protein solubility. Protein concentration effects are well-described by Smoluchowski's collision equation. The aggregation of partially inhibited \u03b1CT demonstrated poisoning behavior. Solute particle radius distributions determined by dynamic laser light scattering indicated that aggregation denends on the supersaturation. A detailed population balance model, accounting for specific and nonspecific quaternary interactions, was developed.
" }, { "name": "Rudolph, Henrik", "degree": "PhD", "year": "1989", "title": "Dynamics of Rotationally Resolved Multiphoton Ionization Processes in Molecules", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272013-104333878", "creators": [ { "name": { "family": "Rudolph", "given": "Henrik" }, "id": "Rudolph-Henrik", "display_name": "Rudolph, Henrik" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Okumura", "given": "Mitchio" }, "id": "Okumura-M", "orcid": "0000-0001-6874-1137", "role": "member", "display_name": "Okumura, Mitchio" } ], "option_major": [ "chemistry" ], "doi": "10.7907/981t-6997", "abstract": "This dissertation presents the results of studies of several rotationally-resolved resonance enhanced multiphoton ionization (REMPI) processes in some simple molecular systems. The objective of these studies is to quantitatively identify the underlying dynamics of this highly state-specific process which utilizes the narrow bandwidth radiation of a laser to ionize a molecule by first preparing an excited state via multiphoton absorption and subsequently ionizing that state before it can decay. Coupled with high-resolution photoelectron spectroscopy, REMPI is clearly an important probe of molecular excited states and their photoioniza tion dynamics.
\r\n\r\nA key feature of our studies is that they are carried out using accurate Hartree-Fock orbitals to describe the photoelectron orbitals of the molecular ions. The use of such photoelectron orbitals is important in rotationally-resolved studies where the angular momentum coupling in the photoelectron orbital plays a significant role in the photoionization dynamics. In these studies the Hartree-Fock molecular molecular photoelectron orbitals are obtained by numerical solution of a Lippmann-Schwinger integral equation.
\r\n\r\nStudies reported here include investigations of (i) ionic rotational branching ratios and their energy dependence for REMPI via the A2\u03a3+(3s\u03c3) and D2\u03a3+(3p\u03c3)states of NO, (ii) the influence of angular momentum constraints on branching ratios at low photoelectron energies for REMPI via low-J levels of the resonant intermediate state, (iii) the strong dependence of photoelectron angular distributions on final ionic rotational state and on the alignment in REMPI of the A2\u03a3+ state of NO, (iv) vibrational state dependence of ionic rotational branching ratios arising from rapid orbital evolution in resonant states (E'2\u03a3+(3p\u03c3) of CH), (v) the influence of rovibronic interactions on the rotational branching ratios seen in REMPI via the D2\u03a3+(3p\u03c3) state of NO, and (vi) effects of laser intensity on the photoionization dynamics of REMPI.
" }, { "name": "Scherer, Norbert Franz", "degree": "PhD", "year": "1989", "title": "Time-Resolved Studies of Molecular Reaction Dynamics and Development of Experimental Methodology", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11302006-091037", "creators": [ { "name": { "family": "Scherer", "given": "Norbert Franz" }, "id": "Scherer-Norbert-Franz", "display_name": "Scherer, Norbert Franz" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5JGV-E964", "abstract": "The six research topics presented in the following chapters are concerned with several diverse problems of molecular reaction dynamics in isolated gas-phase environments. The scope of the studies ranges from performing direct measurements of bond-breakage on electronically dissociative potential energy surfaces, to monitoring the time-course of a restricted geometry bimolecular reaction. The common experimental method used in all of the studies has been a variant of pump-probe time-resolved spectroscopy. The underlying theme of the endeavors has been threefold: 1) To gain a better understanding of the role of intramolecular dynamics that precede or are commensurate with the reaction dynamics; 2) To begin to appreciatiate the observable manifestations of specific features of the reactive potential energy surface; and 3) To utilize the specific temporal behavior to elucidate quantitative information for the said potential surface.
\r\n\r\nThe studies of molecular dissociation on repulsive electronic surfaces has lead to a quantification of the timescale for primary steps in reaction processes. Moreover, transform limited temporal/spectral studies have begun to focus on specific long-range reaction fragment interactions in a state-specific manner. The latter endeavor has identified a mechanism for the reaction-fragment(s) interaction in the near-asymptotic product region.
\r\n\r\nPredissociative reaction and intramolecular dynamical behavior has been studied on ground potential energy surfaces. Overtone excitation of the OH-stretch mode of hydrogen peroxide enables molecular ground state excitation and state-specific detection of the OH reaction product. These investigations point out the potential of this picosecond pump-probe method for directly elucidating the intramolecular energy redistribution process and the possibility for direct investigation of the long-range tail region of the free-radical recombination potential surface.
\r\n\r\nThe investigation of a spatially oriented bimolecular reaction has conclusively shown that the IH-OCO reaction proceeds by way of the [HOCO]\u2020 reaction complex species. The close proximity of the van der Waals bound reactants produces unique multi-body interactions not found in the gas phase but which may arise in condensed phases. Moreover, these investigations have obtained evidence for a unique reaction reasonance (which is analogous to a shape-resonance) feature. The presence of such a resonance in the reaction entrance channel region affects the temporal behavior and yield of product formation.
" }, { "name": "Selman, Mary", "degree": "PhD", "year": "1989", "title": "Preparation and Characterization of and Intramolecular Electron Transfer in a Pentaammineruthenium Derivative of Candida krisei Cytochrome c", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262013-151906759", "creators": [ { "name": { "family": "Selman", "given": "Mary" }, "id": "Selman-Mary", "display_name": "Selman, Mary" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hpxj-n706", "abstract": "A semisynthetic binuclear metalloprotein has been prepared by appending the pentaammineruthenium moiety to histidine 39 of the cytochrome c from the yeast Candida krusei. The site of ruthenium binding was identified by peptide mapping. Spectroscopic and electrochemical properties of the derivative indicate the protein conformation is unperturbed by the modification. A preliminary (minimum) rate constant of 170s-1 has been determined for the intramolecular electron transfer from ruthenium(II) to iron(III), which occurs over a distance of at least 13\u00c5 (barring major conformational changes). Electrochemical studies indicate that this reaction should proceed with a driving force of ~170mV. The rate constant is an order of magnitude faster than that observed in horse heart cytochrome c for intramolecular electron transfer from pentaammineruthenium(II)(histidine 33) to iron(III) (over a similar distance, and with a similar driving force), suggesting a medium or orientation effect makes the Candida intramolecular electron transfer more favorable.
" }, { "name": "Shanks, Jacqueline Vanni", "degree": "PhD", "year": "1989", "title": "Metabolic Engineering Applications of in vivo \u00b3\u00b9P and \u00b9\u00b3C NMR Studies of Saccharomyces cerevisiae", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01242007-080430", "creators": [ { "name": { "family": "Shanks", "given": "Jacqueline Vanni" }, "id": "Shanks-Jacqueline-Vanni", "display_name": "Shanks, Jacqueline Vanni" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." }, { "name": { "family": "Bertani", "given": "Giuseppe" }, "id": "Bertani-G", "role": "member", "display_name": "Bertani, Giuseppe" } ], "option_major": [ "chemeng" ], "doi": "10.7907/tcbh-r327", "abstract": "Noninvasive, multicomponent measurements are required for characterization of the results from metabolically manipulated organisms. The consequences of genetic manipulation by mutation and by introduction of recombinant plasmids to Saccharomyces cerevisiae is explored by \u00b3\u00b9P and \u00b9\u00b3C nuclear magnetic resonance (NMR) spectroscopy.
\r\n\r\nThe in vivo NMR measurements should be quantified and detailed as much as possible. With this intent, analysis techniques of the in vivo \u00b3\u00b9P NMR spectrum are developed. A systematic procedure is formulated for estimating the relative intracellular concentrations of the sugar phosphates in S. cerevisiae based upon the \u00b3\u00b9P NMR spectrum. In addition, in vivo correlations of inorganic phosphate chemical shift with the chemical shifts of 3-phosphoglycerate, \u03b2-fructose 1,6-diphosphate, fructose 6-phosphate, and glucose 6-phosphate are determined. Elucidation of the cytoplasmic and vacuolar components of inorganic phosphate in the \u00b3\u00b9P NMR spectrum of S. cerevisiae is another method of analysis that was developed. Concentrations and pH values for these components may be determined from this method. An in vivo correlation relating the inorganic phosphate chemical shift of the vacuole with the chemical shift of the resonance for pyrophosphate and the terminal phosphate of polyphosphate (PP\u2081) is established. Extension of these strategies to other cellular systems should be straightforward.
\r\n\r\nTransient measurements provided by \u00b3\u00b9P NMR are applied to reg1 mutant and standard strains. The reg1 mutation will allow the expression of a cloned gene on a plasmid under the control of a GAL promoter in the presence of glucose. Despite similar values of ATP and cytoplasmic pH, the transient profiles of glucose 6-phosphate, fructose 6-phosphate, fructose 1,6-diphosphate, and 3-phosphoglycerate were very different for the two strains during anaerobic catabolism of glucose. The glucose uptake step or hexokinase step appears to be altered in the reg1 strain. The reg1 strain also catabolized galactose faster than the standard strain. These results concur with the hypothesis that the reg1 product operates early in the regulatory circuitry for glucose repression.
\r\n\r\n\u00b3\u00b9P and \u00b9\u00b3C NMR measurements are used to analyze the performance of recombinant strains in which the glucose phosphorylation step had been altered. The strain with hexokinase PI had higher rates of glucose consumption and ethanol production in comparison to healthy diploid strains in the literature. The hexokinase PII strain that had the highest in vitro enzyme activity for glucose phosphorylation did not have the highest glucose consumption rate or ethanol production. The differences observed in in vivo utilization of the glucose phosphorylation capacity among the strains are insensitive to cytoplasmic pH and levels of cytoplasmic inorganic phosphate, sugar phosphates, and total ATP. Regulation of hexokinase PII by magnesium-free ATP appears to account for the differences observed with respect to the strain containing this enzyme.
" }, { "name": "Shin, Seung Koo", "degree": "PhD", "year": "1989", "title": "Experimental and Theoretical Studies of Silylenes, Silicenium Ions, and Organometallic Reactive Intermediates", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-115104264", "creators": [ { "name": { "family": "Shin", "given": "Seung Koo" }, "id": "Shin-Seung-Koo", "display_name": "Shin, Seung Koo" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sdj1-2y57", "abstract": "Fourier transform ion cyclotron resonance spectroscopy has been used to investigate thermochemistry and relative stabilities of silylenes, silaethylene, and silicenium ions in the gas phase. Proton affinities of silylene, methylsilylene and silaethylene have been derived from studies of kinetics and thermochemistry of proton transfer from the corresponding silicenium ions to a series of n-donor bases with well-established gas-phase base strengths. Values of proton affinities combined with the known heats of formation of the corresponding silicenium ions yield heats of formation of silylene, methylsilylene, and silaethylene. Experimental results for the relative stability between methylsilylene and silaethylene are corroborated by ab initio generalized valence bond (GVB)-configuration interaction (CI) calculations which indicate that silaethylene is more stable than methylsilylene. Hydride affinities of the methyl-substituted silicenium ions have been precisely determined from examination of kinetics and equilibria of hydride-transfer reactions of methyl-substituted silanes with various hydrocarbons having well-established gas-phase hydride affinities. The result shows that the silicenium ions are significantly more stable than the corresponding carbonium ions in the gas phase with H\u207b as a reference base.
\r\n\r\nPhotoelectron spectroscopy and mass spectrometry have been employed to identify the gas-phase reactive intermediate in the chiorosilane chemical vapor deposition under the heterogeneous flash vacuum pyrolytic condition. The result indicates that dichlorosilylene and hydrogen chloride are the major gas-phase products and monochlorosilylene is not an abundant gas-phase intermediate.
\r\n\r\nThe ab initio theoretical methods have been used to calculate the equlibrium ge-ometries and singlet-triplet splittings of chlorine- and fluorine-substituted silylenes and methylenes. The GVB-dissociation consistent CI (DCCI) method has been developed to accurately predict singlet-triplet energy gaps within 1 kcal/mol error.
\r\n\r\nFinally, we have employed Fourier transform ion cyclotron resonance spec-troscopy combined with a line tunable CW CO\u2082 laser to isolate the coordinatively unsaturated organometallic intermediates and examine structures, reactivities, and spectroscopic properties of the isolated intermediates for the methyl-migratory decarbonylation reaction and ligand displacement reaction. The results show that the CF\u2083 group is an ideal infrared chromophore to investigate the infrared photochemistry of organometallic complexes, L\u2099M-CF\u2083, structures, and reaction mechanisms of their coordinatively unsaturated intermediates containing metal-bonded CF\u2083 groups. The infrared multiphoton dissociation spectra of the isolated intermediates containing metal-bonded CF\u2083 group are presented.
" }, { "name": "Sipes, Christopher N.", "degree": "Masters", "year": "1989", "title": "Real-time measurements of a bimolecular reaction", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-095849815", "creators": [ { "name": { "family": "Sipes", "given": "Christopher N." }, "id": "Sipes-C-N", "display_name": "Sipes, Christopher N." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3527-zy08", "abstract": "A method is described for the initiation of a bimolecular reaction with a laser. This allows the time resolution of bimolecular kinetics with ultrafast laser spectroscopy. Such kinetics are described for the case of \r\nH + CO_2 => OH + CO. The rise in OH is measured and examined via the proper intermediate-mediated kinetics -- the \"biphasic\" expression. The effect of restricting the impact parameter of the hydrogen atom on the carbon dioxide is also considered." }, { "name": "Smith, David Charles", "degree": "PhD", "year": "1989", "title": "Electronic Structure and Photochemical Reactivity of Binuclear Metal Complexes", "advisor": "Goddard, William A., III; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-142520920", "creators": [ { "name": { "family": "Smith", "given": "David Charles" }, "id": "Smith-David-Charles", "display_name": "Smith, David Charles" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "co-advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/q1gz-dn84", "abstract": "A valence bond (VB) \"weak coupling\" model of the electronic structure for [Ir\u2082(TMB)\u2084](B(C\u2086H\u2085)\u2084)\u2082 is developed and generalized to the class of dimeric systems in which the metals are nonbonded, in a formal sense, and can be viewed as weakly coupled. With the VB model, the energies and widths of the previously observed optical absorption bands can be rationalized; in addition, plausible assignments are made for bands that were not interpreted satisfactorily or not observed in earlier work. The VB model does not change any of the molecular orbital-based interpretations of the thermal chemistry, photochemistry, or photophysics of these systems.
\r\n\r\nPhotophysical characterization of the 1,3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a finds a system quite comparable to other binuclear d\u2078 complexes. Both fluorescence (\u03bb\u2098\u2090\u2093 735 nm, \u03c4 ~ 70 \u00b1 30 ps) and phosphorescence (\u03bb\u2098\u2090\u2093 1080 nm, \u03c4 = 210 \u00b1 20 ns) are observed.
\r\n\r\nThe relatively long lifetime of the \u00b3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a suggests that it should be able to participate in bimolecular photochemical reactions. The diradical-like structure of the excited state, an electron (or oxidizing hole) localized on the exterior of the M\u2082 unit (the d\u03c3* orbital) and an electron localized in the interior of the dimer cage (the p\u03c3 orbital), implies that one-electron chemistry will be observed. Reactions of the ground state follow two-electron pathways, similar to those observed for mononuclear d\u2078 complexes.
\r\n\r\nThe \u00b3(d\u03c3*p\u03c3) excited state of Ir\u2082(TMB)\u2084\u00b2\u207a is found to be a powerful reductant, E\u2070(Ir\u2082(TMB)\u20843+/3(Ir\u2082(TMB)\u2084\u00b2\u207a)*) ~ 1.0 V (SSCE). Excited-state electron- transfer quenching by pyridinium acceptors is observed to follow classical Marcus theory for outer-sphere electron transfer. No \"inverted\" behavior is found. The bimolecular electron-transfer reaction is highly nonadiabatic, \u03ba ~ 0.0001, because of the large donor-acceptor separation, ~ 8 \u00c5. The results for Ir\u2082(TMB)\u2084\u00b2\u207a are discussed in comparison to those for [Ir(\u00b5-pz)COD]\u2082.
\r\n\r\nIr\u2082(TMB)\u2084\u00b2\u207a is found to react photochemically with alkyl halides. Although the \u00b3(d\u03c3*p\u03c3) excited state is a good reductant, outer-sphere electron transfer seems unlikely (E\u2070(RX/RX\u2022-) < -1.5 V (SSCE)). An SRN1 pathway has been suggested to explain the alkyl halide photoreduction reaction observed for metal complexes with E\u2070(M\u2082+/3M\u2082*) < -1.5 V (SSCE); however, atom transfer to the \u00b3(d\u03c3*p\u03c3) excited state is the favored reaction mechanism for the alkyl halide photoreduction reaction of Ir\u2082(TMB)\u2084\u00b2\u207a. The generality of this reaction is discussed.
\r\n\r\nWhile there is some ambiguity as to the primary photoprocess for alkyl halide photoreactivity, \u00b3(d\u03c3*p\u03c3) excited-state hydrogen-atom transfer has been established as the mechanism of the reaction of Ir\u2082(TMB)\u2084\u00b2\u207a and a number of organic substrates. The atom-transfer reactivity of the \u00b3(d\u03c3*p\u03c3) excited state is attributed to the presence of a hole in the d\u03c3* orbital, analogous to the \u00b3n\u03c0* state of organic ketones. Interaction of the oxidizing hole with the electron pair of the C-H bond is the presumed pathway.
\r\n\r\nElectrochemical oxidation of Rh\u2082(TMB)\u2084\u00b2\u207a generates the d\u2078-d\u2077 species Rh\u2082(TMB)\u2084\u00b3\u207a. This complex reacts with 1,4-cyclohexadiene to abstract a hydrogen atom mimicking the initial step of the \u00b3(d\u03c3*p\u03c3) photoreaction. The importance of this result is discussed in terms of energy storage systems and extension of the range of hydrocarbon oxidations with binuclear d\u2078 complexes.
\r\n\r\nThe d\u2077-d\u2077 dihydride product obtained from the photoreaction of Ir\u2082(TMB)\u2084\u00b2\u207a and 1,4-cyclohexadiene is isolated and characterized. In addition to NMR, UV-Vis, IR, and Raman spectra, the complex is characterized crystallographically. The reactivity of this complex is also discussed.
" }, { "name": "Sogo, Steven G.", "degree": "Masters", "year": "1989", "title": "Studies of novel methods of gene transfer and gene regulation in eukaryotic cells", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-075936771", "creators": [ { "name": { "family": "Sogo", "given": "Steven G." }, "id": "Sogo-S-G", "display_name": "Sogo, Steven G." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p38j-0a87", "abstract": "No abstract." }, { "name": "St. Clair, Cynthia Strong", "degree": "PhD", "year": "1989", "title": "Electrochemical and Electron Transfer Investigations of Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262013-120637323", "creators": [ { "name": { "family": "St. Clair", "given": "Cynthia Strong" }, "id": "St-Clair-Cynthia-Strong", "display_name": "St. Clair, Cynthia Strong" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/0zvh-aw13", "abstract": "A study of the pH and temperature dependence of the redox potentials of azurins from five species of bacteria has been performed. The variations in the potentials with pH have been interpreted in terms of electrostatic interactions between the copper site and titrating histidine residues, including the effects of substitutions in the amino acid sequences of the proteins on the electrostatic interactions. A comparison of the observed pH dependences with predictions based on histidine pK\u2090 values known for Pseudomonas aeruginosa (Pae), Alcaligenes denitrificans (Ade), and Alcaligenes faecalis (Afa) azurins indicates that the Pae and Ade redox potentials exhibit pH dependences in line with electrostatic arguments, while Afa azurin exhibits more complex behavior. Redox enthalpies and entropies for four of the azurins at low and high pH values have also been obtained. Based on these results in conjuction with the variable pH experiments, it appears that Bordetella bronchiseptica azurin may undergo a more substantial conformational change with pH than has been observed for other species of azurin.
\r\n\r\nThe temperature dependence of the redox potential of bovine erythrocyte superoxide dismutase (SOD) has been determined at pH 7.0, with potassium ferricyanide as the mediator. The following thermodynamic parameters have been obtained (T = 25\u00b0C): E\u00b0' = 403\u00b15 mV vs. NHE, \u0394G\u00b0' = -9.31 kcal/mol, \u0394H\u00b0' = -21.4 kcal/mol, \u0394S\u00b0' = -40.7 eu, \u0394S\u00b0'_(rc) = -25.1 eu. It is apparent from these results that \u0394H\u00b0', rather than \u0394S\u00b0', is the dominant factor in establishing the high redox potential of SOD. The large negative enthalpy of reduction may also reflect the factors which give SOD its high specificity toward reduction and oxidation by superoxide.
" }, { "name": "St. Clair, Martin A.", "degree": "PhD", "year": "1989", "title": "Synthetic and Structural Studies of Permethylscandocene and Permethyltantalocene Derivatives", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262013-094527536", "creators": [ { "name": { "family": "St. Clair", "given": "Martin A." }, "id": "St-Clair-Martin-A", "display_name": "St. Clair, Martin A." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/192V-TK10", "abstract": "Cp*\u2082Sc-H reacts with H\u2082 and CO at -78\u00b0C to yield Cp*\u2082ScOCH\u2083. A stepwise reduction of CO to an alkoxide is observed when CO reacts with Cp*\u2082ScC\u2086H\u2084CH\u2083-p to give the \u03b7\u00b2-acyl Cp*\u2082Sc(CO)C\u2086H\u2084CH\u2083-p, which then reacts with H\u2082 to produce Cp*\u2082ScOCH\u2082C\u2086H\u2084CH\u2083-p. Cp*\u2082ScCH\u2083 and Cp*\u2082ScH(THF) react with CO to give uncharuncharacterizable products. Cp*\u2082ScH and Cp*\u2082ScCH\u2083 react with Cp\u2082MCO (M = Mo, W) to give scandoxycarbenes, Cp\u2082M=C(CH\u2083)OScCp*\u2082, while a wide variety of Cp*\u2082ScX (X = H, CH\u2083, N(CH\u2083)\u2082, CH\u2082CH\u2082C\u2086H\u2085) reacts with CpM(CO)\u2082 (M = Co, Rh) to yield similar carbene complexes. An x-ray crystal structure determination of Cp(CO)Co=C(CH\u2083)-OScCp*\u2082 revealed a \u00b5\u00b2: \u03b7\u00b9, \u03b7\u00b9 carbonyl interaction between the Co-CO and Sc.
\r\n\r\nCO\u2082 inserts cleanly into Sc-phenyl bonds at -78\u00b0C to produce a carboxylate complex, Cp*\u2082Sc(O\u2082C)C\u2086H\u2084CH\u2083-p. The structure of this compound was determined by x-ray crystallographic techniques.
\r\n\r\nExcess C\u2082H\u2082 reacts with Cp*\u2082ScR (R = H, alkyl, aryl, alkenyl, alkynyl, amide) at temperatures below -78\u00b0C to form the alkynyl species Cp*\u2082Sc-C\u2261C-H, which then reacts with the remaining acetylene to form polyacetylene. Cp*\u2082Sc-C\u2261C-H further reacts to yield Cp*\u2082Sc-C\u2261C-ScCp*\u2082. This unusual C\u2082 bridged dimer was characterized by x-ray crystallography.
\r\n\r\nAttempts were made to model the C-N bond breaking step of hydrodenitrogenation by synthesizing Cp*\u2082TaH(\u03b7\u00b2-H\u2082C=N(C\u2086H\u2084X)) and studying its rearrangement to Cp*\u2082Ta(=N(C\u2086H\u2084X))(CH\u2083). The 1,2 addition/elimination reactions of Cp*\u2082Ta(\u03b7\u00b2-H\u2082C=N(CH\u2083)H and Cp*\u2082Ta(=X)H (X=O, S, NH, N(C\u2086H\u2085)) were investigated. Cp*\u2082Ta(=NH)H was found to react with D\u2082 to give Cp*\u2082Ta(=ND)H, implying a nonsymmetric amide-dihydride intermediate for the addition/elimination process. Cp*\u2082Ta(=S)H and H\u2082O equilibrate with Cp*\u2082Ta(=O)H and H\u2082S, which allowed determination of the difference in bond strengths for Ta=O and Ta=S. Ta=O was found to be approximately 41 kcals/mole stronger than Ta=S.
" }, { "name": "Stauffer, David Alan", "degree": "PhD", "year": "1989", "title": "The Ion-Dipole Effect is a Force for Molecular Recognition and Biomimetic Catalysis", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10012010-161648037", "creators": [ { "name": { "family": "Stauffer", "given": "David Alan" }, "id": "Stauffer-David-Alan", "display_name": "Stauffer, David Alan" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DCD7-A023", "abstract": "Chapter 1
\r\n\r\nIn aqueous and organic media, electron-rich synthetic macrocycles serve as hosts for positively-charged guests. Binding studies in different solvents have quantified hydrophobic, donor/acceptor, and ion-dipole interactions as forces for molecular recognition. We have found clear evidence for substantial host-guest donor/acceptor \u03c0-stacking interactions (ca. 1.5 kcal/mol) in aqueous media only. The ion-dipole effect is an appreciable driving force (worth up to 3.5 kcal/mol) for molecular recognition in both aqueous and organic media.
\r\n\r\nChapter 2
\r\n\r\nVariable-temperature binding studies were performed to assess enthalpic (\u0394H\u00b0) and entropic (\u0394S\u00b0) contributions to free energies (\u0394G\u00b0) of host-guest complexation. The van't Hoff plots (RlnK\u2090 vs T\u207b\u00b9), which are clearly non-linear, have revealed significant values for the heat capacities (\u0394C\u209a) of complexation in both organic and aqueous media. The \u0394C\u209a values reflect a phenomenon generally overlooked in molecular recognition studies: both \u0394H\u00b0 and \u0394S\u00b0 are strongly temperature-dependent.
\r\n\r\nHydrophobic, donor/acceptor, and ion-dipole interactions are tentatively partitioned into \u0394H\u00b0 and \u0394S\u00b0 contributions at 298K. \"Classic\" hydrophobic binding is characterized by a large, positive \u0394S\u00b0 and a near-zero \u0394H\u00b0 term. Strong donor/acceptor \u03c0-stacking interactions are typically balanced between large, favorable enthalpic and unfavorable entropic contributions. The ion-dipole effect is primarily an enthalpically-driven binding force.
\r\n\r\nChapter 3
\r\n\r\nElectron-rich synthetic macrocyclic host 1 accelerates a class of alkylation reactions in aqueous media. Specifically, host 1 catalyzes the reactions of pyridine-type nucleophiles with alkyl halides in an aqueous pD~9 borate buffer. The rate constants of catalyzed versus uncatalyzed reactions and the binding affinities for substrates and products demand that host 1 binds transition states more tightly than ground states. This extension of molecular recognition through ion-dipole interactions to biomimetic catalysis provides compelling evidence for transition-state stabilization via favorable dipole-dipole interactions in aqueous media.
\r\n\r\nChapter 4
\r\n\r\nA new class of high-symmetry, water soluble, hydrophobic binding sites is described that feature 1,5-substituents on a rigid ethenoanthracene (DEA) framework. These new 1,5-hosts are compared to the analogous 2,6-hosts described in the Ph.D. theses of Petti and Shepodd. Because of more favorable solvation (by water) of amide linker groups that line the cavity, the 1,5-hosts exhibit significantly reduced affinities for all guests considered: only positively-charged guests are bound to any appreciable extent.
\r\n\r\nWhile the binding sites designed herein are composed of topographically well-defined, rigid units to give a chiral host (with a \"greater sense of twist\"), the disposition of the 1,5-substituents allows the collapse of hosts into a \"bowl\" conformation. We therefore suggest that the more successful high-symmetry, hydrophobic binding sites are to be found with 2,6-DEA-constructed hosts rather than with 1,5-DEA-constructed hosts.
\r\n\r\nOne benefit of the synthetic approach taken here is the development of a series of DEA building blocks for the construction of hosts with even more pronounced hydrophobic character.
" }, { "name": "Sweder, Kevin Scot", "degree": "PhD", "year": "1989", "title": "Isolation and Characterization of Proteins that Bind to Yeast Origins of DNA Replication", "advisor": "Campbell, Judith L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232013-141734040", "creators": [ { "name": { "family": "Sweder", "given": "Kevin Scot" }, "id": "Sweder-Kevin-Scot", "display_name": "Sweder, Kevin Scot" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "advisor", "display_name": "Campbell, Judith L." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Emr", "given": "Scott D." }, "id": "Emr-S-D", "role": "member", "display_name": "Emr, Scott D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/d0tj-k332", "abstract": "Yeast chromosomes contain sequences called ARSs which function as origins of replication in vitro and in vivo. We have carried out a systematic deletion analysis of ARS1, allowing us to define three functionally distinct domains, designated A, B, and C. Domain A is a sequence of 11 to 19bp, containing the core consensus element that is required for replication. The core consensus sequence, A/TTTTATPuTTTA/T, is conserved at all ARSs sequenced to date. A fragment containing only element A and 8 flanking nucleotides enables autonomous replication of centromeric plasmids. These plasmids replicate very inefficiently, suggesting that flanking sequences must be important for ARS function. Domain B also provides important sequences needed for efficient replication. Deletion of domain B drastically increases the doubling times of transformants and reduces plasmid stability. Domain B contains a potential consensus sequence conserved at some ARSs which overlaps a region of bent DNA. Mutational analysis suggests this bent DNA may be important for ARS function. Deletion of domain C has only a slight effect on replication of plasmids carrying those deletions.
\r\n\r\nWe have identified a protein called ARS binding factor I (ABF-I) that binds to the HMR-E ARS and ARS1. We have purified this protein to homogeneity using conventional and oligonucleotide affinity chromatography. The protein has an apparent molecular weight of 135kDa and is present at about 700 molecules per diploid cell, based on the yield of purified protein and in situ antibody staining. DNaseI footprinting reveals that ABF-I binds sequence-specifically to an approximately 24bp sequence that overlaps element Bat ARS1. This same protein binds to and protects a similar size region at the HMR-E ARS.
\r\n\r\nWe also find evidence for another ARS binding protein, ABF-III, based on DN asei footprint analysis and gel retardation assays. The protein protects approximately 22bp adjacent to the ABF-I site. There appears to be no interaction between ABF-I and ABF-III despite the proximity of their binding sites.
\r\n\r\nTo address the function of ABF-I in DNA replication, we have cloned the ABF-I gene using rabbit polyclonal anti-sera and murine monoclonal antibodies against ABF-I to screen a \u03bbgt11 expression library. Four EcoRI restriction fragments were isolated which encoded proteins that were recognized by both polyclonal and monoclonal antibodies. A gene disruption can now be constructed to determine the in vivo function of ABF-I.
" }, { "name": "Thorp, H. Holden", "degree": "PhD", "year": "1989", "title": "The Photochemistry of Dioxorhenium(V)", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272013-140559569", "creators": [ { "name": { "family": "Thorp", "given": "H. Holden" }, "id": "Thorp-H-Holden", "display_name": "Thorp, H. Holden" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-N-S", "orcid": "0000-0001-5245-0538", "role": "member", "display_name": "Lewis, Nathan Saul" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vm0m-vr10", "abstract": "The excited-state properties of trans-ReO2(py)4+ (ReO2+) in acetonitrile solution have been investigated. The excited-state absorption spectrum of ReO2+ is dominated by bleaching of the ground state MLCT and d-d systems. The reduction potential of ReO22+/+* is estimated from emission and electrochemical data to be -0.7 V (SSCE). The ReO2+ excited state efficiently reduces methylviologen and other pyridinium and olefin acceptors. The resulting Re(VI) species oxidizes secondary alcohols and silanes. Acetophenone is the product of sec-phenethyl alcohol oxidation.
\r\n\r\nThe emission properties of ReO2+ in aqueous solutions of anionic and nonionic surfactants have been investigated. The emission and absorption maxima of ReO2+ are dependent on the water content of its environment. Emission lifetimes vary over four orders of magnitude upon shifting from aqueous to nonaqueous environments. The emission lifetime has a large (8.6) isotope effect (k(H2O)/k(D2O)) that reflects its sensitivity towards the environment. These properties have been used to develop a model for the interactions of ReO2+ with sodium dodecyl sulfate (SDS). A hydrophobic ReO2+ derivative, ReO2(3-Ph-py)4+, has been used to probe micelles of nonionic surfactants, and these results are consistent with those obtained with SDS.
\r\n\r\nThe emission properties of ReO2+ in Nafion perfluorosulfonated membranes have been investigated. Absorption and emission spectroscopy indicate that the interior of the membrane is quite polar, similar to ethylene glycol. Two well-resolved emission components show different lifetimes and different isotope effects, indicative of varying degrees of solvent accessibility. These components are taken as evidence for chemically distinct regions in the polymer film, assigned as the interfacial region and the ion cluster region.
\r\n\r\nThe unsubstituted pyridine complex shows monophasic, \u03c4 = 1.7 \u00b5s, emission decay when bound to calf thymus DNA. Switching to the 3-Ph-py complex yields a biphasic emission decay (\u03c41 = 2.4 \u00b5s, \u03c42 = 10 \u00b5s) indicative of an additional, solvent-inaccessible binding mode. Photoinduced electron transfer to methylviologen leads to oxidative cleavage of the DNA as detected by gel electrophoresis. Electrochemical and spectrophotometric techniques used with organic substrates also can be used to monitor the oxidation of DNA. Abstraction of the ribose 4' hydrogen by ReO22+ is a possible mechanism.
" }, { "name": "Totten, Nancy Susanne Demcak", "degree": "Masters", "year": "1989", "title": "Examining the transferrin-transferrin receptor system as a possible mechanism for cell specific targeting with liposomes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-094148072", "creators": [ { "name": { "family": "Totten", "given": "Nancy Susanne Demcak" }, "id": "Totten-N-S-D", "display_name": "Totten, Nancy Susanne Demcak" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2qfc-mj80", "abstract": "This research focuses on targeting capabilities which may be applied for delivery of liposomes to T cells. Two methods of targeting were investigated. The first involved IgG purified from goat antisera to aportion of the viral envelope of Human Immunodeficiency Virus (HIV). The \r\nIgG was derivatized with the N-hydroxysuccinimide ester of palmitic acid (NHSP) to increase its hydrophobicity so that it could be incorporated into the lipid bilayer of egg phosphatidylcholine liposomes.\r\n\r\nThe second method used transferrin to coat liposomes made from egg phosphatidylcholine and egg phosphatidylethanolamine, 5:1 weight ratio, respectively. In this method the transferrin receptor (TfR) serves as a \r\ntarget for the delivery of transferrin (Tf) coated liposomes to cells.\r\n\r\nFrom previous observations made at the City of Hope as well as data from a resent paper, HIV infected cells appear to have an increased affinity for Tf. This increased affinity is most likely associated with an increase in cell surface TfRs. The H-9 cell line, which can be infected with HIV, has been characterized for the number of TfRs per cell and for the binding of Tf.\r\n\r\nAttaching IgG or Tf to a liposome will alter the protein structure. Thus, the receptor-ligand affinity characteristics of IgG as well as the affinity of iron for Tf and of Tf-Fe for TfR will change. As a result, the \r\ntype of association which links IgG or Tf to the liposome will affect the targeting ability of the IgG or Tf coated liposomes. Many methods of associating IgG with liposomes have been studied. The method of choice is one of the most successful ways for the use of liposome delivery. It involves the attachment of palmitoyl chains to the IgG \r\nfollowed by insertion of the now hydrophobic IgG into the lipid membrane. Only a few procedures for attaching Tf and liposomes have previously been tried. I have examined a new method for attaching Tf to liposomes, involving the use of water soluble carbodiimide. The crosslinking of Tf and liposome has been observed with a maximum efficiency of 1 Tf molecule for 4 liposomes. For both IgG and Tf coated liposomes, an average diameter of 45-50nm was determined.\r\n" }, { "name": "Trimmer, Mark S.", "degree": "PhD", "year": "1989", "title": "Mechanistic and Reactivity Studies of Bent Metallocene Complexes of Niobium and Tantalum", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232013-111400988", "creators": [ { "name": { "family": "Trimmer", "given": "Mark S." }, "id": "Trimmer-Mark-S", "display_name": "Trimmer, Mark S." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bads-b915", "abstract": "A variety of olefin hydride complexes of niobium and tantalum has been prepared in order to study their reactivity and to gain insight into organometallic reaction mechanisms. Examination of a series of ethylene and propylene complexes of niobocene (Cp\u2082Nb; Cp = \u03b7\u2075-C\u2085H\u2085), permethylniobocene (Cp*\u2082Nb; Cp* = \u03b7\u2075-C\u2085(CH\u2083)\u2085), tantalocene, and permethyltantalocene has indicated that there are both large electronic and steric effects deriving from the metal (and its ancillary ligands) in the olefin insertion (\u03b2-migratory insertion) process. Furthermore, a thermodynamic and kinetic analysis has been completed for a series of substituted styrene complexes of niobocene in order to better understand the important electronic properties of the olefin. The results are in accord with a concerted four-center process with only moderate charge development.
\r\n\r\nThe special case of \u03b2-migratory insertion of a hydride ligand into coordinated benzyne has also been studied for the permethyltantalocene system. The coordinatively unsaturated (sixteen electron) phenyl tautomer, which is made accessible by the facile benzyne hydride insertion reaction, readily reacts with a variety of ligands, L, to afford Cp*\u2082 Ta(C\u2086H\u2085)L complexes (L = CO, O\u2082, NC\u2261R, :CH\u2082, H\u2082, etc.). This family of compounds exhibits interesting reactivity (a-migratory insertion, O\u2082 activation, and reductive elimination) which is discussed in some detail.
\r\n\r\nFinally a series of paramagnetic seventeen electron Cp*\u2082 TaX\u2082 (X = halide, alkyl, hydride) complexes, and the corresponding cationic and anionic species, have been prepared and studied. The odd electron neutral complexes exhibit surprising thermal stability and undergo very little reactivity. While the chemistry of the anionic compounds is almost completely dominated by their potent reducing power, that of the cations is quite diverse and amenable for study. Therefore the syntheses and reactivity (1,2-eliminations, ligand insertions, and deprotonation reactions) of these coordinatively unsaturated sixteen electron species are presented.
" }, { "name": "Vogelaar, Nancy Swick", "degree": "PhD", "year": "1989", "title": "Structural and Mechanistic Motifs in Membrane Proteins: The Three-Dimensional Modelling of Rhodopsin, Band 3, and the Nicotinic Acetylcholine Receptor", "advisor": "Goddard, William A., III; Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272013-134530519", "creators": [ { "name": { "family": "Vogelaar", "given": "Nancy Swick" }, "id": "Vogelaar-Nancy-Swick", "display_name": "Vogelaar, Nancy Swick" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "co-advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mgah-n841", "abstract": "Because so little is known about the structure of membrane proteins, an attempt has been made in this work to develop techniques by which to model them in three dimensions. The procedures devised rely heavily upon the availability of several sequences of a given protein. The modelling procedure is composed of two parts. The first identifies transmembrane regions within the protein sequence on the basis of hydrophobicity, \u03b2-turn potential, and the presence of certain amino acid types, specifically, proline and basic residues. The second part of the procedure arranges these transmembrane helices within the bilayer based upon the evolutionary conservation of their residues. Conserved residues are oriented toward other helices and variable residues are positioned to face the surrounding lipids. Available structural information concerning the protein's helical arrangement, including the lengths of interhelical loops, is also taken into account. Rhodopsin, band 3, and the nicotinic acetylcholine receptor have all been modelled using this methodology, and mechanisms of action could be proposed based upon the resulting structures.
\r\n\r\nSpecific residues in the rhodopsin and iodopsin sequences were identified, which may regulate the proteins' wavelength selectivities. A hinge-like motion of helices M3, M4, and M5 with respect to the rest of the protein was proposed to result in the activation of transducin, the G-protein associated with rhodopsin. A similar mechanism is also proposed for signal transduction by the muscarinic acetylcholine and \u03b2-adrenergic receptors.
\r\n\r\nThe nicotinic acetylcholine receptor was modelled with four trans-membrane helices per subunit and with the five homologous M2 helices forming the cation channel. Putative channel-lining residues were identified and a mechanism of channel-opening based upon the concerted, tangential rotation of the M2 helices was proposed.
\r\n\r\nBand 3, the anion exchange protein found in the erythrocyte membrane, was modelled with 14 transmembrane helices. In general the pathway of anion transport can be viewed as a channel composed of six helices that contains a single hydrophobic restriction. This hydrophobic region will not allow the passage of charged species, unless they are part of an ion-pair. An arginine residue located near this restriction is proposed to be responsible for anion transport. When ion-paired with a transportable anion it rotates across the barrier and releases the anion on the other side of the membrane. A similar process returns it to its original position. This proposed mechanism, based on the three-dimensional model, can account for the passive, electroneutral, anion exchange observed for band 3. Dianions can be transported through a similar mechanism with the additional participation of a histidine residue. Both residues are located on M10.
" }, { "name": "Wade, Warren Stanfield", "degree": "PhD", "year": "1989", "title": "Sequence Specific Complexation of B DNA at Sites Containing G,C Base Pairs", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242013-102113951", "creators": [ { "name": { "family": "Wade", "given": "Warren Stanfield" }, "id": "Wade-Warren-Stanfield", "display_name": "Wade, Warren Stanfield" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9kdn-0y27", "abstract": "A series of eight related analogs of distamycin A has been synthesized. Footprinting and affinity cleaving reveal that only two of the analogs, pyridine-2- car box amide-netropsin (2-Py N) and 1-methylimidazole-2-carboxamide-netrops in (2-ImN), bind to DNA with a specificity different from that of the parent compound. A new class of sites, represented by a TGACT sequence, is a strong site for 2-PyN binding, and the major recognition site for 2-ImN on DNA. Both compounds recognize the G\u2022C bp specifically, although A's and T's in the site may be interchanged without penalty. Additional A\u2022T bp outside the binding site increase the binding affinity. The compounds bind in the minor groove of the DNA sequence, but protect both grooves from dimethylsulfate. The binding evidence suggests that 2-PyN or 2-ImN binding induces a DNA conformational change.
\r\n\r\nIn order to understand this sequence specific complexation better, the Ackers quantitative footprinting method for measuring individual site affinity constants has been extended to small molecules. MPE\u2022Fe(II) cleavage reactions over a 10\u2075 range of free ligand concentrations are analyzed by gel electrophoresis. The decrease in cleavage is calculated by densitometry of a gel autoradiogram. The apparent fraction of DNA bound is then calculated from the amount of cleavage protection. The data is fitted to a theoretical curve using non-linear least squares techniques. Affinity constants at four individual sites are determined simultaneously. The distamycin A analog binds solely at A\u2022T rich sites. Affinities range from\r\n10\u2076-10\u2077 M\u207b\u00b9 The data for parent compound D fit closely to a monomeric binding curve. 2-PyN binds both A\u2022T sites and the TGTCA site with an apparent affinity constant of 10\u2075 M\u207b\u00b9. 2-ImN binds A\u2022T sites with affinities less than 5 x 10\u2074 M\u207b\u00b9. The affinity of 2-ImN for the TGTCA site does not change significantly from the 2-PyN value. At the TGTCA site, the experimental data fit a dimeric binding curve better than a monomeric curve. Both 2-PyN and 2-ImN have substantially lower DNA affinities than closely related compounds.
\r\n\r\nIn order to probe the requirements of this new binding site, fourteen other derivatives have been synthesized and tested. All compounds that recognize the TGTCA site have a heterocyclic aromatic nitrogen ortho to the N or C-terminal amide of the netropsin subunit. Specificity is strongly affected by the overall length of the small molecule. Only compounds that consist of at least three aromatic rings linked by amides exhibit TGTCA site binding. Specificity is only weakly altered by substitution on the pyridine ring, which correlates best with steric factors. A model is proposed for TGTCA site binding that has as its key feature hydrogen bonding to both G's by the small molecule. The specificity is determined by the sequence dependence of the distance between G's.
\r\n\r\nOne derivative of 2-PyN exhibits pH dependent sequence specificity. At low pH, 4-dimethylaminopyridine-2-carboxamide-netropsin binds tightly to A\u2022T sites. At high pH, 4-Me\u2082NPyN binds most tightly to the TGTCA site. In aqueous solution, this compound protonates at the pyridine nitrogen at pH 6. Thus presence of the protonated form correlates with A\u2022T specificity.
\r\n\r\nThe binding site of a class of eukaryotic transcriptional activators typified by yeast protein GCN4 and the mammalian oncogene jun contains a strong 2-ImN binding site. Specificity requirements for the protein and small molecule are similar. GCN4 and 2-lmN bind simultaneously to the same binding site. GCN4 alters the cleavage pattern of 2-ImN-EDTA derivative at only one of its binding sites. The details of the interaction suggest that GCN4 alters the conformation of an AAAAAAA sequence adjacent to its binding site. The presence of a yeast counterpart to jun partially blocks 2-lmN binding. The differences do not appear to be caused by direct interactions between 2-lmN and the proteins, but by induced conformational changes in the DNA protein complex. It is likely that the observed differences in complexation are involved in the varying sequence specificity of these proteins.
" }, { "name": "Wang, Nam Sun", "degree": "PhD", "year": "1989", "title": "Mathematical and Experimental Studies of Microbial Processes with Lag Effects", "advisor": "Stephanopoulos, Gregory N.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06112007-143619", "creators": [ { "name": { "family": "Wang", "given": "Nam Sun" }, "id": "Wang-Nam-Sun", "display_name": "Wang, Nam Sun" } ], "advisors": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "advisor", "display_name": "Stephanopoulos, Gregory N." } ], "committee": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "chair", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7mez-bd45", "abstract": "Unlike most chemical reaction dynamics, microbial behavior depends not only on the present state of the environment surrounding a microorganism but, more importantly, on its past history as well. Herein lies a major obstacle in the modeling of a biological process with a simple set of equations. By incorporating a culture's past history in the form of a time-lag kernel, a novel approach to bioprocess identification and modeling is formulated. A time-lag kernel is included in the state equations, and a generalized method of mathematical simplification via the transformation of an integro-differential equation to a set of first-order ODE's is developed. The time-lag convolution integral arises during the process of transforming a structured, mechanistic model into an equivalent unstructured model as a result of lumping. The resulting model possesses the combined advantages of the simplicity of an unstructured, lumped-parameter model and the predictive power of a complex structured model. The experimental determination of the kernel is performed by cultivating Saccharomyces cerevisiae in a chemically defined medium of either glucose or ethanol as the limiting carbon source and in a tightly controlled environment of temperature and pH. All the model parameters can be feasibly resolved with a simple set of experiments. The validity of the time-lag modeling approach is clearly demonstrated experimentally by its superior capability in predicting the various transient responses under different modes of operation. Seemingly unreproducible experiments are shown to be united when time-lag effects are taken into consideration. This modeling work fits within the general framework of on-line computer parameter estimation, control, and optimization of a biochemical reactor. As such, the proposed modeling approach to biological systems identifies the cause-effect relationship more clearly and is well suited for process control purposes.
" }, { "name": "Watnick, Paula Ivonne", "degree": "PhD", "year": "1989", "title": "Cooperative Properties of Lipid Bilayers: Collective Director Fluctuations and the Effects of Hydrophobic Mismatch in Protein/Lipid Membrane Systems", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072014-135012645", "creators": [ { "name": { "family": "Watnick", "given": "Paula Ivonne" }, "id": "Watnick-Paula-Ivonne", "display_name": "Watnick, Paula Ivonne" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j3wj-vz40", "abstract": "Cooperative director fluctuations in lipid bilayers have been postulated for many years. \u00b2H-NMR T\u2081\u207b\u00b9, T\u2081\u03c1\u207b\u00b9, and T\u2082\u207b\u00b9; measurements have been used identify these motions and to determine the origin of increased slow bilayer motion upon addition of unlike lipids or proteins to a pure lipid bilayer.
\r\n\r\nThe contribution of cooperative director fluctuations to NMR relaxation in lipid bilayers has been expressed mathematically using the approach of Doane et al.\u00b9 and Pace and Chan.\u00b2 The T\u2082\u207b\u00b9's of pure dimyristoyllecithin (DML) bilayers deuterated at the 2, 9 and 10, and all positions on both lipid hydrocarbon chains have been measured. Several characteristics of these measurements indicate the presence of cooperative director fluctuations. First of all, T\u2082\u207b\u00b9 exhibits a linear dependence on S\u00b2CD. Secondly, T\u2082\u207b\u00b9 varies across the \u00b2H-NMR powder pattern as sin\u00b2 (2\u03b2), where , \u03b2 is the angle between the average bilayer director and the external magnetic field. Furthermore, these fluctuations are restricted near the lecithin head group suggesting that the head group does not participate in these motions but, rather, anchors the hydrocarbon chains in the bilayer.
\r\n\r\nT\u2082\u207b\u00b9 has been measured for selectively deuterated liquid crystalline DML hilayers to which a host of other lipids and proteins have been added. The T\u2082\u207b\u00b9 of the DML bilayer is found to increase drastically when chlorophyll a (chl a) and Gramicidin A' (GA') are added to the bilayer. Both these molecules interfere with the lecithin head group spacing in the bilayer. Molecules such as myristic acid, distearoyllecithin (DSL), phytol, and cholesterol, whose hydrocarbon regions are quite different from DML but which have small,neutral polar head groups, leave cooperative fluctuations in the DML bilayer unchanged.
\r\n\r\n\r\nThe effect of chl a on cooperative fluctuations in the DML bilayer has been examined in detail using \u00b2H-NMR T\u2081\u207b\u00b9, T\u2081\u03c1\u207b\u00b9, and T\u2082\u207b\u00b9; measurements. Cooperative fluctuations have been modelled using the continuum theory of the nematic state of liquid crystals. Chl a is found to decrease both the correlation length and the elastic constants in the DML bilayer.
\r\n\r\nA mismatch between the hydrophobic length of a lipid bilayer and that of an added protein has also been found to change the cooperative properties of the lecithin bilayer. Hydrophobic mismatch has been studied in a series GA'/lecithin bilayers. The dependence of \u00b2H-NMR order parameters and relaxation rates on GA' concentration has been measured in selectively deuterated DML, dipalmitoyllecithin (DPL), and DSL systems. Order parameters, cooperative lengths, and elastic constants of the DML bilayer are most disrupted by GA', while the DSL bilayer is the least perturbed by GA'. Thus, it is concluded that the hydrophobic length of GA' best matches that of the DSL bilayer. Preliminary Raman spectroscopy and Differential Scanning Calorimetry experiments of GA'/lecithin systems support this conclusion. Accommodation of hydrophobic mismatch is used to rationalize the absence of HII phase formation in GA'/DML systems and the observation of HII phase in GA'/DPL and GA'/DSL systems.
\r\n\r\n1. J. W. Doane and D. L. Johnson, Chem. Phys. Lett., 6, 291-295 (1970).
\r\n\r\n2. R. J. Pace and S. I. Chan, J. Chem. Phys., 76, 4217-4227 (1982).
" }, { "name": "Wittrup, Karl Dane", "degree": "PhD", "year": "1989", "title": "Plasmid Propagation in the Yeast Saccharomyces cerevisiae: Flow Cytometry Studies and Segregated Modeling", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212007-131607", "creators": [ { "name": { "family": "Wittrup", "given": "Karl Dane" }, "id": "Wittrup-Karl-Dane", "display_name": "Wittrup, Karl Dane" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Rothenberg", "given": "Ellen V." }, "id": "Rothenberg-E-V", "orcid": "0000-0002-3901-347X", "role": "member", "display_name": "Rothenberg, Ellen V." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/KQYB-CX46", "abstract": "The baker's yeast Saccharomyces cerevisiae is potentially a very useful host for the production of pharmaceutical proteins by recombinant DNA technology. One requirement for efficient overproduction of a foreign protein in yeast is a stable recombinant DNA vector which is maintained at a high number of copies per cell. The rational design of such vectors requires knowledge concerning their propagation in a cell population. The purpose of this work is to develop mathematical and experimental tools for the study of multicopy plasmid propagation, and to apply these tools to the investigation of a particular type of yeast vector: a conditional centromere plasmid.
\r\n\r\nA method for measuring the distribution of plasmid copy number in yeast populations was developed, using \u03b2-galactosidase activity as a marker for plasmid copy number. Enzyme activity is assayed at the single-cell level using a fluorogenic substrate and flow cytometry. The relationship between single-cell fluorescence and enzyme activity is described by a mathematical reaction-diffusion model.
\r\n\r\nA segregated mathematical modeling framework was established to link measured copy number distributions with probabilistic models of single-cell plasmid replication and partitioning. Simplifications of the general integral-partial differential population balance equations were obtained for a discrete state variable, resulting in a linear system of ordinary differential equations.
\r\n\r\nFlow cytometry and segregated modeling were applied to the study of a conditional centromere plasmid. This type of plasmid can be amplified to high copy number by unequal partitioning, but the amplified copy number state is unstable in the absence of selection pressure. A segregated model of this plasmid's propagation was shown to be consistent with experimental observations. The conceptual model of plasmid instability suggests changes in the attributes of the host cell and plasmid construction to improve stability at high copy number. A segregated mathematical model of this type is necessary for the design of bioreactor operating conditions that optimize productivity.
" }, { "name": "Worthen, Denise Lynne", "degree": "Masters", "year": "1989", "title": "Lactose binding to the E. coli symport protein Lac permease", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-093118312", "creators": [ { "name": { "family": "Worthen", "given": "Denise Lynne" }, "id": "Worthen-D-L", "display_name": "Worthen, Denise Lynne" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kkcr-mc09", "abstract": "Lac permease is a symport protein which responsible for the active accumulation of lactose in E. coli. The protein utilizes the energy from the downhill translocation of protons to drive uphill accumulation of lactose. This work reports the direct measurement by proton NMR of lactose binding to lac permease of E. coli membrane vesicles. The technique allows the determination of the K_d of lactose binding to lac permease binding sites. The results presented here show that the assay is specific for lac permease binding sites and that the assay can distinguish differences in binding affinity for different site specific mutants of lac permease. Determination of the Kd for lactose binding is important in determining which residues are important for lactose binding.\r\n" }, { "name": "Xavier, Isaac de Melo, Jr.", "degree": "PhD", "year": "1989", "title": "Electron Energy-Loss Spectroscopy Study of Polyatomic Molecular Systems Under Pyrolytic Conditions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232013-093350784", "creators": [ { "name": { "family": "Xavier", "given": "Isaac de Melo, Jr." }, "id": "Xavier-Isaac-de-Melo-Jr", "display_name": "Xavier, Isaac de Melo, Jr." } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4wx9-6j66", "abstract": "The technique of variable-angle, electron energy-loss spectroscopy has been used to study the electronic spectroscopy of the diketene molecule. The experiment was performed using incident electron beam energies of 25 eV and 50 eV, and at scattering angles between 10\u00b0 and 90\u00b0. The energy-loss region from 2 eV to 11 eV was examined. One spin-forbidden transition has been observed at 4.36 eV and three others that are spin-allowed have been located at 5.89 eV, 6.88 eV and 7.84 eV. Based on the intensity variation of these transitions with impact energy and scattering angle, and through analogy with simpler molecules, the first three transitions are tentatively assigned to an n \u2192 \u03c0* transition, a \u03c0 - \u03c3* (3s) Rydberg transition and a \u03c0 \u2192 \u03c0* transition.
\r\n\r\nThermal decomposition of chlorodifluoromethane, chloroform, dichloromethane and chloromethane under flash-vacuum pyrolysis conditions (900-1100\u00b0C) was investigated by the technique of electron energy-loss spectroscopy, using the impact energy of 50 eV and a scattering angle of 10\u00b0. The pyrolytic reaction follows a hydrogen-chloride \u03b1-elimination pathway. The difluoromethylene radical was produced from chlorodifluoromethane pyrolysis at 900\u00b0C and identified by its X̃\u00b9A\u2081 \u2192 Ã\u00b9B\u2081 band at 5.04 eV.
\r\n\r\nFinally, a number of exploratory studies have been performed. The thermal decomposition of diketene was studied under flash vacuum pressures (1-10 mTorr) and temperatures ranging from 500\u00b0C to 1000\u00b0C. The complete decomposition of the diketene molecule into two ketene molecules was achieved at 900\u00b0C. The pyrolysis of trifluoromethyl iodide molecule at 1000\u00b0C produced an electron energy-loss spectrum with several iodine-atom, sharp peaks and only a small shoulder at 8.37 eV as a possible trifluoromethyl radical feature. The electron energy-loss spectrum of trichlorobromomethane at 900\u00b0C mainly showed features from bromine atom, chlorine molecule and tetrachloroethylene. Hexachloroacetone decomposed partially at 900\u00b0C, but showed well-defined features from chlorine, carbon monoxide and tetrachloroethylene molecules. Bromodichloromethane molecule was investigated at 1000\u00b0C and produced a congested, electron energy-loss spectrum with bromine-atom, hydrogen-bromide, hydrogen-chloride and tetrachloroethylene features.
" }, { "name": "Zietlow, Miriam Heinrichs", "degree": "PhD", "year": "1989", "title": "Chemistry of Low-Valent Platinum Dimers", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282013-161114555", "creators": [ { "name": { "family": "Zietlow", "given": "Miriam Heinrichs" }, "id": "Zietlow-Miriam-Heinrichs", "display_name": "Zietlow, Miriam Heinrichs" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j4bj-3046", "abstract": "Physical and chemical properties of low-valent platinum dimers, namely [Pt\u2082(P\u2082O\u2085H\u2082)\u2084]\u2074\u207b and Pt\u2082(\u00b5-dppm)\u2082Cl\u2082, have been investigated using a variety of structural and spectroscopic techniques.
\r\n\r\nPlatinum(II) d\u2078-d\u2078 dimers have been shown to exhibit much thermal and photochemical reactivity. Chapter 2 describes studies aimed at elucidating the excited state reduction potenetial of [Pt\u2082(P\u2082O\u2085H\u2082)\u2084]\u2074\u207b, Pt\u2082, in organic media. By conducting excited state electron transfer studies using derivatized pyridiniums and benzophenones, the excited state reduction potential has been estimated to be ~2 V. The Pt\u2082 complex undergoes partial oxidation to form Pt(II,III) linear chains. Chapter 3 describes the structural and spectroscopic techniques used to determine the translational symmetries of these [Pt\u2082(P\u2082O\u2085H\u2082)\u2084]\u2074\u207b (X = Cl, Br), Pt\u2082X, chains. Pt\u2082Br has been found to be intermediate between (AAB)\u2099 and (AABCCB)\u2099, while, Pt\u2082Cl is of (AABCCB)\u2099 translational symmetry. Investigations into the electronic transitions of Pt\u2082Cl and Pt\u2082Br were conducted using high pressure techniques and are presented in Chapter 4. The Pt\u2082X electronic spectrum exhibits bands attributable to the reduced Pt\u2082 complex and the oxidized Pt\u2082X\u2082 complex ([Pt\u2082(P\u2082O\u2085H\u2082)\u2084X\u2082]\u2074\u207b) along with an intervalence charge-tranfer band characteristic of a mixed-valence solid.
\r\n\r\nPhotophysical investigations of a new luminescent chromophore, Pt\u2082(\u00b5-dppm)\u2082Cl\u2082, a d\u2079-d\u2079 dimer, and its analogs are described in Chapter 5. The absorption band directly responsible for the observed emission is believed to be very weak and, as of yet, unobserved. Attempts to determine the spin multiplicty and approximate energy of this unobserved transition are described in Chapter 6. Excited-state energy transfer studies indicate that this absorption band is a triplet transition at -13,000 cm\u207b\u00b9. Although, the Pt\u2082(\u00b5-dppm)\u2082Cl\u2082 excited state is non-luminescent in fluid solution, it has been shown to undergo thermal electron transfer to tetracyanoethylene and photoinduced electron transfer to methylviologen. These experiments are presented in Chapter 7. Preliminary studies, described in Chapter 8, of non-bridged d\u2079-d\u2079 platinum(I) dimers have shown that [Pt\u2082(CNCH\u2083)\u2086]\u00b2\u207a serves as a versatile precursor in the synthesis of new d\u2078-d\u2078 A-frame complexes.
" }, { "name": "Adkins, Carol Leslie Jones", "degree": "PhD", "year": "1988", "title": "Use of a Continuous Stirred Tank Reactor for the Study of Aqueous Aerosol Chemistry", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042009-080025691", "creators": [ { "name": { "family": "Adkins", "given": "Carol Leslie Jones" }, "id": "Adkins-Carol-Leslie-Jones", "display_name": "Adkins, Carol Leslie Jones" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Okuyama", "given": "Kikuo" }, "id": "Okuyama-K", "role": "member", "display_name": "Okuyama, Kikuo" }, { "name": { "family": "Morgan", "given": "James J." }, "id": "Morgan-J-J", "role": "member", "display_name": "Morgan, James J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/8cpt-ce77", "abstract": "Atmospheric aerosol chemistry is important in areas ranging from urban air pollution to cloud formation. It has long been supposed that droplet-phase reactions account for a significant fraction of the atmospheric conversion of SO\u2082 to sulfate. Among such reactions is the manganese-catalyzed aqueous-phase oxidation of SO\u2082. Whereas the role of aqueous phase SO\u2082 oxidation in the dilute solutions characteristic of fog and cloud droplets (diameter > 10 \u00b5m) has been reasonably well established, the role of comparable reaction in submicron aerosols is uncertain. In this thesis a reactor system is developed to carry out gas-aerosol reactions under humid, ambient-like conditions. The apparatus consists of a continuous stirred tank reactor (CSTR) in which the growth of the aqueous aerosol is measured. Absence of mass transfer limitation, coagulation, and nucleation ensure that particle growth is direct evidence of reaction. Special care is taken to minimize size biasing of the aqueous aerosol in the electrostatic classifier used to measure the reactor feed and effluent distributions. Aerosol behavior in the reactor is modeled assuming an ideal CSTR and, given the solution thermodynamics and equilibrium chemistry, the effluent distribution can be predicted using one of the proposed reaction rate mechanisms.
\r\n\r\nExperiments were performed using a pure MnSO\u2084 or a MnSO\u2084-Na\u2082SO\u2084 mixture feed aerosol. The relative humidity ranged from 86 to 94% and 0.1 ppm < pSO\u2082, < 50 ppm. The slow, approximately constant reaction rate of Bronikowski and Pasiuk-Bronikowska (1981) (R ~ 2 x 10\u207b\u2074 Ms\u207b\u00b9) was found to best predict the observed growth over the entire range of operating conditions. The various rate expressions proposed for this system in the literature resulted in varying estimates of growth. When reactor conditions were similar to those at which the rate expression was determined, the agreement between the predicted and observed distributions improved. This indicates that use of a rate expression beyond its specified range may result in erroneous predictions.
\r\n" }, { "name": "Anslyn, Eric Van", "degree": "PhD", "year": "1988", "title": "Mechanistic, Synthetic and Theoretical Studies of High Valent Metallacycles and metal Alkylidenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-094841353", "creators": [ { "name": { "family": "Anslyn", "given": "Eric Van" }, "id": "Anslyn-Eric-Van", "orcid": "0000-0002-5137-8797", "display_name": "Anslyn, Eric Van" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/m7kp-4g32", "abstract": "The primary focus of this thesis is on the mechanism of olefin metathesis and ring opening metathesis polymerizations. In addition, several reactions of metal alkylidenes and metallacycles which are not traditionally viewed as part of the olefin metathesis reaction are presented. Olefin metathesis involves the 2+2 cycloaddition of metal alkylidenes with olefins and the 2+2 cycloreversion of metallacyclobutanes. These reactions are becoming common place in organometallic reaction mechanisms and join the traditional oxidative additions, reductive eliminations, ligand substitutions, intramolecular insertions, nucleophilic attacks on coordinated ligands and ligand fluxtionalities as the commonly sited organometallic reactions. A current goal of organometallic chemistry is to understand the influence of oxidation state, electron count, ligand sterics, ligand electronics and substituent effects upon each of these reactions.
\r\n\r\nThe knowledge of mechanisms is essential to be able to understand and rationally manipulate chemical processes. The knowledge also allows for the capability to catagorize mechanistic theories as an organizing device for understanding organometallic chemistry as a whole. Organometallic chemistry, however, is not easily catagorized due to the large complexity of bonding types and structures that inorganic chemistry produces. The work in this thesis has utilized some techniques of physical organic chemistry to study mechanisms and reactive intermediates. These techniques include kinetics, substituent effects, isotope effects, stereochemical studies and theoretical calculations.
\r\n\r\nOrganic chemistry has greatly benefited from the advent and subsequent development of the pericyclic theory for the understanding of covalent bonding, frontier orbitals and symmetry. These same notions have met with various levels of success in organometallic chemistry. The success of theoretical studies in organometallic systems very often depends upon the level of electron correlation and the extent to which the exchange integrals are calculated. The theory presented in this thesis utilizes a fully ab initio method with electron correlation. The structure of organometallic complexes is examined as a function of the nodal planes of the individual metal ligand bonds and their influence on the bonding of other ligands within the same complex. In addition, reactivity of the complexes are probed as a function of the symmetry and energy of the bonding and empty orbitals.
\r\n\r\nIn chapter one, data and speculations relating to the mechanism of cleavage of titanocene metallacyclobutanes is presented. The reactive intermediate is postulated to be a titanocene methylidene-olefin adduct. Chapter two further expands upon these mechanistic studies by presenting the kinetics and polydispersities of the ring opening metathesis polymerizations of slightly strained olefins. Chapter three presents work which utilizes ab initio electronic structure theory calculations to determine the energetics of the 2+2 cycloaddition of molybdenum alkylidene and imido complexes with olefins. In chapters 4, 5 and 6, reactivity different than the normal cycloadditions of metal alkylidenes and cycloreversions of metallacycles is examined. In chapter 4, an electron transfer mechanism for the reaction of titanocene methylidene with activated halides is presented. Chapter 5 discusses the reactivity of titanocene methylidene with inorganic carbonyls. The titanocene methylidene does not perform methylene transfer as is seen with organic carbonyls, but instead, the resultant oxametallacycle rearranges to yield a titanocene ketene complex. Finally, in chapter six, ab initio electronic structure theory calculations are again presented. They are used to explore the interconversion of a metallacyclobutadiene to a metallatetrahedrane. The two complexes are found to be energetically similar due to a balance between the strength of \u03c3 and \u03c0 bonds and the role of strain and resonance effects. Each chapter was written as an individual study and thus includes an Abstract, Introduction, Results and Discussion section and a Summary or Conclusion. Thus, this thesis presents work that attempts to add a little more knowledge to the mechanistic and theoretical understanding of organometallic reaction mechanisms.
\r\n" }, { "name": "Antypas, William George, Jr.", "degree": "PhD", "year": "1988", "title": "Nuclear Magnetic Resonance Studies of Biological Systems", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-100334158", "creators": [ { "name": { "family": "Antypas", "given": "William George, Jr." }, "id": "Antypas-William-George-Jr", "display_name": "Antypas, William George, Jr." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j4ep-gn92", "abstract": "Chapter 1: pH Homeostasis in Human Red Blood Cells
\r\n\r\nThe intracellular pH of normal and homozygous sickle cell red blood cells was measured in cell suspensions in plasma by NMR. Freshly drawn, metabolically active red cells maintain a transmembrane pH gradient that differs significantly from the expected Donnan equilibrium proton distribution. In the physiologically important extracellular pH range of 7.12 to 7.57 the intracellular pH is maintained within the narrow range of 7.20 to 7.37. Outside of this range, the intracellular pH is linearly dependent on the extracellular pH. Thus, red cells maintain an intracellular pH that is closer to 7.3 over the entire extracellular pH range than is expected from the Donnan equilibrium ion distribution. The ligation state of cellular hemoglobin shifted the position of the intra- vs extra-cellular pH relationship, but did not alter the ability of the cells to regulate intracellular pH. Deoxygenation of normal red blood cells resulted in an intracellular pH increase of 0.05 \u00b1 0.02 compared to oxygenated cells over the extracellular pH range 7.00 to 7.80. Metabolically depleted cells are unable to maintain a non-Donnan equilibrium proton distribution. The regulation of intracellular pH was regained by restoring cellular ATP levels. Sickle cell blood demonstrated the same ability to regulate intracellular pH as was observed in normal blood. Deoxygenation of sickle cell blood also resulted in a net increase in intracellular pH. However, gelation of the sample prevented accurate intracellular pH measurements of completely deoxygenated sickle cell samples.
\r\n\r\nChapter 2: Measurements of Cell Volume by Nuclear Magnetic Resonance
\r\n\r\nThe Mean Hemoglobin Concentration (MHC) of red blood cells was measured non-invasively and non-destructively by NMR. The difference between intracellular and extracellular proton relaxation rates provides the basis for the determination of the MHC in red blood cells. T1 relaxation times were measured at a proton frequency of 200 MHz. The T1 relaxation time for water protons in serum is 2.20 \u00b1 0.20 seconds. The T1 relaxation time of water protons in red blood cell pellets is 0.64 \u00b1 0.15 seconds. In red blood cell lysate, the T1 relaxation time is 0.77 \u00b1 0.11 seconds. The observed water T1 relaxation data from red blood cell samples under various conditions were fit to the complete equation for the time-dependent decay of magnetization for a two-compartment system including chemical exchange. The MHC for each sample was calculated from the hematocrit and the intracellular water fraction as determined by NMR. MHC values obtained in this manner ranged from 25% to 29% by volume for normal red blood cells in serum, in agreement with published values. The use of proton NMR to determine MHC values directly and non-destructively provides a method to evaluate the effect of various agents on the MHC in viable cells and has wide applicability to the study of antisickling agents in intact cells. The ability to monitor cell volume and to follow the effect of agents known to affect ion transport (valinomycin, nystatin, amiloride, etc.) on cell volume has enormous experimental potential.
\r\n\r\nChapter 3: 31P NMR Studies of the Binding Site of anti-Phosphorylcholine Antibodies
\r\n\r\nThe binding of the phosphorylcholine (PC) analogue, 2-(trimethylphosphonio)-ethylphosphate (phosphorylphosphocholine, PPC) to the PC binding myeloma proteins TEPC-15, McPC 603, and MOPC 167 was studied by 31P NMR. Binding of PPC to each of the proteins results in an observed phosphate chemical shift that is identical to the shift observed when PC is bound. Thus, the specific binding interactions of the phosphate subsite of the proteins with PC are maintained when PPC is bound. The chemical shift and titration behavior of the phosphonium resonance of PPC was studied as a probe of the choline subsite of these proteins. PPC bound to TEPC-15 or MOPC 167 exhibits a +0.1 ppm upfield shift from the free hapten. In contrast, PPC binding to McPC 603 results in a +2.7 ppm upfield shift that titrates with a pKa of 3.6. The shape of the titration curve indicates that the ionizations of 2 protons of equal pKa are responsible for the observed titration. Three acidic residues provide the major contribution to the choline subsite in both TEPC-15 and MOPC 167. The amino acid substitution ASP99H \u2192 Asn in the third hypervariable region of McPC 603 destroys the spatial symmetry of the choline subsite in McPC 603. The symmetry of the charge distribution of the choline subsite that is lost by this substitution is restored at low pH by titrating the negative charges of Glu35H and Glu59H.
" }, { "name": "Ascoli, Edward Paul", "degree": "PhD", "year": "1988", "title": "The Effects of a Planar Wall on the Low Reynolds Number Motion of Solid Particles, Drops and Bubbles", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-11062007-130109", "creators": [ { "name": { "family": "Ascoli", "given": "Edward Paul" }, "id": "Ascoli-Edward-Paul", "display_name": "Ascoli, Edward Paul" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "James", "given": "David F." }, "id": "James-David-F", "role": "member", "display_name": "James, David F." } ], "option_major": [ "chemeng" ], "doi": "10.7907/jch2-wy37", "abstract": "This thesis focuses on the low Reynolds number interaction of solid particles, deformable drops and bubbles with a rigid plane boundary. In chapters I, II and III we use a numerical technique which employs a boundary integral equation reformulation of Stokes system. In particular, the kernels in the integral reformulation derive from the Green's function corresponding to a no-slip planar boundary. Motion is assumed axisymmetric about the line perpendicular to the plane and through the drop or particle center.
\r\n\r\nWe consider the solid particle case in chapter I. Particle velocity is prescribed and the resultant hydrodynamic force on the particle calculated. The results are discussed in the context of near and far field asymptotic theories as well as existing numerical techniques.
\r\n\r\nIn chapter II deformable drop motion via buoyancy is examined and the time evolution of drop shape is obtained. Interfacial tension is assumed constant. Emphasis is placed on the details of drop \"dimpling\". In particular, at the initial stages of dimpling, pressure variation normal to the wall is found to be significant in the film trapped between the drop and the wall. Thin-film analytic theories neglect this variation in pressure. The consequences of neglect of this pressure variation are discussed.
\r\n\r\nIn the appendix to chapter II we develop a thin-film asymptotic theory for the buoyancy driven motion of a bubble toward a planar wall. The consequences of this theory are related to the results of chapter II. This work is still in progress, and for this reason it is relegated to an appendix.
\r\n\r\nThermocapillarity provides the mechanism for drop motion and deformation in chapter III. Surface tension is allowed to vary with temperature and the drop is placed in a non-constant temperature field. The effects of physical parameters on drop evolution are discussed.
\r\n\r\nChapter IV is a digression from low Reynolds number wall effects. Here we examine a numerical technique developed by Ryskin and Leal for generating boundary-fitted orthogonal coordinate grids. Specifically, we present a proof of the existence of a boundary-fitted orthogonal grid for the case when the ratio of \"scale factors\" is of product form.
\r\n" }, { "name": "Bagajewicz, Miguel Jorge", "degree": "PhD", "year": "1988", "title": "Studies on Hot Gas H\u2082S Removal Sorbents in Fixed-Bed Reactors at High Temperatures", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11062007-103728", "creators": [ { "name": { "family": "Bagajewicz", "given": "Miguel Jorge" }, "id": "Bagajewicz-Miguel-Jorge", "display_name": "Bagajewicz, Miguel Jorge" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WZZJ-H326", "abstract": "Experimental and theoretical studies in the field of fuel gas desulfurization at high temperatures are presented. The performance of different oxides as sorbents for high temperature H2S removal is evaluated. A fixed-bed microreactor was used for this purpose. Basically, streams containing different H2S concentrations were passed through the reactor and the outlet H2S concentration was measured as a function of time. Comparisons between observed and theoretical maximum conversion values are used as a measure of sorbent H2S removal efficiencies.
\r\n\r\nMost of the work was devoted to study zinc oxide and vanadium oxide, but other sorbents were also investigated. ZnO was studied because of its high equilibrium constant for sulfidation. High surface alumina-supported ZnO and high surface bulk ZnO were tested. Alumina-supported ZnO proved to have a smaller desulfurization capacity than bulk ZnO. In the case of V2O5, chemisorption of H2S on reduced vanadium oxide, rather than bulk sulfide formation, was found to be the mechanism of sulfur removal. Adsorption-desorption measurements were carried out in this case to investigate the behavior of the sorbent.
\r\n\r\nThe regeneration step, which restores the oxide by means of oxidation of the spent sulfide, was also studied in detail. The rate of ZnS oxidation was measured using a thermogravimetric analyzer. For the range of temperatures 650-700\u00b0C, the rate of reaction was consistent with Langmuir kinetics. The activation energy and the free energy of oxygen chemisorption were determined. An undesirable side reaction during oxidative regeneration is sulfate formation. The kinetics of this reaction was also investigated by thermogravimetric measurements.
\r\n\r\nTheoretical studies dealing with reaction and diffusion processes in pellets and fixed-bed reactors were conducted, to a large extent motivated by the need to describe desulfurization processes. One chapter is devoted to a survey of exact and approximate solutions for an isothermal fixed-bed gas-solid reactor. Approximate analytical solutions to a class of models of reaction and diffusion inside sorbent pellets are presented next. The last chapter is devoted to a traveling wave solution describing reaction fronts inside non-isothermal fixed-bed reactors. This provides a good analytical approach for the prediction of conditions for the formation of zinc sulfate during the regeneration of ZnS.
\r\n" }, { "name": "Baker, Brenda Faye", "degree": "PhD", "year": "1988", "title": "Sequence Specific Cleavage of Double Helical DNA N-Bromoacetyldistamycin", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01222013-095919666", "creators": [ { "name": { "family": "Baker", "given": "Brenda Faye" }, "id": "Baker-Brenda-Faye", "display_name": "Baker, Brenda Faye" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3c0t-vj26", "abstract": "This thesis is concerned with the design, synthesis, and mechanism of interaction of sequence specific double helical DNA cleaving molecules. The design of sequence specific cleaving molecules for double helical DNA requires the attachment of DNA cleaving moieties to sequence specific DNA binding molecules. The degree of cleavage specificity is in part controlled by the cleavage moiety. With this in mind attention is focused on attachment of a nondiffusible cleavage moiety, specifically an electrophile, to a sequence specific binding unit. Electrophilic attack of DNA nucleophiles, such as the N-3 of adenine or the N-7 of guanine, results in cleavage of the backbone via depurination.
\r\n\r\nN-Bromoacetyldistamycin (BD) is designed to place an electrophile in the minor groove within adenine-thymine rich regions in close proximity to the N3 of adenine. The electrophile, bromoacetyl, is attached at the amino end of tris-N-methylpyrrolcarboxamide, a tripeptide binding unit from the natural product distamycin A.
\r\n\r\nA general synthetic scheme has been devised which allows for synthesis of the isotopically labeled compounds (carbon 13 and 14) and the other halide derivatives, iodo and chloro, for purposes of product characterization and kinetic analysis.
\r\n\r\nAffinity cleavage studies by high resolution gel electrophoresis show that BD has a high degree of cleavage specificity. Out of 334 bases in a 167 b.p. restriction fragment, from the pBR322 plasmid, cleavage occurs primarily (80%) at a single adenine after 10 hours at 37 degrees. In order to understand this high degree of specificity the mechanistic details of the reaction have been explored.
\r\n\r\nUnder longer reaction times and higher temperatures cleavage occurs at other adenines of the 167 b.p. restriction fragment. The amount of cleavage at any given adenine is dependent upon the leaving group as shown with the hydroxy, chloro, iodo and mesyl derivatives, where Br > I \u2243 Ms > Cl >>> OH.
\r\n\r\nElectrophilic attack of double helical DNA by BD occurs at the N3 of adenine. In this regard, carbon 14labeled BD was utilized to compare the products from the BD/free base adenine reaction and the BD/DNA reactions. 99% enriched [15N3]-adenine, 99% enriched N-Bromo-[2-13C]-acetyldistamycin, and subsequently the four isotopic combinations of the distamycin-adenine adduct were synthesized to determine the site of alkylation by proton, carbon 13, and nitrogen 15 NMR. The adenine adduct exists in the amino form (N6) as shown by NMR of the 15N6 labeled adduct.
\r\n\r\n3-(Acetyldistamycin)-adenine is the sole released product from the reaction of BD with a 15 base pair oligonucleotide, which contains the site of major cleavage from the 167 b.p. restriction fragment.
\r\n\r\nDNA products at each stage of the reaction and workup procedure were monitored by high resolution gel electrophoreses of radioactively labeled DNA. The alkylated DNA-distamycin intermediate has been detected. The DNA end products were determined enzymatically with phosphatases verifying that both the 3' and 5' DNA termini are phosphates as expected for an alkylation/depurination reaction followed by base workup.
\r\n\r\nThe reaction of the N-haloacetyldistarnycins (Cl, Br, and I) with double helical DNA which results in strand cleavage has four experimentally distinguishable steps: 1) binding, 2) covalent attachment to adenine, 3) release of the adenine adduct, and 4) strand cleavage. Steps one through three were quantitatively analyzed using a synthetic oligonucleotide that contained the site of major cleavage (one binding site) of the 167 restriction fragment. In this system the binding constant for BD measures as K = 5.5 x 105 M-1. The rate of akylation is first order (k = 1.94 x 10-2 h-1, 37\u00b0C) and the rate of adenine adduct release is first order (7.76 x 10-2 h-1, 37\u00b0C).
\r\n\r\nThe cleavage specificities of the synthetic molecule, N-Bromoacetyldistamycin, and the natural product, CC1065 were compared on the 167 b.p. restriction fragment. After a reaction time of one hour at 37\u00b0C, CC1065 cleaves at 21 adenines whereas BD shows only a minute amount of cleavage at one adenine.
\r\n\r\n" }, { "name": "Brusich, Mark John", "degree": "PhD", "year": "1988", "title": "Theoretical Insights into the Bonding in Thorium Organometallic Complexes: A Comparison with Group IV Transition Metal Chemistry", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-085412529", "creators": [ { "name": { "family": "Brusich", "given": "Mark John" }, "id": "Brusich-Mark-John", "display_name": "Brusich, Mark John" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemistry" ], "doi": "10.7907/89jn-7f38", "abstract": "In this thesis a detailed ab initio theoretical study of organothorium chemistry is presented. The first part is devoted to examining both the bonding in and the reaction chemistry of various substituted thorium complexes. Using the chlorine ligand as a model for the usual cyclopentadienyl groups found in these systems, we examine the bonding of hydrogen and methyl ligands to thorium. Frequent comparisons with the experimental results on similar species are made. In addition, by contrasting the bonding in the thorium complexes with the bonding in the analogous Group IVB systems, a qualitative and quantitative picture of bonding, as the atomic number of the metal becomes larger, can be obtained. The reaction chemistry is studied via two different sets of processes. In the first, the deuterium (D2) exchange reaction with a thorium-hydrogen bond is examined. Several studies have been done previously, both experimentally and theoretically, on the Group IVB exchange reactions. Hence, there is enough information to see trends and to make predictions about relative reaction rates. Also, from our investigation the effect that different types of ligands have on the activation barrier to reaction can be ascertained.
\r\n\r\nIn the second part of the thesis, the factors that go into stabilizing bond formation are discussed concerning both main group elements and transition metals, including actinides. In particular, the process of bond formation between hydrogen atom and the alkali metals is compared with the same process in the Group IVB-hydrogen and thorium-hydrogen saturated complexes. The main difference between the alkali metal and the transition metal bonds with hydrogen is the bond strength trends with increasing atomic number. For the alkali metals the bond energies decrease down the column, yet for the transition metals and thorium it is the reverse. The conclusion is that the shape of the mostly d in character transition metal bonding orbitals is such that better overlap can be achieved with hydrogen as the orbitals become more diffuse. In the alkali metals the bonds can be described as s\u2014s bonds whose overlap decreases with increasing diffuseness.
\r\n" }, { "name": "Bulls, Al Ray", "degree": "PhD", "year": "1988", "title": "Carbon-Hydrogen Bond Activation by Peralkylhafnocene and Peralkylscandocene Derivatives", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01172013-130132630", "creators": [ { "name": { "family": "Bulls", "given": "Al Ray" }, "id": "Bulls-Al-Ray", "display_name": "Bulls, Al Ray" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZSJW-KC36", "abstract": "Chapter 1
\r\n\r\nThermal decomposition of Cp*2Hf(CH2C6H5)2 (Cp* = (\u03b75-C5Me5)) in benzene-d6\r\ncleanly affords toluene and hafnabenzocyclobutene [chemical symbol; see abstract in scanned thesis for details]. Deuterium\r\nlabeling of the benzyl ligands indicates that decomposition of Cp*2Hf(CY2C6H5)2 (Y = H, D)\r\nproceeds primarily by \u03b1-H abstraction to form a permethylhafnocene benzylidene\r\nintermediate [Cp*2Hf=CHC6H5], which rapidly rearranges to the\r\nmetallated-cyclopentadienyl, or \"tucked-in\" benzyl complex\r\nCp*(\u03b75,\u03b71-C5Me4CH2)HfCH2C6H5. The observed product arises from rearrangement of\r\nCp*(\u03b75,\u03b71-C5Me4CH2)HfCH2C6H5 to its tautomer [chemical symbol; see abstract in scanned thesis for details]. A series of meta\r\nsubstituted benzyl derivatives of the proposed metallated cyclopentadienyl intermediates,\r\nCp*(\u03b75,\u03b71-C5Me4CH2)HfCH2C6H4X (X = H, CH3, CF3, NMe2), has therefore been prepared.\r\nThe kinetics of their conversion to [chemical symbol; see abstract in scanned thesis for details] have been examined in order to\r\nprobe the nature of the transition state for aryl C-H bond activation which occurs in the final\r\nsteps of the rearrangement. The rates are found to be insensitive to the nature of X,\r\nsuggesting that the benzyl \u03c0 system is not attacked by the electrophilic hafnium center along\r\nthe reaction coordinate for C-H bond activation. The structure of\r\nCp*(\u03b75,\u03b71-C5Me4CH2)HfCH2C6H5, as determined by single crystal X-ray diffraction\r\ntechniques, indicates that the complex is best described as a Hf(IV) derivative containing an\r\n\u03b75,\u03b71-C5Me4CH2 Iigand, rather than a Hf(ll) \u03b76-fulvene adduct.\r\nCp*(\u03b75,\u03b71-C5Me4CH2)HfCH2C6H5 crystallizes in the triclinic space group P1̅ (a= 9.084(2), b\r\n= 10.492(2), c = 12.328(1) \u00c5; \u03b1 = 95.81(1), \u03b2 = 96.60(1), \u03b3 = 91.15(2); Z = 2). Least-squares\r\nrefinement led to a value for R of 0.048 (I > 3\u03c3I) and a goodness-of-fit of 4.37 for 4029\r\nindependent reflections.
\r\n\r\nChapter 2
\r\n\r\nThermolysis of the singly metallated complex\r\nCp*(\u03b75,\u03b71-C5Me4CH2)Hf(CH2CMe3) in toluene affords neopentane and the doubly\r\nmetallated complex Cp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)2)Hf. The structure of\r\nCp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)2)Hf, as determined by single-crystal X-ray diffraction\r\ntechniques, confirms that metallation has occurred at adjacent methyl groups of the same\r\npentamethylcyclopentadienyl ring. Cp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)2)Hf crystallizes in the space\r\ngroup P2/c (a= 13.775(4) \u00c5, b = 9.516(1) \u00c5, c = 14.183(6) \u00c5; \u03b2 = 103.965(31)\u00b0, z = 4). Least\r\nsquares refinement led to a value for R of 0.036 (I > 3\u03c3i) and a goodness-of-fit of 2.66 for\r\n1984 independent reflections. Cp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)2)Hf and Cp*(\u03b75,\u03b71-C5Me4CH2)Hfl\r\ncleanly insert one equivalent of ethylene into the hafnium methylene carbon bond to form\r\nthe propyl bridged species Cp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)(CH2CH2CH2))Hf and\r\nCp*(\u03b75,\u03b71-C5Me3CH2CH2CH2)Hfl, respectively.\r\nCp*(\u03b75,\u03b71,\u03b71-C5Me3(CH2)(CH2CH2CH2))Hf reacts with excess ethylene to cleanly afford\r\n[chemical symbol; see abstract in scanned thesis for details]. Deuterium labeling experiments suggest that\r\nthis reaction occurs via an \u03b1-H abstraction to generate the alkylidene intermediate\r\nCp*(\u03b75,\u03b71-C5Me4CH2CH2CH=)Hf, which rapidly traps ethylene to form the observed\r\nproduct. The metallated phenyl complex Cp*(\u03b75,\u03b71-C5Me3CH2)HfC6H5 has been shown to\r\nbe in equilibrium with the benzyne complex Cp*2Hf(\u03b72-C6H4). Heating benzene-d6\r\nsolutions of Cp*(\u03b75,\u03b71-C5Me3CH2)HfC6H5 in the presence of ethylene traps the benzyne\r\nintermediate and generates the hafnacyclopentene [chemical symbol; see abstract in scanned thesis for details].
\r\n\r\nChapter 4
\r\n\r\nRelative bond dissociation energies (BDEs) have been obtained by equilibrating\r\nearly transition metal alkyls and hydrides with H2 or the C-H bonds of hydrocarbons. Thus,\r\nin benzene solution Cp*2HfH2 (Cp* = (\u03b75-C5Me5)) equilibrates with Cp*2Hf(C6H5)H and\r\ndihydrogen. From the enthalpy of the reaction, \u0394H\u00b0 = +6.0(3), the Hf-H (BDE) is calculated\r\nto be 0.8(3) kcal\u00b7mol-1 stronger than the Hf-C6H5 BDE. Relative Sc-C6H5 and Sc-alkyl\r\nBDEs have been estimated from the equilibration of the metallated complex\r\nCp*(\u03b75,\u03b71-C5Me4CH2CH2CH2)Sc, C6H6 and Cp*(\u03b75-C5Me4CH2CH2CH3)Sc(C6H5), the\r\nSc-C6H5 BDE being 16.6(3) kcal\u00b7mol-1 stronger than the Sc-CH2CH2CH2C5Me4 BDE. From\r\na similar reversible intramolecular metallation of Cp*(\u03b75-C5Me4CH2CH2CH3)HfH2 to give\r\nCp*(\u03b75,\u03b71-C5Me4CH2CH2CH2)HfH and dihydrogen, the Hf-H BDE is estimated to be 23.0(3)\r\nkcal\u00b7mol-1 stronger than the Hf-CH2CH2CH2C5Me4 BDE. The equilibration of\r\nCp*(\u03b75-C5Me4CH2C6H5)Sc-C\u2261CCMe3 with the metallated scandocene derivative\r\nCp*(\u03b75,\u03b71-C5Me4CH2-o-C6H4)Sc and tert-butylacetylene lies very far towards\r\nCp*(\u03b75-C5Me4CH2C6H5)Sc-C\u2261CCMe3, so that only a lower limit for the relative Sc-alkynyl\r\nand Sc-aryl BDEs may be determined: BDE(Sc-alkynyl) - BDE(Sc-aryl) \u2265 29(5) kcal\u00b7mol-1.\r\nThese early transition metal-hydrocarbyl (M-R) BDEs correlate with the corresponding H-R\r\nBDEs (i.e. M-alkynyl > M-aryl > M-alkyl); however, the M-R BDEs increase more rapidly with\r\ns character than does the H-R BDEs. The origin of this effect is not known, but it is\r\nundoubtedly also responsible for the characteristically high M-H BDEs for transition metal\r\nhydride compounds. In an effort to probe the polarity of Sc-aryl bonds a series of\r\nscandocene derivatives capable of reversibly metallating at either of two differently\r\nsubstituted benzyl groups was prepared. The equilibrium constants for these metallated\r\nderivatives: (\u03b75,\u03b71-C5Me4CH2-o-C6H3-p-X)(\u03b75-C5Me4CH2C6H4-m-CH3)Sc \u21cc\r\n(\u03b75-C5Me4CH2C6H4-m-X)(\u03b75,\u03b71- C5Me4CH2-o-C6H3-p-CH3)Sc (X= H, CF3, NMe2) were\r\ndetermined. The small dependence of Keq on the nature of X suggests that the Sc-aryl\r\nbond is essentially covalent with only a slight ionic character.
" }, { "name": "Cannizzo, Louis Fiscel", "degree": "PhD", "year": "1988", "title": "Titanium Carbenes: Reactions with Selected Carbonyl Compounds and Ring-Opening Metathesis Polymerization of Cyclic Olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-080224143", "creators": [ { "name": { "family": "Cannizzo", "given": "Louis Fiscel" }, "id": "Cannizzo-Louis-Fiscel", "display_name": "Cannizzo, Louis Fiscel" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x7cz-vr92", "abstract": "The reaction of \"(C5H5)2Ti=CH2\" with acid anhydrides and imides yielded several useful organic transformations, including stereoselective ring formation applicable to alkaloid synthesis. Further studies developed an in situ preparation of Tebbe's reagent for large-scale methylenation of ketones and esters. Additionally, the reaction of proton sources with titanacyclobutanes was briefly surveyed and found to give both ring-opened and carbene-trapped products.
\r\n\r\nThe polymerization of strained cyclic olefins initiated by metal carbenes was investigated. Endcapping of polynorbornene produced by titanacyclobutanes was followed by UV and NMR. These analyses along with molecular weight measurements established the high efficiency of the endcapping reaction and the absence of polymer degradation during the reaction. The ring-opening polymerization of cyclopentene by titanacyclobutanes gave polymers that were close to being monodisperse. Kinetic studies showed that the rate of polymerization was first order in cyclopentene. Block copolymers (both A-B and A-B-A) containing monodispersed segments were synthesized with alternating \"hard\" and \"soft\" blocks. In these block copolymerization studies the polymerization of exo-dicyclopentadiene by titanacyclobutanes was shown to be a true \"living\" system. The polymerization of norbornene by the tungsten alkylidene, W(CHtBu)(NAr)[OCMe(CF3)2)2 (Ar=2,6-diisopropylphenyl), was investigated and found not to be a living system. Finally, the heteroolefin, N-methyl-7-azabenzonorbornadiene, was ring-opened metathesis polymerized and the resulting polymer dehydrogenated and doped to give a conducting material (10-3 to 10-4 Scm-1).
" }, { "name": "Chan, Hong-Man", "degree": "PhD", "year": "1988", "title": "Numerical Study of Quiescent and Sheared Sedimenting Suspensions", "advisor": "Leal, L. Gary; Herbolzheimer, Eric", "url": "https://resolver.caltech.edu/CaltechETD:etd-11062007-132325", "creators": [ { "name": { "family": "Chan", "given": "Hong-Man" }, "id": "Chan-Hong-Man", "display_name": "Chan, Hong-Man" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "co-advisor", "display_name": "Herbolzheimer, Eric" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/c07k-ws42", "abstract": "In this thesis we reported the results of our investigation into the behavior of particles settling in a quiescent and sheared suspensions using a molecular-dynamics-type simulator. The effects of varying the concentration over the range of 0.0025 to 0.05, and the shear rate between 0.0 and 20.0 on the average particle velocity, the diffusion coefficient, the variance of the particle velocity, the average particle-distribution function, the particle-distribution-correlation time, and the average velocity and variance autocorrelation times are reported. We found that the first correction to the sedimentation velocity for concentration (c) depended upon c rather than c1/3, and that no structure with a length scale of O(ac(-1)/3) developed in the particle-distribution function. Shearing the suspension caused a nonuniform particle-angular distribution to form, and the particle correlation times and the diffusion coefficients to decrease. Using the diffusion coefficient from the simulations, we modelled the spreading of the interface between the supension and the clear fluid region. We found that the spreading of the interface could cause misinterpretation of the experimental measurements of the sedimentation velocity, and that this might explain the discrepancies among the experimental data.
\r\n\r\nIn building the simulator, we needed to determine what effects N, the number of particles used in the simulator, have on the simulation results. Neither the sedimentation velocity, nor the average particle-distribution function changed when N varied from 27 to 125. However, we found that both the variance of the particle velocity and the diffusion coefficent grew with N. We have shown that for an homogeneous suspension, these statistics will converge, although the number of particles needed may still be very large, especially in the low concentration range which we are interested in.
\r\n" }, { "name": "Claeys, Ivan Lode Andr\u00e9 Maria", "degree": "Masters", "year": "1988", "title": "Experimental and Numerical Study of Molecular Rotational Diffusion in Gel-Like Media", "advisor": "Arnold, Frances Hamilton; Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02122025-215432111", "creators": [ { "name": { "family": "Claeys", "given": "Ivan Lode Andr\u00e9 Maria" }, "id": "Claeys-Ivan-Lode-Andr\u00e9-Maria", "display_name": "Claeys, Ivan Lode Andr\u00e9 Maria" } ], "advisors": [ { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "advisor", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/fdsw-x095", "abstract": "The hindered rotational diffusion of biopolymers in porous or fibrous media\r\nplays a significant role in many industrial and natural processes. Nuclear magnetic\r\nrelaxation experiments can be used to investigate how the gel matrix impedes the\r\ntumbling of molecules trapped in its pores. Indeed, molecular motions influence\r\nthe relaxation rate by causing fluctuations of the local magnetic field experienced\r\nby the nuclear spins. Hence a measurement of relaxation times allows one to monitor\r\nthe rotational diffusion of rigid molecules in gels and to detect matrix-induced\r\nanisotropic behavior. Experiments examining the 31P relaxation of cGMP trapped\r\nin polyacrylamide gels showed more than a threefold decrease in the rotational diffusion\r\ncoefficient when the gel concentration was brought from zero to 30%. Similar\r\nexperiments in agarose gels prove that nuclear magnetic relaxation measurements\r\ncan effectively be used to extract valuable information about rotational diffusion\r\ninside gels.
\r\n\r\nA Stokesian dynamics simulation of molecular diffusion in fibrous environments\r\nwill complement the experimental studies. The mobility interactions between prolate\r\nspheroids in low Reynolds number linear flows have been derived. The expressions\r\nare exact at the level of forces, torques and stresslets, and the results are cast\r\nin a form suitable for numerical calculations. This extension of Stokesian dynamics\r\nto non-spherical particles forms the groundwork for computationally efficient,\r\nhydrodynamically accurate simulations of suspensions of rodlike particles.
" }, { "name": "Clawson, Leigh Ellen", "degree": "PhD", "year": "1988", "title": "Studies on the Reactivity of Titanocene Alkylidenes and Titanocene Alkyl Chlorides", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01172013-151800515", "creators": [ { "name": { "family": "Clawson", "given": "Leigh Ellen" }, "id": "Clawson-Leigh-Ellen", "display_name": "Clawson, Leigh Ellen" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/a114-qy61", "abstract": "The scope and limitations of the reaction of titanocene methylidene with ketones were investigated. Easily enolizable ketones are methylenated quantitatively and isolated in high yield. This reagent also demonstrates chemoselectivity for ketones over esters and regioselectivity for less hindered ketones. Enolates are produced by proton transfer to the methylidene from very sterically (but not particularly acidic) ketones.
\r\n\r\nA simple one-pot method for the production of a geminal dimethylated center from a ketone and two equivalents of titanocene methylidene has been developed. This is a very sterically restricted process that is complementary to similar reactions using other organometallic reagents.
\r\n\r\nThe heterocyclic compounds, benzothiazole and benzoxazole, react with titanocene methylidene, presumably to form aza-metallacycles, which then undergo a \u03b2-elimination to form novel metallacycles. This reaction is not general for other compounds with an X-C=N linkage (X=O, S).
\r\n\r\nFundamental processes involved in Ziegler-Natta polymerization have been investigated in a homogeneous Ti/Al-based model system. Lewis acid catalyzed olefin insertion was studied with titanocene alkenyl chlorides. This reaction is irreversible. Deuterium-labelling experiments provide support for the direct insertion mechanism. The reverse process, \u03b2-alkyl elimination, was also examined with titanocene methylcyclobutyl chloride. This process is also irreversible with no competing \u03b2-hydrogen elimination.
\r\n\r\nNMR studies were performed to probe the nature of the interaction between titanocene alkenyl chlorides and alkyl aluminum chloride cocatalysts in the intramolecular olefin insertion. This system is a model for the active site in Ziegler-Natta polymerization. A Lewis acid concentration dependence on the reaction is observed. A possible explanation for this concentration dependence is presented.
" }, { "name": "Cline, Joseph Isaac, III", "degree": "PhD", "year": "1988", "title": "Photodissociation Dynamics of Triatomic van der Waals Molecules", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-155753371", "creators": [ { "name": { "family": "Cline", "given": "Joseph Isaac, III" }, "id": "Cline-Joseph-Isaac-III", "display_name": "Cline, Joseph Isaac, III" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/f38f-hb60", "abstract": "The spectroscopy and vibrational predissociation dynamics of triatomic van der Waals molecules are studied experimentally and theoretically at the state-to-state level of detail.
\r\n\r\nLaser-induced fluorescence spectra of HeCl2 are measured and the geometry and vibrational predissociation rate are obtained by a rotational analysis of the spectra and the determination of homogenous linewidths. A laser pump-probe technique is used to measure the vibrational and rotational state population distribution of the product Cl2. Although the Cl2 fragment has little rotational energy, its rotational distribution is bimodal. A symmetry selection rule for the dissociation results from the symmetry of the He \u2022 \u2022 \u2022 Cl2 van der Waals potential. Quantum mechanical calculations on a realistic potential energy surface are successful in modeling the experimental spectroscopy and dynamics.
\r\n\r\nThe vibrational predissociation dynamics of NeCl2 is also measured using the pump-probe technique. In this case the Cl2 fragment shows significantly more rotational excitation than in the dissociation of HeCl2. The rotational distributions are bimodal and are relatively independent of the energy of the prepared state. The NeCl2 binding energy is estimated from thresholds for the populations of fragment rotational levels.
\r\n\r\nThe vibrational predissociation of NeBr2 is studied by dispersing the fluorescence of the Br2 fragment. The product Br2 is rotationally cold. The closure of vibrational product channels is used to determine the binding energy of the molecule.
" }, { "name": "Da Silva, Nancy Anderson", "degree": "PhD", "year": "1988", "title": "Host-Plasmid Interactions and Regulation of Cloned Gene Expression in Recombinant Cells", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11062007-104408", "creators": [ { "name": { "family": "Da Silva", "given": "Nancy Anderson" }, "id": "Da-Silva-Nancy-Anderson", "display_name": "Da Silva, Nancy Anderson" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/pze3-dp83", "abstract": "Host-plasmid interactions and the regulation of cloned gene expression have been studied in recombinant cells, primarily Saccharomyces cerevisiae. The plasmids employed contain the inducible yeast GAL1, GAL10, or hybrid GAL10-CYC1 promoter cloned upstream of the Escherichia coli lacZ gene (for \u03b2-galactosidase). The promoters are controlled by the galactose regulatory circuit, and the yeast strains contain a reg1 mutation which interferes with catabolite repression. Therefore, cloned lacZ gene expression could be induced by galactose addition to glucose-containing medium. Batch and continuous fermentations were performed to study the effects of cloned gene product synthesis on the host cell, and to determine the important factors influencing the kinetics of growth, induction, and cloned gene product formation.
\r\n\r\nThe inducer (galactose) level had a strong influence on cloned lacZ gene expression. In batch culture, the initial specific rate of \u03b2-galactosidase synthesis increased with galactose concentration. A galactose concentration of 0.4% (in 0.4% glucose medium) was sufficient for high levels of expression that were approximately proportional to plasmid number (to an average plasmid number of at least 10). The relative galactose level, or galactose/glucose ratio, was also important, and cloned gene expression increased as this ratio increased.
\r\n\r\nPlasmid stability and promoter strength were also important factors. \u03b2-galactosidase production from an ARS1 plasmid was an order of magnitude lower than for the same plasmid with the 2\u00b5 origin. The effects of promoter strength were studied in both batch and continuous fermentations. Although at the expense of a growth rate reduction of 16%, the rate of expression from the stronger GAL1 promoter in batch culture was 3-5 times higher than for the GAL10 or GAL10-CYC1 promoters. In continuous culture, steady-state, \u03b2-galactosidase specific activity with the GAL1 promoter was 2-4 times greater than that for the GAL10-CYC1 promoter. Despite lower plasmid stability (72% versus 86%) and lower biomass concentration (0.98 versus 1.2 g/L), productivity was approximately 3 times higher with the stronger GAL1 promoter system.
\r\n\r\nCarbon-limited continuous fermentations were utilized to study the effects of dilution rate and induction of cloned gene expression on the recombinant system. Selection for faster growing cells, and the concentrations of glucose and galactose, were important in determining chemostat dynamics. For the GAL10-CYC1 promoter system, biomass concentration and \u03b2-galactosidase specific activity increased with decreasing dilution rate. The biomass trend is apparently due to the growth efficiency obtained at the various dilution rates, and the utilization of the inducer as an additional carbon source. Plasmid stability dropped after induction of lacZ gene expression and decreased with decreasing dilution rate. Despite lower plasmid stability and flow rate, overall productivity (activity/L/hr) was substantially higher at low dilution rate.
\r\n\r\nA temperature-sensitive (ts) strain of S. cerevisiae was constructed and characterized. In this strain, cloned lacZ gene expression can be induced by either a temperature-shift (T-shift) from 30\u00b0C to 35\u00b0C or by galactose addition. In batch culture at 35\u00b0C, cloned gene expression induced by T-shift was comparable or better than that observed for galactose induction under the same conditions. Higher levels were observed, however, for galactose induction at the preferred temperature of 30\u00b0C. At either temperature, the best levels of \u03b2-galactosidase synthesis were obtained for the ts strain in galactose-containing medium.
\r\n\r\nTheoretical yield factors have been estimated for recombinant cells to investigate the effect of plasmid-directed synthesis on metabolic stoichiometry. The analysis is based upon detailed accounting of ATP utilization for nutrient uptake and biosynthesis. The microorganism considered was E. coli; however, the method can be extended to other organisms for which metabolic ATP requirements can be reasonably estimated.
" }, { "name": "Dubs, Richard Leslie", "degree": "PhD", "year": "1988", "title": "Single- and Multiphoton Ionization Processes in Molecules", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-144750308", "creators": [ { "name": { "family": "Dubs", "given": "Richard Leslie" }, "id": "Dubs-Richard-Leslie", "display_name": "Dubs, Richard Leslie" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/63a3-d438", "abstract": "This dissertation is theoretical in nature and can be separated into two main areas: 1) single- and multiphoton ionization studies of a novel photoelectron effect, and 2) single-photon ionization studies of simple clusters as models for adsorbate photoemission. The first area centers on the phenomenon of circular dichroism in photoelectron angular distributions (CDAD). CDAD is shown to exist from oriented linear molecules, adsorbed atoms, and aligned atoms and molecules in the gas phase. The calculations presented here are the first to demonstrate the experimental feasability of CDAD studies. CDAD is shown to be a measurable effect which exists because the photoelectron collection direction can break the symmetry of these otherwise highly symmetric systems. As a direct result of the work presented here, CDAD has now been observed experimentally. Coupled with resonantly enhanced multiphoton ionization (REMPI), CDAD is shown to be a powerful probe of unknown alignment in gas phase atomic and molecular samples. The second area of research focuses on the simple oriented molecules NiCO and NiN\u2082 as models for the corresponding adsorbate systems. These simple models provide insight into features observed in the experimental angle-resolved photoemission spectra.
" }, { "name": "Evard, Dwight David", "degree": "PhD", "year": "1988", "title": "Structure and Dynamics of Several Rare Gas-Halogen van der Waals Molecules", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01222013-092417239", "creators": [ { "name": { "family": "Evard", "given": "Dwight David" }, "id": "Evard-Dwight-David", "display_name": "Evard, Dwight David" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/90wr-zj81", "abstract": "The structure and dynamics of several rare gas-halogen van der Waals molecules have been studied in the six laser-free jet expansion experiments which are described in this thesis. High resolution (0.01 cm\u207b\u00b9 spectra were obtained for one B \u2190 X transition of both NeBr\u2082 and NeCl\u2082, in order to determine the structure and lifetime of these complexes in the ground and excited states. NeCl\u2082 was studied extensively at moderate resolution (0.05 cm\u207b\u00b9 to probe the potential energy surface and the correlation of the van der Waals bond with the covalent bond. The lifetime of metastable vibrationally excited NeBr\u2082 X(\u03bd = 1) was determined directly by measuring its concentration as a function of distance from the source to the detection region. A pump-probe technique was used to study ArCl\u2082 to probe the structure and dynamics of the complex. Ar\u2099Cl\u2082 (n = 1, 2, 3) was studied to test the validity of the bond-bond additivity model of binding for the complex. This set of experiments has provided a great deal of information on the nature of the structure and dynamics of the complexes.
" }, { "name": "Hair, Sally Reid", "degree": "PhD", "year": "1988", "title": "Experimental and Theoretical Studies of van der Waals Molecule Photodissociation", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182013-160624319", "creators": [ { "name": { "family": "Hair", "given": "Sally Reid" }, "id": "Hair-Sally-Reid", "display_name": "Hair, Sally Reid" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/anb1-sr68", "abstract": "Three studies are reported on the vibrational predissociation of polyatomic van der Waals complexes. In the first, the ethylene dimer and rare gas-ethylene complexes are treated theoretically, using a local mode quantum mechanical technique. The ethylene dimer exhibits extensive mixing between the initially excited \u03bd\u2087 vibration and nearby combinations of the \u03bd\u2081\u2080 and van der Waals vibrations, while the rare gas- ethylene complexes do not. Mixing is extensive enough in the ethylene dimer to spread the oscillator strength of the \u03bd\u2087 vibration over a 10 cm\u207b\u00b9 region of the spectrum, in agreement with the experimentally observed band.
\r\n\r\nThe second study is a low resolution photodissociation experiment on the ethylene-methane complex. The spectra observed by exciting the \u03bd\u2087 ethylene vibration of C\u2082H\u2084-CH\u2084, C\u2082H\u2084-CH\u2082D\u2082, and C\u2082H\u2084-CD\u2084 all exhibit the same width. This indicates that the shapes and widths of the observed spectra are not determined by unresolved or power-broadened rotational structure. This result underscores the importance of vibrational coupling in the dissociation process.
\r\n\r\nThe final study is a laser pump-probe experiment on the Ne\u2082Cl\u2082 and Ne\u2083Cl\u2082 complexes. The Ne\u2082Cl\u2082 complex has a distorted tetrahedral geometry, as determined from high resolution, excitation spectra. Excitation shift arguments suggest a structure for Ne\u2083Cl\u2082 with the three neon atoms encircling the Cl\u2082 bond axis. The total van der Waals bond energy of the Ne\u2082Cl\u2082 complex is found to be between 145.6 and 148.6 cm\u207b\u00b9. When energetically possible, the Ne\u2082Cl\u2082 complex can dissociate by losing a single quantum of Cl\u2082 stretching energy. This indicates that the two neon atoms do not dissociate by two independent \"half-collisions.\" The Cl\u2082 fragment rotational excitation is found to depend only weakly on the energy available to the fragments.
\r\n\r\n\r\n" }, { "name": "Hannoun, Betty Jane Miller", "degree": "PhD", "year": "1988", "title": "Ethanol Production by Saccharomyces cerevisiae Immobilized in Calcium Alginate", "advisor": "Stephanopoulos, Gregory N.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11082007-092627", "creators": [ { "name": { "family": "Hannoun", "given": "Betty Jane Miller" }, "id": "Hannoun-Betty-Jane-Miller", "display_name": "Hannoun, Betty Jane Miller" } ], "advisors": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "advisor", "display_name": "Stephanopoulos, Gregory N." } ], "committee": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "chair", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/53yk-0e29", "abstract": "Glucose and ethanol diffusion coefficients in calcium alginate were measured in a diffusion cell using the lag time method. The diffusion coefficients decreased as the alginate concentration increased. Glucose and ethanol concentrations had no effect on the diffusion coefficients. Also the presence of 20% dead yeast cells had no effect on the diffusion coefficients.
\r\n\r\nExperiments were conducted under anaerobic conditions to determine the intrinsic, specific rates of growth, glucose uptake, and ethanol production for Saccharomyces cerevisiae immobilized in calcium alginate. The simultaneous processes of diffusion and reaction were analyzed in an alginate membrane to determine the intrinsic, specific growth and reaction rates from glucose and ethanol concentration measurements made outside the alginate phase. Under anaerobic conditions, the specific growth rate of immobilized S. cerevisiae decreased by 20% compared to the growth rate for suspended cells. The specific glucose uptake rate and specific ethanol production rate increased by a factor of four (4) compared to suspended cells. The ethanol yield remained the same and the biomass yield decreased to one-fifth (1/5) the yield for suspended cells.
\r\n\r\nFurther experiments were conducted under aerobic conditions to investigate the effects of dissolved oxygen concentration on the specific rates of growth, glucose uptake, and ethanol production of immobilized S. cerevisiae. Oxygen appears to affect immobilized cells similarly to the way it affects suspended cells.
\r\n\r\nA mathematical model was developed to quantify the effects of oxygen, glucose, and ethanol on the intrinsic, specific rates of growth, glucose uptake, and ethanol production of immobilized cells. The model was tested using S. cerevisiae immobilized in calcium alginate beads in a well-mixed batch reactor. The mathematical model accurately predicts the bulk fluid glucose and ethanol concentrations.
\r\n\r\nThe mathematical model for intrinsic, specific rates of growth, glucose uptake, and ethanol production was used to simulate the behavior of a continuous plug flow reactor and a continuous stirred tank reactor for ethanol production by S. cerevisiae immobilized in calcium alginate beads. Unsteady-state reactor operation was considered. The effects of bead size, feed glucose concentration, residence time, and dissolved oxygen concentration on reactor performance were investigated.
\r\n\r\n\r\n" }, { "name": "Heil, Ann Terese", "degree": "Masters", "year": "1988", "title": "Movement of a Spherical Brownian Particle Between Infinite Parallel Plates: Hindered Dispersion and Sedimentation", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192013-151818424", "creators": [ { "name": { "family": "Heil", "given": "Ann Terese" }, "id": "Heil-A-T", "display_name": "Heil, Ann Terese" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/gypy-h364", "abstract": "The dispersion of an isolated, spherical, Brownian particle immersed in a\r\nNewtonian fluid between infinite parallel plates is investigated. Expressions are\r\ndeveloped for both a 'molecular' contribution to dispersion, which arises from\r\nrandom thermal fluctuations, and a 'convective' contribution, arising when a shear\r\nflow is applied between the plates. These expressions are evaluated numerically\r\nfor all sizes of the particle relative to the bounding plates, and the method of\r\nmatched asymptotic expansions is used to develop analytical expressions for the\r\ndispersion coefficients as a function of particle size to plate spacing ratio for small\r\nvalues of this parameter.
\r\n\r\nIt is shown that both the molecular and convective dispersion coefficients decrease\r\nas the size of the particle relative to the bounding plates increase. When the\r\nparticle is small compared to the plate spacing, the coefficients decrease roughly\r\nproportional to the particle size to plate spacing ratio. When the particle closely\r\nfills the space between the plates, the molecular dispersion coefficient approaches\r\nzero slowly as an inverse logarithmic function of the particle size to plate spacing\r\nratio, and the convective dispersion coefficent approaches zero approximately\r\nproportional to the width of the gap between the edges of the sphere and the\r\nbounding plates.
\r\n" }, { "name": "Hipes, Paul Gregory", "degree": "PhD", "year": "1988", "title": "Three Dimensional Atom-Diatom Reactive Scattering Calculations Using Symmetrized Hyperspherical Coordinates", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:01222013-110555654", "creators": [ { "name": { "family": "Hipes", "given": "Paul Gregory" }, "id": "Hipes-Paul-Gregory", "display_name": "Hipes, Paul Gregory" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2S8G-PJ87", "abstract": "The focus of this thesis is the use of symmetrized hyperspherical coordinate techniques in the accurate calculation of differential cross sections for the reactive collision of an atom with a diatomic molecule in three-dimensional space. A single set of symmetrized hyperspherical coordinates treats all regions of configuration space in an equivalent inelastic scattering problem which is conceptually and computationally easier to handle.
\r\n\r\nThe work described here represents the first successful application of any accurate hyperspherical coordinate methodology to atom-diatom reactive scattering in three-dimensional space. This methodology has permitted the calculation of zero total angular momentum (J = 0) partial wave transition probabilities and associated phases over a significantly larger range of collision energies (up to 1.6 eV total energy) than previously possible for the system H + H\u2082. The numerical stability of the treatment is sufficiently high to permit the first lifetime matrix analysis of the resonance structure of H + H\u2082 based on scattering matrices from our accurate calculations. This analysis reveals a series of 6 resonance states in the J = 0 partial wave, some of which have not been seen before. The symmetrized hyperspherical coordinate methodology is presented in detail. A selection of surface functions and scattering results for J = 0 H + H\u2082 using the LSTH potential energy surface are presented and discussed. In addition, a small number of results from the Porter-Karplus potential energy surface are also given.
\r\n" }, { "name": "Hu, Mickey ChienTsung", "degree": "PhD", "year": "1988", "title": "I. The E. coli Lac Operator-Repressor System is Functional for Control of Gene Expression in Animal Cells. II. Molecular Cloning and Characterization of the Mouse Skeletal Muscle (\u03b1) Actin Gene", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01232013-085319311", "creators": [ { "name": { "family": "Hu", "given": "Mickey ChienTsung" }, "id": "Hu-Mickey-ChienTsung", "display_name": "Hu, Mickey ChienTsung" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Wold", "given": "Barbara J." }, "id": "Wold-B-J", "role": "member", "display_name": "Wold, Barbara J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2a59-9p43", "abstract": "We have investigated the use of the E. coli lac operator-repressor system to regulate the expression of genes introduced into mammalian cells by gene transfer. We find that the bacterial lac repressor protein encoded in a suitable expression vector is synthesized in mammalian cells in culture, assembles into a tetramer, enters the nucleus to some extent, and represses expression of another gene that has one or several lac operator sequences inserted into any one of several sites in the promoter region of the gene. Derepression can be achieved by exposure of the cells to IPTG. From a practical point of view of an inducible genetic switch, this system confers an induction level of somewhere between 10- and 20-fold in most of the cases we have tested. That is not better than those that have been achieved with heat shock, mouse mammary tumor virus, and metallothionein promoters. There may, however, be some situations and some promoters for which the use of the lac operator system is advantageous. We have also shown that this lac control system can be used to regulate the expression of genes introduced into Xenopus oocytes by micro-injection.
\r\n\r\nAt present, we have been trying to revise this system by using a newly developed promoter containing a symmetric lac operator sequence inserted at the various strategic points within the human metallothionein IIA promoter and enhancer regions, which consist of several positive control elements, in order to achieve induction ratios of a factor of 100 or more. We have also generated a new lacI gene which encodes a repressor containing at its carboxyl terminus the nuclear localization signal of the SV40 large-T antigen. Overall, by combining the newly developed lac control promoters with the new repressor producing cell lines, we hope to generate an inducible expression system with large induction ratios that can be used as a general genetic switch in the future.
\r\n\r\nIn section II, the nucleotide sequence of the mouse skeletal muscle (\u03b1) actin gene is presented and discussed.
\r\n" }, { "name": "Iverson, Brent Lee", "degree": "PhD", "year": "1988", "title": "1. Nonenzymatic Cleavage of Single-Stranded DNA to Nucleotide Resolution. 2. Novel Base Specific DNA Cleavage Reactions", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01242013-083723752", "creators": [ { "name": { "family": "Iverson", "given": "Brent Lee" }, "id": "Iverson-Brent-Lee", "display_name": "Iverson, Brent Lee" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pd8h-vx39", "abstract": "Part 1
\r\n\r\nA new strategy for the complementary-addressed modification of nucleic acids was investigated involving the enzymatic incorporation of a modified 2'-deoxynucleotide 5'-triphosphate molecule into oligonucleotide strands. These modified 2'-deoxynucleotide 5'-triphosphate compounds (and hence the strands into which they were incorporated) carried a latent reactive group in the form of a methylthioether function. The methylthioether function was activated by treatment with cyanogen bromide to enable alkylation of a complementary nucleic acid strand. The alkylation was shown to involve methyl group transfer and upon piperidine treatment resulted in the cleavage of the DNA at essentially a single residue on the target strand. The system was found to be capable of cleaving oligonucleotides as well as long pieces (5386 bases) of single-stranded DNA to nucleotide resolution.
\r\n\r\nPart 2
\r\n\r\nTwo novel base specific DNA cleavage reactions were discovered and investigated. The first is an A specific reaction caused by K\u2082PdCl\u2084 at low pH. The second is a photochemical reaction with \"GG\" specificity caused by some nitroaromatic and Co(III) compounds. Reaction of DNA with K\u2082PdCl\u2084 at low pH followed by a piperidine workup produces specific cleavage at adenine residues. Product analysis revealed the K\u2082PdCl\u2084 reaction involves selective depurination at adenine, affording a gapping reaction analogous to the other chemical DNA sequencing reactions. Adenine residues methylated at the exocyclic amine (N6) react with lower efficiency than unmethylated adenine in an identical sequence. This simple protocol specific for A may be a useful addition to current chemical sequencing reactions. Photolysis of DNA in the presence of 4-nitroveratrole, 3-nitroanisole or Co(III) compounds such as Co(III)(NH\u2083)\u2086 followed by a piperidine workup produces cleavage of the DNA with \"GG\" specificity, that is the 5'-G of 5'-GG-3' sequences is preferentially attacked. Product analysis revealed that the aromatic guanine base is decomposed into numerous fragments, and the nitroaromatic compound is apparently not consumed in the reaction. An electron transfer mechanism is proposed to account for the photochemical reaction at 5'-GG-3' sequences.
" }, { "name": "Iverson, Sheila Anne", "degree": "PhD", "year": "1988", "title": "Blue Copper Proteins: Gene Synthesis and Expression", "advisor": "Dervan, Peter B.; Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01222013-153725842", "creators": [ { "name": { "family": "Iverson", "given": "Sheila Anne" }, "id": "Iverson-Sheila-Anne", "display_name": "Iverson, Sheila Anne" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "co-advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z0s5-h938", "abstract": "A new strategy has been developed to facilitate the total synthesis of genes. The approach involves the synthesis of segments of the gene which are cloned into a vector for amplification and proof-reading. The construction of the gene proceeds from both ends toward the middle. In the synthesis, a segment of the gene is cloned into the vector and amplified; the resulting vector now contains a newly cloned segment which importantly includes unique internal restriction sites. The vector can be opened at these sites to allow insertion of an additional segment of the structural gene. A combination of three procedures: opening, cloning, amplification, constitutes a \"step\" of the synthesis, and a sequence of such \"steps\" leads to the synthesis of the total gene.
\r\n\r\nMany unique restriction sites have been designed into the gene thusly synthesized, as their presence will greatly facilitate the use of cassette mutagenesis in subsequent structure/function studies of the protein encoded by the synthetic gene.
\r\n\r\nThis synthetic strategy has several attractive features. In principle it can be used for the construction of genes of essentially any length and, allows proof-reading and correction of errors at intermediate stages in synthesis. This approach thereby avoids some of the problems inherent in the more traditional strategy in which many segments of synthetic DNA are annealed, ligated together and inserted into a vector, followed by a hoped for isolation from the many species inevitably present in the resulting mixture of synthetic genetic material of a clone containing DNA with the desired sequence.
\r\n\r\nThis stepwise approach has been applied to the synthesis of a gene for the blue copper protein, plastocyanin, of poplar leaf. The synthetic gene has been expressed in a fusion with a region of protein A under control of the \u03bbR promoter.
\r\n" }, { "name": "Kang, In Seok", "degree": "PhD", "year": "1988", "title": "Bubble Dynamics and Breakup in Straining Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-11072007-112829", "creators": [ { "name": { "family": "Kang", "given": "In Seok" }, "id": "Kang-In-Seok", "display_name": "Kang, In Seok" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Saffman", "given": "Philip G." }, "id": "Saffman-P-G", "role": "member", "display_name": "Saffman, Philip G." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/y91q-ff03", "abstract": "The dynamics and breakup of a bubble in axisymmetric flow fields has been investigated using numerical and analytical techniques. In particular, the transient bubble deformation, oscillation, and overshoot effects are considered in conjunction with the existence of steady-state solutions.
\r\n\r\nTo explore the dynamics of a bubble with a high degree of deformation, a numerical technique suitable for solving axisymmetric, unsteady free boundary problems in fluid mechanics has been developed. The technique is based on a finite-difference solution of the equations of motion on a moving orthogonal curvilinear coordinate system, which is constructed numerically and adjusted to fit the boundary at any time. For example, the steady and unsteady deformations of a bubble in uniaxial and biaxial straining flows are examined for wide ranges of the Reynolds number and the Weber number. The computations reveal that a bubble in a uniaxial straining flow extends indefinitely if the Weber number is larger than a critical value (W > Wc). Furthermore, it is shown that a bubble may not achieve a stable steady state even at subcritical values of the Weber number if the initial state is sufficiently different from the steady state. Potential flow solutions for uniaxial straining flow show that an initially deformed bubble undergoes oscillatory motion if W < Wc, with a frequency of oscillation that decreases as the Weber number increases and equals zero at the critical Weber number.
\r\n\r\nIn contrast to the uniaxial straining flow problem, a bubble at a finite Reynolds number in a biaxial straining flow has a stable steady state even though the deformation is extremely large. However, it is found that a bubble in a biaxial straining flow in the potential flow limit has exactly the same steady-state shape as in a uniaxial straining flow and a critical Weber number for breakup exists. Comparison of the results for the cases of high Reynolds numbers with the potential flow results suggests that the potential flow solution does not provide a uniformly valid approximation to the real flow at a high Reynolds number in the biaxial straining flow.
\r\n\r\nAs a complementary analytical study to the numerical analysis, the method of domain perturbations is used to investigate the problem of a nearly spherical bubble in an inviscid, axisymmetric straining flow. The steady-state solutions suggest the existence of a limit point at a critical value of the Weber number. Furthermore, the asymptotic analysis for oscillation has provided a formula of oscillation frequency for the principal mode such as \u03c9\u00b2 = \u03c9\u00b2\u2080(1 - 0.31W), where \u03c9\u2080 is the oscillation frequency of a bubble in a quiescent fluid.
\r\n\r\nTo include the weak viscous effect on the oscillation, a general formula for viscous pressure correction for a spherical bubble in an arbitrary axisymmetric flow has been derived in terms of the vorticity distribution. This formula has been applied to obtain the drag coefficient CD = 48/R by directly integrating the normal stress over the surface for a spherical bubble in a uniform streaming flow at a high Reynolds number, which has so far been possible only via indirect macroscopic balances. The direct method also reveals that the drag coefficient up to O(R)\u207b\u00b9 depends only on the O(1) vorticity distribution right on the bubble surface, and is independent of the vorticity distribution inside the fluid.
\r\n\r\nFinally, a voidage bubble in a fluidized bed is considered in the low Reynolds number limit. The problem has been formulated as a generalized drop problem with one additional parameter. The analysis shows that the steady and unsteady deformations in the creeping flow limit are exactly the same as the conventional drop problem even though the flow fields are different. The effect of the additional parameter on deformation first appears when inertial effects are considered.
\r\n" }, { "name": "Khundkar, Lutfur Rahman", "degree": "PhD", "year": "1988", "title": "Microcanonical Rates of Unimolecular Reactions Studied by Time-Resolved Photofragment Spectroscopy", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-083918", "creators": [ { "name": { "family": "Khundkar", "given": "Lutfur Rahman" }, "id": "Khundkar-Lutfur-Rahman", "display_name": "Khundkar, Lutfur Rahman" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zfwr-rk30", "abstract": "The use of modern technology in the study of classic problems in chemistry has afforded researchers the opportunity to understand the dynamics of reactions on a molecular level. This thesis represents one such instance, where the combination of pulsed lasers and molecular beams has made the study of ultrafast reactions of isolated molecules possible.
\r\n\r\nThe optical technique is, in essence, a two pulse pump-probe method. One of the pulses resonantly excites the molecule to be studied, while the second one, delayed in time, measures the population in either the excited parent state or some quantum state of the product. The sample is cooled in a supersonic expansion and observed under collisionless conditions. Atomic and molecular species may be detected by laser-induced fluorescence (LIF) or resonantly-enhanced multiphoton ionization (REMPI), followed by mass-selective detection. The temporal evolution of the state being probed is mapped out as the delay between the pulses is varied. The resolution of this method is determined by the temporal widths of the two pulses, typically ~ 8 picoseconds in the studies presented here.
\r\n\r\nThe technique, termed Time-Resolved Photofragment Spectroscopy (TRPS), has been used to study a number of unimolecular reactions under collisionless conditions. Microcanonical rates of the reaction NCNO \u2192 CN + NO have been measured for excitation energies near threshold. The rates are compared with predictions of various statistical theories, including a recently proposed variational method. State-selected studies of the production of iodine atoms in the UV photodissociation of 1,2\u2014diiodotetrafluoroethane indicate the existence of a bound intermediate, the iodoperfluoroethyl radical. Energy dependent rates show that the amount of internal energy in the intermediate may be varied by changing excitation conditions, thereby affecting the rate of its decomposition. Time and frequency-resolved studies of the photodissociation of methyl iodide show evidence that perturbed species in a dissociating system (so-called transition-state species) may be observed by this technique.
" }, { "name": "Klippenstein, Stephen Jacob", "degree": "PhD", "year": "1988", "title": "Theoretical Studies of Chemical Reaction Dynamics", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062013-161416978", "creators": [ { "name": { "family": "Klippenstein", "given": "Stephen Jacob" }, "id": "Klippenstein-Stephen-Jacob", "display_name": "Klippenstein, Stephen Jacob" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/dbrd-wj15", "abstract": "In this thesis theoretical models a.re developed and/or applied to the study of the dynamics of a variety of chemical reactions. First, a semiclassical model is developed to describe the effect of mutual orientation of the donor and acceptor on the rate of electron transfer between two large aromatic groups. The next reaction considered is that of gas phase H-atom transfer reactions. In this case a comparison is made of two previously developed approximations for the treatment of the particular case of H-atom transfer between two heavy particles.
\r\n\r\nThe next topic involves the study of the rate of intramolecular vibrational redistribution of energy. First, an iterative procedure is developed for determining more and more accurate effective Hamiltonians for the description of the dynamics. The foundation of this method is the separation of the basis states into resonant and nonresonant sets followed by an adiabatic approximation for the dynamics of the off-resonant set. A second study involves the application of artificial intelligence techniques to the choice of a small set of basis states which are the states of greatest importance to the redistribution dynamics.
\r\n\r\nThe remainder of the thesis is devoted to the study of those unimolecular dissociation/free radical recombination reactions which contain highly flexible transition states. For these reactions, a method for determining the quantum partition function for the transition state in terms of path integral ratios is developed and applied to the study of the thermally activated methyl radical recombination. Subsequently, a method is developed for determining the number of states, for the transition state, at a given energy and angular momentum. The basis of the method is the use of conventional Euler angle coordinates in the Monte Carlo evaluation of phase space integrals. This method is applied to the NCNO, CH\u2082CO, and H\u2082O\u2082 photodissociation processes. Also presented is a discussion of both the trend of the location of the transition state with increasing energy and the possible influence of excited potential energy surfaces.
\r\n" }, { "name": "Korber, Bette Tina Marie", "degree": "PhD", "year": "1988", "title": "Regulation of Class I Genes by Interferons", "advisor": "Hood, Leroy E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01252005-085241", "creators": [ { "name": { "family": "Korber", "given": "Bette Tina Marie" }, "id": "Korber-Bette-Tina-Marie", "orcid": "0000-0002-2026-5757", "display_name": "Korber, Bette Tina Marie" } ], "advisors": [ { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "advisor", "display_name": "Hood, Leroy E." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "member", "display_name": "Hood, Leroy E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FWT2-VC76", "abstract": "Major histocompatibility (MHC) class I gene expression is increased in response to interferons. In order to identify critical regulatory regions in mouse MHC (H-2) class I genes, the 5' flanking region and the DNA downstream of the transcription initiation site were analyzed separately. The promoters of H-2Dd and H-2Ld were linked to the reporter gene chloramphenicol acetyl transferase (CAT). Conversely, the H-2Ld structural gene was linked to non-interferon regulated promoters. These constructs were transfected into several different cell lines, and their ability to respond to interferons was assessed. Both regions, 5' and 3' of the transcriptional initiation site, were able to independently contribute to the regulation of class I genes by interferons. The basal levels of expression, interferon inducibility. and the relative contributions of the 3' and 5' responses to overall interferon regulation, were cell-type dependent.
\r\n\r\nSequence analysis of the 5' flanking region of class I genes led to the identification of multiple DNA motifs that are highly homologous to regulatory elements found in other genes. The H-2Dd promoter contains a TATA bog, CAAT elements, enhancer regions, and an interferon consensus sequence that is found in the promoters of many genes that are regulated by interferons. Deletion analysis and expression studies of the H-2Dd promoter revealed several interesting regulatory features of the interferon consensus sequence. It was required for both type I (alpha and beta) and type II interferon (gamma) responses. In some cell types an additional sequence was required for a type I interferon response; this sequence is located 5' and adjacent to the interferon consensus sequence. Type II interferon action was independent of this upstream sequence in all cell-types tested. Therefore the promoter controlled response to interferons is complex and the nature of the response depends both on the type of interferon and the cell-type being tested.
\r\n\r\nWe have noted that an interferon consensus sequence homology exists in the promoters of interferon genes. As interferons have a capacity to be auto-regulatory, we propose a model of gene regulation by interferons that incorporates what our studies and others have shown about the regulation of class I genes by interferon, and what is known about the regulation of interferon genes themselves.
\r\n" }, { "name": "Kruppa, Gary Hermann", "degree": "PhD", "year": "1988", "title": "Photoelectron Spectroscopy of Reactive Intermediates", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02202013-105931312", "creators": [ { "name": { "family": "Kruppa", "given": "Gary Hermann" }, "id": "Kruppa-Gary-Hermann", "display_name": "Kruppa, Gary Hermann" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "chair", "display_name": "Weitekamp, Daniel P." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jytn-vs45", "abstract": "Photoelectron Spectroscopy (PES) has been used to investigate the structure and thermochemistry of a number of alkyl radicals and their corresponding carbonium ions. The radicals have been produced by flash vacuum pyrolysis of alkyl nitrites. The shape of the first band in the photoelectron spectrum of a free radical is related to the structural changes that take place in forming the carbonium ion from the radical. The ionization potentials obtained from the photoelectron spectra of the radicals are combined with gas phase ion thermochemistry data to obtain alkyl radical heats of formation. The thermochemical data thus obtained is used to discuss substituent and structural effects on the stability of radicals and carbonium ions. In many cases the thermolytic decomposition pathways of the alkyl radicals have been elucidated using PES. The application of the PES technique to the analysis of reactive intermediates present in heterogeneous thermolysis mixtures is also discussed.
\r\n\r\nChapter 1 presents an introduction to the technique employed in these studies, and a review of the studies performed in this laboratory. Chapter 2 presents results on the thermochemistry and structure of the 1- and 2-adamantyl radicals. The tricyclic 1-adamantyl radical and carbonium ion are important as model bridgehead compounds, and the question of the amount of strain energy caused by the non-planarity of the radical and ion center has been of great interest. The first bands in the photoelectron spectra of the o-, m- and p-methylbenzyl radicals are presented in Chapter 3. The methyl substituent effects on the stabilities of the radicals and ions are discussed.
\r\n\r\nIn Chapter 4 results on investigations of heterogeneous processes in Chemical Vapor Deposition (CVD) systems using the chlorosilanes as feed gases are discussed. SiCl\u2082 is found to be the major silicon containing reactive intermediate produced by surface reactions at 600 - 1100 \u00b0C in CVD systems using dichlorosilane and trichlorosilane as feed gases.
\r\n\r\nChapter 5 presents the spectra of the 1- and 2-methylnaphthyl radicals. The relative stabilities of the radicals and carbonium ions are discussed based on proton affinities determined by Fourier transform mass spectrometric equilibrium studies, combined with ionization potentials obtained from photoelectron spectra of the radicals.
\r\n" }, { "name": "Laughlin, Daniel Lee", "degree": "PhD", "year": "1988", "title": "Control System Design for Robust Performance Despite Model Parameter Uncertainties: Application to Cross-Directional Response Control in Paper Manufacturing", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-11212007-094804", "creators": [ { "name": { "family": "Laughlin", "given": "Daniel Lee" }, "id": "Laughlin-Daniel-Lee", "display_name": "Laughlin, Daniel Lee" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" } ], "option_major": [ "chemeng" ], "doi": "10.7907/cps9-m559", "abstract": "The problem of robust performance analysis is solved for SISO control systems with uncorrelated model parameter uncertainties. The robust performance problem is formulated in a manner consistent with structured singular value \u00b5-analysis - for SISO systems this means restricting the magnitude of a weighted closed-loop sensitivity function. The solution to the problem is graphical in nature and well suited to a computer-aided controller-design procedure. It utilizes region boundaries on the complex plane that contain specified sets of process models at each frequency. An algorithm is presented for locating the region boundaries corresponding to model transfer-functions with uncertain real coefficients and time-delay. Convergence and containment properties of the algorithm are proven.
\r\n\r\nThe region-based analysis is combined with the Internal Model Control design procedure to form a controller synthesis method for robust performance. Tradeoffs between performance and robustness are transparent to the designer in the proposed synthesis method. Useful tables of controller parameters are presented in tabular form for a wide range of parameter uncertainty levels in a first-order-with-time-delay model. The controller resulting from the IMC design procedure is compared with the \u00b5-optimal controller. Although the new synthesis procedure is generally applicable to SISO systems, it can be used to design decentralized controllers for MIMO systems with uncertain scalar dynamics and symmetric interactions. The particular application of cross-machine-direction basis-weight control in paper manufacturing is discussed in detail. Robust performance and robust failure tolerance of desirable decentralized controllers for this system are proven.
\r\n" }, { "name": "Lederman, Steven Mark", "degree": "PhD", "year": "1988", "title": "Artificial Intelligence in Quantum Intramolecular Dynamics with Application to a Heavy Central Mass Problem", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03082013-103249804", "creators": [ { "name": { "family": "Lederman", "given": "Steven Mark" }, "id": "Lederman-Steven-Mark", "display_name": "Lederman, Steven Mark" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8333-3M02", "abstract": "This dissertation consists in effect, of three parts, each involving some aspect of intramolecular vibrational relaxation. The first section contains simple approximate statistical formulas for the density of vibrational and rovibrational states by symmetry type for non-linear molecules. A modified Whitten-Rabinovitch estimate of the density of states by symmetry type for linear molecules is also derived. Sample calculations are given, which serve to demonstrate the accuracy of all formulas given. In the second section, a 4-coordinate model is presented and is used to treat the vibrational energy redistribution in a molecule with a heavy central metal atom. Local group modes are identified using perturbation theory, and their dynamical separation and importance in analyzing energy redistribution is noted. A comparison of classical and quantum calculations on the model system is also given. In the third section, artificial intelligence methods are used to treat the time-evolution of intramolecular quantum dynamics. Comparison is made of several AI search algorithms and of evaluation functions, proposed here, in an application to the study of quantum intramolecular vibrational relaxation. The methods developed are applied to an 11-coordinate heavy central mass problem and are used to treat both vibrational quantum beats and \"dissipative\" intramolecular energy transfer.
" }, { "name": "Lester, Julia Catherine", "degree": "PhD", "year": "1988", "title": "Hydrodynamic Dispersion in Concentrated Sedimenting Suspensions", "advisor": "Brady, John F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08012006-113003", "creators": [ { "name": { "family": "Lester", "given": "Julia Catherine" }, "id": "Lester-Julia-Catherine", "display_name": "Lester, Julia Catherine" } ], "advisors": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "advisor", "display_name": "Brady, John F." } ], "committee": [ { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "chair", "display_name": "Brady, John F." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/hv2d-rx78", "abstract": "The hydrodynamic dispersion in concentrated sedimenting suspensions is investigated by numerical simulation. The particle Reynolds number is zero, and the P\u00e9clet number is infinite (the particles are non-Brownian). Particle trajectories are calculated by Stokesian dynamics. Stokesian dynamics is a molecular-dynamics-like simulation that provides an accurate representation of the suspension hydrodynamics. Detailed in this thesis is a technique that accelerates the convergence of the mobility interactions among particles in an infinite suspension. The simulations are of a monolayer of identical spheres sedimenting in the plane of the monolayer. Relative motion among the spheres arises from hydrodynamic interactions. The displacement related to this relative motion may constitute a random walk, giving rise to diffusive behavior of the spheres. This hydrodynamically induced self-diffusivity has been seen in sheared suspensions of non-Brownian, neutrally buoyant spheres.
\r\n\r\nResults of the numerical simulations show that the motion of spheres in sedimenting suspensions is also diffusive. The diffusion coefficient is relatively insensitive to the nature of the microstructure, as expressed by the pair-distribution function and the short-time, self-diffusion coefficient. The coefficient of diffusion decreases as the concentration increases for concentrated suspensions (it increases in the shear case). The ratio of the diffusion coefficient to the velocity variance of the spheres should be proportional to the time scale of the diffusive interactions. The diffusion time scale and the diffusion velocity scale (the square root of the velocity variance) both decrease as the concentration increases. In the shear case, the velocity scale (sphere radius multiplied by the shear rate) is independent of concentration, and the time scale (the product of the square of the concentration and the inverse of the shear rate) increases with increasing concentration. At the lowest concentrations, the spheres whose centers are separated by less than 2.05 radii prefer to align in the direction of sedimentation. At the highest concentrations, the preferred alignment is in the perpendicular direction.
" }, { "name": "Lewis, Michael Robert", "degree": "Masters", "year": "1988", "title": "Synthesis of modified ribonucleosides and oligoribonucleotide hybridization probes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132010-091809823", "creators": [ { "name": { "family": "Lewis", "given": "Michael Robert" }, "id": "Lewis-M-R", "display_name": "Lewis, Michael Robert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0x5t-me74", "abstract": "Two strategies for the construction of chemically modified, DNA cleaving oligoribonucleotide probes are described. In the first strategy, the synthetic substrate 5-(3-aminoallyl)uridine 5'-triphosphate (AA-UTP, 1) is reacted with RNA polymerase II to synthesize an aminoallyl-oligoribonucleotide, and the DNA cleaving moiety is introduced by nonspecific, posttranscriptional derivatization of the primary amine groups of the modified RNA. The second strategy involves the incorporation of a modified ribonucleoside 3',5'-bisphosphate, covalently tethered to a DNA cleaving functionality, into an oligoribonucleotide by reaction with T4 RNA ligase. A general method for the chemical synthesis of ribonucleoside 3',5'-bisphosphates was developed. Using this method, uridine 3',5'-bisphosphate (pUp, 2) was synthesized in six steps with an overall yield of 14%. A modified pUp derivative, 5-(3-(3-nitrophenoxy)acetamidoally1)-, uridine 3',5'-bisphosphate (NA-pUp, 12), was also synthesized with an overall yield of 3% for nine steps. The RNA polymerase substrate 1 was prepared by known methods and tested for compatibility with 17 RNA polymerase II in an in vitro \"run-off' transcription system. The incorporation of AA-UTP by 17 RNA polymerase was found to be less efficient than that of uridine 5'-triphosphate (UTP), in contrast to results reported for SP6 RNA polymerase. In vitro transcription synthesis of oligoribonucleotides and aminoallyl-oligoribonucleotides by SP6 RNA polymerase gave irreproducible results. In the Ti RNA polymerase system, transcription synthesis produced heterogeneous mixtures of oligoribonucleotides or aminoallyl-oligoribonucleotides. Analysis of the transcription products by high-resolution gel electrophoresis showed that the distribution of transcripts did not vary significantly with buffer conditions or template end structure.\r\n" }, { "name": "Loewenberg, Michael", "degree": "PhD", "year": "1988", "title": "A Theoretical Study of Reaction and Diffusion in Microstructured Materials", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-135258", "creators": [ { "name": { "family": "Loewenberg", "given": "Michael" }, "id": "Loewenberg-Michael", "display_name": "Loewenberg, Michael" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5tgx-2d57", "abstract": "A fundamental study of heterogeneous reaction and diffusion in random, microstructured materials has been conducted. A detailed, ensemble averaging approach has been developed for the analysis of diffusion-controlled reactions. The method was used to determine the reactant flux into a bounded or semi-infinite medium containing a dilute suspension of reactive, spherical particles under steady-state or transient conditions. The influence of the boundary was given explicit, detailed consideration and the results were compared with a mean-field treatment. Physical motivation is provided by the process of ash vaporization during pulverized coal combustion. The analysis was subsequently extended to study the decay of an initially uniform distribution of reactant which allows comparison with other theoretical approaches. The result suggests that the present method reproduces the solution to this well-known problem by a seemingly simpler, more physical approach. The configurational averaging technique was employed in a study of heterogeneous reaction in a porous material under diffusion-controlled conditions. The porous solid is assumed to have a bimodal pore structure with a random, isotropic distribution of cylindrical macro-pores. The results are relevant to the pulverized combustion of char from softening coals. In the diffusion-controlled limit, the results coincide with a simpler, single pore model.
\r\n\r\nA simplified model of char combustion has been developed which treats pore diffusion and growth coupled to gas-phase heat and mass transport. An efficient model-based algorithm was developed for the determination of oxidation rates from combustion data. These models were applied in two studies involving well-defined laboratory combustion experiments.
\r\n" }, { "name": "Mayo, Stephen Leon", "degree": "PhD", "year": "1988", "title": "Electron Transfer in Structurally Engineered Metalloproteins", "advisor": "Campbell, Judith L.; Gray, Harry B.; Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04292004-095332", "creators": [ { "name": { "family": "Mayo", "given": "Stephen Leon" }, "id": "Mayo-Stephen-Leon", "orcid": "0000-0002-9785-5018", "display_name": "Mayo, Stephen Leon" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "advisor", "display_name": "Campbell, Judith L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "co-advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "co-advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YJKW-3133", "abstract": "This thesis is concerned with experimental approaches for studying electron transfer in metalloproteins. The material presented traces the development of experimental techniques aimed at elucidating the mechanism of intramolecular metalloprotein electron transfer. The first chapter includes a reprint of an Inorganic Chemistry paper that describes the bimolecular reaction of small inorganic redox complexes with blue-copper proteins. The second chapter illustrates the use of covalently attached redox probes for studying rate-distance relationships. And the third chapter documents our progress in using genetic methods to structurally engineer yeast iso-1 cytochrome c into an idealized system for studying the distance dependence of intramolecular electron-transfer events.
" }, { "name": "McAdon, Mark Herbert", "degree": "PhD", "year": "1988", "title": "New Concepts of Metallic Bonding", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302009-113153689", "creators": [ { "name": { "family": "McAdon", "given": "Mark Herbert" }, "id": "McAdon-Mark-Herbert", "display_name": "McAdon, Mark Herbert" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Cross", "given": "Michael Clifford" }, "id": "Cross-M-C", "role": "member", "display_name": "Cross, Michael Clifford" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jtpr-6m88", "abstract": "This thesis presents results derived from ab initio wavefunctions, leading to new concepts of metallic bonding \u2014 real-space concepts that do not require \"thinking in reciprical (k) space.\" As the first step in this study of metallic bonding, Hartree-Fock and generalized valence bond wavefunctions are presented for ring clusters composed of monovalent atoms (Cu, Ag, Au, Li, and Na). These results show that one-dimensional metals need not exhibit Peierls instabilities, charge density waves, or spin density waves. In addition, magnon spectra calculated using various wavefunctions are compared with each other and with magnon spectia obtained with simple nearest-neighbor Ising and Heisenberg hamiltonians.
\r\n\r\nGeneralized valence bond wavefunctions for small metal clusters lead to the conclusion that, for metallic systems, the valence electrons occupy interstitial regions \u2014 bond midpoints for one-dimensional systems, triangular hollows for two-dimensional systems, and tetrahedral hollows for three-dimensional systems. The new concepts of metallic bonding are summarized by a set of rules for the valence sp electrons of metallic systems. These rules are used to derive the low-lying isomers of small metal clusters, and are expected to prove useful in predicting the chemistry and catalytic properties of such systems. Applying these rules to bulk metals leads to a new explanation of the solubility limits governing alloys of monovalent, divalent, trivalent, and tetravalent atoms. These rules are expected to prove valuable in describing the localized states in metals and alloys such as defects or interfaces.
\r\n" }, { "name": "McKinley, Lindsay K.", "degree": "Masters", "year": "1988", "title": "A study of several 1,3-cyclobutanediyls by ft-ir and computational techniques", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04062010-131315633", "creators": [ { "name": { "family": "McKinley", "given": "Lindsay K." }, "id": "McKinley-L-K", "display_name": "McKinley, Lindsay K." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/q9v0-5082", "abstract": "We have studied the photolytic decomposition of 2,3-diazabicyclo[2.2.1]hept-2-ene (Closs' azo) by FT-IR spectroscopy. While no transient species were detected, the photolysis product was exclusively bicyclopentane, as compared to Closs' result of 1:30 cyclopentene: bicyclopentane. The reasons for this difference are unclear; it may be due to our choice of argon for a matrix material. It has been previously shown that argon increases ISC rates compared to the first row elements.\r\n\r\nWe have also studied the photolytic decomposition of 1,4-diethy1-2,3-diazabicyclo[2.1.1]hex-2-ene. In this case, we have evidence that an intermediate exists, probably the diazenyl biradical formed by cleavage of a C-N bond. This intermediate has been detected by its decay to the starting diazene with a half-life of roughly 2 min. During the course of this investigation, the 1,4-diethyl diazene has been synthesized using a slight variation of methods previously developed in our group.\r\n\r\nWe have partially redesigned the FT-IR spectrometer in order to facilitate our investigations. Specifically, we have used a lens and mirror system to allow for photolysis inside the spectrometer of compounds deposited on the Displex window. This adaptation greatly reduces the time required for spectral acquisition.\r\n\r\nFinally, we have undertaken an ab initio study of the biradical 1,3-dietheny1-1,3-cyclobutanediy1 at the Hartree-Fock level. The results of the study show a high concentration of spin density on the ring carbons of the triplet. This difference with experimental results might be ameliorated by an inclusion of configuration interaction, specifically an MCSCF treatment." }, { "name": "Northrop, Paul Scott", "degree": "PhD", "year": "1988", "title": "A Fundamental Study of Char Combustion: Changes in Particle Morphology during Oxidation", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11142007-092219", "creators": [ { "name": { "family": "Northrop", "given": "Paul Scott" }, "id": "Northrop-Paul-Scott", "display_name": "Northrop, Paul Scott" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Zukoski", "given": "Edward E." }, "id": "Zukoski-E-E", "role": "member", "display_name": "Zukoski, Edward E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5R3H-DV43", "abstract": "This thesis presents a study of the morphological changes that occur in selected coal chars during oxidation at low temperature (725K-875K) and at high temperature (1400K-1600K). Gas adsorption and mercury porosimetry were the primary means by which these changes were monitored. An attempt was made to relate the observed reactivity of the char in oxygen to the evolving porous structure of the char. Initial pore structure was varied by using three different raw coals: a lignite, a subbituminous and high volatile A bituminous coal. In the case of the bituminous coal, pore structure was varied further by using different pyrolysis temperatures. Of course, while there were differences in the physical structure of the chars, there were differences in the chemical structure as well. In order to account for this, the chemical nature of the chars was monitored, using elemental analysis and oxygen chemisorption.
\r\n\r\nThe results of this study indicate that, at low temperatures, the rate of oxidation of the subbituminous and bituminous chars is proportional to the BET surface area beyond 20% conversion. The lignite char did not show such simple behavior because of the presence of large amounts of ash. For the high-temperature case, reaction appeared to be confined to the exterior of the particle and to the interior of the macropores.
\r\n\r\nTime-temperature histories of individual lignite char particles were obtained with a two-color pyrometer. A simplified model of single- particle-char combustion was used in conjunction with statistical analysis to infer kinetic parameters from the experimental time-temperature traces.
" }, { "name": "Parker, Garth Rockwood, Jr.", "degree": "PhD", "year": "1988", "title": "Determination of Nascent H\u2082 Rovibrational Distributions by Laser Induced Fluorescence: Applications to Formaldehyde Photodissociation and Hydrogen Exchange Reactions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122013-093032947", "creators": [ { "name": { "family": "Parker", "given": "Garth Rockwood, Jr." }, "id": "Parker-Garth-Rockwood-Jr", "display_name": "Parker, Garth Rockwood, Jr." } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ht1t-df04", "abstract": "Individual quantum states of H\u2082 have been detected using the technique of Laser Induced Fluorescence. This technique is extremely sensitive, with a detection sensitivity of 6 x 10\u2078 states cm\u207b\u00b3 in a probed volume of 0.029 cm\u00b3 with a signal-to-noise ratio of 3. This technique is also accurate. A spectrum of room temperature H\u2082 had a rotational temperature of 305.8 \u00b1 3.0 K. LIF detection of H\u2082 was used to study the H\u2082CO photodissociation reaction under essentially collision-free conditions. Following excitation of the rR\u2083 bandhead of the 2\u00b9\u20804\u00b3\u2080 transition at 30388.5 cm\u207b\u00b9, the principal product was ortho-H\u2082. States as high as v = 4, J = 5 were seen. Within the v = 1 channel, the rotational distribution peaked at J = 3. Following excitation of the rR\u2084 bandhead of the 2\u00b9\u20804\u00b3\u2080 transition at 30396.7 cm\u207b\u00b9, the principal product was para-H\u2082. This is the first report of the para-H\u2082 distribution following H\u2082CO dissociation. The rotational distribution is similar to that for ortho-H\u2082 and peaks at J = 4 within v = 1 channel. This result contradicts a recent theoretical calculation that predicted that the para-H\u2082 distribution would be bimodal with a minimum at J = 6. Quantitative analysis of higher vibrational levels was hampered by a lack of spectroscopic knowledge (both transition energies and intensities) when the the B̅ and C̅ states perturb each other. Attempts to use LIF to study the hydrogen exchange reaction have been unsuccessful.
" }, { "name": "Parmeter, John Ethan", "degree": "PhD", "year": "1988", "title": "The Organometallic Chemistry of the Ru(001) Surface", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182013-115728432", "creators": [ { "name": { "family": "Parmeter", "given": "John Ethan" }, "id": "Parmeter-John-Ethan", "display_name": "Parmeter, John Ethan" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xv82-qr39", "abstract": "The organometallic chemistry of the hexagonally close-packed Ru(001) surface has been studied using electron energy loss spectroscopy and thermal desorption mass spectrometry. The molecules that have been studied are acetylene, formamide and ammonia. The chemistry of acetylene and formamide has also been investigated in the presence of coadsorbed hydrogen and oxygen adatoms.
\r\n\r\nAcetylene is adsorbed molecularly on Ru(001) below approximately 230 K, with rehybridization of the molecule to nearly sp\u00b3 occurring. The principal decomposition products at higher temperatures are ethylidyne (CCH\u2083) and acetylide (CCH) between 230 and 350 K, and methylidyne (CH) and surface carbon at higher temperatures. Some methylidyne is stable to approximately 700 K. The preadsorption of hydrogen does not alter the decomposition products of acetylene, but reduces the saturation coverage and also leads to the formation of a small amount of ethylene (via an \u03b7\u00b2-CHCH\u2082 species) which desorbs molecularly near 175 K. Preadsorbed oxygen also reduces the saturation coverage of acetylene but has virtually no effect on the nature of the molecularly chemisorbed acetylene. It does, however, lead to the formation of an sp\u00b2-hybridized vinylidene (CCH\u2082) species in the decomposition of acetylene, in addition to the decomposition products that are formed on the clean surface. There is no molecular desorption of chemisorbed acetylene from clean Ru(001), hydrogen-presaturated Ru(001), or oxygen-presaturated Ru(001).
\r\n\r\nThe adsorption and decomposition of formamide has been studied on clean Ru(001), hydrogen-presaturated Ru(001), and Ru(001)-p(1x2)-O (oxygen adatom coverage = 0.5). On clean Ru(001), the adsorption of low coverages of formamide at 80 K results in CH bond cleavage and rehybridization of the carbonyl double bond to produce an \u03b7\u00b2(C,O)-NH\u2082CO species. This species is stable to approximately 250 K at which point it decomposes to yield a mixture of coadsorbed carbon monoxide, ammonia, an NH species and hydrogen adatoms. The decomposition of NH to hydrogen and nitrogen adatoms occurs between 350 and 400 K, and the thermal desorption products are NH\u2083 (-315 K), H\u2082 (-420 K), CO (-480 K) and N\u2082 (-770 K). At higher formamide coverages, some formamide is adsorbed molecularly at 80 K, leading both to molecular desorption and to the formation of a new surface intermediate between 300 and 375 K that is identified tentatively as \u03b7\u00b9(N)-NCHO. On Ru(001)-p(1x2)-O and hydrogen-presaturated Ru(001), formamide adsorbs molecularly at 80 K in an \u03b7\u00b9(O)-NH\u2082CHO configuration. On the oxygen-precovered surface, the molecularly adsorbed formamide undergoes competing desorption and decomposition, resulting in the formation of an \u03b7\u00b2(N,O)-NHCHO species (analogous to a bidentate formate) at approximately 265 K. This species decomposes near 420 K with the evolution of CO and H\u2082 into the gas phase. On the hydrogen precovered surface, the \u0397\u00b9(O)-NH\u2082CHO converts below 200 K to \u03b7\u00b2(C,O)-NH\u2082CHO and \u03b7\u00b2(C,O)-NH\u2082CO, with some molecular desorption occurring also at high coverage. The \u03b7\u00b2(C,O)-bonded species decompose in a manner similar to the decomposition of \u03b7\u00b2(C,O)-NH\u2082CO on the clean surface, although the formation of ammonia is not detected.
\r\n\r\nAmmonia adsorbs reversibly on Ru(001) at 80 K, with negligible dissociation occurring as the surface is annealed The EEL spectra of ammonia on Ru(001) are very similar to those of ammonia on other metal surfaces. Off-specular EEL spectra of chemisorbed ammonia allow the \u03bd(Ru-NH\u2083) and \u03c1(NH\u2083) vibrational loss features to be resolved near 340 and 625 cm\u207b\u00b9), respectively. The intense \u03b4g(NH\u2083) loss feature shifts downward in frequency with increasing ammonia coverage, from approximately 1160 cm\u207b\u00b9 in the low coverage limit to 1070 cm\u207b\u00b9 at saturation. In coordination compounds of ammonia, the frequency of this mode shifts downward with decreasing charge on the metal atom, and its downshift on Ru(001) can be correlated with the large work function decrease that the surface has previously been shown to undergo when ammonia is adsorbed. The EELS data are consistent with ammonia adsorption in on-top sites. Second-layer and multilayer ammonia on Ru(001) have also been characterized vibrationally, and the results are similar to those obtained for other metal surfaces.
" }, { "name": "Perez, Dianne Marie", "degree": "PhD", "year": "1988", "title": "Structure-Function Studies of Serine Hydrolases: Synthesis of a Gene for \u03b1-Lytic Protease and the Purification and Characterization of a Mutant \u03b2-Lactamase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182013-143408752", "creators": [ { "name": { "family": "Perez", "given": "Dianne Marie" }, "id": "Perez-Dianne-Marie", "display_name": "Perez, Dianne Marie" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/brjj-5n58", "abstract": "The author has constructed a synthetic gene for \u03b1-lytic protease. Since the DNA sequence of the protein is not known, the gene was designed by using the reverse translation of \u03b1-lytic protease's amino acid sequence. Unique restriction sites are carefully sought in the degenerate DNA sequence to aid in future mutagenesis studies. The unique restriction sites are designed approximately 50 base pairs apart and their appropriate codons used in the DNA sequence. The codons used to construct the DNA sequence of \u03b1-lytic protease are preferred codons in E. coli or used in the production of \u03b2-lactamase. Codon usage is also distributed evenly to ensure that one particular codon is not heavily used. The gene is essentially constructed from the outside in. The gene is built in a stepwise fashion using plasmids as the vehicles for the \u03b1-lytic oligomers. The use of plasmids allows the replication and isolation of large quantities of the intermediates during gene synthesis. The \u03b1-lytic DNA is a double-stranded oligomer that has sufficient overhang and sticky ends to anneal correctly in the vector. After six steps of incorporating \u03b1-lytic DNA, the gene is completed and sequenced to ensure that the correct DNA sequence is present and that no mutations occurred in the structural gene.
\r\n\r\n\u03b2-lactamase is the other serine hydrolase studied in this thesis. The author used the class A RTEM-1 \u03b2-lactamase encoded on the plasmid pBR322 to investigate the roll of the conserved threonine residue at position 71. Cassette mutagenesis was previously used to generate all possible amino acid substitutions at position 71. The work presented here describes the purification and kinetic characterization of a T71H mutant previously constructed by S. Schultz. The mutated gene was transferred into plasmid pJN for expression and induced with IPTG. The enzyme is purified by column chromatography and FPLC to homogeneity. Kinetic studies reveal that the mutant has lower kcat values on benzylpenicillin, cephalothin and 6-aminopenicillanic acid but no changes in km except for cephalothin which is approximately 4 times higher. The mutant did not change siginificantly in its pH profile compared to the wild-type enzyme. Also, the mutant is more sensitive to thermal denaturation as compared to the wild-type enzyme. However, experimental evidence indicates that the probable generation of a positive charge at position 71 thermally stabilized the mutant.
\r\n" }, { "name": "Petti, Michael Anthony", "degree": "PhD", "year": "1988", "title": "Studies in Molecular Recognition", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04272006-160954", "creators": [ { "name": { "family": "Petti", "given": "Michael Anthony" }, "id": "Petti-Michael-Anthony", "display_name": "Petti, Michael Anthony" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wvhj-nb98", "abstract": "A new class of water-soluble organic molecules containing hydrophobic binding sites is described. These host molecules, macrocycles assembled from 2,6-dihydroxy-9,10-dihydro-9,10-(1,2-dicarbomethoxy)-ethenoanthracene 8, can possess a hydrophobic cavity having a grossly right- (or left-)handed sense of twist. We believe this dissymmetric helical cavity could provide a means for chiral discrimination between the enantiomers of a racemate in aqueous solution.
\r\n\r\nBy varying the shape and size of the hydrophobic receptor site, such questions as the the roles of \u03c0-stacking, hydrophobicity and rigidity in molecular recognition are examined. The physical properties of these structures and their binding affinities for various guest molecules in aqueous solution are presented.
\r\n\r\nThese molecules have an especially high affinity for the aliphatic guest adamantyltrimethylammonium iodide (ATMA). In addition, this guest is an elegant probe of host geometry in the binding event. Several lines of evidence indicate that ATMA associates with these hosts in different geometries. Variable-temperature binding studies indicate that the binding of ATMA to hosts 4CMESO and 5CMESO displays a \"non-classical hydrophobic effect.\"
\r\n\r\nFurther studies with other alkyltrimethylammonium salts explore the role of guest shape, size, rigidity and charge on Ka. Studies involving variations of host structure suggest that rigidity, hydrophobicity, charge and donor-acceptor effects can significantly affect Ka.
\r\n\r\nTwo hosts of very similar structure, a p-xylyl-linked macrocycle (P-D) and a trans-1,4-dimethylenecyclohexyl-linked macrocycle (C6-L) are compared. Evidence for a new host geometry, efficient at encapsulating flat aromatic molecules, similar in shape to a naphthalene, is presented. These hosts efficiently bind aromatic heterocyclic guests (e.g., indole, quinoline, isoquinoline) and the N-methyl analogues. In this study, P-D displays an added affinity for the cationic guests. This additional ion-dipole effect is worth at least 1 kcal/mol in binding free energy. The binding of aromatic heterocycles is shown to be driven by donor-acceptor \u03c0-stacking interactions and hydrophobic effects.
\r\n\r\nThus, high binding affinities are achieved by a combination of forces without resorting to the use of highly lipophilic guests. These hosts maintain a clear separation of hydrophilic and hydrophobic groups, thereby eliminating the generally quite strong electrostatic interactions seen in other synthetic host systems.
\r\n\r\nSynthetic strategies to novel building blocks for new host structures are presented. These strategies could allow for the preparation of hosts having different solubility profiles, different aggregation properties and enhanced binding characteristics.
" }, { "name": "Reardon, Kenneth Frederick", "degree": "PhD", "year": "1988", "title": "Deactivation and Regeneration Kinetics during Bioconversions by Immobilized Clostridium acetobutylicum", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11072007-104847", "creators": [ { "name": { "family": "Reardon", "given": "Kenneth Frederick" }, "id": "Reardon-Kenneth-Frederick", "display_name": "Reardon, Kenneth Frederick" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Lidstrom", "given": "Mary E." }, "id": "Lidstrom-M-E", "role": "member", "display_name": "Lidstrom, Mary E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" } ], "option_major": [ "chemeng" ], "doi": "10.7907/REWV-EA22", "abstract": "The physiology and catabolic rates of calcium alginate-immobilized Clostridium acetobutylicum were studied under a variety of conditions, with an emphasis on the relationships between the activity and the environment of the immobilized cells during bioconversions of nitrogen-free glucose media and also during periods of activity regeneration under defined conditions. A number of experimental and analytical techniques were used to investigate these relationships, including measurements of product formation and substrate (glucose and nitrogen) consumption, quantification of immobilized cell concentrations by direct counts of several morphological types, and the in situ measurement of intracellular NAD(P)H-dependent fluorescence. In addition, a framework for the analysis of metabolic pathway rates from product and substrate concentration data was developed and applied to both suspended and immobilized cell cultivations of C. acetobutylicum.
\r\n\r\nTwo C. acetobutylicum strains were used in this work; one was the type strain, the sporogenous ATCC 824, and the other was ATCC 39236, which was found to be oligosporogenous. When the immobilized cell bioreactor feed was a medium deficient in nitrogen and required vitamin sources (to maintain the immobilized cells in a non-growing but viable state), the major causes of product-forming activity loss were initial cell lysis and sporulation; the latter effect was minor in the ATCC 39236 experiment. The addition of ammonia or ammonia plus vitamins to the feed during a regeneration period increased the total activity of the immobilized cell preparation, and this increased activity was not always due to cell growth.
\r\n\r\nThe patterns of product formation during repeated cycles of bioconversion (on nitrogen-free medium) and activity regeneration were discussed in terms of the changes in the adenylate energy charge that occurred in the course of alternating periods of nitrogen starvation and surplus. Product formation during bioconversion periods was affected by environmental conditions such as pH and the presence of some intermediate metabolites in the feed; these effects were related to distinct features of the C. acetobutylicum metabolic pathways. This work shows that knowledge of the metabolism and the underlying physiological responses of the cell to environmental changes can be used to understand and predict cell behavior.
\r\n" }, { "name": "Reyes, Vicente Mendoza", "degree": "PhD", "year": "1988", "title": "Transcription and Processing of Transfer RNA in S. cerevisiae", "advisor": "Abelson, John N.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112013-111743236", "creators": [ { "name": { "family": "Reyes", "given": "Vicente Mendoza" }, "id": "Reyes-Vicente-Mendoza", "display_name": "Reyes, Vicente Mendoza" } ], "advisors": [ { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "advisor", "display_name": "Abelson, John N." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Abelson", "given": "John N." }, "id": "Abelson-J-N", "role": "member", "display_name": "Abelson, John N." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3md6-cn17", "abstract": "A collection of studies on tRNA transcription and splicing in the yeast S. cerevisiae are presented. These studies employ a combination of recombinant DNA, oligonucleotide-directed mutagenesis and in vitro synthetic technologies applied using the reverse genetics approach. Chapter I introduces the reader to these topics. In Chapter II, an attempt to solve the puzzle of tandem tRNA gene transcription in yeast is described. This tandem, the S. cerevisae tRNAArg-tRNAAsp gene pair, is transcribed solely by use of the upstream gene promoter signals, giving rise to a dimeric precursor which is processed into two mature tRNA molecules, much like prokaryotic systems. A collection of specific point and deletion mutations were constructed to answer the question of why the downstream tRNAAsp gene is apparently inactive. Our results show that it is so only in this configuration; the tRNAArg and spacer sequences, which constitute its upstream flanking sequences in this arrangement, seem inhibitory to the independent activity of the tRNAAsp gene. Taken together, these results emphasize the importance of flanking regions in eukaryotic tRNA gene transcription. In Chapter III, the construction and characterization of a heterologous system for the in vitro synthesis of pre-tRNA are presented. A strong bacteriophage T7 promoter was fused to a S. cerevisiae pre-tRNAPhe gene. We show that pre-tRNAPhe is synthesized efficiently from this system by the cognate T7 RNA polymerase, and that this RNA has the correct sequence, mature terminii, and is spliced efficiently and accurately by our in vitro splicing system, which consists of highly purified tRNA splicing endonuclease and ligase enzymes. In Chapter IV, an extensive investigation on tRNA splicing substrate specificity is described. A collection of 15 carefully-designed mutant pretRNAPhe genes were constructed, and then transcribed and analyzed as above. We find that the endonuclease recognizes two highly conserved, surface residues in pre-tRNAPhe-U8 and C56-and probably contacts these bases during the splicing reaction. We also find that splice site selection by this enzyme is a function of the length of the anticodon stem, and thus proceeds by a simple distance measurement mechanism. We have evidence that this measuring process commences in the thoracic region of the pre-tRNA, where the endonuclease probably binds. Finally, we demonstrate that the highly conserved purine residue 3' proximal to the anticodon may be important for cleavage at the nearby 5' splice site.
\r\n" }, { "name": "Seressiotis, Alexandros", "degree": "PhD", "year": "1988", "title": "Mathematical Models Based on Molecular Processes of the Cell", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11132007-082406", "creators": [ { "name": { "family": "Seressiotis", "given": "Alexandros" }, "id": "Seressiotis-Alexandros", "display_name": "Seressiotis, Alexandros" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Bertani", "given": "Giuseppe" }, "id": "Bertani-G", "role": "member", "display_name": "Bertani, Giuseppe" } ], "option_major": [ "chemeng" ], "doi": "10.7907/a9re-yr49", "abstract": "A necessary first step in modeling the metabolic reaction network is a systematic procedure for determining the different reaction sequences which connect two metabolites. A software system (MPS) has been designed on the principles of artificial intelligence in order to address the problem of analysis and synthesis of metabolic pathways leading from one carbon-containing metabolite to another. MPS can be used to predict on a qualitative basis the effects of adding or deleting enzymatic activities to or from the cellular environment, to extract information about metabolic regulation, and to direct experiments in metabolic engineering. The main principles that have been used for the development of MPS are described along with case studies demonstrating the capabilities and potential applications of such a software system. The examples will examine carbon catabolic pathways and amino acid biosynthetic pathways. The catabolic pathways example concentrates on the conversion of glucose 6-phosphate to pyruvate. The output from MPS, which synthesized the classical catabolic pathways along with possible variations, leads to the identification of required genotypes/sets of enzymes that convert glucose 6-phosphate to pyruvate with different ATP and NAD(P)H coupling. The amino acid examples refer to the production of L-alanine from pyruvate and the identification of alternative pathways that perform this bioconversion.
\r\n\r\nThe appropriate use of controllable promoters and plasmid origins of replication provide an opportunity for identifying operating strategies that maximize productivity of unstable recombinant cultures. This is demonstrated by first developing a kinetic model for product formation in recombinant cultures that exhibit both segregational and structural instability, and subsequently by identifying operating conditions that maximize productivity with respect to the base case (uncontrollable promoter and plasmid origin of replication).
\r\n\r\nFinally, an approach is being made to examine the validity of traditional-macroscopic relationships for the description of equilibrium cellular processes. A model is described that addresses these processes from a statistical point of view and results of this model are compared with analogous results obtained from traditional methods applied to a subset of the reactions that characterize the control mechanisms of the lac promoter.
\r\n" }, { "name": "Shanks, Brent Howard", "degree": "PhD", "year": "1988", "title": "Reactor Input Manipulation for Developing Models for Catalytic Reactions", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11092007-141214", "creators": [ { "name": { "family": "Shanks", "given": "Brent Howard" }, "id": "Shanks-Brent-Howard", "display_name": "Shanks, Brent Howard" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pf3v-jt53", "abstract": "A variety of phenomenological experimental methods are employed to construct and validate kinetic models for heterogeneous catalytic reaction systems. Both static input and stimulus-response experiments are performed with particular emphasis placed on the novel feedback-induced bifurcation method. These techniques are applied to CO oxidation on Rh/Al\u2082O\u2083 and Ag/Al\u2082O\u2083 to identify kinetic models that are able to reproduce transient as well as steady-state experimental data.
\r\n\r\nStatic input experiments for CO oxidation on supported Rh, reduced at 170\u00b0C, reveal oscillatory responses for some inlet conditions. Two adsorbed CO species, linear and dicarbonyl forms, are observed with the linearly adsorbed CO shown from step-response experiments to be more reactive than CO adsorbed in the dicarbonyl form. The oscillations seem to be driven by surface temperature fluctuations rather than by interconversion between the adsorbed CO species.
\r\n\r\nSteady-state and step-response experiments at 147\u00b0C are used to estimate and to bound parameters in two reaction models that were previously postulated for CO oxidation on supported Ag. Data from feedback-induced steady-state bifurcation experiments are reproduced well by both models but neither reaction model is able to reproduce closed-loop Hopf bifurcation data. Also, long-time-scale transients observed in some step-response experiments are not accurately simulated by either model. A new model is proposed for CO oxidation on Ag/Al\u2082O\u2083, which incorporates a slow reversible step that forms an adsorbed oxygen species that blocks reaction sites. This model is able to reproduce the long-time-scale dynamics and a variety of cycled feedstream experiments.
\r\n\r\nThe feedback-induced bifurcation method is also applied to the CO oxidation reaction on supported Rh. After reducing the Rh/Al\u2082O\u2083 catalyst at 500\u00b0C, only linearly adsorbed CO is observed. Measurements of the fractional coverage of CO and the gas-phase CO are used for feedback control. The closed-loop bifurcation data are used to discriminate between two reaction models for CO oxidation on supported Rh, which are determined from steady-state experiments. Higher order dynamics resulting from closed-loop operation are also observed. The usefulness of various types of experimental feedback-induced bifurcations, as applied to model development, is discussed.
\r\n\r\nFinally, the feedback-induced bifurcation method is used to generate basis oscillations that are subjected to forced periodic operation. This provides a process in which entrainment behavior can be systematically examined. Experimental and simulated entrainment responses are compared and are found to be in close agreement.
\r\n" }, { "name": "Shepodd, Timothy Jon", "degree": "PhD", "year": "1988", "title": "Studies in Molecular Recognition: Hydrophobic Binding of Water-Soluble Guests by High Symmetry, Chiral Hosts", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03072013-150951099", "creators": [ { "name": { "family": "Shepodd", "given": "Timothy Jon" }, "id": "Shepodd-Timothy-Jon", "display_name": "Shepodd, Timothy Jon" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "member", "display_name": "Myers, Andrew G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/cgn8-6h63", "abstract": "A new class of high-symmetry, water-soluble receptors has been synthesized. The enantiomerically pure hosts are D\u2082-symmetric and are synthesized in 8 steps with an overall yield of 5-10%. An asymmetric Diels-Alder reaction between di-(+)-menthyl fumarate and 2,6-di-t-butyldimethylsiloxyanthracene leads to two diastereomeric Diels-Alder adducts that are elaborated to the key intermediates: (+)- and (-)-2,6-dihydroxy-11,12-dicarbomethoxy-9,10-ethenoanthracene. A number of hosts are synthesized from these intermediates when they are connected by variable linker units. These hosts possess chiral cavities (receptor sites) surrounded by an array of substituted aromatic rings.
\r\n\r\nThe ability of these hosts to complex water-soluble guests with different sizes, shapes, and degrees of preorganization has been quantified by NMR. The electron-rich hosts have a general affinity for electron-deficient guests. Hosts P and M show a moderate hydrophobic-type attraction towards a variety of aromatic and aliphatic guests (3-4 kcal/mol). Host P shows an added attraction towards trimethylammonium (TMA) substituted guests. In almost all cases studied, NMR-shift patterns indicate that when the hostguest complex forms, the polar TMA group lies deepest within the electron-rich, yet hydrophobic, receptor.
\r\n\r\nHosts P and M have a strong attraction towards adamantyltrimethylammonium iodide (ATMA). PR and PS have binding viaffinities of 6.6 \u00b1 0.2 kcal/mol with ATMA and bind the guest, encapsulated within the receptor site, in one guest orientation. MR and MS have binding affinities of 5.5 \u00b1 0.2 kcal/mol with ATMA and bind the guest in a non-specific fashion, yet they demonstrate a preferred attraction towards the TMA group of the guest.
\r\n\r\nAromatic-linked hosts PR, PS, MR and MS show an enhanced ion-dipole attraction towards charged quinolinium-type, flat aromatic guests as compared to neutral ones (P \u2248 1 kcal/mol and M \u2248 2 kcal/mol). Host C, with aliphatic linkers, does not experience an enhanced attraction to the charged flat guests.
\r\n\r\nHosts PR and PS demonstrate enantioselective binding with certain guests. For one case, a simple model for the cause of the enantioselectivity is presented.
" }, { "name": "Sluka, James P.", "degree": "PhD", "year": "1988", "title": "Design, Synthesis and Characterization of Sequence Specific DNA Cleaving Agents", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112013-144406216", "creators": [ { "name": { "family": "Sluka", "given": "James P." }, "id": "Sluka-James-P", "display_name": "Sluka, James P." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4mj0-ec33", "abstract": "Chapter I: Synthetic, Sequence Specific DNA Cleaving Peptides
\r\n\r\nSynthetic peptides based on the sequence specific DNA binding domain of Hin recombinase have been prepared which are equiped with ethylenediaminetetraacetic acid (EDTA) at the amino terminus. Covalent attachment of EDTA converts the sequence specific DNA binding pep tides into peptides which are capable of DNA strand scission in the presence of iron II, a reducing agent and molecular oxygen. The EDTA-equiped peptides cleave DNA at Hin binding sites and provide information on the nucleotide postion and groove identity of the modified amino acid residue when bound to DNA. The EDTA-peptides were also competent at DNA double strand cleavage, which is a useful characteristic for identifying binding sites on large DNA fragments (>5000 base pairs). A general procedure for the incorporation of an EDTA equiped lysine residue at any position in a synthetic peptide is also described.
\r\n\r\nResults with 22 synthetic peptides indicate that Hin specifically recognizes a minor groove 5'-AAA sequence in its binding site with the peptide sequence Arg-Pro-Arg. Furthermore, the minor groove recognition event contributes substantially to the overall binding affinity. The possibility that minor groove recognition of tracks of A's by the peptide sequence Arg-Pro- Arg (and similar sequences), may be a common recognition motif in sequence specific DNA binding proteins is discussed.
\r\n\r\nChapter II: Distamycin-Actinomycin Hybrid Affinity Cleaving Molecules
\r\n\r\nOne approach to the design of sequence specific DNA binding molecules that read large sequences of double helical DNA is to couple DNA binding units of similar or diverse base pair specificities. Covalent attachment of his- and tris-N-methylpyrrolecarboxamides (based on the sequence specific DNA binding antibiotics Netropsin and Distamycin) and an aromatic phenoxazone intercalator (based on the sequence specific DNA intercalator Actinomycin) creates hybrid DNA binding minor groove and intercalation compounds. Using the affinity cleaving method we find that a first generation hybrid, bis-(EDTA-distamycin-glycyl)phenoxazone, binds the sequence 5'-TTATGGTTAA-3' which is consistent with simultaneous minor groove binding of the two tripyrrolecarboxamide units and intercalation of the phenoxazone moeity. Along with the targeted trimeric binding, the first generation hybrid also gave substantial monomeric/ dimeric binding, and exihibited only modest sequence specificity on large DNA fragments.
\r\n\r\nIn an attempt to reduce monomeric and dimeric binding, a second generation hybrid was prepared. Replacement of one pyrrolecarboxamide with a \u03b3 aminobutyric acid moeity, bis(EDTA-netropsin-glycyl)phenoxazone, generated a hybrid molecule which showed a reduced tendency for monomeric and dimeric DNA binding modes. The second generation hybrid binds to sequences of the form 5'-(A/T)\u2084GT(A/T)\u2084-3' and 5'-(A/T)\u2084CT(A/T)\u2084-3' and showed substantially improved sequence specificity on large DNA fragments relative to the first generation hybrid.
\r\n\r\nChapter III: Bleomycin-Distamycin Hybrid Affinity Cleaving Molecules
\r\n\r\nHybrids of the sequence specific DNA binding bithiazole domain of Bleomycin and tris-N-methylpyrrolecarboxamide of Distamycin are described. The hybrids address the issue of whether or not the bithiazole unit of the GC specific Bleomycin is a minor groove binding function. By the affinity cleaving method we find that hybrids in which the bithiazole is attached to either the amino or carboxy terminus of the tris-N-methylpyrrolecarboxamide, do not significantly alter the sequence specificity of the pyrrolecarboxamide domain. The results indicate that either the bithiazole unit is not a minor groove binding function in the same sense as the tripyrrolecarboxamide, or, alternatively, the bithiazole does not include all of the required sequence specific DNA recognition elements of Bleomycin.
\r\n\r\nChapter IV: Studies in Metalloporphyrin Mediated Affinity Cleaving
\r\n\r\nMetalloporphyrins are known to cause DNA strand scission using a variety of central metals, and various reducing and oxidizing cofactors. To investigate if a metalloporphyrin can replace an EDTA\u2022Fe chelate in an affinity cleaving molecule, a metalloporphyrin-Distamycin (PD) was prepared. PD\u2022Fe showed very inefficient DNA cleavage compared to EDTA\u2022Fe equiped affinity cleaving compounds. Additionally, PD\u2022Fe showed no detectable sequence specific DNA cleaving ability. PD\u2022Fe was also less efficient at DNA strand scission than ferriprotoporphyrin itself, which indicates that the DNA binding domain (tripyrrolecarboxamide) and cleaving domain (metalloporphyrin) are interfering with each other\u2019s function in the affinity cleaving compounds.
\r\n" }, { "name": "Snyder, \u200cGary James", "degree": "PhD", "year": "1988", "title": "2,4-Dimethylene-1,3-Cyclobutanediyl and 2,4-Dimethylenebicyclobutane. Synthesis, Spectroscopy, and Reactivity of a Triplet Biradical and Its Covalent Isomer", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202013-082024971", "creators": [ { "name": { "family": "Snyder", "given": "\u200cGary James" }, "id": "Snyder-\u200cGary-James", "display_name": "Snyder, \u200cGary James" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4ftp-kr64", "abstract": "The preparation and direct observation of triplet 2,4-dimethylene-1,3-cyclobutanediyl (1), the non-Kekul\u00e9 isomer of benzene, is described. The biradical was generated by photolysis of 5,6-dimethylene-2,3-diazabicyclo[2.1.1]hex-2-ene (2) (which was synthesized in several steps from benzvalene) under cryogenic, matrix-isolation conditions. Biradical 1 was characterized by EPR spectroscopy (\u200c\u200c\u200c\u200c\u200c\u2502D/hc\u2502 = 0.0204 cm\u207b\u00b9, \u2502E/hc\u2502 = 0.0028 cm\u207b\u00b9) and found to have a triplet ground state. The \u0394ms = 2 transition displays hyperfine splitting attributed to a 7.3-G coupling to the ring methine and a 5.9-G coupling to the exocyclic methylene protons. Several experiments, including application of the magnetophotoselection (mps) technique in the generation of biradical 1, have allowed a determination of the zero-field triplet sublevels as x = -0.0040, y = +0.0136, and z = -0.0096 cm\u207b\u00b9), where x and y are respectively the long and short in-plane axes and z the out-of-plane axis of 1.
\r\n\r\nTriplet 1 is yellow-orange and displays highly structured absorption (\u03bbmax = 506 nm) and fluorescence (\u03bbmax = 510 nm) spectra, with vibronic spacings of 1520 and 620 cm\u207b\u00b9 for absorption and 1570 and 620 cm\u207b\u00b9 for emission. The spectra were unequivocally assigned to triplet 1 by the use of a novel technique that takes advantage of the biradical's photolability. The absorption \u0454 = 7200 M\u207b\u00b9 cm\u207b\u00b9 and f = 0.022, establishing that the transition is spin-allowed. Further use of the mps technique has demonstrated that the transition is x-polarized, and the excited state 1s therefore of B1g symmetry, in accord with theoretical predictions.
\r\n\r\nThermolysis or direct photolysis of diazene 2 in fluid solution produces 2,4-dimethylenebicyclo[l.l.0]butane (3), whose \u00b9H NMR spectrum (-80\u00b0C, CD\u2082Cl\u2082) consists of singlets at \u03b4 4.22 and 3.18 in a 2:1 ratio. Compound 3 is thermally unstable and dimerizes with second-order kinetics between -80 and -25\u00b0C (\u2206H\u2021 = 6.8 kcal mol\u207b\u00b9), (\u2206S\u2021 = -28 eu) by a mechanism involving direct combination of two molecules of 3 in the rate-determining step. This singlet-manifold reaction ultimately produces a mixture of two dimers, 3,8,9-trimethylenetricyclo[5.1.1.02,5]non-4-ene (75) and trans-3,10-dimethylenetricyclo[6.2.0.02,5]deca-4,8-diene (76t), with the former predominating. In contrast, triplet-sensitized photolysis of 2, which leads to triplet 1, provides, in addition to 75 and 76t, a substantial amount of trans-5,10-dimethylenetricyclo[6.2.0.03,6]deca-3,8-diene (77t) and small amounts of two unidentified dimers.
\r\n\r\nIn addition, triplet biradical 1 ring-closes to 3 in rigid media both thermally (77-140 K) and photochemically. In solution 3 forms triplet 1 upon energy transfer from sensitizers having relatively low triplet energies. The implications of the thermal chemistry for the energy surfaces of the system are discussed.
\r\n" }, { "name": "Stern, Jennifer E.", "degree": "PhD", "year": "1988", "title": "Aerosol Formation and Growth in Aromatic Hydrocarbon/NO\u2093 Systems", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12282004-153051", "creators": [ { "name": { "family": "Stern", "given": "Jennifer E." }, "id": "Stern-Jennifer-E", "display_name": "Stern, Jennifer E." } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "member", "display_name": "Grosjean, Daniel" } ], "option_major": [ "chemeng" ], "doi": "10.7907/417v-ke62", "abstract": "The formation of secondary organic aerosol in the atmosphere remains one of the most poorly understood aspects of the air pollution problem in urban areas. Photooxidation of gas-phase emissions produces low vapor pressure species that are converted to the aerosol phase either by homogeneous nucleation of new particles or by condensation onto existing particles. One of the goals in studying aerosol dynamics in atmospheric systems is to determine the factors that govern which of these two pathways dominates in the conversion of gas-phase species to the aerosol phase.
\r\n\r\nWe have conducted an extensive series of experiments aimed at elucidating the physics of atmospheric organic aerosol formation. An outdoor smog chamber was used to study the formation and growth of secondary aerosol resulting from the photooxidation of aromatic hydrocarbons (toluene, m-xylene, ethyl benzene, and 1,3,5-trimethyl benzene) in the presence of NO\u2093. In the experiments, particular emphasis was given to the effect of primary aerosol on the subsequent aerosol evolution in the system. We observed that with a sufficient number concentration of initial seed particles in the system, homogeneous nucleation could be suppressed and all gas-to-particle conversion occurred via condensation onto the seed particles.
\r\n\r\nAerosol yields by mass from the gas phase were calculated for each experiment. These yields were somewhat dependent on the initial hydrocarbon/NO\u2093 ratio in each experiment, which is an indication of the system reactivity. Average yields for each aromatic species were: toluene - 4.8%, m-xylene - 3.5%, ethyl benzene - 1.9%, and 1,3,5-trimethyl benzene - 2.4%. These results are in good agreement with previous determinations of aerosol yield for the toluene and m-xylene systems.
\r\n\r\nSeveral models were used to describe the observed aerosol dynamics. An integral model assuming a monodisperse aerosol, developed by Warren and Seinfeld (1984, 1985b), was used to determine apparent saturation vapor pressures of condensible species from the observations of nucleation events. Overall predictions of final number concentrations with the integral model, based on these saturation vapor pressures, were fairly close to the experimentally observed number concentrations.
\r\n\r\nAn analysis of the rate of aerosol growth was carried out for those experiments exhibiting uniform condensational growth. This analysis provided estimates for the gas-phase partial pressures of the condensible species, which could be compared with the integral model vapor pressures to give approximate saturation ratios during these periods of growth.
\r\n\r\nFull aerosol size distribution simulations were performed using the sectional model ESMAP (Warren and Seinfeld, 1985a), based on the work of Gelbard et al. (1980). Number concentrations resulting from these predictions were higher than those of the integral model, since the condensation rate on a polydisperse aerosol is smaller than that on a monodisperse distribution, leading to a higher nucleation rate. Comparisons of predicted and observed size, distributions during the course of each experiment were limited in accuracy by the numerical diffusion associated with current versions of the sectional model.
" }, { "name": "Stone, Howard Alvin", "degree": "PhD", "year": "1988", "title": "Dynamics of Drop Deformation and Breakup in Time-Dependent Flows at Low Reynolds Numbers", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02052007-081432", "creators": [ { "name": { "family": "Stone", "given": "Howard Alvin" }, "id": "Stone-Howard-Alvin", "display_name": "Stone, Howard Alvin" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Saffman", "given": "Philip G." }, "id": "Saffman-P-G", "role": "member", "display_name": "Saffman, Philip G." }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ER01-9F37", "abstract": "This thesis is concerned with time-dependent free-boundary problems at low Reynolds numbers. The primary objective is to use a combined experimental and numerical investigation to examine the deformation and breakup characteristics of a single phase Newtonian liquid drop suspended in a second immiscible Newtonian fluid undergoing a prescribed linear flow. Two related studies grew naturally out of this work and are also discussed here: (1) an analytic and numerical examination of the behaviour of concentric double emulsion droplets in linear flows, and (2) an introduction to the effect surfactants have on drop deformation in extensional flows.
\r\n\r\nSpecifically, the breakup of a Newtonian liquid drop is studied under well defined flow conditions. Experiments are performed in a computer-controlled four-roll mill and a detailed numerical investigation using the boundary integral method is presented. Particular attention is given to the dynamics of drop breakup and many experimental and numerical examples are shown of the actual fragmentation process. Transient effects associated both with nonspherical initial shapes and time-dependent velocity gradients are studied. Although the time-dependent velocity fields are limited to step changes in flow conditions, these investigations provide valuable insight into the breakup phenomenon and are a necessary first step toward understanding more complicated flow situations. The effects of viscosity ratio, flow-type and capillary number are discussed thoroughly. Overall, these studies of drop breakup provide a nice illustration of the influence of an interfacial-tension-driven flow that arises because of curvature variations along the fluid-fluid interface (the interfacial tension is constant). The interaction of this interfacial-tension-driven flow with the prescribed time-dependent velocity field produces very interesting breakup processes, often without large scale stretching of the drop. Also, for highly elongated drops, finite-amplitude capillary waves are observed experimentally and numerically.
\r\n\r\nThe study of drop deformation and breakup leads naturally to consideration of other systems involving deformable miscrostructures. Double emulsion droplets, which arise in applications involving liquid membranes, are frequently treated by drawing analogies with the known behaviour of single phase droplets. We present a fundamental investigation of concentric double emulsion drops in extensional flows. The analytic results allow calculation of the first effects of flow-induced deformation and the effective viscosity of a dilute emulsion of these particles. The analysis suggests interesting deformation and interaction of the two drop surfaces so a numerical investigation of the finite deformation of these particles is described. The critical capillary number for breakup is determined, the dependence on physical and flow parameters is outlined and possible mechanisms for breakup are discussed that differ from the single phase droplet results. Finally, the effect of different flow-types, i.e., uniaxial or biaxial extensional flows, is shown in some instances to suggest breakup of the inner droplet even though the outer droplet maintains a steady shape.
\r\n\r\nThe thesis closes with an introduction to the effect surface-active agents have on drop deformation. Because the distribution of surfactant along the fluid-fluid interface produces interfacial tension variations, the calculation of the drop shape as a function of time is intimately coupled with the convection and diffusion of surfactant along the drop surface. We present an approximate numerical procedure to study finite deformations and surfactant transport. The results are not extensive but suggest several interesting aspects of the deformation of drops due to the presence of surfactant.
\r\n" }, { "name": "Stoos, James Arthur", "degree": "PhD", "year": "1988", "title": "Particle Dynamics near Fluid Interfaces in Low-Reynolds Number Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02022007-110333", "creators": [ { "name": { "family": "Stoos", "given": "James Arthur" }, "id": "Stoos-James-Arthur", "display_name": "Stoos, James Arthur" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" } ], "option_major": [ "chemeng" ], "doi": "10.7907/bdpc-8734", "abstract": "Numerical solutions for the creeping motion of a spherical particle in a linear axisymmetric straining flow normal to a deformable interface are presented for a range of viscosity ratios, capillary numbers and Bond numbers. The parameter ranges investigated have applications in areas of flotation (small interface deformation) and material processing (large interface deformation). The accuracy of previous solutions for flotation problems, which neglect interface deformation is considered, along with the magnitude and form of interface deformation \"defects\" that may appear in material processing applications involving fluids containing bubbles or small particles.
\r\n\r\nNumerical solutions for the equilibrium particle-interface configuration for a neutrally buoyant spherical particle contacting a deformable fluid/gas interface in a linear axisymmetric straining flow at low Reynolds number are presented for a range of contact angles and capillary numbers. These solutions may have applications both in flotation separation processes and in contact angle and surface tension measurement. In addition, the accuracy of simply combining previous results for particle detachment due to particle buoyancy with the results for particle detachment due to viscous forces is considered. The equilibrium configuration is especially sensitive to the inclusion of a small amount of flow for small contact angles and for capillary numbers near the critical capillary number.
\r\n\r\nTrajectories of small spherical particles around a spherical drop (bubble and solid) are calculated from an approximate solution employing a matched asymptotic expansion. Viscous interaction is seen to have a large effect on the trajectory around a solid collector and a small effect on the trajectory around a bubble. Previous solutions are found to be in error in their prediction of an increase in the capture efficiency because of viscous interactions; the capture efficiency decreases significantly in this case.
\r\n\r\nFinally, the trajectories of particles around bubbles and the capture of particles by bubbles is investigated experimentally.
" }, { "name": "Swager, Timothy Manning", "degree": "PhD", "year": "1988", "title": "Precursor Routes to Conducting Polymers from the Ring-Opening Metathesis Polymerization of Cyclic Olefins", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08152005-160834", "creators": [ { "name": { "family": "Swager", "given": "Timothy Manning" }, "id": "Swager-Timothy-Manning", "orcid": "0000-0002-3577-0510", "display_name": "Swager, Timothy Manning" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/KF6P-FC76", "abstract": "Chapter 1 provides an introduction to the field of conductive polymers. The perspective is that of a chemist who is also interested in the physics of conductive polymers. The concepts discussed in this chapter are referred to throughout the other chapters, and should be a good primer for newcomers to this field as well as a reference to the literature for others. This chapter sets the stage for the theme of this thesis, which is the use of soluble precursor polymers in the synthesis of conductive polymers. Recent work was cited in this chapter which is not available in existing reviews of conductive polymers.
\r\n \r\nThe method of ring-opening metathesis polymerization (ROMP) is discussed in Chapter 2. The concepts discussed therein are again referred to throughout the following chapters. The ideas of catalyst matching for different monomers are discussed, and particular emphasis is given to the steric requirements of the catalysts.
\r\n\r\nThe ROMP of derivatives of dimethylene cyclobutene is discussed in Chapter 3. However, the primary focus of the chapter is on the polymer polydiisopropylidenecyclobutene. This material is distinctly different from other conductive polymers in the fact that it has a structure consisting of triene units that are mutually orthogonal to each other. A detailed study of this material with a variety of spectroscopies and measurements is presented.
\r\n \r\nThe synthesis of polybenzvalene, and the isomerization of this material to polyacetylene, is discussed in Chapter 4. This work constitutes a new precursor method to this fundamentally important polymer, as well as a demonstration of the far reaching scope of ROMP. Polybenzvalene is also a high energy material and has unusual explosive properties which are also discussed.
\r\n\r\nIn Chapter 5, new precursor routes to conductive polymers based on the elimination and hydrolysis of ketals are presented. This work has been primarily focused on structural chemistry and how to best transform the precursor polymers into conductive polymers. The majority of the effort has been focused on the, poly (quinone bisketals); however, another example of this concept is presented briefly.
\r\n" }, { "name": "Treco, Brian G. R. T.", "degree": "PhD", "year": "1988", "title": "Production of Transition Metal Oxidants through Design and Synthesis of Polyanionic Chelating Ligands", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132013-111018743", "creators": [ { "name": { "family": "Treco", "given": "Brian G. R. T." }, "id": "Treco-Brian-G-R-T", "display_name": "Treco, Brian G. R. T." } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/R8X9-3306", "abstract": "Ligand design criteria for stabilization of high valent metals have been developed\r\nand applied to osmium, copper, and cobalt. Ligands have been designed to have\r\nfavorable coordination properities, be noninnocent, and be resistant to oxidative\r\ndegradation.
\r\n\r\nA new subset of ligands has been synthesized, these being called Class II polyanionic\r\nchelating (PAC) ligands. These ligands possess two N-amido donors and two\r\nalkoxy donors. Both units have pKa's of approximately 18 and so would be expected\r\nto be very powerful donors. A number of ligands of this type have been developed\r\nwith 5,5,5; 5,6,5; 6,5,6; and 6,6,6 coordination geometries. The key steps in all of\r\nthe syntheses are coupling of highly hindered carboxylic acids with highly hindered\r\ndiamines.
\r\n\r\nIt is found that the 5,5,5; 5,6,5; and 6,5,6 coordinating ligands all stabilize\r\nOs(VI) monooxo compounds. The 5,6,5 and 6,5,6 coordinating ligands also stabilize\r\nOs(IV) complexes of octahedral geometry. The 6,6,6 ligands of this type do not\r\ncoordinate to osmium. Of the 5,6,5 ligands, the most interesting results have been\r\nobtained with H\u2084HMPA-DMP, or 2,4-bis-hydroxymethylpropamido-2,4-dimethyl-\r\n3-pentanone. Reaction of this with potassium osmate produces Os(VI)(\u03b7\u2074-HMPA-DMP)O. This molecule has been structurally characterized. It assumes a distorted\r\nsquare pyramidal geometry with the metal atom 0.8 \u00c5 above the plane formed by\r\nthe four donor atoms of the PAC ligand. The distortion appears to occur by pyramidalization\r\nat the amide nitrogen atoms, as is shown by the \u03c7N values (17.0\u00b0\r\nand 9.1\u00b0). Os(HMPA-DMP)O undergoes a number of interesting reactions. It is\r\ncleanly converted to the trans-K\u2082Os(\u03b7\u2074-HMPA-DMP)O\u2082 species with base; it can be\r\nelectrochemically reduced to a stable (although highly air-sensitive) Os(V) species;\r\nand it can be chemically reduced to produce trans-Os(IV)(\u03b7\u2074-HMPA-DMP)L\u2082 complexes\r\nwhere L can be a wide variety of pyridines. These Os(IV) compounds may\r\nbe oxidized chemically or electrochemically to produce Os(V) compounds. The\r\nOs(V)/(IV) potential may be precisely controlled by appropriate choices of L allowing\r\nproduction of tunable oxidants. It is also observed that these Os(IV) compounds\r\nreact with molecular oxygen to regenerate the Os(VI) monooxo species. The compounds\r\ncatalytically reduce molecular oxygen and oxidize triphenylphosphine to\r\ntriphenylphosphine oxide. Kinetic studies are consistent with a rate-determining\r\nstep involving dissociation of a pyridine ligand from the trans-Os(IV)(\u03b7\u2074-HMPA-DMP)\r\nL\u2082 species to generate a vacant coordination site to which oxygen may bind.\r\nThe reaction has been examined with a variety of pyridine ligands. The rate of\r\nair oxidation decreases with increased electron donor ability of substituents on the pyridine ring, kobs being 1.9(1) X 10\u207b\u2076 min\u207b\u00b9 for the compound synthesized from\r\n4-bromopyridine and kobs for compounds synthesized with dialkylaminopyridines being\r\nvirtually too small to measure. Similar Os(VI) monooxo and octahedral Os(IV)\r\ncompounds have been synthesized with a number of other Class II PAC ligands.\r\nThe Os(IV) and Os(VI) compounds produced in this work have been compared to\r\nsimilar species produced with Class I PAC ligands.
\r\n\r\nThe Class II PAC ligands have also been used to stabilize trivalent copper.\r\nA number of such compounds have been synthesized (one of which, [TPP][Cu(\u03b7\u2074\r\n-HMPA-B)]) has been structurally characterized) and compared with the corresponding\r\nClass I compounds. While no Cu(III)-Class I PAC complexes were stable (although\r\nreversible Cu(III) /(II) were observed in these cases), the Class II PAC ligands\r\nled to stable Cu(III) complexes, exhibiting Cu(III) /(II) potentials as low as -1.06 V\r\nvs Fe\u207a /Fe. Such potentials are much lower than have been seen for any complexes\r\nsynthesized to date with first-row donor atoms. The [TMA][Cu(III)(HMPA-DMP)]\r\ncomplex is an example of a Cu(III) compound with a completely innocent ligand\r\ncomplement. In this case, resonance structures from lower oxidation states are not\r\npossible thus enabling the oxidation state in this complex to be unambiguously\r\nassigned as +III.
\r\n\r\nThe Class II PAC ligands stabilize cobalt in the rare trivalent, square planar\r\nform. These compounds, while paramagnetic with two unpaired spins, may be\r\ncharacterized by proton NMR. One such complex, Na[Co(III)(HMPA-B)] has been\r\ncharacterized by X-ray crystallography. These compounds catalyze the epoxidation\r\nof styrene using iodosoarenes as the stoichiometric oxidants.
\r\n" }, { "name": "Witt, Stephan N.", "degree": "PhD", "year": "1988", "title": "The Mechanism of Cytochrome c Oxidase-Catalyzed Dioxygen Reduction", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03072013-140610712", "creators": [ { "name": { "family": "Witt", "given": "Stephan N." }, "id": "Witt-Stephan-N", "display_name": "Witt, Stephan N." } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "chair", "display_name": "Hopfield, John J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h1m5-ms09", "abstract": "Cytochrome c oxidase plays a primary role in energy transduction in most organisms. Free-energy is conserved by the oxidase in the form of a sizeable electrochemical hydrogen ion gradient across the inner mitochondrial membrane, which is generated during cytochrome c oxidase-catalyzed dioxygen reduction. In order to understand the energetics of cytochrome c oxidase-dependent energy conservation, the mechanism of cytochrome c oxidase-catalyzed dioxygen reduction must be understood in complete detail.
\r\n\r\nWe investigated the kinetics and mechanism of cytochrome c oxidase-catalyzed dioxygen reduction at low temperatures (180-210 K) in order to determine the kinetic barriers to intramolecular electron transfer and to elucidate the structural details of the dioxygen intermediates which form at the dioxygen reduction site during a single turnover. Our results show that electron transfer to the dioxygen reduction site is possible from either of the low-potential metal centers. Upon transfer of the third electron to the dioxygen reduction site at low temperatures two reactive dioxygen intermediates form in sequence at the dioxygen reduction site. In both intermediates, dioxygen is at the three-electron level of reduction. The kinetics of the conversion between the two reactive intermediates were examined in detail. The conversion between these two reactive species is highly activated, although en tropically assisted. Our results suggest that the cleavage of the dioxygen bond in the first three-electron-reduced intermediate results in the formation of the second three-electron-reduced intermediate. By studying the reoxidation of partially reduced cytochrome c oxidase at low temperatures, we also demonstrate that the rate of electron transfer within the oxidase is dependent on the nature of the trapped dioxygen intermediate at the dioxygen reduction site. Finally, the method used for the low-temperature kinetic experiments utilizes carbon monoxide as an inhibitor. Our investigation of the reoxidation of fully reduced cytochrome c oxidase reveals that carbon monoxide is not an innocent spectator molecule over the course of the reoxidation of the oxidase. Specifically, the dissociation of carbon monoxide from the binuclear dioxygen reduction site is the rate-limiting step at low temperatures; and the second three-electron-reduced intermediate is thought to oxidize carbon monoxide to carbon dioxide at low temperature to produce a novel, readily detectable state of the enzyme.
\r\n\r\nWe discovered that reactive partially reduced states of dioxygen may also be trapped at the dioxygen reduction site of cytochrome c oxidase at more ambient conditions (273-298 K) under a variety of experimental conditions. Combined chemical and spectroscopic results show that a reactive intermediate is produced at the dioxygen reduction site of cytochrome c oxidase when partially reduced cytochrome c oxidase is reoxdized with dioxygen and upon treatment of the oxidase with excess hydrogen peroxide. The trapped intermediate exhibits identical reactivity with carbon monoxide as the second three-electron-reduced intermediate which formed upon reoxidation of the fully reduced enzyme at low temperature. These results demonstrate that the same reactive three-electron-reduced dioxygen intermediate may be trapped at the dioxygen reduction site of cytochrome c oxidase either upon intramolecular electron transfer of the third electron to the peroxidic adduct, which is trapped at the binuclear site, or via an intermolecular reaction between the peroxidic adduct and hydrogen peroxide. This latter reaction is thought to involve the reduction of the enzymatic peroxidic adduct via a direct one-electron transfer from hydrogen peroxide. Our combined chemical and spectroscopic results are consistent with a binuclear dioxygen reduction site composed of a ferryl/cupric couple for the second three-electron-reduced dioxygen intermediate. Finally, we exploited the unique reaction between the second three-electron-reduced intermediate and carbon monoxide to probe the coordination sphere of the copper center at the reactive dioxygen reduction site of cytochrome c oxidase.
" }, { "name": "Youngquist, Robert Scott", "degree": "PhD", "year": "1988", "title": "Sequence Specific Recognition and Cleavage of DNA by Synthetic Molecules", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132013-142505168", "creators": [ { "name": { "family": "Youngquist", "given": "Robert Scott" }, "id": "Youngquist-Robert-Scott", "display_name": "Youngquist, Robert Scott" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "role": "chair", "display_name": "Myers, Andrew G." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Parker", "given": "Carl Stevens" }, "id": "Parker-C-S", "role": "member", "display_name": "Parker, Carl Stevens" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/m1pc-hr68", "abstract": "DNA recognition is an essential biological process responsible for the regulation of cellular functions including protein synthesis and cell division and is implicated in the mechanism of action of some anticancer drugs. Studies directed towards defining the elements responsible for sequence specific DNA recognition through the study of the interactions of synthetic organic ligands with DNA are described.
\r\n\r\nDNA recognition by poly-N-methylpyrrolecarboxamides was studied by the synthesis and characterization of a series of molecules where the number of contiguous N-methylpyrrolecarboxamide units was increased from 2 to 9. The effect of this incremental change in structure on DNA recognition has been investigated at base pair resolution using affinity cleaving and MPE\u2022Fe(II) footprinting techniques. These studies led to a quantitative relationship between the number of amides in the molecule and the DNA binding site size. This relationship is called the n + 1 rule and it states that a poly-N-methylpyrrolecarboxamide molecule with n amides will bind n + 1 base pairs of DNA. This rule is consistent with a model where the carboxamides of these compounds form three center bridging hydrogen bonds between adjacent base pairs on opposite strands of the helix. The poly-N-methylpyrrolecarboxamide recognition element was found to preferentially bind poly dA\u2022poly dT stretches; however, both binding site selection and orientation were found to be affected by flanking sequences. Cleavage of large DNA is also described.
\r\n\r\nOne approach towards the design of molecules that bind large sequences of double helical DNA sequence specifically is to couple DNA binding subunits of similar or diverse base pair specificity. Bis-EDTA-distamycin-fumaramide (BEDF) is an octaamide dimer of two tri-N-methylpyrrolecarboxamide subunits linked by fumaramide. DNA recognition by BEDF was compared to P7E, an octaamide molecule containing seven consecutive pyrroles. These two compounds were found to recognize the same sites on pBR322 with approximately the same affinities demonstrating that fumaramide is an effective linking element for N-methylpyrrolecarboxamide recognition subunits. Further studies involved the synthesis and characterization of a trimer of tetra-N-methylpyrrolecarboxamide subunits linked by \u03b2-alanine ((P4)\u2083E). This trimerization produced a molecule which is capable of recognizing 16 base pairs of A\u2022T DNA, more than a turn and a half of the DNA helix.
\r\n\r\nDNA footprinting is a powerful direct method for determining the binding sites of proteins and small molecules on heterogeneous DNA. It was found that attachment of EDTA\u2022Fe(II) to spermine creates a molecule, SE\u2022Fe(II), which binds and cleaves DNA sequence neutrally. This lack of specificity provides evidence that at the nucleotide level polyamines recognize heterogeneous DNA independent of sequence and allows SE\u2022Fe(II) to be used as a footprinting reagent. SE\u2022Fe(II) was compared with two other small molecule footprinting reagents, EDTA\u2022Fe(II) and MPE\u2022Fe(II).
\r\n" }, { "name": "Asselt, Allan van", "degree": "PhD", "year": "1987", "title": "Reactions of Oxygen Containing Ligands in the Coordination Sphere of Permethylhafnocene and Permethyltantalocene", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02192014-152435840", "creators": [ { "name": { "family": "Asselt", "given": "Allan van" }, "id": "Asselt-Allan-van", "display_name": "Asselt, Allan van" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "chair", "display_name": "Collins, Terrence J." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PF6E-KV88", "abstract": "A series of terl-butylperoxide complexes of hafnium, Cp*2Hf(R)(OOCMe3) (Cp* = ((\u03b75-C5Me5); R = Cl, H, CH3, CH2CH3, CH2CH2CH3, CH2CH2CH2CH3, CH2CHMe2, CH=CHCMe3, C6H5, meta-C6H3(CH2)2) and Cp*(\u03b75-C5(CH3)4CH2CH2CH2)Hf(OOCMe3), has been synthesized. One example has been structurally characterized, Cp*2Hf(OOCMe3)CH2CH3 crystallizes in space group P21/c, with a = 19.890(7)\u00c5, b = 8.746(4)\u00c5, c = 17.532(6)\u00c5, \u03b2 = 124.987(24)\u00b0, V = 2498(2)\u00c53, Z = 4 and RF = 0.054 (2222 reflections, I > 0). Despite the coordinative unsaturation of the hafnium center, the terl-butylperoxide ligand is coordinated in a mono-dentate ligand. The mode of decomposition of these species is highly dependent on the substituent R. For R = H, CH2CH3, CH2CH2CH3, CH2CH2CH2CH3, CH2CHMe2 a clean first order conversion to Cp*2Hf(OCMe3)(OR) is observed (for R CH2CH3, \u0394H\u01c2 = 19.6 kcal\u2022mol-1, \u0394S\u01c2 = -13 e.u.). These results are discussed in terms of a two step mechanism involving \u03b72-coordination of the terl-butylperoxide ligand. Homolytic O-O bond cleavage is observed upon heating of Cp*2Hf(OOCMe3) R (R = C6H6, meta-C6H3(CH3)2). In the presence of excess 9,10-dihydroanthracene thermolysis of Cp*2Hf(OOCMe3)C6H6 cleanly affords Cp*2Hf(C6H6)OH and HOCMe3 (\u0394H\u01c2 = 22.6 kcal\u2022mol-1, \u0394S\u01c2 = -9 e.u.). The O-O bond strength in these complexes is thus estimated to be 22 kcal\u2022mol-1.
\r\n\r\nCp*2Ta(CH2)H, Cp*2Ta(CHC6H5)H, Cp*2Ta(C6H4)H, Cp*2Ta(CH2=CH2)H and Cp*2Ta(CH2=CHMe)H react, presumably through Cp*2Ta-R intermediates, with H2O to give Cp*2Ta(O)H and alkane. Cp*2Ta(O)H was structurally characterized: space group P21/n, a= 13.073(3)\u00c5, b = 19.337(4)\u00c5, c = 16.002(3)\u00c5, \u03b2 = 108.66(2)\u00b0, V = 3832(1)\u00c53, Z = 8 and RF = 0.0672 (6730 reflections). Reaction of terlbutylhydroperoxide with these same starting materials ultimately yields Cp*2Ta(O)R and HOCMe3. Cp*2Ta(CH2=CHR)OH species are proposed as intermediates in the olefin hydride reactions. Cp*2Ta(O2)R species can be generated from the reaction of the same starting materials and O2. Lewis acids have been shown to promote oxygen insertion in these complexes.
" }, { "name": "Axup, Andrew William", "degree": "PhD", "year": "1987", "title": "Laser Flash Spectroscopy of Zinc/Ruthenium Myoglobins: An Investigation of Distance and Medium Effects on Photoinduced Long-Range Intraprotein Electron Transfers", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052019-103258317", "creators": [ { "name": { "family": "Axup", "given": "Andrew William" }, "id": "Axup-Andrew-William", "display_name": "Axup, Andrew William" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1a3m-hb31", "abstract": "An experimental investigation of the distance dependence of long-range intramolecular electron transfer in ruthenium-modified zinc myoglobins has been performed. The zinc/ruthenium-modified metalloproteins were prepared by substitution of zinc-mesoporphyrin IX diacid (ZnP) into four previously characterized pentaammineruthenium(III) (a5Ru) derivatives of sperm whale myoglobin (Mb). The derivatives are a5Ru(His-48)Mb, a5Ru(His-12)Mb, a5Ru(His-116)Mb, and a5Ru(His-81)Mb. Pulsed laser excitation of the zinc myoglobin produces the long-lived and highly reducing triplet excited state (3ZnP*). Electron transfer from this triplet to the ruthenium, 3znP*-Ru3+ \u2192 ZnP+-Ru2+ (\u0394E\u00b0 \u2245 0.8 V), was measured by time-resolved transient absorption techniques. The observed electron-transfer rates are 7.0 x 104, 100, 89, and 85 s-1 for the His-48, -12, -116, and -81 derivatives, respectively, at 25\u00b0C The electron-transfer distances were evaluated using computer modelling in which rotation about the C\u03b1-C\u03b2 bond of the imidazole side chain in the ruthenium-modified histidines is restricted by nonbonded repulsions with atoms at the protein surface. Recent crystallographic results for a5Ru(His-48)Mb indicate that the histidine has considerable rotational flexibility. The estimated accessible distances, both heme edge to inner coordination sphere ligand (e-e) and metal-to-metal (m-m), are as follows. For the His-48 derivative, the e-e range is 13.4-16.6 \u00c5 and the m-m range is 18.6-24.1 \u00c5; His-12 ranges are 22.1-22.4 \u00c5 and 28.8-30.4 \u00c5; His-116 ranges are 18.9-20.4 \u00c5 and 23.1-27.8 \u00c5; and His-81 ranges are 19.0-19.4 \u00c5 and 26.3-26.9 \u00c5. In addition, the orientation angles (\u03b8) of the electron-transfer pathways with relation to the heme plane at a position of closest approach are 25\u00b0 (His-48), 20\u00b0 (His-12), 35\u00b0 (His-116), and 25\u00b0 (His-81). Fitting the rate data to an exponential distance dependence yields the expression ket = 8 x 109 exp(-\u03b2(R-4)) s-1, where \u03b2 = 1.2 \u00c5-1 and R - 4 \u2265 0 (R is the minimum e-e distance in \u00c5). The electron-transfer rate in a5Ru(His-12)Mb(ZnP) is anomalously high (100 vs. 2 s-1 predicted by the rate-distance equation), thereby indicating that the 3ZnP*-Ru3+ electronic coupling may be enhanced by an intervening tryptophan residue that lies parallel-planar to the heme along the reaction pathway. Activation enthalpies calculated from the temperature dependences of the electron-transfer rates over the range 5-40\u00b0C are 1.7 \u00b1 1.6 (His-48), 4.7 \u00b1 0.9 (His-12), 5.4 \u00b1 0.4 (His-116), and 5.6 \u00b1 2.5 (His-81) kcal mol-1. Dynamic flexibility of the protein region containing His-48 may reduce the activation enthalpy with respect to the other more rigidly located derivatives.
" }, { "name": "Burger, Barbara J.", "degree": "PhD", "year": "1987", "title": "Olefin Insertion and \u03b2-Elimination Reactions of Permethylniobocene Olefin Hydride and Permethylscandocene Alkyl Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01162008-111854", "creators": [ { "name": { "family": "Burger", "given": "Barbara J." }, "id": "Burger-Barbara-J", "display_name": "Burger, Barbara J." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BJEC-TH82", "abstract": "Permethylniobocene styrene hydride complexes, Cp*2Nb(CH2=CHC6H4-m-X)H (Cp* = C5Me5, X = CH3, NMe2, CF3) have been prepared and their rates of olefin insertion measured by coalescence techniques. The rates compare favorably with those measured for the analogous para-substituted complexes, suggesting that electronic effects in the transition state are largely inductive in nature. The crystal structure of Cp*2Nb(CH2=CHC6H5)H was determined. The phenyl ring of the styrene is twisted out of resonance with the olefin to avoid unfavorable steric interactions with the bulky Cp* rings.
\r\n\r\nThe rates of ethylene insertion in the Sc-C bond for Cp*2ScR (R = CH3, CH2CH3, CH2CH2CH3 have been measured at low temperature by 13C NMR; the second order rate constants (M-1 sec-1, -80\u00b0C. The slow rate for the ScCH2CH3 complex is attributed to a ground state stabilization by a \u03b2-C-H interaction.
\r\n\r\nThe \u03b2-hydrogen elimination rates for a series of permethylscandocene alkyl complexes Cp*2ScCH2CH2R (R = H, CH3, CH2CH3, SiMe3, C6H5, C6H4-p-CH3, C6H4-p-CF3, and C6H4-p-NMe2) were measured by trapping kinetics. A transition state for the \u03b2-hydrogen elimination was proposed where there is a partial positive charge on the \u03b2-carbon and the hydrogen is transferred to the scandium center as H-.
\r\n\r\n[Cp*2ScH] catalyses the ring opening of methylenecyclopropane and methylenecyclobutane. The ring opening (\u03b2-alkyl elimination) is reversible in the case of methylenecyclobutane. Addition of one equivalent of methylenecyclopentane to [Cp*2ScH] results in the formation of the scandium cyclopentylmethyl complex. This complex undergoes preferential \u03b2-alkyl (reversibly) over \u03b2-hydrogen elimination due to the unfavorable steric congestion encountered in the transition state of the latter.
\r\n\r\n[Cp*2ScH] reacts rapidly at -80\u00b0C with ethyl vinyl ether and vinylfluoride to generate an equimolar mixture of the Cp*2ScX(X = OEt, F, respectively) and Cp*2ScCH2CH3. No intermediates are seen in these reactions and two mechanisms, one involving a \u03b2-X ethyl intermediate and one invoking direct \u03c3-bond metathesis are proposed to account for the products. With vinyldiphenylphosphine, the initial product of insertion, Cp*2ScCH2CH2PPh2 is stable at low temperature; upon warming, this complex undergoes \u03b2-PPh2 elimination.
" }, { "name": "Carroll, Steven S.", "degree": "PhD", "year": "1987", "title": "The Construction and Kinetic Analysis of Specific Mutants of \u03b2-Lactamase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08302019-102809124", "creators": [ { "name": { "family": "Carroll", "given": "Steven S." }, "id": "Carroll-Steven-S", "display_name": "Carroll, Steven S." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2mg4-x771", "abstract": "Mutants of RTEM-1 \u03b2-lactamase, an enzyme responsible for bacterial resistance to \u03b2-lactam antibiotics, have been constructed by cassette mutagenesis. \u03b2-Lactamases have been classified into three groups based on catalytic and structural similarities. Class A B-lactamases, of which the RTEM-1 enzyme is a member, maintain a conserved triad of amino acids about the active site serine, Ser-Thr-X-Lys, where X is not conserved. Endonuclease restriction sites flanking the codons of the active site residues were used to remove the portion of the \u03b2-lactamase gene coding for the wild-type active site sequence. A duplex strand of synthetic oligonucleotides spanning the removed region of the gene and coding for the desired mutations was ligated in place of the wild-type sequence. Subsequent chemical sequencing of the mutated plasmids by the Maxam-Gilbert technique confirmed the presence of the mutations.
\r\n\r\nA mutant converting Thr71 to cysteine, designated Thr71 \u2192 Cys, was constructed and shown to impart to cells a phenotype resistant to high levels of ampicillin (>350 mg/L). Purification of the mutant to homogeneity was accomplished using plasmid pJN which contains the \u03b2-lactamase gene under control of the tac promoter and the gene for kanamycin resistance. Cells were grown at 37\u00b0C and induction was carried out at 30\u00b0C to reduce protein losses due to the thermal instability of the mutant. The Thr71 \u2192 Cys mutant retains 12% of the efficiency of the wild-type enzyme on benzylpenicillin 3% on cephalothin, and 9% on 6-aminopenicillanic acid. The mutant has an altered pH activity profile, with activity declining more rapidly at alkaline pH than for the wild-type enzyme. The mutant is susceptible to inactivation by the sulfhydryl reagent pCMB under conditions where the activity of the wild-type enzyme is not affected. The mutant is inhibited competitively by borate ion. The Thr71 \u2192 Cys mutant is less stable to thermal denaturation than the wildtype enzyme, as are all other mutants at position 71.
\r\n\r\nThe conserved lysine at position 73 of \u03b2-lactamase was replaced with all other amino acids and an amber stop codon by cassette mutagenesis using synthetic oligonucleotides containing a mixture of bases in place of the lysine codon. After ligation the mixtures of plasmids were used to transform E. coli to tetracycline resistance. Plasmids derived from one hundred colonies were sequenced by the Maxam-Gilbert method. Because of an uneven mixture of bases in the mixed codon not all twenty amino acids were located in the first one hundred colonies. Mutants Lys73 \u2192 Asp, Glu and Pro were constructed separately using the same three fragment ligation scheme. None of the mutants at position 73 were able to confer to cells a phenotype resistant to even low levels of ampicillin. Western blot analysis of whole cell extracts revealed mutants with all nineteen amino acid replacements present in amounts not significantly different from the amount of the wild-type enzyme.
\r\n\r\nPurification of mutants Lys73 \u2192 Arg and Cys was accomplished with the use of plasmid pJN and the tac promoter. Kinetic analysis revealed both mutants maintain 0.01% of the activity of the wild-type enzyme on benzylpenicillin. The Michaelis constant, KM, was not significantly different from the value of the wild-type. The Lys73 \u2192 Cys mutant was slightly less stable to thermal denaturation than the wildtype enzyme. The pH-activity profile of the. Lys73 \u2192 Cys mutant showed a maximum at pH 8.3 while the wild-type activity is maximal at pH 6.5. Treatment of the Lys73 \u2192 Cys mutant with ethylenimine, which converts cysteine to aminoethylcysteine, under mildly denaturing conditions resulted in a dramatic increase in specific activity of the mutant. Purification of the derivatized mutant by anion exchange on FPLC and kinetic analysis showed the derivatized mutant regained 62% of the catalytic efficiency of the wild-type enzyme.
" }, { "name": "Carter, Emily Ann", "degree": "PhD", "year": "1987", "title": "Finesse in Quantum Chemistry: Accurate Energetics Relevant for Reaction Mechanisms", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-11212003-111159", "creators": [ { "name": { "family": "Carter", "given": "Emily Ann" }, "id": "Carter-Emily-Ann", "display_name": "Carter, Emily Ann" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/GVJQ-6Y71", "abstract": "A general, systematic approach for calculating accurate energetics for chemical processes within the framework of ab initio electronic structure theory is presented. The correlation-consistent configuration interaction (CCCI) method utilizes generalized valence bond wavefunctions as the starting point for the CI, which emphasizes the inclusion of only the dominant correlations dictated by the physics of the problem. The CI expansion truncates quickly, so that processes involving polyatomic molecules, which could not be addressed with conventional CI methodology, may now be treated easily.
\r\n\r\nA variety of applications of the method are presented, including the prediction of bond energies, electronic excitation energies, and energetics of chemical reactions, for both organic and transition metal-containing molecules. In cases where experimental data are available, the agreement is generally excellent (within 1-5 kcal/mol). We have used these quantitative results, along with qualitative aspects of the wavefunctions, to assess the bonding in and reactivity of a series of organic, organometallic, and inorganic molecules. These studies have produced a number of simple concepts useful for predicting the stability and reactivity of ligands attached to transition metals. Finally, key mechanistic pathways in two transition metal-catalyzed reactions have been examined using the CCCI approach: (i) the chain initiation step for the Fischer-Tropsch synthesis of hydrocarbons; and (ii) the Ag-catalyzed olefin epoxidation reaction.
\r\n" }, { "name": "Chang, Yie-Hwa", "degree": "PhD", "year": "1987", "title": "Studies of the Roles of Residues 71 and 72 of RTEM-1 Beta-Lactamase and the Structure-Function Relationships between Beta-Lactamases and D,D-Carboxypeptidases by Mutagenesis", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08302019-140132981", "creators": [ { "name": { "family": "Chang", "given": "Yie-Hwa" }, "id": "Chang-Yie-Hwa", "display_name": "Chang, Yie-Hwa" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/k85q-w423", "abstract": "The technique of site-directed mutagenesis, including oligonucleotide-directed mutagenesis and cassette mutagenesis, enables us to make any possible structural alterations at desired sites in proteins whose genes have been cloned. This technique when combined with biochemical and X-ray crystallographic analysis has been proved to be a very powerful tool for studying the structure-function relationships in proteins. Using this technique, I have studied some functional requirements of RTEM-1 betalactamase and the structure-function relationships between beta-lactamases and D,D-carboxypeptidases.
\r\n\r\nBeta-lactamases can catalyze the hydrolysis of the amide bond in the beta-lactam ring of penam and cephem antibiotics. The precise catalytic mechanism of these enzymes is still unclear; the specific amino acid residues, in addition to the active site Ser, involved in binding or catalysis remain unknown.
\r\n\r\nIn Chapter I, to study the role of a conserved residue 71, Thr, of RTEM-1 beta-lactamase, I have changed this residue into Ile, Leu and Met, respectively, using oligonucleotide-directed mutagenesis. The results indicate that although the Thr residue may not be directly involved in binding or catalysis, both the methyl and the hydroxyl group on the beta-carbon of Thr71 play a very important role in stabilizing the conformation of the wild-type RTEM-1 beta-lactamase; in this regard, the methyl group seems more important than the hydroxyl group.
\r\n\r\nIt has been proposed that beta-lactamases may have evolved from D,D-carboxypeptidases. Recently, structural data became available for comparing a penicillin-binding-protein (or a D,D-carboxypeptidase) from Streptomyces R61 with class A beta-lactamases from B. licheniformis 749/C and B. cereus 561. The significant similarity found by X-ray crystallography in the spatial arrangement of the elements of secondary structure in these proteins strongly supports the hypothesis described above. Interestingly, there are conserved triads for both class A beta-lactamases and D,D-carboxypeptidases in the immediate vicinity of the active site Ser; the one for class A beta-lactamases is Ser-Thr-Xaa-Lys; however, the one for D,D-carboxypeptidases is Ser-Xaa-Thr-Lys.
\r\n\r\nIn Chapter II, to further study the roles of residues 71 and 72 of RTEM-1 beta-lactamases and to study the possibility of creating a substantial D,D-carboxypeptidase activity within the background of beta-lactamase structure, I have changed the diad Thr71Phe72 of RTEM-1 beta-lactamase into Thr71thr72 and the D,D-carboxypeptidase-like sequences, Leu71Thr72 and Ile71Thr72. The results indicate that although these two residues may not be directly involved in binding or catalysis, they may play a very important role in keeping the active site Ser and the conserved Lys residue in the correct orientation for efficiently catalyzing the hydrolysis of the beta-lactam antibiotics by beta-lactamases. Moreover, none of these mutant beta-lactamases shows detectable D,D-carboxypeptidase activity, suggesting that I may have to change more than two amino acid residues around the active site Ser of RTEM-1 beta-lactamase to generate a mutant beta-lactamase which can catalyze appreciable D,D-carboxypeptidase activity.
\r\n\r\nIn Chapter III, to further study the structure-function relationships between beta-lactamases and D,Dcarboxypeptidases, I constructed a hybrid protein by the replacement of a polypeptide chain containing 29 amino acid residues (from residue 47 to 75, in the number system of Ambler) of RTEM-1 beta-lactamase with the corresponding sequence containing 30 amino acid residues of PBP-5 of E. coli. The results indicate that beta-lactam antibiotics can not only induce the catalytic activity of this hybrid protein but also stabilize the conformation of this protein. The purified hybrid protein shows about 10-3 of the specific activity of the wild-type beta-lactamase against benzylpenicillin and, interestingly, given the objective, this hybrid protein also shows about 1.8% of the D,D-carboxypeptidase activity of the wild-type PBP5 of E. coli. Furthermore, this hybrid protein shows no detectable transpeptidase activity, suggesting that the alpha-G helix in D,D-carboxypeptidase may play an important role in the transpeptidation reaction.
" }, { "name": "Chiang, Huey-jenn", "degree": "PhD", "year": "1987", "title": "Studies of the Thermodynamics of Some Native and Ruthenated Metalloproteins by Spectroelectrochemistry", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312019-170145504", "creators": [ { "name": { "family": "Chiang", "given": "Huey-jenn" }, "id": "Chiang-Huey-jenn", "display_name": "Chiang, Huey-jenn" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8fcf-kt72", "abstract": "The thermodynamic parameters of redox centers in some metalloproteins have been investigated using spectroelectrochemical techniques, with the employment of an OTTLE (Optically Transparent Thin-Layer Electrode) cell. With the aid of various carefully selected mediators, the temperature dependence of the formal redox potentials of type I copper (blue copper) ions in Rhus vernicifera (tree) laccase, as well as in native and in pentaammineruthenium-modified azurins from Pseudomonas aeruginosa, have been measured. Similar experiments have been carried out for the heme site of cis-[Ru(en)2(OH)(His)]-horse heart cytochrome c (en: ethylenediamine; His: histidine). Cyclic voltammetry has been used to study the pH-dependence of the formal redox potentials of the appended ruthenium ion in cis-[Ru(en)2(OH)(His)]-horse heart cytochrome c. Finally, the synthesis and spectroelectrochemistry of sperm whale myoglobin reconstituted with [Ru(MpIX)(DMSO) dicarboxylic acid]- moiety (MpIX: mesoporphyrin IX; DMSO: dimethyl sulfoxide) have also been carried out.
" }, { "name": "Chow, Christopher Vincent", "degree": "PhD", "year": "1987", "title": "The Flow of a Liquid Jet in a Homogenous Suspension", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02282008-133645", "creators": [ { "name": { "family": "Chow", "given": "Christopher Vincent" }, "id": "Chow-Christopher-Vincent", "display_name": "Chow, Christopher Vincent" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "chair", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7wzj-t748", "abstract": "The theoretical and experimental work summarized in this thesis examine the flow of a vertical jet issuing into a suspension of particles. For small particle Reynolds numbers, a relative velocity (between the particle and the bulk suspension) that is a function of concentration only, and an initially homogeneous suspension, the flow field divides into regions of pure fluid and suspension, and hence, a buoyancy force is exerted on the lighter pure fluid jet. The governing two-phase flow equations are solved in different asymptotic limits to show that the jet acquires increasing plume-like characteristics as it flows downstream. A linear stability analysis on the plume-like flow solution showed that there is no critical flow parameter below which this flow is stable. The experimental work was conducted so that comparisons could be made with the theoretical predictions. The experimentally measured spreading rates of the pure fluid region agree quite well with those predicted by the theory, and verify the effect of the buoyancy force on the jet. As predicted by the stability analysis, all of the plume-like flows were unstable. Quantitative comparisons of the experimentally measured amplification rates with those predicted by the theory were inconclusive. However, the qualitative effects of buoyancy, initial jet momentum, and particle concentration in the suspension were observed to be destabilizing, as predicted by the theory.
" }, { "name": "Cohen, Mark Daniel", "degree": "PhD", "year": "1987", "title": "Studies of Concentrated Electrolyte Solutions Using the Electrodynamic Balance", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03202008-105002", "creators": [ { "name": { "family": "Cohen", "given": "Mark Daniel" }, "id": "Cohen-Mark-Daniel", "display_name": "Cohen, Mark Daniel" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Morgan", "given": "James J." }, "id": "Morgan-J-J", "role": "member", "display_name": "Morgan, James J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5ZEY-MH91", "abstract": "An electrodynamic balance has been used to measure the water activity as a function of solute concentration at 20 \u00b0C for eleven single-electrolyte aqueous solutions - NaCl, NaBr, KCl, KBr, NH4Cl, Na2SO4, (NH4)2SO4, CaCl2, MnCl2, MnSO4 and FeCl3 - and three mixed-electrolyte aqueous solutions - NaCl-KCl, NaCl-KBr, and NaCl-(NH4)2SO4. The measurements were performed by levitating single, charged, 20-micron diameter droplets of these solutions within the balance and measuring the mass of the particles as a function of the surrounding relative humidity. The deliquescence behavior of the particles was also observed.
\r\n\r\nHeterogeneous nucleation was inhibited due to the absence of container walls and because the small droplets were less likely than a bulk sample to contain foreign particles. Thus, this technique allowed the thermodynamics of highly concentrated solutions to be studied. For most of the solutions, water activity measurements were made to higher solute concentrations than have previously been reported. At low concentrations, the results were consistent with previously published data. Nucleation theory was used to estimate the surface excess free energy and critical nucleus size from the measured supersaturation at which nucleation occurred.
\r\n\r\nFor the single-electrolyte solutions, the dependence of the solute activity coefficient on concentration was calculated, and the features of this dependence are discussed in relationship to ionic hydration and association. Several semi-empirical electrolyte solution models were tested against the data, and it was found that salt-specific model parameters estimated from low concentration data could not be reliably used to predict the solution behavior at high concentrations. However, with estimated parameters based on the full range of the data, the models were able to represent the experimental data for single-electrolyte solutions to within the uncertainty in the measurements.
\r\n\r\nThree models of mixed-electrolyte solutions \u2014 the Zdanovskii-Stokes-Robinson, Reilly-Wood-Robinson and Pitzer methods \u2014 agreed well with the experimental data for the NaCl-KCl and NaCl-KBr systems over the range of concentration that the models could be applied. The mixing rules' predictions were consistent with the experimental observations for the NaCl-(NH4)2SO4 particles assuming a small amount of water was retained in the dry state.
" }, { "name": "Dandy, David Stewart", "degree": "PhD", "year": "1987", "title": "Intermediate Reynolds Number Free-Surface Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-03042008-083806", "creators": [ { "name": { "family": "Dandy", "given": "David Stewart" }, "id": "Dandy-David-Stewart", "display_name": "Dandy, David Stewart" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Brown", "given": "Robert A." }, "id": "Brown-Robert-A", "role": "member", "display_name": "Brown, Robert A." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Meiron", "given": "Daniel I." }, "id": "Meiron-D-I", "role": "member", "display_name": "Meiron, Daniel I." } ], "option_major": [ "chemeng" ], "doi": "10.7907/frtp-v339", "abstract": "The buoyancy driven motion of a deformable viscous drop at intermediate Reynolds numbers has been studied using numerical techniques. The motion was assumed to be steady and rectilinear, and a pseudo-implicit method was used to solve the Navier-Stokes equations. Cases for a variety of values of the Reynolds number, Weber number, viscosity ratio and density ratio have been considered. The calculations reveal that the shape of the drop is most heavily dependent on the Weber number, attaining spheroidal capped shapes at 0(1) Reynolds numbers, and flattened ellipsoidal shapes at higher Reynolds numbers. Two mechanisms are observed for vorticity production at the interface of the drop\u2014curvature and the no-slip condition\u2014and the no-slip mechanism is a more efficient source of vorticity. When there is sufficient vorticity produced, a detached closed streamline wake forms at the back of the drop, in contrast to the attached wakes seen on inviscid bubbles and solid particles.
\r\n\r\nTo further explore the role of vorticity production in wake formation, numerical computations were done on flow past inviscid bubbles of fixed shape. It was found that attached recirculating wakes existed at intermediate Reynolds numbers and these wakes could not be predicted by either low or high Reynolds number asymptotic theories. The numerical results indicate that the mechanism responsible for flow separation at modest Reynolds numbers may be different than that present at high Reynolds numbers.
\r\n\r\nBecause of the inherent difficulties in solving the Navier-Stokes equations using successive approximation schemes, and to investigate the behavior of solutions of these equations on the dimensionless parameters, a Newton's method scheme has been developed and tested successfully on the steady buoyancy driven motion of an inviscid bubble; an arc length continuation method has also been implemented. Calculations indicate that the scheme achieves quadratic convergence.
\r\n\r\nLast, a numerical technique has been developed for the study of the creeping motion of drops and particles in the presence of a rigid plane boundary. This method is based upon the distribution of point forces on the surface of the body and the use of a Green's function to obtain the unknown velocity and stress on the body surface, without having to consider the rigid boundary.
\r\n" }, { "name": "Dussault, Patrick H.", "degree": "PhD", "year": "1987", "title": "Approaches to the Total Synthesis of Aplysiatoxin", "advisor": "Ireland, Robert E.; Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04122019-170707466", "creators": [ { "name": { "family": "Dussault", "given": "Patrick H." }, "id": "Dussault-Patrick-H", "display_name": "Dussault, Patrick H." } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "co-advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Myers", "given": "Andrew G." }, "id": "Myers-A-G", "orcid": "0000-0001-9602-6915", "role": "member", "display_name": "Myers, Andrew G." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zta1-3f55", "abstract": "Approaches to the synthesis of the polyacetate tumor promoter aplysiatoxin (1a) are described. The spiroketal framework was convergently constructed in a heteroatom Diels-Alder cyclization to afford spiroketal 11. The desired spirocenter stereochemistry was achieved, in a key reaction pitting steric strain against the anomeric effect, by acid-catalyzed isomerization of spiroketal 12 to spiroketal13. Subsequent manipulation furnished alcohols 16A and 16B, which were the starting materials for investigations into macrocyclization and introduction of the C-3 lactol. 16A and 16B were efficiently converted to macrolactones 23A and 23B. The macrolactones were deprotected and brominated to furnish 27A and 27B, representing both possible C-15 epimers of 3-desoxyaplysiatoxin methyl ether. Attempted removal of the phenol methyl ether proved impossible. Nuclear Overhauser effect difference spectra on 27B showed signal enhancements within the rigid spiroketal framework analogous to those observed in derivatives of the natural product. Attempted transannular remote oxidation of C-3 using a C-9 alkoxy radical derived from the nitrite ester of 16B afforded, as the predominant product, the C-9 ketone resulting from fragmentation of the initial alkoxy radical; an alternate route involving allylic oxidation of the C-3 hydroxyethyl sidechain of 16A or 16B also failed to functionalize the C-3 position. Circular dichroism (CD) spectra of 16A and 16B imply that alcohol 16B contains the natural (S) stereochemistry at the C-15 methyl ether.
\r\n\r\n[Chemical structures 1a, 11, 12, 13, 16A, 16B, 23A, 23B, 27A, and 27B. See abstract in scanned thesis for details.]
" }, { "name": "Edelstein, Sergio", "degree": "PhD", "year": "1987", "title": "Adsorption of Sulphur Dioxide and Reduction of Sulphate on Alumina and Alkali-Alumina at High Temperatures", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-082025", "creators": [ { "name": { "family": "Edelstein", "given": "Sergio" }, "id": "Edelstein-Sergio", "display_name": "Edelstein, Sergio" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4CFM-WQ54", "abstract": "Several interrelated problems in connection with the treatment of sulfur dioxide at temperatures between 700 and 800\u00b0C were studied. The interaction of SO2 with Al2O3 was studied experimentally using B.E.T., thermogravimetry and temperature-programmed desorption. Adsorption takes place through a wide range of binding energies, with some SO2 adsorbing irreversibly at temperatures below 800\u00b0C. The amount adsorbed depends on the surface history and thermal treatment. An adsorption isotherm based on a bimodal energy distribution provides an adequate description of the equilibrium process.
\r\n\r\nThe chemical composition, sulfation and regeneration of an alkali-alumina sorbent for sulfur dioxide were studied using thermogravimetry, gas chromatography, and X-ray photoelectron spectroscopy. The active sorbent consists of a thin layer of sodium and lithium aluminates supported on alumina. The rate of sulfation is proportional to the SO2 concentration in the gas, up to [SO2] \u2248 5000 ppm. The activation energy of the sulfation is E = 21.6 kcal/mole. The sulfated sorbent was regenerated by reduction with CO at 700-800\u00b0C. Sulfur removal from the sorbent and distribution of gaseous products were measured at different alkali loadings, temperatures and CO concentrations. The reduction takes place in two consecutive stages through a complex reaction network in which the alumina support plays a decisive role, both as a reactant and as a catalyst. A simplified reaction network is used as a basis for a kinetic model that provides an adequate description of the reduction process at moderate sorbent loadings.
" }, { "name": "Engstrom, James Robert", "degree": "PhD", "year": "1987", "title": "The Influence of Surface Structure and Adlayer Composition on the Kinetics and Mechanisms of Gas-Surface Reactions", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-03122008-080659", "creators": [ { "name": { "family": "Engstrom", "given": "James Robert" }, "id": "Engstrom-James-Robert", "display_name": "Engstrom, James Robert" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6b69-ch24", "abstract": "The theoretical formulation of a frequency response technique, based on surface temperature modulation, for the study of the kinetics of elementary gas-surface reactions is described in detail. The formalism is developed for analyzing adsorption, desorption, and both unimolecular and bimolecular surface reactions. The technique possesses a distinct advantage over competitive techniques, such as modulated molecular beam reactive scattering, since the evaluation of activation barriers for elementary surface reactions is straightforward even in the presence of strong nonlinearities and requires no knowledge of the composition and/or configuration of the adlayer. The technique has been employed successfully to investigate the adsorption, desorption and oxidation of CO on the Pt(110)-(1x2) surface. The oxidation of CO has been studied with emphasis on examining the kinetics of the elementary bimolecular surface reaction CO(a) + O(a) \u2192 CO2(g). The activation energy is found to correlate well with the oxygen adatom concentration, the variation being quite nonlinear. This nonlinear variation is interpreted as a manifestation of the dominant role that the local configuration of the reactants play in determining the reaction dynamics. It is suggested that the power of the technique can be increased significantly by either coupling it with time-resolved, surface-sensitive spectroscopies or employing localized (e.g., laser) heating techniques to provide the modulation in surface temperature. The chemisorption of hydrogen on both the Ir(111) and Pt(110)-(1x2) surfaces has been examined by employing primarily thermal desorption mass spectrometry. Comparisons of the results obtained on the (111) and (110)-(1x2) surfaces of both iridium and platinum suggest strongly that local surface structure has a profound influence on the kinetics of adsorption of hydrogen on these surfaces. Surface structure also influences greatly the desorption kinetics of hydrogen via the mediation of \"through-metal\" adatom-adatom interactions. In particular, both attractive and repulsive interactions are clearly manifest within the higher binding energy \u03b22-adstates on the (110)-(1x2) surfaces, these \u03b22 states associated with adsorption into one-dimensional channels which are composed of high-coordination \"trough\" sites. However, only repulsive interactions were apparent on the (111) surfaces or for the lower binding energy \u03b21-adstates on the (110)-(1x2) surfaces, these \u03b21 states associated with adsorption on the (111) microfacets. The hydrogenolysis of several alkanes and cycloalkanes has been examined on both the (111) and (110)-(1x2) single crystalline surfaces of iridium for hydrocarbon partial pressures near 1 Torr, hydrogen partial pressures near 100 Torr, and surface temperatures between 400 and 700 K. The choice of these two surfaces has proven to be decisive for the unambiguous assessment of the effects of surface geometry on both catalytic activity and selectivity. Concerning the hydrogenolysis of alkanes, excepting the special case of n-butane on Ir(110)-(1x2), a mechanism involving a rate-limiting unimolecular C-C bond cleavage in an adsorbed, dehydrogenated hydrocarbon fragment describes well the variations in both the specific activity and selectivity of hydrogenolysis with variations in the reactant partial pressures. In cases where similar activities and selectivities are observed over the two surfaces, essentially identical reaction intermediates (mechanisms) are implicated. On the other hand, in cases where different activities and/or selectivities are observed over the two surfaces, distinct reaction intermediates (mechanisms) are implicated. In the particular case of the reaction of n-butane, the selectivity for ethane was identified explicitly with the participation (concentration) of low-coordination-number metal surface atoms. It is suggested that the intermediate that leads to the high selectivity for ethane is a mononuclear metallacycle pentane; the formation of this intermediate is sterically forbidden on (111) surfaces. Concerning the hydrogenolysis and hydrogenation of cycloalkanes, the Ir(110)-(1x2) surface possesses a greater specific activity (per metal surface atom basis) with respect to the Ir (111) surface for both the hydrogenation (to propane) and the hydrogenolysis (to methane and ethane) of cyclopropane. This result is interpreted by invoking a greater intrinsic activity (for these reactions) for the low-coordination-number metal surface atoms that are present in higher concentrations on Ir(110)-(1x2).
\r\n\r\nUnlike the reactions of alkanes, for cyclopropane under \"severe\" reaction conditions (i.e., large hydrocarbon-to-hydrogen partial pressure ratios and/or high temperatures), a transformation in the composition of the adlayer occurs, with the coverage of the carbonaceous residue increasing from one-half of a monolayer to nearly a full monolayer. Concomitant with the adlayer transformation, the selectivity of the reaction of cyclopropane and hydrogen shifts dramatically from methane (hydrogenolysis) to propylene (isomerization). The dominance of the (relatively facile) isomerization channel on the \"carburized\" surface is interpreted as a manifestation of a weakened interaction between the metal surface and the relevant adsorbed reaction intermediates.
" }, { "name": "Grosz, Ron", "degree": "PhD", "year": "1987", "title": "Biochemical and Mathematical Modeling of Microaerobic Continuous Ethanol Production by Saccharomyces cerevisiae", "advisor": "Stephanopoulos, Gregory N.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-120209", "creators": [ { "name": { "family": "Grosz", "given": "Ron" }, "id": "Grosz-Ron", "display_name": "Grosz, Ron" } ], "advisors": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "advisor", "display_name": "Stephanopoulos, Gregory N." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Hoffman", "given": "Allan S." }, "id": "Hoffman-A-S", "role": "member", "display_name": "Hoffman, Allan S." } ], "option_major": [ "chemeng" ], "doi": "10.7907/29dc-ay81", "abstract": "The effect of the aeration intensity in the vicinity of 1Oppb of dissolved oxygen upon the steady state, continuous ethanol production by Saccharomyces cerevisiae is explored. The specific ethanol productivity increased by 30 to 50% as the aeration rate was reduced, but decreased to the original level as the aeration was further reduced to the lowest rates. These metabolic changes occurred when the respiration rate contributed negligibly to ATP energy production, excluding the Pasteur mechanism, and when the residual glucose level saturated the glucose transporter, excluding glucose kinetics as the cause.
\r\n\r\nTo expose the mechanism of the metabolic changes, the intracellular concentrations of ethanol, glycerol, ATP, glucose 6-phosphate, pyruvate, and NADH, the activities of the hexokinase, alcohol dehydrogenase, fumarase, and isocitrate dehydrogenase, and the cell viability were assayed. Rate-limiting steps were identified by the accumulation of upstream and the depletion of downstream metabolites. The enzyme activity and cofactor measurements elucidated the causes of the rate limitation.
\r\n\r\nBased on the assays, the metabolic acceleration with decreasing aeration was the result of an increasing glucose transporter activity, and ATP was the most likely activator. The reversal at yet lower aerations resulted from the continued accumulation of ATP until the downstream glycolytic kinases were inhibited.
\r\n\r\nHigh concentrations of silicone polymer antifoam decreased the resistance to glycerol transport across the cell membrane, enhancing glycerol production at the expense of ethanol production. Such cultures attained lower ATP concentrations.
\r\n\r\nThe biomass concentration in the fermentor was occasionally found to undergo hysteresis, characterized by extinction and ignition as critical aeration rates were passed. Hysteresis and associated phenomena were prevented by the addition of yeast extract and the removal of the antifoam from the medium. The higher ATP concentration of the low antifoam culture and the biosynthetic intermediates of yeast extract must participate in this transition.
\r\n\r\nMathematical models account for all observed phenomena. Featured by the model are the ATP activation of the glucose transporter, ATP wastage by ATPases and such processes, and oxygen induction of ATP waste reactions. Singularity theory was invoked to account for the transition from the hysteresis to monotonic biomass versus aeration bifurcation diagrams.
" }, { "name": "Hills, Malina Manon", "degree": "PhD", "year": "1987", "title": "Characterization of Reaction Intermediates and Adsorbate Interactions on the Ru(001) Surface", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-03032008-141343", "creators": [ { "name": { "family": "Hills", "given": "Malina Manon" }, "id": "Hills-Malina-Manon", "display_name": "Hills, Malina Manon" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinstein", "given": "Alan Jay" }, "id": "Weinstein-Alan-J-Physics", "orcid": "0000-0002-0928-6784", "role": "chair", "display_name": "Weinstein, Alan Jay" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7afx-0m86", "abstract": "The adsorption and reaction of ethylene and methylamine on the Ru(001) surface have been investigated in order to characterize reaction intermediates and adsorbate interactions. Experiments were conducted under ultrahigh vacuum conditions using electron energy loss spectroscopy and thermal desorption mass spectrometry. Molecularly chemisorbed ethylene is di-\u03c3-bonded and the carbon atoms of the ethylene are rehybridized to sp3. Upon annealing to room temperature, ethylene forms ethylidyne (CCH3) and acetylide (CCH) via unstable \u03b72-CHCH2 and \u03b72-CCH2 intermediates. These species decompose below 400 K to carbon adatoms and methylidyne (CH) with concurrent evolution of hydrogen.
\r\n\r\nThe interactions of ethylene and its decomposition intermediates with hydrogen and also with carbon monoxide have been explored. Hydrogen and carbon monoxide reduce the adsorption and decomposition of ethylene by blocking adsites. Neither coadsorbed hydrogen nor carbon monoxide alter the identities of the decomposition intermediates, although the selectivity of the reaction is altered. Thus on the clean, hydrogen-precovered and carbon monoxide-precovered Ru(001) surfaces, ethylene tends to decompose via sp3-hybridized, \u03b72-bonded intermediates.
\r\n\r\nOxygen overlayers perturb the electronic structure of the Ru(001) surface, changing both the bonding of coadsorbates and the decomposition intermediates. For example, ethylene adsorbed molecularly on the Ru(001)-p(2x2)O surface is sp2-hybridized and \u03c0-bonded. This ethylene dehydrogenates to ethylidyne which forms vinylidene (CCH2). The vinylidene is coordinated to the surface via one carbon atom with \u03c0-electron donation from the carbon-carbon double bond to the surface occurring. Thus the presence of oxygen changes the nature of the molecularly adsorbed ethylene and the decomposition intermediates, favoring sp2-hybridized, \u03b71-bonded adspecies. This result holds also for adspecies such as acetylene, acetone and formaldehyde and is discussed using the Dewar-Chatt-Duncanson model.
\r\n\r\nMethylamine adsorbed on the Ru(001) surface is coordinated through the lone pair of electrons on the nitrogen atom. This species dehydrogenates to a CH2NH2 intermediate at 300 K, that dehydrogenates to CHNH2 upon annealing to 350 K. The lone pair of electrons, previously located on the nitrogen, are delocalized over the ruthenium-carbon and carbon-nitrogen bonds of CHNH2. This species decomposes below 400 K via two competing pathways, forming carbon adatoms and ammonia or dehydrogenating to side-on bonded C=N with concurrent evolution of hydrogen.
" }, { "name": "Jain, Rakesh", "degree": "PhD", "year": "1987", "title": "Direct Observation and Reactions of Organic Biradicals Generated from Novel Bicyclic Azoalkanes", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02252019-123337280", "creators": [ { "name": { "family": "Jain", "given": "Rakesh" }, "id": "Jain-Rakesh", "display_name": "Jain, Rakesh" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z16r-7e62", "abstract": "Thermolysis of 2,3-diazabicyclo[2.1.1]hex-2-ene (14) in the gas phase produces highly vibrationally excited (chemically activated) bicyclo[1.1.0]butane (30). The excited 30 rearranges to butadiene, in competition with collisional deactivation by a bath gas. Quantitative modeling using RRKM theory and a stepladder model for collisional deactivation indicates that of the substantial amount of excess energy available to the products of thermolysis of 14, the great majority lies in the hydrocarbon fragment (30). Within the framework of a mechanistic criterion developed previously by Bauer, this result suggests that 14 decomposes by a stepwise, one-bond cleavage involving an intermediate diazenyl biradical. We have also synthesized 16, the dimethyl derivative of 14, and studied its thermal decomposition. As predicted by RRKM calculations, gas phase thermolysis of 16 does not produce chemically activated 1,3-dimethylbicyclobutane (31).
\r\n\r\nIrradiation of frozen solutions of 1,4-dialkyl-2,3-diazabicyclo[2.1.1]hex-2-enes (16-19) in the cavity of an ESR spectrometer between 4 and 25 K produces the corresponding triplet 1,3-dialkyl-1,3-cyclobutanediyls (20-23). The spectra display zero-field splitting parameters, |D/hc| = 0.112 cm-1 and |E/hc| = 0.005 cm-1. Hyperfine coupling can be resolved in some of these spectra and can be simulated using a computer program which has been developed for the purpose. The decay of the ESR signals between 4 and 25 K is nonexponential and shows very little dependence on temperature. A novel approach for analyzing the matrix-site effect is used and evidence is provided for quantum-mechanical tunneling in the decay process.
\r\n\r\nMatrix isolation photolysis of 2,3-diazabicyclo[2.2.1]hept-2-ene-7 \u2013spiro-cyclopropane (24) and 2,3 diazabicyclo[2.2.1]hept-2-ene-7,5'-spirobicyclo[2.1.0]pentane (25) between 4 and 35 K produces triplet ESR signals which are thermally stable up to 150 K. Independent generation from direct precursors 7-ethylidene-2,3-diazabicyclo[2.2.1 ]hept-2-ene (71) and 7-cyclobutylidene-2,3-diazabicyclo[2.2.1]hept-2-ene (72) confirms the assignment of the ESR signals to triplet biradicals 2-ethylidene-1,3-cyclopentanediyl (28) and 2-cyclobutylidene-1,3-cyclopentanediyl (29), respectively. Interpretable hyperfine coupling is observed and can be simulated, providing direct information about the electronic structures of these biradicals. The mechanism proposed for the formation of 28 and 29 from 24 and 25 involves two biradical rearrangements; a cyclopropylcarbinyl-type ring opening followed by a 1,2-H shift. Neither of these rearrangements can occur via thermal activation at such low temperatures. Chemical activation and quantum-mechanical tunneling are proposed to explain the reactivity of the intermediary biradicals.
\r\n" }, { "name": "Keech, John Tyler", "degree": "PhD", "year": "1987", "title": "High Valent Osmium Complexes Incorporating a Tetradentate Tetraanionic Chelating Ligand; Stabilization Modification Resulting from the Formation of Non-Planar Amides", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262010-145408928", "creators": [ { "name": { "family": "Keech", "given": "John Tyler" }, "id": "Keech-John-Tyler", "display_name": "Keech, John Tyler" } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "chair", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/A4N9-5E16", "abstract": "A new tetradentate tetraanionic chelating ligand has been synthesized: 1,2-bis(3,5-dichloro-2-hydroxybenzamido)-4,5-dichlorobenzene, H4CHBA-DCB. This ligand is one of a class of polyanionic chelating (PAC) ligands synthesized by the Collins group for stabilizing high valent metal centers. H4CHBA-DCB has an aromatic framework that is chlorinated for added chemical resistance. Reacting equimolar amounts of H4CHBA-DCB and K2[Os(OH)4(O)2] coordinates the ligand as trans-K2[Os(\u03b74-CHBA-DCB)(O)2], 3. Compound 3 undergoes reversible protonation at an oxo ligand to produce trans-K[Os(\u03b74-CHBA-DCB)(O)(OH)], 4. Compound 4 reacts with solid MgSO4 and forms the square-pyramidal mono-oxo complex Os(\u03b74-CHBA-DCB)(O), 5. Most oxidizing agents, with the exception of bromine, decompose 3 into a black amorphous material. Bromination of 3 produces a compound similar to 4 and is proposed to be trans-K[Os(\u03b74-CHBA-DCB)(O)(OBr)], 6. Triphenylphosphine readily reduces Os(VI)3 to a neutral Os(IV) complex, trans-Os(\u03b74-CHBA-DCB)(PPh3)2, 7. The ancillary phosphine ligands of 7 prove to be substitutionally labile and can be exchanged for other Lewis bases (e.g., py, t-Bupy, bipy, dppe, and t-BuNC) to produce a series of Os(IV) complexes. Using cyclic voltammetry, the formal potentials of the Os(V/IV), Os(IV/III), and Os(III/II) couples are determined in CH2Cl2. In liquid SO2, the formal potentials of the Os(V/IV), Os(2+/+), and Os(3+/2+) couples are measured for three compounds, the highest potential being at +1.70 V vs. Fc+/Fc or ca. +2.4 V vs. NHE. A fourth irreversible couple is observed at +2.12 to +2.20 V vs. Fc+/Fc. These osmium complexes display temperature-independent paramagnetism.
\r\n\r\nOs(IV) complexes with bidentate ligands (e.g., bipy and dppe) and Lewis acid ligands (t-BuNC) form cis complexes where the (\u03b74-CHBA-DCB)4- ligand is non-planar, and the auxiliary ligands are cis to one another. Two such complexes have been crystallographically characterized: cis-\u03b2-Os(\u03b74-CHBA-DCB)(bipy), 11, and cis-\u03b1-Os(\u03b74-CHBA-DCB)(PPh3)(t-BuNC), 14. Compound 11 crystallizes with 0.5 equiv EtOH solvate in the triclinic space group P1̅ with a = 10.860(3) \u00c5, b = 12.633(3) \u00c5, c = 12.844(4) \u00c5, \u03b1 = 117.42(2)\u00b0, \u03b2 = 90.42(3)\u00b0, \u03b3 = 95.90(3)\u00b0, V = 1552.2(7) \u00c53, Z = 2, Dcalc = 1.97 g/cm3, and Rf = 0.047 (I > 0; 2888 reflections). Compound 14 crystallizes in the orthorhombic space group Pbca with a = 22.09(2) \u00c5, b = 19.92(2) \u00c5, c = 19.40(2) \u00c5, V = 8537(4) \u00c53, Z = 8, Dcalc = 1.69 g/cm3, and Rf = 0.063 (I > 0; 1564 reflections). These structures contain novel non-planar amide groups. The amount of deformation in each amide is quantified by a torsion angle analysis. Two bonding changes cause the amide non-planarity: amide C-N bond rotation and pyramidalization of the amide nitrogen atom. Consistent with the presence of non-planar amides, unusually high amide carbonyl stretching frequencies are observed (1650-1695 cm-1), which imply that amide delocalization stabilization has been restricted.
\r\n\r\nThe cis-\u03b1 and trans isomers of [Os(\u03b74-CHBA-DCB)(t-Bupy)2]+ are in equilibrium with one another. From the measured equilibrium constant of 1.3 (in favor of the trans) and the formal reduction potentials for each isomer, the equilibrium constants for the interconversion of the neutral (3.4 x 103), anionic (2.4 x 1011), and dianionic (2.0 x 1015) species are derived. The trend in equilibrium constants shows that the cis-\u03b1 ligand set is increasingly favored as the metal is oxidized. A linear free energy relationship (LFER) is established between the cis-\u03b1 ⇆ trans equilibrium constants of Os(\u03b74-CHBA-DCB)(p-X-py)2 [X = MeO, t-Bu, Et, Me, H, Br, Cl, Ac] and both Fischer \u03c3̅ (\u03c1 = -2.10, r = 0.948) and Hammett \u03c3p (\u03c1 = -1.60, r = 0.949) substituent parameters. The formal potentials of the Os(V/IV), (IV/III), and Os(III/II) couples of both the cis-\u03b1 and trans isomers also correlate with \u03c3̅ constants, showing that the electron density at the metal center is perturbed in a predictable manner by the pyridine substituents. These LFERs show that the isomerization equilibria are controlled by electronic demand for stabilization at the metal center with the cis-\u03b1 ligand set being more electron-donating than the trans set. This difference apparently results from the increased localization of the amide nitrogen lone pair due to restricted amide delocalization in the non-planar amide groups of the cis-\u03b1 isomers. The localized lone pair probably enhances \u03c3- and \u03c0-bonding between the amide nitrogen atoms and the osmium center. The balance between the stabilization derived from the cis-\u03b1 isomer and the destabilization incurred from restricted amide delocalization may determine which isomer is thermodynamically most stable.
\r\n\r\nThe mechanism for the interconversion of cis-\u03b1 and trans isomers is probed through kinetic rate measurements and ligand exchange studies. Most of the results suggest that an intramolecular \"twist\" mechanism, T, requiring no ligand dissociation steps, controls the isomerization processes. The mechanism explains why no cis-\u03b2 isomers are detected during the isomerization of cis-\u03b1 and trans isomers. The activation parameters are derived for the cis-\u03b1 \u2192 trans isomerizations of three systems: Os(\u03b74-CHBA-DCB)(t-Bupy)2 (\u0394H\u2260 = 21.6(19) kcal/mol; \u0394S\u2260 = -10(6) eu), Os(\u03b74-CHBA-DCB)(O =PPh3)2 (\u0394H\u2260 = 21.6(2) kcal/mol; \u0394S\u2260 = 0.3(6) eu), and [Os(\u03b74-CHBA-DCB)(O =PPh3)2]+ (\u0394H\u2260 = 23.7(6) kcal/mol; \u0394S\u2260 = + 17(2) eu). This suggests that the different rates of isomerization result from entropic differences in the transition state, not enthalpic differences. That is, the t-Bupy system has the \"tightest\" transition state, as evidenced by the most negative \u0394S\u2260, and consequently the slowest isomerization rate. The rates are observed to be faster in the d3 Os(V) phosphine oxide system than in its d4 Os(IV) analog.
" }, { "name": "Lee, Tai-yong", "degree": "PhD", "year": "1987", "title": "Estimation of Petroleum Reservoir Properties", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03012008-135126", "creators": [ { "name": { "family": "Lee", "given": "Tai-yong" }, "id": "Lee-Tai-yong", "display_name": "Lee, Tai-yong" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" }, { "name": { "family": "Chen", "given": "Wen H." }, "id": "Chen-Wen-H", "role": "member", "display_name": "Chen, Wen H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/gs7z-gy70", "abstract": "Numerical algorithms are developed to estimate petroleum reservoir properties such as absolute permeability, porosity, and relative permeabilities based on the noisy pressure and flow data. Regularization and spline approximation of spatially varying parameters are employed to convert the ill-posed nature of the problem to a well-posed one. A stabilizing functional with gradient operator is used to measure the non-smoothness of the parameter estimates. The number of spline coefficients along each spatial direction is chosen to be as much as the number of meshes for the reservoir PDE's. New history matching algorithms are developed that determine the regularization parameter during the computation without requiring a priori information and improve the parameter estimates stepwise. A partial conjugate gradient method is employed for the estimation of a single set of parameters, and the steepest descent algorithm is used for the simultaneous estimation of absolute and relative permeabilities. A rough parametric sensitivity analysis is carried out for the simultaneous estimation to improve the convergence. Numerical tests are carried out to estimate the parameters in single- and two-phase reservoirs for the different choices of the stabilizing functionals, the regularization parameters, and the degrees of spline approximation; and the effects of the observation error, the observation time, and the configuration of the observation points are investigated. The results show that the new algorithms generate better parameter estimates over the various possible choices of the estimation conditions.
" }, { "name": "Leland, Burton Alan", "degree": "PhD", "year": "1987", "title": "Photoinduced Electron Transfer: Synthetic Models of the Primary Processes in Photosynthesis", "advisor": "Dervan, Peter B.; Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02252019-100631121", "creators": [ { "name": { "family": "Leland", "given": "Burton Alan" }, "id": "Leland-Burton-Alan", "display_name": "Leland, Burton Alan" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "co-advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ncrh-n123", "abstract": "A general synthetic method is presented for the preparation of a series of meso-phenyloctamethylporphyrin-linker-quinone compounds for investigation of intramolecular photoinduced electron transfer rates by picosecond fluorescence spectroscopy. Distance effects were investigated through the incorporation of zero, one, or two bicyclo[2.2.2]octyl linker units separating the porphyrin and quinone. Addition of one bicyclo[2.2.2]octyl linker decreases kET by at least a full order of magnitude. The addition of a second bicyclo[2.2.2]octyl linker unit decreases the electron transfer rate by 500 to \u22651700. Investigation of solvent effects on the electron transfer rate, as obtained from the picosecond fluorescence lifetimes of the compounds, indicate weak solvent dependencies as expected for electron transfer from a neutral initial state. Conversely, dramatic solvent dependencies are expected for the back transfer rates in these compounds. Investigation of temperature effects on the electron transfer rate revealed a relatively temperature insensitive electron transfer rate (nuclear tunneling). This is the first synthetic porphyrin-quinone compound to date to exhibit electron transfer quenching at low temperatures. The nonexponential emission decays of samples at 77K in frozen solvent matrices are proposed to arise from an ensemble of rotational conformations between the porphyrin donor and the benzoquinone acceptor, which is well described by an angle-modulated decay analysis. The dependence of kET on the precise geometric orientation of the donor and acceptor reinforces the nonadiabatic nature of these transfers. Exothermicity effects for a structurally homologous series of porphyrin-benzoquinones prepared by the general synthetic method in four solvents of varying polarity indicate large changes in the electron transfer rate with small changes in the driving force at low exothermicities, followed by a relatively \u0394G\u00b0 insensitive region. At the highest exothermicity case studied, a modest decrease in the electron transfer rate was observed. No dramatic evidence for the inverted region was observed for the photoinduced electron transfer from the porphyrin excited singlet transfer to the quinone acceptor over the range of exothermicity studied (0.5 \u2264 \u0394G\u00b0rel \u2264 1.1 eV (benzene)). A comparison of the results with classical and semiclassical theories is presented.
\r\n\r\n" }, { "name": "Lynch, Diane Lynn", "degree": "PhD", "year": "1987", "title": "Dynamics of Single and Multiphoton Ionization Processes in Molecules", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-212202129", "creators": [ { "name": { "family": "Lynch", "given": "Diane Lynn" }, "id": "Lynch-Diane-Lynn", "display_name": "Lynch, Diane Lynn" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7grh-zk17", "abstract": "Single-photon and resonant multiphoton ionization\r\nstudies, which can now be carried out using synchrotron\r\nradiation and lasers, respectively, are providing important\r\ndynamical information on molecular photoionization. We\r\nhave studied the underlying dynamical features of these\r\nionization processes using Hartree-Fock continuum orbitals\r\ngenerated using the Iterative Schwinger Variational method\r\nfor solving the photoelectron collisional equations. Our\r\nsingle-photon studies examine the important role that\r\nshape and autoionizing resonances play in molecular photoionization,\r\nwhile the multiphoton studies investigate the\r\nionization dynamics of excited electronic states.
\r\n\r\nWe have demonstrated the subtle nature of shape\r\nresonances in polyatomic systems such as C2H2 and C2N2,\r\nwhere the possibility of multiple resonances in a single\r\nchannel is observed. In addition, these resonant states\r\ninduce the breakdown of the Franck-Condon approximation as\r\nwell as the frozen core approximation in K-shell\r\nionization, as illustrated in our vibrationally resolved\r\nstudies of CO and the K-Shell studies of N2 and CO2,\r\nrespectively. Critical comparisons with other theoretical\r\nresults and available experimental data have been made for\r\nthese systems.
\r\n\r\nMolecular autoionizing resonances are known to\r\ndominate regions of the photoionization spectra. We have\r\nadapted and applied a generalization of the Fane treatment\r\nfor autoionization to molecular systems. Results for H2\r\nand C2H2 autoionizing resonances are presented and\r\ndiscussed.
\r\n\r\nResonant enhanced multiphoton ionization (REMPI) is\r\ncurrently being used to study the dynamics of state-selected\r\nphotoionization processes by laser excitation to\r\nspecific vibrational and rotational levels. As first\r\napplications of a quantitative analysis for molecular\r\nREMPI we have studied several ionization schemes in H2,\r\nsuch as (3+1) REMPI via the C1\u220fu state, (2+1) REMPI via\r\nthe B1\u03a3u+ state, and (2+1) REMPI via the double-well\r\nE,F1\u03a3g+ state. These ab initio studies are very useful in g\r\nunderstanding the underlying dynamics of molecular REMPI,\r\ne.g., the observed non-Franck-Condon behavior of the\r\nvibrational branching ratios in the C1\u220fu and E,F1\u03a3g+\r\nstates can be primarily attributed to the internuclear\r\ndistance dependence of the electronic transition moments.\r\nWe compare and discuss our theoretical results with the\r\navailable experimental data.
" }, { "name": "Mandler, Jorge Anibal", "degree": "PhD", "year": "1987", "title": "Robust Control System Design for a Fixed-Bed Catalytic Reactor", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03212008-092922", "creators": [ { "name": { "family": "Mandler", "given": "Jorge Anibal" }, "id": "Mandler-Jorge-Anibal", "display_name": "Mandler, Jorge Anibal" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "member", "display_name": "Morari, Manfred" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/czeb-7c12", "abstract": "The design of control systems in the face of model uncertainty is addressed. A methodology for the design of robust control schemes is outlined, which employs the Structured Singular Value as an analysis tool and Internal Model Control as the synthesis framework. This methodology is applied to the design of control systems for a fixed-bed, laboratory, catalytic methanation reactor. The design procedure allows a clear insight on the fundamental limits to closed-loop performance and provides controllers with explicit stability and performance guarantees for the case of plant-model mismatch.
\r\n\r\nThe overall controller design effort is initiated with a careful mathematical modeling of the system. The original nonlinear partial differential equations are converted through collocation techniques into a nonlinear ordinary-differential/algebraic equation system amenable to dynamic simulation. Interactive software is developed for the open- and closed-loop simulation of general nonlinear differential-algebraic systems, which provides an efficient means to simulate the reactor model. Linearization and control-relevant model reduction techniques are applied to arrive at models appropriate for the control studies.
\r\n\r\nBoth the single-input single-output and the multivariable case are addressed. Three different control configurations are investigated in the context of the single- pass operation of the reactor. In each case-study presented, the controller design procedure is divided into four steps: first, the definition of the control objectives, which not only leads to the selection of the appropriate control configuration but also determines the most adequate design techniques to employ; second, a nominal design step, in which the system-inherent limitations to the closed-loop performance are highlighted; third, a characterization of the uncertainty and the use of this information in the design of robust controllers; and, fourth, the evaluation of the designs through nonlinear simulations.
\r\n\r\nThe thesis describes the first application of structured singular value-based analysis techniques to a chemical reactor system and is in essence the first comprehensive study of the application of robust control to fixed-bed reactors. The power of the new mathematical theory for robust control system design is demonstrated. It is shown that the design of control systems for complex, distributed systems such as the methanation reactor can be addressed in a practical way, and low-order controllers be adequately obtained, which possess near-optimal characteristics when applied in a realistic environment of uncertainty and unavailability of measurements.
\r\n" }, { "name": "Marshall, Janet Layne", "degree": "PhD", "year": "1987", "title": "Spectroscopy and Photochemistry of Pyrazolyl-Bridged Binuclear Iridium(I) Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02192019-111735898", "creators": [ { "name": { "family": "Marshall", "given": "Janet Layne" }, "id": "Marshall-Janet-Layne", "display_name": "Marshall, Janet Layne" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/63cx-a405", "abstract": "Spectroscopic studies of a series of pyrazolyl-bridged and substituted-pyrazolyl-bridged binuclear iridium(I) complexes indicate that the description of the metal-metal interactions in previously studied D4h d8-d8 rhodium(I), iridium(I), and platinum(II) species may be extended to these lower symmetry (C2v) d8-d8 molecules. Specifically, the 1A1(d\u03c3)2 (d\u03c3*)2 ground state exhibits weak metal-metal bonding, and the lowest excited states are a singlet (1B2) and triplet (3B2) derived from the (d\u03c3)2(d\u03c3*)1(p\u03c3)1 electronic configuration. The 1B2 and 3B2 excited states, which are expected to feature strong metal-meta1 bonding, are 1uminescent at ambient temperature in fluid solution.
\r\n\r\nElectronic absorption and emission spectroscopic studies and photophysical investigations of the emissive singlet and triplet excited states of bis(1,5-cyclooctadiene)bis(\u00b5-pyrazolyl)diiridium(I), [Ir(\u00b5-pz)(COD)]2, and analogous substituted-pyrazolyl complexes are presented in Chapter 2. The absorption spectrum of [Ir(\u00b5-pz)(COD)]2 exhibits an intense band attributable to 1A1 \u2192 1B2 at 498 nm (\u03b5 = 8100 M-1cm-1). Both fluorescence (\u03bbmax = 558 nm, \u03a6em = 0.0001, \u03c4 < 20 ps) and phosphorescence (\u03bbmax = 684 nm, \u03a6em = 0.0078, \u03c4 = 250 ns) from the 1B2 and 3B2 excited states, respectively, are observed at ambient temperature for this complex. The absorption and emission spectra of the substituted-pyrazolyl complexes show similar features. In addition, ground-state resonance Raman studies of these complexes suggest the presence of a reasonable metal-metal bonding interaction in the formally nonbonded binuclear center; excitation into the bands corresponding to the metal-metal localized 1A1 \u2192 1B2 transition results in resonance-enhancement of vibrations at frequencies of of 58 cm-1 to 80 cm-1 that are assigned to \u03bd(Ir-Ir ).
\r\n\r\nThe long lifetime of the 3B2(d\u03c3*p\u03c3) excited state of [Ir(\u00b5-pz)-(COD)]2 implies that it should be able to participate in bimolecular reactions. The results presented in Chapter 3 show that this strongly reducing excited state undergoes photoinduced electron transfer with a variety of substrates including reversible electron transfer to one-electron acceptors such as methyl viologen and pyridinium monocations. For pyridinium acceptors with reduction potentials ranging from -0.67 V to -1.85 V vs. SSCE, the rates of electron-transfer quenching range from a diffusion-limited rate of 2.0 x 1010 M-1s-1 to 1.1 x 106 M-1s-1 and obey Marcus-theory predictions for outer-sphere electron transfer in the \"normal free-energy region.\" However, the rates do not decrease as predicted for the \"inverted free-energy region.\" With acceptors such as halocarbons, the unproductive back-electron-transfer reaction can be circumvented, and net two-electron, photoinduced electron transfer yields iridium(II)-iridium(II) oxidative addition products.
\r\n\r\nChapter 4 focuses on spectroscopic and photophysical investigations of pyrazolyl-bridged binuclear iridium(I) complexes containing carbon monoxide ligands. Spectroscopic studies of tetracarbonylbis(\u00b5-pyrazolyl)diiridium(I), tetracarbonylbis(\u00b5-3-methylpyrazolyl)diiridium(I), and tetracarbonylbis(\u00b5-3,5-dimethylpyrazolyl)diiridium(I) reveal interesting features in the electronic absorption spectra at ambient temperature and 77 K that may be assigned to d\u03c0(xz,yz) \u2192 [\u03c3(pz), \u03c0*(CO)] transitions and predominantly metal-metal localized \u03c3*(dz2) \u2192 [\u03c3(pz),\u03c0* (CO)] transitions that reflect the degree of metal-meta1 interaction. Photophysical studies of the emissive 1,3B2(d\u03c3* p\u03c3) excited states suggest that a higher-energy d-d excited state may provide a pathway for thermal deactivation of these states.
" }, { "name": "Masek, Brian B.", "degree": "PhD", "year": "1987", "title": "The Static and Dynamic Conformational Properties of Some (1,5)-Naphthalenophanes", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-134845027", "creators": [ { "name": { "family": "Masek", "given": "Brian B." }, "id": "Masek-Brian-B", "display_name": "Masek, Brian B." } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/avbq-t834", "abstract": "The Molecular Mechanics (MM) method has been applied to several dioxa-(1,5)-naphthalenophanes (1: n=14, 15, and 16, referred to as C14, C15, and C16 respectively). A systematic search, which considered many low-lying conformations, lead to the conclusion that there is no significant statistical contribution to the large negative activation entropies observed for the enantiomerization reactions of C14 and C15.
\r\n\r\nSimple rules from the conformational analysis of large-ring alkanes indicated relatively few possible low energy conformations. Evaluation of the structures by MM lead to predictions about the ground state conformations of C14-C16. For C16, the [9373] conformation is predicted to be the preferred conformation, with the [8383] conformation near in energy. For C15, a class of ring expanded or contracted structures, related to higher and lower homologues, are found to be lowest in energy. Two structures, [83163] and [83712], were predicted to be the lowest in energy. For C14, the [8363] conformation is predicted to be the ground state.
\r\n\r\nX-ray diffraction shows the conformation of C16 in the solid state to be [9363]. Fully refined structures were not obtained for C14 and C15 because of disorder. Therefore, a method based on 13C chemical shifts in the solid state was applied. Solid state CP-MAS 13C NMR correctly identifies the conformation of C16 as [9373]. In addition, the 13C shifts indicate the conformation of C14 to be [8363], as predicted. For C15, only the ring expanded or contracted class of conformations is consistent with the 13C NMR data.
\r\n\r\nThe kinetics for the jump-rope reaction of an N,N,N',N'-tetramethyldiamino-(1,5)-naphthalenophane (2) have been obtained by DNMR in D2O, CD3CN, and CD3OD. The solvent has little or no effect on the derived activation parameters. However, large differences between 2 and C14 were noted. The differences were rationalized as being due to a change in the ground state from the [8363] conformation in C14 to the [5555] conformation in 2.
\r\n\r\nFinally, the kinetics of the jump-rope reaction of a gem-dimethyl substituted dioxa-(1,5)-naphthalenophane (3) were investigated. Comparison with C15 indicates no changes were induced in the activation parameters for the process.
" }, { "name": "Meinhart, James Douglas", "degree": "PhD", "year": "1987", "title": "Synthesis and Reactivity of Titanocene Methylene Complexes and Bis(\u03b7\u2075-Cyclopentadienyl) Titanacyclobutenes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-165401033", "creators": [ { "name": { "family": "Meinhart", "given": "James Douglas" }, "id": "Meinhart-James-Douglas", "display_name": "Meinhart, James Douglas" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/16dt-2465", "abstract": "Syntheses of several bis(\u03b75-cyclopentadienyl) titanium methylene phosphine complexes are reported. The titanium methylene phosphine complexes are generated from themolysis of titanacyclobutanes in the presence of excess phosphine. Spectral data and reactivity are consistent with a methylene phosphine complex rather than an ylide complex.
\r\n\r\nBis(\u03b75-cyclopentadienyl) titanacyclobutenes are readily synthesized by treatment of sources of \"Cp2TiCH2\" with disubstituted alkynes. A variety of stable titanacyclobutenes were synthesized containing aryl, alkyl, and etherial substituents. Titanacyclobutenes, unlike the related titanacyclobutanes, do not reform \"Cp2TiCH2\" thermally.
\r\n\r\nTitanacyclobutenes insert carbon monoxide, forming an acyl intermediate which rearranges to a titanocene vinyl ketene complex. A trimethylphosphine adduct of one of the ketene complexes was characterized by x-ray diffraction techniques. The carbonylation mechanism involves insertion of carbon monoxide into the more accessible titanium-carbon bond, followed by intra-molecular attack of the vinyl group to the acyl. Insertion of t-butyl isocyanide into a titanacyclobutene yields a cyclic imino-acyl complex, which was also characterized by x-ray diffraction. The vinyl ketene complexes react with many unsaturated substrates (alkynes, ethylene, and aldehydes) to form new organotitanium species.
\r\n\r\nTitanacyclobutenes react with ketones and aldehydes via 1,2-addition to yield titanium oxacyclohexenes. Aldehydes form both titanium-oxygen and titanium-carbon regioisomers. The organic ligand may be removed from the titanium to give homo-allylic alcohols in good yield. Nitriles also insert into titancyclobutenes to roduce titanium imidocyclohexenes.
" }, { "name": "Middlemas, David S.", "degree": "PhD", "year": "1987", "title": "Topographical Studies of the Nicotinic Acetylcholine Receptor", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04172019-103221069", "creators": [ { "name": { "family": "Middlemas", "given": "David S." }, "id": "Middlemas-David-S", "display_name": "Middlemas, David S." } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/se3p-8191", "abstract": "All four subunits of the nicotinic acetylcholine receptor in membrane vesicles isolated from Torpedo californica have been labeled with the photoactivated hydrophobic probe, [3H]adamantanediazirine, which selectively labels regions of integral membrane proteins in contact with the hydrocarbon core of the lipid bilayer. As all of the homologous subunits are exposed to the lipid bilayer, it is probable that they each interact with the surrounding membrane in a similar fashion.
\r\n\r\nAll four subunits of the acetylcholine receptor in membrane vesicles isolated from Torpedo californica have been labeled with [3H]cholesteryl diazoacetate. As this probe incorporates into lipid bilayers analogously to cholesterol, this result indicates that acetylcholine receptor interacts with cholesterol. This investigation also demonstrates that this probe is a useful reagent for studying the interaction of cholesterol with membrane proteins.
\r\n\r\nSince the photogenerated carbene is situated near the lipid-water interface, this probe has potential as a topographic tool for mapping membrane protein structure. The labeling studies with both [3H]adamantanediazirine and [3H]cholesteryl diazoacetate support the concept that the acetylcholine receptor is a pseudosymmetric complex of homologous subunits, all of which interact with and span the membrane.
\r\n\r\nThe syntheses of the fluorine-containing agonists for the Torpedo californica nicotinic acetylcholine receptor, fluoroacetylcholine bromide and p-fluorophenyltrimethylammonium iodide, are described. It is demonstrated that both are agonists using a cation flux assay with acetylcholine receptor enriched membrane vesicles. The potential for their use in ligand binding studies using 19F NMR spectroscopy is discussed.
\r\n\r\nThe affinity cleavage reagent, p-thiocyanophenyltrimethylammonium iodide, specifically cleaves a peptide bond of the nicotinic acetylcholine receptor in membrane vesicles isolated from Torpedo californica. It is demonstrated that this reagent is an agonist using a cation flux assay. The cleavage is blocked by stoichiometric quantities of \u03b1-bungarotoxin. The yield of the cleavage reaction is reduced with addition of the agonist, phenyltrimethylammonium iodide. This affinity cleavage reaction provides evidence for a low-affinity binding site for agonists on the 60K subunit.
" }, { "name": "Neitzel, James Joseph", "degree": "PhD", "year": "1987", "title": "The Expression, Stability, and Enzymatic Activity of Specific Beta-Lactamase Mutants", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162019-152444688", "creators": [ { "name": { "family": "Neitzel", "given": "James Joseph" }, "id": "Neitzel-James-Joseph", "display_name": "Neitzel, James Joseph" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "member", "display_name": "Hood, Leroy E." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/E6R6-4J57", "abstract": "Three catalytic site mutants (ser 70 to thr, thr 71 to ser, and the double mutant ser 70 to thr-thr 71 to ser) of the pBR 322 beta-lactamase were purified to homogeneity. These mutant proteins were unstable and could only be obtained from E. coli at 30\u00b0C, rather than the normal growth temperature of 37\u00b0. The use of the strong tac promoter increased the yield of the thr 71 to ser mutant protein. This promoter was coupled with a kanamycin resistance gene to create a new vector for the expression of inactive beta-lactamase mutants. A new purification protocol for the pBR 322 lactamase was devised. By replacing an early ion-exchange chromatography column with an ammonium sulfate precipitation, it was possible to isolate unstable beta-lactamases in high yield.
\r\n\r\nThe ser 70 to thr mutant and the double mutant show no catalytic activity and do not form an acyl enzyme intermediate. However, they do still retain the ability to bind benzylpenicillin. The thr 71 to ser mutant is active. The Km values for benzylpenicillin and cephalothin hydrolysis are unchanged from the wild-type enzyme, while the kcat values are approximately 15% of the wild-type value. This mutant also cleaves the poor substrate cefoxitin, again with no significant change in Km, but with kcat reduced to 8% of the wild-type value. Examination of the pre-steady state burst during cefoxitin hydrolysis showed that the thr 71 to ser enzyme acylated at the same rate and to at least 80% of the extent of the wild-type enzyme. Direct measurement of the deacylation rate confirmed that a reduction in the deacylation rate is responsible for the lowered reaction rate in this mutant protein. Additionally, this protein lost catalytic activity at elevated temperature more rapidly than the wild-type enzyme.
\r\n\r\nThe denaturation of the active thr 71 to ser mutant was observed in more detail. This enzyme thermally denatures at 45\u00b0, a temperature 10 to 15\u00b0 lower than that required to denature the wild-type enzyme. This mutant is also more susceptible to digestion by thermolysin, trypsin, and those proteases present in vivo in the periplasmic space of E. coli. The enzyme also loses activity at a urea concentration of 2 M, whereas the wild-type enzyme is still active at urea concentrations greater than 4 M. The inactive mutants ser 70 to thr and ser 70 to thr-thr 71 to ser are even more susceptible to proteolytic attack by E. coli proteases in vivo.
\r\n\r\nA mutant pBR 322 beta-lactamase lacking the disulfide bond found in the wild-type enzyme was also purified to homogeneity. This protein showed no alterations in catalytic activity relative to the wild-type enzyme at temperatures below 40\u00b0. Above this temperature, this enzyme rapidly lost activity. This enzyme was also more susceptible to proteolytic attack at elevated temperature. However, this enzyme is more resistant to thermal and proteolytic denaturation than the thr 71 to ser mutant betalactamase.
" }, { "name": "Ni, Ching-Long", "degree": "PhD", "year": "1987", "title": "Electrocatalytic Reduction of Dioxygen at Chemically Modified Electrodes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07102015-095638444", "creators": [ { "name": { "family": "Ni", "given": "Ching-Long" }, "id": "Ni-Ching-Long", "display_name": "Ni, Ching-Long" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/EPT0-NF02", "abstract": "The kinetics of the reduction of O2 by Ru(NH3)6+2 as catalyzed by cobalt(II) tetrakis(4-N-methylpyridyl)porphyrin are described both in homogeneous solution and when the reactants are confined to Nafion coatings on graphite electrodes. The catalytic mechanism is determined and the factors that can control the total reduction currents at Nafion-coated electrodes are specified. A kinetic zone diagram for analyzing the behavior of catalyst-mediator-substrate systems at polymer coated electrodes is presented and utilized in identifying the current-limiting processes. Good agreement is demonstrated between calculated and measured reduction currents at rotating disk electrodes. The experimental conditions that will yield the optimum performance of coated electrodes are discussed, and a relationship is derived for the optimal coating thickness.
\r\n\r\nThe relation between the reduction potentials of adsorbed and unadsorbed cobalt(III) tetrakis(4-N-methylpyridyl)porphyrin and those where it catalyzes the electroreduction of dioxygen is described. There is an unusually large change in the formal potential of the Co(III) couple upon the adsorption of the porphyrin on the graphite electrode surface. The mechanism in which the (inevitably) adsorbed porphyrin catalyzes the reduction of O2 is in accord with a general mechanistic scheme proposed for most monomeric cobalt porphyrins.
\r\n\r\nFour new dimeric metalloporphyrins (prepared in the laboratory of Professor C. K. Chang) have the two porphyrin rings linked by an anthracene bridge attached to meso positions. The electrocatalytic behavior of the diporphyrins towards the reduction of O2 at graphite electrodes has been examined for the following combination of metal centers: Co-Cu, Co-Fe, Fe-Fe, Fe-H2. The Co-Cu diporphyrin catalyzes the reduction of O2 to H2O2 but no further. The other three catalysts all exhibit mixed reduction pathways leading to both H2O2 and H2O. However, the pathways that lead to H2O do not involve H2O2 as an intermediate. A possible mechanistic scheme is offered to account for the observed behavior.
" }, { "name": "O'Connor, Kim Claire", "degree": "PhD", "year": "1987", "title": "The Effects of Immobilization on Structure and Substrate Activation of Glutamate Dehydrogenase", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03042008-094030", "creators": [ { "name": { "family": "O'Connor", "given": "Kim Claire" }, "id": "O'Connor-Kim-Claire", "display_name": "O'Connor, Kim Claire" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Arnold", "given": "Frances Hamilton" }, "id": "Arnold-F-H", "orcid": "0000-0002-4027-364X", "role": "member", "display_name": "Arnold, Frances Hamilton" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/qavk-kj50", "abstract": "Structure and substrate activation of bovine liver glutamate dehydrogenase were investigated when the enzyme was in its native state or was covalently bound via primary amino groups to a solid Sepharose bead. In this research, the enzyme was covalently bound directly to CNBr-activated Sepharose 4B or indirectly, via a six-carbon spacer arm, to CH-activated Sepharose 4B. Electron spin resonance spectroscopy was employed to study structure. This study required spin labeling glutamate dehydrogenase with either 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl or 4((4-(chloromercurio)benzoyl)amino)-2,2,6,6-tetramethyl-1-piperidinyloxy. Substrate activation of the deamination of glutamate by NAD was visible in Lineweaver-Burk plots of inverse rate vs. inverse substrate concentration.
\r\n\r\nThe electron spin resonance spectrum of glutamate dehydrogenase spin labeled with 2,2,6,6-tetramethyl-4-oxopiperidine-1-oxyl was a composite consisting primarily of two populations of spin labels with outer peak separations of 33 gauss (population A) and 69 gauss (population B). For the native enzyme in solution, population A accounted for 10% of the spectrum. This percentage increased to 21 when the active site was saturated with substrates during spin labeling and increased to 34 when the enzyme was immobilized to either CNBror CH-activated Sepharose. The roles of aspecific labeling and structural heterogeneity in these spectral changes were discussed. Modification of the native and immobilized enzyme with pyridoxal 5'-phosphate characterized the binding site(s) for the spin label. Deconvolution of experimental spectra into populations A and B divulged a subpopulation of labels with a mobility unlike those of the two principal components. Linear combinations of the deconvoluted line shapes for populations A and B successfully represented all spectra of glutamate dehydrogenase from this and previous investigations.
\r\n\r\nConformational change in glutamate dehydrogenase was investigated by spin labeling the enzyme at cysteine 319 with 4((4-(chloromercurio)benzoyl)-amino)-2,2,6,6-tetramethyl-1-piperidinyloxy. Electron spin resonance spectra of spin-labeled glutamate dehydrogenase showed that immobilization of the enzyme on CNBr-activated Sepharose 4B suppressed conformational change induced by GTP and NADPH and profoundly altered that induced by aketoglutarate. Moreover, the spectrum of the immobilized enzyme provides evidence for structural heterogeneity at cysteine 319.
\r\n\r\nCovalently binding glutamate dehydrogenase to CNBr- and CH-activated Sepharose 4B altered the substrate activation pattern of the biocatalyst. Specifically, the sharp discontinuity, which characterizes Lineweaver-Burk plots of free enzyme kinetics with NAD as the varied substrate, became elongated when the biocatalyst was attached to either support. The elongated transition region contains two inflection points and resembles substrate activation of several other allosteric oligomers. Under the same experimental conditions, glutamate induced varying degrees of abrupt activation in immobilized glutamate dehydrogenase and inhibited the enzyme in solution. The intensity of this activation is inversely proportional to the rate constant of the biocatalyst-Sepharose conugate. These modified activation patterns may be due in part to increased structural heterogeneity and altered conformational change. The above kinetic results are free of mass transport effects: the external effectiveness factor was unity, the observable Thiele modulus was less than 2.0 \u2022 10-4, and reaction- generated pH change was less than 0.01 for all data reported in this paper.
\r\n" }, { "name": "Onuchic, Jos\u00e9 Nelson", "degree": "PhD", "year": "1987", "title": "New aspects of the theory of electron transfer reaction dynamics", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242006-162144", "creators": [ { "name": { "family": "Onuchic", "given": "Jos\u00e9 Nelson" }, "id": "Onuchic-Jos\u00e9-Nelson", "orcid": "0000-0002-9448-0388", "display_name": "Onuchic, Jos\u00e9 Nelson" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hcep-rh59", "abstract": "This thesis deals basically with some new aspects of the electron transfer theory. It is divided into four parts: (1) Chapter I gives an introduction to the electron transfer problem; (2) Chapter II addresses the subject of how nuclear dynamics influences the electron transfer rate; (3) Chapter III explains how to calculate electron transfer matrix elements for non-adiabatic electron transfer systems, in particular protein systems; and (4) Chapter IV discusses some preliminary ideas about new problems I intend to work on the future.
\r\n\r\nIn Chapter II the following dynamical problems are addressed. For the case of one overdamped reaction coordinate, the problem of adiabaticity and non-adiabaticity is considered in details. For an underdamped reaction coordinate, a preliminary discussion is given. All this formalism is developed using a density matrix formalism and path integral techniques. One of the advantages of using this formalism is that, by analyzing the spectral density, we can connect our microscopic Hamiltonian with macroscopic quantities. It also gives us a natural way of including friction in the problem. We also determine when the Hopfield semiclassical or the Jortner \"quantum\" models are good approximations to the \"complete\" Hamiltonian. In the limit that the reaction coordinates are \"classical,\" we discuss how we can obtain the Fokker-Planck equation associated with the Hamiltonian.
\r\n\r\nBy adding more than one reaction coordinate to the problem (normally two), several other problems are studied. The separation of \"fast\" quantum modes from \"slow\" semiclassical modes, where the fast modes basically renormalize the electronic matrix element and the driving force of the electron transfer reaction, is discussed. Problems such as exponential and non-exponential decay in time of the donor survival probability, and the validity of the Born-Oppenheimer and Condon approximations are also carefully addressed. This chapter is concluded with a calculation of the reaction rate in the inverted region for the extreme adiabatic limit.
\r\n\r\nIn Chapter III we discuss calculations of electronic matrix elements, which are essential for the calculation of non-adiabatic rates. It starts with a discussion of why, through bond rather than through space, electron transfer is the important mechanism in model compounds. Also, it explains why tight-binding Huckel calculations are reasonable for evaluating these matrix elements, and why, through space and through bond, matrix element decays with distance have a different functional dependence on energy. Bridge effects due to different hydrocarbon linkers are also calculated.
\r\n\r\nThis chapter concludes with a model for the calculation of matrix elements in proteins. The model assumes that the important electron transfer \"pathways\" are composed of both, through bond and through space parts. Finally, we describe how medium (bridge) fluctuations may introduce a new form of temperature dependence by modulating the matrix element.
\r\n\r\nIn Chapter IV we discuss some experimental results obtained for electron transfer in the porphyrin-phenyl-(bicyclo[2.2.2]octane)n-quinone molecule, and we propose some new experiments that should help to clarify our interpretation. It concludes with some preliminary discussions of how we can include entropy in the finite mode formalism described in Chapter II, and how we intend to use the formalism described in Chapter III in order to understand electron transfer in real protein systems.
" }, { "name": "Paciello, Rocco Angelo", "degree": "PhD", "year": "1987", "title": "Synthesis and Reactivity of Electron-Rich Ruthenium and Iron Half-Sandwich Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-091323168", "creators": [ { "name": { "family": "Paciello", "given": "Rocco Angelo" }, "id": "Paciello-Rocco-Angelo", "display_name": "Paciello, Rocco Angelo" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/exhb-6f18", "abstract": "Late transition metal organometallic complexes, Cp*(PR3)2MX (Cp* = \u03b75-C5Me5), with highly electron donating ligand sets have been synthesized and their reactivity studied. Synthetic routes which allow systematic variation of metal (Ru, Fe), phosphines (PMe3, PEt3, PnBu3, PMe2Ph, DMPE), and sigma-bonded ligands (halide, hydride, alkyl, heteroatom) have been developed.
\r\n\r\nThermally and photochemically induced ligand loss from these complexes has been studied. Trapping and C-H bond activation chemistry have been observed for the transient [Cp*(PR3)MX] complexes produced upon ligand loss. The reactivity of analogous ruthenium and iron complexes is compared and discussed.
\r\n\r\nThe Ru(IV) complex, Cp*(PMe3)RuH3, has been prepared and isolated. This complex is found to catalyze H-D exchange, and hydrogenations of unsaturated organic species. The analogous Fe(IV) complex, Cp*(PMe3)FeH3, has been prepared and observed spectroscopically. Hydrogen bonding modes in these polyhydrides are discussed. Highly fluxional Cp*(PMe3)FeH3 is proposed to be in equilibrium with Cp*(PMe3)Fe(\u03b72-H2)H.
\r\n\r\nAn equilibrium method for the determination of relative Ru-X and Ru-Y bond strengths in Cp*(PMe3)2RuX has been developed. A linear correlation of Ru-X to H-X bond strengths has been found over a wide range of ligands, X. The relationship is found to be general for a number of metal centers.
\r\n\r\nA study of the kinetics of phosphine exchange for Cp*(PMe3)2RuX has been undertaken. The rate of phosphine loss can be abstracted from a treatment of the kinetics of approach to equilibrium. Lone pairs on X are found to promote ligand dissociation. Dative bond dissociation enthalpies are obtained if small, and constant, barriers for ligand recombination are assumed. The functional group approximation used in solution thermochemical studies is found to break down when large changes are made in the steric constraint at the metal center.
" }, { "name": "Peake, Geoffrey Tower", "degree": "PhD", "year": "1987", "title": "Studies of the Donor Properties of New Polyanionic Chelating Ligands through the Synthesis and Characterization of Osmium Complexes", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-094659896", "creators": [ { "name": { "family": "Peake", "given": "Geoffrey Tower" }, "id": "Peake-Geoffrey-Tower", "display_name": "Peake, Geoffrey Tower" } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/68mt-5y71", "abstract": "The synthesis, characterization, physical and chemical properties of osmium complexes containing highly donating polyanionic chelating (PAC) ligands are discussed.
\r\n\r\nThe tetradentate tetraanionic ligand HBA-B (H4HBA-B \u2261 1,2-bis(2-hydroxybenzamido)benzene) coordinates to osmium to form a variety of complexes. Reaction of H4HBA-B with K2[Os(OH)4(O)2] gives an osmium(VI) trans-dioxo complex coordinating the PAC ligand through two deprotonated phenol groups and two deprotonated amide groups. Reduction of the dioxo species with triphenylphosphine gives the neutral osmium(IV) species trans-Os(\u03b74-HBA-B)(PPh3)2 (3). This complex is an excellent starting material to make a series of osmium(IV) complexes because of the lability of the phosphine ligands. Ligand exchange reactions with nitrogen-base ligands, anionic two-electron donor ligands, mono- and bidentate phosphines, \u03c0-acid ligands, and bipyridines are observed. Most of the osmium(IV) PAC ligand complexes prepared are paramagnetic with \u03bceff ~1 BM. The paramagnetic osmium(IV) species all exhibit well-resolved, paramagnetically shifted NMR spectra. The complex trans-Os(\u03b74-HBA-B)(PPh3)(py) (5) has twelve inequivalent sets of protons, all of which are on aromatic rings. The twelve resonances are observed in the 1H NMR spectrum in the range +11 to -5 ppm. The results of 2D-COSY and difference NOE experiments allow the complete assignment of the 1H NMR spectrum.
\r\n\r\nElectrochemical studies of these osmium(IV) complexes, and the coordination chemistry observed indicate that these PAC ligands are very good electron donors to osmium. The Os(IV/III) reversible couples for the neutral osmium(IV) species have potentials m the range -0.9 to -0.7 V vs. Fc+/Fc. The cation/neutral reversible couples have potentials in the range +0.2 to +0.35 V vs. Fc+/Fc, but probably cannot be called Os(V/IV) couples. Reaction of 3 with carbon monoxide produces a rare osmium(IV) carbonyl complex, cis-\u03b1-Os(\u03b74-HBA-B)(PPh3)(CO) (10). Reaction of t-butylisocyanide with 3 gives the analogous mono-phosphine mono-isocyanide. The stability of these complexes in an indication of the strong donating nature of the PAC ligand.
\r\n\r\nA crystal structure of 10 shows it to have a cis-\u03b1 coordination geometry. Complexes with cis geometries can also be made by reacting 3 with bidentate ligands, such as dppe. Cis-\u03b1 and cis-\u03b2 osmium complexes of the HBA-B PAC ligand, and other PAC ligand complexes, contain the first nonplanar amide ligands. We have defined three causes for the formation of nonplanar amide ligands: (1) structural requirements of the metal center (for instance coordination of a bidentate dppe ligand forcing a cis geometry), (2) depletion of electron density from the metal center (either by oxidation or coordination of an electron withdrawing ligand), causing the amide ligands to adopt the more highly donating nonplanar structure and offset the depletion of electron density at the metal, (3) steric interactions forcing deformation of the amide ligand to a nonplanar state.
\r\n\r\nThe syntheses of osmium complexes containing the CHBA ligand (H2CHBA \u2261 3,5-dichloro-2-hydroxybenzamide) are discussed. Several complexes, including trans-Os(\u03b72-CHBA)2(PBu3)2 (26) and trans-Os(\u03b72-CHBA)2(OPBu3)2 (27), have been prepared in attempts to make a long-lived catalyst for the electrochemical oxidation of alcohols. The cyclic voltammetric experiments with 26 and 27 in the presence of alcohol are discussed. It appears that 27 exhibits catalytic behavior and 26 does not. A detailed study probing the catalysis has not been done.
\r\n\r\nThe results of reactions between K2[Os(OH)4(O)2] and ligands similar to 2-(2-hydroxyphenyl)imidazole are reported. The reactions give neutral osmium(VI) trans-dioxo complexes containing two 2-(2-phenoxy)imidazole ligands coordinated as bidentate monoanions through a phenoxy ligand and an imidazole ligand. This coordination mode contrasts with that observed for osmium complexes of 2-(3,5-dichloro-2-hydroxyphenyl)-5,6-dichlorobenzimidazole, which coordinates as a dianion.
" }, { "name": "Peretti, Steven William", "degree": "PhD", "year": "1987", "title": "Theoretical Modeling and Experimental Investigation of Host-Plasmid Interactions in Recombinant Escherichia coli", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03102008-130217", "creators": [ { "name": { "family": "Peretti", "given": "Steven William" }, "id": "Peretti-Steven-William", "display_name": "Peretti, Steven William" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Emr", "given": "Scott D." }, "id": "Emr-S-D", "role": "member", "display_name": "Emr, Scott D." }, { "name": { "family": "Bertani", "given": "Giuseppe" }, "id": "Bertani-G", "role": "member", "display_name": "Bertani, Giuseppe" } ], "option_major": [ "chemeng" ], "doi": "10.7907/M1F6-R062", "abstract": "Microbial metabolism has been mathematically represented with sufficient mechanistic rigor to allow consideration of the ramifications of introducing recombinant vectors on host cell metabolic activity. The model was first verified using details of transcription and translation sufficiently stringent to test the simulation of RNA polymerase equilibrium distribution on promoter regions and the activation of ribosomes by binding of mRNA.
\r\n\r\nPlasmids were added to the formulation, and the dependence of productivity and growth rate was simulated. The results show good agreement with those obtained by other researchers. This model structure was then used to simulate potentially beneficial metabolic engineering scenarios in an attempt to identify those processes limiting productivity for recombinant systems. Simulation results indicate that transcription is the metabolic bottleneck that limits product synthesis. In addition, the most efficient strategy for enhancing plasmid product synthesis was shown to be increasing the efficiency of plasmid mRNA translation.
\r\n\r\nAn asynchronous population was simulated in order to study the transient behavior of the cell model. Based on plasmid-free simulation results, the model accurately reflects the predominant metabolic structure for control of macromolecular synthesis. Transient response considerations for plasmid-containing populations suggest that dynamic reactor operation, in the form of induction of plasmid promoter activity, leads to transient accumulation of product which exceeds that attained during the subsequent balanced growth.
\r\n\r\nFinally, the effect of different plasmid copy numbers and of the concommitant expression of a constitutive plasmid-borne gene were investigated experimentally. Radio-labeling techniques combined with filter hybridizations were used to study the transcription rate from the \u03b2-lactamase promoter as well as the level of corresponding mRNA present in the cell. Coupled with product activity measurements, the stability of the plasmid-derived message, as well as the efficiency of its translation into protein are reduced significantly as copy number increases.
" }, { "name": "Pjura, Philip", "degree": "PhD", "year": "1987", "title": "X-Ray Crystallographic Studies of DNA-Drug and DNA-Protein Interactions", "advisor": "Dickerson, Richard E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-113724052", "creators": [ { "name": { "family": "Pjura", "given": "Philip" }, "id": "Pjura-Philip", "display_name": "Pjura, Philip" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "member", "display_name": "Dickerson, Richard E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wpt7-9h98", "abstract": "I. Cisplatin-12mer
\r\n\r\nCisplatin (cis-diamminodichloroplatinum[II]) is a widely used antineoplastic agent, which is believed to work by means of covalent interaction with DNA. Complexes of this compound were made with the B-DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G by diffusion of the drug into pregrown DNA crystals, and a structure determined to 2.6 Angstrom resolution by molecular replacement. Cisplatin was found to bind with partial occupancy at three discrete sites: G16 (61%), G4 (30%) and G10 (22%), in each case by means of a single covalent bond from the metal to guanine N7 in the major groove. The square plane of the metal complex ligands is rotated out of the plane of the guanine base, with one of the ligands that is cis to the guanine N7, presumably an amine, in a position to make a hydrogen bond with guanine 06; the long metal-06 distance precludes the possiblilty of a direct metal-06 bond. The DNA structure itself is essentially undisturbed by the metal binding; the only change is a slight notion of the bound guanines outward into the major groove toward the metals, resulting in a slight opening up of the groove but without pulling the base-pairs out of the helix stack. The structure shows that it is not possible for a direct N7-to-N7 crosslink between two adjacent bases by the metal to exist in an intact B-DNA double-helix. It is suggested that the observed structure is a primary mode of binding of the drug, which then could become this postulated active form upon disruption of the DNA duplex.
\r\n\r\nII. Lac headpiece-operator complex
\r\n\r\nThe lac repressor protein of E. coli controls expression of the genes necessary for lactose utilization by the organism. It is a tetramer of four identical subunits of 355 amino acids each, each of which is divided into a 51 amino acid N-terminal DNA-binding, or \"headpiece\" domain and a 300 residue C-terminal regulatory region, or \"core.\" In the presence of 1M Tris.HCl pH 7.5 and 30% glycerol, the headpiece can be isolated intact by proteolytic digestion and is believed to retain its specific DNA binding properties for the lac operator site. A large-scale purification scheme for the headpiece protein has been developed, using a specific protease-affinity column to eliminate all residual proteolytic activity from the prep, thus making it possible to isolate large quantities of the protease-sensitive fragment in stable form for crystallization trials. Attempts to crystallize the protein by itself resulted only in fibrous microcrystals. But cocrystallization trials with a 21 base-pair lac operator DNA oligomer yielded what appear to be small cocrystals, too small to characterize, under conditions in which neither the protein nor the DNA by themselves would crystallize.
\r\n\r\nIII. Hoechst 33258-Complex with DNA 12mer
\r\n\r\nHoechst 33258 is a widely used histological stain that forms a fluorescent complex with DNA, showing strong preference for AT-rich regions. Crystals were grown of a 1:1 complex of the dye with the B-DNA 12rner C-G-C-G-A-A-T-T-C-G-C-G, and a structure was determined to 2.2 Angstrom resolution. The compound was found to bind noncovalently in the minor groove, with its aromatic phenol and two benzimidazole rings spanning three bases of the A-A-T-T region, and its aliphatic piperazine ring binding in the adjacent C-G-C-G region. Three hydrogen bond contacts were found to bridge between adjacent base-pairs, the bridging resembling that by water molecules in the native structure. This bridging of base pairs was achieved via three amine groups on the dye. These all undoubtedly help to stabilize the interaction, but the shape of the compound allows a good hydrogen bonding interaction of normal length through only one of these contacts. The piperazine ring, because of its orientation perpendicular to the other rings, is unable to bind into the narrower minor groove of the AT region and must bind in the wider CG minor groove. In a second conformation of the dye, also seen in the structure, the piperazine ring points out of the minor groove because of a rotation of the benzimidazole ring to which it is attached around its bond to the other benzimidazole. In this orientation, the piperazine ring no longer makes contact with the DNA, and therefore the drug is not restricted to binding at a site containing GC base-pairs. As a result, it could bind within a region of contiguous AT base-pairs without the problem of steric clash due to the piperazine ring.
" }, { "name": "Prairie, Michael Roland", "degree": "PhD", "year": "1987", "title": "Steady-State and Transient Methods for Modeling Chemical Reactions on Supported Catalysts", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-131434", "creators": [ { "name": { "family": "Prairie", "given": "Michael Roland" }, "id": "Prairie-Michael-Roland", "display_name": "Prairie, Michael Roland" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Babcock", "given": "Charles D." }, "id": "Babcock-C-D", "role": "chair", "display_name": "Babcock, Charles D." }, { "name": { "family": "Beck", "given": "James L." }, "id": "Beck-J-L", "role": "member", "display_name": "Beck, James L." }, { "name": { "family": "Jennings", "given": "Paul C." }, "id": "Jennings-P-C", "role": "member", "display_name": "Jennings, Paul C." }, { "name": { "family": "Hall", "given": "John F." }, "id": "Hall-J-F", "role": "member", "display_name": "Hall, John F." }, { "name": { "family": "Knowles", "given": "James K." }, "id": "Knowles-J-K", "role": "member", "display_name": "Knowles, James K." }, { "name": { "family": "Sabersky", "given": "Rolf H." }, "id": "Sabersky-R-H", "role": "member", "display_name": "Sabersky, Rolf H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/x3zp-aa54", "abstract": "A systematic experimental strategy based on fluid-phase measurements is proposed for modeling dynamic behavior of heterogeneous catalytic reactions. The strategy utilizes steady-state rate, step-response, cycled-feedstream, and feedback-induced bifurcation techniques. Ethylene hydrogenation on Pt/Al2O3 was studied using this strategy. In addition, transmission infrared spectroscopy is applied to investigate support effects which accompany ethylene hydrogenation on Pt/Al2O3, and to the detailed study of CO adsorption, desorption and oxidation on Rh/Al2O3. The proposed experimental strategy combined with surface infrared spectroscopy provides a very powerful means for identification and validation of dynamic kinetic models.
\r\n\r\nObserved bifurcation behavior can be accurately attributed to a model for the catalytic reaction only if each dynamic element in the closed-loop experimental hardware is properly accounted for. Accordingly, time delay and feedback gain were the manipulated parameters in a feedback-induced bifurcation scheme aimed at validating a dynamic model for an experimental gas-phase reactor flow system without reaction. The apparatus consists of an isothermal, stirred, fixed-bed reactor, mass flow controllers, an infrared gas analysis system, and a computerized data acquisition and control system. Experimental bifurcations to sustained oscillations show that the stability of the reactor system is strongly influenced by delay. The relationships of time delay to Hopf bifurcation gains and frequencies provide a very sensitive basis for model comparisons.
\r\n\r\nSteady-state, step-response, feedback-induced Hopf bifurcation and forced concentration cycling experiments were applied to study ethylene hydrogenation over 0.05% Pt/Al2O3 at 80\u00b0C. Step-response experiments indicate a time scale of 5000 s which is associated with chemisorbed hydrogen. Conversely, feedback-induced Hopf bifurcation data indicate this time scale to be on the order of 1 s in magnitude. In the overall strategy of dynamic modeling, the two techniques are complementary since each inherently focuses on an opposite region in the spectrum of time scales for the reactor system. Cycling the feedstream composition resulted in improvement of the time-average reaction rate for the ethylene hydrogenation reaction compared to steady-state reactor operation.
\r\n\r\nSteady-state, step-response and Hopf bifurcation data are also presented for 0.5% Pt/Al2O3 at 30\u00b0C and compared with results for the 0.05% Pt/Al2O3 catalyst. A single value of 2.5 s for the surface time constant associated with chemisorbed hydrogen is sufficient for modeling behavior on 0.5% Pt/Al2O3, whereas the lower-loaded 0.05% Pt/Al2O3 catalyst requires two very different values. In addition, the 0.5% catalyst was used to demonstrate the general result that small discrepancies between the actual and chosen reference steady state give rise to imperfect, cusp-like bifurcations. Steady-state bifurcation data are also shown to be useful for discriminating among rival kinetic models.
\r\n\r\nEthylene hydrogenation on spillover-activated alumina is proposed as an explanation for the very slow transient behavior observed for 0.05% Pt/Al2O3. Transmission infrared spectroscopy was used to study hydrogen spillover dynamics on 0.05% Pt/Al2O3 at 80\u00b0C via hydroxyl/deuteroxyl exchange. Ethylene in the gas-phase markedly slows the rate of spillover. The presence of ethylene likely reduces the concentration of platinum-adsorbed hydrogen adatoms, the precursors of hydrogen spilled onto alumina, due to catalytic hydrogenation on the platinum. Surface transport of hydrogen atoms on spillover-activated alumina is proposed as an explanation for the very slow transient behavior observed for ethylene hydrogenation on 0.05% Pt/Al2O3. Infrared spectra exhibit characteristics of both hydroxyl and deuteroxyl groups for reactor feed containing only D2 and C2H4. This observation confirms the existence of a dissociative ethylene adsorption process.
\r\n\r\nA section of the thesis unrelated to ethylene hydrogenation investigates modeling applications of transmission infrared spectoscopy (TIR) by applying it to study adsorbed CO on Rh/Al2O3 during CO chemisorption, steady-state, step-response, and forced-cycling oxidation experiments at 900 torr. At 300\u00b0C, the catalyst initially supported primarily a dicarbonyl CO species, but after use exhibited spectra characteristic of a surface mostly covered by linearly bound CO. A model that describes transient, diffusion-influenced CO adsorption and desorption for the supported catalyst is presented. It suggests that the CO desorption energy depends linearly on coverage, and that the magnitude of this dependence is a function of temperature. Observed rate dependence on bulk CO concentration for O2 effluent levels of 0.5% and 0.25% is interpreted considering the effects of internal and external mass transport at 300\u00b0C. Step-response and forced-cycling oxidation experiments across stoichiometric conditions exhibit oxygen and CO storage effects characteristic of CO oxidation catalysts. Data indicating autonomous oscillation of CO coverage and CO2 production are also presented.
" }, { "name": "Rivera, Daniel Eduardo", "degree": "PhD", "year": "1987", "title": "Modeling Requirements for Process Control", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-140158", "creators": [ { "name": { "family": "Rivera", "given": "Daniel Eduardo" }, "id": "Rivera-Daniel-Eduardo", "display_name": "Rivera, Daniel Eduardo" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" } ], "option_major": [ "chemeng" ], "doi": "10.7907/KS5Q-PJ57", "abstract": "Modeling and control system design have traditionally been viewed as distinct, independent problems. Not all model characteristics, however, are relevant to the control system design problem. One can expect, then, that parsimonious, more effective controllers are possible if control considerations are incorporated in the modeling stage.
\r\n\r\nThe synergism of dynamic modeling and process control, as pertaining to the fields of low-order controller design, model reduction, and model identification, is investigated in this thesis. The guiding theoretical framework is the robust control paradigm using the Structured Singular Value, which addresses controller design in the presence of model uncertainty.
\r\n\r\nThe main contribution of this thesis is the development of a control-relevant model reduction methodology. The effectiveness of reduction is increased by incorporating the closed-loop performance/robustness specifications, plant uncertainties, and setpoint/disturbance characteristics explicitly as weights in the reduction procedure. The efficient computation of the control-relevant reduction problem is indicated and illustrated with examples taken from the control of a methanation reactor and a binary distillation column.
\r\n\r\nA low-order controller design methodology for single-input, single-output plants is also presented. The basis for this methodology is the combination of the control-relevant reduction problem with the Internal Model Control (IMC) design procedure. The relationship between low-order IMC controllers and classical feeback compensators is examined. It is shown that for many models common to the process industries, the controllers obtained from the low-order compensator design technique are of the PID type.
\r\n\r\nFinally, a model identification methodology is established using spectral time series analysis to obtain plant transfer function and uncertainty estimates directly from experiments. The control-relevant model reduction procedure can then be used to fit the \"full-order\" frequency response to a \"reduced-order\" parametric model. Model validation for control purposes is achieved by insuring that the robustness condition is satisfied.
\r\n" }, { "name": "Sageev Grader, Gideon", "degree": "PhD", "year": "1987", "title": "Fourier Transform Infrared Spectroscopy of a Single Aerosol Particle", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03052008-111804", "creators": [ { "name": { "family": "Sageev Grader", "given": "Gideon" }, "id": "Sageev-Grader-Gideon", "display_name": "Sageev Grader, Gideon" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/de8x-sp79", "abstract": "Throughout this thesis, the phenomenon of radiation-induced particle size change is studied both on a theoretical as well as experimental level. The thrust of this study is aimed at using the size changes due to heat absorption to develop a technique for obtaining the particle chemical composition.
\r\n\r\nThe experiments here involve charged particles, generated with an impulse jet, and trapped by the electric field of an electrodynamic balance. The particles under study are all aqueous solutions of non-volatile salts, where upon heating a partial evaporation of water occurs. The evaporation and subsequent condensation processes are modeled in both the continuum and the transition regimes. The models developed are tested and the agreement between theory and experimental results is demonstrated. The models are also used to extract the values of the water, thermal, and mass accommodation coefficients from the data. The results for the thermal accommodation show that its value is near unity, however the corresponding results for the mass accommodation are not conclusive.
\r\n\r\nA method is developed for obtaining the molecular composition of a single suspended microparticle by Fourier transform infrared spectroscopy. The particle is irradiated simultaneously by the infrared output from a Michelson interferometer and the visible light from a dye laser. The laser is tuned to an edge of an optical resonance of the particle while the IR beam is chopped. Through evaporation and condensation the chopped IR beam causes a size modulation of the droplet, which in turn induces a fluctuation in the laser light scattered from the particle. The scattered light is detected at 90\u00b0 with a photomultiplier, and the amplitude of the light fluctuation is measured with a lock-in amplifier. The lock-in signal is then inverted by a discrete fast Fourier transform routine (FFT), to yield the particle absorption spectrum. Spectra of (NH4)2SO4 droplets at different solute concentrations are presented.
\r\n" }, { "name": "Schilling, Jerald Bruce", "degree": "PhD", "year": "1987", "title": "Experimental and Theoretical Aspects of Hydrocarbon Activation by Transition Metal Ions in the Gas Phase", "advisor": "Beauchamp, Jesse L.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062009-094101367", "creators": [ { "name": { "family": "Schilling", "given": "Jerald Bruce" }, "id": "Schilling-Jerald-Bruce", "display_name": "Schilling, Jerald Bruce" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "co-advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kechris", "given": "Alexander S." }, "id": "Kechris-A-S", "role": "chair", "display_name": "Kechris, Alexander S." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Luxemburg", "given": "W. A. J." }, "id": "Luxemburg-W-A-J", "role": "member", "display_name": "Luxemburg, W. A. J." }, { "name": { "family": "Taylor", "given": "Hugh P." }, "id": "Taylor-H-P", "role": "member", "display_name": "Taylor, Hugh P." }, { "name": { "family": "Anderson", "given": "David J." }, "id": "Anderson-D-J", "role": "member", "display_name": "Anderson, David J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vazp-zt83", "abstract": "The reactions of several gas-phase metal cations with small hydrocarbons have been studied using ion beam mass spectrometric techniques. We also present several theoretical studies into the sigma bonding between the first and second row transition metal ions and H and CH3.
\r\n\r\nChapter II discusses the three cations, europium, praseodymium, and gadolinium in an attempt to understand the role of f electrons in the reactivity of gas-phase lanthanide ions. Eu+ and Pr+ are found to be unreactive with alkanes while Gd+ readily activates both C\u2014H and C\u2014C bonds. The unreactive metals have only one non-4f valence electron. Oxidative addition of a C\u2014H bond to these metals requires a strong bond to an f electron. Gd+, with two non-4f valence electrons need not use the 4f electrons and is seen to be very reactive. This reactivity behavior indicates that the 4f electrons of the lanthanides play little role in alkane activation due to the formation of weak sigma bonds.
\r\n\r\nIn Chapter III and VI, we discuss the reasons for the unreactivity of gas-phase chromium ions. Molybdenum ions which have a very similar electrons structure are found to activate C\u2014H bonds of alkanes. The metal ions are studied from the standpoint of gas-phase reactivity as well as the theoretical description of the bonding in the hydride and dihydride ions. The two metals are found to differ greatly in the strength of the sigma bonds that they form to hydrogen. The oxidative addition of C\u2014H and C\u2014C bonds to Cr+ is endothermic due to the extremely weak bonds formed to the metal ion.
\r\n\r\nChapters IV and V report systematic, ab initio, generalized valence bond and configuration interaction calculations on the first and second row transition metal hydrides. The bonding in these systems is seen to depend on a number of factors including: (1) the electronic structure of the metal ions; (2) the sizes of the metal s and d orbitals and the effect on the intrinsic strength of the metal\u2014hydrogen bond; and (3) the mediation of the intrinsic bond strengths by the loss of high spin exchange energy.
\r\n\r\nChapter VII presents a theoretical comparison between the metal hydride ions and metal methyl ions. The present theoretical study indicates that for a variety of metal systems, the metal\u2014hydrogen and metal\u2014carbon bonds are very similar, both from the standpoint of metal orbital hybridization as well as bond dissociation energy.
\r\n" }, { "name": "Skogestad, Sigurd", "degree": "PhD", "year": "1987", "title": "Studies on Robust Control of Distillation Columns", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-104731", "creators": [ { "name": { "family": "Skogestad", "given": "Sigurd" }, "id": "Skogestad-Sigurd", "display_name": "Skogestad, Sigurd" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Sideris", "given": "Athanasios" }, "id": "Sideris-A", "role": "member", "display_name": "Sideris, Athanasios" }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." } ], "option_major": [ "chemeng" ], "doi": "10.7907/WS2X-Z786", "abstract": "Distillation is undoubtedly the most important unit operation in chemical engineering. During design a significant effort is normally put into steady-state optimization of the column with respect to its size, feed location and reflux ratio. However, operating the column close to this optimal point requires reasonably tight control of the product compositions. This is usually not achieved in industrial practice due to stability problems. Improved strategies for distillation control offer a viable means for significant economic savings as compared to the existing ad hoc techniques. This thesis addresses robust control of distillation columns in the face of model-plant mismatch caused by model uncertainty, nonlinearity and changes in operating conditions. The robust control paradigm, introduced by Doyle and coworkers, is used as the basis for controller design and analysis. An important tool is the Structured Singular Value (SSV) which enables the evaluation of a plant's achievable control performance. This provides a consistent basis for comparing controllers and design alternatives. Achievable performance is also related to other commonly used measures such as the RGA and the condition number.
\r\n\r\nPhysical insight is used to derive low-order column models which address the issues most important for feedback control. It is shown that the dynamic behavior can be explained in terms of the fundamental difference between external and internal flows. This difference manifests itself both at steady-state and in the dynamic response. Furthermore, the initial response, which is of principal importance for feedback control, is affected much less by changes in the operating conditions than is the steady-state response. The initial response is even less markedly affected when logarithmic compositions are used.
\r\n\r\nAn important issue in distillation control is which two of the possible five manipulated inputs should be selected for composition control; each configuration may yield entirely different control performance. Issues which must be addressed include model uncertainty and dynamic response as well as rejection of flow disturbances by the level loops.
\r\n\r\nFinally, a design method for robust decentralized controllers, which generalizes the SSV-interaction measure of Grosdidier and Morari, is introduced. Each loop is designed independently such that robust performance of the overall system is guaranteed.
" }, { "name": "Sponsler, Michael Bradley", "degree": "PhD", "year": "1987", "title": "Synthesis, EPR Spectroscopy, and Matrix-Isolation Decay Kinetics of Triplet Cyclobutanediyls", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08082025-174515566", "creators": [ { "name": { "family": "Sponsler", "given": "Michael Bradley" }, "id": "Sponsler-Michael-Bradley", "orcid": "0000-0001-7181-1650", "display_name": "Sponsler, Michael Bradley" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/me26-sd58", "abstract": "Chapter 1
\r\n\r\nBicyclo[1.1.1]pentanone (11) has been prepared in two\r\nsteps, the key reaction being the ozonolysis of\r\n2-phenylbicyclo[1.1.1)pentan-2-ol (24). The microwave\r\nspectra of five isotopic species of 11 have been obtained,\r\nallowing a complete rs structure determination for the heavy\r\natoms. Analysis of Stark-effect measurements has shown the\r\ndipole moment to be along the a principle inertial axis with\r\na magnitude of 3.164(5) D. These results are compared with\r\nthose obtained using molecular mechanics (MM2), MNDO, and\r\nHartree-Fock ab initio theory with STO-3G and 3-21G basis\r\nsets. On heating, 11 undergoes cycloreversion to allylketene\r\n(31). The activation parameters and solvent effects for this\r\nprocess suggest that the reaction is concerted and that the\r\ntransition state is relatively nonpolar. The predominant\r\nphotochemical pathway for 11 is decarbonylation to\r\nbicyclobutane (34). Cycloreversion to 31 is a minor\r\nreaction mode. Both the thermal and photochemical results\r\nare rationalized by considering the high strain energy and\r\nnovel geometrical features of 11 and, in the latter case, the\r\nunusually high energy of its 1(n\u03c0*) state.
\r\n\r\nChapter 2
\r\n\r\nAb initio theoretical methods have been applied to\r\ncyclobutanediyl. The geometry of the triplet biradical was\r\noptimized under the constraints of D2h symmetry. At the\r\noptimum geometry, the singlet-triplet energy gap was found to\r\nbe 1.74 kcal/mol, with the ground state being the triplet.\r\nThe closure reaction to bicyclo[1.1.0]butane (34) was\r\ninvestigated using a linear synchronous transit reaction\r\ncoordinate. A barrier of 6.6 kcal/mol was obtained for the\r\nsinglet surface, representing an upper limit to the actual\r\nbarrier. Calculations on 1,3-dimethylcyclobutanediyl (12)\r\nshow that the methyl groups do not strongly affect the\r\nsinglet-triplet gap, reducing it to 1.47 kcal/mol.
\r\n\r\nChapter 3
\r\n\r\nThe synthesis and EPR spectroscopy of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) are\r\ndescribed and compared with results for other\r\ncyclobutanediyls. The triplet biradicals were generated by\r\nphotolysis of the appropriate 2,3-diazabicyclo[2.1.1]hex-\r\n2-enes (47) in frozen-solvent matrices at cryogenic\r\ntemperatures. A general synthetic scheme allowing the\r\npreparation of many diazenes has been developed. The key\r\nstep is the photochemical addition of methyltriazolinedione\r\nto 1,3-dicarbomethoxybicyclo[1.1.0]butane (49), giving the\r\ndicarbomethoxyurazole 15. The triplet EPR spectra offer\r\nvaluable insights into the electronic structure of the\r\ncyclobutanediyls and the role played by the substituents.\r\nBoth zero-field splitting and hyperfine coupling emerge as\r\nsensitive gauges for determining the distribution of spin\r\ndensity in the biradicals.
\r\n\r\nChapter 4
\r\n\r\nThe nonexponential decay kinetics of 1,3-divinyl- and\r\n3-ethyl-1-vinylcyclobutanediyl (46-Vin and -EV) has been\r\nquantitatively analyzed in the 20-54 K temperature range\r\nusing two methods based upon a distribution of first-order\r\nrate constants. A numerical procedure for fitting of decay\r\ntraces based upon an assumption of distribution shape has\r\nbeen modified to allow fitting of the signal growth during\r\nphotolysis as well as the decay. This method successfully\r\nreproduced our data using a variety of distribution shapes.\r\nA new method for analysis of dispersive kinetics, called\r\ndistribution slicing, has been developed. This method allows\r\ndetailed determination of distribution shapes and is\r\ncomplementary to decay-trace fitting in several other ways.\r\nThe two methods have been combined to eliminate several\r\nproblems encountered in the separate methods, allowing the\r\ndetermination of approximate activation parameters. An\r\napproximate log A value of 7.5 was determined for the decay\r\nof 46-Vin along with most-probable activation energies in\r\nthe range 1.2 to 1.7 kcal/mol, depending on the matrix\r\nmaterial. Using the same log A value, 46-EV gives\r\nmost-probable activation energies of 1.4 and 0.9 kcal/mol in\r\nMTHF and heptane, respectively. The stability of these\r\nbiradicals relative to the dialkyl cyclobutanediyls was\r\nrationalized in terms of hypothetical potential energy\r\nsurfaces.
" }, { "name": "Toby, Brian H.", "degree": "PhD", "year": "1987", "title": "Studies of Molecular Bonding, Interactions and Decomposition Reactions on the (001) Surface of Ruthenium", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:02122014-142619432", "creators": [ { "name": { "family": "Toby", "given": "Brian H." }, "id": "Toby-Brian-H", "display_name": "Toby, Brian H." } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R50B-J328", "abstract": "The interactions of N2, formic acid and acetone on the Ru(001) surface are studied using thermal desorption mass spectrometry (TDMS), electron energy loss spectroscopy (EELS), and computer modeling.
\r\n\r\nLow energy electron diffraction (LEED), EELS and TDMS were used to study chemisorption of N2 on Ru(001). Adsorption at 75 K produces two desorption states. Adsorption at 95 K fills only the higher energy desorption state and produces a (\u221a3 x \u221a3)R30\u00b0 LEED pattern. EEL spectra indicate both desorption states are populated by N2 molecules bonded \"on-top\" of Ru atoms.
\r\n\r\nMonte Carlo simulation results are presented on Ru(001) using a kinetic lattice gas model with precursor mediated adsorption, desorption and migration. The model gives good agreement with experimental data. The island growth rate was computed using the same model and is well fit by R(t)m - R(t0)m = At, with m approximately 8. The island size was determined from the width of the superlattice diffraction feature.
\r\n\r\nThe techniques, algorithms and computer programs used for simulations are documented. Coordinate schemes for indexing sites on a 2-D hexagonal lattice, programs for simulation of adsorption and desorption, techniques for analysis of ordering, and computer graphics routines are discussed.
\r\n\r\nThe adsorption of formic acid on Ru(001) has been studied by EELS and TDMS. Large exposures produce a molecular multilayer species. A monodentate formate, bidentate formate, and a hydroxyl species are stable intermediates in formic acid decomposition. The monodentate formate species is converted to the bidentate species by heating. Formic acid decomposition products are CO2, CO, H2, H2O and oxygen adatoms. The ratio of desorbed CO with respect to CO2 increases both with slower heating rates and with lower coverages.
\r\n\r\nThe existence of two different forms of adsorbed acetone, side-on, bonded through the oxygen and acyl carbon, and end-on, bonded through the oxygen, have been verified by EELS. On Pt(111), only the end-on species is observed. On dean Ru(001) and p(2 x 2)O precovered Ru(001), both forms coexist. The side-on species is dominant on clean Ru(001), while O stabilizes the end-on form. The end-on form desorbs molecularly. Bonding geometry stability is explained by surface Lewis acidity and by comparison to organometallic coordination complexes.
\r\n\r\n\r\n\r\n" }, { "name": "Tsai, Wilman", "degree": "PhD", "year": "1987", "title": "Interactions of Ammonia with Platinum and Ruthenium Surfaces", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-100902", "creators": [ { "name": { "family": "Tsai", "given": "Wilman" }, "id": "Tsai-Wilman", "display_name": "Tsai, Wilman" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4Y3N-2321", "abstract": "Specific reaction rates (cm-2-s-1) of the catalytic decomposition of ammonia, the isotopic exchange between ammonia and deuterium, and the inhibition of the decomposition of ammonia by hydrogen (with ammonia to hydrogen partial pressure ratios varying from 1:1 to 1:4) on a polycrystalline platinum wire have been measured in a continuous stirred tank microreactor at pressures between 5 x 10-7 and 0.6 Torr and temperatures between 400 and 1200 K. At relatively low temperatures and/or high pressures, nitrogen adatoms are the dominant surface species, and the recombinative desorption of nitrogen controls the rate of decomposition of ammonia. At relatively high temperatures and/or low pressures, the surface coverage of all species is low, and a competition between the desorption of molecular ammonia and the cleavage of an N-H bond of molecularly adsorbed ammonia controls the rate of reaction. The kinetics of decomposition of ammonia as well as the results for the NH3 + D2 exchange reaction are described quantitatively by a mechanistic model employing independently measured adsorption-desorption parameters of NH3 and H2, and desorption parameters of N2. The model was extended to incorporate the nitrogen coverage-dependence of the rate coefficient of hydrogen desorption to describe the inhibition of the decomposition by hydrogen. The hydrogenation of NH2(a) to produce molecularly adsorbed ammonia is predicted to be the dominant factor in the inhibition of the decomposition of ammonia.
\r\n\r\nThe kinetics of adsorption and desorption of deuterium have been studied on Pt(110)-(1x2) surfaces on which various fractional coverages of nitrogen adatoms were deposited via the decomposition of ammonia at 400 K. Nitrogen selectively blocks the high temperature \u03b22-state of deuterium prior to poisoning the low temperature \u03b21-state. No evidence of a 'long-range' electronic perturbation of the surface by the nitrogen adatoms was found. The adsorption kinetics of deuterium on both clean and nitrogen-precovered Pt(110)-(1x2) surfaces were Langmuirian. Nitrogen modifies the preexponential factor and the activation energy of desorption of deuterium on Pt(110)-(1x2) by essentially rescaling the effective coverage of the deuterium. The results are consistent with findings from previous studies of the inhibition of the decomposition of ammonia by hydrogen on polycrystalline platinum.
\r\n\r\nSteady-state specific reaction rates have also been measured for the catalytic decomposition of ammonia on a Ru(001) surface at pressures of 10-6 and 2 x 10-6 Torr and temperatures between approximately 500 and 1250 K. Qualitatively, the kinetics are similar to those observed for ammonia decomposition on the polycrystalline platinum surface. Based on thermal desorption measurements during the steady-state decomposition of ammonia at 2 x 10-6 Torr, nitrogen adatoms are the dominant surface species, and the recombinative desorption of nitrogen is the major (and probably the only) elementary reaction that produces molecular nitrogen. The mechanistic model developed previously describes accurately the pressure and temperature dependence of both the decomposition kinetics and the measured steady-state coverage of nitrogen adatoms.
\r\n\r\nThe isotopic exchange reaction between 15NH3 and deuter m at steady-state has been studied on Ru(001) for a partial pressure ratio of ammonia to deuterium of 4:1 with a total pressure of 2.5 x 10-6 Torr at temperatures between 380 and 720 K. All three exchange products were observed, and a dissociative exchange mechanism was found to describe quantitatively the experimental data. This mechanistic model is discussed in terms of a potential energy diagram that describes the catalytic decomposition (or synthesis) of ammonia on Ru(001). The energy levels of and the activation barriers separating the chemisorbed intermediates in the ammonia decomposition and synthesis reactions, namely, NH3, NH2+H, NH+2H, N+3H are determined, and the dissociative chemisorption of molecular nitrogen on Ru(001) is found to be activated with an activation energy estimated to be approximately 5 kcal-mol-1 in the limit of zero surface coverage of nitrogen adatoms. Direct comparsion between the estimated barrier for the dissociative adsorption of nitrogen on polycrystalline platinum and Ru(001) surfaces indicates clearly that ruthenium is a superior catalyst to platinum for the synthesis of ammonia.
" }, { "name": "Vajo, John J.", "degree": "PhD", "year": "1987", "title": "Mechanistic Studies of Heterogeneously Catalyzed Reactions of Ammonia and Acetic Acid on Platinum Surfaces", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-173425189", "creators": [ { "name": { "family": "Vajo", "given": "John J." }, "id": "Vajo-John-J", "display_name": "Vajo, John J." } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vayx-4k53", "abstract": "The design and operation of a versatile microreactor capable of studying the rates of both steady-state and batch heterogeneous reactions on a wire, a foil or a single crystalline surface at pressures between 10-7 and 1000 Torr are described. The residence time distribution of the microreactor was characterized in order to evaluate the validity of using the continuous stirred tank reactor approximation to calculate reaction rates.
\r\n\r\nAbsolute reaction rates (i.e. the rate-per-unit catalyst surface area) have been measured for both the catalytic decomposition of NH3 and ND3 and the NH3 + D2 exchange reaction over a polycrystalline platinum wire. The pressure was varied between 5 x 10-7 and 0.5 Torr, and the temperature ranged from 400 to 1200 K. At relatively low pressures and/or high temperatures, the order of the decomposition reaction is unity with respect to ammonia, and the reaction rate is dictated by a competition between the surface reaction and the desorption of molecularly adsorbed ammonia. Under these conditions a primary isotope effect was observed for the decomposition of ND3. At relatively high pressures and/or low temperatures, the reaction rate is independent of ammonia pressure, and the recombinative desorption of nitrogen controls the rate of ammonia decomposition. The measured kinetics of the NH3 + D2 exchange reaction were employed together with adsorption-desorption parameters of NH3, N2 and H2 to develop a mechanistic model that describes the reaction rate over the entire (wide) range of conditions studied.
\r\n\r\nSteady-state absolute reaction rates are reported also for the catalytic decomposition of NH3 on the Pt(110)-(1x2) single crystalline surface at pressures between 1 x 10-6 and 2.6 x 10-6 Torr and at temperatures between 400 and 1000 K. Qualitatively, the kinetics is similar to those observed for ammonia decomposition on the polycrystalline platinum surface. Thermal desorption measurements conducted during the steady-state decomposition reaction demonstrate directly that nitrogen adatoms are the predominant surface species, and that the recombinative desorption of nitrogen is the major elementary reaction that produces molecular nitrogen.
\r\n\r\nThe decomposition of CH313COOH at 7 x 10-4 Torr on a polycrystalline platinum wire at temperatures between 300 and 900 K was examined in the microreactor. The major reaction products on the initially clean surface are 13CO, CO, 13CO2, H2 and adsorbed carbon-12. The adsorbed carbon accumulates on the surface until the reactions that produce these products are poisoned by the graphitic overlayer that is formed. On the graphitized platinum surface, acetic acid dehydrates catalytically to ketene and water. The relative quantities of 13CO and 13CO2 that are formed depend both on the surface temperature and on the surface carbon coverage.
\r\n\r\nThe catalytic dehydration of acetic acid to ketene was investigated over a graphitized polycrystalline platinum surface at pressures between 8 x 10-7 and 7 x 10-4 Torr and temperatures between 500 and 800 K. Steady-state absolute reaction rates, thermal desorption measurements, and the reactivities of functionally related compounds suggest that the reaction proceeds via an irreversibly adsorbed intermediate, which is formed by dissociation of the oxygen-hydrogen bond of acetic acid. For temperatures below 540 K at pressures of 3.5 x 10-4 Torr and above, the rate of decomposition of the surface intermediate controls the overall rate of the reaction. At 675 K or above for the entire range of pressures studied, the rate of dehydration is determined by a competition between the rates of desorption and surface reaction of molecularly adsorbed acetic acid.
" }, { "name": "Voth, Gregory Alan", "degree": "PhD", "year": "1987", "title": "Theoretical Studies of Intramolecular Dynamics and Energy Redistribution", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11292006-135710", "creators": [ { "name": { "family": "Voth", "given": "Gregory Alan" }, "id": "Voth-Gregory-Alan", "display_name": "Voth, Gregory Alan" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/MD4H-AZ79", "abstract": "By virtue of various theoretical techniques, the fundamental mechanisms responsible for intramolecular vibrational energy redistribution (IVR) in isolated molecules are studied in this thesis. One such mechanism, the nonlinear resonance, is examined in some detail for several systems. In particular, nonlinear stretch-bend resonances in a series of isotopically substituted methanes are predicted to have a large effect on the spectral properties of those molecules. By using a semiclassical analysis, the general properties of stretch-bend interactions are further examined, and the quantum mechanical manifestations of classical resonances are characterized in detail. A related problem, the role of classical resonances in the multiphoton absorption process by an anharmonic oscillator, is also analyzed.
\r\n\r\nIn addition, it is demonstrated that the quantum mechanical coupled equations which describe the fundamental IVR process may be simplified. This simplification is achieved by virtue of an \"adiabatic\" approximation for those state amplitudes which are sufficiently off-resonant with (i.e., different in energy from) the experimentally prepared quantum state. The approximate coupled equations are based on an effective Hamiltonian which contains renormalized self-energies and interactions between the zeroth-order quantum states. This formalism may be applied to describe the quasidissipative flow of probability out of an initially prepared vibrational state in a large molecule, and it may also be adapted to treat multiphoton absorption processes in polyatomic molecules when one or more lasers are present.
" }, { "name": "Walzl, Kerry Neil", "degree": "PhD", "year": "1987", "title": "Variable-Angle Electron Energy-Loss Spectroscopy of Polyatomic Molecular Systems", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292019-111940086", "creators": [ { "name": { "family": "Walzl", "given": "Kerry Neil" }, "id": "Walzl-Kerry-Neil", "display_name": "Walzl, Kerry Neil" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pzpj-5b50", "abstract": "The technique of variable-angle electron energy-loss spectroscopy has been used to study the electronic spectroscopy and structure of both open- and closed-shell molecules. The experiments were performed using incident electron beam energies between 25 eV and 100 eV and at scattering angles between 0\u00b0 and 90\u00b0. Energy-loss regions from 0 eV to 16 eV were examined. Spin-forbidden, dipole symmetry-forbidden/quadrupole symmetry-allowed, and super-excited transitions were investigated by this method.
\r\n\r\nThe three small carbonyl compounds formaldehyde (CH2O), acetaldehyde (C2H4O), and acetone (C3H6O) were studied in the energy-loss region from 0 eV to 16 eV. Low-lying spin-forbidden n \u2192 \u03c0* and \u03c0 \u2192 \u03c0* transitions were located on the basis of the angular behavior of their relative differential cross sections. High-lying (autoionizing in the case of formaldehyde) dipole symmetry-forbidden states were also assigned on the basis of differential cross section behavior. The effect of methyl substitution on the transition energies was also noted and discussed.
\r\n\r\nFive dicarbonyl compounds (biacetyl, acetylacetone, acetonylacetone, 1,2-cyclohexanedione, 1,4-cyclohexanedione) were investigated by this spectroscopic method in order to locate their low-lying spin-forbidden transitions. The energy difference between the lowest spin-allowed and spin-forbidden n \u2192 \u03c0* excitations in the cyclic dicarbonyls was found to be much larger than in the acyclic dicarbonyls; this difference was discussed.
\r\n\r\nThe spectrum of the methyl radical CH3 was investigated by the same technique as the carbonyls except that the radical was generated by pyrolysis. Three source compounds were tried (tetramethyl tin, ethyl nitrite, di-t-butylperoxide) with temperatures ranging from ambient to 800\u00b0C. Using di-t-butylperoxide at a pyrolysis temperature of about 300\u00b0C, relative differential cross sections for the lowest allowed 2A'1 \u2190 2A\"2 3s Rydberg transition (5.73 eV) were determined at incident energies of 50 eV and 25 eV. The differential cross sections for this band do not indicate the presence of any underlying spin-forbidden transition.
\r\n\r\nFinally, preliminary investigations of the spectroscopy of pyridazine and cyclohexanone were undertaken. For pyridazine, a new low-lying spin-forbidden excitation was observed. The low-lying spin-forbidden transitions of cyclohexanone were also observed along with tentative relative differential cross sections at 30 eV and 50 eV. Rydberg bands in this molecule converging to the first ionization potential were seen and the positions tabulated.
\r\n" }, { "name": "Wang, Hsin", "degree": "PhD", "year": "1987", "title": "M\u00f6ssbauer and Spectroscopic Studies of Yeast Cytochrome Oxidase", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302019-125418569", "creators": [ { "name": { "family": "Wang", "given": "Hsin" }, "id": "Wang-Hsin", "display_name": "Wang, Hsin" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "chair", "display_name": "Hopfield, John J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jfrs-d493", "abstract": "Cytochrome oxidase from baker's yeast is investigated by M\u00f6ssbauer spectroscopy, complemented by EPR, flash photolysis, and spectroelectrochemical studies. While the M\u00f6ssbauer spectrum of cytochrome \u03b1 can be described with one set of parameters, at least three components were identified for cytochrome \u03b13 in the native enzyme: a functional coupled site, a high spin ferric ion with the antiferromagnetic coupling disrupted, and a low spin ferrous ion. Photolysis experiments indicate that the CO-recombination at the functional cytochrome \u03b13 in yeast is a slow process with an activation energy of 33 kJ/mol, similar to that observed previously in the beef heart enzyme. The structure of this site is therefore very similar in both enzymes. However, the M\u00f6ssbauer spectrum of the this site in yeast cannot be explained by the current spin Hamiltonian model that describes the widely accepted spin-coupling hypothesis. The shortcoming of this model is pointed out and discussed. The assignment of the reduced low spin heme to a degraded form of cytochrome \u03b13 is strengthened by photolysis studies, which reveal a second fast CO-rebinding site with a peak activation energy (13 kJ/mol) similar to that of myoglobin, and by spectroelectrochemical measurements, which demonstrate that the redox potential of the degraded cytochrome \u03b1 is low rather than high as previously thought. Based on these findings in yeast oxidase and previous inactivation reports on beef heart oxidase, a global change in the structures of all of the metal centers during denaturation is suggested. The redox behavior of the normal cytochrome \u03b1 in the CO-inhibited enzyme is well-explained by a 2-site interaction model which has also been applied successfully in the beef heart enzyme. The redox potential of cytochrome \u03b1 in yeast is found to be roughly 45 mV higher than that in beef heart. A comparative EPR and M\u00f6ssbauer study of the reoxidation of the fully-reduced yeast enzyme is also presented. The reoxidation course is well-described by the mechanism proposed for the beef heart enzyme and a few intermediates are suggested by the M\u00f6ssbauer study.
" }, { "name": "Waymouth, Robert Mebane", "degree": "PhD", "year": "1987", "title": "Synthesis and Reactivity of Alkylaluminum Adducts of Zirconium Ketene and Ketone Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142008-080353", "creators": [ { "name": { "family": "Waymouth", "given": "Robert Mebane" }, "id": "Waymouth-Robert-Mebane", "display_name": "Waymouth, Robert Mebane" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/PDGW-2Q40", "abstract": "A family of alkylaluminum adducts of zirconium ketene and ketone complexes has been prepared. Treatment of dimeric bis(cyclopentadienyl)zirconium ketene complexes with alkylaluminum reagents affords trinuclear Zr2Al bridging ketene complexes of formula [Cp2Zr(C,O-\u03b72-OCCHR)]2(\u03bc-AlR2)(\u03bc-X). X-Ray structural characterization of these complexes reveals several novel features. Two zirconium ketene ligands are spanned by symmetric dialkylaluminum and hydride, chloride, or methyl ligands to form slightly puckered 6-membered rings. A notable feature of these structures is the coordination of the bridging ligand X (H, Cl, or Me), which is characterized by a large Zr-X-Zr angle and an unusual hybridization for the bridging methyl group. The coordination of this methyl group represents a new bonding geometry for carbon, a trigonal-bipyramidal configuration between two metal centers. This geometry models intermediates in alkyl transmetallations that proceed with inversion and implies that transmetallations with inversion should be facile for electrophilic metal centers.
\r\n\r\nThe bridging methyl complex [CP2Zr(C,O-\u03b72-OCCHCH2CMe3)]2(\u03bc-AlMe2)(\u03bc-CH3) reacts with acetylene to give an oxymetallacyclopentene. Carbonylation of the bridging methyl complex produces an acyl-enol complex\u2014an unprecedented transformation for a group 4 ketene complex and one that is relevant to the behavior of ketene intermediates over Fischer-Tropsch catalysts.
\r\n\r\nZirconium chloro acyl complexes react with alkylaluminum reagents to give alkyl-aluminum adducts of zirconium ketone complexes. Mechanistic studies of this reaction provide strong support for a stepwise mechanism involving transmetallation to form a zirconium alkyl acyl complex followed by reductive coupling of the zirconium alkyl and acyl ligands. A significant feature of these studies is the observation that aluminum reagents dramatically accelerate the reductive coupling of zirconium alkyl and acyl ligands.
\r\n\r\nThe ketone complexes react readily with olefins, alkynes, and ketones in reactions that should prove useful in organic synthesis. Insertion of ethylene into the zirconium ketone ligand yields oxymetallacyclopentanes, which can be hydrolyzed to tertiary alcohols. Insertion of alkynes into the zirconium ketone ligand affords oxymetallacyclopentenes. Terminal alkynes react with high regioselectivity to give oxymetallacyclopentenes with the alkyl substituent \u03b1 to the metal center. Hydrolysis of these complexes yields tertiary allyl alcohols. The ketone complexes couple with organic ketones to give diolates. Hydrolysis of the diolates affords 1,2-diols. These results demonstrate that zirconium ketone complexes, in contrast to later transition metal ketone complexes, induce the reductive coupling of organic carbonyl substrates to give diolates, a reaction that may prove useful for the preparation of 1,2-diols.
\r\n\r\nTrinuclear Zr2Al ketone complexes are formed in the reaction of two equivalents of alkyl acyl zirconium complexes and one equivalent of an aluminum reagent. These complexes appear structurally similar to the trinuclear Zr2Al ketene complexes discussed above.
\r\n" }, { "name": "Zafiriou, Evanghelos", "degree": "PhD", "year": "1987", "title": "A Methodology for the Synthesis of Robust Control Systems for Multivariable Sampled-Data Processes", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-140832", "creators": [ { "name": { "family": "Zafiriou", "given": "Evanghelos" }, "id": "Zafiriou-Evanghelos", "display_name": "Zafiriou, Evanghelos" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Caughey", "given": "Thomas Kirk" }, "id": "Caughey-T-K", "role": "member", "display_name": "Caughey, Thomas Kirk" }, { "name": { "family": "Doyle", "given": "John Comstock" }, "id": "Doyle-J-C", "role": "member", "display_name": "Doyle, John Comstock" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/m08p-9102", "abstract": "The problem of the synthesis of multivariable controllers which are robust with respect to model-plant mismatch is addressed. A two-step design procedure based on the Internal Model Control (IMC) structure is used. In the first step the IMC controller is designed assuming no modeling error, and in the second step the IMC filter is designed to preserve the closed-loop characteristics in spite of model-plant mismatch.
\r\n\r\nTwo alternatives are provided for the first step. One of them allows the designer to satisfy structural performance specifications, in terms of the structure of the closed-loop interactions, their magnitude and duration. The closed-loop transfer function matrix is directly designed. The method requires only standard linear algebra operations and includes the construction of the IMC or the feedback controller in state-space. The second approach involves the minimization of the appropriately weighted H2-norm of the sensitivity transfer function matrix, that relates the errors to the external inputs (setpoints or disturbances). A method is given for the meaningful selection of a full matrix weight so that the H2-error is minimized for a set of external input directions and their linear combinations. The procedure is extended to open-loop unstable systems. In both approaches, special care is taken to avoid intersample rippling.
\r\n\r\nThe design of the filter in the second step is formulated as an optimization problem over the filter parameters. The objective function is constructed by using the Structured Singular Value theory so that the maximum singular value of the sensitivity transfer function remains bounded in spite of modeling error. The selection of the frequency bound is based on the properties of the design that was obtained in the first step. Analytic gradient expressions have been developed for the objective function. The optimization problem is an unconstrained one, solved with standard gradient search techniques. An iterative method for the selection of the appropriate sampling time is proposed, which explicitly takes into account model uncertainty information and performance specifications.
\r\n" }, { "name": "Anton, Alan Brad", "degree": "PhD", "year": "1986", "title": "Studies of Overlayer Vibrational Structure and Identification of Adsorbed Reaction Intermediates Via Electron Energy Loss Spectroscopy", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-110807", "creators": [ { "name": { "family": "Anton", "given": "Alan Brad" }, "id": "Anton-Alan-Brad", "display_name": "Anton, Alan Brad" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/6yr9-e416", "abstract": "Electron energy loss vibrational spectroscopy (EELS) and thermal desorption mass spectrometry (TDMS) have been used to investigate the chemisorption of several molecules on the hexagonally close-packed Ru(001) surface. The adsorption of N2, O2, and N2 with O2 and CO was investigated to characterize the chemical state of adsorbed molecules, including their interactions with the substrate and with their adsorbed neighbors, through effects manifest in their vibrational spectra. The adsorption of (Ch3)2CO and H2CO and their subsequent thermal decomposition was investigated to identify the structures of reactive and non- reactive adsorbed intermediates, to identify the products of surface reactions and their structures, to identify surface reaction mechanisms, and to correlate reactivity with the structure of adsorbed intermediates.
\r\n\r\nN2 binds to the Ru(001) surface at on-top sites with its molecular axis perpendicular to the surface. In contrast to results reported for the isoelectronic molecule CO on the same surface, however, \u03bd(NN) decreases with increasing surface coverage, a result which is explained in terms of increasing population of the 1\u03c0g antibonding orbital of N2 with increasing surface coverage.
\r\n\r\nThe vibrational spectra of ordered p(2x2) and p(1x2) overlayers of oxygen adatoms on Ru(001) were studied via comparison of experimental EEL spectra to vibrational spectra calculated with a Green's function lattice dynamical technique. The results identify features due to coupling of the overlayers to substrate phonons and illustrate a unique effect of adsorption site symmetry which distinguishes the vibrational spectra of the two overlayers.
\r\n\r\nEELS and TDMS results used in conjunction to determine the effects of interactions between contrasting adsorbates in mixed adlayers of N2 with oxygen and N2 with CO on Ru(001). Preadsorbed oxygen produces a strong chemical effect on subsequently adsorbed N2, stabilizing \u03c3-donation while destabilizing 1\u03c0g-backdonation in the N2-surface bond. Preadsorbed N2 increases the ability of the Ru surface atoms to backdonate electron density into the 2\u03c0 orbital of subsequently adsorbed CO, producing values of \u03bd(CO) which are lower than are observed under any circumstances for the adsorption of CO on the clean Ru(001) surface.
\r\n\r\nAdsorption of (Ch3)2CO on the clean Ru(001) surface produces \u03b72-bonded molecular acetone which decomposes to CO, carbon and hydrogen upon heating the surface. If the surface is instead precovered with a p(2x2) oxygen overlayer, a significant fraction of the subsequently adsorbed acetone exists in an \u03b71-bonded configuration which, like \u03b71 acetone observed on the clean Pt(111) surface, desorbs molecularly upon heating. These results demonstrate in a quantifiable way how the reactivity of the Ru(001) surface can be modified by the presence of a coadsorbed species, and that the change in reactivity can be correlated with the selectivity of the surface toward reactive (\u03b72) and nonreactive (\u03b71) intermediate bonding configurations.
\r\n\r\nAdsorption of the chemically similar molecule H2CO on Ru(001) produces many effects analogous to those observed for (Ch3)2CO adsorption: \u03b72 bonding is observed on the clean surface and \u03b71 bonding is observed when the surface is precovered with a p(2x2) oxygen overlayer. The H2CO is more reactive than (Ch3)2CO, however, decomposing at low coverages and low temperature on the clean surface to give hydrogen and CO before any molecular adsorption is observed. At coverages intermediate between total decomposition and near monolayer saturation, where the \u03b72-H2CO species is observed, partial decomposition to yield an \u03b72-HCO species is observed. The results have important implications for the mechanistic understanding of CO hydrogenation reactions catalyzed under heterogeneous conditions.
" }, { "name": "Baldwin-Zuschke, Brenda Janet", "degree": "Masters", "year": "1986", "title": "Investigations of the Effect of Antigen Binding Upon Tryptophan Reactivity in Immunoglobulin G", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052010-153132274", "creators": [ { "name": { "family": "Baldwin-Zuschke", "given": "Brenda Janet" }, "id": "Baldwin-Zuschke-Brenda-Janet", "display_name": "Baldwin-Zuschke, Brenda Janet" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pwp3-7532", "abstract": "A ^3H/^(14)C-labelled reagent that reacts specifically with tryptophan residues, was used to monitor the reactivity of tryptophans in the Fc and Fab portions of IgG upon binding DNP-gly, (DNP)_1-cytochrome c, and (DNP)_8-cytochrome c. Binding of monovalent antigen caused a decrease in the reactivity of tryptophan residues in the Fc by 18%; binding of multivalent antigen caused decreases in the reactivity of tryptophan residues in Fc by 21% and Fab by 12%. Experiments to elucidate the interaction between IgG and complement component C4 were attempted.\r\n\r\nFuture studies include further characterization of (DNP)_1-cytochrome c and-the complement fixation capability of IgM-ABPC22 with monovalent antigen. Also planned is an investigation of the interaction of C4 with IgM in soluble antibody-antigen complexes." }, { "name": "Beratan, David Nathan", "degree": "PhD", "year": "1986", "title": "The Theory of Long Distance Electron Transfer Reactions", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012014-082222627", "creators": [ { "name": { "family": "Beratan", "given": "David Nathan" }, "id": "Beratan-David-Nathan", "orcid": "0000-0003-4758-8676", "display_name": "Beratan, David Nathan" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/FF39-DP24", "abstract": "The rate of electron transport between distant sites was studied. The rate depends crucially on the chemical details of the donor, acceptor, and surrounding medium. These reactions involve electron tunneling through the intervening medium and are, therefore, profoundly influenced by the geometry and energetics of the intervening molecules. The dependence of rate on distance was considered for several rigid donor-acceptor \"linkers\" of experimental importance. Interpretation of existing experiments and predictions for new experiments were made.
\r\n\r\nThe electronic and nuclear motion in molecules is correlated. A Born-Oppenheimer separation is usually employed in quantum chemistry to separate this motion. Long distance electron transfer rate calculations require the total donor wave function when the electron is very far from its binding nuclei. The Born-Oppenheimer wave functions at large electronic distance are shown to be qualitatively wrong. A model which correctly treats the coupling was proposed. The distance and energy dependence of the electron transfer rate was determined for such a model.
\r\n" }, { "name": "Blair, David Francis", "degree": "PhD", "year": "1986", "title": "Progress Toward Elucidating the Mechanisms of Energy Transduction in Cytochrome c Oxidase", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08162019-111201815", "creators": [ { "name": { "family": "Blair", "given": "David Francis" }, "id": "Blair-David-Francis", "display_name": "Blair, David Francis" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "chair", "display_name": "Hopfield, John J." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/g33b-bw96", "abstract": "The exothermic transfer of four electrons from cytochrome c to dioxygen is catalyzed in eucaryotes by mitochondrial cytochrome c oxidase. A large fraction of the energy made available from these electron transfers is conserved in the form of a proton electrochemical gradient across the mitochondrial inner membrane. Two energy-conserving mechanisms operate in cytochrome c oxidase: First, the electron transfers to dioxygen are themselves electrogenic, since the electrons originate from the outer side of the membrane while the protons required to produce water originate from the inner side. Second, the electron transfers are coupled to the active transport across the membrane of additional protons, perhaps as many as one for every electron transferred. In this work, investigations which are intended to contribute to a detailed understanding of the mechanisms of energy transduction in cytochrome c oxidase are described.
\r\n\r\nCytochrome c oxidase performs its catalytic functions with the assistance of four metal ion sites. The redox thermodynamic properties of three of these sites have been extensively characterized by spectroelectrochemical methods. A fairly complex interactive scheme involving all four metal centers is required to account for the observed thermodynamic behavior. Via measurements of reduction potential temperature dependences, it is found that the standard entropies of reduction of the two sites which have been suggested to play a role in proton pumping (cytochrome a and CuA) are unusually large and negative, suggesting that a substantial protein-ordering conformational change accompanies their reduction. The reduction potential of cytochrome a is only moderately pH-dependent, indicating that its reduction is not stoichiometrically coupled to proton uptake.
\r\n\r\nThe energy made available for transduction by the oxidase comes primarily from the exothermic transfer of electrons from the metal centers to dioxygen. The mechanism of these electron transfers has been examined in a detailed kinetic study of the reaction of the enzyme with dioxygen at low temperatures. Two different reaction intermediates have been found in which dioxygen is reduced to the same, namely, the three-electron level. The conversion between these two intermediates is rather highly activated but is promoted by entropic factors. It is suggested that this step corresponds to the breaking of the oxygen-oxygen bond. Earlier suggestions that electrons may be transferred via multiple pathways through the enzyme have been confirmed and extended. An examination of the reaction of partially reduced samples of the oxidase with dioxygen indicates that the rates of internal electron transfer within the oxidase are different at different steps in dioxygen reduction. Multiple pathways and step-dependent rates are expected to have important implications for the mechanisms of energy conservation by the oxidase.
\r\n\r\nThe steady-state kinetics of a simple model for redox-linked proton pumping has been examined in a final chapter. In this analysis, special emphasis was given to the importance of controlling electron flows through the transducing site. The consideration of electron flows results in some novel conclusions which assist in rationalizing the results of the redox thermodynamic study. It is expected that the analysis should also contribute to the design and interpretation of further experiments intended to reveal the mechanisms of proton pumping.
\r\n" }, { "name": "Blake, Geoffrey A.", "degree": "PhD", "year": "1986", "title": "On the Chemical Composition of Interstellar Molecular Clouds: A Millimeter and Submillimeter Spectral Line Survey of OMC-1", "advisor": "Phillips, Thomas G.; Pickett, Herbert M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12092003-145807", "creators": [ { "name": { "family": "Blake", "given": "Geoffrey A." }, "id": "Blake-Geoffrey-A", "orcid": "0000-0003-0787-1610", "display_name": "Blake, Geoffrey A." } ], "advisors": [ { "name": { "family": "Phillips", "given": "Thomas G." }, "id": "Phillips-T-G", "role": "advisor", "display_name": "Phillips, Thomas G." }, { "name": { "family": "Pickett", "given": "Herbert M." }, "id": "Pickett-Herbert-M", "role": "advisor", "display_name": "Pickett, Herbert M." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Phillips", "given": "Thomas G." }, "id": "Phillips-T-G", "role": "member", "display_name": "Phillips, Thomas G." }, { "name": { "family": "Pickett", "given": "Herbert M." }, "id": "Pickett-H-M", "role": "member", "display_name": "Pickett, Herbert M." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Scoville", "given": "Nicholas Zabriskie" }, "id": "Scoville-N-Z", "orcid": "0000-0002-0438-3323", "role": "member", "display_name": "Scoville, Nicholas Zabriskie" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0F73-PJ76", "abstract": "The same basic principles govern the chemical and physical evolution of systems throughout the universe. However, the dissimilar conditions on the Earth and in the interstellar medium lead to remarkably different chemical compositions for these two environments. While less familiar than terrestrial chemistry, the study of the chemical composition of the interstellar medium is important because it bears directly on the understanding of phenomena as diverse as star formation, galactic structure and dynamics, and the cosmological origin of the universe, in addition to providing a unique opportunity to investigate a number of fundamental chemical and physical processes.
\r\n\r\nWe present here results from a millimeter and submillimeter spectral line survey of the core of the Orion molecular cloud (OMC-1). The millimeter-wave survey, conducted at the Owens Valley Radio Observatory (OVRO), covers a 55 GHz interval in the 1.3 mm (230 GHz) atmospheric window and contains emission from 29 molecules. Together with the frequency selective submillimeter observations of H2D+ (372.4 GHz), Cl (492.2 GHz), NH3 (572.5 GHz), and HCl (625.9 GHz) performed aboard NASA's Kuiper Airborne Observatory, over 800 emission lines have been detected from 33 chemically distinct species during the course of this work. The uniformly calibrated results from the unique and extensive OVRO spectral line survey place significant constraints on models of interstellar chemistry, and have allowed the chemical composition of the various regions in OMC-1 to be definitively characterized.
\r\n\r\nA global analysis of the observed abundances has shown that the markedly different chemical compositions of the kinematically distinct Orion subsources may be simply interpreted in the framework of an evolving, initially quiescent, gas-phase chemistry influenced by the process of massive star formation. The chemical composition of the extended Orion cloud complex is similar to that found in a number of other objects, but the central regions of OMC-1 have had their chemistry selectively altered by the high velocity outflow from the young star(s) embedded deep within the interior of the molecular cloud. Detailed arguments are presented in this thesis which relate the seemingly disparate chemical compositions of the individual regions to each other and to the expected physical manifestations of the circumstellar mass loss, and which suggest that similar mechanisms may operate in other molecular clouds as well.
\r\n\r\nBy performing supporting laboratory spectroscopy to supplement existing millimeter-wave catalogues only 33 of the over 800 lines remain unidentified, in contradiction to earlier expectations which had predicted that the near millimeter-wave spectrum of molecular clouds would contain hundreds of strong, unidentifiable emission features. It is probable that a number of the unidentified lines left in the OVRO survey are due to transitions between states of either isotopically substituted or highly excited abundant and complex molecules such as CH3OH, CH3OCH3, and HCOOCH3 whose rotational spectra are poorly known at present. The very small percentage and weak strength of the unidentified lines implies that the dominant chemical constituents visible at millimeter wavelengths have been identified in the Orion molecular cloud.
\r\n\r\nAlso presented are high resolution laboratory millimeter, submillimeter, and far-infrared absorption spectra of the transient molecular species OH, CN, HOC+, and HCO, The zero-field pure rotational spectrum of the OH radical was observed, for the first time, with a frequency agile far-infrared laser sideband spectrometer which promises to revolutionize high resolution spectroscopy at submillimeter and far-infrared wavelengths, while the HOC+ molecular ion was synthesized in a novel glow discharge cell that increases ion abundances by roughly two orders of magnitude as compared with those produced by previously reported methods. Studies of several ions produced in the new discharge cell have provided a theory of the mechanism responsible for the ion enhancement. Sixty-five transitions of CN in its first four vibrational states have been observed, allowing a detailed examination of vibrational and electronic effects in this astrophysically important free radical. The investigation of HCO is the first extensive zero-field analysis of the formyl radical, and is one of the very few millimeter and submillimeter laboratory studies of a non-linear free radical performed to date.
" }, { "name": "Cave, Robert J.", "degree": "PhD", "year": "1986", "title": "A Theoretical Model for Orientation Effects in Electron Transfer Reactions", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08302019-110545286", "creators": [ { "name": { "family": "Cave", "given": "Robert J." }, "id": "Cave-Robert-J", "display_name": "Cave, Robert J." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s9zp-mj05", "abstract": "In this thesis, the development and application of a model for the examination of orientation effects in electron transfer reactions are considered. The model is designed to describe broad features of the electronic interactions between large molecules, where the transferred electron is delocalized in both reactant and product.
\r\n\r\nThe model employs spherical or oblate-spheroidal potentials of constant depth for the donor and acceptor sites. The Schrodinger equation is solved for the exact eigenfunctions of such a potential, and the electron transfer matrix element, TBA, is calculated us1ng these wavefunctions. TBA is the principal distance and orientation dependent quantity in current theories of nonadiabatic electron transfer. By comparison of results obtained using spherical and spheroidal wells, il was determined that both orbital shape and well shape (i.e., molecular shape) effects are important in determining the magnitude and orientation dependence of TBA.
\r\n\r\nThe model was used to examine orientation dependence in electron transfer reactions between porphyrins and porphyrin derivatives. TBA was examined for a variety of mutual orientations, including: 1) face-to-face transfers, where it was found that TBA for forward transfer from photoexcited reactants was considerably larger than Lhat for back transfer to yield ground state products, 2) edge-to-edge orientations, and 3) models of possible initial donor-acceptor pairs in a bacterial photosynthetic electron transfer system (Rhodopseudomonas viridis). It was observed that TBA was a sensitive function of orbital shape and orientation.
\r\n\r\nIn order to simplify the model, a semiclassical approximation was examined for the donor and acceptor wavefunctions, for both the spherical- and spheroidal-well states. The accuracy of the approximation supports the interpretations of the results obtained from the exact calculations. It also substantially reduced the calculational time involved.
" }, { "name": "Celii, Francis Gabriel", "degree": "PhD", "year": "1986", "title": "I. IR Photodissociation Spectroscopy of Large van der Waals Clusters. II. UV Laser-Induced Photochemistry of Fe(CO)\u2085 on Single Crystal Surfaces", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-153133005", "creators": [ { "name": { "family": "Celii", "given": "Francis Gabriel" }, "id": "Celii-Francis-Gabriel", "display_name": "Celii, Francis Gabriel" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nz14-wz74", "abstract": "Chapter 2 is a summary of vibrational predissociation spectra of weakly bound clusters containing either CF3I or CF3Br. Spectra indicative of ArCF3I, KrCF3I, (CF3I)2, ArCF3Br and (CF3Br)2 clusters are presented with comparison to the matrix-isolation spectra of CF3I and CF3Br.
\r\n\r\nThe infrared photodissociation technique can be applied to the study of weakly bonded clusters which do not absorb in the infrared by attaching an IR chromophore; this work is presented in Chapter 3. Vibrational predissociation spectra of large clusters of Ar, Kr, N2 and CH4 containing a single CH3F or C2H4 chromophore are obtained as a function of cluster size. The IR spectra distinguish three regimes of cluster size in the CH3F case. The dissociation profiles yield information on the chromophore environment and the lifetime of the excited vibration. The clusters are gas-phase analogies to the matrix-isolation technique, although differences between the two are consistent with the presumed icosahedral cluster geometry, and \"matrix\" and \"surface\" sites are distinguishable.
\r\n\r\nChapter 4 presents the application of a simple two-level-with-decay model to the photodesorption of weakly bound adsorbates on crystal surfaces. Feasibility estimates are reported and establish that vibrational predissociation of the excited adsorbes can be induced in the infrared, where energy quenching mechanisms on surfaces can be quite fast. The effect of these quenching mechanisms on the lineshapes present the opportunity to probe the processes with the use of the photodesorption technique. Extraction of the phenomenological rate constants is described. Also reported are attempts to observe photodesorption induced by low-power lasers.
\r\n\r\nThe photodecomposition of Fe(CO)5 on three single crystal surfaces, sapphire (Al2O3), Si(100) and Ag(110), using UV irradiation is described in Chapter 5. The quenching of excited electronic states of adsorbates is expected to be quite different on the surfaces, yet dissociation of the Fe(CO)5 is observed in all cases. The results allow determination of the dissociation mechanism and also imply that the Fe(CO)5 dissociation rate is ultra-fast (< 10-13). Extensions of this initial investigation are discussed.
" }, { "name": "Chi, Bo Kyung", "degree": "PhD", "year": "1986", "title": "The Motion of Immiscible Drops and the Stability of Annular Flow", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-10102005-095730", "creators": [ { "name": { "family": "Chi", "given": "Bo Kyung" }, "id": "Chi-Bo-Kyung", "display_name": "Chi, Bo Kyung" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Ottino", "given": "Julio M." }, "id": "Ottino-Julio-M", "role": "member", "display_name": "Ottino, Julio M." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/932J-DA86", "abstract": "The creeping motion of a neutrally buoyant drop in Poiseuille flow is studied numerically using the boundary integral technique. The effects of the viscosity ratio, interfacial tension and drop size on steady shapes and velocities of the deformed drop are considered. Particular attention is given to cases involving large deformation which occurs when the interfacial tension becomes small. The critical value of the capillary number, for a given viscosity ratio, above which a steady shape for the drop does not exist is determined.
\r\n\r\nThe stability of annular flow of two fluids of different viscosities through a circular tube is studied. The instability considered in the present study occurs at the interface between two fluids. Linear stability analysis is carried out for axisymmetric disturbances when the mechanisms of instability due to a viscosity difference between two fluids and interfacial tension are simultaneously present. The growth factor of instability is nonlinear in the viscosity ratio and the interfacial tension because the governing equations and boundary conditions are linearized with respect to a disturbance amplitude function, but not linearized with respect to the viscosity ratio and the interfacial tension. The effects of the viscosity ratio, interfacial tension, radius ratio and Reynolds number on the stability of the interface as well as the modes of maximum instability are studied.
\r\n\r\nNumerical study of the axisymmetric approach of a deformable drop toward a deformable interface under the action of a constant buoyancy force is carried out using the boundary integral technique. Unlike the previous film drainage theories, governing equations are applied in all fluids including the drop, lower bulk and upper bulk fluids. Therefore, physical properties of the drop fluid and the upper bulk fluid, which are neglected in the film drainage theories, are included in the present study. The influence of the viscosity ratio and interfacial tension is considered. Three distinct mechanisms of film drainage are identified: rapid drainage where the film between the drop and the interface is thinnest at the centerline and the film thickness increases with radial distance, uniform drainage where the region of uniform film thickness appears and persists during further approach of the drop toward the interface, and dimpled drainage where the film is thinnest at a rim radius rather than at the centerline.
\r\n" }, { "name": "Dunlap, Paul N.", "degree": "PhD", "year": "1986", "title": "Studies of Flow Modification and Polymer Conformation in Extensional Flows of Dilute Polymer Solutions", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-03212008-080541", "creators": [ { "name": { "family": "Dunlap", "given": "Paul N." }, "id": "Dunlap-Paul-N", "display_name": "Dunlap, Paul N." } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "member", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Sabersky", "given": "Rolf H." }, "id": "Sabersky-R-H", "role": "member", "display_name": "Sabersky, Rolf H." }, { "name": { "family": "Peng", "given": "S. T." }, "id": "Peng-S-T", "role": "member", "display_name": "Peng, S. T." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2v8j-nf26", "abstract": "This is a study of the coil-stretch transition of macromolecules in dilute solutions which are subjected to extensional flows and of the effects of the polymer molecules on the flow fields. The flow fields are produced in a four-roll mill, two-roll mills of several different gap width to roller radius ratios, and a cylindrical Couette device. These flows are laminar, and approximately two-dimensional linear flows covering the range of flow types with different amounts of extension and vorticity from pure extension to simple shear flow. The two-roll mills were constructed to extend the previously accessible range of flow types to those with only slightly more extension than vorticity, i.e., much nearer to simple shear flow. The flows are characterized by using homodyne light scattering spectroscopy to directly measure velocity gradients fields. The degree of polymer extension is monitored using flow birefringence measurements.
\r\n\r\nStudies using 100 ppm polystyrene in viscous solvents show that the flow birefringence data for all the different strong flows (simple shear is a weak flow) correlate with the eigenvalue of the velocity gradient tensor. Extensional flow birefringence data for the same polymer in different solvents correlate with the Zimm relaxation time based on the intrinsic viscosity. When the polymers are sufficiently extended there is a distinct onset of measurable decreases in the velocity gradients. A necessary condition for this to occur is a very high level of domain overlap between the extended molecules. If we estimate this by the volume concentration of circumscribed spheres, \u03c6eff (i.e., the sphere diameter equals the extended length of the polymer), the onset of an effect of polymer on the flow does not occur until \u03c6eff ~ 4000-6000. Nevertheless, our measurements show that dilute polymer solutions do inhibit the development of large strain rates in regions of persistent extensional flow.
\r\n\r\nStudies using sodium polystyrenesulfonate in glycerol with various amounts of added sodium chloride show the range of coil-stretch behavior that can occur as a function of the equilibrium conformation of the polyelectrolyte. With high ionic strength solutions, the polyelectrolyte behavior is the same as that of nonionic polymers. As the ionic strength decreases and the equilibrium dimensions increase, the onset of the coil-stretch transition shifts to much lower shear rates. With no added salt, the expanded coil approaches free-draining behavior with a monotonic increase of flow birefringence with increasing shear rate instead of the distinct onset point usually observed. These low ionic-strength solutions also exhibit overshoots in the birefringence on startup of simple shear flow.
\r\n\r\nThe flow birefringence data have been compared with predictions of the nonlinear elastic dumbbell model with various combinations of constant or conformation-dependent friction laws, internal viscosity, strain-inefficient rotation, and Coulombic charges on the beads. It seems that all of the models studied work well in pure extension where the coil-stretch process largely governed by the limited amount of total strain (or finite residence time) in the flow. However, in flows with considerable vorticity, the details of the hydrodynamic interaction between beads and solvent and the rotational motion of the deforming dumbbell become very important in determining the behavior of the model. Thus the birefringence data in the flows near simple shear flow provide more stringent tests of the models than flows with no vorticity. In flows slightly more extensional than simple shear flow, none of the more advanced models gives entirely satisfactory comparisons with the data. In this flow regime, the best comparisons with data are obtained with the simple FENE dumbbell. Some evidence that the current modeling approach (and conformation-dependent hydrodynamic friction) is basically sound was found. The charged dumbbell model is able to describe the large difference in behavior between highly charged polyelectrolytes and those with excess added salt only if a conformation-dependent friction law is included.
" }, { "name": "Economou, Constantin George", "degree": "PhD", "year": "1986", "title": "An Operator Theory Approach to Nonlinear Controller Design", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-083200", "creators": [ { "name": { "family": "Economou", "given": "Constantin George" }, "id": "Economou-Constantin-George", "display_name": "Economou, Constantin George" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "chair", "display_name": "Morari, Manfred" }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Thompson", "given": "Peter M." }, "id": "Thompson-Peter-M", "role": "member", "display_name": "Thompson, Peter M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/2ewe-dp19", "abstract": "Strong similarities between control theory and the theory on the solution of operator equations have been observed and basic results in control theory have been derived from operator theory arguments. The purpose of this work is to investigate the theory of controller design as an application of basic operator theory principles and to establish a unified framework in which control theory can benefit from a \"rich\" operator theory. The major impact is anticipated in nonlinear feedback control theory: controller design can be formulated as selection of an iterative algorithm to solve a nonlinear operator equation corresponding to the control objective. As an example, controllers induced by the method of successive substitution and the Newton method are introduced and the corresponding analysis and synthesis issues are studied. Applied to linear systems, the proposed concepts have a straightforward interpretation in terms of familiar notions in linear controller design theory. Applications are presented and extensions of the current results are suggested to conclude the thesis.
" }, { "name": "Ellis, Walther Robert, Jr.", "degree": "PhD", "year": "1986", "title": "Spectroelectrochemical Studies of Heme and Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062025-201831641", "creators": [ { "name": { "family": "Ellis", "given": "Walther Robert, Jr." }, "id": "Ellis-Walther-Robert", "display_name": "Ellis, Walther Robert, Jr." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "chair", "display_name": "Hopfield, John J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fqg8-e811", "abstract": "A complete characterization of the redox thermodynamics of a metalloprotein\r\ninvolves the determination of the effects of pH, ionic\r\nstrength, and temperature. In particular, variable-temperature reduction\r\npotential measurements yield the enthalpic and entropic contributions\r\nto EO, which, in turn, are related to kinetic activation\r\nparameters.
\r\n\r\nIn Chapter II of this thesis, the design of a versatile\r\nspectroelectrochemical apparatus for high precision measurements of\r\nmetalloprotein reduction potentials is described. A stainless steel\r\nshroud, necessary for anaerobic measurements, is used to house either\r\nof two types of spectroelectrochemical cells: a thin-layer optically\r\ntransparent electrode cell, or a two cm. stirred cell (useful for\r\nobserving weak chromophores). Both types of cells are suitable for\r\nvariable-temperature measurements using either absorption or circular\r\ndichroism spectroscopy. The latter offers a useful alternative to\r\nabsorption spectroscopy since redox mediators, which are almost always\r\nnecessary for electrochemical experiments on metalloproteins, are\r\ngenerally not optically active and therefore will not interfere with\r\nthe acquisition of protein circular dichroism spectra.
\r\n\r\nSpectroelectrochemical measurements for a selection of paradigmatic \r\nhemoproteins are presented in Chapter III. Horse heart\r\ncytochrome c is shown to yield redox thermodynamic parameters in excellent\r\nagreement with results of calorimetric determinations. Data\r\nfor R. palustris cytochrome c' and myoglobin are also presented\r\nand discussed with reference to extant spectroscopic and kinetic data, and\r\ncrystal structure determinations for these proteins. \u0394SO does not\r\ncorrelate with protein surface charge, unlike the well-known correlation\r\nof \u0394SO with charge for transition metal complexes. Instead, it\r\nis suggested that \u0394SO is (at least in part) determined by redox-linked\r\nprotein conformational changes. Next, redox thermodynamic parameters\r\nfor the azurins from A. denitrificans and A. faecalis are presented.\r\nThe azurin data show that proton uptake (in the region pKaox\r\nless than pH less than pKared) accompanying the reduction of the copper site decreases \u0394SO\r\nslightly. This observation is discussed in light of crystallographic\r\nstudies on \"blue\" copper proteins.
\r\n\r\nChapter IV discusses the problems of temperature and metal-metal\r\ninteractions associated with the equilibrium redox behavior of multisite\r\nmetalloproteins. An analogy between allosteric ligand binding\r\nand allosteric electron binding (i.e., reduction) is used to analyze\r\nNernst plots exhibiting unusual slopes. In interactive situations,\r\nthe conventionally defined reduction potential is not a simple\r\nthermodynamic quantity. This formalism is used in a discussion of the\r\nequilibrium redox interactions displayed by the optically visible\r\nmetal centers (CuA, Fe a, Fe a3) in cytochrome c oxidase. The commonly\r\naccepted \"neoclassical\" model, which only incorporates interaction\r\nbetween Fe a and Fe 3, is shown to be incorrect. The importance\r\nof temperature (leading to varying entropies of reduction for different\r\nmetal sites in a protein) is illustrated by a (NH3)5Ru(His-48)-derivative\r\nof sperm whale myoglobin. Kinetic and thermodynamic data\r\nfor this two-site protein lead to an estimate of 20 kcal/mol for the\r\nreorganizational enthalpy of the iron heme in myoglobin. This value\r\nsubstantially larger than the 7-8 kcal/mol estimate for horse\r\ncytochrome c, and is most likely due to a ligation change upon reduction\r\nof myoglobin wherein the axial water molecule dissociates from\r\nthe iron center.
\r\n\r\nA detailed discussion of the pH, ionic strength, and temperature\r\ndependences of the formal reduction potentials of the CuA, Fe a. and\r\nFe a3 centers in cytochrome oxidase is the topic of Chapter V. These\r\nresults are compared with values for other protein copper and heme\r\nsites and are discussed within the context of the known structural\r\nfeatures and reactivity of the enzyme.
" }, { "name": "Finch, William C.", "degree": "PhD", "year": "1986", "title": "Synthesis and Reactivity of Transition Metal Methylidene Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062009-112330268", "creators": [ { "name": { "family": "Finch", "given": "William C." }, "id": "Finch-William-C", "display_name": "Finch, William C." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/t0fa-0414", "abstract": "The reaction of metal oxo complexes with methylenation agents, \"Cp2TiCH2\" and CH2PPh3, was investigated as a means to generate new transition metal methylidene complexes. With \"Cp2TiCH2\", only when the oxo complex has ancillary ligands of the proper electronic and steric characteristics, as in WO(CH2XMe3)4(X = C, Si), is clean reaction observed producing \u00b5-O-\u00b5-CH2 complexes. Otherwise the many reaction pathways available to the Cp2TiCH2 fragment lead to complex reaction mixtures. The oxo ligand is inert to attack by CH2PPh3 which instead acts as a powerful alkylating agent in the transition metal systems investigated.
\r\n\r\nThe effect of cyclopentadienyl ring substitution on the reactivity of titanocene metallacyclobutanes was also investigated. The observed decrease in reactivity of these compounds with increasing methyl substitution of their cyclopentadienyl rings is related to the increasing destabilization of the transition state between metallacycle and methylidene-olefin complex upon substitution. This destabilization arises from the \"reductive\" nature of the formation of methylidene-olefin complex from metallacycle.
\r\n" }, { "name": "Forester, Lynn", "degree": "PhD", "year": "1986", "title": "An Inelastic Electron Tunneling Spectroscopic Study of the Interactions of Cyclic Hydrocarbons with a Zirconium Polymerization Catalyst Supported on Aluminum Oxide", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-04112008-133837", "creators": [ { "name": { "family": "Forester", "given": "Lynn" }, "id": "Forester-Lynn", "display_name": "Forester, Lynn" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Lambe", "given": "John" }, "id": "Lambe-John", "role": "member", "display_name": "Lambe, John" } ], "option_major": [ "chemeng" ], "doi": "10.7907/fj5a-m086", "abstract": "Inelastic electron tunneling spectroscopy (IETS) has been used to investigate the temperature and exposure-dependent reactions of two cyclic hydrocarbons, cyclohexene and 1,3-cyclohexadiene, with Zr(BH4)4 supported on Al2O3, a known olefin polymerization catalyst.
\r\n\r\nThe interactions of cyclohexene with the adsorbed catalyst have been studied at exposures of 150, 1200 and 6000 Torr s at temperatures ranging from 298 to 623 K. At 150 Torr s and 298 K, the adsorbed cyclohexene is clearly an unsaturated hydrocarbon and cyclohexene coordination to the Zr catalyst does not require an appreciable displacement of BH4 ligands. There is evidence of both tridentate and bidentate BH4 stretching vibrations. The initial complex formed by the adsorbed cyclohexene is probably a \u03c0-complex. The IET spectra support this conclusion as well as the possibility of conversion to a \u03b73-allyl ligand. The unsaturated surface species are converted to a saturated hydrocarbon at intermediate and high exposures of cyclohexene. The saturated specie accumulates on the surface as a function of both exposure and substrate temperature and the spectra show no olefinic increases in intensity. The saturated specie has been identified as polycyclohexene, a saturated polymer consisting of cyclohexane rings formed by homopolymerization.
\r\n\r\nThe interactions of 1,3-cyclohexadiene with Zr(BH4)4 supported on v have been studied at exposures of 150 and 6000 Torr s. Adsorbed 1,3-cyclohexadiene has been shown to form an unsaturated hydrocarbon similar to cyclohexene at moderate exposures which continues to accumulate on the surface as a function of temperature. At high exposures, evidence has been presented that the catalyst may initiate the polymerization of 1,3-cyclohexadiene to form poly-1,3-cyclohexadiene. As with cyclohexene, there is no apparent saturation limit as based on increases in the intensity of key hydrocarbon spectral features and on junction resistance. Adsorbed 1,3-cyclohexadiene continues to accumulate on the surface as a function of temperature at 6000 Torr s. The spectral intensity of the ring breathing modes increases dramatically and their variability in position provide evidence of different types of substituted rings. Adsorption of 1,3-cyclohexadiene perturbs the catalyst much more than cyclohexene, promoting the disassociation of the BH4 ligands.
\r\n\r\nDesign changes and improvements to a high vacuum system used for the fabrication of tunnel junctions, as well as a detailed account of the experimental procedures, are described. Programs for computer spectral analysis are presented.
\r\n" }, { "name": "Fourkas, John Theodore", "degree": "Masters", "year": "1986", "title": "Polycyclic Peroxides and Planar Nitrogens", "advisor": "Schaefer, William P.; Chan, Sunney I.; Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282010-132203527", "creators": [ { "name": { "family": "Fourkas", "given": "John Theodore" }, "id": "Fourkas-John-Theodore", "orcid": "0000-0002-4522-9584", "display_name": "Fourkas, John Theodore" } ], "advisors": [ { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "co-advisor", "display_name": "Schaefer, William P." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "co-advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GMVG-R955", "abstract": "1,6-diaza-3,4,8,9,12,13-hexaoxabicyclo[4.4.4] tetradecane (hexamethylene triperoxide diamine or HMTD) was found, by a single crystal x-ray study, to have planar bridgehead nitrogen atoms. In order to study this planarity, a synthesis was developed for HMTD analogs. Crystals structures were obtained for three of these analogs, 1,6-diaza-3,4,8,9-tetraoxabenzotricyclo[4.4.2]dodec-11-ene (benzene tetramethylene diperoxide diamine or BTDD), 1,8-diaza-10,11,14,15- tetraoxatricyclo[6.4.4.0^(2,7)]hexadecane (cyclohexyl tetramethylene diperoxide diamine or CTDD), and 1,6-diaza3,4,8,9-hexaoxabicyclo[4.4.2]dodecane (hexamethylene diperoxide diamine or HMDD). These structures show that the planarity at the bridgehead nitrogen atoms of HMTD is no coincidence. MM2, a molecular mechanics program, was used to show that this planarity is not expected from simple force considerations. MNDO was used to model the molecule considering molecular orbitals. Finally, nuclear magnetic resonance techniques were used to obtain the energy of activation for inversion of HMTD and to determine the nuclear quadrupole coupling constants of the bridgehead nitrogen atoms at different temperatures, and thus their relative\r\nplanarity.\r\n\r\n" }, { "name": "Gajda, Gregory Joseph", "degree": "PhD", "year": "1986", "title": "An Inelastic Electron Tunneling Spectroscopic Investigation of Inorganic and Organometallic Molybdenum Complexes Adsorbed on Aluminum Oxide Surfaces", "advisor": "Weinberg, William Henry; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-124552652", "creators": [ { "name": { "family": "Gajda", "given": "Gregory Joseph" }, "id": "Gajda-Gregory-Joseph", "display_name": "Gajda, Gregory Joseph" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/2evk-b965", "abstract": "The design, construction and operation of an integrated glove box-based tunnel\r\njunction fabrication system are described. This versatile, all stainless steel,\r\nultrahigh vacuum compatible system provides both vapor and liquid phase\r\nadsorption capabilities with a wide variety of molecules. The differences between\r\nadsorption from the liquid phase under an inert atmosphere and in the laboratory\r\natmosphere are illustrated by spectra from junctions prepared with\r\nethanolamine (2-amino-ethanol). A rapid (~ 10 s) and accurate (~ 1%) constant\r\nmodulation current tunnel junction spectrometer displays the obtained spectrum\r\non a storage oscilloscope. The design of these electronics is discussed, and\r\nthe ability to rapidly optimize the lock-in detector phase setting simplifies the\r\nmeasurement of inelastic electron tunneling spectra. The use of a numerical\r\nfirst derivative routine to remove the linear background slope in tunneling spectra\r\nis described, and its ability to determine peak positions in the processed\r\nspectra is discussed.
\r\n\r\nMolybdenum hexacarbonyl adsorbs reversibly on hydroxylated alumina surfaces\r\nat 22\u00b0C to form a carboxylic acid-type adspecies . An estimate of the heat\r\nof adsorption energy, 15 \u00b1 3 kcal/mole, is derived from the desorption kinetics.\r\nHeating the alumina surface to 140 \u00b1 2\u00b0C during adsorption produces thick\r\n(> 500 \u00c5) molybdenum films. Heating the surface to 100\u00b0C during adsorption\r\nproduces decomposition products which consist of molybdenum oxides and subcarbonyls,\r\ndepending on the decomposition parameters (time and post-heating\r\nsequence). The decomposition products show no reaction with 2 Torr of\r\nethylene at 100\u00b0C even after one hour.
\r\n\r\nAt 22\u00b0C, molybdenum oxytetrachloride adsorbs and reacts with the surface\r\nhydroxyl groups on the alumina to form a dioxo-bridged molybdenum dichloro\r\ncomplex, which desorbs slowly at 295 K. Heating during the adsorption produces\r\npoorly reproducible molybdenum suboxide compounds. At 22\u00b0C molybdenum\r\ndioxodichloride adsorbs from the vapor phase and reacts with surface\r\nhydroxyl groups on the alumina to form a molybdenum oxide which reacts\r\nreadily with background water vapor. Heating the surface during exposure produces\r\na partially polymerized oxide which still reacts with background water\r\nvapor. Heating the exposed surfaces in vacuum dehydrates the oxide and\r\nincreases the extent of oligomerization. The oxides show no reaction with 2 Torr\r\nof ethylene at 100\u00b0C after 30 minutes, or with acetic acid at 10-1 Torr after five\r\nminutes at 22\u00b0C. Exposure to 5 x 10-2 Torr of 4-t-butylpyridine for 100 s at 22\u00b0C\r\nresults in complete desorption of the oxide.
" }, { "name": "Geller, Anthony Sigmund", "degree": "PhD", "year": "1986", "title": "A Study of the Creeping Motion of a Sphere Normal to a Deformable Fluid-Fluid Interface: Deformation and Breakthrough", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-135633", "creators": [ { "name": { "family": "Geller", "given": "Anthony Sigmund" }, "id": "Geller-Anthony-Sigmund", "display_name": "Geller, Anthony Sigmund" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brady", "given": "John F." }, "id": "Brady-J-F", "orcid": "0000-0001-5817-9128", "role": "member", "display_name": "Brady, John F." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Ottino", "given": "Julio M." }, "id": "Ottino-Julio-M", "role": "member", "display_name": "Ottino, Julio M." } ], "option_major": [ "chemeng" ], "doi": "10.7907/88xv-sk72", "abstract": "The creeping motion of a sphere normal to a deformable fluid-fluid interface has been studied using numerical and experimental techniques. A numerical method based on the distribution of point force singularities at fluid surfaces, the boundary integral method, has been applied to sphere motion in the presence of an interface subject to the constraint of either constant velocity normal to the interface, or constant non-hydrodynamic body force normal to the plane of the undeformed interface. Cases for several values of the viscosity ratio, density difference, and interfacial tension between the two fluids are considered. Calculations reveal two distinct modes of interface deformation: a film drainage mode in which fluid drains away in front of the sphere leaving an ever thinning film, and a tailing mode where the sphere passes several radii beyond the plane of the initially undeformed interface, while remaining encapsulated by the original surrounding fluid which is connected with its main body by a thin thread-like tail behind the sphere. We consider the influence of the viscosity ratio, density difference, interfacial tension and starting position of the sphere in determining which of these two modes of deformation will occur.
\r\n\r\nExperiments were performed for a rigid sphere translating normal to a deformable fluid-fluid interface with large capillary number. The motion of fluid at the interface in both the axial and radial directions was recorded as was the total force on the sphere. The experimental results were compared to boundary integral calculations of the interface position and force on the sphere, employing both a fully mobile and completely immobile model for interfacial dynamics. These comparisons indicate significant reduction in the interface mobility for the experimental system.
\r\n\r\nIn order to increase our understanding of the actual breakthrough process, a third model for interfacial dynamics was developed. The latest model includes the disjoining pressure in the normal stress jump boundary condition. Preliminary calculations indicate that dispersion forces can result in a change in the calculated mode of breakthrough, converting tailing cases to the film drainage mode. Further, for the range of parameters studied here, the effect of dispersion forces was relatively small until the sudden onset of motion of the interface toward the sphere caused breakthough.
" }, { "name": "Gelles, Jeff Daniel", "degree": "PhD", "year": "1986", "title": "The Cu\u1d00 Site in Cytochrome c Oxidase: Its Role in Coupling Electron Transport to Proton Pumping", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10112019-095757311", "creators": [ { "name": { "family": "Gelles", "given": "Jeff Daniel" }, "id": "Gelles-Jeff-Daniel", "orcid": "0000-0001-7910-3421", "display_name": "Gelles, Jeff Daniel" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vr49-7048", "abstract": "Cytochrome c oxidase contains a copper-ion electron transfer site, CuA, which has previously been found to be unreactive with externally added reagents under conditions in which the protein remains structurally intact. We have studied the reaction of cytochrome oxidase with sodium p-hydroxymercuribenzoate (pHMB) and found that the reaction proceeds, under appropriate conditions, to give an excellent yield of a particular derivative of the CuA center which has electron paramagnetic resonance and near-infrared absorption spectroscopic properties which are distinctly different from those of the unmodified center. Spectroscopic and chemical characterization of the other metal-ion sites of the enzyme reveals little or no effect of the pHMB modification on the structures of and reactions at those sites. Of particular interest is the observation that the modified enzyme still displays a substantial fraction of the native steady-state activity of electron transfer from ferrocytochrome c to O2. Although the modified copper center retains the ability to receive electrons from the powerful reductant Na2S2O4 and to transfer electrons to O2, it is not significantly reduced when the enzyme is treated with milder (higher potential) reductants such as NADH/phenazine methosulfate or the physiological substrate ferrocytochrome c.
\r\n\r\nCuA exhibits many spectroscopic and chemical properties which make it highly atypical of cuproprotein active sites; the singular nature of this site has prompted speculation about the importance of the structural peculiarities of this metal-ion center in the catalytic cycle of the enzyme. In this work, we demonstrate that the unusual features of this site are not prerequisites for competent catalysis of electron transfer and O2 reduction by the enzyme. These observations suggest that a secondary electron transfer pathway not involving CuA exists between the cytochrome c and oxygen binding sites which can function at a rate at least 20% of the total turnover rate of the native enzyme.
\r\n\r\nCytochrome c oxidase converts free energy released in respiratory electron transport into a metabolically useful form by contributing to the potential gradient across the mitochondrial inner membrane. Both a process involving electron transfer linked proton pumping and a process involving electron transfer from ferrocytochrome c to O2 contribute to the potential gradient. Taken together with those from other recent studies, the results of the experiments support a model for electron transfer in cytochrome oxidase in which CuA and Fea are parts of separate, parallel electron transport pathways between cytochrome c and the cytochrome oxidase O2 reduction site. This model has important implications for the role of CuA in respiratory energy transduction by cytochrome oxidase. It suggests that CuA is the best candidate among the four metal center sites in cytochrome oxidase to be the site of redox-linked proton pumping.
\r\n\r\nIn order to explore more fully the mechanistic aspects of energy transduction in cytochrome oxidase, we propose a complete chemical mechanism for the enzyme's proton pump. The mechanism achieves pumping with chemical reaction steps localized at a single redox site within the enzyme; no indirect coupling through protein conformational changes is required. The proposed mechanism is based on a novel redox-linked transition metal ligand substitution reaction. The use of this reaction leads in a straightforward manner to explicit mechanisms for achieving all of the processes determined by Blair, et al. (D.F. Blair, J. Gelles, and S.I. Chan, Biophys. J., in press) to be needed to accomplish redox-linked proton pumping. These processes include: 1) modulation of the energetics of protonation/deprotonation reactions and modulation of the energetics of redox reactions by the structural state of the pumping site; 2) control of the rates of the pump's redox reactions with its electron transfer partners during the turnover cycle (gating of electrons); and 3) regulation of the rates of the protonation/deprotonation reactions between the pumping site and the aqueous phases on the two sides of the membrane during the reaction cycle (gating of protons). The model is the first proposed for the cytochrome oxidase proton pump which is mechanistically complete and specific enough that a realistic assessment can be made of how well the model pump would function as a redox-linked energy transducer. This assessment is accomplished via analyses of the thermodynamic properties and steady-state kinetics expected of the model. These analyses demonstrate that the behavior of a pump based on the model would be very similar to that observed of cytochrome oxidase both in the mitochondrion and purified preparations. Specifically, calculation of the properties of the model pump at equilibrium demonstrates that the behavior expected of the model pump in an electrochemical titration is the same as that observed for the CuA center: a nearly pH-independent midpoint potential of approximately 290 mV. An analysis of the performance of the pump during steady-state turnover demonstrates that the model pump is expected to function efficiently and with good power output under physiological conditions, and that its properties under conditions of varying load are similar to those observed in experiments on respiring mitochondria and on purified cytochrome oxidase reconstituted into artificial lipid vesicles.
\r\n\r\nAlthough the analysis presented here concerns only a single model of a redox-linked proton pump, it leads to some important general conclusions regarding the mechanistic features of such pumps. The first is that a workable proton pump mechanism does not require large protein conformational changes. Another conclusion is that a redox-linked proton pump need not display a pH-dependent midpoint potential as has frequently been assumed. A final conclusion is that mechanisms for redox-linked proton pumps that involve transition metal ligand exchange reactions are quite attractive because such reactions readily lend themselves to the linked gating processes necessary for proton pumping.
\r\n\r\nSeveral of the results of this research form the basis of a new approach to studying the role of CuA in energy transduction by cytochrome oxidase. I describe several continuing experimental programs based on this method, and summarize the goals, experimental design, and progress of these studies. I conclude by considering the physiological significance of the new conceptions about the role of CuA in energy transduction by cytochrome oxidase arising from this research.
" }, { "name": "Georgopoulos, Panagiotis Gerasimou", "degree": "PhD", "year": "1986", "title": "Mathematical Studies of Photochemical Air Pollution", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02012007-092322", "creators": [ { "name": { "family": "Georgopoulos", "given": "Panagiotis Gerasimou" }, "id": "Georgopoulos-Panagiotis-Gerasimou", "display_name": "Georgopoulos, Panagiotis Gerasimou" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "List", "given": "E. John" }, "id": "List-E-J", "role": "member", "display_name": "List, E. John" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" } ], "option_major": [ "chemeng" ], "doi": "10.7907/71dn-x264", "abstract": "In Part I a new, comprehensive model for a chemically reacting plume, is presented, that accounts for the effects of incomplete turbulent macro- and micro- mixing on chemical reactions between plume and ambient constituents. This \"Turbulent Reacting Plume Model\" (TRPM) is modular in nature, allowing for the use of different levels of approximation of the phenomena involved. The core of the model consists of the evolution equations for reaction progress variables appropriate for evolving, spatially varying systems (\"local phenomenal extent of reaction\"). These equations estimate the interaction of mixing and chemical reaction and require input parameters characterizing internal plume behavior, such as relative dispersion and fine scale plume segregation. The model addresses deficiencies in previous reactive plume models. Calculations performed with the TRPM are compared with the experimental data of P.J.H. Builtjes for the reaction between NO in a point source plume and ambient O3, taking place in a wind tunnel simulating a neutral atmospheric boundary layer. The comparison shows the TRPM capable of quantitatively predicting the retardation imposed on the evolution of nonlinear plume chemistry by incomplete mixing. Part IA (Chapters 1 to 3) contains a detailed description of the TRPM structure and comparisons of calculations with measurements, as well as a literature survey of reactive plume models. Part IB (Chapters 4 to 7) contains studies on the turbulent dispersion and reaction phenomena and plume dynamics, thus exposing in detail the underlying concepts and methods relevant to turbulent reactive plume modeling. New formulations for describing in-plume phenomena, such as the \"Localized Production of Fluctuations Model\" for the calculation of the plume concentration variance are included here.
\r\n\r\nPart II (Chapter 8) presents a collection of distribution-based statistical methods that are appropriate for characterizing extreme events in air pollution studies. Applications to the evaluation of air quality standards, formulation of rollback calculations, and to the use of plume models are included here.
" }, { "name": "Gilliom, Laura R.", "degree": "PhD", "year": "1986", "title": "Titanacyclobutanes Derived from Strained, Cyclic Olefins: A New Living Polymerization System", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10112019-151903746", "creators": [ { "name": { "family": "Gilliom", "given": "Laura R." }, "id": "Gilliom-Laura-R", "display_name": "Gilliom, Laura R." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bem4-z181", "abstract": "Reaction of precursors of \"Cp2Ti=CH2\" (Cp = \u03b75-C5H5) with cyclobutene yields polybutadiene. The preparation of the titanacyclobutane 3 by the addition of 3,3-dimethylcyclopropene to \"Cp2Ti=CH2\" is described. When phosphines PMeR2 (R = Me, Ph) are added to 3, phosphine adducts of the isomeric \u03b1-substituted titanium-carbene compound are obtained. Reaction with AlMe2Cl affords a heterobimetallic complex. Poly(dimethylpropenamer) is produced from reaction of 3 with excess olefin. The observed reactivity is consistent with productive cleavage of the metal-containing ring in 3 to \"Cp2Ti=CHC(CH3)2CHCH2.\"
\r\n\r\nTitanacyclobutanes 7 and 11 have been prepared from the reaction of norbornene with precursors of \"Cp2Ti=CH2\" and with metallacycle 3, respectively. On thermolysis, both 7 and 11 produce products consistent with the intermediacy of \u03b1-substituted titanocene-carbene compounds. Thermolysis at 65\u00b0C in the presence of excess norbornene affords ring-opened polynorbornene with a cis to trans ratio of 38:62. The polymerizations are highly efficient in catalyst and yield polymers of controlled molecular weight. Polymer prepared from 11 shows polydispersities as low as 1.07 based on gel permeation chromatography versus polystyrene standards. The molecular weight distributions of polymers obtained with 7 are always broader than those obtained with 11. The kinetics of both polymerizations are zero-order in monomer with \u0394G\u2021338 = 24 kcal/mol, \u0394H\u2021 = 27 kcal/mol, and \u0394S\u2021 = 9 e.u. Polymerization with 7 shows an induction period corresponding to a first-order decay of 7 with t1/2 = 80 min at 65\u00b0C, whereas the polymerization with 11 is linear throughout. Simultaneous incorporation of d2-norbornene into the polymer by all active sites confirms that this system is best described as a living polymer. The polymerization mechanism is discussed as an olefin metathesis with rate-limiting cleavage of trisubstituted titanacyclobutanes affording high energy carbene intermediates.
\r\n\r\nReaction of endo-dicyclopentadiene with \"Cp2Ti=CH2\" and 3 affords titanacyclobutanes 15 and 16 with exclusive addition to the bicyclic double bond. The X-ray diffraction study of 15 indicates a puckered metal-containing ring. Polymerization of endo-dicyclopentadiene occurs with cleavage of the bicyclic ring system. Preliminary results demonstrate that cyclopentene can be polymerized with 3 at high monomer concentrations. The polymerization of norbornadiene to a linear ring-opened polymer is described. Reaction of these catalysts with 1,4-epoxy-1,4-dihydronapthalene occurs at the double bond and yields oligomers.
\r\n\r\nAnalysis of the microstructure of polymers prepared from methyl-norbornenes indicates that the double bonds in these polymers are predominantly trans. The catalysts exhibit a moderate head-to-tail selectivity. The preferred tacticity of dyads at trans double bonds is racemic while that at cis double bonds is meso.
" }, { "name": "Gipson, Stephen Lloyd", "degree": "PhD", "year": "1986", "title": "Electrochemical Studies Related to the Design of New Inorganic Oxidants", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10112019-162918098", "creators": [ { "name": { "family": "Gipson", "given": "Stephen Lloyd" }, "id": "Gipson-Stephen-Lloyd", "display_name": "Gipson, Stephen Lloyd" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "chair", "display_name": "Collins, Terrence J." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fyz2-qc15", "abstract": "The electrochemistry of complexes designed to address important questions in the field of oxidation chemistry has been examined. There is a need for new ligands capable of forming stable complexes with high oxidation state metal centers for the development of new oxidants with enhanced selectivity and reactivity for the oxidation of organic substrates. The electrochemistry of complexes of a family of potentially tetradentate tetraanionic ligands was examined to probe their reactivity, stability to oxidation and ability to stabilize high-valent metal centers.
\r\n\r\nAn osmium(IV) complex of the ligand 1,2-bis(3,5-dichloro-2-hydroxybenzamido) ethane (CHBA-Et) was found to undergo degradation of the ligand upon oxidation to Os(V) in CH2Cl2. In the presence of alcohols or water this oxidative degradation proceeded in a selective and stepwise fashion through a number of intermediate complexes which were isolated and characterized. The identification of the intermediates allowed a detailed mechanism for the degradation, accounting for both the products and their diastereomeric distribution, to be proposed. The final products of the oxidative degradation and subsequent hydrolysis reactions were found to contain bidentate dianionic 3,5-dichloro-2-hydroxybenzamido ligands (CHBA) and to be catalysts for the electrochemical oxidation of alcohols. These catalysts, and analogs prepared chemically, catalyzed the selective electrochemical oxidation of alchols to aldehydes and ketones, but had limited lifetimes. During the catalytic oxidation reactions the catalysts decomposed to unknown, inactive products. The maximum catalyst lifetime observed corresponded to the oxidation of approximately 150 moles of benzyl alcohol to benzaldehyde per mole of catalyst.
\r\n\r\nThe oxidative degradation of the CHBA-Et ligand was eliminated by replacement of the ethylene bridge with a dichlorobenzene bridge. Osmium (IV) complexes of the new ligand, 1,2-bis(3,5-dichloro-2-hydroxy-benzamido)-4,5-dichlorobenzene (CHBA-DCB) displayed reversible oxidations to Os(V) in CH2Cl2. Complexes of the non-chlorinated analog of this ligand, HBA-B, also displayed reversible oxidations to Os(V). There is some question about the oxidation state assignment in these complexes since oxidized forms of the ligands could contribute to the structure ofthe complexes and so reduce the formal oxidation state assignment of the metal. It is believed that at least the CHBA-DCB ligand forms true Os(V) complexes.
\r\n\r\nControlled potential oxidation of complexes such as Os(CHBA-DCB)(pyridine)2 led to partial isomerization from the trans to the cis-alpha isomer. This isomerization is believed to be triggered by the decrease in electron density at the metal center upon oxidation. Because of restriction of amide resonance in the nonplanar form of the ligand, it is a better electron donor in the cis-alpha isomer and so isomerization helps offset the loss of electron density caused by oxidation. A similar decrease in electron density and isomerization to the cis-alpha isomer is observed upon coordination of electron-withdrawing ligands to the Os(IV) complexes. Reduction of some of these cis-alpha Os(IV) complexes can cause isomerization to the more planar cis-beta isomer. An approximate correlation between the electron donating ability of the monodentate ligands and the equilibrium constant for the trans/cis-alpha isomerization at Os(V) was demonstrated. This observation indicates that the isomerization is primarily, but not exclusively, under electronic control.
\r\n\r\nBecause of the limited anodic range of the CH2Cl2 used as a solvent for the electrochemical studies of the CHBA-DCB complexes, no anodic activity past the Os(V/IV) couples could be observed. Therefore, the electrochemistry of some of these complexes was examined in liquid SO2 which has an anodic range to about +4 V vs. 8CE. The complexes displayed additional reversible oxidations in SO2, but these oxidations are believed to be ligand-localized. The complex Os(CHBA-Et)(pyridine)2 and its degradation products were also examined in SO2 and were found to display additional reversible oxidations not observable in CH2Cl2.
\r\n\r\nComplexes of the tetradentate tetraanionic ligands with cobalt(III) were also studied. These complexes could be oxidized to stable Co(IV) compounds. A second oxidation observed in acetonitrile and CH2Cl2 did not produce a stable Co(V) complex. In liquid SO2 the cobalt complexes displayed four reversible oxidations.
\r\n\r\nChemically modified electrodes were prepared from some of the complexes studied. The most stable electrodes were prepared by reductive electropolymerization of the complex K[Os(CHBA-Et)(4-vinylpyridine)2]. These electrodes showed stable electrochemical responses in acetonitrile, CH2Cl2 and aqueous media, but were not stable in nonaqueous acidic media or upon oxidation to Os(V). Because of the sensitivity to acid, these polymer modified electrodes could not be converted to the catalyst compounds.
" }, { "name": "Grosdidier, Pierre", "degree": "PhD", "year": "1986", "title": "Interaction Measures for Systems Under Decentralized Control", "advisor": "Morari, Manfred", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192008-093230", "creators": [ { "name": { "family": "Grosdidier", "given": "Pierre" }, "id": "Grosdidier-Pierre", "display_name": "Grosdidier, Pierre" } ], "advisors": [ { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "advisor", "display_name": "Morari, Manfred" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "role": "chair", "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xhj6-3x76", "abstract": "Multivariable controllers are often avoided in the chemical process industries in favor of simpler diagonal or block-diagonal controllers. Such \"decentralized\" controllers are desirable because they result in control systems with fewer tuning parameters and greater failure tolerance. However, the ensuing simplicity in controller design must be weighted against the interactions which result from ignoring the off-diagonal system blocks. These can lead to performance deterioration and even instability. The purpose of an Interaction Measure (IM) is to indicate under what conditions the stability of the diagonal loops/blocks will guarantee that of the complete system.
\r\n\r\nOne such measure, the Relative Gain Array (RGA), has found widespread acceptance both in industry and academia despite its empirical basis. This measure, in fact, has sound theoretical justifications. Rigorous relationships are derived in this study linking the RGA to closed-loop stability and robustness with respect to model uncertainty.
\r\n\r\nUsing the notion of Structured Singular Value, a new dynamic IM is also defined for multi-variable systems under feedback with diagonal or block-diagonal controllers. This measure, the \u00b5 IM, can be used to select the \"best\" variable pairings for the controller as well as predict the stability of the decentralized control system. Its steady-state value also provides a sufficient condition for achieving offset-free performance with the closed-loop system. The relationship of this new IM with Rijnsdorp' IM and Rosenbrock's Direct Nyquist Array is clarified.
\r\n\r\nFinally, it is shown how the \u00b5 IM, in conjunction with the RGA, can form the basis of a novel and useful methodology for the design of decentralized controllers.
" }, { "name": "Ho, Suzzy Chen Hsi", "degree": "PhD", "year": "1986", "title": "Synthesis and Reactivity of Transition of Metal Homo- and Heterobinuclear Ketene Complexes", "advisor": "Dougherty, Dennis A.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152019-104421637", "creators": [ { "name": { "family": "Ho", "given": "Suzzy Chen Hsi" }, "id": "Ho-Suzzy-Chen-Hsi", "display_name": "Ho, Suzzy Chen Hsi" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bmj9-a007", "abstract": "The rearrangement of \u03b2-phenyltitanacyclobutane (1) to \u03b1-phenyltitanacyclobutane (2) is shown through labeling experiments to proceed by a stepwise mechanism. Ring opening of 1 to the metalmethylidene species followed by readdition of styrene affords both complexes 1 and 2.
\r\n\r\nThe reaction of titanacyclobutanes with oxidizing agents produces cyclopropanes in good yield. The stereochemistry of this reaction has been investigated using cis-2,3-dimethyltitanacyclobutane and trans-2-deutero-3-phenyltitanacyclobutane. By the use of 2H NMR, the stereochemistry of each step of the reaction has been determined.
\r\n\r\nThe crystal and molecular structure of zirconaenolate anion Cp2Zr(\u03b72-OCCH2-O,C)CH3Na\u20222 THE prepared by deprotonation of the corresponding acyl complex has been determined. The reactivity of this anion with electrophilic reagents is studied. Reaction with alkyl halides leads to C-substituted acyl complexes. Reaction with metal chlorides L2M(CH3)Cl leads to binuclear ketene complexes (Cp2ZrCH3)(\u00b5-\u03b72-OCCH2-O,C)-(MCH3L2) (M = Zr, Pt; L = Cp, phosphines). The mechanism for the formation of these complexes and their reactivities are discussed in detail.
\r\n\r\nThe interaction of phosphonium and sulfoxonium ylides with acyl complexes of titanium and zirconium is examined. Reaction of Cp2Zr(COR)R' (R,R' = akyl, aryl) with CH2P\u03c63 and CH2SO(CH3)2 gives enolate complex Cp2Zr(OCR=CH2)R'. Treatment of titanocene chloro acyls with CH2SO(CH3)2 affords ketene complexes which react with excess ylides to give titanaoxacyclobutanes. The structure of titanaoxacyclobutane is determined by Dynamic NMR techniques. The zirconium chloro acyls react with CH2SO(CH3)2 to give mixtures of ketene and enolate complexes. Both react further with the ylides to yield zirconaoxacyclobutanes.
" }, { "name": "Hood, Diane Marie", "degree": "PhD", "year": "1986", "title": "Calculation of e\u207b-H Atom Scattering Processes Using Hyperspherical Coordinates", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172019-161305619", "creators": [ { "name": { "family": "Hood", "given": "Diane Marie" }, "id": "Hood-Diane-Marie", "display_name": "Hood, Diane Marie" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xj5h-me61", "abstract": "A method is presented for accurately solving the Schr\u00f6dinger equation for the scattering of an electron from a hydrogen atom in three dimensions, which uses hyperspherical coordinates. Our motivation for using this new technique is that previous methods -- coupled channel expansions using target atom eigenfunctions,1 polarization functions and pseudostates,2 and variational methods3 -- have all proven unsatisfactory. The coupled channel calculations tend to have difficulty obtaining convergence with respect to basis set size, and the variational method interjects spurious resonances. Previous applications of hyperspherical coordinates4 have used methods that, while adequate for computing the energy level of the bound state of H-, are not appropriate to full scattering calculations.
\r\n\r\nWe have obtained converged surface functions at a set of discrete values of the hyperradius, which acts as a parameter. The surface functions are further expanded in a basis set that involves 1-dimensional functions of the hyperspherical angle, which are obtained by a finite difference method.
\r\n\r\nThe surface functions have been used to expand the scattering functions. The resulting coupled equations are solved numerically. The wavefunctions are obtained separately at each energy and are converged with respect to the number of basis functions used. Calculations performed so far give converged results for J = 0 through J = 5 up to the n = 4 threshold. The method is both accurate and efficient, and has been implemented on a VAX 11/780 with an FPS164 attached processor.
\r\n\r\nBoth the magnitude and phase of elements of the scattering matrix have converged. Integral cross sections have been obtained for energies up to the n = 4 threshold of hydrogen. Feshbach resonances have been detected below each threshold, and they have been characterized and classified.
\r\n\r\n1P. G. Burke, S. Ormonde, and W. Whitaker, Proc. Phys. Soc. 92, 319, (1967).
\r\n2S. Geltman and P. G. Burke, J. Phys. B 3, 1062, (1970).
\r\n3J. Callaway, Phys. Rev. A 26, 199, (1982).
\r\n4C. D. Lin, Phys. Rev. A 23, 1585, (1981).
\r\n\r\n" }, { "name": "Hookham, Philip Alan", "degree": "PhD", "year": "1986", "title": "Concentration and Velocity Measurements in Suspensions Flowing through a Rectangular Channel", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-11132007-105408", "creators": [ { "name": { "family": "Hookham", "given": "Philip Alan" }, "id": "Hookham-Philip-Alan", "display_name": "Hookham, Philip Alan" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "member", "display_name": "Corcoran, William Harrison" } ], "option_major": [ "chemeng" ], "doi": "10.7907/hv1g-s887", "abstract": "A method to measure particle concentrations in dilute to moderately concentrated transparent liquid-solid suspensions was developed. The method uses a dual-beam laser-Doppler anemometer system. Particle concentrations were determined by counting the number of signals from fluorescently-dyed tracer particles per unit time. Using this method, both the velocities and concentrations of suspended particles were obtained.
\r\n\r\nVelocity and concentration measurements were made in suspensions of neutrally-buoyant polystyrene-divinylbenzene spheres 27, 50, and 70 \u00b5m in diameter flowing in a rectangular channel with 800 \u00b5m spacing between walls. Measurements were made in the central plane of the flow channel, thus approximating two-dimensional flow. Dilute-suspension (particle volume fraction \u03a6m = 0.001) experiments were performed both at Reynolds numbers that were low enough so that inertial effects were unimportant (particle Reynolds number Rep < 10-3), and Reynolds numbers at which inertial effects were significant (Rep = 10-3-10-1). Concentrated-suspension (\u03a6m = 0.02-0.25) experiments were done at low Rep only.
\r\n\r\nFor the dilute suspensions at low Re, small peaks in the concentration distributions were found near the flow channel walls, which were attributed to an entrance effect. At higher Re, lateral migration of particles due to inertia was observed. The spheres migrated toward a lateral equilibrium position about 0.6 times the distance from the flow channel centerline to the walls, as demonstrated previously by others. The measured concentration profiles were compared to a previously published theory for the lateral migration of a single sphere, and it was found that the peaks near the equilibrium positions in the measured concentration distributions were somewhat broader than those predicted by the theory, presumably due to particle-particle interactions.
\r\n\r\nNon-uniform concentration profiles were observed for the concentrated suspensions. The concentration profiles became somewhat peaked in the center of the channel as \u03a6m and/or sphere diameter increased, particularly for the 50 and 70 \u00b5m sphere suspensions, and for these suspensions the velocity profiles were blunted for \u03a6m \u2265 0.10. A model velocity profile calculation indicated that the shape of the concentration profiles could satisfactorily account for the shape of the velocity profiles, except possibly for the suspensions of 70 \u00b5m spheres.
\r\n" }, { "name": "Hopkins, Michael David", "degree": "PhD", "year": "1986", "title": "The Energetics, Structures, and Dynamics of the \u03b4\u03b4* Excited States of Quadruply Bonded Dimers", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03102005-131755", "creators": [ { "name": { "family": "Hopkins", "given": "Michael David" }, "id": "Hopkins-Michael-David", "display_name": "Hopkins, Michael David" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DVSC-0Z70", "abstract": "The results of an experimental investigation of the electronic structures of the M2X4L4 (M = Mo, W; X = Cl, Br I; L = uncharged \u03c3-donor ligand) class of quadruply bonded metal dimers are reported. These results are interpreted within a theoretical framework that is general for all types of weakly interacting orbitals; this is set out in Chapter I. In Chapter II we lay the structural foundation for this investigation by presenting the crystal structures of Mo2Br4(PMe3)4 and Mo2I4(PMe3)4 and comparing their bonding parameters with those previously reported for Mo2Cl4(PMe3)4. Resonance Raman and far-infrared spectral data of these complexes are also reported; comparisons to the available structural data indicate that the metal-metal distance and diatomic force constants, which are fingerprint parameters for the characterization of metal-metal interactions, display different ligand sensitivities. This chapter concludes with a discussion of the energies and intensities of the 1(\u03b4 \u2192 \u03b4*) transitions of these complexes, cast both in terms of their molecular structures as well as within the framework of existing theories of the electronic structural significance of these latter two spectroscopic properties. The data for the M2X4L4 complexes lead to a reevaluation of these standard interpretations, and a new postulate, based on charge transfer mixing, is put forth that more adequately accounts for the energies and intensities of the 1(\u03b4 \u2192 \u03b4*) transitions of nearly all quadruply bonded dimers. The 3(\u03b4\u03b4*) state is discussed briefly in Chapter III, wherein it is shown that differing magnetic and spectroscopic properties of the Mo2X4(PMe3)4 and diphosphine-bridged \u03b2-Mo2X4(dmpe)2 dimers are readily accounted for by the simple theoretical framework set out in Chapter I. The analysis of these data leads to experimental estimates of the energies of the 3(\u03b4\u03b4*) states of these compounds: L = PMe3, E = 5200 c-1; L = dmpe, E = 500 cm-1. In Chapter IV we consider the photophysical properties of the 1(\u03b4\u03b4*) state in light of its energetics relative to the 3(\u03b4\u03b4*) and \u03b42 states. Of particular interest is the finding that the photophysical properties of these complexes are perturbed by the nature of the coordination sphere to a different extent than are their 1(\u03b4 \u2192 \u03b4*) energies and intensities. The extensive series of M2X4L4 complexes studied allows the estimation of the intrinsic radiative and nonradiative decay properties of this chromophore. Chapter V contains the main body of this thesis, namely the analysis of the high-resolution electronic spectra of the M2X4L4 complexes. The unprecedented vibronic detail revealed by these spectra is interpreted using the conceptual base developed over the preceding four chapters, and results in the proposal of a double-well potential energy surface for the 1(\u03b4\u03b4*) state along nontotally symmetric coordinates; this arises from sudden polarization. In the final chapter, the photochemical manifestations of this new excited state description are outlined. Material that supplements the discussion in Chapters I-VI is presented in the appendices.
\r\n" }, { "name": "Joran, Alvin David", "degree": "PhD", "year": "1986", "title": "Photochemical Electron Transfer at Fixed Distance: A Synthetic Model of the Photosynthetic Primary Process", "advisor": "Dervan, Peter B.; Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052015-135421366", "creators": [ { "name": { "family": "Joran", "given": "Alvin David" }, "id": "Joran-Alvin-David", "display_name": "Joran, Alvin David" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "co-advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/chrv-qx20", "abstract": "A series of meso-phenyloctamethylporphyrins covalently bonded at the 4'phenyl position to quinones via rigid bicyclo[2.2.2]octane spacers were synthesized for the study of the dependence of electron transfer reaction rate on solvent, distance, temperature, and energy gap. A general and convergent synthesis was developed based on the condensation of ac-biladienes with masked quinonespacer-benzaldehydes. From picosecond fluorescence spectroscopy emission lifetimes were measured in seven solvents of varying polarity. Rate constants were determined to vary from 5.0 x 109 sec-1 in N,N-dimethylformamide to 1.15 x 1010 sec-1 in benzene, and were observed to rise at most by about a factor of three with decreasing solvent polarity. Experiments at low temperature in 2-MTHF glass (77K) revealed fast, nearly temperature-independent electron transfer characterized by non-exponential fluorescence decays, in contrast to monophasic behavior in fluid solution at 298K. This example evidently represents the first photosynthetic model system not based on proteins to display nearly temperature-independent electron transfer at high temperatures (nuclear tunneling). Low temperatures appear to freeze out the rotational motion of the chromophores, and the observed nonexponential fluorescence decays may be explained as a result of electron transfer from an ensemble of rotational conformations. The nonexponentiality demonstrates the sensitivity of the electron transfer rate to the precise magnitude of the electronic matrix element, which supports the expectation that electron transfer is nonadiabatic in this system. The addition of a second bicyclooctane moiety (15 \u00c5 vs. 18 \u00c5 edge-to-edge between porphyrin and quinone) reduces the transfer rate by at least a factor of 500-1500. Porphyrinquinones with variously substituted quinones allowed an examination of the dependence of the electron transfer rate constant \u03baET on reaction driving force. The classical trend of increasing rate versus increasing exothermicity occurs from 0.7 eV \u2264 |\u0394G0'(R)| \u2264 1.0 eV until a maximum is reached (\u03baET = 3 x 108 sec-1 rising to 1.15 x 1010 sec-1 in acetonitrile). The rate remains insensitive to \u0394G0 for ~ 300 mV from 1.0 eV \u2264 |\u0394G0\u2019(R)| \u2264 1.3 eV, and then slightly decreases in the most exothermic case studied (cyanoquinone, \u03baET = 5 x 109 sec-1).
\r\n" }, { "name": "Kang, Heon", "degree": "PhD", "year": "1986", "title": "Gas Phase Studies of Hydrocarbon Oxidation by Chromium Oxide Cation", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07262010-154826937", "creators": [ { "name": { "family": "Kang", "given": "Heon" }, "id": "Kang-Heon", "display_name": "Kang, Heon" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M9HQ-9749", "abstract": "An ion beam reactive scattering technique is used to study organometallic reactions in the gas phase. Detailed investigations of the reactions of CrO+ with hydrocarbons are reported. CrO+ formed by surface ionization oxidizes both alkenes and alkanes larger than methane with a high degree of selectivity compared with other first-row transition metal oxides. Analyses of reaction energetics are facilitated by determination of ancillary thermochemical data, including Cr+-O and CrO+-H bond dissociation energies.
\r\n\r\nChapter II presents an analysis of the reactions of CrO+ with alkenes. Major reaction channels include allylic hydrogen abstraction by CrO+ and oxidative cleavage of double bonds to form aldehydes and smaller alkenes.
\r\n\r\nChapter III describes selective oxidation of saturated hydrocarbons by CrO+. Major product channels include alcohol formation, dehydrogenation, and loss of alkanes and alkenes. Reaction intermediates in which alkyl C-H bonds add across the Cr+-O bond are proposed.
\r\n\r\nChapter IV presents studies of reactions of transition metal ions (Ti, V, Cr, Fe, Co, and Ni) with organosilanes in the gas phase. These reactions often lead to formation of metal silylenes as major products. An examination of reaction thermochemistry provides estimates for metal-silylene bond dissociation energies. Relationships between the reactivities, metal-silylene bond energies, and the electronic structures of the metal ions are discussed.
\r\n\r\nChapter V describes a novel source which generates metal atom and ion beams by focusing a CO2 TEA laser onto a solid metal target. Kinetic energy distributions of laser-generated atoms and atomic ions are measured using time-of-flight techniques. Possible mechanisms for the metal ion production as well as aspects of employing the laser-generated beams for gas phase reaction studies are discussed.
" }, { "name": "Keelan, Brian William", "degree": "PhD", "year": "1986", "title": "High Resolution Laser Spectroscopy of Supersonic Jet-Cooled Molecules", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-111202", "creators": [ { "name": { "family": "Keelan", "given": "Brian William" }, "id": "Keelan-Brian-William", "display_name": "Keelan, Brian William" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n788-xq67", "abstract": "The phenomenon of intramolecular vibrational redistribution (IVR) is currently of significant theoretical and practical interest. Consideration of a simple model raises several important questions about the coupling mechanisms responsible for NR. A review of recent work indicates that these questions are best addressed using complimentary high resolution spectral and temporal experiments, as have been reported elsewhere for only two large molecules. Thus, a tunable laser - free jet apparatus capable of producing fluorescence excitation, dispersed fluorescence, and rotational band contour spectra was constructed and is described in detail herein. High resolution spectral. data obtained using this apparatus is presented for five molecules for which complimentary temporal data is now available: stilbene, diphenylbutadiene, anthracene\u2014h10, anthracene-9d1, and anthracene\u2014d10. Analysis of the spectral data yields information about coupling mechanisms which is relevant to the questions proposed initially.
\r\n\r\nThe results obtained support the following conclusions for these molecules: (1) anharmonic coupling predominates at ranges of \u2248 1 - 10 cm-1, but Coriolis coupling may also be important at shorter ranges; (2) molecular symmetry influences coupling by limiting the number of nearby levels with which a given level may interact; and (3) coupling is more extensive at higher vibrational densities of states due .to the increased number of levels of the appropriate symmetry lying within the effective coupling range of a given level.
" }, { "name": "Lima, Marco Aurelio Pinheiro", "degree": "PhD", "year": "1986", "title": "Dynamics of Electron-Molecule Collisions", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-165338290", "creators": [ { "name": { "family": "Lima", "given": "Marco Aurelio Pinheiro" }, "id": "Lima-Marco-Aurelio-Pinheiro", "orcid": "0000-0002-3602-1546", "display_name": "Lima, Marco Aurelio Pinheiro" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/T10Z-7D32", "abstract": "We have developed a multichannel formulation for low-energy electron-molecule collisions based on the Schwinger variational method. An important feature of this formulation is that it is capable of dealing with some important aspects of electron-molecule collisions such as electronically inelastic scattering and nonlinear targets. The formulation also allows for the inclusion of a substantial number of closed electronic channels to represent polarization effects, which are very important at low-impact energies.
\r\n\r\nTo assess the accuracy with which polarization is represented in this formulation we have calculated elastic integral and differential cross sections for e \u2014 H2 collisions. We have obtained very good agreement between our results and available theoretical and experimental data. We have also examined the shape resonances in e \u2014 CO and e \u2014 N2 collisions, where polarization plays a very important role in determining the resonance parameters.
\r\n\r\nOur first application to electron-nonlinear molecule collisions was for e \u2014 CH4 scattering. At the static-exchange level of approximation our differential cross sections are in very good agreement with existing measurements at about 7 eV and higher energies. For incident energies below this an interesting feature of the small angle differential cross sections is seen only when polarization effects are included in the calculation. We have also obtained elastic differential and momentum transfer cross sections for e \u2014 H2O scattering. Our calculated differential cross sections agree well with available experimental data, which extend only to 120\u00b0. The differential cross sections, particularly at 15 and 20 eV, show significant backward peaking. This peaking occurs in the experimentally inaccessible region beyond scattering angle of 120\u00b0, and, as we will see, it has an important implication in the determination of momentum transfer cross sections.
\r\n\r\nWe also obtained differential and integral cross sections for the electron impact excitation of the b3\u03a3+u, a3\u03a3+g, c3\u03a0u and B1\u03a3+u states of H2 at the two state approximation. In contrast to the triplet excitations, the B1\u03a3+u is a dipole-allowed transition, a feature which introduces several new interesting aspects. Our results for the excitation of the b3\u03a3+u and B1\u03a3+u states are in good agreement with experimental data at all energies.
\r\n\r\nThe results we obtained with the Schwinger multichannel method are very encouraging and illustrate the potential utility of these calculated cross sections. The results of such studies can clearly complement experimental efforts to determine absolute values of these electron-molecule scattering cross sections.
" }, { "name": "Lyons, William Lee", "degree": "Masters", "year": "1986", "title": "The Construction and Testing of a Hartley Oscillator for Measuring Temperatures in Free-Floating Objects", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-225256027", "creators": [ { "name": { "family": "Lyons", "given": "William Lee" }, "id": "Lyons-William-Lee", "display_name": "Lyons, William Lee" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/bnw4-2s92", "abstract": "Several modified Hartley oscillators were constructed from inexpensive,\r\neasily obtained materials and were calibrated for use as wireless temperature\r\nprobes. Three classical experiments involving heat conduction inside solid\r\nspheres were performed to test the oscillators' accuracy. Excellent agreement\r\nwas found between theoretical and oscillator-measured temperature profiles.\r\nFurther experiments were made in which the oscillator was embedded in a\r\nneutrally-buoyant, free-floating solid in order to gain insight into the\r\nThermal history and motion of an object in a confined, heated liquid. These\r\nexperiments demonstrated the device's usefulness as a free-floating\r\ntemperature probe with potential applications in studies of natural convection\r\nand sterilization of enclosed foodstuffs." }, { "name": "Natter, Russell Lawrence", "degree": "Masters", "year": "1986", "title": "Allocations of Computational and Graphical Methods for Separation Processes Calculations and Education", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082026-213006452", "creators": [ { "name": { "family": "Natter", "given": "Russell Lawrence" }, "id": "Natter-Russell-Lawrence", "display_name": "Natter, Russell Lawrence" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/mwp6-z058", "abstract": "Two computer programs were developed to teach\r\nseparation processes and to solve related problems. The\r\nfirst, SEPTECH, uses the Fenske-Underwood-Gilliland method\r\nto find stage requirements and column operating parameters\r\nof a multicomponent distillation tower given feed stream\r\ninformation and desired product purities. The second\r\nprogram was designed to achieve specific educational goals.\r\nA robust educational program was developed that was a\r\ngeneral, flexible, fast, understandable, and easy to use\r\ntool for problem solving. This program, MCTHIELE, utilizing\r\nMcCabe-Thiele graphical solution techniques, was used in a\r\nsenior level chemical engineering course and proved to be a\r\nvery successful learning tool." }, { "name": "O'Loughlin, Michael John", "degree": "PhD", "year": "1986", "title": "The Determination of Atom-Molecule Interaction Potentials from Total Differential Cross Sections", "advisor": "Sparks, Randal K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162019-162014129", "creators": [ { "name": { "family": "O'Loughlin", "given": "Michael John" }, "id": "O'Loughlin-Michael-John", "display_name": "O'Loughlin, Michael John" } ], "advisors": [ { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "advisor", "display_name": "Sparks, Randal K." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/eg4t-an16", "abstract": "A newly constructed crossed molecular beams apparatus has been used to measure total (elastic plus inelastic) differential cross sections for collisions between rare gas atoms and methane and chlorine molecules. The total differential cross sections were then used in an iterative trial and error potential fitting program to determine the interaction potentials between these species. In the rare gas-methane study (Chapter 2), the methane molecule has been approximated as being a spherical entity, and the standard equations and techniques have been applied to simulate the laboratory scattering distributions from an assumed isotropic potential. The isotropic potentials determined in this manner are compared with some recently proposed anisotropic potentials for these systems. In the rare gas-chlorine study (Chapter 3), anisotropic potentials have been determined using the infinite order sudden approximation and a Legendre parameter expansion of a central field potential. The resulting potentials compare rather favorably with what is known about these potential surfaces from photodissociation experiments.
" }, { "name": "Reid, Brian Paul", "degree": "PhD", "year": "1986", "title": "Elastic, Inelastic, and Photofragment Scattering from Crossed Molecular Beams", "advisor": "Sparks, Randal K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-145508172", "creators": [ { "name": { "family": "Reid", "given": "Brian Paul" }, "id": "Reid-Brian-Paul", "display_name": "Reid, Brian Paul" } ], "advisors": [ { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "advisor", "display_name": "Sparks, Randal K." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Weitekamp", "given": "Daniel P." }, "id": "Weitekamp-D-P", "orcid": "0000-0003-0079-8000", "role": "member", "display_name": "Weitekamp, Daniel P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xz77-2x37", "abstract": "Three sets of crossed molecular beam scattering experiments are described. In the first experiment, total differential cross sections are measured for collisions between two methane molecules. Treating the scattering as elastic, these cross sections are used to determine an isotropic intermolecular potential energy function for the methane-methane system. The second experiment involves the measurement of total differential cross sections and time-of-flight spectra for neon-chlorine scattering. These data are modeled using the infinite order sudden approximation for rotationally inelastic scattering, and an anisotropic potential function for neon-chlorine is determined. In the third experiment, the angular and time-of-flight distributions for the products of the three-body photofragmentation of 1,2-diiodotetrafluoroethane at 266 nm are measured. These data are analyzed to determine the product translational energy distributions.
" }, { "name": "Schultz, Steve Chester", "degree": "PhD", "year": "1986", "title": "Site Saturation Mutagenesis of Residue 71 in \u03b2-Lactamase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232019-174017653", "creators": [ { "name": { "family": "Schultz", "given": "Steve Chester" }, "id": "Schultz-Steve-Chester", "display_name": "Schultz, Steve Chester" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "member", "display_name": "Davidson, Eric H." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/c3a0-kd54", "abstract": "A method was developed to \"saturate\" a particular residue in a protein with all possible amino acid substitutions. The method essentially involves introducing into the gene at the codon for the residue of interest a mixture of nucleotides: A, C, G, and T at the first two positions, C and G at the third position. This mixture of oligonucleotides can be readily introduced into the gene as a cassette when restriction sites are conveniently nearby. This method was used to saturate residue 71 in the pBR322 encoded \u03b2-lactamase. The first step was introduction of restriction sites into pBR322 that flank the codon for residue 71: an Ava I site at 3972 and a Sca I site at 3937. The DNA fragment between these residues was removed and replaced with a mixture of synthetic double-stranded oligonucleotides that included 32 codons for residue 71 (codons for all 20 amino acids and the amber codon). The method was nearly 100% efficient for introducing this set of mutations and the observed distribution of codons indicates that the various codons were introduced at equal frequencies.
\r\n\r\nClass A \u03b2-lactamases, which include the pBR322 encoded enzyme, contain a conserved triad (Ser-Thr-x-Lys) at the catalytic site; this site includes Ser 70 whose hydroxyl group opens the \u03b2-lactam ring. This study focuses on the conserved Thr 71, whose role in the activity of \u03b2-lactamase was previously unknown. Mutants with all 19 possible amino acid substitutions at residue 71 were generated as described above and characterized by the in vivo penam and cephem antibiotic resistance they provided to E. coli LS-1 cells. Surprisingly, cells producing any of 14 of the mutant enzymes display appreciable resistance to ampicillin; only cells with mutants having Tyr, Trp, Asp, Lys, or Arg at residue 71 had no observable resistance to ampicillin. However, all of the mutants are less stable to cellular proteases than the wild type enzyme. These results suggest that Thr 71 is not essential for binding or catalysis but is important for stability of the \u03b2-lactamase protein. An apparent change in the substrate specificity of the various mutant enzymes indicates that residue 71 influences the region of the protein that accommodates the side chain attached to the \u03b2-lactam ring of the substrate.
\r\n\r\nTo study the role of the naturally occurring disulfide bond in stabilizing \u03b2-lactamases that contain mutations at residue 71, a Cys 77 \u2192 Ser mutation was introduced into all 19 of these mutants. The resulting doubly mutant proteins were analyzed for their ability to confer resistance to ampicillin in vivo and the relative quantities of the mutant enzymes in whole cell extracts were analyzed by antibody stains of electrophoretic blots. Although the activity and stability of the single mutant Cys 77 \u2192 Ser is indistinguishable from the wild type enzyme in physiological conditions, the doubly mutant proteins are much less stable than the analagous single mutants that contain a disulfide bond. Apparently, the presence of the disulfide bond in \u03b2-lactamase enables the enzyme partially to overcome instabilities arising from mutations at residue 71. The results presented here also demonstrate that Thr at residue 71 performs a unique and essential role in the stability of \u03b2-lactamase.
" }, { "name": "Seo, Jin-Ho", "degree": "PhD", "year": "1986", "title": "Investigations of Plasmid-Host Cell Interactions in Recombinant Escherichia coli Populations", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03102008-104251", "creators": [ { "name": { "family": "Seo", "given": "Jin-Ho" }, "id": "Seo-Jin-Ho", "orcid": "0000-0002-4206-6046", "display_name": "Seo, Jin-Ho" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/RGTN-X895", "abstract": "Plasmid-host cell interactions have been characterized experimentally for recombinant Escherichia coli populations. The plasmids used contain pMB1 replication origins and propagate in E. coli at different copy number levels ranging from 12 to 408. Host E. coli HB101 strains transformed with those plasmids were used throughout this research.
\r\n\r\nThe specific growth rate and amount of cloned-gene product (\u03b2-lactamase) were determined in batch cultivations as a function of plasmid copy number. Maximum specific growth rates in LB and M9 media were reduced monotonically for increasing plasmid content per cell. The maximum specific growth rate for a recombinant strain with copy number 408 was reduced by 25% relative to the plasmid-free strain. The ratio of \u03b2-lactamase specific activity to plasmid content, as a measure of the overall efficiency of plasmid-gene expression, declines by a factor of 7 as the copy number increases from 12 to 408. The relationship between copy number and cloned-gene product activity can be reasonably approximated by a parabolic equation, with approximately linear proportionality for copy numbers up to 60 but subsequently with reduction in the product/copy number ratio.
\r\n\r\nInvestigations of environmental effects on plasmid content and \u03b2-lactamase activity have also been done in batch and continuous bioreactors. Plasmid copy number decreased when specific growth rate was increased by varying medium composition in a batch fermentor, or when dilution rate (inverse of residence time) was increased by increasing medium flow rate in a continuous fermentor. The response of plasmid-gene product formation to growth conditions in these two different reactor types is interesting. Batch experiments showed that the specific activity of \u03b2-lactamase is a gradual decreasing function of specific growth rate, whereas product activity has a maximum with respect to dilution rate in chemostat growth. Comparative analysis of genetic and environmental effects implies that both plasmid content and growth conditions should be taken into account in determining the productivity of recombinant cell populations.
\r\n\r\nFurther insight into the host-vector interactions was obtained by exploring plasmid amplification behavior and cell-cycle characteristics in the recombinant strains. Chloramphenicol-derived amplification kinetics were measured using flow cytometry, which allows direct determination of the total cellular DNA content after staining with mithramycin, a DNA-specific fluorescent dye. Both rates of plasmid amplification and final contents of amplified plasmids were found to be proportional to the average initial plasmid copy number obtained at steady-state growth.
\r\n\r\nThe measurements of the cell-cycle parameters in E. coli cells were performed using experimentally determined single-cell DNA content frequency functions in connection with mathematical analysis of cell growth. Plasmid-containing cells exhibit C and D times that are approximately 14 and 24 percent, respectively, smaller than corresponding values in the plasmidfree host. Mean cell sizes and cell mass at the point of replication initiation decrease 38 and 18 percent, respectively, relative to plasmid-free cells. These results agree qualitatively with the previous findings with E. coli B/r carrying F plasmids of various sizes. Interestingly, the effects of plasmid presence on C, D, average cell size, and initiation mass were found to be approximately independent of plasmid copy number in these host-vector systems.
\r\n\r\nFinally, mathematical description of plasmid propagation in cells which reproduce by binary fission was presented using a segregated, population balance model. With the population balance equations, the probability of plasmid loss, distribution of cellular plasmid content, and specific rate of product synthesis were determined based on different single-cell models of plasmid replication, partition, and gene expression. Control modes of plasmid replication during cell growth markedly affect the distribution of plasmid content and accordingly the specific rate of gene product synthesis. The degree of selection required for stable maintenance of plasmidharboring populations was derived by analyses that focused on the transient growth of plasmid-containing and plasmid-free cells in partially selective medium.
" }, { "name": "Siu, Gerald", "degree": "PhD", "year": "1986", "title": "Antigen Receptors on Lymphocytes", "advisor": "Hood, Leroy E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242019-102816056", "creators": [ { "name": { "family": "Siu", "given": "Gerald" }, "id": "Siu-Gerald", "display_name": "Siu, Gerald" } ], "advisors": [ { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "advisor", "display_name": "Hood, Leroy E." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "member", "display_name": "Hood, Leroy E." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Meyerowitz", "given": "Elliot M." }, "id": "Meyerowitz-E-M", "orcid": "0000-0003-4798-5153", "role": "member", "display_name": "Meyerowitz, Elliot M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p1zd-zh51", "abstract": "The structure and evolution of a small VH gene family called the T15 family was analyzed. It was determined that although selection pressure appeared to be operating to maintain the coding region sequence of these VH gene segments, these gene segments were diverging from one another very rapidly. Sequences were identified in the 5' flanking region that were conserved between all VH gene segments and were hypothesized to be important for immunoglobulin heavy-chain gene transcription. Related sequences were identified in immunoglobulin VL gene segment and histone H2B 5' flanking regions, implying coordinate expression between these genes and the immunoglobulin heavy chain genes.
\r\n\r\nThe structure, organization, evolution, and the generation of diversity in the genes encoding the T-cell antigen receptor were analyzed. The T-cell antigen receptor consists of two chains, referred to as the \u03b1 and \u03b2 chains. Each chain consists of two regions, a variable region and a constant region, that are encoded by two different genes. The gene that encodes the variable region of the \u03b2 chain was found to consist of three gene segments, denoted V\u03b2, D\u03b2, and J\u03b2. The V\u03b2 gene segment encodes the first 280-300 bp, the D\u03b2 gene segment encodes the next 10-15 bp, and the J\u03b2 gene segment encodes the final 50 bp of the variable region gene. The rearrangement event that juxtaposes these gene segments during lymphocyte differentiation appears to be mediated by the same recognition signals that mediate immunoglobulin V gene rearrangement.
\r\n\r\nDiversity was found to be generated in at least three different manners in the V\u03b2 gene. Combinatorial joining permits the rearrangement of different V, D and J gene segments to each other to provide different V gene sequences. Deletion of nucleotides from the ends of the germline gene segments and the random addition of nucleotides at the junction of the rearrangement event are two other mechanisms for generating diversity. A comparison of a rearranged V gene with the corresponding germline gene segments showed that with the exception of the junctions, the sequences were identical. Therefore, there is no evidence that somatic hypermutation, the random addition of point mutations to the V gene during late stages of B lymphocyte differentiation, is utilized by the T-cell antigen receptor as it is by immunoglobulins.
\r\n\r\nThe initial stage of V\u03b2 gene formation was found to be the rearrangement of the D\u03b2 gene segment to the J\u03b2 gene segment. Both germ line D\u03b2 gene segments appear to have promoters in the 5' flanking regions that can often result in the transcription of a 1.0 kb mRNA containing D\u03b2-J\u03b2-C\u03b2 sequences after D\u03b2-J\u03b2 rearrangement. This 1.0 kb mRNA message is present at a high level in the thymus but at lower levels in the spleen, lymph nodes, and in mature T cells, implying that this message or a protein product encoded by this message may be important in T cell ontogeny.
\r\n\r\nAnalysis of the protein sequences of the variable regions of the \u03b1 and \u03b2 chains revealed conserved amino acids that are found in all variable region genes. Many of these amino acids were found to be important for V domain structure in immunoglobulins and may be important for the structure of the V\u03b1-V\u03b2 domain as well. In addition, analyses of the \u03b2-strand forming potential and the relative hydrophobicity of the side chains of the amino acids that make up the T-cell antigen receptor variable regions have indicated that these properties are very similar to those of the immunoglobulin variable regions. These analyses indicate that the immunoglobulin and T-cell receptor antigen-binding regions may be very similar in structure to each other.
" }, { "name": "Smith, Michael Glenn", "degree": "PhD", "year": "1986", "title": "Approaches to the Syntheses of the Acyltetramic Acid Antibiotics Streptolydigin, Tirandamycin A, and Tirandamycin B", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012019-123946315", "creators": [ { "name": { "family": "Smith", "given": "Michael Glenn" }, "id": "Smith-Michael-Glenn", "display_name": "Smith, Michael Glenn" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w9jw-bw56", "abstract": "An approach to the syntheses of several acyltetramic acid antibiotics is presented. The approach is partially based on a previous synthesis of tirandamycic acid. It involves an ester enolate Claisen rearrangement of an intermediate derived from D-glucose to establish the requisite relative and absolute stereochemical configurations. An application of the Sharpless asymmetric epoxidation reaction is also involved, and is noteworthy due to its success as an intramolecular kinetic resolution of two available allylic alcohols.
\r\n\r\nA total synthesis of streptolic acid is presented as evidence of the viability of the synthetic scheme employed. A formal synthesis of tirandamycin A is also presented. Furthermore, the sequence employed is shown to provide an excellent approach to tirandamycin B.
\r\n\r\nA novel de-benzylation is also reported. The reagent lithium di-tert-butylbiphenyl is demonstrated to accomplish the deprotection of benzyl ethers rapidly and efficiently.
\r\n" }, { "name": "Stille, John Robert", "degree": "PhD", "year": "1986", "title": "The Synthetic Versatility of Titanocene Methylidene Sources and Their Utility in the Total Synthesis of Capnellene", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242019-114145318", "creators": [ { "name": { "family": "Stille", "given": "John Robert" }, "id": "Stille-John-Robert", "display_name": "Stille, John Robert" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s4ds-5j77", "abstract": "The development and application of a synthetically useful metallacycle are described. Using this metallacycle reagent to generate the reactive titanocene methylidene, the methylenation of dialkyl carbonates occurs, producing ketene ketals. The transformation of carbonates to ketene ketals varies dramatically with the O-alkyl substituents on the carbonate. Due to the sensitivity of titanocene methylidene toward steric interference, conversion is substantially higher for dimethyl carbonate than for diphenyl carbonate. Restricting the carbonates to the s-trans, s-trans conformation, such as in cyclic carbonates, the steric effects are completely overcome.
\r\n\r\nThe reaction of titanocene methylidene sources with acid chloride substrates produces the titanocene chloride enolate of the corresponding methyl ketone. Enolate formation occurs specifically at the methyl group, resulting in only the kinetic enolate, even in a case where the thermodynamic enolate would be stabilized by conjugation to aromatic functionality. Enolate formation with an \u03b1-chiral acid chloride followed by hydrolysis showed that less than 0.5% racemization had occurred. The titanocene methylidene selectively attacks the acid chloride functional group even when an ester carbonyl is present. Condensation of the enolate with aldehydes occurs regiospecifically to produce \u03b2-hydroxy ketones. Titanocene methylidene also methylenates silyl esters to produce the corresponding kinetic silyl enol ether.
\r\n\r\nUsing a reported method for the generation of bridged titanocene alkylidene complexes, the first trisubstituted titanacyclobutane has been isolated and characterized. A general method by which titanocene alkylidene complexes may be prepared has also been investigated. The transmetallation of 1,1-dimetallo complexes of aluminum and zinc to titanocene chloride, forming the heterobimetallic bridged alkylidenes, was also studied. Although the aluminum complexes do not afford bridged complexes, the 1,1-dizincalkyls appear to undergo transmetallation to give a species which will methylenate ketone functionality.
\r\n\r\nCyclopentadiene compounds, tethered to \u03b1,\u03b2-unsaturated ester functionality, have been prepared by the direct alkylation of the corresponding iodide with cyclopentadienylmagnesium chloride. The cyclopentadienyl Grignard reagent does not display the undesired reactions found to occur with the use of the more basic compounds of lithium and sodium; the organometallic reagent does not catalyze the isomerization of the cyclopentadiene isomers. Alkylation of the iodide is preferred over Michael Addition to the unsaturated ester functional group, but using the corresponding tosylate, conjugate addition is the more prominent reaction. Several functionalized cyclopentadienes are prepared which differed in tether length. These substrates readily undergo intramolecular [4+2] cycloaddition at mild temperatures to produce tricyclic ring systems. The cycloaddition will proceed at even lower temperatures if catalyzed by diethylaluminum chloride. Pathways of cycloaddition favor incorporation of the tether linkage into a five- or six-membered ring.
\r\n\r\nThe reaction of titanocene methylidene with norbornene substrates containing endo ester substituents results in metallacycle formation with the strained olefin. The regiochemistry of the cycloaddition to the strained olefin can be completely controlled through the use of a 1-methyl substituent. Thermolysis of these metallacycles proceeds predominantly by ring-opening metathesis of the norbornene substrate to produce a titanocene alkylidene intermediate. This intermediate is subsequently trapped by the intramolecular ester substituent to produce the corresponding bicyclo[3.2.0]heptene enol ether. Similar results are obtained using substituted titanocene alkylidene complexes. The intermediate trisubstituted metallacycles display an enhanced propensity for ring-opening metathesis to occur.
\r\n\r\nThe synthetic versatility of titanocene methylidene is demonstrated in the total synthesis of (\u00b1)\u0394(9,12)-capnellene from \u03b1,\u03b1-dimethyl-\u03b3-butyrolactone. Using the intramolecular cycloaddition of the appropriate functionalized cyclopentadiene, the relative stereochemistry of all four asymmetric centers in the natural product is established. Ring-opening metathesis of the resulting strained olefin by titanocene methylidene, followed by intramolecular trapping of the intermediate titanocene alkylidene, produces the required skeleton for capnellene. Only standard modification of existing functionality is required to obtain the reported ketone precursor. Methylenation of this ketone with titanocene methylidene occurs much more efficiently than with the standard Wittig reagent to produce capnellene. This synthesis of capnellene is the first reported to establish the relative stereochemistry of all four asymmetric centers using a single cycloaddition step. The use of titanocene methylidene has led to an efficient synthesis of (\u00b1)\u0394(9,12)-capnellene in 20% overall yield.
" }, { "name": "Sylwester, Alan Paul", "degree": "PhD", "year": "1986", "title": "Matrix Isolation and Characterization of 1,1-Diazenes", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10252019-122237282", "creators": [ { "name": { "family": "Sylwester", "given": "Alan Paul" }, "id": "Sylwester-Alan-Paul", "display_name": "Sylwester, Alan Paul" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/52cm-3b89", "abstract": "CHAPTER 1
\r\n\r\nThe photochemical generation, matrix isolation and direct spectroscopic characterization of H2NN 3 is reported. UV (VIS filtered) photolysis of carbamoyl azide 15 in a rigid glass (2-MTHF, 80\u00b0K) generates blue-violet 3. The electronic absorption spectrum of 3 reveals a structured absorption curve \u03bbmax = 636 nm, \u03bb0,0 = 695 nm for the n-\u03c0* transition of 3. This transition is blue shifted in a more polar glass (2-MTHF:nPrCN, 1:1, 80\u00b0K) to \u03bbmax = 624 nm, \u03bb0,0 = 681 nm. The argon matrix FT-IR spectrum of 3 shows bands at 2865.55, 2807.20, 1863.20, 1574.16, and 1003.07 cm-1 (1:2000, Ar, 10\u00b0K). The characteristic N=N stretch for 3 at 1574.16 demonstrates the considerable double bond character in the 1,1-diazene. Incorporation of a terminal 15N label into H2N-15N 3-15N shifts the N=N stretch to 1547.64 cm-1. The argon matrix infrared spectra of 3, 3-15N, 3-d2, and 3-d2-15N are reported. Thermal decomposition of 3 (2-MTHF, 90\u00b0K) affords 2-tetrazene (\u03bbmax = 260 nm), trans HNNH 1 (\u03bbmax = 386 nm) and an unidentified species (\u03bbmax = 480 nm). Subsequent thermolysis (>100 K) affords NH3, N2H4, N+H4N-3, H2 and N2 products. Oirect irradiation of 3 in a glass (2-MTHF = 77\u00b0K) with visible light affords H2, N2, and trans-HNNH 1. Photodecomposition of matrix isolated 3 (Ar, 10\u00b0K) with visible light in the presence of CO affords formaldehyde (H2CO), trans-HNNH 1, H2, and N2. This represents the first direct observation of thermal and photochemical interconversion of H2N2 isomers.
\r\n\r\nCHAPTER 2
\r\n\r\nPreliminary studies of the low temperature matrix isolation and spectroscopic characterization of 1,1-dimethyldiazene 7 and l, 1-di-isopropyldiazene 18 are reported. The UV (VIS filtered) photolysis of carbamoyl azides 13 and 17 in a rigid medium (organic glass, 80\u00b0K or Ar matrix, 10\u00b0K) provides a new general method for the photochemical generation of reactive 1,1-diazenes. This photochemical route is considered to proceed via the photo-Curtius rearrangement of a carbamoyl azide to an aminoisocyanate followed by photodecarbonylation to a 1,1-diazene and carbon monoxide. Electronic absorption spectroscopy (2-MTHF, 80\u00b0K) reveals structured absorption curves (n-\u03c0*) \u03bbmax = 556 nm, \u03bb0,0 = 643 nm for 7 and \u03bbmax = 504 nm, \u03bb0,0 = 620 nm for 18. 1,1-Dimethyldiazene 7 was independently generated by UV (VIS filtered) photolysis of (Z)-3,3-dimethyl-1-phenyltriazene-1-oxide 16 to afford 7 and nitrosobenzene. Matrix isolation FT-IR spectroscopy (Ar, 10\u00b0K) reveals the characteristic N=N stretch for 7 at 1600.96 cm-1. Incorporation of a terminal 15N label shifts this stretch to 1581.83 cm-1. The N:N stretch for 18 at 1600.92 cm-1 is 15N shifted to 1579.46 cm-1. Photochemical decomposition of 7 (Ar, 10\u00b0K) yields the infrared bands of ethane and an unidentified species (U) which is subsequently photolyzed to ethane. The effects of substitution on the electronic transitions and R2N=N stretches of 1,1-diazenes correlates with the trends of the isoelectronic carbonyl compounds. Thermolysis of 7 and 18 (2-MTHF, 90\u00b0K) yields red-orange 9 (\u03bbmax = 464 n, \u03b5 \u2243 3000 M-1 cm-1) and 30 (\u03bbmax = 474 nm, \u03b5 \u2243 3000 M-1 cm-1), respectively. These species are tentatively identified as the azomethinimine tautomers of the 1,1-diazenes with \u03b1-hydrogens. Irradiation of 7 and 18 at their n-\u03c0* transitions in the visible (2-MTHF, 80\u00b0K) also initially yields 9 and 30, respectively, in addition to the hydrocarbon products expected from nitrogen extrusion. Subsequent bimolecular decomposition of 9 (Ea = 8.2 \u00b1 0.5 kcal/mol, log10 A = 1.8 \u00b1 0.6) yields tetramethyl-2-tetrazene 19. Bimolecular decomposition of 9-d6 (Ea = 8.6 \u00b1 0.5 kcal/mol, log10 A = 1.4 \u00b1 0.6) reveals a deuterium isotope effect kH/kD = 6.7 at 190\u00b0K for loss of 9. Thermal decomposition of 30 affords hydrocarbon products 32, 33, and 34 expected for nitrogen extrusion from 1,1-diazene 18. The activation parameters for unimolecular decomposition of 30 are Ea = 16.8 \u00b1 0.5 kcal/mol, log10 A = 11.8 \u00b1 0.3.
\r\n\r\nCHAPTER 3
\r\n\r\nThe low-temperature 15N NMR spectrum of the 1,1-diazene, N-(2,2,6,6-tetramethylpiperidyl)nitrene (1) is reported. The 15N double- and mono-labeled 1,1-diazenes 1a and 1b were synthesized. The nitrene and amino nitrogens of 1 have resonances in dimethyl ether at -90\u00b0C at 917.0 and 321.4 ppm, respectively, downfield from anhydrous 15NH3, affording a chemical-shift difference of 595 ppm for the directly bonded nitrogen nuclei. The chemical shift of the ring nitrogen is consistent with an amino nitrogen whose lone pair is largely delocalized. The large downfield shift of the nitrene nitrogen is consistent with a large paramagnetic term due to a low-lying n-\u03c0* transition.
" }, { "name": "Thompson, Douglas Kelvin", "degree": "Masters", "year": "1986", "title": "Attempts to Synthesize Cyclic Group 8 Metallaesters", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262013-145326002", "creators": [ { "name": { "family": "Thompson", "given": "Douglas Kelvin" }, "id": "Thompson-Douglas-Kelvin", "display_name": "Thompson, Douglas Kelvin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/24t5-yc44", "abstract": "In studying a proposed carbon monoxide reduction scheme\r\nan attempt has been made to synthesize bifunctional group 8 transition metal carbonyl complexes containing intramolecular nucleophiles. The incorporation of alkoxide nucleophiles through cyclopentadienyl ligands was hoped to encourage attack on carbonyl ligands thereby forming cyclic metallaesters. The attempts to synthesize these substituted cyclopentadienyl group 8 transition metal complexes have thus far been unsuccessful.
\r\n" }, { "name": "Thompson, Mark Edward", "degree": "PhD", "year": "1986", "title": "Synthesis and Investigations into the Reactivity of Electron Deficient Organoscandium Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10252019-155031892", "creators": [ { "name": { "family": "Thompson", "given": "Mark Edward" }, "id": "Thompson-Mark-Edward", "display_name": "Thompson, Mark Edward" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "chair", "display_name": "Collins, Terrence J." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wcaf-jd79", "abstract": "A new class of coordinatively unsaturated, monomeric scandium complexes, (Cp*2ScR (Cp* = \u03b75-C5(CH3)5; R = H, alkyl, aryl, halide) have been prepared. Cp*2ScCl is prepared by the reaction of ScCl3(THF)3 with LiCp*, and Cp*2ScR (R = CH3, C6H5, C6H4CH3, CH2C6H5) by the reaction of Cp*2ScCl with the appropriate organoalkali reagent. Cp*2ScR complexes react readily with H2 to give RH and Cp*2ScH. The hydride ligand exchanges rapidly with hydrogen gas and inserts olefins to give alkyl complexes (e.g. Cp*2ScCH2CH3). Cp*2ScH reacts with allene to give Cp*2Sc(\u03b73-CH2CH=CH2). Cp*2ScR and Cp*2ScH react with pyridine to give Cp*2Sc(C,N-\u03b72-C5H4N). The crystal structure of this complex was determined and is reported herein.
\r\n\r\nSpectroscopic data for Cp*2ScCH3 and Cp*2ScCH2CH3 and crystallographic data for the former indicate that the methyl ligand is bound to scandium in a conventional manner, while the ethyl ligand may participate in an agostic interaction.
\r\n\r\nThe reactions of scandium alkyl, aryl and hydride complexes were investigated. H/D exchange between H2, arenes and the 1\u00b0 and 2\u00b0 C-H bonds of alkanes is catalyzed by Cp*2ScH. In C6H6 solution Cp*2ScH and Cp*2ScC6H5 are in equilibrium, \u0394H\u00b0 = 6.7 \u00b1 0.3 kcal/mole and \u0394S\u00b0 = 1.5 \u00b1 0.1 e.u.. Thus in this system a scandium-hydride bond is 1.5 \u00b1 0.4 kcal/mole stronger than a scandium-phenyl bond. Cp*2ScCH3 reacts with a wide range of hydrocarbons (RH) by C-H bond activation to give CH4 and Cp*2ScR (RH = 13CH4, arenes, styrenes, propyne). From the reactions of Cp*2ScCH3 with styrenes, the activation parameters (\u0394H\u2021 = 11.5-12.6 kcal/mole, \u0394S\u2021 = -34 to -38 e.u.) for these C-H activation reactions were determined. A deuterium isotope effect of 2.9 is observed for the intermolecular activation of C-H in the reaction of Cp*2ScCH3 with benzene. Very small differences in the rates of vinylic C-H bond activation for CH2=CHC6H4X-para (X = CF3, OCH3), and the aryl C-H bonds of C6H5X (X = CF3, H, CH3, N(CH3)2), as well as the positional nonselectivity for the activation of the meta and para C-H bonds of toluene indicate that the scandium center does not interact substantially with the \u03c0-system of these substrates in the transition states for these reactions. Thus for these sterically encumbered organoscandium compounds, sp2 C-H bond activation occurs without formation of a \u03c0-complex. A general mechanism for these C-H and H-H activation reactions is proposed, and is termed \"\u03c3-bond metathesis\".
\r\n\r\nThe reactions of Cp*2ScR complexes {R = hydride, alkyl, aryl) with small olefins and alkynes were examined. The hydride, methyl and benzyl complexes function as ethylene polymerization catalysts, while Cp*2ScC6H5 does not react. Cp*2ScH and Cp*2ScCH3 react stoichiometrically with propene by a series of insertion and vinylic C-H activation reaction. The final scandium product in both cases is trans-Cp*2ScCH=CHCH3. The scandium allyl complex, Cp*2Sc(\u03b73-CH2CH=CH2), is not observed and is not a reaction intermediate.
" }, { "name": "Tolbert, Margaret A.", "degree": "PhD", "year": "1986", "title": "Mechanisms and Energetics of Alkane Activation by Transition Metal Ions in the Gas Phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282019-140307646", "creators": [ { "name": { "family": "Tolbert", "given": "Margaret A." }, "id": "Tolbert-Margaret-A", "display_name": "Tolbert, Margaret A." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3047-z490", "abstract": "The mechanisms and energetics of alkane activation by transition metal ions in the gas phase are studied using an ion beam apparatus. These investigations concentrate on the reactivity of several early first row transition metal ions (Sc+, Ti+, V+) and the second row group 8-10 metal ions (Ru+, Rh+, Pd+). The reaction mechanisms are probed using deuterium labelled alkanes. Experimental and theoretical metal-ligand bond dissociation energies are used to help interpret the observed metal ion reactivities.
\r\n\r\nChapter II provides a detailed study of the reactions of Ru+, Rh+ and Pd+ with alkanes. The reactivity observed is contrasted to that of their first row congeners Fe+, Co+ and Ni+.
\r\n\r\nChapter III presents a determination of the heterolytic, M+-H-, and homolytic, M-H, bond dissociation energies for the first and second row group 8-10 metals. A correlation is found between the homolytic bond energies and the metal atom promotion energy to a state derived from an s1dn electronic configuration.
\r\n\r\nChapter IV examines the reactions of Ti+ and V+ with alkanes and deuterium labelled alkanes. Dehydrogenation mechanisms and deuterium isotope effects are explored.
\r\n\r\nChapter V reports the unusual reactivity of Sc+ with alkanes. The ability of Sc+ to form two strong metal-ligand sigma bonds results in alkane activation processes which are not observed for most other transition metal ions.
" }, { "name": "Varney, Michael David", "degree": "PhD", "year": "1986", "title": "Approach to the Synthesis of Chlorothricolide: Synthesis of (\u00b1)-19,20-Dihydro-24-O-methylchlorotricolide, methyl ester, ethyl carbonate", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02272019-121930852", "creators": [ { "name": { "family": "Varney", "given": "Michael David" }, "id": "Varney-Michael-David", "display_name": "Varney, Michael David" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h9ke-rp15", "abstract": "An approach to the total synthesis of the 14-membered macrolide antibiotic aglycon chlorothricolide is presented. Key steps from the two halves to (\u00b1)-19,20-Dihydro-24-O methylchlorothricolide, methyl ester, ethyl carbonate include initial esterification across the C1 and C25 carbons followed by macrodilactonization across the C17 and C14 carbons. Ester enolate Claisen rearrangement and subsequent decarboxylation afforded the intact lactone. Functionalization of the top half is explored.
\r\n\r\nThe ester enolate Claisen rearrangement of propionate derivatives of resolved 1-(t-butyldimethylsilyl)-trans-2-butene-1-ol is reported. Subsequent protiodesilation of the reduced and protected Claisen products resulted in the formation of 2,3-dimethyl-4-pentenyl ethers. Thus, the secondary \u03b1-silyl alcohol has functioned as a chiral primary alcohol equivalent.
\r\n\r\nThe Claisen rearrangement of vinyl ethyl derivatives of 5-tert-butyl-1-(hydroxymethyl)-1-cyclohexene is reported. The standard allyl vinyl ether conditions as well as the triethyl orthoacetate and ester enolate variants of the Claisen rearrangement all resulted in the formation of cis(axial)-4-tert-butylcyclohexyl-substituted systems. Thus, in sterically unbiased cases, this [3.3] sigmatropic process results in the axial attachment of the side chain in a cyclohexyl system.
" }, { "name": "Wardle, Robert Budge", "degree": "PhD", "year": "1986", "title": "Approach to the Synthesis of the Acyltetramic Acid Antibiotic Bu-2313", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11082019-144704211", "creators": [ { "name": { "family": "Wardle", "given": "Robert Budge" }, "id": "Wardle-Robert-Budge", "orcid": "0000-0002-2602-0603", "display_name": "Wardle, Robert Budge" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/rne7-j668", "abstract": "An approach to the synthesis of the bicyclononane portion of the 3-acyltetramic acid antibiotic Bu-2313 is presented. The highly unstable \u03b1-ketoaldehyde obtained by Swern oxidation of the diol 30 was allowed to condense with the unreactive \u03b1-ketophosphoranylidene 18 affording the enedione 31. The silyl ether was cleaved and the hydroxyl caused to add to the enedione in a five-exo fashion to form the tetrahydrofuran. The combination of functional groups necessary for ketal formation was investigated showing that the system does not form the desired ketal in most circumstances (Table I). Given the correct functional group array, it was shown that the ketalization is more favorable with the stereochemistry of the natural product.
" }, { "name": "Warren, Dale Ross", "degree": "PhD", "year": "1986", "title": "Nucleation and Growth of Aerosols", "advisor": "Seinfeld, John H.; Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03212008-085926", "creators": [ { "name": { "family": "Warren", "given": "Dale Ross" }, "id": "Warren-Dale-Ross", "display_name": "Warren, Dale Ross" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "co-advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "member", "display_name": "Grosjean, Daniel" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0edp-5481", "abstract": "This thesis discusses the formation of aerosol particles by homogeneous nucleation of supersaturated vapor, and the subsequent or simultaneous growth of particles by condensation. Experiments, theory, and numerical simulations are used to approach the underlying goal of understanding the aerosol evolution process in photochemically reactive systems, such as Los Angeles smog.
\r\n\r\nA comprehensive size-sectionalized model was developed for simulating the evolution of a multicomponent aerosol size distribution through homogeneous nucleation, condensational growth, coagulation, and various deposition mechanisms. When applied to atmospheric photochemistry, the model predicted that the number of new particles nucleated is controlled by the ratio between the rates of homogeneous nucleation and condensational growth. A simple model was devised for predicting the number and size evolution of particles which would be formed by a burst of homogeneous nucleation. An interesting aspect of the model was its prediction of suppression of homogeneous nucleation by seed aerosol through bulk vapor depletion. Later these predictions were verified qualitatively in two systems. One was a physiochemically well characterized system where nucleation was driven by a high initial supersaturation ratio, in which nucleation was faster than predicted by classical nucleation theory, and suppression of nucleation was only slight. The second system was our outdoor smog chamber.
\r\n\r\nIn a large outdoor smog chamber, toluene and NOx were allowed to photochemically react. Gas phase concentrations and the resulting aerosol distribution were followed with time, for various initial concentrations of reactants and seed aerosol. A few thousand seed particles per cm3 (sub-ambient concentrations) were sufficient to suppress homogeneous nucleation that would have resulted in several times as many particles. Operation of the chamber in dual mode allowed the influence of a single parameter, varied between the two sides of the bag, to be clearly observed, thus avoiding many of the difficulties that arise from comparing experiments conducted at different times and different temperature and sunlight histories.
" }, { "name": "Allison, Janet Noel", "degree": "PhD", "year": "1985", "title": "Theoretical Studies of Heterogeneous Catalysis of Molybdates", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192009-083321412", "creators": [ { "name": { "family": "Allison", "given": "Janet Noel" }, "id": "Allison-Janet-Noel", "display_name": "Allison, Janet Noel" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wpmx-ff05", "abstract": "Chapter 1: We use thermochemical results from ab initio quantum chemical calculations (generalized valence bond) to examine the reaction mechanism for
\r\n\r\nH3COH + \u00bd O2 \u2192 H2CO + H2O
\r\n\r\nas catalyzed by MoO3. We find that surface dioxo sites
\r\n\r\n[Chemical structure; see abstract in scanned thesis for details.]
\r\n\r\nare critical to activating the methanol, but we find that the Trifiro proposal of a single site-single step process
\r\n\r\n[Chemical structure; see abstract in scanned thesis for details.]
\r\n\r\nis not favorable (\u2206H \u2243 +31.5 kcal). Our conclusion is that the catalytic site involves two adjacent surface dioxo units (the dual dioxo site), with each dioxo site extracting one H in a sequence of steps. The required dual dioxo site exists on the (010) surface of MoO3 but does not exist on the other low index surfaces. This mechanism is supported by atmospheric pressure experimental studies which indicate that MoO3 (010) is selective for CH2O products. A detailed sequence of reaction steps and the associated thermochemistry is proposed.
\r\n\r\nChapter 2: Molybdates involving various metal additives play a dominant role in such industrially important catalytic processes as selective oxidation (propene to acrolein) and ammoxidation (propene to acrylonitrile); however, the details of the reaction mechanism and of the surface sites responsible are yet quite uncertain. In order to establish the thermo-chemistry and detailed mechanistic steps involved with such reactions, we have performed ab intitio quantum chemical calculations [generalized valence bond (GVB) and configuration interaction (CI)]. These studies indicate a special importance of multiple surface dioxo Mo sites (possessing two Mo-O double bonds and hence spectator oxo groups) arranged together so as to provide the means for promoting the sequence of transformations.
\r\n\r\nChapter 3: Extensive ab initio calculations have been carried out on molybdenum (VI, V and IV) complexes containing oxygen and nitrogen. A detailed description of the bonding of oxo, nitrido and imido terminally attached ligands to molybdenum is presented. These results are used to explain the preferred geometries of complexes as well as the periodic trends as ligands to molybdenum are varied from O, N, NH.
\r\n\r\nChapter 4: We find that the ground state of MoN (4\u2211-) has a covalent triple bond where the \u03c3 bond is dz2-like on the Mo, leading to a quartet state with unpaired electrons in the Mo 5s, Mo 4d\u03b4xy and Mo 4d\u03b4x2-y2 orbitals. The first excited state (4\u03a0) corresponds to the 5p\u03c0 \u2190 5s excitation. The calculated properties of Re = 1.60 \u00c5, \u03c9e = 1100 cm-1, De = 4.07 eV, and \u2206E (4\u03a0-4\u2211- = 2.128 eV are in good agreement with recent experimental results (Re = 1.63 \u00c5 and \u2206E = 2.011 eV). Particularly interesting is a dramatic nonmonotonic change of dipole moment with distance (\u00b5 = -3.123 D at Re = 1.60 \u00c5, -5.982 D at R = 2.60 \u00c5 and \u00b5 = -0.176 D at R = 5.0 \u00c5. This effect is explained.
\r\n" }, { "name": "Baar, Roger Bennett", "degree": "PhD", "year": "1985", "title": "Synthesis and Characterization of a Ruthenium-EDTA Dimer by Spectral and Electrochemical Techniques", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01022019-103725460", "creators": [ { "name": { "family": "Baar", "given": "Roger Bennett" }, "id": "Baar-Roger-Bennett", "display_name": "Baar, Roger Bennett" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bh22-fp76", "abstract": "Section I
\r\n\r\nThe synthesis of a ruthenium-edta dimer is described. The dimer is shown to be the one-electron oxidized product of two [Ru(III)edta(OH2)]- monomers. The dimer was shown to contain one unpaired spin by magnetic susceptibility and esr spectroscopy indicating spin pairing between the two ruthenium metal centers. A band was detected in the near infrared that analyzed for a Class III complex indicating that the dimer is truly delocalized and that the oxidation state on each ruthenium is 3.5. The band was much narrower than predicted for a delocalized, Class II complex and its position did not exhibit any solvent dependence. The optical spectrum indicated some similarity with other formally Ru(III)-Ru(IV) dimers indicating that the formation of this type of dimer is favored regardless of the type of auxiliary ligands attached to the ruthenium.
\r\n\r\nThe change in the optical spectrum upon raising the pH indicated a pKa of 10.32 for the dimer. This, taken in conjunction with the infrared, the raman and the nmr results indicated that the dimer was \u00b5-oxo bridged at low pH and was, most likely, \u00b5-oxo, \u00b5-hydroxo bridged at higher pH.
\r\n\r\nWhen an excess of Ce(IV) was added to a solution of the dimer the catalytic evolution of dioxygen was observed. The dimer also catalyzed the disproportionation of hydrogen peroxide.
\r\n\r\nSection II describes the electrochemistry of Ru(III)edta and the dimer. Cyclic voltammetry, polarography and rotating ring-disk electrode (RRDE) voltammetry were used to characterize the oxidation and reduction of each of the two complexes. The electrochemical oxidation of Ru3Y produced the dimer after one Faraday per two moles of ruthenium. The catalytic evolution of dioxygen was also observed at a platinum electrode. The step-wise reduction of the dimer to produce Ru(II)edta is also described. The combined use of the RRDE with digital simulations of the mechanism of reduction yielded the rate constants for the rate of breakup of the intermediates. A spectro-electrochemical experiment also showed that the dimer can be oxidized further to produce a Ru(IV)-Ru(IV) dimer.
" }, { "name": "Ball, Denice", "degree": "Masters", "year": "1985", "title": "Hydrodynamically Modulated Rotating Disk Electrodes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-111648791", "creators": [ { "name": { "family": "Ball", "given": "Denice" }, "id": "Ball-Denice", "display_name": "Ball, Denice" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wg42-fk22", "abstract": "Hydrodynamically modulated rotating disk electrodes (HMRDE) have been studied and utilized with a basic system. Experimental results follow the theoretical predictions fairly closely with a few exceptions. HMRDE is useful in reducing complications due to background currents. The goal of HMRDE in this report is separation of currents due to surface responses from diffusion controlled currents. Some measure of success was obtained by incorporation of Ru(NH_3)^(3+)_6 into a Nafion film. However, the sine wave and square wave modulations are cumbersome and highly inefficient. Once the rotator is interfaced to the IBM 90004 for experimental control and data collection, separation of surface response using HMRDE will be feasible on a practical time scale." }, { "name": "Barudi, Samir Elias", "degree": "PhD", "year": "1985", "title": "Steady and Pulsatile Flow in a Glass Model of an Artery Bifurcation", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-04142008-144909", "creators": [ { "name": { "family": "Barudi", "given": "Samir Elias" }, "id": "Barudi-Samir-Elias", "display_name": "Barudi, Samir Elias" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "chair", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Harrison", "given": "Earl C." }, "id": "Harrison-Earl-C", "role": "member", "display_name": "Harrison, Earl C." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/p655-8w88", "abstract": "Velocity measurements were made in the downstream branch of a symmetric rigid glass model of an artery bifurcation for both steady and pulsatile flows. A laser Doppler anemometer was used to make the measurements. The symmetric model had a bifurcation angle of 90\u00b0 and an area ratio (ratio of daughter tubes cross sectional area to mother tube cross sectional area) of 1.2. The Reynolds numbers based upon the upstream flow investigated for steady flow were 600, 1200, 1800, 2400 and 3000 with flow division percentages of 70%, 60%, 50%, 40%, 30% in the branch being studied. For pulsatile flow only a 50/50 division between daughter tubes was employed and the mother tube average Reynolds numbers (Reynolds number based on velocity averaged in time and space) used were 900 and 450. The Womersley parameter for the pulsatile flow studies was 33. Measurements of velocity versus time were also made for steady flow to allow for a better understanding of the nature of the unsteadiness in the flow just after the bifurcation.
\r\n\r\nThis study shows the existence of secondary motions that play a very important role in the development of the flow and in the magnitude of shear stresses at the wall near the outside of the branch. The magnitude of these secondary velocities could reach up to 50% of average mother tube velocities. A small separation region near the outside wall is evident, from the steady flow data, that varies in size depending on the flow conditions present at the time. Helical motions are seen within this area. The velocity versus time plots for steady flows show very large fluctuations in the value of axial and vertical velocities near the outside part of the flow. These fluctuations can be as large as 500% of the value of the local average velocities, and thus show that even for steady flows very large fluctuations in the shear stress are present at the outside wall. No evidence was obtained to show that these fluctuations were periodic in nature. In pulsatile flow, the separation region plays a very dominant role during diastole and is not present during systole. The shear stresses for pulsatile flow at the inside wall are very high and unidirectional while at the outside wall they are oscillatory and low in absolute value.
" }, { "name": "Bentley, Barry Jerome", "degree": "PhD", "year": "1985", "title": "Drop Deformation and Burst in Two-Dimensional Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-04112008-112307", "creators": [ { "name": { "family": "Bentley", "given": "Barry Jerome" }, "id": "Bentley-Barry-Jerome", "display_name": "Bentley, Barry Jerome" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Acrivos", "given": "Andreas" }, "id": "Acrivos-Andreas", "role": "member", "display_name": "Acrivos, Andreas" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2axg-ce38", "abstract": "The deformation and burst of small fluid droplets suspended in a second immiscible fluid undergoing a steady linear shearing motion are discussed. The effects of Capillary number, ratio of fluid viscosities, and flow type are considered both experimentally and theoretically.
\r\n\r\nThe experiments are unique in that a spectrum of strong two-dimensional flows (those with the magnitude of the strain rate exceeding that of the vorticity) was considered. These flows were generated in a four roll mill specifically designed for the experiments. Previous investigations had been limited to one specific strong flow owing to the difficulty in holding drops stationary at the stagnation point in such flows. We overcame this obstacle by using a computer interfaced to a digital video camera to locate the drops in the flow field and adjust the roller speeds to effect an inferential feedback control scheme. It is believed that the control system implemented for the present experiments could be adapted to a variety of fluid flow experiments with similar control problems.
\r\n\r\nDrop deformation and burst experiments were performed for viscosity ratios ranging from 0.001 to 27., and flows with ratio of vorticity to strain rate ranging from zero to 0.667. In a typical experiment a drop went through a succession of increasingly deformed steady shapes as the Capillary number was slowly increased with the flow type constant. The appearance of the drop was recorded photographically. In most cases, a Capillary number was reached where no steady shape was possible, and this was recorded as the critical Capillary number for drop burst. In a few cases with high viscosity ratio and large vorticity to strain rate ratio, drop burst was impossible. In cases where burst occurred, the transient motion of the drops at the critical Capillary number was observed. The drops continued to deform, but did not break into fragments until the flow was turned off. They then either fragmented or returned to the spherical shape through a complex interfacial tension driven motion.
\r\n\r\nThe experimental deformation and burst observations were compared to the predictions of several available theories. Separate theories apply to cases where the deformation is small (nearly spherical drops) or large (threadlike drops). Comparisons to existing numerical results for one particular viscosity ratio are also included. Agreement between the experimental observations and the predictions of the theories was very good.
\r\n" }, { "name": "Boland, John James", "degree": "PhD", "year": "1985", "title": "Experimental and Theoretical Developments in Extended X-Ray Absorption Fine Structure (EXAFS) Spectroscopy", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232014-143633362", "creators": [ { "name": { "family": "Boland", "given": "John James" }, "id": "Boland-John-James", "display_name": "Boland, John James" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "McGill", "given": "Thomas C." }, "id": "McGill-T-C", "role": "member", "display_name": "McGill, Thomas C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YGM3-F114", "abstract": "To obtain accurate information from a structural tool it is necessary to have an understanding of the physical principles which govern the interaction between the probe and the sample under investigation. In this thesis a detailed study of the physical basis for Extended X-ray Absorption Fine Structure (EXAFS) spectroscopy is presented. A single scattering formalism of EXAFS is introduced which allows a rigorous treatment of the central atom potential. A final state interaction formalism of EXAFS is also discussed. Multiple scattering processes are shown to be significant for systems of certain geometries. The standard single scattering EXAFS analysis produces erroneous results if the data contain a large multiple scattering contribution. The effect of thermal vibrations on such multiple scattering paths is also discussed. From symmetry considerations it is shown that only certain normal modes contribute to the Debye-Waller factor for a particular scattering path. Furthermore, changes in the scattering angles induced by thermal vibrations produces additional EXAFS components called modification factors. These factors are shown to be small for most systems.
\r\n\r\nA study of the physical basis for the determination of structural information from EXAFS data is also presented. An objective method of determining the background absorption and the threshold energy is discussed and involves Gaussian functions. In addition, a scheme to determine the nature of the scattering atom in EXAFS experiments is introduced. This scheme is based on the fact that the phase intercept is a measure of the type of scattering atom. A method to determine bond distances is also discussed and does not require the use of model compounds or calculated phase shifts. The physical basis for this method is the absence of a linear term in the scattering phases. Therefore, it is possible to separate these phases from the linear term containing the distance information in the total phase.
\r\n" }, { "name": "Chang, Karl Kho-Chung", "degree": "PhD", "year": "1985", "title": "Calcium-Ion Exchange of Coal for Retention of Sulfur During Combustion", "advisor": "Gavalas, George R.; Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-08092006-145027", "creators": [ { "name": { "family": "Chang", "given": "Karl Kho-Chung" }, "id": "Chang-Karl-Kho-Chung", "display_name": "Chang, Karl Kho-Chung" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." }, { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "co-advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "member", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/X4W7-D106", "abstract": "The kinetics of calcium-ion exchange of coal and the combustion of calcium-exchanged coals in a laminar flow furnace were investigated. Particle diffusion was found to be the rate-determining step for the process of ion exchange. A diffusion model gave good agreement with observed rates of ion exchange. Diffusion of ions in PSOC 680, a bituminous coal, was observed to be much slower than in PSOC 623, a lignite.
\r\n\r\nRetention of sulfur during combustion of calcium-exchanged coals was observed to increase with increasing particle residence and oxygen concentration in the combustion gas. Chemical reaction was found to be the rate-determining step in the capture of SO2 by CaO in coal ash. The results of this study were interpreted in a proposed mechanism for the release and capture of SO2.
" }, { "name": "Coolbaugh, Thomas Smith", "degree": "PhD", "year": "1985", "title": "Nucleophilic Activation of Carbon Monoxide: Synthesis, Characterization and Reactivity of Intramolecular Group VI Metallaesters", "advisor": "Bercaw, John E.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12172018-123100783", "creators": [ { "name": { "family": "Coolbaugh", "given": "Thomas Smith" }, "id": "Coolbaugh-Thomas-Smith", "display_name": "Coolbaugh, Thomas Smith" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/aps3-bk95", "abstract": "An investigation of the design and reactivity of bifunctional transition metal complexes pertinent to homogeneous reduction of carbon monoxide is presented. Oxygen nucleophiles were incorporated into Group VI metal carbonyl complexes via cyclopentadienyl ligands.
\r\n\r\nNeutral molybdenum dimers yield no intramolecular nucleophilic interaction between an alcohol, attached by different bridging arm lengths, and the metal carbonyl fragment. A crystal structure of the propanol substituted cyclopentadienyl molybdenum tricarbonyl dimer (space group P1, a = 7.487 \u00c5,\r\nb = 7.713 \u00c5, c = 10.902 \u00c5, \u03b1 = 99.3600\u00b0, \u03b2 = 81.460\u00b0, \u03b3 = 115.260\u00b0, V = 563.0 \u00c53, Z = 1) indicates only an intermolecular hydrogen bond between alcohols.
\r\n\r\nThe synthesis of the cationic compounds, [CpRM(CO)3L]+BF-4 is reported, where M = Mo, W and R = -(CH2)\u03b7 - OH with n = 1-3. Deprotonation of the alcohols leads to intramolecular metallaester formation for the methylene and ethylene bridged compounds. The equilibria established upon reaction with external alcohols are reported as are the thermodynamic parameters associated with the process.
\r\n\r\nCrystal structures of the metallaesters bridged by a methylene (space group P21/n, a = 7.867 \u00c5, b = 17.083 \u00c5, c = 17.768 \u00c5, \u03b2= 100.959\u00b0, V = 2344.4 \u00c53, Z = 4) and ethylene group (space group P21/n, a = 8.127 \u00c5, b = 16.823 \u00c5, c = 17.623 \u00c5, \u03b2 = 101.980\u00b0, V = 2357.1 \u00c53, Z = 4) are presented. A comparison of the structures is given.
\r\n\r\nReaction of the intramolecular metallaesters with molecular hydrogen produces no volatile products. Reaction with stoichiometric hydride sources yields compounds of relevance to carbon monoxide reduction. Reactions with Me+ and water are presented, the latter giving rise to a stoichiometric analog of the water-gas shift reaction.
" }, { "name": "Dalbadie-McFarland, Gloria", "degree": "PhD", "year": "1985", "title": "Structural Requirements for Protein Function Studied by In Vitro Mutagenesis on Beta-Lactamase", "advisor": "Davidson, Eric H.; Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052019-162706704", "creators": [ { "name": { "family": "Dalbadie-McFarland", "given": "Gloria" }, "id": "Dalbadie-McFarland-Gloria", "display_name": "Dalbadie-McFarland, Gloria" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "advisor", "display_name": "Davidson, Eric H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "co-advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Riggs", "given": "Arthur D." }, "id": "Riggs-Arthur-D", "role": "member", "display_name": "Riggs, Arthur D." }, { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "member", "display_name": "Davidson, Eric H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/jhx0-q907", "abstract": "The study of naturally occurring variants of proteins has been successfully used for a long time to assign roles to structural elements in a protein and to correlate functional requirements with the nature of these structural elements.
\r\n\r\nAdvances in techniques for DNA synthesis and DNA sequencing, along with the development of recombinant DNA techniques now allow one to clone the gene for a protein and then to modify it at will. In this way, presumably any and all aminoacid substitutions can be engineered into any protein whose gene has been cloned, characterized and expressed.
\r\n\r\nBeta-lactamase has been used as a model system in which to study the feasibility of the approach, and it has been demonstrated that not only is it possible to introduce specific predetermined changes in the structure of a protein, but that these mutants can in turn serve as substrates for further modifications. An inactive enzyme can be used to search for a broad range of structural requirements by imposing selective conditions that require a function for the survival of the host organism for the mutant protein.
\r\n\r\nFour variants of beta lactamase, one of which is catalytically active, have been obtained by site specific mutagenesis. In the inactive mutants the conserved active site sequence -ser70-thr71- was altred to either -thr70-ser71-, -thr70-thr-71- or -arg-70-thr71-; a variant in which a disulfide bond was removed by mutating one of the only two cysteines in E. coli beta-lactamse to serine was found to be active. In addition, a revertant to activity has been obtained from one of the the inactive mutants (-thr70-ser71-). The revertant is different in aminoacid sequence (-ser70-ser71-) and in some of its properties from the wild type enzyme while still having catalytic activity. No revertants with aminoacid substitutions at a secondary site were found.
\r\n\r\nBoth the catalytically active revertant and the mutant lacking the disulfide bridge were found to have reduced thermal stability. The rate of secretion of three of these mutants (ser70\u2192thr, thr71\u2192ser and ser70\u2192thr/thr71\u2192ser) was compared to that of the wild type beta lactamase and no significant differences were found. The -arg70-ser71- mutant will be used to identify chemical mutagens and carcinogens that induce GC to TA transversions by collaborators P. L. Foster and D. Botstein.
" }, { "name": "Davison, Brian Henry", "degree": "PhD", "year": "1985", "title": "Dynamics and Coexistence of Microbial Mixed Cultures", "advisor": "Stephanopoulos, Gregory N.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102008-092241", "creators": [ { "name": { "family": "Davison", "given": "Brian Henry" }, "id": "Davison-Brian-Henry", "orcid": "0000-0002-7408-3609", "display_name": "Davison, Brian Henry" } ], "advisors": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "advisor", "display_name": "Stephanopoulos, Gregory N." } ], "committee": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "chair", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/EC5N-4Y46", "abstract": "Various methods of establishing a persistent mixed culture were examined in continuous culture. A well-defined system consisting of Esherichia coli and Saccharomyces cerevisiae was used. The primary interaction was competition for glucose, the rate limiting nutrient. When this was the only interaction no coexistence is possible in a well mixed fermentor at constant conditions (i.e., a chemostat).
\r\n\r\nThe two microorganisms while competing for glucose were maintained in a stable cycle of coexistence by alternating the growth advantage between the two organisms by oscillating the pH in a chemostat. Pure culture experiments found S. cerevisiae to be insensitve to pH between 5 and 4.3 with a maximum specific growth rate (Umax) of 0.4/hr; while Umax of E. coli decreased from 0.6/hr at pH 5 to 0.1/hr at pH 4.3. Steady state and crossinoculation chemostat runs at a dilution rate of 0.17/hr confirmed the expectation that the mixed culture system is unstable at constant pH with E. coli dominating at pH 5 and S. cerevisiae dominating at pH 4.3. Three pH oscillation experiments were performed at D=0.17/hr with 1 gm/1 glucose feed. The 16 hr/16 hr cycle was stable for six periods with a stable alternating cycle of E. coli and S. cerevisiae being quickly established. A 18 hr pH5./14 hr pH4.3 cycle was found to be stable with smaller yeast concentrations. A 6hr/6hr cycle was found unstable with yeast washout. Simulation results were compared with these runs and were used to predict the onset of instability. Oscillations of pH can force stable persistence of a competing mixed culture that is otherwise unstable. Thus time varying conditions are experimentally demonstrated to be one explanation for competitive coexistence.
\r\n\r\nA mixed culture of Saccharomyces cerevisiae and Esherichia coli was established in a stable coexistence steady state in a chemostat under constant operating conditions at higher feed concentrations. The species competed for glucose, the growth limiting resource, and produced acetate and ethanol. The acetic acid was shown to be very inhibitory to E. coli in pure culture at pH 5 while ethanol inhibition was only marginal. No significant inhibition of S. cerevisiae growth was observed by either acetate or ethanol. Pure culture paramenters were measured and used in the analysis. Linearized stabilty analysis for the case when both organisms produce the inhibitor showed that a transition through three stable outcomes was possible as the feed concentration is lowered. Experimental studies verified these predictions and successive transitions from a yeast growth steady state, to a coexistence steady state, and to a E. coli growth steady state were obtained by lowering the glucose concentration in the feed from 10 to 5 to 2.5 g/l. This dynamic behavior is distinctly different form other competition-inhibition combinations and demostrates for the first time that coexistence is possible due to substrate competition and product inhibition.
\r\n\r\nA bioreactor with simultaneous fermentation and cell recycle was investigated. The reactor consisted of a typical fermentor and an attached inclined side-arm that allowed enhanced sedimentation. Due to the enhanced sedimentation in the side-arm settler the cells precipitate quickly and flow back into the reactor. A virtually cell free broth can be withdrawn through the side-arm while maintaining both a high flowrate and a high cell density. Continuous fermentations with S. cerevisiae demonstrated these features and the possibility of high cell densities at flowrates that ordinarially would lead to washout. Ethanol productivities and yields were high. Increased resistance to contamination was feasible and tested using E. coli as the model contaminant.
\r\n\r\nThis new reactor with size-selective properties was found to allow a coexistent mixed culture of Esherichia coli and Saccharomyces cerevisiae. The larger yeast population was retained and recycled at high efficiencies, while the smaller yet faster growing bacteria were removed preferentially through the side-arm. Stability analysis indicated that the coexistence of this system could be stable only if the yeast removal rate as a function of biomass was concave up. This would occur if growth continued in the side-arm. Another experimental system was devised to measure this removal rate function. A negative removal rate (i.e., a net addition of yeast to the fermentor) was observed at low biomass indicating growth in the settler and explaining the stability of the coexistence steady state.
\r\n\r\nA mixed culture, that was unstable during pure competition under constant well-mixed conditions as expressed in the Competitive Exclusion Principle, was made to persist indefinitely by the use of time-varying conditions (such as pH oscillations), or the addition of other interactions (such as inhibition), or the design of spatially nonuniform reactors (such as the side-arm settler).
" }, { "name": "Doran, Pauline Mavis", "degree": "PhD", "year": "1985", "title": "Effects of Immobilization on the Metabolism of Yeast", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-111952", "creators": [ { "name": { "family": "Doran", "given": "Pauline Mavis" }, "id": "Doran-Pauline-Mavis", "orcid": "0000-0002-8682-4929", "display_name": "Doran, Pauline Mavis" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5445-rc32", "abstract": "The composition and kinetic properties of Saccharomyces cerevisiae were found to be substantially different when the cells were immobilized on gelatin. Batch fermentation experiments conducted in a gradientless reaction system allowed comparison of immobilized cell and suspended cell performance.
\r\n\r\nIn complete nutrient medium, the specific rate of ethanol production by the immobilized cells was 40-50% greater than for the suspended yeast. The immobilized cell consumed glucose twice as fast as the suspended cells, but their specific growth rate was reduced by 45%. Yields of biomass from the immobilized cell population were lower at one-third the value for the suspended cells.
\r\n\r\nCellular composition was also affected by immobilization. Measurements of intracellular polysaccharide levels showed that the immobilized yeast stored larger quantities of reserve carbohydrates and contained more structural polysaccharide than suspended cells. Flow cytometry was used to obtain DNA, RNA and protein frequency functions for suspended and immobilized cell populations. These data showed that the immobilized cells have higher ploidy than cells in suspension. The level of stable, double-stranded RNA in immobilized cells was only one-quarter that measured for suspended cells. The observed changes in immobilized cell metabolism and composition may have arisen from disturbance to the yeast cell cycle by cell attachment, causing alterations in the normal patterns of yeast bud development, DNA replication and synthesis of cell wall components.
\r\n\r\nRecovery from hydroxyurea-induced DNA synthesis inhibition was indicated by measurements of growth rate, DNA content and light scatter properties. The immobilized cells quickly developed an effective means for overcoming hydroxyurea-induced inhibition of replication, and proceeded to synthesize large amounts of DNA while still in the presence of the inhibitor. Stable RNA levels for immobilized cells remained low at 25% of the measured quantity for hydroxyurea-treated suspended cells. Synthesis of protein and RNA was not adversely affected in either cell type. Suspended cell protein pools increased by a factor of 1.8 following inhibition, while the immobilized cells contained 2.6 times the level of protein before hydroxyurea treatment.
\r\n\r\nFermentation properties of immobilized and suspended cells were changed by hydroxyurea. The specific rate of ethanol production by immobilized cells increased by an average of 24%, while, for the suspended cells, specific productivity was up to three times higher. Glucose consumption rates for both cell types also increased under the influence of hydroxyurea. Suspended cell polysaccharide content was reduced by 65%, while the immobilized cells, in contrast, contained 30% more polysaccharide after hydroxyurea treatment.
\r\n\r\nBiotin starvation of immobilized yeast was effective in reducing synthesis of DNA. Biotin-deficient immobilized S. cerevisiae contained approximately the same quantity of DNA as starved suspended cells, while RNA and protein levels were reduced. Glycerol was synthesized at the expense of ethanol during fermentation by biotin-deficient immobilized and suspended cells.
\r\n\r\nThe character and occurrence of glycolytic oscillations were affected by immobilization. Endogenous metabolism by immobilized cells gave rise to relaxation oscillations in the absence of external substrate. Addition of glucose to starved immobilized yeast also generated relaxation-type behaviour, while suspended cells produced only sinusoidal waveforms. Interpretation of these immobilized cell dynamics is discussed in terms of the kinetics and regulatory properties of energy metabolism in yeast.
" }, { "name": "Falke, Joseph John", "degree": "PhD", "year": "1985", "title": "The Behavior and Structure of the Band 3 Anion Transport Site: a \u00b3\u2075Cl and \u00b3\u2077Cl NMR Study", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112019-112435563", "creators": [ { "name": { "family": "Falke", "given": "Joseph John" }, "id": "Falke-Joseph-John", "orcid": "0000-0002-3704-4694", "display_name": "Falke, Joseph John" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/j15r-rw02", "abstract": "The transport of ions across cellular and organellar membranes is a widespread and fundamental process in biology. The goal of the present work is a molecular picture describing the ion translocation event in band 3, the most heavily used ion transport protein in typical vertebrate systems. The strategy employed involves 35Cl NMR, which is shown both theoretically and experimentally to be a sensitive probe of two microscopic events: 1) the migration of Cl- from solution to the vicinity of a macromolecular binding site, and 2) the binding of Cl- to the site. The technique reveals 35Cl- linebroadening due to two classes of Cl- binding sites on isolated, native red cell membranes. One class is composed solely of low affinity Cl- binding sites of unknown function (KD > > 0.5 M), while the other class is composed solely of band 3 transport sites (KD = 80 \u00b1 20 mM) which are identified by their affinity for substrate (Cl-), competing substrates (HCO-3, F-, Br-, I-) and inhibitor (4,4'-dinitrostilbene-2,2'-disulfonate, or DNDS). A 35Cl NMR method is developed to ascertain the sidedness of Cl- binding sites relative to a compartment barrier such as a membrane: this approach shows that the low-affinity and transport sites are each found on both surfaces of the membrane.
\r\n\r\nThe sequence of events in the Cl- transport cycle is investigated by monitoring the behavior of the transport sites when the concentration of DNDS, p-nitrobenzenesulfonate (pNBS), Cl-, Br-, or H+ is varied. DNDS and pNBS, which are known to bind to outward-facing transport sites, each recruit all of the transport sites on both sides of the membrane to the inhibited outward-facing conformation, indicating that the inward- and outward-facing transport sites observed in the absence of inhibitor are merely different conformations of a single site. In addition, the transport sites on both sides of the membrane together behave like a homogeneous population of sites when [Cl-], [Br-], or pH is varied. These results are quantitatively consistent with the pingpong model for the transport cycle (Gunn and Frolich (1979) J. Gen. Physiol. 74, 351-374), in which a single transport site alternates between the inward- and outward-facing states and can only change states when occupied by bound anion. The rates of Cl- binding and dissociation at both inward- and outward-facing transport sites are investigated with 35Cl and 37Cl NMR, and it is shown that each of these rates exceeds 105 events sec-1 site-1 -- much faster than the known turnover rate of the chloride transport cycle (430 events sec-1 site-1, 0\u00b0C). Assuming that the rates of the influx and efflux half-turnovers of the transport cycle differ by 102 or less, it follows that the translocation of the chloride*transport site complex is the rate-limiting step in both half-turnovers (see Figure).
\r\n\r\nThe structure of the transport machinery is investigated using transport inhibitors and proteases. The reversible inhibitor niflumic acid (NIF) has no effect on the transport site linebroadening: this inhibitor slows the translocation of bound Cl- in both the influx and efflux half-turnovers. The covalent, arginine-specific reagents phenylglyoxal (PG) and 1,2-cyclohexanedione (CHD) each eliminate the transport site linebroadening: PG modifies an essential residue in the transport site and CHD slows the migration of Cl- between the site and solution. The observed PG-sensitivity and pH-dependence of the transport site linebroadening (pKA = 11.1 \u00b1 0.1, [Cl-] = 250 mM) indicate that an arginine residue provides the positive charge in at least one conformation of the transport site. A search is conducted for the minimal structure containing the intact transport site: this search begins with the removal of an innessential part of the transport domain, followed by monitoring of the transport site linebroadening for change. A variety of treatments leave some or all of the transport site linebroadening intact, including: 1) removal of the red cell membrane nonintegral proteins, 2) proteolytic removal of the soluble N-terminal domain of band 3, or 3) extensive proteolysis of band 3 by papain, which reduces band 3 to its transmembrane peptides (3-9 kDa). These results indicate that the essential arginine, as well as all other residues essential for Cl- migration and binding to the transport site, are located on the papain-generated transmembrane peptides. The structural data presented here strongly support a picture in which the transport site, including the essential arginine, is buried in the membrane where it is resistant to proteolysis; and access of the buried site to solution Cl- is provided by a channel that can be blocked by CHD. In summary, the minimal sequence of events in the Cl- transport cycle can be schematically illustrated by
\r\n\r\n[Illustration. See abstract in scanned thesis for details]
\r\n\r\nA model is also presented that describes the molecular details of the ion translocation event: the translocation is proposed to begin when the transport site positive charge is neutralized by anion binding, so that a sliding hydrophobic barrier can move past the site and thereby expose the site to the opposite solution, as illustrated by
\r\n\r\n[Illustration. See abstract in scanned thesis for details]
\r\n\r\nA sliding barrier model could explain the translocation event in many other membrane transport systems as well.
" }, { "name": "Felker, Peter Mark", "degree": "PhD", "year": "1985", "title": "Picosecond Dynamics of Intramolecular Vibrational-Energy Redistribution (IVR) in Jet-Cooled Molecules", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072008-152253", "creators": [ { "name": { "family": "Felker", "given": "Peter Mark" }, "id": "Felker-Peter-Mark", "orcid": "0000-0002-4907-7231", "display_name": "Felker, Peter Mark" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x48p-n096", "abstract": "Theoretical and experimental results concerning the dynamical manifestations of intramolecular vibrational-energy redistribution (IVR) in the temporally resolved fluorescence of jet-cooled molecules are presented. A first concern is with the derivation of the characteristics of the beat-modulated fluorescence decays which arise from multilevel vibrational coupling within a molecule. Relations connecting quantum beat frequencies, phases, and modulation depths to coupling parameters are presented. Likely sources of deviations of experimental results from theoretical predictions are considered. And, the direct link between IVR and time-resolved fluorescence experiments is discussed with emphasis placed on the physical interpretation of vibrational quantum beats and the nature of IVR as a function of vibrational energy in a molecule. Secondly, the results of picosecond time-resolved measurements of IVR on jet-cooled anthracene at different excess energies are reported and analyzed. The nature of IVR as a function of vibrational energy, the relevant timescales for the process, and the details of pertinent vibrational couplings are determined. Thirdly, experimental and theoretical results pertaining to the role of molecular rotations in IVR are presented. Finally, experimental results on jet-cooled t-stilbene are reported and analyzed with the aim of assessing the generality of our theoretical treatment and the anthracene results.
" }, { "name": "Flanagan, Dorothy Jean", "degree": "PhD", "year": "1985", "title": "The Angular Resolved Photoelectron Spectroscopy of Various Polyatomic Molecular Systems", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052019-112244749", "creators": [ { "name": { "family": "Flanagan", "given": "Dorothy Jean" }, "id": "Flanagan-Dorothy-Jean", "display_name": "Flanagan, Dorothy Jean" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/f9mq-vz30", "abstract": "This thesis describes the study of the angular resolved photoelectron spectroscopy of a series of polyatomic molecules. The spectrometer consists of a He I radiation source, a scattering chamber, and a rotatable detection system which includes a set of electrostatic lenses, a hemispherical electrostatic kinetic energy analyzer and an electron multiplier. Angular distributions are determined from the variation in intensity as the detection system is rotated about the center of the scattering chamber.
\r\n\r\nThe theory of photoionization is discussed semiclassically, as the interaction of an atom or molecule treated quantum mechanically with a classical radiation field. Some recent calculations of the asymmetry parameter for valence electrons are briefly reviewed.
\r\n\r\nPhotoelectron angular distributions were measured for acetylene, propyne, 1-butyne, and 2-butyne. The asymmetry parameters of propyne, 1-butyne, and 2-butyne have been determined for the first time. Trends in the asymmetry parameter, ionization potentials and band shapes were studied. It was determined that the parity favoredness rules of Chang failed to account for the behavior of the asymmetry parameter of the molecule despite the symmetry of the molecule. Instead, acetylene and its alkylated analogs follow the trends in \u03b2 observed in studies of the methylated ethenes.
\r\n\r\nAdditionally, the semi-empirical rule that the \u03b2 values of \u03c0 orbitals are higher than for \u03c3 orbitals was violated in this series. Acetylene and propyne possess \u03c3 orbital with \u03b2 values significantly higher than the \u03c0 orbitals.
\r\n\r\nTwo principal substituent effects were observed: 1) a systematic decrease in the first ionization potential and 2) a similar decrease in the asymmetry parameter of the X̃ band with increasing alkylation.
\r\n\r\nThe photoelectron angular distributions were measured for formaldehyde, acetaldehyde, and acetone. The asymmetry parameter has been determined for the first time for acetaldehyde, and, with the exception of the first band, for acetone.
\r\n\r\nThis study has shown that the beta values of the X̃ nO bands of these molecules are, within experimental error, invariant with respect to methyl substitution, results that are consistent with the nonbonding characteristics of the molecular orbitals. The à \u03c0C = O bands, however, show a strong decrease in the asymmetry parameter of approximately 0.2 per methylation in a manner similar to that observed previously in the methylated ethenes and ethynes. The expected systematic decrease in first ionization potential with substitution was also observed.
\r\n\r\nLastly, HAM/3 calculations were performed to determine the ionization potentials of some substituted carbonyls and to examine the excitation energies of ethylene and its methyl and fluoro derivatives to evaluate the method's usefulness to studies in electron impact spectroscopy.
\r\n\r\nThere was generally good agreement between the ionization potential calculated by this method and experimentally determined values. Agreement between the calculated values of the excitation energies and the experimental were reasonable but the method was not sensitive enough to reproduce the trends observed with increasing substitution of the chromophore.
" }, { "name": "Garvey, James F.", "degree": "PhD", "year": "1985", "title": "The Production and Characterization of an Intense Hyperthermal Beam of H\u2083 Molecules and of H Atoms", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02132012-111043915", "creators": [ { "name": { "family": "Garvey", "given": "James F." }, "id": "Garvey-James-F", "display_name": "Garvey, James F." } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/r4n1-8762", "abstract": "The simplest bimolecular reaction involving neutral reagents is the reaction
\r\n\r\nH + H2 \u2192 H2 + H.
\r\n\r\nThis system, because of its simplicity and fundamental significance in chemical dynamics, has been the subject of extensive accurate ab initio theoretical quantum mechanical calculations and the results obtained have been used to test approximate theories of reaction dynamics. However, this system has proved difficult to study experimentally due to its high activation barrier (~ .33 eV) and its small reactive cross section (~ 1 x 10-16 cm2. Because of these factors, state-to-state reaction dynamics have only become feasible recently.
\r\n\r\nIn order to study this reaction in a crossed molecular beam experiment, a means of generating an intense beam of H atoms is essential. This thesis documents the design and operation of a hydrogen arc discharge for generating such a beam. The method consists of using a high power arc discharge to create a high temperature (~ 12,000 K) plasma in which H2 molecules can be dissociated into atoms. By using an arc source of the type developed by Kunth, a stable, intense, hyperthermal H atom beam has been successfully produced. Section 2 of this thesis discusses the design and operation of the apparatus and Section 3 of the thesis discusses the characterization of the hydrogen atoms within the beam. The laboratory energy distribution function of these atoms was determined approximately, and spans the range from 0.5 eV to about 12 eV. The total intensity of this beam is of the order of ~1022 atoms/sterad/sec. With such an intense and energetic beam, a wealth of chemical dynamical experiments may now become feasible.
\r\n\r\nIn the course of developing this intense beam of hydrogen atoms, the source was found to also produce metastable H3 molecules. This is the first direct, unambiguous observation of such a specie in a molecular beam, and is discussed in Section 4. Translational energy analysis of this H3 molecule indicates an energy distribution similar to that of the H atoms, suggesting that the lifetime of H3 is of the order of 40 \u00b5sec or longer. We also observed emission spectra from the Rydberg states of H3 identified previously by Herzberg. This is spectroscopic evidence for the presence of this neutral molecule in our beam. The only know state of H3 capable of having the long lifetime observed is 2p 2A\"2, the second excited state of this species.
\r\n\r\nIn addition, we detected this molecule by a variety of other independent techniques. It has long been known that alkali metal atoms with low ionization potential will ionize upon collision with a metal surface having a high work function. The 2p 2A\"2 state of H3 has an IP of ~ 3.7 eV and is expected to behave in a similar way. As a result, surface ionization of metastable 3 has been observed for for a variety of metals and is reported in this thesis. From that low IP one would also expect that the metastable H3 should be photoionizable using an appropriate light source. In this thesis we report the generation of H+3 through irradiation of the beam with the light from a high intensity mercury lamp. Lastly, since the metastable H3 is in a Rydberg state, it would be expected to exhibit a large total scattering cross section due to the diffuse nature of the Rydberg orbital. Such cross sections were measured by the attenuation of the H3 beam as it passed through a gas cell.
\r\n\r\nSection 5 describes the first observation of the electronic spectrum of WH. This emission spectrum was due to WH formed by the presence of the tungsten anode and cathode which are heated too close to its melting point by the arc discharge. Analysis of this spectrum has given rotational constants and bond distances for the electronic states of the mono-hydride involved in the observed transisiton. Due to relativistic terms in the potential, the theoretical calculation of WH has proved difficult to date. Recently a reliable potential for W has been generated such that our experimental bond distances will provide an important empirical check for any further theoretical calculations performed on this system. Likewise, the arc source may be employed in the future as a means of generating new metal hydride emission spectra.
\r\n\r\nAppendix A of the thesis details the design and construction of the inhomogeneous magnet to serve in the future as a velocity selector for the hyperthermal hydrogen beam in our crossed beam experiment. Using such a Stern-Gerlach magnet as a velocity selector, the dynamics of the H + H2 reaction can be probed as a function of translational energy of the reactants. Appendix B grew out of an interesting Ch 227 project and will now become a theoretical paper. Exact quantum mechanical calculations of the collinear reaction Be + FH (\u03bd = 0, 1) have been performed and the effects of reagent translational and vibrational excitation on reaction probabilities and product state distributions are examined. These quantum mechanical results are compared with those of quasi-classical trajectory calculations reported previously.
" }, { "name": "Hannoun, Betty Jane Miller", "degree": "Masters", "year": "1985", "title": "Diffusion Coefficients of Glucose and Ethanol in Cell-Free and Cell-Occupied Calcium Alginate Membranes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:06272025-211525361", "creators": [ { "name": { "family": "Hannoun", "given": "Betty Jane Miller" }, "id": "Hannoun-Betty-Jane-Miller", "display_name": "Hannoun, Betty Jane Miller" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9gpk-a215", "abstract": "The diffusivities of glucose and ethanol in cell-free and cell-occupied membranes of calcium alginate were measured in a diffusion cell. The lag time analysis was employed. Diffusivities decreased with increasing alginate concentration and were comparable to those in water for a 2% alginate membrane. Glucose and ethanol concentrations had no effect on the respective diffusion coefficients. The ratio of ethanol diffusivity to glucose diffusivity in 2% and 4% alginate agreed closely to the inverse ratio of the hydrodynamic radii for the two molecules in water indicating that the hydrodynamic theory of diffusion in liquids may be applicable to diffusion in dilute alginate gels. Also the presence of 20% dead yeast cells had no effect on the diffusivities. The data reported can be used to study reaction and diffusion in immobilized cell reactors and cell physiology under immobilized conditions." }, { "name": "Hanratty, Maureen Alice", "degree": "PhD", "year": "1985", "title": "Investigations of the Mechanisms and Energetics for Transition Metal Ion Mediated Reactions", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012019-115455977", "creators": [ { "name": { "family": "Hanratty", "given": "Maureen Alice" }, "id": "Hanratty-Maureen-Alice", "display_name": "Hanratty, Maureen Alice" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "chair", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6mqm-3w23", "abstract": "Multiphoton infrared activation has been used to probe the potential energy surfaces for the reactions of stable Co(C5H10)+ adducts, formed by ligand exchange reactions in an ion cyclotron resonance spectrometer. These investigations are discussed in Chapter II. Infrared activation effected with a cw CO2 laser is highly selective, with dissociation occurring only by the lowest energy pathway.
\r\n\r\nChapter III describes the use of product translational energy release distributions to investigate the potential energy surfaces for elimination of H2 and small hydrocarbons from ionic cobalt and nickel complexes with alkanes. The measurements were made using a reverse geometry double focusing mass spectrometer. For dehydrogenation reactions, both the shape of the kinetic energy release distribution and the maximum kinetic energy release appear to be correlated with the reaction mechanism. Statistical RRKM theory is used to model the observed kinetic energy release distributions.
\r\n\r\nThe kinetic energy release distributions associated with loss of H2 and small hydrocarbons from Co(C5H10)+ complexes are presented in Chapter IV. The results from the ionic cobalt-alkene adducts are compared with the kinetic energy release distributions for the ionic cobalt-alkane complexes discussed in Chapter III. Collision induced dissociation is also employed to characterize the Co(C5H10)+ adducts.
\r\n\r\nThe formation and reactions of iron and nickel clusters containing up to four metal atoms with a varying number of CO ligands are discussed in Chapter V. Ion-molecule condensation reactions result in the rapid formation of polynuclear metal carbonyl clusters which lose CO when exposed to infrared or visible radiation. The reactivity of these ligated species is markedly different from that of the bare metal ion. The potential of this method for generating very specific unsaturated cluster compounds is demonstrated.
\r\n\r\n" }, { "name": "Kalema, William Samson", "degree": "PhD", "year": "1985", "title": "A Study of Coal Oxidation", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102008-081200", "creators": [ { "name": { "family": "Kalema", "given": "William Samson" }, "id": "Kalema-William-Samson", "display_name": "Kalema, William Samson" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemeng" ], "doi": "10.7907/kr3w-an09", "abstract": "Three coals were oxidized in a fluidized bed, using air at temperatures from 175\u00b0C to 280\u00b0C and total pressures from 126 kPa. to 274 kPa., for periods of up to 24 hours. An infra-red analyzer was used to measure concentrations of carbon oxide gases in the fluidizing stream. Both CO and CO2 rates declined with time and increased with total pressure. The CO2/CO ratio increased with oxidation temperature.
\r\n\r\nOxidation at 200\u00b0C for 12 hours caused about a 10% loss in coal heating value; with most of that loss occurring in the first two hours. The loss of heating value correlated well, according to Dulong's formula, with the decrease in carbon and hydrogen content. The total and carboxylic ion-exchange capacities of the coal increased significantly with oxidation. The enhanced cation exchange capacity could be used to introduce calcium or other cations, which could help reduce emissions of sulfur oxides during coal combustion by foaming sulfates in the ash.
\r\n\r\nFTIR spectra of coal samples were obtained using diffuse reflectance spectroscopy and peak overlap was reduced significantly using the fourier self-deconvolution technique, The spectra of oxidized coal samples showed the progressive reduction in the intensities of aromatic, methyl, and methylene C-H peaks and the appearance or enhancement of a number of carbonyl peaks.
\r\n\r\nCarbon-13 NMR spectra of solid coal samples were obtained using the cross-polarization technique together with magic-angle spinning, and carbon aromaticities were estimated which, when combined with analyses for carbon and ash content, allowed the calculation of overall consumption of aromatic and aliphatic carbon. Both aromatic carbon and aliphatic carbon were consumed, even at 175\u00b0C. This finding disproved a previous theory that aromatic rings were oxidized only above 225\u00b0C.
\r\n" }, { "name": "Koerting, Charles Frederick", "degree": "PhD", "year": "1985", "title": "Variable-Angle Electron Spectroscopic Studies of Various Polyatomic Molecular Systems", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02132014-084828083", "creators": [ { "name": { "family": "Koerting", "given": "Charles Frederick" }, "id": "Koerting-Charles-Frederick", "display_name": "Koerting, Charles Frederick" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YP9D-ED80", "abstract": "The complementary techniques of low-energy, variable-angle electron-impact spectroscopy and ultraviolet variable-angle photoelectron spectroscopy have been used to study the electronic spectroscopy and structure of several series of molecules. Electron-impact studies were performed at incident beam energies between 25 eV and 100 eV and at scattering angles ranging from 0\u00b0 to 90\u00b0. The energy-loss regions from 0 eV to greater than 15 eV were studied. Photoelectron spectroscopic studies were conducted using a HeI radiation source and spectra were measured at scattering angles from 45\u00b0 to 90\u00b0. The molecules studied were chosen because of their spectroscopic, chemical, and structural interest. The operation of a new electron-impact spectrometer with multiple-mode target source capability is described. This spectrometer has been used to investigate the spin-forbidden transitions in a number of molecular systems.
\r\n\r\nThe electron-impact spectroscopy of the six chloro-substituted ethylenes has been studied over the energy-loss region from 0-15 eV. Spin-forbidden excitations corresponding to the \u03c0 \u2192 \u03c0*, N \u2192 T transition have been observed at excitation energies ranging from 4.13 eV in vinyl chloride to 3.54 eV in tetrachloroethylene. Symmetry-forbidden transitions of the type \u03c0 \u2192 np have been oberved in trans-dichloroethyene and tetrachlor oethylene. In addition, transitions to many states lying above the first ionization potential were observed for the first time. Many of these bands have been assigned to Rydberg series converging to higher ionization potentials. The trends observed in the measured transition energies for the \u03c0 \u2192 \u03c0*, N \u2192 T, and N \u2192 V as well as the \u03c0 \u2192 3s excitation are discussed and compared to those observed in the methyl- and fluoro-substituted ethylenes.
\r\n\r\nThe electron energy-loss spectra of the group VIb transition metal hexacarbonyls have been studied in the 0 eV to 15 eV region. The differential cross sections were obtained for several features in the 3-7 eV energy-loss region. The symmetry-forbidden nature of the 1A1g \u2192 1A1g, 2t2g(\u03c0) \u2192 3t2g(\u03c0*) transition in these compounds was confirmed by the high-energy, low-angle behavior of their relative intensities. Several low lying transitions have been assigned to ligand field transitions on the basis of the energy and angular behavior of the differential cross sections for these transitions. No transitions which could clearly be assigned to singlet \u2192 triplet excitations involving metal orbitals were located. A number of states lying above the first ionization potential have been observed for the first time. A number of features in the 6-14 eV energy-loss region of the spectra of these compounds correspond quite well to those observed in free CO.
\r\n\r\nA number of exploratory studies have been performed. The \u03c0 \u2192 \u03c0*, N \u2192 T, singlet \u2192 triplet excitation has been located in vinyl bromide at 4.05 eV. We have also observed this transition at approximately 3.8 eV in a cis-/trans- mixture of the 1,2-dibromoethylenes. The low-angle spectrum of iron pentacarbonyl was measured over the energy-loss region extending from 2-12 eV. A number of transitions of 8 eV or greater excitation energy were observed for the first time. Cyclopropane was also studied at both high and low angles but no clear evidence for any spin-forbidden transitions was found. The electron-impact spectrum of the methyl radical resulting from the pyrolysis of tetramethyl tin was obtained at 100 eV incident energy and at 0\u00b0 scattering angle. Transitions observed at 5.70 eV and 8.30 eV agree well with the previous optical results. In addition, a number of bands were observed in the 8-14 eV region which are most likely due to Rydberg transitions converging to the higher ionization potentials of this molecule. This is the first reported electron-impact spectrum of a polyatomic free radical.
\r\n\r\nVariable-angle photoelectron spectroscopic studies were performed on a series of three-membered-ring heterocyclic compounds. These compounds are of great interest due to their highly unusual structure. Photoelectron angular distributions using HeI radiation have been measured for the first time for ethylene oxide and ethyleneimine. The measured anisotropy parameters, \u03b2, along with those measured for cyclopropane were used to confirm the orbital correlations and photoelectron band assignments. No high values of \u03b2 similar to those expected for alkene \u03c0 orbitals were observed for the Walsh or Forster-Coulson-Moffit type orbitals.
" }, { "name": "Krafft, Terry Edward", "degree": "PhD", "year": "1985", "title": "The Design Multianionic Chelating Ligands for the Production of Inorganic Oxidizing Agents, Synthesis, Structure and Reactivity of Osmium Complexes Derived from a Tetradentate Ligand", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302019-091842152", "creators": [ { "name": { "family": "Krafft", "given": "Terry Edward" }, "id": "Krafft-Terry-Edward", "display_name": "Krafft, Terry Edward" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/sts6-x769", "abstract": "The design of multianionic chelating ligands for use in high valent transition metal chemistry is discussed. Possible application of such ligands to problems in inorganic oxidation chemistry is addressed. A class of potentially tetradentate tetraanionic ligands was synthesized. The ligand 1,2-bis(3,5-dichloro-2-hydroxybenzamido)ethane (H4CHBA-Et), 1, was found to coordinate to osmium as a tetradentate tetraanion in the oxidation states (II), (III), (IV), (V), and (VI). X-ray crystal structures of two osmium(IV) complexes of this ligand are reported. The \u00b5-oxo dimer, K2({Os(\u03b74-CHBA-Et)(OPPh3)}2-O], 3, features octahedral osmium with the tetradentate tetraanionic ligand 1 coordinated to the equatorial positions and the potassium ions in unusual coordination environments. The structure of octahedral Os(\u03b74-CHBAEt)(py)2,5, shows the ligand 1 coordinated in the same fashion with pyridines in the axial positions.
\r\n\r\nCompound 5 and all of the osmium(IV) compounds reported here exhibit well-resolved paramagnetically shifted NMR spectra. The 1H NMR data suggest the possibility of an unusual \u03c0-backbonding interaction from osmium(IV) to pyridine. Electrochemical data indicate that ligand 1 and related ligands have a profound effect on the osmium redox couples which are found at significantly lower potentials than with other ligands.
\r\n\r\nControlled potential oxidation of 5 in the presence of water or alcohol was found to trigger a series of irreversible chemical and electrochemical transformations in which the ethane backbone of the ligand is oxidized in a selective and stepwise fashion. Several key intermediates have been isolated, independently synthesized and characterized. The first intermediate isolated, Os(\u03b74-CHBA-ethylene)(py)2, 7, results from dehydrogenation of the ligand bridge. An X-ray crystal structure of this material is reported and significant features are discussed. In the second isolated intermediate the unsaturated ethylene bridge of 7 has been oxidized to a trans-1,2-diether in compound 8. A crystal structure of the related trans-1,2-hydroxy-alkoxy complex, 8*, has been performed. Cleavage of the bridge carbon-carbon bond in 8 yields the final oxidation products cis-\u03b1 and trans-Os(\u03b72-Fo-CHBA)2-(py)2, 9 and 9', in which the amide nitrogen of each bidentate ligand is substituted with a formyl group. t-Bupy derivatives of both isomers have been characterized by X-ray crystal structure determinations. The diastereomeric distribution is determined by the nature of the alcohol in solution during the electrolysis. Mechanistic aspects of the ligand oxidation process are addressed.
\r\n\r\nCompounds 9 and 9' can be converted to catalysts for the electrochemical oxidation of alcohols. The catalysts were found to be the osmium(IV) compounds cis-\u03b1- and trans-Os(\u03b72-CHBA)2(t-Bupy)2, 11 and 11', which are formed by a selective stepwise hydrolysis of the two formyl groups in 9/9'. A crystal structure of 11' shows the primary amide group of 3,5-dichloro-2-hydroxybenzamide, H2CHBA, to be coordinated through nitrogen. Chemical synthesis of the catalysts was pursued by coordination of H2CHBA to osmium. Two of the ligands coordinate to osmium(VI) as bidentate dianions in the complex K2 (Os(\u03b72-CHBA)2(O)2), 12, which can be converted to 11', 15 and the compounds trans and cis-Os(\u03b72-CHBA)2(t-Bupy)(Ph3P=O), 13 and 14. Compound 15 has been formulated as the dimer Os2(\u03b72-CHBA)4(t-Bupy)4.
\r\n\r\nCompounds 11, 11', 13 and 14 are catalysts for the electrochemical oxidation of alcohols. The catalytic system selectively oxidizes benzyl alcohol to benzaldehyde without further oxidation to benzoic acid or benzyl esters. Approximately 150 molecules of benzyl alcohol are oxidized during the lifetime of the catalyst, 11, but activity with other alcohols is quite low. The synthesis, characterization and properties of the above osmium compounds and significant features of the catalytic system are reported.
\r\n\r\n" }, { "name": "Lagnado, Ronald Robert", "degree": "PhD", "year": "1985", "title": "The Stability of Two-Dimensional Linear Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-03272008-105253", "creators": [ { "name": { "family": "Lagnado", "given": "Ronald Robert" }, "id": "Lagnado-Ronald-Robert", "display_name": "Lagnado, Ronald Robert" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "chair", "display_name": "Brennen, Christopher E." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DDJC-PE17", "abstract": "This thesis presents the results of a theoretical and experimental investigation concerned with the hydrodynamic stability of extensional flows. In particular, model extensional flows in the class of two-dimensional linear flows are considered. These flows may be classified by a parameter \u03bb ranging from \u03bb = 0 for simple shear flow to \u03bb = 1 for pure extensional flow.
\r\n\r\nIn Chapter I, a linear stability analysis is given for an unbounded Newtonian fluid undergoing two-dimensional linear flows. The linearized velocity disturbance equations are analyzed to yield the large-time asymptotic behavior of spatially periodic initial disturbances. The results confirm the established fact that simple shear flow (\u03bb = 0) is linearly stable. However, it is found that unbounded extensional flows in the range 0 < \u03bb \u2264 1 are unconditionally unstable. Spatially periodic initial disturbances which have lines of constant phase parallel to the inlet streamline of the basic flow and have sufficiently small wavenumbers in the direction normal to the plane of the basic flow must grow exponentially in time. A complete analytical solution of the vorticity disturbance equation is obtained for the case of pure extensional flow (\u03bb = 1).
\r\n\r\nChapter II presents a linear stability analysis for an Oldroyd-type fluid undergoing two-dimensional linear flows throughout an unbounded region. The effects of fluid elasticity on extensional-flow stability are considered. The time derivatives in the constitutive equation can be varied continously from co-rotational to co-deformational as a parameter \u03b2 varies from 0 to 1. It is again found that unbounded flows in the range 0 < \u03bb \u2264 1 are unconditionally unstable with respect to spatially periodic initial disturbances that have lines of constant phase parallel to the inlet streamline in the plane of the basic flow. For small values of the Weissenberg number, only disturbances with sufficiently small wavenumbers \u03b1s in the direction normal to the plane of the basic flow give rise to instability. However, for certain values of \u03b2, there exist critical values of the Weissenberg number above which flows are unstable for all values of the wavenumber \u03b1s.
\r\n\r\nThe results of an experimental investigation of the flow of a Newtonian fluid in a four-roll mill are found in Chapter III. The four-roll mill may be used to generate an approximation to two-dimensional linear flow in a central region between the rollers. A photographic flow-visualization technique was employed to study the stability of a pure extensional flow (\u03bb = 1). Two four-roll mills with different ratios of roller length to gap width between adjacent rollers (namely, L/d = 3.39 and 12.73) were used in order to study end effects on flow stability. At sufficiently small Reynolds numbers the flow in both devices is essentially two- dimensional throughout most of the region between the rollers, except near the top and bottom bounding surfaces where three-dimensional flow involving four symmetrically positioned vortices appears. The vertical extent of this two- dimensional flow gradually diminishes and the vortices grow in size and strength as the Reynolds number is increased up to a quasi-critical range. An increase in Reynolds number through this quasi-critical range results in an abrupt transition to a steady three-dimensional flow throughout the entire region between the rollers. The three-dimensionality is significantly less pronounced in the device with L/d = 12.73, however. At sufficiently high Reynolds numbers beyond the quasi-critical range, the flow becomes unsteady in time and eventually turbulent.
" }, { "name": "Leone, Joseph Anthony", "degree": "PhD", "year": "1985", "title": "Studies in Photochemical Smog Chemistry: I. Atmospheric Chemistry of Toluene. II. Analysis of Chemical Reaction Mechanisms for Photochemical Smog", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042006-093443", "creators": [ { "name": { "family": "Leone", "given": "Joseph Anthony" }, "id": "Leone-Joseph-Anthony", "display_name": "Leone, Joseph Anthony" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Grosjean", "given": "Daniel" }, "id": "Grosjean-D", "role": "member", "display_name": "Grosjean, Daniel" }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/swb9-yg26", "abstract": "This study focuses on two related topics in the gas phase organic chemistry of importance in urban air pollution. Part I describes an experimental and modeling effort aimed at developing a new explicit reaction mechanism for the atmospheric photooxidation of toluene. This mechanism is tested using experimental data from both indoor and outdoor smog chamber facilities. The predictions of the new reaction mechanism are found to be in good agreement with both sets of experimental data. Additional simulations performed with the new mechanism are used to investigate various mechanistic paths, and to gain insight into areas where our understanding is not complete. The outdoor experimental facility, which was built to provide the second set of experimental data, consists of a 65 cubic meter teflon smog chamber together with full instrumentation capable of measuring ozone, nitrogen dioxide, nitric oxide, peroxyacetyl nitrate (PAN), carbon monoxide, relative humidity, temperature, aerosol size distributions, and of course toluene and its photooxidation products.
\r\n\r\nIn Part II, we present a theoretical analysis of lumped chemical reaction mechanisms for photochemical smog. Included is a description of a new counter species analysis technique which can be used to analyze any complex chemical reaction mechanism. When applied to mechanisms for photochemical smog, this analysis is shown capable of providing answers to previously inaccessible questions such as the relative contributions of individual organics to photochemical ozone formation. The counter species analysis is applied to six existing mechanisms for photochemical smog to determine why they predict substantially different degrees of emission controls to achieve the same desired air quality under identical conditions. For each mechanism critical areas are identified that when altered bring the predictions of the various mechanisms into much closer agreement. Finally, a new lumped mechanism for photochemical smog is developed and tested against experimental data from two smog chamber facilities. Advantages of this mechanism relative to the existing lumped mechanisms are discussed.
\r\n" }, { "name": "Low, John James", "degree": "PhD", "year": "1985", "title": "Theoretical Studies of Oxidative Addition and Reductive Elimination", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232009-095454256", "creators": [ { "name": { "family": "Low", "given": "John James" }, "id": "Low-John-James", "orcid": "0000-0001-6598-5347", "display_name": "Low, John James" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XR1N-CM33", "abstract": "Chapter 1: Ab initio calculations (Hartree-Fock, generalized valence bond, and configuration interaction), utilizing relativistic core potentials, have been used to follow the oxidative addition of H2 to Pt(PH3)2. We find an activation barrier of 2.3 kcal/mol and an exothermicity of 15.9 kcal/mol. From examination of the geometries and wavefunctions, we find that up to the transition state the H-H bond is still intact. The role of the Pt s1d9 and d10 states in oxidative addition is described, and the effects of including electronic correlation are discussed. The implications for reductive elimination of the dimethyl and hydridomethyl complexes are also discussed.
\r\n\r\nChapter 2: Ab initio calculations have been carried out on MR2 complexes (where M = Pd or Pt and R = H or CH3) to model concerted reductive coupling from MR2L2 complexes (where L is a substituted phosphine). The results of these calculations support the following two conclusions. (1) The differences in the driving force for reductive elimination from Pd(II) and Pt(II) complexes with the same R groups is very close (0-4 kcal/mol) to the difference in the s1d9-d10 state splittings of these elements (32 kcal/mol). Thus reductive elimination is exothermic from Pd complexes (since Pd prefers d10) and endothermic from Pt complexes (since Pt prefers s1d9), where the metal product is in its d10 state. This supports the conclusion, derived from qualitative considerations of generalized valence bond wavefunctions, that Pt(II) and Pd(II) complexes have their metal atoms in a s1d9 configuration and the metal atoms in Pt(0) and Pd(0) complexes are in a d10 configuration. (2) The activation barriers for C-C coupling are approximately twice that for C-H coupling. There are essentially no barriers for processes involving H-H bonds. The origin of this trend is the directionality of the methyl sp3 orbital, which destabilizes the transition state for the case where an M-C bond is being converted to a C-C or C-H bond. Conversely, the spherical H 1s is orbital can form multicenter bonds easily, allowing it to break M-H bonds while forming an H-H bond and leading to low intrinsic barriers. These results are consistent with the experimentally observed trends.
\r\n\r\nChapter 3: Ab initio calculations were carried out on Pt(CH3)2(Cl)2(PH3)2 and on various Mt(R1)(R2)(PH3)2 complexes (where Mt = Pd or Pt; R1, R2 = H or CH3) in order to elucidate the differences in reductive H-C and C-C coupling from Pd(II), Pt(II), and Pt(IV) complexes. These studies explain why (1) reductive C-C coupling is facile for Pd(II), favorable for Pt(IV), and unobserved for Pt(II) systems, while (2) reductive H-C coupling is facile for Pt(II) and Pd(II) systems, and (3) oxidative addition is favorable only for addition of H2 to Pt(0) systems.
\r\n\r\nChapter 4: Ab initio calculations were carried out on CHx and NHx molecular fragments on small clusters of Ni atoms (Ni13 and Ni14), as a model for chemisorption on the Ni(100) surface. The results presented here show that these species make strong \u03c0 bonds to the surface which cause methylidyne and imidogen to be the most stable CHx and NHx, species on this surface. The results have also been used to estimate \u2206H0f for various intermedates important for methanation and ammonia decomposition on Ni surfaces.
" }, { "name": "Lynch, Edward Douglas", "degree": "PhD", "year": "1985", "title": "Sedimentation in Quiescent and Sheared Suspensions", "advisor": "Herbolzheimer, Eric", "url": "https://resolver.caltech.edu/CaltechETD:etd-03272008-090808", "creators": [ { "name": { "family": "Lynch", "given": "Edward Douglas" }, "id": "Lynch-Edward-Douglas", "display_name": "Lynch, Edward Douglas" } ], "advisors": [ { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "advisor", "display_name": "Herbolzheimer, Eric" } ], "committee": [ { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "chair", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/5h7h-5652", "abstract": "This thesis explores how the average sedimentation velocity u0 of a monodisperse suspension of spheres depends on the volume fraction of solids c and on the application of shear to the suspension and considers how changes in the sedimentation velocity reflect changes in the microscale distribution of particles in the suspension. For dilute, quiescent, monodisperse suspensions of spheres with radius a greater than 2\u00b5m, previous experimental measurements of u0 are well-correlated by the result
\r\n\r\nu0 = us(1 - c1/3)
\r\n\r\nwhere us is the Stokes settling velocity of the spheres (cf. Barnea, E. and Mizrahi, J., Chem. Eng. J. 5, 171-189 (1973)). Although none of the previous theoretical predictions are in even rough accord with this result, this type of behavior is shown to be consistent with that of a suspension having a pair-probability function changing over a length scale of O(ac-1/3), which is comparable to the average interparticle spacing. A molecular-dynamics-type simulation is employed to show that multiparticle hydrodynamic interactions can create this type of microscale \"structure\" in a sedimenting suspension. This thesis also presents the first results for the influence of bulk flow on non-flocculating sedimenting suspensions. In a uniaxial extensional flow, a dilute suspension which is being sheared sufficiently rapidly for the effect of the shear to dominate the effect of multiparticle hydrodynamic interactions is shown to settle with velocity
\r\n\r\nu0 = us(1 - 4.52c) + o(c).
\r\n\r\nThis increase in u0 results because the pair-probability function now changes over a length scale of O(a), not of O(ac-1/3). Experimental measurements presented here of the sedimentation velocity as a function of particle volume fraction and dimensionless shear rate in the simple shear flow created by a Couette device agree remarkably well with this result.
" }, { "name": "Martin, Craig Timothy", "degree": "PhD", "year": "1985", "title": "The Structures of Cu\u2090 and Cytochrome a\u0332 in Cytochrome c Oxidase", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052019-144431487", "creators": [ { "name": { "family": "Martin", "given": "Craig Timothy" }, "id": "Martin-Craig-Timothy", "display_name": "Martin, Craig Timothy" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/eft1-pp43", "abstract": "Cytochrome c oxidase contains four metal centers, two heme irons and two copper centers. The two low-potential centers, CuA and cytochrome a, function in the transfer of electrons from cytochrome c to the oxygen binding site within cytochrome oxidase. Although almost nothing is currently known about the mechanism of proton pumping in cytochrome oxidase, it is very likely that at least one of these low-potential metal centers is directly involved in the translocation of protons across the inner mitochondrial membrane. Essential to a complete understanding of the mechanisms of electron transfer and proton pumping in cytochrome oxidase is a knowledge of the structures of the involved metal centers.
\r\n\r\nIn this work, the spectroscopic tool of electron nuclear double resonance (ENDOR) is used in conjunction with the direct incorporation of isotopically substituted amino acids into the yeast protein to determine the identities of ligands to CuA and cytochrome a in cytochrome oxidase. For cytochrome a, the incorporation of [1,3-15N2]histidine into the yeast protein results in the appearance of an ENDOR signal associated with hyperfine coupling to the histidine ring 15N, thereby unambiguously identifying histidine as an axial ligand to cytochrome a. Comparison of this result with similar results in the native and 15N-substituted bis-imidazole model compounds metmyoglobin-imidazole and bis-imidazole tetraphenyl porphyrin, provides strong evidence that cytochrome a is coordinated by two axial histidine ligands.
\r\n\r\nSimilar studies on the effect of the incorporation of [1,3-15N2]histidine into yeast cytochrome oxidase demonstrate that histidine is a ligand to CuA. The incorporation of [\u03b2,\u03b2-2H2]cysteine into the protein reveals that the two strongly coupled protons previously observed in the ENDOR spectrum of CuA (H. L. Van Camp, et al. (1978) Biochim. Biophys. Acta 537, 238) can be assigned to the methylene protons on cysteine, proving conclusively that cysteine is a ligand to [\u03b2-13C]cysteine-substituted protein. These results, combined with the resolution in the native enzyme of a new hyperfine coupling to a third strongly coupled proton for CuA, provide strong evidence for the coordination of two cysteine ligands to CuA.
\r\n\r\nArmed with the identification of one histidine and two cysteine ligands to CuA, we present a model for the physical and electronic structure of the oxidized CuA center. This model is characterized by the delocalization of a substantial amount of unpaired spin density away from the copper atom and into an orbital between the two cysteine sulfur ligands. This model satisfactorily explains many of the unusual spectroscopic features of CuA and should prove to be of use in future studies of the nature of the CuA site.
\r\n\r\nWith the positive identification of ligands to cytochrome a and CuA, we have analyzed the available protein sequence data for the subunits of cytochrome oxidase from a wide variety of organisms, and are able to reach some conclusions regarding the physical location of these metal centers in the subunit structure of the protein. The cysteine ligand(s) to CuA most certainly derive from the two conserved cysteine residues in subunit II. Furthermore, it is predicted that all of the metal centers in cytochrome oxidase cannot be located in subunit II, and are quite likely shared with subunit I. Finally, we present a model for the protein coordination of CuA in which the two cysteine sulfur ligands to CuA originate in two cysteine residues which are physically adjacent on the face of an \u03b1-helix in subunit II.
" }, { "name": "Mathre, David John", "degree": "PhD", "year": "1985", "title": "I. The Disastereoselective Alkylation of Chiral 2-Oxazolidinone Imide Enolates. II. Efforts Directed Toward the Enantioselective Total Synthesis of Ferensimycin B", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02202019-093314396", "creators": [ { "name": { "family": "Mathre", "given": "David John" }, "id": "Mathre-Davis-John", "display_name": "Mathre, David John" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x5a5-z913", "abstract": "The diastereoselective alkylation of chiral 2-oxazolidinone imide enolates is described. The requisite chiral N-acyl 2-oxazolididones are prepared from readily available amino acid and amino alcohol precursors. The lithium and sodium enolates, derived from these chiral imides, react in a highly diastereoselective manner with a variety of electrophiles. Furthermore, the diasteromers are often separable by liquid chromateography affording products with a diastereomeric purity \u2265 99:1. Several methods are described for the non\u2013destructive removal of the chiral auxiliary to afford enantiomerically pure alcohols, aldehydes, carboxylic acids, acid chlorides, esters, hydrazides, and ketones. Through the use of chiral imides 16 and 20 either of the enantiomeric products can be obtained.
\r\n\r\n[Structural formula. See abstract in scanned thesis for details.]
\r\n\r\nAn approach to the enantioselective total synthesis of the poly- ether ionophore antibiotic ferensimycin B (2) is described. The synthesis employs the diastereoselective alkylation and aldol condensation of chiral 2-oxazolidinone imide enolates to both construct the carbon backbone and generate the necessary stereo- centers. This research has culminated in the preparation of the advanced intermediate 49.
\r\n\r\n[Structural formula. See abstract in scanned thesis for details.]
\r\n\r\nAn enantioselective total synthesis of (R) and (S)-thiorphan [N-(1-oxo-2-mercaptomethyl-3-phenylpropyl)glycine] via a six-step sequence is reported. The key step, establishing the absolute stereochemistry, is the diastereoselective alkylation of the enolate derived from chiral 2-oxazolidinone imide 16 (R = PhCH2) or 20 (R = PhCH2) with benzyl bromomethyl sulfide. The level of alkylation diastereoselection is in excess of 95:5.
" }, { "name": "McDade, Christine", "degree": "PhD", "year": "1985", "title": "Synthetic, Kinetic and Mechanistic Studies in Early Transition Metal Systems. I. \u03b1- and \u03b2-Hydrogen Elimination Reactions in Derivatives of Permethyltitanocene, -Zirconocene, and -Hafnocene. II. The Reactions of Aluminum Alkyls with Derivatives of Permethylniobocene", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02202014-135322611", "creators": [ { "name": { "family": "McDade", "given": "Christine" }, "id": "McDade-Christine", "display_name": "McDade, Christine" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "chair", "display_name": "Collins, Terrence J." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/B308-3A48", "abstract": "The thermal decomposition of Cp*2Ti(CH3)2 (Cp* \u2261 \u019e5-C5Me5) toluene solution follows cleanly first-order kinetics and produces a single titanium product Cp*(C5Me4CH2)Ti(CH3) concurrent with the evolution of one equivalent of methane. Labeling studies using Cp*2Ti-(CD3)2 and (Cp*-d15)2Ti(CH3)2 show the decomposition to be intramolecular and the methane to be produced by the coupling of a methyl group with a hydrogen from the other TiCH3 group. Activation parameters, \u0394H\u2021 and \u0394S\u2021, and kinetic deuterium isotope effects have been measured. The alternative decomposition pathways of \u03b1-hydrogen abstraction and a-hydrogen elimination, both leading to a titanium-methylidene intermediate, are discussed.
\r\n\r\nThe insertion of unactivated acetylenes into the metal-hydride bonds of Cp*2MH2 (M = Zr, Hf) proceeds rapidly at low temperature to form mono- and/or bisinsertion products, dependent upon the steric bulk of the acetylene substituents. Cp*2M(H)(C(Me) = CHMe), Cp*2M(H)(CH = CHCMe3), Cp*2M(H)-(CH = CHPh), Cp*2M(CH = CHPh)2, Cp*2M(CH = CHCH3)2 and Cp*2Zr-(CH = CHCH2CH3)2 have been isolated and characterized. To extend the study of unsaturated-carbon ligands, Cp*2M(C \u2261 CCH3)2 have been prepared by treating Cp*2MCl2 with LiC \u2261 CCH3. The reactivity of many of these complexes with carbon monoxide and dihydrogen is surveyed. The mono(2-butenyl) complexes Cp*2M(H)(C(Me) = CHMe) rearrange at room temperature, forming the crotyl-hydride species Cp*2M(H)(\u019e3-C4H7). The bis(propenyl) and bis(l-butenyl) zirconium complexes Cp*2Zr(CH = CHR)2 (R = CH3, CH2CH3) also rearrange, forming zirconacyclopentenes. Labeling studies, reaction chemistry, and kinetic measurements, including deuterium isotope effects, demonstrate that the unusual \u03b2-hydrogen elimination from an sp2-hybridized carbon is the first step in these latter rearrangements but is not observed in the former. Details of these mechanisms and the differences in reactivity of the zirconium and hafnium complexes are discussed.
\r\n\r\nThe reactions of hydride- and alkyl-carbonyl derivatives of permethylniobocene with equimolar amounts of trialkylaluminum reagents occur rapidly producing the carbonyl adducts Cp*2Nb(R)(COAlR'3) (R = H, CH3, CH2CH3, CH2CH2Ph, C(Me) = CHMe; R' = Me, Et). The hydride adduct Cp*2NbH3\u2022AlEt3 has also been formed. In solution, each of these compounds exists in equilibrium with the uncomplexed species. The formation constants for Cp*2Nb(H)(COAlR'3) have been measured. They indicate the steric bulk of the Cp* ligands plays a deciding factor in the isolation of the first example of an aluminum Lewis acid bound to a carbonyl-oxygen in preference to a metalhydride. Reactions of Cp*2Nb(H)CO with other Lewis acids and of the one:one adducts with H2, CO and C2H4 are also discussed.
\r\n\r\nCp*2Nb(H)(C2H4) also reacts with equimolar amounts of trialkyl-aluminum reagents, forming a one:one complex that 1H NMR spectroscopy indicates contains a Nb-CH2CH2-Al bridge. This adduct also exists in equilibrium with the uncomplexed species in solution. The formation constant for Cp*2Nb+(H)(CH2CH2Al-Et3) has been measured. Reactions of Cp*2Nb(H)(C2H4) with other Lewis acids and the reactions of Cp*2Nb+(H-(CH2CH2Al-Et3) with CO and C2H4 are described, as are the reactions of Cp*2Nb(H)(CH2 = CHR) (R = Me, Ph), Cp*2Nb(H)(CH3C \u2261 CCH3) and Cp*2Ti-(C2H4) with AlEt3.
" }, { "name": "Norbeck, Daniel Word", "degree": "PhD", "year": "1985", "title": "Progress Toward the Total Synthesis of Polyether Ionophore Antibiotics", "advisor": "Grubbs, Robert H.; Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052019-154201556", "creators": [ { "name": { "family": "Norbeck", "given": "Daniel Word" }, "id": "Norbeck-Daniel-Word", "display_name": "Norbeck, Daniel Word" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "co-advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "chair", "display_name": "Ireland, Robert E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/92jg-h841", "abstract": "Several subunits for the convergent synthesis of polyether ionophore antibiotics via the ester enolate Claisen rearrangement of furanoid and pyranoid carboxylic acids and glycals are prepared from carbohydrates. Key steps from D-fructose to the monensin spiroketal include the ester enolate Claisen rearrangement of a glycal propionate, expansion of a furanoid to a pyranoid ring, and the acid catalyzed equilibration of a bicyclic ketal to a spiroketal. An alternative approach, entailing the hetero-Diels-Alder condensation of a 2-methylenetetrahydropyran and acrolein is thwarted by facile isomerization to the endocyclic enol ether. The monensin bis-tetrahydrofuran is prepared from D-xylose and Dmannose. In the key step, in situ silylation of an ester enolate with a beta leaving group allows the tetrahydrofuran rings to be joined by Claisen rearrangement. The monensin tetrahydropyran is prepared from D-fructose and then joined to the bis-tetrahydrofuran by the ester enolate Claisen rearrangement. Methodology for the radical induced, reductive decarboxylation of the resulting acid via its phenyl selenoester is described. Anomeric stabilization of the intermediate tetrahydrofuran-2-yl radical is an important factor in the stereochemical outcome of this process. Reduction of 2,3-Q-(1-methylethylidene)furanosyl and pyranosyl chloride with lithium 4,4'-di-t-butylbiphenyl affords the corresponding glycals in high yield. The direct addition of nucleophilic reagents to crude Swern oxidation reaction mixtures circumvents the deleterious side reactions characteristic of highly reactive carbonyl compounds. Hexylglyoxal, produced by Swern oxidation of 1,2-octanediol, condenses with methyl (triphenylphosphoranylidene)acetate to give the \u03b3-oxo-crotonate. Addition of methyl magnesiun bromide to an unstable 2-ketofuranoside delivers the branched chain carbohydrate derivative. The transient existence of monomeric trimethylsilyl formaldehyde, generated at -78\u00b0C by Swern oxidation of trimethylsilylmethanol, is established by isolation of a Wittig condensation product.
" }, { "name": "Pichaichanarong, Puvin", "degree": "PhD", "year": "1985", "title": "Reactions of Phenoxy Radicals Under Coal Liquefaction Conditions", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102008-152250", "creators": [ { "name": { "family": "Pichaichanarong", "given": "Puvin" }, "id": "Pichaichanarong-Puvin", "display_name": "Pichaichanarong, Puvin" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Allen", "given": "David Thomas" }, "id": "Allen-David-Thomas", "orcid": "0000-0001-6646-8755", "role": "member", "display_name": "Allen, David Thomas" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6nqa-0445", "abstract": "This thesis presents the results of model compound studies that address the rate parameters for hydrogen abstraction involving phenoxy radicals, and the products, pathways, and kinetics of phenoxy radical recombination, under coal liquefaction conditions. Thermolysis of selected mixtures of model compounds containing functionalities found in coal-related materials were conducted in a batch reactor at temperatures between 250 and 450\u00b0C. The reaction products were analyzed by GC, HPLC, GCMS, and NMR, with emphasis on the identification of radical recombination products. Reactions were modeled by free radical mechanisms and rate parameters at liquefaction temperatures for hydrogen abstraction and recombination reactions involving phenoxy radicals were determined.
\r\n\r\nPhenoxy radicals were found to be more reactive than benzyl radicals, rapidly abstracting hydrogen atoms to form stable molecules. Hydrogen abstraction by a phenoxy radical from a phenol was faster than from a hydrocarbon. Application of the rate parameters determined for one model compound mixture to other systems of compounds indicated good match with experimental data.
\r\n\r\nAnalysis of the recombination products revealed that, when no good hydrogen donor solvents were available, phenoxy-phenoxy radical recombination products were more abundant than phenoxy-benzyl recombination products. Certain differences and similarities were observed between the behavior of single-ring aromatics and their condensed-ring counterparts. Whereas phenol was quite stable at 400\u00b0C, 1-naphthol was found to undergo considerable conversion. A mechanistic scheme for 1-naphthol decomposition was proposed which accounted for the major reaction products. Thermolysis of various model compound mixtures indicated similar patterns exhibited by single-ring and double-ring aromatics with respect to the pathways of oxygen-oxygen and oxygen-carbon free radical recombination.
\r\n\r\nBimolecular reverse disproportionation was demonstrated to be satisfactory in explaining naphthol conversion. Furthermore, dehydration accounted for furan formation and concerted reactions could possibly be involved in naphthalene formation. Thus, in addition to unimolecular dissociation reactions, several pathways exist for the thermal reactions of oxygen compounds.
\r\n\r\nThese model compound studies indicated that the results of a simple model compound mixture could give insight into the understanding of a more complex reaction network. This insight will ultimately provide the link between model compound results and the reactions of coal-related materials.
\r\n" }, { "name": "Smith, Maile Elizabeth", "degree": "PhD", "year": "1985", "title": "The Schwinger Variational Principle Applied to Molecular Photoionization", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01232019-115959754", "creators": [ { "name": { "family": "Smith", "given": "Maile Elizabeth" }, "id": "Smith-Maile-Elizabeth", "display_name": "Smith, Maile Elizabeth" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/4m95-c614", "abstract": "We have developed a method based upon the Schwinger Variational Principle to study molecular photoionization and electron molecule scattering. We obtain exact static-exchange solutions to the equations for the continuum orbitals within the Hartree-Fock approximation, and from these we derive cross sections and angular distributions for both of the above processes. We have applied this method to photoionization of the valence levels of three different systems.
\r\n\r\nThe first application of this method is in a study of the photoionization of the valence levels of NO. For photoionization of the 5\u03c3 level we find that the magnitudes of the cross sections for the resulting b3\u03a0 and A1\u03a0 states of NO+ are not in the statistical 3:1 ratio and that the position of the peaks in the shape resonances appear at significantly different photoelectron kinetic energies. The differences are a reflection of the sensitivity of the shape resonances to small changes in the exchange component of the molecular ion potential. We also examined photoionization of the 2\u03c0 and 4\u03c3 levels of NO and found that these levels, along with the 5\u03c3, exhibit shape resonances in the \u03c3 continuum.
\r\n\r\nVibrationally resolved branching ratios and vibrational state-specific asymmetry parameters for photoionization of the 5\u03c3 level of CO are presented. The agreement between these results and the measured data was obscured by autoionization peaks superimposed upon the region of the spectrum in which the experiment was performed. The limited experimental data which are not obscured by autoionization, agree quite well with our results.
\r\n\r\nFinally, a study of the photoionization of the 5\u03c3 level of CO adsorbed on a nickel surface is reported. Approximating this system by the linear triatomic molecule NiCO leads to cross sections and angular distributions which are in good agreement with experimental data. The use of polarized, highly tunable synchrotron radiation along with detection at various angles yields far more information than can be obtained from the photoionization of the same molecule in the gas phase. With this technique it is possible to determine the adsorbate geometry, resolve partial channels, and resolve the photoemisison from two degenerate orbitals of different symmetries, simply by making appropriate choice of the polarization and collection angles. Examples of these techniques are discussed.
" }, { "name": "Spies, George Harlan", "degree": "PhD", "year": "1985", "title": "I. Studies on the Coordination of Bis-hydroxybenzamido Chelating Ligations to Chromium, Iron, and Osmium. II. A Survey of the Organometallic Chemistry of Osmium Tetraoxide", "advisor": "Bercaw, John E.; Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01182019-103133548", "creators": [ { "name": { "family": "Spies", "given": "George Harlan" }, "id": "Spies-George-Harlan", "display_name": "Spies, George Harlan" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "co-advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s19j-2033", "abstract": "The coordination chemistry of chromium, iron, and osmium with bis-hydroxybenzamido chelating ligands was investigated. Two types of complexes were obtained on reacting CrCl3 \u2022 6H2O with 1,2-bis(3,5-dichloro-2-hydroxybenzanido)-ethane ((H)4CHBA-Et). A neutral dimeric complex, in which two chelates bridge two metal centers, was discovered and characterized by X-ray crystallography. This is the first molecule in which both forms of monodentate organic amide coordination (i.e., O-bound and N-bound coordination) have been found. The N-bound amide was shown to be a better \u03c3-donor. This is the first well-characterized example of N-coordination to chromium(III).
\r\n\r\nA second complex, which is a precursor to the neutral dimer, has not been fully characterized. It may also be dimeric. Similar complexes, with different bis-hydroxybenzamido ligands, have been examined. Iron(III) species, synthesized from these ligands and FeCl3, appear to be analogous to the latter chromium(III) compounds.
\r\n\r\nX-ray crystallographic studies have complemented investigations into the coordination chemistry of these bis-hydroxybenzamido ligands with several transition metals. In addition to the dimeric chromium(III) complex, in which the ligand bridges two metal centers, many osmium(IV) complexes were found with the bis-hydroxybenzamido ligands coordinated to one metal center as a planar tetradentate tetraanion. These structures exhibited the first examples of bonds between osmium(IV) and an N-coordinated organic amide ligand and a phenoxide ligand. One such complex, a \u00b5-oxo dimer, was found with potassium ions in unusually low coordination environments (i.e., four- and five-coordinate). Oxidation of trans-Os( CHBA-Et)(py)2 subsequently resulted in crystals of a new con1plex with a hydroxy and a methoxy group on the ethylene unit bridging the amide nitrogen atoms of the chelated ligand. The bond distances and angles for this molecule are very similar to those of its precursor, trans-Os(CHBA-Et)(py)2. The ligand, (H)4 CHBA-Et, was found to cocrystallize with pyridinium chloride. This structure has provided a benchmark for comparison with complexed chelates; few significant differences were observed.
\r\n\r\nThe fusion of 2,3-bis(2-hydroxy-benzamido)-2,3-butane with (NH4)2OsCl6 (T > 300\u00b0C) resulted in the formation of an osmium(IV)-imidazoline complex.
\r\n\r\nAlso examined was the organometallic chemistry of osmium tetraoxide. Oxidation of low valent carbonyl complexes with the quinuclidine adduct of osmium tetraoxide resulted in attack of both the low valent metal and a carbonyl ligand with the formation of \u00b5-CO2 mixed-valent complexes. The surprising stability of this new type of CO2 complex is kinetic in origin as den1onstrated by the chemistry of a series of compounds. Decomposition with loss of CO2 was observed for more labile metal complexes. In the absence of nitrogenous bases, oxidation of Ru(CO)3(PPh3)2 with osmium tetraoxide resulted in the formation of what is believed to be a tetranuclear complex. The low valent metal center and a coordinated carbonyl ligand were oxidized.
\r\n\r\nOne other mode of reactivity was discovered. Oxidative addition of osmium tetraoxide to Pt(PPh3)2(C2H4) displaced the ethylene ligand with the formation of a \u00b5-oxo bridged tetranuclear complex. These and other potential modes of OsO4 reactivity with organometallic and inorganic complexes are discussed.
" }, { "name": "Szuromi, Phillip David", "degree": "PhD", "year": "1985", "title": "Studies of Hydrocarbon Reactions on Low-Index Iridium and Platinum Surfaces", "advisor": "Goddard, William A., III; Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:01072019-124055656", "creators": [ { "name": { "family": "Szuromi", "given": "Phillip David" }, "id": "Szuromi-Phillip-David", "display_name": "Szuromi, Phillip David" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "co-advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ndxy-rb82", "abstract": "The interaction of hydrocarbons with the (110)-(1x2) and (111) surfaces of iridium and the (110)-(1x2) surface of platinum has been studied under ultrahigh vacuum conditions. The principle experimental techniques employed were thermal desorption mass spectrometry and low energy electron diffraction.
\r\n\r\nChapter 2 describes the extension of previous studies of the adsorption and reaction of ethane and propane on the Ir(110)-(1x2) surface to the normal isomers of butane, pentane, hexane and heptane. At low coverages, each of these alkanes undergoes dissociative chemisorption at 130 K. At higher coverages, molecular adsorption occurs as well. Thermal desorption spectra of hydrogen are similar in many respects for the dissociatively adsorbed overlayers of all six of these paraffins. Both desorption-limited and reaction-limited adstates of hydrogen are observed, the latter being associated with the dehydrogenation of hydrocarbon fragments on the surface. Ethane, butane and hexane form high temperature adstates, the associated fragments of which are low in hydrogen content, while those for propane, pentane and heptane contain relatively more hydrogen. This difference may be explained by extending a model for dehydrogenation which has been proposed previously [T. S. Wittrig, P. D. Szuromi and W. H. Weinberg, J. Chem. Phys. (76), 3305 (1982)] for understanding the dissociative adsorption of other saturated hydrocarbons on this surface.
\r\n\r\nChapter 3 discusses cyclopropane, propylene, propyne and allene on the reconstructed Ir(110)-(1x2) surface. Annealing adlayers of these hydrocarbons (at low coverages) leads to the formation of surface hydrogen and hydrocarbon fragments of approximate stoichiometry C3H2. The importance of the \u03b22 adsite of hydrogen on this surface of iridium has been demonstrated further by inhibition studies with hydrogen, CO and surface carbon. The close-packed Ir(111) surface dehydrogenates propylene, but neither propane nor cyclopropane adsorb dissociately under the same reaction conditions, indicating a strong effect for the activation of carbon-hydrogen bonds of alkanes.
\r\n\r\nChapter 4 describes the investigation of this strong effect of surface geometry on the dissociative adsorption of alkanes on surfaces of platinum. Previous work (L. E. Firment, Ph.D. Thesis, Univ. of California, Berkeley, 1976) shows that the close-packed Pt(111) surface does not dehydrogenate the normal alkanes through octane under ultrahigh vacuum conditions. On the reconstructed Pt(110)-(1x2) surface, low coverages of n-butane and n-pentane adsorb dissociatively at approximately 200 K to form surface hydrogen and hydrocarbon fragments, whereas only molecular adsorption is observed for ethane and propane. Inhibition of this reaction by precoverages of hydrogen suggests strongly that carbon-hydrogen bond activation is the initial reaction step, and occurs at the same adsite as for the adsorption of hydrogen at lower coverages. Thus for both iridium and platinum the availability of high coordination adsites on the (110)-(1x2) surface appears to lower the kinetic barriers that must be overcome to activate carbon-hydrogen bonds in alkanes. Differences in the electronic structure of the two metals manifest themselves in such details as the magnitude of that kinetic barrier.
" }, { "name": "Tsou, Yu-Min", "degree": "PhD", "year": "1985", "title": "Thermodynamic and Kinetic Studies of Redox Reactions within Polyelectrolyte Coatings on Electrodes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01112019-110100839", "creators": [ { "name": { "family": "Tsou", "given": "Yu-Min" }, "id": "Tsou-Yu-Min", "display_name": "Tsou, Yu-Min" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/c31b-xm06", "abstract": "The formal potentials of several redox couples incorporated in coatings of a perfluorocarboxylate on graphite electrodes are measured and compared with the formal potentials of the same couples in homogeneous solution. For every redox couple investigated, the difference observed agrees with that calculated from the Nernst equation with the independently measured ratio of incorporation coefficients of the two halves of the couple. The dependences of the shifts in formal potentials on the nature of the incorporated complex ion, the ionic strength, and the temperature are also determined. They indicate that the incorporation equilibrium is governed by electrostatic and hydrophobic interactions that act in opposite directions. The incorporation of most cations examined is driven by large increases in entropy which overcome the usually unfavorable enthalpy changes.
\r\n\r\nThe mediated oxidation of ascorbate by Os(bpy)33+ incorporated in Nafion coatings on graphite electrodes is examined. Attempts to account for the magnitude of the mediated ascorbate oxidation currents in terms of current models and theories are only partially successful. As the ascorbate concentration is increased, the limiting oxidation currents at coated rotating disk electrodes do not increase as rapidly as expected on the basis of the models. Some possible reasons for this deviant behavior are suggested. The implications of the results on the general utility of Nafion-coated electrodes in electrocatalysis are presented.
\r\n\r\nThe heterobinuclear complex [formula; see abstract in scanned thesis for details] is synthesized and used as a probe to gain the insight into the diffusional behavior of redox reactants within polymeric coatings. Its diffusion coefficient within Nafion coatings is measured chronocoulometrically in all three of its possible redox states (RuIIILFeIII, RuIIILFeII, RuII LFeII). The three oxidation states exhibit large differences in their diffusional rates. Possible origins of the differences and their concentration dependences that are considered include intermolecular electron self- exchange, single- file diffusion and electrostatic cross-linking. Both enhancement and depression of charge transport rates produced by electron transfer cross-reactions between the fully oxidized and fully reduced complex are observed and compared with those calculated on the basis of a simple model. Reasonable agreement is obtained. The important effect that intermolecular cross-exchange reactions can exert on the diffusive flux of reactants is demonstrated.
" }, { "name": "Weston, Theresa Ann", "degree": "PhD", "year": "1985", "title": "The Regeneration of High Temperature Sulfur Dioxide Sorbents: the CO Reduction of Supported Alkali Sulfates", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032019-104846124", "creators": [ { "name": { "family": "Weston", "given": "Theresa Ann" }, "id": "Weston-Theresa-Ann", "orcid": "0000-0002-9822-7355", "display_name": "Weston, Theresa Ann" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Voecks", "given": "Gerald E." }, "id": "Voecks-Gerald-E", "orcid": "0009-0008-9371-5756", "role": "member", "display_name": "Voecks, Gerald E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/cen1-hb98", "abstract": "The chemical reactions involved in the regeneration step of a high temperature SO2 removal process have been investigated. In particular, the CO reduction of supported alkali sulfates has been studied. Thermogravimetric measurements have yielded the time-resolved composition of sorbent and gaseous products during reduction with 10% CO at 700 and 800\u00b0C. FTIR was used to identify reaction intermediates . A flow microreactor was used to compare gaseous product selectivity between SO2, COS and elemental sulfur of sorbents reduced with 1 and 10% CO at 700 and 800\u00b0C.
\r\n\r\nThe experimental results show regeneration; i.e., sulfur removal is greatly increased by the presence of lithium in the sorbent material. Reaction between the support and the alkali material greatly influences the degree of regeneration. Support materials are apparently active in the catalysis of the reduction of SO2 to elemental sulfur and the reaction between elemental sulfur and CO to form COS, and therefore, influences the product selectivity. A reaction scheme which qualitatively explains the experimental results is proposed.
\r\n" }, { "name": "Winniczek, Jaroslaw W.", "degree": "PhD", "year": "1985", "title": "Anisotropic Interaction Potentials between Helium and Linear Molecules from Crossed Beam Experiments", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:01222019-123545387", "creators": [ { "name": { "family": "Winniczek", "given": "Jaroslaw W." }, "id": "Winniczek-Jaroslaw-W", "display_name": "Winniczek, Jaroslaw W." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5nvw-ym37", "abstract": "Anisotropic interaction potentials between helium and linear molecules have been studied experimentally and theoretically to examine the relationship between the potential and the scattering differential cross-section, and to extract these potentials from crossed-molecular beam data.
\r\n\r\nChapter 2 presents the measurement of total (elastic and inelastic) differential scattering cross sections for He + CO2, CS2, OCS at a relative collision energy of about 65 meV with a crossed molecular beam apparatus. Anisotropic interaction potentials were extracted from these data, by way of an infinite order sudden approximation analysis. Several different anisotropic potential models were used in this analysis. The necessity for considering the anisotropy in the position of the well minimum as well as of its depth is demonstrated. A potential is proposed for He + OCS that reflects the symmetry of OCS, with a minimum number of modeling parameters.
\r\n\r\nIn Chapter 3 a detailed sensitivity analysis of the total and rotational state-to-state differential cross-section (DCS) is performed on an empirical potential energy surface for He + CO2. The infinite order sudden approximation is used to calculate the cross-sections. The sensitivity analysis consists of: 1) a large scale modification of the parameters that determine the anisotropic potential, and 2) an infinitesimal variation of these parameters to obtain a relative sensitivity function for the DCS. From these we demonstrate the effect each potential parameter has on the cross-sections. Despite the fact that this highly quantum system displays no classical effects such as rainbow scattering, we have shown that the quantal DCS oscillations contain significant information regarding the depth and width of the potential well and its anisotropy. Much of this information can be extracted from total-DCS scattering data. However the rotationally inelastic DCS contain a substantial amount of additional information regarding the shape of the potential energy surface.
\r\n\r\nSome of the conclusions reached in Chapter 3 indicate that the measuring of rotationally inelastic differential cross-sections can provide significantly greater insight into the nature of the potential than does the total DCS. In Chapter 4 we develop the means for simulating experimentally observable data from the potential for a given set of apparatus conditions. In Chapter 5 we describe modifications made to the crossed-beam apparatus in order to observe this inelasticity and present preliminary results for He + CO2.
" }, { "name": "Yang, Seung-Man", "degree": "PhD", "year": "1985", "title": "Hydrodynamics and Brownian Motion of Small Particles Near a Fluid-Fluid Interface", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-06302005-124544", "creators": [ { "name": { "family": "Yang", "given": "Seung-Man" }, "id": "Yang-Seung-Man", "display_name": "Yang, Seung-Man" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jvmx-rd64", "abstract": "The general problems of particle motion in the vicinity of a flat, non-deforming fluid interface is studied. The approximate singularity method used by previous workers in this research group has been generalized to consider the motion of a sphere in any linear velocity field compatible with the existence of the undisturbed flat interface, and the motion of slender rod-like particles which undergo an arbitrary translation or rotation in either a quiescent fluid or in a linear flow. The theory yields the hydrodynamic mobility tensors which are necessary to describe Brownian movement near a phase boundary, as well as general trajectory equations for sedimenting particles near a fluid interface with an arbitrary viscosity ratio. These approximate solution results are in good agreement with both exact-solutions where they are available and experimental data for motion of a sphere near a rigid plane wall. Among the most interesting results for motion of slender bodies is the generalization of Jeffery orbit equations for linear simple shear flow.
\r\n\r\nThe Brownian motion of a sphere in the presence of a deformable fluid interface is also examined. First, the fluctuation-dissipation theorem is derived for the random distortions of interface shape that are caused by spontaneous thermal impulses from the surrounding fluids. This analysis is carried out using the method of normal modes in conjunction with a Langevim type equation for the Brownian particle, and results in the prediction of autocorrelation functions for the location of the interface, for the random force acting on the particle (evaluated by a generalization of the Faxen's law), and for the particle velocity. The particle velocity correlation, in turn, yields the effective diffusion coefficient due to random fluctuations of the interface shape. Finally, we investigate the effects of interface deformation that are induced by the impulsive motion of a sphere that is undergoing Brownian motion. In this phase of our study, we consider both the spatially modified hydrodynamic mobility which occurs as a consequence of hydrodynamic interactions, and influence on the mean-square displacement of the Brownian particle of the interface relaxation back towards the flat equilibrium configuration after an initial deformation that is caused by the particle motion.
" }, { "name": "Zietlow, Thomas Christopher", "degree": "PhD", "year": "1985", "title": "Photophysics and Electrochemistry of d\u2074 Metal Clusters", "advisor": "Gray, Harry B.; Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042019-095546695", "creators": [ { "name": { "family": "Zietlow", "given": "Thomas Christopher" }, "id": "Zietlow-Thomas-Christopher", "display_name": "Zietlow, Thomas Christopher" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x6gp-2861", "abstract": "The metal-ligand and metal-metal interactions in d4 metal cluster systems have been examined using emission spectroscopy and electrochemical techniques. A detailed picture of the electronic structure of the hexanuclear molybdenum and tungsten clusters has not yet been achieved, but significant insight has been obtained through studying the effects of ligand, temperature, and molecular structure on the properties of the emissive excited state. Through these studies, and through analogy to the (d4)2 quadruply bonded molybdenum and tungsten dimers, the dynamics of the excited state, and its relevance to the chemistry out of that state, can be better understood.
\r\n\r\nThe work done on the excited state properties of the Mo6X2-14 (X = Cl, Br, I) clusters is outlined in Chapter 2. The energy of the emissive excited state is independent of halide ligand and is best described as a metallocalized state with very little ligand character. Energy transfer quenching data have determined that the emissive excited states are spin triplets.
\r\n\r\nThe unusual emissive behavior of the tungsten series W6X8Y2-6 (X, Y = Cl, Br, I) is discussed in Chapters 3 and 4. The energy of the emissive states order: W6Cl2-14 (1.83 eV) < W6Br2-14(1.85 eV) < W6I2-14(2.05 eV), the opposite trend from that expected by including charge transfer character into the transition. Variation of axial and facial halides leads to the conclusion that the \u00b53-bridging halides dominate the electronic structure of the cluster, but that the axial halides have a strong influence on the non-radiative rate. The structural studies show that the W-W bonds are longer in the W6I2-14 cluster than in the W6Cl2-14 structure, indicating that the metal-metal bond overlap is not the sole determining factor in the energy of the emitting excited states.
\r\n\r\nChapters 5, 6, and 7 describe the chemistry and properties of derivatives of these hexanuclear clusters. The W6Br-14 anion has been synthesized and its crystal structure determined. The effect of alkylphosphine ligands on the electrochemistry and photophysics of the Mo6Cl12 cluster has been found to be very small. Although the Mo5Xn-13 (n = 1, 2, 3) clusters do not appear to have any interesting photochemical properties, the observation of the splitting between spin-orbit states in a high nuclearity cluster has implications in the photochemistry of the hexanuclear clusters.
\r\n\r\nFinally, the last two chapters describe work done on the electrochemistry of Mo2X4 (PR3) 4 dimers. An unexpected ordering of the redox potentials is ascribed to \u03c0-backbonding from the metal center to the halide ligand. Efficient electrogenerated chemiluininescence has been observed for several of these dimers.
" }, { "name": "Zinck, Jennifer Joanne", "degree": "PhD", "year": "1985", "title": "A Study of the Dynamics of the Interaction of CH\u2084 with the (111) Surface of Rh and the (110) Surface of Ir", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032019-120826233", "creators": [ { "name": { "family": "Zinck", "given": "Jennifer Joanne" }, "id": "Zinck-Jennifer-Joanne", "display_name": "Zinck, Jennifer Joanne" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wzmc-9m54", "abstract": "A study of the dynamics associated with the activated dissociative adsorption of CH4 on the (111) surface of Rh and the (110) surface of Ir has been performed in ultrahigh vacuum (UHV), using laser excitation and molecular beam techniques.
\r\n\r\nChapter 2 describes an experiment in which gas phase CH4 is laser excited to the \u03bd3 excited vibrational state (8.63 kcal/mole) in a collisionless environment, and also, collisionally deactivated to the 2\u03bd4 state (7.46 kcal/mole), in a He atmosphere. Hydrogen thermal desorption spectra from a Rh(111) surface exposed to the excited gas indicate that. within the experimental limits of detection, no enhancement of dissociative adsorption of CH4 is obtained by excitation to the \u03bd3, 2\u03bd4 (or \u03bd4) vibrational states.
\r\n\r\nChapter 3 consists of the description of an ultrahigh vacuum-molecular beam apparatus constructed for the study of gas-surface dynamics. The ultrahigh vacuum chamber is a three level system of custom design. Level I is a load lock for introducing and retrieving the sample, to and from the UHV chamber. The molecular beam axis crosses the UHV chamber at Level II, and also crosses the axis of the ionizer of a quadrupole mass spectrometer detector. Low-energy electron diffraction optics are also mounted at Level II. Auger electron spectroscopy may be performed at Level III. An extended travel UHV sample manipulator has been designed and constructed, which allows translation of the sample to all three levels of the UHV system. The molecular beam line is of a nozzle source design, with three separate chambers which are pumped differentially. A chopper motor, for incident beam modulation, is mounted in the third beam chamber directly adjacent to the UHV chamber, and allows time-of-flight measurements.
\r\n\r\nChapter 4 describes an experiment in which the role of translational energy in the chemisorption of CH4 on Ir(110) is studied via the use of molecu1ar beams of CH4 seeded in H2 and He. A probability of dissociative adsorption below 10-4 is associated with a CH4 beam which has an average translational energy of approximately 10 kcal/mole.
\r\n\r\nThe results of Chapters 2 and 4 point to the existence of a barrier to dissociative adsorption of CH4 that is greater than 10 kcal/mole of total energy, on the surfaces studied. A combination of vibrational and translational activation of CH4 may be required for dissociative adsorption on Rh(111) and Ir (110).
" }, { "name": "Askew, Deidre Ann", "degree": "Masters", "year": "1984", "title": "Electrochemistry of Adsorbed Organic Dye Molecules", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-082538471", "creators": [ { "name": { "family": "Askew", "given": "Deidre Ann" }, "id": "Askew-Deidre-Ann", "display_name": "Askew, Deidre Ann" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3yjq-7a97", "abstract": "Molecular luminescence has been used to study the mechanism of charge transfer in electrode-bound films and coatings. This sensitive, fast technique enables one to observe occurrences on the electrode surface which could not be observed with conventional electrochemical or spectroelectrochemical methods. In general, electrodes should be excellent quenchers of fluorescence due to energy transfer or electron transfer. We want to examine the mechanism of the surface quenching of the fluorescence. By reproducibly adsorbing a known amount of an organic dye of high quantum yield to the electrode surface, one should be able to determine if electron transfer is a pathway in the quenching mechanism by varying the potential of the electrode. This report describes the electrochemistry of several organic dyes adsorbed on graphite electrodes which could be used for the luminescence studies. Methylene blue adsorption and electrochemistry are studied in detail. The methylene blue system is excellent in terms of adsorption characteristics. Adsorption isotherms are presented which show the range of surface coverage, \u0393, that one can achieve. Methylene blue also has clean reversible electrochemistry to facilitate spectroelectrochemical experiments. However, methylene blue has a small fluorescence quantum yield and short fluorescence lifetime. This may make it a poor choice for luminescence experiments. Several other organic dyes were studied. While their electrochemistry is not as clean as that of methylene blue, their fluorescence quantum yields are much higher." }, { "name": "Audett, Jay Douglas", "degree": "PhD", "year": "1984", "title": "(2,2-Dimethylcyclopropyl)carbinyl Grignard Reagents and the Reactivity of Osmium Tetraoxide and Peroxycarboxylic Acids with Low Valent Iridium Compounds", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122018-101217195", "creators": [ { "name": { "family": "Audett", "given": "Jay Douglas" }, "id": "Audett-Jay-Douglas", "display_name": "Audett, Jay Douglas" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/z4g9-cb82", "abstract": "The formation and rearrangement of Grignard reagents from (2,2-dimethylcyclopropyl)carbinyl halide have been studied. The Grignard reagent from the chloride, 2,2-dimethyl-3-butenyl-1-magnesium chloride, demonstrates the carbanionic influence on the Grignard rearrangement. The bromide yielded no Grignard reagents, only the disproportionated hydrocarbons 4-methyl-1-pentene and 2-methyl-1,4-pentadiene. The dominating radical side reactions for the bromide may be attributed to the weaker carbon-bromine bond which gives rise to complete bond rupture\r\naccompanying single-electron transfer from magnesium.
\r\n\r\nThe reactions of several oxidizing agents with Vaska's complex and its derivatives have been investigated. Interesting results with osmium tetraoxide and peroxycarboxylic acids are described. Osmium tetraoxide reacts with Vaska's complex in the presence of pyridine to form a dinuclear, bridging carbon dioxide complex. Characterization is accomplished with 13C,31P, and 1H NMR, in addition to infrared labeling studies. Derivatization of\r\nthis complex with methyl trifluoromethanesulfonate resulted in amethylation of the carbon dioxide moiety giving the structurally characterized dinuclear carbene complex. The reaction of peroxycarboxylic acids with Vaska's complex under a variety of conditions has yielded a series of compounds. When Vaska's complex is exposed to at least two equivalents of\r\nperoxycarboxy lie acid, carbon monoxide is oxidized to carbon dioxide and the iridium product is chlorobis(m- chlorobenzoato)bis(triphenylphosphine)-iridium(III). When the reaction is performed in the presence of excess tetrafluoroboric\r\nacid, carbon monoxide oxidation is prevented and the observed\r\nproduct is chloro(m-chlorobenzoato)carbonylbis(triphenylphosphine)iridium(III)\r\ntetrafluoroborate. The p-methylbenzoato analogue of this compound has been structurally characterized, and the reactions of nucleophiles with these iridium cations are described. The series of reactions performed with peroxycarboxylic acid suggest a previously unconsidered mechanism for the formation of chlorobis(m-chlorobenzoato)bis(triphenylphosphine)iridium(III)\r\nfrom Vaska's complex and the peroxycarboxylic acid.
\r\n" }, { "name": "Banerjee, Utpal", "degree": "PhD", "year": "1984", "title": "Alamethicin: Secondary Structure in Solution and Interactions with Phospholipid Membranes", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292018-120530235", "creators": [ { "name": { "family": "Banerjee", "given": "Utpal" }, "id": "Banerjee-Utpal", "display_name": "Banerjee, Utpal" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9y1x-zh89", "abstract": "The icosapeptide alamethicin [sequence included in scanned thesis' abstract, p. v] isolated from the fungus Trichoderma viride induces voltage-gated ionic conductance in black lipid film membranes (Latorre, R. & Alvarez, D. (1981) Physiol. Rev. 61, 77). Single-channel measurements have indicated that passive ion transport across membranes is mediated by alamethicin channels that fluctuate between several conduction states. While these studies provide phenomenological description of the nature of alamethicin-assisted ionic conduction, very few studies probed the molecular structure of this peptide and the nature of its interaction with lipid membranes. These issues are addressed in the present investigation.
\r\n\r\nAn analysis of the proton magnetic resonance spectrum is undertaken. Two-dimensional NMR is employed to achieve a complete assignment of the protons in the molecule to NMR resonances. The spectral assignment is a necessary first step towards molecular interpretations.
\r\n\r\nMeasurement of coupling constants and two-dimensional NOE's suggest a half-helical, half-extended dimeric structure for the molecule in methanol. This proposed model for the secondary structure, consistent with the NMR data as well as a line of other experimental observations erstwhile published, predicts that (a) the amide protons of residues 15 through 20 are intermolecularly hydrogen-bonded with the corresponding residues of the opposing molecule to create a rigid, extended parallel \u03b2-pleated structure for the C-terminal end of the molecule; (b) the proline at position 14 breaks the continuity of this structure, and amino acids 10 through 14 are forced into an open, non-hydrogen-bonded conformation, and (c) amino acids 3 through 9 are folded into an \u03b1-helix, with Gln-7 side chains from the two strands in the right juxtaposition to facilitate a hydrogen bond between them. The resultant structure is highly amphipathic: one face is completely hydrophobic with the aliphatic side chains exposed, whereas the other face is primarily hydrophilic with polar side chains and peptide groups lining the extended \u03b2-sheet region.
\r\n\r\nThe dimeric structure is further supported by relaxation measurements that indicate that the N-acetyl methyl groups at the N-termini of the two helices in the dimer have distinct proton spin-spin relaxation times. This difference is eliminated once the dimers are dissociated with urea.
\r\n\r\nSpectral assignments in water are complicated by broadened NMR signals due to aggregation. Standard two-dimensional and decoupling techniques for assignments are inadequate for this case. A successful assignment is achieved by solvent titration from methanol. No changes in coupling constants are noted during the titration, and it is expected that the conformation in water is similar if not identical, to that in methanol. Relaxation measurements in water are consistent with a tightly bound dimeric unit that micellises to larger aggregates.
\r\n\r\nThe interaction of alamethicin with multilayers is inferred from a spectroscopic investigation of the phospholipid bilayer prepared from dimyristoyllecithin (DML) in the presence and absence of alamethicin, and, for contrast, in the presence of other membrane active molecules. The dynamics and conformation of phospholipid head group and chains are examined by P31 and H2 NMR. A P31 line shape calculation has helped identify the dependence of the spectrum on various motional, relaxation and conformational parameters.
\r\n\r\nAs part of the investigation of lipid packing and dynamics in membranes, small bilayer vesicles are also studied. Proton NMR indicates that the outside-facing and inside-facing leaflets of the bilayer in small vesicles have lipids packed in different densities. This is due to the differences in the extent and sign of curvature of the two leaflets. At the high field at which this NMR study is undertaken, the differences in packing show up as distinct proton peaks from the inside and outside chain methylene and methyl groups nthat differ in width and in chemical shift.
\r\n\r\nFinally, the interaction of alamethicin with DML multilayers is characterized by P31, H2 and H1 NMR and Raman spectroscopy. The reduction in chemical shift anisotropy (\u0394\u03c3) of the P31 signal is interpreted in terms of an interaction of the peptide at the water-membrane interface that causes a change in the average head group orientation. Deuterium NMR shows no changes in quadrupolar splittings (and hence C-D order parameters) of the chain deuterons, and Raman spectroscopy shows no change in the gauche-trans ratio of methylene segments in the chain. These results are contrasted with P31 and H2 NMR of the gramicidin S/DML system that shows polymorphism due to partial disruption of the multilayer structure and the chlorophyll A/DML system that exhibits a 7\u00b0 C change in phase transition temperature as a clear indication of incorporation of the phytol chain into the bilayer.
\r\n\r\nTaken together, these experiments unequivocally indicate that the peptide interacts with lipid bilayers at the lipid-water interface. The proposed amphiphilic aggregated solution structure for the peptide is ideally suited for such an interaction. Inasmuch as the conductance characteristics of alamethicin are only explained in terms of transmembrane pore formation, it is proposed that the large dipole moment of this aggregate facilitates the transfer of the peptide into the bilayer once a gradient of field is applied.
\r\n" }, { "name": "Bartroli, Javier Francisco", "degree": "PhD", "year": "1984", "title": "Stereoselective Aldol Condensations via Boron Enolates. The Syntheses of (+)-Prelog-Djerassi Lactone and (+)-Tylonolide", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11092018-094859390", "creators": [ { "name": { "family": "Bartroli", "given": "Javier Francisco" }, "id": "Bartroli-Javier-Francisco", "display_name": "Bartroli, Javier Francisco" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3v27-xh37", "abstract": "The use of boron enolates of chiral N-acyl oxazolidinones i and ii in highly stereoselective aldol condensations is described. Mild base hydrolysis of the products affords optically pure erythro \u03b2-hydroxy acids and the chiral auxiliary, which can be reconverted into i or ii in one step.
\r\n\r\nThe utility and scope of these reactions is demonstrated by the total syntheses of (+)-Prelog-Djerassi lactone and (+)-Tylonolide, cyclic 5,20-hemiacetal .
\r\n\r\n[Chemical structures included in scanned thesis' abstract, p. v.]
\r\n" }, { "name": "Bassett, Mark Elliott", "degree": "PhD", "year": "1984", "title": "Mathematical Modeling of Atmospheric Aerosol Equilibria and Dynamics", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11092005-105529", "creators": [ { "name": { "family": "Bassett", "given": "Mark Elliott" }, "id": "Bassett-Mark-Elliott", "display_name": "Bassett, Mark Elliott" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "member", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9mvc-2t06", "abstract": "Atmospheric aerosols consist of submicron-sized particles occurring at number concentrations of the order of 105 cm-3 and mass concentrations of the order of 100 \u00b5g m-3. These aerosols, when occurring in urban areas, consist of aqueous solutions of sulfate, nitrate, ammonium, organic constituents, and certain metals. This thesis is a contribution toward our ability to describe mathematically the formation and growth of such atmospheric aerosols. Since a substantial fraction of the mass of urban aerosols consists of sulfate, nitrate, ammonium and water (Stelson and Seinfeld, 1981), the description of the dynamics of such an aerosol is an important place to initiate the development of aerosol models. The size and composition distribution of atmospheric aerosols are governed by a combination of thermodynamics and kinetics. A detailed treatment of the thermodynamics of the atmospheric sulfate/nitrate/ammonium/water system is presented. Based on this treatment, models are developed to predict the equilibrium quantity, composition, state, and size of the aerosol given gas phase properties. Aerosol kinetics are approached by solution of the General Dynamic Equation for the aerosol sized distribution using the sectional method of Gelbard and Seinfeld. In the most general kinetic model presented, the evolution of the size and composition of an atmospheric sulfate aerosol is predicted under power plant plume conditions. Users manuals for the computer codes comprising the models developed here are given in the Appendix.
" }, { "name": "Berry, Donald Harry", "degree": "PhD", "year": "1984", "title": "Studies of the Reactivity of Permethylzirconocene Complexes with Binuclear Transition Metal Carbonyl Compounds", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242018-111901394", "creators": [ { "name": { "family": "Berry", "given": "Donald Harry" }, "id": "Berry-Donald-Harry", "orcid": "0000-0001-6732-3726", "display_name": "Berry, Donald Harry" } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/yahb-n031", "abstract": "The low valent permethylzirconocene complex {Cp*2ZrN2}2N2 (Cp*\u2261\u03b75-C5Me5) reacts with binuclear transition metal carbonyl compounds of the general formula Cp2M2(CO)x (Cp\u2261\u03b75-C5H5) to produce trinuclear complexes. Two major modes of reactivity are observed. Compounds with M-M bonds that are easily reduced such as (CpM(CO)3)2 (M = W, Mo) react with {Cp*2ZrN2}2N2 to produce trinuclear species in which two CpM(CO)3 anions are connected to a Cp*2Zr dication via \u00b52-(C-\u03b71; O-\u03b71) carbonyl bridges. The structure of the molybdenum complex has been determined by single crystal X-ray diffraction methods. These trinuclear complexes are also produced in the reaction of the Cp*2ZrRR'(R,R' = H,alkyl) with two equivalents of the hydride complexes CpM(CO)3H\u00b7 The dinuclear complexes Cp*2M(H)(CpMo(CO)3)(M = Zr, L = PMe3; M = Hf, L = CO) have been similarly prepared by treatment of the zirconium or hafnium dihydride with the corresponding molybdenum hydride. The trinuclear complexes react with HX (X = Cl, OH) to produce CpM(CO)3H and Cp*2ZrX2.
\r\n\r\nThe other mode of reactivity between {Cp*2ZrN2}2N2 and metal dimers is observed with (CpM(CO)2)2 (M = Fe, Ru). In these cases trinuclear complexes are produced in which two carbonyl ligands are reductively coupled yielding an O2C2 moiety bridging the three metals. This coupling is reversible and the Zr(II) intermediate can be trapped with CO or other metal dimers. The iron analog is also produced in the reaction of Cp*2ZrI2 with Na(CpFe(CO)2).
\r\n\r\nThe reaction of {Cp*2ZrN2}2N2 with the bridging methylene complex cis-Cp2Ru2(CO)3(CH2) does not result in carbonyl coupling, yielding instead what appears on the basis of spectroscopic data to be a \u03c0-complex between permethylzirconocene and cis-Cp2Ru2(CO)3(CH2) held together only by \u00b52-(C-\u03b71; C,O-\u03b72) bridging carbonyl ligands.
\r\n\r\nThe ruthenium carbonyl coupled product, Cp*2Zr(O2C2)Ru2Cp2(CO)2, reacts under H2 to produce the bridging zirconoxy carbene complex trans-Cp2Ru2(CO)3(C(H)OZr(H)Cp*2). This complex is fluxional on the 1H and 13C NMR timescales. \u0394G\u2021 for this process is 14.0(2) kcal\u00b7mol-1 at -4\u00b0C. The fluxionality is best explained by a process involving a terminal carbine intermediate. The carbene formation is reversible, and treatment with D2 results in label incorporation in both the hydride and carbene hydrogen positions. Reaction with CO produces Cp*2Zr(CO)2, (CpRu(CO)2)2 and presumably H2. Treatment with BF3 or HBF4 results in C-O scission and produces the bridging methylene complex Cp2Ru2(CO)3(CH2). Labeling studies indicate both methylene hydrogens originate on zirconium. This bridging methylene complex can be synthesized in 60% yield by treatment of (CpRu(CO)2)2 with LiBEt3H in toluene.
\r\n" }, { "name": "Brinza, David Edward", "degree": "PhD", "year": "1984", "title": "I. Millimeter Microwave Spectroscopy of Radicals. II. Laser Spectroscopy of the Van der Waals Molecule Ne-Cl\u2082", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242018-130045424", "creators": [ { "name": { "family": "Brinza", "given": "David Edward" }, "id": "Brinza-David-Edward", "display_name": "Brinza, David Edward" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Pickett", "given": "Herbert M." }, "id": "Pickett-H-M", "role": "member", "display_name": "Pickett, Herbert M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/b03t-1z96", "abstract": "The temperature dependence of the linewidth parameter for the pressure broadening of ClO rotational transitions was investigated. As determined from millimeter microwave spectroscopy, the value of the linewidth parameter at 218 K is 4.44\u00b10.23 MHz/torr. The width parameter varies according to T-0.75\u00b10.2 over the temperature range 200-350 K. A similar study was carried out for oxygen self-broadening and broadening by nitrogen. The stronger temperature dependence for the self-broadened case suggests a resonant spin-flip or exchange process is important in the collisional broadening.
\r\n\r\nThe measurement of microwave spectra of the CS radical, as produced in the ArF excimer laser photolysis (193 nm) of CS2 was attempted. No spectra for the vibrationally excited CS molecules produced in the photolysis could be observed, presumably due to relatively slow rotational relaxation of the CS fragment.
\r\n\r\nThe van der Waals molecule Ne-Cl2 has been studied by molecular beam laser spectroscopy. Fluorescence features ~6 cm-1 to higher energy of the Cl2B-X band origins are attributed to Ne-Cl2. Band shape analysis supports a T-shaped molecular structure. The metastable vibrationally excited molecule Ne-Cl2(X1 \u03a3+, \u03bd\" = 1) has been spectroscopically observed. The time-of-flight from the nozzle indicates the lifetime of the complex to be greater than 10-5 sec.
\r\n" }, { "name": "Buttry, Daniel Alan", "degree": "PhD", "year": "1984", "title": "Effects of Electron Exchange on the Photochemical, Electrochemical and Electrocatalytic Responses of Polymer Modified Electrodes ", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312018-105602325", "creators": [ { "name": { "family": "Buttry", "given": "Daniel Alan" }, "id": "Buttry-Daniel-Alan", "orcid": "0000-0002-6915-6914", "display_name": "Buttry, Daniel Alan" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/x5vq-d546", "abstract": "A spectroelectrochemical method is presented which may be used to measure the concentrations of the two oxidation states of a redox couple in a polymer film. The method is applied to Ru(bpy)32+ in Nafion films on transparent tin oxide electrodes. Measurements of the emission of this complex in Nafion films on graphite and tin oxide electrodes are used to obtain information about the quenching of Ru(bpy)32+* by Ru(bpy)33+. Features of the luminescence which yield insight into the structure of the Nafion film are discussed.
\r\n\r\nExperiments are described which bear on the question of when electron self-exchange reactions can contribute to the propagation of electrons through polymer films on electrodes. The results of experiments on the Co(bpy)32+/+ couple are discussed in terms of a theory derived by Dahms and Ruff et al. which describes the contribution of electron self-exchange reactions to diffusion in mixtures containing both halves of a redox couple.
\r\n\r\nThe propagation of charge through polymer films by electron exchange cross-reactions between different redox couples which are co-incorporated into a polymer film on an electrode is discussed. Two experimental examples of this phenomenon are presented.
\r\n\r\nAn electrocatalytic application of a polymer modified electrode is described. Cobalt tetraphenylporphyrin is incorporated into a Nafion film on a graphite electrode, and this porphyrin is used to catalyze the two-electron electroreduction of dioxygen. Enhanced catalytic currents are observed when an electron mediator (Ru(NH3)63+) is added to the film. This mediator serves to shuttle electrons between the electrode and the relatively immobile catalyst sites. The performance of electrocatalysts in polymer films is discussed with emphasis on ways to enhance stability without sacrificing efficiency.
" }, { "name": "Casassa, Michael Paul", "degree": "PhD", "year": "1984", "title": "Infrared Photodissociation of Van der Waals Molecules", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262018-123200794", "creators": [ { "name": { "family": "Casassa", "given": "Michael Paul" }, "id": "Casassa-Michael-Paul", "display_name": "Casassa, Michael Paul" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Samson", "given": "Sten Otto" }, "id": "Samson-Sten-Otto", "role": "member", "display_name": "Samson, Sten Otto" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n43s-1339", "abstract": "Infrared photodissociation of van der Waals molecules is investigated using low power cw infrared lasers. Information gained concerns the dynamics of vibrational predissociation and the van der Waals interactions. Clusters formed in supersonic molecular beams are irradiated for approximately 0.5 msec and the fraction of clusters remaining intact is measured as a function of laser wavelength and power. Detailed homogeneous and inhomogeneous line shape models are presented and used to analyze the results. Effects such as fluence broadening and orientational inhomogeneity are described.
\r\n\r\nVan der Waals molecules studied include dimeric clusters of ethylene with rare gases, hydrogen halides and non-hydrogen bonding polyatomic molecules. Homogeneous widths of clusters excited near the \u03bd7 frequency of free ethylene correspond to lifetimes ranging from 0. 44 psec for (C2H4)2 to greater than 10 psec for Ne\u2022C2H4. These are attributed to vibrational predissociation constrained by conservation of angular momentum. Other conceivable broadening mechanisms are discussed.
\r\n\r\nSpectra obtained by exciting the \u03bd7 mode in different types of ethylene clusters are quite dissimilar. Lineshape analysis indicates that the \u03bd7 transition in (C2H4)2 occurs as a hybrid band. The same transition in (C2H4\u00b7HF occurs as a perpendicular band. The rare gas-ethylene clusters are less rigid than the others and excitation of hindered internal rotation of C2H4 accompanies the \u03bd7 absorption. All of the ethylene clusters exhibit blue shifts and intensity enhancement, as compared to \u03bd7 absorption by free ethylene, which are attributed largely to electrostatic interactions.
\r\n" }, { "name": "Clark, Douglas S.", "degree": "PhD", "year": "1984", "title": "Molecular Level Investigations and Mathematical Modeling of Immobilized \u03b1-Chymotrypsin Preparation, Utilization and Deactivation", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11082005-133605", "creators": [ { "name": { "family": "Clark", "given": "Douglas S." }, "id": "Clark-Douglas-S", "orcid": "0000-0003-1516-035X", "display_name": "Clark, Douglas S." } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "chair", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/0z80-4946", "abstract": "Radiation-mediated grafting of polyacrolein onto polymethyl methacrylate microspheres activated the particles for chymotrypsin immobilization. Treatment of porous polystyrene/magnetite particles with polyacrolein produced very small enzyme loading enhancement and significantly increased substrate diffusional resistance. These results nonetheless demonstrate the feasibility of obtaining grafted materials and of utilizing this approach to improve the capacity of microspheres for protein immobilization.
\r\n\r\nEnzyme immobilization on a more conventional support material, CNBr-activated Sepharose 4B, was studied extensively. Specific activities and the amounts of active immobilized enzyme were determined for several different preparations of \u03b1-chymotrypsin immobilized on CNBr-activated Sepharose 4B. Electron paramagnetic resonance (EPR) spectroscopy of free and immobilized enzyme with a spin label coupled to the active site was used to probe the effects of different immobilization conditions on the immobilized enzyme active site configuration. Specific activity of active enzyme decreased and rotational correlation time of the spin label increased with increasing immobilized enzyme loading. Enzyme immobilized using an intermediate six-carbon spacer arm exhibited greater specific activity and spin label mobility than directly coupled enzyme. The observed activity changes due to immobilization were completely consistent with corresponding active site structure alterations revealed by EPR spectroscopy.
\r\n\r\nWhen EPR spectra were recorded in the presence of indole, direct evidence for the existence of two distinct forms of active \u03b1-chymotrypsin immobilized on CNBr-activated Sepharose 4B was obtained. The indole EPR spectra of five different spin-labeled immobilized enzyme formulations were all resolved into the same two spectral components. Both subpopulation spectra were approximately identified experimentally, and the subpopulation exhibiting greatly restricted spin-label motion was shown also to be relatively inaccessible to solvent. Using overall specific activity data and subpopulation fractions from EPR spectral analysis, the specific activity of the more constricted immobilized enzyme active form was shown to be approximately fifteen times smaller than that of the other class of immobilized enzyme molecules with an indole EPR spectrum similar to that of chymotrypsin in solution. Variations in overall specific activity of formulations with different loadings and different supports result entirely from changes in the proportions of the same two subpopulations of immobilized enzyme molecules.
\r\n\r\nDeactivation in aliphatic alcohols of \u03b1-chymotrypsin and \u03b1-chymotrypsin-CNBr Sepharose 4B conjugates was also studied by several characterization methods. Active site titration measurements, which were used to determine the amount of catalytically active enzyme, revealed appreciable differences between the deactivation kinetics of free and immobilized chymotrypsin. In all cases for the immobilized enzyme, the kinetics of active enzyme disappearance differed significantly from first-order. Interestingly, the estimated intrinsic activity of immobilized chymotrypsin remaining active after different exposure times to 50% n-propanol solution increased somewhat as a result of exposure to alcohol. These findings were complemented by direct information, provided by EPR spectroscopy, on the effects of alcohols on the active site configuration of spin-labeled chymotrypsin. EPR spectra of the free enzyme illustrated the appearance in different alcohol solutions of different enzyme forms with different active site structures. EPR experiments also showed that denaturation of immobilized chymotrypsin was accompanied by unfolding of the active site that followed similar multistep kinetics as the loss of active enzyme.
\r\n\r\nFurther insight into the deactivation in 50% n-propanol of immobilized \u03b1-chymotrypsin was provided by analyses that focused on the behavior of the two distinct active forms of immobilized enzyme, designated here A and B, identified previously. Raw data provided by EPR spectroscopy clearly show that the relative quantities of active chymotrypsin-A and active chymotrypsin-B change as a result of exposure to alcohol, with the relative quantity of the B form increasing with time. These and additional results provide evidence that the distribution of A and B forms is a function of active enzyme loading but independent of the means used to obtain the loading. Different kinetic models in conjunction with experimental observations consistently indicate that the activity of enzyme form B, by far the more active enzyme form, does not change significantly during the initial 60 min. of catalyst deactivation but then decreases appreciably.
\r\n\r\nFinally, theoretical analyses of enzyme immobilization, more general in scope than the \u03b1-chymotrypsin work, were also performed. Enzymes are often immobilized on the internal surfaces of porous solid supports by immersing enzyme-free particles in a well-mixed solution of enzyme. The ensuing impregnation process involves coupled transient mass transfer and surface attachment of enzyme. Mathematical models were employed to explore the influences of process parameters on the amount of enzyme loaded and the distribution of immobilized enzyme within the support particles. Nonuniform loading of the support occurs under some conditions, particularly when diffusion of unattached enzyme through the support is restricted by the large size of the enzyme relative to the accessible cross-sectional area of the support's pores. This is significant since the distribution of enzyme within the support particle influences the overall activity and stability of the immobilized enzyme catalyst. The models developed here may also be used to describe removal of reversibly immobilized enzyme during washing or utilization of the immobilized enzyme catalyst.
" }, { "name": "Durand, Richard Raymond, Jr.", "degree": "PhD", "year": "1984", "title": "Catalysis of the Electroreduction of Dioxygen by Monomeric and Dimeric Cobalt Porphyrins", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072016-152635305", "creators": [ { "name": { "family": "Durand", "given": "Richard Raymond, Jr." }, "id": "Durand-Richard-Raymond", "display_name": "Durand, Richard Raymond, Jr." } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/h738-ft41", "abstract": "Mechanistic aspects of the catalytic electroreduction of dioxygen by monomeric and dimeric cobalt porphyrins were investigated. The catalysts were examined while either adsorbed to graphite electrodes or dissolved in concentrated acids.
\r\n\r\nMonomeric cobalt(II) porphyrins adsorbed to graphite electrodes were found to reduce dioxygen to hydrogen peroxide. Cyclic and rotating disk voltammetry were used to examine the kinetics and mechanism of the catalyzed reactions. These monomeric catalysts exhibited behavior atypical of simple redox catalysis.
\r\n\r\nThe mechanisms by which the reduction of dioxygen at graphite electrodes is catalyzed by cofacial dicobalt and related porphyrins has been investigated. The products of the reductions, the electrode potential where the reduction proceeds and the mechanistic role of protons were among the topics examined. A comparison of the behavior of several new cofacial metalloporphyrins has led to a more detailed proposal for the mechanisms by which they operate.
\r\n\r\nMonomeric and dimeric cobalt porphyrins have been dissolved in trifluoromethanesulfonic acid (5.6 M) and concentrated phosphoric acid without demetalation. The electrocatalytic reduction of dioxygen by solutions of the catalysts was examined by rotating disk and ring-disk voltammetry. The dissolved metalloporphyrins provide improved stability to the catalysts.
\r\n\r\nThe reaction of a cobalt(II) complex with superoxide was examined electrochemically in a non-aqueous electrolyte. The affinity of superoxide for cobalt(II) has been demonstrated by cyclic voltammetry. The results of this study were related to mechanisms of dioxygen reduction in aqueous media.
" }, { "name": "Fitzsimmons, Brian Joseph", "degree": "PhD", "year": "1984", "title": "The Total Synthesis of the Enantiomer of Lasalocid A", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12072018-114316546", "creators": [ { "name": { "family": "Fitzsimmons", "given": "Brian Joseph" }, "id": "Fitzsimmons-Brian-Jopseph", "display_name": "Fitzsimmons, Brian Joseph" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/w5gn-5650", "abstract": "A convergent total synthesis of the enantiomer of the\r\nnaturally occurring polyether antibiotic Lasalocid A (X-537A) and preliminary results of the biological testing of this compound are reported.
\r\n" }, { "name": "Goodgame, Marvin Mark", "degree": "PhD", "year": "1984", "title": "Exchange Forces in Transition-Metal Bonding", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232009-150307132", "creators": [ { "name": { "family": "Goodgame", "given": "Marvin Mark" }, "id": "Goodgame-Marvin-Mark", "display_name": "Goodgame, Marvin Mark" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "McGill", "given": "Thomas C." }, "id": "McGill-T-C", "role": "member", "display_name": "McGill, Thomas C." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xs72-nm31", "abstract": "We have examined multiple bonds (\u03c3, \u03c0, and \u03b4) to transition metals and find that intra-atomic exchange forces on these metals are crucial for correct prediction of ground states and that a proper description of these terms is required for a quantitative understanding of bond energies.
\r\n\r\nOur calculations on models for bridged Fe porphyrin dimers show that intra-atomic exchange forces on the Fe's are critical to the explanation for the dramatic differences in the Fe-Fe coupling for \u00b5-oxo and \u00b5-nitrido bridged Fe porphyrin dimers. The qualitative bonding concepts obtained are used to predict properties of the \u00b5-carbido bridged Fe porphyrin dimer.
\r\n\r\nIn most cases, the interactions responsible for bonding lead to antifer'romagnetic coupling between the d orbitals localized on adjacent centers, resulting in overall low-spin couplings. However, some extended metal systems (eg. metallic Ni) lead to net ferromagnetic interactions between d orbitals localized on different centers. In order to elucidate these effects, we have examined the direct and indirect d-d couplings in the Ni4 cluster as a function of bond distance. We find that ferromagnetic coupling dominates in a region of bond distance around the bulk Ni value of 2.5 \u00c5 with antiferromagnetic coupling dominating for short R (by 2.0 \u00c5) and for long R (by 3.5 \u00c5). The dominant interactions responsible for ferromagnetic coupling involve spin polarization of the conduction band (s-like), supporting a model for ferromagnetism in bulk metallic systems very similar to the Ruderman-Kittel model for magnetic impurities.
\r\n\r\nThe dimers Cr2 and Mo2 provide the most dramatic illustration of the importance of exchange forces in bonding. With six unpaired electrons on each atom, there is the potential for up to six covalent bonds. However, formation of d-d covalent bonds requires a concomitant loss in intra-atomic d-d exchange energy. The net result is a double well where the long-R minimum (3 \u00c5 is dominated by s-s pairing (no loss of intra-atomic d-d terms) while the short-R minimum (1.7 to 1.9 \u00c5) involves a strong quintuple bond of d orbitals plus an antibonding s-s interaction. To properly handle the intra-atomic exchange terms during this transition from long R with local high-spin coupling to small R with dominant singlet pairing within bonding pairs presents a formidable challenge to ab initio computation. To carry out such studies, we have extended the GVB and related approaches of ab initio calculations and have also developed a simple approximate method of including the electron correlation missing in GVB wavefunctions that provides a quantitatively accurate description of these systems.
\r\n\r\nThe effects studied here should be of comparable importance for multiple bonds involving transition metals, lanthanides, and actinides bonding to each other and to such ligands as CR2, CR, O, N, and NR. Correlation terms beyond GVB are most important for the least electronegative ligands. Thus, the proper treatment of intra-atomic exchange and of interatomic d-d coupling should be of considerable importance in studies of heterogeneous and homogeneous catalytic systems.
" }, { "name": "Gray, Murray Ross", "degree": "PhD", "year": "1984", "title": "The Effects of Moisture and Ash Content on the Pyrolysis of a Wood Derived Material", "advisor": "Flagan, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11152005-102832", "creators": [ { "name": { "family": "Gray", "given": "Murray Ross" }, "id": "Gray-Murray-Ross", "orcid": "0000-0003-2431-7312", "display_name": "Gray, Murray Ross" } ], "advisors": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "advisor", "display_name": "Flagan, Richard C." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Qader", "given": "Shaik A." }, "id": "Qader-Shaik-A", "role": "member", "display_name": "Qader, Shaik A." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZEMV-CV64", "abstract": "Moisture and ash are always present in wood to some extent, but their affect on its chemical behavior is not fully known. The influence of moisture and ash on the thermal degradation of wood was investigated by pyrolyzing samples of ground wood waste in a batch fluid-bed reactor at between 320 and 470\u00b0C in helium at 101-104 kPa. The wood samples were heated at about 300\u00b0C/min. so that drying and pyrolysis were simultaneous, Woodex\u00ae pellets were used in this study because their density was suitable for fluid-bed tests.
\r\n\r\nIn ash-free samples moisture suppressed the formation of pyrolysis tar at temperatures above 390\u00baC and increased the yield of char, relative to dry samples. A model for the behavior of free radicals during pyrolysis is proposed which gives qualitative agreement with the observed effect of temperature. The ion-exchange capacity of wood was used to disperse calcium atoms in the polymer matrix, which increased the formation of aqueous product during pyrolysis at the expense of tar by enhancing dehydration and fragmentation reactions. The native mineral components in the wood waste gave effects equivalent to calcium.
\r\n\r\nThe effect of moisture on char yield was independent of the ash components, but the yield of tar from Woodex containing moisture and ash exhibited a minimum at 390\u00b0C. Below 390\u00b0C the water hydrated catalyst sites to reduce reactivity. A kinetic model for hydration gave qualitative agreement with the observed effects of temperature. Above 390\u00b0C the degradation of tar became independent of the availability of catalyst sites, and was suppressed by the effect of water on the concentration of tar within the particles, and on the equilibrium of dehydration reactions.
" }, { "name": "Gurer, Cigdem", "degree": "PhD", "year": "1984", "title": "Time Dependent and Equilibrium Stress-Strain Behavior of Rubbers in Moderately Large Deformations", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252004-105813", "creators": [ { "name": { "family": "Gurer", "given": "Cigdem" }, "id": "Gurer-Cigdem", "display_name": "Gurer, Cigdem" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "chair", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/e0xe-8w83", "abstract": "In this work, time dependent and equilibrium stress-strain properties of elastomeric networks are investigated for moderately large deformation. A two network potential is proposed, which constitutively describes stress-strain behavior at elastic equilibrium. The potential is applied to time dependent deformations thorough a molecular model.
\r\n" }, { "name": "Handly, Neal Bruce", "degree": "Masters", "year": "1984", "title": "Studies of Regulatory Networks in Cells: Roles of Ions and Small Molecules", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122010-113308417", "creators": [ { "name": { "family": "Handly", "given": "Neal Bruce" }, "id": "Handly-Neal-Bruce", "display_name": "Handly, Neal Bruce" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nwzk-dr03", "abstract": "No abstract." }, { "name": "Hanle, Daniel Dale", "degree": "PhD", "year": "1984", "title": "In Vitro Fluid Dynamics of Prosthetic Aortic Heart Valves in Steady and Pulsatile Flow", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-11092005-152937", "creators": [ { "name": { "family": "Hanle", "given": "Daniel Dale" }, "id": "Hanle-Daniel-Dale", "orcid": "0000-0002-5167-8220", "display_name": "Hanle, Daniel Dale" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "chair", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Harrison", "given": "Earl C." }, "id": "Harrison-Earl-C", "role": "member", "display_name": "Harrison, Earl C." }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/JC5A-5J46", "abstract": "Velocity measurements were made in vitro using a laser-Doppler anemometer downstream from prosthetic aortic heart valves with distinctly different designs. The valves studied were an Ionescu-Shiley tri-leaflet bioprosthesis, a Bj\u00f6rk-Shiley convexo-concave tilting-disc prosthesis, a Smeloff caged-ball prosthesis, and a St. Jude bi-leaflet prosthesis. Velocity measurements were made in steady and in pulsatile flow using a Newtonian fluid with a viscosity of 0.001 kg/ms. Velocity components in all three coordinate directions were measured at 305 locations distibuted systematically across a cross section of the flow system at an axial distance of 31.8 mm downstream from the valve mount. This systematic approach to the data acquisition allowed a detailed analysis of the disturbed flow fields generated by each of the four valves. Large shear stresses were estimated in the bulk flow which were potentially hemolytic and which could potentially activate platelet chemical-release reactions.
\r\n\r\nA well-controlled, comparative analysis of the steady-flow and pulsatile-flow velocity results revealed that measurements made in steady flow could be used to approximate the dynamics of pulsatile flow during the middle of the pulse cycle only. Shear stresses estimated for steady flow were found to be an upper bound on those estimated for pulsatile flow.
\r\n\r\nA comparison of the pressure-drop and regurgitant-flow characteristics of these four valves showed that there was a significant range in the hydrodynamic performance of these prostheses. The St. Jude prosthesis generated the lowest pressure drop among the four valves studied while the Smeloff prosthesis generated the largest. The St. Jude prosthesis also allowed the least amount of regurgitant flow of the three valve designs which, when closed, did not totally occlude their orifice for flow. Because it has a totally-occluding design, the lonescu-Shiley bioprosthesis allowed the least regurgitant flow of the valves studied. The Smeloff prosthesis allowed the largest amount of regurgitant flow of the valves studied.
" }, { "name": "Hertzberg, Robert P.", "degree": "PhD", "year": "1984", "title": "Cleavage of DNA with Methidiumpropyl-EDTA", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102018-114702204", "creators": [ { "name": { "family": "Hertzberg", "given": "Robert P." }, "id": "Hertzberg-Robert-P", "display_name": "Hertzberg, Robert P." } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vcna-tp03", "abstract": "Attachment of ethylenediaminetetraacetate (EDTA) to the DNA intercalator methidium creates an efficient DNA cleaving molecule, methidiumpropyl-EDTA (MPE). MPE\u00b7Fe(II) (10-7 M) single strand cleaves supercoiled pBR-322 plasmid DNA (10-5 M) in the presence of O2, converting it to 56% open circular DNA. In the presence of 1 mM dithiothreitol (DTT) and O2, MPE\u00b7Fe(II) (10-8 M) converts supercoiled pBR-322 DNA (10-5 M) to 97% open circular and 3% linear DNA. MPE\u00b7Mg(II) binds to sonicated calf thymus DNA with a binding affinity of 1.2 x 10-5 M-1 and binding site size of 1.9 base pairs, and unwinds supercoiled PM2 plasmid DNA with an unwinding angle of 11\u00b0 \u00b1 3\u00b0.
\r\n\r\nThe reaction conditions for DNA cleavage and factors affecting the cleavage efficiency by MPE\u00b7Fe(II) have been determined. The cleavage is dependent on Fe(II) and O2, inhibited by chelating agents, enhanced by reducing agents (ascorbate > DTT > NADH), inhibited by catalase, partially inhibited by radical scavengers, relatively unaffected by sodium concentration, and optimum at pH 7.4 (in Tris\u00b7HCl buffer). MPE\u00b7Fe(II) cleaves DNA in a relatively non-sequence specific manner, with significantly lower sequence specificity than the enzyme DNAse I, and is a useful footprinting tool for the determination of small molecule binding sites on naturally occurring heterogeneous DNA.
\r\n\r\nThe products from the cleavage reaction of MPE\u00b7Fe(II) with DNA have been characterized. The results demonstrate that each strand scission produces a free nucleotide base, a 5' phosphoryl group, and a mixture of 3' phosphoryl and 3' phosphoglycolic acid groups left on the polynucleotide chain. Very little malondialdehyde or base-propenals are produced. These products are consistent with the intermediacy of hydroxyl radical in the strand scission reaction.
\r\n" }, { "name": "Ikeda, Richard Alan", "degree": "PhD", "year": "1984", "title": "I. Bismethidium Intercalators: the Binding of Nucleic Acids and II. Experiments in the Design of Site Specific DNA Cleaving Agents", "advisor": "Campbell, Judith L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122018-122020454", "creators": [ { "name": { "family": "Ikeda", "given": "Richard Alan" }, "id": "Ikeda-Richard-Alan", "orcid": "0000-0003-4015-5528", "display_name": "Ikeda, Richard Alan" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "advisor", "display_name": "Campbell, Judith L." } ], "committee": [ { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "chair", "display_name": "Campbell, Judith L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xp0y-6y73", "abstract": "CHAPTER I
\r\nPart I
\r\n\r\nBis(methidium)spermidine (BMSpd), an analog of ethidium bromide in which two phenanthridine chromophores are tethered by a 10 \u00c5 Spermidine linker, has been synthesized and characterized in order to test the effect of linker length on DNA binding. Like bis(methidium)spermine (BMSp),1 a dimer with a 15 \u00c5 tether, BMSpd unwinds DNA 36.5\u00b0. Unlike BMSp, the binding of BMSpd to calf thymus DNA, poly dG\u00b7poly dC, poly rA\u00b7poly dT, and poly dA\u00b7poly dT is complicated. At 0.4 M (M+) and pH 7, the binding site sizes and binding constants of BMSpd range from 2.75 base pairs (calf thymus DNA) to 4.0 base pairs (rA\u00b7dT, dG\u00b7dC) and 5 x 105 M-1 (dA\u00b7dT) to 6 x 106M-1 (r A\u00b7dT). These affinities are on the average, ten times higher than the analogous affinities of ethidium bromide and 300 times less than the binding constants of BMSp. The most dramatic change occurs in the binding specificity of BMSpd. Whereas, BMSp binds poly rA\u00b7dT 1440 times more tightly than poly dA\u00b7dT, the spermidine analog (BMSpd) binds poly rA\u00b7dT only 10 times more tightly than poly dA\u00b7dT.
\r\n\r\nPart II
\r\n\r\nThe ethidium dimers, bis(methidium)spermine (BMSp) and bis(methidium)spermidine (BMSpd), were found to site selectively inhibit DNase I and a variety of restriction enzymes on the plasmid pBR322. In contrast to the dimers, the monomer, ethidium bromide (EB), shows no site selective action in competition with any of the enzymes tested. The sites preferentially inhibited by BMSp and BMSpd appear to be in the first third of the plasmid. These observations and the clustering of inhibited restriction sites then suggests that selective inhibition may be due to the recognition or perturbation of DNA secondary structure.
\r\n\r\nCHAPTER II
\r\n\r\nThe compounds methidiumpropyl-EDTA, distamycin-EDTA, and pentaN-methylpyrrolecarboxamide-EDTA are three representative examples of a class of rationally designed DNA cleaving agents. By appending an iron chelator to different DNA binding vehicles certain properties of the resulting DNA cleaving agent can be controlled. Methidiumpropyl-EDTA randomly single strand cleaves DNA with high efficiency. Distamycin-EDTA nicks at 5 base pair recognition sites, and penta-N-methylpyrrolecarboxamide-EDTA double strand cleaves DNA at 6 base pair recognition sites. The success of these compounds led to the design of a controlled site cleaving agent, oligonucleotide-EDTA.
\r\n\r\nThe construction of the molecule was approached in two ways, synthetically and enzymatically. Synthetically, the oligonucleotide-EDTA was constructed by known nucleotide triester methodology. Enzymatically, a modified uridine, EDTA-dUTP, was incorporated into a DNA fragment. Unfortunately, neither strategy yielded an active DNA cleaving agent. These failures, however, do not directly reflect on the viability of an oligonucleotide-EDTA. It is possible that an extended research effort will uncover the methods needed to create an active oligonucleotide-EDTA.
\r\n" }, { "name": "Kaiser, Robert James, Jr.", "degree": "PhD", "year": "1984", "title": "Nuclear Magnetic Resonance and Kinetic Studies of the Catalytic Mechanism of the Serine Proteases", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11162018-115223569", "creators": [ { "name": { "family": "Kaiser", "given": "Robert James, Jr." }, "id": "Kaiser-Robert-James", "display_name": "Kaiser, Robert James, Jr." } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xg11-xg51", "abstract": "Kinetic and nuclear magnetic resonance experiments on the catalytic mechanism of the serine proteases have been carried out using alpha lytic protease, a bacterial serine protease. 13C NMR measurements indicate that His 57, and not Asp 102, is the residue titrating with pKa 6.7 in the free enzyme. However, when alpha lytic protease is complexed with transition state analogs (peptide aldehydes and benzeneboronic acid), the pKa of this residue can shift to lower values. This shift can be at least as large as 1.8 pK units, and suggests that the enzyme may behave differently in the presence of substrate, especially in its transition state or intermediate forms, than it does in its absence.
\r\n\r\nThe reaction of elastase with specific peptide p-nitroanilides is biphasic, indicating the buildup of a tetrahedral intermediate in a pre-steady state reaction, followed by linear turonver. The intermediate accumulates to about 20-25% of the total amount of substrate bound to the enzyme. The ability for the substrate to make favorable contacts along an extended portion of the enzyme binding site is important in the observation of the buildup of this intermediate.
\r\n\r\n13C NMR studies on model compounds for the Asp 102-His 57 dyad in water and in DMSO solution indicate that pKa reversal of the two ionizable groups can occur under conditions of moderate dielectric and high polrity. Overall, the results indicate that the \"charge relay\" mechanism may be operative in cases where the substrate can make precise extended contacts with the enzyme.
\r\n" }, { "name": "Khanna, Rohit", "degree": "PhD", "year": "1984", "title": "Control Model Development for Packed Bed Chemical Reactors", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05152003-160535", "creators": [ { "name": { "family": "Khanna", "given": "Rohit" }, "id": "Khanna-Rohit", "display_name": "Khanna, Rohit" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Morari", "given": "Manfred" }, "id": "Morari-M", "orcid": "0000-0002-7696-5058", "role": "member", "display_name": "Morari, Manfred" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VK3Y-QN30", "abstract": "Although control algorithms have been conceived for industrial chemical systems, their acceptance by industry has been slow due to a lack of direct experimental evidence of their effectiveness and to volumes of conflicting, or at least incompatible, recommendations on control structure design. This thesis provides the basis for a concerted theoretical and experimental program in multivariable process control structure design for packed bed chemical reactors by presenting an in-depth control analysis of a practical, multivariable, distributed parameter system-the heat conduction problem defined by the simple diffusion equation-using both frequency-domain and time-domain analyses and the formulation, numerical solution, and analysis of a detailed model for packed bed reactors, along with reduction to a low-order state-space representation suitable for on-line process control.
\r\n\r\nThe study of the heat conduction system allowed for consideration of various control design techniques and the relation between measurement structure and control system design. This study shows that the choice of measurements and their locations significantly affects the optimal control design and the usefulness of the different design techniques and the importance of an accurate process model and the necessity of model reduction to a low-order state-space representation for control structure design and implementation.
\r\n\r\nThe second portion of this study provides a detailed mathematical modeling analysis of packed bed catalytic reactors that significantly extends previous studies in the detail of the model and in the consideration of all aspects of the model development and reduction to a state-space control representation. The general view that modeling simplifications are desired since they lead to a reduction in numerical solution effort is contested, and it is shown that many simplifications are no longer necessary with today's advanced computational capabilities. A unified approach to dynamic reactor modeling is developed and its importance in the accurate description of dynamic and steady state reactor behavior, in the investigation of reactor start-up or the effects of process disturbances, and in the development of an accurate reduced state-space model for the design of control structures to stabilize the reactor under various disturbances or to provide optimal system recovery from input changes is shown.
\r\n" }, { "name": "Kravaris, Constantine (Costas)", "degree": "PhD", "year": "1984", "title": "Identification of Spatially-Varying Parameters in Distributed Parameter Systems", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01092007-104956", "creators": [ { "name": { "family": "Kravaris", "given": "Constantine (Costas)" }, "id": "Kravaris-Constantine-Costas", "orcid": "0000-0003-0951-9493", "display_name": "Kravaris, Constantine (Costas)" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Caughey", "given": "Thomas Kirk" }, "id": "Caughey-T-K", "role": "member", "display_name": "Caughey, Thomas Kirk" } ], "option_major": [ "chemeng" ], "doi": "10.7907/m0kv-m285", "abstract": "Identification of spatially-varying parameters in distributed parameter systems given an observation of the state is as a rule an ill-posed problem in the sense of Hadamard. Even in case when the solution is unique, it does not depend continuously on the data. The identification problem that motivated this work arises in the description of petroleum reservoirs and subsurface aquifers; it consists of identifying the spatially-varying parameter \u03b1(x,y) in the diffusion equation ut = (\u03b1ux)x + (\u03b1uy)y + f given an observation of u at a discrete set of spatial locations.
\r\n\r\nThe question of uniqueness of \u03b1 (identifiability problem) is first investigated. The analysis is restricted to the one-dimensional version of the above equation i.e. to ut = (\u03b1ux)x + f and an observation of u at a single point. The identifiability problem is formulated as an inverse Sturm-Liouville problem for (\u03b1y')' + \u03bby = 0. It is proved that the eigenvalues and the normalizing constants determine the above Sturm-Liouville operator uniquely. Identifiability and non-identifiability results are obtained for three special cases.
\r\n\r\nThe problem of constructing stable approximate solutions to identification problems in distributed parameter systems is next investigated. The concept of regularization, widely used in solving linear Fredholm integral equations, is developed for the solution of such problems. A general regularization identification theory is presented and applied to the identification of parabolic systems. Two alternative numerical approaches for the minimization of the smoothing functional are investigated: (i) classical Banach space gradient methods and (ii) discretized minimization methods. The latter use finite-dimensional convergent approximations in Sobolev spaces and are based on an appropriate convergence theorem. The performance of the regularization identification method is evaluated by numerical experiments on the identification of spatially-varying diffusivity \u03b1 in the diffusion equation.
" }, { "name": "Kuo, Chia-lam", "degree": "PhD", "year": "1984", "title": "Use of Temperature Sensitive Mutants to Study Yeast DNA Replication", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212018-100547724", "creators": [ { "name": { "family": "Kuo", "given": "Chia-lam" }, "id": "Kuo-Chia-lam", "display_name": "Kuo, Chia-lam" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Emr", "given": "Scott D." }, "id": "Emr-S-D", "orcid": "0000-0002-5408-6781", "role": "member", "display_name": "Emr, Scott D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gekb-yq20", "abstract": "An improved in vitro DNA replication system in Brij-treated Saccharomyces cerevisiae has been used to screen a random population of temperature-sensitive strains for mutants specifically defective in DNA synthesis. Twenty mutants defective in in vitro DNA synthesis have been isolated. Seven of them fall into three complementation groups -- cdc2, cdc8, and cdc16 -- involved in the control of the cell-division cycle. Because synthesis in vitro represents propagation of replication forks active in in vivo at the time of permeabilization, our findings that cdc2 and cdc16 mutants can incorporate dTMP into DNA in such permeabilized cells at 23\u00b0c but not at 37\u00b0c supports the conclusion that these two mutations directly affect DNA synthesis. Such an involvement was previously suggested by in vivo analysis for CDC2 but was less clear for CDC16. The usefulness of our screening procedure is further demonstrated by the isolation of replication mutants in previously undescribed complementation groups. One strain shows a serious defect in in vivo DNA synthesis but normal RNA synthesis.
\r\n\r\nThe in vitro system has also been used to purify the CDC8 protein. cdc8 mutant strains are temperature-sensitive for DNA chain elongation and the CDC8 gene product is required for DNA synthesis in vitro in permeabilized yeast cells. Extracts of wild-type A364a yeast restore DNA synthesis in Brij-treated cdc8 mutant. A small, heat-stable protein responsible for this complementation has been partially purified from wild-type cells.
\r\n\r\nThe CDC8 gene has been isolated on recombinant plasmids. The yeast-E. coli shuttle vector YCp50 was used to prepare a recombinant plasmid pool containing the entire yeast genome. Plasmids capable of complementing the temperature-sensitive cdc8-1 mutation were isolated by transformation of a cdc8-1 mutant and selection for clones able to grow at the nonpermissive temperature. The entire complementing activity is carried on a 0.75-kilobase fragment, as revealed by deletion mapping and DNA sequencing. This fragment lies 1 kilobase downstream from the well characterized sup4 gene, a gene known to be genetically linked to CDC8 thus confirming the cloned gene corresponds to the chromosomal CDC8 gene. Two additional recombinant plasmids that complement the cdc8-1 mutation but that do not contain the 0.75-kilobase fragment or any flanking DNA were also identified in this study. These plasmids may contain genes that compensate for the cdc8-1 mutation.
\r\n\r\nBy the following criteria, we have shown that thymidylate kinase, which catalyzes the phosphorylation of thymidine-5'-monophosphate to thymidine-5'-diphosphate in the pathway of synthesis of dTTP from dTMP, is the product of the CDC8 gene. First, transformed strains carrying the CDC8 gene on a stable high-copy-number plasmid express higher levels of both the gene transcript and the kinase activity than does wild type. Secondly, extracts of strains bearing different alleles of cdc8 show no detectable thymidylate kinase activity. Third, the DNA sequence of CDC8 gene reveals an open reading frame that encodes a protein of 216 amino acids with the same amino terminal sequence as thymidylate kinase purified from yeast.
" }, { "name": "Le, Anthony Trung", "degree": "Masters", "year": "1984", "title": "Synthesis of the \u03b2-Ketoimides and their Chemical Transformations", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-082952526", "creators": [ { "name": { "family": "Le", "given": "Anthony Trung" }, "id": "Le-Anthony-Trung", "display_name": "Le, Anthony Trung" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/canh-7y33", "abstract": "No abstract." }, { "name": "Lee, Chi-Woo", "degree": "PhD", "year": "1984", "title": "Adsorption and Electrochemistry of BIS-1, 10-Phenanthroline Complexes of Copper (I,II) and Fungal Laccase A", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11272018-091510836", "creators": [ { "name": { "family": "Lee", "given": "Chi-Woo" }, "id": "Lee-Chi-Woo", "orcid": "0000-0002-0821-9344", "display_name": "Lee, Chi-Woo" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/f4sv-x904", "abstract": "This thesis is an outcome of the efforts directed toward the theme \"Electrocatalysis of dioxygen reduction by copper- containing molecules adsorbed on graphite electrodes.\"
\r\n\r\nIn the first part, an electrochemical measurement of the rate of electron exchange between Cu(phen)2+ adsorbed on graphite and Cu(phen)2++ in solution is described. The rate constant was estimated to be ca. 105 M-1 s-1 by using rotating disk voltammetry. The origin of the previously reported but widely discrepant values (5 x 107 M-1 s-1 and 50 M-1 s-1) in the literature is discussed, and a new estimate of ca. 104 M-1 s-1 is obtained by applying Marcus theory in a form that allows explicitly for differences in reorganization energy between the oxidized and reduced halves of the reacting redox couples. The electrocatalytic studies of dioxygen reduction by Cu(phen)2+ could not be done due to the low signal-to-noise ratio.
\r\n\r\nIn the second part, the bioelectrocatalytic reduction of molecular oxygen by reduced fungal laccase A immobilized on pyrolytic graphite is described. The reduction produces exclusively water in the potential range studied (< 0 V vs. SSCE). The catalytic activity reaches its maximum at pH 3~4, and the lower limit on rate constant for the reduction in this pH range was estimated to be 1.5 x 104 M-1 s-1.
\r\n\r\nThree appendices describe (i) potential step hydrodynamic chronocoulometry, (ii) a new method to determine the self- exchange rate constant for the redox couple in which the coordination numbers depend on the oxidation states, and (iii) a novel electrochemical method of detecting H2O2.
\r\n" }, { "name": "Lyberatos, Gerasimos", "degree": "PhD", "year": "1984", "title": "Dynamic and Steady-State Bifurcation for Modeling Chemical Reaction Systems", "advisor": "Bailey, James E.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01112007-103406", "creators": [ { "name": { "family": "Lyberatos", "given": "Gerasimos" }, "id": "Lyberatos-Gerasimos", "orcid": "0000-0003-1663-4035", "display_name": "Lyberatos, Gerasimos" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "co-advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Cohen", "given": "Donald S." }, "id": "Cohen-D-S", "role": "member", "display_name": "Cohen, Donald S." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/bspw-np07", "abstract": "Chemical reaction systems often exhibit nonlinear dynamic phenomena such as multiple steady states and different types of nonlinear oscillations. Furthermore, nonlinear dynamic models are essential for control and input optimization of chemical reactors. Methods of bifurcation theory are used for analysis of the nonlinear behavior of chemical reaction systems and for chemical reactor model discrimination and identification. The latter objective is attained by forcing \"tame\" chemical systems to bifurcate and provide valuable information about the nonlinear system nature. Discrimination between rival kinetic models is demonstrated and a strategy for accurate parameter estimation is developed. The problem of steady-state bifurcation to multiple steady states in the event that the original model equations are not reducible to a single algebraic equation is attacked using the simple geometrical method of Newton Polyhedra. This method is particularly useful for analysis of feedback induced steady-state bifurcations. The theory of normal forms is used to illustrate that systems when close to bifurcation exhibit even locally their non-linear characteristics. The most common types of bifurcation phenomena are discussed and the minimum number of feedback (or system) parameters that must be varied to attain the various bifurcational structures is determined. Systems that are easily reducible to normal forms (simpler locally equivalent polynomial systems) are identified with distinctive advantages for the study of steady state and eigenvalue structure close to bifurcation. The analogy between some chemical systems and a particle's motion in a potential field is exploited to gain special insights into the chemical systems' dynamics. Chemical examples include nitrous oxide decomposition on NiO catalyst, consecutive-competitive reaction systems in a CSTR, parallel nonisothermal reactions of arbitrary order in a CSTR, reactions between adsorbed chemical species, coupled oscillating autocatalytic CSTRs and a class of feedback regulated enzymatic reaction systems.
\r\n" }, { "name": "McElwee-White, Lisa Ann", "degree": "PhD", "year": "1984", "title": "Theoretical and Experimental Assessment of the Viability of 1,4,6,9-Spiro[4.4]Nonatetrayl as a Reactive Intermediate", "advisor": "Dervan, Peter B.; Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262009-151524640", "creators": [ { "name": { "family": "McElwee-White", "given": "Lisa Ann" }, "id": "McElwee-White-Lisa-Ann", "display_name": "McElwee-White, Lisa Ann" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "chair", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nytz-bf09", "abstract": "Qualitative molecular orbital (MO) theory predicts that 1,4,6,9-spiro[4.4]nonatetrayl (7) should be stabilized via spiroconjugative interaction of the four radical p orbitals. In addition to this thermodynamic stabilization, energetic barriers are predicted for closure to either of the closed shell forms.
\r\n\r\nThe electronic structure of 7 has been investigated using ab initio electronic structure theory. The spiro-conjugative interaction of the four radical centers is evidenced by a large orbital splitting. However, spiroconjugation does not confer upon the structure the electronic properties of a biradical, contrary to qualitative MO considerations. Structure 7 possesses the six, low-lying (covalent) states that characterize a tetraradical. Spiroconjugation does strongly influence the relative energies of these six states, and does lead to a small but significant stabilization of the molecule. Possible modes of ring closure and closed shell isomers of 7 are also discussed.
\r\n\r\nDirect photolysis of spiro[bis(2,3-diazabicyclo[2.2.1]-hept-2-ene)-7,7'] (17) leads to loss of a single equivalent of N2 and ring closure of the resulting biradical to 2,3-diazabicyclo[2.2.11hept-2-ene-7,5'-spirobicyclo[2.1.0]-pentane (19). Generation of the triplet biradical by sensitized photolysis results in a competition between ring closure to 19 and a 1,2-alkyl shift to ,9-diazatricyclo-[5.2.2.02,6)]undeca-2,8-diene (23). While direct photolysis and thermolysis of 19 yield primarily ring closure product, sensitized photolysis leads to a series of biradical-to-biradical rearrangements that ultimately produce 2,3-divinyl-cyclopentene (24). Deuterium labeling studies indicate competing mechanistic pathways for this reaction. Rationalization of the label distribution requires one of two unprecedented processes: frontside radical attack on a C-C bond or intermediacy of 1,4,6,9-spiro[4.4]nonatetrayl.
" }, { "name": "Moonan, William Kevin", "degree": "PhD", "year": "1984", "title": "Superposition of the Effects of Time, Temperature, and Pressure in Polymetric Materials", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06152004-145433", "creators": [ { "name": { "family": "Moonan", "given": "William Kevin" }, "id": "Moonan-William-Kevin", "display_name": "Moonan, William Kevin" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "chair", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Knauss", "given": "Wolfgang Gustav" }, "id": "Knauss-W-G", "role": "member", "display_name": "Knauss, Wolfgang Gustav" }, { "name": { "family": "Chang", "given": "W. V." }, "id": "Chang-W-V", "role": "member", "display_name": "Chang, W. V." } ], "option_major": [ "chemeng" ], "doi": "10.7907/e970-mg79", "abstract": "Stress relaxation was studied in torsion under superposed hydrostatic pressure using a newly constructed device. Combination of these measurements with the determination of expansivities and compressibilities and with earlier measurements of stress relaxation in tension leads to verification of the description of the combined effects of temperature and pressure on shear relaxation by an extension of the classical free volume theory. The predictions of an extension of the Adam-Gibbs theory to the pressure domain are also compared with the data. This theory is not as successful in predicting superposition. The data are also examined in light of an adaptation of the Simha-Somcynsky equation of state to the free volume theory. Prediction of the effect of pressure by the theory requires a single adjustable parameter. It was possible to calculate the free volume parameters of several polymers without use of information from high pressure experiments.
" }, { "name": "Moore, Eric Jan", "degree": "PhD", "year": "1984", "title": "Synthetic, Structural and Mechanistic Studies of Interactions of Carbon, Nitrogen, and Oxygen Nucleophiles with Bis-Pentamethylcyclopentadienyl Zirconium and Hafnium Derivatives", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082013-141952473", "creators": [ { "name": { "family": "Moore", "given": "Eric Jan" }, "id": "Moore-Eric-Jan", "display_name": "Moore, Eric Jan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/18vn-5737", "abstract": "The reactivity of permethylzirconocene and permethylhafnocene complexes with various nucleophiles has been investigated. Permethylzirconocene reacts with sterically hindered ketenes and allenes to afford metallacycle products. Reaction of these cummulenes with permethylzirconocene hydride complexes affords enolate and \u03c3-allyl species, respectively. Reactions which afford enolate products are nonstereospecific, whereas reactions which afford allyl products initially give a cis-\u03c3-allyl complex which rearranges to its trans isomer. The mechanism of these reactions is proposed to occur either by a Lewis Acid-Lewis Base interaction (ketenes) or by formation of a \u03c0-olefin intermediate (allenes).
\r\n\r\nPermethylzirconocene haloacyl complexes react with strong bases such as lithium diisopropylamide or methylene trimethylphosphorane to afford ketene compounds. Depending on the size of the alkyl ketene substituent, the hydrogenation of these compounds affords enolate-hydride products with varying degrees of stereoselectivity. The larger the substituent, the greater is the selectivity for cis hydrogenation products.
\r\n\r\nThe reaction of permethylzirconocene dihydride and permethylhafnocene dihydride with methylene trimethylphosphorane affords methyl-hydride and dimethyl derivatives. Under appropriate conditions, the metallated-ylide complex 1, (\u03b75-C5(CH3)5)2Zr(H)CH2PMe2CH2, is also obtained and has been structurally characterized by X-ray diffraction techniques. Reaction of 1 with CO affords (\u03b75-C5(CH3)5)2Zr(C,O-\u03b72-(PMe3)HC=CO)H which exists in solution as an equilibrium mixture of isomers. In one isomer (2), the \u03b72-acyl oxygen atom occupies a lateral equatorial coordination position about zirconium, whereas in the other isomer (3), the \u03b72-acyl oxygen atom occupies the central equatorial position. The equilibrium kinetics of the 2 \u2192 3 isomerization have been studied and the structures of both complexes confirmed by X-ray diffraction methods. These studies suggest a mechanism for CO insertion into metal-carbon bonds of the early transition metals.
\r\n\r\nPermethylhafnocene dihydride and permethylzirconocene hydride complexes react with diazoalkanes to afford \u03b72-N,N'-hydrazonido species in which the terminal nitrogen atom of the diazoalkane molecule has inserted into a metal-hydride or metal-carbon bond. The structure of one of these compounds, Cp*2Zr(NMeNCTol2)OH, has been determined by X-ray diffraction techniques. Under appropriate conditions, the hydrazonido-hydride complexes react with a second equivalent of diazoalkene to afford \u03b7'-N-hydrazonido-\u03b72-N,N'-hydrazonido species.
" }, { "name": "Moser, David Randall", "degree": "PhD", "year": "1984", "title": "Regulation of ColEl Plasmid DNA Replication in Escherichia coli", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302018-183325232", "creators": [ { "name": { "family": "Moser", "given": "David Randall" }, "id": "Moser-David-Randall", "display_name": "Moser, David Randall" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/bf0f-4378", "abstract": "A number of plasmid copy-number mutants have been characterized in order to gain insight into the mechanism by which initiation of plasmid DNA synthesis is regulated. One nutant, pFHllB, which has a 12-fold higher copy number than the homologous wildtype plasmid, RSF1050, contains 16 additional base pairs within a region of the plasmid that has been shown to be essa1tial for norrral replication. The insertion nutation lies approximately 500 base tairs upstream of the origin of DNA synthesis within the coding region of a small untranslated RNA, RNA I. The copy-number nutation is recessive and can be complemented both in cis and in trans by the wild-type RNA I gene. The results of the complementation studies reveal that replication of the ColE1-type plasmids is regulated by a mechanism of negative control in which RNA I functions as a repressor of plasmid DNA synthesis.
\r\n\r\nThe target of RNA I inhibition is believed to be near the 5' end of a second plasmid transcript, RNA II. RNA II transcription begins 555 base pairs upstream of the replication origin and terminates several hundred base pairs downstream of the origin. RNA II can be processed by RNase H to generate a primer for the initiation of DNA synthesis by DNA polymerase I. Purified RNA I has been shown to inhibit primer formation in vitro. Dominant high copy-number mutants of a specially-constructed plasmid, pDM247, contain single base-pair changes within a seven base-pair sequence of the RNA II coding region. The altered nucleotides in RNA II are located within the single-stranded loop of a prominent hairpin structure that can form near the 5' end of the transcript. A romplenentary hairpin structure exists in RNA I. A model for RNA I-RNA II interaction involving base pairing of loop structures has been proposed.
\r\n\r\nA single base-pair mutation has been identified in a plasmid which has a temperature-sensitive high ropy-number phenotype. The ts mutant exhibits normal copy control in cells growing at the permissive temperature of 30\u00b0C but replicates uncontrollably in cells shifted to the nonpermissive temperature, 37\u00b0C. Runaway replication of plasmid DNA is lethal to the host cells within 3-4 hours after the temperature shift. The orp mutation (for over-replication) affects both the RNA II transcript and the promoter for RNA I. RNA I promoter-galK fusion studies indicate that the mutation does not create a temperature-sensitive promoter. It has been proposed that the orp mutation creates a thermosensitive secondary structure in RNA II. The breakdown of this structure at the higher temperature renders the plasmid insensitive to replication inhibition by RNA I. Secondary mutations which suppress the temperature-sensitive phenotype have been isolated. These mutations also affect nucleotides within RNA II.
\r\n\r\nA small plasmid-encoded polypeptide also plays a role in plasmid copy number control. Although this protein, referred to as the rop gene product, is not essential for regulation of plasmid DNA replication (the deletion of the rop gene causes only a three to five-fold increase in plasmid copy number), its presence in the cell can suppress lethal DNA over-replication of the temperature-sensitive copy number mutant. This suppression was used as the basis of a selection for rop insensitive mutants. The identification of point mutations within the RNA I coding region of these mutants is consistent with the hypothesis that the product of the rop gene modulates the interaction between RNA I and the primer precursor.
" }, { "name": "Nocera, Daniel George", "degree": "PhD", "year": "1984", "title": "Spectroscopy, Electrochemistry, and Photochemistry of Polynuclear Metal-Metal Bonded Complexes", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02012005-160716", "creators": [ { "name": { "family": "Nocera", "given": "Daniel George" }, "id": "Nocera-Daniel-George", "orcid": "0000-0001-5055-320X", "display_name": "Nocera, Daniel George" } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/T14G-4N32", "abstract": "The spectroscopic, electrochemical, and photochemical properties of two d4 metal polynuclear complex systems were investigated: the quadruple bond complex, Re2Cl82-, and the M6X142- halide cluster ions of molybdenum(II) and tungsten (II).
\r\n\r\nThe vibrationally structured luminescence spectrum of Re2Cl82- at 5 K has confirmed that emission arises from the \u03b4\u03b4* singlet state. Both Re2Cl82- and electronically excited Re2Cl82- (Re2Cl82-*) undergo facile one-electron oxidation and reduction reactions. Aromatic amines quench Re2Cl82-* luminescence and a Marcus analysis of the steady state quenching rate constants suggest that Re2Cl83-|D+ is formed in the quenching reaction and that the ion-pair decays rapidly by back electron transfer. The luminescence of Re2Cl82-* is also quenched by electron acceptors (TCNE and chloranil) in nonaqueous solutions, forming Re2Cl8- and reduced acceptor. The back electron transfer reactions are near the diffusion controlled limit. Electrochemical measurements suggested that photogenerated Re2Cl8- anion could be trapped by Cl- to produce Re2Cl92-, thereby circumventing the efficient back reaction. Irradiation (\u03bb > 600 nm) of nonaqueous solutions of Re2Cl82- and chloranil or TCNE in the presence of excess Cl- does, indeed, produce Re2Cl92- in quantitative yield. Photolysis reactions employing a quencher (e.g. 2,3-dichloro-5,6-dicyano-benzoquinone) possessing a redox couple with a potential greater than that of Re2Cl9-/2- (0.53 vs. SCE) yielded Re2Cl9- as a final product. Thus, a single low energy photon facilitates a two-electron oxidation of Re2Cl82-. Direct two-electron oxidation of Re2Cl82-* by chlorine atom transfer reagents such as PtCl62- to produce Re2Cl9- was also attempted. Irradiation (\u03bb > 590 nm) of dichloromethane solutions containing Re2Cl82- and PtCl62- quantitatively yield Re2Cl9-. Qualitative kinetic experiments measuring the wavelength dependence of the reaction rate suggest that the photochemical reaction proceeds by a free radical pathway involving the 3A2u ligand field excited state of PtCl62- and does not involve an atom transfer reaction mechanism. These experiments are not without their ambiguities, however, and further areas of research are discussed. The crystal structure analysis of NBu4Re2Br9 is also presented.
\r\n\r\nThe M6X142- (M=Mo,W; X=Cl,Br,I) ions are intensely luminescent in the solid state and solution and the photophysical properties of the six cluster ions are documented. These results in conjunction with those of the EPR spectra of the electrochemically generated M6X14- anions are discussed in terms of recent theoretical models for the electronic structure of the cluster ions. Electrochemical experiments were also conducted and showed the M6X142- cluster ions to undergo reversible single-electron oxidation reactions. For Mo6Cl142- a quasi-reversible one-electron reduction wave was observed in addition to its oxidation wave. The electrochemical and photophysical properties of Mo6Cl142- suggested electrogenerated chemiluminescent behavior of the cluster ion. Emission, characteristic of Mo6Cl142-*, is observed upon electrochemical generation of Mo6Cl14- and Mo6Cl143-.
\r\n" }, { "name": "Pearson, Laurence Timothy", "degree": "PhD", "year": "1984", "title": "A Model for the Lateral Organization of Protein Molecules in Lipid Bilayers", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12142018-113612227", "creators": [ { "name": { "family": "Pearson", "given": "Laurence Timothy" }, "id": "Pearson-Laurence-Timothy", "display_name": "Pearson, Laurence Timothy" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/k7m9-xb92", "abstract": "Interactions between membrane bound proteins are examined using freeze-fracture etch electron microscopy. The pair distribution functions (PDF's) of protein particles in natural and synthetic membrane systems are examined, and compared with PDF's that are calculated from potential energy functions. In particular, PDF's calculated from the hard-disc only interaction between particles serve as a useful reference for determining whether particle interactions are attractive or repulsive. Of particular interest is the possibility that the lipid bilayer membrane mediates protein interactions. A model is presented for a lipid-mediated interaction that predicts that if protein molecules perturb the bilayer membrane away from its equilibrium (protein free) configuration and that if the perturbation is propagated laterally through the membrane over a sufficient distance, then an attractive interaction is the result.
\r\n\r\nThe model is tested on recombinants of cytochrome c oxidase with dimyristoyl phosphatidyl choline and glycerol and with cardiolipin. Each recombinant is frozen from above the phase transition temperature of the lipid, so the membranes are expected to be fluid. Aggregation of protein into patches is seen, but all PDF's are indicative of a long-ranged repulsion. The model must be modified to account for the repulsion, a modification that would explain the observations in the inclusion of a vector membrane order parameter, namely lipid tilt, into the model. Tilt perturbation can be described by using the formalism already developed for describing nematic and smectic liquid crystals. A repulsive interaction between protein particles that is analogous to that seen between Schlieren textures in liquid crystals can be shown to occur if protein molecules induce tilt deformations in the bilayer around their boundaries.
" }, { "name": "Perry, Joseph Walter", "degree": "PhD", "year": "1984", "title": "Nature and Energy Redistribution of Highly Vibrationally Excited Polyatomic Molecules", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04032008-111559", "creators": [ { "name": { "family": "Perry", "given": "Joseph Walter" }, "id": "Perry-Joseph-Walter", "orcid": "0000-0003-1101-7337", "display_name": "Perry, Joseph Walter" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YDWZ-Z639", "abstract": "This thesis is a primarily experimental study of the spectroscopy and dynamics of highly vibrationally excited molecules in the ground and excited electronic states. Linear spectroscopic studies have been performed on CH-stretching overtones of medium and large sized molecules in the gas and solid phases. Also new time-resolved methods based on nonlinear uultiphoton ionization spectroscopy have been applied on the picosecond time-scale to the study of ultrafast intramolecular vibrational-energy redistribution (IVR) in isolated molecules.
\r\n\r\nThe first observation of high-energy CH stretching overtones of molecules in low-temperature solids is reported. Spectra of the \u03bdCH = 5 transitions of many aromatic molecules at ~2K reveal homogeneously broadened bands which are assigned to inequivalent local modes by studies of same isotopically substituted molecules. Typical linewidths give population lifetimes of ~50 fs for aromatic compared to 100-200 fs for methyl CHs in these large molecules. The polarization ratios of durene CH overtones are in good agreement with those predicted with the localized bond-mode transition moments.
\r\n\r\nOvertone spectra of some gas-phase deuterated methanes and tetramethyl compounds have been studied. Spectra of CHD3 have shown severe vibrational mixing at \u03bdCH = 6 and 7 with an apparent tuning of the Fermi-resonance between |\u03bdCH> and discrete stretch-bend combination states, e.g., |(\u03bd-1)CH, 2bend>. Nonetheless, the lifetime of the CHD3 overtones must be long (≥5 ps) as evidenced by the narrow resolution limited linewidths. The splitting of the |6,0>± states of CH2D2 is inferred to be <10 cm-1 and shows that the coupling of the CH oscillators is relatively weak in agreement with theoretical prediction. In general, the results on the CH overtones indicate a significant role of CH stretch-normal mode coupling in the spectra and dynamics.
\r\n\r\nPicosecond pump and probe multiphoton ionization is developed for the study of IVR in isolated molecules. Experimental evidence for IVR is presented. Nonexponential decay of vibronic states of S1 trans-stilbene is analyzed in terms of a population rate equation and time-dependent Franck-Condon factor description of IVR. The thermally-averaged IVR time constant is about 2 ps. Also, the excess vibrational energy dependence of the S1 trans-stilbene isomerization rate is determined for total vibrational energy of 2000 to 4500 cm-1 and good agreement is found with calculated thermally averaged rates based on independent results on jet-cooled molecules.
" }, { "name": "Roddick, Dean Michael", "degree": "PhD", "year": "1984", "title": "Synthesis, Structure, and Reactivity of Hydride and Phosphide Complexes of Hafnium and Zirconium", "advisor": "Collins, Terrence J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222018-111603289", "creators": [ { "name": { "family": "Roddick", "given": "Dean Michael" }, "id": "Roddick-Dean-Michael", "orcid": "0000-0002-5981-4178", "display_name": "Roddick, Dean Michael" } ], "advisors": [ { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "advisor", "display_name": "Collins, Terrence J." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wbgr-yd42", "abstract": "A series of alkyl hydride complexes Cp*2Hf(H)R (R=Et, CH2CHMe2, CH2CH2Ph; Cp* = \u03b7-C5Me5) have been prepared by reaction of Cp*2HfH2 with the appropriate olefin. The reactions of these compounds with H2 and C2H4 follow those of the previously reported zirconium isobutyl hydride, Cp*2Zr-(H)CH2CHMe2, giving Cp*2HfH2 and metallacyclopentane Cp*2Hf-CH2CH2CH2CH2, respectively, plus one equivalent alkane. All alkyl hydrides examined exhibit high thermal stability and decompose only slowly at 80\u00b0C. The thermolysis of Cp*2Hf(H)CH2CHMe2 yields a 1:1 mixture of Cp*2HfH2 and a metallacyclobutane complex Cp*2HfCH2CH(Me)CH2. A proposed mechanism for the formation of Cp*2HfCH2CH(Me)CH2 is given, involving initial \u03b3-H abstraction from the isobutyl methyls of Cp*2Hf(H)CH2CHMe2. Cp*2HfH2 also reacts cleanly with t-butylacetylene to form a remarkably stable alkenyl hydride complex, Cp*2Hf(H)CH=CHtBu. The reactivity of Cp*2Hf(H)CH=CHtBu with H2 and C2H4 is similar to that observed for the related alkyl hydrides. The hydride complexes Cp*2Hf(H)Ph and Cp*2Hf-(H)CH2CMe3 have been conveniently prepared by the metathesis of Cp*2HfH2 with PhLi and LiCH2CMe3, respectively.
\r\n\r\nCp*2HfH2 reacts cleanly with allene to form the \u03c0-allyl hydride Cp*2Hf(H)(\u03b73-CH2CHCH2). 1H and 13C NMR data as well as labeling studies indicate that Cp*2Hf(H)(\u03b73-CH2CHCH2) is highly fluxional, and isostructural to Cp*2Zr(H)(\u03b73-CH2CHCH2). The crystal structure of Cp*2Hf(H)(\u03b73-CH2CHCH2) is presented. The coordination of the allyl ligand is confirmed to be trihapto, with notably asymmetric Hf-C(allyl) distances (2.38, 2.48, 2.57 A). The final R index is 0.049. The hydride ligand has been reliably located, and represents the first structurally characterized example of a terminal Hf-H bond.
\r\n\r\nCp*2Zr(H)CH2CHMe2 has been shown to react cleanly with CO to form the enolate hydride Cp*2Zr(H)OCH=CHCHMe2. A proposed mechanism for formation of Cp*2Zr(H)OCH=CHCHMe2 involves hydride migration via the initially formed acyl hydride Cp*2Zr(H)(\u03b72-C(O)CH2CHMe2) to give a \u03c0-coordinated aldehyde complex Cp*2Zr(\u03b72-OCHCH2CHMe2), which subsequently \u03b2-H eliminates to give the observed product. Support for the intermediacy of a \u03c0-aldehyde complex in this transformation is provided by the reaction of Cp*2M(H)CH2CHMe2 (M=Zr, Hf) with excess CO under controlled conditions to give moderately stable \u03c0-aldehyde carbonyl complexes Cp*2M(CO)(\u03b72-OCHCH2CHMe2). Thermolysis of Cp*2Hf(CO)(\u03b72-OCHCH2CHMe2) results in a novel coupling reaction to form the enediolate Cp*2HfOC(CH2CHMe2)CHO. The coordinatively unsaturated zirconium \u03c0-aldehyde intermediate Cp*2Zr(\u03b72-OHCCH2-CHMe2) is also implicated in the reactions of acyl hydride Cp*2Zr(H)(\u03b72-C(O)CH2CHMe2) with trapping substrates C2H4, MeC\u2261CMe, H2, and HC\u2261CtBu upon warming to give Cp*2Zr(OCH(-CH2CHMe2)CH2CH2), Cp*2Zr(OCH(CH2CHMe2)C(Me)=C(Me)), Cp*2Zr-(H)OCH2CH2CHMe2, and Cp*2Zr(C\u2261CtBu)OCH2CH2CHMe2, respectively. Carbonylation of the alkenyl hydride Cp*2Hf(H)CH=CHtBu did not yield an aldehyde complex, but rather the metallacycle Cp*2Hf(OHC=CHCH(tBu)). Mechanistic interpretations of these and related reactions are presented.
\r\n\r\nA series of mono-ring, terminal phosphide complexes of hafnium have been prepared. Reaction of Cp*HfCl3 with one equivalent or excess LiPtBu2 yields deeply-colored phosphide complexes Cp*HfCl2(PtBu2) and Cp*HfCl(PtBu2)2, respectively. Alkyl and aryl derivatives of Cp*HfCl2 (PtBu2), Cp*HfR(Y)(PtBu2) (R=Y=Me; Y=Cl, R-CH2CMe, CH2Ph, Ph), are prepared either by direct alkylation, or from the corresponding chloro-alkyls Cp*ClnR3-n. Cp*HfMe2(PtBu2) reacts slowly with H2 to form a highly insoluble methyl hydridophosphide dimer, [Cp*HfMe(\u00b5-H)(\u00b5-PtBu2)]2. The crystal structure of [Cp*HfMe(\u00b5-H)(\u00b5-PtBu2)]2 reveals a symmetric-bridged Hf2P2 core with Hf-P distances of 2.805, 2.807 A. The hydride ligands have been tentatively located and form an assymetric Hf2H2 bridge (Hf-H = 2.12, 2.33 A) orthogonal to the planar Hf2P2 moiety. The final R index is 0.066. Hydrogenolysis of alkyl derivatives Cp*HfClR(PtBu2) (R = CH2CMe3, CH2Ph) affords an analogous chlorothydridophosphide dimer, [Cp*HfCl(\u00b5-H)(\u00b5-Pt Bu2)]2. Treatment of Cp*HfCl(PtBu2)2 with H2 leads to rapid cleavage of Hf-P bonds and formation of [Cp*HfCl(\u00b5-H)(\u00b5-PtBu2]2. Cp*HfCl2(PtBu2) also reacts with H2, albeit slower, to give products derived from initially-formed Cp*HfCl2H.
\r\n\r\nThe relatively low Hf-P bond energy suggested by hydrogenolysis reactions in these systems is further indicated by the reaction of Cp*HfCl2(PtBu 2) with CO to form the CO-insertion product, Cp*HfCl2 (\u03b72-C(O)PtBu2). The crystal structure of Cp*HfCl2(\u03b72-C(O)PtBu2) exhibits dihapto carboxyphosphide functionality, with Hf-C = 2.203 and Hf-O = 2.117 A. The P-C(acyl) bond is 0.08 A shorter than P-C(alkyl) values, and suggests a significant P-\u03c0 interaction. This has been confirmed by variable temperature studies, which reveal a substantial (10.7 kcal/mol) barrier to rotation about the P-C(acyl) bond.
" }, { "name": "San, Ka-Yiu", "degree": "PhD", "year": "1984", "title": "Studies on the On-Line Identification and Optimal Control of Bioreactors", "advisor": "Stephanopoulos, Gregory N.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01082007-153733", "creators": [ { "name": { "family": "San", "given": "Ka-Yiu" }, "id": "San-Ka-Yiu", "display_name": "San, Ka-Yiu" } ], "advisors": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "advisor", "display_name": "Stephanopoulos, Gregory N." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Hoffmann", "given": "Michael R." }, "id": "Hoffmann-M-R", "orcid": "0000-0001-6495-1946", "role": "member", "display_name": "Hoffmann, Michael R." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." } ], "option_major": [ "chemeng" ], "doi": "10.7907/b5p1-5c02", "abstract": "An integrated approach is presented for the on-line estimation of the state of a biochemical reactor from presently attainable real-time measurements. Elemental and macroscopic balances are used for the determination of the total rate of growth and state-of-the-art estimation techniques are subsequently employed for the elimination of process and measurement noise and the estimation of the state variables and unknown culture parameters. The proposed approach is very flexible in that as new sensors become available they can be easily incorporated within the present framework to estimate new variables or improve the accuracy of the old ones. The method does not require any model for the growth kinetics and is very sucessful in accurately estimating the above variables in the presence of intense noise and under both steady state and transient conditions. Computer simulation as well as experimental results obtained from this study clearly demonstrate the superb performance of such estimation methodology. State estimates obtained by the proposed method can be used for the development of adaptive optimal control schemes as well as for basic studies of the characteristic properties of microbial cultures.
\r\n" }, { "name": "Schultz, Jocelyn Chupka", "degree": "PhD", "year": "1984", "title": "Photoelectron Spectroscopy of Alkyl and Alkenyl Free Radicals", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032018-091338203", "creators": [ { "name": { "family": "Schultz", "given": "Jocelyn Chupka" }, "id": "Schultz-Jocelyn-Chupka", "display_name": "Schultz, Jocelyn Chupka" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/r2r1-k971", "abstract": "The first bands of the photoelectron spectra of simple alkyl and alkenyl free radicals, produced by pyrolysis of organic nitrites, are presented. Thermochemical and structural information about the corresponding carbocations in the gas phase are obtained from interpreting the spectra. In particular, adiabatic ionization potentials are combined with radical heats of formation to obtain heats of formation of the cations. The photoelectron band shapes are discussed in terms of structural changes occurring upon ionization. The focus of this work is\u00b7 the study of isomeric radicals. Their photoelectron spectra allow the characterization of a series of carbocations with well-defined structures, namely those which closely resemble the radicals, even when the cations can rearrange with little or no activation energy to more stable forms. Radical thermal rearrangement and decomposition pathways are also studied.
\r\n\r\nChapter I provides a brief introduction to the field of photoelectron spectroscopy of transient species, including a compilation of photoelectron data of transient species, and an introduction to the specific work presented in this thesis. Chapter II presents the photoelectron spectra of the C4H7 radicals 1-methylallyl, 2-methylallyl, allylcarbinyl and cyclobutyl radical, which provide information about the corresponding C4H+7 carbocations in the gas phase. These cations are of longstanding interest in the cyclopropylcarbinyl, cyclobutyl and allylcarbinyl interconversions observed in solvolysis reactions. The photoelectron spectra of 1-propyl, 1-butyl, isobutyl, neopentyl and 2-butyl radicals are presented in Chapter III. The corresponding primary cations are of particular interest because they are often postulated as intermediates or transition states in gas-phase and solution isomerization processes.
\r\n\r\nChapter IV describes the application of photoelectron spectroscopy to the study of low-pressure gas-surface reactions. Organic radicals, as well as stable products, have been detected directly after exiting the catalyst bed. Allylic hydrogen abstraction by heated bismuth oxide catalyst forms gas-phase allyl and 2-methylallyl radicals from propylene and isobutylene in the presence of oxygen. Mechanistic information is obtained by varying the catalyst temperature and reactant partial pressures.
\r\n" }, { "name": "Schultz, Peter G.", "degree": "PhD", "year": "1984", "title": "I. Ground and Excited State Studies of Persistent 1,1-Diazenes. II. Design of Sequence Specific DNA Cleaving Molecules", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252004-112048", "creators": [ { "name": { "family": "Schultz", "given": "Peter G." }, "id": "Schultz-Peter-G", "display_name": "Schultz, Peter G." } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6vcz-qs72", "abstract": "CHAPTER I
\r\n\r\nDirect studies of the ground and excited state properties of kinetically persistent l,l-dialkyldiazenes are reported. The electronic absorption spectrum of N-(2,2,5,5-tetramethylpyrrolidyl)nitrene 3 reveals a structured absorption band for the n,\u03c0* transition: \u03bbmax = 497 nm, \u03bb0,0 = 572 nm (\u03bbmax = 20 \u00b1 3) in CH2Cl2; \u03bb0,0 = 552 nm in i-PrOH. The infrared spectrum shows a strong absorption at 1638 cm-1, providing evidence that the 1,1-diazene N-N stretch has considerable double bond character. The major products resulting from pyrolysis of 3 at 0\u00b0C are isobutylene 21, tetramethylcyclobutane 20, and tetrazene 24, consistent with unimolecular and bimolecular decomposition pathways. The activation parameters for unimolecular fragmentation are: log A = 12.4 \u00b1 0.4, Ea = 19.0 \u00b1 0.6 kcal mole-1 in Et2,O; log A = 12.1 \u00b1 0.3; Ea = 19.1 \u00b1 0.4 kcal mole-1 in THF; log A = 10.9 \u00b1 0.3, Ea = 16.8 \u00b1 0.5 kcal mole-1 in hexane. The activation parameters for the bimolecular dimerization of 3 could not be measured, however log A = 3.8 \u00b1 0.7 and Ea = 6.4 \u00b1 0.9 kcal mole-1 for the dimerization of N-(2,2,6,6-tetramethylpiperidyl)nitrene 2 in CDCl3.
\r\n\r\nThe fluorescence spectrum of 3 has a 0-0 band at 607 nm which is the maximum. The spacing between the peaks at 607 and 672 nm is consistent with the N=N stretch of S0 obtained from the infrared spectrum. The fluorescent quantum yields are \u03a6F = 2 x 10-3 (MTHF, -78\u00b0C), 7 x 10-8 (CFCl3, -196\u00b0C) and 1 x 10-3 (EPA, -196\u00b0C). The fluorescent lifetime of 3, \u03c4F is 5 x 10-9 sec (CFCl3, -78\u00b0C) and 2.3 x 10-8 sec (CFCl3, -196\u00b0C). Direct irradiation of 3 in the visible (-78\u00b0C) affords 54% 21, 44% 20, and tetrazene 24, again consistent with unimolecular and bimolecular decomposition pathways. Triplet sensitized photolysis affords a high cleavage/closure ratio: 74% 21 and 24% 20. An approximate quantum yield for decomposition of 3 on direct irradiation (-78\u00b0C) is \u03a6D = 1.1 x 10-2.
\r\n\r\nD,1-N(2,5-diethyl-2,5-dimethylpyrrolidyl)nitrene 26 has a structured visible absorption with \u03bbmax at 507 nm. The maximum of the fluorescence spectrum is 620 nm, \u03a6F = 9 x 10-3 (MTHF, -196\u00b0C). Direct and sensitized irradiation of 26 in the visible (-78\u00b0C) affords closure, cleavage, and disproportionation products as well as tetrazene. The retention of configuration in the cyclobutane products was 98% and 68% for direct and sensitized decompositions, respectively. This spin correlation effect indicates that kISC < < kN2 (S1), consistent with the large calculated S1-T1 gap in 1,1-diazenes. Comparison of these results with those in the literature for the isomeric 1,2-diazene provides information on the nature of intersystem crossing in nonconjugated diradicals. The deactivation rates for S1 of 1,1-diazene 3 have been determined: kIC = 2 x 108 sec-1 (-78\u00b0C); kF = 3 x 105 sec-1; kDIM ~ 8 x 107 M-1 s-1 (-78\u00b0C); kN2 ~ 3 x 105 sec-1 (-78\u00b0C); ET \u2264 31 kcal mole-1.
\r\n\r\nThe photochemistry of the six-membered ring cyclic 1,1-diazene 2 was also examined.
\r\n\r\nCHAPTER II
\r\n\r\nThe ability of restriction endonucleases to cleave double helical DNA on opposite strands at or near 4-6 base pair recognition sequences makes possible DNA sequencing, gene isolation and recombinant DNA technology. Studies aimed at defining those elements necessary for the design of synthetic double strand DNA cleaving molecules with defined target sequences and binding site sizes are described.
\r\n\r\nThe covalent modification of sequence specific DNA binding molecules with a chelated metal capable of redox chemistry generates bifunctional DNA cleaving molecules. Attachment of EDTA to the amino or carboxy terminus of the N-methylpyrrole oligopeptide distamycin A affords distamycin-EDTA (DE) and EDTA-distamycin (ED), respectively. DE\u2022Fe(II) and ED\u2022Fe(II) (10-6M) sequence specifically single strand cleave pBR-322 plasmid DNA (10-5 bp) in the presence of O2 and dithiothreitol (DTT). Cleavage occurs over three to five base pairs adjacent to a five base pair 5'-XXTTT-3' (X = A or T) binding site and is consistent with oxidative degradation of the deoxyribose. Analysis of the DNA cleavage patterns generated by DE\u2022Fe(II) and ED\u2022Fe(II) (high resolution denaturing gel electrophoresis) provides information on the location, size, and orientations of distamycin binding sites on DNA. This direct method for defining small molecule binding sites on DNA, \"DNA affinity cleaving\", is compared to methidiumpropyl-EDTA\u2022Fe(II) (MPE\u2022Fe(II)) footprinting. A model for distamycin binding is proposed.
\r\n\r\nAttachment of EDTA to the amino terminus of a penta-N-methylpyrrole peptide yields P5E. In the presence of O2 and DTT, P5E\u2022Fe(II) (10-8M bp) converts supercoiled pBR-322 DNA (10-3M) to 40% open circular DNA, indicating that cleavage is catalytic, with a minimum of nine turnovers. P5E\u2022Fe(II) sequence specifically double strand cleaves linear pBR-322 DNA (4362 base pairs) into discrete fragments. The cleavage sites are located at 4.3, 4.2, 3.3, 3.2 kb (major) and 2.6, 2.4, 2.0, 1.8 kb (minor). P5E\u2022Fe(II) binds preferentially to 6-7 base pair poly(dA)\u2022poly(dT) sites.
\r\n\r\nEBD and BED consist of two N-methylpyrrole tripeptide units coupled at the amino termini via a flexible linker with EDTA tethered to one or both carboxy termini, respectively. BED\u20222Fe(II) and EBD\u2022Fe(II) cleave pBR-322 (10-5M bp) DNA at nanomolar concentrations. These reagents cleave linear pBR-322 plasmid DNA at 4.3 and 3.3 kb to afford discrete fragments. BED\u2022Fe(II) and EBD\u2022Fe(II) bind as dimers to 8-9 base pair A+T sites and monomers to 5-6 base pair A+T sites.
" }, { "name": "Shih, Thomas Loong", "degree": "PhD", "year": "1984", "title": "Use of Enantioselective Aldol Condensations: Efforts Directed Towards the Total Synthesis of Ionomycin", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10192018-103740684", "creators": [ { "name": { "family": "Shih", "given": "Thomas Loong" }, "id": "Shih-Thomas-Loong", "display_name": "Shih, Thomas Loong" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vhx3-s283", "abstract": "The amino acid derived N-acyl oxazolidones were found to be excellent chiral enolate synthons in the aldol condensation. The dialkylboron enolates of these imides exhibit very high levels of asymmetric induction and diastereoselection. However, the use of N-acetyl oxazolidones resulted in much lower diastereoselection. In these cases, substitution of N-acetyl oxazolidones with N-\u03b1-thiomethylacetyl oxazolidones (followed by Raney Nickel desulfurization) restored the high level of stereoselection.
\r\n\r\nApplication of this methodology to the total synthesis of ionomycin is described.
" }, { "name": "Soto Gonzalez, Jorge", "degree": "PhD", "year": "1984", "title": "Mechanistic Aspects of the Ziegler-Natta Polymerization", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07072014-083212737", "creators": [ { "name": { "family": "Soto Gonzalez", "given": "Jorge" }, "id": "Soto-Gonzalez-Jorge", "display_name": "Soto Gonzalez, Jorge" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AXPG-AG37", "abstract": "The isotope effect on propagation rate was determined for four homogeneous ethylene polymerization systems. The catalytic system Cp2Ti(Et)Cl + EtAlCl2 has a kHp/kDp = 1.035 \u00b1 0.03. This result strongly supports an insertion mechanism which does not involve a hydrogen migration during the rate determining step of propagation (Cossee mechanism). Three metal-alkyl free systems were also studied. The catalyst I2(PMe3)3Ta(neopentylidene)(H) has a kHp/kDp = 1.709. It is interpreted as a primary isotope effect involving a non-linear \u03b1-hydrogen migration during the rate determining step of propagation (Green mechanism). The lanthanide complexes Cp*2LuMe\u2022Et2O and Cp*2YbMe\u2022Et2O have a kHp/kDp = 1.46 and 1.25, respectively. They are interpreted as primary isotope effects due to a partial hydrogen migration during the rate determining step of propagation.
\r\n\r\nThe presence of a precoordination or other intermediate species during the polymerization of ethylene by the mentioned metal-alkyl free catalysts was sought by low temperature NMR spectroscopy. However, no evidence for such species was found. If they exist, their concentrations are very small or their lifetimes are shorter than the NMR time scale.
\r\n\r\nTwo titanocene (alkenyl)chlorides (hexenyl 1 and heptenyl 2 were prepared from titanocene dichloride and a THF solution of the corresponding alkenylmagnesium chloride. They do not cyclize in solution when alone, but cyclization to their respective titanocene(methyl(cycloalkyl) chlorides occurs readily in the presence of a Lewis acid. It is demonstrated that such cyclization occurs with the alkenyl ligand within the coordination sphere of the titanium atom. Cyclization of 1 with EtAlCl2 at 0\u00b0C occurs in less than 95 msec (ethylene insertion time), as shown by the presence of 97% cyclopentyl-capped oligomers when polymerizing ethylene with this system. Some alkyl exchange occurs (3%). Cyclization of 2 is slower under the same reaction conditions and is not complete in 95 msec as shown by the presence of both cyclohexyl-capped oligomers (35%) and odd number \u03b1-olefin oligomers (50%). Alkyl exchange is more extensive as evidenced by the even number n-alkanes (15%).
\r\n\r\nCyclization of 2-d1 (titanocene(hept-6-en-1-y1-1-d1)chloride) with EtAlCl2 demonstrated that for this system there is no \u03b1-hydrogen participation during said process. The cyclization is believed to occur by a Cossee-type mechanism. There was no evidence for precoordination of the alkenyl double bond during the cyclization process.
\r\n" }, { "name": "Steigerwald, Michael Louis", "degree": "PhD", "year": "1984", "title": "2\u209b + 2\u209b Reactions at Transition Metals", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01032007-142600", "creators": [ { "name": { "family": "Steigerwald", "given": "Michael Louis" }, "id": "Steigerwald-Michael-Louis", "orcid": "0000-0001-6337-2707", "display_name": "Steigerwald, Michael Louis" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/S0HZ-TF05", "abstract": "A study of the suprafacial 2 + 2 reaction at transition metal centers is presented. It is demonstrated that this reaction is allowed and proceeds with a low activation energy if the reacting transition metal-to-substituent bond is covalent, nonpolar, and has a large component at transition nickel d-orbital character. These chains are evinced by examination of 2s + 2s reactions at M-H bonds. Those systems in which M can use d orbitals show lower barriers to the 2s + 2s reaction than those in which M cannot use d orbitals.
\r\n\r\nThe importance of the electronic structure of the metal-to-substituent bond is highlighted by a study of dichorotitanacyclopropane. This molecule, being a metallacyclopropane, can undergo 2s + 2s reactions which one unavailable to a simple olefin.
\r\n\r\nStudies concerning the importance of 2s + 2s reactivity in the organic chemistry of nickel, and in the Ziegler-Natta polymerization of simple olefins are presented.
\r\n\r\nIt is suggested that the principle of maximum bonding (the Woodward-Hoffmann rules) implies the conservation of transition metal covalency in low-energy catalytic cycles.
" }, { "name": "Swartz, Barry Allan", "degree": "PhD", "year": "1984", "title": "Free Jet Expansion Laser Spectroscopy of van der Waals Molecules Containing Ne and Br\u2082", "advisor": "Sparks, Randal K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312018-092920492", "creators": [ { "name": { "family": "Swartz", "given": "Barry Allan" }, "id": "Swartz-Barry-Allan", "display_name": "Swartz, Barry Allan" } ], "advisors": [ { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "advisor", "display_name": "Sparks, Randal K." } ], "committee": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "chair", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "McGill", "given": "Thomas C." }, "id": "McGill-T-C", "role": "member", "display_name": "McGill, Thomas C." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mp06-am61", "abstract": "Fluorescence excitation spectra of complexes of Ne and Br2 containing up to four Ne atoms have been measured. The van der Waals molecules were synthesized in a free jet expansion and excited with tunable excimer-pumped dye laser radiation. Features attributable to van der Waals complexes by virtue of their intensity dependences on molecular beam stagnation pressure appear shifted to the blue of band origins of the B3\u03a0o+g \u2190 X1\u03a3+g transition of all three isotopic species of Br2. Spectra were recorded for transitions (11-0) through (30-0) of Br2 which show that the specral shifts of the complexes relative to the Br2 band origins increase with increasing v'. NeBr2 shifts range from 5.5 to 8.8 cm-1. The spectral widths of the van der Waals features also increase with v' from a laser bandwidth limited value of 0.10 cm-1 for NeBr2 (16-0) to 3.1 cm-1 for (27-0). This indicates a greater than order of magnitude change in the lifetimes of these complexes with level of vibrational excitation which is disucssed in relation to recent theories on the dynamics of weakly bound systems. Estimates of 73 and 64 cm-1 were obtained for the van der Waals bond dissociation energy for the ground and excited electronic states, respectively.
\r\n" }, { "name": "Templeton, Michael Karpovich", "degree": "PhD", "year": "1984", "title": "The Identification of Stable Reaction Intermediates on Aluminum Oxide Surfaces with Inelastic Electron Tunneling Spectroscopy", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-01262007-130514", "creators": [ { "name": { "family": "Templeton", "given": "Michael Karpovich" }, "id": "Templeton-Michael-Karpovich", "display_name": "Templeton, Michael Karpovich" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Lambe", "given": "John" }, "id": "Lambe-John", "role": "member", "display_name": "Lambe, John" }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" } ], "option_major": [ "chemeng" ], "doi": "10.7907/et22-8s13", "abstract": "The stable surface intermediates that were formed in several heterogeneous reactions on aluminum oxide films were identified with inelastic electron tunneling spectroscopy. The heterogeneous reactions included associative and dissociative adsorption, nucleophilic substitution, surface catalyzed elimination, hydrolysis and hydrogenolysis. Primarily two chemisorption systems are discussed. These are cyclopropane carboxylic acid on aluminum oxide and phosphonate esters on aluminum oxide. In conjunction with the temperature and exposure dependence of the stable reaction intermediates, the nature of these reactions and the aluminum oxide surface are discussed.
\r\n\r\nThe temperature and exposure dependent interaction of cyclopropane carboxylic acid with alumina surfaces has been studied with inelastic electron tunneling spectroscopy. Cyclopropane carboxylate and n-butane carboxylate were the only adsorbed species formed, as determined by a comparison with tunneling spectra of n-butane carboxylic acid and cyclopropane carboxylic acid coadsorbed on alumina. The n-butane carboxylate results from hydrogenolysis of the cyclopropyl ring of the adsorbed cyclopropane carboxylate with hydrogen supplied by surface hydroxyl groups. The relative populations of the two surface species are strongly dependent upon coverage and temperature.
\r\n\r\nThe adsorption of gaseous dimethyl methyl phosphonate (DMMP) on aluminum oxide film surfaces has been investigated with inelastic electron tunneling spectroscopy. Surface temperatures ranged between 200 K and 673 K, and exposures ranged between 3 x 10-4 and 10 Torr-s. Tunneling spectra of deuterium labeled DMMP, perdeutero methyl alcohol, methyl methyl phosphonic acid, methyl phosphonic acid and trimethyl phosphine oxide, all adsorbed on aluminum oxide surfaces, were used to clarify the structures of the species resulting from the adsorption and decomposition of DMMP. At 200 K, DMMP is adsorbed molecularly with high surface coverages. At surface temperatures above 295 K, DMMP is adsorbed dissociatively in low coverages. Surface temperatures above 473 K lead to the dealkylation of the dissociatively adsorbed adspecies, which results in the formation of adsorbed methyl phosphonate.
\r\n\r\nInelastic electron tunneling spectroscopy was used to examine comparatively the adsorption and reaction of three phosphonate esters on aluminum oxide surfaces which were synthesized by the plasma oxidation of aluminum metal films. The phosphonate esters were diisopropyl methyl phosphonate (DIMP), dimethyl methyl phosphonate (DMMP) and diphenyl methyl phosphonate (DPMP). The adsorption temperatures ranged from 200 to 673 K. The exposures of gaseous DIMP and DMMP were 1.0 Torr-s, while DPMP was exposed to the surface as a 0.025 M solution in hexane. DIMP was found to adsorb associatively in low coverages at 295 K, whereas at 373 K, DIMP was found to adsorb dissociatively in low coverages as isopropyl methyl phosphonate. Above 373 K the isopropyl methyl phosphonate decomposed to the metastable hydroxy methyl phosphonate, which, in turn, decomposed completely to the methy phosphonate above 573 K. Although the dissociative adsorption temperature was lower (295 K), adsorbed DMMP decomposed similarly through the hydroxy methyl phosphonate to form the methyl phosphonate. However, in this case the hydroxy methyl phosphonate was a short-lived intermediate. DPMP was found to adsorb dissociatively at 295 K, and the adsorbed species formed is stable through 673 K. Consistent with these observations, mechanisms for the adsorption and decomposition of phosphonate esters on aluminum oxide are proposed that involve P-O bond cleavage upon adsorption but O-C bond cleavage upon decomposition of the adspecies.
\r\n\r\nA versatile tunnel junction fabrication system is described. A temperature controller which resistively heats the aluminum oxide films by passing a current through the underlying aluminum film is presented. Computer software for spectral analysis is discussed.
\r\n" }, { "name": "Turner, Steve Ronald", "degree": "Masters", "year": "1984", "title": "Nitrogen Protecting Groups in the Ester Enolate Claisen Rearrangement of Amino Esters. Synthesis of a Furanomycin Derivative", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-081412450", "creators": [ { "name": { "family": "Turner", "given": "Steve Ronald" }, "id": "Turner-Steve-Ronald", "display_name": "Turner, Steve Ronald" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x02s-jt53", "abstract": "No abstract." }, { "name": "Van Dyke, Michael W.", "degree": "PhD", "year": "1984", "title": "MPE\u2022Fe(II) Footprinting: Drug Binding Sites on Native DNA", "advisor": "Davidson, Eric H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12052018-113900386", "creators": [ { "name": { "family": "Van Dyke", "given": "Michael W." }, "id": "Van-Dyke-Michael-W", "orcid": "0000-0003-0306-4002", "display_name": "Van Dyke, Michael W." } ], "advisors": [ { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "advisor", "display_name": "Davidson, Eric H." } ], "committee": [ { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "chair", "display_name": "Davidson, Eric H." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Simon", "given": "Melvin I." }, "id": "Simon-M-I", "role": "member", "display_name": "Simon, Melvin I." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vy36-rq29", "abstract": "Many small molecules, such as antibiotics used in cancer chemotherapy, are believed to execute their therapeutic action through binding to the DNA template and impeding the progress of transcription and replication. While it is possible by spectroscopic means to determine the overall affinities and stoichiometries of these small molecule/DNA interactions, the exact locations and sizes of these sites of interaction are not known. The analogous question of protein: DNA binding specificities has been answered through the use of DNase I footprinting. This technique combines DNase I cleavage of protein protected DNA fragments and Maxam-Gilbert sequence determination methods, relying on the relatively low specificity of DNase I in a partial digestion and the ability of DNA-bound proteins to prevent phosphodiester bond hydrolysis between the base pairs they cover.
\r\n\r\nReported within is a direct technique, MPE\u2022Fe(II) footprinting, which allows the determination of the preferred binding sites of several small molecules on heterogeneous double helical DNAs. Methidiumpropyl EDTA [MPE], in the presence of ferrous ion and oxygen efficiently creates single-strand breaks in double helical DNA and with significantly lower sequence specificity than DNase I. Utilizing MPE\u2022Fe(II) as a small synthetic scissor one is capable of footprinting the preferred locations and binding site sizes of small molecules bound on native DNA.
\r\n\r\nThe small molecules actinomycin D, chromomycin A3, distamycin A, echinomycin, mithramycin, netropsin, and olivomycin have been shown to demonstrate sequence specific MPE\u2022Fe(II) cleavage inhibition, thus allowing a determination of their preferred binding sites and site sizes. Actinomycin D was found to have a minimum site size of 3 base pairs and an absolute guanine requirement in its binding site. Distamycin A and netropsin demonstrated equivalent binding specificities, preferring contiguous A+T rich regions of 5 base pairs in length. Chromomycin A3, mithramycin, and olivomycin all shared similar binding specificities, demonstrating typically 3 base pair binding site sizes and preferring a 5'-GC-3' sequence within. Echinomycin protected a minimum of 4 base pairs; nearly all sites containing a central 5'-CG-3' sequence with 5'-CCGG-3' being favored. All footprints demonstrated an opposite strand asymmetry with overprotection on the 3' end. From a collection of their preferred binding sites, binding models for these small molecules have been derived.
\r\n\r\nMPE\u2022Fe(II) footprinting has been compared with DNase I footprinting in their ability to determine the binding specificities of both small molecules and proteins. While DNase I exhibits a slightly greater sensitivity, MPE\u2022Fe(II) footprinting provided greater resolving capacity and importantly more precisely defined the binding locations and sizes of small molecule: DNA complexes. Both methods provided similar information in the case of a sequence-specific DNA binding protein, lac repressor. Investigations were also undertaken to study the effects of altered DNA conformation (Z-form DNA; binding cooperativity of different small molecules) on the interactions of small molecules with native DNA.
" }, { "name": "Winkler, Jay Richmond", "degree": "PhD", "year": "1984", "title": "Spectroscopy and Photochemistry of Metal-Oxo Complexes", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-02272006-082939", "creators": [ { "name": { "family": "Winkler", "given": "Jay Richmond" }, "id": "Winkler-Jay-Richmond", "orcid": "0000-0002-4453-9716", "display_name": "Winkler, Jay Richmond" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DE5E-2Y69", "abstract": "Electronic spectroscopic, photophysical, and photochemical investigations of two types of metal-oxo complexes are described. The electronic absorption spectra of various molybdenyl ions (MoO3+ were measured in crystals and solutions. These spectra clearly support 2B1(x2-y2) \u2190 2B2(xy) and 2E(xz, yz) \u2190 2B2(xy) assignments for the two weak bands near 25,000 and 14,000 cm-1, respectively, in these molecules. A Franck-Condon analysis of the 2B1 \u2190 2B2 band in the 5 K single crystal absorption spectrum of (Ph4As)MoOCl4 indicated a 0.07(1) \u00c5 elongation of the metal-chloride bond in the excited state. Crystalline (Ph4As)MoOCl4 luminesces from the lower energy component of a split 2E(xz, yz) state with a lifetime of 160 ns at 300 K, increasing to 1.4 \u00b5s at 5 K. No luminescence was detected from any molybdenyl ion in solution.
\r\n\r\nThe electronic absorption and emission spectra of trans-ReO2L4z (L = CN-, z = 3-; L = 1/2(ethylenediamine), z = +; L = pyridine, z = +; L = 4-picoline, z = +; L = 4-t-butylpyridine, z = +) were also measured in crystals and solutions. The lowest energy absorption bands are assigned to components of a split 3Eg[(eg)1(b2g)1] state (ground state 1Ag1g[(b2g)2]). Emission from at least two of these components was identified in the cyanide and pyridine complexes and only the ethylenediamine complex failed to luminesce. Franck-Condon analyses of the emission spectra indicated ca. 0.1 \u00c5 elongations of each Re-O bond in the 3Eg excited states. The lifetime of the 3Eg state varies from 10 to 300 \u00b5s in crystals and is ca. 10 \u00b5s for trans-ReO2L4z species in aprotic solvents. Protons efficiently quench the luminescence of these molecules. Experiments directed toward photoinduced oxygen atom transfer chemistry are also described.
\r\n" }, { "name": "Allen, David Thomas", "degree": "PhD", "year": "1983", "title": "Modeling the Reactions of Coal Liquids", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08312006-082647", "creators": [ { "name": { "family": "Allen", "given": "David Thomas" }, "id": "Allen-David-Thomas", "orcid": "0000-0001-6646-8755", "display_name": "Allen, David Thomas" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." } ], "option_major": [ "chemeng" ], "doi": "10.7907/ph4t-rb90", "abstract": "This thesis begins the development of a new approach to the kinetic modeling of complex hydrocarbon mixtures. The approach is based on functional group reactions and its implementation involves three steps. The first step is to characterize complex hydrocarbon mixtures, such as coal-derived liquids, heavy oils and shale oils, in terms of their constituent functional groups. A methodology is defined for estimating functional group concentrations from elemental analysis and NMR data. Mass spectra, infared spectra, separation yields and other analytical data may also be incorporated into the concentration estimates. The methodology is demonstrated for a heavy oil and for a wide variety of coal liquids.
\r\n\r\nThe concentrations provide a starting point for kinetic modeling. The second step of the modeling procedure is to determine the rates and pathways of the reactions of the functional groups by investigating the reactions of pure compounds containing the same functionalities. The reactions of a number of these model compound systems were examined. The studies focused on the reactions of atomic hydrogen under conditions appropriate to coal liquefaction.
\r\n\r\nThe final step in the modeling is the development of a mathematical model which can predict changes in functional group concentrations given initial concentrations and reaction rates. This is outside the scope of this thesis, but general guidelines and valid simplifications are discussed.
\r\n" }, { "name": "Anderson, Julie Ann", "degree": "Masters", "year": "1983", "title": "A Total Synthesis of Spiro[Bis(2,3-Diazabicyclo[2.2.1]-Hept-2-Ene-7,7']", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-142818016", "creators": [ { "name": { "family": "Anderson", "given": "Julie Ann" }, "id": "Anderson-Julie-Ann", "display_name": "Anderson, Julie Ann" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cqp3-1k14", "abstract": "The total synthesis of spiro[bis(2,3-diazabicyclo[2.2.1]-hept-2-ene)-7,7\u2019] from trans-1,4-dibromo-2-butene was accomplished. One advantage of this synthetic route is that it can be carried out on a relatively large scale. Another advantage is that the synthesis is flexible. With a few minor modifications, one can generate various C\u2089H\u2081\u2082 spiro ring system derivatives." }, { "name": "Barger, Paul Theron", "degree": "PhD", "year": "1983", "title": "The Reactivity of Zirconium Hydrides with Transition Metal Carbonyls", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262018-130043347", "creators": [ { "name": { "family": "Barger", "given": "Paul Theron" }, "id": "Barger-Paul-Theron", "display_name": "Barger, Paul Theron" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/qvev-5987", "abstract": "The reactivity of bis(pentamethylcyclopentadienyl) zirconium hydride complexes with a variety of Group VIII transition metal carbonyls has been investigated. These reactions are observed to follow two distinct pathways; one involving reductive loss of the zirconium hydrides as H2, the other proceeding by. hydride transfer to the carbon atom of a carbonyl to afford CO reduction. Treatment of CpM(CO)2 (M=Co, Rh, RuH) with Cp2*ZrH2 or [Cp2*ZrN2]2N2(Cp=C5H5, Cp*=C5Me5) give the \"early\" and \"late\" metal dimers, CpM(CO)2ZrCp2*: with elimination of H2 or N2. The X-ray crystal structure of CpCo(CO)2ZrCp2*; is reported and shows that this molecule contains a Co-Zr single bond bridged by a conventionally bound \u03bc-CO and a four-electron donating \u03bc-\u03b71, \u03b71 CO. The reactions of Cp2*ZrHX (X=F, Cl) with these carbonyls proceed by the second pathway to give oxycarbene complexes, Cp(CO)M=CHO-Zr(X)Cp2* (M=Co, Rh). These compounds demonstrate that the zirconium hydride reduction of a Group VIII metal carbonyl is reversible; an equilibrium is observed between the carbene complexes and the starting metal dicarbonyl and ziconium hydride. Treatment of CpM(CO)(PMe3)H or CpM(CO)2CH3 (M=Fe, Ru) with Cp2*ZrH2, in the presence of PMe3, affords Cp(PMe3)2M-CH2O-Zr(H)Cp2* or Cp2*Zr(OCH=CH2)H. The mechanisms of the transformation are proposed to involve initial formation of an iron or ruthenium oxycarbene intermediate which undergoes migratory insertion into the metal hydride or alkyl bond followed by phosphine trapping or \u03b2-elimination to give the observed products.
\r\n\r\nSeveral zirconium oxycarbene complexes have been prepared by the reduction of the corresponding zirconium carbonyl by Cp2*ZrH2. These molecules represent some of the first isolable examples of Group IV metal to carbon multiple bonding. The X-ray crystal structure of Cp2(PMe3)Zr=CHO-Zr(I)Cp2* \u2022 C6H6 is reported. Treatment of Cp2(CO)Zr=CHO-Zr(H)Cp2* with MeI or Cp2(PMe3)Zr=CHO-Zr(I)Cp2* with CO gives a new product, the structure of which has been shown by X-ray diffraction to be Cp2*ZrOCH=C(Zr(I)Cp2*)O. The mechanism for this transformation has been shown to involve an intramolecular coupling of carbene and carbonyl ligands on a zirconium center to give a zirconium ketene intermediate, which rearranges to the observed product. In the presence of pyridine the ketene intermediate can be trapped to give the isolable Cp2(pyr)Zr(O=C=CHO-Zr(H)Cp2*).
" }, { "name": "Becker, Nancy Newton", "degree": "PhD", "year": "1983", "title": "\u00b9\u2075N Nuclear Magnetic Resonance Studies of the Liver Alcohol Dehydrogenase-NAD\u207a-Pyrazole Complex", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262018-161343127", "creators": [ { "name": { "family": "Becker", "given": "Nancy Newton" }, "id": "Becker-Nancy-Newton", "display_name": "Becker, Nancy Newton" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nnx8-q333", "abstract": "The structures of the liver alcohol dehydrogenase (LADH)-NAD+-pyrazole and LADH-NAD+-4-ethylpyrazole complexes were investigated by 15N nuclear magnetic resonance (NMR) spectroscopy. 15N chemical shifts were obtained for 15N-labeled inhibitors and 15N-labeled coenzyme bound in the enzyme ternary complexes. The structures of the two inhibitor complexes were found to be very similar. 15N chemical shifts of various pyrazole derivatives were determined. 15N NMR studies of model pyrazole derivative-zinc chloride complexes were carried out to determine the effect of zinc complexation on the pyrazole N2 chemical shift. The N1 nicotinarnide resonance of the coenzyme of the LADH-NAD+-pyrazole complex was 96 ppm upfield from that of NAD+ in solution and only 13 ppm downfield from that of NADH in solution, demonstrating formation of a derivative of dihydronicotinamide. The 15N chemical shift of the pyrazole N1 of the ternary complex when compared to other pyrazole derivatives indicated bond formation between pyrazole N1 and the nicotinarnide ring of the coenzyme. The 15N shift of the pyrazole N1 of the model pyrazole-NAD+ adduct, N-benzyl-1,4-dihydro-4-pyrazolylnicotinarnide, was 5.8 ppm downfield from that of N1 of the enzyme ternary complex. The 15N chemical shift of the pyrazole N2 of the ternary complex compared to pyrazole derivatives in solution was shielded by more than 40 ppm, demonstrating direct complexation of N2 to the active-site zinc. The results of model zinc complex studies indicated 60-100% inner-sphere coordination of the pyrazole N2 to the active-site zinc in the ternary complex.
" }, { "name": "Begley, Tadhg Pulcarious", "degree": "PhD", "year": "1983", "title": "Bispecific, Cleavable, Protein DNA Crosslinker, Psoralen-Diol-Nitroveratrole. A Probe of Bacteriophage Structure", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10202010-084119498", "creators": [ { "name": { "family": "Begley", "given": "Tadhg Pulcarious" }, "id": "Begley-Tadhg-Pulcarious", "orcid": "0000-0001-5134-2623", "display_name": "Begley, Tadhg Pulcarious" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BPQM-KP51", "abstract": "The synthesis of a cleavable, photochemically activated, bispecific protein-DNA crosslinking reagent, psoralen-diol-nitroveratrole (PDN) is described. The reagent crosslinks the capsid proteins to the packaged DNA in bacteriophage T7. The SDS dissociated crosslinked phage appears under the electron microscope as a rosette with the phage head at the center. DNA from the crosslinked phage does not enter agarose gels in the absence of SDS. Treatment of the crosslinked phage with proteinase K or cleavage of the crosslink with sodium periodate restores the gel mobility of the DNA to that of the non-crosslinked phage DNA. No evidence for protein-protein crosslinking was obtained when the protein composition of crosslinked and non-crosslinked phage was compared by polyacrylamide gel electrophoresis. No evidence for DNA-DNA crosslinking was obtained when the frequency of crossed BglI restriction fragments for the crosslinked and non-crosslinked phage was compared by electron microscopy. An attempt was made to analyze the distribution of protein crosslinked to intraphage DNA. It was not possible to carry out this analysis by electron microscopy as the non-crosslinked phage gave too high a background of phage heads attached to the DNA. Sodium periodate treatment of the crosslinked DNA-protein complex failed to give detectable levels of protein on a silver stained polyacrylamide gel.
\r\n\r\nThe phage head of bacteriophage \u03bb was also crosslinked to the DNA by treatment with PDN and irradiation at long wavelength (> 360 nm). The crosslink was cleaved by sodium periodate. However, proteinase K treatment did not remove the protein from the DNA. Evidence is presented indicating that the \u03bb phage head is exceptionally stable to dissociation. Preliminary crosslinking results are presented for simian virus 40.
" }, { "name": "Bowman, Robert Clark, Jr.", "degree": "PhD", "year": "1983", "title": "Solid-State Proton Nuclear Magnetic Resonance Studies of Hydrogen Site Occupancies, Electronic Structure Properties, and Diffusion Behavior in Transition Metal Hydrides", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-05152003-105639", "creators": [ { "name": { "family": "Bowman", "given": "Robert Clark, Jr." }, "id": "Bowman-Robert-Clark", "orcid": "0000-0002-2114-1713", "display_name": "Bowman, Robert Clark, Jr." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Johnson", "given": "William Lewis" }, "id": "Johnson-W-L", "role": "member", "display_name": "Johnson, William Lewis" }, { "name": { "family": "Rhim", "given": "Won-Kyu" }, "id": "Rhim-Won-Kyu", "role": "member", "display_name": "Rhim, Won-Kyu" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w68b-2750", "abstract": "Solid-state NMR techniques have been used to measure the proton lineshapes, Knight shifts, and relaxation times in several transition metal hydrides. The objective of these studies is to obtain a better understanding of the roles of host metal structure and substitutional alloying on the hydrogen site occupancy, the electronic structure properties, and diffusion mechanisms.
\r\n\r\nAn improved method for observing the rigid-lattice proton lineshapes and extracting the second moments has been developed. Comparisons of the experimental second moments for polycrystalline samples with the values calculated from Van Vleck formulas for nuclear dipolar interactions have indicated that only tetrahedral interstitial sites are occupied by the protons in TiHx, ZrHx, crystalline TiCuH0.94, Ti2CuH1.9, and Zr2PdHx (with x < 2) while both tetrahedral and octahedral sites can be occupied in amorphous a-TiCuH1.4, Ti2CuH2.6, and Zr2PdHx (x > 2).
\r\n\r\nThe proton Knight shifts and low-temperature spin-lattice relaxation times have been related to the local densities of electron states at the Fermi levels N(EF) in Ti1-yVyHx, TiCr1.8Hx, TiCr1.9Hx, TiCuHx, Ti2CuHx, ZrHx, and Zr2PdHx. The dominant conduction electron hyperfine interaction for protons is a transferred \"core-polarization\" of the paired hydrogen 1s electrons through spin exchange with the unpaired metal d electrons. The proton NMR parameters have confirmed that decreases in N(EF) through a Jahn-Teller type mechanism are associated with the temperature and composition dependent tetragonal distortions in Ti1-yVyH1.95 and ZrHx (where 1.75 \u2264 x \u2264 2.0). The proton NMR results are consistent with recent band theory calculations and photoemission spectra. Unusual N(EF) increases with hydrogen content, which are supported by independent magnetic susceptibility data, have been observed in TiCr1.8Hx, TiCr1.9Hx, and Ti2CuHx. The proton parameters suggest that significant differences in N(EF) for the crystalline and amorphous phases of TiCuHx and Zr2PdHx may reflect a smearing of energy levels in the disordered phases.
\r\n\r\nThe proton rotating-frame relaxation times for Ti1-yCuyHx indicate both crystal structure and hydrogen site occupancies greatly influence diffusion behavior. A significant enhancement in hydrogen mobility for amorphous a-TiCuH1.4 has been confirmed; but, short range order is probably retained in the structure of a-TiCuH1.4. Reductions in activation energies are observed when octahedral sites exist in the diffusion paths between tetrahedral sites.
" }, { "name": "Crump, James Gleason, III", "degree": "PhD", "year": "1983", "title": "Aerosol Deposition, Growth, and Dynamics in the Continuous Stirred Tank Reactor", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122006-145635", "creators": [ { "name": { "family": "Crump", "given": "James Gleason, III" }, "id": "Crump-James-Gleason-III", "display_name": "Crump, James Gleason, III" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "chair", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gelbard", "given": "Fred M." }, "id": "Gelbard-Fred-M", "role": "member", "display_name": "Gelbard, Fred M." }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/yd9e-2s32", "abstract": "This work examines three related topics in aerosol science. First, a continuous stirred tank reactor (CSTR) for studying the dynamics of chemically reacting aerosol systems is described. This apparatus is designed to allow aerosols to react under conditions of controlled temperature and relative humidity and is applied to the study of growth of aqueous manganese sulfate aerosols in a humid atmosphere containing sulfur dioxide. From experimental data the rate of conversion of sulfur dioxide to sulfuric acid in manganese sulfate aerosols is deduced.
\r\n\r\nSecond, a new algorithm for inversion of aerosol size distribution data is presented. This algorithm is well suited to the ill-posed nature of the data inversion problem and is shown to give results superior to those obtained using conventional methods. This inversion technique is applied to the analysis of aerosol growth data.
\r\n\r\nFinally, the general steady state coagulation equations with particle sources and sinks are examined and shown to admit physically unrealistic solutions in some cases. General conditions are then given which insure the existence of physically acceptable solutions and these solutions are shown to have large particle tails that decay exponentially.
" }, { "name": "Daub, John Powell", "degree": "PhD", "year": "1983", "title": "The Total Synthesis of Macrolide Antibiotics", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-095416829", "creators": [ { "name": { "family": "Daub", "given": "John Powell" }, "id": "Daub-John-Powell", "display_name": "Daub, John Powell" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/87f1-5d52", "abstract": "An approach to the total synthesis of macrolide antibiotics via the key spiroketal intermediates i and ii, which possess all of the stereochemistry for the macrolides 10-deoxymethynolide (iii) and methynolide (iv), is described. Initially, the exocyclic enol ether v, which through hetero-Diels-Alder condensation with an \u03b1,\u03b2-unsaturated carbonyl compound would lead to these spiroketals i and ii, was prepared stereoselectively in optically pure form from 4,6-O-benzylidene-D-allal and was converted into the Prelog-Djerassi lactone (vi) by way of stereochemical confirmation. The low reactivity of this sensitive enol ether v toward hetero-Diels-Alder condensation led to the development of a new, high yield spiroketal synthesis through hetero-Diels-Alder condensation of the keto-enol ether vii with hetero-dienes; and, in this manner, the spiroketals i and ii were prepared stereoselectively. Cleavage of these spiroketals i and ii by thioketal exchange with 1,2-ethanedithiol led to seco-acid derivatives for the synthesis of the macrolides iii and iv. Additionally, a formal total synthesis of the antibiotic methymycin is achieved.
\r\n\r\n[See abstract in scanned thesis for chemical diagrams referenced above.]
" }, { "name": "Dodge, John Austin", "degree": "PhD", "year": "1983", "title": "The Synthesis and Characterization of Binuclear Copper(I) Complexes as Models for Protein Active Sites", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-101145351", "creators": [ { "name": { "family": "Dodge", "given": "John Austin" }, "id": "Dodge-John-Austin", "display_name": "Dodge, John Austin" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "member", "display_name": "Gagne, Robert R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/v7jq-zn64", "abstract": "A series of coordinatively unsaturated copper(I) complexes of binucleating nitrogenous ligands have been examined as potential models for protein active sites. The first complex discussed is derived from the ligand N,N,N',N'-tetrakis(2-pyridylmethyl)-ethylenediamine (TPEN). The binuclear copper(I) complex Cu2(TPEN)2+ reversibly binds two equivalents of carbon monoxide, giving an adduct which displays a pair of CO stretching absorptions at 2097 and 2107 cm-1. Both Cu2(TPEN)(BF4)2 and its carbonyl adduct have been examined by single-crystal X-ray diffraction. Each copper atom of Cu2(TPEN)2+ is bound in a highly asymmetric environment, with an intramolecular copper-copper separation of 2.78\u00c5. In the carbonyl adduct the metal-ligand bonds have rearranged, each copper has assumed a pseudotetrahedral geometry, and there is no longer any direct metal-metal interaction.
\r\n\r\nAnother complex, Cu2(CHXNpy)2+, has been prepared with a ligand analogous to TPEN, but with trans-1,2-cyclohexanediamine substituted for ethylenediamine. A second cyclohexanediamine-based ligand, CHXNbim, has been prepared which contains four benzimidazole groups rather than pyridine. Both Cu2(CHXNpy)2+ and Cu2(CHXNbim)2+ exhibit temperature dependent proton magnetic resonance spectra. The fact that fast exchange is observed only well above room temperature, in spite of the high lability of copper(I), is attributed to the sterically constrained nature of the ligands. Like Cu2(TPEN)2+, Cu2(CHXNpy)2+ forms a dicarbonyl adduct, but it is of lower stability. The benzimidazole complex Cu2(CHXNbim)2+ does not react with carbon monoxide and reacts only slowly with oxygen. Furthermore, unlike Cu2(TPEN)2+ and Cu2(CHXNpy)2+, Cu2(CHXNbim)2+ shows no tendency to disproportionate. This high stability is likely due to a combination of steric and electronic factors, which are discussed.
\r\n\r\nFinally, a series of complexes having different xylylene \"backbones\" have been synthesized and examined. Each ligand contains four biologically relevant imidazole groups. All of the complexes react rapidly with carbon monoxide and oxygen (irreversibly in the latter case). In contrast with another known xylylene-based complex containing pyridine groups, the reaction with oxygen occurs without ligand hydroxylation. Factors which could contribute to the reactivity difference are discussed.
" }, { "name": "Doxsee, Kenneth Martin", "degree": "PhD", "year": "1983", "title": "Homogeneous Carbon Monoxide Reduction \u2013 Catalyst Design Strategies", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012019-123348372", "creators": [ { "name": { "family": "Doxsee", "given": "Kenneth Martin" }, "id": "Doxsee-Kenneth-Martin", "display_name": "Doxsee, Kenneth Martin" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fexn-4820", "abstract": "A new approach to the activation of carbon monoxide toward homogeneous reduction by hydrogen is presented. Attack at transition metal bound carbon monoxide by nucleophiles generates anionic carbene complexes; hydrogenation of such complexes should give rise to products derived from reduced carbon monoxide. Model stoichiometric reactions using lithium dimethylamide as the activating nucleophile and various binary transition metal carbonyls have been found to give rise to varying amounts of methanol, dimethylformamide (DMF), and trimethylamine, products derived from reduction of carbon monoxide (as confirmed by carbon-13 labeling), under exceptionally mild conditions [35 psi H2, 130 \u00b0C, tetrahydrofuran or hexamethylphosphoric triamide (HMPA) solvent]. In the Cr(CO)6/LiNMe2 system in HMPA, trimethylamine appears to be formed by hydrogenation of the primary product DMF by a chromium carbonyl hydride anion. In support of this, the pentacarbonyl chromium hydride anion, (CO)5CrH-, has been found to quantitatively reduce N,N-dialkylamides to the corresponding amines under the above hydrogenation conditions.
\r\n\r\nNucleophiles weaker than LiNMe2 do not give rise to the desired activation of carbon monoxide for homogeneous reduction. Attempts to drive unfavorable equilibria through the use of bifunctional nucleophiles are reported. Intramolecular delivery of weaker nucleophiles has also been investigated in a series of functionalized arene chromium tricarbonyl complexes; no sign of the desired nucleophilic attack at carbon monoxide is obtained, though interesting reductive degradations and couplings of arenes are observed.
\r\n\r\nThe electrochemical oxidation of a series of arene chromium and arene tungsten tricarbonyl complexes has been examined. Studies regarding the oxidatively-promoted decomposition of the chromium complexes are reported. Extension of these studies to the tungsten analogs has led to the observation of metal coordination sphere expansion upon one-electron oxidation, an observation of fundamental significance with regards to recent reports of dramatic reaction rate enhancements in odd-electron organometallic systems. The relationship of coordination sphere expansion to these and other problems of current mechanistic organometallic chemical interest, including the oxidative instability of arene chromium tricarbonyl complexes, is discussed.
" }, { "name": "Duan, Daniel C.", "degree": "PhD", "year": "1983", "title": "Evidence for a Stereospecific 1,2-Elimination Reaction in a 1,1-Diazene. Synthesis and Decomposition of [N-Phenyl-(Threo-(and Erythro)-2-Deuterio-1-Methylpropl)Amino]Nitrene", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-103344869", "creators": [ { "name": { "family": "Duan", "given": "Daniel C." }, "id": "Duan-Daniel-C", "display_name": "Duan, Daniel C." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/zbfn-1t36", "abstract": "CHAPTER 1:
\r\n\r\nThe mechanism of the formal 1,2-elimination reaction of 1,1-diazenes to alkenes is examined. 'fue syntheses and decomposition of [N-phenyl-(1-methylpropyl)amino]nitrene (6), [N-phenyl(erythro-2-deuterio-1-methylpropyl)amino]nitrene (7) and [N-phenyl-(threo-2-deuterio-1-methylpropyl)amino]nitrene (8) are reported. Oxidation of 1-(1-methylpropyl)-1-phenylhydrazine (9) with nickel peroxide at 100\u00b0C affords 1-butene, trans-2-butene, cis-2-butene, butane and benzene in ratios of 0.59:0.30:0.097:0.005:1.00. Reaction of the corresponding benzenesulfonamide 10 with base at 100\u00b0C affords similar ratios. Oxidation of 1-(erythro-2-deuterio-1-methylpropyl)-1-phenylhydrazine (14) at 100\u00b0C affords 1-butene, trans-2-butene (100\u00b12% d1) and cis-2-butene (2.8\u00b12% d1), and butane in ratios of 0.67:0.30:0.03:0.004. Oxidation of 1-(threo-2-deuterio-1-methylpropyl)-1-phenylhydrazine (20) at 100\u00b0C affords 1-butene, trans-2-butene (1.8\u00b12% d1) and cis-2-butene (97.9\u00b12% d1) and butane in ratios of 0.77:0.11:0.11:0.009. Reaction of the corresponding benzenesulfonamides 15 and 21 with base at 100\u00b0C affords similar results. Primary kinetic isotope effects for 2-butene formation from the erythro and threo 1,1-diazene diastereomers were 3.5 and 3.4, respectively. The 1,1-diazene 1,2-elimination reaction studied here is a stereospecific cis elimination process.
\r\n\r\nCHAPTER 2:
\r\n\r\nAn attempt was made to observe chiral induction in a gas phase IR multiphoton photolysis using a circularly polarized output from a TEA CO2 laser. The molecule studied was trans-1,2-divinylcyclobutane (1) in the gas phase at 0.6 torr. Racemic samples were photolyzed at 977 cm-1 (=CHR bending) with 75 focused (0.8-0.9J) pulses. This resulted in about 33% conversion to 1,3-butadiene (2), 4-vinylcyclohexene (3) and 1.5-cyclooctadiene (4). A large number of samples were combined and the 1 (44mg) and 3 (6mg) were isolated by VPC. Neither showed optical activity.
\r\n\r\nCHAPTER 3:
\r\n\r\nThe possibility that triazolenitrenes (2) are involved in the photodecomposition of s-tetrazines (1) is considered. It was found that oxidation of 1-amino-2,5-diphenyl-1,3,4-triazole (5) in the presence of tetramethylethylene gave a high yield of triazolenitrene trapping product 6. Photolysis of 3,6-diphenyl-1,2,4,5-tetrazine (4) under these conditions failed to yield the adduct 6. Unsuccessful attempts were also made to prepare (2,5-di-tert-butyl-1,3,4-triazolidyl)nitrene (7) as a persistent species at low temperatures.
" }, { "name": "Ennis, Michael Dalton", "degree": "PhD", "year": "1983", "title": "I. Asymmetric Alkylation Reactions of Chiral Imide Enolates. II. Efforts Directed Toward the Total Synthesis of (+)-Macbecin I", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032019-124939824", "creators": [ { "name": { "family": "Ennis", "given": "Michael Dalton" }, "id": "Ennis-Michael-Dalton", "display_name": "Ennis, Michael Dalton" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pqm8-7286", "abstract": "The preparation of chiral N-acyl oxazolidones 6 and 7 from readily available amino acid precursors is described. Reaction of the alkali metal enolates derived from these chiral imides with alkyl halides and acid chlorides exhibit high levels of kinetic diastereoselection. Chromatographic enrichment
\r\n\r\n[chemical structure; see abstract in scanned thesis for details]
\r\n\r\naffords alkylated and acylated products of \u2265 99:1 diastereomeric purity. Non-destructive cleavage of the chiral auxiliary is accomplished by a variety of means to afford optically active products.
\r\n\r\nThe use of chiral imides 6 and 7 in the synthesis of the ansa-antibiotic macbecin-I (1) is described. The synthesis makes use of the iterative application of highly stereoregulated aldol condensations of N-acyl oxazolidones for the construction of the ansa-bridge of 1. This project has culminated in the preparation of the advanced acyclic intermediate 46.
\r\n\r\n[Chemical structures; see abstract in scanned thesis for details.]
" }, { "name": "Goldberg, Aaron Henry", "degree": "Masters", "year": "1983", "title": "Physical and Theoretical Studies of Localized Organic Biradicals", "advisor": "Dougherty, Dennis A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-114150617", "creators": [ { "name": { "family": "Goldberg", "given": "Aaron Henry" }, "id": "Goldberg-Aaron-Henry", "display_name": "Goldberg, Aaron Henry" } ], "advisors": [ { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "advisor", "display_name": "Dougherty, Dennis A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w5h0-qg02", "abstract": "Section I. Introduction.\r\n\r\nSection II. Singlet-triplet energy gaps in localized 1,3-biradicals have been investigated using ab initio electronic structure theory. Analysis of both the molecular orbital and generalized valence bond wavefunctions allows one to follow the complex interplay between through-bond and through-space interactions. When the two effects are of similar magnitude, a triplet ground state is possible. However, when one significantly dominates the other, a singlet ground state is expected. Extension of the analysis to other systems and the implications of the results for experimental studies of localized biradicals are discussed.\r\n\r\nSection III. Several unsuccessful attempts to observe the triplet cyclobutane- and cyclohexane-1,3-diyls through low temperature photolysis of the corresponding azo and azoxy compounds are reported. The reasons for these failures are considered together with their implications for the observation of other localized biradicals.\r\n\r\nSection IV. Photolysis of either 7-(2,3-diazabicyclo[2.2.1]hept-2-ene) spirocyclopropane or 7-(2,3-diazabicyclo[2.2.1]hept-2-ene) spiro-5'-bicyclo[2.1.0]pentane in a glassy matrix at 8\u00b0K leads to observation of a triplet ESR spectrum.. Both signals exhibit zero-field splitting parameters which are typical of delocalized systems (|D/hc| = 0.0255 and |E/hci| = 0.003\r\ncm^(-1)). In addition, they are stable at temperatures well in excess of 85\u00b0K. Several possible sources of the two spectra are discussed.\r\n\r\nSection V. A program for the ab initio calculation of zero-field splitting parameters in localized biradicals is developed. The results for several 1,3-biradicals are presented.\r\n" }, { "name": "Halle, Linda F.", "degree": "PhD", "year": "1983", "title": "Studies of the Energetics and Mechanisms of Organometallic Reactions in the Gas Phase", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012019-144753562", "creators": [ { "name": { "family": "Halle", "given": "Linda F." }, "id": "Halle-Linda-F", "display_name": "Halle, Linda F." } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/29x4-wk61", "abstract": "An ion beam apparatus is used to study reactions of the three first row group 8 atomic metal ions, Fe+, Co+, and Ni+, as well as the diatomic FeH+ species, with small organic molecules. The kinetic energy dependence of these processes is examined. Analysis of the thresholds for endothermic reactions yields bond strengths of the metal ion to various substituent groups. The thermochemical information derived in this manner and from more qualitative observations is used to assess the mechanisms by which these ions react with small organic molecules.
\r\n\r\nChapter I provides a brief summary of some of the organometallic systems previously studied using the ion beam apparatus. Chapter II presents the culmination of our studies of reactions of the first row group 8 metal ions with alkanes in which the extensive use of deuterium and 13C-labeled compounds provides further elaboration of the mechanisms by which these ions activate carbon-carbon and carbon-hydrogen bonds.
\r\n\r\nChapter III examines the consequences of incorporating a carbonyl group into the hydrocarbon from investigations of the reactions of Co+ with aldehydes and ketones. Analysis of products formed at high relative kinetic energies are used in conjunction with thermochemical estimates to infer mechanistic details and construct qualitative reaction coordinate diagrams for the interactions of Co+ with carbonyl compounds.
\r\n\r\nChapter IV represents an extension of our determinations of metal-carbon bond strengths to include fluorinated substituents. In particular, measurements of the Ni+-CH2 and N+-CF2 bond energies are reported. The implication of these carbene bond strengths for the metathesis of fluorinated olefins is discussed.
\r\n\r\nChapter V reports the first ion beam experiment of an organometallic fragment, the FeH+ species. Thermochemical information is obtained from reactions involving proton transfer from, and hydride transfer to, FeH+. We find that oxidative addition of FeH+ to D2 or hydrocarbons via Fe(IV) or four-centered intermediates is not a facile process, while reversible insertion of olefins into Fe+-H occurs with moderate cross section at low energies. Preliminary results for the reactions of FeH+ with alcohols, aldehydes, and ethers are also discussed.
" }, { "name": "Heckendorn, Debra Kay", "degree": "Masters", "year": "1983", "title": "Experiments Directed Towards the Total Synthesis of Chlorothricolide", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-081945536", "creators": [ { "name": { "family": "Heckendorn", "given": "Debra Kay" }, "id": "Heckendorn-Debra-Kay", "display_name": "Heckendorn, Debra Kay" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/q3v3-m204", "abstract": "The attempted synthesis of a differentially protected \"top half\", i, of chlorothricolide is described. The key step necessary for this synthesis was the spirocyclization of the anhydride ii, to prepare the protected tetronic acid iii.\r\n\t\t\t\r\n\t" }, { "name": "Kanne, Robert McNamara", "degree": "Masters", "year": "1983", "title": "Studies of the Enzyme Laccase", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-090654360", "creators": [ { "name": { "family": "Kanne", "given": "Robert McNamara" }, "id": "Kanne-Robert-McNamara", "display_name": "Kanne, Robert McNamara" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8yyp-a776", "abstract": "Rhus Vernicifera laccase was purified to an \r\nA_(280)/A_(614) ratio of 15.2. A procedure was then used \r\nto selectively remove the Type 2 copper and 70% of \r\nit was removed as judged by EPR. The treated enzyme \r\nshowed decreased absorbance in the 330 nm, region, \r\nwhich is associated with the Type 3 site, The blue \r\ncolor was observed to reversibly bleach on occasion, \r\napparently due to autoreduction of the Type 1 copper. \r\nThe fluorescence of the Type 2 depleted laccase was \r\nincreased 60% over that of the native protein.\r\nSince fluorescence quenching is often associated\r\nwith binding of a metal to a protein site, fluorescence \r\nwas used to monitor the attempted substitution of \r\ncobalt and nickel into the Type 2 site, There is\r\nsome evidence that cobalt can occupy the Type 2 site.\r\n" }, { "name": "Krauss, Eric Martin", "degree": "PhD", "year": "1983", "title": "Conformation and Function of Gramicidin S, a Peptide Antibiotic which Mediates Phase Transfer of Nucleotides and Nucleic Acids", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172019-173615812", "creators": [ { "name": { "family": "Krauss", "given": "Eric Martin" }, "id": "Krauss-Eric-Martin", "display_name": "Krauss, Eric Martin" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/d8tf-3k19", "abstract": "Gramicidin S (GrS; cyclo-(Val1-Orn2-Leu3-D-Phe4-Pro5)2) is a cyclosymmetric decapeptide antibiotic synthesized by mature cultures of the gram-positive spore former, Bacillus brevis. Its amphiphilic character and antiparallel \u03b2-pleated conformation in solution are experimentally established, but the extent of internal hydrogen bonding, the structural basis of its cytotoxicity and the physiological role in the producer organism remain unelucidated. These issues are addressed in the present investigation.
\r\n\r\nThe secondary structure of GrS is studied by a combination of proton exchange kinetics and vibrational spectroscopy. Dispersion in amide proton exchange rates provides a means of synthesizing variably N-deuterated GrS congeners, the isotopic composition of which are determined quantitatively by NMR. Difference IR of Me2SO solutions then affords isolation of residue-specific peptide group vibrations. Two pairs of equivalent hydrogen bonds with donor groups Leu NH and Val NH are identified, and their geometry and energetics characterized. The \u03b2-pleated conformation is thus shown to be stabilized by the maximum of four transannular hydrogen bonds.
\r\n\r\nThe solution conformation of the functionally essential ornithine side chains is then investigated by 1H and 15N NMR spectroscopy at 11.7 Tesla. Rotational averaging of the chemical shifts of the Orn C\u03b4H2 protons is incomplete, the degree to which the apparent motility of the side chain is limited varying inversely with the ability of the solvent to compete for hydrogen bonding donor or acceptor sites. Methylation of GrS to give [N\u03b4-trimethylornithyl2,2']-GrS results in an upfield shift of 3.5 ppm in the 15N resonance of Pro in MeOH and abolishes the correlation of the Orn C\u03b4H2 splitting with solvent basicity. The data are consistent with the presence of intramolecular Orn N\u03b4H3+--O=C D-Phe hydrogen bonds, each with formation constant ~1.1 in MeOH at 23\u00b0C, and exerting a substantial charge relay effect on the Pro 15N chemical shift. Proton exchange kinetics and nuclear Overhauser enhancement measurements indicate that these hydrogen bonds are formed in the i \u2192 i + 2 sense. Estimates for the Orn side chain torsional angles in the intramolecularly hydrogen bonded configuration are given, and the possible origin of the Orn C\u03b4H2 chemical shift inequivalence discussed.
\r\n\r\nThe studies of the solution conformation raise the possibility that the biological actions of GrS involve complexation of polyvalent anions; Orn N\u03b4H3+--O=C D-Phe hydrogen bonding might then ensure a critical intercationic distance (6-8 \u00c5) which is complementary to the architecture of the anionic species. Indeed, it is shown that GrS binds nucleotides in water to yield a complex which partitions into organic solvents. The observed phase transfer efficiencies at a given pH increase in the order AMP < ADP < ATP. The lipophilic complexes have well-defined stoichiometries, which are determined to be 1:1 for ADP-GrS at pH 7 and ATP-GrS at pH 3 and 1:2 for ATP-GrS at pH 7. The interaction is primarily ionic, involving coordination of the Orn N\u03b4H3+ groups of the peptide and the phosphoryl groups of the nucleotide, with little contribution from the nucleoside moiety. The nucleotide complexes are sparingly soluble in water, and self-associate extensively in CHCl3, most likely by cross-\u03b2 aggregation, to yield large, ribbonlike aggregates which give rise to broad NMR, resonances. structures for the 1:1 and 1:2 complexes are proposed. In the latter, two GrS molecules envelop the nucleotide, orienting their apolar faces externally in opposite directions, while the lateral faces retain considerable polar character and direct aggregation in organic media. The 1:1 complex possesses a single apolar face and is less lipophilic. Binding constants are estimated by simulation of the extraction data.
\r\n\r\nA novel interaction between GrS and nucleic acids is subsequently characterized which, like that between GrS and nucleotides, exploits both the dicationic and amphiphilic properties of the peptide. Complex formation between calf thymus DNA and GrS is demonstrated by (i) phase transfer to CHCl3 of ultrasonically irradiated DNA and (ii) inhibition of phase transfer to CHCl3 of ATP by either native or ultrasonically irradiated DNA. The stoichiometry of the interaction is 2:1 (DNA-P/GrS) as expected for a predominantly electrostatic mode of binding. The extraction-competition data suggest that the affinity of GrS for DNA is considerably higher than it is for free nucleotides. It is proposed that during dormancy stoichiometric binding by GrS ensheaths the bacterial chromosome in a dense peptide matrix possessing a highly apolar external surface, which should constitute an effective barrier against chemical degradation.
\r\n\r\nIn order to elucidate the molecular basis for GrS toxicity in vivo microbiological studies of GrS and analogues derivatized at ornithine are undertaken. The minimum lethal concentrations of GrS, [N\u03b4-trimethylornithyl2,2']-GrS, and [N-acetylornithyl2]-GrS in a standard bioassay employing Staphylococcus aureus in nutrient broth are compared. In addition, the time course of attenuation of the culture by GrS and the dependence of the minimum lethal concentration on initial cell concentration are determined. A model for GrS action is proposed involving internalization and formation of cytotoxic lipophilic complexes with polyanionic substrates , possibly nucleotides. The limiting antibiotic potencies at zero initial cell concentration and apparent extraction constants for nucleotides estimated in vitro are shown to be consistent with this model.
" }, { "name": "Lambert, William Roger", "degree": "PhD", "year": "1983", "title": "Picosecond Excitation and Quantum Beats of Molecules in Supersonic Molecular Beams", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechETD:etd-04092008-152954", "creators": [ { "name": { "family": "Lambert", "given": "William Roger" }, "id": "Lambert-William-Roger", "display_name": "Lambert, William Roger" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ans8-4e87", "abstract": "An understanding of the mechanisms responsible for intramolecular vibrational redistribution in polyatomic molecules has important implications for the efficacy of mode selective laser chemistry. In this thesis the application of picosecond laser excitation and supersonic molecular beam techniques to the investigation of the intramolecular dynamics of large polyatomic molecules is presented. Specifically, the first investigations on quantum interference effects observed in the energy and time resolved fluorescence following coherent picosecond laser excitation to intermediate excess energies in the first excited singlet state manifold are reported. The observation of quantum beats in anthracene and trans-stilbene indicates that at moderate excess energies, the effective density of rotational and vibrational states is quasi-discrete, even though the predominant relaxation dynamics reflect properties associated with the statistical limit. The relationship of internal temperatures and vibronic level structure to the quantum beats is investigated. The potential for using quantum interference effects as a probe of intramolecular energy and phase redistribution is emphasized.
\r\n\r\nThe design and construction of a supersonic molecular beam apparatus developed for the application of pulsed picosecond excitation and fluorescence detection are also presented. In as much as the free jet expansion conditions perturb the internal dynamics of the diluent molecules, an understanding of the hydro- and thermodynamics of the expansion is essential. The influence of the expansion conditions on intermolecular collisional processes complex formation, and internal temperatures is discussed with respect to the intramolecular dynamics of anthracene.
" }, { "name": "Marritt, William Alan", "degree": "PhD", "year": "1983", "title": "The Syntheses and Characterization of Binuclear Clathrochelate Complexes", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302018-160040560", "creators": [ { "name": { "family": "Marritt", "given": "William Alan" }, "id": "Marritt-William-Alan", "display_name": "Marritt, William Alan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "member", "display_name": "Gagne, Robert R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xpqf-ns89", "abstract": "A series of binuclear clathrochelate complexes, MA(II)MB(II)L+, have been synthesized and characterized for the purpose of examining electrostatic, magnetic, and electronic delocalization effects in binuclear complexes. The clathrochelating ligand, L3-, is a bicyclic Schiff-base compound derived from 3 equiv of 2-hydroxy-5-methylisophthalaldehyde and 2 equiv of 2,2',2\"-triaminotriethylamine (tren). The following MA(II)MB(II)L+ complexes were prepared by combinations of metal-ion template, metathesis, and insertion reactions: homonuclear complexes with MA = MB = Mn, Fe, Co, Cu, Zn, and Cd; heteronuclear complexes with MA = Mn, MB = Co, Ni, Zn, Cd, and Mg; MA = Fe, MB = Mn, Co, Ni, Cu, Zn, Cd, and Mg; MA = Cu, MB = Mn, Co, Ni, Zn, Cd, and Mg. In addition, syntheses and characterization are reported for the binuclear Cu(II)Cu(II)LH2+ complex and mononuclear complexes of the non-deprotonated ligand, MLH3n+, with M = Na(I), Mn(II), Mn(III), Fe(II), Fe(III), Co(II), Ni(II), Cu(II), Zn(II), Cd(II), and Mg(II).
\r\n\r\nThe MA redox potentials of the Mn(III)/Mn(II), Fe(III)/Fe(II), and Cu(II)/Cu(I) couples were determined by cyclic voltammetry and differential pulse voltammetry for three series containing both homonuclear and heteronuclear complexes, Mn(II)MB(II)L+, Fe(II)MB(II)L+, and Cu(II)MB(II)L+. Within experimental error, the average of the MA redox potentials for each series of heteronuclear complexes was the same as that for the corresponding homonuclear complex. This result suggests that there is no measurable stabilization of Mn(III)Mn(II)L2+, Fe(III)Fe(II)L2+, and Cu(I)Cu(II)L with respect to mixed-valent heteronuclear analogues.
\r\n\r\nThe magnetic properties of a series of four homonuclear MA(II)MB(II)L+ complexes were examined by variable temperature susceptibility measurements (MA = MB = Mn, Fe, Co, and Cu). In all cases, weak antiferromagnetic coupling between the metal centers was observed (-33.5 cm-1 < J < -0.8 cm-1). The weakness is attributed to limited overlap of metal orbitals with those of the bridging atoms.
" }, { "name": "Mayer, James Moers", "degree": "PhD", "year": "1983", "title": "Synthesis, Characterization, and Reactivity of New Hydride Compounds of Tantalum (V)", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03212012-094858041", "creators": [ { "name": { "family": "Mayer", "given": "James Moers" }, "id": "Mayer-James-Moers", "orcid": "0000-0002-3943-5250", "display_name": "Mayer, James Moers" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DR9V-G528", "abstract": "A series of (pentamethylcyclopentadienyl)tantalum bis(phosphine) polyhydride complexes, Cp*TaL2H4 (L = PMe3, PMe2(C6H5), P(OMe)3, and L2 dmpe; Cp* = \u03b75 - C5(CH3)5) and Cp*Ta(PMe3)2H3Cl, have been prepared by high pressure hydrogenation of Cp*TaMe4 or Cp*TaMe3Cl in the presence of L. The hydride ligands are more hydridic than protic in character. All of the compounds react with acetone and methanol to afford isopropoxide and methoxide complexes, respectively. Reactions with carbon monoxide yield carbonyl hydride and dicarbonyl compounds resulting from sequential reductive elimination of dihydrogen. Hydrogenation of ethylene is observed, as well as catalytic dimerization of ethylene to 1-butene. Most reactions of these eighteen-electron polyhydride complexes are thought to involve rate-determining loss of a phosphine ligand. Evidence is presented in support of coordination of acetone to tantalum prior to its reduction to isopropoxide. By contrast, methanol can react qirectly with the coordinatively saturatedtantalum hydride species to generate H2.
\r\n\r\nLow temperature and high field NMR spectroscopy has been used to investigate the coordination geometries of these polyhydride complexes and some niobium analogues. Using symmetry arguments, the spectra indicate a Cs structure with equivalent phosphorus atoms for complexes with monodentate phosphine ligands. This is consistent with an X-ray crystal structure of Cp*Ta(PMe3)2H4, in which the hydride ligands were not located. A different Cs structure, with inequivalent phosphorus atoms, is indicated for compounds with the bidentate dmpe ligand.
\r\n\r\nThe reactions of Cp*TaMe3Cl (1) with a variety of alkali metal alkoxide, alkylamide, and alkyl reagents have been examined. Reaction with LiNMe2 produces Cp*Ta(NMe2)Me3, but this decomposes at 25\u00b0C to an imine (or metallaazirane) complex, Cp*Ta(CH2NMe)Me2. The decomposition is a first-order, unimolecular process with a large kinetic isotope effect kH/kD = 9.7). Monoalkylamides (LiNHR) react with 1 to form imido complexes Cp*Ta(NR)Me2. Reaction of 1 with lithium diisopropylamide forms a bridging methylene complex, Cp*Me2Ta(\u00b5CH2)(\u00b5H)2TaMe2Cp*. The alkoxide compounds Cp*Ta(OR)Me3 (R = Me, CHMe2, CMe3) are very stable and decompose only over 100\u00b0C. Alkyl complexes are stable only if the alkyl group does not have \u03b2-hydrogens. The rates of hydrogen abstraction or elimination processes in this system correlate with the nature of the atom bound to tantalum: for reactions involving a \u03b2-hydrogen the order is C > N > O while \u03b1-hydrogen abstraction reactions appear to vary in the reverse order, N > C. These rates seem to reflect the thermodynamic preferences in these compounds.
\r\n\r\nHydrogenation of the imido compounds (Cp*Ta(NR)Me2) in the presence of phosphine ligands yield the first examples of imido-hydride complexes, Cp*Ta(NR)H2(L) (L = PMe3, PMe2(C6H5), R = CMe3, CH2CM3). An alkyl-hydride complex, Cp*Ta(CH2NMe)Me(PMe3)H, has also been prepared. The reaction of Cp*TaMe3(OCMe3) with hydrogen forms an unusual asymmetric dimer, Cp*(Me3CO)2HTa(\u00b5H)2 TaH3Cp*, which has been characterized by NMR and IR spectroscopies.
\r\n\r\nThe tantalum hetero-olefin complexes Cp*Ta(CH2NMe)Me2 and Cp*Ta(OCMe2)Me2 react readily with olefins, aldehydes, and nitriles. A number of five- and seven-atom metallacycles have been prepared.
" }, { "name": "McGee, Dennis Emmett", "degree": "PhD", "year": "1983", "title": "Diol Dehydratase: Purification, Structural Characterization, and Mechanism of Action", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082021-204133329", "creators": [ { "name": { "family": "McGee", "given": "Dennis Emmett" }, "id": "McGee-Dennis-Emmett", "display_name": "McGee, Dennis Emmett" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xkz2-e227", "abstract": "Abstract to Chapter I
\r\n\r\nA new isolation procedure for propanediol dehydratase increases by a factor of about 16 the yield of enzyme obtainable from Klebsiella pneumoniae; the enzyme thus isolated has a specific activity of 95 \u00b1 4 units/mg. The apoenzyme consists of four different subunits with molecular weights of 60 K, 51 K, 29 K, and 15 K daltons in the ratio of 2:1:2:2, respectively. In this new procedure, care was taken to prevent the partial proteolysis of the propanediol dehydratase which seems to occur in earlier procedures. The other novel aspect recognizes that the enzyme is associated with the cell membrane. Accordingly, after gentle sonication, the membrane fragments are separated from cytosol, and the enzyme is solubilized by extraction with buffers containing detergent. The amino acid compositions and N-terminal amino acid sequences for each of the subunits was also determined. From the amino acid compositions of the individual subunits, diol dehydratase appears to be a peripheral membrane protein.
\r\n\r\nAbstract to Chapter II
\r\n\r\nWhen diol dehydratase holoenzyme is inactivated by reaction with radioactive glycerol, one mole of glycerol appears to become tightly associated with each 250,000 daltons of the holoenzyme complex with a significant loss of tritium from C-2 being observed. However, denaturation of the inactivated complex releases the modified glycerol from the protein, indicating that the protein is not covalently modified by the inactivator. Similar experiments were carried out with radioactive isobutylene glycol, but due to the high level of nonspecific labeling, the results were not as definitive.
\r\n\r\nAs described in Chapter I, former isolation procedures (Abeles, 1966; Poznanskaya et al., 1979) yielded enzyme which had been proteolysed. For this reason inactivation studies employing various deuterated derivatives of glycerol and isobutylene glycol, as well as a new class of inactivators represented by hydroxyacetone and dihydroxyacetone, were carried out with native enzyme to compare results from similar studies with proteolysed enzyme (Bachovchin et al., 1977; Moore, 1979). It was found that proteolysis had little effect on the constants associated with the glycerol inactivation, but an enormous effect on the constants describing the inactivation by isobutylene glycol.
\r\n\r\nThe results of the radiolabeling studies and kinetic experiments are consistent with the formation of a secondary alkylcobalamin upon inactivation of diol dehydratase by glycerol. Kinetic evidence also suggests that the inactivation of diol dehydratase by isobutylene glycol occurs after the abstraction of hydrogen from C-1, but before the substrate rearranges.
\r\n\r\nAbstract to Chapter III
\r\n\r\nA reinvestigation of trace label experiments with native diol dehydratase isolated by the method of McGee and Richards (1981) (see Chapter I) has shown that the probability of net intramolecular transfer for tritium is 0.33 \u00b1 0.02 as opposed to the value of about 0.03 obtained earlier (Frey et al., 1967a) with an enzyme preparation obtained by a different method. Our observed value of 0.33 is about 20 times larger than what one would predict on the basis of the mechanism for the migration of hydrogen given in the Introduction to this thesis. In contrast, tritium washout experiments, similar to those conducted by Essenberg et al. (1971), yielded a value of kHH/kHT = 29 \u00b1 2 which is approximately the value predicted by Moore et al. (1979). Also, tritium washout experiments were carried out in such a way that, in addition to the C-5' hydrogens of adenosylcobalamin containing tritium, any other multiple-hydrogen reservoirs should have contained tritium as well. These experiments yielded identical results to those in which only the C-5' hydrogens contained reactable tritium; therefore, it appears that only the C-5' hydrogens of C-5' deoxyadenosine participate directly in catalysis.
\r\n\r\nAlso, the tritium isotope effect on the first hydrogen transfer was determined to be 6.1 \u00b1 0.5 by measuring the isotopic enrichment in unreacted [1-3H]-1,2-propanediol as a function of the extent of reaction. The results of our study suggest that the generally accepted pathway for catalysis, which proceeds through the C-5' deoxyadenosine hydrogen reservoir, constitutes about 95% of the catalytic events with unlabeled substrate; however, there appears to be an alternate catalytic pathway whose contribution to catalysis can be enhanced by isotopic substitution at C-1 of substrate.
" }, { "name": "McIntyre, Daniel Keith", "degree": "PhD", "year": "1983", "title": "Synthesis and Characterization of 1,1-Di-Tert-Butyldiazene", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022013-142422017", "creators": [ { "name": { "family": "McIntyre", "given": "Daniel Keith" }, "id": "McIntyre-Daniel-Keith", "display_name": "McIntyre, Daniel Keith" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/y54d-s069", "abstract": "The synthesis and direct observation of 1,1-di-tert-butyldiazene (16) at -127\u00b0C is described. The absorption spectrum of a red solution of 1,1-diazene 16 reveals a structured absorption band with \u03bbmax at 506 nm (Me2O, -125\u00b0C). The vibrational spacing in S1 is about 1200 cm-1. The excited state of 16 emits weakly with a single maximum at 715 nm observed in the fluorescence spectrum (Me2O:CD2Cl2, -196\u00b0C). The proton NMR spectrum of 16 occurs as a singlet at 1.41 ppm. Monitoring this NMR absorption at -940 \u00b1 2\u00b0C shows that 1,1-diazene 16 decomposes with a first-order rate of 1.8 x 10-3 sec-1 to form isobutane, isobutylene and hexarnethylethane. This rate is 108 and 1034 times faster than the thermal decomposition of the corresponding cis and trans 1,2-di-tert-butyldiazene isomers. The free energy of activation for decomposition of 1,1-diazene 16 is found to be 12.5 \u00b1 0.2 kcal/mol at -94\u00b0C which is much lower than the values of 19.1 and 19.4 kcal/lmole calculated at -94\u00b0C for N-(2,2,6,6-tetramethylpiperidyl)nitrene (3) and N-(2,2,5,5-tetramethylpyrrolidyl)nitrene (4), respectively. This difference between 16 and the cyclic-1,1-diazenes 3 and 4 can be attributed to a large steric interaction between the tert-butyl groups in 1,1-diazene 16.
\r\n\r\nIn order to investigate the nature of the singlet-triplet gap in 1,1-diazenes, 2,5-di-tert-butyl-N-pyrrolynitrene (22) was generated but was found to be too reactive towards dimerization to be persistent. In the presence of dimethylsulfoxide, however, N-pyrrolynitrene (22) can be trapped as N-(2,5-di-tert-butyl-N'-pyrrolyl)dimethylsulfoximine (38). N-(2,5-di-tert-butyl-N'-pyrrolyl)-d6-dimethylsulfoximine (38-d6) exchanges with free dimethylsulfoxide at 50\u00b0C in solution, presumably by generation and retrapping of pyrrolynitrene 22.
\r\n" }, { "name": "Mitchell, Mark Allen", "degree": "PhD", "year": "1983", "title": "Interhelical DNA-DNA Crosslinking of Bacteriophage Lambda: Bis(monoazidomethidium)octaoxahexacosanediamine and Bis(psoralen)nonaethyleneoxy ether, Probes of Packaged Nucleic Acid", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112006-153134", "creators": [ { "name": { "family": "Mitchell", "given": "Mark Allen" }, "id": "Mitchell-Mark-Allen", "display_name": "Mitchell, Mark Allen" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mtd8-tb22", "abstract": "A strategy for determining the structure of packaged bacteriophage DNA is developed. The synthesis and characterization of two new interhelical crosslinking reagents, bis(monoazidomethidium)-octaoxahexacosanediamine (BAMO) (13) and bis(psoralen)nonaethyleneoxy ether (BPNE) (7) are reported. Both BAMO and BPNE are capable of crosslinking neighboring DNA helices within intact bacteriophages \u03bb and T7. BAMO crosslinks packaged bacteriophage \u03bb DNA at low binding levels (r = 0.01 BAMO/bp) and can be photolyzed quickly (0.5-1 hr) with light of low energy (\u03bb > 400 nm) to yield 17% crosslinked structures as observed under the electron microscope after isolation and restriction cleavage of the crosslinked DNA. BPNE yields 10% crosslinked structures when incubated for three hours with bacteriophage \u03bb at a binding ratio of r = 0.28 BPNE/bp, photolysed for five hours (\u03bb = 365 nm), followed by isolation and restriction digestion of the crosslinked DNA.
\r\n\r\nMethodology necessary to uniquely locate the site of crosslinking along the bacteriophage genome has also been developed. Directional measurements of restriction fragments have been carried out on photomicrographs of fragments labeled specifically at one end with electron dense avidin spheres. The avidin spheres are attached to the restriction fragments by incorporating a biotin containing nucleotide (Bio-dUTP) into the restriction fragment using T4 polymerase under standard labeling conditions. Subsequent restriction cleavage generates fragments labeled at one specific end. Incubation of avidin spheres with these biotinylated restriction fragments results in avidin sphere binding specifically to the labeled end of the fragments.
\r\n\r\nWe have begun to generate interhelical nearest neighbors maps from the measured crosslink positions for bacteriophages \u03bb and T7. Models have been constructed for packaged T7 DNA according to the coaxial solenoid and coil of coils models discussed in the literature. Hypothetical interhelical nearest neighbors maps from these models have been prepared.
" }, { "name": "Moll, David Jerry", "degree": "PhD", "year": "1983", "title": "One- and Two-Color Laser Spectroscopy with Photoacoustic and Multiphoton Ionization Detection", "advisor": "Janda, Kenneth C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-175021360", "creators": [ { "name": { "family": "Moll", "given": "David Jerry" }, "id": "Moll-David-Jerry", "display_name": "Moll, David Jerry" } ], "advisors": [ { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "advisor", "display_name": "Janda, Kenneth C." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/60wm-py84", "abstract": "The techniques of pulsed photoacoustic spectroscopy and multiphoton ionization spectroscopy have been used to study several types of weak optical transitions in the ultraviolet or visible spectral regions for gas phase molecules. Both one- and two-color experiments have been performed. The one-color experiments involved the study of high vibrational overtones and spin-forbidden transitions. The two-color experiments demonstrated the application of photoacoustic detection of stimulated emission pumping for populating high vibration levels of the ground electronic state. Two-color experiments were also used to study excited state absorption processes in aniline.
\r\n\r\nPulsed laser photoacoustic spectra of CD3H in the region of the \u2207vCH = 5, 6, and 7 CH stretch overtones were obtained. These overtones and nearby combination bands displayed sharp rotational structure, indicating a minimum excited state population relaxation time of 5 x 10-12 sec. A combination sum analysis was used to generate excited state rotational constants B'. These constants reflect the geometries of the excited states, and therefore provide a sensitive probe of the mixing between various zero order excited states.
\r\n\r\nPhotoacoustic detection was used to monitor a stimulated emission pumping process in p-difluorobenzene. Using the Ã1B2u 5' state as an intermediate state, several vibrational levels of the ground electronic state were populated. The photoacoustic technique is an attractive alternative to other techniques because of its sensitivity, simplicity, and its ability to differentiate between stimulated emission pumping and excited state absorption.
\r\n\r\nTime-resolved excited state absorption studies were performed on aniline using the multiphoton ionization and photoacoustic detection techniques. Signals from both of these techniques were measured as a function of the time delay between two laser pulses of different wavelength. The first pulse excited the S1 0-0 transition. The second pulse excited either S1 or a triplet state produced by intersystem crossing, depending on the time delay between pulses. Both ionization and dissociation processes were observed. By varying the conditions of excitation, it appears that a given amount of energy can be selectively channeled into either ionization or dissociation pathways. These results were explained using a simple Franck Condon factor model.
\r\n\r\nThe application of pulsed laser photoacoustic spectroscopy to the study of weak absorptions in the visible and ultraviolet spectral regions was investigated. Photoacoustic spectra of triplet states in CS2, SO2, biacetyl, and thiophosgene were obtained. An attempt to detect the ã3B1u state in benzene, produced instead a two-photon spectrum of several Rydberg states. It was discovered that the sensitivity of the pulsed photoacoustic technique for extremely weak absorptions is limited by the increased probability of multiphoton absorption when high intensities are used.
\r\n\r\nFinally, in two appendices, the detection of the ã3A2 state in CS2 by the multiphoton ionization technique is presented. The CS2 study demonstrates the utility of the multiphoton ionization technique for detecting spin-forbidden transitions at high resulution and with great sensitivity.
" }, { "name": "Olson, Wendy Ann", "degree": "Masters", "year": "1983", "title": "The Synthesis and Reactivity of New Niobium (V) Polyhydrides", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-145411166", "creators": [ { "name": { "family": "Olson", "given": "Wendy Ann" }, "id": "Olson-Wendy-Ann", "display_name": "Olson, Wendy Ann" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e6p9-e788", "abstract": "The synthesis of new niobium polyhydrides by high pressure hydrogenation of Cp*NbMe_4 in the presence of trapping phosphines is reported. The complexes Cp*NbL_2H_4, L=PMe_3, PMe_2Ph, PMe_2Cy, and L_2=bis(dimethylphosphino)ethane, are described. They exchange D_2 into the hydride positions, and react hydridically with methanol and acetone to give alkoxide species. Reactions with CO give reduced metal carbonyl phosphine complexes. All these reactions (except the reaction with methanol) appear to proceed with loss of phosphine as the rate limiting step. Reactions of the hydride species with group VI carbonyls, and with ethylene, are presented. The novel reactivity of Cp*Nb(PMe_2Ph)_2H_4 with H_2 to give Cp*Nb(PMe_2Cy)_2H_4 is discussed." }, { "name": "Ott, Kevin Curtis", "degree": "PhD", "year": "1983", "title": "Some Mechanistic and Synthetic Aspects of the Interaction of Lewis Acids with Bis-Cyclopentadienyltitanium(IV) Alkyls and Bis-Cyclopentadienyltitanacyclobutanes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012019-155844929", "creators": [ { "name": { "family": "Ott", "given": "Kevin Curtis" }, "id": "Ott-Kevin-Curtis", "display_name": "Ott, Kevin Curtis" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/fxvt-ac87", "abstract": "Titanocene dichloride has been shown to react cleanly with two equivalents of AlMe3 to produce the Lewis acid stabilized titanium methylene [chemical formula; see abstract in scanned thesis for details]. Due to the interest in the utility of this complex in Wittig-type chemistry, in the metathesis of olefins, and in the synthesis of titanacyclobutanes, a study of the mechanism of formation of the complex was carried out. The proposed mechanism for formation of 1 involves an intramolecular proton abstraction by an Al-Me bond from a Ti-CH3 group in the intermediate Cp2TiMeCl\u2022AlMe3. The effect of Cp-ring substitution and halide substitution on the reaction rate along with a deuterium isotope effect of 3 and a large negative entropy of activation were consonant with the proposed mechanism.
\r\n\r\nSpecifically labelled titanacyclobutanes were prepared, and the cleavage reaction with AlMe2Cl to yield 1 as studied. It was found that cleavage occurred with a secondary deuterium isotope of 1.2 to 1.6 (depending upon the titanacyclobutane) and exhibited bimolecular kinetics. Surprisingly, the stereochemistry of the titanacyclobutanes was completely scrambled before cleavage to 1 and olefin. A mechanism for this isomerization was proposed to involve a rapid and reversible trans-metallation of a Ti-C bond with AlMe2Cl, producing a 3-aluminapropyltitanocene chloride. Following rapid inversion at the carbon adjacent to aluminum, the racemized 3-aluminapropyltitanocene chloride could cleave to 1 or close to yield isomerized titanacyclobutane.
\r\n\r\nThe \u03b2,\u03b2-disubstituted titanacyclobutanes proved to be good sources of the Cp2TiCH2 unit, as indicated by their ready formation of bis-\u00b5-CH2-bis-Cp2Ti (2). Some chemistry and photochemistry of 2 are reported. The Cp2TiCH2 moiety is readily trapped with transiton metal or main group metal Lewis acids such as Cp^TiCl3 or Me3SnCl to produce compounds such as [Cp2TiCl]-\u00b5-CH2-[Cp*TiCl2] (3) and Cp2Ti(CH2SnMe3)Cl. Cp2TiCH2 may also be trapped as the methylene phosphine adduct Cp2Ti(=CH2)PEt3 (4).
\r\n\r\nThe compounds 2 and 3 react with CO to yield insertion products which contain bridging ketene ligands which w ere characterized spectroscopically. Compound 4 also reacts with CO to produce the mononuclear ketene Cp2Ti(\u03b72-CH2CO) in low yield.
" }, { "name": "Paffett, Mark Thomas", "degree": "PhD", "year": "1983", "title": "Electrochemistry of Molybdenum Aquo Ions", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012019-171533510", "creators": [ { "name": { "family": "Paffett", "given": "Mark Thomas" }, "id": "Paffett-Mark-Thomas", "display_name": "Paffett, Mark Thomas" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/hv5n-dz91", "abstract": "The electrochemical behavior of selected molybdenum aquo ions in acidic media is examined in relation to solution structure.
\r\n\r\nThe electrochemistry of Mo(VI) in non-complexing aqueous electrolytes is usually severely complicated by the oligomerization and subsequent adsorption of the reactant. This problem can be circumvented by employing dilute (\u2264 10-4 M) solutions of Mo(VI) in 1 to 2 M trifluoromethanesulfonic acid. Under these conditions staircase voltammograms and pulse polarograms exhibit single, reversible waves that are consistent with the one-electron reduction of an unadsorbed, monomeric Mo(VI) species. The pH dependence of the reduction potentials suggests that two protons are consumed in the reduction of each Mo(VI). The monomeric Mo(V) reduction product undergoes spontaneous dimerization with a rate constant estimated as 103 M-1 s-1. It also reduces perchlorate and nitrate anions at a significant rate.
\r\n\r\nThe Mo2(V)/Mo2(III) redox couple in acidic solution involves an overall four electron-six proton transfer connecting the two participants. This redox process is characterized by extreme electrochemical irreversibility. Reduction of the Mo2(V) aquo ion to the Mo2(III) aquo ion proceeds with \u03b1na equal to 0.73 and a proton reaction order of 1.4. A chemical step with an inverse dependence on proton concentration precedes the reoxidation of aquo Mo2(III) to aquo Mo2(V). Plausible mechanisms are given for these observations.
\r\n\r\nThe trinuclear ions containing Mo(IV), Mo3O4(H2O)4+9(Mo3(IV)) and an oxalato derivative, Mo3O4(C2O4)3(H2O) 2-3, can be reversibly reduced in acidic media to trinuclear Mo(III) species. The reductions involve two sequential electron transfer steps with formal potentials that are pH dependent:
\r\n\r\n[chemical equations; see abstract in scanned thesis for details].
\r\n\r\nTwo waves are evident in voltammograms and polarograms of Mo3O4(C2O4)3(H2O)2-3 but with Mo3(IV) the two formal potentials are too close together to observe separate waves. However, logarithmic analysis of the shapes of normal pulse polarograms allowed the two formal potentials to be evaluated. The reductions of both complexes are believed to be accompanied by protonation of the bridging and capping oxo-ligands. The new, trinuclear Mo3(III) species resulting from the three-electron reduction of Mo3(IV) exhibits a characteristic EPR spectrum. The mixed-valent intermediate, Mo3(III, III, IV), is diamagnetic. Possible structural changes that accompany the addition of electrons and protons to Mo3IV) are discussed.
" }, { "name": "Pesthy, Andrew John", "degree": "PhD", "year": "1983", "title": "Aerosol Formation and Growth in Laminar Flow", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09062006-080949", "creators": [ { "name": { "family": "Pesthy", "given": "Andrew John" }, "id": "Pesthy-Andrew-John", "display_name": "Pesthy, Andrew John" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "chair", "display_name": "Flagan, Richard C." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "member", "display_name": "Seinfeld, John H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/X6ZW-RA12", "abstract": "A detailed theoretical analysis of aerosol nucleation and growth in laminar flow, including the important aspects of mass and energy transfer and aerosol size distribution dynamics, is presented. Simulations of dibutyl phthalate aerosol formation and growth in a laminar flow cooled tube, in the presence and absence of seed particles, are carried out using the classical and Lothe-Pound theories of homogeneous nucleation. The competition between new particle formation and vapor growth onto seed particles is explored in detail. The mathematical model is compared to experimental measurements of aerosol volume distribution and dibutyl phthalate mass balance for a laminar flow cooled tube without seed particles. The model with Lothe-Pound theory shows fair agreement with the mass balance data, but over-predicts the total aerosol number concentration by four orders of magnitude.
" }, { "name": "Runnels, John Hulett", "degree": "Masters", "year": "1983", "title": "Investigation of Coriolis Mixing in Benzene", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-084636927", "creators": [ { "name": { "family": "Runnels", "given": "John Hulett" }, "id": "Runnels-John-Hulett", "display_name": "Runnels, John Hulett" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yxqj-6804", "abstract": "An explanation for some recent observations in the \r\nelectronic absorption spectrum of benzene by Schlag and \r\ncoworkers is proposed. Several vibrational lines of the \r\nS_0 to S_1 transition have been studied by these authors with the Doppler\u2014free, two\u2014photon technique developed earlier. The resolution of this technique is so high that individual \u0394 J=0, \u0394 K=0 rotational lines in the Q\u2014branch of a given vibrational transition may be seen in the electronic absorption spectrum. A major progression in the two\u2014photon spectrum is the 14^1_0 1^n_0 progression. It was found that the 14^1_0 1^0_0 and 14^1_0 1^1_0 transitions had well\u2014resolved rotationalstructure, but the 14^1_0 1^2_0 transition had reduced, not well \r\nresolved rotational structure--except for the prominent K=0 \r\nlines for small to medium values of J. This suggested to \r\nus Coriolis mixing. The model presented here utilizes a \r\nsuggestion of Riedle et al.The Coriolis coupling to \r\nneighboring vibrational states is followed by a rapid \r\nradiationless depletion of these states, consistent with \r\nthe decreased fluorescence yield observed by Wunsch et al. \r\nEstimates are made of the density of states of the various \r\nsymmetries; these estimates are then used to estimate the \r\nextent of the relevant Coriolis mixing. The model results \r\nin a large decrease in intensity of non\u2014zero K lines\r\nrelative to the K=0 lines for the 14^1_0 1^2_0 transition, but not for the 14^1_0 1^0_0 and 14^1_0 1^1_0 transitions, in agreement with the experimental observations, making a few assumptions discussed below, but without the use of adjustable parameters. Predictions are then made for the rotational structure of other strong transitions in the two\u2014photon spectrum of benzene.\r\n" }, { "name": "Ryskin, Gregory", "degree": "PhD", "year": "1983", "title": "A Numerical Study of Bubble Deformation in Steady Axisymmetric Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-04132004-142806", "creators": [ { "name": { "family": "Ryskin", "given": "Gregory" }, "id": "Ryskin-Gregory", "display_name": "Ryskin, Gregory" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "chair", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Keller", "given": "Herbert Bishop" }, "id": "Keller-H-B", "role": "member", "display_name": "Keller, Herbert Bishop" }, { "name": { "family": "Wu", "given": "Theodore Yao-tsu" }, "id": "Wu-T-Y-T", "role": "member", "display_name": "Wu, Theodore Yao-tsu" }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "member", "display_name": "Leal, L. Gary" } ], "option_major": [ "chemeng" ], "doi": "10.7907/rrsq-e746", "abstract": "This work is devoted to the development and application of the numerical technique suitable for solution of the free-boundary problems, i.e. those in which the shape of the boundary should be determined as a part of the solution. The technique is based on a finite-difference solution of the equations of the problem on an orthogonal curvilinear coordinate system, which is also constructed numerically and always adjusted so as to fit the current boundary shape. The same orthogonal mapping approach may also be used to construct orthogonal coordinates fitted to boundaries of known but complicated shapes.
\r\n\r\nThe technique is applied to two classical problems of fluid mechanics -- deformation of a gas bubble rising through a quiescent fluid due to buoyancy, and deformation of a gas bubble in a uniaxial extensional flow. For the rising bubble, the shapes and flow fields are computed for Reynolds numbers 1 \u2264 R \u2264 200 and Weber numbers up to 20 at the lower Reynolds numbers and up to 10 at Reynolds numbers 50, 100 and 200. The most interesting results of this part are those demonstrating the phenomenon of flow separation at a smooth free surface. This phenomenon does not appear to have been theoretically predicted before, in spite of its importance for understanding the mechanics of free-surface flows.
\r\n\r\nIn the case of a bubble in a uniaxial extensional flow, the computations show that at Reynolds numbers of order 10 and higher the deformation of a bubble proceeds in a way qualitatively different from the low Reynolds number regime studied previously; the bubble bursts at a relatively early stage of deformation never reaching the highly elongated shapes observed and predicted at low Reynolds numbers. It is shown also that for this problem the solution at Reynolds number of order 100 is already quite close to the potential flow solution which can be easily obtained using the present technique.
" }, { "name": "Siders, Paul David", "degree": "PhD", "year": "1983", "title": "Theory of Outer-Sphere Electron-Transfer Reactions", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012019-155724801", "creators": [ { "name": { "family": "Siders", "given": "Paul David" }, "id": "Siders-Paul-David", "display_name": "Siders, Paul David" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "chair", "display_name": "Marcus, Rudolph A." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mgjj-rj90", "abstract": "Classical, semiclassical and quantum theories of outer-sphere electron-transfer reactions in polar media are discussed. For each, the Franck-Condon overlap factors for the hexaamminecobalt, hexaaquoiron and hexaammineruthenium self-exchange rates and for the cross-reaction of hexaaquoiron(II) with tris(2,2\u2019-bipyridine)ruthenium(III) are evaluated and compared. The quantum effect on the rates is small in the region of moderate driving force; the \"normal\" \u0394Go region. Direct-sum and saddle-point evaluations of the quantum Franck-Condon factors are made and compared. The saddle-point approximation is shown to be an excellent approximation in the cases considered.
\r\n\r\nQuantum effects in homogeneous outer-sphere electron transfer reactions in the region of large negative \u0394Go (the \"inverted\" region) are considered. The results of quantum, semiclassical and classical calculations on model systems are presented. A sequence of highly exothermic photoinduced reactions of tris(2,2'-bipyridyl) complexes is discussed with regard to the possible importance of quantum effects and of alternate reaction pathways in understanding the failure of the sequence of reactions to exhibit pronounced \"inverted\" behavior. A mechanism leading to electronically excited products provides a possible explanation for the large discrepancy.
\r\n\r\nThe theory of highly exothermic homogeneous outersphere electron-transfer reactions is discussed for transfers occurring over a range of distances. A finite rate of diffusion of reactants and their long-range force are treated by solving the reaction-diffusion equation numerically for the reactant pair distribution function. Steady-state solutions are compared with experimental data. On the basis of short-time solutions it is proposed that experiments which measure electron-transfer rates at short times following the onset of reaction improve the possibility of observing the inverted effect in bimolecular systems.
\r\n\r\nThe effect of the reactants' relative orientation on the electron-transfer rate is considered. Reactants are modeled as oblate-spheroidal potential wells of constant, finite depth. Energy levels and wavefunctions are obtained for an electron localized in such a well. The electronic matrix elements that govern electron transfer within a nonadiabatic quantum theory are evaluated. Significant orientational preferences are predicted for electron transfer between nonspherical donor and acceptor sites.
" }, { "name": "Strader, David John", "degree": "PhD", "year": "1983", "title": "Studies on the Mechanism of Complement Activation by Murine Immunoglobulin G", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062025-213025282", "creators": [ { "name": { "family": "Strader", "given": "David John" }, "id": "Strader-David-John", "display_name": "Strader, David John" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h30s-4x87", "abstract": "UPC-10 myeloma protein, a murine immunoglobulin of the IgG class,\r\nand its carbohydrate antigen, levan, have been used to define the nature\r\nof classical complement activation by IgG. A four step purification\r\nprocedure was developed for the myeloma protein to minimize albumin\r\ncontamination and to insure the structural integrity of the purified\r\nantibody. In addition, methods were developed for the isolation of\r\nlevan from perennial ryegrass and Aerobacter levanicum; a novel\r\ntechnique employing water-soluble sulfonated polystyrene was used to\r\nprepare levan oligosaccharides which were then fractionated according to\r\nmolecular weight. Association constants were determined for the binding\r\nof various levan preparations to UPC-10 myeloma protein, thereby\r\nallowing an initial understanding of the antigen-antibody interactions\r\nobserved in this system.
\r\n\r\nFurther experiments explored the role of antigen-antibody complexes\r\nin classical complement activation. An extremely sensitive assay of\r\nhemolytic complement activity employing radiolabeled erythrocytes was\r\ndeveloped to allow the use of limited quantities of antigen in these\r\nstudies. Mixtures of antibody and bacterial levan were found to fix\r\ncomplement only in strictly defined concentration ratios, while no\r\ncomplement fixation was observed when conditions of antigen-excess were\r\npresent, thereby establishing the aggregation of antibody molecules as a\r\nnecessary, if not sufficient, step for this activity. A more detailed\r\nanalysis with sized levan oligosaccharides confirmed this requirement\r\nfor aggregation and indicated that the molecular weight of the levan\r\noligosaccharides is an important determinant of its ability to assemble\r\nantibody molecules into active complexes. Direct observations of such\r\nantigen-antibody complexes were made through the use of analytical\r\nultracentrifugation, establishing that all of the levan oligosaccharides\r\ncapable of inducing complement fixation by IgG molecules were also able\r\nto assemble the antibody molecules into multimeric antibody complexes.\r\nThus, these studies find no evidence for a purely conformational\r\nmechanism for the expression of complement activation by murine IgG, and\r\ninstead confirm that aggregation of antibody molecules is required for\r\nthis effector function.
" }, { "name": "Straus, Daniel Albert", "degree": "PhD", "year": "1983", "title": "Synthesis and Reactivity of Bis(cyclopentadienyl)titanacyclobutanes and Ketene Complexes of Bis(cyclopentadienyl)titanium and Bis(cyclopentadienyl)zirconium", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-122031306", "creators": [ { "name": { "family": "Straus", "given": "Daniel Albert" }, "id": "Straus-Daniel-Albert", "display_name": "Straus, Daniel Albert" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1jtq-cj35", "abstract": "The synthesis of several titanacyclobutanes of the types [chemical formula; see abstract in scanned thesis for details] and [chemical formula; see abstract in scanned thesis for details] (Cp = \u03b75-C5H5, R = alkyl) is described. The stability of several of these, as well as some metallacycles of the type [chemical formula; see abstract in scanned thesis for details], has been measured and is discussed in terms of the structure of these species. The reaction of some titanacyclobutanes with dimethylaluminum chloride in the presence of diethyl ether and tetrahydrofuran was investigated, and is discussed in terms of a scheme for olefin metathesis involving an aluminum co-catalyst. The thermolysis, acidolysis and reactions with bromine and iodine have been studied for a number of these metallacycles. The mechanism of the reaction with iodine is considered in some detail.
\r\n\r\nTitanacyclobutanes of the type [chemical formula; see abstract in scanned thesis for details] and [chemical formula; see abstract in scanned thesis for details] are known to catalyze degenerate metathesis of terminal olefins. The activity of the titanacyclobutanes in non-degenerate olefin metathesis has been investigated here. The titanacyclobutanes have been found to metathesize cis- and trans-2,8-decadiene with some stereospecificity. This process is very inefficient and the reasons for this are discussed in terms of the stability and reactivity of various titanacyclobutanes, which model presumed intermediates in this reaction.
\r\n\r\nThe carbonylation of several titanacyclobutanes has been examined in detail and leads to insertion of two molecules of carbon monoxide to produce cyclic enediolate products in all cases when carbon monoxide is present in excess. Acidolysis and oxidation of these enediolates affords 2-hydroxycyclopentanones and 1,2-cyclopentanediones, respectively. Under conditions where the carbon monoxide concentration is limited, cyclobutanones and titanocene dicarbonyl are formed. A mechanism which explains these observations is presented. Carbon monoxide insertion has been found to proceed with retention of stereochemistry at migrating carbon.
\r\n\r\nKetene complexes have been prepared by treatment of chloro and bromo acyl complexes of titanocene, zirconocene and decamethylzirconocene with strong bases. In this manner (Cp2Ti(OCCH2))n (Cp2Zr|OCCHC(CH3)3|)2 and (\u03b75-C5Me5)2Zr(OCCH2)(C5H5N) have been synthesized. The reactivity of these complexes with hydrochloric acid, hydrogen, ethylene and acetylene is discussed. Reaction of Cp2Zr(COCH3)CH3 with CH2PPh3 gives the enolate complex Cp2Zr(OC(CH2)CH3)CH3 and PPh3. Reaction of Cp2Zr(COCH3)CH3 with NaN(TMS)2 gives the anion Cp2Zr(COCH2)CH3-, which is alkylated with methyl iodide to produce Cp2Zr(COCH2CH3)CH3.
" }, { "name": "Suobank, David Walter", "degree": "PhD", "year": "1983", "title": "A Quantitative, Comparative Study of Sound Produced in vitro by Pulsatile Flow in and Around Prosthetic, Aortic Heart-Valves", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12142006-094228", "creators": [ { "name": { "family": "Suobank", "given": "David Walter" }, "id": "Suobank-David-Walter", "display_name": "Suobank, David Walter" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Harrison", "given": "Earl C." }, "id": "Harrison-Earl-C", "role": "member", "display_name": "Harrison, Earl C." }, { "name": { "family": "Yoganathan", "given": "Ajit P." }, "id": "Yoganathan-Ajit-P", "role": "member", "display_name": "Yoganathan, Ajit P." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/q5r7-a318", "abstract": "A quantitative, comparative study was made of sound produced in vitro by pulsatile flow in and around three designs of prosthetic aortic heart-valves. Designs studied were 25mm Bjork-Shiley, 24mm Smeloff and Starr-Edwards model 2400 valves. A digital method for the analysis of the sounds using the fast Fourier transform is presented and applied. Results are examined in both the time domain and a variety of formats in the frequency domain. Formats include original time vs. amplitude plots, power-density spectra, power-distribution functions, a 3-D (three-dimensional) surface of power-frequency-time, auxiliary views of these 3-D surfaces, and a 3-D, power-distribution surface showing the difference between two 3-D, power-distribution surfaces. Enhanced distinguishability of sound was clearly shown by the 3-D, power-difference surface which provided a very convenient means for the overall comparison of two sounds.
\r\n\r\nAttention was given to understanding effects of valvar and pulsatile conditions upon the frequency characteristics of the opening, systolic, and closing sounds. Failure modes were simulated and resulting changes of the sounds were examined. Simulated overgrowth was placed on the inner apical surface of the Starr-Edwards model 2400 valve and on the upstream struts of the Smeloff valve. Results showed that the sounds produced provided information pertinent to the simulated malfunction.
\r\n\r\nEffects of pulse rate, mean flow-rate, and mean aortic pressure associated with the normal valvar sounds were investigated. Results were interpreted in terms of the known physical changes of the valve and known changes of the pulsatile state. Under alternate pulsatile states, the total power of the opening and closing sounds were influenced primarily by the rate of change of the ventricular pressure prior to these events. The difference between systolic sounds was much greater than between opening and closing sounds for cases involving changes of the stroke volume for each normal valve design. An increase in systolic flow rate produced a corresponding increase in the power of peaks in the spectra of the systolic sound for each design. The location of peaks within the power density spectra of opening, systolic and closing sounds were more similar during the studies of alternate, non-normal, pulsatile states of normal valves than they were during the studies of normal/abnormal valves under normal pulsatile states.
\r\n\r\nVisualization of the valve and particle trajectories and simultaneous recording of sound, flow rate, and upstream and downstream pressure, provided direct evidence of the cause of many of the acoustical events. Strouhal numbers were estimated from center-frequencies of resonance peaks associated with sounds that were related to periodic vortex shedding in flows past the struts, annular gaps and phonocatheter.
\r\n\r\nThe overall results indicate that the method used could distinguish changes of valvar and pulsatile states for each of the valvar designs that were studied.
" }, { "name": "Voter, Arthur Ford", "degree": "PhD", "year": "1983", "title": "The Resonating Valence Bond Model of Molecules and Reactions", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-133042163", "creators": [ { "name": { "family": "Voter", "given": "Arthur Ford" }, "id": "Voter-Arthur-Ford", "display_name": "Voter, Arthur Ford" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d754-h174", "abstract": "This thesis presents an ab initio generalization of Pauling's theory of resonance, the generalized resonating valence bond (GRVB) method. In GRVB, we optimize a wavefunction of the form
\r\n\r\n\u03a8TOT = CA \u03a8A + CB \u03a8B
\r\n\r\nwhere \u03a8A and \u03a8B are multiconfigurational wavefunctions with arbitrary overlap. This type of wavefunction has been considered unfeasible for more than a few electrons due to the n! computational dependence of evaluating the matrix element < \u03a8A | H | \u03a8B >. We reduce this dependence to ~n5 by biorthogonalizing the orbitals in each determinant pair. GRVB is ideally suited to describing systems which require a resonance of more than one bonding structure, such as benzene, molecules with three-electron bonds, and reaction transition states. Besides yielding a conceptually simple avefunction, we find that GRVB yields quantitative results for processes in which the dominant differential correlation is a resonance effect. For example, the GRVB barrier heights for the HCl + H and HF + H exchange reactions are each within one kcal of the basis set limit, in contrast to the orthogonal configuration interaction (CI) approaches which require hundreds or thousands of configurations to achieve the same accuracy. We also present application to the three-electron bonding in noble gas dimer ions, and various other examples.
" }, { "name": "Willett, Brian Christopher", "degree": "PhD", "year": "1983", "title": "Electron Transfer Rates and Adsorption in the Electrochemistry of Cobalt-2,2'-Bipyridine, Ruthenium Ammine Thiocyanate Complexes and cis-[(C\u2085H\u2085)Fe(CO)P(C\u2086H\u2085)\u2082]\u2082", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042019-130341164", "creators": [ { "name": { "family": "Willett", "given": "Brian Christopher" }, "id": "Willett-Brian-Christopher", "display_name": "Willett, Brian Christopher" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/t7fp-5z02", "abstract": "In Part I of this thesis, the electrochemical properties of cobalt(I)-2,2'-bipyridine and cobalt(I)-6,6'-dimethyl-2,2'-bipyridine complexes were investigated, including their reactions with reducible substrates and their adsorption on mercury electrodes.
\r\n\r\nElectron transfer rate constants measured for cyclooctatetraene and cis-[(C5H5)Fe(CO)P(C6H5)2]2, molecules which undergo large intramolecular rearrangements upon electron transfer, in non-aqueous solvents with various tetraalkylammonium salts as supporting electrolytes are presented in Part II. The electrode kinetics were measured by cyclic voltammetry, chronocoulometry and AC impedance techniques. Values of the rate constants found were as large as 0.30 cm/sec.
\r\n\r\nSynthesis and adsorption behavior of several novel substituted ruthenium ammine complexes are discussed in Part III. The adsorption on mercury was used to distinguish between the two thiocyanate linkage isomers, Ru(NH3)5NCS2+ and Ru(NH3)5SCN2+. The coordination properties of ruthenium(II) were used to prepare trans-Ru(NH3)4(NCS))4-vinyl- pyridine)Ru(EDTA), a binuclear ruthenium species.
" }, { "name": "Bair, Raymond Alan", "degree": "PhD", "year": "1982", "title": "Part A. Theoretical Studies of the X-Ray Absorption Edge in Copper Complexes. Part B. Electron Correlation Consistent Calculation of Bond Dissociation Energies", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03222018-144512817", "creators": [ { "name": { "family": "Bair", "given": "Raymond Alan" }, "id": "Bair-Raymond-Alan", "display_name": "Bair, Raymond Alan" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/ez8r-aj04", "abstract": "Part A: In order to elucidate the nature of the transitions involved in the x-ray absorption edge of molecular systems, we have used ab initio methods to examine the discrete transitions corresponding to the atomic 1s \u2192 3d, 4s, 4p, 5s, and 5p transitions and the corresponding shakeup processes for Cu atom and for a Cu(II) model system, CuCl2. The three common features of the K edge are described by the calculations. For CuCl2, the lowest strong transitions have the character 1s \u2192 4p (f = 0.00133). About 7.5 eV lower is a group of transitions involving 1s \u2192 4p simultaneous with ligand-to-metal shakedown. About 18.7 eV below the main peak is a weak (65 times weaker) quadrupole-allowed transition corresponding to 1s \u2192 3d (i.e., 1s23d9 \u2192 1s13d10. In each case the spectral feature has been assigned to an allowed transition. Previously, the middle transition was assigned as 1s \u2192 4s, whereas in this study the 1s \u2192 4s transition was calculated to be too weak to be observed. We propose that the observed peak is due to the allowed transition involving 1s \u2192 4p plus shakedown.
\r\n\r\nPart B: Ab initio generalized valence bond (GVB) and configuration interaction (CI) methods have been used to develop a generally applicable method for directly calculating bond energies. Particular effort has been put into obtaining a scheme in which all correlation terms that change upon dissociation of a particular bond are included consistently. The method uses in an essential way the localized orbitals from a GVB calculations, and is readily applicable to large systems [e.g., (CH3)3C-C(CH3)3]. To test our method, we selected two benchmark series of compounds, where the experimental bond energies are well known. Calculated bond energies are reported for the R-H bonds of CH4, NH3, H2O, and HF, which are low by 3.5, 2.5, 3.0, and 2.7 .kcal/mol, respectively. We also report calculations of the R-R bond energies of C2H6, N2H4, H2O2, and F2, which are low by 0.1, -3.2, -1.8, and 0.8 kcal/mol, respectively. In the application of our method, we have calculated all of the O-O, O-C, and O-H bond energies of HOOH, CH3OOH, CH3OOCH3, CH3OH, C2H5OH (O-H only), and CH3O-. Finally, we obtain the electron affinities of F, OH, and CH3O with the same techniques.
" }, { "name": "Becker, Michael McClellan", "degree": "PhD", "year": "1982", "title": "I. Molecular Recognition of Nucleic Acid by BMSP. II. Sequence Specific B \u2192 H \u2192 A Allosteric Transitions in DNA", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102018-162757284", "creators": [ { "name": { "family": "Becker", "given": "Michael McClellan" }, "id": "Becker-Michael-McClellan", "display_name": "Becker, Michael McClellan" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/s7mc-ka23", "abstract": "Chapter One
\r\n\r\nBis(methidium)spermine (BMSp), a dimer of two intercalating monomers of ethidium bromide (EB) connected by a spermine link has been synthesized and characterized. The results of these studies clearly demonstrate that both monomers of BMSp simultaneously intercalate nucleic acid, substantially enhancing both its binding affinity and specificity. Under physiological conditions both the binding affinity and specificity of BMSp are similar to DNA binding regulatory proteins. Thus BMSp represents one of the first rationally designed drugs which may selectively inhibit or alter gene expression.
\r\n\r\nThe binding affinity, binding cooperativity, binding site size, and visible spectrum of BMSp are found to vary with nucleic acid conformation. Both BMSp and EB are shown to bind H and A conformations of nucleic acid much more tightly than B conformations. As a result, both compounds induce sequence specific B \u2192 H \u2192 A allosteric transitions in DNA.
\r\n\r\nChapter Two
\r\n\r\nA sensitive experimental technique which can accurately estimate equilibrium binding isotherms is described. Ligand-macromolecule interactions are monitored by classical indirect techniques over a broad ratio of LT/M, where LT is the total ligand concentration and M is the macromolecule concentration. When analyzed at constant X, where X is some physical property of ligand which is proportional to its concentration, the dependence of LT on M can be used to estimate the binding densities and free ligand concentrations characterizing the ligand-macromolecule interaction. In contrast to classical indirect and direct techniques, accurate binding isotherms can be estimated over a wide range of binding densities for tightly or weakly bound ligands. When the binding of ethidium bromide to polyd(C-G) and polydCdG is examined by this technique, previously undetected allosteric transitions are revealed.
\r\n\r\nChapter Three
\r\n\r\nEvidence for a new conformational family of Watson-Crick DNA is presented. Termed H or hybrid DNA, such DNA is postulated to be an intermediate in the interfamily B \u2192 A transition. Hybrid DNA is characterized by a 2'-endo (3' \u2192 5') 3'-endo alteration in sugar pucker every base pair and may also be an intermediate in DNA melting, DNA kinking, and drug intercalation. The ease with which DNA undergoes a B \u2192 H \u2192 A transition is found to vary greatly with its sequence. On the basis of these results, the equilibrium stability, rather than the structure of Watson-Crick DNA is postulated to vary greatly with base sequence.
" }, { "name": "Berdan, Clarke, II", "degree": "PhD", "year": "1982", "title": "Study of the Creeping Motion of a Sphere in the Presence of a Deformable Fluid/Fluid Interface", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202006-142454", "creators": [ { "name": { "family": "Berdan", "given": "Clarke, II" }, "id": "Berdan-Clarke-II", "display_name": "Berdan, Clarke, II" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Brennen", "given": "Christopher E." }, "id": "Brennen-C-E", "role": "member", "display_name": "Brennen, Christopher E." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" } ], "option_major": [ "chemeng" ], "doi": "10.7907/hetj-r497", "abstract": "The creeping motion of a rigid sphere in the presence of a deformable fluid/fluid interface has been considered using theoretical, experimental and numerical techniques. Solutions for small perturbations in shape, for an initially flat interface, are obtained to calculate the additional forces and torques on a sphere rotating and translating both normal to and parallel with a slightly deformed interface. The interfacial shape as well as the forces and torques are calculated as a function of sphere position and interfacial deformation parameters, viscosity ratio, capillary number, and ratio of Bond number to capillary number. The interface deformation was found to yield no correction to the torque or parallel force on the sphere for any combination of sphere motion. The interface deformation did yield a force directed away from the interface for all sphere motions which generate a deformation for the interface.
\r\n\r\nA new direct force measurement experimental apparatus is used to study the normal motion of a rigid sphere approaching a deformable interface under conditions of constant interfacial deformation parameters. The sphere was lowered at a constant velocity and the force on the body was measured as a function of the interface shape and values of the deformation parameters.
\r\n\r\nStudy of the translation of a nonrotating sphere parallel with a fluid/fluid interface, experiencing finite amplitude deformations, utilizes a numerical collocation technique. The forces and torques on the body are calculated as a function of body displacement from the interface and the interface deformation parameter (ratio of Bond number to capillary number). The interface shapes are determined and the forces and torques on the sphere are calculated.
" }, { "name": "Biller, Scott Adams", "degree": "PhD", "year": "1982", "title": "An Approach to the Total Synthesis of (\u00b1)-Naphthyridinomycin A", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10312002-152412", "creators": [ { "name": { "family": "Biller", "given": "Scott Adams" }, "id": "Biller-Scott-Adams", "display_name": "Biller, Scott Adams" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/mref-rb43", "abstract": "An approach to the total synthesis of the quinone antibiotic (\u00b1)-naphthyridinomycin A is described. This research has thus far culminated in the preparation of the advanced, pentacyclic intermediate 93. The structure of phenol 93 was secured by an X-ray crystallographic study of its benzoate ester. Intermediate 93 was constructed from tricyclic lactam 21, phenol 19a and methyl glyoxalate, employing a stereoselective amidoalkylation reaction and an intramolecular Friedel-Crafts alkylation as key transformations. With regard to the amidoalkylation step, several new methods for the generation of acylimmonium ions were developed in the course of model studies. The synthesis of tricyclic lactam 21 from the readily available bicyclic \u03b2-lactam 31 was accomplished via a 13-step sequence, which included several interesting intramolecular reactions.
" }, { "name": "Brittain, William Joseph", "degree": "PhD", "year": "1982", "title": "I. Rearrangement of Cyclopropyldiphenylmethyllithium and 4,4-Diphenyl-3-Buten-1-Yllithium. II. Deuterium Isotopic Perturbation of the Cyclopropylmethyl-Cyclobutyl Carbocation", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102018-165616024", "creators": [ { "name": { "family": "Brittain", "given": "William Joseph" }, "id": "Brittain-William-Joseph", "display_name": "Brittain, William Joseph" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/1c58-f235", "abstract": "PART I
\r\n\r\nCyclopropyldiphenylrnethyllithium was prepared directly from cyclopropyldiphenylmethane by trimethylsilylmethyllithium metalation or indirectly by transmetalation of cyclopropyldiphenylmethylpotassium. The organolithium is stable in tetrahydrofuran, dimethyl ether, or 2-methyltetrahydrofuran and exists predominately as loose ion pairs. In diethyl ether or isopropyl methyl ether, cyclopropyldiphenylmethyllithium isomerizes to 4,4-diphenyl-3-buten-1-yllithium; a process that can be reversed by addition of tetrahydrofuran. 4,4-Diphenyl-3-buten-1-yllithium is unstable in most solvents; in cyclopentane, \u03b2-elimination of lithium hydride and ortho-cyclisation were major reaction pathways. The solvent dependence of the organolithium rearrangement can be adequately explained by three principle equilibria; the rearrangement occurring in contact ion pairs.
\r\n\r\nPART II
\r\n\r\nIonization of (2E,2Z,3Z-d3-cyclopropyl)methanol. 9, in SbF5-SO2ClF-SO2F2 afforded primarily one stereoisomer (endo-C4H4D3+) of the trideuterated cyclopropylmethyl-cyclobutyl carbocation. Ionization of (2,2-d2-cyclopropyl)-1-d-methanol, 10, in SbF5-SO2ClF-SO2F2 produces a 1:1 mixture of endo- and exo-C4H4D3+. The low-temperature 1H, 2H, and 13C NMR spectra of both C4H4D3+ stereoisomers are reported. The methine resonance (13CH) of exo-C4H4D3+ is shifted 0.4 ppm downfield from unlabeled cation, C4H7+, while the endo-C4H4D3+ resonance is coincident with the corresponding carbon in C4H7+. This can be taken as evidence for the deuterium isotopic perturbation of the equilibrium between bicyclobutonium, 2, and bisected cyclopropylmethyl, 4, structural isomers. The deuterium perturbation of equilibria involving structurally similar, nondegenerate isomers is a larger effect and induces dramatic changes in the methylene carbon resonances. The 13C resonance corresponding to the mondeuterated carbon (13CH2) is shifted in opposite directions relative to C4H7+ in endo- and exo-C4H4D3+. Endo-C4H4D3+ slowly isomerizes to exo-C4H4D3+; a lower limit for the rotation barrier in C4H4D3+ is 14 \u00b1 1 kcal/mol. The endo-hydrogens in endo-C4H4D3+ were assigned to the high-field methylene resonance in the 1H spectrum of this ion in contrast to previous assignments by other workers. The results of this NMR study of C4H4D3+ carbocations are consistent with two rapidly equilibrating structures, 2 and 4, of C4H4D3+ under stable-ion conditions.
" }, { "name": "Cohen, Steven Alan", "degree": "PhD", "year": "1982", "title": "Organotitanium and Niobium Chemistry. I. Structure and Reactivity of a Titanium Ethylene Complex. II. Reactivity of Decamethyl Niobocene Derivatives", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02132014-115308678", "creators": [ { "name": { "family": "Cohen", "given": "Steven Alan" }, "id": "Cohen-Steven-Alan", "display_name": "Cohen, Steven Alan" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/3DDT-0252", "abstract": "The synthesis and X-ray diffraction study of bis(pentamethylcyclopentadienyl) ethylene titanium (I) are reported. This complex represents the first example of an isolable ethylene adduct of a group IV metal, a key intermediate in Ziegler-Natta olefin polymerization schemes. While treatment of I with ethylene leads to only traces of polymer after months, I participates in a wide range of stoichiometric and catalytic reactions. These include the catalytic conversion of ethylene specifically to butadiene and ethane and the catalytic isomerization of alkenes. Detailed studies have been carried out on the stoichiometric reactions of I with nitriles and alkynes. At low temperatures, nitriles react to form metallacycloimine species which more slowly undergo a formal 1,3-hydrogen shift to generate metallacycloeneamines. The lowest energy pathway for this rearrangement is an intramolecular hydrogen shift which is sensitive to the steric bulk of the R substituent. The reactions of I with alkynes yield metallacyclopentene complexes with high regioisomer selectivity. Carbonylation of the metallacyclopentene (\u03b7-C5Me5)2TiC(CH3)=C(CH3)CH2CH2 under relatively mild conditions cleanly produces the corresponding cyclopentenone and [C5(CH3)5]2Ti(CO)2. Compounds derived from CO2 and acetaldehyde have also been isolated.
\r\n\r\nThe synthesis and characterization of bis-(\u03b7-pentamethylcyclopentadienyl) niobium(III) tetrahydroborate (II) are described and a study of its temperature-dependent proton NMR spectroscopic behavior is reported. The complex is observed to undergo a rapid intramolecular averaging process at elevated temperatures. The free energy of activation, \u0394G\u2260 = 16.4 \u00b1 0.4 kcal/mol, is calculated. The reinvestigation of a related compound, bis(\u03b7-cyclopentadienyl)niobium(III) tetrahydroborate, established \u0394G\u2260 = 14.6 \u00b1 0.2 kcal/mol for the hydrogen exchange process. The tetrahydroborate complex, II reacts with pyridine and dihydrogen to yield (\u03b7-C5Me5)2NbH3 (III). The reactivity of III with CO and ethylene is reported.
\r\n" }, { "name": "Conner, Benjamin Norman", "degree": "PhD", "year": "1982", "title": "Iodo-CCGG: A Single Crystal Structure of A-DNA", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142018-150830492", "creators": [ { "name": { "family": "Conner", "given": "Benjamin Norman" }, "id": "Conner-Benjamin-Norman", "display_name": "Conner, Benjamin Norman" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "chair", "display_name": "Dickerson, Richard E." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3t68-dc11", "abstract": "Iodo-CCGG was synthesized by the triester method and crystallized in space group P43212. Electron density maps were phased using the anomalous scattering from the iodines and refined with the Jack-Levitt constrained refinement program. The final crystallographic R factor was 16.5% for 2 \u03c3 data and 19.9% for all data.
\r\n\r\nSolution of the structure revealed the first fragment of A-DNA to be seen in a single crystal. The helix has a 2.2\u00c5 rise per residue, 10.6 base pairs per turn, and an average propeller twist of 17\u00b0. A total of 86 water molecules were located in the crystal. Of these, 47 were within 3.5\u00c5 of the ICCGG molecule. A second layer of hydration is formed by water molecules which are within 3.5\u00c5 of two or more first layer water molecules. The hydration sites on ICCGG are ordered based on the relative strengths of DNA to water bonds. as judged by their bond lengths.
\r\n\r\nICCGG packs together with the bottom of one helix in the minor groove of another. The packing scheme indicates that the minor groove of A-DNA is a relatively hydrophobic site. This fact may be important in the recognition of A-DNA by proteins and drugs.
\r\n\r\nA list of refined coordinates of ICCGG is given in the appendix.
" }, { "name": "Dow, William Clinton", "degree": "PhD", "year": "1982", "title": "Total Synthesis of \u03b2-Chamigrene", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05142018-155247666", "creators": [ { "name": { "family": "Dow", "given": "William Clinton" }, "id": "Dow-William-Clinton", "display_name": "Dow, William Clinton" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "chair", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/6kmn-mt31", "abstract": "A total synthesis of the sesquiterpene (\u00b1)-\u03b2-Chamigrene is described. A key step is the preparation of spiroketone ii through Claisen rearrangement of the vinyl-substituted cycloheptapyran i. A modified Meinwald-Cava ring contraction sequence is used for the intramolecular elaboration of a functionalized one-carbon unit at the hindered alpha flank of the spirocycle. This procedure affords ester iii. Alternate reaction pathways available to the reactive ketene intermediate are also discussed. These results are compared with observations made in a previously reported synthesis of aphidicolin.
\r\n\r\n[Chemical structure included in scanned thesis' abstract, p. iv.]
" }, { "name": "Gleeson, James William", "degree": "PhD", "year": "1982", "title": "I. A Nuclear Magnetic Resonance Study of Metal Carbonlys in the Solid State, and II. Studies of the Surface Chemistry of Rhodium Supported on Alumina", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05152018-092853858", "creators": [ { "name": { "family": "Gleeson", "given": "James William" }, "id": "Gleeson-James-William", "display_name": "Gleeson, James William" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vmgw-qf86", "abstract": "Part I
\r\n\r\nThe principal components of the 13C nuclear magnetic resonance chemical shift tensors of metal carbonyls containing between one and six metal atoms were determined from the powder patterns of the solid compounds. The tensors of terminally-bound CO groups are highly anisotropic (380 \u00b1 60 ppm) and nearly axially symmetric. The tensors of bridging CO groups are much less anisotropic, due to significant asymmetry in the electron orbitals about the CO internuclear axis. The tensors vary only slightly for different transition metals. There is no intramolecular rearrangement of the metal carbonyls in the solid state at frequencies \u2273 10kHz, except in Fe3(CO)12.
\r\n\r\nPart II
\r\n\r\nThe surface chemistry of rhodium supported on alumina was studied using infrared spectroscopy and quantitative measurements of the gases adsorbed and evolved during various procedures. First, the behavior of alumina-supported Rh upon heating in the presence of CO, CO2, O2 and H2 was studied. The loss in the capacity to adsorb CO after heating to 525 K increases in the order O2, H2, vacuum < CO2 < CO. Upon heating in CO, some CO is oxidized to CO2 with oxygen from the surface, while the dicarbonyl-forming RhI is reduced to Rh\u00b0. The Rh\u00b0 agglomerates, accounting for the substantial loss in capacity to adsorb CO. Upon heating in CO2, the dicarbonyl-forming RhI is also deactivated. There is little loss in the capacity to adsorb CO upon heating in H2, O2 or vacuum.
\r\n\r\nSecond, the adsorption of H2S and its interaction with CO on Rh supported on alumina was studied. The dissociation of H2S on the Rh at 300 K produces H2 and is inhibited by preadsorbed CO. Rh also facilitates the reaction of H2S with surface oxygen below or at 373 K, in which water is produced. After exposure of the Rh to H2S, CO adsorbs in the linear, but not in the dicarbonyl or bridging modes. Exposure of a CO-precovered surface to H2S displaces much of the bridging CO, but only slowly removes the dicarbonyl and linear CO. Exposure to H2S strongly inhibits the removal of adsorbed CO by O2, but exchange of adsorbed and gas phase CO occurs readily.
" }, { "name": "Jones, Melvin O.", "degree": "Masters", "year": "1982", "title": "The Factors Important to Catalysis by Serine Proteases: Structure of Diisopropylfluorophosphate-Inhibited Bovine Trypsinogen Refined at 2.1 \u00c5 Resolution", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-075029250", "creators": [ { "name": { "family": "Jones", "given": "Melvin O." }, "id": "Jones-Melvin-O", "display_name": "Jones, Melvin O." } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4703-tc82", "abstract": "Crystals of bovine trypsinogen inhibited with diisopropylfluorophosphate (DFP) were grown at pH 7 and x-ray intensity data to 2.1 \u00c5 resolution were collected. The reflections were assigned the phases determined by Kossiakoff (1977) for the isomorphous native trypsinogen structure. Using difference fourier techniques, the resulting protein structure was refined to a residual of 18.2%. As expected, a comparison between (DIP)-trypsinogen and the native trypsinogen structures shows all the structural differences to be in the catalytic site region. However, the structure of the catalytic region was expected to be quite similar to that of DFP-inhibited bovine trypsin at neutral pH, but there exist some marked differences.
\r\n\r\nIn trypsin, one of the isopropyl groups of the inhibitor is analogous to the leaving group of a specific substrate and is hydrolyzed off the inhibitor. In the resulting monoisopropylphosphoryl (MIP)-trypsin, the inhibitor is oriented with a non-esterified phosphoryl oxygen in the oxyanion stabilization site as expected for a tetrahedral intermediate in proteolysis. His 57 N\u03b52 points toward the phosphoryl oxygen at the leaving group site, and is in a position suitable for proton donation to the leaving group.
\r\n\r\nBy contrast, the inhibitor on DIP-trypsinogen remains intact and the presence of electron density at each of the three possible isopropyl locations indicates that the groups of the inhibitor are less specifically oriented. After independent refinement of each of the three possible orientations, the favored orientation was with isopropyl groups near the oxyanion and leaving group sites and the non-esterified phopsphoryl oxygen hydrogen-bonded through two solvent molecules to Ser 214 O. The imidazole ring of His 57 is displaced from its native position at the catalytic site out into the solvent region where it forms hydrogen-bonds to Tyr 94 0 and through a solvent molecule to Ser 214 O. Ser 195 O\u03b3 has moved closer to the position occupied by the His 57 imidazole in native trypsinogen and MIP-trypsin.
\r\n\r\nBoth statistical variation in orientation of the inhibitor and movement of Ser 195 O\u03b3 toward the native imidazole site can be explained by the nonfunctionality of the oxyanion binding site in trypsinogen.
\r\n\r\nThe difference between DIP-Tgen and MIP-trypsin thus suggests both non-productive transition state or substrate binding and stereochemical incompatability between the tetrahedral intermediate and the native imidazole site as possible contributors to the relative inactivity of the proenzyme.
\r\n\r\nConversely, and of more general importance, these results emphasize the importance of exact stereochemical alignment in generating a functional catalytic enzyme.
" }, { "name": "Kaffes, Nicholas Alexandrou", "degree": "PhD", "year": "1982", "title": "Steam Reforming of Methane on a Ni Catalyst Suspended in Molten Sodium Phosphates", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07122018-151932188", "creators": [ { "name": { "family": "Kaffes", "given": "Nicholas Alexandrou" }, "id": "Kaffes-Nicholas-Alexandrou", "display_name": "Kaffes, Nicholas Alexandrou" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "chair", "display_name": "Bailey, James E." }, { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "member", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/9t7k-ge62", "abstract": "A molten salt bath was used to carry out the methane steam reforming reaction in the 800-l000\u00b0C range. The rate of methane pyrolysis was also determined under the same conditions to compare it to the rate of steam reforming. The molten salt baths used included a eutectic mixture of sodium pyrophosphate and sodium metaphosphate, a eutectic mixture of potassium pyrophosphate and potassium metaphosphate, a mixture of Na2O, P2O5 and V2O5 and a mixture of Na2O, P2O5 and NiO. Additional experiments were conducted in empty reactors.
\r\n\r\nIt was found that the rate of pyrolysis was not affected by any of the salt systems.The rate of the steam reforming reaction was low, about 10% of the pyrolysis rate, for the empty reactors and for all the salt systems except the system Na2O-P2O5-NiO under reducing conditions. Under reducing conditions, the nickel of this system was reduced to' metallic Ni which catalyzed the CH4-H2O reaction.
\r\n\r\nX-ray diffraction, electron microscope and electron microprobe analysis studies confirmed the hypothesis that under oxidizing conditions nickel was dissolved in the melt and under reducing conditions solid nickel particles were formed which were suspended in the melt. These particles were exposed to the reactant gases on bubble surfaces.
\r\n\r\nThis novel catalytic steam reforming system is especially suitable for handling residual oils of high sulfur and heavy metal content. The sulfur is captured by the salt melt whereas the nickel catalyst is regenerated by repeated cycles of dissolution into and reduction from the melt.
" }, { "name": "Kaye, Jack Alan", "degree": "PhD", "year": "1982", "title": "Theoretical Studies of Chemical Reaction Dynamics", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:02152012-151600900", "creators": [ { "name": { "family": "Kaye", "given": "Jack Alan" }, "id": "Kaye-Jack-Alan", "display_name": "Kaye, Jack Alan" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vkds-vb56", "abstract": "The collinear collision of an atom with a diatomic molecule has been studied within the frameworks of quantum and classical mechanics. Three major topics have been investigated.
\r\n\r\nIn part I, the collinear collision of hydrogen atoms with hydrogen fluoride (and singly deuterium substituted variants of this system) have been studied in the exchange channel by coupled-channel quantum mechanical calculations using a realistic (high barrier) potential energy surface. We have also investigated the effect on the dynamics of varying the barrier height of the potential energy surface.
\r\n\r\nIn part II, we consider the characterization of low energy resonances in the collinear H + H2 and F + H2(HD, DH, D2) systems. A variety of characterization techniques are used; the most useful proves to be the variation with energy of the eigenvalues of the collision lifetime matrix.
\r\n\r\nIn part III, we develop the method of hyperspherical coordinates for the study of collinear reactive atom-diatomic molecule collisions. The method is tested for the H + H2 system, and is applied to a model system above the threshhold for collision-induced dissociation and to reactions in which a light atom (hydrogen) is transferred between two heavy ones. Systems of this type studied include I + HI and Br + HCl; we also consider some aspects of the dynamics in the Cl + HCl system. We develop the formalism to extract the physical scattering wave function from the method and present preliminary results of probability densities and probability current densities on the H + H2 system. We also consider the formulation of the method in the adiabatic representation and examine both numerically and analytically the behavior of the coupling matrices at large values of the propagation variable. Convergence properties of the method are investigated in detail for the H + H2 and F + H2 systems. Quasi-classical trajectory calculations have been used to help understand the results obtained and to determine the importance of quantum mechanical effects.
\r\n" }, { "name": "Kralik, James Gregory", "degree": "PhD", "year": "1982", "title": "An Investigation of the Applied Chemistry of the Reactions of Coal and Nitrogen Dioxide with a Particular Emphasis on Oxidative Desulfurization", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-11232005-112642", "creators": [ { "name": { "family": "Kralik", "given": "James Gregory" }, "id": "Kralik-James-Gregory", "display_name": "Kralik, James Gregory" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "chair", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Kalvinskas", "given": "John J." }, "id": "Kalvinskas-John-J", "role": "member", "display_name": "Kalvinskas, John J." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/r7z7-6s05", "abstract": "The physical and chemical changes in coal resulting from mild oxidation at ambient conditions with NO2 were studied. Various liquid phases were used as transport media for the NO2. Subsequent to the oxidation, the coal was subjected to a wash with aqueous Na2CO3 at ambient conditions. Particular attention was given to the desulfurization of the coal. A mathematical model of the reactions between NO2 and coal at temperatures less than 100\u00b0C and a pressure of 1 atm was developed from the experimental data. This model included the simultaneous diffusion and reaction of NO2 in the solid-coal matrix and considered pore diffusion not to be controlling. The elemental composition and the energy content, after processing were extensively examined. The effect of the NO2 treatment on the pore structure was established.
\r\n" }, { "name": "Lucchese, Robert Ross", "degree": "PhD", "year": "1982", "title": "The Iterative Schwinger Variational Method Applied to Electron-Molecule Continuum Processes", "advisor": "Marcus, Rudolph A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062011-113312144", "creators": [ { "name": { "family": "Lucchese", "given": "Robert Ross" }, "id": "Lucchese-Robert-Ross", "display_name": "Lucchese, Robert Ross" } ], "advisors": [ { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "advisor", "display_name": "Marcus, Rudolph A." } ], "committee": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "chair", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Marcus", "given": "Rudolph A." }, "id": "Marcus-R-A", "orcid": "0000-0001-6547-1469", "role": "member", "display_name": "Marcus, Rudolph A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/JS31-4A21", "abstract": "We have developed the iterative Schwinger variational method to study electron-molecule scattering problems within the Hartree-Fock approximation. The method is based on the iterative use of the Schwinger variational principle and can obtain exact static-exchange scattering solutions. This approach has been implemented using standard single-center expansion techniques. We present results using the Schwinger variational expression for e-He and e-He+ collisions and find very rapid convergence of the phase shifts with increasing basis set size. We then discuss the iterative use of the Schwinger variational expression and give results for e-H2 and e-H+2 scattering which show very rapid convergence of the iterative method. We have applied this method to low energy 3-CO2 scattering and obtained differential and integral elastic scattering cross sections. We determined that the 2\u03c0u shape resonance in this system occurs at an energy of 5.39 eV with a width of 0.64 eV in contrast to previously published static-exchange results.
\r\n\r\nWe have also used the iterative Schwinger variational method to study the valence shell photoionization of N2 and CO2 as well as the K-shell photoionization of CO2. These results agree well with available experimental data. The vibrational branching ratios for photoionization of 3\u03c3g level of N2 were found to agree quantitatively with experimental measurements when an adequate number of internuclear spacings were considered. The effects of vibrational averaging on 4\u03c3g photoionization of CO2 were also studied. A detailed comparison of the results obtained using the Schwinger method and other theoretical methods for studying photoionization has been made.
\r\n\r\nThe iterative Schwinger variational method has proven to be an accurate and efficient method for obtaining Hartree-Fock level scattering solutions, and it has allowed us to study electron-molecule continuum processes in more detail and for larger systems than previously possible.
" }, { "name": "Marks, David Neil", "degree": "PhD", "year": "1982", "title": "Transition Metal Complexes of 1, 3-bis (2'-pyridylimino) Isoindolines and Their Use as Alcohol Oxidation Catalysts", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07122018-160904951", "creators": [ { "name": { "family": "Marks", "given": "David Neil" }, "id": "Marks-David-Neil", "display_name": "Marks, David Neil" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "chair", "display_name": "Gagne, Robert R." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" } ], "option_major": [ "chemistry" ], "doi": "10.7907/swwe-jf28", "abstract": "Condensation of 1, 2-dicyanobenzene and 2-amino-4-methylpyridine resulted in the formation of a ligand, 4'-MeLH, which in its anionic or neutral form functions as a tridentate chelate. Metal complexes were prepared with metal to ligand ratios of 1:1 and 1:2. The 1:1 complexes also contain acetate or chlorides as ligands while in the 1:2 complex the two tridentate ligands provide a pseudooctahedral environment about the metal ion. An analogous binucleating ligand was prepared by reaction of 1, 2, 4, 5-tetracyanobenzene and 2-amino-4-s-butylpyridine. This ligand, as a dianion, is capable of binding two metal ions, providing three coordination sites for each. Complexes were prepared in which the remaining coordination sites are either occupied by 4'-MeLH, resulting in two six-coordinate metal ions, or by an acetate ligand. Mononuclear and binuclear complexes were prepared with Mn(II), Fe(II), Co(II), Co(III), Ni(II), Cu(II), Zn(II), Ru(II), and Ru(III). Mixed-metal complexes containing Ru(II) were also prepared. Magnetic, spectral and electrochemical properties of these molecules were investigated.
\r\n\r\nThe ruthenium complex, (4'-MeLH)RuCl3, catalyzes the autoxidation of alcohols in basic alcoholic solution. The reaction is general, resulting in the oxidation of primary and secondary alcohols, with the principal products being aldehydes and ketones. The catalytic reaction is affected by the strength of the base used and its coordinating ability. The best results were obtained using sodium ethoxide as a base. Turnover numbers of 10-30 per day were observed in one atmosphere of oxygen at ambient temperature; with larger turnover numbers at higher temperatures. More than 200 turnovers were observed in the oxidation of ethanol at the ambient temperature with little or no loss of catalytic activity. Dimeric complexes of Ru(II) and Ru(III) were isolated from ethanolic solutions. These complexes were characterized and their role in the catalytic reaction is discussed.
\r\n\r\nThe Ru(III) complex, (4'-MeLH)RuCl3, also catalyzes the electrochemical oxidation of alcohols in basic alcoholic solution. The best results were obtained with 2, 6-lutidine as the base. The electrochemical oxidation was carried out at a carbon electrode immersed in an alcoholic solution at 0.8-1.0 V vs. nhe. In the absence of catalyst, negligible current was observed. The catalyzed electrochemical oxidation was general, oxidizing primary and secondary alcohols, with the principal products being aldehydes and ketones. More than 20 catalytic cycles were completed with the current remaining at 75% of its initial value. The Ru(III) complex exhibits reversible one-electron oxidation waves in nonalcoholic solvents in the presence or absence of 2, 6-lutidine. The electrochemistry in alcohols and nonalcohols is discussed, and a possible pathway for the catalytic electrochemical oxidation is presented.
\r\n\r\n" }, { "name": "Maverick, Andrew William", "degree": "PhD", "year": "1982", "title": "Spectroscopy and Photochemistry of Polynuclear Metal Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03092005-130854", "creators": [ { "name": { "family": "Maverick", "given": "Andrew William" }, "id": "Maverick-Andrew-William", "display_name": "Maverick, Andrew William" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PBEA-8W62", "abstract": "The photochemical and spectroscopic properties of two classes of polynuclear metal complexes have been studied.
\r\n\r\nMolybdenum and Tungsten Cluster Halides: The cubic ions Mo6Cl142-, Mo6Br142-, and W6Cl142- are luminescent, with lifetimes approaching 200 \u03bcs in solution at room temperature. The luminescent excited state of Mo6Cl142- is probably associated with a transition localized on the central Mo6 core. Both this excited state and the corresponding ground state undergo facile one electron oxidation. These features make the cluster ions attractive for experiments in photochemical energy storage. Also discussed is evidence from magnetic and spectroscopic studies bearing on the electronic structures of the cluster ions.
\r\n\r\nRhodium Isocyanide Complexes: Various thermal and photochemical reactions in the system Rh2b42+ - Rh4b86+ - Rh2b44+ (b = 1,3-diisocyanopropane) have been examined. The possibility of photocatalytic hydrogen production sensitized by Rh2b42+ and Rh4b86+, previously shown to produce H2 stoichiometrically on irradiation in strongly acidic solution, was explored. Experiments were also conducted with Rh2(TMB)42+ (TMB = 2,5-diisocyano-2,5-dimethylhexane) in the hopes of accomplishing similar energy storage reactions. The equilibria in acidic aqueous solution involving these species as well as oligomers of intermediate oxidation state were also studied. Kinetic studies of the reduction of Rh2b44+ by H2 and of thermal and photochemical oxidation of Rh4b86+ by O2 were inconclusive.
\r\n" }, { "name": "McGee, Lawrence Ray", "degree": "PhD", "year": "1982", "title": "Diastereoselective and Enantioselective Aldol Condensations with Bis-Cyclopentadienyl Zirconium Enolates", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212019-154636979", "creators": [ { "name": { "family": "McGee", "given": "Lawrence Ray" }, "id": "McGee-Lawrence-Ray", "display_name": "McGee, Lawrence Ray" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "member", "display_name": "Gagne, Robert R." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Collins", "given": "Terrence J." }, "id": "Collins-T-J", "role": "member", "display_name": "Collins, Terrence J." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/e2qn-kh88", "abstract": "Bis-cyclopentadienyl zirconium enolates undergo aldol condensation to afford erythro aldol adducts regardless of enolate configuration. Enolates of chiral amides afford high levels of asymmetric induction at the erythro stereo-centers. Mild hydrolysis of the chiral auxiliaries occurs via intramolecular assistance by hydroxyl neighboring groups in the chiral auxiliary. The absolute configurations of the erythro-aldol products have been determined by independent correlations to compounds of known absolute configuration. A cyclic metal-centered transition state model has been developed which accounts for the stereoselectivity observed with zirconium enolates.
" }, { "name": "Millar, David Philip", "degree": "PhD", "year": "1982", "title": "Picosecond Studies of Molecular Energy Transfer, Reorientation, and Internal Motion Dynamics", "advisor": "Hopfield, John J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04042008-131831", "creators": [ { "name": { "family": "Millar", "given": "David Philip" }, "id": "Millar-David-Philip", "display_name": "Millar, David Philip" } ], "advisors": [ { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "advisor", "display_name": "Hopfield, John J." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." } ], "option_major": [ "chemistry" ], "doi": "10.7907/NSA9-8028", "abstract": "This thesis describes the development and characterization of mode- locked CW dye lasers and their application to time-resolved studies of molecular reorientation in liquids, electronic energy transfer in solution, and the internal motions of nucleic acids. Both passive and synchronous mode-locking are found to produce slightly structured pulses with coherence times \u0394tc ~ 0.8 psec, and pulse envelope widths \u0394tp ~ 2 to 3 psec.
\r\n\r\nThe dynamics of reorientation of cresyl violet in alcohol solvents is directly studied on the picosecond time scale. The observed rotational correlation function decays as a single exponential, with a rotational relaxation time that is linearly dependent on solvent viscosity. Rotation times calculated from hydrodynamics are a factor of 2 smaller than observed. The discrepancy is attributed to hydrogen-bonding interactions with the solvent that cause additional friction.
\r\n\r\nElectronic energy transfer between cresyl violet donors and azulene acceptors in solution is studied. The excited donor decay is in excellent agreement with the Rirster dipole-dipole model over the time range from 2 psec to 10 nsec. The critical transfer distance inferred from the decay Ro = 26\u00c5 agrees well with the value calculated from the spectral properties, Ro = 27\u00c5. The increased energy transfer rate in fluid solutions due to translational motion is accurately predicted by the approximate solution to a diffusion equation for the donor excitation. However, the energy transport due to donor-donor transfer was nondiffusive on the picosecond time scale.
\r\n\r\nThe dynamics of the torsional and bending motions of nucleic acids are studied by sub nanosecond time-dependent fluorescence depolarization of intercalated ethidium bromide. The non exponential relaxation behavior is observed for the first time, and is in excellent agreement with the theoretical predictions of an elastic model for DNA internal motions. The intrinsic torsional rigidity of calf thymus DNA is C = 1.43 \u00b1 0.11 x 10-19 erg.cm. The torsional rigidity is shown to be sensitive to details of primary, secondary, and tertiary nucleic acid structure. The polyelectrolyte contribution to the torsional rigidity of DNA has been measured for the first time.
" }, { "name": "Mitch, Charles Howard", "degree": "PhD", "year": "1982", "title": "The Application of Metallated Enamines to the Synthesis of Morphine Alkaloids", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-103306929", "creators": [ { "name": { "family": "Mitch", "given": "Charles Howard" }, "id": "Mitch-Charles-Howard", "display_name": "Mitch, Charles Howard" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "chair", "display_name": "Evans, David A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vf0x-tn08", "abstract": "Metallated enamines have been used to prepare a number of morphine-based analgesics, including efficient entry to the 4a-phenylisoquinolines and morphinans. Stereocontrolled formation of both cis and trans-fused perhydroisoquinolines has been accomplished by either kinetic or thermodynamic protonation of the corresponding octahydroisoquinoline. Reaction of 4a-phenyloctahydroisoquinolinium perchlorates with diazomethane afforded the expected aziridinium perchlorate with a component of direct cyclization to the morphinan structure also observed. Kornbloom oxidation to the \u03b1-amino-aldehyde was accomplished on treatment of the aziridinium salts with dimethyl-sulfoxide. The aldehydes were cyclized to the morphinan structure on reaction with boron trifluoride etherate, providing ready access to intermediates used by Gates in his pioneering total synthesis of morphine.
" }, { "name": "Najdzionek, Jan Stanley", "degree": "PhD", "year": "1982", "title": "Electrochemistry of Some Rhodium(I) Complexes", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07132018-094917474", "creators": [ { "name": { "family": "Najdzionek", "given": "Jan Stanley" }, "id": "Najdzionek-Jan-Stanley", "display_name": "Najdzionek, Jan Stanley" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." } ], "option_major": [ "chemistry" ], "doi": "10.7907/pqye-xp04", "abstract": "The electrochemistry of Rh[C6H5)2P(CHx)nP(C6H5)2]2 Y where Y = CF3SO-3 or ClO-4, x = 2 with n = 1, 2, 3, 4 and x = 1 with n = 2 was examined and compared with that of Co[(C6H5)2P(CHx)2P(C6H5)2]2 where x = 1 and 2. Cyclic voltammetric (CV), chronoamperometric (CA), polarographic (including D.C., normal and differential pulse) and bulk electrolytic experiments were performed and the results show that all of these Rh(I) phosphine complexes are reduced in a two-electron process.
\r\n\r\nCV and CA measurements were used to determine the heterogeneous electron transfer rate constants for Rh[(C6H5)2P(CH2)2P(C6H5)2]2. The values determined were 0.0092 and 0.0087 cm/sec, respectively, and the results are discussed in relation to the Butler-Volmer formulation of electrode kinetics.
\r\n\r\nFluorescence measurements were made on the above rhodium complexes for n = 1, 3 and 4 at room temperature and at 77 K. None emit under ambient conditions in solution but the compound containing ligands with a single methylene unit backbone emitted at 77 K with a lifetime of 20 microseconds. The UV-Visible spectrum of reduced Rh(DPP)+2, the most stable of the reduced complexes, displayed a very intense absorption at 450 nm which was assumed to be charge-transfer in origin.
\r\n\r\nThe two-electron reduction of Rh2(2,5-dimethyl-2,5-diisocyanohexane)2+4 produced a unique species in which a CN- ion has been lost resulting in the formation of a cyclohexylimine ligand which bridges the metal atoms through the imine function. The strain imposed on the TMB ligand backbone forces the rhodium atoms to have the strongest interaction of any of the Rh(Br)+4 compounds studied [Rh(l)-Rh(2) = 2.970(1)\u00c5]. Linear isocyanide carbon-nitrogen distances range from 1.153(9) to 1.175(9) \u00c5 while the imine carbon-nitrogen is extended slightly to 1.254(9) \u00c5.
" }, { "name": "Nee, Michael Wei-Kuo", "degree": "PhD", "year": "1982", "title": "I. Reactions of Bicyclo[3.3.0]octenyl Tosylates II. Nitrogen-15 Nuclear Magnetic Resonance Investigations of Organic Reactions", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-111927806", "creators": [ { "name": { "family": "Nee", "given": "Michael Wei-Kuo" }, "id": "Nee-Michael-Wei-Kuo", "display_name": "Nee, Michael Wei-Kuo" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/82re-5t35", "abstract": "PART I
\r\n\r\nA. Elimination Reactions of 6-Bicyclo[3.2.0]-2-heptenyl Tosylates
\r\n\r\nThe 6- and 7-bicyclo[3.3.0]-2-octenyl tosylates with 2,4,6-trimethylpyridine have been reported to yield mixtures of bicyclo[3.3.0]octa-2,6-diene and bicyclo[3.3.0]octa-2,7-diene. Under the same conditions, the stereoisomeric 6-bicyclo[3.2.0]-2-heptenyl tosylate gives ring-opened products, 1,3,5-cycloheptatriene and 5-ethylidene-1,3-cyclopentadiene.
\r\n\r\nB. Acetolysis of Some Bicyclo[3.3.0]-2-octenyl Tosylates
\r\n\r\nThe products of the acetolysis of the stereoisomeric 6-,7-, and 8-bicyclo[3.3.0]-2-octenyl tosylates are reported. These tosylates were themselves stable to skeletal rearrangements, but were found to undergo 1,2-hydride shifts and elimination solvolysis.
\r\n\r\nPART II
\r\n\r\nAssignment of the Nitrogen-15 Nuclear Magnetic Resonances of Biotin and Unequivocal Synthesis of (+)-[1-15N]Biotin
\r\n\r\nThe 15N NMR spectra of biotin, desthiobiotin, and 2-imidazolidinone were measured. Assignment of the resonances of biotin and desthiobiotin was achieved by off-resonance decoupling. The biotin assignment was confirmed by measurement of biotin specifically labeled with 15N at N1.
\r\n\r\nPART III
\r\n\r\nA 15N Nuclear Magnetic Resonance Study of the Base-Catalyzed -NH2 Exchange Reactions of Acetamide and Thioacetamide
\r\n\r\nThe base-catalyzed -NH2 exchange reactions of acetamide and thioacetamide were studied by 15N nuclear magnetic resonance spectroscopy by use of line-shape analysis. The 15N NMR spectra of these primary amides at intermediate exchange rates were broad doublets, which indicated that the two amide protons were exchanging at different rates. The line-shape analysis indicated that the ratio of exchange rates was 6 \u00b1 1 for acetamide and 3 \u00b1 1 for thioacetamide.
\r\n\r\nPART IV
\r\n\r\nDetermination of the Binding Interactions of cis-[Pt(NH3)2Cl2] with Nucleosides by 15N Nuclear Magnetic Resonance Spectroscopy
\r\n\r\nThe 15N NMR chemical shifts and 15N-195Pt coupling constants of several platinum(II)-ammine complexes were measured. The magnitude of the coupling constants were dependent on the trans ligand. A similar dependence on the trans ligand was found for the 15N chemical shifts of the coordinated ammonia ligands. The magnitude of the 15N platinum coordination shift was proportional to the 15N protonation shift of the ligand. Cis-[Pt(NH3)2Cl2] was found to bind to guanosine through N7 and another nitrogen site. The drug also binds to N3 of cytidine and to all four of the nitrogen sites of adenosine. No evidence was found to support chelate binding of nucleosides by cis-[Pt(NH3)2Cl2].
" }, { "name": "O'Steen, Byron Lance", "degree": "PhD", "year": "1982", "title": "I. Depolarized Light Scattering Studies of Rotational-Translational Coupling in Liquids Composed of Small Anisotropic Molecules. II. Investigation of the Coupling Between Reorientation and Longitudinal Modes in the Brillouin Spectra of Liquids Composed of Anisotropic Molecules", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09142006-110153", "creators": [ { "name": { "family": "O'Steen", "given": "Byron Lance" }, "id": "O'Steen-Byron-Lance", "display_name": "O'Steen, Byron Lance" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "chair", "display_name": "Leal, L. Gary" }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "member", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Corngold", "given": "Noel Robert" }, "id": "Corngold-N-R", "role": "member", "display_name": "Corngold, Noel Robert" }, { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "member", "display_name": "Pings, Cornelius J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/wda1-bj76", "abstract": "Part I
\r\n\r\nIn an attempt to better understand the molecular interactions governing the behaviour of the coupling parameter R measured in light scattering experiments, the depolarized (lVH) spectra for a series of liquids composed of small aromatic molecules, very similar in size and shape, have been measured. The molecules studied here were generally monosubstituted benzene and pyridine derivatives. All were found to exhibit the doublet structure indicative of dynamic coupling between molecular reorientation and shear modes, or more simply, rotational-translational coupling. The degree of this coupling is measured by a parameter R (0 \u2264 R \u2264 1) which is often thought of as the fraction of the shear viscosity attributable to reorientational motion. From the depolarized spectra the coupling parameter R, collective reorientation frequency, and low frequency shear viscosity were determined.
\r\n\r\nThe values of R were found to vary from 0.24 to 0.55 for the liquids studied here. This range is nearly as broad as that observed in all previous studies, which have included such diverse molecules as carbon disulfide, tri-phenyl phosphite, and the highly anisotropic liquid crystal MBBA. This suggests that size and shape considerations, or steric forces, are not the primary factor in determining the degree of rotational-translational coupling as measured by light scattering. If this is indeed the case then other non-steric interactions must be producing the observed variation in R. With this in mind, we have examined possible electrostatic interactions. A simple correlation with dipole moment was not found to exist. Instead it appears that the variation in R can only be understood by consideration of the detailed molecular charge distribution. This is determined to a large extent by resonance interactions with the aromatic ring which are generally reflected in the change of dipole moment from the aliphatic compound (CH3-R) to its aromatic analog (C6H5-R).
\r\n\r\nBased upon resonance structure arguments and our own experimental results, it is concluded that the anomolously large R values found for pyridine from the lHH depolarized spectrum might well be correct and the more orthodox lVH measurements in error. If this assertion is indeed correct, then the reliability of rotational-translational coupling measurements by lVH depolarized light scattering must be considered questionable for weakly scattering molecules such as pyridine.
\r\n\r\nPart II
\r\n\r\nThe coupling of reorientational motion to longitudinal modes was investigated by studying the Brillouin spectra of aniline and p-anisaldehyde over a wide range of scattering angles. The primary goal of these studies was to attempt to confirm the microscopic theory of orientational relaxation in the polarized spectrum. Theoretically it has been shown that for symmetric tops the coupling between longitudinal modes and reorientation in the polarized spectrum is identical to that between shear modes and reorientation in the depolarized spectrum. Thus the Brillouin scattering studies performed here also provide an internal check on the consistency of the 2-variable molecular theory for depolarized scattering and the corresponding theory of orientational relaxation in the Brillouin spectrum. Aniline and p-anisaldehyde were chosen for this investigation since their depolarized spectra at the temperature of interest are well described by the simple 2-variable molecular theory coupling shear modes to orientation. The collective reorientation frequency for both liquids could easily be varied in the low gigahertz range by operating at temperatures near the freezing point. Thus the effects of orientational relaxation in the propagation of longitudinal waves (1 - 10 GHz) should be observable in an angular study of the Brillouin spectra. Moderate viscosites and large rotational-translational couplings also made these liquids attractive from an experimental standpoint since these quantities determine the relaxation strength.
\r\n\r\nOur results for attenuation and velocity of the longitudinal waves demonstrate that there is indeed relaxation in the shear viscosity as predicted by theory. However, shear relaxation in addition to that due to reorientational motion is indicated by the k-dependence of the attenuation results. This stands as an apparent contradiction to the depolarized results which suggest that only orientational relaxation should be important under these conditions. Since the different relaxation effects cannot be unambiguously separated here, a detailed confirmation of orientational relaxation theory could not be obtained.
" }, { "name": "Perkins, Thomas Gardner", "degree": "PhD", "year": "1982", "title": "Nuclear Magnetic Resonance Investigations: Structure, Function, and Dynamics", "advisor": "Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-141617618", "creators": [ { "name": { "family": "Perkins", "given": "Thomas Gardner" }, "id": "Perkins-Thomas-Gardner", "display_name": "Perkins, Thomas Gardner" } ], "advisors": [ { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "chair", "display_name": "Richards, John H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/23sy-qt80", "abstract": "PART I
\r\n\r\nCarbon-13 nuclear magnetic resonance (nmr) spectroscopy has been used to investigate the chemical shifts and spin-lattice relaxation times (T1) of 13CO bound to two derivatives of protoheme IX. The chemical shift is a function of the nature of the ligand trans to the 13CO and of the solvent. T1 measurements of the complex 1-methylimidazole-protoheme IX dimethyl ester-13CO reveal that Chemical Shift Anisotropy (CSA) is the dominant relaxation mechanism for the heme bound 13CO. The aniostropy of the chemical shift tensor, \u0394\u03c3, for the 13CO was found to be 584 \u00b1 132 ppm. The chemical shifts are compared with those obtained for 13CO bound to the monomeric hemoglobin from the marine annelid Glycera dibranchiata.
\r\n\r\nPART II
\r\n\r\nCarbon-13 nuclear magnetic resonance (nmr) spectroscopy has been used to reinvestigate the spin-lattice relaxation times (T1) of 13CO bound to human hemoglobin (HbA) and sperm whale myoglobin. It has been found that the Chemical Shift Anisotropy (CSA) and Dipole-Dipole (D-D) relaxation mechanisms contribute to the observed T1 for the protein-bound 13CO. This observation can explain the lack of an observable nuclear Overhauser effect (NOE) for 13CO bound to HbA. A reanalysis of the previously determined relaxation times indicates that \u0394\u03c3 = 194 \u00b1 37 ppm and reff = 1.81 \u00b1 0.02 \u00c5 for 13CO bound to HbA. The significance of these results in relation to the postulated nucleophilic base interaction between the distal residue His-E7 and the protein bound CO is also discussed.
\r\n\r\nPART III
\r\n\r\nThe spin-lattice relaxation (T1) times for 13CO bound to New Zealand white rabbit hemoglobin (HbR) and the monomeric hemoglobin from the marine annelid Glycera dibranchiata (Hb-II) have been investigated. It has been found that the anisotropies of the chemical shift tensor, \u0394\u03c3, in each protein are vastly different. These results support the existence of a nucleophilic interaction between His-E7 and the heme-bound 13CO in HbR. In addition, the geometry and rate of internal motion for 13CO bound to HbR have also been obtained.
\r\n\r\nPART IV
\r\n\r\nThe pH dependence of the carbon-13 nuclear magnetic resonance (nmr) chemical shift for the C-2 carbon of selectively carbon-13 enriched histidine biosynthetically incorporated into the catalytic triad of the serine protease, \u03b1-lytic protease, has been reinvestigated at three magnetic fields. The spectra acquired at all fields yield a value for 1J13C-H at pH ~ 5 which is consistent with full protonation of the active site imidazole ring of His57 at this pH. Hence, the catalytically important ionization of pKa ~ 6.7 can be assigned to His57. At 125.76 MHz and pH \u227e 5, the carbon-13 spectrum of the enriched enzyme reveals two other structural forms of the histidine side chain within the protein which are not observed at lower fields. The presence of these species can explain previous carbon-13 nmr results which yielded an abnormally low pKa value for the catalytic histidine.
\r\n\r\nPART V
\r\n\r\nA general method is presented for obtaining the exchange rates for chemical systems undergoing slow exchange on the nuclear magnetic resonance (nmr) timescale. As an example of the generality of the method, 31P nmr spectroscopy has been used to measure the rate of exchange for the system [chemical equation included in scanned thesis' Abstract, p. xvii]. The exchange rates obtained with this method are compared to those measured using lineshape analysis.
\r\n\r\nPART VI
\r\n\r\nThe binding of (R,S) d5-ethanol (CD3CHDOD) to horse liver alcohol dehydrogenase (LADH) has been studied using 500.13 MHz 1H nuclear magnetic resonance (nmr) spectroscopy. In the presence of reduced nicotinamide adenine dinucleotide (NADH) the C-1 proton resonance moves such that the extrapolated chemical shift for the C-1 proton of the ethanol bound to the enzyme-coenzyme complex is shifted 0.82 \u00b1 0.08 ppm upfield from the free ethanol resonance. The chemical shifts for the (R) and (S) hydrogens of the bound ethanol do not differ by more than 0.16 ppm.
\r\n\r\nPART VII
\r\n\r\nThe structure of a formaldehyde-crosslinked dimer of verapamil, a Ca+2 channel blocker, has been determined using 500.3 MHz 1H nuclear magnetic resonance (nmr) spectra. The structure has been found to be asymmetric and, as with monomeric verapamil, possess a rigid conformation.
" }, { "name": "Reible, Danny David", "degree": "PhD", "year": "1982", "title": "Investigations of Transport in Complex Atmospheric Flow Systems: I. Small Scale Studies of Diffusion through Porous Media, Impact of Fumehood Exhaust Reentry on Indoor Air Quality, and Pollutant Transport Near an Isolated Island. II. Pollutant Transport in Mountain-Valley and Coastal Regions of California", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12212006-103605", "creators": [ { "name": { "family": "Reible", "given": "Danny David" }, "id": "Reible-Danny-David", "display_name": "Reible, Danny David" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Roshko", "given": "Anatol" }, "id": "Roshko-A", "role": "member", "display_name": "Roshko, Anatol" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/X6WE-JD66", "abstract": "This thesis details some applications of tracer techniques from laboratory scale studies of diffusion in porous media to the analysis of the transport and dispersion of pollutants in the mountain-valley and coastal environments that form the majority of the state of California.
\r\n\r\nChapter 1 describes a technique for estimating gaseous diffusivities in porous media that is based on the general solution to Fick's second law for diffusion in a tube between two well-mixed volumes. In beds of essentially non-porous particles, the ratio of the measured effective diffusivity to the air diffusivity of a gas was found to be proportional to the bed porosity raised to the 1.43 power, a result in agreement with previous studies on similar materials. High moisture content (>15-20% moisture in sand) was found to significantly reduce the gas diffusivity with respect to that found in dry materials.
\r\n\r\nChapter 2 indicates the importance of ventilation system imbalance upon the reentrainment of pollutants exhausted from a building. Tracer was released from a fumehood in a \"clean\" room at the Jet Propulsion Laboratory. Indoor concentrations as high as 235 PPB/gr-mole tracer released/hr were observed due to infiltration of the exhausted tracer. This concentration is about an order of magnitude higher than has been observed in buildings with more balanced ventilation systems. Predictions of single and multi-compartment stirred-tank models were compared to the dynamics of the tracer infiltration. A simple one-compartment model provided a better description of the infiltration dynamics than a three-compartment model suggested by the design of the ventilation system.
\r\n\r\nChapter 3 describes a series of atmospheric tracer studies of the transport and dispersion of pollutants over the ocean and near an isolated island cape. The experiments were designed to determine the impact of local sources on a background air quality sampling program. The horizontal dispersion of the tracer over the ocean surface could be approximated by the Gaussian plume model assuming a neutrally stable atmosphere, in general agreement with the expected atmospheric stability. Tracer releases from the surface of the isolated cape indicated that an essentially well-mixed separated zone existed above and downwind of the cape. The height of this zone extended to 35-40% above the height of the cape, about the same height as the wake downwind of an isolated building. Limited mixing between the separated zone and the freestream resulted in a sharp concentration gradient above this height.
\r\n\r\nChapter 5 indicates the difficulties of describing the behavior of pollutants in complex terrain. A series of tracer experiments conducted in the northern and central California Coastal Mountains are described. The Gaussian plume model could be used to describe the dispersion of the tracer during strong, unidirectional winds. During an elevated tracer release, however, wind directional shear with altitude led to plume bifurcation, with the majority being transported through a stable nighttime drainage layer to ground level. The transport through the stable layer occurred at a vertical velocity of about 2 cm/s, surprisingly rapid transport between stably stratified layers of the atmosphere.
\r\n\r\nChapter 6 describes the uncertainties associated with mass balance and Gaussian parameter estimates from tracer data. The uncertainty in the calculated final result can be less than the errors (assumed random) associated with any individual experimental measurement, indicating that such calculations can be made with greater accuracy than would initially be expected.
\r\n\r\nChapter 7 details the transport of pollutants in the San Joaquin Valley during stable wintertime conditions. The relatively limited net ventilation of the valley indicates that pollutants can remain within the valley for several days subsequent to their release. During one tracer experiment, about 50% of the released tracer was observed to be well-mixed within the southern valley about 72 hours after the beginning of the release. The most significant ventilation mechanism for the valley during the winter was the occasional passage of low pressure frontal systems. Long periods without frontal system passage can lead to significant pollutant buildup.
\r\n\r\nChapter 8 describes the transport of pollutants in the San Joaquin Valley during summertime conditions. While much more effectively ventilated than during the winter, the increased solar insolation leads to significant ozone levels within the valley. A strong influx of air at the northern mouth of the valley is balanced during the day by a corresponding efflux at its southern end and by daytime upslope flow on the Sierra Nevada Mountains. At night, an eddy forms in the southern valley due to low level stabilization and terrain blockage of the afternoon efflux over the southern boundary of the valley. This eddy grows as more air is entrained from the influx at the northern mouth of the valley. An accelerated layer of air aloft also develops during the night due to surface layer stabilization and decoupling. These dynamic flow structures are significant factors in the transport and dispersion of pollutants in the valley during the summer.
\r\n\r\nChapter 9 details the impact of the San Joaquin Valley on the northern Mojave Desert. The transport of pollutants from the southern valley was linked through both tracer and aerosol data to the rapid nighttime reduction in visibility in the northern Mojave Desert. Unlike winter conditions, most of the pollutants in the southern valley were transported out of the valley within a day after their release.
\r\n\r\nChapter 10 describes the impact on the Sierra Nevada Mountains of pollutant sources within the San Joaquin Valley. Tracer released within the valley was efficiently transported upslope, impacting National Park and Forest areas. The maximum concentrations observed upslope could be approximated with the Gaussian plume model, assuming very unstable atmospheric conditions. Nighttime stabilization arrested the upslope movement of the tracer and led to slope and valley impacts throughout the night. The limited nighttime ventilation of the slopes may result in the significant ozone concentrations typically observed at slope sites throughout the night.
\r\n\r\nChapter 11 describes the transport characteristics of the Sacramento Valley, the northern half of the California Central Valley. Tracer experiments indicated that San Francisco Bay area pollutants have only a small effect on the air quality in the Sacramento Valley. A midday flow divergence over Sacramento resulted in tracer impacts in both the northern part of the valley and the slopes northeast of the city. A counterclockwise eddy that forms in the southern valley during the morning was a potential mechanism for recirculating aged pollutants within the valley. During one tracer experiment, most of the released tracer was trapped within an elevated layer of air, a potentially important mechanism for multi-day impacts of pollutants.
\r\n\r\nChapter 12 evaluates the transport of pollutants in the Santa Barbara Channel off the coast of southern California. Limited vertical mixing combined with diurnal wind reversals resulted in multi-day onshore impacts of the tracer released offshore. Efficient lateral mixing of the tracer during wind reversals led to a widespread coastal impact from a single point source. The existence of many point sources could result in a diluted background concentration (i.e. after wind reversals) that equals or exceeds the concentration directly downwind of a single source.
\r\n\r\nChapter 13 develops a two layer model of the atmosphere that semi-quantitatively incorporates much of the basic transport structure observed in the above studies. The method of characteristics and the method of moments were used to examine the implications of the model. The model indicates that the air aloft must be considered in order to accurately predict the impact of a pollutant source, especially when considering the multi-day or long range impact of the source.
" }, { "name": "Rianda, Ronald", "degree": "PhD", "year": "1982", "title": "Electronic Transitions of Molecules by Electron Impact and Multiphoton Ionization Spectroscopy", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-134206825", "creators": [ { "name": { "family": "Rianda", "given": "Ronald" }, "id": "Rianda-Ronald", "display_name": "Rianda, Ronald" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." }, { "name": { "family": "Sparks", "given": "Randal K." }, "id": "Sparks-Randal-K", "role": "member", "display_name": "Sparks, Randal K." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b7ed-jg16", "abstract": "The experimental work discussed in this thesis is concerned primarily with the detection of electric dipole forbidden transitions of molecules in the gas phase. The thesis is divided into two parts. The first part describes measurements made using the technique of low-energy, variable-angle, electron impact spectroscopy. The second part describes investigations performed using resonance enhanced multiphoton ionization (REMPI) spectroscopy.
\r\n\r\nThe low-energy variable-angle electron impact technique has been used to study the electronic spectroscopy of molecules. Both dipole allowed and dipole forbidden transitions have been investigated. Transitions having excitation energies from 0 eV to 20 eV have been studied using incident electron beam energies ranging from 25 eV to 75 eV and scattering angles from 0\u00b0 to 80\u00b0. Molecules studied included nitric oxide (NO), uranium hexafluoride (UF6), tungsten hexafluoride (WF6), nitrogen dioxide (NO2), hydrogen cyanide (HCN), acetonitrile (CH3CN), propionitrile (C2H5CN), butyronitrile (C3H7CN), and malononitrile (CH2(CN)2).
\r\n\r\nWeak structure was observed in the spectrum of nitric oxide between 5.22 eV and 5.60 eV. These bands have been assigned as vibronic bands belonging to the X2\u03c0 \u2192 a4\u03c0 transition. Additional structure extending from 5.7 eV to about 7 eV was assigned to the X2\u03c0 \u2192 b4\u03a3- transition. Several higher lying transitions were observed which have been tentatively assigned as doublet \u2192 quartet in nature.
\r\n\r\nIn order to elucidate the electronic structure of uranium hexafluoride the electron impact spectra at UF6 and WF6 were determined. Eleven features were observed in UF6 with intensity maxima at 3.26, 4.2, 4.7, 5.8, 7.0, 7.86, 9.26, 11.01, 11.75, 12.5 and 13.2 eV. Features were observed in the spectrum at 7.25, 7.9, 8.5, 9.85, 11.75, 12.6 and 13.5 eV. Comparison of the spectra indicate that the primary contribution to transition intensity in UF6 above 5.8 eV and in WF6 results form charge transfer excitations from fluorine p orbitals to metal d orbitals. Tentative assignments based on previous theoretical studies are made.
\r\n\r\nA previously unreported doublet \u2192 quartet transition was observed at 4.49 eV in the electron impact spectrum of NO2, in excellent agreement with theoretical calculations. Doublet \u2192 doublet transitions were observed with maxima at 2.95, 5.81, 7.48, 8.64, 9.69, 10.52, 10.68, 10.94 and 11.20 eV in agreement with previous studies.
\r\n\r\nThe series of C \u039e N containing molecules, Aydrogen cyanide, acetonitrile, malononitrile, propionitrile and butyronitrile, have also been studied using the electron impact technique. Results for hydrogen cyanide are in excellent agreement with previous work. Previously undetected singlet \u2192 triplet transitions of acetonitrile, propionitrile and butyronitrile are reported. In addition the first study of the electronic spectrum of malononitrile is reported.
\r\n\r\nTwo appendices to Part One are included. The first of these reports the results of generalized valence bond and configuration interaction studies of the low lying states of ammonia. The second appendix discusses an electron impact study of the electronically excited states of 1,3,5-cycloheptatriene.
\r\n\r\nPart Two of this thesis describes the theory of multiphoton ionization and reports results obtained using this technique. The application of REMPI spectroscopy to the detection of spin forbidden transitions is examined. It is shown in a study of the X1\u03a3+g \u2192 a3A2 state of CS2 to offer potential for the detection of spin forbidden transitions at high resolution and with great sensitivity.
\r\n\r\nFinally a preliminary study of the two-photon resonance enhanced multiphoton ionization of p-xylene is reported. Several elements of the X1Ag \u2192 1B2u transition observed previously in benzene and p-difluorobenzene are reported.
\r\n" }, { "name": "Rice, Steven Frederick", "degree": "PhD", "year": "1982", "title": "Optical Spectroscopic Studies of Square Planar d\u2078 Dimers", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03102005-155606", "creators": [ { "name": { "family": "Rice", "given": "Steven Frederick" }, "id": "Rice-Steven-Frederick", "display_name": "Rice, Steven Frederick" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z2CJ-J714", "abstract": "The single crystal polarized absorption spectra of rhodium(I) diisocyanide dimers presented confirm the assignment of Mann and Gray for the intense visible absorption band as 1A1g \u2192 1A2u. The structured 1A1g \u2192 3A2u absorption band in RH2(b)4(Bph4)2 shows the 3A2u excited state to have a metal-metal vibrational frequency of 149 cm-1. This is compared to the 85 cm-1 ground state frequency which results in the orbital assignment of this transition as d z2\u03c3* \u2192 pz\u03c3. The excited state has an internuclear bond distance .31 \u00c5 shorter than that of the ground state. The bonding description obtained through the analysis of the spectra depicts a ground state that is formally nonbonding stabilized through configurational interaction with a low lying, strongly bonded excited state.
\r\n\r\nThe 3A2u state in these dimers has a pronounced phosphorescence with a 77K lifetime of 20 \u03bcsec. The quantum yields and lifetimes are very temperature sensitive with several 300K lifetimes of about 10 nsec. This temperature dependence, characteristic of a strong coupling limit, is interpreted in terms of a nonradiative pathway depopulating the 3A2u through another excited state associated with a dz2 \u2192 dx2-y2 transition.
\r\n\r\nA compound isoelectronic with these rhodium diisocyanides, Pt2(H2P2O5)4-4, is shown to have a similar metal-metal interaction in both the ground and lowest excited states. Recent results regarding the low temperature photophysics of this compound have been verified and extended through an analysis of the vibronically structured 3A2u \u2192 1A1g luminescence. The 3A2u state is demonstrated to have an internuclear distance of 2.71 \u00c5, .21 \u00c5 shorter than that of the ground state. The metal-metal vibrational frequency in the 3A2u is 155 cm-1, distinctly higher than the 110 cm-1 of the ground state.
\r\n" }, { "name": "Sand, Irving D.", "degree": "PhD", "year": "1982", "title": "Investigation of the Mechanism of Complement Activation by Immunoglobulin G", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162018-161819743", "creators": [ { "name": { "family": "Sand", "given": "Irving D." }, "id": "Sand-Irving-D", "display_name": "Sand, Irving D." } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p8jz-sj81", "abstract": "The synthesis of a tryptophan specific reagent, dimethyl (2-hydroxy-3-methyl-5-nitrobenzyl) sulfoniurn bromide, is described. The synthetic route incorporated 3H and 14C. The reagent was shown to specifically benzylate tryptophan which was either in solution as a free amino acid or in a protein. Physicochemical properties of the reagent which may be related to its specificity were examined.
\r\n\r\nEvidence is presented that a conformational change occurs in mouse IgG2a when antigen binds and that this change is a necessary condition for the activation of the complement cascade. A 3H/14C-labeled, tryptophan-specific reagent was used to monitor the reactivity of tryptophans in the Fc region of the immunoglobulin. This reactivity correlated with the ability of the antibody to fix complement. Thus binding monovalent and multivalent antigens caused decreases in the reactivity of Fc tryptophan residues by 15% and 22%, respectively. Hapten had no effect on the reactivity of these residues. After reduction and alkylation of disulfide bonds in the IgG to an extent which abolished the antibody's ability to fix complement, the reactivity of Fc tryptophan did not change when monovalent antigen was bound. The Fc tryptophan reactivity of similarly reduced and alkylated IgG increased by 25% when multivalent antigen was bound.
\r\n\r\nA combined classical-alternate pathway assay was developed which distinguishes effects on those components preceeding C3 in the complement cascade from effects on C3 and later components. When antigen-antibody aggregates were assayed by this method, fixation was observed in both the classical and alternate pathways. However, when oligomers of mouse IgG2a produced by chemical crosslinking were assayed, no fixation of the components of the alternate pathway was observed. The time course of classical pathway fixation by these synthetic oligomers indicates that some of the components preceding C3 in the cascade were being enzymatically degraded.
" }, { "name": "Sekera, Michael H.", "degree": "Masters", "year": "1982", "title": "Cationic Cyclization Involving a Remote Allene Function in the Trifluoroethanolysis of 5,6-heptadien-1-yl p-toluenesulfonate", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03282010-113717103", "creators": [ { "name": { "family": "Sekera", "given": "Michael H." }, "id": "Sekera-Michael-H", "display_name": "Sekera, Michael H." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dnmp-1s53", "abstract": "In order to determine whether a remote allene function would undergo intramolecular nucleophriftsubstitution, 5,6-heptadien-1-yl p-toluenesulfonate (14) was synthesized and solvolyzed. The major products of the trifluoroethanolysis of 14 were the cyclic trifluoroethyl ethers of 2-methylenecyclohexanol (24) and 1-cyclohexenemethanol (25). The minor product was the direct displacement product, 5,6-heptadien-1-yl 2,2,2-trifluoroethyl ether (23). The cyclic triflurorethyl ethers were also obtained from the solvolysis of two arenesulfonate esters of 24 and 25, the alcohols having been synthesized by an independent route. Kinetic data showed a rate enhancement for 14 relative to its saturated analog." }, { "name": "Siddoway, Mark Alan", "degree": "PhD", "year": "1982", "title": "The Gasification of Carbonaceous Materials in Molten Sodium Phosphate", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232007-132837", "creators": [ { "name": { "family": "Siddoway", "given": "Mark Alan" }, "id": "Siddoway-Mark-Alan", "display_name": "Siddoway, Mark Alan" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Allen", "given": "Clarence R." }, "id": "Allen-C-R", "role": "chair", "display_name": "Allen, Clarence R." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3t1x-qd32", "abstract": "The gasification rates of petroleum coke, char, and residual oil were measured in molten sodium phosphate. Both oxygen and steam were used as oxidants, and a variety of reactor configurations were studied. Reactors consisted of fused ceramic parts sealed into a reactor configuration using castable refractory.
\r\n\r\nThe reaction rate of carbon particles in a bubbling molten phosphate slurry was found to depend upon the rate of particle-bubble contacting. Upon contact, direct conversion of carbon particles with the gas phase occurs due to the large carbon-molten sodium phosphate contact angle (136\u00b0). The potential flow solution for flow around a bubble where particles are assumed to follow the streamlines gave a consistent picture of bubble-particle contacting. The reactivity of the carbon in the bulk liquid was found to be negligible due to the low solubility of oxygen in the melt.
\r\n\r\nGas phase (no salt) results were generated to establish base cases and to examine treatment effects on the reactivity of green sponge and green needle cokes. The reactivities of both were favorably affected by toluene extraction and adversely affected by calcination to 1300 K. Extraction decreased the agglomerating nature of the sponge coke. Both extracts were largely aromatic with the needle coke extract being more so.
\r\n\r\nMolten sodium phosphate was found to catalyze the gasification of petroleum coke by steam and by oxygen. Such catalytic effects are limited due to the large carbon-salt contact angle and may be obscured in slurry reactors by the rate of particle-bubble contacting being slow. The steam reforming of residual oil revealed that the carbonized product in the molten salt phase closely resembled sponge petroleum coke (as produced by delayed coking).
\r\n\r\nCold model experiments employing water and polymeric beads revealed that dilute slurries of small, non-wetting particles decreased the rise velocity of single bubbles and increased the rate of bubble coalescence in swarms. Dilute slurries of wetting particles had no effect in either case.
\r\n" }, { "name": "Smith, Terrance Patrick", "degree": "PhD", "year": "1982", "title": "Syntheses and Characterization of a Series of Binuclear Iridium Complexes", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252009-153626", "creators": [ { "name": { "family": "Smith", "given": "Terrance Patrick" }, "id": "Smith-Terrance-Patrick", "display_name": "Smith, Terrance Patrick" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "member", "display_name": "Marsh, Richard Edward" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xc18-n193", "abstract": "A binuclear iridium(I) isocyanide complex has been synthesized and its photophysics and chemistry have been synthesized and its photophysics and chemistry have been investigated. The complex Ir2(TMB)2+4 (TMB = 2.5-dimethyl 2,5 diisocyanohexane), possesses an intense absorption band maximizing at 625 nm in the visible region. Excitation into this feature results in two long wavelength luminescence bands at 735 nm and 1080 nm. The longer wavelength feature has been assigned as phosphorescence (E(3A2) \u2192 A1(1A1)) from the lowest electronic excited state; the lifetime of this state is 200 ns and is independent of temperature between 77 K and 298 K. In contrast, the E(3A2) excited state of the analogous rhodium complex exhibits a dramatic temperature dependence. This difference is ascribed to the proximity of ligand field states to the lowest excited state; in the rhodium case the ligand field states are thermally accessible whereas for the iridium case they lie at much higher energy.
\r\n\r\nThe d8 - d8 iridium complex oxidatively adds a variety of small molecules (e.g. I2, Br2, Cl2, CH3I, HCl). The reactivity is quite similar to that of the analogous rhodium system (Rh2(TMB)2+4). One interesting difference is the fact that the HC1 adduct of Rh2(TMB)2+4 is directly observable only at low temperature. Nonetheless, a similar hydride species is postulated as an important intermediate in the production of hydrogen in another binuclear rhodium system.
\r\n\r\nA number of spectroscopic methods have been employed to explore the bonding in symmetric oxidative addition adducts. A linear correlation between metal-metal-force constant and intermetallic distance has been uncovered. The structure of the iodine adduct, Ir2(TMB)4I2(BPh4)2, has been determined; the intermetallic distance 2.803(4) \u00c5. Also dynamic 1H NMR reveals that binuclear complexes containing the TMB ligand are rapidly undergoing conformation changes at ambient temperatures; the activation barriers for this process range from 12 to 15 kcal/mole.
" }, { "name": "Soesanto, Tonny", "degree": "Masters", "year": "1982", "title": "The Measurement of Time Dependent Poisson's Ratio", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11222004-145049", "creators": [ { "name": { "family": "Soesanto", "given": "Tonny" }, "id": "Soesanto-Tonny", "display_name": "Soesanto, Tonny" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/YZTZ-MA69", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nInterest in accurate measurements of the time-dependent Poisson's ratio of polymers arises because it is a component commonly needed in stress analysis and it appears in most theories predicting the behavior of filled materials and composites. Because of the paucity of data and the difficulties in determining [...](t) experimentally, it has been customary in the past to treat [...](t) as a constant. This is unsatisfactory theoretically and inadequate for accurate work.\r\n\r\nAn apparatus has been constructed that enables us to measure tensile relaxation modulus, E(t), and time-dependent Poisson's ratio, [...](t), simultaneously on the same specimen under the same experimental condition. The apparatus, which contains several novel features, is essentially in working condition. Experiments will be made on a series of selected polymers.\r\n\r\nWe hope to be able to determine the bulk relaxation modulus, K(t), and the shear relaxation modulus, G(t), from measurements of E(t) and [...](t). A method for solving the appropriate convolution integrals to determine K(t) and G(t) is already available. It would be desirable to compare the calculated G(t) and K(t) with direct measurements. The latter are very difficult. Direct measurements of G(t) will be made in a torsional relaxometer on the same specimen but not under identical conditions. Nevertheless, these data will be useful as a check on our measurements and our method of calculation.\r\n\r\nThis work will allow a comparison to be made between shear and bulk relaxation via the spectral functions. The measurements will ultimately form the basis for the development of a theory of bulk relaxation in polymeric materials." }, { "name": "Stelson, Arthur Wesley", "degree": "PhD", "year": "1982", "title": "Thermodynamics of Aqueous Atmospheric Aerosols", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09062006-113244", "creators": [ { "name": { "family": "Stelson", "given": "Arthur Wesley" }, "id": "Stelson-Arthur-Wesley", "display_name": "Stelson, Arthur Wesley" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "chair", "display_name": "Seinfeld, John H." }, { "name": { "family": "Cass", "given": "Glen Rowan" }, "id": "Cass-G-R", "role": "member", "display_name": "Cass, Glen Rowan" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Morgan", "given": "James J." }, "id": "Morgan-J-J", "role": "member", "display_name": "Morgan, James J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/m9ac-pe87", "abstract": "A novel application of classical thermodynamics is presented to understand the distribution of aerosol forming material between the gas and aerosol phases in the polluted troposphere. The particular system studied involves NH4NO3 and its interactions with the environmental variables, temperature, relative humidity, droplet pH and aqueous (NH4)2SO4 concentration. In Chapter 1, the theoretical temperature dependence of the solid NH4NO3 dissociation constant is compared to ambient ammonia-nitric acid partial pressure products and general agreement is shown. Also, temperature is demonstrated to be a determining factor for ambient aerosol nitrate formation. Chapter 2 discusses how an urban aerosol can be chemically characterized and that the aqueous electrolytic aerosol solutions are very concentrated (> 8 molal). Thus, any attempt to model ion interactions in aerosol solutions must be able to represent the concentrated solution regime. The ammonia-nitric acid partial pressure product for concentrated NH4NO3-HNO3-H2O solutions is shown to be sensitive to relative humidity but not to pH (1-7) in Chapter 3. Since the ammonia-nitric acid partial pressure product is insensitive to pH, the NH4NO3 dissociation constant over NH4NO3-H2O solutions should typify the ammonia-nitric acid partial pressure product above slightly acidic solutions. The NH4NO3 dissociation constant temperature and relative humidity dependence is evaluated and compared to ambient data in Chapter 4. General agreement between the predictions and the data exists but the possible effect of additional solutes in aerosol droplets is evident. Since NH4NO3 and (NH4)2SO4 are present in atmospheric particles of similar size, it is appropriate to calculate the effect of (NH4)2SO4 on the relative humidity dependence of the NH4NO3 dissociation constant. Chapter 5 shows the presence of (NH4)2SO4 reduces the amount of ammonia and nitric acid in the gas phase and that the NH4NO3 dissociation constant is only 40% less for a 0.5 (NH4)2SO4 ionic strength fraction in aqueous solution. Also, methods for predicting the particle growth, the solution density and the refractive index of NH4NO3-(NH4)2SO4-H2O solutions are outlined in Chapter 5. Good accordance between experimental data and predictions is demonstrated indicating the possible applicability of these techniques to more complex multicomponent solutions.
\r\n\r\nIn the Appendices, a density prediction technique for (NH4)2SO4-H2SO4-H2O solutions is presented since this aspect of ambient aerosols is not contained in the major thrust of this work.
" }, { "name": "Whatley, Gary Eugene", "degree": "PhD", "year": "1982", "title": "An Experimental Study of Eddy Diffusivities and Eddy Viscosities for Cases of Anisotropic and Non-Homogeneous Turbulence in Suspension Flow", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122006-091243", "creators": [ { "name": { "family": "Whatley", "given": "Gary Eugene" }, "id": "Whatley-Gary-Eugene", "display_name": "Whatley, Gary Eugene" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "chair", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Herbolzheimer", "given": "Eric" }, "id": "Herbolzheimer-E", "role": "member", "display_name": "Herbolzheimer, Eric" }, { "name": { "family": "Flagan", "given": "Richard C." }, "id": "Flagan-R-C", "orcid": "0000-0001-5690-770X", "role": "member", "display_name": "Flagan, Richard C." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/entr-8p75", "abstract": "An experimental study on the motion of small particles, about 120 microns in size, in turbulent pipe flow was completed. The goal of the study was to determine the effects of the anistropic, non-homogeneous turbulence generated by the pipe wall on the motion and diffusion of the particles. Measurements of the mean and rms velocities in the r, \u03b8, and z directions were made on flows with Reynolds numbers of 8,400, 12,500, 16,700 and 20,900 for both the continuous and disperse phases. Values of eddy diffusivities for the particles and eddy viscosities for the continuous phase were determined.
\r\n\r\nExperimental data were obtained for the continuous phase (de-ionized water) in order to characterize the four flows used. All velocity measurements on the water were made at axial positions in the flow channel where the flows were fully developed. Mean velocities in the z direction were found to be well represented by the equation u+ = 4.0 + 2.9 ln y+ over the range from y+ = 50 to 550 where u+ is a dimensionless velocity,
Mean velocity measurements of the PVC particles showed that the velocity profiles of the particles did not develop as quickly as the velocity profiles of the fluid phase. Experimentally measured rms velocities of the particles in the r, \u03b8, and z directions were obtained at several radial positions across the channel. Other investigators have measured rms velocities of particles at the center of the channel or have calculated them from diffusion data which yields average rms velocities.
\r\n\r\nIn the experiments performed in the study the values of the axial rms velocities of the particles were found to be smaller than the same values for the liquid. The r and \u03b8 components for the particles did not exhibit constant relationships with the water as did the z component. The radial diffusion of the PVC particles outward from a point source was found to be inhibited after an initial diffusion distance. The eddy-diffusion coefficients for the initial zone of diffusion were 0.31, 0.48, 0.66, and 0.72 cm2/sec, respectively for the four different Reynolds numbers. Values of the turbulent Schmidt numbers calculated over the same region of flow were 0.45, 0.42, 0.47, and 0.74 respectively. The eddy-diffusion coefficients determined for the region of flow in which the inhibition occurred were respectively found to be 0.13, 0.17, 0.22, and 0.25 cm2/sec. The corresponding values for the turbulent Schmidt numbers calculated with the diffusion coefficients from the region of inhibited spread were 1.39, 1.54, 1.54, and 1.56.
" }, { "name": "Wight, Charles Albert", "degree": "PhD", "year": "1982", "title": "Chemical Applications of Infrared Laser Photochemistry", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172018-114924220", "creators": [ { "name": { "family": "Wight", "given": "Charles Albert" }, "id": "Wight-Charles-Albert", "display_name": "Wight, Charles Albert" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/gskp-8c88", "abstract": "Infrared multiphoton electron detachment reactions of gas phase carbanions are investigated using the techniques of ion cyclotron resonance spectroscopy. Ions are spatially confined in a low pressure environment for up to several seconds during irradiation with the unfocused output of a line tunable continuous wave CO2 laser. Analysis of the photodetachment yields as a function of irradiation time, neutral gas pressure, laser intensity and laser wavelength have revealed details of the multiphoton excitation process as well as radiative and collisional relaxation mechanisms. The emphasis for many of these studies is on the wavelength dependence of multiphoton electron detachment yields since the resulting infrared spectra are sensitive probes of molecular structure for distinguishing and identifying isomeric anions. An introduction to low power infrared photochemistry of ions is given in Chapter I.
\r\n\r\nIn Chapter II this technique is used to obtain infrared multiphoton electron detachment spectra of two C7H7- isomers, benzyl and cycloheptatrienyl anions. In the first known example where infrared spectra have been used to probe mechanistic details of an ion-molecule reaction, deprotonation of norbornadiene by CH3O- is shown to yield a mixture of benzyl and cycloheptatrienyl anions.
\r\n\r\nA closer examination of multiphoton electron detachment kinetics is the subject of Chapter III. The results are interpreted in terms of a kinetic model which is developed to describe low power multiphoton excitation and vibrational relaxation. Radiative relaxation of benzyl anion does not appear to be significant at laser intensities greater than 10 W /cm2 and collisions with neutral molecules are only moderately effective in deactiviating vibrationally excited anions.
\r\n\r\nIdentification of cis and trans butenyl anions in Chapter IV demonstrates the sensitivity of this technique for differentiating molecular structures. Deprotonation of cis-2-butene by NH2- forms the cis anion while deprotonation of trans-2-butene results in a mixture of cis and trans C4H7-. The multiphoton electron detachment spectrum of a third isomer, 2-methylallyl anion, is also presented.
\r\n\r\nVibrational relaxation of allyl anion, C3H5- is probed by infrared laser photodetachment techniques in Chapter V. In contrast to the results for benzyl anion in Chapter III, the radiative relaxation of 53 s-1 for allyl anion shows this to be the dominant mechanism for relaxation at pressures below 10-5 torr.
" }, { "name": "Williams, Ellen D.", "degree": "PhD", "year": "1982", "title": "Studies of Chemical Adsorption Using Low-Energy Electron Diffraction", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09302005-132833", "creators": [ { "name": { "family": "Williams", "given": "Ellen D." }, "id": "Williams-Ellen-D", "display_name": "Williams, Ellen D." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/DYY3-MQ42", "abstract": "Both experimental and computational studies based on low-energy electron diffraction (LEED) have been performed to determine the nature of order in chemically adsorbed overlayers. These studies have been directed towards obtaining a better understanding of adatom-adatom interactions by measurement of their most obvious manifestations; change in overlayer order during adsorption and co-adsorption, island formation, and order-disorder phenomena.
\r\n\r\nThe effect of the co-adsorption of hydrogen on the ordering of CO on Rh(111) has been studied using LEED and thermal desorption mass spectrometry. The results indicate that the adsorption of CO proceeds via a physically adsorbed intermediate. In addition, there is a strong repulsive interaction between CO molecules and hydrogen atoms co-adsorbed on Rh(111). This interaction is apparent at distances up to 2.7-3.1 \u00c5 indicating that it is a through-metal effect.
\r\n\r\nA series of LEED patterns has been observed during the adsorption of sulfur on the reconstructed IR(110)-(1x2) surface. The structure observed at lowest coverages has a p2mg symmetry. This allows a determination of the absolute coverage, and indicates a probable binding site for the sulfur atoms.
\r\n\r\nA Monte Carlo simulation of the order-disorder behavior of oxygen on W(110) has been performed. General expressions relating the values of the interaction energies to the transition temperatures for a lattice gas with first, second and third neighbor interactions have been determined. Symmetry considerations in selecting a model for the interaction energies are discussed.
\r\n\r\nThe effect of the ordering of adsorbed molecules into small islands on the LEED beam profile has been determined. In the limit of a random distribution of island positions the overall intensity is shown to be the weighted sum of the intensities from the individual islands. Computer simulations of island-containing overlayers have been used to determine the effect on the beam profiles of deviations from a random distribution of islands.
\r\n\r\nExperimental studies of island formation for CO on Ru(001) have been performed. The finite size of the ordered islands has a strong effect on the order-disorder behavior. Quantitative measurements of this effect have allowed a determination of the island size distribution and thus, the mean island size as a function of coverage.
\r\n" }, { "name": "Wittrig, Thomas Stephen", "degree": "PhD", "year": "1982", "title": "An Investigation of the Interaction of Water and of Saturated Hydrocarbons with the (110) Surface of Iridium", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-09112006-132454", "creators": [ { "name": { "family": "Wittrig", "given": "Thomas Stephen" }, "id": "Wittrig-Thomas-Stephen", "display_name": "Wittrig, Thomas Stephen" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "chair", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." } ], "option_major": [ "chemeng" ], "doi": "10.7907/7J0D-GQ82", "abstract": "The interactions of the reconstructed Ir(110)-(1x2) surface with water and with saturated hydrocarbons have been studied in an ultrahigh vacuum environment. The techniques of thermal desorption mass spectrometry (TDMS), ultrahigh photoelectron spectroscopy (UPS), X-ray photoelectron spectroscopy, contact potential difference measurements and low-energy electron diffraction (LEED) were utilized.
\r\n\r\nChapter 2 describes a refinement in the technique for modelling the kinetics of desorption of adsorbed species by an Arrhenius construction. The functional dependence of the energy of desorption and the rate coefficient on the surface coverage are accounted for. An explicit example is provided.
\r\n\r\nThe interaction of water with the Ir(110)-(1x2) surface is discussed in Chapter 3. It is shown that at most, 6% of the adsorbed water dissociates upon adsorption at a temperature of 130 K. Water does dissociate to OH groups when adsorbed on an Ir(110)-(1x2) surface with preadsorbed oxygen. Water exhibits a constant probability of adsorption for all submonolayer coverages. There exist four distinct thermal desorption states of water on the clean Ir(110)-(1x2) surface. A qualitative model is put forth to rationalize the complex thermal desorption behavior.
\r\n\r\nThe remaining chapters describe investigations of the adsorption and reaction of saturated hydrocarbons on Ir(110)-(1x2). Chapter 4 presents the results of a study of the interaction of cyclopropane and Ir(110). Chapter 5 considers the coadsorption of hydrogen and cyclopropane on Ir(110). Finally, Chapter 6 presents the results of a study of the adsorption and reaction of ethane, propane, isobutane and neopentane on Ir(110). These saturated hydrocarbons dissociated on the surface at some temperature below 130 K. In each case, this dissociation reaction is poisoned by the presence of adsorbed hydrogen on the surface. This leads to the identification of an active site for hydrocarbon dissociation on the surface. As the surface is heated, the carbon remains adsorbed on the surface and the hydrogen desorbs as H2. For ethane, one thermal desorption peak of H2 is observed that corresponds to hydrogen adsorbed in \u03b22 hydrogen adsites on the metal surface. This thermal desorption peak is observed for the remaining hydrocarbons, as well as two other thermal desorption states associated with hydrogen that exists in partially dehydrogenated hydrocarbon fragments present on the surface. No hydrocarbon species other than the one initially adsorbed were observed to desorb from the surface under any of the conditions reported in this work.
" }, { "name": "Yocom, Kathryn Mary", "degree": "PhD", "year": "1982", "title": "The Synthesis and Characterization of Inorganic Redox Reagent-Modified Cytochromes C", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10082012-092613083", "creators": [ { "name": { "family": "Yocom", "given": "Kathryn Mary" }, "id": "Yocom-Kathryn-Mary", "display_name": "Yocom, Kathryn Mary" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Hopfield", "given": "John J." }, "id": "Hopfield-J-J", "role": "member", "display_name": "Hopfield, John J." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/5tfv-gx02", "abstract": "A stable complex is formed between pentaammineruthenium(III) and the imidazole moiety of histidine-33 in cytochrome c. This complex is the major mono-substituted product of the reaction between aquopentaammineruthenium(II) and horse heart cytochrome c at pH 7. It is isolated and purified by ion exchange chromatography on CM-cellulose. High-pressure liquid chromatography of the tryptic hydrosylate of the modified cytochrome c is shown to be an effective method for the identification of the pentaammineruthenium binding site. The spectrum of the modified peptide mimics that of the pentaamminehistidineruthenium(III) model complex. Spectro-electrochemical and optical absorption measurements show that the integrity of the native structure in the vicinity of the heme c group is maintained in the ruthenium-modified protein. The reduction potentials of the two redox sites of the modified protein, derived from cyclic voltammetric measurements at a gold electrode in the presence of 4,4'-bipyridyl, are: heme c (Fe3+/2+), 0.26 V; Ru(NH3)5(His-33)3+/2+, 0.15 V (vs. NHE). A-15 \u00c5 separation between the two redox sites in this system is estimated from molecular models of cytochrome c. It is suggested that the specificity, stability, and redox properties exhibited by aquopentaammineruthenium(II) render it an ideal protein modification reagent for the production of \"synthetic\" multisite metalloproteins.
\r\n\r\nThe criterion of product stability is not met by the aquopentacyanoferrate(II) ion. The products isolated from the reaction of this reagent with cytochrome c are believed to be a mixture of histidine and methionine substitution products, and ionic association complexes. The relatively rapid dissociation of the pentacyanoferrate(II) moiety from the protein severely limits the extent to which the products can be characterized.
\r\n\r\nThe synthesis of a cobalt(III)-cytochrome c complex is described. Tetrachloroplatinate(II) reacts specifically with methionine-65. Pyridine-4-carboxylatopentaamminecobalt(III) is subsequently reacted with the platinum center. Unfortunately, the cobalt(II) form of the derivative is substitution labile, and the redox properties of the cobalt complex are highly unfavorable.
\r\n\r\nIntermolecular reductions of horse heart cytochrome c, Pseudomonas aeruginosa cytochrome c(551), Pseudomonas aeruginosa azurin, and Rhus verniaifera stellacyanin by hexaammineruthenium(II) are reported. Rate constants and activation parameters are presented. The results are discussed in terms of electron transfer distances for metalloprotein redox reactions.
" }, { "name": "Agard, David Andrew", "degree": "PhD", "year": "1981", "title": "Approaches to Macromolecular and Supramolecular Structure Determination", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03022018-140501638", "creators": [ { "name": { "family": "Agard", "given": "David Andrew" }, "id": "Agard-David-Andrew", "orcid": "0000-0003-3512-695X", "display_name": "Agard, David Andrew" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "chair", "display_name": "Dickerson, Richard E." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-Robert-M", "role": "member", "display_name": "Stroud, Robert M." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9psf-0a04", "abstract": "All of the common techniques for obtaining structural information from macromolecular and supramolecular objects suffer from one type of drawback or another. X-ray and neutron diffraction methods have the phase problem (only the amplitude and not the phase angle of the complex diffraction vector can be experimentally observed). Low-dose 3-dimensional electron microscopy suffers from the inability to collect a complete data set due to instrumental limitations. Although light microscopy allows the sample to be kept under biological conditions (compare with standard electron microscopic techniques), the low resolution has limited its appeal to more qualitative aspects of ultrastructure analysis.
\r\n\r\nAll of these limitations can be considered as a lack of information in the Fourier space domain. A generalized mathematical approach is presented where global real-space constraints are utilized to ameliorate this loss of information. In simple cases (one-dimensional analysis) it is possible to solve the phase problem, and in more complex cases (two- and three-dimensional analyses) the added real-space information is used to augment the experimentally derived data. The iterative Fourier refinement scheme was chosen as it represents the most versatile means for incorporating global knowledge concerning the real-space behavior of the object.
\r\n\r\nThis approach was used to solve the three-dimensional x-ray structure of the snake polypeptide neurotoxin \u03b1-Bungarotoxin, the one dimensional transmembrane electron density profile. for acetylcholine receptor containing membranes, and to solve the missing cone problem of electron microscopic structure analysis.
\r\n\r\nReal-space constraints were also incorporated into an iterative deconvolution scheme used both for image processing and for the quantitative analysis of overlapping gel electrophoretogram peaks. None of this work would have been possible if the information supplied by real-space constraints had not been utilized . The approaches presented to these problems are general ones and should be applicable to other systems.
" }, { "name": "Berman, D. Wayne", "degree": "PhD", "year": "1981", "title": "I. Thermochemistry and Reaction Kinetics of Disolvated Protons by Ion Cyclotron Resonance Spectroscopy. II. Thermochemical Studies of Small Fluorocarbons by Photoionization Mass Spectrometry", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042015-131748215", "creators": [ { "name": { "family": "Berman", "given": "D. Wayne" }, "id": "Berman-D-Wayne", "display_name": "Berman, D. Wayne" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/grqm-wy30", "abstract": "The disolvated proton, H(OH2)2+ is employed as a chemical reagent in low pressure (\u02c2 10-5 torr) investigations by ion cyclotron resonance spectroscopy. Since termolecular reactions are absent at low pressure, disolvated protons are not generally observed. However H(OH2)2+ is produced in a sequence of bimolecular reactions in mixtures containing H2O and one of a small number of organohalide precursors. Then a series of hydrated Lewis bases is produced by H3O+ transfer from H(OH2)2+. In Chapter II, the relative stability of hydrated bases containing heteroatoms of both first and second row elements is determined from the preferred direction of H3O+ transfer between BH(OH2)+ complexes. S and P containing bases are shown to bind H3O+ more weakly than O and N bases with comparable proton affinities. A simple model of hydrogen bonding is proposed to account for these observations.
\r\n\r\nH+ transfer from H(OH2)2+ to several Lewis bases also occurs at low pressure. In Chapter III the relative importance of H3O+ transfer and H+ transfer from H(OH2)2+ to a series of bases is observed to be a function of base strength. Beginning with CH3COOH, the weakest base for which H+ transfer is observed, the importance of H+ transfer increases with increasing proton affinity of the acceptor base. The nature of neutral products formed from H(OH2)2+ by loss of H+ is also considered.
\r\n\r\nChapters IV and V deal with thermochemistry of small fluorocarbons determined by photoionization mass spectrometry. The enthalpy of formation of CF2 is considered in Chapter IV. Photoionization of perfluoropropylene, perfluorocyclopropane, and trifluoromethyl benzene yield onsets for ions formed by loss of a CF2 neutral fragment. Earlier determinations of \u0394H\u00b0f298 (CF2) are reinterpreted using updated thermochemical values and compared with results of this study. The heat of formation of neutral perfluorocyclopropane is also derived. Finally, the energetics of interconversion of perfluoropropylene and perfluorocyclopropane are considered for both the neutrals and their molecular ions.
\r\n\r\nIn Chapter V the heats of formation of CF3+ and CF3I+are derived from photoionization of CF3I. These are considered with respect to ion-molecule reactions observed in CF3I monitored by the techniques of ion cyclotron resonance spectroscopy. Results obtained in previous experiments are also compared.
\r\n" }, { "name": "Bone, Russell Leslie", "degree": "PhD", "year": "1981", "title": "Kinetics and Mechanism of the Co-Oxidation of Aldehydes and Model Organic Sulfur Compounds in Studies Related to the Oxo-Desulfurization of Fuel Oil and Coal", "advisor": "Corcoran, William Harrison; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052006-105445", "creators": [ { "name": { "family": "Bone", "given": "Russell Leslie" }, "id": "Bone-Russell-Leslie", "display_name": "Bone, Russell Leslie" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "co-advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "member", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Kalvinskas", "given": "John J." }, "id": "Kalvinskas-John-J", "role": "member", "display_name": "Kalvinskas, John J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/68ap-3w86", "abstract": "Reaction rates and mechanisms in the oxidation of organic sulfur compounds by perbenzoic acid generated in situ from benzaldehyde autoxidation were investigated. Dibenzothiophene and diphenyl sulfide were utilized as model sulfur compounds typical of those present in residual oil and coal. The aromatic nature of a fuel medium was simulated by bromobenzene solvent. Reaction samples were quantitatively analyzed primarily by means of high-pressure liquid chromatography. Diffusion of oxygen, peracid decomposition, and direct oxidation of aldehyde by peracid were found to limit the formation of peracid. Activation energies for decomposition of the peracid and for direct oxidation of the aldehyde by peracid were obtained and used to explain the maximum in oxidation efficiency with respect to temperature observed for dibenzothiophene. Perbenzoic acid was found to be selective in oxidizing diphenyl sulfide and dibenzothiophene to the corresponding sulfoxides and sulfones. At 75\u00b0C, diphenyl sulfide was only oxidized approximately twice as rapidly as dibenzothiophene, in contrast with the higher rates reported by other investigators. Both sulfur compounds were found to inhibit the rate of benzaldehyde autoxidation.
" }, { "name": "Brown, Duncan William", "degree": "PhD", "year": "1981", "title": "Synthesis and Matrix Isolated Photolysis of 2,3-Dimethylbicyclo[2.2.0]Hexa-2,5-Diene-1,4-Dicarboxylic Acid Anhydride: A Potential Precursor to 2,3 -Dimethyl-1,4-Dehydrobenzene", "advisor": "Bergman, Robert G.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032014-135236367", "creators": [ { "name": { "family": "Brown", "given": "Duncan William" }, "id": "Brown-Duncan-William", "display_name": "Brown, Duncan William" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2spb-1x47", "abstract": "The synthesis of the first member of a new class of\r\nDewar benzenes has been achieved. The synthesis of 2,3-\r\ndimethylbicyclo[2.2.0]hexa-2,5-diene-1, 4-dicarboxylic acid\r\nand its anhydride are described. Dibromomaleic anhydride\r\nand dichloroethylene were found to add efficiently in a\r\nphotochemical [2+2] cycloaddition to produce 1,2-dibromo-\r\n3,4-dichlorocyclobutane-1,2-dicarboxylic acid. Removal\r\nof the bromines with tin/copper couple yielded dichloro-\r\ncyclobutenes which added to 2-butyne under photochemical\r\nconditions to yield 5,6-dichloro-2,3-dimethylbicyclo [2.2.0]\r\nhex-2-ene dicarboxylic acids. One of the three possible\r\nisomers yielded a stable anhydride which could be dechlorinated\r\nusing triphenyltin radicals generated by the photolysis\r\nof hexaphenylditin.
\r\n\r\nPhotolysis of argon matrix isolated 2,3-dimethylbicyclo\r\n[2.2.0]hexa-2, 5-diene-1,4-dicarboxylic acid anhydride produced\r\ntraces whose strongest bands in the infrared were at\r\n3350 and 600 cm^(-1). This suggested the formation of terminal\r\nacetylenes. The spectra of argon matrix isolated E- and Z-\r\n3,4-dimethylhexa-1,5-diyne-3-ene and cis-and trans-octa-\r\n2,6-diyne-4-ene were compared with the spectrum of the\r\nphotolysis products. Possibly all four diethynylethylenes\r\nwere present in the anhydride photolysis products. Gas chromatograph-mass spectral analysis of the volatiles from the anhydride photolysis again suggested, but did not\r\nconfirm, the presence of the diethynylethylenes.
\r\n" }, { "name": "Brown-Wensley, Katherine Ann", "degree": "PhD", "year": "1981", "title": "Formation of Bonds to Carbon at Transition Metal Centers", "advisor": "Dervan, Peter B.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03022018-142501266", "creators": [ { "name": { "family": "Brown-Wensley", "given": "Katherine Ann" }, "id": "Brown-Wensley-Katherine-Ann", "display_name": "Brown-Wensley, Katherine Ann" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "co-advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "member", "display_name": "Gagne, Robert R." } ], "option_major": [ "chemistry" ], "doi": "10.7907/sz44-eg97", "abstract": "The reactions of Cp2TiCH2Al(Me)2Cl 1, Cp2TiCH2C(R) = CR 2, and Cp2TiCH2CHRCH2 3 with organic carbonyl compounds are explored. 1 with carbonyl, in a Wittig-type reaction, exchanges methylene for oxygen and yields alkenes; no intermediates can be observed. When treated with carbonyl, 2a (R = \u00d8) inserts O = C into the Ti-CH2 bond, generating oxytitanacyclohexenes. Other metallacyclobutenes similarly insert carbonyl; or, if RC \u2261 CR is labile, exchange methylene for oxygen, producing alkenes. 3a (R = t-butyl) with carbonyl compounds also exchanges methylene for oxygen, and the mechanism of this reaction is explored. 3a is in equilibrium with a titanocene-carbene-olefin complex 11, which is trapped by ketones. 11 is also in equilibrium with titanocene carbene 12 and free olefin; 12 is trapped by esters (as well as ketones}. The formation of 11 is rate-determining. Formation of 12 from 11, trapping of 11 by ketone, and the reverse reaction, formation of 3a from 11 are all competitive. Trapping of 12 by esters is competitive with the reverse reaction, formation of 11 from 12 and olefin. Relative rates of reaction of several ketones and esters are determined.
\r\n\r\nA new platinum vinyl complex, L2Pt(CH = CH2) Me 3 (L = PMe2\u00d8) is prepared by treatment of the known L2Pt(CH = CH2)Cl with MeLi at low temperatures. Oxidative addition of MeI to the platinum (II) complex 3 generates L2Pt(CH = CH2)Me2I 4\u00b7 The thermal decomposition of 4 is examined, and the relative amounts of ethane and propene formed lead to the conclusion that a vinyl group reductively eliminates twenty times faster than methyl.
\r\n\r\nCpCr(NO)2Me is treated with various ligands in an attempt to see insertion of NO into the Cr-Me bond. A clean reaction is observed with PMe3. Instead of insertion, deoxygenation of NO by PMe3 generates O = PMe3 and, ultimately, CpCr(NO) (:NMe) - (PMe3) 5a\u00b7 Similar reactions occur with CpCr(NO)2R, R = n-hexyl, isobutyl, \u00d8, Thermal decomposition of 5a or treatment with H+ generates CH4.
" }, { "name": "Brudvig, Gary Wayne", "degree": "PhD", "year": "1981", "title": "The Nature and Distribution of the Metal Centers in Cytochrome C Oxidase", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052026-232935897", "creators": [ { "name": { "family": "Brudvig", "given": "Gary Wayne" }, "id": "Brudvig-Gary-Wayne", "orcid": "0000-0002-7040-1892", "display_name": "Brudvig, Gary Wayne" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yms5-jw04", "abstract": "Cytochrome c oxidase is the terminal oxidase in the mitochondrial\r\nelectron transport chain. Its function is to catalyze\r\nthe four electron reduction of O2 to water and under coupled\r\nconditions the energy released in this reaction is used in the\r\nsynthesis of adenosine triphosphate. The enzyme contains four\r\nmetal centers, two heme a's and two coppers, all of which are\r\ninequivalent. In this work, the structure of the metal centers\r\nand the distances between the metals has been investigated by\r\nthe use of electron paramagnetic resonance (EPR) and optical\r\nspectroscopy.
\r\n\r\nCytochrome a3 and Cua3 together form the O2 binding site.\r\nIn the fully oxidized enzyme these two metals do not exhibit an\r\nEPR signal due to the strong antiferromagnetic exchange interaction\r\nbetween these closely associated metal ions. NO has been\r\nused as a spin probe to uncouple Cua3 from cytochrome a3. In\r\nthe course of these studies it was found that the enzyme\r\ncatalyzed both the oxidation and reduction of NO. The analysis\r\nof these reactions has provided a new insight into the catalytic\r\nfunction of cytochrome\u00a3 oxidase and the implications of these\r\nexperiments on the mechanism of O2 reduction is discussed. It\r\nalso was found that NO binds specifically to one conformation of\r\nthe oxidized enzyme. This specificity has allowed the conformations\r\nof the oxidized enzyme to be investigated. Three conformations\r\nwere found to form sequentially when the reduced enzyme\r\nwas reoxidized by O2. It is proposed that these conformations\r\ndiffer in the nature of the ligand bridging between cytochrome a3\r\nand Cua3; the final state being one in which a \u03bc-oxo ligand\r\nbridges between the two metal ions.
\r\n\r\nCua is involved in transferring electrons from cytochrome c\r\nto the O2 binding site. The structure of Cua has been of considerable\r\ninterest .because this site has very unusual EPR\r\nproperties. The effect of sulfhydryl binding reagents on the Cua\r\ncenter EPR signal has been examined. These experiments together\r\nwith an analysis of the EPR parameters of the native site, indicate\r\nthat Cua is best described as a Cu(I)-sulfur radical complex\r\nin the oxidized enzyme. A model for the Cua center is proposed\r\nin which a Cu(I) is ligated to two neutral histidine nitrogens\r\nand two cysteine sulfurs, one a cysteinate and the other a thiyl\r\nradical, in a near tetrahedral geometry.
\r\n\r\nThe distance between the metal centers was investigated by\r\nexamining the electron spin relaxation properties of the Cua\r\ncenter by the method of continuous saturation. The dipolar\r\ninteraction of a rapidly relaxing site (either of the two hemes)\r\ncan dramatically increase the relaxation rate of a slowly\r\nrelaxing site (the Cua center) if the sites are in close proximity.\r\nIt is concluded that cytochrome a is within 13 \u00c5 of the Cua\r\ncenter, and that the cytochrome a3-Cua3 site is more than 10 \u00c5\r\nfrom either the Cua center or cytochrome a.
" }, { "name": "Carson, Douglas Glenn", "degree": "PhD", "year": "1981", "title": "Solid State NMR at High Magnetic Fields Using Multiple Pulse Techniques", "advisor": "Vaughan, Robert W.; Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10102006-095702", "creators": [ { "name": { "family": "Carson", "given": "Douglas Glenn" }, "id": "Carson-Douglas-Glenn", "display_name": "Carson, Douglas Glenn" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Rhim", "given": "Won-Kyu" }, "id": "Rhim-Won-Kyu", "role": "member", "display_name": "Rhim, Won-Kyu" }, { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "orcid": "0000-0002-4571-6884", "role": "member", "display_name": "Rossman, George Robert" }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemeng" ], "doi": "10.7907/172t-m550", "abstract": "Part I of this thesis is concerned with measuring the proton chemical shift in solids using a homebuilt high field (6.3 tesla) multiple pulse spectrometer. The distinctive features of the spectrometer are described. The chemical shift tensors for the carboxylic protons in potassium hydrogen malonate, potassium hydrogen oxydiacetate, and potassium hydrogen dicrotonate are reported as determined by multiple pulse experiments. The isotropic part of the chemical shifts relative to a spherical sample of TMS and the anisotropies for the three compounds are -20.5(5), -19.6(7), -18.2(7), and 27.6(6), 28.3(9), 28.9(9) ppm respectively.
\r\n\r\nPart II of this thesis presents a two pulse double quantum nuclear magnetic resonance (NMR) experiment which is designed to measure the Pake doublet splitting in systems of isolated proton pairs which are inhomogeneously broadened. This experiment is applied to the water molecules in the channels of a single crystal of cordierite as a function of orientation and temperature to obtain structural information about the water molecules. Based on the NMR data, the water molecules are found to exhibit substantial anisotropic motion at room temperature and combined with previously reported infrared absorption data, a two site hopping model is proposed where the water spends 85% of its time with its proton-proton vector parallel to the channels and 15% of its time perpendicular. The difference in free energy between these two sites is 0.8 kcal/mole.
\r\n\r\nAverage hamiltonian theory is extended to cover the case of strongly coupled proton-pair systems by transforming the hamiltonian to the dipolar pair-toggling reference frame. It is found that the residual dipolar hamiltonian for the Burum-Rhim 24-pulse cycle is governed by a four-body interaction and any other multiple pulse cycle based on phase alternated WAHUHA 4-pulse cycles will do no better than the 24-pulse cycle at reducing the residual dipolar hamiltonian.
" }, { "name": "Casewit, Carla Jutta", "degree": "PhD", "year": "1981", "title": "I. Electrophilic Reactions of p-Toluenesulfonyl Azide. II. \u00b9\u2075N and \u00b9\u00b3C Nuclear Magnetic Studies of Aryldiazonium Compounds Effect of Substituent, Solvent and 18-Crown-6", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01112005-143434", "creators": [ { "name": { "family": "Casewit", "given": "Carla Jutta" }, "id": "Casewit-Carla-Jutta", "display_name": "Casewit, Carla Jutta" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/nyft-yr23", "abstract": "Part I
\r\n\r\nElectrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nSection 1. Review of Electrophilic Reactions of p-Toluenesulfonyl Azide
\r\n\r\nThe electrophilic reactions of p-toluenesulfonyl azide are reviewed using the principles of hard and soft acids and bases (HSAB).
\r\n\r\nSection 2. The Reaction of p-Toluenesulfonyl Azide with the Sodium Salt of p-Toluenesulfonamide
\r\n\r\nA number of concurrent reactions of p-toluenesulfonyl azide-3-15N (I-3-15N) with the sodium salt of p-toluenesulfonamide were followed by 15N NMR. I-2-15N is formed as a result of a degenerate diazo transfer by I-3-15N to p-toluenesulfonamide anion. p-Toluenesulfonamide anion also reacts with 1-3-15N to give di-p-toluenesulfonamide and azide ion. The 15-N-labeled azide ion exchanges with I to give I-1-15N. I also reacts with azide ion, yielding dinitrogen and p-toluenesulfinate anion. The sulfinate salt reacts readily and reversibly with I to give 1,3-di-p-toluenesulfontriazene anion, which provides another pathway for interconversion of 1-3-15N and I-1-15N.
\r\n\r\nSection 3. The Reaction of p-Toluenesulfonyl Azide with Potassium Azide
\r\n\r\nThe reaction of p-toluenesulfonyl azide with potassium azide-1-15N has been examined in toluene and dichloromethane by 15N NMR. In addition to azide-ion exchange leading to 1-1-15N and I-3-15N, the formation of 1-2-15N is indicated. Two mechanisms for this novel scrambling are proposed. Azide-ion metathesis involving reversible formation of an N-Pentazole derivative from I and azide ion, followed by azide exchange could account for the formation of 1-2-15N. Alternatively, a scrambling route involving the reversible addition of p-toluenesulfonylnitrene to 1-3-15N can be envisioned. The inhibition of scrambling in dichloromethane by addition of iodide ion suggests that a discrete p-toluenesulfonyl azide \u2013 azide ion intermediate is involved in any case.
\r\n\r\nPart II
\r\n\r\n15N and 13C Nuclear Magnetic Resonance Studies of Aryldiazonium Compounds. Effect of Substituent, Solvent and 18-Crown-6.
\r\n\r\n15N and 13C shifts induced by addition of one equivalent of 18-crown-6 have been determined for several para-substituted aryldiazonium fluoborates in dimethylformamide. The \u03b1-nitrogen (N1) and para carbon (C4) shift upfield and the \u03b2-nitrogen (N2) and C1 shift downfield on complexation. The effect of solvent on the positions of the 15N and 13C resonances of p-(n-butyl)benzenediazonium fluoborate are small. The influence of substituents on the 15N chemical shifts is relatively large and comparable to the effect of 18-crown-6. These 13C and 15N results, in conjunction with previous spectroscopic studies indicate that the crown ether complexed aryldiazonium cation is electronically more diazonium-like and less diazo-like than the uncomplexed form.
" }, { "name": "Drew, Horace Rainsford, III", "degree": "PhD", "year": "1981", "title": "The High Resolution Structure of DNA by Single-Crystal X-Ray Methods", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-111249837", "creators": [ { "name": { "family": "Drew", "given": "Horace Rainsford, III" }, "id": "Drew-Horace-Rainsford-III", "display_name": "Drew, Horace Rainsford, III" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "member", "display_name": "Dickerson, Richard E." }, { "name": { "family": "Samson", "given": "Sten Otto" }, "id": "Samson-Sten-Otto", "role": "member", "display_name": "Samson, Sten Otto" }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/vkqm-0f09", "abstract": "The crystal structures of two synthetic DNA oligomers have been solved and refined. The first, a tetramer of base sequence d(CpGpCpG) or CGCG, crystallizes as four-base-pair fragment of left-handed Z' double helix. It differs from the Z helix adopted by the related hexamer sequence CGCGCG in that the pucker of guanine sugar rings is C1'-exo rather than C3'-endo. Crystals of the tetramer, grown from an exceptionally high-salt solution, incorporate excess magnesium chloride. The magnesium cations do not appear to play any structural role, but chloride anions, bound to guanine 2-amino groups in the minor groove, may induce the C3'-endo/C1-exo guanine sugar pucker change via electrostatic repulsion of a nearby phosphate oxygen.
\r\n\r\nA second compound, the dodecamer CGCGAATTCGCG, crystallizes as slightly more than a full turn of right-handed B-DNA. The fact that both CGCG ends of this molecule remain right-handed, without a trace of any conformational instability, implies that left-right interfaces and left-handed helical regions might be rare or nonexistent in a DNA polymer of mixed sequence.
\r\n\r\nAlthough the dodecamer double helix is smoothly deformed into a radius of curvature of 110 \u00c5, bending has little effect on local helix parameters. Instead, the sequence of bases along the chain plays a more important role in helix variability. Purine sugars exhibit the C2'-endo pucker of classical B-DNA, but pyrimidine sugars are distorted into a conformation intermediate between 01'-endo and C1'-exo. Because sugar pucker and glycosyl angle are closely related parameters, this small difference in sugar pucker leads to subtle sequence-specific variations in base pair position and helix twist. In general, pyrimidine-purine steps open to the minor groove, while purine-pyrimidine steps open to the major.
\r\n\r\nOrdered water molecules are an integral part of the CGCGAATTCGCG structure, and they are found more in the grooves of the helix than in the first coordination shell of phosphate groups. Major groove waters are predominantly monodentate, but those in the GAATTC minor groove are organized into a single cooperative network or \"spine\" that extends from the surface of the base pairs to beyond the helical radius of phosphate oxygens. The inner two shells of this network exhibit hydrogen-bonded geometries which are likely to be specific for an uninterrupted stretch of A/T base pairs.
" }, { "name": "Eidem, Penny Kristen", "degree": "PhD", "year": "1981", "title": "An Investigation of the Photochemistry and Structures of Selected Second and Third Row Transition Metal Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072018-093217287", "creators": [ { "name": { "family": "Eidem", "given": "Penny Kristen" }, "id": "Eidem-Penny-Kristen", "display_name": "Eidem, Penny Kristen" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1s9g-cn19", "abstract": "Examination of the electronic spectrum of IrCl3-6 has led to a reassignment of the electronic transitions involved. The band at 206 nm, formerly assigned as the spin allowed \u03c0L to metal eg transition, is shown to be 1t1u (\u03c3) \u2192 2eg(z2, x2 - y2) [1A1g \u2192 1T1u]. Low temperature spectra revealed the presence of additional features at 250 and 278 nm. These are ascribed to the 1t2u (\u03c0) \u2192 2eg(z2, x2 - y2) [1A1g \u2192 1T1u] and 1t2u (\u03c0) \u2192 2eg(z2, x2 - y2) [1A1g \u2192 3T1u] transitions, respectively. Irradiation (\u03bb = 254 nm) of 1-12 M HCl solutions of IrCl3-6 yields IrCl2-6 and H2. Since the excited state populated at this wavelength has been shown to be ligand to metal charge transfer in nature, the reactive intermediate is proposed to he an Ir(II) species with a chlorine atom still formally bound. Photolysis of the reaction product, IrCl2-6 in HCl results in the formation of IrCl3-6 and Cl2. This reaction prevails regardless of wavelength of excitation. The reactive state is again LMCT in nature. Coupling of these reactions effects a reversible photochemical hydrohalic acid splitting catalyst.
\r\n\r\nThe photochemistry of Mo(III), Mo(IV), Mo(V) in aqueous solution was investigated, and these ions were shown to be photochemically inert. Structural characterizations via Raman spectroscopy and X-ray ahsorption edge and EXAFS were undertaken. The Mo(II) structure is shown to be q quadruply bound dinuclear species. The Mo(III) is singly bonded with hydroxy bridges. Data for the Mo(V) ion are typical for oxobridged dinuclear compounds. In strong acid, Mo(IV) is shown to exist as a trinuclear species. As the pH of the medium is increased, the Mo-Mo amplitude decreased, indicating possible cluster fragmentation. In basic solution, a major structural change occurs. The presence of halide ions had no effect on the spectra.
\r\n\r\nRu3(CO)12 reacts photochemically in the presence of olefins, CO, and H2 to catalyze the hydroformylation reaction. Typical yields are 1.5 x 10-3 moles of aldehydes in a 2:1 linear to branched chain ratio. A heterogeneous catalyst can also be effected by photoinduced fragmentation of the cluster in the presence of PV4P. Attachment of a Ru-CO moiety was confirmed by IR and elemental analysis. The first step in catalyst activation was shown to be formation of Ru(CO)4 olefin with a quantum yield of 0.03 for 1-pentene. Subsequent steps involved formation of a hydride-olefin complex, rearrangement to a hydride alkyl, \"CO insertion,\" and reductive elimination of aldehyde. Olefin isomerization and alkane production are also seen under reaction conditions. Formation of larger ruthenium carbonyl clusters led to catalyst deactivation. Photolysis of Ru3(CO)12 in the presence of H2 led to the formation of \u03b1H4-Ru4(CO)12. This molecule can also effect catalysis of the hydroformylation reaction, although yields are an order of magnitude less than for the parent cluster.
" }, { "name": "Eigenberg, Kenneth Eugene", "degree": "PhD", "year": "1981", "title": "The Interaction of Chlorophyll \u03b1 with Lipids in Model and Natural Membrane Systems", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072018-163009985", "creators": [ { "name": { "family": "Eigenberg", "given": "Kenneth Eugene" }, "id": "Eigenberg-Kenneth-Eugene", "display_name": "Eigenberg, Kenneth Eugene" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/p7ns-0z05", "abstract": "Chlorophyll a is the principal photosynthetic pigment of plants and most algae. Despite its importance relatively little is known about its organization or environment within the photosynthetic membrane. A variety of evidence suggests that a significant portion of the chlorophyll may be associated with the lipid portion of the photosynthetic thylakoid membrane. The topic of the interaction of chlorophyll with lipid membranes, both model and natural, forms the basis of this thesis.
\r\n\r\nIt is found that chlorophyll a can be incorporated into model phospholipid bilayer membranes at up to 40 mole percent. Both multilamellar and small vesicular bilayer forms can be prepared and characterized. The phase diagram of the chlorophyll a/distearoylphosphatidylcholine (DSPC) bilayer system, obtained by differential thermal analysis, is complex and indicates that below the solidus phase transition chlorophyll a and DSPC form a compound phase with a composition of 40 mole pe-rcent chlorophyll a. A thermodynamic simulation of the phase diagram yields an estimate for the strength of the chlorophyll a-DSPC interaction. Nuclear magnetic resonance studies, utilizing the shift effect on nearby nuclei due to the large ring current magnetic anisotropy of chlorophyll, demonstrate that compound formation results from a coordination interaction between the DSPC phosphate and the central magnesium atom of chlorophyll a which has an obligatory requirement for an additional axial ligand.
\r\n\r\nThe optical properties of chlorophyll a are modified by its inclusion into bilayers and change at the bilayer phase transition. Compared to chlorophyll a in organic solution, chlorophyll a in bilayers has absorption maxima which are strongly red-shifted and a greatly reduced fluorescence. The red-shift is most pronounced and fluorescence is lowest below the solidus phase transition temperature. Several possible causes of these changes in optical properties are discussed. Because the optical properties of chlorophyll a/DSPC bilayers in the compound phase duplicate the optical properties of bulk in vivo chlorophyll quite well, this system constitutes an attractive model of the photosynthetic chlorophyll antenna.
\r\n\r\nEvidence for the location of a pool of chlorophyll in a lipid environment comes from the 13C-NMR spectrum at 90.5 MHz of the photosynthetic thylakoid membrane from spinach. Specific lipid and chlorophyll resonances are observed and assigned but no protein resonances are found. It can be estimated that at least 30% of the plant chlorophyll contributes to the high resolution spectrum with the remainder presumably broadened by association with membrane proteins. The resonance linewidths of the observed chlorophyll phytol chains are approximately the same as those of the lipid hydrocarbon chains indicating that their motional states are similar and suggesting that this fraction of chlorophyll is lipid bound or at most only loosely associated with membrane proteins.
" }, { "name": "Frommer, Jane Elizabeth", "degree": "PhD", "year": "1981", "title": "Syntheses and Reactions of Polymer-Bound Molybdenum Complexes and Hydrogenolyses of an Alkynyl Cobalt Carbonyl Cluster", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08052009-075725", "creators": [ { "name": { "family": "Frommer", "given": "Jane Elizabeth" }, "id": "Frommer-Jane-Elizabeth", "display_name": "Frommer, Jane Elizabeth" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MD7N-W189", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nCo3(CO)9CCH2C(CH3)3 (1) was prepared and its hydrogen- mediated decomposition was studied. 1 reacted with hydrogen in aromatic solvents (60\u00b0C, 2-7 atm H2) to yield three products: 3,3-dimethylbutene (2), 2,2-dimethylbutane (3), and 4,4- dimethylpentanal (4). The final ratio of alkene to alkane to aldehyde was approximately 2.5 : 1.5 : 1.0. Kinetic data collected from both NMR- and vpc-monitored experiments indicated first order decomposition of starting material 1 and a hydrogen pressure dependence for the rate of appearance of total products. Nearly total inhibition of the hydrogenation was observed in the presence of carbon monoxide (CO:H2, 3.7:3.7 atm, 60\u00b0C). However, at elevated temperatures (85\u00b0), under the same CO/H2 atmosphere, aldehyde (4) production became the predominant reaction pathway at the expense of earlier-formed olefin 2. Incorporation of independently added olefins in the hydrogenation of 1 suggested the intermediacy of olefin in aldehyde and alkane production.\r\n\r\nA polystyrene-attached n[superscript 5}-cyclopentadienyl(tricarbony1)-hydridomolybdenum complex (P-6) was prepared and its reactions with several THF-soluble bases were investigated. Enolates of \u03b2-dicarbonyl compounds quantitatively deprotonated P-6, giving polymer-bound salts of the corresponding anion ([...]-Cp(CO)3Mo[...], P-7). Equilibration studies involving polymers P-6 and P-7 and their soluble monomeric analogues in THF demonstrated that little change in pKa was induced by binding the molybdenum hydride to the polymer. Even though the polymer-supported partners in these experiments were not soluble and therefore rendered the reactions heterogeneous, the systems adhered reasonably well to conventional equilibrium behavior, as exhibited by a simple equilibrium analysis which yielded effectively constant Keq values. A polymer-bound carboxylic acid (P-1) and its conjugate base (P-2) also displayed essentially conventional equilibrium dynamics." }, { "name": "George, Patricia Margaret", "degree": "PhD", "year": "1981", "title": "Electron Attachment Reactions and Photochemistry of Transition Metal Carbonyls in the Gas Phase and on Surfaces", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072018-173514299", "creators": [ { "name": { "family": "George", "given": "Patricia Margaret" }, "id": "George-Patricia-Margaret", "display_name": "George, Patricia Margaret" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Janda", "given": "Kenneth C." }, "id": "Janda-K-C", "role": "member", "display_name": "Janda, Kenneth C." } ], "option_major": [ "chemistry" ], "doi": "10.7907/yp54-sc75", "abstract": "Mechanistic studies of photoassisted and electron-assisted deposition of thin metal films, from organometallic compounds at low pressures have been carried out. Various types of spectroscopy and microscopy are used to characterize the complex processes occurring during film formation. Chapter I gives an introduction emphasizing the importance of such an approach.
\r\n\r\nChapter II details some of the experimental methods used in this study. The three major techniques which were used to evaluate metal films deposited in this manner were Rutherford backscattering spectrometry, X-ray photoelectron spectroscopy and energy dispersive X-ray microprobe analysis. A summary of the methodology associated with each is given and background information is supplied for necessary measurements and calculations.
\r\n\r\nChapter III details the photoassisted mechanism which involves three stages: initiation, propagation and termination of film growth. Initiation is thought to occur primarily by the formation and subsequent reaction of photoelectrons and by photodecomposition. At low pressures formation and reaction of photoelectrons probably dominates while at higher pressures photodecomposition becomes increasingly important. The organometallic compounds are thought to react with electrons by dissociative electron capture, forming negative ions that decompose further to produce thin metal films. Propagation appears to involve a thermally active catalyst capable of effecting a number of turnovers in the dark before termination occurs. The limiting step appears to be loss of remaining CO ligands and the metal species is on the surface.
\r\n\r\nChapter IV examines the dissociative electron attachment reactions of transition metal carbonyls. Dissociative electron attachment rates are measured for the transition metal carbonyls V(CO)6, Cr(CO)6, Fe(CO)5, Ni(CO)4, Mo(CO)6 and W(CO)6. Rates are measured as a function of the pressure of CO2 added to relax epithermal electrons. Derived thermal rate constants for the process M(CO)n \u2192 M(CO)-n-1 + CO are 0.6, 3.0, 2.0, 2.0, 1.3 and 1.2 x 10-7 cm3 molecule-1 s-1, respectively. The differences in these rate constants may be attributed to the different stabilities of the molecular anion with regard to dissociation versus autodetachment. The measured rate of thermalization of electrons by CO2 varies with the metal carbonyl used and depends on the variation of the dissociative electron capture cross section with electron energy. Each system is thus tightly coupled in that the electron energy distribution is determined not only by collisional processes involving CO2 but varies as well with the energy dependent depletion of the distribution by reactant species.
" }, { "name": "Hardy, Richard Randolph", "degree": "PhD", "year": "1981", "title": "Studies of the Specificities and Function of Immunoglobulins: I. Relationship Between Structures and Specificity in Dinitrophenyl-Binding Mouse Myeloma Immunoglobulins. II. Effector Function Triggering in Immunoglobulins", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082018-102024886", "creators": [ { "name": { "family": "Hardy", "given": "Richard Randolph" }, "id": "Hardy-Richard-Randolph", "display_name": "Hardy, Richard Randolph" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "member", "display_name": "Hood, Leroy E." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wcn5-3w02", "abstract": "Chapter 1:
\r\n\r\nThis chapter presents the background to part I (chapters one through six) in which the structure of the antibody binding site and the specific interactions that occur between the site and antigen are considered.
\r\n\r\nChapter 2:
\r\n\r\nThe relation between structure and specificity of antibodies has been explored by 19F NMR studies of the binding of trifluoromethyl analogues of nitrophenyl haptens to the three mouse myeloma immunoglobulins M315, M460, and X25. Haptens were used with trifluoromethyl groups located at the ortho or para positions of the phenyl ring or attached to the side chain, two atoms removed from the ring (i.e., -NHCH2CF3). The changes in chemical shift between hapten free in solution and bound to antibody are sensitive to microenvironment and range from 1.7-ppm downfield to 1-ppm upfield. The shifts of p-trifluoromethylnitrophenyl haptens bound to M315 and M460 are both large downfield shifts, which are likely caused by van der Waals interaction and ring-current effects, particularly from tyrosine-34 (L); these haptens do not show similar shifts when bound to X25 which has a deletion of tyrosine-34 (L). Other differences in the binding of the aromatic rings of haptens by M315, M460, and X25 are observed and their origins considered. The importance of hydrogen bonding in the thermodynamic affinity of antibody for hapten has been estimated by comparisons of binding affinities for haptens with trifluoromethyl groups in place of nitro groups.
\r\n\r\nChapter 3:
\r\n\r\nA protein modification reagent, tetranitromethane, has been employed to specifically nitrate a binding site tyrosine residue in three nitrophenyl-specific myeloma proteins. The nitration does not significantly alter the affinity for hapten, which rules out a hydrogen bond from this tyrosine to the hapten. In the case of M315 and X25, 19F resonances on labelled haptens are specifically perturbed from the native protein position, which is interpreted to indicate proximity of the reporter group and the modified tyrosine. A method is described for the introduction of reporter groups into the protein by a reduction of the nitrotyrosine to aminotyrosine.
\r\n\r\nChapter 4:
\r\n\r\nProton nuclear magnetic resonance has been employed to observe perturbations of methylated nitrophenyl haptens that take place on binding to three nitrophenyl-specific myeloma proteins. A comparison of the previously observed 19F shifts from fluorinated haptens with these proton shifts permits the separation of the proton ring current shifts from the fluorine paramagnetic component. The paramagnetic component, which is large and different for each protein, is ascribed either to van der Waals crowding or to charge transfer interaction or a combination of the two.
\r\n\r\nChapter 5:
\r\n\r\nThe contribution of charge transfer to the 19F paramagnetic shift has been examined by the use of model complexes. Hapten with tryptophan methyl ester model complexes allows determination of the total shift by comparison of methyl and trifluoromethyl shifts. This demonstrated that the para-substituted shift was much larger than the ortho-substituted shift, which is similar to the result found in the protein study. A computer program was employed to determine the intensity and position of the charge transfer absorption band in these model complexes and with the three proteins. The intensity of the charge transfer interaction appears to correlate with the size of the 19F paramagnetic shift. The difference in shift between the ortho- and para-substituted positions is attributed to the particular resonance structures that are important in binding. The association constants of the model complexes were employed to decompose the binding energies of several haptens for the three proteins, and this analysis indicated a hydrogen bond between hapten and antibody for M315 but not M460 or X25.
\r\n\r\nChapter 6:
\r\n\r\nThe nitration study (Chapter 3) indicated a particular tyrosine (Tyr-33H) was near the chain reporter group of the hapten when bound to M315. This result, in combination with the charge transfer data, was used to modify a model of the M315 binding site. A computer graphics system was employed to assemble the first heavy chain hypervariable loop with the tyrosine reoriented so as to fit next to the hapten. The resulting structure, when analyzed by a Diamond refinement energy minimization program, was more precisely fit to standard X-ray coordinates than the original structure.
\r\n\r\nChapter 7:
\r\n\r\nThis chapter presents background on effector function and effector function triggering, which is the subject of the final two chapters. The importance of the integration of antigen binding with cellular effector function is described and several effector functions are mentioned. The two major theories of effector triggering are outlined.
\r\n\r\nChapter 8:
\r\n\r\nComplement fixation studies on the nitrophenyl-specific myeloma protein A22 (and IgM) have shown that both mono- and poly-substituted antigens trigger fixation. This result contrasts with previous work on IgG that demonstrated that only antigens capable of forming complexes could trigger complement fixation. This apparent discord is resolved when one considers that the IgM is already aggregated (as compared to IgG) and so does not require further aggregation after the binding of antigen in order to fix complement. The binding of a single monosubstituted antigen per IgM was sufficient for triggering and the triggering could be competitively inhibited by hapten. The fixation did not occur through the alternate pathway. A DNP-specific hybridoma IgG2a protein acted as a control such that, over the entire dilution range employed in this study, no complement was fixed with the monosubstituted antigen, while with polyvalent antigen considerable fixation occurred.
\r\n\r\nChapter 9:
\r\n\r\nA cell culture line of MOPC 460 has been established by alternate growth in animals and in culture. A cell culture line of MOPC 315 has been established by somatic cell fusion of the MOPC 315 cells with a nonsecreting myeloma that can grow in culture. Secreting cells were selected by a solid phase radioimmunoassay. Two hybridoma lines secreting DNP-specific IgG were also employed in this study. 13C-enriched tryptophan was incorporated into large-scale cultures of these cells and their secreted immunoglobulin was thereby enriched in 13C tryptophan. The various proteins were isolated by affinity chromatography of the spent culture fluid and then studied by 13C NMR. NMR of the isolated protein revealed an envelope of resonances near the position of free tryptophan, but shifted over a 10 parts-per-million range. Observations of the proteins with and without monovalent antigen showed large changes in the envelope for the IgG2a protein (a complement fixing class), but only slight changes for the IgG1 (a non-fixing class). Reduction of the IgG2a produced large changes in the envelope as did papain fragmentation. The results generally support the concept that a conformational change is associated with antigen binding (at least in the IgG2a subclass) and may constitute a major part of the triggering of effector function.
" }, { "name": "Herndier, Brian", "degree": "PhD", "year": "1981", "title": "Activation of Cell Function: Pharmacological Agents Which Degranulate Mast Cells and Cause Skeletal Muscle to Contract", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-113544116", "creators": [ { "name": { "family": "Herndier", "given": "Brian" }, "id": "Herndier-Brian", "display_name": "Herndier, Brian" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "member", "display_name": "Hood, Leroy E." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/9txk-fw43", "abstract": "Chapter I
\r\n\r\nThis chapter presents a general introduction to the cellular metabolism of calcium with particular reference to the concept of calcium pools. The importance of the ionized calcium pool of the cytosol in determining the specific function of cells and tissues is discussed.
\r\n\r\nA model for stimulus-release coupling in mast cells is presented. Excitation-contraction (EC) coupling in skeletal muscle is defined and the fundamental premises required for a theory on EC coupling are given. The two basic theories of excitation-contraction coupling are briefly reviewed.
\r\n\r\nChapter II
\r\n\r\nWe have discovered a new class of drugs which induce the release of 3H-serotonin in mast cells. Verapamil, previously described as a \"specific calcium antagonist\", was found to release 3H-serotonin from mast cells. Our study investigated and compared verapamil and compound 48/80, a drug previously known to be a potent degranulator of mast cells.
\r\n\r\nThis investigation revealed that low concentrations of verapamil inhibited the spontaneous release of 3H-serotonin and efflux of 86Rb+ in mast cells. High concentration of verapamil caused an increase in the rate of the release of 3H-serotonin and 86Rb+ from mast cells. Compound 48/80 causes only an increase in the release 3H-serotonin and 86Rb+-efflux. The effect of compound 48/80 and verapamil on the rate of 86Rb+-efflux in mast cells was investigated.
\r\n\r\nThe significance of these results is discussed. Verapamil, at low concentrations, is thought to act as a \"specific Ca channel blocker\". The increase in 86Rb+ efflux from mast cells induced by high concentration of verapamil suggests an increase in concentration of cytosolic Ca++. The mobilization of calcium into the cytosolic pool is believed also to trigger the release of 3H-serotonin from the mast cell. We propose that verapamil is not simply a calcium antagonist in mast cells but also has the ability at higher concentrations to cause an increase in ionic or cytosolic Ca2+.
" }, { "name": "Highe, Albert John", "degree": "PhD", "year": "1981", "title": "Ionic Motion in Solid Electrolytes: A Solid State NMR Study of Sodium and Lithium in \u03b2-Alumina", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-120827730", "creators": [ { "name": { "family": "Highe", "given": "Albert John" }, "id": "Highe-Albert-John", "display_name": "Highe, Albert John" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Cole", "given": "Terry" }, "id": "Cole-Terry", "role": "member", "display_name": "Cole, Terry" } ], "option_major": [ "chemistry" ], "doi": "10.7907/w0cr-8h87", "abstract": "Solid state NMR techniques have been used as a microscopic probe of the structural and dynamical properties of the mobile cations in the solid electrolyte \u03b2-alumina. The first order quadrupole shifts in the (\u00b13/2 \u2194 \u00b11/2) transitions in the spin 3/2 nuclei sodium and lithium have allowed the electric field gradients (EFG) for the nominal Beevers and Ross (BR) and mid-oxygen (MO) sites to be characterized. The details of the EFG's for and the distribution of cations among BR and MO sites reflect the differences in the potential wells for lithium and sodium in \u03b2-alumina. In particular, unlike sodium, the MO site for lithium is lower in energy than the BR site which results in a different structural arrangement of lithium ions. In sodium \u03b2-alumina, the equilibrium position for sodium in the BR site is displaced from the three-fold symmetry axis. It is believed that this is due to the presence of nearby MO-MO pairs. Furthermore, an activation energy of 0.04 eV is observed for the motion of sodium ions among the displaced BR sites which is associated with the correlated motion of MO-MO pairs. The effects of a second motional process with an activation energy of 0.08 eV are observed in both lithium and sodium spectra which are associated with the motion of cations among BR and MO sites. The interaction of cations in MO-MO pairs was further investigated by observing the effect of varying the ratio of lithium and sodium in mixed lithium-sodium \u03b2-alumina on the distribution of cations among the available sites. The results were interpreted using a theory previously developed to explain the mixed-alkali effect in glasses and indicate that there is a strong interaction between unlike MO-MO pairs which governs the cation site distribution and raises the activation energy for conduction.
" }, { "name": "Howard, Thomas R.", "degree": "Masters", "year": "1981", "title": "Reactions of an Aluminum Stabilized Titanium Alkylidene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-081003488", "creators": [ { "name": { "family": "Howard", "given": "Thomas R." }, "id": "Howard-Thomas-R", "display_name": "Howard, Thomas R." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/48f6-5a82", "abstract": "[Introduction] In recent years there has been a great deal of interest in organometallic alkylidene complexes as they are one of the postulated intermediates for the currently accepted mechanism of metathesis. Our interest was drawn to an aluminum stabilized titanium alkylidene because it had been reported to catalyze metathesis and to demonstrateother novel reactivity. This paper reports our results in the study of the chemistry of this complex." }, { "name": "Huggins, John Mitchell", "degree": "PhD", "year": "1981", "title": "A Study of Fundamental Reaction Pathways for Transition Metal Alkyl Complexes. I. The Reaction of a Nickel Methyl Complex with Alkynes. II. The Mechanism of Aldehyde Formation in the Reaction of a Molybdenum Hydride with Molybdenum Alkyls", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09302025-210640682", "creators": [ { "name": { "family": "Huggins", "given": "John Mitchell" }, "id": "Huggins-John-Mitchell", "display_name": "Huggins, John Mitchell" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5pj3-sn83", "abstract": "I. This study reports the rapid reaction under mild\r\nconditions of internal or terminal alkynes with methyl (acetyl-\r\nacetonato) (triphenylphosphine) nickel (1) in either aromatic or\r\nether solvents. In all cases vinylnickel products 2 are formed\r\nby insertion of the alkyne into the nickel-methyl bond. These\r\ncomplexes may be converted into a variety of organic products\r\n(e.g. alkenes, esters, vinyl halides) by treatment with\r\nappropriate reagents. Unsymmetrical alkynes give selectively the\r\none regioisomer with the sterically largest substituent next to\r\nthe nickel atom. In order to investigate the stereochemistry of\r\nthe initial insertion, ax-ray diffraction study of the reaction\r\nof 1 with diphenylacetylene was carried out. This showed that the\r\nvinylnickel complex formed by overall trans insertion was the\r\nproduct of the reaction. Furthermore, subsequent slow\r\nisomerization of this complex, to a mixture of it and the\r\ncorresponding cis isomer, demonstrated that this trans addition\r\nproduct is the kinetic product of the reaction. In studies with\r\nother alkynes, the product of trans addition was not always\r\nexclusively (or even predominantly) formed, but the ratio of the\r\nstereoisomers formed kinetically was substantially different from\r\nthe thermodynamic ratio. Isotope labeling, added phosphine, and\r\nother experiments have allowed us to conclude that the mechanism\r\nof this reaction does involve initial cis addition. However, a\r\ncoordinatively unsaturated vinylnickel complex is initially\r\nformed, which can undergo rapid, phosphine-catalyzed cis-trans\r\nisomerization in competition with its conversion to the isolable\r\nphosphine-substituted kinetic reaction products.
\r\n\r\nII. The reaction of CpMo(CO)3H (la) with CpMo(CO)3R (2, R =\r\nCH3, C2H5) at 5O\u00b0C in THF gives the aldehyde RCHO and the dimers\r\n[CpMo(CO)3]2 (3a) and [CpMo(CO)2]2 (4a). Labeling one of the\r\nreactants with a methylcyclopentadienyl ligand it was possible to\r\nshow that the mixed dimers MeCpMo (CO)3-CO)3MoCp (3b) and\r\nMeCpMo (CO)2\u2261(CO)2MoCp (4b) are the predominant kinetic products\r\nof the reaction. Additionally labeling the carbonyl ligands of la\r\nwith 13CO led to the conclusion that all three of the carbonyl\r\nligands in la end up in the tetracarbonyl dimers 4a if the\r\nreaction is carried out under a continuous purge of argon.\r\nTrapping studies failed to find any evidence for the intermediacy\r\nof either [CpMo(CO)3]- or [CpMo(CO)3]+ in this reaction. A\r\nmechanism is proposed that involves the initial migration of the\r\nalkyl ligand in 2 to CO forming an unsaturated acyl complex which\r\nreacts with la to give a binuclear complex containing a three\r\ncenter-two electron Mo-H-Mo bond. This complex then selectively\r\nlooses a carbonyl from the acyl molybdenum, migrates the hydride\r\nto that same metal, and forms a metal-metal bond. This binuclear\r\ncomplex with the hydride and acyl ligands on one metal\r\nreductively eliminates aldehyde, and migrates a carbonyl ligand,\r\nto give 4a directly. The other product 3a is formed by addition\r\nof two molecules of free CO to 4a.
" }, { "name": "Ibbotson, Dale Edward", "degree": "PhD", "year": "1981", "title": "A Fundamental Study of NO Reduction with Hydrogen over Ir(110)", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12142006-084027", "creators": [ { "name": { "family": "Ibbotson", "given": "Dale Edward" }, "id": "Ibbotson-Dale-Edward", "display_name": "Ibbotson, Dale Edward" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Stephanopoulos", "given": "Gregory N." }, "id": "Stephanopoulos-G-N", "role": "member", "display_name": "Stephanopoulos, Gregory N." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemeng" ], "doi": "10.7907/xnsj-m676", "abstract": "The heterogeneously catalyzed reduction of NO with hydrogen over Ir(110), as well as the chemisorption of the individual reactants and some of the products, has been studied at low pressures (<10-5) torr). The experiments were performed with several surface sensitive probes-thermal desorption mass spectrometry (TDS), contact potential difference (CPD) measurements, LEED, X-ray and UV photoelectron spectroscopies and Auger electron spectroscopy.
\r\n\r\nChapter 2 describes the chemisorption of hydrogen on Ir(110). The Ir(110)-(1x2) reconstructed surface is stable in hydrogen at pressures from 10-9 to 10-5 torr and surface temperatures from 130 to 1000 K, the conditions investigated. Absolute coverage measurements indicate the saturation density at 130 K on Ir(110) is (2.2\u00b10.2)x1015 atoms cm-2. Thermal desorption measurements indicate hydrogen obeys second order desorption kinetics and exhibits two features, \u03b21 and \u03b22 states, with intensities 2:1, respectively, which exchange isotopically with one another. However, \u03b22 hydrogen obeys first order adsorption kinetics with an initial probability of adsorption So equal to unity, while \u03b21 hydrogen has an So equal to 7x10-3 and obeys second order kinetics. Rate parameters for hydrogen desorption from Ir(110) show a sympathetic increase up to at least half of saturation for the \u03b22 state where Ed and \u03bdd assume values of 23 kcal-mole-1 and 1.5x10-2cm2-s-1, respectively. For the \u03b21 state, Ed = 17-100 kcal-mole-1 from 0 equal to 0.4-0.7 and \u03bdd maintains an average value of 10-7 cm2-s-1. The CPD and UPS measurements are used to infer probable binding sites for the \u03b21 and \u03b22 states of hydrogen which are consistent with the absolute coverage determined from TDS.
\r\n\r\nChapter 3 discusses the interaction of hydrogen and CO on Ir(110). The co-adsorption of hydrogen and CO was undertaken to understand the effects of a model poison, CO, for hydrogen chemisorption. The adsorption of hydrogen on adsorbed CO, or vice versa, causes less hydrogen to occupy the \u03b22 state and shifts the occupancy to the \u03b21 state preferentially. An apparent increase in the probability of adsorption of hydrogen in the \u03b21 state occurs for small CO coverages. At high CO coverages, the Ir(110) surface is poisoned to hydrogen adsorption. Exposing CO to preadsorbed hydrogen causes the binding energy of hydrogen to decrease with increasing CO exposure. Eventually, hydrogen is displaced from the surface for sufficient CO exposures. The induced dipole of hydrogen is unaffected by CO compared to the clean surface, as measured by the CPD. The results indicate CO poisons \u03b22 sites for hydrogen by a simple site blocking mechanism and may exclude \u03b21 sites at high CO coverages by a hydrogen-CO repulsive interaction.
\r\n\r\nChapter 4 presents the results for the molecular chemisorption of N2 and the coadsorption of N2 with hydrogen on Ir(110) at low temperatures. Photoelectron spectroscopy shows molecular levels of N2 at 8.0 (5\u03c3 + 1\u03c0) and 11.8 (4\u03c3) eV in the valence band and at 399.2 eV with a satellite at 404.2 eV in the N(1s) region. The kinetics of adsorption and desorption of N2 show that both precursor kinetics and interadsorbate interactions are important for this chemisorption system. Adsorption occurs with So equal to unity up to saturation coverage (4.8X1014 cm-2) and thermal desorption gives rise to two peaks. The activation energy for desorption varies between 8.5 and 6.0 kcal-mole-1 at low and high coverages, respectively. Results of the co-adsorption of N2 and hydrogen indicate that adsorbed N2 resides in the missing row troughs on Ir(110) - (1x2). Furthermore, N2 is displaced by hydrogen, and the \u03b22 state of hydrogen blocks virtually all N2 adsorption.
\r\n\r\nChapter 5 considers the chemisorption of NO on Ir(110). Adsorption of NO on Ir(110) proceeds by presursor kinetics with So equal to unity independent of surface temperature. Saturation of Ir(110) is achieved in molecular form at 9.6x1014 cm-2 below 300 K. Approximately 35% of a saturated overlayer desorbs as NO in two peaks with equal intensities. The balance desorbs as N2 and O2 where N2 begins to desorb after the first peak of NO is nearly completed. Estimates were made of the activation energies for the various surface reactions that occur as the surface is heated. At low coverages of NO, N2 desorbs with E equal to 36 kcal-mole-1. The activation energy for the dissociation of NO is near 25 kcal-mole-1 for a saturated overlayer, but varies for smaller coverages of NO. Desorption of NO at saturation is associated with energies of 23 and 33 kcal-mole-1 for the two peaks. The first peak represents desorption of NO from an oxygen-free surface and the second peak represents, at least in part, the recombination of nitrogen and oxygen adatoms on a partially oxidized surface. Oxygen tends to stabilize NO to dissociation and desorption as N2, as reflected in TDS. Moreover, UPS and CPD results indicate NO is stabilized on oxygen overlayers compared to the clean Ir(110) surface.
\r\n\r\nChapter 6 discusses the reaction of NO and deuterium to form N2, ND3 and D2O over Ir(110). In addition, the competitive co-adsorption of NO and deuterium and the thermal desorption of the resulting overlayer were performed to gain further insight into the observed steady state rates of reaction, via TDS and CPD measurements. Small precoverages of deuterium do not affect the adsorption kinetics of NO on Ir(110) but do cause more N2 to desorb relative to NO at saturation on the clean surface. Deuterium will adsorb on a saturated overlayer of NO. However, deuterium is strongly blocked from adsorbing on an Ir(110) surface that has both NO and oxygen adsorbed, which is a condition that occurs for some steady state reaction conditions. Under steady state conditions, the reduction of NO shows a marked hysteresis as the surface temperature is cycled for a large enough value of R(PD2/PNO). A plateau in the reduction rate appears at some T that persists as T decreases until at lower values of T the rate falls irreversibly. For larger values of R, ND3 is produced between 470 - 630 K and competes strongly with N2 production. Otherwise, N2 and D2O are the only products of the reduction reaction. Tentative explanations of the empirical rate models derived from the steady state rate data are discussed in light of XPS, UPS and LEED results that are presented as well.
" }, { "name": "Kanamori, Keiko", "degree": "PhD", "year": "1981", "title": "\u00b9\u2075N Nuclear Magnetic Resonance Studies of the Active Sites of Enzymes and In Vivo Nitrogen Metabolism", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09182025-000702960", "creators": [ { "name": { "family": "Kanamori", "given": "Keiko" }, "id": "Kanamori-Keiko", "orcid": "0000-0001-6931-724X", "display_name": "Kanamori, Keiko" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ryxe-9852", "abstract": "To determine whether the catalytic zinc of carboxypeptidase A (CPA) is complexed to the active-site tyrosine (Tyr-248) in solution, a 15N probe, an arsanilazo group enriched in 15N at both azo nitrogens, has been selectively coupled to Tyr-248 with retention of full catalytic activity, and the resulting arsanilazotyrosyl-248 carboxypeptidase A (Zn.Azo-CPA) studied by 15N NMR spectroscopy over pH range from 7.0 to 10.3. Its azo nitrogen resonances, Na (proximal to Tyr-248) and NB (distal), show 8.3 ppm and 23.5 ppm shielding respectively relative to the corresponding resonances of apoarsanilazotyrosyl-248 carboxypeptidase A at pH 8.8. By comparison with the 15N shifts of a model azotyrosine and its zinc complex, these shift differences indicate substantial complexation of the azotyrosyl-248 with the catalytic zinc at pH 8.8. Consistent with such complexation is the fact that the azo nitrogen resonances of Zn.Azo-CPA show large deshieldings on addition of a slowly hydrolyzing substrate glycyl-L-tyrosine or an inhibitor \u03b2 -phenylpropionate, each of which binds to the catalytic zinc and therefore is expected to break any azotyrosine-Zn complex. The results demonstrate unequivocally that the molecular basis for the properties of Zn.Azo-CPA observed by other spectral techniques is a Zn-azotyrosyl-248 complex, with the N\u03b2 nitrogen (and presumably the phenolic oxygen) as ligand to zinc. Furthermore, the high sensitivity of 15N shifts to coordination with zinc permits at least a semi-quantitative estimate of the degree of azotyrosine-Zn complexation and indicates that the major conformation of \u03b6 n.Azo-CPA, and by implication, of CPA in solution could be the one in which the active-site tyrosine is complexed to zinc, in contrast to the major conformation in the crystalline enzyme in which the Tyr-248 hydroxyl is 17 \u00c5 from the zinc.
" }, { "name": "Koelsch, Peter Martin", "degree": "PhD", "year": "1981", "title": "Use of Masked Quinones in Organic Synthesis: Efforts Directed Towards the Synthesis of Tropolonoid Natural Products", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082018-144257927", "creators": [ { "name": { "family": "Koelsch", "given": "Peter Martin" }, "id": "Koelsch-Peter-Martin", "display_name": "Koelsch, Peter Martin" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/v5ga-5777", "abstract": "The application of quinone-derived substrates as building blocks for the synthesis of tropolonoid natural products is described. A preparation of the terpene \u03b2-dolabrin involving electrocyclic ring-opening of a bicyclo[4.l.0]heptenone enolate is outlined. A number of approaches to the recently characterized alkaloid imerubrine involving a highly efficient annelation procedure to form the benzazulenoid carbocyclic skeleton are also discussed.
\r\n\r\n[Chemical structure; see abstract in scanned thesis for details.]
" }, { "name": "Kreh, Robert Paul", "degree": "PhD", "year": "1981", "title": "The Synthesis, Electrochemistry and Reactivity of Binuclear Copper(I) Complexes as Mimics of Protein Active Sites", "advisor": "Gagn\u00e9, Robert R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292025-224718353", "creators": [ { "name": { "family": "Kreh", "given": "Robert Paul" }, "id": "Kreh-Robert-Paul", "display_name": "Kreh, Robert Paul" } ], "advisors": [ { "name": { "family": "Gagn\u00e9", "given": "Robert R." }, "id": "Gagn\u00e9-R-R", "role": "advisor", "display_name": "Gagn\u00e9, Robert R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ffc7-y238", "abstract": "A series of binuclear copper(I) complexes has been synthesized and characterized as potential models for binuclear copper protein sites.
\r\n\r\nThe first group of compounds was prepared by the condensation of 2-hydraxy-5-methylisophthalaldehyde with a variety of primary amines (RNH2) followed by the addition of Cu(CH3CN)4BF4 and pyrazolate (pz), 3, 5-dimethyl pyrazolate (Me2pz) and 7-azaindolate (aza)\r\nanions (X) to yield [Equation. See abstract in scanned thesis for details]. A crystal and molecular structural analysis of [Equation. See abstract in scanned thesis for details] (R = 2-(2'-pyridyl)ethyl) showed each copper bound to the phenoxide oxygen, as well as to one imine and one pyrazolate nitrogen. The pyridine nitrogens were not coordinated to copper, but an intermolecular Cu-Cu interaction (2.97 \u00c5) was observed. Overall coordination about copper(I) is best described as highly distorted pyramidal, with long axial (Cu-Cu) coordination. The copper-copper interaction appears to be associated with a ca. 600 nm (solid state) absorption which is not present in solution or in the solid state for compounds with bulky \"side arms\" (R). All compounds are proposed to be three-coordinate in solution, but they have exhibited no tendency to bind additional ligands such as CO or pyridine. Most of the binuclear copper(I) complexes gave quasi-reversible electrochemical behavior, with two distinct one-electron processes. The reduction potentials were varied over a wide range by modifications of the sidearms (R) and the bridge (X), with the most positive potentials observed for R = t-butyl and X = 3, 5-dimethylpyrazolate (Ef1 = +O.239, Ef2 = + O.80 V vs. nhe). Biological implications of the observed reactivities and redox properties of these compounds are discussed.
" }, { "name": "Lisensky, George Clark", "degree": "PhD", "year": "1981", "title": "Reactions of Multidentate-Ligand Copper(I) Complexes with Dioxygen", "advisor": "Gagn\u00e9, Robert R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10242025-212603541", "creators": [ { "name": { "family": "Lisensky", "given": "George Clark" }, "id": "Lisensky-George-Clark", "display_name": "Lisensky, George Clark" } ], "advisors": [ { "name": { "family": "Gagn\u00e9", "given": "Robert R." }, "id": "Gagn\u00e9-R-R", "role": "advisor", "display_name": "Gagn\u00e9, Robert R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8662-xh16", "abstract": "Syntheses, isolation, and characterization of several copper(I)\r\ncomplexes with multidentate ligands (including macrocycles), and their\r\nreactions with dioxygen are reported. A binuclear dioxygen complex\r\nwas obtained from 1, 1-difluoro-4, 5, 11, 12-tetramethyl-1-bora-3, 6, 10, 13-\r\ntetraaza-2, 14-dioxo-cyclctetradeca-3, 5, 10, 12-tetraenato copper(I) in\r\ndichloromethane solution at -79\u00b0 C. In the absence of excess dioxygen\r\nup to 40% of regenerated copper(I) has been observed upon warming.\r\nAt room temperature the stoichiometry O2/Cu is greater than 1.0 and\r\nincreases with solvent basicity. At large triphenylphosphine to copper\r\nratios the uptake is decreased and at low ratios the uptake is enhanced.\r\nThe macrocyclic complex 5, 7, 7, 12, 14, 14-hexamethyl-1, 4, 8, 11-tetra-azacyclctetradeca-\r\n1, 4, 8, 11-tetraene copper(I) perchlorate in the solid\r\nstate or in dichloromethane solution at -79\u00b0 C is ketonated in either of\r\ntwo positions. The 3, 5, 7, 7, 10, 12, 14, 14-octamethyl derivative is\r\nketonated in only one position. Similar reactions are observed for the\r\n4, 11-diene copper(I) complexes as well as partial oxidative dehydrogenation." }, { "name": "Lockhart, Thomas Paul", "degree": "PhD", "year": "1981", "title": "The Chemistry of 1,4-Dehydrobenzenes", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072025-210733150", "creators": [ { "name": { "family": "Lockhart", "given": "Thomas Paul" }, "id": "Lockhart-Thomas-Paul", "display_name": "Lockhart, Thomas Paul" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/35fh-q724", "abstract": "Upon heating, alkyl substituted cis 1,2-diethynyl olefins\r\nundergo cyclization to yield reactive 1,4-dehydrobenzenes; the\r\nproducts isolated may be derived from either unimolecular or\r\nbimolecular reactions of the intermediate. Z-4,5-Diethynyl-4-\r\noctene (19) undergoes rearrangement to yield 2,3-di-n-propyl-1,4-\r\ndehydrobenzene (33). Solution pyrolysis of 19 in inert aromatic\r\nsolvents produces three unimolecular products, (Z-dodeca-4,8-\r\ndiyn-6-ene (23), benzocyclooctene (25) and o-allyl-n-propylbenzene\r\n(26)) in high yield. When 1,4-cyclohexadiene is\r\nadded to the pyrolysis solution as a trapping agent, high yields\r\nof the reduced product o-di-n-propylbenzene (28) are obtained.\r\nThe kinetics of solution pyrolysis of 19 in the presence and\r\nabsence of trapping agent establish that 2,3-di-n-propyl-1,4-\r\ndehydrobenzene is a discrete intermediate on the pathway leading\r\nto products. When the reaction was run in the heated probe of an\r\nNMR spectrometer, CIDNP was observed in 26. This observation,\r\nalong with kinetic and chemical trapping evidence, indicates the\r\npresence of two additional intermediates, formed from 33 by\r\nsequential intramolecular [1,5] hydrogen transfer, on the pathway\r\nto products. The observation of CIDNP, coupled with the\r\nreactivity exhibited by 33 and the other two intermediates,\r\nimplicates a biradical description of these molecules.
\r\n\r\nTwo approaches have been used to determine the spin state(s)\r\nof 1,4-dehydrobenzenes produced in the solution reaction of\r\ndiethynyl olefins. The first method relies on the \"spin\r\ncorrelation effect\" which postulates a relationship between the\r\nspin state of a caged radical pair and the ratio of cage and\r\nescape reactions (C/E) which may occur in the pair. When the\r\n2,3-di-n-propyl-1,4-dehydrobenzene biradical abstracts hydrogen\r\nfrom 1,4-cyclohexadiene, a radical pair is generated. If a\r\nmixture of l,4-cyclohexadiene-do and -d4 is employed it is\r\npossible, by performing a VPC-MS analysis, to determine the ratio\r\nC/E leading from the radical pair to the reduced product, 28.\r\nApplying this method to the reaction of 19, C/E was found to be\r\n0.6, independent of the concentration of 1,4-cyclohexadiene\r\n(between 0.1 and 10 M) in the chlorobenzene reaction solution.\r\nThis result suggests the presence of the singlet state of 33 in\r\nthe reaction of 19. Independent support for this analysis came\r\nfrom the reaction of 3,4-dimethyl-1,5-diyn-3-ene (38) in\r\nhexachloroacetone sol vent in an NMR probe. The major product,\r\nl,4-dichloro-2,3-dimethylbenzene (39), obtained by chlorine\r\nabstraction from the sol vent, showed polarization (emission) in\r\nthe aromatic protons. The interpretation of this result is\r\nstraightforward and indicates solvent trapping of the singlet\r\nstate of the intermediate 2,3-dimethyl-1,4-dehydrobenzene. Both\r\nof these experiments indicate that only the singlet state of 1,4-\r\ndehydrobenzenes is generated upon thermal reaction of diethynyl\r\nolefins. The failure to observe evidence for the triplet state\r\nof the 1,4-dehydrobenzenes under the reaction conditions requires\r\nthat, if the triplet is the ground electronic state, the rate of\r\nintersystem crossing from the singlet must be <109 sec-1.
" }, { "name": "Miller, James Arthur", "degree": "PhD", "year": "1981", "title": "Studies on Ligand Binding to the Histrionicotoxin and the Agonist Binding Sites of Membrane Bound Acetylcholine Receptor from Torpedo californica", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132018-105051819", "creators": [ { "name": { "family": "Miller", "given": "James Arthur" }, "id": "Miller-James-Arthur", "display_name": "Miller, James Arthur" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Campbell", "given": "Judith L." }, "id": "Campbell-J-L", "orcid": "0000-0001-8291-5551", "role": "member", "display_name": "Campbell, Judith L." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wd5n-dn51", "abstract": "Chapter I
\r\n\r\nThe binding of various alkylguanidines to the histrionicotoxin site of the membrane bound acetylcholine receptor of Torpedo californica was studied. These results, along with data obtained on the binding of several histrionicotoxin derivatives, were used to formulate a model of ligand to binding to the receptor's histrionicotoxin site.
\r\n\r\nAn azido derivative of histrionicotoxin was used in an attempt to photoaffinity label the histrionicotoxin site. The effect of the agonist carbamylcholine on incorporation of this label was investigated.
\r\n\r\nChapter II
\r\n\r\nProton magnetic resonance was used to monitor binding of choline, a known partial agonist, to acetylcholine receptor-enriched membrane preparations from Torpedo californica electroplax. The interaction between choline and receptor led to a broadening of the resonance of the choline methyl groups and this effect was reversed by \u03b1-bungarotoxin, a quasi-irreversible antagonist of the acetylcholine receptor. From the concentration dependence of line broadening the equilibrium dissociation constant for choline was obtained (Kd = 190 \u00b1 65 \u03bcM). The temperature dependence of the parameters observed in the choline titrations gave an enthalpy of binding \u0394H < 1.5 kcal/mol and allowed estimates for the dissociation rate constant of the receptor-choline complex (kdiss > 1.6 x 103 S1) and the respective activation energy, Ea (kdiss) \u2248 5.5 kcal/mol. The association of other ligands with the membrane-bound receptor could also be studied by observing effects of varying concentrations of such ligands on the choline methyl group linewidth at a constant choline concentration.
\r\n\r\nChapter III
\r\n\r\nMembrane fragments from the electric organ of Torpedo californica were purified so that the only protein components remaining were the four homologous acetylcholine receptor subunits of 40,000, 50,000, 60,000 and 65,000 daltons. The change in agonist affinity induced by carbamylcholine and the rate of this change, especially in the presence of local anesthetics, were studied and compared to the corresponding properties of membranes containing additional protein components. The results were consistent with the notion that desensitization, as defined by conversion to a state of higher ligand affinity of the acetylcholine receptor, and modulation of the kinetics of this effect by local anesthetics are dependent only on the receptor protein in its native environment.
" }, { "name": "Morse, Randall Heywood", "degree": "PhD", "year": "1981", "title": "EPR Spectroscopic Studies of the Active Sites of Some Heme- and Copper-Containing, Oxygen-Binding Proteins", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132018-112023831", "creators": [ { "name": { "family": "Morse", "given": "Randall Heywood" }, "id": "Morse-Randall-Heywood", "orcid": "ORCID ID\tFirst Name\tLast Name\tOther Names\tAffiliations 0000-0003-0000-8718", "display_name": "Morse, Randall Heywood" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "member", "display_name": "Gray, Harry B." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/7cva-0k93", "abstract": "All oxygen-utilizing proteins contain copper, iron, or both, at the oxygen-bonding sites. The ligand environment and geometry about the metal centers in these proteins must be crucial in determining their individual functions. This thesis reports studies in which the ligand nitric oxide is used as a spin probe to investigate the structure of the oxygen-binding sites of myoglobin and some inorganic heme analogues, and of tree and fungal laccase and cytochrome c oxidase.
\r\n\r\nNitric oxide reacts with heme iron in ferrous hemeproteins such as hemoglobin and myoglobin, to form six-coordinate paramagnetic complexes. Chapter II reports investigations on the EPR spectra of the nitric oxide complexes of ferrous myoglobin, cytochrome c, and Fe(II) protoporphyrin IX-imidazole, which change with temperature over the range 30-180 K. This temperature dependence could be due to motional/relaxation effects or to a chemical equilibrium. To resolve this matter, the technique of factor analysis was used to deconvolute the temperature-dependent EPR spectra. By this method it has been found that all of the spectra for any given complex can be reproduced by adding together varied amounts of two signals, demonstrating that the variation of the EPR spectra with temperature is due to an equilibrium between two species. The two species differ in enthalpy by no more than about 2 kcal/mol. The observed signals are interpreted as arising from two six-coordinate conformers of the nitrosylheme\u2219nitrogen base complexes, differing primarily in the position of the iron with respect to the ligands and to the heme plane. The anomalous behavior of the terminal respiratory enzyme cytochrome c oxidase, which exhibits only one EPR signal independent of temperature, suggests that the NO-oxygen may interact with the cuprous ion at the cytochrome a3-Cua3 site of the enzyme. These results have implications for studies in general on oxygen-carrying proteins.
\r\n\r\nIn addition to being a strong-field ligand, NO is also a reactive molecule which can be oxidized to NO-2 and NO-3, and reduced to N2O, N2 and NH3. Chapter III details investigations of the reactions of NO with the copper-containing oxidases tree and fungal laccase, as well as with tree laccase depleted in type 2 copper. The oxidation states of the enzymes were monitored by EPR and optical spectroscopy, and the reaction products of NO were determined by NMR and mass spectroscopy. These studies show that NO reduces all three copper sites of fungal laccase. In addition, NO forms a specific complex with the reduced type 2 copper. NO similarly reduces all of the copper sites in tree laccase, but it also oxidizes the reduced sites produced by ascorbate or NO reduction. A catalytic cycle is set up in which N2O, NO-2 and various forms of the enzyme are produced. On freezing of fully reduced tree laccase in the presence of NO, the type 1 copper becomes reoxidized. This reaction does not occur with the enzyme depleted in type 1 copper, suggesting that it involves intramolecular electron transfer from the type 1 copper to NO bound to the type 2 copper. When the half-oxidized tree laccase is formed in the presence of NO, a population of molecules exists which exhibits a type 3 EPR signal. A triplet EPR signal is also seen in the same preparation, and is attributed to a population of the enzyme molecules in which NO is bound to the reduced copper of a half-oxidized type 3 copper site. The implications of these results towards the structures of tree and fungal laccase are discussed.
\r\n\r\nNitric oxide has also been used to probe the structure of the metal centers of cytochrome c oxidase, resulting in the discovery of three stable conformations of the oxidized enzyme [G. W. Brudvig, T. H. Stevens, R. H. Morse and S. I. Chan (1981) Biochemistry 20, in press]. These conformat1onsdiffer in the structure of the cytochrome a3-Cua3 site, which is the site of oxygen reduction, and are distinguishable by EPR spectroscopy. Two of the diagnostic EPR signals are unusual in that they cannot be interpreted simply in terms of normal Cu(II) or Fe(III) EPR signals. The \"g5\" conformation identified as a transient species occurring upon reoxidation of the reduced enzyme by O2 [R. W. Shaw, R. E. Hansen and H. Beinert (1978) J. Biol. Chem. 253, 6637-6640] similarly exhibits an EPR signal not subject to simple interpretation. In view of the complexity of these three EPR signals, they are most likely due to the coupled cytochrome a3+3-Cua3+2 site of the oxidized enzyme. Chapter IV describes calculations of the energy levels of, and allowed EPR transitions from, the cytochrome a3-Cua3 site under various conditions of exchange coupling and dipolar coupling, as a function of other parameters such as the magnitude of the rhombic zero-field splitting of the heme iron and distance between the two metal ions. On the basis of these calculations, one of the three unusual EPR signals from oxidized cytochrome c oxidase is deduced to arise from a strongly exchange-coupled (|J| > 200 cm-1) cytochrome a3+3-Cua3+2 site, one from a weakly exchange-coupled (|J| > 0.25 cm-1) cytochrome a3+3-Cua3+2 site, and one from an admixture of S = 5/2 and S = 3/2 states of the cytochrome a3+3 site.
" }, { "name": "Nelson, John Victor", "degree": "PhD", "year": "1981", "title": "I. The Stereochemistry of the [3,3] Sigmatropic Rearrangement of 1,5-Diene-3-Alkoxides. II. Stereoselective Aldol Condensations via Dialkylboron Enolates", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09192025-213350260", "creators": [ { "name": { "family": "Nelson", "given": "John Victor" }, "id": "Nelson-John-Victor", "display_name": "Nelson, John Victor" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/93mv-cf69", "abstract": "A study was carried out on the [3,3] sigmatropic\r\nrearrangement of the potassium salts of the four diastereomers\r\n(both cis,trans and erythro,threo) of 1-(1-methoxy-\r\n2-butenyl)-2-cyclohexen-l-o1. It was found that these\r\nrearrangements proceed in a concerted fashion predominately\r\nvia chair-like transition states to give diastereomers of\r\n3-(3-methoxy-l-methyl-2-propenyl)-cyclohexanone. The\r\napplication of these modified oxy-Cope rearrangements to\r\nthe synthesis of (\u00b1)-erythro-juvabione is reported.
\r\n\r\nA detailed investigation of the enolization of a\r\nvariety of ketones and carboxylic acid derivatives with\r\ndialkylboryl triflates in the presence of a tertiary amine\r\nand the subsequent aldol condensations of these boron\r\nenolates was conducted. The stereochemistry of the\r\nenolates formed from acyclic ketones was found to be\r\ndependent on the structure of the ketone, the dialkyl-boryl\r\ntriflate, and the tertiary amine. A mechanism for\r\nthe enolization involving initial coordination of the\r\nboryl triflate to the ketone carbonyl with subsequent\r\ndeprotonation by the amine is proposed to explain the\r\nresults . The boron enolates derived from these acyclic\r\nketones undergo aldol condensation with a number of\r\naldehydes in good yield, Consistently good correlation\r\nwas observed between the enolate geometry and the product\r\naldol stereochemistry for these acyclic ketones regardless\r\nof the structure of the ketone or the boron ligands.\r\nHowever, for the boron enolate derived from cyclohexanone\r\nthe aldol stereoselectivity was dependent on the boron\r\nligands and the solvent. In this case, the use of a\r\ncyclopentylthexylboron enolate in tetrahydrofuran as\r\nsolvent resulted in complete stereocontrol in the condensation. \r\nAlthough simple esters and amides cannot be\r\nenolized with the triflate reagents, tert-butyl thio-propionate\r\nwas readily converted to the trans-enolate.\r\nThe stereoselectivity of the aldol condensations of this\r\nenolate are also dependent on the boron ligands and the\r\nsolvent; again, the proper choice of these parameters\r\nallowed total stereocontrol of the condensation, It\r\nwas found that carboxylic acids could be converted to\r\nthe dialkyl boron enediolates and the aldol condensations\r\nof these species were used to probe the relative reactivity\r\nof cis- and trans-enolates.
" }, { "name": "Olbricht, William Lee", "degree": "PhD", "year": "1981", "title": "The Motion of Macromolecules and Immiscible Drops in Creeping Flow", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052006-091257", "creators": [ { "name": { "family": "Olbricht", "given": "William Lee" }, "id": "Olbricht-William-Lee", "display_name": "Olbricht, William Lee" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jnx5-8786", "abstract": "Experimental studies were conducted on the creeping motion of immiscible drops of a Newtonian liquid through a circular tube. The mobility of the drop, the additional pressure gradient owing to the presence of the suspended drop, and the deformation and breakup of the drop were determined as a function of the drop size, flow rate and viscosity ratio, for both Newtonian and viscoelastic suspending fluids. Two tube geometries were employed to generate kinematically distinct flows. First, the effects of density differences between the fluids were studied in a tube of constant diameter for comparison with available results for neutrally buoyant drops. Surprisingly small density differences produced highly eccentric drop positions, and the data, including the steady shape of the drop, were correlated with the gap width between the drop and the tube wall using simple lubrication approximations. The results suggest the presence of both viscometric and time-dependent non-Newtonian effects for the viscoelastic suspending fluid. Experiments were then conducted for the case where the diameter of the tube varies periodically with axial position. The conformation of the drop depends strongly on the value of the inverse capillary number. For small values of this parameter, the shape of the drop, and hence, the measured quantities were periodic and in-phase with the drop's passage through the oscillatory tube. When the inverse capillary number was large, a drop suspended in a Newtonian fluid became highly elongated and eventually broke into several fragments. Under the same conditions, a drop suspended in a viscoelastic fluid did not elongate, but instead, developed tails which issued satellite drops. The effect of increasing the polymer concentration in the suspending fluid was to stabilize the tails. The different conformations of the drop produced qualitatively different behavior for the additional pressure gradient and drop mobility. The observed dispersion processes appeared as onset phenomena at critical values of the material parameters.\r\n\r\nThe dynamics of fluid systems which are comprised of a suspended material in a Newtonian continuous phase were investigated theoretically. Important dynamical phenomena for such fluids are often a consequence of significant flow-induced deformation and/or orientation of the suspended elements. Hence, conditions under which large-scale distortion of the microstructure occurs were predicted via criteria for the flow strength, which is a measure of the form and magnitude of the velocity gradient tensor. The form of the criteria depends on the model chosen to describe the microstructure, but the properties which describe the specific fluid system enter only as parameters. Thus, the theoretical framework encompasses a wide class of fluids including macromolecular solutions and particulate suspension. Two examples illustrate the approach: the macromolecular stretching induced by a turbulent flow and the breakup of immiscible liquid drops in a shear field." }, { "name": "Phichitkul, Charunya", "degree": "PhD", "year": "1981", "title": "Catalytic Activity and Deactivation Mechanisms of Supported NiO in CH\u2084 Oxidation", "advisor": "Bailey, James E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10042006-154422", "creators": [ { "name": { "family": "Phichitkul", "given": "Charunya" }, "id": "Phichitkul-Charunya", "display_name": "Phichitkul, Charunya" } ], "advisors": [ { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "advisor", "display_name": "Bailey, James E." } ], "committee": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "chair", "display_name": "Gavalas, George R." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Voecks", "given": "Gerald E." }, "id": "Voecks-Gerald-E", "role": "member", "display_name": "Voecks, Gerald E." }, { "name": { "family": "Bailey", "given": "James E." }, "id": "Bailey-J-E", "role": "member", "display_name": "Bailey, James E." } ], "option_major": [ "chemeng" ], "doi": "10.7907/kmv4-kb66", "abstract": "The partial oxidation of CH4 was studied using a commercial Ni/\u03b1-Al2O3 catalyst. The results show that two operating regimes can be maintained: a low-conversion regime where CO2 and H2O are formed and a high-conversion regime where CO, CO2, H2 and H2O are formed. The latter regime is established by \"catalytic light-off\" which among other conditions depends on temperature, feed composition and catalyst activity. Prior to light-off, the catalyst is in the NiO form. Following light-off, the catalyst is in NiO form near the inlet and metallic form further downstream. A series of NiO/\u03b1-Al2O3, and NiO/ZrO2 catalysts were prepared by impregnation and calcination in air between 750 and 1050\u00b0C. These catalysts were characterized by the BET method, O2 chemisorption, X-ray diffraction, electron microscopy and ESCA. Test analyses indicate that the supported NiO particles are made up of a large number of small crystallites which become more dispersed after reduction and reunite after oxidation. The activity of these catalysts for CH4 oxidation under pre-light-off conditions was found to decrease dramatically with increasing calcination temperature. However, the calcined catalysts can be reactivated by reduction in H2 prior to reaction. The change in activity is attributed mainly to the change in specific activity of NiO which is explained in terms of the change in excess oxygen content.
" }, { "name": "Rapp\u00e9, Anthony Kay", "degree": "PhD", "year": "1981", "title": "Theoretical Studies of Homogeneous Catalysis by Transition Metal Complexes", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02032005-112022", "creators": [ { "name": { "family": "Rapp\u00e9", "given": "Anthony Kay" }, "id": "Rapp\u00e9-Anthony-Kay", "display_name": "Rapp\u00e9, Anthony Kay" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "chair", "display_name": "Goddard, William A., III" }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "member", "display_name": "Bercaw, John E." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "member", "display_name": "Beauchamp, Jesse L." } ], "option_major": [ "chemistry" ], "doi": "10.7907/8kc4-gq42", "abstract": "CHAPTER 1: Extensive ab initio calculations (double zeta plus polarization function basis with correlated wavefunctions) on the oxidation of hydrocarbons by chromyl chloride are combined with standard thermochemical methods to predict the energetics for oxidation of alkanes, alcohols, and alkenes. Additional results are presented on the analogous oxidations by molybdyl chloride. A common feature of all these reactions is identified and explained.
\r\n\r\nCHAPTER 2: Extensive ab initio calculations (double zeta plus polarization function basis with correlated wavefunctions) on the olefin metathesis reaction with high valent Mo and W catalysts are combined with standard thermochemical methods to predict the energetics of potential intermediates. The active catalyst is identified and explained together with several subsidiary features of the reaction manifold.
\r\n\r\nCHAPTER 3: A unifying generalized valence bond view of transition metal ligand bonding is presented as well as the energetics and structural characteristics of several ligand types. Additionally, the energetics for several ligand exchange reactions of potential synthetic utility are presented.
" }, { "name": "Reimer, Jeffrey Allen", "degree": "PhD", "year": "1981", "title": "The Development of Novel Nuclear Magnetic Resonance Techniques for the Study of Solids, Thin Films and Surfaces with Particular Application to Amorphous Semiconducting Silicon-Hydrogen Films", "advisor": "Baldeschwieler, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062018-123026017", "creators": [ { "name": { "family": "Reimer", "given": "Jeffrey Allen" }, "id": "Reimer-Jeffrey-Allen", "display_name": "Reimer, Jeffrey Allen" } ], "advisors": [ { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "advisor", "display_name": "Baldeschwieler, John D." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "member", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Cole", "given": "Terry" }, "id": "Cole-Terry", "role": "member", "display_name": "Cole, Terry" }, { "name": { "family": "McGill", "given": "Thomas C." }, "id": "McGill-T-C", "role": "member", "display_name": "McGill, Thomas C." }, { "name": { "family": "Baldeschwieler", "given": "John D." }, "id": "Baldeschwieler-J-D", "role": "member", "display_name": "Baldeschwieler, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/c2h9-0m19", "abstract": "Part 1
\r\n\r\nProton magnetic resonance data are presented for twenty different plasma-deposited amorphous silicon-hydrogen films. The two phase compositional inhomogeneity observed in these films is found to be independent of film thickness down to less than 1\u03bc. Models for various structural configurations show that these films contain heavily monohydride clustered regions such as divacancies and voids, as well as (SiH2)n and SiH3 local bonding configurations. The presence of the divacancies in films showing predominantly monohydride vibrational modes provides some insight into the controversy over the assignment of the 2090 cm-1 vibrational mode. The films also contain regions in which monohydride groups are distributed at random. Based on changes in a film whose proton NMR lineshapes are metastable as deposited, a model based on strain relief is proposed for film development which explains the ubiquitous presence of the two phase inhomogeneity. Examination of the changes in proton NMR data as a function of deposition conditions furnishes new insight on the role SiH2 and SiH+x groups have in models for the gas phase reactions involved in the developing films. Finally, p- or n-type doping is found to increase the the hydrogen content of the films, and, under heavy p-type doping with diborane, boron clustering may occur within the films. Proton NMR lineshapes are also presented as a function of annealing temperature up to 650\u00b0C. The data indicate that hydrogen diffuses internally before major evolution occurs, that transfer of hydrogen occurs from a heavily clustered phase to a dilute phase coincident with evolution and that evolution occurs initially from the heavily clustered phase. Internal hydrogen diffusion is found to be concomitant with the reduction in paramagnetic center density.
\r\n\r\nSilicon-29 and hydrogen magic angle sample spinning experiments on amorphous silicon-hydrogen films (involving cross-polarization and homonuclear multiple pulse techniques respectively) fail to yield quantitative determinations of local silicon-hydrogen bonding environments. However, the 29Si data are qualitatively consistent with infra-red assignments of (SiH2)n groups. Furthermore, the lack of significant line narrowing for the 29Si spectra upon magic angle sample spinning shows that there are large chemical shift dispersions, indicative of the disorder in the amorphous lattice.
\r\n\r\nProton spin-lattice relaxation data are presented for several plasma deposited amorphous silicon-hydrogen films when (i), homonuclear dipolar interactions are suppressed, (ii), deuterium is isotopically substituted for hydrogen, and (iii), films are annealed. These data are consistent with a model in which proton nuclei are relaxed by hydrogen-containing disorder modes. Analysis of these data shows that the density of disorder modes is ~30% higher in the low hydrogen density domain and that more than one hydrogen nucleus is associated with each disorder mode. The behavior of T1 upon annealing indicates that a small fraction of unpaired spins or \"dangling bonds\" may be associated with the disorder modes. These results suggest that the role of hydrogen in amorphous silicon is more complex than passivation of \"dangling bond\" intrinsic defects.
\r\n\r\nFinally, proton magnetic resonance data are presented for the hydrogen alloys of plasma-deposited amorphous boron, carbon, silicon carbide and silicon nitride. Linewidth and lineshape analysis leads to the conclusion that hydrogen nuclei are clustered in a-Si/C:H, a-C:H, and a-Si/N:H. Both a-Si/C:H and a-C:H data show hydrogen exists in two phases. Modeling of linewidths in a-Si/C:H indicates that the two phases are heavily hydrogenated carbon clusters imbedded in a weakly hydrogenated a-Si lattice. In addition, evidence is presented for the presence of motionally narrowed hydrogen spectra in a-Si/N:H, a-B:H, and a-C:H. It is suggested that the hydrogen nuclei giving rise to these spectra are associated with disorder modes.
\r\n\r\nPart 2
\r\n\r\nThe production of heteronuclear dipolar modulated chemical shift spectra of specific protons within polycrystalline solids is described by consideration of explicit double resonance pulse schemes which remove both heteronuclear and homonuclear dipolar interactions. These spectra furnish an accurate method of determining bond distances in local environments of complicated chemical systems. When used in conjunction with selectively observed chemical shift spectra, these schemes present a means for characterization of both geometrical and electronic properties in the solid state. To demonstrate the utility of these experiments, selective proton observed NMR results are presented for the carbonyl protons of adsorbed formic acid on ammonium-Y zeolite and the hydrogen bonded proton in polycrystalline acetanilide. Chemical shift information for the adsorbed formic acid shows a chemisorbed species consistent with formate ions. The data for the amide bond in polycrystalline acetanilide show a hydrogen bond with a chemical shift anisotropy of 17.7 ppm and a N-H distance of 1.05 \u00b1 0.01 \u00c5.
" }, { "name": "Robinson, Randy Richard", "degree": "PhD", "year": "1981", "title": "Sequence Analysis of a tRNA Gene Cluster: Drosophila Leucine-tRNA Genes contain Intervening Sequences", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09152025-181743359", "creators": [ { "name": { "family": "Robinson", "given": "Randy Richard" }, "id": "Robinson-Randy-Richard", "display_name": "Robinson, Randy Richard" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p9cn-c915", "abstract": "A recombinant DNA phage containing a cluster of Drosophila\r\nmelanogaster tRNA genes has been isolated and analyzed. In situ\r\nhybridization localizes this phage to chromosomal region 50AB, a known\r\ntRNA site. Nucleotide sequencing of the entire Drosophila tRNA coding\r\nregion reveals seven tRNA genes spanning 2.5 kb of chromosomal DNA.\r\nThis cluster is separated from other tRNA regions on the chromosome\r\nby at least 2.7 kb on one side, and 9.6 kb on the other. Two tRNA genes\r\nare nearly identical and contain intervening sequences in the anticodon\r\nloop. These two genes are assigned to be tRNALeu genes because of\r\nsignificant sequence homology with yeast tRNA3Leu, and secondary structure\r\nhomology with yeast tRNA3Leu intervening sequences. In addition, an 8\r\nbase sequence (AAAAUCUU) is conserved in the same location in the inter-\r\nvening sequences of Drosophi1a tRNALeu genes and a yeast tRNA3Leu gene.\r\nSimilar sequences occur in all other tRNAs containing intervening\r\nsequences. The remaining five genes are identica1 tRNAIle genes, which\r\nare identical to a tRNAIle gene from chromosomal region 42A. The 5'\r\nflanking regions are only weakly homologous, but each set of isoacceptors\r\ncontains short regions of strong homology approximately 20 nucleotides\r\npreceding the tRNA coding sequences: GCNTTTTG preceding tRNAIles; and\r\nGANTTTGG preceding tRNALeus. The genes are irregularly organized on both\r\nDNA strands; spacing regions are divergent in sequence and length.\r\nPreliminary in vitro transcription experiments with isolated restriction\r\nfragments demonstrate that both tRNALeu genes and at least two of the\r\nfive tRNAIle genes are selectively transcribed in vitro by cytoplasmic\r\nextracts from HeLa cells." }, { "name": "Schlup, John Robert", "degree": "PhD", "year": "1981", "title": "The Nature of Fluorinated Oxide Catalysts: A Nuclear Magnetic Resonance Investigation", "advisor": "Chan, Sunney I.; Vaughan, Robert W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09282006-095624", "creators": [ { "name": { "family": "Schlup", "given": "John Robert" }, "id": "Schlup-John-Robert", "display_name": "Schlup, John Robert" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." }, { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." } ], "committee": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "chair", "display_name": "Chan, Sunney I." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "member", "display_name": "Grubbs, Robert H." } ], "option_major": [ "chemeng" ], "doi": "10.7907/b77t-rz15", "abstract": "Fluorination of oxide catalysts has been shown to drastically change the catalytic properties of these materials. The catalytic activity of these materials has been studied using a wide variety of reactions. Research on fluorinated oxides has focused upon improving product yields and product selectivity and upon obtaining a better understanding of the unmodified oxide catalyst as changes due to fluorination are observed. The purpose of this investigation has been to demonstarate the utility of pulsed nuclear magnetic resonance (NMR) spectroscopy as a direct spectroscopic probe of the local chemical environment of the hydroxyl groups and the fluorine atoms of these materials.
\r\n\r\nQuantitative analysis of the hydroxyl group and fluorine atom concentrations of these materials is difficult. Most techniques used previously require temperatures in excess of 1200 K and result in destruction of the sample. NMR has been shown to be an effective non-destructive quantitative tool. Precision of 5% has been demonstrated with samples containing as few as 5 x 1018 hydrogen or fluorine atoms.
\r\n\r\nThe chemical shift interaction has shown that the fluorine forms covalent bonds to the silicon and aluminum atoms of silica, alumina, and various aluminosilicates. If an aluminosilicate contains 11 wt% alumina, only SiF and SiOH species are observed. SiF, SiOH, AlF, and Al0H species are observed for aluminosilicates containing 48 wt% alumina. The SiF bond is identical for all fluorinated silicas and aluminosilicates calcined at 873 K. The Carr-Purcell-Meiboom-Gill data show that the hydroxyl groups are well isolated from one another for all samples. The same is true for the fluorine atoms.
\r\n\r\nThe decay constants of the hydrogen and fluorine 90\u00b0-\u03c4-180\u00b0and Carr-Purcell-Meiboom-Gill experiments differ by at least a factor of ten. Therefore, the nuclei are experiencing fluctuations in their local magnetic fields, probably as a result of anisotropic motion or diffusion. The behavior of the spectra observed at temperatures between 110 K and 290 K is very dependent upon the type of oxide, the degree of fluorination, and the calcining temperature.
" }, { "name": "Smith, Duane Donald", "degree": "PhD", "year": "1981", "title": "Optical Dephasing and Energy Transfer in Ordered and Disordered Solids: Studies by Laser Spectroscopy and Optical-Microwave Double Resonance", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072008-141328", "creators": [ { "name": { "family": "Smith", "given": "Duane Donald" }, "id": "Smith-Duane-Donald", "display_name": "Smith, Duane Donald" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1gza-t381", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nElectronic energy transfer and optical dephasing of ordered and disordered molecular crystals is studied theoretically and experimentally. Data on impurity band transport are presented which are consistent with the Anderson transition. The effect of dimensionality on trap-trap energy transfer thresholds is experimentally measured and modeled.\r\n\r\nExperiments focus on 1,4-dibromonaphthalene whose lowest triplet exciton is quasi-one-dimensional. Steady state and transient line narrowing laser spectroscopy provide the first unequivocal measurement of the inelastic scattering rate amongst the band states. The inelastic scattering rate (intraband exchange rate) is slow and of the order of 10 [...]sec at 20 K. Further, the elastic scattering rate is ~10 psec at 20 K and is describable as Raman scattering by ~ a 42 cm[...] phonon. It is significant that there is a six order of magnitude separation of time scales for the elastic and inelastic scattering, demonstrating that pure dephasing dominates the intraband exchange. From the broadening and the lack of a relative shift of the two sublattice [...] absorptions, it is concluded that the interband exchange rate is negligible compared to the pure dephasing. It is found that disordering [...] DBN with up to 16% [...] DBN, the inelastic scattering rate is unaltered, being 10 gsec at 20 K! Pumping the [...] state of the upper sublattice, relaxation is exclusively to the [...] state of the lower sublattice, implicating single phonon resonant relaxation.\r\n\r\nFor heavily trap-disordered DBN (up to 24% [...]/[...]) it is found that (1) excitation migration is step-wise incoherent, (2) energy transfer to deep traps is best fit with a [...] energy transfer rate, (3) there are no mobility edges in the trap inhomogeneous profile and (4) an upper limit for the trap homogeneous linewidth at 1.3 K is 9 Ghz.\r\n\r\nUsing lifetimes and temperature-dependent lineshapes, optical dephasing of F and [...] center triplet states in CaO is is consistent with Raman scattering by effective oscillators of 89 and 151 cm[...], respectively.\r\n\r\nVibrational dephasing of the CO stretch for benzophenone matrix-isolated in 4,4'-dibromodiphenyl ether at 2.1 K was investigated with a novel application of emission spectroscopy. It was found that the total dephasing rate of the CO stretch was linear in the CO quantum number, consistent with recent theoretical predictions for carbonyl moieties.\r\n" }, { "name": "Stevens, Amy Elizabeth", "degree": "PhD", "year": "1981", "title": "Fundamental Studies of Reactive Intermediates in Organometallic Chemistry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262018-131940882", "creators": [ { "name": { "family": "Stevens", "given": "Amy Elizabeth" }, "id": "Stevens-Amy-Elizabeth", "display_name": "Stevens, Amy Elizabeth" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XKHS-2M38", "abstract": "The techniques of ion cyclotron resonance spectroscopy and \r\nphotoionization-mass spectrometry are used to characterize the \r\nthermochemistry and reactivity of transition metal and organometallic \r\nspecies in the gas-phase. Chapter I gives an introduction emphasizing \r\nthe need for physical studies of these compounds. An assessment of\r\nthe differences in chemical properties and reactivity between the gas \r\nphase and solution is also made.
\r\n\r\nChapter II details the properties and reactions of (CO)5MnR\r\n(R = H, CH3) determined using the techniques of ion cyclotron \r\nreso\u00adnance spectroscopy. An examination of the products (CO)5Mn(R)H+, \r\n(CO)4Mn(R)H+, and (CO)5Mn+ which result from proton transfer with \r\nvarying exothermicity to (CO)5MnR permits several thermochemical \r\nand mechanistic inferences. In particular the prcton affinities of\r\nthese species are derived and the mechanism of reductive elimination \r\nof RH from the conjugate acids is detailed.
\r\n\r\nAn examination of processes involving negative ions yields the\r\nheterolytic bond energies D[(CO)5Mn--R+]. The hydride is found to be an exceptionally strong acid in the gas phase.
\r\n\r\nPositive and negative ion mass spectra and ion-molecule\r\nreactions are reported briefly.
\r\n\r\nChapter III presents the results of an ion cyclotron-resonance \r\ntrapped ion study of the kinetics of proton transfer from MnH+ (formed\r\nas a fragment ion from HMn(CO)5 by electron impact) to bases of \r\nvarying strength. Deprotonation is rapid with bases whose proton\r\naffinity exceeds 196 \u00b1 3 kcal mol-1. Using this value for PA[Mn]\r\nyields the homolytic bond dissociation energy D[Mn+-H] =\r\n53 \u00b1 3 kcal mol-1.
\r\n\r\nIn Chapter IV the results of a photoionization mass\u00ad\r\nspectrometric determination of the ionization potentials and selected \r\nfragment ion appearance potentials of (CO)5MnR where R = H , CH3,\r\nCH2F, CHF2 and CF3 are presented. A comparison of the appearance\r\npotential of (CO)5Mn+ from all five species yields the metal-carbon \r\nbond dissociation energies relative to the metal-hydrogen bond\r\ndissociation energy with no additional thermochemical data. Using \r\nthe literature value D0[(CO)5Mn-H ] = 57 kcal/mol gives \r\nD0[(CO)5Mn-R] = 44, 32, 33, and 42 kcal/mol, respectively.\r\nFragmentation thresholds for the metal carbene fragment ions\r\n(Co)5MnCXY+ where X, Y = H or F are analyzed to yield the fluoride \r\nand hydride affinities of these species. Ion cyclotron resonance\r\nspectroscopy is used to examine hydride and fluoride transfer\r\nreact ions involving these carbenes to corroborate the photoionization \r\ndata. The carbene bond dissociation energies D0[(CO)5Mn+-CXY] \r\ndecrease from 104 to 98 to 82 kcal/moL with successive substitution \r\nof F for H .
\r\n\r\nIn Chapter V the proton affinities of twenty organotransition \r\nmetal complexes in the gas phase are reported. Combined with \r\nadiabatic ionization potentials, these data yield metal-hydrogen \r\nhemolytic bond energies for the sixteen species for which protonation \r\noccurs on the metal center. These bond energies range from 53 to\r\n87 kcal/mol. Bond energies increase on going from a first-row\r\ncomplex to its second-row homologue, but no increase is seen on \r\ngoing to the third-row metal. The metal-hydrogen bond energy\r\ndecreases markedly with increasing oxidation state of the same metal. \r\nComparison to isoelectronic neutral complexes is made.
\r\n\r\n\r\n\r\n\r\n\r\n" }, { "name": "Stevens, Tom Hall", "degree": "PhD", "year": "1981", "title": "The Structure of the Metal Centers in Cytochrome c Oxidase", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132018-142618023", "creators": [ { "name": { "family": "Stevens", "given": "Tom Hall" }, "id": "Stevens-Tom-Hall", "display_name": "Stevens, Tom Hall" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "chair", "display_name": "Gray, Harry B." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Attardi", "given": "Giuseppe" }, "id": "Attardi-G", "role": "member", "display_name": "Attardi, Giuseppe" } ], "option_major": [ "chemistry" ], "doi": "10.7907/g9ms-c954", "abstract": "Mitochondrial cytochrome c oxidase catalyzes the four-electron reduction of oxygen to water. The functional form of the protein contains two copper ions and two heme irons. Two of these metal centers, cytochrome a3 and Cua3, constitute the oxygen reduction site. The other two metal centers, cytochrome a and Cua, are involved in electron transfer from cytochrome c to the oxygen reduction site. It is the structure and function of these four metal centers in cytochrome c oxidase which is the subject of this thesis.
\r\n\r\nThe metal centers constituting the oxygen reduction site of cytochrome c oxidase have traditionally been difficult to study because their coupled nature renders them EPR silent. It is shown that nitric oxide can uncouple these metal centers, and under appropriate conditions renders both metal centers observable by EPR. One of the nitric oxide complexes is an NO-bridge complex, demonstrating that the oxygen reduction site is between the two metal centers. Furthermore, this NO-bound complex allows us to calculate a distance between the metal centers of about 5 \u00c5. Finally, with 15N-his isotopically labeled yeast oxidase it is shown that the fifth endogenous ligand to cytochrome a3 is a histidine.
\r\n\r\nThe copper metal center involved in electron transfer, Cua, is shown to have a cysteine and a histidine as ligands. The substitution of 12CD2-cysteine into yeast oxidase does not perturb the eight line hyperfine pattern first seen on the Cua EPR signal at 3 GHz. This demonstrates that the S = 1/2 center interacting with Cua is probably cytochrome a at a distance of 10-13 \u00c5. These studies represent the first time that ligands to any of the metal centers in cytochrome c oxidase have been unequivocally elucidated.
" }, { "name": "Taber, Terry Ray", "degree": "PhD", "year": "1981", "title": "The Total Synthesis of A-23187 and Related Enantioselective Aldol Condensations", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072018-142839331", "creators": [ { "name": { "family": "Taber", "given": "Terry Ray" }, "id": "Taber-Terry-Ray", "display_name": "Taber, Terry Ray" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dougherty", "given": "Dennis A." }, "id": "Dougherty-D-A", "orcid": "0000-0003-1464-2461", "role": "member", "display_name": "Dougherty, Dennis A." } ], "option_major": [ "chemistry" ], "doi": "10.7907/xcz4-1016", "abstract": "A-23187 is a calcium specific ionophore which was isolated from Streptomyces chartreusis. The total synthesis of A-23187 and synthesis of related diacid ionophores are discussed.
\r\n\r\n[Chemical structure included in scanned thesis' Abstract, p. v.]
\r\n\r\nThe synthetic approach used for A-23187 required stereoselective aldol condensations. In this regard, the development of enantioselective aldol condensations with boron enolates is detailed. The general applications of such condensations are also discussed.
" }, { "name": "Takacs, James Michael", "degree": "PhD", "year": "1981", "title": "Approaches to Asymmetric Synthesis. The Diastereoselective Alkylations of Chiral Propionamide Enolates", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05092018-115015856", "creators": [ { "name": { "family": "Takacs", "given": "James Michael" }, "id": "Takacs-James-Michael", "display_name": "Takacs, James Michael" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-David-A", "role": "member", "display_name": "Evans, David A." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "member", "display_name": "Ireland, Robert E." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." } ], "option_major": [ "chemistry" ], "doi": "10.7907/f2kf-9406", "abstract": "Enantioselective propionate alkylation, as a method to control acyclic methyl~bearing stereocenters, is achieved via the diastereoselective alkylation of chiral propionamide enolates. The factors which control stereoselective enolization, diastereotopic differentiation of the enolate system, and selective cleavage of the chiral auxiliary are discussed. The application to the preparation of simple chiral carboxylic acids proceeds with the highest optical yields yet reported.
\r\n\r\n" }, { "name": "Thiel, Patricia Ann", "degree": "PhD", "year": "1981", "title": "Adsorption, Co-Adsorption and Catalytic Reactions on Rh(111) and Ru(001) Surfaces", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03222018-134525550", "creators": [ { "name": { "family": "Thiel", "given": "Patricia Ann" }, "id": "Thiel-Patricia-Ann", "display_name": "Thiel, Patricia Ann" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "chair", "display_name": "Bercaw, John E." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "member", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" }, { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "member", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8m9w-p414", "abstract": "The adsorption of oxygen, hydrogen, carbon monoxide , nitric oxide and water on Rh(111) and Ru(001) surfaces has been studied using the techniques of high-resolution electron energy loss spectroscopy, low-energy electron diffraction, Auger electron spectroscopy, ultraviolet photoelectron spectroscopy and thermal desorption mass spectrometry. In many cases co-adsorption experiments have provided insight into the nature of interaction between different adsorbates, with potential implications for heteroqeneous catalytic reaction mechanisms.
\r\n\r\nThe interaction of oxygen with Rh(111) consists of adsorption, irreversible thermally induced ordering and disordering phenomena, dissolution into the subsurface region and desorption. The thermodynamic parameters which describe these phenomena have been investigated. The forms of the kinetic rate expressions for the catalytic reaction of adsorbed oxygen with hydrogen are different for ordered and disordered arrays of oxygen adatoms. In agreement with co-adsorption studies of hydrogen and oxygen, and supported by studies of hydrogen chemisorption on clean Rh(111), this implies that the rate of adsorption of hydrogen is sensitive to the structure of the adsorbed oxygen lattice.
\r\n\r\nTwo forms of molecularly adsorbed NO are readily distinguished on a Ru(001) surface by the frequencies of the nitrogen-oxygen stretching vibrations, which can then be used to observe the influence of co-adsorbates. Oxygen, nitrogen and hydrogen adatoms compete selectively for the adsites which are occupied by multiply-coordinated NO, whereas CO competes for adsites occupied by the singly-coordinated molecular NO. Carbon monoxide can even induce conversion of adsorbed molecular NO from sites of single coordination to sites of multiple coordination with the metal substrate.
\r\n\r\nWater interacts with the Ru(001) surface to form chemisorption bonds, but it also forms intermolecular hydrogen bonds which are of comparable strength. This leads to formation of layered, hydrogen bonded aggregates at all coverages. The properties of the first two layers are distinct from those of the subsequent ice multilayers, and a specific structural model for the hydrogen bonded lattices is proposed. A thermally induced ordering effect is observed which is analogous to the vitreous-to-cubic phase transformation of bulk ice.
" }, { "name": "Trentacosti Presti, Florence L.", "degree": "PhD", "year": "1981", "title": "Cholesterol's Important Influence on Structure and Function of Membrane Lipids", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112026-182051620", "creators": [ { "name": { "family": "Trentacosti Presti", "given": "Florence L." }, "id": "Trentacosti-Presti-Florence-L", "display_name": "Trentacosti Presti, Florence L." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8taz-wp08", "abstract": "Cholesterol is an important component of all animal membranes,\r\nboth cellular and intracellular. This ubiquitous amphiphilic sterol may\r\nconstitute up to 50% of the total lipid in some biological membranes.\r\nHowever, its exact role in the structure and function of membranes is unknown,\r\nin spite of intensive study of cholesterol's effects on model and\r\nnatural membrane systems in the last decade. Previous investigations have\r\nexamined the often rather indirect effects of cholesterol on overall\r\nmembrane properties, such as permeability. This work attempts to determine\r\nthe local influence of cholesterol molecules on the dynamical properties of\r\nthose lipids in their immediate environment.
\r\n\r\nElectron spin resonance (ESR) spectroscopy was employed to monitor\r\nthe behavior of 3-nitroxide cholestane (CSL), a cholesterol-like spin label\r\nmolecule, incorporated into various phospholipid-cholesterol multi-bilayer\r\nmembranes. Being more cholesterol-like than lipid-like, the cholestane spin\r\nlabel may provide information about the cholesterol-rich regions of the\r\nbilayer, which phospholipid spin probes may not even enter. This is the\r\nfirst thorough, systematic study of the effects of cholesterol concentration\r\non the thermal behavior of phospholipid multilayers dispersed in excess\r\nwater (the state most closely simulating the natural membrane environment)\r\nby ESR spectroscopy. Differential scanning calorimetry (DSC) was also used\r\nto examine phospholipid multilayers with incorporated CSL.
\r\n\r\nPlots of 2A\u22a5 versus temperature yielded S-shaped transition curves\r\ncentered around 20\u00b0c for all the lipids studied. The lipid gel-liquid\r\ncrystal transition was also present at the appropriate temperature.\r\nAddition of cholesterol results in gradual increase of temperature of the\r\nCSL-induced transition, but addition of 25 mole% cholesterol or more resulted\r\nin disappearance of the main gel-liquid crystal transition. The spin\r\nlabel-induced 20-degree transition was also observed by DSC, corroborating\r\nthe ESR results. Peaks were broad, with a small enthalpy change.
\r\n\r\nIt is suggested, from evidence accumulated in this work and\r\nreported in the literature, that cholesterol-lipid domains with a 1:2\r\nstoichiometry begin coalescing with addition of even small amounts of sterol.\r\nThese regions are composed of cholesterol molecules, each complexed to a\r\nsingle lipid molecule and loosely associated with a second lipid. Lipid\r\nwhich is complexed to cholesterol does not melt, whereas lipid associated\r\n0 with CSL does melt - around 20\u00b0 C. Boundary lipid around the complex domains\r\nand the lipid loosely associated with 1:1 complex undergo a broad, uncooperative\r\ntransition slightly above the free lipid melting temperature. At\r\nabout 20 mole% cholesterol content, there is no more free bulk lipid in the\r\nsystem; only complexed lipid and boundary lipid remain and the main gel-liquid\r\ncrystal transition disappears. When 33 1/3 mole% cholesterol is\r\npresent, boundary lipid around the complex domains also disappears. As more\r\ncholesterol is added, the loosely associated lipid molecules still left\r\naround the complex pairs decrease in number as more 1:1 complex units are\r\nformed. At 50 mole% cholesterol, the last uncomplexed lipid molecules are\r\ngone, and further addition of the sterol results in separation of cholesterol\r\ncrystals from the bilayer.
" }, { "name": "Vasilakos, Nikolaos Petrou", "degree": "PhD", "year": "1981", "title": "Coal Desulfurization by Selective Chlorinolysis", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-09192006-130811", "creators": [ { "name": { "family": "Vasilakos", "given": "Nikolaos Petrou" }, "id": "Vasilakos-Nikolaos-Petrou", "display_name": "Vasilakos, Nikolaos Petrou" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "chair", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "member", "display_name": "Gavalas, George R." }, { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "member", "display_name": "Shair, Fredrick H." }, { "name": { "family": "Kalvinskas", "given": "John J." }, "id": "Kalvinskas-John-J", "role": "member", "display_name": "Kalvinskas, John J." } ], "option_major": [ "chemeng" ], "doi": "10.7907/05PE-T991", "abstract": "The desulfurization of coal by selective oxidation under slurry-phase chlorination conditions was investigated. Chemical reaction was found to be the rate-controlling step in carbon-tetrachloride chorination at 25\u00b0C for coal particles less than 150 \u00b5 in diameter. For larger particle sizes, a transition from chemical to intraparticlemass-transfer control was observed. The nitrogen-surface area of the coal decreased significantly as a result of the chlorination reaction.
\r\n\r\nThe reaction mechanism and the desulfurization patterns of chlorinolysis were studied under model-reaction and coal-chlorination conditions. Possible complete desulfurization schemes were considered.
\r\n\r\nThe role of solvents both in increasing the efficiency of the coal treatment and in providing alternative paths for coal beneficiation processes was also examined. The results of this study were interpreted within the frame of the solubility-parameter theory, utilizing the new experimental technique of solubility-parameter spectroscopy.
" }, { "name": "Adler, George", "degree": "PhD", "year": "1980", "title": "NMR Studies of Cooperativity in Hemoglobin", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112020-012735380", "creators": [ { "name": { "family": "Adler", "given": "George" }, "id": "Adler-George", "display_name": "Adler, George" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "chair", "display_name": "Dervan, Peter B." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "member", "display_name": "Raftery, Michael A." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/089e-bj69", "abstract": "PART I
\r\n\r\nIn this part the binding of ligands, like oxygen and carbonmonoxide to hemoglobin and myoglobin, and the connection between the physiological functions and the structure of these proteins are discussed. The allosteric models, which have been proposed to explain the cooperative binding of oxygen, and the effect of single residue mutations on the structure of hemoglobin are reviewed. Finally, questions which have not yet been satisfactorily answered are raised about the structure and function of hemoglobin.
\r\n\r\nPART II
\r\n\r\nThe binding of carbon monoxide to rabbit hemoglobin and to trifluoroacetonylated rabbit hemoglobin has been studied by \u00b9\u00b3C NMR and by \u00b9\u2079F NMR. The \u00b9\u00b3C NMR studies show that CO binds preferentially to the \u03b2 chains of rabbit hemoglobin in the absence of effectors such as 2,3-diphosphoglycerate (DPG) and inositol hexaphosphate.
\r\n\r\nThe \u00b9\u2079F spectrum of trifluoroacetonylated human adult hemoglobin, at low CO or O\u2082 ligation, indicated preferential a chain ligation (Huestis and Raftery, 1973, Biochemistry 12, 2531). There is a linear relationship between the fraction of the ligated signal of trifluoroacetonylated rabbit hemoglobin as monitored by \u00b9\u2079F NMR and the overall ligation detected by optical density measurements at 650 nm. Therefore, the trifluoroacetonyl label does not, in the case of rabbit hemoglobin, distinguish initial \u03b2 ligation from random ligation.
\r\n\r\nBoth in the absence of and in the presence of DPG, the \u00b9\u2079F spectra of partially ligated trifluoroacetonylated rabbit hemoglobin reveal only two significant resonances. These two resonances, which correspond to the deoxy (tense) and ligated (relaxed) structures of hemoglobin, are joined by two additional resonances when inositol hexaphosphate is added to the solution. The new resonances are presumably due to hemoglobin in intermediate structures between the relaxed and tense states.
\r\n\r\nThe \u00b9\u2079F chemical shifts of the deoxy and ligated TF labelled hemoglobin change due to the addition of organic phosphates. This observation implies that the organic phosphates bind to hemoglobin in both the deoxy and the ligated states.
\r\n\r\nPART III
\r\n\r\nTitrations of trifluoroacetonyl labelled human deoxy-, oxy-, carbonmonoxy-, nitrosylhemoglobin, aquamethemoglobin and cyanomethemoglobin have been followed by \u00b9\u2079F NMR. The titration curve of trifluoroacetonyl human deoxyhemoglobin (HbTF) in the presence or absence of 2,3-diphosphoglycerate (DPG) is similar to that found by Huestis and Raftery (Proc. Natl. Acad. Sci. USA (1972) 69, 1887). Nitrosyl-, oxy-, and carbonmonoxy-HbTF in the absence of effectors exhibit pH dependence only below pH 5.5. The addition of inositol hexaphosphate (IHP) resulted in large upfield shifts of the fluorine resonance of HbTF(NO)\u2084, HbTF(O\u2082)\u2084. In addition, the fluorine signal of HbTF(CO)\u2084 and HbTF(O\u2082) exhibited large linewidths which is evidence for the exchange between two structures. The addition of DPG to HbTF(NO)\u2084 below pH 7.4 results in the appearance of a second resonance which indicates the presence of two different protein structures.
\r\n\r\nThe titration of the labelled aquarnethemoglobin in the presence or in the absence of DPG supports the results of Huestis and Raftery (1972). In the presence of IHP trifluoroacetonyl Hb\u207a(CN\u207b)\u2084 shows a complicated \u00b9\u2079F spectra which suggests that cyanornethernoglobin can have three different structures. The implication of these results on the mechanism of cooperativity and on the two state model is discussed.
\r\n\r\nPART IV
\r\n\r\nThe intracellular pH, and the binding of intracellular 2,3-diphosphoglycerate (2,3-DPG) to hemoglobin are studied in AA and SS blood. There is no significant difference in the intracellular pH of AA and SS erythrocytes in the fully oxygenated state. However, in the \u00b3\u00b9P spectrum of deoxygenated AA blood the resonance due to 2-P of 2,3-DPG is downfield, while in the \u00b3\u00b9P spectrum of deoxygenated SS blood this resonance is upfield, from the chemical shift of the same phosphorous signal in oxygenated blood. This difference in \u00b3\u00b9P chemical shifts is likely due to a lower intracellular pH of the SS erythrocytes relative to the AA erythrocytes.
" }, { "name": "Armentrout, Peter Bruce", "degree": "PhD", "year": "1980", "title": "Mechanistic and Thermochemical Studies of the Reactions of Transition Metal Ions and Uranium Ions with Small Molecules in the Gas Phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192024-230500054", "creators": [ { "name": { "family": "Armentrout", "given": "Peter Bruce" }, "id": "Armentrout-Peter-Bruce", "display_name": "Armentrout, Peter Bruce" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bcv3-5t71", "abstract": "An ion beam apparatus is employed to study the reactions of\r\nmetal ions with small molecules. The experiments yield reaction\r\ncross sections as a function of ion kinetic energy. Simple models\r\nare developed in Chapters IV and VI to interpret the energy dependent\r\ncross sections for endothermic reactions. Analysis of reaction\r\nthresholds using these models yields thermochemical data of interest.\r\nChapter I is a brief introduction to these topics.
\r\n\r\nChapter II describes the reactions of U+ and UO+ with O2, CO,\r\nCO2, COS, CS2 and D2O. Results are in good accord with literature\r\nthermochemistry except for the exothermic reactions of UO+ with\r\nCO2 and COS to yield UO+2 where an energy barrier is observed. In\r\nChapter III, the collision induced dissociation of UO+ and UO+2\r\nimpacting on Ar is studied.
\r\n\r\nChapters IV, V and VIII report experiments of metal ions, Ba+\r\nNi+ and Co+, respectively, reacting with hydrogen. Interpretation of\r\nreaction thresholds for production of the metal hydride yields metal\r\nhydrogen bond energies. A large energy dependent isotope effect is\r\nobserved in the reaction of Ni+ with HD (Chapter V).
\r\n\r\nIn Chapters VI-VIII, results for reactions of Co+ with organic\r\nmolecules are presented. Chapter VI concerns the formation of CoCH+2\r\nby reaction of Co+ with ethene, cyclopropane and ethylene oxide. The\r\nbond energy of the cobalt carbene ion is derived. Chapters VII and\r\nVIII discuss the reactions of Co+ with alkanes. The emphasis in\r\nChapter VII is the ion beam instrument as a probe of the potential\r\nenergy surface of complex organometallic reactions. Chapter VIII is\r\na comprehensive thermochemical and mechanistic study of the interactions\r\nof Co+ with saturated hydrocarbons. Several bond energies\r\nbetween Co+ and hydrocarbons are derived and a general mechanism\r\nfor the reactions proposed.
" }, { "name": "Auburn, Pamela Rae", "degree": "Masters", "year": "1980", "title": "Synthesis, Characterization, and Reactivity of Permethyltitanocene Monoethylene Complex", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-140317486", "creators": [ { "name": { "family": "Auburn", "given": "Pamela Rae" }, "id": "Auburn-Pamela-Rae", "display_name": "Auburn, Pamela Rae" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/q8e0-k091", "abstract": "No abstract." }, { "name": "Brown, Frank Ripley, Jr.", "degree": "PhD", "year": "1980", "title": "Macrocyclic Lactone Formation through Sulfide Contraction: Synthesis of (\u00b1)-Diplodialide A", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142026-100640811", "creators": [ { "name": { "family": "Brown", "given": "Frank Ripley, Jr." }, "id": "Brown-Frank-Ripley-Jr.", "display_name": "Brown, Frank Ripley, Jr." } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/t4z3-ef78", "abstract": "A methodology for the synthesis of macrocyclic\r\n\u03b2-ketolactones from \u03c9-hydroxythioamides is described. The\r\nhydroxythioamides were esterified with chloroacetyl chloride,\r\nand the resulting chloroesters underwent Eschenmoser\r\nsulfide contraction when treated with sodium iodide, diisopropylethylamine,\r\nand triethyl phosphite in acetonitrile.\r\nThe \u03b2-ketolactones were obtained in 25-58% yield. The\r\nutility of the method was demonstrated by the synthesis of\r\ndiplodialide A." }, { "name": "Chan, Paul Chun-Ho", "degree": "PhD", "year": "1980", "title": "Non-Newtonian Migration of a Deformable Drop in Shearing Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-12122006-093505", "creators": [ { "name": { "family": "Chan", "given": "Paul Chun-Ho" }, "id": "Chan-Paul-Chun-Ho", "display_name": "Chan, Paul Chun-Ho" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/a85a-qg94", "abstract": "The lateral migration of a deformable drop suspended in a unidirectional shearing flow of a slightly non-Newtonian fluid has been considered both theoretically and experimentally. Analytical expressions for the migration velocity due to the separate effects of drop deformation and fluid viscoelasticity were obtained for a two-dimensional flow, and then extended to the case of a general quadratic flow. The direction and magnitude of the migration velocity was calculated for the particular cases of Poiseuille flow in a tube and linear shear flow, and compared with experimental data.\r\n\r\nThe Couette flow problem was studied experimentally. The size of the inner rotor of the Couette device was varied systematically to assess the role of velocity profile curvature on drop migration. Both deformation and non-Newtonian effects were considered. In all cases, the agreement between experimental results and theoretical predictions was very good. Significant observations that were not reported in previous studies include the migration of a deformable Newtonian drop to an equilibrium position between the centerline and the inner rotor, and the close competition between normal stress and shape deformation contributions for the case of a Newtonian drop in a non-Newtonian fluid." }, { "name": "Cherpeck, Richard Eugene", "degree": "PhD", "year": "1980", "title": "Studies Directed Toward the Total Synthesis of Histrionicotoxin", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04092026-205433905", "creators": [ { "name": { "family": "Cherpeck", "given": "Richard Eugene" }, "id": "Cherpeck-Richard-Eugene", "display_name": "Cherpeck, Richard Eugene" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dh0c-9d30", "abstract": "Histrionicotoxin (HTX) is a unique alkaloid secreted\r\nfrom the skin glands of the arrow poison frog, Dendrobates\r\nhistrionicus. This base has been found to be a highly\r\nactive venom as well as a mucosal tissue irritant toward\r\nboth mammals and reptiles. Syntheses of perhydrohistrionicotoxin\r\n(H12-HTX), which exhibits all of the biological\r\nactivities that histrionicotoxin does, and a photoaffinity\r\nlabeled derivative of H12-HTX are described.
\r\n\r\nAn approach to the synthesis of the cis-enyne moieties\r\nin HTX is presented. This method utilizes the stereoselective\r\nsynthesis of \u03b2-hydroxy acid derivatives obtained\r\nvia the boron enolates of 3-acyl-oxazolidine-2-ones.
\r\n\r\nSee PDF abstract for figure.
" }, { "name": "Chung, Ernest Ying-Chee", "degree": "PhD", "year": "1980", "title": "Experimental Investigations of the Transport Properties of Flow Suspensions: l. Measurement of Velocity Distributions of Suspension Flows in a Rectangular Channel. II. Experimental Study of the Effective Thermal Conductivity in Shear Flow of a Suspension. III. The Use of Fluorescence Correlation Spectroscopy to Measure Molecular Diffusion and Velocity Distributions", "advisor": "Corcoran, William Harrison; Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-10132006-090651", "creators": [ { "name": { "family": "Chung", "given": "Ernest Ying-Chee" }, "id": "Chung-Ernest-Ying-Chee", "display_name": "Chung, Ernest Ying-Chee" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/k2rw-rc28", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThis study was directed towards the understanding of transport properties of flowing suspensions. The first part of the thesis detailed the experimental study undertaken to investigate the characteristics of flowing suspensions. An experimental method capable of measuring the velocities of both the dispersed and suspending phases of a flowing suspension was first developed. The method was shown to be capable of measuring the velocity distributions of moderately concentrated suspensions. By using a modified laser Doppler anemometer, the velocity distribution of the suspended fluid was approximated by measuring the velocity of small fluorescent tracers, while the scattered signal from the suspended particles gave a direct measurement of their velocity distribution. Suspensions of rigid latex spheres, red blood cells, and ghost red blood cells were used. The observed behavior of the different suspensions were similar. However, the behavior of suspensions of rigid latex spheres showed a stronger dependence on the concentration of suspended particles, and a dependence on flow rates which was not observed with suspensions of ghost cells.\r\n\r\nThe second part of the thesis describes the measurements of the effective thermal conductivity of sheared suspensions of rigid spherical particles. The objective was to verify the theoretical prediction of Leal (1973) for a dilute suspension undergoing shear at low particle Peclet number, and to extend the range of the experiments to conditions beyond the scope of the theory. Surprisingly, reasonable agreement with the theoretical prediction was observed even for suspensions of moderate concentrations ([...] 0.25) and higher Peclet numbers: (Pe ~ 0(1)). The trend of the data, however, verifies the obvious fact that the theory does not completely describe the transport behavior at higher concentrations and Peclet numbers. The range of quantitative applicability of Leal's result is apparently only for Pe < 0.01 and [...] < 0.01, but the changes in the effective thermal conductivity in this domain were too small to be measured in our apparatus.\r\n\r\nIn the third part of the thesis, an analysis on the use of fluorescence correlation spectroscopy to measure molecular diffusion and velocity distributions in a sheared flow is presented. The superior spatial resolution of the method allows local measurements of molecular diffusion and/or velocity distributions. The method can also be used to measure self-diffusion of the suspended particles in a sheared suspension." }, { "name": "Croasmun, William Robert", "degree": "PhD", "year": "1980", "title": "The Physical State of Hydrocarbons and Chlorophyll a Incorporated in Phospholipid Bilayers as Determined by Nuclear Magnetic Resonance Spectroscopy", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02272026-234959087", "creators": [ { "name": { "family": "Croasmun", "given": "William Robert" }, "id": "Croasmun-William-Robert", "display_name": "Croasmun, William Robert" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4scc-d620", "abstract": "Several classes of non-protein lipophilic\r\nmolecules interact with biological membranes in physiologically\r\nimportant ways. Nuclear magnetic resonance\r\nhas been used to investigate the physical state of two\r\nmodel membrane systems composed of a phosphatidylcholine\r\nand a lipophile.
\r\n\r\nThe motional state of straight-chain hydrocarbons\r\nin phospholipid bilayers has been studied by deuterium\r\nNMR. Wide-line 2H spectra have been obtained for multilamellar\r\ndispersions of dipalmitoylphosphatidylcholine\r\ncontaining perdeuterated hydrocarbons and fatty acids\r\nten and sixteen carbons in length. Hydrocarbon spectra\r\nshow three or four resolved quadrupolar splittings as\r\nwell as a central maximum whose intensity increases with\r\nhydrocarbon concentration. The maximum quadrupolar\r\nsplitting is two to three times less than that observed\r\nfor fatty acids. These data indicate two pools of hydrocarbon\r\nin the bilayer which are in slow exchange on the\r\n2H NMR timescale. The central maximum corresponds to\r\nhydrocarbons in an isotropic motional state and may be\r\nassigned to micro-droplets of hydrocarbon between the\r\ntwo monolayers of the bilayer. The various quadrupolar\r\nsplittings indicate a flexibility gradient along the\r\nhydrocarbon chain and may be assigned to hydrocarbon\r\nlying parallel to the fatty acid chains of the lipid.\r\nThe magnitude of the splittings, and the fact that the\r\ntwo ends of the hydrocarbon show equivalent splittings\r\nmay be accounted for by either a rapid end-for-end flip\r\nof the molecule within one monolayer or sliding of the\r\nmolecule between monolayers of the bilayer. To conduct\r\nthese experiments, a 2H NMR spectrometer for observation\r\nof wide-line spectra utilizing a solid-echo pulse\r\nsequence and quadrature phase detection has been constructed.
\r\n\r\nChlorophyll-containing phospholipid bilayers\r\nhave been investigated as a model system for light-harvesting\r\nantenna chlorophyll in vivo. The red shift\r\nof the chlorophyll visible absorption band observed\r\nin vivo is best duplicated by the model system at\r\ntemperatures below the gel to liquid crystalline phase\r\ntransition of the bilayer. The phase diagram of the two\r\ncomponent bilayer as determined by differential thermal\r\nanalysis shows a double eutectic with compound formation\r\naround 40 mole% chlorophyll. 31P, 13C and 1H magnetic\r\nresonance measurements confirm that phase separation\r\noccurs below the transition temperature and suggest that\r\nin the compound phase the chlorophyll Mg is coordinated\r\nby the phosphate of the lipid headgroup. The constant\r\ncomposition of the compound phase, the interaction of\r\nchlorophyll with lipid and the possibility of spatial\r\nordering of chlorophylls in the compound make it an\r\nattractive antenna model.
" }, { "name": "Duncan, Thomas Michael", "degree": "PhD", "year": "1980", "title": "The Nature of Molecules Adsorbed on Catalytic Surfaces: Pulsed Nuclear Magnetic Resonance and Infrared Absorbance Studies", "advisor": "Vaughan, Robert W.; Weinberg, William Henry; Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10272006-080057", "creators": [ { "name": { "family": "Duncan", "given": "Thomas Michael" }, "id": "Duncan-Thomas-Michael", "display_name": "Duncan, Thomas Michael" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." }, { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/mbvt-4g35", "abstract": "The nature of molecules adsorbed on high surface catalysts have been studied with infrared absorbance and nuclear magnetic resonance (NMR) techniques. The well-separated infrared vibrational spectra have been used mainly to identify the various surface species by comparison with known compounds. The frequency shifts in the molecular stretching modes indicate the strengthening or weakening of the bonds of the molecules upon adsorption. The NMR spectra have been used to quantify the distributions among the surface states and to describe the motional properties of the adsorbed molecules. The NMR data were obtained through the application of several recently developed multiple-pulse techniques. By analyzing the spin-lattice relaxation times, the dipolar interactions, and the chemical shift anisotropies, it has been possible to separate the overlapping NMR spectra and determine the molecular symmetries, bond lengths, and the nature of the adsorption site. The results of these two techniques were combined to describe the adsorbed states of CO on Rh dispersed on Al2O3, and the distribution of formic acid on zeolite surfaces. The infrared spectroscopy confirmed the previous indentification of three surface CO states; linear and bridged sites that form on Rh atoms in clusters on the Al2O3, and dicarbonyl species on isolated Rh atoms. The desorption rate at 295 K is very slow. All three states readily exchange with CO(g) at 295 K, but only the dicarbonyl species exchanges at temperatures below 200 K. H2CO decomposed on the dispersed Rh into adsorbed CO states, with no evidence of any HxCO surface states, though there was further demonstration of isolated Rh atom sites. The 13C NMR results quantified the distribution of the three surface sites, and thus calibrated the infrared absorbances, as well as the local motions on the three sites. The infrared spectra of formic acid on the Y zeolites suggested the presence of unidentate and bidentate formate species on the surface. The bidentate structure was the dominant species on the more catalytically active zeolite. The combination of the results of several multiple-pulse NMR techniques are analyzed to measure the site distribution between the unidentate and bidentate species, as well as to further describe the bidentate formate ion. The bidentate structure is bonded to the Al atoms rather than the Si atoms, has a structure similar to formate salts, and a more acidic carbonyl hydrogen, relative to formic acid." }, { "name": "Elliott, Janet Ruth", "degree": "PhD", "year": "1980", "title": "Interactions of Perhydrohistrionicotoxin with Acetylcholine Receptors from Torpedo Californica electroplax", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012026-205521313", "creators": [ { "name": { "family": "Elliott", "given": "Janet Ruth" }, "id": "Elliott-Janet-Ruth", "display_name": "Elliott, Janet Ruth" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3jk4-va70", "abstract": "Electrophysiological evidence has shown that the histrionicotoxins\r\nreversibly block neuromuscular transmission, acting only in\r\nthe presence of agonists (Albuquerque, E. X., Barnard, E. A., Chiu,\r\nT. H., Lapa, A. J., Dolly, J. 0., Jansson, S.-E., Daly, J., and\r\nWitkop, B. (1973) Proc. Natl. Acad. Sci. USA 70, 949-953). The use\r\nof tritiated perhydrohistrionicotoxin (H12-HTX) and the fluorescent\r\nprobe ethidium bromide allowed biochemical characterization of the\r\nH12-HTX binding site in postsynaptic membranes and after detergent\r\nextraction.
\r\n\r\n[3H]H12-HTX bound with high affinity (KD ~ 0.5 \u03bcM) to acetyl-\r\ncholine receptor (AcChR) enriched membranes isolated from Torpedo\r\ncalifornica electroplax. The ratio of a-bungarotoxin sites to H12-HTX\r\nsites was 4:1. This stoichiometry implied that one H12-HTX bound per\r\nAcChR dimer. H12-HTX was not competitive with \u03b1-bungarotoxin or\r\nagonists, but the agonist recognition site and the H12-HTX site were\r\nconformationally linked. The KD for [3H]H12-HTX was decreased\r\ntwofold in the presence of carbamylcholine in concentrations sufficient\r\nto convert the receptor to the form having high affinity for agonists.\r\nDecahydrohistrionicotoxin increased the binding of [3H] acetylcholine.\r\nH12-HTX had no effect on [3H] carbamylcholine binding. In this system\r\nthe twofold higher affinity of H12-HTX for the membrane in the high\r\naffinity state was not sufficient to strongly affect the process of agonist\r\ninduced conversion from the low affinity state to the high affinity state\r\nfor agonists (in vitro \"desensitization\"). 3 \u03bcM H12-HTX did not\r\ndirectly desensitize nor did it accelerate the rate of agonist induced\r\ndesensitization or decelerate the rate of recovery from agonist induced\r\ndesensitization. 30 \u03bcM H12-HTX did not directly desensitize nor did it\r\naccelerate the rate of agonist induced desensitization or decelerate the\r\nrate of recovery from agonist induced desensitization. 30 \u03bcM\r\nH12-HTX increased the rate of in vitro desensitization only slightly.
\r\n\r\nLocal anesthetics displaced [3H]H12-HTX bound to membranes in\r\nan apparently competitive fashion. The presence of carbamylcholine\r\nsufficient to convert the receptor to the high affinity state for agonists\r\nmodulated the apparent KIs for some local anesthetics. The differences\r\nin their apparent affinities for the low and high affinity states of\r\nthe receptor roughly paralleled the effects of these local anesthetics on\r\nthe rate of carbamylcholine induced \"desensitization\" (Blanchard,\r\nS. G., Elliott, J., and Raftery, M. A. (1979) Biochemistry, in press).\r\nFor example dibucaine, which greatly accelerated the rate of conversion\r\nto the high affinity state, bound 17-fold more tightly to the high\r\naffinity state, and tetracaine, which slowed the rate of conversion,\r\nbound 20-fold more tightly to the low affinity state. This phenomenon\r\nmay not have been due to a specific binding, since the detergent Triton\r\nX-100 also blocked [3H]H12-HTX binding and accelerated in vitro\r\n\"desensitization\" at micromolar concentrations.
\r\n\r\nSpecific ethidium bromide fluorescence was quenched by H12-HTX\r\nwith an apparent KI very similar to the KD determined by direct\r\nbinding studies. This quenching was probably due to a change in the\r\nenvironment of the bound ethidium rather than an actual displacement.\r\n
\r\n\r\n[3H]H12-HTX binding could be extracted from AcChR enriched\r\nmembranes by the detergent sodium cholate. Binding activity was\r\nsensitive to detergent concentration and was only recovered at low\r\ncholate concentrations where some aggregation occurred. The ratio\r\nof \u03b1-bungarotoxin sites to H12-HTX sites remained 4:1, though the KD\r\n(1.6 \u03bcM) was higher than with membranes. The cholate extracts were\r\nfractionated by several techniques, yielding an enrichment of AcChR.\r\nTreatment of cholate extracts with an \u03b1-bungarotoxin-Sepharose resin\r\nremoved H12-HTX and \u03b1-bungarotoxin binding activities in parallel.
\r\n\r\nTreatment of AcChR enriched membranes with base selectively\r\nremoved most non-AcChR polypeptides without affecting [3H]H12-HTX\r\nbinding. This provided positive identification of the H12-HTX binding\r\ncomponent with the AcChR, eliminating the possibility that the binding\r\nsite was located on the 43,000 Mr polypeptide found in native membranes.\r\nThe local anesthetics dibucaine and tetracaine displaced\r\n[3H]H12-HTX bound to base treated membranes with unaltered KIs\r\nCarbamylcholine modulated the affinity of the membranes for H12-HTX\r\nand the local anesthetics. [3H]H12-HTX binding could be reconstituted\r\nfrom cholate extracts of treated membranes. Thus the high affinity\r\nH12-HTX site appears to be located on one or more of the AcChR\r\npolypeptides, and reconstitution of that binding site from detergent\r\nextracts does not require the presence of the 43,000 Mr polypeptide.
\r\n\r\n[3H]H12-HTX binding was largely unaffected by reduction and\r\nalkylation of AcChR enriched membranes, a treatment which reduced\r\n\u03b1-bungarotoxin binding activity. It was likewise unaffected by treatment \r\nof the membranes with the carboxyl-modifying reagent trimethyl\r\noxonium tetrafluoroborate. Divalent cations (Ca2+, Mg2+) increased\r\nthe affinity of membranes for [3H]H12-HTX about twofold. [3H]H12-HTX \r\nbinding was little affected by changes in NaCl concentration of the\r\nbuffer.
" }, { "name": "Evans, Howard Edwin", "degree": "PhD", "year": "1980", "title": "The Development and Utilization of Inelastic Electron Tunneling Spectroscopy as a Tool for Investigating Fundamental Catalytic Processes", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252006-153643", "creators": [ { "name": { "family": "Evans", "given": "Howard Edwin" }, "id": "Evans-Howard-Edwin", "display_name": "Evans, Howard Edwin" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4jhn-ad98", "abstract": "A diverse number of reactant/catalyst systems have been investigated utilizing inelastic electron tunneling spectroscopy (IETS) to probe the vibrational structures of the various surface species. Catalytic systems studied were selected for their relevance to important industrial reactions, as well as to demonstrate the versatily of IETS and to expand the range of its known applications. These studies include observation of an ethoxide-to-acetate transformation above 470K for ethanol on alumina, demonstrating that IETS can effectively monitor surface reactions. Unique characterization of surface acetates formed on alumina by ethanol, acetic acid and acetaldehyde is obtained via analysis of IET spectra, as is information on the initial adsorption mechanism for each of the three species. Results obtained for ethanol adsorption on alumina-supported silver particles extend the use of IETS into new areas of supported metal catalysis. Characterization of the silver particles was accomplished utilizing transmission electron microscopy. Most significant, perhaps, are the studies of Zr(BH4)4 supported on aluminum oxide. This is the first reported instance of IETS being utilized to characterize the structure of a supported complex; and, indeed, represents one of the few structural studies performed thus far for this increasingly important class of catalysts. Interactions of ethylene, acetylene and propylene with the Zr(Bh4)4/Al2O3 (a known polymerization catalyst under certain conditions) were examined with the resultant observation of polyacetylene formation. The alumina films utilized in IETS studies were characterized by X-ray photoelectron spectroscopy to facilitate comparisons to actual commercial aluminas." }, { "name": "Evitt, Eric Robert", "degree": "PhD", "year": "1980", "title": "Insertion and Thermal Decomposition Reactions of Cyclopentadienylcobalt (III) Dialkyl Complexes", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202026-165214989", "creators": [ { "name": { "family": "Evitt", "given": "Eric Robert" }, "id": "Evitt-Eric-Robert", "display_name": "Evitt, Eric Robert" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sbv2-pc06", "abstract": "PMe3 replaces PPh3 in CpCo(PPh3) (Me)2 (1, Cp = \u019e5-\r\nC5H5) in a dissociative substitution reaction to give CpCo\r\n(PMe3) (Me)2; the first order rate constant for PPh3 loss\r\nfrom 1 is 4 x 10-4 sec-1 at 30\u00b0C in toluene-d8. Dialkyl\r\ncomplex 1 doubly alkylates CO in an intrarnolecular process\r\nto give acetone in high yield; this proceeds via CO substitution\r\nin 1 to give the spectroscopically observed intermediate\r\nCpCo(CO) (Me)2 (6), followed by migratory insertion,\r\nand reductive elimination from an acyl-alkyl complex.\r\nHeating and then carbonylating mixtures of 1-d0 and\r\n1-d6 (deuterated methyl groups) in benzene revealed the\r\npresence of an intermolecular methyl exchange process in 1.\r\nWe have reinvestigated the reaction of .2:_ with diphenylacetylene\r\nand, in addition to the organometallic products observed by\r\nprevious workers, isolated two new organic products 2,3-\r\ndiphenyl-1-butene (11) and Z-2,3-diphenyl-2-butene; these\r\nproducts account for >95% of the methyl groups in starting\r\n1 and were formed in the ratio 14:1 in the absence of added\r\nPPh3. Additional experiments designed to probe the mechanism\r\nof product formation led to the following conclusions: (1)\r\nhigh yield stereospecific double alkylation of diphenylacetylene\r\nis a feasible process; (2) reactions of 11 in this\r\nsystem involve two diastereomeric \u019e2-olefin complexes which\r\nare interconvertible only by dissociation of the olefinic\r\nligand from the metal; (3) hydrogen shifts involved in the\r\nCp(PPh3)Co-catalyzed isomerization of alkenes occur more\r\nrapidly than dissociation of the alkene from the metal center;\r\nand (4) interconversion of \u019e3-allyl complexes via rotation in\r\n\u019e1-allyl complexes is much slower than hydrogen transfer and\r\nproduct formation. Ethylene reacts with 1 to give methane,\r\npropene, and the new ethylene complex CpCo(PPh3) (C2H4) (14);\r\nthis was independently generated by thermal PPh3 or photochemical\r\nCO substitution in CpCo(PPh3)2 and CpCo(CO) (PPh3),\r\nrespectively. The production of propene from ethylene and\r\n1 is a model for the chain-growth step in the Ziegler-Natta\r\npolymerization of olefins. The products can be explained by\r\na classical mechanism involving insertion of ethylene into\r\na cobalt-carbon a-bond or an alternative one involving\r\nethylene addition to an intermediate metal-carbene complex\r\nformed by a-elimination. Labeling experiments in this system\r\nhave shown propene is formed by transfer of one intact methyl\r\ngroup to ethylene, in agreement with the classical view.\r\nThermal decomposition of 1 is competitive with the alkylation\r\nof ethylene and gives mostly methane, abstracting the fourth\r\nmethane hydrogen from the cyclopentadienyl ring. The decomposition\r\nhas been monitored by 1H NMR spectroscopy in the\r\npresence of added PPh3 and ethylene (conditions where no\r\npropene is generated) and CpCo(PPh3) (C2H4) (Cp' = \u019e5CH3C5H4)\r\nand Cp'Co(PPh3) (Me)2 have been observed spectroscopically\r\nand identified as the primary and secondary products of the\r\ndecomposition, respectively. Together, these reactions show\r\nreductive elimination in alkyl-acyl and alkyl-vinyl complexes\r\nis more favorable than alkyl-alkyl reductive elimination\r\nand this is attributed to the ability of the former systems\r\nto donate an additional pair of electrons to the metal center\r\nin the reductive elimination transition state.
\r\n\r\n\u019e5-cyclopentadieny(triphenylphosphine)cobaltacyclopentane\r\n(18) has been prepared by reaction of CpCo(PPh3)I2 with 1,4-\r\ndilithiobutane at low temperature. This metallacycle is\r\nthermally more sensitive than its dimethyl analog 1 and decomposes\r\nto give 1-butene which is subsequently isomerized\r\nby the organometallic products to a mixture of 2-butenes.\r\nIn this system, ethylene insertion cannot compete with thermal\r\ndecomposition, but CO and diphenylacetylene insertion can.\r\nCO reacts with 18 to give cyclopentanone via the CO substituted\r\nanalog of 18; this has been observed spectroscopically\r\nand builds up to a greater degree than the dimethyl analog\r\nobserved during the reaction of 1 with CO. Diphenylacetylene\r\nreacts with 18 to give the expected products of double alkylation,\r\n1,2-diphenylcyclohe.xene and 2,3-diphenylcyclohexene,\r\nand Z-1,2-diphenyl-1,5-hexadiene as well. The latter product\r\nis presumably derived from \u03b2-elimination in an intermediate\r\nmetallacycloheptene which also generates the cyclohexenes\r\nvia reductive elimination.
" }, { "name": "Fuller, Gerald Gendall", "degree": "PhD", "year": "1980", "title": "I. Dynamics of Flowing Polymer Solutions. II. The Measurement of Velocity Gradients by Homodyne Light Scattering Spectroscopy", "advisor": "Leal, L. Gary; Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12112006-152815", "creators": [ { "name": { "family": "Fuller", "given": "Gerald Gendall" }, "id": "Fuller-Gerald-Gendall", "display_name": "Fuller, Gerald Gendall" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" }, { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/5PPN-JZ62", "abstract": "This thesis is presented in two parts. In the first part the results of flow birefringence experiments and modelling efforts on both concentrated and dilute polymer solutions are discussed. The second part presents theoretical developments and complementary experiments which demonstrate the utility of the technique of homodyne light scattering spectroscopy to the measurement of velocity gradients in laminar flow fields.
\r\n\r\nThe flow birefringence experiments were performed using a four roll mill which was designed in order to allow the simulation of a wide range of two dimensional flows ranging from purely extensional flows to purely rotational flows. Flow visualization and homodyne light scattering spectroscopy experiments were used to characterize the flow fields.
\r\n\r\nUsing this device the flow birefringence of concentrated polyethylene/water and polystyrene/tricresyl phosphate solutions was measured. Birefringence measurements of the Polyox solutions over a wide range of flow types indicated that the birefringence could be well correlated against the eigenvalue of the velocity gradient tensor, in agreement with model calculations. Transient experiments were performed in which the birefringence was measured as purely extensional flows were started from rest. Both polymer/solvent systems showed a pronounced overshoot in the birefringence. Turbidity measurements were also performed on the polyox solutions and a 30% increase in the turbidity was measured which persisted for many hours after the cessation of flow (whereas the birefringence decayed to zero in a fraction of a second). This increased turbidity and its persistence with time suggests the occurence of flow induced crystallization of the polymer.
\r\n\r\nThese experiments involving concentrated polymer systems were compared to model calculations using the Yamamoto network theory. Several choices of the polymer entanglements creation and destruction functions were analyzed and it is demonstrated that analytical results can be obtained using these choices. A variety of nonlinear phenomena can be predicted including the correlation of the of purely extensional flows. The predicted response of the stress tensor is also presented and discussed.
\r\n\r\nFlow birefringence experiments were also carried out in the dilute concentration range. Measurements were taken on three molecular weight samples (2-8x10^6 MW, MW/MN=1.14-1.3) in a viscous polychlorinated biphenyl solvent in the range of 50-100 ppm subjected to a wide range of two dimensional flows. The birefringence was again found to be well correlated against the eigenvalue of the velocity gradient tensor. The normalized birefringence, corrected for concentration, ([delta]n/nc), was observed to approach a saturation value at high velocity gradients in purely extensional flow. This saturation value was independent of both the molecular weight and the concentration c, in agreement with theory. In addition, the magnitude of the saturation value is consistent with nearly fully extended chains and suggests extensions in the range of 20-50 times the rest state size. The experiments were complemented by simple dumbbell model calculations which incorporated the nonlinear spring, internal viscosity and variable hydrodynamic friction. The model was found to simulate the experimental data very well if the effects of molecular weight distribution and finite transit times in the flow were taken into account.
\r\n\r\nThe results of a detailed investigation of the dumbbell model used to analyze the dilute solution experiments is also included. The effects of the nonlinear spring, variable friction factor and internal viscosity to the response of the dumbbell to steady state and transient two dimensional flows are exposed. A perturbation solution for the dumbbell with a small amount of internal viscosity is presented and it is demonstrated that this problem can be solved analytically.
\r\n\r\nThe technique of homodyne light scattering spectroscopy applied to suspensions in laminar flow is investigated. It is demonstrated both theoretically and experimentally that use of this method allows direct measurement of velocity gradients without the need for differentiating velocity data which is the normal method used. This technique was used to characterize the spatial distribution of velocity gradients existing in the four roll mill simulating purely extensional flow.
" }, { "name": "Gerwer, Alexander Sherwin", "degree": "Masters", "year": "1980", "title": "A Discrete Basis Set Technique for Calculating Photoionization Cross Sections Utilizing Moment Theory", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042010-123305037", "creators": [ { "name": { "family": "Gerwer", "given": "Alexander Sherwin" }, "id": "Gerwer-Alexander-Sherwin", "display_name": "Gerwer, Alexander Sherwin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E1ZA-6224", "abstract": "No abstract." }, { "name": "Grunthaner, Paula Jean", "degree": "Masters", "year": "1980", "title": "I. Isolation of LAC Operator DNA. II. XPS Investigation of the GaAs/Native Oxide and Si/Metal Interfaces", "advisor": "Dickerson, Richard E.; Mayer, James Walter", "url": "https://resolver.caltech.edu/CaltechTHESIS:07142025-221617617", "creators": [ { "name": { "family": "Grunthaner", "given": "Paula Jean" }, "id": "Grunthaner-Paula-Jean", "display_name": "Grunthaner, Paula Jean" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." }, { "name": { "family": "Mayer", "given": "James Walter" }, "id": "Mayer-J-W", "role": "advisor", "display_name": "Mayer, James Walter" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7tzy-bv05", "abstract": "Chapter I
\r\n\r\nA procedure is presented for the large scale isolation of cloned\r\n29 base-pair lac operator DNA from plasmid DNA. The methodology is\r\ngeneral and may be used to isolate other cloned DNA fragments as well.
\r\n\r\nInitial ultraviolet difference experiments with lac repressor\r\nprotein are also presented. Solvent perturbation is used to locate\r\nthe tyrosine and tryptophan residues.
\r\n\r\nChapter II
\r\n\r\nThe chemical structure of the thin native oxide of GaAs (30 - 40 \u00c5)\r\nhas been investigated using x-ray photoelectron spectroscopy. Both\r\nwet chemical and argon ion bombardment techniques have been used to\r\ndepth profile the oxide structure. The composition of the oxide is\r\nfound to be quite complex and the distribution of the various species\r\nas a function of oxide thickness is discussed.
\r\n\r\nA Fouries transform data reduction technique based on linear\r\nprediction has been used to develop possible explanations for the\r\nexperimentally observed chemical shifts and composition layers.\r\nEvidence is found for the presence of As2O3, Ga2O3, and the mixed\r\noxide GaAsO4.
\r\n\r\nChapter III
\r\n\r\nA systematic investigation of the bonding properties of selected\r\ntransition metal silicides on single crystal Si substrates is proposed.\r\n4He+ back scattering, XPS, and x-ray excited AES will be used to\r\ncharacterize both the bulk and interfacial bonding properties. Initial\r\nexperiments are presented to demonstrate the feasibility of the approach.
" }, { "name": "Grunthaner, Paula Jean", "degree": "PhD", "year": "1980", "title": "The Chemical Structure of Metal/Semiconductor Interfaces as Determined by X-Ray Photoelectron Spectroscopy", "advisor": "Mayer, James Walter", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232025-170156584", "creators": [ { "name": { "family": "Grunthaner", "given": "Paula Jean" }, "id": "Grunthaner-Paula-Jean", "display_name": "Grunthaner, Paula Jean" } ], "advisors": [ { "name": { "family": "Mayer", "given": "James Walter" }, "id": "Mayer-J-W", "role": "advisor", "display_name": "Mayer, James Walter" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0458-3943", "abstract": "The chemical nature of transition metal/silicon interfaces has\r\nbeen investigated using x-ray photoelectron (XPS) and Rutherford\r\nbackscattering (RBS) spectroscopy, In particular, the Ni/Ni2Si,\r\nSi/Ni2Si, and Ni/Si transitional regions have been examined in detail.\r\nThe effect of oxygen impurities on the Ni/NiSi interface has been\r\nstudied using ion implantation and 16O(d,\u03b1)14N nuclear reactions in\r\nconjunction with XPS and RBS. Preliminary results on the Pd/Pd2Si and\r\nPt/Pt2Si interfaces are presented and contrasted to the Ni system.
\r\n\r\nA technique for studying silicide/silicon and silicide/metal interfaces\r\nhas been developed in the course of this work. The approach\r\nexploits the exponential attenuation of photoemission intensities to\r\ndynamically monitor the advancing planar silicide growth front during\r\nthe in situ growth of the silicide. The technique allows the examination\r\nof a realistic interface bounded on either side by an extended solid\r\nwithout the chemical and structural perturbations caused by conventional\r\ndepth profiling methods. The local chemical environment of both the\r\nsilicon and transition metal atoms has been established through analysis\r\nof the observed binding energy shifts in the photoemission spectra\r\n4He+ backscattering has been used to follow the progression of the thin\r\nfilm reaction and to provide quantitative information on atomic composition.
\r\n\r\nThe Ni/Ni2Si interface was examined using both amorphous and\r\ncrystalline Si as a substrate. In each case, it was demonstrated that\r\nthe Si atoms in the transition region are in a substantially more Ni-rich\r\nenvironment than that found for Si in Ni2Si. These regions are again\r\nof graded composition. The first Si 2p signal observed is consistent\r\nwith a metallic-like Si substituted in the fee lattice of Ni metal.\r\nThe essential difference between the Ni/Ni2Si interface using a crystalline\r\nsubstrate as compared to an amorphous substrate is that the former\r\nis 2 - 3 times narrower (0.6\u03bb) than the latter (1.5\u03bb).
\r\n\r\nThe as-deposited Ni/Si interface was investigated by monitoring\r\nthe evolution of the Ni and Si core levels as multiple monolayers of Ni\r\nwere deposited on Si (100). The data indicate the presence of a chemically\r\ngraded transition region which ranges in stoichiometry from Ni\r\natoms bound in the Si interstitial voids on the (100) Si side of the\r\ninterface to Si atoms substituted in the Ni metal lattice on the Ni\u00b0\r\nside of the interface.
\r\n\r\nThe chemical nature of the Ni/Si interface as a function of the\r\nsubstrate temperature was also examined. It was shown that substantial\r\nchemical interaction occurs between the Ni and Si substrate at temperatures \r\nas low as 100\u00b0 K. Ni metal was deposited on an inert substrate\r\nto demonstrate that aggregation effects were not responsible for the\r\nobserved chemical shifts.
\r\n\r\nThe dependence of the Ni 2p binding energy on the substrate temperature\r\nalso demonstrated that the initial Ni atom deposited on the Si\r\nsurface must drop into the interstitial Si voids rather than being\r\nbound on the surface. The behavior of the Ni 2p binding energy as a\r\nfunction of Ni coverage at elevated substrate temperatures suggests the\r\npresence of several distinct Ni environments.
\r\n\r\nThe effect of oxygen impurities on the Ni/Ni2Si interface was\r\ninvestigated via ion implantation using XPS, RBS, and 16O(d,\u03b1)14N\r\nnuclear reactions. It was shown that 2.2 x 1016 O/cm2 are sufficient\r\nto block the diffusion of the Ni metal and thereby inhibit the silicide\r\nreaction. The data demonstrate that as the advancing Ni/Ni2Si interface\r\nencounters oxygen in the Ni film, silicon suboxides are formed. As\r\nmore oxygen is encountered, SiO2 is formed. When a sufficient layer of\r\nSiO2 has formed, the Ni metal is no longer able to diffuse through to\r\nthe Si/Ni2Si interface to continue the solid phase reaction.
\r\n\r\nPreliminary results for the Pd/Pd2Si and Pt/Pt2Si interfaces are\r\npresented and contrasted to those found for the Ni/Ni2Si system. The\r\ndata suggest that, as the Ni case, the limiting environment for Si at\r\nthe Pd/Pd2Si interface is metallic-like with a high ligancy. We\r\npropose this is a Si atom substituted in the fee lattice of Pd metal.\r\nThe Si atoms at the Pt/Pt2Si interface, on the other hand, rest in a\r\nsite of substantially lower coordination number in the fee Pt lattice.\r\nThis is suggestive of an interstitial defect site.
\r\n\r\nBoth the Pd/Pd2Si and Pt/Pt2Si interfaces are found to be graded\r\nin composition. Estimations of these widths indicate that the metal/\r\nsilicon interface widths decrease in the order Ni > Pt > Pd.
" }, { "name": "Hinsberg, William Dinan, III", "degree": "PhD", "year": "1980", "title": "The Synthesis, Spectroscopic Observation and Chemical Reactivity of N-(2,2,6,6-Tetramethylpiperidyl)Ni trene", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252016-112114482", "creators": [ { "name": { "family": "Hinsberg", "given": "William Dinan, III" }, "id": "Hinsberg-William-Dinan-III", "display_name": "Hinsberg, William Dinan, III" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3R32-XC97", "abstract": "1,1-Dialkyldiazenes (aminonitrenes, N-nitrenes)\r\nunlike their more stable 1,2-dialkyldiazetle isomers\r\n(azo compounds) have not yet been isolated or detected\r\nby spectroscopic methods, but rather are assumed\r\nintermediates based on a substantial body of chemical\r\nevidence. The first direct observation of a 1,1-\r\ndialkyldiazene is described here. The visible spectrum\r\nat -78\u00b0 of N-(2,2,6,6-tetramethylpiperidyl)nitrene (33)\r\n(\u03bbmax = 541 nm) provides experimental evidence on (1)\r\nthe energy required for the n + \u03c0* electronic\r\ntransition, and (2) the vibrational spacing of the\r\nfirst electronically excited state. The infrared spectrum\r\nat -78\u00b0 (14N=14N stretch at 1595 cm-1; 14N=15N\r\nstretch at 1569 cm-1) provides evidence that the 1,1-\r\ndiazene has considerable N=N double bond character\r\nin the ground state.
\r\n\r\nThe first kinetic study of the thermal decomposition\r\nof a 1,1-dialkyldiazene is described. The\r\ntemperature dependence of the unimolecular rate (k1)\r\nof fragmentation of 33 was examined in three different\r\nsolvents and kinetic evidence for a direct bimolecular\r\npathway for the formation of 1,1 \"-azo-2,2,6,6-tetra-\r\nmethylpiperidine 41 from 33 is provided. The activation\r\nparameters for the unimolecular fragmentations\r\nare log A = 11.6 \u00b1 0.5, Ea = 16.9 \u00b1 0.7 in n-hexane,\r\nlog A = 13.7 \u00b1 0.3, Ea = 20.0 \u00b1 0.4 in Et20, log A=\r\n13.6 \u00b1 0.3, Ea = 20.1 \u00b1 0.4 kcal/mole in THF. Using\r\ncomputer simulation it is found that the curved\r\nportions of the tn A vs. time plots may be modelled as\r\ncompetitive unimolecular and bimolecular reactions\r\n(kobs = k1 + k2[33]). In Et20 at -16\u00b0, k1 = 5.03 x\r\n10-4 sec-1 and k2 = 5.0 x 10-2 liter/mole-sec.
\r\n\r\nAlso reported are proton and carbon-13 nuclear\r\nmagnetic resonance data for 33, along with the results\r\nof a preliminary study of its photoreactivity.
" }, { "name": "Ingle, David Michael", "degree": "PhD", "year": "1980", "title": "Investigations of Four-Coordinate and Five-Coordinate Nickel(I) Macrocyclic Ligand Complexes", "advisor": "Gagn\u00e9, Robert R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07182025-170908470", "creators": [ { "name": { "family": "Ingle", "given": "David Michael" }, "id": "Ingle-David-Michael", "display_name": "Ingle, David Michael" } ], "advisors": [ { "name": { "family": "Gagn\u00e9", "given": "Robert R." }, "id": "Gagn\u00e9-R-R", "role": "advisor", "display_name": "Gagn\u00e9, Robert R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/17rv-gv36", "abstract": "The affinity for the binding of carbon monoxide as a fifth ligand\r\nto several formally-nickel(I) complexes of tetraazamacrocyclic ligands\r\nhas been studied; CO binding constants measured in DMF range from\r\nzero to 105. Reduced nickel complexes, which may occur either as\r\nfour-coordinate nickel(I) species or, for those ligands having conjugated\r\n\u03b1-diimine moieties, as four-coordinate nickel(II)-stabilized\r\nligand radicals, have been found to bind carbon monoxide as a fifth\r\nligand, forming paramagnetic, presumably five-coordinate nickel(I)\r\ncarbonyl complexes. Intramolecular electron transfer appears to\r\noccur upon the binding of CO to several of the four-coordinate nickel(II)stabilized\r\nligand radicals to give five-coordinate nickel(I) carbonyl complexes.\r\nIntramolecular electron transfer within a four-coordinate\r\nframework appears to occur for one complex, [1, 1,-difluoro-4, 5, 12, 13-\r\ntetramethyl-1-bora-3, 6, 11, 14-tetraaz a-2, 15-dioxacyclopentadeca-3, 5, 11,-\r\n13, -tetraenato] nickel(I), for which the nickel(I) form appears to lie\r\n0. 75 \u00b1 0.15 kcal/mole higher in energy than the nickel(II) ligand radical\r\nform.
\r\n\r\nThese nickel complexes have been characterized by elemental\r\nanalysis, bulk magnetic susceptibility, carbon monoxide binding constants,\r\nelectron paramagnetic resonance spectroscopy, electronic\r\nabsorption spectroscopy, infrared spectroscopy, and electrochemical\r\nanalysis. These nickel complexes appear to be quite analogous to\r\ntheir copper counterparts. On the basis of chemical and physical\r\nsimilarities to the nickel complexes, particularly with respect to\r\ntheir infrared spectra, four-coordinate copper complexes may be formally\r\ndescribed as either copper(I) or copper(III)-stabilized ligand\r\ndianion species, depending on the ligand system, although both copper\r\nspecies have very similar chemical properties.
\r\n\r\nA discussion of EHMO calculations on the system is included.\r\nIn the four-coordinate Ni(II) ligand radical the HOMO is a ligand \u03c0*\r\norbital having some metal character; in the five-coordinate Ni(I)\r\ncarbonyl complexes, the HOMO is the dx2-y2 orbital.
\r\n\r\nAn approach to the synthesis of cofacial dimethylglyoxime dimer\r\ncomplexes using 1, 4-bis(difluoroboro)butane is included in Appendix\r\nn.
" }, { "name": "Jain, Ravi", "degree": "PhD", "year": "1980", "title": "Mathematical Modeling and Experimental Studies of Thermal Reactions of Coal", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12112006-085017", "creators": [ { "name": { "family": "Jain", "given": "Ravi" }, "id": "Jain-Ravi", "display_name": "Jain, Ravi" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HAV6-QD05", "abstract": "This dissertation discusses theoretical and experimental research on coal pyrolysis.\r\n\r\nIn the theoretical part, a mathematical model based on coal's chemical structure and its reactions is developed for computer simulation of pyrolysis. Firstly, the important organic functional groups of carbon, hydrogen and oxygen in medium and high rank coals are organized into a conceptual model for coal's chemical structure. Using the principles of thermochemistry of free radicals as guidelines, the important categories of chemical reactions in coal pyrolysis are postulated. A set of 41 series-parallel reactions represents the chemical change. It is concluded that there is no a priori distinction between volatiles and non-volatiles in a coal. They are both formed from the same chemical structure, and are basically an inevitable consequence of each other's formation.\r\n\r\nFor the purpose of mathematical modeling, coal is considered to be a population of randomly distributed functional groups on a matrix. A scheme based on statistical transformations is devised to compute concentrations of reacting configurations before and during pyrolysis. The rates of reactions are expressed in terms of these concentrations. Differential equations governing the rate of change of state variables with pyrolysis time are formulated and numerically integrated on the computer. Pyrolysis results are predicted in terms of the state variables.\r\n\r\nThe dependence of the yield and composition of volatiles on (a) transport parameters like particle size and pressure, and (b) kinetic parameters like time, temperature and time-temperature history, is investigated experimentally. Gaseous products are analyzed using chromatography, while tar is characterized by GPC, NMR and elemental analysis.\r\n\r\nBasic research on coal helps in developing a general \"theory\" about its structure and chemical behavior. It enhances our ability to meet process, economic and environmental goals in coal's industrial utilization." }, { "name": "Lee, Seong Hee", "degree": "PhD", "year": "1980", "title": "I. Motion of a Sphere in the Presence of a Plane Interface. II. Modeling of Non-Isothermal Turbulent Flows", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-10102006-105459", "creators": [ { "name": { "family": "Lee", "given": "Seong Hee" }, "id": "Lee-Seong-Hee", "display_name": "Lee, Seong Hee" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7k89-yq91", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I:\r\n\r\n The motion of a sphere in the presence of a fluid/fluid interface is studied. First, a solution is derived for a point force near a plane interface. Then the solution is extended to include the higher-order terms which are required to describe the motion of a solid sphere. Singularities of higher orders at the center of the sphere are obtained by using the method of reflections. This method yields asymptotic solutions for the general motion of a sphere in the presence of an interface.\r\n\r\n A general solution for Stokes' equation in bipolar coordinates is also derived, and then applied to the arbitrary motion of a sphere in the presence of a plane fluid/fluid interface. The drag force and hydrodynamic torque on the sphere are then calculated for four specific motions of the sphere; namely, translation perpendicular and parallel to the interface and rotation about an axis which is perpendicular and parallel, respectively, to the interface. These numerically exact solutions are compared with the previous approximate solutions. The latter can be generalized to a variety of particle shapes, and it is thus important to assess their accuracy for this case of spherical particles where an exact solution can be obtained.\r\n\r\nPart II:\r\n\r\n The second-order, mean Reynolds stress turbulence closure approximation is extended to non-isothermal turbulent flows with negligible buoyancy. We apply the method of invariant modeling [Lumley and Khajeh-Nouri (1974)] to systematically model the various higher order moments in the governing equations. This approach yields a general form for each unknown correlation in the transport equations of [...] and [...] each containing many terms with parameters that must be determined from experimental data. For practical application, it is necessary to reduce the number of terms. In the present work, the most important terms are filtered from the general model for each unknown moment and their parameters are evaluated based on experimental data.\r\n \r\n A semi-analytical method is used to derive models for the triple correlations of fluctuating velocity and temperature in a nonisothermal turbulent flow based upon the exact equations which govern their transport and production processes. In this study, these governing equations are transformed to a set of coupled linear algebraic equations for [...], [...], [...], and [...] by assuming: (1) a quasi-Gaussian structure for the fourth-order moments, (2) slow variations of the mean flow in the streamwise direction, (3) negligible convection of the triple correlations, and (4) certain simple models for the remaining higher-order correlations. A model for the triple correlations can thus be obtained by solving the set of linear algebraic equations." }, { "name": "Ma, Charlotte K. Lowe", "degree": "PhD", "year": "1980", "title": "Crystallographic Studies of Iodide-Containing Quasi-One-Dimensional Conductors", "advisor": "Samson, Sten Otto", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112018-114630678", "creators": [ { "name": { "family": "Ma", "given": "Charlotte K. Lowe" }, "id": "Ma-Charlotte-K-Lowe", "display_name": "Ma, Charlotte K. Lowe" } ], "advisors": [ { "name": { "family": "Samson", "given": "Sten Otto" }, "id": "Samson-Sten-Otto", "role": "advisor", "display_name": "Samson, Sten Otto" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P2PA-7060", "abstract": "The crystal structures of three iodide-containing quasi-one-dimensional conductors, (tetrathiotetracene)2(iodide)3 (high disorder), tetrathiotetracene-iodide, and (hexamethylenetetraselenofulvalene)-(iodide)x were solved by single crystal X-ray diffraction methods. These three iodides are single charge-carrier conductors and allow a comparison of such competing effects as disorder, interchain coupling, and overlap.
\r\n\r\nThe crystal structure of metallic (tetrathiotetracene)2(iodide)3 (high disorder), TTT2I3 (h.d.), was solved at room temperature (~294\u00b0 K), 164\u00b0 K, 74\u00b0 K, and at 19\u00b0 K. At all four temperatures the lattice symmetry remained orthorhombic and the structures were successfully refined in the space group Cmca. During slow cooling the diffuse layer lines were also carefully monitored. In contrast to TTFC10.67, even with slow cooling the iodide chains do not three-dimensionally order, and there are no distortions in the TTT lattice to 19\u00b0 K. A model of the iodide chains is presented which explains the positions and intensities of the diffuse layer lines and also explains why three-dimensional ordering at low temperatures is not observed.
\r\n\r\nThe structure of semiconducting tetrathiotetracene-iodide (TTTI) was studied at room temperature. The structure consists of two ordered lattices which are incommensurate along \u2192c, the stacking axis. The unit cell dimensions for Lattice 1 (triclinic, C-l) are a = 13.028(2), b =\r\n16.445(2), c = 3.643(1) \u00c5 and \u03b1 = 90.81(1)\u00b0, \u03b2 = 96.11(1)\u00b0, and \u03b3 = 91 .11(1)\u00b0. For Lattice 2, c \u2243 4.78 \u00c5. The positions of all of the layer lines, including the two \u201csixth\u201d layer lines, which are observed on X-ray oscillation photographs of crystals of TTTI rotated about \u2192c, can be explained by the presence of two lattices. The measured density dm \u2243 2.09 g/cm3 and refinement of the [001] projection (hk0 reflections) confirmed that the overall stoichiometry is TTTI (1:1). For a complete data set collected with copper K\u03b1 radiation, the refinement of Lattice 1 converged to R = 0.102. For the 1132 reflections with Fo2 > 3\u03c3(Fo2), R = 0.081. The overlap between adjacent TTT cations in the same stack in TTTI is significantly different from that observed in TTT2I3 (h.d.). There is also very little interchain coupling in TTTI.
\r\n\r\nHexamethylenetetraselenofulvalene-iodide, HMTSF-Ix, is triclinic, P-l, with the unit cell parameters a = 8.056(4), b = 12.740(4), c = 8.016(3) \u00c5 and \u03b1 = 81.72(4)\u00b0, \u03b2 = 67.73(5)\u00b0, and \u03b3 = 102.64(4)\u00b0. For a complete data set of 4213 reflections collected with monochromatized molybdenum K\u03b1 radiation to 2\u03b8 = 60\u00b0 the structure refined to R = 0.097. For 2042 reflections with Fo2 > 3\u03c3(Fo2), R = 0.051. The hydrogen atoms were not located. There is disordered iodide and solvent at 1/2,1/2,1/2. The HMTSF cations stack along \u2192a. A new type of alternating overlap between adjacent HMTSF molecules was observed. The magnitude of the d.c. electrical conductivity at room temperature suggests that this phase of HMTSF-Ix is semiconducting.
\r\n\r\nThese iodide-containing structures show three different types of iodide behavior in quasi-one-dimensional conductors. In TTT2I3 (h.d.) the slip-stacking and large interchain coupling favor formation of a metallic state at high temperatures. At low temperatures the disordered iodide chains have a major effect on the transport properties by allowing states to exist in the semiconductor band gap. In TTTI the iodides are no longer disordered but still dominate the physical properties by causing a modulation of the TTT lattice. There is very little interchain coupling in TTTI. In HMTSF-Ix the iodide is probably of minor importance.
" }, { "name": "Moore, Hsiao-Ping Hsu", "degree": "PhD", "year": "1980", "title": "Correlation of Structure and Function of the Acetylcholine Receptor from Torpedo californica", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122025-230449808", "creators": [ { "name": { "family": "Moore", "given": "Hsiao-Ping Hsu" }, "id": "Moore-Hsiao-Ping-Hsu", "display_name": "Moore, Hsiao-Ping Hsu" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hz20-rb32", "abstract": "The interaction of a cholinergic depolarizing agent, bromoacetylcholine, with acetylcholine receptor enriched membrane fragments and Triton-solubilized, purified AcChR from T. californica has been studied. The reagent bound to membrane-bound AcChR reversibly with an apparent dissociation constant of 16 \u00b1 l nM at equilibrium. This 600 - fold higher affinity for the receptor than found from physiological studies (Kactivation \u224310 \u03bcM, Karlin (1973) Fed. Proc~ 32, 1847- 1853) can be attributed to a ligand induced affinity change of the membrane-bound receptor upon preincubation with bromoacetylcholine. At equilibrium [3H] bromoacetylcholine bound to half the number of a-bungarotoxin sites present in the preparation without apparent positive cooperativity and this binding was competitively inhibited by acetylcholine.
\r\nIn the presence of dithiothreitol [3H] -bromoacetylcholine irreversibly alkylated both membrane-bound and solubilized, purified acetylcholine receptor, with a stoichiometry identical to that for reversible binding. The labeling was inhibited by acetylcholine and \u221d-bungarotoxin. SDS-polyacrylamide gel electrophoresis of the labeled acetylcholine receptor showed that only the 40,000 dalton subunit contained the label. From these results it is concluded that the 40,000 dalton subunit represents a major component of the agonist binding site of the receptor.
" }, { "name": "Neilson, Paul Vincent", "degree": "Masters", "year": "1980", "title": "Electrochemistry of Polymer-Metal Complexes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052010-111723098", "creators": [ { "name": { "family": "Neilson", "given": "Paul Vincent" }, "id": "Neilson-Paul-Vincent", "display_name": "Neilson, Paul Vincent" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HS95-4691", "abstract": "Polymeric ligands, Polyethylenimine (PEI) and Chitosan, were studied for possible applications in the modification of electrode surfaces in relation to the three main goals:
\r\n\r\n1. metal ion scavenging
\r\n2. to find a system which catalyzes O2 reduction
\r\n3. understanding of electron transfer in polymer-metal films.
A-23187 is a calcium specific ionophore isolated from Streptomyces chartreusis. Syntheses of model\r\nsystems containing the 1, 7-dioxaspiro[5.5]undecane ring system and the total synthesis are discussed. Based on results from the total synthesis the absolute configuration of A-23187 is assigned.
\r\n\r\nA new ionophore, X-14547A, was recently discovered which, like A-23187, contains a pyrrole ketone subunit. Kew methodology designed to introduce the pyrrole unit via an N-protected 2-pyrrylcuprate is presented.
\r\n\r\nSee PDF of thesis for figure.
\r\n\r\n[6S*-{6\u03b1(2S*,3S*),8\u03b2(R*),9\u03b2,11\u03b1}]-5-(Methylamino)-2-[{3,9,11-trimethyl-8- |l-methyl-2-oxo-2-(1H-pyrrol-2-yl)-ethyl |-1,7-dioxaspiro[5.5]undec-2-yl}methyl]-4-benzoxazole-carboxylic acid.
" }, { "name": "Sailasuta Scott, Napapon", "degree": "PhD", "year": "1980", "title": "Spectroelectrochemical Studies of Metalloenzymes and Polymer-Coated Graphite Transparent Electrodes", "advisor": "Gray, Harry B.; Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202026-221839671", "creators": [ { "name": { "family": "Sailasuta Scott", "given": "Napapon" }, "id": "Sailasuta-Scott-Napapon", "orcid": "0000-0001-7611-9233", "display_name": "Sailasuta Scott, Napapon" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sz22-a066", "abstract": "Thermodynamic parameters of metalloprotein electron transfer reactions,\r\nnamely reduction potentials, enthalpies and entropies, are determined\r\nby means of spectroelectrochemical techniques. The studies\r\nconcentrate on blue copper protein (Rhus vernicifera stellacyanin,\r\nPhaseolus vulgaris plastocyanin and Pseudomonas aeruginosa azurin), and\r\nc-type cytochromes (horse heart cytochrome c, Pseudomonas aeruginosa\r\ncytochrome c-551 and cytochrome oxidase). The results show that within\r\nthe same class of metalloprotein studied, i.e., blue copper protein and\r\ncytochrome c, the observed enthalpy and entropy changes can be used as\r\ncriteria for determining solvent access of the metal centers. The more\r\naccess the metal center has to the solvent, the less negative enthalpy\r\nand entropy changes are associated with its reduction process. The\r\nincrease in solvent access of the metal center is in the order\r\ncytochrome cd < cytochrome c-551 ~ cytochrome c and azurin < plastocyanin\r\n< stellacyanin. The conclusions agree well with those from kinetic\r\nstudies.
\r\n\r\nThe reduction potentials of heme b5 of liver sulfite oxidase have\r\nbeen determined. The potentials of the intact enzyme and those in which\r\nthe molybdenum moeity has been removed are very similar, indicating that\r\nthere is no interaction such as to alter the reduction potential of heme\r\nb5 between the heme and molybdenum prosthetic groups. The reduction of\r\nthe heme b5 of chicken liver sulfite oxidase by Fe(EDTA)2- has also been\r\ninvestigated. The rate of electron transfer has been analyzed within\r\nthe framework of the relative Marcus theory of outer sphere electron\r\ntransfer. The electrostatic corrected self-exchange rate constant is\r\ntwo orders of magnitude greater than the corresponding value of cytochrome c\r\nindicating more accessibility of the heme of sulfite oxidase\r\nthan in those of cytochrome c. The activation parameters have also\r\nbeen determined. It is proposed that electron transfer mechanism employed\r\nby heme b5 of sulfite oxidase is very similar to that employed\r\nby cytochrome c, i.e., via exposed heme edge.
\r\n\r\nSpectroelectrochemical studies of the polymer-coated graphite\r\ntransparent electrodes have been performed. The amount of polymer\r\nadsorbed on electrode surface was determined spectrally. The rates of\r\nattachment and detachment of Ru(III)(EDTA) to and from the pyridine\r\ngroup on the polymer backbone were studied. It was found that reactivity\r\nof the formation and detachment of Ru(EDTA) complex was less than\r\nthe corresponding homogeneous reactions. The electrochemical properties\r\nof such electrodes were also reported.
" }, { "name": "Santilli, Don S.", "degree": "PhD", "year": "1980", "title": "Synthesis and Thermal Decomposition of CIS-3,4,5,6-Tetrahydropyridazine-3,4-d\u2082", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162026-224332678", "creators": [ { "name": { "family": "Santilli", "given": "Don S." }, "id": "Santilli-Don-S", "display_name": "Santilli, Don S." } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/az6w-hq89", "abstract": "Chapter I
\r\n\r\nThe stereospecific syntheses of cis-tetrahydropyridazine-\r\n3,4-d2 (6) and cis- and trans-cyclobutane-1,2-d2 are reported.\r\nThe thermal decomposition of cis-tetrahydropyridazine-3,4-\r\nd2 (6) (gas phase, 439\u00b0) affords 67.1 \u00b1 0.9% cis-ethylenel,\r\n2-d2, 16.1 \u00b1 0.8% trans-ethylene-1,2-d2, 9.4 \u00b1 0.4% ciscyclobutane-\r\n1,2-d2, 7.4 \u00b1 0.4% trans-cyclobutane-1,2-d2.\r\nThe relative rates of rotation, cleavage, and closure for\r\nthis 1,2-diazene generated tetramethylene-d2 are\r\nk(cleavage)/k(closure) = 2.2 \u00b1 0.2 and k(rotation)/\r\nk(closure = 12 \u00b1 3. An extra stereospecific cleavage component\r\n(46%) superimposed on the 1,4-biradical pathway (54%)\r\nfrom the parent tetrahydropyridazine was found, similar to\r\nthat observed in the 3,4-dimethyl-3,4,5,6-tetrahydropyridazine\r\nthermal reactions. Finally, the experimental data\r\nfor the parent 1,4-biradical, tetramethylene, are compared\r\nto calculated values in the literature.
\r\n\r\nChapter II
\r\n\r\nThe gas phase pyrolysis of 3,3,4,4-tetramethyldiazetine\r\nhas been performed in the inlet system of a photoelectron\r\nspectrometer. By analysis of the observed internal energy\r\ncontent of the nascent nitrogen and 2,3-dimethyl-2-butene\r\nproducts, estimates on the limits of the amount of reaction\r\nexothermicity released to vibration of the nitrogen\r\nfragment could be made. It appears that nitrogen acquires\r\nvery little of the available energy and the implications of\r\nthis result are discussed in terms of a model which has been\r\nproposed for distinguishing concerted and stepwise decomposition\r\nof azo compounds.
" }, { "name": "Scheller, Richard Henry", "degree": "PhD", "year": "1980", "title": "Studies of Cloned Repetitive DNA Sequences in the Sea Urchin Genome", "advisor": "Davidson, Eric H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11052004-110125", "creators": [ { "name": { "family": "Scheller", "given": "Richard Henry" }, "id": "Scheller-Richard-Henry", "display_name": "Scheller, Richard Henry" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "advisor", "display_name": "Davidson, Eric H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3X73-XY07", "abstract": "The sequence organization, evolution, and transcription of cloned repetitive DNA elements in sea urchin were studied.
\r\n\r\nTotal S. purpuratus DNA was reassociated such that only the reiterated sequences were duplex. The flanking single-stranded DNA was digested with S1 nuclease and synthetic Eco RI sites were ligated to the ends. These molecules were cloned in RSF2124 and recombinants were selected by their Amp+Col- phenotype. These clones ranged in reiteration frequency from 3 to 12,000 copies per haploid genome. The mean intrafamilial divergence was as low as 4[degrees]C for some families which could be attributed entirely to polymorphism. Other families contained members that showed greater divergence, some as high as 25\u00b0C.
\r\n\r\nNine randomly selected sequences were found to be transcribed in oocyte RNA, gastrula hnRNA, and intestine hnRNA. The concentrations of these transcripts are tissue specific and unlike single copy sequences both strands were represented in the RNAs. The transcripts were longer than the repetitive elements themselves indicating linkage to single copy sequences.
\r\n\r\nThe number of copies per haploid genome was determined in S. franciscanus and L. pictus in addition to the parent species. The ratio of the reiteration frequency in S. purpuratus to S. franciscanus ranged from about 20 to 1. The copies remaining in S. franciscanus and L. pictus genomes were, however, conserved relative to average single copy DNA sequence.
\r\n\r\nThe plasmid clones were used to select individual family members from total genomic [lambda] libraries and their characteristics were investigated. Families 2034 and 2108 were found to be members of the long repetitive sequence class. The 2034 elements exist in clustered arrays while the 2108 family is dispersed. The 2109 elements were shown to be largely of the short repetitive class, however, about 10% of the members occur in long repetitive regions.
\r\n\r\nThe interspersed elements were found to be flanked by low reiteration frequency or single copy sequences. Thus, a large number of genomic regions are physically linked via the 2109 repetitive sequences. The implications of these findings with respect to evolution and gene regulation are many-fold and are discussed in detail in the following chapters.
" }, { "name": "Scott, Robert Allen", "degree": "PhD", "year": "1980", "title": "Metalloprotein Electron Transfer. Cytochrome aa\u2083 Reduction Kinetics and Theoretical Formulation of Distance Dependence", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302026-221600061", "creators": [ { "name": { "family": "Scott", "given": "Robert Allen" }, "id": "Scott-Robert-Allen", "orcid": "0000-0003-2236-1336", "display_name": "Scott, Robert Allen" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/j4fy-6v83", "abstract": "The kinetics of anaerobic reduction of beef heart mitochondrial\r\ncytochrome c oxidase (cytochrome aa3) by hexammine\r\nruthenium(II) (RuA62+) were measured. At wavelengths in the\r\nSoret and at 605 nm the kinetics are biphasic, neither phase\r\nexhibiting (pseudo-)first order behavior. A complete nonlinear\r\noptimization analysis showed that the slow phase obeyed\r\nstrict second order kinetics, the fast phase being apparently\r\nmore complex. Kinetic difference spectra observed for the\r\nRuA62+ reduction of native and cyanide-treated enzyme clearly\r\ndemonstrate that the fast phase is due to reduction of cytochrome\r\na3+ while the slow phase is due to reduction of a33+.\r\nThe slow phase is independent of RuA62+ concentration with a\r\nsecond order rate constant of (1.04 \u00b1 .06) x 105 M-1-s-1 (25\u00b0C)\r\nand activation parameters \u25b3H\u2260 = 16.6 \u00b1 0.6 kcal-mol-1, \u25b3S\u2260=\r\n+20.2 \u00b1 2.0 cal-deg-1-mol-1 (pH = 6.0 (cacodylate), \u03bc = 0.10 M)\r\nfor native aa3. The oxidized-cyanide derivative gave a second order rate\r\nconstant of (1.99 \u00b1 .06) x 104 M-1-s-1 (pH = 6.0 (cacodylate), \u03bc =\r\n0.10 M, 25\u00b0C). Analysis of the fast phase as a second order\r\ndecay gave temperature-independent second order rate constants\r\nwhich are linearly dependent on RuA62+ concentration. The\r\nthird order rate constant from this fit is (1.68 \u00b1 .02) x 1011\r\nM-2-s-1 (pH = 6.0 (cacodylate), \u03bc = 0.10 M, 25\u00b0C). The second\r\norder slow phase is interpreted as involving intermolecular\r\nelectron transfer between half-reduced (cytochrome a reduced)\r\nspecies in reduction of cytochrome a3.
\r\n\r\nA detailed description of the nonlinear least squares\r\noptimization techniques used for analysis of the cytochrome\r\naa3 kinetics is given along with a general description of a\r\ncomplete kinetics analysis computer routine package. Emphasis\r\nis placed on correct error analysis and weighting procedures.
\r\n\r\nIn addition, a theoretical description of the dependence\r\nof the rate of metalloprotein electron transfer on the distance\r\nover which the transfer must occur is presented. The\r\nexponential dependence of rate on distance derived in several\r\ntheoretical formulations of electron tunneling in biological\r\nsystems is assumed and several known cases of metalloprotein\r\nelectron transfer with small molecule reagents are examined\r\nto determine the distance of transfer. The results are compared\r\nwith known structural data and discussed in terms of\r\nthe accessibility of protein metal sites to external reagents.
" }, { "name": "Strader, Catherine Boxley Devine", "degree": "PhD", "year": "1980", "title": "Investigations of the Structural Properties of the Acetylcholine Receptor and its Polypeptide Subunits from Torpedo Californica", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102025-234919185", "creators": [ { "name": { "family": "Strader", "given": "Catherine Boxley Devine" }, "id": "Strader-Catherine-Boxley-Devine", "display_name": "Strader, Catherine Boxley Devine" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n480-zm70", "abstract": "Microsequence analysis of the four polypeptide subunits of the acetylcholine receptor from Torpedo californica electroplax was performed and demonstrated a striking amino acid homology among these four chains. Further sequence analysis of both membrane-bound and Tritonsolubilized,\r\nchromatographically purified receptor was used to measure the stoichiometry of the subunits. The values determined for the two preparations of receptor were the same: the ratio of the four subunits (40,000: 50,000:60,000:65,000 daltons) is 2:1:1:1, indicating a value of255,000 daltons for the molecular weight of the receptor, in agreement with experimentally determined values. These results demonstrate that the acetylcholine receptor is a pentamer composed of five subunits, two being identical and the other three being structurally related to them by sequence homology. Genealogical analysis suggests that divergence from a common ancestral gene occurred early in the evolution of the receptor. This shared ancestry argues compellingly that each of the four subunits plays a functional role in the receptor's physiological action." }, { "name": "Thaisrivongs, Suvit", "degree": "PhD", "year": "1980", "title": "The Total Synthesis of Lasalocid A", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212025-183359737", "creators": [ { "name": { "family": "Thaisrivongs", "given": "Suvit" }, "id": "Thaisrivongs-Suvit", "display_name": "Thaisrivongs, Suvit" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1y06-c253", "abstract": "A total asymmetric synthesis of the \"right half ketone\"\r\nof the stereo-complex polyether antibiotic, lasalocid A, is\r\ndescribed. The [3,3] sigmatropic rearrangements of 0-silylketene\r\nacetals derived from esters of 1,4-anhydro-pent-1-enitols\r\n(furanoid glycals) and 1,5-anhydro-hex-1-enitols (pyranoid glycals)\r\nprovided \u03b1-substituted-2,5-dihydrofuran-2-acetic acid and\r\n\u03b1-substituted-5,6-dihydro-2H-pyran-2-acetic acid derivatives.\r\nThe products are key structural elements which are present in\r\npolyether antibiotics. The furanoid and pyranoid glycals were\r\nconveniently prepared by reductive fragmentation of 2,3-0-(1-methylethylidene)-\r\nfuranosyl and pyranosyl chlorides. The synthetic\r\nscheme is highly convergent, utilizing a building-block\r\napproach with stereo- and regioselective carbon-carbon bond\r\nformation between the subunits." }, { "name": "Threlkel, Richard S.", "degree": "PhD", "year": "1980", "title": "Early Transition Metal Organometallic Reactivity. Catalytic Acetylene Hydrogenation and Dimerization. Carbene Migratory Insertion Reactions", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-222717548", "creators": [ { "name": { "family": "Threlkel", "given": "Richard S." }, "id": "Threlkel-Richard-S", "display_name": "Threlkel, Richard S." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ay0x-zs17", "abstract": "[Not transcribed]" }, { "name": "Tiefenbruck, Grant Fred", "degree": "PhD", "year": "1980", "title": "The Translational Motion of Particles in a Viscoelastic Liquid", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-10302006-092427", "creators": [ { "name": { "family": "Tiefenbruck", "given": "Grant Fred" }, "id": "Tiefenbruck-Grant-Fred", "display_name": "Tiefenbruck, Grant Fred" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/65jz-qx04", "abstract": "The translational motion of two different particles at low Reynolds number in a viscoelastic liquid is studied. The first study is an experimental investigation of the motion of a slender rod near a vertical wall. When the rod is not too near the wall, its motion is found to be in qualitative agreement with theoretical solutions for the motion of a rod in an unbounded second-order fluid. When the rod is nearer to the wall, its motion is shown to correspond qualitatively to a simple superposition of the motion in an unbounded second-order fluid and the motion in a Newtonian fluid near a vertical wall.\tThe second study is a numerical solution of the equations governing the motion of a solid sphere and a spherical bubble in a viscoelastic fluid of infinite extent. The computed solutions are compared with analytic solutions obtained by asymptotic methods. It is found that many quantities are described quite well by the asymptotic theory considerably beyond the expected range of validity. Many features of the flow can be described by the model fluid behavior in shear and extensional flows." }, { "name": "Upton, Thomas Hallworth", "degree": "PhD", "year": "1980", "title": "Theoretical Studies of Chemisorption Processes on Nickel Surfaces", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-140133915", "creators": [ { "name": { "family": "Upton", "given": "Thomas Hallworth" }, "id": "Upton-Thomas-Hallworth", "display_name": "Upton, Thomas Hallworth" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bvbb-m935", "abstract": "Part I: Generalized Valence Bond and Configuration Interaction calculations are reported for the zero valent nickel complexesNiC_2H_2, NiC_2H_4, Ni_2C_2H_4, and Ni_2C_2H_2. It is found that the NiC_2H_2 and NiC_2H_4 a coordination complex is formed in which the ligand \u03c0 orbital delocalizing into an empty Ni 4sp orbital. The 4s^13d^9 configuration of the Ni atom is stabilized. Bond energies of 16.7 and 14.2 kcal are found for the two complexes, respectively. In both complexes, the ligand is very weakly distorted, a result that is supported by complementary experimental data characterizing the IR and UV-visible spectral properties of NiC_2H_4 and thNi_2C_2H_4 \u03c0-complex.\r\n\r\nAcetylene is coordinated to Ni_2 in both di-\u03c3 and di-\u03c0 bonded form, for which bond energies of 23 and 60 kcal (relative to C_2H_2 + 2Ni) are found, respectively.\r\n\r\nConfiguration interaction calculations are also reported characterizing all ligand valence ionization levels for theNiC_2H_2, NiC_2H_4 and Ni_2C_2H_2 complexes. Excellent agreement is found between the UPS results for chemisorbed ethylene and the NiC_2H_4 calculated spectrum. \"Bonding shifts\" are found to result from a differential screening effect.\r\n\r\nPart II: Extensive generalized valence bond (GVB) and configuration interaction calculations (POL-CI) have been carried out for the lowest states of Ni_2 and Ni_2^+ for bond lengths from 1.6 to 4.0 \u00c5. The six lowest states of Ni_2 are found to be essentially degenerate with an average equilibrium bond length r_e = 2.04 \u00c5 and D_e = 2.92 eV. A ^4\u03a3^+_g ground state is found for the ion with a bond length R_e = 1.96 \u00c5 and dissociation energy D_e = 4.14 eV. The bonding of Ni is dominated by the interactions of the 4s orbital on each Ni with each Ni of Ni_2 corresponding to a (4s)^1(3d)^9 configuration. The lowest states lead to singly occupied \u03c3 orbitals on each center with other 3d occupations leading to 100 electronic states within about 1.0 eV of the ground state.\r\n\r\nHartree-Fock calculations are also reported, characterizing the low-lying states of an Ni_8 cluster. It is found that the 4s^13d^9 valence configuration of the Ni atom is strongly stabilized, and that here too, the 3d orbitals remain localized and are of secondary importance in the bonding.\r\n\r\nAs a result of these findings, further first principles calculations have been carried out characterizing the \"conduction band\" properties of high and low symmetry clusters up to Ni_(87). Macroscopic properties [ionization potential (IP), electron affinity (EA), bandwidth, and cohesive energies are not sensitive to cluster geometry, and except for EA, show definite convergence towards the bulk limit by Ni_(87) .\r\nEven for Ni_(87), the EA is over 2.5 eV smaller than the IP, and the origin of this effect is discussed.\r\n\r\nPart III: First Principles Hartree-Fock and Generalized Valence Bond Calculations are reported for the bonding of atomic H, Cl, Na, 0, and S on high symmetry sites of the Ni(100) face using an Ni_(20) cluster as a model. All of the adsorbates are found to prefer the fourfold site, with bond energies (D_e) of 3.04, 4.9, 1.3, 3.63, and 4.34 eV, respectively. Bond distances are 0.78, 1.38, 2.7, 0.88, and 1.24 \u00c5 above the surface, which are (except for Na) in excellent agreement with available experimental data. Vibrational frequencies of 73, 17, 30, 46, and 37 meV are found for each adsorbate, respectively. Decreasing site coordination is found to uniformly increase vibrational frequencies, and bond distances while decreasing bond energies. The data are analyzed through the introduction of the concepts of site acidity and basicity, and it is found that site basicity increases with increasing coordination. This trend is responsiale for the observed preference of each adsorbate for high coordinate sites, and it is expected that donor adsorbates (such as CO) would show a reverse trend. The data for Na are found to be in poor agreement with the analogous bulk data, confirming the prediction from Part II.0 that small particles should behave differently from the bulk when bonded to highly electropositive species.\r\n\r\nPart IV: A technique is presented for carrying out ab initio Hartree-Fock calculations on systems of infinite three-dimensional periodicity. The method represents an adaptation of standard molecular basis set expansion techniques and fully utilizes translational and point group symmetry to simplify the calculations. It is shown that the expression for total energy may be written as a sum of pairwise interactions between neutral charge units consisting of a nucleus and a localized compensating electronic charge. The resulting sums are rapidly convergent. The technique is illustrated with sample calculations on face-centered cubic lattices of hydrogen, lithium, and sodium. Generalization to systems of lower symmetry is discussed.\r\n" }, { "name": "Watson, Albert Theodore", "degree": "PhD", "year": "1980", "title": "Estimation of Two-Phase Petroleum Reservoir Properties", "advisor": "Seinfeld, John H.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10102006-104201", "creators": [ { "name": { "family": "Watson", "given": "Albert Theodore" }, "id": "Watson-Albert-Theodore", "display_name": "Watson, Albert Theodore" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/004X-2856", "abstract": "The estimation of petroleum reservoir properties on the basis of production rate and pressure observations at the wells is an essential component in the prediction of reservoir behavior. The reservoir properties to be estimated appear as parameters in the partial differential equations describing the flow of fluids in the reservoir. The estimation of these properties is referred to variously as the inverse or identification problem or as history matching. In this dissertation, new results have been obtained pertaining to the estimation of petroleum reservoir properties.\r\n\r\nMost of the prior analysis of the reservoir parameter estimation problem has been confined to reservoirs containing a single fluid phase, e.g., oil. We consider here reservoirs that contain two fluid phases, e.g., oil and water. The parameters to be estimated in such a case are the porosity and permeability, which depend on spatial location, and the saturation-dependent relative permeabilities. In this work we treat two basic problems in reservoir parameter estimation: (1) establishing the ability to estimate the desired parameters (so-called identifiability), and (2) developing and testing a new algorithm, based on optimal control theory, to carry out the estimation.\r\n \r\nIn regard to problem (1), we have extended the classic analytical (Buckley-Leverett) solution for incompressible flow to heterogeneous reservoirs. Analysis for an incompressible water flooding situation shows that the spatially varying properties at locations behind the saturation front have an effect on the pressure solution. The spatially varying properties can be uniquely determined based on data taken up to the time of water breakthrough. Only an integral value of the porosity can be determined from the water-oil ratio data alone; however, the spatially varying porosity may be determined when the initial saturation varies with location. The values of the relative permeabilities which are identifiable, and the information about the relative permeabilities obtained for other intervals of saturation, is established. Analytical expressions are derived for the sensitivity of the pressure and water-oil ratio observations to parameters appearing in functional forms of the relative permeabilities. When the relative permeabilities are represented as exponential functions, the coefficients and exponents can be uniquely determined.\r\n\r\nFor problem (2), an algorithm is developed for the estimation of porosity, permeability and the relative permeabilities for two-phase, compressible reservoirs. This work represents the first study for which relative permeabilities have been estimated based on a model generally used to represent fluid flow in petroleum reservoirs. An objective function, composed of the weighted sum of squares of the deviations between the observed and calculated values of pressure and water-oil ratio, is minimized by a first-order gradient method based on optimal control theory. The algorithm is tested for one and two-dimensional hypothetical water floods. The algorithm performed well for problems in which the porosity, permeability and relative permeability exponents were simultaneously estimated. The increase from one to two spatial variables does not appear to change the properties of the estimation problem. Small observation errors are shown not to significantly affect the convergence of the estimates." }, { "name": "White, Mary Ann", "degree": "PhD", "year": "1980", "title": "The Formation of Carbon-Carbon and Carbon-Nitrogen Bonds Mediated by Organometallic Cobalt Complexes", "advisor": "Bergman, Robert G.; Grubbs, Robert H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192024-221442048", "creators": [ { "name": { "family": "White", "given": "Mary Ann" }, "id": "White-Mary-Ann", "display_name": "White, Mary Ann" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." }, { "name": { "family": "Grubbs", "given": "Robert H." }, "id": "Grubbs-R-H", "orcid": "0000-0002-0057-7817", "role": "advisor", "display_name": "Grubbs, Robert H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mtgw-1g08", "abstract": "Binuclear cobalt complexes of the general formula\r\n[CpCo(CO)R]2 (Cp = \u019e5 C5H5) have been prepared and the reactivity of\r\nthese complexes has been investigated. Thermal decomposition of\r\n[CpCo(CO)(CH3)]2 in a variety of organic solvents leads to good yields\r\nof acetone (a process involving the formation of two new carbon-carbon\r\nbonds). The mechanism of this decomposition and that of analogous\r\ncomplexes where R = CH3CH2 and CF3CH2 has been elucidated. The\r\ncarbonylation reactions of these complexes have also been examined.
\r\n\r\nThe reaction of either CpCo(CO)2 or [CpCo(NO)]2 with NO and a\r\nvariety of olefins yields cobalt complexes containing 1, 2-dinitroso\r\nligands which are derived from the alkene substrate. Thus two new\r\ncarbon-nitrogen bonds are formed. The scope of this reaction is\r\nsurveyed and methods for removal of the 1, 2-dinitroso ligand, with the\r\nnewly formed carbon-nitrogen bonds intact, are investigated.
" }, { "name": "Abe, Amy", "degree": "PhD", "year": "1979", "title": "I. Structural Analysis Using \u00b9\u2075N NMR Spectroscopy II. An Investigation of the Interaction of Grignard Reagents with Mesityl Ketones", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012018-155039057", "creators": [ { "name": { "family": "Abe", "given": "Amy" }, "id": "Abe-Amy", "display_name": "Abe, Amy" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "chair", "display_name": "Ireland, Robert E." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "member", "display_name": "Richards, John H." }, { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "member", "display_name": "Dervan, Peter B." }, { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "member", "display_name": "Dickerson, Richard E." } ], "option_major": [ "chemistry" ], "doi": "10.7907/m0ya-bx45", "abstract": "PART I. Structural Analysis Using 15N NMR Spectroscopy
\r\n\r\nThe proton-coupled, natural-abundance 15N NMR spectra of three series of compounds were examined with emphasis on obtaining conformational, structural and configurational data.
\r\n\r\nAmino acids and peptides. Chemical shifts of aliphatic amino acids and glycyl dipeptides followed typical \u03b1, \u03b2, and \u03b3-substituent effects. Vicinal 15N\u03b1, H\u03b2 coupling constants were obtained for seven amino acids and Gly-X dipeptides which possess ~ither a single or three equivalent \u03b2-protons. Average vicinal couplings were obtained for amino acids with diastereotopic \u03b2-protons. Conformational preferences for the rotamers about the C\u03b1 - C\u03b2 bond of threonine and allothreonine were found by extending the traditional Pachler analysis to allow for interaction among substituents through treating both population and torsion angle as variables. Hydrogen-bond formation between the hydroxyl and the carboxylate was favored over that between the hydroxyl and nitrogen for both amino acids.
\r\n\r\nBiotin. The proton on the N1' nitrogen of biotin exchanges more readily with solvent than that on the sterically-hindered N3' nitrogen. The order of exchange was established through correlation of the nitrogen NMR resonances with the ureido proton resonances by variable single-frequency decoupling of the ureido protons and through assignment of the proton spectrum by homonuclear-decoupling experiments. Assignment of the nitrogen resonances in biotin (N1' = 285.6 ppm and N3' = 294.7 ppm) and desthiobiotin (N1' = 279.3 ppm and N3' = 285.0 ppm) was achieved with the aid of single-frequency, proton-decoupled nitrogen resonances with partial NOE.
\r\n\r\nOximes. The large difference between two-bond 15N, H\u03b1 coupling constants for the E- and Z-isomers of the oximes allows the configurations of aldoximes to be assigned from geminal couplings obtained from the 15N NMR spectra and also the configuration of O-alkylaldoximes from nitrogen spectra in which the protons on the alkyl group are selectively decoupled.
\r\n\r\nPART II. An Investigation of the Interaction of Grignard Reagents with Mesityl Ketones
\r\n\r\nThe reaction of acetomesitylene with benzyl Grignard reagent was reinvestigated because of uncertainty in the mechanism and site of addition of the benzyl moiety. The addition product was identified as mesitylmethylbenzylcarbinol as is consistent with a \"normal\" addition to the ketone proceeding through an initial ketone-Grignard reagent complex.
" }, { "name": "Allison, Judith Lee", "degree": "PhD", "year": "1979", "title": "An Investigation into the Bonding of Copper(I) Macrocycles to Fifth Ligands", "advisor": "Gagn\u00e9, Robert R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04042026-194836204", "creators": [ { "name": { "family": "Allison", "given": "Judith Lee" }, "id": "Allison-Judith-Lee", "display_name": "Allison, Judith Lee" } ], "advisors": [ { "name": { "family": "Gagn\u00e9", "given": "Robert R." }, "id": "Gagn\u00e9-R-R", "role": "advisor", "display_name": "Gagn\u00e9, Robert R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yz9j-9e70", "abstract": "The properties and reactivities of an unusual copper(I) macrocyclic complex have been investigated. The complex, Cu(LBF2) ([l,l-difluoro- 4,S,ll,12-tetramethyl-l-bora-3,6,10,13-tetraaza-2,14-dioxo-cyclo-tetradeca-3,S,10,12-tetraenato]copper(I)), reacts with carbon monoxide to form an isolable complex, Cu(LBF2)CO. The crystal structure of Cu(LBF2)CO, which was previously determined, shows a square-pyramidal geometry around copper(I) with an apical carbon monoxide and four basal nitrogens.
\r\n\r\nThe crystal and molecular structure of the four-coordinate complex, Cu(LBF2), was determined. The copper binds to the four nitrogens of the macrocycle in a distorted square-planar array. The nitrogens are twisted toward a tetrahedron with resulting dihedral angles of 23 and 27\u00b0 between the two sets of planes defined by copper and two adjacent nitrogens. The amount of the tetrahedral distortion is limited by the macrocycle's steric limitations.
" }, { "name": "Baillargeon, David Joseph", "degree": "PhD", "year": "1979", "title": "Oxy Anion-Accelerated Rearrangements", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05012015-142954149", "creators": [ { "name": { "family": "Baillargeon", "given": "David Joseph" }, "id": "Baillargeon-David-Joseph", "display_name": "Baillargeon, David Joseph" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9M01-KJ80", "abstract": "The alkali metal salts of 1,5-hexadien-3-ols undergo\r\naccelerated Cope rearrangements to the enolates of \u03b4, \u03b5-unsaturated\r\ncarbonyl compounds. The generality of the\r\nrearrangement was investigated in numerous systems,\r\nparticularly acyclic cases, and the effect of changes in\r\nsubstituents, counterions, solvents, and geometrical\r\nstructures were noted and discussed. Applications of\r\nthis methodology in synthesis included the synthesis of\r\nthe insect pheromone frontalin, the preparation of\r\nselectively monoprotected 1,6-dicarbonyl compounds from\r\n4-methoxy- and 4-phenylthio-1,5-hexadien-3-ols, and the\r\nconstruction of complex ring structures such as a D-homo-estratetraenone\r\nderivative.
\r\n\r\nThermochemical estimates of the energetics of anionpromoted\r\nalkoxide fragmentations were made, and in all\r\ncases heterolytic cleavage was favored over hemolytic\r\ncleavage by 8.5-53 kcal/mol. The implication of these\r\nand other thermochemical estimates is that the anionic\r\noxy-Cope rearrangement occurs via a concerted mechanism\r\nrather than a dissociation-recombination process. The\r\nconcepts of anion-induced bond weakening were successfully\r\napplied to an accelerated [1,3]-shift of a dithiane fragment\r\nin a cyclohexenyl system. Trapping experiments\r\ndemonstrated that > 85% of the [1,3]-shift occurred within\r\na solvent cage. Attempts at promoting an intramolecular\r\nene reaction using the potassium salts of 2,7-octadien-1-o1\r\nand 2,8-nonadien-1-o1 were unsuccessful. A general review\r\nof anion-promoted bond reorganizations and anion substituent\r\neffects is also presented.
" }, { "name": "Bencala, Kenneth Edward", "degree": "PhD", "year": "1979", "title": "I. Linear Distributed Parameter Filtering: Observation Processes and Boundary Conditions for Engineering Systems. II. Statistical Analysis of Air Pollutant Observations and Model Predictions", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02172026-231434100", "creators": [ { "name": { "family": "Bencala", "given": "Kenneth Edward" }, "id": "Bencala-Kenneth-Edward", "display_name": "Bencala, Kenneth Edward" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/r2fc-1237", "abstract": "Part I
\r\n\r\nThe linear distributed parameter filtering problem is considered\r\nfor systems of engineering interest. In particular, the boundary conditions\r\nand observation processes considered represent those encountered\r\nin practice. The intent is to consolidate the theoretical results relevant\r\nto engineering applications and to provide a unified structure to\r\nfacilitate implementation of these results through a complete and consistent\r\nset of formal derivations. When necessary, previous results are\r\nextended.
\r\n\r\nThe types of observation processes considered are
\r\n\r\n- continuous time, discrete space
\r\n\r\n- discrete time, discrete space.
\r\n\r\nThe discrete time case includes both instantaneous and limited time\r\naverage observations. And the discrete space case includes both pointwise\r\nand integral observations. Based on the orthogonal projection lemma,\r\nthe minimum variance estimate is derived.
\r\n\r\nTo examine the effect of stochastic boundary conditions, second\r\norder systems with mixed and Dirichlet boundary conditions\r\nare considered.
\r\n\r\nPart II
\r\n\r\nAspects of air quality analysis that must be characterized with\r\nstatistical methods are considered. The evaluation of air quality models\r\nis considered in detail . First, an evaluation framework is developed.\r\nThe significance of evaluations of validity, accuracy and efficiency are\r\ndiscussed. Then, the specific aspect of accuracy assessment is addressed.\r\nThe emphasis is placed on practical and objective methods. An extensive\r\npackage of specific methods is set forth for use with air quality models.\r\nThe package has been coded in FORTRAN. A description of the code is\r\nincluded.
\r\n\r\nIn an attempt to increase the understanding of characterizations of\r\nlong-term data, observed frequency distributions of air pollutant concentration\r\nlevels are critically analyzed with respect to their statistical\r\ndescription. It is demonstrated that several common distributions\r\ncan be used to fit observed data, one of which is the popular log-normal\r\ndistribution. The observation that concentration distributions for all\r\naveraging times are approximately log-normal can be explained if the\r\nshort averaging time data are themselves assumed to be log-normally distributed.\r\nThe near log-normality of pollutant concentration frequency\r\ndistributions can be explained on the basis of the near log-normality of\r\nwind speed distributions, although this explanation does not establish\r\nthat wind speed distributions are solely responsible for observed concentration\r\ndistributions. It is concluded that pollutant concentration\r\nfrequency distributions are the result of complex phenomena and cannot be\r\npredicted exactly, but that the approximate log-normal character of the\r\ndistributions is useful from a practical point of view and can be understood\r\nqualitatively on the basis of the relation between wind speed and\r\nconcentration.
" }, { "name": "Berg, Beckie E.", "degree": "Masters", "year": "1979", "title": "Carbon Monoxide Reduction by Sixteen Electron d-Zero Tantalum Complexes. Acrylonitrile Cyclodimerization by Tris(triphenylphosphine) Tetramethylene Ni(II)", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-082613027", "creators": [ { "name": { "family": "Berg", "given": "Beckie E." }, "id": "Berg-Beckie-E", "display_name": "Berg, Beckie E." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qqt5-e721", "abstract": "[Part I] The sixteen electon, d-zero complexes Ta(COT)Me_3 and (\u03b7^5-C_5Me_5)Ta(C_3H_5)Me_3 were prepared and treated with carbon monoxide. The prep of Ta(COT) Me_3 gave irreproducibly small yields and upon treatment with CO paramagnetic material was observed. The prep of (\u03b7^5-C_5Me_5)Ta(C_3H_5)Me_3 resulted in yellow crystals in a red oil and these could not be separated.\r\n(\u03b7 ^5C_5Me_5)Ta(C_3H_4Me)Me_3 was then made. This complex decomposes to the trimethylene methane species (\u03b7^5-C_5Me_5)Ta(C_3H_3Me)Me_2, and upon treatment with CO gave an unknown white solid product.\r\n\r\n[Part II] Tris(triphenylphoshine) tetramethylene Ni(II) was made and treated with acrylonitrile. 1, 2 dicyanocyclobutane was produced\r\nin a cis:trans mixture of 45:55 and was isolated by preparative GC. The product was rarely observed and the reaction of nickel metallocycle with acrylonitrile was not catalyzed by acid, base, or Ni(O)." }, { "name": "Burum, Douglas Peter", "degree": "PhD", "year": "1979", "title": "Nuclear Spin Dynamics and Thermodynamics of Pulsed NMR in Solids", "advisor": "Vaughan, Robert W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04302007-153624", "creators": [ { "name": { "family": "Burum", "given": "Douglas Peter" }, "id": "Burum-Douglas-Peter", "display_name": "Burum, Douglas Peter" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "appliedphys" ], "doi": "10.7907/MF8E-RD37", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe investigations presented in this thesis deal with two basic topics of solid state NMR: coherent averaging of nuclear spin interactions by rf irradiation, and the application of thermodynamics in strongly time dependent interaction frames. In each case new theoretical insights are presented, and these lead to the development of new experiments.\r\n\r\nAfter a general introduction, an extension of coherent averaging theory called the principle of pulse cycle decoupling is presented. This principle greatly facilitates the design and analysis of compound experiments, i.e. techniques which are combinations of several smaller experiments. A number of multiple pulse experiments are analyzed using pulse cycle decoupling and several new techniques are introduced, including 24-pulse and 52-pulse cycles which have a greater ability to resolve anisotropic chemical shifts in solids than any experiment previously developed. The 52-pulse cycle is used to measure proton chemical shift spectra for polycrystalline ice, C6H12, C5H10 and polyethylene. This new technique is also used to study proton chemical shifts in single crystals of gypsum, [...].\r\n\r\nThe second topic considered in this thesis is the application of thermodynamics to NMR experiments in which the amplitude of the applied rf irradiation is varied in a strongly non-adiabatic fashion. Sources of artificial spin heating are analyzed and methods of eliminating these effects are demonstrated. A calculation is presented of the spin-lattice relaxation time during one basic type of multiple pulse irradiation. Techniques based on this calculation are introduced which measure relaxation times in the laboratory frame, [...], and the rotating frame, [...]. A method for determining the first moment of an NTIR spectrum is also developed. These new techniques are demonstrated using a variety of materials, including CaF2 and C6F6.\r\n\r\nA simple yet highly flexible pulse sequence generator which is capable of producing all the pulse sequences described in this thesis as well as many more complicated experiments is described in the Appendix." }, { "name": "Carter, Boyd Jay", "degree": "PhD", "year": "1979", "title": "The Substitution Kinetics and Electronic Absorption Spectroscopy of Some Molybdenum and Tungsten Bis-Dinitrogen Complexes", "advisor": "Bercaw, John E.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02042026-163248982", "creators": [ { "name": { "family": "Carter", "given": "Boyd Jay" }, "id": "Carter-Boyd-Jay", "display_name": "Carter, Boyd Jay" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tt5j-me28", "abstract": "The electronic absorption spectra of ttans-[M(N2)2(dpe)2],\r\ntrans-[Mo(N2)(RCN)(dpe)2], and cis-[M(N2)2(PMe2Ph)4] (M = Mo, W;\r\ndpe = (C6H5)2PCH2CH2P(C6H5)2; PMe2Ph = P(CH3)2C6H5) were measured\r\nand assigned. All of the charge transfer (CT) transitions were\r\nmetal-to-ligand CT transitions. The lowest energy CT transition\r\nin each spectrum was assigned as a M \u2192 Pd\u03c0 CT transition, and\r\nthe low energy shoulders on this transition were assigned as\r\nligand field transitions. The highest energy CT transition was\r\nassigned as a M \u2192 N2\u03c0* CT transition in each case.
\r\n\r\nThe kinetics and mechanisms for the substitution of nitriles\r\nfor dinitrogen in trans-[M(N2)2(dpe)2] and cis-[M(N2)2(PMe2Ph)4]\r\nwere studied. In the reaction of trans-[Mo(N2)2(dpe)2] with\r\nnitriles, one dinitrogen was replaced by a nitrile. All of\r\nthe kinetic data support an SN1 dissociative mechanism. The\r\nanalogous reaction with trans-[WN2)2(dpe)2] was found to proceed\r\nonly photochemically, with the loss of one dinitrogen induced\r\nby population of the 1,3Eg state. In the reactions of cis-\r\n[M(N2)2(PMe2Ph)4] with nitriles, both dinitrogen ligands were\r\nreplaced by nitriles. The reaction mechanism for both compounds\r\nconsists of two consecutive SN1 dissociative steps.
\r\n\r\nThe reactions of cis-[W(N2)2(C6H5CN)(PMe2Ph)4], cis-\r\n[W(C6H5CN)2(PMe2Ph)4], and trans-[Mo(N2)(C6H5CN)(dpe)2] with\r\nanhydrous HCl were also studied. The reaction of the latter\r\ncompound with HCl to yield [Mo(Cl)(N2H2)(dpe)2] was particularly\r\nnoteworthy.
" }, { "name": "Chan, Chi Ming", "degree": "PhD", "year": "1979", "title": "A Theoretical and Experimental Investigation of Surface Structures and Gas-Surface Interactions", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:04242026-224520918", "creators": [ { "name": { "family": "Chan", "given": "Chi Ming" }, "id": "Chan-Chi-Ming", "orcid": "0000-0002-3835-8345", "display_name": "Chan, Chi Ming" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1nd5-g410", "abstract": "The object of this thesis is to study gas-surface interactions in\r\ngeneral, and the geometrical structures of surface and overlayers in\r\nparticular. Low-energy electron diffraction is employed to determine the\r\nstructure of both clean metal surfaces and overlayers. In addition, an\r\nanalysis of thermal desorption mass spectrometry is presented.
\r\n\r\nIn part II, a convolution-transform method of LEED analyses is described \r\nwhich has proved to be able to determine either contraction or\r\nexpansion of the crystal surface. The results of analyses of clean\r\nAl(110), Ag(110), Ni(110), Rh(111) and Pt(111) surfaces obtained by this\r\nmethod are comparable with those obtained by more complicated dynamical\r\ncalculations~ Our results indicate that both (111) surfaces have the\r\nsame structure as the bulk with a slight expansion or contraction of the\r\ntopmost layer of atoms by less than 5% of the bulk interlayer spacing.\r\nThe analyses of the fcc(110) surfaces reveal that a contraction of 4%, 5%\r\nand 7% of the bulk interlayer spacing occurs on the Al(110), Ni(110) and\r\nAg(110) surfaces.
\r\n\r\nIn part III, the atomic arrangement of general surfaces of Ir is\r\ndiscussed, namely, the (111), the reconstructed (110)-(1x2), and the\r\nunreconstructed (110) surface. Also, the surface structure of atomic\r\noverlayers of both oxygen and sulfur on these surfaces have been analyzed.\r\nFinally, the Debye temperature characteristics of both these surfaces\r\nof clean iridium are presented and compared.
" }, { "name": "Claudio, Antonia R.", "degree": "PhD", "year": "1979", "title": "The Acetylcholine Receptor and its Role in Induction of Experimental Autoimmune Myasthenia Gravis", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02032026-160531236", "creators": [ { "name": { "family": "Claudio", "given": "Antonia R." }, "id": "Claudio-Antonia-R", "display_name": "Claudio, Antonia R." } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "chair", "display_name": "Raftery, Michael A." }, { "name": { "family": "Brockes", "given": "Jeremy P." }, "id": "Brockes-Jeremy-P", "orcid": "0000-0002-3395-5159", "role": "member", "display_name": "Brockes, Jeremy P." }, { "name": { "family": "Hudspeth", "given": "A. James" }, "id": "Hudspeth-A-J", "role": "member", "display_name": "Hudspeth, A. James" }, { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "member", "display_name": "Mitchell, Herschel K." }, { "name": { "family": "Owen", "given": "Ray David" }, "id": "Owen-R-D", "role": "member", "display_name": "Owen, Ray David" }, { "name": { "family": "Revel", "given": "Jean-Paul" }, "id": "Revel-J-P", "role": "member", "display_name": "Revel, Jean-Paul" } ], "option_major": [ "bioch" ], "doi": "10.7907/pm26-ex97", "abstract": "I. Rabbit antibodies were produced against purified acetylcholine receptor\r\n(AcChR) and each of the four acetylcholine receptor subunits from Torpedo\r\ncalifornica. Using the technique of double immunodiffusion in agar, specific- and\r\ncross-reactivities were observed between these antibodies and purified acetylcholine\r\nreceptor and receptor subunits from Torpedo californica, Torpedo marmorata,\r\nTorpedo nobiliana, and Narcine brasiliensis. The specificity of each of the four\r\nanti-subunit antibodies was shown, suggesting the lower molecular weight polypeptide\r\nchains of the AcChR were not degradation products of the higher molecular\r\nweight polypeptide chains. The study also demonstrated conservation of AcChR\r\nand AcChR subunit antigenic determinants in the four electric rays investigated.
\r\n\r\nII. Experimental autoimmune myasthenia gravis (EAMG) has been induced\r\nin a wide variety of animals using AcChR purified from a variety of electric organ\r\nand muscle sources. Electrophoresis of sodium dodecyl sulfate (SDS) polyacrylamide\r\ngels heavily loaded with purified AcChR often reveals the presence of minor\r\ncontaminants. To test if these contaminants or any other components present\r\nin Torpedo californica AcChR preparations could induce EAMG, solubilized T.\r\ncalifornica membrane fragments were depleted of AcChR by passage over an\r\na-bungarotoxin resin and then injected into Lewis rats in an attempt to induce\r\nEAMG. The results demonstrated that some of the minor contaminants present\r\nin purified AcChR preparations were antigenic but EAMG could not be induced\r\nwith preparations enriched in these contaminants or containing other T. californica\r\nnon-AcChR components.
\r\n\r\nIII. Antisera prepared in rabbits and Lewis rats against Torpedo californica\r\nAcChR (purified and denatured to various degrees) were tested for the ability\r\nto inhibit [125I] \u03b1-bungarotoxin (\u03b1-BuTx) binding to native and detergent solubilized\r\nT. californica AcChR. Similar inhibition studies were performed using antisera\r\nand antigen-binding fragments (Fabs) directed against each of the four isolated\r\nAcChR subunits. None of these antisera or Fabs could inhibit \u03b1-BuTx binding\r\nto native AcChR. Antisera and Fabs directed against AcChR could inhibit a\r\nmaximum of 50% \u03b1-BuTx binding to solubilized AcChR. The results using Fabs\r\nindicated the inhibition was not due to antibody-mediated aggregation of AcChR\r\nmolecules. A strong correlation was seen between animals with EAMG and the\r\nability of their antisera to inhibit 5096 of \u03b1-BuTx binding to AcChRs. The results\r\nindicated that particular antigenic determinants on AcChRs could induce EAMG\r\nand that these determinants were lost with SDS denaturation of AcChR.
" }, { "name": "Dooley, David Marlin", "degree": "PhD", "year": "1979", "title": "Spectroscopic and Magnetic Studies of the Coordination Environment and Electronic Structure of Copper Sites in Blue Copper Oxidases", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072026-144145965", "creators": [ { "name": { "family": "Dooley", "given": "David Marlin" }, "id": "Dooley-David-Marlin", "display_name": "Dooley, David Marlin" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tt3g-fs12", "abstract": "Low temperature absorption, circular dichroism, and\r\nmagnetic circular dichroism measurements have been made\r\non the multicopper oxidases Rhus vernicifera laccase,\r\nPolyporus versicolor laccase, and human ceruloplasmin.\r\nNear infrared bands have been observed that are assigned\r\nto ligand field transitions of the type 1 (blue) Cu(II).\r\nThe low energies of these bands, when considered together\r\nwith the EPR g values, are consistent only with a\r\ntetragonally (D2d) distorted tetrahedral geometry for\r\ntype 1 Cu(II). Analysis and comparison of data obtained\r\non the blue oxidases and single blue copper proteins\r\nindicate that three kinds of blue copper may be\r\ndistinguished spectroscopically and electrochemically.\r\nNo evidence of inequivalent type 1 sites was found in\r\nnative or azide inhibited ceruloplasmin.
\r\n\r\nModified forms of the laccases and ceruloplasmin,\r\nin which the type 1 copper is specifically reduced or\r\nremoved, were also investigated. Absorption and circular\r\ndichroism bands were observed that are attributed to the\r\ntypes 2 and 3 copper ions. Distorted tetrahedral geometry\r\nmay be ruled out for these sites as no near infrared\r\nbands were present. Observed transitions are consistent\r\nwith tetragonal six, five or square planar four coordination.\r\nSuperhyperfine in the EPR spectra of modified ceruloplasmins\r\nestablished three or four nitrogen atoms as ligands of\r\nt he type 2 Cu(II). Binding of up to two fluoride ions\r\nby ceruloplasmin type 2 copper was also demonstrated .
\r\n\r\nMagnetic susceptibility measurements on Rhus vernicifera\r\nlaccase showed the type 3 coppers to be diamagnetic from\r\n5-260 K. If the type 3 site is formulated as an antiferromagnetically\r\ncoupled Cu(II) pair then J \u2265 500 cm-1.\r\nData were also obtained on Limulus polyphemus oxyhemocyanin\r\nwhich require a lower limit on J of 550 cm-1. Curie law\r\nbehavior of the susceptibility of Rhus laccase at low\r\ntemperatures indicates that types 1 and 2 copper must\r\nbe separated by several angstroms and are not bridged\r\nby a common ligand(s) in the native protein. However,\r\nbinding of fluoride at the type 2 site in both Rhus and\r\nPolyporus laccase perturbs the type 1 circular dichroism\r\nspectrum. This may reflect catalytically significant\r\nconformational changes designed to facilitate intramolecular\r\nelectron transfer.
" }, { "name": "Gelbard, Fred", "degree": "PhD", "year": "1979", "title": "The General Dynamic Equation for Aerosols", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112012-114024411", "creators": [ { "name": { "family": "Gelbard", "given": "Fred" }, "id": "Gelbard-Fred", "display_name": "Gelbard, Fred" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/WJMB-2D76", "abstract": "This work focusses on developing and solving the conservation\r\nequations for a spatially homogeneous aerosol. We begin by developing\r\nthe basic equations, and in doing so, a new form of the conservation\r\nequation or General Dynamic Equation (GDE), termed the discrete-continuous\r\nGDE, is presented. In this form, one has the ability to\r\nsimulate aerosol dynamics in systems in which processes are occurring\r\nover a broad particle size spectrum, typical of those found in the\r\natmosphere. All the necessary kinetic coefficients needed to solve\r\nthe GDE are discussed and the mechanisms for gas-to-particle conversion\r\nare also elucidated.
\r\n\r\nParticle growth rates limited by gas phase diffusion, surface\r\nand volume reactions are discussed. In the absence of coagulation,\r\nanalytic solutions for the above particle growth rates, arbitrary\r\ninitial and boundary conditions, arbitrary sources, and first order\r\nremoval mechanisms are developed.
\r\n\r\nTo account for all processes, numerical solutions are required.\r\nTherefore, numerical techniques and the errors associated with the\r\nnumerical solution of the GDE are discussed in detail. By comparing\r\nthe numerical solution to both analytical solutions for simplified\r\ncases and smog chamber data, it is shown that the numerical techniques\r\nare highly accurate and efficient.
\r\n\r\nTechniques for simulating a sulfuric acid and water aerosol are\r\npresented. By application of the discrete-continuous GDE, the effect\r\nof neglecting cluster-cluster agglomeration, and the effect of a\r\npreexisting aerosol on the nucleation rate of a sulfuric acid and\r\nwater aerosol are studied. The effects of coagulation are also elucidated\r\nby simulating the system with the full continuous GDE and the\r\nanalytic solution to the continuous GDE in the absence of coagulation.\r\nFairly good agreement between the predicted and experimentally observed distributions is obtained.
\r\n\r\nFinally, an exact solution to the continuous form of the GDE for\r\na multicomponent aerosol for simplified cases is developed.
\r\n" }, { "name": "Harding, Lawrence Brook", "degree": "PhD", "year": "1979", "title": "Ab Initio Studies of Excited States and Reactions of Organic Molecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-132537342", "creators": [ { "name": { "family": "Harding", "given": "Lawrence Brook" }, "id": "Harding-Lawrence-Brook", "display_name": "Harding, Lawrence Brook" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/19z3-cp09", "abstract": "Part A: Extensiveab initio calculations (double zeta, plus polarization function basis with correlated wave functions) on the addition of ^1O_2 ethylene are combined with standard thermochemical methods of estimating substituent effects to predict the energetics of the addition of ^1O_2 to substituted olefins. The results include estimates for peroxy biradical, open 1,4-zwitterion and perepoxide intermediates. It is concluded that only the first two play a role in this reaction. Detailed comparisons of the theoretical predictions with experimental results are also reported.It is shown that many aspects of the stereospecificity and regiospecificity can be understood assuming a biradical intermediate or transition state.\r\n\r\nPart B: Generalized valence bond (GVB) and configuration interaction (CI) calculations using an extensive basis [double zeta plus polarization functions (DZd)] have been carried out on peroxymethylene (H_2COO) often referred to as carbonyl oxide or as the Criegee intermediate), dioxirane, and dioxymethylene (OCH_2O). The ab initio thermochemical results are combined with existing thermochemical data to analyze possible modes of ozonolysis. The predicted heat of formation of peroxymethylene is 29.1 kcal, indicating that the dissociation of the primary ozonide to form peroxymethylene biradical and formaldehyde is 9 kcal endothermic. The ring state, dioxirane, is predicted to be 36 kcal below peroxymethylene with dioxymethylene lying 15 kcal above the ring state. Gas phase experimental results are shown to be consistent with the predicted thermochemistry. In addition, solution phase results on the stereospecificity of ozonolysis are shown to ae consistent with a biradical intermediate.\r\n\r\nPart C: Large basis set configuration interaction, bending potential curves for three states (^3B_1, ^1A_1, and ^B_1) of netural CH_2 and one state (^2B_1) of CH_2^- are reported. Vibronic calculations using these potential curves are found to lead to excellent agreement with the observed ^1B_1 - ^1A_1 spectrum. Similar calculations on the ^3B_1 - ^2B_1 and ^1A_1 - ^2B_1 photoelectron spectra indicate the presence of hot bands in the observed negative ion spectrum. Reassignment of the observed spectrum based on these calculations leads to the prediction of ^1A_1 - ^3B_1 splitting of O. 38 \u00b1 0.05 eV.\r\n\r\nPart D: The ground and valence excited states of ketene (H_2CCO) were studied using ab initio generalized valence bond (GVB) and configuration interaction (GVB-CI) wavefunctions. The character and properties of the states are analyzed in terms of the GVB wave- functions. The calculated vertical excitation energies (in eV) are 3.62 ^3(n \u2192 \u03c0*) or ^3A_2, 3.69 ^1(n \u2192 \u03c0*) or ^1A_2, 5.39 and 3(n \u2192 \u03c0*) or 1 ^3A_1, and 7.37 ^3(\u03c0 \u2192 \u03c0*) or 2^3A_1. (Here \u03c0 indicates a \u03c0-like orbital in the plane of the molecule.) These results are in excellent agreement with the observed electron impact excitation energies, 3.8 (^1A_2) and 5.35 ev (^3A_1). Note in particular the small separation (0.07 eV) of the ^3A_2 and ^1A_2 states (0.5 eV for H_2CO) and the 2-eV separation in the \u03c0 \u03c0* triplet states in the two planes. The calculated ground state dipole moment, 1.62 D, is in fair agreement with the experimental value of 1.41 D. The calculated dipole moments of the ^3A_2, ^1A_2, 1 ^3A_1, and 2 ^3A_1 excited states are 2.76, 3.43, 2.43 and 0.27 D respectively.\r\n\r\nPart E:\tAb inito configuration interaction (GVB-CI) methods are used to study the excited Rydberg states of formaldehyde formed by exciting out of either the n or \u03c0 orbital into the various 3s, 3p, and 3d-like Rydberg orbitals. The resulting excitation energies are in good agreement (within ~ 0.1 eV) with the available experimental results. Calculated oscillator strengths are in fair agreement with experiment. Two states ^1(\u03c0\u2192\u03c0*) and ^1(\u03c0\u21923s) are calculated to lie between 10.7 and 10.8 eV, corresponding closely to a broad unassigned peak in the electron impact spectrum (10.5-11.0 eV). We have assigned other peaks in the electron impact spectrum at 11.4-19.n eV and 12.5-12.8 eV as resulting from (\u03c0\u21923p) and (\u03c0\u21923d) transitions, respectively.\r\n" }, { "name": "Houle, Frances Anne", "degree": "PhD", "year": "1979", "title": "Studies of Alkyl Free Radicals and Reaction Mechanisms by Photoelectron Spectroscopy", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11022009-081650291", "creators": [ { "name": { "family": "Houle", "given": "Frances Anne" }, "id": "Houle-Frances-Anne", "display_name": "Houle, Frances Anne" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zppe-fp18", "abstract": "Application of vacuum ultraviolet photoelectron spectroscopy (UPS) to the study of simple alkyl free radicals and organic reaction mechanisms is described. A brief overview of the field of UPS of chemical transients, including a survey of the relevent literature, and a general introduction to topics covered in this thesis are given in Chapter 1. \r\n\r\nChapters 2, 4 and 5 present results of UPS investigations of the first photoelectron bands of alkyl radicals produced by pyrolysis of the corresponding alkyl nitrites. Spectra have been obtained for methyl, ethyl, 1-propyl, 2-propyl, tert-butyl, cyclopentyl, cyclohexyl and 2-norbornyl radicals. Adiabatic ionization potentials determined for these species are used to calculate heats of formation of the ions, heterolytic bond dissociation energies of the corresponding alkanes, and proton affinities of the corresponding olefins. The shapes of the bands are discussed qualitatively in terms of structural differences between neutrals and positive ions. \r\n\r\nChapter 3 is a discussion of the lowest energy conformations of ethyl and tert-butyl radicals. In particular, ESR and theoretical results from the literature are used to discuss the question of the planarity of alkyl radical centers. \r\n\r\nChapters 4 and 6 present results of studies of the thermal decomposition mechanisms of 2-norbornyl, cyclopentyl and cyclohexyl radicals. Pyrolysis of the radicals is readily observed under the conditions necessary for their generation. The mechanisms deduced from the spectra are compared to those resulting from studies using classical techniques. \r\n\r\nIn Chapter 7, experiments designed to assess the fate of reaction exothermicity in the pyrolysis of some strained azo compounds are described. The results indicate that very little of the available energy is released to vibration of the N_2 fragment. The implications of this observation for the transition states of the reactions that were studied are discussed." }, { "name": "Johnson, Gilbert Collier", "degree": "PhD", "year": "1979", "title": "Approaches to the Elucidation of the Nature of 1,4-Dehyrobenzene", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302026-223031889", "creators": [ { "name": { "family": "Johnson", "given": "Gilbert Collier" }, "id": "Johnson-Gilbert-Collier", "display_name": "Johnson, Gilbert Collier" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wpgh-0v33", "abstract": "Two approaches to the generation of 1,4-dehydrobenzene are\r\ndescribed. The first, involving an attempted cycloreversion to\r\ngenerate initially the bicyclic form of the title compound,\r\n\"butalene,\" gave negative results. The second approach, pyrolysis\r\nof various substituted hexene-diynes to generate substituted\r\n1,4-dehydrobenzenes, gave evidence for the intermediacy\r\nof the 1,4-dehydrobenzene diradical in the formation of several\r\nisomerization products. A novel 1,2 silicon shift is proposed\r\nto give rise to other products through the intermediacy of\r\nsubstituted 1,3-dehydrobenzenes." }, { "name": "Jones, Carol Ruth", "degree": "PhD", "year": "1979", "title": "The Syntheses and Thermal Decompositions of Six-Membered Cyclic Diacyl Peroxides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08072008-145712", "creators": [ { "name": { "family": "Jones", "given": "Carol Ruth" }, "id": "Jones-Carol-Ruth", "display_name": "Jones, Carol Ruth" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R2WT-EV58", "abstract": "meso- and d1-2,3-Dimethylsuccinyl peroxides (5) and (6), cis- and trans-1,2-hexahydrophthaloyl peroxides (7) and (8), and bicyclo[3.1.0]hexanediacyl peroxide (9) have been synthesized. Products of their thermal decomposition in dichloromethane and THF suggest they decompose by a stepwise mechanism via the intermediacy of a carboxy diradical. The decomposition of erythro- and threo-2,3-dimethylpropiolactone was stereospecific and requires that the pathway and/or intermediate in this decomposition be different from that of the decomposition of peroxides (5) and (6). Thermal decomposition of (5)-(8) in methanol afforded saturated and unsaturated methyl ethers. Mechanisms involving the intermediacy of a radical cation are discussed.\r\n\r\nDirect and sensitized irradiation of (5)-(8) were performed. The peroxides were quite photolabile. Benzophenone, anthracene, and tetracene were effective sensitizers. An electron transfer rather than an energy transfer mechanism for the effectiveness of anthracene and tetracene is proposed.\r\n\r\nInduced decomposition of the cyclic diacyl peroxides by triphenylphosphine and dimethylsulfide to stereo-specifically lead to the corresponding cyclic anhydrides was observed.\r\n\r\nCopper (I) rapidly induced the decomposition of peroxides (5)-(8) to afford the corresponding olefins in low to moderate yields.\r\n\r\nInduced decomposition of peroxides (5)-(8) by aromatic hydrocarbons was observed. Emission of light was observed from the reaction of d1-(6) and rubrene. The observations are consistent with chemically initiated electron transfer luminescence (CIEEL)." }, { "name": "Jones, William Davidson, II", "degree": "PhD", "year": "1979", "title": "Reactivity Patterns of Transition Metal Hydrides and Alkyls", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152026-230341334", "creators": [ { "name": { "family": "Jones", "given": "William Davidson, II" }, "id": "Jones-William-Davidson-II", "orcid": "0000-0003-1932-0963", "display_name": "Jones, William Davidson, II" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yj3c-pw50", "abstract": "The complex PPN+CpV(CO)3H- (Cp=n5-C5H5) has been\r\nprepared in 70% yield by sodium reduction of CpV(CO)4\r\nfollowed by protonation of the resulting dianion [CpV(CO)3]2-\r\nwith water and cation exchange with PPN+Cl-. The physical\r\nproperties and chemical reactions of PPN+CpV(CO)3H- have\r\nbeen investigated. The sodium salt of CpV(CO)3H- is contact\r\nion-paired in the solid state and in THF; dissociation\r\nof solvent-separated pairs occurs on conversion to the PPN+\r\nsalt or dissolution in polar solvents such as HMPA. \r\nPPN+CpV(CO)3H- reacts with a wide range of organic halides,\r\nresulting in substitution of the halogen atom by the hydrogen of CpV(CO)3H-.\r\nThe organometallic products of these\r\nreactions are the vanadium halides PPN+[CpV(CO)3X]-. In\r\nsome cases a second organometallic product is observed;\r\nthis material is the binuclear bridging hydride PPN+\r\n[CpV(CO)3]2 H-, and it is formed by reaction of the kinetic\r\nproduct CpV(CO)3X- with starting CpV(CO)3H- present in the\r\nreduction solutions. Irradiation of CpV(CO)4 in the\r\npresence of CpV(CO)3H- provides an alternate route to\r\nbridging hydride [CpV(CO)3]2 H-. Competition experiments\r\nagainst PPh3 have shown that CpV(CO)3H- reacts more rapidly\r\nthan the phosphine with transient, coordinatively unsaturated\r\nCpV(CO)3, but thermodynamically PPh3 is the better ligand.\r\nThe borohydride salt PPN+[CpV(CO)3BH4]- has also been\r\nprepared, by treating CpV(CO)4 with NaBH4 and by treating\r\nCpV(CO)3H- with BH3THF. The mechanism of the reaction\r\nbetween CpV(CO)3H- and organic halides has been investigated\r\nin detail, and compared in several cases with halide\r\nreductions carried out using tri-n-butyltin hydride.\r\nRelative reactivity, stereochemistry, cyclization and\r\ntrapping studies demonstrate that in almost all cases,\r\nthe reduction reaction proceeds via free radical intermediates.\r\nAs in the R3SnH case, these intermediates are\r\ngenerated in a chain process, and are trapped by hydrogen\r\ntransfer from CpV(CO)3H-. The absolute rate constant for\r\nthis transfer step can be estimated to be ca. 2 X 107 M-1\r\nsec-1, nearly an order of magnitude larger than the rate\r\nconstant for hydrogen transfer from tri-n-butyltin hydride.\r\nReduction of cyclopropylcarbinyl bromide appears to be\r\nexceptional, and probably proceeds by a two-electron mechanism,
\r\n\r\nSodium amalgam reduction of CpRh(CO)2 or a mixture of\r\nCpRh(CO)2 and CpCo(CO)2 affords two new anions, PPN+\r\n[Cp2Rh3(CO)4]- and PPN+[Cp2RhCo(CO)2]-. The latter compound appears to be physically and chemically similar to the known\r\nPPN+[Cp2Co2(CO2]-, whereas the former posesses the same\r\nsubstructure bridged by a Rh(Co)2 unit. Both anions\r\nreact with CH3I producing acetone via CpRh(CO)(CH3)2\r\nor CpCo(CO)(CH3)2. In addition, the compounds Cp2RhCo(CO2R2\r\n(R=CH3, CH2CF3) are formed upon alkylation of [Cp2RhCo(CO)]+\r\nand are observed to decompose to CpRh(CO)(CH2CF3)2 and\r\nCpCo(CO)(CH2CF3)2.
\r\n\r\nCpMo(CO)3H has been found to react with CpMo(CO)3R\r\n(R=CH3, C2H5, CH2C6H5; 2a, 2b, 2c) at 25-50\u00b0C to quantitatively\r\nproduce aldehyde RCHO and the dimers [CpMo(CO)3]2\r\nand [CpMo(CO)3]2. Evidence is presented indicating that\r\naldehyde formation occurs by insertion of CO into the Mo-R\r\nbond followed by hydride transfer by 1 forming an intermediate \r\nacyl hydride. The intermediate acyl CpMo(CO)2(COR)\r\nalso reacts with ethylene and CpMo(CO)3H producing ketones\r\nR-C-C2H5. A mechanism is proposed for these reactions and\r\na comparison with the cobalt analogues in the hydroformylation\r\nprocess discussed.
\r\n\r\nThe reactions of PPN+CpV(CO)3H- with some transition\r\nmetal carbonyls, alkyl and acyls are studied. In almost\r\nall cases substitution of hydride (H-) for CO is observed.\r\nThe chemistry of CpMo(CO)3H with similar compounds is also\r\nexamined and compared with that of CpV(CO)3H-. In general,\r\nCpV(CO)3H- appears to transfer a hydrogen atom to the\r\nmetal radical anion formed in an electron transfer process 5\r\nwhereas CpMo(CO)3H- transfers hydride in a 2-electron process\r\nto a vacant coordination site. The chemical consequences\r\nare that CpV(CO)3H- generally reacts with metal alkyls to\r\ngive alkanes via. intermediate alkyl hydride species whereas\r\nCpMo(CO)3H reacts with metal alkyls to produce aldehyde,\r\nvia an intermediate acyl hydride species.
" }, { "name": "Koval, Carl Anthony", "degree": "PhD", "year": "1979", "title": "Synthesis, Electrochemistry, and Physical Studies of Graphite Electrodes with Chemically Modified surfaces and Copper Complexes with Macrocyclic Ligands", "advisor": "Anson, Fred C.; Gagn\u00e9, Robert R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012026-175907655", "creators": [ { "name": { "family": "Koval", "given": "Carl Anthony" }, "id": "Koval-Carl-Anthony", "display_name": "Koval, Carl Anthony" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Gagn\u00e9", "given": "Robert R." }, "id": "Gagn\u00e9-R-R", "role": "advisor", "display_name": "Gagn\u00e9, Robert R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/smpc-8t32", "abstract": "The attachment of various molecules to graphite surfaces and\r\nthe electrochemistry exhibited by the attached species are discussed\r\nin Part I.
\r\n\r\nSection I-A
\r\n\r\nAromatic compounds such as 9,10-phenanthrenequinone are\r\nirreversibly adsorbed onto pyrolytic graphite electrodes. Cyclic\r\nvoltammetry is used to illustrate the differences in electrochemical\r\nreJponse between surface and solution species. Integration of\r\nthe current used to oxidize or reduce the molecules on the surface\r\naffords measurement of surface concentrations, which are typically 10-10\r\nto 10-11 moles/cm2. The use of differential pulse voltammetry to study\r\nsurface electrochemistry is introduced.
\r\n\r\nSection I-B
\r\n\r\nProcedures are presented for attaching pyridinepentaammineruthenium{II)\r\ncomplexes to graphite electrodes by covalent bonding and irreversible ad sorption.\r\nCyclic voltammetry and differential pulse voltammetry are used\r\nto compare the electrochemical behavior of the attached complexes and to\r\nmeasure surface concentrations . Different orientations of the anisotropic\r\ngraphite affect the quantity of reactant that can be attached as well as\r\nthe voltammetric responses. On \"edge plane\" pyrolytic graphite the covalently\r\nbound and irreversibly adsorbed ruthenium complexes reach coverages\r\n0f 1.5 x 10-10 and 1.6 x 10-9 moles/cm2, respectively. The coverage for\r\nthe adsorbed complex on \"basal plane\" graphite is 3.5 x 10-10 moles/cm2.\r\nThe covalent attachment procedure is unsuccessful on this surface,\r\npresumably due to the lack of surface oxides. Attachment by irreversible\r\nadsorption yields larger quantities of complex on the electrode surface\r\nbut the covalently attached complex persists on the surface for a longer\r\ntime; t1/2 = 313 and 1080 min, respectively.
\r\n\r\nSection I-C
\r\n\r\nThe catalytic reduction of oxygen in acidic aqueous solution at several\r\nmodified pyrolytic graphite surfaces is examined using a rotating ring-disc\r\nelectrode. Surfaces coated with 9,10-phenanthrenequinone and Ru(III)(edta)\r\nafford no catalysis. Adsorbed Fe(III) protoporphyrin IX catalyzes the\r\nreduction of oxygen to water at ~0.2 V. Catalytic properties of modified\r\ngraphite and platinum surfaces are compared .
\r\n\r\nThe synthesis, electrochemistry and physical properties of a variety\r\nof Cu(II) and Cu(I) complexes are presented in Part II. The physical\r\nstudies reveal several unusual properties of the Cu(I) complexes.
\r\n\r\nSection II-A
\r\n\r\nMeasurements of formal reduction potentials are compared for several\r\ninorganic systems using cyclic voltammetry, d.c. polarography, differential\r\npulse voltammetry, and potentiometry. For the type of copper complexes\r\nbeing studied, d.c. polarography is judged to be the most reliable\r\ntechnique, especially in the electrochemical m~asurement of CO binding\r\nconstants. The potential of the oxidation of ferrocene to ferricenium\r\nion is suggested as a practical reference against which to report the\r\npotentials of other couples.
\r\n\r\nSection II-B
\r\n\r\nThe synthesis of an oxo-bridged copper(II)-copper(I) mixed- valence\r\nion and its carbon monoxide adduct is reported along with preliminary\r\nobservations concerning electronic and electron paramagnetic resonance\r\nspectra of the ions.
\r\n\r\nSection II-C
\r\n\r\nMore complete physical studies of the mixed-valence system introduced\r\nin Section II-B are presented. Electrochemistry is used to synthesize the\r\ncopper(I)-copper(I) state of the molecule and to obtain formal reduction\r\npotentials (-0.518 V and -0.908 V) for the two copper atoms. The CO\r\nbinding constant for the copper(II)-copper(I) complex is measured\r\npolarographically and found to be 2.82 x 104. All complexes are characterized\r\nby elemental analysis, infrared spectroscopy, magnetic susceptibility\r\nand electronic spectroscopy. Temperature-dependent electron\r\nparamagnetic resonance spectra of the mixed- valence complex provide an\r\nestimated intramolecular electron transfer rate of 2.2 x 1010 sec-1 at\r\n298\u00b0K.
" }, { "name": "Kuehne, Donald L.", "degree": "PhD", "year": "1979", "title": "Selective Transport of Sulfur Dioxide through Polymer Membranes", "advisor": "Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212026-211042969", "creators": [ { "name": { "family": "Kuehne", "given": "Donald L." }, "id": "Kuehne-Donald-L", "display_name": "Kuehne, Donald L." } ], "advisors": [ { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/xkjs-zz88", "abstract": "The purpose of this research was to identify and characterize\r\npolymeric materials which are selective to SO2 for possible\r\napplications in the monitoring or control of SO2 emissions from\r\nstationary sources. Preliminary studies indicated that polyacrylate\r\nand cellulose triacetate were very selective to SO2. The SO2\r\nsolubility of polyacrylate was 0.215 lb/lb (25\u00b0C, 1 atm), comparable\r\nto the SO2 solubilities of sulfolane (tetrahydrothiophene-1,1-dioxide)\r\nand polyethylene glycol, two excellent SO2 solvents.
\r\n\r\nTo achieve the high SO2 transport rates required for a membrane\r\nseparation process, two techniques were investigated for preparing\r\nultrathin films of these polymers. Polyacrylate films were cast\r\non mercury, and cellulose triacetate films were formed on glass\r\nplates which were withdrawn at constant velocity from dilute polymer\r\nsolutions. The glass plate technique was also used to make composite\r\nfilms consisting of a 0.2-0.5 \u03bcm layer of polyacrylate over a\r\n0.002-0.005 \u03bcm layer of cellulose triacetate. All the films were\r\nplaced on microporous filter materials for support.
\r\n\r\nThe performance of the membranes was initially determined by\r\nmeasuring their permeability to pure N2, CO2, and SO2. The N2 and\r\nCO2 permeabilities were nearly independent of pressure, but the SO2\r\npermeability increased rapidly with increasing pressure. The SO2\r\npermeation data were correlated with two- and three-parameter\r\nexponential models. The three-parameter model had the same functional\r\nform as the free volume theory and gave a better fit to the data than\r\nthe two-parameter model. The SO2 permeability was affected by\r\nprevious conditioning of the membranes and time-dependent processes\r\noccurring in the polymer. There was evidence that some SO2 molecules\r\nbecame immobilized in clusters within the membranes.
\r\n\r\nThe composite membranes were also tested with binary mixtures of\r\nN2 and SO2 at 10 atm upstream pressure with a steady-state flow\r\nsystem. A typical membrane produced an enriched permeant stream of\r\n2% SO2 from 0.1% SO2 upstream, 35% from 2%, and over 90% from 10%.\r\nN2 permeation was enhanced by the presence of SO2, but the presence\r\nof N2 inhibited SO2 permeation at high SO2 partial pressures.\r\nInteractions between N2 and SO2 made it difficult to accurately\r\npredict the permeation rates of the mixtures from data for the pure\r\ngases.
\r\n\r\nThe composite membranes were superior in performance to the\r\nsingle-layer membranes and those developed by others for SO2\r\nseparations; however, they were unable to meet the stringent design\r\ngoals for combustion and smelter gas cleaning. The unique properties\r\nof the composite membranes do make them attractive for instrumentation\r\nand other specialty applications.
" }, { "name": "Levin, Deborah Ann", "degree": "PhD", "year": "1979", "title": "Ab Initio Calculations of Processes in Low Energy Electron-Molecule Scattering", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212026-200051749", "creators": [ { "name": { "family": "Levin", "given": "Deborah Ann" }, "id": "Levin-Deborah-Ann", "orcid": "0000-0002-6109-283X", "display_name": "Levin, Deborah Ann" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k96t-xc35", "abstract": "Chapter I
\r\n\r\nCalculations are reported for low energy e-N2 scattering cross\r\nsections in the static-exchange approximation. The approach used\r\ninvolves solving the Lippmann-Schwinger equation for the transition\r\noperator in a sub-space of Gaussian functions. New features of\r\nthe method are analytic evaluation of matrix elements of the free\r\nparticle Green's function and analytic transformation to obtain\r\nsingle-center expansion coefficients for the scattering amplitude.\r\nResults are presented for the total elastic and rotational excitation\r\ncross sections and the momentum transfer cross section for incident\r\nelectron energies of 0.5 to 10 eV. Comparison with other theoretical\r\nand experimental data is included.
\r\n\r\nThe second paper of this chapter presents cross sections for\r\ne--CO scattering in the static exchange approximation. The method\r\nof calculation is the T-matrix discrete-basis-set method as updated\r\nby Fliflet, Levin, Ma and McKoy (previous paper) along with the\r\nvariational correction approach of Fliflet and McKoy. We extract\r\nthe 2\u03c0 resonance parameters at equilibrium internuclear separation\r\nand compare with other theoretical and semi-empirical results.\r\nMomentum transfer cross sections are compared with the experimental\r\ndata of Land and the theoretical calculation of Chandra.
\r\n\r\nChapter II
\r\n\r\nResults are presented in this first paper for rotational and\r\nvibrational-rotational excitation of H2 by electron impact in the\r\nstatic-exchange approximation. Using the T-matrix discrete-basis-set\r\napproach as described in the first paper of Chapter I we solve\r\nthe fixed-nuclei scattering problem at several internuclear separations.\r\nComparisons of our results with the experimental data of Linder and\r\nSchmidt and with other calculated results are given.
\r\n\r\nIn the second paper of this chapter we obtain vibrational and\r\nvibrational-rotational excitation cross sections of N2 by electron\r\nimpact via the 2\u03a0g resonance in the static-exchange approximation.\r\nTo obtain highly accurate phase shifts in the \u03a0g channel we use the\r\nvariational correction of Fliflet and McKoy applied to the discrete-basis-\r\nset method of Fliflet, Levin, Ma and McKoy. As in e-H2\r\nvibrational excitation, the approach involves solving the fixed-nuclei\r\nscattering problem at several internuclear separations.\r\nFrom these calculations one extracts the parameters necessary to\r\ncalculate resonant vibrational cross sections in a compound state\r\nmodel. Our results are compared with the experimental data of\r\nWong et al., and other theoretical calculations.
\r\n\r\nFinally, the last paper discusses a simple model to include\r\npolarization effects in shape resonances. The position and width\r\nof the 2eV shape resonance in e-N2 scattering are calculated by\r\nsolving the T-matrix equations with the static-exchange field of\r\nthe N2 case of the N2- compound state. Resonance parameters\r\nobtained at the equilibrium separation of the molecule agree well\r\nwith semi-empirical results. Most importantly, the procedure can\r\nbe readily applied at several internuclear separations.
\r\n\r\nChapter III
\r\n\r\nAs was mentioned in Chapter I, an important refinement of\r\nthe original T-matrix method is the analytic evaluation of Gaussian\r\nmatrix elements of the free particle Green's function. Previous\r\ncalculations evaluated these matrix elements by a numerical\r\nquadrature which was in practice restricted to cases of axial\r\nsymmetry. In this chapter the derivation of a method for generating\r\nhigher order Gaussian matrix elements is presented. Although this\r\nprocedure is applicable to polyatomic systems, we list here only\r\nthe types of matrix elements necessary for \u03a3, \u03a0 and \u0394 symmetries\r\nof a linear molecule.
\r\n\r\nChapter IV
\r\n\r\nIn this chapter a method for obtaining scattering wave functions\r\nat arbitrary energies is presented. Minimization of the variance\r\nintegral for a trial wave function expanded in discrete basis functions\r\nonly provides a criterion for choosing the expansion coefficients of\r\nthe wave function. By using a separable representation of the\r\nscattering potential only one new class of matrix elements appears\r\nin the evaluation of the variance integral which is not already\r\nrequired in the diagonalization of the Hamiltonian. The method is\r\napplied to some model potentials and to s-wave scattering for helium\r\nin the static-exchange approximation.
" }, { "name": "Moore, Kevin William", "degree": "PhD", "year": "1979", "title": "The Mechanism of Action of Adenosylcobalamin-Dependent Diol Dehydratase. I. Glycerol and other Substrate Analogs as Substrates and Inactivators of Diol Dehydratase: Kinetics, Stereospecificity, and Mechanism. II. Hydrogen Transfer in the Inactivation of Diol Dehydratase by Glycerol. III. Hydrogen Transfer in Catalysis by Diol Dehydratase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03162026-223828895", "creators": [ { "name": { "family": "Moore", "given": "Kevin William" }, "id": "Moore-Kevin-William", "display_name": "Moore, Kevin William" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/efx4-ad25", "abstract": "Chapter I
\r\n\r\nA number of vicinal diols were found to react with\r\npropanediol dehydratase, typically resulting in the conversion\r\nof enzyme-bound adenosylcobalamin to cob(II)alamin\r\nand formation of aldehyde or ketone derived from substrate.\r\nMoreover, most are capable of effecting the irreversible\r\ninactivation of the enzyme. The kinetics and mechanism of\r\nproduct formation and inactivation were investigated.\r\nGlycerol, found to be a very good substrate for diol dehydratase\r\nas well as a potent inactivator, atypically,\r\ndid not induce cob(II)alamin formation to any detectable\r\nextent. With glycerol, the inactivation process was accompanied\r\nby conversion of enzyme-bound adenosylcobalamin\r\nto an alkyl or thiol cobalamin, probably by substitution\r\nof an amino acid side chain near the active site for the\r\n5'-deoxy-5'-adenosyl ligand on the cobalamin. The inactivation\r\nreaction with glycerol as the inactivator exhibits\r\na deuterium isotope effect of 14, strongly implicating\r\nhydrogen transfer as an important step in the mechanism\r\nof inactivation. The isotope effect on the rate of product\r\nformation was found to be 8. Experiments with isotopically\r\nsubstituted glycerols indicate that diol dehydratase distinguishes\r\nbetween \"R\" and \"S\" binding confonnations, the\r\nenzyme-(R)-glycerol complex being predominantly responsible\r\nfor the product-forming reaction, while the enzyme-(S)-\r\nglycerol complex results primarily in the inactivation reaction.\r\nA comparative study of the reaction of IIieso- and\r\ndl-2,3-butanediols with diol dehydratase shows that the\r\nstereospecificity of hydrogen abstraction during inactivation \r\nis the same as that of catalysis, suggests that hydrogen \r\nabstraction from C-1 of substrate may be concerted with\r\ncleavage of the carbon-cobalt bond, and further suggests\r\nthat formation of a carbon-cobalt bond between coenzyme\r\nand substrate is not obligatory for catalysis. Mechanistic\r\nimplications are discussed. A method for removing\r\nenzyme-bound hydroxycobalamin that is nondestructive to the\r\nenzyme and a technique for measuring the binding constants\r\nof (R)- and (S)-1,2-propanediols are presented.
\r\n\r\nChapter II
\r\n\r\nWe have investigated the kinetic characteristics of\r\nthe inactivation of the adenosylcobalamin-dependent enzyme\r\npropanediol dehydratase by glycerol, (RS)-1,1-dideuterioglycerol,\r\n(R)-1,1-dideuterioglycerol, (S)-1,1-dideuterioglycerol,\r\nand perdeuterioglycerol in the absence of substrate and in the presence of 1,2-propanediol and 1,1-dideuteriopropanediol.\r\nSubstitution of deuterium for hydrogen at C-1 of 1,2-propanediol or at the pro-(R) hydroxymethyl\r\ngroup of glycerol has no effect on the apparent\r\ndissociation constants KI and KG, respectively, of the holo-enzyme-\r\nsubstrate complexes. In contrast, the same substitution\r\nat the pro-(S) hydroxymethyl group of glycerol increases\r\nthe value of the apparent KG. The results suggest\r\nthat the binding of only the pro-(S) conformation is perturbed\r\nby this latter substitution. In the presence of a competL1g\r\nsubstrate, this KG is observed to vary as a function of\r\nglycerol concentration in a manner indicating that kinetic\r\nterms involving steps of the reaction subsequent to binding\r\nof substrate contribute to determining its value. The inactivation\r\nkinetics obtained with these glycerols in the\r\npresence of 1,2-propanediol and 1,1-dideuterio-1,2-propanediol\r\nimply that hydrogen (or deuterium) attached to\r\nC-1 of 1,2-propanediol participates in the inactivation\r\nprocess and contributes to the expression of a kinetic\r\nisotope effect on the rate of inactivation. The mechanism\r\nfor this inactivation must involve the cofactor as an intermediate\r\nhydrogen carrier, presumably in the form of 5'-deoxyadenosine.\r\nMoreover, a mechanism involving a rate determining\r\ntransfer of hydrogen from an intermediate\r\ncontaining three equivalent hydrogens accounts for the results.\r\nWhen diol dehydratase holoenzyme is inactivated by\r\n[1-3H]-glycerol, 5'-deoxyadenosine which is enriched in\r\ntritium by a factor of 2.1 over that in glycerol can be\r\nisolated from the reaction mixture.
\r\n\r\nChapter III
\r\n\r\nStudies (Chapter II; Bachovchin et al. (1978)\r\nBiochemistry 17, 2218) of the mechanism of inactivation of\r\nadenosylcobalamin-dependent dial dehydratase have led to\r\nthe development of a general method to describe the kinetics\r\nof a reaction pathway containing a reservoir of mobile\r\nhydrogen. Analysis by this method of catalytic rate measurements\r\nfor mixtures of 1,2-propanediol and 1,1-dideuteriol,\r\n2-propanediol supports a mechanism involving an intermediate\r\nwith three equivalent hydrogens, in which hydrogen\r\ntransfer from this intermediate to product is the major\r\nrate-contributing step. The results of this analysis predict\r\nthat diol dehydratase should exhibit a tritium isotope\r\neffect of 4.5, a prediction which was verified experimentally.\r\nOther results using tritium as a trace label (Essenberg\r\net al. (1971) J. Am. Chem. Soc. 93, 1242) are discussed\r\nin light of these deuterium isotope studies. Results of\r\nanalogous experiments employing mixtures of glycerol and\r\nperdeuterioglycerol as substrates suggest that during\r\ncatalysis with this substrate, neither hydrogen abstraction\r\nfrom C-1 of glycerol nor from the intermediate is strictly\r\nrate determining.
" }, { "name": "Morse, Corinne Sue", "degree": "Masters", "year": "1979", "title": "I. On the Lifetime of 1,4-Diradicals. Attempted Trapping of Tetramethylene. II. Six-Membered Cyclic Diacyl Peroxides. Thermal Decomposition of 1,2,3,4-Tetrahydrophthaloyl Peroxide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212010-111536797", "creators": [ { "name": { "family": "Morse", "given": "Corinne Sue" }, "id": "Morse-Corinne-Sue", "display_name": "Morse, Corinne Sue" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tjxn-bg94", "abstract": "Part I. Thermochemical calculations suggest that the \r\ndepth of the potential well for tetramethylene 1,4-diradical can be probed by trapping the intermediate with sulfur dioxide. This was attempted using N-azacyclopentylmethane sulfonamide (1) as the precursor to tetramethylene. Gas chromatographic evidence for the presence of sulfolane in the decomposition of 1 in sulfur dioxide could not be confirmed by gc/ms and results were not reproducible. It is suggested that a precursor which decomposes more cleanly than 1 will be necessary in order to get quantitative results from a trapping experiment.\r\n\r\nPart II. 1,2,3,4-Tetrahydrophthaloyl peroxide (13) has been synthesized. Thermal decomposition of 13 gave hydrocarbon yields of 5%. No evidence was found for lactone formation, but the presence of anhydride and epoxide products suggests that bimolecular redox chemistry is occurring.\r\n\r\nThe possibility of \u03c0\u03c0^* cyclohexadiene formation in the\r\nthermal decomposition of 13 is discussed. Evidence was not found which suggests that this is occurring.\r\n\r\nInduced decomposition of 13 by rubrene resulted in\r\nemission of light consistent with chemically initiated electron exchange luminescence (CIEEL).\r\n" }, { "name": "Nicol, Ann Tryon", "degree": "PhD", "year": "1979", "title": "Solid States NMR Studies of Metal Hydrides", "advisor": "Vaughan, Robert W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162026-031614166", "creators": [ { "name": { "family": "Nicol", "given": "Ann Tryon" }, "id": "Nicol-Ann-Tryon", "display_name": "Nicol, Ann Tryon" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/swmm-ay26", "abstract": "Both conventional and multiple pulse proton NMR studies of the compounds H2Os3(CO 10, H4Ru4(CO)12, and H4Os4(CO)12 as well as multiple pulse studies of CaH2, SrH2, and BaH2 are reported.
\r\n\r\nChemical shift tensors for protons directly bonded to heavy metal atoms in the metal carbonyl compounds are found to have an isotropic value close to that observed in solution and are found to have an anisotropy of less than 30 ppm. The temperature dependent spectra of\r\nH4Ru4(CO)12 indicates the presence of anisotropic proton reorientation at room temperature. The isotropic proton chemical shift for the ionic solids CaH2, SrH2, and BaH2 are found in the range \u014d= 0 ppm to \u014d= -10 ppm, and a trend in the isotropic value to shift toward higher field as a function of cation electronegativity is noted.
\r\n\r\nStructured proton NMR lineshapes, observed by conventional pulse NMR, are reported for the metal cluster carbonyl compounds; and the results are interpreted in terms of four dipolar coupled spin \u00bd nuclei. Contributions to the lineshapes from heteronuclear dipolar interaction with a Zeeman perturbed quadrupolar nucleus, indirect nuclear coupling, and restricted motion are discussed.
" }, { "name": "Oken, Carol Ann", "degree": "Masters", "year": "1979", "title": "The Partial Amino Acid Sequence of the Heavy Chain Variable Region of J558, a Dextran-Binding Myeloma Protein", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-105228867", "creators": [ { "name": { "family": "Oken", "given": "Carol Ann" }, "id": "Oken-Carol-Ann", "display_name": "Oken, Carol Ann" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8rs6-5e55", "abstract": "No abstract." }, { "name": "Olafson, Barry Duane", "degree": "PhD", "year": "1979", "title": "A Molecular Description of Oxygen Binding to Hemoglobin", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-093719542", "creators": [ { "name": { "family": "Olafson", "given": "Barry Duane" }, "id": "Olafson-Barry-Duane", "display_name": "Olafson, Barry Duane" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7fss-rj50", "abstract": "We discuss the bonding of O_2 to hemoglobin (Hb) at the molecular level. The ideas presented here are the results of ab initio calculations on idealized portions of the Hb molecule.\r\n\r\nThe bond between Fe and O_2 is formed by coupling a triplet state of Fe to the triplet ground state of O_2. The electronic structure of the FeO_2 moiety is analogous to that of ozone. We show how the ozone model is in agreement with the EPR data for MnO_2 and CoO_2, predicting unpaired spin density on the Mn for the former molecule, and unpaired spin density on the O_2 ligand in CoO_2. Our calculations lead to a bound molecule with very little transfer of electron density onto the O_2 ligand. Valence bond ideas also indicate the similarity between HbO_2 and the formal Fe(III) complexes of HbOH and HbCN.\r\n\r\nThe heme plane and axial imidazole ligand are seen to play a key role in promoting reversible O_2 binding. The effective size of high- spin Fe is not found to play a major role in the O_2 binding process. The Fe remains in the heme plane for four-coordinate molecules, regardless of the local spin state about the Fe. The Fe moves out of the heme plane for five-coordinate complexes in order to keep a strong dative bond to the axial ligand while reducing the nonbonded repulsions between the heme plane and the axial ligand. The spin state change on Fe is found to occur, not because the Fe moves into the plane of the porphyrin, but because the formation of the FeO_2 bond reduces the number of local exchange interactions that stabilize the high-spin state. The role of the coordination sphere of Fe pertaining to the chemistry of the Hb molecule is to reduce the energy separation between the atomic states. It makes an intermediate-spin state accessible for bond formation and thereby provides a mechanism by which an O_2 molecule can easily and reversibly bind to Hb. Neither the diamagnetic (t_(2g))^6 excited state of Fe nor the excited singlet state of O_2 play a role in the formation of the FeO_2 bond.\r\n\r\nWe show how movement of the proximal imidazole, long thought to initiate the change in quaternary structure of Hb, is also responsible for the reduced O_2 affinity in the T quaternary form of Hb. Assuming that protein forces hinder the movement of the axial ligand leads to the calculation of protein forces in the T and R quaternary forms, and a prediction of the movement of Fe upon a change in the quaternary structure. This movement of the Fe center is found to be on the order of 0.05 \u00c5. Based upon the structural studies of Perutz and co-workers we show how the different protein forces in the T and R quaternary forms can be traced to a small number of hydrogen bonds and salt bridges. This allows us to present a model that displays the molecular origin for the cooperative binding effect. Transferring these protein forces to the coboglobin molecule allows us to calculate the magnitude of the cooperative effect in this metal-substituted Hb. The predicted cooperative effect is found to be in excellent agreement with the experimentally determined value.\r\n\r\nThe ozone model of transition metal-O_2 binding leads to the prediction of a second metal-O_2 stretching band between 1000-1200 cm^(-1). It has also been used to tentatively assign the near-infrared and z- polarized ultraviolet-visible spectra of HbO_2, HbCN, and HbCO.\r\n" }, { "name": "Orlowski, Thomas Edward", "degree": "PhD", "year": "1979", "title": "New Techniques in Coherent Optical Spectroscopy: Optical Dephasing and Radiationless Processes in Molecules", "advisor": "Zewail, Ahmed H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04082008-084228", "creators": [ { "name": { "family": "Orlowski", "given": "Thomas Edward" }, "id": "Orlowski-Thomas-Edward", "display_name": "Orlowski, Thomas Edward" } ], "advisors": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "advisor", "display_name": "Zewail, Ahmed H." } ], "committee": [ { "name": { "family": "Zewail", "given": "Ahmed H." }, "id": "Zewail-A-H", "role": "chair", "display_name": "Zewail, Ahmed H." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "member", "display_name": "Robinson, G. Wilse" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "member", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "member", "display_name": "McKoy, Basil Vincent" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1KE1-7557", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe objectives of this thesis are to develop new high-resolution (\u00b1 3 MHz) coherent nonlinear optical spectroscopic techniques and to utilize them to examine the nature of line broadening processes in optical transitions of isolated large and small molecules. By measuring the coherent and incoherent transients observed either in the forward direction along the laser beam (absorption) or at right-angles to the exciting beam (emission), these techniques allow one to determine optical [...] (the longitudinal relaxation time) and optical [...] (the transverse relaxation time). From [...] and [...] one can obtain under certain circumstances, both the radiative and nonradiative [...] contributions as well as the pure dephasing [...] contribution to the total homogeneous linewidth [...] of the optical transition.\r\n\r\nTwo molecules are examined in detail. Iodine was chosen to demonstrate the new techniques because its conventional spectroscopy is well-known and to examine dephasing and decay processes important for small molecules. It was studied in the gas phase and in a molecular beam. Condensed phase experiments were performed on single crystals of pentacene isolated in a p-terphenyl host to obtain information about the nature of radiationless transitions and dephasing processes important in this large molecule.\r\n\r\nThe optical transition that was studied in iodine is [...]. Using LADS (Laser Acoustic Diffraction Spectroscopy) for obtaining nanosecond time resolution with a narrowband single-mode dye laser and the IRD (Incoherent Resonance Decay) method whereby population dynamics and the coherence in the system can be obtained by monitoring the spontaneous emission, the following Stern-Volmer relationship was obtained for iodine:\r\n\r\n[...] = (0.783 \u00b1 0.032) + (0.0143 \u00b1 0.0005) P(mtorr).\r\n\r\nThis relationship provides a zero-pressure radiative lifetime of 1.28 \u00b1 0.05 [...]sec and a nonradiative collisional quenching cross section of [...] = 70 \u00b1 2 [...]. These results agree with those obtained in previous studies with broadband excitation indicating that excitation bandwidth is unimportant for [...] processes in small molecules. Using the electrooptic method of laser frequency switching, an optical nutation was observed in iodine whose Rabi oscillation frequency [...] provided the dipole moment for the transition ([mu] = 0.05 Debye) after determining the laser field amplitude [...]. The Rabi frequency was also obtained from a coherent oscillation observed on top of the IRD signal in iodine at low pressure. This oscillation decayed by [...] and the overall IRD signal provided [...] such that both the coherence and decay of the system were obtained simply by monitoring the spontaneous emission. The homogeneous linewidth of the transition was measured using the 3-pulse photon echo method. At 10 mtorr pressure it was found to be 579 kHz. This is almost three orders of magnitude less than the inhomogeneous (Doppler) linewidth of ca. 400 MHz. Molecular beam experiments provided the radiative lifetime (1.24 \u00b1 0.02 [...]sec) of iodine in a collisionless environment from which the radiative contribution (22%, 128 kHz) to the total homogeneous linewidth was obtained. Assuming that radiative losses from the lower level of the system can be neglected it was also determined that 38 kHz (7%) of the homogeneous linewidth is due to non-radiative relaxation (inelastic scattering) and a dramatic 413 kHz (71%) is due to pure dephasing [...] as a result of elastic scattering processes. Finally an OFID (optical free induction decay) was observed in the molecular beam whose decay indicated that [...]. Therefore, in a collisionless environment, the only dephasing process for iodine is spontaneous emission (i.e., no intramolecular dephasing processes exist).\r\n\r\nThe optical transition that was studied in pentacene [...] exhibits four sites in a p-terphenyl host. The lowest energy site at 16,887 cm[...] has the following characteristics at 1.8[...]K:\r\n\r\n[...] = 24.9 \u00b1 2 nsec; [...] = 44 \u00b1 2 nsec, and [mu] = 0.7 \u00b1 0.1 Debye.\r\n\r\nExperiments in this system are categorized into two time regimes for theoretical analysis: a transient coherence regime where the observed decay is comparable with [...] and [...], and a steady-state coherence regime where transient dephasing is complete and the off-diagonal elements of the density matrix have decayed to their steady-state values in the presence of the laser field. The Wilcox-Lamb method is used to derive rate equations ([...] dependent) from the density matrix equations of motion. These equations describe the population dynamics in the pentacene level structure ([...] = ground state, [...] = excited singlet state and [...] = triplet manifold) and upon averaging them over the inhomogeneous linewidth of the transition and then using them to fit experimental decay curves one obtains:\r\n\r\n[...] = 24.9 \u00b1 2 nsec and [...] = 15.7 [...]sec,\r\n\r\nthe time constants for spontaneous emission to [...] and crossing into [...], respectively. OFID and nutation expressions are presented for the pentacene level structure and when appropriate averaging is done over both the inhomogeneous linewidth and the laser beam spatial profile, good fits can be obtained for the experimental transients. At 1.8[...]K it was determined that [...] = [...]. Therefore, as in iodine at zero pressure, spontaneous emission is the only dephasing process in pentacene at low temperature. At higher temperature, however, a strongly temperature dependent dephasing process takes place with an onset at 3.7[...]K. A theoretical treatment of the various dephasing channels is presented that explains the observed temperature dependence of [...] in pentacene and attributes pure dephasing to an anisotropy in the scattering amplitudes between the ground and excited states. Optical site selection of the pentacene transitions has been observed and is related to vibrational relaxation and homogeneous and inhomogeneous broadening in this system. Studies of the homogeneous broadening of the vibronic line 267 cm[...] above the lowest energy site indicate that vibrational relaxation is fast (psec) in the excited singlet manifold of pentacene. Finally from more than ten independent experiments including narrow and broad band excitation, on- and off-resonance scattering, Zeeman effect measurements and the transient decay as a function of excess energy in the molecule, a more complete picture of the pentacene level structure is given. It is proposed that the slow decay\t[...] observed during narrowband excitation represents intersystem crossing to nearby triplet manifolds after the transient coherence of the \"two-level\" system [...] has decayed. Furthermore, the decay of the primary state prepared in these experiments is not sensitive to the bandwidth or the coherence properties of the excitation source.\r\n" }, { "name": "Roberts, Daryl Lynn", "degree": "PhD", "year": "1979", "title": "Sulfur Dioxide Transport through Aqueous Solutions", "advisor": "Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022026-072046797", "creators": [ { "name": { "family": "Roberts", "given": "Daryl Lynn" }, "id": "Roberts-Daryl-Lynn", "orcid": "0000-0001-5667-6083", "display_name": "Roberts, Daryl Lynn" } ], "advisors": [ { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1zqn-mh71", "abstract": "A theory for the rate of SO2 transport through aqueous\r\nsolutions has been developed based on measurements of the\r\nsteady-state flux of SO2 through aqueous films of known\r\ncomposition. Conditions in most of the experiments were\r\ntypical of flue gas desulfurization (FGD) scrubbers.
\r\n\r\nAqueous films, in the form of agar gels or soaked\r\npolyethylene filters, were mounted in a diffusion cell.\r\nHumidified nitrogen with a known mole fraction of SO2 (ySO2,o)\r\nflowed through one side of the cell. Clean, humidified N2\r\nflowed through the other side, sweeping away SO2 passing\r\nthrough the films. Films of water and solutions of neutral\r\nand alkaline sodium salts (0.1-2.0M NaCl, 10-3-3.0M NaOH,\r\nNaHSO3, or Na2SO3) were studied with ySO2 = 10-4, 2\u00b710-4, 5\u00b710-4, and 10-3.
\r\n\r\nIn alkaline solutions, the transport by sulfur-containing\r\nions was up to 1300 times larger than the contribution of\r\ndissolved SO2 molecules. The chemical reactions of SO2 that\r\nform these ions have previously been regarded as instantaneous\r\n(i.e., at equilibrium). Equilibrium theory, however, over-predicts\r\nthe observed flux through alkaline solutions by up\r\nto a factor of seven. A new non-equilibrium boundary layer\r\nanalysis (NEBLA) has been developed to account for this\r\ndeviation. This analysis treats the boundary layers as regions\r\nwhere the conversion from molecular SO2 to sulfur-containing\r\nions (and vice-versa) is frozen. The NEBLA is the first\r\nanalysis to predict the flux for a system that has non-linear\r\nkinetics and is far from the limits of both zero and instantaneous\r\nchemical reactions.
\r\n\r\nFor water and NaCl solutions, data agreed with an\r\nanalytical expression for the flux based on the equilibrium\r\napproximation. This expression accounts for the (diffusion-induced)\r\npotential gradient. The potential gradient increases\r\nthe effective diffusivity of HSO3- by approximately 73%. With\r\nthis assist, HSO3-; is responsible for 80% to 95% of the net\r\nflux. The agreement of the water and neutral solution data\r\nwith equilibrium theory shows that the deviation from equilibrium\r\nin the alkaline solutions is a pH effect.
\r\n\r\nBecause the transport theory has been developed for a\r\none-dimensional film, it can be most easily adapted to the\r\nfilm model that is employed in the absorption literature.\r\nIn this way, the theory can be used to predict absorption\r\nrates of SO2 in FGD scrubbers and by bodies of water, rain,\r\nplumes, lung mucus, and plants.
" }, { "name": "Rogers, Christopher Bruce", "degree": "Masters", "year": "1979", "title": "Biosynthetic studies of human fetal hemoglobin", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-090030827", "creators": [ { "name": { "family": "Rogers", "given": "Christopher Bruce" }, "id": "Rogers-C-B", "display_name": "Rogers, Christopher Bruce" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9vhd-4p65", "abstract": "Previous investigators have found unbalanced synthesis of Hb F, with \u03b3 chain synthesized from 30% to 68% as efficiently as \u03b1 chain. In this report, biosynthetic studies of 9 umbilical cord bloods and 6 sickle-cell bloods with elevated levels of Hb F gave an efficiency of 47 \u00b1 3% for \u03b3-chain synthesis relative to \u03b1-chain synthesis.\r\n\r\nAmino acid analysis of the minor zones in chain separation chromatograms showed that two peaks, one eluting before and one after \u03b3 chain, contain products of \u03b3-chain mRNA. These peaks, however, are insufficient to explain the discrepancy in \u03b3-chain synthesis.\r\n\r\nA likely explanation for the reduced \u03b3-chain synthesis is that \u03b3-chain mRNA may have a shorter effective lifetime than \u03b1 - or \u03b2-chain mRNA. There would thus be a progressive imbalance in Hb F synthesis after the blood cell leaves the bone marrow and mRNA synthesis stops.\r\n\r\nA timed study of a single cord blood, with times ranging from 2.5 minutes to 4 hours, showed that incorporation of radioactivity into acetylated \u03b3 chain begins at a high value and decreases with respect to unmodified \u03b3 chain. This implies that the \u03b3 chain may be modified either on the ribosome or shortly after release, but in any case earlier than 2.5 minutes after the start of incubation.\r\n" }, { "name": "Sheard, Sarah A.", "degree": "Masters", "year": "1979", "title": "Angle Resolved Photoemission Calculations", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-100441032", "creators": [ { "name": { "family": "Sheard", "given": "Sarah A." }, "id": "Sheard-Sarah-A", "display_name": "Sheard, Sarah A." } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JECM-5E41", "abstract": "No abstract." }, { "name": "Thomas, Glenn E.", "degree": "PhD", "year": "1979", "title": "The Chemisorption of Carbon Monoxide, Oxygen and Nitric Oxide on the Ruthenium (001) Surface", "advisor": "Weinberg, William Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162026-173912462", "creators": [ { "name": { "family": "Thomas", "given": "Glenn E." }, "id": "Thomas-Glenn-E", "display_name": "Thomas, Glenn E." } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/dsb8-c685", "abstract": "The vibrational energies of small molecules adsorbed on the Ru(001)\r\nsurface were studied by means of inelastic electron scattering. The\r\ninstrument used to carry out this work is an electron spectrometer of the\r\nKuyatt-Simpson type. The design and operation of this instrument, which\r\nis capable of carrying out a number of electron spectroscopies important in\r\nchemisorption research, is discussed in detail.
\r\n\r\nThe vibrations of carbon monoxide, oxygen and nitric oxide chemisorbed\r\non the basal plane of Ru provide insight into their chemical structures.\r\nCarbon monoxide exhibits the carbon-oxygen stretching frequency (1980 cm-1 -\r\n2080 cm-1) characteristic of a linear CO, with a single carbon-metal bond.\r\nThis is true at all coverages, although at saturation coverage the low-energy\r\nelectron diffraction pattern shows that the adsorbed CO overlayer is\r\nout of registry with the substrate. An interadsorbate interaction is\r\nproposed to explain the observed increase in the carbon-oxygen stretching\r\nfrequency of 100 cm-1 with coverage.
\r\n\r\nOxygen is adsorbed dissociatively on Ru(001) and exhibits a single\r\ncoverage-dependent stretching frequency of approximately 570 cm-1. The\r\nlow frequency indicates that atomic oxygen is bonded in a bridged or\r\nthreefold site. A study of chemisorbed oxygen over the temperature range,\r\n100 K to 1000 K, shows the existence of energy gain peaks in the electron\r\nenergy distribution.
\r\n\r\nNitric oxide adsorbs molecularly at 130 K but dissociates at approximately\r\n400 K, depending on coverage. Comparison with the stretching\r\nfrequencies of metal nitrosyls suggests that NO is bound in a threefold\r\nor bridged site at low coverage and as a linear NO with a single metal-nitrogen \r\nbond at high coverage. The vibrational spectrum of adsorbed NO\r\nchanges irreversibly if the surface is heated to a temperature below the\r\nonset of desorption (depending on coverage). A mechanism is proposed\r\nfor this in which the bridged NO dissociates at room temperature and the\r\natomically bound nitrogen and oxygen atoms block further dissociation.
" }, { "name": "Tyler, David Ralph", "degree": "PhD", "year": "1979", "title": "The Photochemistry and Electronic Structures of Metal Carbonyl Cluster Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03162026-181948664", "creators": [ { "name": { "family": "Tyler", "given": "David Ralph" }, "id": "Tyler-David-Ralph", "display_name": "Tyler, David Ralph" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cdy5-4p05", "abstract": "The electronic structures and spectra of the M3(CO)12 (M = Fe,\r\nRu, Os) complexes are discussed. Using techniques such as single\r\ncrystal polarized spectroscopy and MCD spectroscopy it is shown\r\nthat the two lowest energy electronic transitions in these complexes\r\nare the \u03c3 \u2192 \u03c3* (xz (bonding) \u2192 xz (antibonding)) and \u03c3*' \u2192 \u03c3*\r\n(z2 (antibonding) \u2192 xz (antibonding)) transitions.
\r\n\r\nPhotolysis of Ru3(CO)12 leads to fragmentation of the cluster\r\ncomplex; however, a photochemical study of Os3(CO)12 showed that\r\nOs - CO dissociation is a more efficient photoprocess than Os - Os\r\nbond cleavage. The different photochemical behaviors of the two\r\ncluster complexes is ascribed to their different lowest excited\r\nstates. The lowest excited state of Ru3(CO)12 is \u03c3 \u2192 \u03c3*, a state\r\nwhich certainly leads to metal-metal bond cleavage. The \u03c3*' \u2192 \u03c3*\r\nstate is lowest in Os3(CO)12. Electronic excitation to this state\r\ndoes not lead to efficient cluster fragmentation.
\r\n\r\nThe effects of bridging ligands on photochemical metal-metal\r\nbond cleavage were also studied. It was found that the bridging\r\nCO groups prevent photofragmentation of the (h5-C5H5)2Fe2(CO)4\r\nmolecule and also of the Fe3(CO)112- complex. In the latter molecule,\r\nFe-CO dissociation is the primary photoprocess. In the case of\r\n(h5-C5H5)2Fe2(CO)4, the primary photoproduct is a CO-bridged dimer which has no metal-metal bond.
" }, { "name": "Williams, Roger Macauley", "degree": "PhD", "year": "1979", "title": "Crystallographic Order and Disorder in Quasi-One-Dimensional Conductors", "advisor": "Samson, Sten Otto; Gordon, Joseph", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102018-143101993", "creators": [ { "name": { "family": "Williams", "given": "Roger Macauley" }, "id": "Williams-Roger-Macauley", "display_name": "Williams, Roger Macauley" } ], "advisors": [ { "name": { "family": "Samson", "given": "Sten Otto" }, "id": "Samson-Sten-Otto", "role": "advisor", "display_name": "Samson, Sten Otto" }, { "name": { "family": "Gordon", "given": "Joseph" }, "id": "Gordon-Joseph", "role": "advisor", "display_name": "Gordon, Joseph" } ], "committee": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "chair", "display_name": "Anson, Fred C." }, { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "member", "display_name": "Vaughan, Robert W." }, { "name": { "family": "Gagne", "given": "Robert R." }, "id": "Gagne-Robert-R", "role": "member", "display_name": "Gagne, Robert R." }, { "name": { "family": "Gordon", "given": "Joseph" }, "id": "Gordon-Joseph", "role": "member", "display_name": "Gordon, Joseph" }, { "name": { "family": "Samson", "given": "Sten Otto" }, "id": "Samson-Sten-Otto", "role": "member", "display_name": "Samson, Sten Otto" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FPJF-PM42", "abstract": "Stacked, conducting isocyanide complexes of rhodium(I) were synthesized and characterized by x-ray diffraction and electrical measurements. Good crystals of orthorhombic [Rh(CNCHCH2)4]ClO4, with a0 = 8.81 \u00c5, b0 = 22.85 \u00c5, c0 = 12.70 \u00c5, were obtained and a structural refinement was carried out in space group Immm. The rhodium chain is nearly uniform (Rh-Rh = 2.94 \u00c5) and ligands and anions show considerable disorder. The room temperature conductivity is -2 \u03a9-1 cm-1 and conductivity is activated. The moderately high conductivity of [Rh(CNCHCH2)4]ClO4 is due to the presence of a low-lying conduction band rather than a non-integral rhodium oxidation state.
\r\n\r\nThe disorder, tetragonal phase of (TTF)Clx, a0 = 11.19 \u00c5, c0 = 3.60 \u00c5, was studied for compositions x = 0.67, x = 0.70. A room\r\ntemperature structural refinement in space group P42/mnm revealed eclipsed stacking of TTF cations and extremely high disorder of chlorides in channels. Low temperature studies revealed ordering of chloride ions for both compositions. (TTF)Cl0.67 undergoes an incomplete structural transition to a monoclinic symmetry phase at ~250\u00b0 K. Ordering of chloride ions occurs at the same temperature. Fast cooling (>1\u00b0 K/hr) results in peak broadening which is apparently due to the very small size of diffracting domains within the crystal. Both small domain size and the inequivalent environments of TTF cations following chloride ordering may contribute to the drop in conductivity observed at the phase transition.
\r\n\r\nStructural refinements of both the subcell (space group Cmca, a0 = 18.47 \u00c5, b0 = 4.95 \u00c5, c0 = 18.30 \u00c5) and full cell (space group Pmc2l, a0 = 18.47 \u00c5, b0 = 9.90 \u00c5, c0 = 18.30 \u00c5) of a low disorder crystal of TTT2I3 were carried out. The iodine chain is highly disordered and all sites have less than full occupancy. The presence of I3- and I2 species in the chain is likely. The resulting aperiodic potential due to the iodide chain may be expected to be retained at low temperature and inhibit a metal-to-insulator transition.
\r\n\r\nElectrochemical crystal-growth experiments involving TTF, TMTSF, and HMTSF gave successful results with the first two donors. Crystals of (TMTSF)Br0.8 and (TMTSF)(SCN)0.5 are isostructural, although the latter exhibits satellite reflections (period = 4.6 x c0) in diffraction patterns. Both structures were refined in space group Cmcm, and the satellite data of (TMTSF)(SCN)0.5 was modeled in space group Cmc2l. Unit cell parameters are a a0 = 9.798 \u00c5, b0 = 23.837 \u00c5, c0 = 7.095 \u00c5, for the bromide and a0 = 9.919 \u00c5, b0 = 24.124 \u00c5, c0 = 7.220 \u00c5, for the thiocyanate. The planes of these cations are perpendicular to the z-axis and consecutive cations slip back and forth by ~1.3 \u00c5 to reduce methyl group steric repulsion.
\r\n\r\nAll of the systems studied are single carrier conductors with conduction along the cation stack and high disorder of anions. The nature of the disorder and its relationship to phase transitions, as well as interchain coupling and stacking in the cation chain, were evaluated in these compounds. Comparison of (TTF)Cl0.67 and (TTT02I3 were especially useful, as both exhibit comparably very short range order of halide ions at room temperature, but different cation stacking arrangements (eclipsed and slipped, respectively) and hence different interchain coupling and electronic bandwidth.\r\nStructural studies at room temperature and low temperature provided an opportunity to understand the important differences in the electrical properties of these two materials.
" }, { "name": "Woodin, Richard Lawrence", "degree": "PhD", "year": "1979", "title": "Ion Cyclotron Resonance Studies of Vibrationally Excited Ions. I. Low Intensity Multiphoton Dissociation of Gas Phase Ions Using CW CO\u2082 Laser Radiation. II. Infrared Radiative Stabilization of Energized Species in the Gas Phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-133235754", "creators": [ { "name": { "family": "Woodin", "given": "Richard Lawrence" }, "id": "Woodin-Richard-Lawrence", "display_name": "Woodin, Richard Lawrence" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cggh-sb21", "abstract": "This thesis is divided into two general topics; vibrational excitation of gas phase molecules using cw CO_2 laser radiation (Chapters II and III) and stabilization of chemically activated species by infrared radiative emission (Chapters IV-VI). Chapter I is a brief introduction to the topics discussed in Chapters II- VI.\r\n\r\nMultiphoton dissociation of molecules is observed using low intensity (1-100 W cm^(-2)) cw CO_2 laser radiation. Ion cyclotron resonance techniques allow gas phase ions to be stored and irradiated for times approaching several seconds prior to mass analysis. Chapter II describes multiphoton dissociation of ions derived from diethyl ether [(C_2H_5)_2O] while Chapter III describes multiphoton dissociation of C_3F_6^+ from perfluoropropylene (C_3F_6). Energy fluence thresholds and cross-sections for multiphoton dissociation measured using low intensity radiation qualitatively agree with similar measurements using megawatt pulsed infrared lasers. For all ions which photodissociate only the lowest activation energy process is observed. Effects of bimolecular interactions, varying laser intensity, and laser wavelength on photodissociation probabilities are explored. At high pressures collisions are observed to deactivate vibrationally excited ions. At low pressures, however, C_3F_6^+ photodissociation is enhanced by collisions. The consequences of collisional enhancement of multiphoton absorption are discussed.\r\n\r\nICR techniques are uniquely suited for studying ion-molecule reactions under nearly collisionless conditions. Chapters IV and V discuss direct association reactions of Li^+ with (C_2H_5)_2CO, CH_3COC_2H_5, (CH_3)_2CO, (CD_3)_2CO, CH_3CHO, and H_2CO at pressures low enough (< 10^(-6) Torr) to preclude collisional stabilization of the chemically activated adduct. The stabilization mechanism is assumed to be via infrared emission, and calculated attachment rates are in good agreement with experiment.\r\n\r\nIn experiments similar to those described above, rates of direct electron attachment to C_6F_6 (perfluorobenzene), C_7F_8 (perfluorotoluene), c-C_4F_8 (perfluorocyclobutane), and C_7F_(14) (perfluoromethylcyclohexane) are measured at low pressure by ICR techniques. Rate constants measured by ICR are found to be one to two orders of magnitudes smaller than high pressure swarm measurements. The results are discussed in terms of radiative stabilization at low pressure versus collisional stabilization at high pressure. Combination of data from time-of-flight, electron beam-swarm, and ICR experiments allows estimates of infrared radiative lifetimes to be made. These fall in the range 0. 4-3. 0 msec, which are typical of infrared radiative processes. Data are also presented for dissociative electron attachment of CCl_4.\r\n" }, { "name": "Yortsos, Yanis Christos", "degree": "PhD", "year": "1979", "title": "Analytical Modelling of Oil Recovery by Steam Injection", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11022004-090942", "creators": [ { "name": { "family": "Yortsos", "given": "Yanis Christos" }, "id": "Yortsos-Yanis-Christos", "display_name": "Yortsos, Yanis Christos" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/T5A4-1W70", "abstract": "This dissertation is concerned with the mathematical modelling of oil recovery by steam injection using analytical techniques.\r\n\r\nAn integral method for generating approximate solutions to the one and two- (three-) dimensional steam injection processes is presented. Due to the qualitatively different character of the problem the one- and two- (three-) dimensional cases are examined separately.\r\n\r\nThe applicability of the method for the determination of the rate of growth of the steam zone volume in one-dimensional systems is considered. An extensive study of the heat transfer in the surroundings and the hot liquid zone is carried out to complement the one-dimensional implementation of the technique. The resulting class of moving boundary problems and their methods of solution are discussed in detail. The results obtained are then combined with the integral technique to derive upper and lower bounds, asymptotic solutions and approximate solutions to the rate of growth of the steam zone. The important physical parameters are identified and their significance in the design of the process is outlined. In particular, the very important effect of heat transport in the surroundings and the hot liquid zone is fully accounted.\r\n\r\nFor two- (three-) dimensional systems, a more detailed version of the integral method is developed to account for the effect of gravity segregation in the determination of the steam front shape. A non-linear partial differential equation that describes the evolution of the steam front shape in gravity dominated systems is derived. The significance of the various physical parameters in the performance of a three-dimensional steam injection process is discussed by providing a solution to the equation derived, in the limit of predominantly viscous flows.\r\n\r\nA critical evaluation of the existing analytical models is presented and the regions of their validity established. The potential of the techniques developed, particularly in the heat transfer area, to treat a class of in-situ thermal methods is also clearly indicated." }, { "name": "Almassy, Robert James", "degree": "PhD", "year": "1978", "title": "Structure Determination and Refinement of Pseudomonas aeruginosa Cytochrome c\u2085\u2085\u2081 at 2.0 A\u030a Resolution", "advisor": "Dickerson, Richard E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172026-225651328", "creators": [ { "name": { "family": "Almassy", "given": "Robert James" }, "id": "Almassy-Robert-James", "display_name": "Almassy, Robert James" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8k3m-9b97", "abstract": "The crystal structure of the protein cytochrome c 5 5 1 from\r\nPseudomonas aeruginosa has been solved by the method of multiple isomorphous\r\nreplacement and refined by constrained difference Fourier\r\n0 methods to an R-factor of 16.2% at 2.0 A\u030a resolution.
\r\n\r\nCrystallization conditions were found at pH 5.6. Three heavy\r\natom derivatives (K2 PtCl4, UO2(NO3)2, \r\nand NaAu(CN)2) were used in the\r\nmultiple isomorphous replacement x-ray diffraction phase analysis. A\r\nlow resolution protein electron density map was calculated. The protein\r\nmain chain was continuous and easily interpreted. The location\r\nof the heme and a few side chains were also determined. The resolution \r\nwas extended to 2.4 A\u030a and a wire model was built to the electron\r\ndensity. The map quality was good and almost all atoms fit into\r\nstrong density. These coordinates were improved by refinement at 2.0 A\u030a\r\nresolution to an R-factor of 16.2%. Additional structural information\r\nwas obtained, including individual isotropic temperature factors,\r\nestimates of coordinate errors, and solvent positions.
\r\n\r\nc 5 5 1 has major changes, compared to eukaryotic c, in the number\r\n(82 compared to 103) and the sequence of amino acids. Residues which\r\nhave been highly conserved in c-type cytochrome structures are altered\r\nor deleted in c 5 5 1. Homology alignment predictions based on sequence\r\nare discussed. Despite these differences, the overall main chain fold\r\nis conserved, with only one major deletion and some minor deletions\r\nand additions.
" }, { "name": "Bakke, Antony Clifford", "degree": "PhD", "year": "1978", "title": "Studies on the Chromatin of the Cellular Slime Mold Dictyostelium Discoideum", "advisor": "Bonner, James Frederick", "url": "https://resolver.caltech.edu/CaltechTHESIS:01242026-214622936", "creators": [ { "name": { "family": "Bakke", "given": "Antony Clifford" }, "id": "Bake-Antony-Clifford", "display_name": "Bakke, Antony Clifford" } ], "advisors": [ { "name": { "family": "Bonner", "given": "James Frederick" }, "id": "Bonner-J-F", "role": "advisor", "display_name": "Bonner, James Frederick" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/rmzz-9k75", "abstract": "This thesis concerns the chromatin of Dictyostelium discoideum which has been characterized chemically, physically, and biochemically. The chromatin was carefully purified by differential centrifugation using nuclease and protease inhibitors followed by a brief, controlled Staphylococcal nuclease digestion. It has a chemical composition in terms of mass of 1.0 part DNA to 0.18 part RNA to 0.98 part histone to 1.02 part nonhistone protein. Its ultraviolet absorption spectrum is typical of chromatins from other eukaryotes.
\r\n\r\nThe histones have been extracted from chromatin with 0.4 N H2SO4 and characterized on three gel systems. Three are equivalent to histones in higher eukaryotes and have the following molecular weights: Hl is 20,000; H3 is 14,900, and H4 is 12,000. Another one is not found in higher eukaryotes, but may be present in lower eukaryotes other than Dictyostelium. It is termed H6 and has a molecular weight of 15,800. There are no equivalents of the higher eukaryotic histones H2a and H2b.
\r\n\r\nThe slime mold histones were also analyzed by ion-exchange chromatography. Hl elutes with the weakly bound proteins, while H3, H4, and H6 elute with the tightly bound peak. No proteins elute with calf thymus histones Hl, H2a, or H2b indicating that slime mold Hl is less basic than calf Hl and confirming that H6 is not equivalent to H2a or H2b.
\r\n\r\nThe chromatin may be separated into two fractions by shearing briefly with Staph. nuclease, centrifuging, reshearing the insoluble pellet, and centrifuging again. The first supernatant contains 5% of the total DNA and is the first sheared chromatin fraction. The second supernatant contains 80% of the DNA. Both fractions have the same histone compositions, but differ in their mass ratios of nonhistone chromosomal proteins (NHCP). The NHCP are characterized on gels and differences are pointed out.
\r\n\r\nA subset of NHCP are extracted and tentatively identified as actin-like and myosin-like proteins on the basis of solubility and molecular weight. The actin-like protein accounts for approximately 5% of the total NHCP mass.
\r\n\r\nThe basic unit of structure in the chromatin is the nucleosome. In Dictyostelium it is 98.6 \u00c5 in diameter and has a sedimentation coefficient of 11.5S. It contains 187 b.p. of DNA consisting of a 137 b.p. core and a 50 b.p. linker. Approximately 50% of the chromatin is protected from Staph. nuclease digestion, but this decreases when protease activity is not inhibited. When the chromatin is melted, four transitions are observed at 54.5\u00b0, 66.7\u00b0, 74.9\u00b0, and 79.7\u00b0. The structure of Dictyostelium chromatin is very similar to that seen in higher eukaryotes.
" }, { "name": "Cannon, David Maxwell", "degree": "Masters", "year": "1978", "title": "NMR Study of Fluoride Ion Diffusion in Potassium-Doped \u03b2-PbF\u2082", "advisor": "Vaughan, Robert W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-111321744", "creators": [ { "name": { "family": "Cannon", "given": "David Maxwell" }, "id": "Cannon-David-Maxwell", "display_name": "Cannon, David Maxwell" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8dgg-dx50", "abstract": "Fluoride ion motion in a KF-doped \u03b2-PbF_2 crystal was studied by measuring the ^(19)F relaxation times T_1, T_2, and T_(1p). Measurements were made on a 56.4 MHz pulsed spectrometer over the temperature range -101\u00b0C to 22\u00b0C; the T_(1p) data were taken in a rotating magnetic field of 6.8 G. Two sets of T_2 data were taken, yielding activation energies of 0.17 \u00b1 0.01 eV and 0.18 \u00b1 0.01 eV. Activation energies obtained from T_1 and T_(1p) data were 0.17 \u00b1 0.01 eV and 0.34 \u00b1 0.02 eV, and a correlation time of 2.9 \u00b5sec was observed at -20\u00b0C, the temperature at which the T_(1p) minimum occurs. Comparison of these data with previously published results shows that potassium-doping is more effective than sodium-doping in activating fluorine motion. It is believed that T_1 relaxation is dominated by a mechanism other than anionic diffusion.\r\n" }, { "name": "Coyle, Catherine Louise", "degree": "PhD", "year": "1978", "title": "Mechanisms of Electron Transfer in Cytochromes and Blue Copper Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302026-033154761", "creators": [ { "name": { "family": "Coyle", "given": "Catherine Louise" }, "id": "Coyle-Catherine-Louise", "display_name": "Coyle, Catherine Louise" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fq3x-yd79", "abstract": "The mechanisms of electron transfer in cytochromes and bluecopper proteins are investigated by examining the oxidation and reduction of horse heart cytochrome c, Pseudomonas aeruginosa cytochrome c551, Rhus vernicifera stellacyanin, Phaseolus vulgaris plastocyanin and Pseudomonas aeruginosa azurin by inorganic redox agents. The rates of electron transfer in these systems have been analyzed within the framework of the relative Marcus theory of outer sphere electron transfer. The activation parameters for these processes have also been examined.
\r\n\r\nThe reduction of Pseudomonas aeruginosa cytochrome c551, by Fe(EDTA)2- has been investigated. The electrostatics-corrected self-exchange rate constant is similar to that obtained for horse heart cytochrome c. The close correspondence indicates that the two proteins employ similar electron transfer mechanisms. It is proposed that this mechanism. involves reagent contact and little protein conformational change at the partially exposed heme edge.
" }, { "name": "Davis, Nicki Lee", "degree": "Masters", "year": "1978", "title": "Investigations into the Structures of Biologically Important Molecules. I. The Crystal Structure of Monoclinic Calcium Pyrophosphate Tetrahydrate. II. The Purification of Glucose-6-Phosphate Dehydrogenase from Human Red Blood Cells. III. A Partial Solution of the Crystal Structure of p-Trimethylammoniumbenzene Sulfonate", "advisor": "Dickerson, Richard E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232010-072850392", "creators": [ { "name": { "family": "Davis", "given": "Nicki Lee" }, "id": "Davis-Nicki-Lee", "display_name": "Davis, Nicki Lee" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FB15-4S36", "abstract": "Chapter I deals with the solution and refinement of the crystal structure of monoclinic calcium pyrophosphate tetrahydrate. The role of the triclinic dihydrate of calcium pyrophosphate as the cause of inflammation in pseudogout is briefly discussed, and a detailed comparison is made between its crystal structure and that of the mono-clinic tetrahydrate, which does not cause disease.\r\n\r\nIn Chapter II, methods for the isolation of the enzyme glucose 6-phosphate dehydrogenase from human red blood cells are described. The problems involved in adapting a small-scale purification procedure to large-scale production are investigated, and solutions proposed. Alternative methods for the purification of the enzyme are developed and tested.\r\n\r\nA partial solution of the crystal structure of p-trimethyl-ammoniumbenzenesulfonate (ZWT) is given in Chapter III. This compound is the product of a solid state rearrangement of methyl-p-dimethyl-aminobenzene sulfonate (ASE). Although the structure of ZWT could not be refined, a trial structure obtained by a direct methods calculation bore a close resemblance to the known structure of the parent compound, MSE. This result was in accord with previous data on the details of the rearrangement reaction.\r\n" }, { "name": "Dawson, Daniel Richard", "degree": "Masters", "year": "1978", "title": "Ultrafast Coherent Transients & Excited State Dynamics in Gases and Solids", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-080339920", "creators": [ { "name": { "family": "Dawson", "given": "Daniel Richard" }, "id": "Dawson-Daniel-Richard", "display_name": "Dawson, Daniel Richard" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E3GT-JD57", "abstract": "I. A new technique utilizing the electro-optic frequency switching of a single mode ( 6 Mhz) dye laser was used to observe free induction decay and optical nutation in iodine gas and optical nutation in an organic mixed crystal (pentacene in p-terphenyl) at low temperature. A new technique, incoherent resonance decay (IRO) was also developed. These experiments allow one to determine T_1 and T_2, the longitudinal and transverse relaxation times of the excited ensemble, in analogy with magnetic resonance. For I_2(g) at O\u2219C; T_l = 2.3 x 10^(-7) sec, T_2 \u2243 1 x 10^(-7) sec. These techniques are limited to a time scale > 10 nsec.\r\n\t\r\nII. The construction and characterization of \"cw\", mode-locked dye laser capable of putting out a continuous train of reproducible sub-picosecond pulses is described. Experiments utilizing this laser for the measurement of picosecond coherent transients and time resolved absorption spectroscopy are proposed.\r\n" }, { "name": "Dwyer, John Patrick", "degree": "PhD", "year": "1978", "title": "Quantum Mechanical Studies of Molecular Scattering", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012026-183146076", "creators": [ { "name": { "family": "Dwyer", "given": "John Patrick" }, "id": "Dwyer-John-Patrick", "display_name": "Dwyer, John Patrick" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/f6qz-1472", "abstract": "This thesis is not about changing the world. Its scope is much\r\nmore modest; we wish only to describe a very small part of it. In fact,\r\nwe will usually restrict ourselves to only three or four atoms at any\r\none time.
\r\n\r\nThis thesis is a collection of seven theoretical studies on elementary\r\nchemical processes. In each of the studies we have used a quantum\r\nmechanical framework to describe a particular chemical system. In\r\nnearly every case we have formulated the problem exactly. That is, we\r\nhave made no mathematical approximations to the governing equations.\r\nBecause these problems are too complex to be solved analytically, we\r\nhave turned to computers to solve them numerically. Once the appropriate\r\nequations have been derived, each study becomes an exercise in\r\nnumerical techniques and computer programming. The crucial step,\r\ninterpretation of the numbers, comes last.
\r\n\r\nIn the first chapter we examine a model that describes energy\r\ntransfer in the collinear collision of two diatomic molecules. In this\r\nsystem the diatomics are homonuclear Morse oscillators and interact\r\nthrough an exponentially repulsive potential. We compare our results\r\nwith previous quantum calculations and find that the older results were\r\nnot converged with respect to the number of basis functions. A comparison\r\nwith the adiabatic approximation of Clarke and Thiele shows that\r\nthe approximate results are reasonably accurate at all but the highest\r\ncollision energies.
\r\n\r\nThe second chapter is a study of the importance of low energy\r\nreaction probabilities in calculating low temperature rate constants. It\r\nlimited to the collinear H + H2 reactive system using a realistic\r\npotential energy surface. We show that the integral which relates\r\nprobabilities to rate constants must be calculated carefully in order to\r\navoid numerical errors. We show that this was not done by other\r\nworkers and has probably led to an incorrect conclusion concerning the\r\nisotope dependence of the transmission coefficient.
\r\n\r\nThe third chapter is a survey of resonances in the reactive\r\nscattering of collinear H + H2 and its symmetric isotopic variants.\r\nFrom the survey we note trends and differences in the resonance\r\nstrengths and positions caused by the various mass combinations.\r\nThis leads us to propose a simple model for collinear scattering which\r\nshould predict resonances. In fact, it correctly predicts their relative\r\nstrengths and their positions to better than 0.08 eV.
\r\n\r\nThe fourth chapter is an extensive study of the effect of barrier\r\nheights on vibrational deactivation in collinear scattering. The five\r\nsurfaces used were for the H + FH system with barriers ranging from\r\n1.5 kcal/mole to 40 kcal/mole. The motivation for the study comes\r\nfrom recently published work which indicates that the correct barrier\r\nin the HFH arrangement channel is much closer to 40 kcal/mole than\r\nthe often used 1.5 kcal/mole. The results indicate that the large barriers\r\nsignificantly reduce the rate of collisional deactivation via reaction,\r\nbut that nonreactive deactivation is roughly constant for a wide\r\nrange of barrier heights.
\r\n\r\nIn Chapter 5 we propose a method to describe collinear breakup\r\ncollisions of the form A + BC \u2192 A + B + C. The method is general and\r\ncan be applied to systems in which the energy is too low to allow\r\ndissociation. It has been applied to the H + H2 reaction and found to\r\naccurately reproduce reaction probabilities at low energies. The\r\ncentral idea is to use a discrete pseudo-vibrational basis set which can\r\ndescribe both bound and continuum states naturally. This preliminary\r\nwork points the way to further calculations.
\r\n\r\nIn the last two chapters we move to three-dimensional collisions.\r\nChapter 6 is a comparison of two independent calculations of reactive\r\nscattering in an actual chemical system, one by Elkowitz and Wyatt\r\n(EW) and the other by Schatz and Kuppermann (SK). The comparison\r\nshows that the results are qualitatively and quantitatively different. It\r\nfurther shows that differences lie in the separate formulations of the\r\nproblem and that the SK method is numerically converged while the EW\r\nis not. We note that the EW method used certain approximations that\r\nwere not investigated and conclude that their results are in error.
\r\n\r\nIn the last chapter we consider the difficulty of doing exact quantum\r\ncalculations for even simple reactive systems and propose a mathematical\r\napproximation that preserves the accuracy of the exact results.\r\nThe approximation arises from the neglect of certain off-diagonal\r\nangular momentum terms in the Hamiltonian and thus reduces the\r\nnumber of coupled equations to be solved simultaneously. We find that\r\nthe computation time can be reduced by as much as a factor of 20.
" }, { "name": "Eisenach, James Conrad", "degree": "Masters", "year": "1978", "title": "1. 0-Substituted Serine and Threonine Residues in Acetylcholine Receptor Protein from Torpedo californica. 2. Synthesis of a New Fluorescent Probe for Ligand Binding to Acetylcholine Receptor from Torpedo californica", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-135021562", "creators": [ { "name": { "family": "Eisenach", "given": "James Conrad" }, "id": "Eisenach-James-Conrad", "display_name": "Eisenach, James Conrad" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0rts-8j78", "abstract": "Part I deals with chemical studies performed on \r\npurified acetylcholine receptor from Torpedo Californica \r\ndesigned to document the presence and nature of 0-substituted serine and threonine residues. Treatment of \r\nreceptor with methylamine in base and analysis of the \r\nproducts formed showed 24 0-substituted serine residues \r\nper 300,000 daltons protein and the presence of 0-substituted serine in all four subunits. The amount of \r\n0-substituted threonine present in receptor was estimated \r\nby treatment with alkaline sodium borohydride, suggesting \r\n25 such residues per 300,000 daltons protein. Evidence \r\nis presented suggesting that at least half of this 0-substitution to serine and threonine is accounted for by\r\n0-glycosyl linkage to carbohydrate chains of short length.\r\n\r\nPart II deals with synthesis of a fluorescent probe \r\nfor ligand binding to acetylcholine receptor. The probe \r\nsynthesized contains a highly fluorescent moiety and a \r\nphoto-induced reactive azide group, and is a suicide \r\nprobe in that it contains an acetylcholine moiety which \r\nshould direct it to the ligand binding site. This latter \r\nmoiety can be removed after reacting the azide to leave\r\na fluorescent probe located adjacent to the ligand \r\nbinding site.\r\n" }, { "name": "Flanagan, James Brian", "degree": "PhD", "year": "1978", "title": "Some Investigations in Theoretical and Experimental Electrochemistry", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302017-163917597", "creators": [ { "name": { "family": "Flanagan", "given": "James Brian" }, "id": "Flanagan-James-Brian", "display_name": "Flanagan, James Brian" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kb90-ht51", "abstract": "This thesis is composed of three distinct topics.\r\nChapters II, III and IV are concerned with the analytical \r\nconsequences of adsorption of reactants at the electrode\r\nsurface with d.c. polarography and normal and differential\r\npulse polarography. Theoretical behavior was calculated\r\nby means of digital simulation and Laplace transform\r\ntechniques. The effects of nonlinear adsorption isotherms\r\nand uncompensated resistance on current-potential response\r\nwas calculated. The reaction Cd+2/Cd (Hg) with adsorption\r\ninduced by the presence of iodide was used as a test system.
\r\n\r\nChapters V and VI are concerned with the electrochemical\r\nbehavior of molecules with more than one center for electron\r\ntransfer. Classical statistical methods were used with\r\ncomputer calculation of results, Problems considered\r\ninclude concentration- and current-potential behavior of:\r\n(1) polymeric species with no interaction between centers;\r\n(2) dimers with interactions; and (3) asymmetric binuclear\r\nmolecules.
\r\n\r\nChapter VII discusses data analysis techniques for\r\n\"large step\" coulostatics in the study of electron transfer\r\nkinetics. The merits of the technique in electrochemistry\r\nare discussed. A method for the use of a numerically\r\ngenerated function as the basis function for nonlinear\r\nregression is discussed.
\r\n\r\nChapter VIII presents a study of alternative methods\r\nof \"small step\" coulostatic data analysis. Strong cross-correlation\r\nwas found between double layer capacitance,\r\ncharge transfer parameters and diffusional parameters.
" }, { "name": "Frueholz, Robert Paul", "degree": "PhD", "year": "1978", "title": "Electronic Spectroscopy of Various Molecular Systems by Low-Energy, Variable Angle, Electron Impact", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042009-104248477", "creators": [ { "name": { "family": "Frueholz", "given": "Robert Paul" }, "id": "Frueholz-Robert-Paul", "display_name": "Frueholz, Robert Paul" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xedy-ks74", "abstract": "The technique of low-energy, variable-angle, electron impact spectroscopy has been used to study the electronic spectroscopy of several groups of molecules. In each of the molecules, spin-forbidden and spin-allowed transitions have been investigated as well as excitations lying above the first ionization potential. Studies were performed at incident electron beam energies between 25 eV and 75 eV,at scattering angles ranging from 0\u00b0 to 80\u00b0. The excitation energy region studied was from 0 eV to energies greater than 15 eV. Molecules investigated were selected because of their inherent spectroscopic interest; elucidation of their spectra would aid in explaining photochemical processes in which they are involved; and in some cases the molecules were of an energy-related nature. Ketene (H_2CCO) is a molecule of particular photochemical interest. Transitions were observed in its spectra at energies of 3. 7 eV, 5.3 eV and 5.86 eV. They are assigned, respectively, to an n \u2192 \u03c0^*, X^1A_1 \u2192 ^1A^2 transition, a \u03c0 \u2192 \u03c0^*, X^1A_1 \u2192 ^3A_1 transition and an n \u2192 3s, singlet \u2192 singlet, Rydberg transition. Both 1, 3, 5-cycloheptatriene and 1,3,5, 7-cyclooctatetraene are also of photochemical interest. They have both been found to be efficient dye laser quenchers and their low-lying triplet states are of importance in these quenching mechanisms. Three singlet \u2192 triplet transitions were located in 1, 3, 5, 7- cyclooctatetraene's spectrum with maxima at 3.05 eV, 4. 05 eV, and 4.84 eV. The spin-allowed transitions are also discussed. In the spectrum of 1,3, 5-cycloheptatriene two triplet states were located at 3.05 eV and 3.95 eV. Electron-impact spectra of benzene and eleven fluorine substituted derivatives were obtained. Each molecule shows an absorption maximum at about 3.9 eV corresponding to a singlet \u2192 triplet, \u03c0 \u2192 \u03c0^*, transition. In benzene, fluorobenzene, o-difluorobenzene, m-difluorobenzene, and 1, 3, 5-trifluorobenzene, an additional singlet \u2192 triplet transition was detected at about 5.7 eV. Three singlet \u2192 singlet transitions analogous to the 4.90 eV, 6.20 eV, and 6.95 eV benzene excitations are seen in each of the fluorine-substituted molecules. The more highly substituted compounds exhibit an additional singlet \u2192 singlet transition which is most clearly observed in the hexafluorobenzene spectrum at 5.32 eV. The electronic spectroscopy of conjugated cis-1, 3-dienyl systems has been investigated by obtaining the spectra of 1, 3-cyclopentadiene, 1, 3-cyclohexadiene, and 1, 3-cycloheptadiene. In each molecule a single low-lying triplet state was detected with maximum intensity at 3.10 eV, 2.94 eV, and 2.99 eV, respectively. The singlet-state spectra were also investigated and discussed in terms of interacting ethylenic units. The spectrum of 1, 3-cyclopentadiene was compared to those of the heterocycles, furan (C_4H_4O), thiophene (C_4H_4S) and pyrrole (C_4H_4NH). 1, 3-Cyclopentadiene's spectrum is best discussed in terms of a cis-1, 3-dienyl system. The electron-impact spectra of cyclohexene and norbornene were obtained along with those of the non-conjugated dienes, 1,4-cyclohexadiene and norbornadiene. In cyclohexene and norbornene a single singlet \u2192 triplet excitation was observed at 4,24 eV and 4.10 eV, respectively. Transitions corresponding to it \u03c0 \u2192 \u03c0 ^* singlet excited states and \u03c0 \u2192 3s Rydberg states were also observed. The spectra of norbornadiene and 1,4-cyclohexadiene are discussed in terms of ethylenic units interacting via through-bond and through-space effects. The lowest feature in the norbornadiene spectrum appears to be due to the superposition of two singlet \u2192 triplet transitions with approximate locations at 3.4 eV and 3.9 eV. In the spectrum of 1, 4-cyclohexadiene, the lowest feature is also believed to result from two singlet \u2192 triplet transitions; however, the transitions overlap so heavily that individual locations could not be determined. Finally, in two appendices the electronic spectroscopy of nitric oxide and UF_6 and WF_6 are discussed. Weak structure in the NO spectrum occurring between 5.22 eV and 5.60 eV has been assigned as vibronic bands belonging to the X^2\u220f \u2192 a^4\u220f transition. Structure with an apparent Franck-Condon envelope extending from 5.70 eV to approximately 7 eV with intensity maxima at 6.29 eV was assigned to the X^2\u220f \u2192 b^4\u03a3^- transition. The UF_6 and WF_6 spectra were discussed in terms of recent calculations and by drawing parallels between the two spectra.\r\n" }, { "name": "Goetze, Andrew Michael", "degree": "PhD", "year": "1978", "title": "Nuclear Magnetic Resonance Studies of Immunoglobulins: I. Structure-Function Relationships in Phosphorylcholine-Binding Mouse Myeloma Antibodies. II. \u00b9\u2079F NMR Studies of Trifluoroacetonylated Immunogloblins as a Probe of Antibody Conformation", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02182026-233013281", "creators": [ { "name": { "family": "Goetze", "given": "Andrew Michael" }, "id": "Goetze-Andrew-Michael", "display_name": "Goetze, Andrew Michael" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n7gm-yp14", "abstract": "Chapter 1
\r\n\r\nThis chapter presents a general introduction\r\nto mouse myeloma proteins, antibody structure, and\r\nthe nature of antibody-antigen interactions. The\r\ncontributions of light and heavy chains to antibody\r\nbinding properties are also discussed and the\r\n3-dimensional structure of the McPC 603 binding\r\nsite is examined in some detail.
\r\n\r\nChapter 2
\r\n\r\nThe interaction of phosphorylcholine-binding\r\nmouse myeloma protein McPC 603 and the isotopically\r\nsubstituted hapten phosphoryl[methyl-13C]choline\r\nhas been investigated using 13C and 31P nuclear\r\nmagnetic resonance spectroscopy. Upon binding to\r\nantibody, upfield shifts of 0.7 and 1.5 ppm are\r\nobserved for the hapten 13C and 31P resonances,\r\nrespectively, and both spectra are in the \"slow\"\r\nexchange limit. Linewidth analysis indicates some\r\nimmobilization of the phosphate group but essentially\r\nunrestricted methyl group rotation for the\r\nbound hapten. Hapten-antibody dissociation rate\r\nconstants of 10 and 38 s-1 are calculated from\r\n13c and 31P NMR spectra, respectively, suggesting\r\nthe possibility of differential dissociation rates\r\nfor the two opposing ends of the phosphorylcholine\r\nmolecule. The NMR data are entirely consistent\r\nwith the known X-ray structure of the McPC 603\r\nFab'-phosphorylcholine complex .
\r\n\r\nChapter 3
\r\n\r\nThe binding site interactions between the\r\nphosphorylcholine-binding mouse myeloma proteins\r\nTEPC 15, W3207, McPC 603, MOPC 167, and MOPC 511 and\r\nthe isotopically subsituted hapten phosphoryl[methyl-13C]choline have been investigated using\r\n13C and 31P nuclear magnetic resonance (NMR)\r\nspectroscopy. Each protein exhibits a unique NMR\r\npattern, but extensive similarities in chemical\r\nshift parameters upon binding of hapten to immunoglobulin\r\nsuggest a significant degree of conservation\r\nof important hapten-binding site interactions.\r\nMoreover, independent binding studies, in conjunction\r\nwith the NMR data, allow construction of\r\na simple model of the binding sites of these antibodies,\r\nanalyzed in terms of the relative strength\r\nof interaction between hapten and two main subsites.\r\nThe NMR evidence supports the view that the heavy\r\nchains of these proteins dominate in interacting with\r\nbound phosphorylcholine.
\r\n\r\nChapter 4
\r\n\r\nWe have determined the pH dependencies of the\r\nbinding affinities of the mouse myeloma immunoglobulins\r\nM603, W3207, T15 and M167 for the haptens phosphorylcholine\r\n(PC) and L-\u03b1-glycerophosphorylcholine (GPC).\r\nThese affinities are generally maximal near neutral\r\npH with the exception of the binding of PC by Ml67\r\nwhich is strongest at pH 5.5. These data have helped\r\nto clarify the nature and relative importance of the\r\nionic interactions between hapten and antibody.
\r\n\r\n31P nuclear magnetic resonance (NMR) techniques\r\nwere used to probe the influence of pH on the microenvironment\r\nof the phosphate group of several haptens\r\nwhen these were bound to M603, W3207, T15, M167 and\r\nM511. The phosphate subsites of M603, W3207 and Tl5\r\nare electropositive and also show other similarities;\r\nthose of M167 and M511 have more electronegative\r\ncharacter than PC experiences in solution. The two\r\nhydrogen bonds known to be formed between M603 and\r\nthe phosphate oxygens of PC are also involved in\r\nbinding GPC and are essentially unaffected by pH in\r\nthe region 3-9. Studies with the hapten 3-trimethyl-\r\namino-1-propanolphosphate show that the binding\r\ncavity of M1 67 is substantially wider than those of\r\nM603, W3207 and T15.
\r\n\r\nThese results lead to a detailed, molecular\r\nmodel of the pH dependent binding of PC and related\r\nhaptens to these antibodies; they further indicate\r\nthe roles of various amino acid residues in defining\r\nthe differing ligand specificities of these\r\nantibodies.
\r\n\r\nChapter 5
\r\n\r\nThe phosphorylcholine (PC) affinities of\r\nseveral hybrid immunoglobulins, formed from recombination\r\nof light and heavy chains from parent\r\nmolecules with PC specificity, have been determined.\r\nThe results indicate a highly specific light-heavy\r\nchain interaction in these antibodies since high PC\r\nbinding affinities are obtained only with autologous\r\nrecombinants or with heterologous recombinants in\r\nwhich both parent molecules have a highly similar\r\nlight chain. It is proposed that the heavy chain\r\nresidues of these immunoglobulins determine both\r\nthe primary PC specificity and the differing fine\r\nspecificities; the important role of the different\r\nlight chains is then to stabilize unique heavy chain\r\nconformations.
\r\n\r\nChapter 6
\r\n\r\nThe domain structure of antibodies, as well\r\nas the localization of various effector functions\r\nto specific antibody regions, are discussed. Evidence,\r\nfrom the literature, for the induction of\r\nconformational changes in the antibody molecule as\r\na result of antigen binding is presented and the\r\npossible nature of such changes is discussed.
\r\n\r\nChapter 7
\r\n\r\nThe six interchain disulfide bonds of TEPC 15\r\nwere trifluoroacetonylated and 19F NMR studies used\r\nto probe the magnetic environments of the trifluoroacetonyl\r\nreporter groups. The use of various\r\nenzymatic fragments of the intact immunoglobulin\r\nenabled the observed fluorine signals to be partially\r\nassigned to the known locations of the disulfide\r\nbonds on the antibody molecule and the distinct\r\nchemical environments seen for the 19F labels are\r\nin good agreement with the known 3-dimensional\r\nstructures of antibodies. No change in environment\r\nof the trifluoroacetonyl groups was observed upon\r\nbinding of TEPC 15 to phosphorylcholine or to\r\nphosphorylcholine conjugated to a protein carrier.\r\nSimilar studies with trifluoroacetonylated MOPC 315\r\nbinding to 2,4-dinitrophenyl-sensitized sheep red\r\nblood cells likewise resulted in no observable\r\nchanges in the 19F NMR spectrum.
" }, { "name": "Hodges, Ronald Vernon", "degree": "PhD", "year": "1978", "title": "Gas Phase Ion-Molecule Chemistry. I. Ion Cyclotron Resonance Investigations of Organophosphorus Compounds. II. Reactions of Aluminum Ions with Alkyl Halides", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06232025-170342003", "creators": [ { "name": { "family": "Hodges", "given": "Ronald Vernon" }, "id": "Hodges-Ronald-Vernon", "display_name": "Hodges, Ronald Vernon" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "abstract": "The properties and reactions of a series of phosphate and phosphite\r\nesters have been studied using the techniques of ion cyclotron\r\nresonance spectroscopy. The positive and negative ion chemistry of\r\nthese species has been examined and their gas phase base strengths\r\n(proton affinities) and adiabatic ionization potentials measured. Effects\r\nof constrained geometry on the base strengths of phosphites are\r\nexplored by comparing a series of cyclic phosphites with acyclic\r\nanalogs. Axial and equatorial phosphorus lone pairs in six membered\r\nphosphite rings differing only by inversion of configuration at phosphorus\r\nare shown to have significantly different base strengths. A\r\nlinear correlation exists between the proton affinities and first adiabatic\r\nionization potentials of all tervalent phosphorus compounds for which\r\ndata are available. This has implications for the electronic structure of\r\nthese species, strongly suggesting that the highest occupied molecular\r\norbital is the phosphorus lone pair. The results of these experiments\r\nare useful in the design of schemes for chemical ionization mass spec trometric\r\nanalysis of phosphorus esters, which include widely used\r\npesticides.
\r\n\r\nAn ion beam apparatus is used to study the gas phase reactions\r\nof aluminum ions with a series of alkyl halides. The variation of product\r\ndistributions with collision energy is reported. The observed reactivity\r\nof aluminum ions is discussed in terms of the electronic structure of\r\naluminum, the reaction thermodynamics and proposed reaction\r\nmechanisms.
" }, { "name": "Hu, Valerie Wailin", "degree": "PhD", "year": "1978", "title": "Structure-Function Studies on Cytochrome c Oxidase: Part I. An Investigation into the Nature of the Metal Sites in Cytochrome c Oxidase using X-Ray Absorption Spectroscopy. Part II. An Investigation into the Lipid Factors Affecting Protein Activity and Respiratory Control in Reconstituted Cytochrome c Oxidase Membranes", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292026-153002263", "creators": [ { "name": { "family": "Hu", "given": "Valerie Wailin" }, "id": "Hu-Valerie-Wailin", "orcid": "0000-0002-3357-0777", "display_name": "Hu, Valerie Wailin" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qxtt-0d68", "abstract": "Cytochrome c oxidase is a membrane-bound enzyme of the mitochondrial \r\nrespiratory chain which is ultimately responsible for almost all of\r\nthe oxygen consumption in aerobic organisms. In a rapid four-electron\r\nprocess, it reduces molecular oxygen to water and, at the same time,\r\ncouples the energy derived from this exothermic reaction with energy conservation\r\nby driving ATP synthesis. The proper functioning of cytochrome\r\noxidase in oxygen reduction and energy coupling requires not only\r\nphospholipids but also an intact, vectorially-oriented membrane. In the\r\nstudy described briefly below, two different aspects of the cytochrome\r\noxidase problem have been examined: 1) the nature of the metal sites in\r\nthe isolated molecule with regard to their participation in the\r\noxidation/reduction process, and 2) the functional role of lipids in the\r\nactivation of the protein.
\r\n\r\nPart I deals with an investigation into the nature of the metal\r\nsites in cytochrome c oxidase. For this purpose, X-ray absorption edge\r\nspectroscopy was employed to examine the oxidation states of the copper\r\nand iron centers in the protein under oxidized, fully-reduced, and\r\npartially-reduced conditions. In addition, the edge spectra of oxidized\r\nand reduced plastocyanin (a \"blue copper\" protein containing a single Cu\r\nion) as well as of a number of model Cu compounds in various oxidation\r\nstates were obtained to establish energy ranges for the several bound to\r\nbound transitions of Cu in the different oxidation states. A comparison\r\nof the fine structure detail in the absorption edge spectra of cytochrome\r\noxidase with those of the models indicates that one of the two\r\ncopper ions in the oxidized protein is in the +1 oxidation state. Upon\r\nreduction of the protein with dithionite, the second copper becomes\r\nCu(I). The Fe K-edge spectra of cytochrome c oxidase reveals a small\r\nshift(~ 2 eV) towards lower energies upon reduction. This is comparable\r\nwith the shift observed for the reduction of the heme iron in\r\ncytochrome c [l]. Studies on the cyanide complexes of cytochrome oxidase\r\nindicate that 1) cyanide has no effect on the Cu K-edge spectrum\r\nof oxidized cytochrome oxidase, 2) the 1s \u2192 3d transition of the Fe edge\r\nof oxidized oxidase is enhanced by the presence of cyanide, and 3) both\r\nof the Cu ions are reduced in the partially-reduced cyanide complex.
\r\n\r\nPart II of this thesis is concerned with an investigation into the\r\nlipid factors affecting protein activity and respiratory control in reconstituted\r\ncytochrome oxidase membranes. Delipidated cytochrome c oxidase\r\nwas reconstituted with various natural and synthetic phospholipids\r\nand several aspects of protein-lipid interactions were studied. In a\r\nwell-defined series of model membranes, it was shown that cytochrome\r\noxidase activity, monitored at a constant temperature, was sensitive to\r\nthe physical state of the lipids, being higher when the lipids were in\r\nthe liquid-crystalline phase. In addition, the temperature at which the\r\nreconstitution was allowed to take place was found to affect the manifestation\r\nof phase-dependent oxidase activity. A passive charge diffusion\r\nmodel has been proposed to explain the observed phenomena.
\r\n\r\nThe effect of protein on the lipid phase transition has also been\r\ninvestigated using light scattering techniques. A heating/cooling\r\nhysteresis in the absorbance versus temperature curves has been attributed\r\nto a reversible aggregation and dispersal of the proteins in the bilayer\r\nwhich is dependent on the physical state of the lipids.
\r\n\r\nSeveral lipid factors have been investigated with regard to their\r\ninfluence on the reconstitution of cytochrome oxidase membranes exhibiting\r\nrespiratory control. It was found that high lipid/protein ratios\r\nand the presence of acidic polar head groups are conducive to the establishment\r\nof respiratory control as evidenced by increased rates of oxygen\r\nconsumption in the presence of chemical uncouplers. In addition, the\r\nmode of vesicle preparation affected the responsiveness of the samples\r\ntowards uncoupling agents.
" }, { "name": "Keil, Mark", "degree": "PhD", "year": "1978", "title": "Interaction Potentials of Helium with Atoms and Molecules from Crossed Beam Experiments", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:02032026-214425569", "creators": [ { "name": { "family": "Keil", "given": "Mark" }, "id": "Keil-Mark", "orcid": "0000-0002-1643-8256", "display_name": "Keil, Mark" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rsgg-db81", "abstract": "This thesis is concerned with the study of van der Waals interactions\r\nbetween He atoms and various atomic and molecular partners.\r\nThese studies involve measuring differential cross sections (DCS) for\r\nscattering of thermal-energy crossed atomic and molecular beams.\r\nAlthough this crossed-beams technique has been used extensively in the\r\npast ten or so years, the accuracy with which it may be used to obtain\r\nvan der Waals potentials for highly quantum systems heretofore has not\r\nbeen examined quantitatively. Under typical experimental conditions,\r\nwe show in Chapter 1 that the attractive minimum region of the potential\r\nis determined to within about \u00b1 10%. However, this accuracy is\r\nattained only when appropriately flexible interatomic potentials are\r\nused in the iterative inversion procedures needed to obtain these\r\npotentials from the DCS scattering measurements. Suitable parametric\r\nrepresentations for the potential are those capable of effectively\r\ndecoupling the attractive minimum region from the adjacent regions of\r\nthe potential. This is particularly important for highly quantum systems\r\nhaving shallow attractive minima, since this is the region most sensitively\r\nprobed by the elastic DCS. The related difficulty of non-uniqueness\r\nfor iteratively derived potential energy curves is circumvented\r\nby introducing these flexible parametric representations. The\r\nrange of interatomic distances actually sampled in the experiment is\r\nfound to be significantly wider than would be expected classically.
\r\n\r\nIn Chapter 2, the above results find practical application in the\r\nanalysis of our measurements for He-Ar scattering. Using two very\r\ndifferent mathematical parameterizations having the appropriate\r\nflexibility to represent the He-Ar interaction, an accurate and substantially\r\nmodel-independent potential is determined. This potential is\r\nsignificantly more accurate than previously proposed ones. By further\r\nusing measurements of properties which are sensitive primarily to\r\nrepulsive interactions of He-Ar, its potential may now be considered\r\nas well known for interatomic separations >2.4\u00c5. (potential energies\r\n< 0.15 eV). This potential provides an accurate description of all\r\navailable gas-phase data for the He-Ar system. The techniques used to\r\nobtain it can easily be extended to the other He-rare gas pair potentials.
\r\n\r\nLater chapters in this thesis emphasize the van der Waals interactions\r\nof He atoms with molecular partners, whose intermolecular\r\npotentials are anisotropic. To be accurately represented, they should\r\ntherefore be parameterized in a dimensionality higher than one . The\r\nimportance of additional degrees of freedom is demonstrated to be\r\nslight for small diatomic partners (N2, O2, CO and NO), for hydrides\r\n(CH4, NH3, H2O), and even for large but highly symmetric molecules\r\n(SF6). In Chapter 3, the small anisotropic contributions to the He-diatomic\r\nintermolecular potentials are determined, using a model in\r\nwhich the locus of the attractive minimum position is represented by an\r\nellipse. In Chapter 4, anisotropies in the He-hydrides and He-SF6\r\npotentials are ignored, maintaining nonetheless a good description of\r\nthe DCS's for these scattering partners.
\r\n\r\nChapter 5 presents a brief study of the He-CO2 van der Waals\r\npotential, which is sufficiently anisotropic to result in a scattering\r\npattern which cannot be fit with central-field models, even very flexible\r\nones. The anisotropic potential extracted from the experiment may be\r\nused to predict rotationally inelastic DCS's for thermal-energy\r\nHe-CO2 collisions.
" }, { "name": "Kinney, Robert James", "degree": "PhD", "year": "1978", "title": "I. Synthesis and Characterization of the New Cyclopentadienyl Vanadium Tricarbonyl Hydride and Methyl Anions and their Reactions with Organic Substrates. II. Monomeric Organometallic Dianions", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01092026-185831925", "creators": [ { "name": { "family": "Kinney", "given": "Robert James" }, "id": "Kinney-Robert-James", "orcid": "0000-0003-1963-5818", "display_name": "Kinney, Robert James" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pygb-k537", "abstract": "The new anionic cyclopentadienyl vanadium tricarbonyl complexes,\r\n(n5C5H5)V(CO)3R-, (R=H,CH3),have been isolated as the phosphineminium\r\nsalts. (n5C5H5)V(CO)3H- reacts with alkyl (primary, secondary, and tertiary),\r\nvinyl and aryl bromides at room temperature in THF to replace\r\nbromine with hydrogen. A gem-dibromocyclopropane was reduced to the\r\nmono-bromide, and acid chlorides were converted to aldehydes with\r\n(n5C5H5)V(CO)3H-. Primary alkyl iodides react more rapidly than the\r\nbromides and aklyl chlorides do not react at all. Alkyl tosylates react\r\nmuch slower than the corresponding bromides. Carbon radicals and\r\n(n5C5H5)V(CO)3Br- as the kinetic organometallic product imply a radical\r\nchain mechanism for these reactions.
\r\n\r\nThe reactions of (n5C5H5)V(CO)3CH-3 and alkylbromides and acyl\r\nchlorides do not produce new carbon-carbon bonds .
\r\n\r\nAttempts to prepare the dianious RM(CO)2-3, M = Cr, Mo; R = norbornadiene\r\nand M = Mo; R = cyclooctatetraene were not successful.
" }, { "name": "Kumar, Sudarshan", "degree": "PhD", "year": "1978", "title": "Optimal Design of Distributed Parameter Measurement Systems", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01262026-234414750", "creators": [ { "name": { "family": "Kumar", "given": "Sudarshan" }, "id": "Kumar-Sudarshan", "display_name": "Kumar, Sudarshan" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/g5zj-8n68", "abstract": "The measurement system design for a process governed by partial\r\ndifferential equations (so called distributed parameter system) consists\r\nof the choice of state variables to be measured, the frequency of measurements,\r\nand the optimal location of sensors. In this work, we consider\r\nthe problem of optimal location of sensors in distributed parameter systems.
\r\n\r\nThe optimal sensor location problem is approached from the point of\r\nview of estimation theory. The objective chosen is the estimation of\r\nthe system state variables with maximum possible accuracy. An upper\r\nbound for the error covariance of the state estimate is derived. Optimal\r\nsensor locations are determined by minimizing this upper bound of\r\nthe error covariance. This approach offers significant savings in computation\r\ntime over the conventional approaches based on direct minimization \r\nof the error covariance. A one-dimensional heat conduction system\r\nis considered as an example. The effect of process dynamics on optimal\r\nsensor locations is studied in detail for that example. The optimal locations\r\nare found to vary for spatially varying measurement noise.
\r\n\r\nTo apply the theory to a technologically important system we consider\r\nthe optimal location of measurements for tubular reactors. The\r\nstate of this system is described by two variables - concentration\r\nand temperature-and is governed by two nonlinear partial differential\r\nequations. For the first time, the optimal sensor location problem for\r\na system with two state variables has been studied. For this problem,\r\nan approach based on discretization of the system equations is developed.\r\nThe feasibility of estimating both concentration and temperature profiles\r\nfrom temperature measurements only is demonstrated. The effect of process\r\nnoise and measurement noise on optimal sensor locations was studied and\r\nit was found that optimal sensor locations move towards region of lower\r\nmeasurement error variance. For the particular set of parameters chosen,\r\nit was found that two optimally located temperature sensors can give a\r\nsufficiently accurate estimate of the concentration and temperature\r\nprofiles.
" }, { "name": "Lamb, Brian Kent", "degree": "PhD", "year": "1978", "title": "Development and Application of Dual Atmospheric Tracer Techniques for the Characterization of Pollutant Transport and Dispersion", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022025-232421338", "creators": [ { "name": { "family": "Lamb", "given": "Brian Kent" }, "id": "Lamb-Brian-Kent", "orcid": "0000-0001-7641-5227", "display_name": "Lamb, Brian Kent" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6djp-n724", "abstract": "Environmental concerns over urban development and industrial\r\ngrowth have resulted in increased interest in atmospheric tracers.\r\nExpanding urban areas in coastal regions make it particularly important\r\nto understand the effects of complex meteorological patterns and rough\r\nterrain upon the transport and dispersion of atmospheric pollutants.\r\nThe purpose of this thesis was to further develop single and double\r\natmospheric tracer techniques which would be economical and efficient\r\nfor large-scale field studies. Sulfur hexafluoride and bromo-trifluoromethane\r\nwere selected as tracers since they are both inert gases\r\ndetectable by electron capture gas chromatography in the parts per\r\ntrillion range . A tracer system was developed which permitted the\r\ncollection and analysis of as many as 1000 air samples per day. This\r\nsystem was then used to demonstrate the application of tracer techniques\r\nto important problems of current interest in both coastal and noncoastal\r\nzones over distances as great as 100 km.
\r\n\r\nAtmospheric tracer studies, conducted in Southern California\r\nduring September, 1975, investigated the possible transport of\r\npollutants between the Los Angeles Basin and the Oxnard Plain. The\r\nSF6 data clearly showed that pollutant transport occurs from the Oxnard\r\nPlain along the Malibu coast into the Los Angeles Basin.
\r\n\r\nA second series of tracer studies using SF6 and CBrF3 were\r\ncompleted within the California Delta Region during September, 1976.\r\nThe purpose of these tests was to analyze the impact of possible\r\nindustrial developments in the Montezuma Hills of the Delta Region.\r\nThe relative impact of existing and proposed industrial sources was\r\ninvestigated by simultaneously releasing CBrF3 from the Montezuma Hills\r\nand SF6 from upwind of the Delta Region. Results indicated that plumes\r\nfrom both areas were carried southeast over Stockton into the San\r\nJoaquin Valley.
\r\n\r\nData from both of the coastal studies indicated that because of\r\nperiods of steady coastal winds, the commonly used Hino correction\r\ngrossly underestimated hourly averaged concentrations computed from\r\n10-second averaged concentrations. Tracer concentrations predicted\r\nfrom the Gaussian plume model overestimated values observed in the\r\nOxnard study because of increased dispersion over rough terrain.\r\nPredicted concentrations showed good agreement with observed values in\r\nthe Delta study where the terrain was relatively flat. When\r\nsufficient data were available, surface air parcel trajectories\r\ndetermined from numerical solutions of the two-dimensional conservation\r\nequation were found to be more accurate than trajectories drawn from\r\nmeteorological streamline maps.
\r\n\r\nFive large-scale tracer studies utilizing SF6 and CBrF3 were\r\nperformed in urban St. Louis during August, 1975, to probe the\r\nrelative impact of emissions from low-level and elevated sources.\r\nReleases of SF6 were used to simulate elevated sources, while\r\nsimultaneous releases of CBrF3 were used to simulate low-level sources.\r\nThe dispersion of emissions from low-level sources was initially\r\nenhanced in contrast to the dispersion of emissions from elevated\r\nsources.
\r\n\r\nAnalysis of the St. Louis t racer data resulted in the development\r\nof the concept of a limit model of air quality. By considering the\r\nrelative impact of different sources and formulating necessary\r\nassumptions in terms of an upper or lower bound , the limit model\r\napproach offers a new perspective upon contemporary air quality\r\nproblems. The application of this concept was demonstrated in the\r\ndevelopment of an upper limit model of the relative impact of elevated\r\nrural sources and low-level urban sources upon urban SO2 levels in\r\nSt. Louis. Results of this application indicated that rural sources\r\ncontribute no more than 25% of the average total urban SO2 concentration,\r\neven though rural sources can dominate urban air quality in portions of\r\nthe urban region during relatively large portions of the time.
\r\n\r\nAs a means of applying experience gained from atmospheric\r\ntracer studies to liquid systems, a method was developed for the\r\ndetermination of the solubility of halogenated compounds in liquids.\r\nSolubilities of SF6 in water measured with this technique were in good\r\nagreement with literature values. The method was used to determine,\r\nfor the first time, values of the solubility of SF6 in a homologous\r\nseries of n-alcohols. The method allows SF6 to be used as a tracer in\r\na number of unique liquid systems including the characterization\r\nof the interfacial exchange rate of gases across the pulmonary membrane\r\nof the lung.
" }, { "name": "McAlister, Donald Robert", "degree": "PhD", "year": "1978", "title": "Organometallic Reaction Mechanisms: Catalytic Cyclotrimerization of Alkynes, Reduction of Carbon Monoxide and Reductive Elimination from an Alkylhydride Complex", "advisor": "Bergman, Robert G.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052026-185527488", "creators": [ { "name": { "family": "McAlister", "given": "Donald Robert" }, "id": "McAlister-Donald-Robert", "display_name": "McAlister, Donald Robert" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "orcid": "0000-0002-3105-8366", "role": "advisor", "display_name": "Bergman, Robert G." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fat2-6j70", "abstract": "Chapter I
\r\n\r\nThe cobaltacyclic compound, (n55-C5H5)Co(C(CH3)=C(CH3)c(CH3)=C(CH3))\r\n(PPh3) (3a), formed by reaction of (n55-C5H5)Co(PPh3)2 (1a) with 2-butyne\r\nis shown to be an efficient catalyst for cyclotrimerization of alkynes\r\nto provide arenes. An investigation of the substitution reactions of\r\nPMe3 and 2-butyne with 1a and with its PMe3 containing congeners (1b and 1c) is\r\nreported. A mechanism consistent with this data and in accord with\r\nthe observed dependence of the rate of formation 3a on PPh3 and 2-\r\nbutyne concentration is proposed.
\r\n\r\nThe kinetics of the cyclotrimerization of 2-butyne catalyzed by\r\n3a both in the presence and absence of excess PPh3 and the kinetics\r\nof substitution of PEt3 for PPh3 in 3a are reported. These results\r\nindicate a mechanism involving rate determining coordination of 2-butyne \r\nto cobalt. In contrast the reaction of C2(CO2Me)2 (dma)\r\nwith the PMe3 substituted analog of 3a,(3c), is shown to proceed without\r\nprior coordination of the alkyne.
\r\n\r\nChapter II
\r\n\r\nBis (pentamethyl cyclopentadienyl)-dihydrido zirconium (IV)\r\n(\u019e5-C5Me5)2ZrH2 (2) forms unstable adducts with PF3 and CO at -80\u00b0.\r\nThe carbonyl adduct (\u019e5-C5Me5)2ZrH2 (CO) yields {(\u019e5-C5Me5)2ZrH}2\r\n(\u03bc-OCH=CHO) and/or (\u019e5-C5Me5)2 ZrH(OCH3 upon warming depending on\r\nconditions. Carbonylation of (\u019e5-C5Me5)2 Zr(CH3)2 2 provides successively\r\n(\u019e5-C5Me5)2 Zr(CH3) (C(=O)CH3) and (\u019e5-C5Me5)2 Zr(OC(Me)=C(Me)O).\r\nReaction of the zirconocyclopentane (\u019e5-C5Me5)2 Zr(CH2(CH2)2CH2 \r\nwith CO affords (\u019e5-C5Me5)2Zr(H) (OCH=CH(CHMe2). Treatment of 2\r\nwith isobutylene gives (\u019e5-C5Me5)2Zr(H) (CH2) (13), which reacts\r\nwith CO to give (\u019e5-C5Me5)2Zr(H) (OCH=CH(CHMe2))(15). The results of\r\n13C and deuterium labeling studies indicate that (\u019e5-C5Me5)2 Zr(H)\r\n(C(=O)CH2CHMe2) is an intermediate in conversion of 13 to 15. The\r\nobserved reaction patterns of alkyl and hydride derivatives of\r\nzirconium with CO are attributed to carbenoid character of the carbonyl\r\ncarbon resulting from an unusual \"side-on\" coordination of acyl or\r\nformyl groups.
\r\n\r\nChapter III
\r\n\r\nThe alkyl hydride complex (\u019e5-C5Me5)2Zr(H)(CH2CHMe2) (5a),\r\nprepared by reaction of (\u019e5-C5Me5)2ZrH2 (4) with isobutylene, is\r\na monomeric, pseudotetrahedral compound. In direct contrast to\r\nother transition metal complexes bearing cis hydride and alkyl ligands\r\nit is reasonably thermally stable. However, isobutane is evolved from\r\nSa upon thermolysis at 75\u00b0. Reaction with H2 or ethylene also results\r\nin generation of isobutane.
\r\n\r\nThe isotopically labeled complexes (\u019e5-C5Me5)2Zr(D)(CH2CDMe2) (5b)\r\nand (\u019e5-C5(CD3)5)2Zr(D)(CH2CD(CH3)2)(5c) are prepared by reaction of\r\nisobutylene with (\u019e5-C5Me5)2ZrD2 and (\u019e5-C5(CD3)5)2ZrD2. respectively.\r\nThe deuterium distribution in isobutanes resulting from thermolysis\r\nof 5a, b and c and from their reactions with H2, D2, C2H4 and C2D4\r\nwere determined. The rates of thermolysis of those complexes are\r\nalso reported. Mechanisms consistent with these data are proposed.\r\nFor the cases of thermolysis and reaction with H2, the suggested\r\nmechanisms are similar to those proposed to account for exchange\r\nprocesses between 4 and a deuterium atmosphere.
" }, { "name": "Moody, Terry William", "degree": "PhD", "year": "1978", "title": "Biochemical Studies of the Nicotinic Acetylcholine Receptor from Torpedo Californica Electroplax", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02262026-183012750", "creators": [ { "name": { "family": "Moody", "given": "Terry William" }, "id": "Moody-Terry-William", "orcid": "0000-0001-6359-7703", "display_name": "Moody, Terry William" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/c7t4-xc17", "abstract": "The ligand binding properties of the acetylcholine (AcCh)\r\nreceptor have been investigated using radioactive cholinergic\r\nligands, radiolabelled a-neurotoxins, and fluorescent decamethonium\r\nanalogues. The radioactive cholinergic ligands appear to bind\r\nwith high affinity to half as many sites as \u03b1-Bungarotoxin (\u03b1-BuTx).\r\nOne possible interpretation of these data is that two distinct classes\r\nof sites are present in equal populations. The results of kinetic\r\nexperiments conducted in this laboratory have shown that the\r\nreceptor binds a-BuTx with a five fold greater second order rate\r\nconstant and binds cholinergic ligands with 2-7 fold lower affinity\r\nto the \"fast\" than to the \"slow\" site.
\r\n\r\nThe binding properties of a series of synthetic bis-3-aminopyridinium-\r\n1,n-alkane fluorescent decamethonium analogues to the\r\npurified receptor were investigated. The probes bind with substantially\r\ngreater affinity to the \"slow\" than to the \"fast\" site, and\r\ntherefore served as useful tools to map the ligand binding topography\r\nof the uslow11 site of the receptor. This site binds the probes\r\nwith increasing affinity as the methylene bridge length (n) increases\r\nfrom 4 to 12 carbons and decreases from 18 to 16 carbons. One\r\npossible interpretation of these data is that when the \"slow\" site\r\nbinds a bifunctional probe such as bis-3-aminopyridiniunr-1,14-tetradecane,\r\nboth ends of the probe interact strongly with the\r\nreceptor. Therefore the \"slow\" site of the receptor may be composed\r\nof at least two subsites.
\r\n\r\nRecently published evidence indicates that the venom\r\nof the krait Bungarus caeruleus contains unique toxic proteins\r\nwhich affect the function of the AcCh receptor in vivo. Therefore\r\nwe undertook the fractionation and purification of various proteins\r\nfrom this venom in order to examine their use as probes of the AcCh\r\nreceptor. Two of the basic components were highly neurotoxic in.\r\nmice and had significant levels of phospholipase-A activity. These\r\ncomponents appear to be similar to the presynaptic neurotoxin \u03b2-BuTx.\r\nTwo other basic components were toxic in mice and also reduced\r\nthe rate of \u03b1-BuTx binding to the purified acetylcholine receptor.\r\nThese components appear to be similar to the postsynaptic neurotoxin\r\n\u03b1-BuTx. Two acidic components display A-type phospholipase activity\r\nand perturb the carbamylcholine binding properties of receptor\r\nenriched membrane preparations. These data indicate that the\r\nfatty acids and/or lysophospholipids released by endogenous or\r\nexogenous phospholipase A may affect the receptor conformation\r\nsuch that the receptor binds carbamylcholine with greater\r\naffinity.
" }, { "name": "Nascimento, Marco Antonio Chaer", "degree": "PhD", "year": "1978", "title": "I. Theoretical studies of photoionization. II. The electronic structure of linear polyenes", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292009-093916795", "creators": [ { "name": { "family": "Nascimento", "given": "Marco Antonio Chaer" }, "id": "Nascimento-M-A-C", "display_name": "Nascimento, Marco Antonio Chaer" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e7dw-3p39", "abstract": "Part I:\r\nThe photoionization cross section is shown to be directly related to the imaginary part of the frequency dependent polarizability. Using this relation, an approximate representation of the frequency-dependent polarizability is constructed from a discrete set of transition frequencies and oscillator strengths. This approximate representation is used in an analytical continuation for complex values of the frequency using a sequence of (N+ J/N) Pade Approximants (with J \u2265 1). Once the representation of the frequency-dependent polarizability in the upper half part of the complex plane is known, we can calculate its value along the real axis and consequently the photo- ionization cross section. The great advantage of the method resides on the fact that the use of a discrete representation for the dynamic polarizability explicitly avoids the use of continuum functions. We have applied this method previously in the calculation of photoionization cross sections for the helium atom in its ground state and in the 2^1S and 2^3S metastable states. Calculations for the CO molecule are in progress. Here we present calculations for the H^- atom. For this system we also computed the dynamic polarizability in the normal dispersion region. A study of the basis set dependence is also presented.\r\n\r\nPart II:\r\nSelf-consistent ab initio generalized valence bond (GVB) and configuration interaction (CI) calculations are presented for the ground states, valence and non-valence states, Rydberg states and \u03c0 positive ion states of trans 1, 3-butadiene and all-trans 1, 3, 5-hexatriene molecules. It is shown that the electronic spectra of these molecules can be rationalized in terms of a few valence excited states and a series of Rydberg states. The first singlet excited states of these molecules (1^1B_u) correspond to non-valence, non-vertical states. It was found that to correctly describe the 1^1B_u and the 2^1A_g (valence) states of these molecules it is necessary to correlate not only the electrons of the \u03c0 system but also the electrons of the (C-C)_\u03c3 subspace. It is also shown that the first two bands of the photoelectron spectrum (PE) of the butadiene molecule and the first three bands of the PE spectrum of hexatriene correspond to ionization out of the occupied \u03c0 orbitals of these molecules. Another important conclusion from our studies is that for this type of system, good quality GVB (n/PP) wavefunctions with the 2n \u03c0 electrons correlated can be obtained by carrying out a Hartree-Fock calculation on the ground state followed by a GVB (n/PP) calculation on just the 2n\u03c0 orbitals (keeping the \u03c3 HF space fixed). From this wavefunction accurate values for the transition energies of the valence states can be obtained. Work on all-trans 1, 3, 5, 7-octatetraene now in progress will provide a good test for this scheme.\r\n" }, { "name": "Parkinson, Bruce Alan", "degree": "PhD", "year": "1978", "title": "Experimental Studies of Interfacial Electrochemistry", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272018-142532405", "creators": [ { "name": { "family": "Parkinson", "given": "Bruce Alan" }, "id": "Parkinson-Bruce-Alan", "orcid": "0000-0002-8950-1922", "display_name": "Parkinson, Bruce Alan" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5byg-v343", "abstract": "Part I. Eu+2, V+2 and Co(NH3)63+ as Electrode Kinetic Probes of the Structure of the Diffuse Layer in Dilute Electrolytes
\r\n\r\nThe structure of the diffuse double layer at positive electrode charges in dilute perchlorate, fluoride, chloride and bromide electrolytes is inferred from the kinetics of oxidation of the Eu+2, V+2 and Co(NH3)63+ cations, Diffuse layer potentials calculated from the measured kinetics of the V+2 and Eu+2 probes disagree, both in magnitude and (in some cases) in sign with potentials calculated from electrocapillary data and Gouy-Chapman-Stern theory. A different kinetic response is observed for Co(NH3)63+ and is attributed to the formation of an ion pair with an adsorbed anion. The possible origin of these effects and their consequences in attempts to apply Frumkin double layer corrections or to detect discreteness-of-charge effects is discussed
\r\n\r\nPart II. The Formation of Polymeric Surface Phases on Mercury Electrodes from Solutions Containing Thioethercarboxylates and White Metal Cations
\r\n\r\nThe adsorption of thioethercarboxylate ligands and complexes formed by these ligands with white metals (Pb+2 in particular) on a mercury surface is investigated, Two distinct phases are apparent in many systems one at positive potentials and the other on more negative electrodes. The large adsorption of metal cations measured in both potential regions is attributed to the formation of a monolayer of polymeric surface phase which has a structure not unlike those observed in the molecular crystals of analogous compounds.
" }, { "name": "Peerce, Pamela J .", "degree": "PhD", "year": "1978", "title": "The Coordination Chemistry and Electrochemistry of Chromium (III) Complexes of Thiobis (Ethylenenitrilo) Tetraacetic Acid", "advisor": "Anson, Fred C.; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072026-103724305", "creators": [ { "name": { "family": "Peerce", "given": "Pamela J ." }, "id": "Peerce-Pamela-J", "display_name": "Peerce, Pamela J ." } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8ceh-nc51", "abstract": "The product of the reaction between Cr(Cl04)3 and the\r\nligand, thiobis(ethylenenitrilo)tetraacetic acid (TEDTA),\r\nwas very dependent on the pH of the reaction mixture.\r\nTwo monomeric isomers and several dimeric species were\r\nidentified. Characterization of the various Cr(III)\r\ncomplexes of TEDTA included an examination of their pH\r\nbehavior, visible and ultraviolet absorption spectra,\r\nsubstitutional !ability with excess azide ion, behavior\r\non a Selectacel anion exchange column, reaction with\r\nheavy metal cations and methyl mercury cation, infra-red\r\nspectra and distinctive electrochemistry. Comparisons\r\nof the behavior of the Cr(III)-TEDTA complexes with those\r\nof the Cr(III) complexes of related ligands, including\r\nEDTA, oxybis(ethylenenitrilo)tetraacetic acid (EEDTA)\r\nand pentamethylenedinitrilotetraacetic acid (PMDTA),\r\nwere very helpful. Based on these data, it was concluded\r\nthat both cis and trans isomers (with respect to the\r\nnitrogens) were formed. In the trans isomer, the sulfur\r\nis forced to be close to the Cr(III) center and\r\ncoordination occurs. At pH 5-9, solutions of the pentadentate\r\ncis isomer are a mixture of the monomeric complex\r\nand an acetate bridged dimer. Confirmation of dimer\r\nformation and a value for the dimerization constant were\r\nobtained from potential step experiments. The structure\r\nof the dimer was strongly supported by the cyclic\r\nvoltammetry which indicated the presence of two nonequivalent\r\nmetal centers in the complex. The other\r\ndimeric species were highly charged and their IR spectra\r\nsuggested that they were oxo-bridged.
\r\n\r\nThe electrochemistry of both the cis and trans\r\nisomers and the acetate bridged dimer was investigated\r\nin detail. Cyclic voltammetry and electrocapillary\r\nmeasurements indicated that trans-CrTEDTA was much more\r\nstrongly adsorbed on mercury electrodes than was cis-CrTEDTA(OH2), \r\ncis-CrTEDTA(OH2) or the acetate bridged\r\ndimer, and that free TEDTA was not adsorbed. Experiments\r\nwith CrEEDTA showed that it was not adsorbed, indicating\r\nthat the Cr(III)-TEDTA complexes were attached to the\r\nelectrode through the sulfur. Quantitative measurements\r\nof the adsorption confirmed all of this. The adsorption\r\nof trans-CrTEDTA increased abruptly over a very narrow\r\nrange of bulk concentrations and was strongest at positively\r\ncharged electrodes. The potential dependence was\r\ncorroborated by the fact that the charge on the electrode\r\nin the presence of the complex was more positive. The\r\nconcentration and potential dependences are attributed\r\nto back bonding from Cr(III) to the thioether sulfur\r\nwhich a-donates electron density to the electrode.\r\nThe abrupt change in the surface coverage over a narrow\r\ncharge of bulk concentration indicates that the adsorption\r\nof trans-CrTEDTA is cooperative.
\r\n\r\nChronocoulometric measurements of the adsorption\r\nof the cis isomer at pH 4 and 7 demonstrated that the\r\nneutral complex was more strongly adsorbed than the anions\r\nespecially at more negative potentials. The adsorption\r\nappeared to increase as the electrode potential was\r\nmade more negative. However, the electrocapillary\r\ncurves were discrepant. Electrode charge measurements\r\nsupported the electrocapillary data. The adsorption\r\nof the cis complex depressed the double layer capacitance\r\nat all potentials. This behavior is similar to that of\r\norganic adsorbates. Although the non-adsorption of\r\nthe free ligand was attributed to steric difficulty 1n\r\nexposing the sulfur atom to the electrode, the fact\r\nthat the La(III) and Zn(II) complexes of TEDTA were\r\nalso not adsorbed shows that the role of Cr(III) in\r\ninducing the adsorption of TEDTA in the cis isomers is\r\ncomplicated.
" }, { "name": "Petersen, Nils Overgaard", "degree": "PhD", "year": "1978", "title": "Studies of Lipid-Lipid Interactions in Phospholipid Bilayer Membranes", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09222004-135757", "creators": [ { "name": { "family": "Petersen", "given": "Nils Overgaard" }, "id": "Petersen-Nils-Overgaard", "display_name": "Petersen, Nils Overgaard" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/V9WW-2180", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nLipid-lipid interactions in bilayer membranes are studied in relation to their influence on (i) the state of motion of phospholipid molecules in the liquid crystalline phase, (ii) the miscibility of different lipids in the various bilayer phases, and (iii) the aggregation and fusion of sonicated bilayer vesicles.\r\n\r\nProton and deuterium order parameters measured for the liquid crystalline phase of unsonicated lipid bilayer membranes are interpreted in terms of two types of acyl chain motions, rapid isomerizations and slower reorientations. The observed order parameters are compatible with 50[degree] angular deflections of the chain with respect to the bilayer normal, coupled with a probability of a trans orientation of a methylene segment in the upper two-thirds of the chain of about 0.8 0.9. The motional model can be shown to account for the dynamic properties of the membrane system as measured by nuclear magnetic relaxation measurements, assuming that the chain isomerization occurs at a rate of [...] while chain reorientation occurs at [...]. Analysis of proton and deuterium linewidth data in terms of this model shows that a bilayer curvature, as induced by sonication, causes an increase in the rate and amplitude of chain reorientation without substantially affecting the isomerization motion along the acyl chain.\r\n\r\nPhase diagrams for lecithin mixtures are inferred from Differential Thermal Analysis measurements. In the liquid crystalline phase all the lecithins form ideal solutions whereas in the gel phases immiscibility occurs when the lecithin acyl chains differ by four or more methylene groups in length.\r\n\r\nCholesterol-lecithin interactions are discussed in terms of the motional model for the lecithin bilayer. A phase diagram for cholesterol-lecithin-water mixtures is proposed and discussed in relation to the currently available data on these mixtures. The condensing effect of cholesterol is interpreted as a decrease in lecithin chain fluctuations.\r\n\r\nChanges in light scattering properites of DRL vesicles at their phase transition are interpreted using the above model of chain motion. The results are compatible with the conclusions derived from the NMR data.\r\n\r\nTime dependent absorbance measurements of DPL vesicles are explained by the colloidal properties of the suspension. It is shown that aggregation consists of both coagulation and flocculation, the latter of which is abolished with di- or trivalent cations. The possibility of controlling vesicle-vesicle fusion by coagulation is discussed." }, { "name": "Peterson, Thomas William", "degree": "PhD", "year": "1978", "title": "Aerosol Dynamics in an Urban Atmosphere", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07182024-181126325", "creators": [ { "name": { "family": "Peterson", "given": "Thomas William" }, "id": "Peterson-Thomas-William", "display_name": "Peterson, Thomas William" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/e8gt-t984", "abstract": "This work examines three aspects of modeling the dynamic behavior of an atmospheric aerosol distribution. First, a steady state, three-dimensional solution of the atmospheric diffusion equation including settling, deposition, and first order removal is presented. The solution is applied to the prediction of airborne concentrations of gaseous and particulate pollutants in the case in which gases are converted to secondary particulate matter . The conversion of sulfur dioxide, nitrogen oxides, and hydrocarbons to particulate sulfate, nitrate, and organics in the Los Angeles atmosphere and urban plume is analyzed.
\r\n\r\nSecond, the dynamic behavior of aerosol size distributions under the influence of coagulation and growth by heterogeneous condensation of gaseous species is studied. Analytical solutions are obtained to the integro-differential equation governing the aerosol size distribution density function. Two modes of coagulation (constant and linear coagulation kernels) and two modes of condensation (growth independent of particle volume and linearly dependent on particle volume) are considered. Also included are simplified mechanisms for nucleation and removal of aerosol particles. The interaction of these mechanisms on aerosol size distributions is elucidated.
\r\n\r\nFinally, a detailed study of heterogeneous condensation on and reaction within an aerosol particle is undertaken. All important mechanisms governing the transfer of pollutants from the gas to the particulate phase are discussed, and the general framework for describing heterogeneous reaction within the particle is constructed. The model is then used to describe growth and composition change of a marine aerosol exposed to SO\u2082, NH\u2083 and H\u2082SO\u2084.
" }, { "name": "Ruark, John Edward", "degree": "Masters", "year": "1978", "title": "Structural Studies of Bacteriophage T7 and T7 Capsids", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03302010-083049438", "creators": [ { "name": { "family": "Ruark", "given": "John Edward" }, "id": "Ruark-John-Edward", "display_name": "Ruark, John Edward" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3nwd-0q45", "abstract": "The structures of bacteriophage T7 and T7 capsids have been investigated by small-angle X-ray scattering. Phage T7 has a radius of 301 \u00b1 2 \u00c5 (excluding the phage tail), and a calculated volume of 1.14 \u00b1.05 x 10^(-16) ml. The radius determined for. T7 phage in solution is about 30% greater than the radius measured from electron micrographs, indicating that considerable shrinkage and distortion occurs during sample preparation for electron microscopy. Thus the volume calculated from X-ray scattering in solution is almost twice that estimated from electron microscope measurements. Capsids that have a phage-like envelope and do not contain DNA were obtained from lysates \r\nof T7-infected E. coli (capsid II) and by separating the capsid component of T7 phage from the phage DNA using temperature shock (capsid IV). These capsids have outer radii of 2[8?]3-289 \u00b1 2 \u00c5 and are thus significantly smaller than the envelope of T7 phage. The thickness of the\r\nenvelopes of two forms of capsid II are 20 and 23 \u00b1 2 \u00c5. The volume in T7 phage available to package DNA is estimated to be 9.2 \u00b1 .4 x 10^(-17) ml or 2.1 times the volume of the B form of T7 DNA.\r\n\r\nA T7 precursor capsid (capsid I), believed to be capable of \r\npulling in DNA, has a smaller outer diameter (261 \u00b1 2 \u00c5) and a thicker envelope (52 \u00b1 4 \u00c5) than capsids II and IV. Capsid I expands when pelleted in the ultracentrifuge, but expansion can be prevented by fixing with glutaraldehyde. A low resolution model for the capsid I envelope \r\nhas been developed." }, { "name": "Sanner, Robert D.", "degree": "PhD", "year": "1978", "title": "Synthetic and Structural Investigations of Dinitrogen, Carbonyl, Olefin, Dichloride, and Hydride Derivatives of Bis(Pentamethylclopentadienyl)Titanium and Zirconium", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072026-224337745", "creators": [ { "name": { "family": "Sanner", "given": "Robert D." }, "id": "Sanner-Robert-D", "orcid": "0000-0001-6703-8079", "display_name": "Sanner, Robert D." } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bjmq-3010", "abstract": "The crystal structures of three compounds containing the (\u03b75 -C5Me5)2M (M = Ti, Zr) moiety have been determined by single crystal X-ray diffraction methods. (\u03b75 -C5Me5)2 TiCl2 has a distorted tetrahedral configuration about titanium comprised of the two chlorine atoms and the centroids of the two \u03b75 -C5Me5 rings. Several ring methyl groups are bent considerably out of the cyclopentadienyl plane away from titanium due to chlorine methyl and inter-ring methyl-methyl crowding. The final R factor was 0. 032. The structure of {(\u03b75 -C5Me5)2Ti}2N2 consists of two (\u03b75 -C5Me5)2Ti moieties bridged by N2 in a linear Ti-N\u2261N-Ti arrangement. The final R index was 0.058. A qualitative molecular orbital treatment of the bonding consistent with the structure is presented. The structure of {(\u03b75 -C5Me5)2ZrN2}2N2 consists of two (\u03b75 -C5Me5)2ZrN2 subunits bridged by a third dinitrogen ligand. Terminal and bridging dinitrogen ligands are bound end-on to zirconium with essentially linear Zr-N\u2261N and Zr-N\u2261N-Zr arrangements. The final R factor was 0. 035. A qualitative picture of the zirconium-dinitrogen bonding consistent with the structure and other physical properties of the compound is presented." }, { "name": "Shippey, Michael Allen", "degree": "PhD", "year": "1978", "title": "Trimethylsilyl Anions: Stereospecific Deoxygenation of Epoxides and Trimethylsilyldehalogenation of Aryl Halides", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01232015-153319101", "creators": [ { "name": { "family": "Shippey", "given": "Michael Allen" }, "id": "Shippey-Michael-Allen", "display_name": "Shippey, Michael Allen" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/g9fx-wb19", "abstract": "I. Trimethylsilylpotassium reacts with epoxides to give olefins with inversion of stereochemistry. The reaction appears to proceed via the potassium \u03b2-silyl alkoxide (2) formed from the S_N2 attack of the silyl anion on the epoxide. Subsequent stereospecific synelimination of 2 affords the olefin of inverted stereo-chemistry. The reaction is convenient and preparatively useful.
\r\nThe byproduct of the reaction, potassium trimethylsilanolate (17), effectively cleaves hexamethyldisilane to yield trimethylsilylpotassium. Since the latter reagent is generated and reacted in situ with epoxides, the overall reaction can be carried out with less than one equivalent of potassium methoxide.
\r\nII. The reaction of aryl halides with trimethylsilyl anions in HMPT provides good yields of aryltrimethylsilanes, useful synthetic intermediates. The choice of metal cation is unimportant. Chlorides and bromides give high yields of silylated products, while iodides give lower yields, with correspondingly increased amounts of reduced products. Arylammonium and arylphosphonium salts also undergo the reaction.
\r\nWe have permissive evidence for the reaction proceeding via both aryl radical and aryl anion intermediates.
\r\n\r\nIII. Trimethylsilyl and trimethylstannyl methoxycarbene complexes of chromium and tungsten have been prepared. One of these, (CO)_5WC(OMe)SnMe_3, reacts with norbornene at 80\u00b0 to afford a new olefin polymer. Efforts to effect the alpha-elimination of the nonmetallic carbene ligands have not yet been successful. Reactions of these carbene complexes with acetone have been investigated.
\r\n" }, { "name": "Spencer, Steven Andrew", "degree": "PhD", "year": "1978", "title": "Studies on a Neurotoxic Protein: the 5 A\u030a Structure of \u03b1-Bungarotoxin", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232026-165627030", "creators": [ { "name": { "family": "Spencer", "given": "Steven Andrew" }, "id": "Spencer-Steven-Andrew", "display_name": "Spencer, Steven Andrew" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1xys-8s92", "abstract": "The neurotoxic venom from the Formosan Banded Krait, Bungarus\r\nmulticinctus, was fractionated into nineteen components by ion-exchange\r\nand gel-filtration chromatography. The thirteen main protein\r\ncomponents were nm on SDS-polyacrylamide gels. Six of these components\r\nproduced banding patterns si1nilar to a-bungarotoxin (a-BuTX),\r\nwhile four produced banding patterns similar to S-bungarotoxin. Three\r\ncomponents did not fit either pattern.
\r\n\r\nCrystallization studies of \u03b1-BuTX were conducted, and crystals\r\nwere obtained throughout the pH range 2.5 to 7.5. However, only near\r\npH 4 were crystals routinely obtained which were large enough to allow\r\nthe \u03b1-BuTX structure to be determined by x-ray diffraction methods.\r\nThe pH 4 crystals contained four molecules in the asymmetric
\r\n\r\nThe pH 4 crystals contained four molecules in the asymmetric\r\nunit. The unit cell dimensions were 69.9 x 76.7 x 44.8 A\u030a. The\r\ncrystals appeared to orthorhombic, but space group identification was\r\ndifficult because the l = odd reflections were generally weak throughout\r\nreciprocal space . These weak reflections resulted from the\r\npresence within the unit cell of two subcells, each of which had\r\napproximately P212121 symmetry. This feature of the crystals considerably\r\ncomplicated the structure determination process . Further\r\ncomplications arose from the presence within the asymmetric unit of a\r\nnoncrystallographic symmetry axis.
\r\n\r\nThe \u03b1-BuTX structure was solved at 5 A\u030a resolution by the method\r\nof multiple isomorphous replacement . Except for a long tail at the\r\ncarboxyl terminus, the toxin molecule fit within an ellipsoid\r\napproximately 40 x 28 x 21 A\u030a. The main features of the electron\r\ndensity map were interpreted by comparison to the structure of another\r\nneurotoxin, erabutoxin b.
" }, { "name": "Sullivan, Sally Anne", "degree": "PhD", "year": "1978", "title": "Ion Cyclotron Resonance Investigations of Negative Ion-Molecule Reactions", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-171813911", "creators": [ { "name": { "family": "Sullivan", "given": "Sally Anne" }, "id": "Sullivan-Sally-Anne", "display_name": "Sullivan, Sally Anne" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mk9r-2065", "abstract": "chapter I
\r\n\r\nIon cyclotron resonance techniques are employed in the examination\r\nof the gas phase reactions of PF3 and OPF3 with anionic bases,\r\nincluding NH2-, OH-, CH3 CH2O-, HNO-, HS-, SF6-, and SF5-.\r\nEvidence is presented which suggests that all reactions proceed by\r\ninitial attack at phosphorous, with products resulting from decomposition\r\nof chemically activated intermediates. The energetics of intermediates\r\ninferred in these processes are related to the Lewis acidities\r\nof OPF3 and PF3. With fluoride ion as a reference base, OPF3 is\r\nfound to be more acidic than PF3 , with D(OPF3-F-) = 58.9 \u00b1 0.4\r\nkcal/mole and D(PF3-F-) = 50 \u00b1 5 kcal/mol.
\r\n\r\nChapter II
\r\n\r\nIon cyclotron resonance techniques are employed to determine\r\nthe gas phase Bronsted and Lewis acidities as well as the Bronsted\r\nbasicity of l-methyl-1, 4 dihydroborabenzene, CH3BC5H6. The ring\r\nproton is found to be highly acidic with PA(CH3BC5H5) = 337 \u00b1 3\r\nkcal/mol. This acidity results from the formation of 6\u03c0 electron\r\naromatic anion CH3BC5H5-, which is isoelectronic with toluene.\r\nBoth the Lewis acidity and proton basicity of the parent molecule\r\nsuggest that there is little interaction between the diene \u03c0 system and\r\nthe electron deficient boron. This is further confirmed by the\r\nsimilarity of both negative and positive ion chemistry of the borabenzene\r\nto that of aliphatic boranes.
\r\n\r\nChapter III
\r\n\r\nIon cyclotron resonance techniques are employed in the\r\ninvestigation of positive and negative ion formation and ion molecule\r\nreactions in sulfuryl halides SO2XY(X, Y = Cl, F). Positive ion\r\nreactivity is discussed in terms of the relative Cl and F bond\r\nstrengths in these species and possible structures of ionic intermediates\r\nand products. Electron attachment processes generate\r\nhalide ion donors such as F2-, Cl2-, SO2F- and SO2 Cl- from sulfuryl\r\nhalides. Negative ion reactivity is dominated by halide transfer\r\nreactions. Halide transfer reactions in mixtures with H CN and\r\nHCl are examined in an attempt to quantify D(SO2-F-) and D(SO2-C-).
" }, { "name": "Thompson, Wayne Julius", "degree": "PhD", "year": "1978", "title": "The Total Synthesis of Chlorotricolide: the Top Half", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02092026-232741458", "creators": [ { "name": { "family": "Thompson", "given": "Wayne Julius" }, "id": "Thompson-Wayne-Julius", "display_name": "Thompson, Wayne Julius" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m8zt-ek15", "abstract": "The total synthesis of the top half of chlorotricolide 2,\r\nis described. The top half 65 was prepared in 14 steps (10%\r\noverall yield) from tartaric acid. The potential usefulness\r\nof this top half in the total synthesis of chlorotricolide\r\nwas demonstrated by connection to bottom half models. Successful\r\ndeprotection of the \u03b1-hydroxy-tetronic acid dimethyl ether\r\nmoiety is also described.
\r\n\r\nSee figures in PDF of thesis.
" }, { "name": "Tobler, Jerry", "degree": "PhD", "year": "1978", "title": "Studies on interaction of Plasminogen with Balb/c 3T3 and SV3T3 Cells in Culture", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03232026-204936777", "creators": [ { "name": { "family": "Tobler", "given": "Jerry" }, "id": "Tobler-Jerry", "display_name": "Tobler, Jerry" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mqz2-kv25", "abstract": "The existence of a specific transformed cell surface-plasminogen\r\ninteraction which has been implicated in many phenotype changes that\r\noccur in cells upon transformation was studied. In addition, the fate\r\nof the plasmin in cell culture medium activated by a cell-derived\r\nplasminogen activator was investigated.
\r\n\r\nAs an initial step, the plasminogen binding to Balb/c 3T3 and\r\nSV3T3 cells was studied using 125I-labeled dog plasminogen. The binding\r\nappears to be independent of the protease-dependent morphological\r\nchange which is exhibited by many transformed cells. The 125I-\r\nplasminogen which bound to the SV3T3 cells was completely degraded\r\nduring three days of incubation to macromolecules which were the same\r\nsize as the large and small chains of active plasmin, and to smaller\r\nfragments including 3-iodo-L-tyrosine. The plasminogen which bound to\r\nthe 3T3 cells was only partially degraded to 3-iodo-L-tyrosine with\r\nintermediate conversion to plasmin-size peptides.
\r\n\r\nThe results of a sublethal cell-surface trypsinization assay,\r\ndeveloped to determine whether the processing of plasminogen by cells\r\nwas a cell-surface phenomenon or an internal process, suggest that the\r\ncell-associated plasminogen was primarily bolll1d to the surfaces of the\r\n3T3 and SV3T3 cells while the macromolecular degradation products were\r\ninside the cells.
\r\n\r\nTherefore, the 3T3 and SV3T3 cells bound, endocytosed and degraded\r\nserum plasminogen. The overall rate of this processing was\r\napproximately twice as fast for the SV3T3 cells as the 3T3 cells. This\r\nbinding and processing of plasminogen does not appear to be a specific\r\nplasma membrane-plasminogen interaction and is known to be independent\r\nof the protease-dependent morphological change.
\r\n\r\nEssentially none of the plasminogen in the 3T3 growth medium was\r\nactivated to plasmin, while a significant amount of the plasminogen in\r\nthe SV3T3 growth medium was activated to plasmin, and subsequently\r\ncomplexed with a serum inhibitor of 47,000 molecular weight. This\r\ninhibitor is covalent, forming a hydroxylamine-dissociable bond.
\r\n\r\nTo investigate whether any active plasmin remained in SV3T3\r\ngrowth medium, a model system of urokinase in situ activation of plasminogen\r\ndesigned to mimic the levels of plasminogen activation observed\r\nin a 48-hour incubation of plasminogen with SV3T3 cells was developed.\r\nSome of the plasmin in this model system incorporated 32P-labeled di-isopropylfluorophosphate,\r\nimplying that active plasmin exists in\r\nSV3T3 cell culture medium and thus may be responsible for the protease-dependent\r\nmorphological change expressed by these cells and other\r\nphenotypic changes which occur upon virus transformation.
" }, { "name": "Trogler, William Charles", "degree": "PhD", "year": "1978", "title": "Electronic Spectroscopy and the Photochemistry of Compounds which Contain Quadruple Metal-Metal Bonds", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03092026-183448574", "creators": [ { "name": { "family": "Trogler", "given": "William Charles" }, "id": "Trogler-William-Charles", "orcid": "0000-0001-6098-7685", "display_name": "Trogler, William Charles" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nr7a-jz27", "abstract": "The electronic spectra and structures of binuclear\r\ntransition metal compounds which contain a quadruple metal-metal\r\nbond are discussed. Experimental results are presented\r\nfor the electric-dipole forbidden transitions of (n-Bu4)2[Re2Cl8],\r\n(n-Bu4)2[Re2Br8], Mo2(O2CCH3)4, Mo2(O2CCD3)4,\r\nMo2(O2CH)4, and Mo2(O2CCF3)4. The near infrared absorption system in\r\nK3Mo2(SO4)4 \u00b7 3.5 H2O has also been analyzed.
\r\n\r\nAqueous acid solutions of Mo2(SO4)44-, Mo2(aq)4+, and\r\nMo2Cl84- yield molecular hydrogen and oxidized molybdenum\r\nproducts upon ultraviolet irradiation. The compounds Mo2Cl4P4\r\n(P = P(n-Bu)3, P(Et)3 and P(Et)(Ph)2) undergo photooxidation to\r\nchloride bridged binuclear Mo(III) compounds subsequent to\r\n254 nm irradiation in chlorocarbon solvents. The nature of these\r\nphotooxidation reactions are examined.
" }, { "name": "Wood, Philip Eric", "degree": "PhD", "year": "1978", "title": "Studies of Mean Reynolds Stress Models of Turbulent Flow", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042026-224939924", "creators": [ { "name": { "family": "Wood", "given": "Philip Eric" }, "id": "Wood-Philip-Eric", "display_name": "Wood, Philip Eric" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6gta-n621", "abstract": "In this thesis a second order turbulence model is described\r\nwhich calculates the mean Reynolds stresses and dissipation rate\r\nfor homogeneous and slightly inhomogeneous shear flows. The higher\r\norder terms which appear in the exact differential (transport)\r\nequations for the Reynolds stresses and dissipation rate are approximated\r\nin terms of the mean velocity gradient, Reynolds stresses and\r\ndissipation rate using some of the principles of invariant modeling.\r\nThe unknown coefficients appearing in the models for the higher\r\norder terms were estimated by a systematic evaluation of the available\r\nexperimental data for homogeneous turbulence. The model was\r\nused to calculate the Reynolds stresses for homogeneous shear flow,\r\nhomogeneous strain and the decay of initially anisotropic turbulence.
\r\n\r\nThe model was further tested by calculating the mean velocity\r\nand Reynolds stresses for two inhomogeneous free shear flows, the\r\ntwo dimensional turbulent jet and the two dimensional wake. The\r\ngoverning model equations were transformed into similarity form.\r\nA calculation procedure is described for the solution of the resulting\r\nset of nonlinear ordinary differential equations.
\r\n\r\nA simplified version of the mean Reynolds stress model was\r\ndeveloped and it was also used to model the plane jet and wake.
" }, { "name": "Yoganathan, Ajit Prithiviraj", "degree": "PhD", "year": "1978", "title": "Cardiovascular Fluid Mechanics: I. Fluid Dynamics of Prosthetic Aortic Valves. II. Use of the Fast Fourier Transform in the Analysis of Cardiovascular Sounds", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-05252004-140334", "creators": [ { "name": { "family": "Yoganathan", "given": "Ajit Prithiviraj" }, "id": "Yoganathan-Ajit-Prithiviraj", "display_name": "Yoganathan, Ajit Prithiviraj" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/TVP6-ZY22", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPressure drops across ten prosthetic aortic heart valves have been measured under both steady and pulsatile flow using two different Newtonian liquids having viscosities of 0.01 dyne sec/cm[superscript 2] and 0.035 dyne sec/cm[superscript 2], respectively. The experimental results and the theory developed indicate that for a given aortic valve it is possible to predict peak systolic and mean systolic pressure drops from experimental pressure-drop data for steady flow. The difference in viscosities of the test fluids, 0.01 and 0.035 dyne sec/cm[superscript 2], seemed to have negligible effect within experimental error on the pressure drops over a range of flow rates from 83.0 cm[superscript 3]/sec to 500.0 cm[superscript 3]/sec.\r\n\r\nA laser-Doppler anemometer was used to study the in vitro velocity profiles in the near vicinity of a Starr-Edwards 1260 ball valve, a Smeloff-Cutter ball valve, a Cooley-Cutter disc valve, and a Bjork-Shiley tilting disc aortic prosthesis. The experiments were conducted under steady flow conditions. The experimental results indicate that all the aortic prostheses studied create very disturbed flow fields and cause large wall and bulk turbulent shear stresses in their near vicinity. If such stresses occur in vivo they could damage the endothelial lining of the ascending aorta, red blood cells and platelets, and could lead to thrombus formation and hemolysis.\r\n\r\nA detailed study of the Bjork-Shiley tilting disc aortic prosthesis reveals that it is possible to correlate the in vitro velocity measurements with two late pathological failure modes observed in recovered Bjork-Shiley aortic prostheses.\r\n\r\nThe fast Fourier transform (FFT) was used in the frequency analysis of the first and second heart sounds in normal man, and the closing sounds of aortic prostheses produced in a pulse duplicator. An initial study indicates that frequency analysis via the FFT technique could be used as a non-invasive diagnostic tool for some cardiovascular problems." }, { "name": "Aristoff, Paul Adrian", "degree": "PhD", "year": "1977", "title": "An Approach to the Total Synthesis of Aphidicolin", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10152025-061722008", "creators": [ { "name": { "family": "Aristoff", "given": "Paul Adrian" }, "id": "Aristoff-Paul-Adrian", "display_name": "Aristoff, Paul Adrian" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rerp-ya50", "abstract": "An approach to the total synthesis of the tetracyclic\r\nditerpene antibiotic aphidicolin i is described. The key\r\nintermediate ii was prepared in 19 steps (3% overall yield)\r\nfrom 2-methoxybenzosuberone. The key step involved the\r\nsolvolysis of a spire system (generated from a Claisen\r\nrearrangement) with participation of a remote double\r\nbond. The desired trans A/B ring fusion was introduced\r\nin the model system iii (18,19-dinoraphidicolan-3-one),\r\navailable from alcohol ii in 7 steps (40% overall yield)." }, { "name": "Attar, Amir", "degree": "PhD", "year": "1977", "title": "The Chemistry of Selective Oxidation of Sulfur Compounds and its Relation to Fuel Desulfurization", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172025-215430915", "creators": [ { "name": { "family": "Attar", "given": "Amir" }, "id": "Attar-Amir", "display_name": "Attar, Amir" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/5923-b957", "abstract": "See thesis PDF for abstract." }, { "name": "Bachovchin, William Walter", "degree": "PhD", "year": "1977", "title": "The Mechanism of Action of Adenosylcobalamin: I. 3-Fluoro-1, 2-Propanediol Dehydrase - Mechanistic Implications. II. Glycerol and Other Substrate Analogues as Substrates and Inactivators for Propanediol Dehydrase. Kinetics, Stereospecificity and Mechanism. III. The Involvement of a 5'-Deoxyadenosine Intermediate Containing Three Equivalent Hydrogens in the Mechanism of Glycerol Inactivation of Propanediol Dehydrase Holoenzyme. IV. Hydrogen Transfer from Enzyme-Bound Adenosylcobalamin as a Partial Rate Limiting Step in Catalysis", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262025-201250378", "creators": [ { "name": { "family": "Bachovchin", "given": "William Walter" }, "id": "Bachovchin-William-Walter", "orcid": "0000-0002-9926-7244", "display_name": "Bachovchin, William Walter" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8fy8-dk59", "abstract": "Part I
\r\n\r\n3-Fluoro-1,2-propanediol has been found to be a\r\nsubstrate for propanediol dehydrase and has very similar\r\nbinding and catalytic constants compared to the natural\r\nsubstrate. The only isolable products of the reaction are\r\nacrolein and inorganic fluoride; with 3-fluoro-3,3-dideuterio-\r\n1,2-propanediol as substrate, only 3,3-dideuterioacrolein\r\nis obtained. These results indicate that the primary\r\nproduct of the reaction is 3-fluoropropionaldehyde which\r\nspontaneously loses hydrogen fluoride to yield acrolein.\r\nThe similar kinetic parameters for the fluorinated as\r\ncompared to the normal substrate suggest that significant\r\ncharge does not develop on the fluorinated or, by implication,\r\nthe natural substrate during any rate-limiting\r\nsteps of the reaction. These results support a radical,\r\nas contrasted to an ionic pathway for reactions involving\r\nadenosylcobalamin and diol dehydrase.
\r\n\r\nPart II
\r\n\r\nA number of vicinal diols were found to react with\r\ndioldehydrase, typically resulting in the conversion of\r\nenzyme-bound adenosylcobalamin to cob(II)alamin and formation\r\nof aldehyde or ketone derived from substrate. Moreover all\r\nare capable of effecting the irreversible inactivation of\r\nthe enzyme. The kinetics and mechanism of product formation\r\nand inactivation were investigated.
\r\n\r\nGlycerol, found to be a very good substrate for diol\r\ndehydrase as well as a potent inactivator, atypically, did\r\nnot induce cob(II)alamin formation to any detectable extent.\r\nWith glycerol the inactivation process was accompanied by\r\nconversion of enzyme-bound adenosylcobalamin to an alkyl\r\nor thiol cobalamin, probably by substitution of an amino\r\nacid side chain near the active site for the 5'-deoxy-5'-adenosyl\r\nligand on the cobalamin.
\r\n\r\nThe inactivation reaction with glycerol as the inactivator\r\nexhibits a deuterium isotope effect of 14, strongly\r\nimplicating hydrogen transfer as an important step in the\r\nmechanism of inactivation. The isotope effect of the rate\r\nof product formation was found to be 8.0.
\r\n\r\nExperiments with isotopically substituted glycerols\r\nindicate that dioldehydrase distinguishes between \"R\" and\r\n\"S\" binding conformations, the enzyme-\"R\"-glycerol complex\r\nbeing predominately responsible for the product-forming\r\nreaction while the enzyme-\"S\"-glycerol complex results\r\nprimarily in the inactivation reaction. Mechanistic implications\r\nare discussed.
\r\n\r\nA method for removing enzyme-bound OH-Cbl that is non-\r\ndestructive to the enzyme and a technique for measuring the\r\nbinding constants of (R)-and (S)-1,2-propanediol are presented.
\r\n\r\nPart III
\r\n\r\nThe kinetics of inactivation of adenosylcobalamin dependent\r\npropanediol dehydrase by glycerol, (RS)-1,1-dideuterioglycerol,\r\n(R)-1,1-dideuterioglycerol, and perdeuterioglycerol\r\nin the presence of 1,2-propanediol and 1,1-dideuterio-1,2-propanediol\r\nwere investigated. The results (lead to the conclusion)\r\nthat hydrogen (or deuterium) located on C-1 of 1,2-propanediol \r\ncan participate in the inactivation-reaction and\r\ncontribute to the expression of an isotope effect on the\r\ninactivation rate constant. The mechanism by which this\r\noccurs must involve the cofactor as intermediate hydrogen\r\ncarrier, presumably in the form of 5'-deoxyadenosine. Moreover,\r\nthe results can be quantitatively accounted for by a\r\nmechanism involving transfer of hydrogen from an intermediate\r\ncontaining three equivalent hydrogens, such as 5'-deoxyadeno-sine,\r\nas the rate-determining step in the inactivation pathway.
\r\n\r\nWhen dioldehydrase holoenzyme is inactivated with 1-3H-glycerol,\r\n5'-deoxyadenosine enriched in tritium by a factor\r\nof 2.1 over that in glycerol can be isolated from the reaction\r\nmixture.
\r\n\r\nPart IV
\r\n\r\nThe rate of catalysis by the adenosylcobalamin dependent\r\nenzyme diodehydrase was determined as a function of the\r\nrelative amounts of 1,1-dideuterio-1,2-propanediol and\r\n1,2-propanediol present in the reaction mixture. The rate\r\nwas found to decrease sharply at low mole fractions of\r\n1,1-dideuterio-1,2-propanediol and slowly approach the\r\nrate observed 1,1-dideuterio-1,2 -propanediol at large mole\r\nfractions of 1,1-dideuterio-1,2-propanediol. We interpret\r\nthis to indicate that hydrogen transfer from enzyme-bound\r\nadenosylcobalamin is at least partially rate limiting\r\nin catalysis.
" }, { "name": "Berg, Jacqueline O.", "degree": "PhD", "year": "1977", "title": "Theory of Radiationless Transitions, Light Scattering and Fluorescence", "advisor": "Robinson, G. Wilse; McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042025-194142166", "creators": [ { "name": { "family": "Berg", "given": "Jacqueline O." }, "id": "Berg-Jacqueline-O.", "display_name": "Berg, Jacqueline O." } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "co-advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2f9g-4260", "abstract": "In the first part of this thesis a purely electronic mechanism by\r\nwhich ~ 20 eV excitations in condensed non-metallic phases relax to\r\nlower energy states is described. The mechanism utilizes an \"energy\r\nfission\" process whereby an ionic or excitonic state splits into two\r\nlower energy states, at least one being of the Frenkel exciton variety.\r\nThese relaxation processes should be important in the pre-chemical\r\nstage in the radiation chemistry of condensed phases. The mechanism\r\nexplains not only the known rapidity of such processes but also suggests\r\nan explanation for the proportionation of the chemistry between ionic\r\nand electronically excited states.
\r\n\r\nIn the second part of this thesis, Green's functions are used to\r\ndiscuss the time and frequency dependence of light scattering and\r\nfluorescence from model systems. In the first section of this part,\r\ntime-dependent scattering from a single resonance using an uncertainty-limited\r\nlight pulse is described. Three terms occur in the time\r\ndependence--one which decays as the resonance, one which decays\r\nlike the light source and a beat term between them which beats at the\r\nfrequency difference between the exciting pulse and the resonance.
\r\n\r\nIn the next section the model is extended to scattering from a\r\ntwo-level system. The frequency dependence of the Rayleigh and\r\nRaman scattering is described, again using excitation from an uncertainty-\r\nlimited light pulse.
\r\n\r\nThe effects of the two-photon states, which lead to the antiresonance\r\nterms in time-independent light scattering, have been evaluated\r\nfor time-dependent light scattering in the next section. Thus a unified\r\ntheory is obtained for time-dependent light scattering of an uncertainty-limited\r\npulse from far off-resonance into the resonance region. The\r\ntheory reduces to the conventional Kramers-Heisenberg second-order\r\nresults if a monochromatic light source is used. The two-photon states'\r\ncontribution to the scattering cross section has the same time dependence\r\nas the light source while the zero-photon state has the timede-pendence\r\npreviously calculated for near-resonance light scattering.
\r\n\r\nIn the next section excitation profiles for Rayleigh and Raman\r\ncross sections have been calculated using the formalism of the\r\nprevious section for an actual diatomic molecule from over 8000 cm-1\r\noff resonance into the resonance region. Several interference effects\r\nare discussed. The usual formula for the scattering cross sections is\r\nshown to lead to errors off resonance if the basis set is truncated.
\r\n\r\nFinally, a new method of calculating the zero-order density\r\nfunction directly from the absorption spectrum has been found and\r\napplied to the origin region of naphthalene's second excited singlet\r\nstate. Results are in good agreement with previous trial-and-error\r\nmethods.
\r\n\r\nMathematical appendices are given which derive the key formulae\r\nneeded in the second part of this thesis.
" }, { "name": "Burke, Jonathan Arno", "degree": "PhD", "year": "1977", "title": "Investigations of the Photochemistry of Mixtures of Methane, Nitrogen and Ammonia with Lyman-Alpha Radiation", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:03202026-160048320", "creators": [ { "name": { "family": "Burke", "given": "Jonathan Arno" }, "id": "Burke-Jonathan Arno", "display_name": "Burke, Jonathan Arno" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pkvs-kt50", "abstract": "In an attempt to investigate possible processes which may have\r\nled to the formation of nitrogen bases on the primitive earth prior to\r\nthe emergence of life, the gas-phase photochemistry of mixtures of\r\nmethane plus nitrogen and methane plus nitrogen plus ammonia was\r\nstudied. Photolyses were performed with Lyman-a light (10.2 eV).\r\nSample pressures varied from 2.5 T to 10.5 T. The compositions\r\nof the starting mixtures were CH4 : N2 = 2.24 : 1, and CH4 : N2 :\r\nNH3 = 1 : 0.61 : 0.12, 1 : 0.63 : 0.20, 1 : 0.62 : 0.24 and\r\n1 : 0.64 : 0.96. From 5 X 10-4 to 3.5 X 10-2 of the initial methane\r\nwas converted into various hydrocarbon products. The products of\r\nthe methane plus nitrogen photolyses yielded only hydrogen and\r\nhydrocarbons as products: no carbon-nitrogen bonds were formed.\r\nThe products of the methane plus nitrogen plus ammonia photolyses\r\nwere similar, but with the addition of small amounts of alkyl nitriles\r\nand no other carbon-nitrogen products. Hydrocarbon product distributions\r\nare in the approximate mole ratio C2H6 : C2H4 : C2H2 :\r\nC3H8 : CH3CN - 1 : 0.30 : 0.10 : 0.10 : 0.01. The two products\r\nC2H4 and C2H2 exhibited marked pressure dependences. A\r\npartial mechanism is proposed." }, { "name": "Chambers, John L.", "degree": "PhD", "year": "1977", "title": "Inhibited Bovine Trypsin, and Bovine Trypsinogen : the Refined Structure and Mechanism of a Not-Too-Serene Protease", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022025-193957018", "creators": [ { "name": { "family": "Chambers", "given": "John L." }, "id": "Chambers-John-L", "display_name": "Chambers, John L." } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/69pr-0q16", "abstract": "Refined three-dimensional structures of diisopropylphosphoryl\r\n(DIP)-inhibited bovine trypsin and of bovine trypsinogen are described,\r\nas determined by x-ray crystallography. A constrained difference\r\nFourier method for rapid, economical protein structure refinement\r\nwas developed and applied to these structures. The refinement\r\nsystem, which has been written to operate on a minicomputer, has\r\nreduced the standard crystallographic R-factor for DIP-trypsin from\r\n47.2% at 2.7 \u00c5 resolution to 21.5% at 1.5 \u00c5 resolution, making it one\r\nof the most highly and inexpensively refined protein structures to\r\ndate. For trypsinogen, R is 31% at 1.9 \u00c5 resolution, and refinement\r\nof both structures is nearing completion. The refined structures,\r\nthe mechanism of serine proteases, and the mechanism of activation of\r\ntheir zymogens are discussed.
\r\n\r\nDuring data collection for the studies described, new, more\r\nefficient techniques of correction for background radiation in\r\nprotein data measured by x-ray diffractometry were developed.
\r\n\r\nAlso presented are the structures of trypsin inhibited by the\r\nmetal ions Ag+ and Cu2+. These ions, which are powerful trypsin and\r\nchymotrypsin inhibitors, bind tightly and specifically at the active\r\nsite of the enzyme, between Asp 102 O\u03b41 and His 57 N\u03b41. They may\r\nthus be used as specific probes of the active site of serine proteases.
" }, { "name": "Cheong, Paul How-Kei", "degree": "PhD", "year": "1977", "title": "A Modeling Study of Coal Pyrolysis", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202026-211950178", "creators": [ { "name": { "family": "Cheong", "given": "Paul How-Kei" }, "id": "Cheong-Paul-How-Kei", "display_name": "Cheong, Paul How-Kei" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0am7-4v78", "abstract": "A model of coal pyrolysis is developed with the elements of (i) structure, (ii) chemical reactions, and (iii) transport.
\r\n\r\n(i) The chemical structure of coal is modeled as aromatic clusters bearing aliphatic side chains, bridges, and phenolic functional groups, consistent with various spectroscopic data and known chemical behavior.
\r\n\r\n(ii) A detailed scheme of thermal free radical reactions leading to the formation of tar, gases and deactivated char is postulated. State variables are defined as concentrations of the participating functional groups to describe the stoichiometry and rates of these reactions.
\r\n\r\n(iii) Macropores and transitional pores partition the coal particle into smaller subunits in which transport of tarry and gaseous products is by means of activated diffusion. The transport model postulates an active surface region of the subunits and a process of renewal of that region. A counting procedure is devised to predict the amount of aromatic fragments that escape from the subunits.
\r\n\r\nThe physicochemical processes are translated into a system of ordinary differential equations in the state variables, parametrized by the initial conditions and appropriate rate parameters. Numerical simulation is performed for two case studies where the necessary parameters are deduced from available pyrolysis and structural data and from additional assumptions.
\r\n\r\nThe model is applicable within the range of primary pyrolysis ((650\u00b0c) and predicts the ultimate weight loss as well as the distribution of products as a function of temperature and coal type. A supplementary model is also formulated for the reaction and transport of volatile materials in the macropores. This model takes into account the effects of the external pressure and the particle size on the evolution of products.
" }, { "name": "Corderman, Reed Roeder", "degree": "PhD", "year": "1977", "title": "Ion Cyclotron Resonance Studies of Inorganic Molecules in the Gas Phase: I. Organotransition Metal Complexes. II. Chain Reactions Involving Ionic Intermediates", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202007-075658", "creators": [ { "name": { "family": "Corderman", "given": "Reed Roeder" }, "id": "Corderman-Reed-Roeder", "display_name": "Corderman, Reed Roeder" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RYFA-1T76", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA brief introduction (Chapter 1) gives a general overview of the results presented in this thesis, and is followed by five chapters which concern ion cyclotron resonance spectroscopy (ICR) studies of transition metal complexes, trifluorophosphine, and methylsilanes in the gas phase. An ancillary study on the photoionization mass spectrometry (PIMS) of the methylsilanes is also included.\r\n\r\nChapter II discusses the gas phase ion chemistry of ([eta superscript 5] - C5H5)NiNO. The dissociative bond energies, D(B-CpNi[superscript +]) [...], are obtained by measuring equilibrium constants for reactions involving CpNi[superscript +] transfer between appropriate base pairs. A wide variety of reactions effected by CpNi[superscript +], including dehydrohalogenation, dehydration, dehydrogenation, decarbonylation, and alkylation processes are observed, and reaction mechanisms proposed.\r\n\r\nChapter III presents a detailed study of the sequential alkylation of CpNi[superscript +] and CpFe[superscript +] by d3-methyl bromide. A reaction mechanism involving oxidative addition of the metal to the weak carbon-bromine [sigma]-bond is presented.\r\n\r\nThe first observed example of a ligand displacement reaction involving an anionic transition metal complex, in which PF3 displaces CO from CpCo(CO)[superscript -], is reported in Chapter IV. This result leads directly to the conclusion that PF3 is a stronger [pi]-acceptor ligand than CO towards CpCo[superscript -] in the gas phase. Additionally, the negative ion chemistry of CpCo(CO)2 both alone and in mixtures with various ligands is presented.\r\n\r\nThe gas phase basicity, or proton affinity, of phosphorus tri-fluoride is determined in Chapter V. The results are discussed in terms of contributions from inductive and hyperconjugative interactions involving p[subscript pi]-d[subscript pi] bonding in HPF3[superscript +]. Ion-molecule reactions of mixtures of PF3 with SiF4, BF3, SF6, NF3, CH3F, and (CH3)2CO are briefly considered; various thermochemical considerations are used to determine the energetics of formation of the PF2[superscript +], PF4[superscript +], and CH3PF3[superscript +] ions observed in these mixtures.\r\n\r\nSeveral examples of gas phase chain reaction which proceed through ionic intermediates are presented in Chapter VI. Chain propagation reactions involve hydride and fluoride transfer between pairs of siliconium ions R1[superscript +] and carbonium ions R2[superscript +], for which D(R1[superscript +]-F[superscript -]) [...] D(R2[superscript +]-F[superscript -]) and D(R1[superscript +]-H[superscript -])[...] D(R2[superscript +]-H[superscript -]).\r\n\r\nPhotoionization efficiency for the low energy fragment ions (P-H)[superscript +], (P-H2)[superscript +], and (P-CH4)[superscript +] for the series of methylsilanes, (CH3)nH4-nSi (n = 0-3), are reported in Chapter VII. Appearance potentials for the (P-H)[superscript + siliconium ion fragments afford accurate calculation of the hydride affinities, D(R3Si[superscript +] -H[superscript -]) of these species." }, { "name": "Davis, James Hubbard", "degree": "PhD", "year": "1977", "title": "Theoretical Studies of Organic Diradicals and the Thermal Rearrangement of Bicyclopropenyls", "advisor": "Bergman, Robert G.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04242012-160948000", "creators": [ { "name": { "family": "Davis", "given": "James Hubbard" }, "id": "Davis-James-Hubbard", "display_name": "Davis, James Hubbard" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KZ6K-7P42", "abstract": "Part A. Generalized valence bond calculations on cyclopropene and vinylmethylene lead to the following conclusions: (1) the allyl-type \u03c0-system is strongly distorted by the presence of the unpaired sigma electron leading to a methylene-like triplet, ^3A^\", but a 1,3-diradical-like singlet state, ^1A^\"; (2) the lowest-lying singlet state of vinylmethylene has the form of a singlet methylene ^1A lying 12 kcal/mole above the triplet ground state, while the diradical singlet state lies at 14 kcal/mole.
\r\n\r\nPart B. Generalized valence bond calculations on trimethylenemethane indicate that the ground state is the planar triplet with the planar singlet state 26 kcal/mole higher. The rotational barrier for the triplet state is 18 kcal/mole, while one component of the planar singlet prefers the bisected geometry by 7 kcal/mole. Oscillator strengths for vertical transitions and ionization potentials are also reported.
\r\n\r\nPart C. Generalized valence bond calculations on vinylidene predict that the ground state is a singlet with a methylene-like triplet at 2 eV higher. With extensive CI calculations, we find CC bond energy of D_0(h_2C=C) = 150.1 kcal/mole and a heat of formation of 111.5 kcal/mole at 298\u00b0K. The dipole moment for the singlet is calculated to be 2.23D, while the dipole moment for the triplet is 0.55D.
\r\n\r\nPart D. Generalized valence bond calculations on aminonitrene indicate that the ground state is a singlet (^1A_1) with a low-lying triplet state (^3A_2) at 15 kcal/mole. We find the nitrogen-nitrogen bond dissociation energy for the singlet state is 70.4 kcal/mole. The dipole moment is found to be 4.036D for the ^1A_1 and 2.351D for the ^3A_2 state of aminonitrene. The ionization potential is calculated to be 9.4 eV.
\r\n\r\nPart E. The kinetic distribution of isomeric xylenes formed on the thermal aromatization of dl- and meso-1,1'-dimethyl-3,3'-bicylopropenyl and of 3,3'-dimethyl-3,3'-bicyclopropenyl has been determined by extrapolation of the time-dependent xylene percentages to zero percent conversion. The data is most consistent with a mechanism involving initial cleavage of one of the cyclopropene rings, followed by expansion of the other ring, closure to Dewar benzene and finally opening of the Dewar to form aromatic products.
" }, { "name": "DeNiro, Michael Joseph", "degree": "PhD", "year": "1977", "title": "I. Carbon Isotope Distribution in Food Chains. II. Mechanism of Carbon Isotope Fractionation Associated with Lipid Synthesis", "advisor": "Epstein, Samuel; Bonner, James Frederick", "url": "https://resolver.caltech.edu/CaltechTHESIS:01272026-230842128", "creators": [ { "name": { "family": "DeNiro", "given": "Michael Joseph" }, "id": "DeNiro-Michael-Joseph", "display_name": "DeNiro, Michael Joseph" } ], "advisors": [ { "name": { "family": "Epstein", "given": "Samuel" }, "id": "Epstein-S", "role": "advisor", "display_name": "Epstein, Samuel" }, { "name": { "family": "Bonner", "given": "James Frederick" }, "id": "Bonner-J-F", "role": "co-advisor", "display_name": "Bonner, James Frederick" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/vxtw-p993", "abstract": "The distribution of carbon isotopes in food chains was investigated\r\nby analyzing animals grown in the laboratory on diets of\r\nconstant isotopic composition. The isotopic composition of an animal\r\nreflects the isotopic composition of its diet, but the animal is\r\ngenerally enriched by about 1 \u2030 in \u03b413C relative to the diet. An\r\nisotopic mass balance exists for an animal-diet system. In three of\r\nfour cases analyzed, the 13C enrichment of the body relative to the\r\ndiet is balanced by a 13C depletion of the respired CO2.
\r\n\r\nThe carbon isotope distribution among different suborganismic\r\ncomponents of animals was also analyzed. The relationships among the\r\n13C/12C ratios of the major biochemical fractions, such as lipid,\r\ncarbohydrate, and protein, appear to be preserved in going from one\r\ntrophic level to the next, but the actual isotopic composition of a\r\nfraction in an animal and its diet can differ considerably. The\r\nrelationship between the carbon isotopic composition of a tissue in\r\na mouse and the carbon isotopic composition of the diet is affected\r\nboth by the type of tissue analyzed and by the diet. The 13C/12C\r\nratios of the biochemical components collagen, chitin, and the insoluble\r\norganic fraction of shells, which are commonly preserved in fossil\r\nmaterial, also show a correlation with the isotopic composition of the\r\ndiet. However, the magnitude of the difference between the 13C/12C\r\nratios of the component and the diet depends on the animal, the diet,\r\nand the biochemical nature of the component.
\r\n\r\nThese results suggest that it will be possible to perform dietary\r\nanalysis based on the relationship between the 13C/12C ratios of\r\nanimals and their diets. The limits of accuracy of this method, as\r\nestablished by the experiments reported here, will restrict its\r\napplication to situations in which the diet is derived from sources\r\nwith large differences in their \u03b413C values, such as terrestrial vs.\r\naquatic organisms and C3 vs. C4 plants. This method should be\r\napplicable in fossil as well as modern situations.
\r\n\r\nThe second part of this study involved the elucidation of the\r\nbasis of the low 13C/12C ratio of the lipid fraction relative to the\r\ncarbon isotopic composition of the whole organism and the other major\r\nbiochemical fractions. Experiments in which E. coli was grown on\r\ncarbon sources which enter at different steps of the metabolic sequence\r\nleading to lipid formation indicate that the carbon isotope fractionation\r\nresulting in the 13C depletion of the lipid fraction occurs during the\r\noxidative decarboxylation of pyruvate to acetyl CoA by the pyruvate\r\ndehydrogenase complex.
\r\n\r\nThe isotopic fractionations occurring during this step were\r\nanalyzed indirectly in a series of in vitro experiments with pyruvate\r\ndecarboxylase. These experiments indicate that:
\r\n\r\n1) An isotopic fractionation of the expected direction and\r\nmagnitude occurs during the pyruvate dehydrogenase step.
\r\n\r\n2) The 13C depletion of the acetyl CoA formed in the reaction\r\nis concentrated primarily in the carbonyl carbon atom, with the\r\nmethyl carbon atom retaining the 13C/12C ratio of pyruvate.
\r\n\r\n3) The difference in the 13C/12C ratios of the methyl and\r\ncarbonyl carbon atoms of acetyl CoA is twice as large as the\r\n13C depletion of the lipid fraction.
\r\n\r\n4) The difference in the 13C/12C ratios of the methyl and\r\ncarbonyl carbon atoms of acetyl CoA is temperature-dependent.
\r\n\r\n5) There will be a large, temperature-dependent difference in\r\nthe carbon isotopic composition of those carbon atoms of lipid\r\ncomponents which derive from the methyl and carbonyl carbon\r\natoms of acetyl CoA.
" }, { "name": "Freiser, Ben Sherman", "degree": "PhD", "year": "1977", "title": "Photochemical Investigations of Ions in the Gas Phase Utilizing Ion Cyclotron Resonance Spectroscopy", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242009-110155", "creators": [ { "name": { "family": "Freiser", "given": "Ben Sherman" }, "id": "Freiser-Ben-Sherman", "display_name": "Freiser, Ben Sherman" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "orcid": "0000-0001-8839-4822", "role": "chair", "display_name": "Beauchamp, Jesse L." }, { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "member", "display_name": "Hammond, George Simms" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "member", "display_name": "Goddard, William A., III" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HMVE-Q508", "abstract": "The photochemistry and photophysical processes of a broad range of ions have been studied in the gas phase using ion cyclotron resonance techniques. A discussion summarizing much of this work, and two papers on related topics are presented.\r\n\r\nIn paper I, \"Acid-Base Properties of Molecules in Excited Electronic States Utilizing Ion Cyclotron Resonance Spectroscopy\", a general method is described for obtaining excited state acid-base properties of molecules and ions in the gas Phase which utilizes ion cyclotron resonance spectroscopy for studying photochemical processes involving ions. These processes, including photodissociation and photodetachment, yield in favorable instances, electronic excitation energies of ions. A comparison of the excitation energies of a base B with the corresponding acid-base complex AB yields the excited state basicity of B. Similarly, a comparison of the excitation energies of a chromophoric acid A with the complex AB yields information about the excited state acidity of A. Studies of the first type are described using the reference acids H[superscript +] and Li[superscript +] with the bases C6H5X (X = H, CN, NH2, CHO, COCH3, NO2, OCH3, O[superscript -], and S[superscript -) pyridine, and ferrocene. In several instances photodissociation spectra of solvated acid-base complexes of the type BLib[with a + above the L] have been obtained and analyzed to determine the effects of further solvation on the excitation spectra of these complexes. A comparison of the gas phase excitation spectra of a number of ions to their solution absorption is made.\r\n\r\nStudies of the second type (excited state acidities) are described using the reference base H[superscript -] with the acids C6H5CO[superscript +] and C6H5CHOH[superscript +]. Calculated changes in acidity and basicity are used to infer changes in electron distributions and dipole moments for excited states, and yield insight into the types of transitions involved. In particular, these studies are used to assess the controversial role played by intra-molecular charge transfer in the lowest two singlet \u03c0\u2192\u03c0* transitions of monosubstituted benzenes. These results are compared with findings from related experiments and calculations when available.\r\n\r\nPaper II, entitled \"Electron Impact Dissociation of Cyanobenzene Radical Cations by Ion Cyclotron Resonance Spectroscopy\", describes using trapped ion cyclotron resonance spectroscopy for the first time to study the electron impact dissociation of ions. Fragmentation of C6H5CN[superscript +] to produce C6H4[superscript +] and HCN is observed to occur at low electron energies (3-9 eV). The extent of dissociation is observed to be linear in emission current, rising from a threshold at 3.0 \u00b1 0.5 eV to a maximum cross section estimated to be 6 \u00c5[superscript 2] at 7.5 \u00b1 0.5 eV. The implications of these results are discussed.\r\n" }, { "name": "Hawke, David Harry", "degree": "Masters", "year": "1977", "title": "Thermal Decomposition of (Presumed) Bismethylene Diazene", "advisor": "Dervan, Peter B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-081150564", "creators": [ { "name": { "family": "Hawke", "given": "David Harry" }, "id": "Hawke-David-Harry", "display_name": "Hawke, David Harry" } ], "advisors": [ { "name": { "family": "Dervan", "given": "Peter B." }, "id": "Dervan-P-B", "orcid": "0000-0001-8852-7306", "role": "advisor", "display_name": "Dervan, Peter B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2F5K-AV65", "abstract": "Thermal high temperature and base induced low temperature de-composition of 1-sulfonamido-2, 3-dimethylaziridines (2, 3) and low temperature oxidation of 1-amino-2,3-dimethylaziridines (4) gives 2-butenes as the major hydrocarbon products (70-99%). The stereo-chemistry of the products is consistent with a stepwise pathway for decomposition of the presumed intermediate bismethylene diazenes (1).\r\n" }, { "name": "Laura, Richard", "degree": "Masters", "year": "1977", "title": "Experiments Directed Toward the Total Synthesis of the Ionophore Antibiotic X-537A", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-155249907", "creators": [ { "name": { "family": "Laura", "given": "Richard" }, "id": "Laura-Richard", "display_name": "Laura, Richard" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/01WN-6H85", "abstract": "A synthetic approach to a portion of the carboxylic ionophore X-537A is discussed. A synthesis of the tetrahydropyran ring of this antibiotic via a Diels-Alder reaction followed by hydroboration is described.\r\n" }, { "name": "Lewis, Nathan Saul", "degree": "Masters", "year": "1977", "title": "The Chemistry of Rhodium and Molybdenum Isocyanide Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09192007-110805", "creators": [ { "name": { "family": "Lewis", "given": "Nathan Saul" }, "id": "Lewis-Nathan-Saul", "orcid": "0000-0001-5245-0538", "display_name": "Lewis, Nathan Saul" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YM4S-K662", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe rhodium isocyanide dimer, [...], has been synthesized and characterized. Like monomeric rhodium isocyanide complexes, the dimer has a tendency to associate in solution and reversibly form oligomers. These oligomers have been detected spectroscopically, and concentration dependences verify their formulation as high aggregates. The dimer also undergoes two-center, two-electron oxidative addition with a variety of reagents, including the halogens, methyl iodide, ethyl iodide, and methyl tosylate. These oxidative adducts have been characterized and studied through a variety of techniques. The dimer, unlike rhodium isocyanide monomers, acts as a base and binds one proton in aqueous solution. Titration data are presented, and an approximate [...] has been obtained. When treated with aqueous acid, visable light (546 nm) photolysis of solutions of [...] yields molecular hydrogen with quantum yields as high as 0.04. The photochemistry is oxygen sensitive, as well as anion dependent. Possible means of exploiting the photoreaction in a solar energy storage scheme is also discussed. In order to better understand the metal-metal interactions in the dimeric species, extended-Huckel molecular orbital calculations were performed on the rhodium dimer, as well as on monomeric fragments with the four isoelectronic metals Ru(O), Pd(II), Co(I), and Ir(I). These results, and their relationship to observed physical properties of the rhodium dimer are discussed in detail." }, { "name": "Mann, Kent Robert", "degree": "PhD", "year": "1977", "title": "An Investigation of the Photochemical and Spectroscopic Properties of Chromium, Molybdenum, Tungsten, and Rhodium Isocyanide Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08132024-203836380", "creators": [ { "name": { "family": "Mann", "given": "Kent Robert" }, "id": "Mann-Kent-Robert", "display_name": "Mann, Kent Robert" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s9tb-gr40", "abstract": "The X-ray crystal structure of Cr(CNPh)6 has been determined.\r\nThe complex crystallizes in the space group R3 with one molecule in\r\nthe unit cell a = b = c = 10.628\u00c5; \u03b1 = \u03b2 = \u03b3 = 111.17\u00b0; V = 861.1 \u00c53.\r\nThe metal atom has crystallographic site symmetry S6 with the MC6\r\nframework forming a perfect octahedron. The Cr-C-N bond angles\r\nare all 174.7\u00b0, the Cr-C bond lengths are 1.933(2)\u00c5, and the C-N\r\nbond length are 1.168(2)\u00c5.
\r\n\r\nBoth infrared spectra, X-ray crystal structure data, and\r\nelectronic absorption spectra are consistent with the operation of a\r\nsecond order Jahn Teller distortion of the ground state of Cr(CNPh)6.\r\nData obtained on the sterically hindered systems Cr(CNDph)6 and\r\nCr(CNIph)6 [Dph = 2,6-dimethylphenyl and Iph = 2,6-diisopropylphenyl]\r\nalso support the operation of a Jahn Teller effect. Similar considerations \r\napply to the Mo and W systems.
\r\n\r\nThe electronic absorption spectra of M(CNAr)6 [M = Cr(0),\r\nMo(0), W(0), Ar = phenyl, ph; 2,6-dimethylphenyl, Dph; and\r\n2, 6-diisopropylphenyl, Iph], Mn(CNP'n)6Cl and [Mn(CNPh)6](PF6)2\r\nare reported. Each of the M(CNAr)6 complexes exhibits intense\r\nallowed metal-to-ligand charge transfer (MLCT) absorption bands\r\nbetween 20.8 and 32.7 kK. The lowest MLCT bands are observed at\r\n29.9 and 31.1 kl( in the electronic spectrum of Mn(CNPh)6+. Low\r\nenergy bands at 18.2 and 20.4 kK in [Mn(CNPh)6]2+ are assigned to\r\nvibronic components of a \u03c3(CNPh) \u2192 d\u03c0 charge transfer transition.\r\nThe unique electronic structural properties of arylisocyanide\r\ncomplexes are apparently related to the \u03c0 conjugation of aromatic\r\nring orbitals with the out-of-plane \u03c0*(CN) function.
\r\n\r\nThe emission and photochemical behavior of M(CNPh)6 and\r\nM(CNIph)6 complexes (M = Cr, Mo, W; Ph = phenyl, Iph = 2,6-\r\ndiisopropylphenyl) has been studied. The complexes of Mo and W\r\nshow emission attributable to an L\u03c0* \u2192 d\u03c0 process in a variety of\r\nsolvents (2-methylpentane, 2-MeTHF, benzene, pyridine) at room\r\ntemperature. Complexes of all three metals show emissions at 77 K\r\nin 2-MeTHF that overlap the MLCT absorption bands. The emission\r\nquantum yields for Mo(CNIph)6 and W(CNIph)6 in 2-MeTHF at 77 K are\r\n0.78 \u00b1 0.08 and 0.93 \u00b1 O.07, respectively. The emission lifetimes\r\nat 77 K ir: 2-methylpentane for the M(CNIph)6 complexes are:\r\n\u03c4(Cr) less than 10 nsec, \u03c4(Mo) 40.2 \u00b1 0.5 \u03bcsec (298 K, 43 \u00b1 2 nsec),\r\n\u03c4(W) 7.6 \u00b1 0.5 \u03bc sec (298 K, 83 \u00b1 2 nsec). Both M(CNPh)6 and\r\nM(CNIph)6 undergo photosubstitution reactions in pyridine solutions.\r\nFormation of M(CNPh)5py and M(CNIph)5py occurs upon irradiation\r\nat 436 nm, with quantum yields decreasing according to a regular\r\npattern [Cr(CNPh)6] (0.23) ~ [Cr(CNIph)6] (0.23) > [Mo(CNPh)6]\r\n(0.055) > [Mo(CNIph)6] (0.022) > [W(CNPh)6] (0.011) >>\r\n[W(CNIph)6] (0.0003). The very small quantum yield for photosubstitution\r\nin the case of W(CNIph)6 is interpreted as an indication\r\nthat the mechanism of formation of W(CNPh)5 has associative\r\ncharacter. Irradiation of M(CNIph)6 at 436 nm in CHCl3 yields the\r\none-electron oxidation products [M(CNIph)6]Cl. The quantum yield\r\nin each case is 0.19 \u00b1 0.01. Similar irradiation of M(CNPh)6 in\r\nCHCl6 gives two-electron oxidation products. For M = Mo, W, the\r\nproducts are identified as the seven-coordinate species [M(CNPh)6Cl] Cl.
\r\n\r\nThe room temperature UV-VIS solution spectra of Rh(CNR)4+\r\n[R = aromatic or aliphatic] have been found not to follow Beer's law.\r\nThis behavior has been attributed to complex oligomerization of the\r\nmonomeric Rh(CNR)4+ units to form species of the type [Rh(CNR)4+]n (n = 1, 2, 3). The extinction coefficients and formation constants\r\nusing the following expressions:
\r\n\r\nM + M K1 \u21c4 D
\r\n\r\nD + M K2 \u21c4 T
\r\n\r\nhave been obtained for the systems R = phenyl in acetonitrile solution;\r\nand R = t-butyl in water solution. The values for the parameters used\r\nare for R = phenyl, K1 = 35 M-1, \u03b52 = 10,500, \u03b52K2 = 183,000 M-1; for R = t-butyl, K1 = 251 M-1, \u03b52 = 16,900.
\r\n\r\nThe nature of the oligomerization is due to a direct metals\r\nmetal interaction of the d8Rh atoms. The band positions for the\r\noligomeric species were found to conform to predictions made by\r\nsimple H\u00fcckel theory.
\r\n\r\nThe synthesis and characterization of a dimeric Rh(I)\r\ncomplex containing the bridging ligand 1,3-diisocyanopropane(bridge)\r\nis reported. In methanol solution, [Rh2(bridge)4]2+ oligomerizes,\r\nand species containing four, six, and eight Rh atoms have been
\r\n\r\nidentified spectroscopically. The dimer, [Rh2(bridge)4]2+, undergoes\r\ntwo center oxidative addition reactions with I2, Br2, and CH3I. The\r\nproducts, [Rh2(bridge)4X2]2+ (X = I, Br) which contain two strongly\r\ncoupled Rh(II) atoms, possess trans stereochemistry. The\r\nmechanism of oxidative addition is thought to involve attack of the\r\nRh(I) on the heavy atom of substrate molecule.
" }, { "name": "Manriquez, Juan Manuel", "degree": "PhD", "year": "1977", "title": "I. The Reduction of Molecular Nitrogen in Binuclear Dinitrogen Complexes of Titanium and Zirconium. II. Hydrogen Reduction of Carbon Monoxide Promoted by Mononuclear Carbonyl and Hydride Complexes of Bis(Pentamethylcyclopentadienyl) Zirconium", "advisor": "Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022026-201950836", "creators": [ { "name": { "family": "Manriquez", "given": "Juan Manuel" }, "id": "Manriquez-Juan-Manuel", "display_name": "Manriquez, Juan Manuel" } ], "advisors": [ { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zzmr-d423", "abstract": "I. The Reduction of Molecular Nitrogen in Binuclear Dinitrogen\r\nComplexes of Titanium and Zirconium.
\r\n\r\nII. Hydrogen Reduction of Carbon Monoxide Promoted by Mononuclear\r\nCarbonyl and Hydride Complexes of Bis(pentamethylcyclopentadienyl)\r\nZirconium.
\r\n\r\nPART I
\r\n\r\nThe synthesis and characterization of (\u019e5-C5Me5)2ZrCl2 (1),\r\n{(\u019e5-C5Me5)2ZrN2}2N2 (2), {(\u019e5-C5Me5)2Zr(CO)}2N2 (3), and\r\n{(\u019e5-C5Me5)2Zr(PF3)}2N2 (4) are described. 1 is prepared from lithium\r\npentamethylcyclopentadienide and zirconium tetrachloride. Sodium\r\namalgam reduction of 1 under N2 yields 2. 3 and 4 are prepared by\r\nsubstitution of the two terminal dinitrogen ligands by CO and PF3,\r\nrespectively. In solution 2 (and 4) exhibits fluxional behavior. The\r\ndynamics of 2 in solution as studied by 1H and 15N NMR shows that 2\r\nundergoes [\u019e5-C5Me5] ring site exchange as a result of the !ability of\r\nthe terminal dinitrogen ligands. A re-investigation of the titanium\r\nsystem analog in solution showed that the complex, originally assigned\r\nthe formula (\u019e5-C5Me5)2TiN2, is in fact analogous to the zirconium \r\ncomplex i.e. {\u019e5-C5Me5)2TiN2}2N2 (5). The product distribution (N2H4, NH3)\r\nfor the reaction of 2, 3, 4, 5, and {\u019e5-C5Me5)2TiN2}2N2 (6) with anhydrous\r\nHCl in toluene is reported. Hydrazine obtained in high yields obtained\r\nfrom the reaction of 2 and 5 with HCl. 6 also gives hydrazine but in\r\nmuch lower yield. Under the same conditions the reaction with HCl\r\nfor the complexes 3 and 4 results in the quantitative release of the\r\ndinitrogen and partial reduction of the terminal ligands. The product\r\ndistribution for the reaction of 2 with HBr, HCl, and H2SO4 each being\r\ncarried out in toluene, diethyl ether and methanol is also reported.\r\n2-(15N2)3 exchanges only terminal dinitrogen ligands with free 14N2 in\r\ntoluene solution at -23\u00b0. Treatment of 2 which is labelled with 15N2\r\nexclusively in the bridge position yields 1.5 mols 14N2, 0.5 mol 15N2,\r\n0.5 mol 14N2H4. The implications of these data\r\nwith regard to the N2 reduction sequence are discussed.
\r\n\r\nThe reactions of 2, 3, 4, and 6 with LiAlH4 are reported. 2\r\ngives hydrazine (0.5 mol) and ammonia (1 mol) after hydrolysis of the\r\nreaction products with HCl. 6 also gives hydrazine and ammonia but \r\nin lower yield. Under the same conditions the reaction of 3 and 4 results \r\nin the evolution of most of the dinitrogen. A study of the reaction\r\nof 2 labelled with 15N2 exclusively in the bridge position showed that\r\nthe hydrazine and ammonia originate from the bridge position.
\r\n\r\nPART II
\r\n\r\nThe synthesis and characterization of (\u019e5-C5Me5)2Zr(CO)2 (1),\r\n(\u019e5-C5Me5)2ZrH2 (2), and [C5(CH3)5] [C5(CH3)4CH2]ZrH prepared from {\u019e5-C5Me5)2ZrN2}2N2 are described. Both 1 and {\u019e5-C5Me5)2Zr(CO)}2N2 react with H2 forming (\u019e5-C5Me5)2Zr(H)(OCH3)(4) in high yield. 2 reacts\r\nwith CO and PF3 at -80\u00b0 to yield (\u019e5-C5Me5)2Zr(H)2(CO) (3) and\r\n(\u019e5-C5Me5)2Zr(H)2(PF3). 3 dimerizes to {(\u019e5-C5Me5)2ZrH}2 (\u00b5-OCH=CHO) aboce -50\u00b0. In the presence of 2, 3 may be reduced to 4. These\r\nobservations are interpreted in terms of a reaction sequence mediated\r\nby the formyl hydride complex (\u019e5-C5Me5)2Zr(H)(CHO) derived from 3\r\nvia migratory insertion. The reaction of 2 with formaldehyde on an\r\nequal molar basis produces a mixture of 4 and (\u019e5-C5Me5)2Zr(OCH3)2.\r\nThe implications of these results with respect to the possible intermediacy\r\nof formaldehyde in the formation of 4 and the plausible mechanisms\r\nfor the formation of 4 and {(\u019e5-C5Me5)2ZrH}2(\u00b5-OCH=CHO) are\r\ndiscussed. The synthesis of (\u019e5-C5Me5)2HfCl2 and (\u019e5-C5Me5)2HfH2 are\r\nreported. A comparison of the bis(pentamethylcyclopentadienyl)\r\nhydrides of group IV with the bis(cyclopentadienyl) hydrides of groups\r\nV, VI, and VII is made. The possible determining factor in the \r\nrearrangement of 3 to (\u019e5-C5Me5)2Zr(H)(CHO) is discussed.
" }, { "name": "McMillen, Thomas Joe", "degree": "PhD", "year": "1977", "title": "The Thermal Constitutive Behavior of Suspensions", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechETD:etd-04092004-154630", "creators": [ { "name": { "family": "McMillen", "given": "Thomas Joe" }, "id": "McMillen-Thomas-Joe", "display_name": "McMillen, Thomas Joe" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0KW1-H250", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in /pdf document.\t\t\t\t\t\r\n\r\nThe bulk thermal constitutive behavior of flowing, neutrally buoyant suspensions is considered theoretically and experimentally. A general theoretical expression relating the macroscopic heat flux in the suspension to microscale velocity and temperature distributions on the length scale of the particles is derived from statistical considerations of the microstructural configuration of the suspension. Evaluation of the relation for specific conditions is discussed with particular attention given to the role of random Brownian motions of the particles. Constraints imposed by simple shear flow are considered, and it is seen that the flowing suspension may not be described by a complete effective conductivity tensor [...].\r\n\r\nThe effective conductivity transverse to the flow of a dilute suspension of slightly deformed droplets is calculated in the limit of small particle Peclet number for the undisturbed bulk shear, [...], and the linear bulk temperature field, [...]. Two distinct cases of small deformation are considered; deformation dominated by interfacial tension forces, and deformation dominated by viscous forces in the drop. The microscale velocity and temperature fields are obtained as regular, asymptotic expansions in the small deformation parameter, [...], the governing thermal energy equation is then solved for small Peclet number using the methods of matched asymptotic expansions. The results obtained display the possible fundamental change in the dominant flow contribution to the effective conductivity due to the deformation in shape of the particles.\r\n\r\nThe bulk heat flux of a dilute suspension of rigid prolate spheroids is evaluated in the limit of small particle Peclet number for the undisturbed shear flow, [...], and the linear bulk temperature fields [...]. Microscale velocity fields near the particle are calculated from the Stokes equations for small particle Reynolds number for arbitrary orientation and rotation of the particles, and temperature distributions for the small, but non-negligible Peclet number by the methods of matched asymptotic expansions. The components of the effective conductivity tensor for a stationary suspension is obtained, and the bulk heat flux due to the temperature gradients orthogonal to the flow evaluated for the case of significant rotational Brownian motion of the particles.\r\n\r\nA rotating cylinder apparatus designed for the investigation of the bulk heat flux transverse to the flow of a suspension undergoing simple bulk shear flow is described, with special consideration given to describing and minimizing secondary effects such as natural convection, particle migration, viscous dissipation, and Taylor instability of the flow. Results obtained for the effective conductivity of suspensions of spherical polystyrene particles suspended in a Newtonian fluid are presented and compared to the theoretical prediction of Leal (1973) for the effective conductivity of dilute suspensions of spherical particles at low particle Reynolds and Peclet numbers." }, { "name": "Moskowitz, Alan Henry", "degree": "Masters", "year": "1977", "title": "The Distribution of Aerosol Nitrate Compounds with Respect to Particle Size: Vaporization Analysis with the Low Pressure Impactor", "advisor": "Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-084112194", "creators": [ { "name": { "family": "Moskowitz", "given": "Alan Henry" }, "id": "Moskowitz-Alan-Henry", "display_name": "Moskowitz, Alan Henry" } ], "advisors": [ { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KGHR-PB47", "abstract": "The atmospheric aerosol was sampled with a low pressure impactor at a coastal, an urban, and an agricultural site in the Los Angeles air basin. The material collected on each stage was analyzed for nitrate by direct vaporization into a chemiluminescent analyzer, sensitive at nanogram levels. The method responds to inorganic nitrate compounds which vaporize or decompose below about 1200\u00b0C. The coastal nitrate size distribution consists mainly of particles which have diameters greater than 2.0 \u00b5M, whereas the nitrate in the agricultural region is found primarily in the submicron range. The urban location, exhibiting characteristics of both coastal and agricultural regions, was bimodal about the 1-2 \u00b5m range. It is believed that the submicron aerosol is ammonium nitrate while the larger size fraction is sodium nitrate." }, { "name": "Murphy, Milton Keith", "degree": "PhD", "year": "1977", "title": "Gas Phase Investigations of the Lewis Acid Properties of Electron Deficient Compounds of Boron, Carbon and Silicon", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042025-164936251", "creators": [ { "name": { "family": "Murphy", "given": "Milton Keith" }, "id": "Murphy-Milton-Keith", "display_name": "Murphy, Milton Keith" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wxyg-3z40", "abstract": "Following a brief overview (Chapter I) which is intended to define\r\nin very general terms the main direction of this thesis, the results of\r\nfour distinct but closely interrelated investigations into the gas phase\r\nchemistry of a variety of Lewis acids of carbon, boron and silicon are\r\npresented.
\r\n\r\nChapter II describes photoionization mass spectrometry studies\r\nof positive ions generated from the fluoromethylsilanes (CH3)nF4-nSi\r\n(n = 1-4). Results provide accurate adiabatic ionizations of the neutrals\r\nand appearance potentials of the parent-minus-methyl fragments\r\ngenerated by photon impact. These data permit the derivation of a\r\nvariety of thermochemical data describing silicon containing species,\r\nincluding estimates of heats of formation of the ionic species, fluoride\r\naffinities (heterolytic bond dissociation energies, D[R+-F-]) of the\r\nvarious siliconium ions (CH3)nF3-nSi+ and ionization potentials of the\r\nsilyl radicals (CH3)nF3-nSi (n = 0-3).
\r\n\r\nChapter III describes ion cyclotron resonance spectroscopy (ICR)\r\nstudies of fluoride transfer reactions observed to occur between various\r\nfluorine and methyl substituted siliconium ions and carbonium ions\r\n(CH3)nF3-nM+ (M = C, Si; n = 0-3). These studies provide the first\r\nexperimental comparisons of the relative stabilities of analogous carbonium\r\nand siliconium ions free from the influence of solvation and\r\nestablish the gas phase ion stability order F3Si+ < CH3SiF2+ < CH3+ <\r\nCF3+ < (CH3)2SiF+ < CH3CF2+ < CH3CH2+ < (CH3)3Si+ < (CH3)2CF+ <\r\n(CH3)3C+ for F- as reference base. In conjunction with quantitative\r\nthermochemical data obtained in the photoionization studies (Chapter II),\r\nthese studies yield insights into the effects of \u03b1 methyl and fluorine\r\nsubstitution on carbon and silicon positive ion centers. Comparisons\r\nof the present results with available hydride affinity data yield insights\r\ninto the influence of the nature of the reference species on the\r\nstrengths of acid-base interactions.
\r\n\r\nChapters IV and V describe trapped-anion ICR investigations of\r\nthe gas phase Lewis acidities of a variety of neutral boranes R3B and\r\nR2FB (where R = CH3, C2H5, i-C3H7, and F) and silanes (CH3)nF4-nSi\r\n(n = 0-3), respectively, using F- as the reference Lewis base. Alkyl\r\nsubstituents are observed to decrease the Lewis acidity of both boron\r\nand silicon acceptor centers relative to fluorine substituents, but the\r\nmagnitude of this effect is found to be more pronounced in the case of\r\nthe silane Lewis acids. For the borane Lewis acids, increasing the\r\nsize of alkyl groups \u03b1 to the acceptor center results in increased\r\nstability (measured as fluoride affinities, D [R3B-F-]) of the borane-fluoride\r\nLewis adducts. The combined results of these two investigations\r\npermit quantification of the observed gas phase ordering of Lewis\r\nacidities BF3 > SiF4 > (i-C3H7)2FB > (i-C3H7)3B > (C2H5)2FB > (C2H5)3B > CH3SiF3 > (CH3)2FB > (CH3)3B > (CH3)3SiF2 > SF4 > (CH3)3SiF for\r\nfluoride ion as the reference base. Interesting insights into the variations\r\nin stabilities of the pentacoordinate silicon anions (CH3)nF5-nSi-\r\n(n = 0-3) are provided by comparisons with available information on\r\nthe isoelectronic neutral fluoromethylphosphoranes (CH3)nF5-nP\r\n(n =0-4).
" }, { "name": "Nascimento, Marco Antonio Chaer", "degree": "Masters", "year": "1977", "title": "Theoretical Studies of Photoionization", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302010-100258173", "creators": [ { "name": { "family": "Nascimento", "given": "Marco Antonio Chaer" }, "id": "Nascimento-Marco-Antonio-Chaer", "display_name": "Nascimento, Marco Antonio Chaer" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FP9D-JD91", "abstract": "The photionization cross-section is shown to be directly related to the imaginary part of the frequency dependent \r\npolarizability.\r\n\r\nUsing this relation, an approximate representation of the frequency-dependent polarizability is constructed from a discrete set of transition frequencies and oscillator strengths, which in turn is used in an analytical continuation procedure for complex values of the frequency. The great advantage of the method resides on the fact that the use of a discrete representation for the dynamic \r\npolarizability explicitly avoids the use of continuum functions.\r\n\r\nThe method is applied to the calculation of the photoionization cross-section for the 2^1S and 2^3S metastable states of the He atom and for the H^- atom. Further improvements of the technique are suggested.\r\n" }, { "name": "Nesbitt, Stephen Lee", "degree": "Masters", "year": "1977", "title": "Thiosilanes as Thioketalization Reagents", "advisor": "Evans, David A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04062010-085409602", "creators": [ { "name": { "family": "Nesbitt", "given": "Stephen Lee" }, "id": "Nesbitt-Stephen-Lee", "display_name": "Nesbitt, Stephen Lee" } ], "advisors": [ { "name": { "family": "Evans", "given": "David A." }, "id": "Evans-D-A", "role": "advisor", "display_name": "Evans, David A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CDYJ-S314", "abstract": "Thiosilanes react efficiently with simple aldehydes and ketones when catalyzed with ZnI_2 to produce thioacetals and thioketals. Steroidal diketones were thioketalized with yields and selectivity superior to other methods when allowed to react with thiosilanes and ZnI_2.\r\n\r\nThe overall thioketalization process proceeds through silyl-hemithioketal intermediates which can be detected and isolated from the reaction mixtures. The isolated silylhemithioketals can be resubmitted to the thioketalization reaction conditions and be converted to thioketals.\r\n" }, { "name": "Reiner, Robert Henry", "degree": "PhD", "year": "1977", "title": "I. Calculation of Vibrational Transition Moments. II. Photochemistry of Vibrationally Excited Hydrogen Iodide. III. Photochemistry of Iodine Monochloride in Hydrogen", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072026-041914218", "creators": [ { "name": { "family": "Reiner", "given": "Robert Henry" }, "id": "Reiner-Robert-Henry", "display_name": "Reiner, Robert Henry" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v0fy-8486", "abstract": "The text of this thesis is divided into three sections.
\r\n\r\nIn Part I, semi-empirical calculations of vibrational transition moments in general and hydrogen halide transition moments in particular are investigated. Semi-empirical transition moments, calculated using traditional approximations for the electric dipole operator, M(R), are compared with the exact vibrational transition moments for two hypothetical molecules in paper 1. The comparisons indicate that applying boundary conditions to an approximate M(R) does not significantly improve the transition moments predicted by that M(R). In paper 2, the same hypothetical molecules are used to evaluate a new method of obtaining M(R) from spectroscopic data, using each rovibrational moment in the vibrational bands rather than just the band centers. This method allows one to obtain an additional term in the Taylor series expansion of M(R), which produces corresponding improvement in the predicted vibrational transition moments. This new method is used on the experimental results available for HI and HF in papers 3 and 4, respectively. Here the rovibrational transition moments are also used to verify and determine the signs of measured transition moments.
\r\n\r\nThe reaction and vibrational relaxation of hydrogen iodide are discussed in Part II of this thesis (paper 5). Thermal and photochemical decomposition studies performed on HI yield the following results: (1) A small first-order component in the dark (thermal) reaction was detected in addition to the well-known second-order component. (2) The activation energy of the second-order reaction component between 660 and 710 K is 52.9\u00b12.8 kcal/mole as compared with the 44 kcal/mole previously reported. (3) While the rate of the HI decomposition was enhanced in the photochemical experiments, a kinetic analysis indicated that this enhancement was due to thermal heating rather than by the reaction of vibrationally excited HI. (4) Theoretical estimates of vibrational reaction and relaxation rates were made suggesting experimental conditions which could lead to observation of vibrational enhancement of this reaction.
\r\n\r\nThe photochemistry of iodine monochloride in hydrogen is the subject of Part III. In paper 6, the quantum yield of HC1 formation in mixtures of IC1 and H2 is remeasured. The results indicate that while earlier conclusions are qualitatively correct, the secondary reactions in the IC1-H2 system are more complicated than previously envisioned. The reaction ratio of IC1 to H2 with C1 at 298.05 K is 1133\u00b1 69. This implies that the reported rate constant for the reaction: C1+ IC1 \u2192 C12 + I, determined by the photolysis of pure IC1 is several orders of magnitude too small.
" }, { "name": "Sankur, Vega Dibag", "degree": "PhD", "year": "1977", "title": "I. Study of Macromolecular Brownian Motion by Laser Light Scattering. II. Light Scattering Investigation of Amorphous Polymethylmethacrylate", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022026-163753886", "creators": [ { "name": { "family": "Sankur", "given": "Vega Dibag" }, "id": "Sankur-Vega-Dibag", "display_name": "Sankur, Vega Dibag" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/459a-3f20", "abstract": "Part I
\r\n\r\nWe have studied the light scattered from dilute solutions of\r\nthree different molecular weight (MW = 2 x 106, 4.1 x 106, 7.1 x 106)\r\npolystyrene molecules in three solvents (cyclohexane, diethylmalonate,\r\n1-chloroundecane) at their respective theta temperatures. The autocorrelation\r\nfunctions collected at small x = k2RG (k is the wave\r\nvector, RG is the radius of gyration) were fitted to a single exponential\r\nfunction decay time which yielded the diffusion coefficients D.\r\nFor concentrations below 1000 \u03bcg/cc, D's were found to be independent\r\nof concentration and to be well represented by a Stokes-Einstein relation\r\nD = kBT/6T\u03c0\u019es\u03beG where \u019es is the solvent viscosity. We determined\r\n\u03be to be 0.70 \u00b1 .02. At higher x, the autocorrelation functions have\r\ncontributions from the first mode of internal motion and analysis of\r\ndata in terms of two exponentials yield the relaxation time of this\r\nmode, \u03c41. \u03c41's were measured for four polystyrene-cyclohexane solutions\r\nwith varying concentrations for both the four and seven million\r\nmolecular weight samples. The relaxation times were found to be independent\r\nof concentration. The same experiment was repeated for both\r\nmolecular weight samples for one solution each in diethylmalonate and\r\nin 1-chloroundecane. The relaxation times obtained agreed well with\r\nthe theoretical predictions based on Rouse-Zimm model. The results\r\nof this research program confirm the accuracy of laser light scattering\r\ntechnique to measure diffusion coefficients of macromolecules. They\r\nalso establish laser light scattering as a new technique for quantitative\r\ndetermination of terminal relaxation time of linear flexible\r\npolymers. The accuracy of these measurements are comparable to those\r\nobtained by viscoelastic methods.
\r\n\r\n\r\nPart II
\r\n\r\nWe have studied the light scattered from amorphous polymethylmethacrylate\r\n(PMMA) using the correlation technique for a range of\r\ntemperatures from 6\u00b0c to 165\u00b0c encompassing the glass transition temperature\r\n(Tg ~ 120\u00b0C). The data were analyzed in terms of two exponential\r\ndecays and the angular dependence of each of the corresponding\r\nrelaxation frequencies was examined. The results for the high frequency\r\nrelaxation mode are angular independent and fall reasonably well on two\r\nstraight lines of different activation energy(~ 8 Kcal/mole at high\r\ntemperatures and ~1 Kcal/mole at low temperatures), indicating the\r\npresence of two coupled relaxation mechanisms. The low frequency relaxation\r\nresults are quite sensitive to the inhomogeneities of\r\nunannealed samples and have in this case irregular angular dependences.\r\nThe angular dependence disappears for samples close to Tg and for\r\nannealed samples. Below Tg this relaxation process has a fairly constant\r\nfrequency of about 3 Hz independent of temperature. Above Tg its\r\nfrequency increases very rapidly with temperature to reach 130 Hz at\r\n165\u00b0C and follows the backbone main-chain relaxation frequency measured\r\nby other techniques. The results of this research program show that\r\nlaser light scattering is a valuable tool to study the various relaxation\r\nmechanisms occuring in solids and supercooled liquids.
" }, { "name": "Stackhouse, Frank A.", "degree": "Masters", "year": "1977", "title": "Solubilization and Partial Characterization of the Tetrodotoxin Binding Component from Electric Eel Electroplaque", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282010-093315226", "creators": [ { "name": { "family": "Stackhouse", "given": "Frank A." }, "id": "Stackhouse-Frank-A", "display_name": "Stackhouse, Frank A." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EGBS-9230", "abstract": "The tetrodotoxin (TTX) binding component from the electroplaque of Electrophorus electricus was solubilized and studied using ^3H-TTX purified by a modified procedure using Bio-Rex-70 at pH 8.7. The best extraction yield was obtained from a solubilization in 1-2% Lubroi-PX, at pH 7.6, for 2 hours, at a membrane fragment concentration equivalent to 2.0 - 2.5 g original wet weight tissue/ml. Gel filtration on Sepharose-6B was used to verify that the TTX binding component was solubilized. The molecular weight of the solubilized component was found to be about 200,000 using 10-43% glycerol gradients. A Sephadex G-50 assay was used to study binding. A K_D of 1.2 nM was obtained for ^3H-TTX binding. This binding was affected by cations in a manner similar to that found by Reed and Raftery\r\n[Biochemistry 15:944-953 (1975)]. The solubilized material was found to be unstable with respect to TTX binding; this stability was affected by the presence of cations and TTX, but not veratridine or procaine.\r\n" }, { "name": "Walch, Stephen Perry", "degree": "PhD", "year": "1977", "title": "Theoretical Studies of Chemisorption", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11092009-084139276", "creators": [ { "name": { "family": "Walch", "given": "Stephen Perry" }, "id": "Walch-Stephen-Perry", "display_name": "Walch, Stephen Perry" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TDQT-V666", "abstract": "PART A: GVB and GVB-Cl wavefunctions (using a double zeta basis) have been obtained as a function of internuclear distance for the lowest three states of NiCO. The wavefunctions lead to a qualitative description in which the Ni atom is neutral with a (4s)^1(3d)^9 atomic configuration. The CO lone pair delocalizes slightly onto the Ni, leading to the 4s-like orbital hybridizing away from the CO. The dir pairs on the Ni are slightly back-bonding to the CO. The three bound states are ^3\u03a3^+, ^3\u220f, and ^3\u0394\r\nconsisting of the singly occupied 4s-like orbital plus a single d hole in a \u03c3, \u03c0, or \u03b4 orbital, respectively. The ground state is found to be ^3\u0394 with calculated R_e = 1.90 \u00c5, D_e = 1.15 eV = 26.5 kcal/mol, and \u03c9_c(Ni-C) = 428 cm^(-1), all reasonable values, although direct information on NiCO is not yet available. The adiabatic excitation energies are calculated as 0.240 eV to ^3\u03a3^+, and 0.293 eV to ^3\u220f. The states with (4s)^2(3d)^8 configurations on the Ni lead to repulsive potential curves with vertical excitation energies in the range of 3.0 to 5.0 eV.\r\n\r\nPART B:\tConfiguration interaction calculations have been carried out for a number of positive ion states of NiCO. These calculations indicate that there are two distinct groups of ionization potentials. The first group involves ionizations out of Ni-like orbitals. The lowest states of this group involve ionization out of a Ni 4s-like orbital leading to a 3d^9 configuration and states of symmetry ^2\u03a3^+, ^2\u220f, and ^2\u0394 depending on whether the 3d-hole is taken in a \u03c3 , \u03c0) or \u03b4 orbital. At the optimum geometry of NiCO, the dissociation energy of NiCO^+ to Ni^+(^2D) and CO is calculated to be 2.26, 2.03 and 2.50 eV for the ^2\u03a3^+, ^2\u220f, and ^2\u0394 states, respectively, in reasonable agreement with the value of 2.10 eV calculated from the experimental heat of formation of NiCO^+. Other states in the first group involve ionization out of Ni 3d orbitals leading to a group of ion states with a width of 3.1 eV. This is in good agreement with the Ni d bandwidth as observed in photoemission experiments. The second group of ion states correlates at large Ni-C separation with the ground state of the Ni atom and various states of CO^+. The principal change as compared with free CO is that the 5\u03c3 ionization (lone pair on the CO) increases in energy by about 2.5 eV, whereas the 4\u03c3 and 1\u03c0 ionizations change only slightly. This leads to the 5\u03c3 and 1\u03c0 ionizations being nearly degenerate, with the 4\u03c3 ionization about 3.0 eV higher, in agreement with the currently accepted interpretation of the photoelectron spectrum of CO chemisorbed on Ni.\r\n\r\nPART C: Geometries for 0 and S overlayers on the (100) and (110) surfaces of Ni have been calculated using ab initio wavefunctions for 0 and S bonded to small clusters of Ni atoms (1 to 5 Ni atoms). The calculated geometries are within 0.07\u00c5 of the results of dynamic LEED intensity calculations, indicating that accurate geometries\r\nof chemisorbed atoms may be obtained from calculations using clusters including only those metal atoms within bonding distance.\r\n\r\nPART D:\tElectronic wavefunctions have been obtained as a function of geometry fora S atom bonded to Ni clusters consisting of l to 4 atoms de-signed to model bonding to the Ni(100) and Ni(110) surfaces. Electron correlation effects were included using the generalized valence bond and configuration interaction methods. Modeling the (100) surface with four Ni atoms, we find the optimum S position to be 1.33\u00c5 above the surface, in good agreement with the value (1.30 \u00b1 0.10\u00c5) from dynamic LEED intensity calculations. The bonding is qualitatively like that in H_2S with two covalent bonds to one diagonal pair of Ni atoms. There is a S p\u03c0 pair overlapping the other diagonal pair of Ni atoms. [Deleting this pair the S moves in to a position 1.04\u00c5 from the surface.] There are two equivalent such structures, the resonance leading to equivalent S atoms and a c(2x2) structure for the S overlayer. The Ni in the layer beneath the surface seems to have little effect (~0.03\u00c5) on the calculated geometry.\r\nThe above model of the bonding suggests that for the (110) surface the S lies along the long edge of the rectangular unit cell (2 coordinate) rather than at the four coordinate site usually assumed. Our calculated position for the S of 1.04\u00c5 is in reasonable agreement with the value from dynamic LEED intensity calculations, 0.93 \u00b10.10\u00c5.\r\nBonding the S directly above a single Ni atom leads to a much weaker bond (D_e = 3.32 eV) than does bonding in a bridge position (D_e = 5.37 eV). \r\n\r\nPART E:\tElectronic wavefunctions have been obtained as a function of geometry for an 0 atom bonded to Ni clusters (consisting of 1 to 5 atoms) designed to model bonding to the Ni(100) and Ni(110) surfaces. Electron correlation effects were included using the generalized valence bond and configuration interaction methods. For the (100) surface, we find that the charge distribution for the full 0 overlayer is consistent with taking a positively charged cluster. The four surface atoms in the surface unit cell and the atom beneath the surface are important in determining the geometry, leading to a Ni^+_50 cluster as the model for the (100) surface. The optimum oxygen position with this model is 0.96\u00c5 above the surface (four-fold coordinate site) in good agreement with the value (0.90\u00b1 0.10\u00c5) from dynamic LEED intensity analysis. The atom beneath the surface allows important polarization effects for the positively charged cluster. The bonding to the surface involves bridging two diagonal surface Ni atoms. There is an 0(2p\u03c0)pair which overlaps the other diagonal pair of Ni atoms leading to nonbonded repulsions which increase the distance above the surface. There are two equivalent such structures, the resonance leading to a c(2 x 2) structure for the 0 over-layer. The above model suggests that for the (110) surface the 0 lies along the long edge of the rectangular unit cell. For this registry with the surface, calculations based on Ni_20 and Ni_30 models indicate that the oxygen is only 0.1\u00c5 above the plane of the surface.\r\n\r\nPART F:\tGeneralized valence bond and configuration interaction wave-functions have been obtained as a function of R for numerous electronic states of NiO. All the lower states are found to involve the (4s)^1(3d)^9 Ni atom configuration and 0 in the (2s)^2(2p)^4 configuration. There are two groups of states. The lower group of states involves pairing singly occupied Mi(4s).and 0(2p \u03c3) orbitals into a (somewhat ionic) sigma bond pair with various pairings of the Ni(3d)^9 and 0(2p\u03c0)^3 configurations. This leads to a number of states including the ground state which we find to be x^3\u03a3^-. (The electronic structure is analogous to that of O_2.) The calculated D_o and R_e for the x^3\u03a3^- state of Ni0 are 89.9 Kcal/mole and 1.60 \u00c5 respectively. The bond energy is in good agreement with the experimental value 86.5 \u00b15 Kcal/mole, while the R_e value is not known experimentally. The higher group of states involve a doubly occupied 0(2p \u03c3) orbital., The Ni(4s) orbital in this case is non-bonding and builds in\r\n4p character to move away from the oxygen orbitals. The bonding mainly involves stabilization of the oxygen orbitals by the Ni(3d)^9 core (somewhat analogously to the bonding in NiC0). Numerous allowed transitions between these states and the states of the lower group are calculated to be in the range 1.0 to 3.0 eV where numerous bands are seen in emission.\r\n\r\n" }, { "name": "Ward, Gerald Wayne", "degree": "PhD", "year": "1977", "title": "Strain Induced Changes in the Permeability of Water Swollen Segmented Polyurethane Elastomers", "advisor": "Corcoran, William Harrison; Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07162004-144020", "creators": [ { "name": { "family": "Ward", "given": "Gerald Wayne" }, "id": "Ward-Gerald-Wayne", "display_name": "Ward, Gerald Wayne" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8SMH-RQ14", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe permeability of water swollen segmented polyurethane membranes has been determined for the solutes urea, glucose, sucrose, and raffinose at 26.5[degrees]C. The permeability of segmented polyurethane membranes; based on poly(oxyethylene glycol) grades 600, 1000, 1500, and 1540; was determined for the swollen unstrained films and for the swollen films at several strains. The free volume theory for diffusion through homogeneously swollen polymers was able to predict the observed changes in membrane permeability with strain for all solutes except urea. The free volume theory fails to predict the urea data accurately because the polyurethanes used absorb urea and therefore the urea can diffuse through the polymer as well as through the solvent, an eventuality not provided for in the free volume theory.\r\n\r\nThe solute reflection coefficient [...], as defined in the theory of thermodynamics of irreversible processes, was determined. The available-area-ratio and the film tortuosity were calculated from the solute reflection coefficient and the film permeability [...]. Neither the available-area-ratio nor the film tortuosity correlate with changes in the film permeability.\r\n\r\nA correlation between [...] and [...] was proposed. It was shown that for [...] the film permeability [...] is inversely proportional to [...]. The proposed correlation is discussed and the suggestion is made that additional experiments be conducted to determine the range in [...] for which the correlation is valid." }, { "name": "Wherland, Scot Edward", "degree": "PhD", "year": "1977", "title": "Metalloprotein Electron Transfer Mechanisms", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292026-205905890", "creators": [ { "name": { "family": "Wherland", "given": "Scot Edward" }, "id": "Wherland-Scot-Edward", "orcid": "0000-0003-1699-5594", "display_name": "Wherland, Scot Edward" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6cx5-4s21", "abstract": "The rates of oxidation and reduction of various metalloproteins\r\n(several cytochromes c azurin, plastocyanin, stellacyanin, and \r\nHiPIP) by inorganic reagents (including Fe(EDTA)2-,\r\nCo(phen)33+, Fe(CN)63-/4-, derivatives of the latter two reagents,\r\nand Ru(NH3)62+) have been analyzed within the framework of the\r\nrelative Marcus theory of outer-sphere electron transfer. This\r\napproach has allowed contributions to the overall free energy of\r\nactivation (the specific activation of the reagent, the thermodynamic\r\ndriving force for the reaction, and the general coulombic\r\ninteractions of the reactants) to be factored out, leaving a quantity\r\nwhich is characteristic of the activation process the protein must\r\nundergo in order to transfer an electron with each reagent. These\r\nanalyses have led to the definition of the \"kinetic accessibility\" of\r\nthe electron transfer sites of several proteins, the order being\r\nstellacyanin \u226b plastocyanin > horse heart cytochrome ~ >\r\nPseudomonas cytochrome c551 > HiPIP \u2245 Pseudomonas azurin.\r\nAs the kinetic accessibility of the proteins decreases, the variety\r\nof apparent electron transfer mechanisms increases. It is\r\nconcluded that the two most important factors in controlling the\r\nreactivity of redox proteins with inorganic reagents (after the three\r\npreviously mentioned contributions are eliminated) are the\r\navailability of extended \u03c0 orbital systems to facilitate orbital overlap\r\nand thus adiabaticity, and the capacity of the reagents to\r\npenetrate the hydrophobic residues surrounding the metal sites in\r\nmany proteins. Protein-protein electron transfer reactions are also\r\nconsidered, as are ionic strength and pH influences on the rate\r\nconstants." }, { "name": "Allen, Mark Andrew", "degree": "PhD", "year": "1976", "title": "Interstellar Space: the Astrochemist's Laboratory", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042003-154350", "creators": [ { "name": { "family": "Allen", "given": "Mark Andrew" }, "id": "Allen-Mark-Andrew", "display_name": "Allen, Mark Andrew" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B5RS-Y551", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn the first part of this thesis, a mechanism for the formation molecules on small (radius [...] ) interstellar grains is proposed. It is suggested that the energy liberated when a chemical bond is formed between two atoms on a grain is transferred to the lattice vibrations of the grain, heating up the grain. The \"hot\" grain, during the time that it is radiatively recooling, may then liberate its adsorbed volatiles. The timescales for molecular desorption from a grain are calculated for OH and CO for four different grain compositions.
\r\n\r\nA simplified H2 formation model is then presented that utilizes this surface reaction mechanism. The resulting value for the formation rate constant R is [...] for dark clouds at 10[degrees]K. The nascent H2 molecules are ejected in excited states in qualitative agreement with Copernicus observations. With the synthesis of H2 the dominant process, a time-dependent treatment of the chemical evolution of a dark cloud with little or no ionizing radiation [...] shows that the clouds require more than 10[^7] years to achieve chemical equilibrium. It is also suggested that the observed residual atomic hydrogen in several dark clouds indicates that the clouds are l0[^6]- l0[^7] years old.
\r\n\r\nThis approach is further developed into an ab initio chemical model for dense interstellar clouds that incorporates 598 grain surface reactions, with small grains again providing the key reaction area. Gas-phase molecules are depleted through collisions with grains. The abundances of 372 chemical species are calculated as a function of time and are found to be of sufficient magnitude to explain most observations. Peak abundances are achieved on timescales on the order of l0[^5]-l0[^6] years, depending on cloud density and kinetic ternperature. The reaction rates for ion-molecule chemistry are approximately the same, therefore indicating that surface and gas-phase chemistry may be coupled in certain regions. The composition of grain mantles is shown to be a function of grain radius. In certain grain size ranges, large molecules containing two or more heavy atoms are more predominant than lighter \"ices\"H_2O, NH_3, and CH_4. It is possible that absorption due to these large molecules in the mantles may contribute to the observed 3[...] band in astronomical spectra.
\r\n\r\nThe second part of this thesis is an account of a radio astronomy observational program to detect new transitions of both previously observed and yet undetected interstellar molecules. The negative results yield order of magnitude upper limits to the column densities of the lower transition states of the various molecules. One special project was the search for the [...] - doublet transitions of the [...] state of OD. The resulting upper limit for the OD/OH column density ratio towards the galactic center is 1/400 and is discussed with reference to theories about deuterium enrichment in interstellar molecules.
\r\n" }, { "name": "Bloch, Ricardo", "degree": "PhD", "year": "1976", "title": "Viscoelastic Behavior of Filled and Unfilled Elastomers in Moderately Large Deformations", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02202004-115154", "creators": [ { "name": { "family": "Bloch", "given": "Ricardo" }, "id": "Bloch-Ricardo", "display_name": "Bloch, Ricardo" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z2CG-8P89", "abstract": "A constitutive model was developed for the description of the viscoelastic (time-dependent) behavior of soft rubberlike materials in moderately large deformations. The model assumes that time shift invariance is preserved in such deformations. Hence, the Boltzmann superposition integral remains valid and time-dependent behavior can be described by incorporating a nonlinear stress-strain law into it. The elastic potential of Blatz, Sharda, and Tschoegl, which is based on a generalized measure of strain, was used for this purpose.\r\n\r\nA slightly plasticized styrene-butadiene copolymer rubber (SBR) was subjected to various modes of deformation in simple tension. The experimental data were compared with the theoretical predictions of the model. The agreement was unprecedentedly good.\r\n\r\nIn the course of this work a curious anomaly was discovered in the behavior of emulsion polymerized compression molded dicumylperoxide cured SBR. This material showed lack of time shift invariance in the region of very small strains in which elastomers generally follow a linear stress-strain law. Normally, non-preservation of time shift invariance is linked with stress-strain nonlinearity. In the anomalous SBR the former effect can be studied free of interference from the other.\r\n\r\nTo test the applicability of the model to filled elastomers, experiments were made on both crosslinked and uncrosslinked SBR filled with a high-structure carbon black. The model, and several generalizations of it, failed to predict the behavior of the filled materials in response to small (theoretically infinitesimal) deformations superposed on a finite stretch. Such experiments may be considered looked upon as sensitive probes with which the behavior of the material may be explored in large deformations. The superposition tests confirmed that in carbon black filled rubbers there exists a network of secondary aggregates of the filler particles which is held together by Van der Waals forces. This network imparts to the filled rubber a thixotropic character with a rebuilding time of about 15 minutes at room temperature. Successful prediction of the properties of such a filled system must await the development of a new constitutive model which incorporates the thixotropic behavior." }, { "name": "Chang, Wenji V.", "degree": "PhD", "year": "1976", "title": "Theoretical and Experimental Studies of the Viscoelastic Behavior of Soft Polymers", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03292004-145730", "creators": [ { "name": { "family": "Chang", "given": "Wenji V." }, "id": "Chang-Wenji-V", "display_name": "Chang, Wenji V." } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/CQ68-V266", "abstract": "The first order approximation of the theory of the so-called simple material describes the viscoelastic behavior of soft polymers in large deformations with twelve time-dependent material functions and three material constants, all functions of the three invariants of the deformation tensor. Restricting consideration to deformations in which time shift invariance is preserved, a series of models was developed which describe the time dependence of the stress through the Boltzmann superposition integral incorporating into it a suitable nonlinear measure of strain. The theory was developed in its most general three-dimensional form. Its predictions for homogeneous deformations were tested in a series of experiments on an uncrosslinked styrene-butadiene copolymer.\r\n\r\nFor the prediction of the viscoelastic behavior of soft polymers the simplest form of the theory requires only one time function, the relaxation modulus. In addition, it requires a strain parameter which is a characteristic material constant. The dependence of this parameter on temperature and other material and experimental variables was examined on hand of estimates from published data as well as from the experimental results reported here.\r\n\r\nSensitive tests in which small (theoretically infinitesimal) deformations were superposed on a finite stretch, allowed a distinction to be made between the two simplest forms of the theory which, in principle, should apply to solidlike and to liquidlike behavior, respectively. Although uncrosslinked styrene-butadiene copolymer behaves in many respects like a liquid, it showed unprecedented excellent agreement with the predictions of the solid model at room temperature. It was concluded that under this condition the liquidlike character of the copolymer is not strong enough to satisfy the special requirements of the liquid model.\r\n\r\nThe new theory allows specific predictions to be made concerning the contribution of internal energy to the restoring force in rubberlike materials. It represents an advance over former theories in that it permits the contribution to be obtained on uncrosslinked as well as on crosslinked soft polymers. Literature data were reviewed and examined in the light of the theory." }, { "name": "Dwyer, John Patrick", "degree": "Masters", "year": "1976", "title": "A Theoretical Study of Collinear Scattering : I. A New Method to Calculate Reactive and Dissociative Cross Sections of Atom Plus Diatom Systems. II. A Reexamination of the Collinear Inelastic Collision of Two Diatomics", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-113051468", "creators": [ { "name": { "family": "Dwyer", "given": "John Patrick" }, "id": "Dwyer-John-Patrick", "display_name": "Dwyer, John Patrick" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E5AG-JH44", "abstract": "In attempting to understand the nature of a chemical reaction, the theoretical chemist is severely limited. Exact quantum mechanical (EQM) 3-D calculations of all but the simplest chemical systems are prohibitively expensive. In addition, accurate potential surfaces are not available for most reactions. Finally, because the cost of computation increases with the collision energy, 3-D investigations are restricted to low energies. To circumvent these difficulties, one might develop approximate theories, or do exact calculations on model systems. The first method permits one to calculate cross sections for real chemical reactions, but it leaves one wondering if the results are correct, since experimental work is often not sophisticated enough to verify (or disclaim) them. The second method has the disadvantage of being \"unreal\". Cross sections for model systems may exhibit properties not found in the real system, while hiding or distorting properties which actually exist. However, EQM calculations on model systems are useful for testing approximate theories.\r\n\r\nIn this thesis we present two calculations on model systems. The first is for the collinear collision of H and H_2 using a realistic potential surface. Although other investigations have calculated reactive and nonreactive cross sections for atom-diatom collisions, their results have been restricted to low energies and have not included dissociation as a possible reaction pathway. We present a general method for calculating reactive, nonreactive and dissociative cross sections for an atom-diatom collision and apply it to the H_3 surface.\r\n\r\nIn part II we present transition probabilities for the nonreactive collinear collision of two identical diatoms. We use a model potential surface, but are able to compare our results to those of other investigators who used an approximate theory." }, { "name": "Finklea, Harry Osborn", "degree": "PhD", "year": "1976", "title": "Mechanisms of Photocurrent Generation at Metal and Semiconductor Electrodes", "advisor": "Gordon, Joseph G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06272025-221955987", "creators": [ { "name": { "family": "Finklea", "given": "Harry Osborn" }, "id": "Finklea-Harry-Osborn", "orcid": "0000-0002-2021-5872", "display_name": "Finklea, Harry Osborn" } ], "advisors": [ { "name": { "family": "Gordon", "given": "Joseph G." }, "id": "Gordon-Joseph-G", "role": "advisor", "display_name": "Gordon, Joseph G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5d1f-5821", "abstract": "An attempt to measure the electrochemical properties of an\r\nexcited molecule is made. Polyaromatics and Ru(bipy)32+are photoexcited\r\nin nonaqueous electrolytes via a monochromatic beam passing\r\nthrough a thin-metal film electrode. It is concluded that observation\r\nof charge transfer from an excited molecule is not possible because of\r\nrapid quenching by energy transfer to the electrode. All observed\r\nphotocurrents in the presence of a light-absorbing solute are explained\r\nby heating of the solution near the interface or the photochemical\r\ngeneration of electroactive products. Anodic and cathodic photocurrents\r\nare observed in the absence of a dye. The mechanism of the latter\r\nprocess entails the formation of excited holes and electrons within the\r\nmetal with their subsequent reaction at the interface. Photoelectron\r\nejection into the solution is also proven by the effects of an electron\r\nscavenger.
\r\n\r\nA related problem is the mechanism of dye-sensitization at a\r\nsemiconductor electrode. The concentration dependence of the photo induced\r\noxidation of the dye rhodamine 6G at a polycrystalline SnO2\r\nelectrode is determined in aqueous and nonaqueous electrolytes.\r\nIn water, the concentration study reveals a slow irreversible buildup\r\nof an adsorbed dye layer. Photocurrent spectra suggest that the\r\nsensitizing species is the monomer within the adsorbed layer, slightly\r\nperturbed by its environment. The adsorbed layer structure is\r\nhypothesized to be localized in clumps. In acetonitrile, onset of\r\nsensitization does not occur until 10-4 M dye concentrations are\r\nreached. Over the next decade of concentration, the photocurrent\r\ncaused by excitation of the electrode decreases by a factor of two,\r\nindicating the formation of a uniform monolayer. Evidence for sensitization\r\nby non-adsorbed molecules is obtained. Again, dilution\r\nreveals an irreversible adsorption process. The observation of\r\nfluorescence quenching of the adsorbed dye as a function of electrode\r\npotential is attempted. The negative results are attributed to the low\r\nquantum yield of the sensitized photocurrent.
" }, { "name": "Hare, Jeffrey Wayne", "degree": "PhD", "year": "1976", "title": "Crystal Field Applications to Biochemical and Geochemical Systems: Electronic Structures of Blue Copper Proteins and Iron Group Olivines", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01122026-221905922", "creators": [ { "name": { "family": "Hare", "given": "Jeffrey Wayne" }, "id": "Hare-Jeffrey-Wayne", "display_name": "Hare, Jeffrey Wayne" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7f37-6553", "abstract": "Part I, Chapter I
\r\n\r\nA helical secondary structure has been found to\r\nbe associated with the metal site in bean plastocyanin.\r\nIt is likely that such structure is also present in\r\nother blue copper proteins. This short section of\r\nhelix is distorted by metal (copper or cobalt) incor\r\nporation, which is probably the result of coordination\r\nto an amide nitrogen or oxygen of the peptide backbone.\r\nThe perturbed helical structure at the site remains\r\nconformationally rigid upon reduction of holoplasto-cyanin\r\nto the copper(I) derivative. Finally, a\r\ncombination of known physical data leads to a picture\r\nof the metal site where copper(II) is bound by histidine-37, \r\nan amide nitrogen or oxygen or one or more of\r\nthe following residues which make up the helix, and by\r\ncysteine-84 and histidine-87 which provide the final\r\ncoordinating positions.
\r\n\r\nPart I, Chapter II
\r\n\r\nNew low energy electronic transitions at ~10000\r\nand 5000 cm-1 have been identified as ligand field\r\nbands of the blue site of the single copper proteins\r\nstellacyanin, plastocyanin and azurin from low temperature\r\nabsorption as well as CD and MCD studies in the\r\nnear-infrared. The well known visible series of\r\nabsorption bands are assigned as charge transfer\r\ntransitions of \u03c0 and \u03c3 character from sulfur to copper\r\nand of \u03c0 character from deprotonated amide nitrogen\r\nto copper, based on comparison of visible absorption\r\nand CD intensities. Ligand field calculations have\r\nshown that the observed d-d excitation energies are\r\nconsistent with a tetrahedral model distorted approximately\r\n4 to 8\u00b0 towards a square plane. A model of the\r\nblue site, which incorporates recent physical evidence\r\nfor specific ligands, is presented. The reduction\r\npotentials have been shown to be influenced, but not\r\ndominated, by ligand field effects.
\r\n\r\nPart I I
\r\n\r\nThe absorption bands of iron, cobalt and nickel\r\nolivines have been separated with respect to metal site\r\non the basis of previous assignments, the absorption\r\nspectra of synthetic and natural triphylites, and the\r\npolarized spectra of magnesium-nickel and magnesium-cobalt\r\nolivines. An effective C2v site symmetry has\r\nbeen shown to adequately describe the band splittings,\r\nbut it fails to completely describe the observed\r\npolarization properties particularly for Co(II). Ligand\r\nfield calculations have resulted in values of B, Dq and\r\nthe low symmetry radial parameters for both the M1 and\r\nM2 sites. Calculation of LFSE's and the ligand field\r\ncontribution to the distribution coefficients of the\r\ncation exchange reactions from these parameters and\r\ncomparison to KD's calculated from x-ray diffraction\r\ndata has led to the conclusion that ligand field\r\nstabilization is the major driving force for cation\r\nordering in olivine.
" }, { "name": "Jones, Richard R.", "degree": "PhD", "year": "1976", "title": "Progress Toward the Synthesis and Characterization of 1,4-Dehydroaromatic Systems: I. 1,4-Dehydrobenzene (Para-Benzene or Butalene); II. 1,4-Dehydrotropyl Cation, Anion and the Bicyclo[3.2.0]heptatrien-3-one", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04142004-135323", "creators": [ { "name": { "family": "Jones", "given": "Richard R." }, "id": "Jones-Richard-R", "display_name": "Jones, Richard R." } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QQ2T-5185", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\t\t\t\t\t\r\nThis thesis concerns the attempted synthesis of two strained nonbenzenoid, conjugated bicyclic systems, 1,4-dehydrobenzene (butalene or para-benzyne, 28) and the 1,4-dehydrotropylium ion (30c). Both 28a and 30c contain a fused cyclobutadiene ring with [...] its accompanying antiaromaticity but overall possess 4n+2 [pi] electrons. The concept of nonbenzenoid aromaticity as it applies to compounds such as these is reviewed. The synthetic approach to 28 and 30 systems is based on the pyrolytic cyclization of a 1,5-hexadiyne moiety to form a dimethylenecyclobutene, thereby introducing the strain and unsaturation of the fused four-membered ring in one step.\r\n\r\nIn Part I, the synthesis and pyrolysis of cis-1,6-dideutero-1,5-hexadiyn-3-ene (cis-60a) is described. By a combination of nmr and ms techniques, it is demonstrated that cis-60a undergoes a degenerate rearrangement at 200?C in the gas phase at atmospheric pressure, interconverting cis-60a with its 3,4-dideuteroisomer cis-60b with an equilibration half-life of 30 sec. None of the single exchange isomer cis-60c or any trans-60 was formed in this pyrolysis. These data require a transition state or intermediate between cis-60a and cis-60b with [...] symmetry, i. e., [...] 1,4-dehydrobenzene. Similarly prepared trans-60a did not undergo isomerization or rearrangement at these temperatures.\r\n\r\nPyrolysis of cis- and trans-60 in solution provided a high yield of benzene in the presence of hydrogen donors at the expense of cis-60. In carbon tetrachloride, para-dichlorobenzene was the major product. In methanol, a 10% yield of benzyl alcohol but no anisole was formed. Since these are typical products of radical abstraction, it is suggested that the symmetrical species implicated in the deuterium scrambling is a true intermediate and of 1,4-benzenediyl structure 28d or e (instead of 28a). [...].\r\n\r\nWhile traces of benzene were seen in the atmospheric and vacuum pyrolysis of cis- and trans-60, no satisfactory gas phase trapping experiment has been performed. Neither have substantial levels of deuterium scrambling been demonstrated in liquid phase pyrolysis. These points together with some indication of the stereospecificity of the benzene forming reaction in solution remain to be answered. The added complication of a possible triplet ground state for the 1,4-benzenediyl (28d) must also be resolved before a truly consistent story can be told. A possible direct route to a triplet 28d, photosensitized irradiation of cis-60a, failed to produce scrambling in competition with a demonstrated approach to the photostationary state. No transfer of acetylenic label was observed also under direct (254 nm) irradiation of cis-60a.\r\n\r\nIn Part II, toward formation of the 1,4-dehydrotropylium ion (30c) as well as the 1,4-dehydrotropyl anion (30a) and the bicyclo [3.2.0]heptatrien-3-one (52), the synthesis of [...] bicyclo[3.2.0]hepta-1,4,6-trienes substituted in the 3-position is discussed. The required 3-substituted 1,2-diethynylcyclopropanes were approached via carbene addition to hexadiynenes, eneynes, and via y-elimination routes. Of these, only the addition of propargyl carbene to methoxybuten-3-yne (150) provided any cyclopropane product. The 3-methoxy-1,2-diethynylcyclopropane (61d) [...] prepared in < 1% isolated yield by this method readily isomerized to the air sensitive 3-methoxybicyclo[3.2.0]hepta-1,4,6-triene (62d) upon pyrolysis under atmospheric pressure flow conditions at 305?C (contact time 10 sec). Attempted formation of 30a by ether cleavage reduction of 62d with potassium led only to polymer without any evidence for formation of an anion. However, treatment of 62d with SbF5 containing a catalytic amount of HOSO2F in a soft matrix at -180?C gave evidence in the nmr of formation of 30c although at such low concentrations that a clear spectrum was not obtained. This interesting result is currently under reinvestigation." }, { "name": "Koeppe, Roger Erdman, II", "degree": "PhD", "year": "1976", "title": "Catalysis by Trypsin", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162010-082819644", "creators": [ { "name": { "family": "Koeppe", "given": "Roger Erdman, II" }, "id": "Koeppe-Roger-Erdman", "display_name": "Koeppe, Roger Erdman, II" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QP6S-7B65", "abstract": "Investigations are reported concerning the mechanism of catalysis by an enzyme of known structure, bovine trypsin. Evidence for proton transfers at the active site residues His 57 and Asp 102 during catalysis is provided by experimental techniques which specifically detect the ionization state of either the carboxyl group or the imidazole ring. The pK_a of Asp 102 in a chemically modified\u2014but still active--form of trypsin is shown to be 6.8 by difference infrared spectroscopic titration. This assignment is facilitated by the use of inhibitory copper (Cu^(++)) ion which lowers the pK_(app) of Asp 102 by binding to trypsin between Asp 102 and His 57, as is demonstrated crystallographically.\r\n\r\nInformation concerning the solvent accessibilities and mobilities of the three imidazole side chains of bovine trypsin is provided by measurements of the pH dependences of the rates of exchange of the ring C-2 protons with tritium in labeled water. Kinetic studies of substrate hydrolysis do not detect the pK_a of His 57 anywhere in the range 3 - 8.5. Pre-incubation of trypsin at low or at high pH shows that the failure to detect the pK_a of His 57 kinetically is not due to a slow pH-dependent conformational change. \r\n\r\nThe implications of the assignment of a pK_a of 6. 8 to Asp 102, and of the pK_a of His 57 being below 3, are discussed with regard to the catalytic mechanism of the serine proteases.\r\n" }, { "name": "Krieger, Monty", "degree": "PhD", "year": "1976", "title": "Serine Proteases: Structure, Mechanism, and Role in Eucaryotic Cell Transformation", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01292025-223653680", "creators": [ { "name": { "family": "Krieger", "given": "Monty" }, "id": "Krieger-Monty", "orcid": "0000-0003-4541-5181", "display_name": "Krieger, Monty" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h6dh-m388", "abstract": "The structure and catalytic mechanism of the serine protease\r\ntrypsin was investigated using x-ray crystallography, enzyme\r\nkinetics and hydrogen isotope exchange. The role of serine proteases\r\nin eucaryotic cell transformation was examined by studying\r\nthe binding of 125I-labeled dog plasminogen to normal and SV40-transformed\r\nBalb/c 3T3 cells.
\r\n\r\nX-ray structural analysis using the difference Fourier technique\r\nshowed that benzamidine, a non-covalent, reversible inhibitor\r\nof trypsin, binds in the specificity binding pocket of the enzyme and\r\nblocks substrate access to the active center. Benzamidine binding\r\nprovided a reasonable model for the binding of specific side chains\r\nand permitted us to construct a model for specific substrate binding.\r\nThe difference Fourier technique was also used to show that silver\r\nions inhibit trypsin by binding between the aspartic acid and histidine\r\nside chains in the catalytic site. This observation was used to\r\nassign difference infrared spectral peaks to the side chain of Asp 102\r\nin the catalytic site. A new level in understanding the catalytic\r\nmechanism was achieved using this information.
\r\n\r\nIn the course of these crystallographic investigations, new,\r\nmore efficient and accurate techniques of data collection were\r\ndeveloped based upon a detailed study of the sources of background\r\nradiation in x-ray diffractometry. These techniques involve new\r\nmethods for reducing and accurately accounting for background\r\neffects.
\r\n\r\nA pH-dependent conformational change could introduce artifacts\r\nin the determination of the pKa's of catalytic groups using\r\neither rapid kinetic or slower spectroscopic techniques. The rate\r\nof N\u03b1-carbobenzoxy-L-lysine-p-nitrophenyl ester (CLNE) hydrolysis\r\nby trypsin over the range pH 2 to pH 5 was observed to test for such\r\na conformational change. Pre-incubating the enzyme at pH 2 and\r\npH 6.9 for up to three hours had no effect on the hydrolysis rate;\r\ntherefore, within these limits, there was no pH-dependent conformational\r\nchange which directly affected catalysis.
\r\n\r\nIn an attempt to determine the pKa of His 57 directly, the\r\nexchange of tritum with the C-2 protons in the histidine side chains\r\nof trypsin was measured. This exchange was found to be slower\r\nthan any previously measured C-2 tritium exchange. The half-time\r\nfor exchange into His 57 was 73 days, and this apparently took\r\nplace when the active site imidazole had rotated\r\naway from its active conformation. The apparent pKa of His 57 in\r\nthis inactive \"out\" conformation was 6.6.
\r\n\r\nIncreased proteolytic activity exhibited by many cells after\r\ntransformation is due to plasminogen activation to the trypsin-like\r\nenzyme plasmin. Plasmin is responsible for a number of morphological\r\nchanges which accompany transformation and some experiments\r\nhave suggested that plasmin or plasminogen might bind to\r\ntransformed cell surfaces in preference to normal cell surfaces.\r\nWe therefore studied the time dependence of plasminogen binding to\r\n3T3 and SV 3T3 cells. The binding to 3T3 cells on a per-cell basis\r\neither decreased during the course of a three-day incubation or decreased\r\nbetween the first and second days and then rose again on the\r\nthird day (\"V\" shaped binding curve). The binding to the SV 3T3\r\ncells was usually \"V\" shaped. After three days of incubation, all of\r\nthe plasminogen bound to the SV 3T3 cells had been degraded while\r\nthere was still substantial plasminogen associated with the 3T3 cells.\r\nThe degradation by the transformed cells was independent of the\r\nplasmin-dependent morphological changes normally exhibited by\r\nthese cells. The uptake of serum plasminogen by the cells apparently\r\ninvolved several processes and may be accompanied by cell-surface\r\nproteolysis in the case of the transformed cells.
" }, { "name": "Kung, James Hsing-Jien", "degree": "PhD", "year": "1976", "title": "Structure of RNA Tumor Virus Genome", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01072026-213406911", "creators": [ { "name": { "family": "Kung", "given": "James Hsing-Jien" }, "id": "Kung-James-Hsing-Jien", "display_name": "Kung, James Hsing-Jien" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a4x7-sy65", "abstract": "Part I of the thesis describes the characterization of the RNA\r\nstructure of the RNA tumor viruses.
\r\n\r\nThe genome of type C RNA tumor viruses is an RNA complex\r\nwhich sediments at \"50-60\"S in a nondenaturing aqueous electrolyte.\r\nUpon exposure to denaturing conditions, it can be dissociated\r\ninto subunits of \"30-40\"S plus small \"4-10\"S RNA's. The structure\r\nand molecular weight of the \"50-60\"S and \"30-40\"S RNA species have\r\nbeen studied by electronmicroscopy, gel electrophoresis and sedimentation\r\nanalysis. It was found that type C viruses, isolated from\r\ndifferent origins (feline, murine, simian and baboon) all contain as\r\ntheir genomes \"50-60\"S RNA species which have similar secondary\r\nstructure patterns. The \"50-60\"S molecule has a molecular length\r\nabout 16-20 Kb (~6x106 daltons) as measured by electronmicroscopy.\r\nIt contains two characteristic secondary structure features (i) a\r\ncentral T-shaped structure (the dimer linkage structure) (ii) two\r\nloops symmetrically positioned on each side of the dimer linkage\r\nstructure. Melting of the dimer linkage structure resulted in a concomitant\r\ndissociation of the 52S molecule into two half-size subunits,\r\neach about 8-10 Kb. PolyA mapping by electronmicroscopy shows\r\nthat the \"50-60\"S molecules contain two polyA segments, one at each\r\nend.
\r\n\r\nThese results suggest that the \"50-60\"S RNA consists of two\r\n8-10 Kb or \"30-40\"S subunits, each with a characteristic secondary\r\nstructure loop. These two subunits which are possibly identical are\r\njoined at their 5' ends within the dimer linkage structure. The primary\r\nnucleotide sequence, the molecular weight and the stability of\r\nthe \"50-60\"S RNA is different for each different virus. Yet, the finding\r\nthat these different viral RNA's contain similar secondary structure\r\npatterns suggests that such features are functionally important.\r\nIf this is true, it is possible that they are present in all type C virus\r\ngenomes.
\r\n\r\nIn part II, an electronmicroscopic technique for studying\r\nsingle-stranded RNA is described. This technique has been applied\r\nto determine the molecular weight, to study the secondary structure\r\nand to map the polyA sequence of RNA isolated from an arbovirus\r\n(Sindbis).
\r\n\r\nThis spreading technique utilizes glyoxal as a denaturing\r\nagent. Glyoxal reacts preferentially with guanine residues of polynucleotides\r\nand blocks their hydrogen binding donor functions. Single-stranded\r\nRNA, after treatment with glyoxal, appears as an extended\r\nfilament whose length can be accurately measured by electronmicroscopy.\r\nBy this means, the molecular weight of Sindbis virus RNA\r\nis determined to be 4.7 \u00b1 0.4 x 106 daltons. Glyoxal treatment is\r\nuseful for the electronmicroscopic mapping of polyA sequences on\r\nRNA molecules, since the RNA is extended without affecting the\r\npolydT binding which is the basis for polyA mapping. Using this method,\r\na polyA sequence has been mapped at one end of Sindbis virus\r\nRNA. Many circular molecules are seen when Sindbis RNA is treated\r\nfor only short periods with glyoxal, then spread for electron\r\nmicroscopy. Under more denaturing conditions, linear molecules\r\nare seen. It is proposed that the two ends of Sindbis viral RNA contain\r\nmutually complementary sequences which normally are base-paired\r\nto form circular molecules. Under the more denaturing conditions\r\nhydrogen bonding is disrupted, which produces linear molecules.
" }, { "name": "Lamkin, Mark Stuart", "degree": "Masters", "year": "1976", "title": "Analogues of 1, 2-Propanediol, Inactivators of Dioldehydrase: I. Studies on the Effect of 3-Halo-1, 2-Propanediols on the Coenzyme B\u2081\u2082 Dependent Dioldehydrase Reaction. II. Studies on the Effect of an Epoxide on Dioldehydrase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052010-084939879", "creators": [ { "name": { "family": "Lamkin", "given": "Mark Stuart" }, "id": "Lamkin-Mark-Stuart", "display_name": "Lamkin, Mark Stuart" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1E2T-TX52", "abstract": "PART I: \r\n3-Chloro-1, 2 -propanediol, 3 -bromo-1, 2-propanediol, and 3-iodo-1, 2-propanediol have been found to bind to dioldehydrase. Dissociation constants are approximately equal in each case. Binding occurs in a manner similar to that of the normal substrate, 1, 2-propanediol. All three compounds behave as competitive inhibitors while 3-chloro-1, 2-propanediol and 3-brom-1, 2-propanediol inactivate the holoenzyme as well. This inactivation process is irreversible and may involve the alkylation of sulfhydryl residues of dioldehydrase. Of the above compounds, only 3-chloro-1, 2-propanediol is converted to product; possibly \u03b2-chloropropionaldehyde is formed.\r\n\r\nPART II: \r\n2, 3-Epoxypropanol (glycidol) has been found to bind to dioldehydrase.\tIts calculated dissociation constant is 8.8 X 10^(-4) M. It binds to dioldehydrase even though it has but one hydroxyl group.\t2, 3-Epoxypropanol behaves as a competitive inhibitor. This compound also inactivates the holoenzyme. Unlike the compounds studied in Part I, it also inactivates the apoenzyme, although at a slower rate. Since epoxides are known to alkylate sulfhydryl groups, the above result suggests the presence of exposed sulfhydryl residues." }, { "name": "Lau, Arthur Lai Yin", "degree": "PhD", "year": "1976", "title": "An Investigation on the Interactions of Alamethicin with Lecithin Bilayers", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12192025-021800392", "creators": [ { "name": { "family": "Lau", "given": "Arthur Lai Yin" }, "id": "Lau-Arthur-Lai-Yin", "display_name": "Lau, Arthur Lai Yin" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p4j6-cd34", "abstract": "The interaction of alamethicin, an extracellular macrocyclic polypeptide found in the fungus Trichoderma viride, with lipid bilayer systems in both unsonicated multilayer and sonicated bilayer vesicle states was investigated with nuclear magnetic resonance spectroscopy and electron microscopy techniques. We found that alamethicin is a surface active agent, which interacts primarily with the polar choline head groups of the lecithin. In its interaction with small sonicated bilayer vesicles (~300\u00c5 in diameter), alamethicin greatly facilitates the aggregation and subsequent fusion of these vesicles. Using europium ion, a lanthanide shift reagent, to probe the detail of this fusion process we found that during the alamethicin-mediated fusion some of the antibiotic molecules became translocated from the extravesicular aqueous medium into the intravesicular space. Alamethicin entrapped in this manner affects the choline methyl proton signals only from the inner half of the bilayer. No evidence was obtained for transmembrane coupling of the two halves of the bilayer or for effects of the incorporation of alamethicin molecules into the hydrophobic core of the bilayer in the absence of a transmembrane potential. In the presence of a potential difference across the bilayer, however, alamethicin is capable of forming ion-conducting channels. Such channels were found to be unidirectional for europium ions at least. A model for the voltage-induced formation of alamethicin pores in lipid bilayers is proposed and this model is discussed in the light of previously reported results of electrical studies on alamethicin-modified black lipid membranes." }, { "name": "McArdle, James Vincent", "degree": "PhD", "year": "1976", "title": "Kinetic Studies of the Oxidation of Horse Heart Cytochrome c(II), Pseudomonas Aeruginosa Cytochrome C\u2085\u2085\u2081(II), and Pseudomonas Aeruginosa Azurin(I) by Tris Complexes of 1,10-Phenanthroline and Modified 1, 10-Phenanthroline with Cobalt(III)", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12062025-081958880", "creators": [ { "name": { "family": "McArdle", "given": "James Vincent" }, "id": "McArdle-James-Vincent", "display_name": "McArdle, James Vincent" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/esv8-9y07", "abstract": "Anaerobic stopped flow kinetic studies of the oxidation of horse\r\nheart cytochrome c(II), Pseudomonas aeruginosa cytochrome c551(II),\r\nand Pseudomonas aeruginosa azurin(I) have been performed. The\r\noxidants were the tris complexes of 1,10-phenanthroline; 5-chloro-\r\n1,10-phenanthroline; 5,6-dimethyl-1,10-phenanthroline; 4,7-dimethyl-\r\n1,10-phenanthroline; and 4,7-di(phenyl-4'-sulfonate)-1,10-phenanthroline\r\nwith cobalt(III).
\r\n\r\nSecond-order rate constants found for the oxidation of the\r\n\r\ncytochromes by Co(phen)33+ give good correlation with rate constants\r\npredicted by Marcus theory. Outer-sphere electron transfer at a site\r\ncommon to both proteins is implied, and this site is proposed to be the\r\nexposed heme edge.
\r\n\r\nRate and activation parameters for the oxidation of the proteins\r\nby all of the above mentioned oxidants were acquired. Reactivities of\r\nthe proteins toward the various oxidants were found to be similar except\r\nfor the oxidant Co(4,7-Me2-phen)33+. Known structural differences\r\nbetween the proteins in the vicinity of the heme edge are proposed to\r\naccount for the reactivity difference found for oxidation by Co(4,7-Me2-phen)33+. No dependence of the activation parameters upon charge\r\nwas observed. Accumulated activation parameters were interpreted\r\nto mean that efficient electron transfer from the cytochromes involves\r\nconsiderable activation energy.
\r\n\r\nIonic strength dependence studies showed that horse heart\r\ncytochrome c(II) has a small positive active site charge, and that\r\nP. aeruginosa cytochrome c551(II) has a small negative active site\r\ncharge.
\r\n\r\nA similar series of oxidation experiments was performed using\r\nP. aeruginosa azurin(I). Once again excellent correlation between\r\nMarcus theory and experiment was found. The occurrence of simple\r\nouter-sphere electron transfer between the three proteins of this study\r\nwas thus indicated. The oxidant Co(phen)33+ was also thereby shown to\r\nbe a suitable reagent for the study of these electron transfer proteins.
\r\n\r\nThe oxidation of azurin(I) was shown to proceed only with\r\nconsiderable protein activation. All modified-phenanthroline oxidants\r\ncause significant perturbation of the activation parameters compared\r\nto those of the unmodified-phenanthroline oxidant. A very sterically\r\ninaccessible electron transfer site for azurin was therefore suggested.
\r\n\r\nTo define the effects of the substitutions on the properties of\r\nthe oxidants, spectral data and reduction potential data were collected.\r\nIn addition, electron transfer studies involving each of the oxidants\r\nwith the reductants Co(terpy)22+ and Ru(NH3)5py2+ were completed.\r\nExcluding charge effects, the oxidants were shown to have only slightly\r\nvarying redox properties.
" }, { "name": "McCurdy, Clyde William, Jr.", "degree": "PhD", "year": "1976", "title": "The Application of Basis Set Methods and Many-Body Theory in Electron-Molecule Scattering", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062026-172939673", "creators": [ { "name": { "family": "McCurdy", "given": "Clyde William, Jr." }, "id": "McCurdy-Clyde-William-Jr", "display_name": "McCurdy, Clyde William, Jr." } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v80f-7v37", "abstract": "Chapter I
\r\n\r\nThe difficulty encountered in electron-molecule scattering, which\r\nis absent from the atomic case, is due to the nonspherical nature of the\r\npotential describing the interaction of an electron with a molecule.\r\nTherefore a prerequisite to the development of an accurate description\r\nof electron-molecule collisions is an efficient method for treating single-particle\r\nscattering from nonspherical potentials.
\r\n\r\nThis chapter describes such a method. The essential idea is the\r\napproximation of the potential by a separable representation in terms of\r\na finite set of square-integrable basis functions. This approximation\r\ngives the kernel of the Lippmann-Schwinger equation a separable\r\nform and allows us to write it as a finite matrix equation. The solution\r\nof this equation by ordinary matrix methods yields a basis set representation\r\nof the transition operator, and the scattering amplitude is\r\neasily calculated using this operator.
\r\n\r\nThis method is applied to the calculation of scattering amplitudes\r\nfor a model two-center Gaussian potential and to e- - H2 elastic scattering\r\nat low energies in the static exchange approximation. The e- - H2\r\nelastic scattering calculation is compared with the results of other\r\nworkers.
\r\n\r\nAn entirely different approach to low-energy, elastic electron-molecule\r\nscattering from homonuclear diatomic molecules is also\r\ndiscussed in this chapter. It is based on the observation that, for\r\nelectron scattering from homonuclear diatomic molecules at low\r\nenergies, angular momentum is approximately conserved in spite of\r\nthe nonspherical nature of the molecule. This observation allows the\r\nextraction of approximate phase shifts for electron scattering in the\r\nstatic exchange approximation from the results of diagonalizing the\r\nHartree-Fock Hamiltonian in a large basis. This method is applied to\r\ne- - H2 and e- - N2 elastic scattering and the results compared with\r\nthose of other workers.
\r\n\r\nChapter II
\r\n\r\nA discussion of the application of many-body theory to electron-atom\r\nand electron-molecule scattering is presented. First a previous\r\nmany-body theory of inelastic scattering is shown in first order to be a\r\nform of the distorted wave approximation. The target atom or molecule\r\nis described in the random phase approximation (RPA), while the distorting\r\npotential for the incident and scattered waves is the Hartree-Fock\r\npotential of the ground state.
\r\n\r\nThe application of many-body theory to elastic scattering is also\r\ndiscussed using a many-body formulation of the Feshbach optical potential.\r\nThe difficulty of constructing Feshbach projection operators for a\r\nsystem of identical particles is overcome by the use of second quantized\r\noperators. Therelationship between this theory and the optical model of\r\nBell and Squires, in which the many-body self-energy serves as an\r\noptical potential, is discussed in detail.
\r\n\r\nChapter III
\r\n\r\nThe application of the RP A form of the distorted wave approximation\r\nto inelastic e- - H2 scattering is described. Differential cross\r\nsections for excitation of the b 3\u2211+u and a 3\u2211+g states are calculated for\r\na range of incident energies from 13 eV to 20 eV. Good agreement is\r\nobtained with the limited experimental data available for the differential\r\ncross section for excitation of the b 3\u2211+u state. The sum of the total\r\ncross sections for the two states is compared with the experimental\r\ncross section for electron impact dissociation of H2, and good agreement\r\nis found. Extensive discussion of the details of the calculation is\r\nincluded.
\r\n\r\nAppendix
\r\n\r\nCross sections in the Born approximation for electron impact\r\nexcitation of CO2 and CO using an RP A description of the target are\r\npresented. Generalized oscillator strengths for several states of CO2\r\nare found to be in agreement with experiment. For CO, substantial\r\ndisagreement exists between theory and experiment for the B 1\u2211+ state.\r\nA possible explanation involving a breakdown of the Born-Oppenheimer\r\napproximation resulting from an avoided crossing is proposed.
" }, { "name": "Miller, Donald Lee", "degree": "Masters", "year": "1976", "title": "An In Vitro Study of the Ionophore Properties of the Acetylcholine Receptor in Torpedo Californica Membrane Fragments", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-091454086", "creators": [ { "name": { "family": "Miller", "given": "Donald Lee" }, "id": "Miller-Donald-Lee", "display_name": "Miller, Donald Lee" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QS6A-C151", "abstract": "An in vitro system for studying the ionophore properties of the nicotinic acetylcholine receptor from the electric organs of Torpedo californica was developed. Efflux of ^(22)Na^+ from microsacs rich in AcChR was studied as a function of the addition of various agonists and antagonists to the medium. In the presence of agonists increased rates of efflux of ^(22)Na^+ occurred, and this affect was abolished in the presence of antagonists. The in vitro response to varying concentrations of carbamylcholine was determined. The desensitization phenomenon occurring in vivo was also found to occur in vitro." }, { "name": "Miller, John Wayne", "degree": "PhD", "year": "1976", "title": "I. A Study of the Effects of Dislocations in Silver on the Rate of Oxidation of Carbon Monoxide. II. A Mechanism for the Formation of Dislocations during the Oxidation of Zinc", "advisor": "Corcoran, William Harrison; Vreeland, Thad", "url": "https://resolver.caltech.edu/CaltechTHESIS:09252017-162443679", "creators": [ { "name": { "family": "Miller", "given": "John Wayne" }, "id": "Miller-John-Wayne", "display_name": "Miller, John Wayne" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Vreeland", "given": "Thad" }, "id": "Vreeland-T", "role": "co-advisor", "display_name": "Vreeland, Thad" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/PDYT-7V46", "abstract": "I. Effect of Dislocations in Silver on the Rate of Oxidation of Carbon Monoxide
\r\n\r\nAn investigation was made to determine the effects of the number of\r\ndislocations in a silver catalyst on the rate of oxidation of carbon\r\nmonoxide. The reaction was catalyzed by the (111) face of several silver\r\ncrystals which had a dislocation density of either 104 cm-2 or 108 cm-2.\r\nActivation of the catalyst was accomplished by alternate treatments of\r\nhydrogen and oxygen at 800\u00b0F.
\r\n\r\nThe reaction was carried out in a pyrex recirculation reactor with\r\na reactant mixture of 75% carbon monoxide and 25% oxygen. Gas chromatography\r\nwas utilized to analyze the reactor gases, and about 1% carbon\r\ndioxide was produced at 170\u00b0F during the time of reaction. Reactor\r\ncomposition data were fitted as a function of time to an expression which \r\nwas developed from a proposed model of the surface kinetics. The model\r\nused the assumptions that there existed adsorption equilibrium and that\r\nthe rate of formation of carbon dioxide was proportional to the number\r\nof carbon monoxide-oxygen sites on the surface.
\r\n\r\nResults of the study indicated that the greatest change to the rate \r\nof reaction was caused by impurities which adsorbed on the catalyst \r\nsurface. During the study the chemical-etch-pit count of silver was \r\nincreased after pretreatment with oxygen. However, other measurements \r\nshowed the dislocation density had remained the same, so comparison of the \r\nreaction rates was made for crystals with different initial dislocation \r\ndensities. This comparison indicated that dislocations did not alter the \r\nrate of reaction, thus dislocations were not considered to be the most \r\nimportant catalytic sites under the conditions of this study.
\r\n\r\nII. A Mechanism for the Formation of Dislocations during the Oxidation of Zinc
\r\n\r\nA study was made of the changes which occurred to an oxidized zinc \r\ncrystal. It was determined that the normal oxide film was thin and epitaxial \r\nbut this film would form many micro-cracks when exposed to an \r\naqueous environment. The rate of subsequent oxidation of the crystal\r\nwas increased because the cracks formed low energy paths for the zinc\r\nto get to the surface. The increased oxidation rate also increased the \r\nnumber of the vacancies in the solid and the vacancies in excess of the \r\nthermodynamic value formed dislocations. The dislocations were in the \r\nshape of loops and spirals, and were presumed to result from the coalescence \r\nof the excess vacancies. Berg-Barrett topography was utilized \r\nto view the dislocations and to investigate the Burgers Vector. The information \r\nfrom both the experimental data and the calculations of the\r\nconfiguration with the lowest energy suggested that the Burgers Vector \r\nwas a full c.
\r\n\r\nAs an addendem to the work on zinc, a discussion is included of \r\na chemical etching solution that was developed to reveal dislocations \r\nwhich intersected the basal plane. The chemical solution worked well \r\nfor surfaces whose orientation was within 0.5 of the basal plane.\r\nEvidence was presented which suggested a one-to-one correspondence \r\nbetween dislocations and etch pits.
\r\n\r\n" }, { "name": "Mintz, Donald Mills", "degree": "PhD", "year": "1976", "title": "Variable Angle Photoelectron Spectroscopy", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:02242017-160501611", "creators": [ { "name": { "family": "Mintz", "given": "Donald Mills" }, "id": "Mintz-Donald-Mills", "display_name": "Mintz, Donald Mills" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n30x-qw67", "abstract": "This thesis describes the design, construction, and performance\r\nof a variable angle photoelectron spectrometer. The experiment consists\r\nof a stationary resonance line lamp, a sample chamber, and a\r\nrotatable electrostatic electron energy analyzer. Experiment operation\r\nis extensively automated through several interfaces to a small on-line\r\ndigital computer.
\r\n\r\nResults are presented for a variety of atomic, diatomic, and\r\npolyatomic sample gases. In the case of Ar, Ne, N2, and CO, higher\r\norder lines in the resonance line lamp produce many peaks which do\r\nnot overlap extensively with those of the principal vacuum-ultraviolet\r\noutput. The additional lamp output lines allow for measurement of the\r\nvariation of the photoelectron angular distribution asymmetry parameter,\r\n\u03b2, with photoelectron energy. Results for Ar and Ne are in\r\ngood agreement with previous theoretical calculations.
\r\n\r\nFor N2, we find a discontinuity in the variation of \u03b2 near 5 eV\r\nphotoelectron energy for the v' = 0 peak of the X2\u03a3+g ionic state.\r\nThe result is interpreted in terms of the possible mechanisms:\r\nautoionization, variation of the electric dipole transition moment with\r\ninternuclear distance, and resonance phenomena. For peaks of the\r\nA2\u220fu ionic state, the variation of \u03b2 with ionic vibrational level\r\nmatches the variation with photoelectron energy. For CO, anomalous\r\nstructure is assigned to higher peaks of the X2\u03a3+\r\nvibrational progression. The dominant mechanism is probably autoionization.
\r\n\r\nPhotoelectron angular distributions were measured for the\r\nseries of olefins: ethylene, isobutylene, 2-methyl,2-butene, and\r\n2, 3-dimethyl, 2-butene. The variation of \u03b2 with electron energy was\r\ninferred by a comparison of data for the four structurally similar\r\nmolecules. In the \u03c32p orbital ionization region of the spectrum, we\r\nfind a similar variation of \u03b2 with electron energy over bands corresponding\r\nto widely varying orbital symmetries. In the \u03c0 orbital\r\nionization region of the spectrum, \u03b2 increases with increasing\r\nelectron energy, taken from the variation of \u03b2 across the vibrational\r\nenvelopes. Accompanying the drop in \u03b2 for \u03c0 ionization with increasing\r\nmethyl substitution is an anomalous drop in \u03b2 at the high\r\nionization potential end of the \u03c32p region which may indicate the\r\npresence of a \u03c3/\u03c0 orbital mixing.
\r\n\r\nPhotoelectron angular distributions were measured for a series\r\nof di-olefins. In the case of allene, we propose the ordering\r\n2e, 3b2, 1e for the three lowest-lying orbitals on the basis of a deconvolution\r\nof the band in the ionization potential range 14-16.5 eV.\r\nA re-examination of 1,3-butadiene supports the \u03c0, \u03c0, \u03c3 energy\r\nordering of low-lying molecular orbitals. The variation of \u03b2 across\r\nthe \u03c32p region in the photoelectron spectra of 1,4-pentadiene and\r\n1, 5-hexadiene supports an earlier notion that through-space interaction\r\nof the \u03c0-bonds dominates through-bond interaction. Spectra\r\nof the \u03c0 region suggest that the interaction between \u03c0 moieties\r\ndecreases in going from 1,4-pentadiene to 1,5-hexadiene.
\r\n\r\nIn an examination of low-lying structure of 1,4-cyclohexadiene,\r\nthe anomalously low \u03b2 value for the lowest \u03c0-ionization band probably\r\narises from \u03c3/\u03c0 mixing.
\r\n\r\nIn an examination of the two low-lying photoelectron bands of\r\npyridine below 11 eV IP, the sharp rise of \u03b2 across the 9-10 eV band\r\nis interpreted in terms of the orbital ordering n, \u03c0, \u03c0.
" }, { "name": "Orlowski, Thomas Edward", "degree": "Masters", "year": "1976", "title": "Vibrational Relaxation of N\u2082 Isolated in an Argon Matrix", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-04082008-114221", "creators": [ { "name": { "family": "Orlowski", "given": "Thomas Edward" }, "id": "Orlowski-Thomas-Edward", "display_name": "Orlowski, Thomas Edward" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4JTQ-3292", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe Raman spectrum of N2 isolated in an argon matrix at 4.2[...]K was obtained using single photon counting techniques and a CW argon ion laser. Attempts at measuring the vibrational relaxation (VR) time for N2 were made by monitoring the Raman intensity from upper vibrational levels as a function of time. Stimulating the Raman process using a rhodamine 6G jet stream dye laser tuned to the Stoke's frequency while simultaneously irradiating with the argon ion laser, was also attempted in an effort to improve Raman intensity. Although an accurate measurement of the VR time awaits a more efficient excitation process (or a more powerful laser), our results indicate a VR time as long as a few minutes is possible for N2 in this environment." }, { "name": "Pietsch, Anton Emil", "degree": "Masters", "year": "1976", "title": "Swept Centerband Decoupling as a Technique in Nuclear Magnetic Double Resonance Spectroscopy", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022010-091249125", "creators": [ { "name": { "family": "Pietsch", "given": "Anton Emil" }, "id": "Pietsch-Anton- Emil", "display_name": "Pietsch, Anton Emil" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8ABZ-3779", "abstract": "A technique of doubly modulated radiofrequency irradiation to achieve nuclear magnetic spin-spin decoupling was developed. The effectiveness of this technique, called Swept Centerband Modulation, was investigated by comparison study with other well known techniques. It was found that swept centerband modulation produced an averaging of single coherent frequency decoupling over an adjustable bandwidth. The conclusion drawn from the study was that this technique is not effective for wide band decoupling but very effective for medium to narrow band selective decoupling experiments." }, { "name": "Reiner, Robert Henry", "degree": "Masters", "year": "1976", "title": "Determination of Multiquantum Vibrational Transition Moments in Hydrogen Iodide and their Significance in its Vibrational Photochemistry", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-075012259", "creators": [ { "name": { "family": "Reiner", "given": "Robert Henry" }, "id": "Reiner-Robert-Henry", "display_name": "Reiner, Robert Henry" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ay4m-0474", "abstract": "Estimates of the band intensities of transitions between the ground and upper vibrational levels (1-9) were made for HI. Calculations were performed with both Morse and RKR oscillator wavefunctions, using various functional approximations for the dipole operator fitted to known experimental results. Absorption measurements using a multiple pass cell placed upper bounds on transition intensities, which were not inconsistent with the calculated values. (Band strengths for HI \u0394V = 8,9 are \r\nless than 5 x 10(-4) cm^(-2) atm(^1)).\r\n\r\nThe feasibility of using these multiquantum vibrational transitions to pump the reaction HI + HI*(v - 8,9) \u2192 H_2 + 2I is discussed.\r\n" }, { "name": "Rothman, Barry Samuel", "degree": "PhD", "year": "1976", "title": "Electrophysiological and Biochemical Studies on the Effects of RNA and Protein Synthesis Inhibitors on the Circadian Rhythm of the Isolated Aplysia Eye", "advisor": "Strumwasser, Felix", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302026-191212444", "creators": [ { "name": { "family": "Rothman", "given": "Barry Samuel" }, "id": "Rothman-Barry-Samuel", "display_name": "Rothman, Barry Samuel" } ], "advisors": [ { "name": { "family": "Strumwasser", "given": "Felix" }, "id": "Strumwasser-F", "role": "advisor", "display_name": "Strumwasser, Felix" } ], "committee": [ { "name": { "family": "Strumwasser", "given": "Felix" }, "id": "Strumwasser-F", "role": "chair", "display_name": "Strumwasser, Felix" }, { "name": { "family": "Benzer", "given": "Seymour" }, "id": "Benzer-S", "role": "member", "display_name": "Benzer, Seymour" }, { "name": { "family": "Davidson", "given": "Eric H." }, "id": "Davidson-E-H", "role": "member", "display_name": "Davidson, Eric H." }, { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "member", "display_name": "Mitchell, Herschel K." }, { "name": { "family": "Wiersma", "given": "Cornelis A. G." }, "id": "Wiersma-C-A-G", "role": "member", "display_name": "Wiersma, Cornelis A. G." } ], "option_major": [ "bioch" ], "doi": "10.7907/ay8x-wp67", "abstract": "The isolated eye of Aplysia californica produces a circadian rhythm\r\nof optic nerve activity. In filtered sea water, at 15\u00b0C, in constant\r\ndarkness, the free-running period of the circadian rhythm is 23.4 hrs.\r\nOptic nerve activity is recorded by means of suction electrode, and is\r\nin the form of spontaneous compound action potentials (CAPs) which vary\r\nin frequency from 0 to 200 per hr.
\r\n\r\nExperiments were designed to test the necessity of macromolecular\r\nsynthesis for the production of the circadian rhythm. Eyes were given\r\na pulse of an inhibitor of RNA or protein synthesis and the effects on\r\nthe circadian rhythm, biochemistry or electrophysiology assayed.
\r\n\r\nWhen eyes were given a 3 hr pulse of actinomycin D (AMD)(4 ug/ml\r\nthe circadian rhythm was inhibited without blocking spontaneous\r\nactivity altogether. Eyes receiving a 3 hr pulse of aflatoxin B1(AFTX)\r\n(16 ug/ml) revealed similar effects in half the cases studied, while in\r\nthe other half a reduced amplitude phase delayed circadian rhythm was\r\nfound. Eyes given a 12 hr pulse of puromycin (PURO) (20-134 ug/ml) or\r\ncycloheximide (CHX) (500-2000 ug/ml) beginning in mid-subjective night\r\nhad their circadian rhythms phase delayed by 12-16 hrs and 6-12 hrs,\r\nrespectively, after the drug pulse was washed out. A phase-response\r\ncurve determined for the effects of a 6 hr PURO (125 ug/ml) pulse showed\r\nthat maximum phase delays were caused by pulses given in late subjective\r\nnight, and maximum phase advances caused by pulses given in early subjective\r\nday.
\r\n\r\nIn biochemical studies, incorporation of 3H-uridine and 14C-leucine\r\nwere measured 1-9, 9-17, 49-57 and 73-81 hrs after the removal of a 3 hr\r\npulse of AFTX (16 ug/ml) or AMD (4 ug/ml). Uridine incorporation was\r\ninhibited by 50-75% from 1 to 17 hrs after an AFTX or AMD pulse, while\r\nleucine incorporation was inhibited by 40-70% from 1 to 81 hrs after an\r\nAFTX pulse, and by about 20% from 49 to 57 hrs after an AMD pulse. At\r\nall other times measured, uridine and leucine incorporation were not\r\nsignificantly different from controls. In other biochemical studies the\u00b7\r\neffects of ?URO and CHX on leucine incorporation were tested by means of\r\na double-label 303-polyacrylamide gel system. When eyes were labeled\r\nduring the last 5 hrs of a 12 hr pulse of PUR.O (20 ug/ml) or CHX (500\r\nug/ml), incorporation was inhibited by about 50%. The distribution of\r\nlabel in the gels of PURO-treated eyes showed increasing inhibition of\r\nincorporation with increasing molecular weight above 75,000 daltons,\r\nwhile in the gels of CHX-treated eyes, incorporation was almost equally\r\ninhibited at all molecular weights. A 12 hr PURO (125 ug/ml) inhibited\r\nleucine incorporation by about 85%, while the distribution of label in\r\nthe gels showed increasing inhibition of incorporation with increasing\r\nmolecular weight above 12,000 daltons. At 12-20 hrs and 20-28 hrs after\r\nthe end of the PURO pulse, incorporation was normal except for a small\r\npeak at 20,000 daltons.
\r\n\r\nThe electrophysiological properties of eyes were tested by recording\r\nspontaneous CAP activity and responses to light pulses at various\r\ntimes before, during and after the administration of a drug pulse.\r\nEight electrophysiological parameters were measured and compared quantitatively\r\nbetween experimental and control eyes. They were the latency,\r\namplitude and frequency of both the phasic and tonic light responses;\r\nand the amplitude and frequency of spontaneous CAP activity. AFTX (3\r\nhrs, 16 ug/ml) induced multiphasic tonic light responses during the\r\ndrug pulse; and when applied during the peak of an activity cycle,\r\nincreased the frequency of spontaneous CAP activity by 35% for the\r\nremainder of the cycle. AMD (3 hrs, 4 ug/ml) caused a 13% increase in\r\nspontaneous CAP amplitude and a 10% decrease in tonic light response\r\nlatency subsequent to its removal. PURO (12 hrs, 20 ug/ml) increased\r\nthe amplitude of the tonic light response by 23% when measured more\r\nthan. 7 hrs after the end of the pulse. CHX (12 hrs, 500 ug/ml) caused\r\na 32% increase in the tonic light response frequency measured 0-7 hrs\r\nafter the end of the pulse, and a 33% decrease in the duration of spontaneous\r\nCAP bursts during the pulse.
\r\n\r\nThe results of these experiments indicate that doses of four inhibitors\r\nof macromolecular synthesis capable of modifying the circadian\r\nrhythm of the eye reduce the incorporation of uridine and/or leucine\r\nand cause only small changes in the electrophysiology of the eye.\r\nThese data suggest that the production of the circadian rhythm of the\r\nAplysia eye is dependent on macromolecular synthesis.
" }, { "name": "Schatz, George Chappell", "degree": "PhD", "year": "1976", "title": "The Quantum Dynamics of Atom Plus Diatom Chemical Reactions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-09012006-080950", "creators": [ { "name": { "family": "Schatz", "given": "George Chappell" }, "id": "Schatz-George-Chappell", "orcid": "0000-0001-5837-4740", "display_name": "Schatz, George Chappell" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2N85-G728", "abstract": "The results of accurate quantum dynamical calculations on one, two and three dimensional atom plus diatomic molecule electronically adiabatic chemical reactions are presented.
\r\n\r\nIn papers 1 and 2, comparisons between quantum, quasi-classical and semi-classical results for the collinear F + H2 and F + D2 reactions, are examined. Paper 3 discusses the role of reactive and nonreactive collisions in producing vibrational deactivation in the collinear H + FH, D + FD, H + FD and D + FH systems.
\r\n\r\nThe extension of reactive scattering calculational methods to atom diatom collisions on a plane and in three dimensions is presented in papers 4 and 6, respectively. In both applications, the Schrodinger equation is solved by a coupled equation method in each of the three equation arrangement channel regions. This is followed by a matching procedure in which the wave function is made smooth and continuous at the boundaries of these regions, In the three dimensional case, the use of body fixed coordinates is crucial to obtaining an efficient coordinate transformation between arrangement channels.
\r\n\r\nApplications of these 2D and 3D methods to the H + H2 exchange reaction are presented in papers 5 and 7. Integral and differential cross sections, reaction probabilities, product and reagent state rotational distributions, and other dynamical information are discussed in the papers, and these results are extensively compared with those of previous quasi-classical, semi-classical and approximate quantum calculations. The results of a very simple angular momentum decoupling approximation are considered in paper 7.
\r\n\r\nIn papers 8 and 9 the relative importance of direct versus resonant (shape or Feshbach) mechanisms for several atom diatom reactions is examined. A number of techniques for characterizing both mechanisms are discussed, including time delays, eigenphase shifts, Argand diagrams and the collision lifetime matrix. Extension of these 1D resonances to the 2D and 3D reactions is examined in paper 10 for the simple case of H + H2.
" }, { "name": "Shu, Winston Rei-Yun", "degree": "PhD", "year": "1976", "title": "Turbulent Chemical Reactions : Application to Atmospheric Chemistry", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01202026-223733813", "creators": [ { "name": { "family": "Shu", "given": "Winston Rei-Yun" }, "id": "Shu-Winston-Rei-Yun", "display_name": "Shu, Winston Rei-Yun" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/c507-9y29", "abstract": "The general problem of predicting the rates of chemical reactions\r\nin turbulent fluid has been studied. Particular attention has been given\r\nto bimolecular (second-order) chemical reactions occurring isothermally.\r\nThe problem of predicting the rates of turbulent chemical reactions has\r\nbeen formulated in both Eulerian and Lagrangian frameworks. The Eulerian\r\nformulation leads to a closure problem in the equations for the moments\r\nof concentrations of the reacting species. The Lagrangian formulation,\r\nwhile circumventing the usual closure problem, is based on a transition\r\nprobability density function of particle displacements which can only be\r\npredicted in the simplest of cases.
\r\n\r\nThe principal result of the work is the development of a new\r\nclosure method for second-order chemical reactions in turbulence. The\r\nmethod is referred to as the diffusion zone model. The essential idea\r\nof the model is that one defines the diffusion zone as that region of\r\nthe fluid in which the reactive species would coexist if they were inert.\r\nThen, chemical reaction is presumed to occur only within the diffusion\r\nzone; outside the diffusion zone the concentrations of the reactive\r\nspecies are identical to those if the species were inert. The diffusion\r\nzone model is tested extensively on available laboratory data and gives\r\ngood agreement.
\r\n\r\nThe diffusion zone closure method is adapted for predicting the\r\nrates of atmospheric chemical reactions occurring in plumes. The effect\r\nof inhomogeneous mixing on the reaction rates is explicitly accounted\r\nfor in the formulation. In assessing this effect, a numerical planetary\r\nboundary layer velocity field is employed as a source of the necessary\r\nturbulence data. The model is applied to predicting the rates of nitric\r\noxide oxidation in a plume from the Morgantown power plant in Maryland.\r\nPredictions are in good qualitative agreement with available measurements\r\non the plume.
" }, { "name": "Staley, Ralph Horton", "degree": "PhD", "year": "1976", "title": "Studies of Acid-Base Ion-Molecule Chemistry Using Ion Cyclotron Resonance Techniques and Photoelectron Spectroscopy", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-095120323", "creators": [ { "name": { "family": "Staley", "given": "Ralph Horton" }, "id": "Staley-Ralph-Horton", "display_name": "Staley, Ralph Horton" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/32NW-ER15", "abstract": "Thermochemical properties related to molecular basicity are examined for series of substituted amines and nitriles using ion cyclotron resonance techniques and photoelectron spectroscopy. Proton affinities PA(B), defined for a base B as the heterolytic bond dissociation energy for removing a proton from the conjugate acid BH^+, and adiabatic ionization potentials, IP(B), are determined. In previously examined series of bases linear relationships have been established between proton affinities and adiabatic first ionization potentials which correspond to removal of an electron from a lone pair localized at the site of protonation. Nitrile proton affinities are found to be linearly related not to the first CN \u03c0 ionization potentials but rather to the adiabatic N lone pair \u03c3 ionization potentials at higher energy. This relationship provides a useful chemical means for the assignment of bands in photoelectron spectra; specific examples are considered and assigned. Homolytic bond dissociation energies D(B^+-H) are obtained using the relation PA(B)-D(B^+-H) = IP(H)-IP(B). Systematic effects of substitution on PA(B), D(B^+-H), and IP(B) are identified and discussed in terms of the intrinsic factors affecting molecular basicity.\r\n\r\nIon cyclotron resonance techniques are also used to measure relative heterolytic bond dissociation energies D(R^+-Br^-) in the gas phase for a series of alkali cations, alkyl carbenium ions, acylcations, and cyclic halonium ions. D(R^+-Br^-) for adamantyl cation is found to be less than for tert-butyl cation. A proton affinity for norbornene of D(B-H^+) = 198.2 \u00b1 2 kcal/mol is determined from which D(R^+-Br^-) = 146.8 \u00b1 2.3 kcal/mol is calculated for norbornyl cation, 14 kcal/mol less than for cyclo-pentyl cation. Relative enthalpies of solvation are estimated via appropriate thermochemical cycles by combining the gas phase data with heats of ionization in fluorosulfuric acid. The results show that solvation enthalpies are related to ion size with smaller ions being better solvated. Relative stabilities of cyclic bromonium ions are the same in the gas phase and solution. Stability increases with increasing ring size and in the three-membered rings with methyl substitution. However, solvent has an appreciable effect in attenuating the observed range.\r\n" }, { "name": "Sukenik, Chaim N.", "degree": "PhD", "year": "1976", "title": "Catalysis of Organic Reactions: Part I: Enhancement of a Solid State Reaction by Proper Orientation within a Crystal. Part II. Micellar Effects on the Stereochemistry and Rate of Aqueous Solvolysis Reactions", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222017-142615284", "creators": [ { "name": { "family": "Sukenik", "given": "Chaim N." }, "id": "Sukenik-Chaim-N", "display_name": "Sukenik, Chaim N." } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QB90-WP98", "abstract": "Part I. The solid state rearrangement of methyl-p-dimethylaminobenzenesulfonate\r\nto the trimethylammoniumbenzenesulfonate zwitterion was studied\r\nby a combination of spectroscopic techniques. NMR, Field Desorption\r\nMass Spectrometry, and X-Ray Crystallography were employed to determine\r\nthe mechanism of this reaction. It was shown to be an intermolecular\r\nnucleophilic displacement whose rate is greatly enhanced by the\r\ncrystallinity of the starting material.
\r\n\r\nPart II. A study of the effects of micelles on the aqueous solvolysis\r\nof alkyl-p-trimethylammoniumbenzenesulfonates revealed that anionic\r\nmicelles could change the rate and stereochemistry of the solvolysis\r\nreaction. The mechanism for the observed rate retardation and induced\r\ndecrease in stereochemical integrity was probed and a unified mechanistic\r\nhypothesis is presented.
" }, { "name": "Surratt, Grover Timothy", "degree": "PhD", "year": "1976", "title": "A Generalized Valence Bond Description of Vacancy and Impurity States in Diamond and Silicon", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-153524672", "creators": [ { "name": { "family": "Surratt", "given": "Grover Timothy" }, "id": "Surratt-Grover-Timothy", "display_name": "Surratt, Grover Timothy" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YCT9-H995", "abstract": "Generalized Valence Bond and Configuration Interaction calculations using a double zeta basis have been performed for the vacancy states of diamond and silicon and for the lithium and boron impurities in silicon. For the vacancy case it was found that the nature of the low-lying electronic states of the positive, negative and neutral charge species is easily understood in terms of simple valence bond concepts. Here the effect of symmetric distortion of the vacancy was included, but no other distortions were included. For those cases in which the ordering of the states is known, the experimental ordering is reproduced by the theoretical results. For the impurity case it is found that boron is strongly bound in a substitutional site whereas lithium is not. In both cases the states of the system can be predicted from a simple valence bond analysis. The calculated results are compared with experiment through the use of a dielectric continuum approximation to correct the energies of charged and ionic states.\r\n" }, { "name": "Vatcha, Sorab Rustom", "degree": "PhD", "year": "1976", "title": "Analysis and Design of Methanation Processes in the Production of Substitute Natural Gas from Coal", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05082026-170122915", "creators": [ { "name": { "family": "Vatcha", "given": "Sorab Rustom" }, "id": "Vatcha-Sorab-Rustom", "display_name": "Vatcha, Sorab Rustom" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/n760-pt75", "abstract": "Methanation, the final major step common to all processes for the\r\nconversion of coal to substitute natural gas, upgrades the sulfur-free\r\nsynthesis gas to comply with the pipeline quality standards:
\r\n\r\n< 0.1 % CO,> 900 BTU/SCF (35.5 MJ/Nm3)
\r\n\r\nA reactor system featuring good temperature control and effective\r\nheat recovery is essential for effecting the strongly exothermic reaction\r\n(CO + 3H2 \u2192 CH4 + H2O) to a high overall conversion. The\r\ndifferent reactor arrangements of the leading processes (currently at\r\nthe pilot plant stage of development) are critically assessed and\r\ncompared: multistage adiabatic packed beds, fluidized bed, Raney nickel\r\ncoated tubes with circulating coolant, and a 3-phase slurry.
\r\n\r\nComputations of reaction equilibria and energy balances are performed\r\nto delineate operating conditions and maximum yields for both\r\nisothermal and adiabatic methanators in the range of total pressures\r\nfrom 50 to 90 atm. The effects of dry recycle and the concurrent shift\r\nreaction on the equilibrium composition and properties of the product\r\nstream from an isothermal methanator are shown. Graphs are provided for\r\npredicting the extent of formation of undesirable nickel carbonyl or\r\ncarbon (as graphite) at equilibrium.
\r\n\r\nOn the basis of a comprehensive literature survey, the intrinsic\r\nkinetics and selectivity are analyzed relative to catalyst properties.\r\nA thermodynamically consistent rate expression is formulated and\r\nemployed in methanator design. It is based on a published rate expression\r\napplicable to a commercial nickel-kieselguhr catalyst, Harshaw\r\nNi-0104T. Transport effects, catalyst deactivation, and their\r\ninfluence on reactor operation are examined. Intrapellet gradients of\r\nconcentration are usually significant while intrapellet temperature\r\ngradients are moderate.
\r\n\r\nA modular process simulator is developed and applied to the design\r\nof a commercial scale methanation system. A two-stage cylindrical\r\nradial flow packed reactor with feed split and cold recycle is selected\r\nfor the simulation studies. It is shown to be superior to the other\r\nconfigurations in many respects, notably by a low pressure drop.\r\nCooler-condensers of the vertical downflow type are designed by a\r\nrigorous finite element algorithm whose accuracy has been validated by\r\ncomparison with experimental results reported in the literature.
\r\n\r\nNearly all the published economic estimates have tended to understate\r\ncosts and there is a need for a uniform, standardized accounting\r\nprocedure. The sensitivities of the (free-market) product gas price to\r\n6 process and economic factors are estimated; it is most sensitive to\r\nthe cost of coal and least sensitive to the debt fraction.
\r\n\r\nSome key problems and promising directions for future research and\r\ndevelopment are identified. The development of more sulfur-tolerant,\r\nlong-lasting catalysts and reliable kinetic data under conditions of\r\nindustrial methanator operation deserve a high priority.
" }, { "name": "Walba, David Mark", "degree": "PhD", "year": "1976", "title": "The Total Synthesis of (\u00b1)-Friedelin", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042017-160036925", "creators": [ { "name": { "family": "Walba", "given": "David Mark" }, "id": "Walba-David-Mark", "display_name": "Walba, David Mark" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YSVW-HF20", "abstract": "The total synthesis of the unsymmetrical pentacyclic\r\ntriterpene friedlein (10) was completed in 31 steps in an overall
\r\n\r\nRefer to pdf for formulas.
\r\n\r\nyield of 0.3%. The route, symbolized by the disconnections \r\noutlined in Chart 4, forms each of the 9 assymetric centers of \r\nfriedelin stereoselectively.
\r\n\r\n\r\nChart 4
\r\n\r\nRefer to pdf for formulas.
\r\n\r\n\r\n" }, { "name": "Weisblat, David Allan", "degree": "PhD", "year": "1976", "title": "Electrophysiology of the Somatic Muscles in the Nematode Ascaris lumbricoides", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302017-144757378", "creators": [ { "name": { "family": "Weisblat", "given": "David Allan" }, "id": "Weisblat-David-Allan", "display_name": "Weisblat, David Allan" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RQ4W-5T91", "abstract": "The electrical activity of the somatic muscles of the\r\nparasitic nematode Ascaris lumbricoides has been investigated.\r\nThe functional muscle syncytium overlying the nerve cord is\r\npreferentially excited by anodal stimulation with an extracellular\r\nelectrode. Cathodal stimulation preferentially excites\r\nthe nerve cord, allowing determination of separate\r\nconduction velocities for the nerve cord and syncytium. The\r\npropagation velocity of the nerve cord is 16.2 \u00b1 1.2 cm/sec;\r\nthat of the syncytium varies with the calcium concentration,\r\nbeing 21.6 \u00b1 1.3 cm/sec for unitary slow waves under normal\r\nconditions. Both values are too high to account for the\r\npropagation of contractile waves in the intact animal.
\r\n\r\nAscaris muscle gives rise to complex spontaneous depolarizations\r\nconsisting of slow waves and graded spike potentials. \r\nOften, the spikes and slow waves are modulated into\r\nperiodic bursts of electrical activity, which gives rise to\r\nrhythmic contractions on a behaviorally significant time\r\nscale. Spikes appear to be mediated exclusively by calcium\r\nions the spike active potential varies with calcium concentration \r\nas expected for a calcium electrode and spikes persist\r\nin sodium-free media. Slow waves can be mediated by\r\neither sodium or calcium ions; they persist when calcium or\r\nsodium are removed separately, but not when both are removed\r\ntogether.
\r\n\r\nIn rhythmically active preparations, a burst of slow\r\nwaves and spikes accompanies each contraction. The modulation\r\nshows dorsal-ventral coordination if the right lateral\r\nline is intact, in accord with known nervous system asymmetry.\r\nAnterior-posterior coordination is also observed.
" }, { "name": "Wendling, Larry Allan", "degree": "PhD", "year": "1976", "title": "I. The Synthesis, Absolute Configuration, and Stereochemistry of Thermal Decomposition of (+)-3R,5R- and (+)-3R,5S-3-Ethyl-5-Methyl-1-Pyrazoline. II. Mechanistic Investigations of the Thermal Decompositions of 2H-Azirines", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02242017-100127779", "creators": [ { "name": { "family": "Wendling", "given": "Larry Allan" }, "id": "Wendling-Larry-Allan", "display_name": "Wendling, Larry Allan" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DFVF-ZS54", "abstract": "I. (+)-3R,5R- and (+)-3R,5S-3-ethyl-5-methyl-1-pyrazolines\r\n(34T and 34C, respectively) have been prepared in optically active\r\nform. Their stereochemistries have been determined by correlation\r\nwith (-)-R-3-hexanol and (-)-R-2-bromohexane. Pyrolysis of these\r\npyrazolines in the gas phase at 292\u00b0 allows a complete study of the\r\nstereochemistry of the 1-pyrazoline decomposition. 34T yields\r\ncis-1-ethyl-2-methylcyclopropane (48C) in nearly racemic form and\r\ntrans-1-ethyl-2-methylcyclopropane (48T) 22.5% optically active\r\nwith predominant inversion of the alkyl groups. 34C yields cis-\r\n1-ethyl-2-methylcyclopropane (48C) 36.5% optically active with\r\npredominant retention of stereochemistry and trans-1-ethyl-2-methycyclopropane\r\n(48T) 14.2% optically active with predominant single\r\ninversion of the ethyl group.
\r\n\r\n\r\nII. A series of phenyl-substituted 2H-azirines: 3,3-dimethyl-\r\n2-phenyl-2H-azirine (33c), 3-methyl-2-phenyl-2H-azirine (33a),\r\n3-ethyl-2-phenyl-2H-azirine (33b), and 2,3-dimethyl-3-phenyl-2H-azirine\r\n(33d) were synthesized and their thermal decompositions\r\nwere investigated. 2-aza-1,3-butadienes were formed as primary\r\npyrolysis products from 33a-c, which indicates that the thermal\r\nreaction proceeds via carbon-carbon bond cleavage leading to iminocarbene\r\nintermediates. 33d yields 2,3-dimethylindole as its only\r\npyrolysis product, which indicates initial carbon-nitrogen bond\r\ncleavage leading to vinyl nitrene: intermediates. Further thermal\r\nreactions of the azabutaaienes to yield olefins and nitriles, and\r\ndihydroisoquinolines were also studied.
" }, { "name": "Willard, Alvin Keith", "degree": "PhD", "year": "1976", "title": "The Ester Enolate Claisen Rearrangement: I. Stereochemical Control Through Stereoselective Enolate Formation. II. Construction of the Prostanoid Skeleton", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042017-161832975", "creators": [ { "name": { "family": "Willard", "given": "Alvin Keith" }, "id": "Willard-Alvin-Keith", "display_name": "Willard, Alvin Keith" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FX8A-9T58", "abstract": "Part I:
\r\n\r\nThe [3,3]-sigmatropic rearrangement of a number of allylic esters\r\n1, as the enolate anions of the corresponding silyl ketene acetals,\r\nproduces the \u03b3,\u03b4-unsaturated acids 2 in 66 - 88% yield. The mild\r\nconditions allow rearrangement of acid sensitive and thermally labile\r\nesters. Rearrangement of ester 1g affords (E)-4-decenoic acid (2g)\r\nwith greater than 99% stereoselectivity. (E)-Crotyl propanoate (12)\r\nleads to erythro-acid 14 when enolization is carried out in THF, but to\r\nthe threo-acid 15 when the solvent is 23% HMPA-THF. Results with a \r\nvariety of esters demonstrate that kinetic enolization with lithium\r\ndiisopropylamide gives selective formation of the geometrical enolate\r\nH in THF and the isomeric enolate I in HMPA-THF. Similar results are \r\nobtained with 3-pentanone. (Scheme I)
\r\n\r\n\r\nPart II:
\r\n\r\nA convergent synthesis of the prostaglandin skeleton is described.\r\nThe ester enolate modification of the aliphatic Claisen rearrangement\r\nis used to form the key C8-C12 bond. Rearrangement of ester 18 provides\r\nthe lactone 29 which is converted to the prostanoid 30. Similarly,\r\nthe lactone 52, a potential intermediate in the synthesis of 12-methyl\r\nPGA1, is obtained from ester 51. Preparation of ester 51 features\r\nClaisen rearrangement of ester 38, which leads to the dienoate 41 after\r\ndesulfenylation. Model studies of reduction of \u03b3,\u03b4-epoxy-\u03b1-\u03b2-unsaturated\r\nesters to \u03b4-hydroxy-\u03b2,\u03b3-unsaturated esters are described. This reduction\r\nis accomplished with lithium in ammonia at -78\u00b0 for conversion of epoxy\r\nester 50 to ester 51. (Scheme II)
\r\n\r\n\r\nScheme I:
\r\n\r\nRefer to pdf for formulas
\r\n\r\n\r\nScheme II:
\r\n\r\nRefer to pdf for formulas
\r\n" }, { "name": "Williamson, Ashley Deas", "degree": "PhD", "year": "1976", "title": "Investigation of Kinetics and Thermochemistry of Ion-Molecule Reactions Using Photoionization Mass Spectrometry", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01232017-162540529", "creators": [ { "name": { "family": "Williamson", "given": "Ashley Deas" }, "id": "Williamson-Ashley-Deas", "display_name": "Williamson, Ashley Deas" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mgxv-k439", "abstract": "Chapter I introduces the methodology of photoionization mass\r\nspectrometry and lists common applications, including study of ionmolecule\r\nreactions. A major advantage of photoionization in the study\r\nof ion chemistry lies in the favorable photoionization threshold laws,\r\nwhich frequently permit accurate knowledge of the internal energy\r\ndistribution of reactant ions. Study of reactions as this distribution is\r\nvaried allows measurement of the effects of reactant ion internal\r\nenergy on the reaction kinetics. The photoionization mass spectrometer\r\nconsists of a discharge lamp, a one-meter normal incidence\r\nvacuum monochromator, and a medium pressure quadrupole mass\r\nspectrometer. The instrument and its operating conditions are detailed.
\r\n\r\nChapter II contains a photoionization study of the reactions of\r\nthe molecular ion in vinyl fluoride to yield the ionic products C3H3F2+,\r\nC3H4F+, and C3H5+. Quantitative measurements are reported of\r\nthe effect of the vibrational state of the reactant ion on the product\r\ndistribution and overall reaction cross section. Reaction cross\r\nsections for all three channels decrease with reactant internal energy.\r\nThe effect on the reaction pathway producing C3H3F2+ is especially\r\npronounced, with 0.19 eV of vibrational excitation being sufficient\r\nto reduce the reaction probability by 80%. Deactivation of vibrationally\r\nexcited reactant ions competes with the reaction and is shown to be\r\nan efficient process.
\r\n\r\nChapter III details a study of the major ion-molecule\r\nreaction pathways in ketene and ketene-d2 by photoionization mass\r\nspectrometry and ion cyclotron resonance spectroscopy. For processes \r\ninvolving the molecular ion, the variation of reaction cross\r\nsection with ion vibrational state is pronounced. The threshold\r\ndetermined for the endothermic process CH2CO+ + CH2CO \u2192\r\nC2H4+ + 2CO provides a novel confirmation of the recent redetermination\r\nof the heat of formation of ketene.
\r\n\r\nIn Chapter IV photoionization efficiency data are presented for\r\nthe parent and major fragment ions in 2,2-difluoropropane and\r\n2-fluoropropane. Appearance potentials for CH3 and CH4 loss may\r\nbe used to relate the heats of formation of the olefin radical cations\r\nand fluorinated ethyl carbonium ions to the parent neutral and to one\r\nanother. A thermochemical cycle allows determination of the proton\r\naffinities of vinyl fluoride and 1,1-difluoroethylene. The fragmentation\r\nthresholds in 2-fluoropropane appear to be too high by\r\n7-9 kcal/mole. standard heats of formation determined by this study\r\nare: (CH3)2CF2, -129.8 \u00b1 3.0 kcal/mole; CH3CF2+, 108.5 \u00b1 3.2\r\nkcal/mole; (CH3)2CF+, 138.0 \u00b1 1.6 kcal/ mole; CH3CHF+, 162.6 \u00b1\r\n1.1 kcal/mole.
" }, { "name": "Winterle, John Scott", "degree": "PhD", "year": "1976", "title": "Excitation Transfer in Organic and Inorganic Systems", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-03112009-140839", "creators": [ { "name": { "family": "Winterle", "given": "John Scott" }, "id": "Winterle-John-Scott", "display_name": "Winterle, John Scott" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8h2g-v390", "abstract": "PART I: \r\n\r\nIron(II) is photooxidized to iron(III) in 0.100 N sulfuric acid in the presence of the photosensitizer tris(2,2'-bipyridine)ruthenium(II) dichloride. Control experiments show that the oxidation must be partly ascribed to a reactive oxygen species generated by interaction of molecular oxygen (dioxygen) with the excited photosensitizer because the oxidation quantum yield varies in strict proportion to the fraction of sensitizer excited states quenched by dioxygen.\r\n\r\nThe reaction was found to be dramatically pH dependent in the range studied (1 to 0). However, the oxidation quantum yield was insensitive to changes in Fe[superscript +2](aq.) in the region 4 x 10[superscript -2] to 2 x 10[superscript -4] M.\r\n\r\nIn 0.100 N H[subscript 2]SO[subscript 4] at 25\t\u00b1 1\u00b0C, the quantum yield for Fe[superscript +3] (aq.) production is 0.077 when extrapolated to 100% sensitizer quenching.\r\n\r\nQuenching of the emissive MLCT state of Ru(bipy)[subscript 3 superscript +2 ] is known to occur by two different mechanisms, energy and charge transfer. In the latter case electron transfer to dioxygen would result in superoxide anion and oxidized sensitizer, both of which rapidly oxidize Fe[superscript +2] (aq.) at pH 1. That this simple mechanism is operative is ruled out by the observed pH dependence since HO[subscript 2], O[...] radical oxidations of iron (II) are acidity independent in the range studied.\r\n\r\nIn view of these considerations it is proposed that hydroperoxyl radicals are produced upon protonation of a transient sensitizer - dioxygen complex which otherwise decays without oxidation-reduction.\r\n\r\nPART II:\r\n\r\n\r\nTrans[underscored], trans[underscored]-2, 4-hexadiene is isomerized to its geometrical isomers when dilute benzene solutions are \u03b3-irradiated. Because the diene receives negligible primary excitation, a solvent-to-solute excitation transfer mechanism must be invoked to explain the isomerization.\r\n\r\nA comparison of the photochemistry and the radiation chemistry of the diene in benzene, demonstrates that the kinetic behavior of trans[underscored], trans[underscored]-2,4-hexadiene under \u03b3-irradiation is consistent with the transfer of triplet solvent electronic excitation.\r\n\r\nThe triplet yield is consistent with recent careful determinations.\r\n\r\nCollateral photochemical experiments demonstrate that the [...] state of benzene does not efficiently isomerize trans[underscored], trans[underscored]-2,4-hexadiene. Thus, the excess isomerization must be contributed by another intermediate.\r\n\r\nBy a process of elimination, an upper excited benzene singlet state is identified as the excitation donor. This choice is confirmed by an excellent concordance of the data with the model for energy transfer.\r\n\r\nTheoretical predictions make such transfer possible, because this energy migration rate in benzene far exceeds that predicted by simple mass diffusion." }, { "name": "Bakshi, Kiran Ravindra", "degree": "PhD", "year": "1975", "title": "Characterization of Acid-Base Catalysts and its Application to Catalyst Poisoning", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12072017-144658705", "creators": [ { "name": { "family": "Bakshi", "given": "Kiran Ravindra" }, "id": "Bakshi-Kiran-Ravinda", "display_name": "Bakshi, Kiran Ravindra" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "orcid": "0000-0003-1468-6835", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VEWJ-1D21", "abstract": "Several commercial aluminas, silica-aluminas and clays are investigated \r\nfrom a standpoint of catalyst characterization and the influence of partial \r\ndeactivation on their activities for dehydration of primary alcohols. The \r\nstates of the various catalysts are characterized by calorimetric titr\u00adations \r\nwith n-butylamine and trichloroacetic acid and the resulting heat of \r\nadsorption curves are utilized to obtain acidity and basicity distributions \r\nfor each catalyst state. A division of these distributions into groups of \r\nsuitable acidic and basic site pairs leads to the development of a correla\u00adtion \r\nbetween the acid-base distributions and the catalyst activities. The postulates \r\nof the correlation are in agreement with the reaction mechanism previously \r\nproposed in the literature.
\r\n\r\nSeveral of these catalysts are subjected to poisoning by ammonia and \r\norganic bases of different strengths. Subsequent evaluation of the acid-base \r\ndistributions of the deactivated catalysts show subtle changes in the basicity \r\ndistributions depending upon the strength of the poison. The cor\u00adrelation \r\ndeveloped earlier is used to predict the activities and selectivities of \r\nthe deactivated catalysts. The good agreement between the predictions and \r\nthe experimental results substantiate the usefulness of the correlation.\r\nSubtle changes in selectivity caused by poisoning have been explained \r\nby the corresponding changes in the acid-base distributions, thus proving \r\nthe importance of such characterization.
\r\n\r\nKinetics of methanol and ethanol dehydration over some of these catalysts \r\nhave been studied to ascertain effects of changes in the catalyst state.\r\nThe rate expression
\r\n\r\nr = kKAcA1/2/(1 + KAcA1/2 + KWcW)
\r\n\r\ndescribes the experimental data for all the catalysts in their fresh as \r\nwell as poisoned states. Significant variations in k, KA and KW are \r\nob\u00adserved depending upon the catalyst states. Comparison of kinetics on fresh and \r\npoisoned catalyst states shows that poisoning increases the KA and KW \r\nfor ether formation in contrast to a decrease in these constants for olefin\r\nformation. These variations are attributed to interactions among poison\r\nmolecules and acid-base site pairs, thereby lending support to the reaction \r\nmechanism. Certain implications of nonseparable kinetics are investigated\r\nto show significant changes in total conversion and product distribution upon \r\nreversal of flow direction through a graded reactor.
\r\n" }, { "name": "Barstad, Paul Arlyn", "degree": "PhD", "year": "1975", "title": "A Current Look at the Biological Basis of Antibody Diversity and Specificity", "advisor": "Hood, Leroy E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12132017-081719269", "creators": [ { "name": { "family": "Barstad", "given": "Paul Arlyn" }, "id": "Barstad-Paul-Arlyn", "display_name": "Barstad, Paul Arlyn" } ], "advisors": [ { "name": { "family": "Hood", "given": "Leroy E." }, "id": "Hood-L-E", "orcid": "0000-0001-7158-3678", "role": "advisor", "display_name": "Hood, Leroy E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/0931-D337", "abstract": "Using automated protein sequence analysis of BALB/c\r\nmyeloma proteins, the genetic basis for antibody specificity\r\nand diversity is investigated. Studies on the N-terminal\r\nregions of the heavy chains from these immunoglobulins reveal\r\nthat a large amount of diversity must exist in the VH regions.\r\nExamination of the heavy and light chain sequences from myeloma\r\nproteins with hapten-binding activities indicates that\r\nthe heavy chain variable region sequence correlates closely\r\nwith all the specificities of intact molecules. The light\r\nchain appears to be less restricted in some specificities,\r\nhowever. The relevance of these data to the proposed \r\nmechanisms of antibody diversity is discussed." }, { "name": "Bogan, Gary Wayne", "degree": "Masters", "year": "1975", "title": "The Synthesis and Solvolytic Investigations of 2-Hexanone-5-(p-N-methylpyridinium) Ether and n-Hexyl-p-carboxybenzenesulfonate", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-092444069", "creators": [ { "name": { "family": "Bogan", "given": "Gary Wayne" }, "id": "Bogan-Gary-Wayne", "display_name": "Bogan, Gary Wayne" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SMH3-TM92", "abstract": "The synthesis and purification of 2-hexanone-5-(p-N-methylpyridinium) ether was accomplished. The reaction of this compound with aqueous NaOH failed to produce the desired products, cis- and trans-2-methylcyclopropylmethyl ketone. It appears that the desired anionic ring closure of the starting material did not take place, but instead, a simple displacement reaction occurred to produce 5- \r\nhydroxyhexan-2-one.\r\n\r\nIn a second project, the synthesis of n-hexyl-p-carboxybenzene-sulfonate was attempted by two different routes. The first route involved esterification of p-carboxybenzenesulfonyl chloride and n-hexanol to form the desired sulfonate. This method proved unsuccessful, and\r\nwas abandoned. The second route involved oxidation of n-hexyl-p-toluenesulfonate to the carboxy compound. This method was successful, producing n-hexyl-p-carboxybenzenesulfonate in about 7% yield. This \r\nmolecule was found to have an approximate half-life of 14 hours when reacted with 1 N aqueous NaOD at room temperature.\r\n" }, { "name": "Bowman, Joel Mark", "degree": "PhD", "year": "1975", "title": "Theoretical Studies of Electronically Adiabatic and Non-Adiabatic Chemical Reaction Dynamics", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:02142012-112644269", "creators": [ { "name": { "family": "Bowman", "given": "Joel Mark" }, "id": "Bowman-Joel-Mark", "display_name": "Bowman, Joel Mark" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6F8N-ZE84", "abstract": "Part I presents several sets of comparisons of semi-classical, quasi-classical and exact quantum reactive scattering calculations for collinear chemical reactions. The possibility of modifying the standard quasi-classical method according to a quantum criterion is investigated. The systems studied are H + H_2, F + H_2, and F + D_2. In addition, a theoretical investigation of the semi-classical S matrix is made.
\r\n\r\nDetails of a quasi-classical current density analysis of the H + H_2 reaction are presented and a comparison with exact quantum results is made.
\r\n\r\nA direct test of two versions of the vibrationally adiabatic theory of chemical reactions is made in Part II for the H + H_2 reaction. The adiabaticity of the symmetric stretch motion of the H_3 transition state is focussed upon. In addition, a determination of the completeness of adiabatic basis sets for scattering calculations is made.
\r\n\r\nThe theory of electronically non-adiabatic chemical reactions is presented in Part III. Quantum calculations of the collinear H^+ + H_2 \u2192 H_2 + H^+ reaction are described. A model and a realistic potential energy surface are employed in these calculations.
\r\n\r\nA fictitious electronically non-adiabatic H + H_2 collinear chemical reaction is treated quantum mechanically. Two potential energy surfaces and a coupling surface are developed for this purpose.
\r\n\r\nThe reaction Ba(^1S) + ON_2(X^1\u03a3) \u2192 BaO(X^1\u03a3) + N_2(X^1\u03a3^+_g), BaO(a^3II) + N_2(X^1\u03a3^+_g) is studied quantum mechanically. The singlet and triplet potential energy surfaces are devised as is a spin-orbit coupling surface. Electronically adiabatic and non-adiabatic transition probabilities are calculated as a function of the initial translational energy of the reagents.
" }, { "name": "Brown, Ronald Jerome", "degree": "PhD", "year": "1975", "title": "I. Quasi-Elastic Light Scattering from Liquids and Liquid Mixtures: a Study of Mass and Thermal Diffusivities. II. Observation of Translational and Intramolecular Diffusion of Circular Duplex DNA by Quasi-Elastic Light Scattering", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12062017-094448880", "creators": [ { "name": { "family": "Brown", "given": "Ronald Jerome" }, "id": "Brown-Ronald-Jerome", "display_name": "Brown, Ronald Jerome" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VKF3-8056", "abstract": "Part I
\r\n\r\nA quasi-elastic light scattering spectrometer has been con\u00adstructed and used to measure the binary mutual diffusion coefficient DAB as a function of concentration in eight binary mixtures and the thermal diffusivity x in nine pure liquids and two binary mixtures. The resulting values are in close agreement with the available bulk\r\nvalues and are accurate to within 3% for mass diffusivities and 5% for thermal diffusivities. Because neither type of measurement is dependent on the imposition of a macroscopic gradient, many of the\r\nproblems associated with conventional bulk measurements are \r\neliminated.
\r\n\r\nDeterminations require less than 2 hours for thermal diffus\u00adivities and 30 minutes for mass diffusivities, in contrast to the more time consuming classical approaches.
\r\n\r\nOn the basis of these experimental results, light scattering spectroscopy is established as an effective tool in the determination of \r\nliquid mass and thermal diffusivities. The technique should have wide industrial application.
\r\n\r\nPart II
\r\n\r\nQuasi-elastic light scattering experiments on solutions of\r\n\u0278X174 RF DNA and PM2 I DNA reveal spectral contributions from \r\ntransla\u00adtional and intramolecular motion. A tentative interpretation of the data in terms of Rouse-Zimm theory indicates lowest order relaxation\r\ntimes qualitatively consistent with theoretical predictions. Further experiments on linear and form II DNA should provide information about the changes in molecular flexibility and translational diffusivity associated with an alteration in conformation.
" }, { "name": "Clough, Roger Lee", "degree": "PhD", "year": "1975", "title": "Preparation and Properties of Molecules Having High Steric Crowding. 1,8-Diphenylnaphthalenes", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122017-144229583", "creators": [ { "name": { "family": "Clough", "given": "Roger Lee" }, "id": "Clough-Roger-Lee", "display_name": "Clough, Roger Lee" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B8WV-Q285", "abstract": "The 1,8-diarylnaphthalenes have distinctive properties and\r\ngeometric features which result from the forced proximity of the \r\nadjacent periaryl rings. We have developed an efficient synthetic\r\nroute to 1,8-diphenylnaphthalene derivatives which involves a direct \r\ncoupling between the phenyl and naphthyl rings with an organonickel \r\ncatalyst. The magnitude of the strain energy resulting from the \r\novercrowding in 1,8-diphenylnaphthalene 1 is determined using \r\ncombustion calorimetry.\tAn X-ray analysis of peri-diphenyl-\r\nacenaphthene 2 is reported. The over crowded phenyl rings of \r\n2 are face to face and nearly perpendicular to the naphthalene ring \r\nplane. Large structural distortions are found, especially in the \r\nnaphthalene framework. A comparison of the geometries of several \r\n1,8-diphenylnaphthalenes having different types of steric interactions \r\nat the 4,5 positions is made, and an analysis of distortions in terms \r\nof induced stress vectors which act throughout the naphthalene \r\nframework is presented. Striking effects in both the proton and C-13 \r\nnmr spectra of derivatives of 1 are found which are correlated with \r\na near-perpendicular solution conformation of the phenyl and naphthyl rings.
\r\n\r\n\r\nThe phenyl rings in derivatives of 1 have surprisingly low\r\nbarriers to a 180\u00b0 rotation about the phenyl-naphthyl bond. \r\nComparison of rotational barrier measurements for analogs and derivatives of 1\r\nincluding the highly strained 1,4,5,8-tetraphenyl-naphthalene, \r\ntogether with other observations, indicates that the\r\ntransition-state to phenyl-ring rotation involves substantial concurrent \r\nwarping of the naphthalene ring as a whole. Substitution in the phenyl\u00ad-ring \r\northo position raises the rotational barrier considerably; cis and tram \r\nrotational isomers of 1,8-di-o-tolylnaphthalene are isolated\r\nand studied.
\r\n\r\n" }, { "name": "Coggiola, Michael John", "degree": "PhD", "year": "1975", "title": "Experimental Investigations of Molecule-Molecule and Electron-Molecule Scattering", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:09222021-222748217", "creators": [ { "name": { "family": "Coggiola", "given": "Michael John" }, "id": "Coggiola-Michael-John", "display_name": "Coggiola, Michael John" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" } ], "option_major": [ "chemistry" ], "doi": "10.7907/r4tc-py47", "abstract": "Part I. Crossed molecular beam methods have been used to measure the differential elastic scattering of molecular hydrogen and deuterium with a number of diatomic and polyatomic secondary molecules. In particular, H2 + O2, SF6, NH3, H2O, CO and CH4 and D2 + O2, SF6, NH3, and H2O were all studied using thermal energy beams. The H2 + NH3 and H2 + SF6 systems were further studied using an H2 beam cooled to liquid nitrogen temperature. In addition, the H2 + SF6 system was remeasured using a beam of cooled para-hydrogen in place of the normal-hydrogen. These studies cover a wide range of anisotropy, size and initial relative collision energy of the scattering partners, as well as the corresponding de Broglie wavelengths. Each system studied yielded rapid quantum oscillations in the differential cross section which were used to determine central-field intermolecular potentials. These potentials were found to be independent of the energy and the hydrogen isotope used as well as their assumed mathematical form. As a result, the effects of anisotropy on the differential elastic scattering of these H2 and D2 systems do not seem important.
\r\n\r\nPart II. Variable angle electron impact spectroscopy has been applied to the systematic study of the electronic structure of the fluoroethylenes. Excitation spectra were obtained at 40 eV and 20 eV or 25 eV impact energies, and scattering angles from 0\u00b0 to 80\u00b0. Each of the molecules shows an absorption maximum between 4.2 eV and 4.7 eV, corresponding to the singlet \u2192 triplet, \u03c0 \u2192 \u03c0* transition similar to the N \u2192 T transition seen in ethylene. A weak absorption at 6.45 eV observed only in monofluoroethylene is assigned to the second singlet \u2192 triplet transition. Also observed in each spectrum is the strong singlet \u2192 singlet N \u2192 V transition, as well as a number of Rydberg features. Beyond the first ionization potential, a number of broad absorption features are observed in each molecule, corresponding to superexcited state transitions. Using a method based on term values, a number of these transitions have been assigned to Rydberg series converging to higher ionization potentials. The implications of these results for the photochemistry of the fluoroethylenes is also discussed.
\r\n\r\nChlorotrifluoroethylene has also been studied by the electron impact method, and the results are similar to those found for trifluoroethylene.
" }, { "name": "Cormack, Donald Edward", "degree": "PhD", "year": "1975", "title": "Topics in Geophysical Fluid Dynamics: I. Natural Convection in Shallow Cavities. II. Studies of a Phenomenological Turbulence Model", "advisor": "Leal, L. Gary; Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212022-000323683", "creators": [ { "name": { "family": "Cormack", "given": "Donald Edward" }, "id": "Cormack-Donald-Edward", "display_name": "Cormack, Donald Edward" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/132p-k784", "abstract": "Part I
\r\n\r\nThe problem of natural convection in a cavity of small aspect ratio with differentially heated end walls is considered. It is shown by use of matched asymptotic expansions that the flow consists of two distinct regimes: a parallel flow in the core region and a second, non-parallel flow near the ends of the cavity. An analytical solution valid at all orders in the aspect ratio, A, is found for the core region, while the first several terms of the appropriate asymptotic expansion are obtained for the end regions. Parametric\r\nlimits of validity for the parallel flow structure are discussed. Asymptotic expressions for the Nusselt number and the single free parameter of the parallel flow solution, valid in the limit as A \u2192 O, are derived.
\r\n\r\nAlso presented are numerical solutions of the full Navier-Stokes equations, which cover the parameter range Pr = 6.983, 10 \u2264 Gr \u2264 2 X 10\u2074 and 0.05 \u2264 A \u2264 1. A comparison with the asymptotic theory shows excellent agreement between the analytical and numerical solutions provided that A \u227e 0.1 and Gr\u00b2Pr\u00b2A\u00b3 ~ 10\u2075. In addition, the numerical solutions demonstrate the transition between the shallow-cavity limit and the boundary-layer limit, A fixed Gr \u2192 \u221e.
\r\n\r\nFinally, the effect of upper surface boundary conditions on the flow structure within differentially heated shallow cavities is examined. Matched asymptotic solutions, valid for small cavity aspect ratios are presented for the cases of uniform shear stress with zero heat flux, uniform heat flux with zero shear stress, and a heat flux linearly dependent on surface temperature with zero shear stress. It is shown that these changes in surface boundary conditions have an important influence on temperature and flow structure within the cavity.
\r\n\r\nPart II
\r\n\r\nThe rational closure technique proposed by Lumley and Khajeh-Nouri (1974), in which each unknown correlation is represented as an expansion about the homogeneous, isotropic state, is applied to the approximate closure of the mean Reynolds stress tensor, and rate of dissipation equations for turbulent flows. The high Reynolds number turbulence model which results is similar in many respects to that presented by Lumley et al. However, a more detailed effort is made to evaluate systematically the numerous parameters. Particular emphasis is placed on the suitability and quality of the experimental data which is used for the estimation of model parameters and on the uniqueness and universality of the resulting parameters.
\r\n\r\nA quantitative comparison of the present turbulence model to those proposed by Daly and Harlow (1970), Hanjalic and Launder (1972b), Shir (1973) and Wyngaard, Cote and Rao (1973), indicates that the present model gives the best overall prediction of the dynamic response for the homogeneous flows of Uberoi (1956, 1957), Champagne, Harris and Corrsin (1970) and Tucker and Reynolds (1968). A further comparison, which evaluates the ability of these turbulence models to predict profiles of the triple-velocity correlation, the rate of intercomponent transfer and the rate of turbulence energy dissipation for inhomogeneous flows indicates that, of the previous turbulence models, that of Hanjalic and Launder is most consistent with the data examined.\r\nHowever, the present model shows promise to yield an even better approximation to the experimental data.
" }, { "name": "Drivas, Peter John", "degree": "PhD", "year": "1975", "title": "Investigation of Atmospheric Dispersion Problems by Means of a Tracer Technique", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262021-223635283", "creators": [ { "name": { "family": "Drivas", "given": "Peter John" }, "id": "Drivas-Peter-John", "display_name": "Drivas, Peter John" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/e0az-n959", "abstract": "The purpose of this thesis was to extend the capabilities of an existing atmospheric tracer technique and to demonstrate the sensitivity and usefulness of this technique by investigating a number of complex atmospheric dispersion problems. These problems ranged from a fairly small scale of about one meter to a quite large scale of about 100 kilometers. The tracer used was sulfur hexafluoride, an inert non-toxic gas detected by means of electron-capture gas chromatography; the air sampling and analysis techniques were developed to permit a minimum detection limit of one part SF6 in 1012 parts of air. Four main atmospheric dispersion problems of environmental significance were studied in detail: ventilation systems in buildings; air flow within the wake downwind of a building; dispersion from an urban highway; and largescale transport and dispersion over the Los Angeles area.
\r\n\r\nTracer experiments involving SF6 were used to obtain quantitative data regarding actual residence time distributions in rooms and hallways, and contamination caused by reentry of laboratory fume hood hood exhausts into a building. Application of a mixing factor was found useful in room ventilation tests, and measured values ranged from 0.3 to 0.7 in small rooms without fans. In one experiment with a roof fume hood exhaust located only 16 feet from the main ventilation intake of a building, 20% of the fumes exhausted were found to reenter the ventilation system.
\r\n\r\nSulfur hexafluoride was used to probe the air flow within the wake downwind of a 12 meter high, three-story building. A reverse-flow circulation was observed with a longitudinal extent downwind of about three building heights; the extent of the recirculation on the roof was confined to less than one-half the width of the building from the downwind edge. The recirculating velocities in the wake were estimated to be about 0.1 - 0.3 those of the prevailing wind at the top of the building. The wake downwind of the building was found to be well-mixed in all three dimensions and exhibited a characteristic exponential dilution time of approximately one minute.
\r\n\r\nA number of quasi-instantaneous line source releases of SF6 were made by an automobile moving along an urban highway in Los Angeles. Concentrations at various distances from 0.4 km to 3.2 km downwind of the highway were recorded at ground level as a function of time. The tracer data were used to test the validity of several theoretical models which can be used in predicting the dispersion from an instantaneous crosswind line source. The model based upon the semi-empirical turbulent diffusion equation, using a power-law vertical velocity profile and a power-law vertical eddy diffusivity profile, was found to provide the best agreement with the data.
\r\n\r\nFinally, sulfur hexafluoride was used as a tracer in a large-scale test over the urban region near Los Angeles. On July 19, 1973, 33.5 kg of SF6 was released over a period of 45 minutes from the city of Anaheim. The transport and dispersion from Anaheim was traced in five neighboring communities including Palm Springs, which at 124 km away was the furthest location tested. A preliminary analysis of the data indicated that the cities of Riverside and Palm Springs possibly lie in a direct path of the pollutant transport from Anaheim.
" }, { "name": "Fillers, Robert Wallace", "degree": "PhD", "year": "1975", "title": "The Effect of Temperature and Pressure on the Linear Viscoelastic Response of Elastomers", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02022004-093227", "creators": [ { "name": { "family": "Fillers", "given": "Robert Wallace" }, "id": "Fillers-Robert-Wallace", "display_name": "Fillers, Robert Wallace" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/G3YM-TA68", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nStress relaxation measurements were made in uniaxial tension under superposed hydrostatic pressures up to 5 kbar at temperatures ranging from -25 to 50[degrees]C. Two lightly filled (Hypalon-40 and Viton-B) and one highly filled elastomer (Neoprene) were studied because their pressure transition lie within the range of the apparatus. The construction and operation of the apparatus are discussed. Measurements on Hypalon and Viton were made either by varying the temperature while maintaining the pressure constant at 1, 1,000, and 2,000 bars, or by holding the temperature constant while varying the pressure from atmospheric to 4,600 bars. The viscoelastic response of Neoprene was measured at 25[degrees]C and pressures up to 4,600 bars.\r\n\r\nThe measurements were converted to a time dependent shear modulus. Time-temperature and time-pressure superposition was then applied to the reduced data to obtain master curves at 1, 1,000, and 2,000 bars. By introducing either the Murnaghan or the Tait equation of state into the free volume theory, an expression was obtained which describes the shift factors, log a[subscript T,P'] resulting from the empirical shifts into the master curves at atmospheric pressure. This equation then gave an excellent prediction of the empirically found shift factors resulting from forming the master curves at 1,000 and 2,000 bars.\r\n\r\nBecause the measurements made as function of temperature and those made as a function of pressure must be consistent, certain ambiguities in the free volume theory have been removed. This leads to an essential improvement in the theory." }, { "name": "Foster, Michael Stewart", "degree": "PhD", "year": "1975", "title": "Properties and Reactions of Some Inorganic and Organometallic Compounds in the Gas Phase", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202007-080247", "creators": [ { "name": { "family": "Foster", "given": "Michael Stewart" }, "id": "Foster-Michael-Stewart", "display_name": "Foster, Michael Stewart" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VAP4-RG14", "abstract": "The gas-phase ion-molecule reactions occurring in several inorganic and organometallic systems have been examined by ion cyclotron resonance (icr) spectroscopy.\r\n\r\nElectron attachment to sulfur hexafluoride under collision-free conditions has been shown to produce stable SF6[superscript -] by a radiative de-excitation process. Halide ion transfer reactions involving anions derived from several covalent sulfur halides produce the hydrogen dihalide anions, XHY[superscript -] (X, Y = halogen), and other interesting anionic dimers. These results have important implications for radiolysis experiments which employ SF6 as an electron scavenger.\r\n\r\nThe ion-molecule reactions of iron pentacarbonyl are characterized by the formation of polynuclear clusters containing up to four iron atoms. Extensive carbon monoxide replacement reactions are also observed with a wide variety of [sigma]- and [pi]-bonding ligands. Fe(CO)5 is shown to have a proton affinity slightly less than that of ammonia.\r\n\r\nThe fragment ions derived from ferrocene undergo charge exchange with the parent neutral and condense with it to form Fe2(C5H5)3[superscript +]. The proton affinity of ferrocene is very high, the molecule being only slightly less basic than methylamine. Some general conclusions are reached about the concept of transition metal basicity.\r\n\r\nThe proton affinity of hydrogen fluoride has been determined as 1 kcal/mole less than that of nitrogen. The anomalous behavior of HF relative to the other hydrogen halides is discussed." }, { "name": "Fronczek, Franklin Robert", "degree": "PhD", "year": "1975", "title": "Structural Studies of Binuclear Cobalt (III) Cyano Complexes", "advisor": "Schaefer, William P.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03252022-181352122", "creators": [ { "name": { "family": "Fronczek", "given": "Franklin Robert" }, "id": "Fronczek-Franklin-Robert", "display_name": "Fronczek, Franklin Robert" } ], "advisors": [ { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "advisor", "display_name": "Schaefer, William P." } ], "committee": [ { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "member", "display_name": "Schaefer, William P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/wc2q-8t48", "abstract": "The crystal structures of six closely related binuclear cobalt(III) complexes have been determined by single crystal X-ray diffraction methods, in order to study the effects of the pentacyano system upon the bonding to various bridging ligands. Studies pertinent to dioxygen bridging ligands include the bis(pentacyanocobalt(III)) structures K5{(CN)5Co2(CN)5}\u00b7H2O and the double salt K8{(CN)5Co2(CN)5} (NO3)2\u00b74H2O, as well as the bis(pentaamminecobalt(III)) structure {(NH3) 5Co2(CN)5}(SCN)4. In all cases, the dioxygen ligands (peroxo and superoxo) are found to bridge to two cobalt atoms in the asymmetric, staggered arrangement, and both planar and nonplanar structures are noted. The structures of two molecules of the type pentacyanocobalt(III)pentaamminecobalt(III) are determined, with the bridging ligands cyanide and thiocyanate. These compounds are (CN)5CoNCCo(NH3)5\u00b7H2O and (CN)5CoSCNCo(NH3)5\u00b7H2O. The preparation and structure of the compound K6{(CN)5Co2(CN)5}\u00b76H2O, containing the new bridging ligand thiosulfite (SSO22-) are reported. This ligand bridges the two cobalt atoms through its two sulfur atoms, and has a geometry similar to that of normal coordinated sulfites. Coordination to cobalt is trans planar." }, { "name": "Ho, Bosco Po-Wai", "degree": "PhD", "year": "1975", "title": "Suspension Mechanics: I. Inertial and Non-Newtonian Migration of Neutrally Buoyant Rigid Spheres in Two-Dimensional Unidirectional Flows. II. The Effect of Viscoelasticity on the Creeping Motion of a Train of Neutrally Buoyant Newtonian Drops through a Circular Tube", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechTHESIS:07152014-151002249", "creators": [ { "name": { "family": "Ho", "given": "Bosco Po-Wai" }, "id": "Ho-Bosco-Po-Wai", "display_name": "Ho, Bosco Po-Wai" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/A0MZ-B010", "abstract": "The lateral migration of neutrally buoyant rigid spheres in two-dimensional unidirectional flows was studied theoretically. The cases of both inertia-induced migration in a Newtonian fluid and normal stress-induced migration in a second-order fluid were considered. Analytical results for the lateral velocities were obtained, and the equilibrium positions and trajectories of the spheres compared favorably with the experimental data available in the literature. The effective viscosity was obtained for a dilute suspension of spheres which were simultaneously undergoing inertia-induced migration and translational Brownian motion in a plane Poiseuille flow. The migration of spheres suspended in a second-order fluid inside a screw extruder was also considered.
\r\n\r\nThe creeping motion of neutrally buoyant concentrically located Newtonian drops through a circular tube was studied experimentally for drops which have an undeformed radius comparable to that of the tube. Both a Newtonian and a viscoelastic suspending fluid were used in order to determine the influence of viscoelasticity. The extra pressure drop due to the presence of the suspended drops, the shape and velocity of the drops, and the streamlines of the flow were obtained for various viscosity ratios, total flow rates, and drop sizes. The results were compared with existing theoretical and experimental data.
" }, { "name": "Ho, Wilson", "degree": "Masters", "year": "1975", "title": "A Theoretical Investigation of Surface Phenomena", "advisor": "Weinberg, William Henry; Cunningham, Steven", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-112323165", "creators": [ { "name": { "family": "Ho", "given": "Wilson" }, "id": "Ho-Wilson", "display_name": "Ho, Wilson" } ], "advisors": [ { "name": { "family": "Weinberg", "given": "William Henry" }, "id": "Weinberg-W-H", "role": "advisor", "display_name": "Weinberg, William Henry" }, { "name": { "family": "Cunningham", "given": "Steven" }, "id": "Cunningham-S", "role": "co-advisor", "display_name": "Cunningham, Steven" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DB7B-FM81", "abstract": "Using the Linear Combination of Atomic Orbitals (LCAO) formalism and \r\nthe tight-binding approximation, we have investigated three separate types \r\nof surface phenomena via the Green's function method and the phase shift \r\ntechnique. We obtain the shift in the energy levels due to the following: \r\n(l) creation of the surface, (2) surface reconstruction, and (3) the adsorption of a single atom. In the first two parts, we study the (001) face \r\nof a two-band crystal with the CsC1 structure, simulating the surface \r\nproperties of semiconductors or insulators. In the third part, we study \r\nthe interaction of a single atom with the (001) surface of a bcc metal.\r\nThe results obtained are contrasted with those obtained from a one-band \r\ncalculation for the (001) surface of a simple cubic crystal. We find that \r\nthe second unoccupied band is of utmost importance in understanding these \r\nsurface phenomena.\r\n" }, { "name": "Kent, Diane Jacalyn", "degree": "Masters", "year": "1975", "title": "Electron Microscope Studies of Chromatin Subunit Particles", "advisor": "Stroud, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202010-093957061", "creators": [ { "name": { "family": "Kent", "given": "Diane Jacalyn" }, "id": "Kent-Diane-Jacalyn", "display_name": "Kent, Diane Jacalyn" } ], "advisors": [ { "name": { "family": "Stroud", "given": "Robert M." }, "id": "Stroud-R-M", "role": "advisor", "display_name": "Stroud, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GVT9-N257", "abstract": "Nuclease resistant chromatin subunits (\u03bd bodies) were isolated from rat liver chromatin after digestion with DNAase II. Electron microscope studies showed them to be similar in size to particles which have been isolated from calf thymus chromatin and also to those seen in native chromatin. \u03bd bodies prepared from native chromatin (\u03bd(+F1) and histone F1-depleted chromatin (\u03bd(-F1)), as well as formaldehyde-fixed products from both these digestions (\u03bd(FF + F1) and \u03bd(FF-F1) were similar in size. For \u03bd(+F1) the diameter was 80 \u00b1 17 \u00c5 (n = 125); for \u03bd(-F1), 87 \u00b1 19 \u00c5 (n = 100); for \u03bd(FF + F1), 96 \u00b1 23 \u00c5 (n = 50); and for \r\n\u03bd(FF \u2013 F1) 81 \u00b1 13 \u00c5 (n = 85). Multimer \u03bd-body fractions did not show any obvious dimers, trimers, etc. , of monomer \u03bd bodies. Sheared, isolated chromatin from rat liver was also examined using electron microscopy and was observed as networks of long thin strands (about 15 \u00c5 wide), interspersed with regions of either coiled single strands or strands covered with protein.\r\n" }, { "name": "Keppel, Robert Andrew", "degree": "PhD", "year": "1975", "title": "Organic Reactions in the Gas Phase. Part I: Decomposition of Isomeric Cis 6,7-dimethyl-2,3-diazabicyclo[3.2.0]hept-2-enes in the Gas Phase. Part II: The Wall-Less Reactor. Part III: Thermal Isomerization of Cyclopropenes", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09042024-184628054", "creators": [ { "name": { "family": "Keppel", "given": "Robert Andrew" }, "id": "Keppel-Robert-Andrew", "display_name": "Keppel, Robert Andrew" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9ske-ad80", "abstract": "Part I: Decomposition of Isomeric Cis 6,7-dimethyl-2,3-diazabicyclo[3.2.0]hept-2-enes in the Gas Phase
\r\n\r\nThe thermal decomposition of the isomeric cis 6,7-dimethyl-2,3-diazabicyclo[3.2.0]hept-2enes was \r\nstudied. In order to account for the products observed,\r\ndual pathways for the decomposition are proposed. The formation of isomeric\r\ncis 2,3-dimethyl-bicyclo[2.1.0] pentanes is explained by a mechanism involving\r\na diradical intermediate. The formation of 2,3-dimethylpenta-1,4-dienes is best\r\nexplained by a stereospecific retro-1,3-dipolar cleavage to an acyclic\r\ndiazo compound which loses nitrogen to form a carbene. The absence of\r\na thermal \"Di-\u03c0-methane pathway is indicated from the products.
\r\n\r\nPart II: The Wall-less Reactor
\r\n\r\nA wall-less reactor was constructed based on one designed\r\npreviously at Kent State. The reactor was modified and used to study\r\nthe unimolecular decomposition of strained hydrocarbons. Cyclopropane\r\nwas found to isomerize to propylene with a rate law of log k =\r\n14.6 -65.1 kcal per mole/\u03b8 over the temperature range of 936 to\r\n1026\u00b0K. The wall-less reactor was also used to study the isomerization of\r\n3,3-dimethylcyclopropene (see abstract of Part III).
\r\n\r\nPart III: Thermal Isomerization of Cyclopropenes
\r\n\r\nThe thermal rearrangement of 3,3-dimethylcyclopropene (6)\r\nwas studied in the wall-less reactor over a temperature range of\r\n608 to 668\u00b0K. The rate law for the isomerization was found to be\r\nlog k = 12.6 -36.2 kcal per mole/\u03b8. 6 isomerized to 86.2% 3-methyl-1-butyne,\r\n12.9% 1-methyl-1,3-butadiene and 0.9% 3-methyl-1,2-butadiene.\r\nThe data were in accord with published results of the\r\nisomerization of 6 in a static thermal reactor.
\r\n\r\nThe thermal rearrangement of 1-methylcyclopropene (14) was\r\ninvestigated by entering the energy surface for the reaction by two\r\nroutes: thermal isomerization of the cyclopropene and pyrolysis of\r\na vinylcarbene precursor, 3-methyl-3-vinyldiazirine (12). The\r\nacyclic C4H6 products from both reactions are \r\nidentical, however the proportions vary greatly. Greater than 99% of the\r\nproduct from the diazirine is the cyclopropene, and the remainder of the\r\nproducts is 1,3-butadiene, 2-butyne and 1,2-butadiene in the\r\nratio of 1:0.6:0.2, respectively. The products from the isomerization of\r\n1-methyl-cyclopropene are the same but in the ratio of 5:93:2, respectively. From\r\nthe data it is concluded that two intermediates exist for the\r\nisomerization, a planar vinylcarbene and a 90\u00b0 rotamer, designated\r\na diradical.
" }, { "name": "Kroon, Paulus Arie", "degree": "PhD", "year": "1975", "title": "I. The Use of Deuterated Phospholipids to Elucidate Lipid-Lipid Interactions in Bilayer Vesicles. II. The Effect of Chain Length on the Secondary Structure of Oligoadenylates", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192011-112852465", "creators": [ { "name": { "family": "Kroon", "given": "Paulus Arie" }, "id": "Kroon-Paulus-Arie", "display_name": "Kroon, Paulus Arie" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y8JR-HG97", "abstract": "Part I: The Use of Deuterated Phospholipids to Elucidate Lipid-Lipid Interactions in Bilayer Vesicles.\r\n\r\nThe motional state of lecithin molecules in single walled bilayer vesicles has been studied by nuclear magnetic resonance spectroscopy. Inter- and intramolecular relaxation rates have been determined for the hydrocarbon chain methylene protons. The intermolecular contribution is much smaller than previously estimated. The data suggest a model in which hydrocarbon chain motion is described by rapid kink formation and diffusion along the chains in addition to slower C-C trans-gauche rotations. A lateral diffusion coefficient of 2.5 - 5.5 x 10^(-8) cm^2 sec^(-1) is estimated. Both linewidths and spin-lattice relaxation rates have been measured for lecithins with different hydrocarbon chain lengths. Above the crystal to liquid crystal phase transition temperature, the linewidths are independent of chain length. This is taken to indicate that the hydrocarbon chain mobility and order are also independent of chain length.\r\n\r\nThe motional state of cholesterol in bilayer vesicles has been studied. Cholesterol dispersed in bilayers consisting of dipalmitoyl lecithin with perdeuterated hydrocarbon chains has an NMR spectrum with well defined features. Two of the five methyl resonances are sharp and clearly resolved. These are assigned to the isopropyl methyls of the hydrocarbon tail. The other methyl resonances are much broader. This is taken to indicate that the hydrocarbon tail is much more mobile and disordered than the steroid nucleus. These conclusions are in agreement with and provide experimental support for the model proposed by Rothman and Engelman, but contrast with recent NMR studies which conclude that both the steroid nucleus and hydrocarbon tail are highly immobilized.\r\n\r\nPart II: The Effect of Chain Length on the Secondary Structure of Oligoadenylates.\r\n\r\nThe oligoadenylates (Ap)_(2_4)A have been studied by proton magnetic resonance (pmr) spectroscopy. All the exterior base protons and a number of the interior base proton resonances have been assigned. The results of this work showed that the adenine bases in these oligoadenylates are intramolecularly stacked at 20\u00b0C with their bases oriented preferentially in the anti conformation about their respective glycosidic bonds. The oligomers were found to associate extensively even at concentrations of 0.02 M, primarily via \"end to end\" stacking. With increasing temperature the oligomer bases destack, but it is argued that this unfolding process cannot be described in terms of a two-state stacked versus unstacked model. Instead, the temperature dependences of the base proton chemical shifts support a base-oscillation model. The relationship between this model and the \"two-state\" model is discussed. Finally, on the basis of the chain-length dependence of the proton chemical shifts of the various adenine bases, it was concluded that subtle variations in the secondary structure of these oligomers exist with increasing chain length. Evidence is presented to show that the effects of distant base shielding are considerably smaller than what was previously estimated. The observed departures from the \"extended dimer\" model are attributed to differences in the relative orientations of the bases with respect to their neighbors in the oligomer." }, { "name": "Martin, Patrick H. S.", "degree": "Masters", "year": "1975", "title": "Studies of atomic and molecular processes and properties in the random phase approximation", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212010-085207566", "creators": [ { "name": { "family": "Martin", "given": "Patrick H. S." }, "id": "Martin-P-H-S", "display_name": "Martin, Patrick H. S." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FASY-ZM58", "abstract": "Part I - Dipole Properties of Atoms and Molecules in the Random Phase Approximation: \r\n\r\nA random phase approximation (RPA) calculation and a direct sum over states is used to calculate second-order optical properties and van der Waals coefficients. A basis set expansion technique is used and no continuum-like functions are included in the basis. However, unlike other methods we do not force the basis functions to satisfy any sum-rule constraints but rather the formalism (RPA) is such that \r\nthe Thomas Reiche-Kuhn sum rule is satisfied exactly. Central attention is paid to the dynamic polarizability from which most of the other properties are derived. Application is made to helium and molecular hydrogen. In addition to the polarizability and van der Waals coefficients, results are given for the molecular anisotropy of H_2, Rayleigh scattering cross sections and Verdet constants as a function of frequency. Agreement with experiment and other theories is good. Other energy weighted sum-rules are calculated and compare very \r\nwell with previous estimates. The practicality of our method suggests its applications to larger molecular systems and other properties.\r\n\r\nPart II - Photoionization Cross Sections for H_2 in the Random Phase Approximation with a Square-Integrable Basis:\r\n\r\nTotal photoionization cross sections for H_2 are calculated in the Random Phase Approximation (RPA) through a numerical analytic continuation procedure applied to the polarizability for complex valuesof the frequency. The representation of the polarizability that is \r\nrequired is obtained from a discrete set of excitation energies and oscillator strengths that satisfies the Thomas-Reich-Kuhn sum rule exactly and other energy-weighted sum rules approximately. The fact that the excitation spectrum is obtained through a solution of the RPA equations with no continuum functions added to the basis makes the method well suited for general molecular photoionization calculations. The results are compared with experiment and good agreement is found.\r\n\r\nPart III - Oscillator Strengths for the X^1\u2211^+ - A^1\u03c0 System in CH^+ from the Equations of Motion Method:\r\n\r\n\tThe equations of motion method is used to study the X^1\u2211^+ - A^1\u03c0 system in CH^+. In a computationally simple scheme, these calculations, which were done in modest sized basis sets, provide transition moments and oscillator strengths that agree well with the best CI calculations \r\nto date.\r\n" }, { "name": "Moon, Richard Bruce", "degree": "PhD", "year": "1975", "title": "Nuclear Magnetic Resonance Studies of Hemoglobin and Red Blood Cell Function", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05182023-164434034", "creators": [ { "name": { "family": "Moon", "given": "Richard Bruce" }, "id": "Moon-Richard-Bruce", "display_name": "Moon, Richard Bruce" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "abstract": "Pulse and Fourier transform nuclear magnetic resonance techniques have been employed to study various aspects of hemoglobin\r\nand red blood cell function.
\r\n\r\nThe binding of 13C-enriched carbon monoxide to myoglobins and hemoglobins from a variety of animal species has been studied by\r\n13C NMR. The environments experienced by 13CO bound to \u03b1 or \u03b2 subunits, the relative facility with which oxygen displaces 13CO, and the relative thermodynamic affinities of the unliganded subunits for 13CO are found to differ. These results clearly demonstrate the various degrees of nonequivalence that may exist between the subunits of normally occurring hemoglobins which must be accounted for in any physical model of hemoglobin ligation if it is to accurately describe hemoglobin function.
\r\n\r\nThe chemical shifts of 13CO bound to reconstituted myoglobins and hemoglobins containing synthetically modified hemes have been\r\nstudied and show that the degree of electronic interaction between the heme and the bound ligand may be modulated by the nature of the surrounding\r\nprotein. T1 and NOE studies indicate that the bound 13CO ligand interacts strongly with the valine residue (E11) and forms a\r\nhydrogen bond with the distal histidine residue (E7) in the ligand binding pocket. These results provide new information about the manner\r\nin which the protein environment controls the chemistry and reactivity of the heme.
\r\n\r\nObservation of the 31P resonances of inorganic phosphate and 2,3-diphosphoglycerate in whole blood has led to the development of\r\na noninvasive technique for the determination of intracellular pH. This technique is generally applicable for the study of intracellular\r\npH in a large number of different cell and vesicle systems.
\r\n\r\nThe reactions of 13C-enriched cyanate with human adult and sickle cell hemoglobins have also been studied by 13C NMR. Results were obtained for the pH dependence of carbamylation for the N-terminal amino groups and lysine residues of these hemoglobins, both\r\nin purified hemoglobin solutions and in whole blood. These studies suggest that maximal effects of cyanate in clinical in vitro treatments\r\nwill be realized when cyanate concentrations are kept below 10-20 mM and reaction pH is in the range 6.5-7.0.
\r\n\r\nNatural abundance 13C NMR has been used to study the solution conformations of human and rabbit hemoglobins. The results suggest\r\nthat average hemoglobin quaternary conformations are ligand dependent. Methemoglobin is found to have a solution quaternary conformation\r\nroughly intermediate between those of oxyhemoglobin and deoxy hemoglobin at neutral pH.
" }, { "name": "Mosher, Oren Allen", "degree": "PhD", "year": "1975", "title": "Electronic Spectroscopy by the Electron Impact Method", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:03052025-235905696", "creators": [ { "name": { "family": "Mosher", "given": "Oren Allen" }, "id": "Mosher-Oren-Allen", "display_name": "Mosher, Oren Allen" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vkjm-pa67", "abstract": "A previously constructed variable angle electron-impact\r\nspectrometer has been rebuilt and used to study electronic excitation\r\nspectra in the energy-loss range from 0 eV to beyond 15 eV for 13\r\nmolecules. Spectra were obtained in the impact energy range from\r\n20 eV to 70 eV and for scattering angles from 0\u00b0 to 80\u00b0. The differential\r\nscattering cross sections were obtained for several low-lying\r\nelectronic transitions and used to determine whether a transition was\r\nspin-allowed or spin-forbidden. Further assignments of some\r\ntransitions were made by comparison of the present results with\r\nearlier theoretical and experimental studies.
\r\n\r\nIn the 1, 3-conjugated polyenes the three lowest energy excited\r\nstates are the 1 3Bu, the 1 3Ag and the 1 3Bu. These states have been\r\nstudied here and produce peaks in the energy-loss spectrum at 3.22\r\neV, 4.91 eV, and 5.92 eV in s-trans-1, 3-butadiene, at 3.14 eV, 4.87\r\neV, and 5.80 eV in 1-trans-3-pentadiene, at 3.20 eV, 4.93 eV, and\r\n5.77 eV in 1, 3-hexadiene, and at 3.11 eV, 4.85 eV, and 5.69 eV in cis-\r\n2-trans-4-hexadiene. The energies of the low-lying transitions in the\r\n1, 3 and 2, 4 non-cyclic dienes are nearly invariant with respect to\r\nalkyl substitution. This indicates that these are \u03c0 \u2192 \u03c0* transitions and\r\nthat the \u03c3,\u03c0 separability approximation is applicable to these\r\nmolecules. In 1, 3-cyclohexadiene the state which is equivalent to the\r\n1 3Ag is not seen but transitions to the states which are equivalent to\r\nthe 1 3Bu and the 1 1Bu states produce peaks at 2.94 eV and 4.94 eV,\r\nrespectively. The shifts in the transition energies from the noncyclic\r\ndiene values are probably associated with the increased closeness\r\nof the two \u03c0 bonds. In 1, 3, 5-hexatriene the energies of the\r\ntransitions to the 3Bu, 1 3Ag, and 1 1Bu states are 2.61 eV, 4.11 eV,\r\nand 5.13 eV, respectively. There was no evidence for a weak\r\nsinglet \u2192 singlet transition below the X1 Ag \u2192 1 1Bu transition in contrast\r\nto the results of recent studies on larger substituted polyenes.
\r\n\r\nSome non 1,3-conjugated polyenes were studied. The \u03c0 \u2192 \u03c0*,\r\nsinglet \u2192 triplet transition produced a peak at 4.25 eV in 1, 4-hexa-\r\ndiene, 4.25 eV in 1,5-hexadiene and 4.29 eV in 1, 4-cyclohexadiene.\r\nThe strong \u03c0 \u2192 \u03c0*, singlet \u2192 singlet transition peaks at 6.84 eV, 7.00\r\neV, and 7.95 eV in these molecules. The results for the non-cyclic\r\ndienes were quite similar to the results in the alkyl substituted\r\nethylenes and again suggest that the \u03c3, \u03c0 separation is valid. For 1,4-\r\ncyclohexadiene, however, the upward shift in the singlet-singlet\r\ntransition energy may reflect the interaction of the two \u03c0 orbitals by\r\nhyperconjugation with the \u03c3CH orbitals. Such an interaction implies\r\na breakdown of the \u03c3,\u03c0 separability approximation.
\r\n\r\nTwo azo compounds (R-N=N-R) have been studied. The first\r\nthree excited states are the 1 3Bg, the 1 1Bg, and a second triplet state.\r\nIn azomethane transitions to these states produce maxima at 2.75 eV,\r\n3.50 eV, and 4.84 eV. The corresponding values in azo-t-butane are\r\n2.67 eV, 3.37 eV, and 4.9 eV. The near equality of the three lowest\r\ntransition energies of these two azo compounds suggests that these\r\nexcitations are primarily due to the azo group electrons.
\r\n\r\nIn propadiene (allene) the 1,2 interaction of the double bonds\r\nproduces two singlet \u2192 triplet transitions with maxima at 4.28 eV and\r\n4.89 eV. The separation of 0.61 eV between these triplet states is\r\nsubstantially smaller than the corresponding splitting of 1.69 eV in\r\n1,3-butadiene indicating a much smaller \u03c0 - \u03c0 interaction due to the\r\nperpendicularity of the \u03c0 molecular orbitals.
\r\n\r\nIn thiophosgene (Cl2CS) a previously unreported singlet \u2192 triplet\r\ntransition was seen at 3.1 eV.
\r\n\r\nThese results illustrate the power of low energy variable angle\r\nelectron-impact spectroscopy in the elucidation of the electronic\r\nstructure of \u03c0-electron molecules.
" }, { "name": "Moss, Barry Joel", "degree": "Masters", "year": "1975", "title": "I. The Generalized Valence Bond Description of O\u2082 II. Configuration Interaction Studies on Low-Lying States of O\u2082", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03312010-111428333", "creators": [ { "name": { "family": "Moss", "given": "Barry Joel" }, "id": "Moss-Barry-Joel", "display_name": "Moss, Barry Joel" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WB95-VY69", "abstract": "I. The Generalized Valence Bond Description of O_2\r\n\r\nAb initio calculations using the generalized valence bond (GVB) method have been carried out for the lowest triplet and singlet states of O_2 at internuclear distances (R) between 2a_o and 6a_o. In contrast to other orbital descriptions, GVB leads correctly to ground state oxygen atoms as the bond length is increased to infinity. This proper behavior requires optimization of the spatial orbitals themselves and of the permutational coupling between them as well. Analysis of the results as a function of R is straightforward. Constructing a simple configuration interaction (CI) wavefunction using the GVB orbitals leads to excellent potential curves, accounting for 94% of the bond dissociation energy. The calculated adiabatic separation of the singlet and triplet states is 1.09 eV compared with the experimental T_e of 1.01 eV.\r\n\r\nII. Configuration Interaction Studies on Low-Lying States of O_2\r\n\r\nConfiguration interaction calculations are reported as a function of R for the nine state of O_2 corresponding to the (3\u03c3_g)^2 (1\u03c0_\u03bc)^4 (1\u03c0_g)^2 and (3\u03c3_g)^2 (1\u03c0_\u03bc)^3 (1\u03c0_g)^3 configurations (X^3\u2211^-_g, a^1\u0394_g, b^1\u2211^+_g, ^1\u2211^-_\u03bc, ^3\u0394_\u03bc, A^3\u2211^+_\u03bc, B^3\u2211^-_\u03bc, ^1\u0394_\u03bc, ^1\u2211^+_\u03bc). By using the generalized valence bond (GVB) orbitals of the X^3\u2211^-_g state we obtain good quality GVB-CI wavefunctions with only a moderate number of configurations(72 to 98 spatial configurations) despite the use of a large basis set (double-zeta plus polarization functions). The calculated D_e for the X^3\u2211^-_\u03bc state is 4.88 eV, 93% of the experimental value. The calculated adiabatic excitation energies are on the average about 0.1 eV from the experimental values.\r\n\r\n\r\n" }, { "name": "Patumtevapibal, Saon", "degree": "PhD", "year": "1975", "title": "Part I: The Construction of a Model-Locked Nd\u00b3\u207a: Glass Laser and Non-Linear Optical Techniques. Part II: Applications of Picosecond Laser Pulses in Chemistry: Vibrational Relaxation Times in Liquid Alkanes and Alkenes", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:02172022-193613745", "creators": [ { "name": { "family": "Patumtevapibal", "given": "Saon" }, "id": "Patumtevapibal-Saon", "display_name": "Patumtevapibal, Saon" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sska-f577", "abstract": "PART I. The construction and qualitative explanation of the pulsed, mode-locked laser are described: the generation of a train of picosecond 1.06\u03bc pulses is achieved by properly aligning a saturable absorber in the Nd3+: glass laser cavity. The pulsewidth, being on a picosecond time scale, has to be measured' by a special two-photon method. In order to make the laser more chemically useful, second harmonic generation of the fundamental (1.06 \u03bc) pulses is necessary. A phase-matched KDP crystal is employed in this process. Some non-linear optical techniques, such as stimulated Raman scattering and self-phased modulation, which generates continuum light from a monochromatic pulses, also enrich the usage of the laser. Azulene experiment is tried with our laser set-up.
\r\n\r\nPART II. The dephasing times and vibrational lifetimes of C-H stretching vibrations are studied systematically in a series of liquid alkanes and alkenes, using the Raman effect. The results indicate that the vibrational energy loss takes place primarily through the methyl groups in these molecules. A preliminary result of the methylene C-H stretch vibrational lifetime is conducted in liquid CD3-CH2-CH2-CD3
" }, { "name": "Powers, Dana Auburn", "degree": "PhD", "year": "1975", "title": "Magnetic Behavior of Basic Iron (III) Compounds: I. Magnetic Behavior of the Basic Iron Sulfates and Basic Iron Chromates. II. Magnetic Behavior of Delta Ferric Oxide Hydroxide", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112015-085855387", "creators": [ { "name": { "family": "Powers", "given": "Dana Auburn" }, "id": "Powers-Dana-Auburn", "display_name": "Powers, Dana Auburn" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0P1Q-WM72", "abstract": "I. The thermomagnetic behavior and infrared spectroscopic features of KFe3(SO4)2(OH)6 (jarosite), (H3O)Fe3(SO4)2 (OH)6 (hydronium jarosite), KFe3(CrO4)2 (OH)6, Fe(OH)SO4 (basic iron sulfate), and Fe(OH)CrO4 (basic iron chromate) are reported. Fe(OH)CrO4 and KFe3(CrO4)2 (OH)6 are shown to be weak ferro magnets with Curie temperatures of 73 and 71 \u00b0K, respectively. This unusual magnetic\r\nbehavior is rationalized in terms of the ionic spin configurations of the phases. Exchange coupling through chromate bridging groups is shown to be weak.
\r\n\r\n\r\nII. The magnetic behavior and the influence of preparative history on the magnetic behavior of \u03b4FeO(OH) is reported. \u03b4FeO(OH) is shown to be a fine-particulate, uniaxial, magnetic species. Magnetization data for this species are shown to be consistent with the existence of magnetically inactive layers surrounding magnetic\r\nparticles.
" }, { "name": "Rawlings, Jill", "degree": "PhD", "year": "1975", "title": "Spectral and Kinetic Studies of Iron-Sulfur Proteins", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11032021-211434335", "creators": [ { "name": { "family": "Rawlings", "given": "Jill" }, "id": "Rawlings-Jill", "display_name": "Rawlings, Jill" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vv7x-np65", "abstract": "Spectral studies of spinach ferredoxin and Chromatium HiPIP in the near infrared region give indications of inequivalence of the iron. The low energy spectrum of ferredoxin is interpreted in terms of one [Fe(III)S4] site, which is the reducible site, and one site, which is not tetrahedral and is nonreducible. A band at 720 nm in the oxidized protein is attributed to the first spin forbidden d-d band of a tetrahedral site, while bands at 820 and 920 nm are assigned to the distorted, nonreducible site. A band at 652 nm in the reduced protein is interpreted as an intervalence transition or a spin forbidden band of the iron(II) site.
\r\n\r\nThe near infrared spectrum of reduced HiPIP has a broad band at 1040 nm. This band is absent in the model compound, (Et4N)2[Fe4S4(SCH2Ph)4] and may be indicative of a slight site inequivalence. However, magnetic studies show an antiferromagnetic coupling very similar to the model, with \u03bce per iron for protein and model agreeing closely.
\r\n\r\nA number of redox reactions of these iron-sulfur proteins with inorganic reagents were studied. The second order rate constant 5 for the reaction of spinach ferredoxin with FeEDTA- is 3.4 x 105 M-1sec-1, while the rate constants for the HiPIP reactions are slower by a factor of 100. The rate constant is 1.7 x 103 M-1sec-1 for the reaction of HiPIP and FeEDTA2- and 2.4 x 103 M-1sec-1 for the HiPIP-Fe(CN)63- reaction. These reactions typically have very small activation enthalpies and very negative activation entropies. Electron tunneling is suggested as a possible mechanism for these reactions.
" }, { "name": "Robertson, Grant Earl", "degree": "PhD", "year": "1975", "title": "Combined Forced and Free Convection in Stratified and Unstratified Flows", "advisor": "Leal, L. Gary; Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062021-232305217", "creators": [ { "name": { "family": "Robertson", "given": "Grant Earl" }, "id": "Robertson-Grant-Earl", "display_name": "Robertson, Grant Earl" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" }, { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/47d4-nd32", "abstract": "The laminar, steady, horizontal flow past a hot or cold two-dimensional body is examined; the fluid is unbounded, diffusive, and viscous. The presence of significant ambient stable temperature (or density) stratification, or significant buoyancy-induced convection, or both, is considered. A detailed understanding of the fundamental structure of such flows is obtained by developing effective analytical and numerical solution procedures.
\r\n\r\nChapter 2: This chapter considers the general problem of stably stratified, Oseen flow at large distances upstream and downstream of a body which is represented as a line sink of horizontal or vertical momentum, or as a line heat source or heat dipole. The analysis is focused on the general properties of the horizontal velocity component, as well as on explicit calculation of the horizontal velocity profiles and disturbance streamfunction fields for varying degrees of stratification. For stable stratifications, the flow fields for all four types of singularities exhibit the common feature of multiple recirculating rotors of finite thicknesses, which leads to an alternating jet structure. both upstream and downstream for the horizontal velocity component and to lee-waves in the overall flow. Self-similar formulae for the velocity, temperature, and pressure at very large distances upstream and downstream are also derived and compared with the Oseen solutions
\r\n\r\nChapter 3: The simultaneous forced and free convection flow of a neutrally- or stably-stratified fluid past a hot or cold horizontal flat plate is investigated by numerically solving the full equations of motion and thermal energy subject only to the Boussinesq approximation. The solutions span the parameter ranges 10 ≤ Re ≤ 100, 0.1 ≤ Pr ≤ 10, -2.215 ≤ Gr/Re5/2 ≤ +2.215, and O ≤ Ri ≤ 6.325, where Re, Pr, Gr, and Ri are based on the overall plate length \u2113 and the ambient free stream fluid properties evaluated at the plate level. For all degrees of stratification a hot plate causes an acceleration of the boundary flow near the plate surface relative to the corresponding forced convection flow, thereby increasing both the local skin friction and heat transfer coefficients. On the other hand, the boundary flow adjacent to a cold plate is decelerated and the local skin friction and heat transfer rate are decreased. This deceleration effect is enhanced by either further cooling or increasing the amount of ambient stratification, Ri, leading to boundary-layer separation in some cases. When the effect of the ambient stratification dominates that of local heating or cooling, the boundary-layer displacement increases for decreasing Ri, due to the buoyancy restoring force lessening, thus diminishing the drag. The dimunition in the drag, for the same decrease in Ri, lessens (increases) by slightly heating (cooling) the plate. When the effect of local heating or cooling dominates that of the ambient stratification, the drag is diminished by increasing Ri. A wave-structure exists only for stably-stratified fluids, with the amplitudes and wavelengths of the waves being decreased for increasing Ri.
" }, { "name": "Schreiber, Loren Bennett", "degree": "PhD", "year": "1975", "title": "A Pulse NMR Trilogy: Anomalies, Anisotropies, and Adsorption", "advisor": "Vaughan, Robert W.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08242021-231334417", "creators": [ { "name": { "family": "Schreiber", "given": "Loren Bennett" }, "id": "Schreiber-Loren-Bennett", "display_name": "Schreiber, Loren Bennett" } ], "advisors": [ { "name": { "family": "Vaughan", "given": "Robert W." }, "id": "Vaughan-R-W", "role": "advisor", "display_name": "Vaughan, Robert W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/avna-2v77", "abstract": "In phase one of this thesis, a systematic method, an extension of the average Hamiltonian formalism, is presented for calculating the effects of pulse errors in the multiple pulse nuclear magnetic resonance (NMR) experiments. Application of this method to account for effects of pulse nonidealities such as phase errors, phase transient effects, pulse size errors, and rf inhomogeneity is found to agree with experimental observation.
\r\n\r\nIn phase two, the proton chemical shift tensor of the hydroxyl proton in calcium hydroxide was measured using multiple pulse NMR techniques. The tensor is axially symmetric with susceptibility corrected components of \u03c3\u22a5 = -9.3 \u00b1 1 ppm and \u03c3\u2225 = +4.7 \u00b1 1 ppm relative to TMS.
\r\n\r\nIn phase three, conventional and multiple pulse NMR techniques were used to examine the hydroxyl protons on a series of high surface area silica-aluminas whose composition varied from 0-100% SiO2. Protons remaining on these materials after being calcined at 500\u00b0 C are found to exist as immobile and isolated hydroxyl groups at room temperature. With the high silica content samples, 100-75% Si02, no AlOH groups were detectable, while on the 50% and lower SiO2 content samples, most protons were A1OH groups; thus, there is indication of a major change in local structure between 75% and 50% silica content.
" }, { "name": "Smith, Jeffrey Bernard", "degree": "PhD", "year": "1975", "title": "Kinetic Theory of Normal Quantum Fluids", "advisor": "Corngold, Noel Robert", "url": "https://resolver.caltech.edu/CaltechTHESIS:07102014-095132104", "creators": [ { "name": { "family": "Smith", "given": "Jeffrey Bernard" }, "id": "Smith-Jeffrey-Bernard", "display_name": "Smith, Jeffrey Bernard" } ], "advisors": [ { "name": { "family": "Corngold", "given": "Noel Robert" }, "id": "Corngold-N-R", "role": "advisor", "display_name": "Corngold, Noel Robert" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SWXM-ZG90", "abstract": "Close to equilibrium, a normal Bose or Fermi fluid can be\r\ndescribed by an exact kinetic equation whose kernel is nonlocal in space and time. The general expression derived for the kernel is evaluated to second order in the interparticle potential. The result is a wavevector- and frequency-dependent generalization of the linear\r\nUehling-Uhlenbeck kernel with the Born approximation cross section.
\r\n\r\nThe theory is formulated in terms of second-quantized phase space operators whose equilibrium averages are the n-particle Wigner distribution functions. Convenient expressions for the commutators and anticommutators of the phase space operators are obtained. The two-particle equilibrium distribution function is analyzed in terms of momentum-dependent quantum generalizations of the\r\nclassical pair distribution function h(k) and direct correlation function c(k). The kinetic equation is presented as the equation of motion of a two -particle correlation function, the phase space density-density anticommutator, and is derived by a formal closure of the quantum BBGKY hierarchy. An alternative derivation using a projection operator is also given. It is shown that the method used for approximating the kernel by a second order expansion preserves all the sum rules to the same order, and that the second-order kernel satisfies the appropriate positivity and symmetry conditions.
\r\n" }, { "name": "Sollenberger, Michael J.", "degree": "Masters", "year": "1975", "title": "Modified effective potentials for transition metal atoms", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-083257156", "creators": [ { "name": { "family": "Sollenberger", "given": "Michael J." }, "id": "Sollenberger-M-J", "display_name": "Sollenberger, Michael J." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HC7N-TD51", "abstract": "No abstract." }, { "name": "Timkovich, Russell", "degree": "PhD", "year": "1975", "title": "The Structure Determination of M. denitrificans Cytochrome C\u2085\u2085\u2080", "advisor": "Dickerson, Richard E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10202022-180817376", "creators": [ { "name": { "family": "Timkovich", "given": "Russell" }, "id": "Timkovich-Russell", "display_name": "Timkovich, Russell" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xmcg-d794", "abstract": "The protein sequence and the three-dimensional folding structure for cytochrome c550 from Micrococcus denitrificans are \r\nreported. The tertiary structure resulted from an x-ray crystallographic determination. Standard protein chemistry techniques were \r\napplied to sequence all the fragment peptides from a tryptic digest of c550. This information was combined with a 2.45 \u00c5 electron density map of the protein where identifying the tryptic fragments in the map led to the correct ordering of the peptides and the final \r\ncomplete sequence.
\r\n\r\nThe crystallization of c550 is described. Three chemical derivatives of the protein were found, PtCl42-; UO22+, and Pt(CN)42-, and these aided in the isomorphous replacement solution to the crystallographic phase problem. The interpretation and refinement of the derivatives to produce an accurate protein map is discussed.
\r\n\r\nThis bacterial c550 possesses a structure similar to the known cytochromes from eukaryotic sources and from a photosynthetic bacterium. The three are contrasted to conclude that for the cytochrome family, there exists a core structure of polypeptide folding. Current proposed mechanisms for the action of c-type cytochromes are rejected as being incompatible with the c550 structure. The view is advocated that the exposed heme edge in cytochrome may be the sole active site for the molecule.
" }, { "name": "Uradnisheck, Julius, III", "degree": "PhD", "year": "1975", "title": "Rates and Mechanisms of Chemical Reactions during Flow of Secondary Treated Sewage Effluent through Porous Beds", "advisor": "Corcoran, William Harrison; McKee, Jack E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03052024-183600060", "creators": [ { "name": { "family": "Uradnisheck", "given": "Julius, III" }, "id": "Uradnisheck-Julius-III", "display_name": "Uradnisheck, Julius, III" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "McKee", "given": "Jack E." }, "id": "McKee-J-E", "role": "advisor", "display_name": "McKee, Jack E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9w4g-z504", "abstract": "A general theory is formulated, based on extensive experimental\r\nand theoretical work, concerning the variation of chemical species\r\nin the top aerated horizon of the soil associated with the intermittent\r\npercolation of a secondary treated sewage effluent containing aqueous\r\nammonium ions.
\r\n\r\nExperimental data are presented to show that the variation of\r\naqueous cations in inorganic percolating solutions is a result of\r\nthe consecutive steps of rapid ion exchange of cations from the\r\nelectric double layer followed by slow ion exchange of chemisorbed\r\ncations diffusing through aluminosilicate mineral structures.
\r\n\r\nHigh concentrations of alkaline earth salts in interstitially\r\nheld solutions when the granitic sand is drained of solution are\r\nshown to be a result of desorption of cations from the sand by aqueous\r\nhydrogen ions generated by the conversion of adsorbed ammonium ions\r\nto nitrite ions by Nitrosomonas. Only a slight amount of mineral dissolution\r\nis shown to occur. Data are also presented to show that when\r\na solution is again percolated through the sand, hydrogen ion desorption\r\nis accompanied by only minimal nitrification.
\r\n\r\nA mathematical model is presented to predict the variation of\r\naqueous calcium, magnesium, sodium, ammonium, nitrate, nitrite, oxygen,\r\nacidity, and bicarbonate ions as well as the bacterial population\r\ndensities, adsorbed cations, and gaseous constituency of a soil column\r\nand solution as an intermittent percolation process is operated.
" }, { "name": "Wadt, Willard Rogers", "degree": "PhD", "year": "1975", "title": "I. The Electronic Structure of the Criegee Intermediate. II. The Electronic Structure of Pyrazine. III. Approximate Integral Methods and Correlated Wavefunctions", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182009-145338541", "creators": [ { "name": { "family": "Wadt", "given": "Willard Rogers" }, "id": "Wadt-Willard-Rogers", "display_name": "Wadt, Willard Rogers" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AKCY-N766", "abstract": "Part 1: The Electronic Structure of the Criegee Intermediate: Ramifications for the Mechanism of Ozonolysis. \r\nGeneralized valence bond (GVB) and configuration interaction (CI) calculations using a double zeta basis set have been carried out on methylene peroxide (H_2COOO), the reactive intermediate in the Criegee mechanism for ozonolysis of olefins. The ground state of methylene peroxide (using an open geometry) is shown to be a singlet biradical rather than a zwitterion. A strong analogy between methylene peroxide and its isoelectronic counterpart, ozone, is developed. The calculations also show that the ring state of methylene peroxide is 1 eV lower than the open form. Moreover, the ring state may reopen to give the dioxy-methane biradical. The ab initio results are combined with thermochemical data in order to analyze the stability of the Criegee intermediate as well as the possible modes of reaction in ozonolysis. With regard to ozonolysis in solution, the mechanism for epoxide formation is elucidated and the possible role of methylene peroxide rearrangement to dioxymethane is considered in interpreting the ^(13)O isotope experiments. With regard to ozonolysis in the gas phase, the production of many of the chemiluminescent species observed by Pitts and co-workers is explained. The production of reactive radicals such as OH and HO_2 in the course of ozonolysis, which may have important consequences for understanding the generation of photochemical air pollution, is also delineated.\r\n\r\nPart 2: The Electronic Structure of Pyrazine: A Valence Bond Model for Lone Pair Interaction.\r\nA valence bond (VB) model is developed to describe the interaction of the lone pair excitations in pyrazine. Extensive ab initio minimal basis set (MBS) configuration interaction (CI) calculations show that the description of the n cations and n\u03c0* states of pyrazine afforded by the VB model is more accurate than that afforded by the molecular orbital (MO) model proffered by Hoffmann. The VB picture of the n cations and n\u03c0* states involves the interaction (resonance) of two equivalent, localized excitations. The resultant splitting is large (1 to 2 eV) because of a light delocalization of the n orbitals induced by the Pauli principle. (The n orbitals are still 90% localized on the nitrogens.) The splitting of the n\u03c0* states is comparable to that of the n cations because the \u03c0* orbital is delocalized, even though the excitation process is localized on one nitrogen. The MBS CI calculations indicate that the lowest ionization potential of pyrazine corresponds to the ^2A_g (n) state. Calculations on the lowest Rydberg states indicate that they involve excitations out of an n orbital rather than a \u03c0 orbital, in opposition to earlier spectroscopic assignments. Finally, the calculations show that the forbidden 1 ^1B_2g (n\u03c0*) states is 1 eV higher than the allowed 1 ^1B_3u (n\u03c0*) state, so that the perturbations observed in the absorption spectrum must be ascribed to another source.\r\n\r\nPart 3: Comparison of INDO and Ab Initio Methods for the Correlated Wavefunctions of the Ground and Excited States of Ozone. \r\nThe validity of using integral approximation schemes in conjunction with correlated wavefunctions has been tested by performing generalized valence bond (GVB) and extensive configuration interaction (CI) calculations with INDO approximate integrals on the ground and excited states of ozone. High quality ab initio calculations have previously shown correlation effects to be extremely important for describing ozone. We find that for the CI wavefunctions the INDO approximation leads to vertical excitation energies- within about 30% [from 0.8 eV too low to 0. 6 eV too high with an RMS error of 0.5 eV], as compared with comparable ab initio calculations. We also found that the INDO GVB wavefunctions lead to bond angles in good agreement with experimental and ab initio calculations, but produced bond lengths that were too short. Most important was the discovery that INDO grossly favors closed geometries as opposed to open geometries, predicting the ground state of ozone to be an equilateral triangle state (even for correlated wavefunctions) with an energy 6 eV below the correct open state!\r\n\r\nPart 4: Comparison of INDO and Ab initio Methods for Correlated Wavefunctions of the Ground and Excited States of Methylene and Ethylene. \r\nThe usefulness of the INDO integral approximation for correlated wavefunctions was tested by carrying out GVB calculations on (1) the three lowest states of methylene as a function of bond angle and (2) the three lowest states of ethylene as a function of the dihedral twist angle. The methylene potential curves obtained with INDO were in good agreement (0.2 eV errors) with ab initio results, while the \r\nethylene curves were very poor (2 to 4 eV errors). Comparison with ab initio calculations revealed two major problems in the INDO method (1) the use of empirical values from atomic spectra for the one-center exchange integrals and (2) the use of only one resonance or \u03b2 parameter per atom.\r\n\r\nPart 5: Approximate Integral Methods and Correlated Wavefunctions\r\nAttempts to develop an approximate integral method that produces reliable results in conjunction with correlated wavefunctions are reported. Two basic lines of approach are pursued: (1) modification (or reparametrization) of INDO and (2) general investigation of truncated integral sets. The integral approximations were tested on the low-lying states of H_2, H_3, C_2, O_2, C_2H_4, O_3, and C_6H_6 using consistently correlated wavefunctions. No approximate method investigated gave satisfactory results on all the systems tested, with the O_3 and C_2 molecules presenting the greatest problems. However, good results, using approximate methods comparable in complexity with INDO, were obtained for describing the potential curves of the low-lying states of H_2, H_3, and C_2H_4. Finally, the calculations revealed two important guidelines for approximate integral methods. (1) Transformation to orthogonal atomic orbitals (especially the one-electron integrals) is necessary prior to any truncation of the integral set. Truncation of the standard nonorthogonal integral set leads to poor results, biasing the calculations toward short bond lengths and closed geometries, (2) Replacement of core electrons with local potentials rather than 2J-K potentials leads to better results, because the need to orthogonalize the valence orbitals to the core is obviated.\r\n" }, { "name": "Yeager, Danny Lee", "degree": "PhD", "year": "1975", "title": "Applications of the Equations of Motion Method", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282022-185309824", "creators": [ { "name": { "family": "Yeager", "given": "Danny Lee" }, "id": "Yeager-Danny-Lee", "display_name": "Yeager, Danny Lee" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xny7-ve74", "abstract": "Part I
\r\n\r\nIn Part I several applications of the equations of motion method for c1osed shell around states are discussed. The equations of motion method is used to study the excitation energies and intensities of formaldehyde, water, and CH+. A formalism is developed for studying intraexcited state transition densities, and applications are made to He and N2. This section is composed of three published manuscripts and two manuscripts submitted for publication.
\r\n\r\nIn H2CO the calculated excitation energies and oscillator strengths agree well with experiment and suggest explanations for some unusual features recently observed in the optical absorption and electron scattering spectrum in the vacuum ultraviolet.
\r\n\r\nTo explain the inelastic feature at 4.5 eV in the spectrum of water and to study its spectrum in some detail, several calculations on the excited states of water using the equations of motion method are made. We conclude that the calculated vertical excitation energy of 6.9 eV for the 3B1 state corresponds to the strong feature at 7.2 eV observed in low-energy electron scattering spectrum. The 4.5 eV inelastic process almost certainly does not correspond to a vertical excitation of water at the ground state geometry. The other excitation energies and oscillator strengths agree well with experiment.
\r\n\r\nThe equations of motion method is used to study the X'\u03a3+ -A'\u03c0 system in CH+. In a computationally simple scheme, these calculations, which were done in modest sized basis sets, provide transition moments and oscillator strengths that agree with the best CI calculations to date.
\r\n\r\nAn approximation for transition moments between excited states consistent with the approximations and assumptions normally used to obtain transition moments between the ground and excited states in the random phase approximation and its higher order approximations is derived . The result is applied to the calculation of the photoionization cross sections of the 23S and 2'S metastable states of helium by a numerical analytical continuation of the frequency dependent polarizability. The procedure completely avoids the need for continuum basis functions. The cross sections agree well with the results of other calculations. We also predict an accurate two-photon decay rate for the 2'S metastable state of helium. The entire procedure is immediately applicable to several problems involving photoionization of metastable states of molecules .
\r\n\r\nWe report the transition moments between the excited states of molecular nitrogen including their dependence on internuclear distance. These moments are calculated non-empirically using a many-body approach --the equations of motion method. These results suggest that it may be simpler to calculate these transition moments and their variation with internuclear distance rather than to attempt to extract this information from available experimental intensity data.
\r\n\r\nPart II
\r\n\r\nA straightforward scheme is developed for extending the equations of motion formalism to systems with simple open shell ground states. Equations for open shell random phase approximation (RPA) are given for the cases of one electron outside of a closed shell in a nondegenerate molecular orbital and for the triplet ground state with two electrons outside of a closed shell in degenerate molecular orbitals. Application to other open shells and extension of the open shell EOM to higher orders are both straightforward. Results for the open shell RPA for lithium atom and oxygen molecule are given.
\r\n\r\nPart III
\r\n\r\nA simple method for directly calculating ionization potentials and electron affinities is discussed. Formulas are given through third order in interaction matrix elements and described in detail . Results are presented for the ionization potentials of He, N2, and OH- using several different approximations.
" }, { "name": "Zana, Erdinc", "degree": "PhD", "year": "1975", "title": "The Motion and Associated Mass Transfer Characteristics of Gas Bubbles in Viscoelastic Liquids", "advisor": "Leal, L. Gary", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172023-213904882", "creators": [ { "name": { "family": "Zana", "given": "Erdinc" }, "id": "Zana-Erdinc", "display_name": "Zana, Erdinc" } ], "advisors": [ { "name": { "family": "Leal", "given": "L. Gary" }, "id": "Leal-L-G", "role": "advisor", "display_name": "Leal, L. Gary" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/exg0-az53", "abstract": "The motion and associated mass transfer characteristics of gas bubbles in viscoelastic liquids is investigated in the limits of Pe << 1 and Pe >> 1. Full numerical and approximate analytical solutions are obtained for Pe << 1 case in order to investigate the roles of shear viscosity, relaxation and retardation times, surface tension and the Henry's law constant on the dissolution rate. It is shown that the collapse characteristics and the behavior of internal pressure in the viscoelastic liquid differ considerably from the case of a purely Newtonian liquid, particularly during the early and late stages of the\r\ndissolution process.
\r\n\r\nThe Pe >> 1 case is studied experimentally. The mass transfer rates from gas bubbles rising in viscoelastic liquids are measured and the data are shown to correlate very well with Weissenberg number. It is also shown that mass transfer rate from a gas bubble is greatly enhanced by viscoelasticity over its value for a Newtonian liquid with the same shear viscosity. The terminal rise velocities of bubbles in viscoelastic liquids are also measured. The well known discontinuity in the bubble rise velocity is fully investigated. It is shown that the magnitude of the velocity discontinuity may be accounted for by considering shear dependent viscosity and viscoelasticity. A tentative explanation for the abruptness of the velocity transition is presented.
\r\n\r\nFinally, the streamline flow visualization experiments for viscoelastic liquids past a solid sphere are presented. The results show that the streamlines are shifted in the upstream direction and the amount of shift increases with viscoelasticity.
" }, { "name": "Bell, Karl Ammon", "degree": "PhD", "year": "1974", "title": "Aerosol Deposition in Models of a Human Lung Bifurcation", "advisor": "Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09282005-162018", "creators": [ { "name": { "family": "Bell", "given": "Karl Ammon" }, "id": "Bell-Karl-Ammon", "display_name": "Bell, Karl Ammon" } ], "advisors": [ { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9165-2r63", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe bifurcations of the human upper respiratory tract are regions in which enhanced local deposition of airborne particles occurs. Existing mathematical models do not characterize these local \"hot spots\", which may be important in the development of certain respiratory diseases, the setting of air quality standards according to particle size, and the diagnosis and therapy of respiratory diseases by aerosols.\r\n\r\nIdealized two-dimensional (\"2-D\") and three-dimensional (\"3-D\") models of the first bifurcation of the human lung with parent and daughter branches were used in theoretical and experimental studies designed to characterize local deposition patterns (Bell and Friedlander, 1973). Mono-disperse latex aerosols, having diameters from 0.088 to 7.6[...], were passed through the experimental models at unsteady flow rates simulating conditions of rest and moderate exercise in humans. Deposited particles were counted by optical and electron microscopy, and the aerosol concentration was measured either by gravimetry or by light scattering photometry. Deposition patterns of the \"3-D\" model data are depicted by computer plotted maps having contours of constant transfer coefficients. Steady potential flow around a wedge was employed to model local deposition by impaction, sedimentation and interception. Steady and quasi-steady laminar boundary layer flows along a wedge were used to model deposition by convective diffusion.\r\n\r\nIn both models data and theory from 0.088 to 7.6[...] for transfer coefficients were similar in trend to curves of deposition efficiency for the entire human lung or the collection efficiency for fibrous filters. Although similar average transfer coefficients are observed in the diffusion and impaction sub-ranges, the deposition patterns are strikingly different. Data < 0.5[...] agreed well with theories of convective diffusion and data > 2[...] agreed fairly well with theories of impaction, sedimentation and interception. The 0.5 - 2.0[...] data fall between the two theories on account of unsteady boundary layer effects not included in the theories. Effects of secondary flows on particle deposition must be taken into account in estimating local nonuniformities and \"hot spots\", however, they can be neglected when calculating the deposition efficiency for each branch. \"3-D\" model theories more accurately approximate the experimental efficiencies than the models of either Landahl or the ICRP Task Group on Lung Dynamics, and all \"3-D\" model theories and deposition patterns can be used to model deposition in the tracheobronchial trees of humans and animals.\r\n \r\nMeasurements indicate that the 150,000 epithelial cells lining the lung wall near the carina receive 25.4 times more 5.7[...] particles than the average over the branch. The corresponding figure falls to 3.8 as particle size is reduced to the diffusion range. The relative intensity of \"hot spots\" calculated for cigarette smoke in the first three generations of the human lung roughly agreed with the frequency that bronchial carcinomas originate in each of these generations. In addition to local deposition rates, the relative rates of dissolution of irritant aerosols are crucial for modeling acute dose-response.\r\n\r\nTo assure a fairly uniform coating of therapeutic or diagnostic aerosol over > 75% of the surface of human airways, unit density particles with diameters < 1[...] can be inhaled at any flow rate. For maximum nonuniformity, least surface coverage, and maximum collection at bifurcations, unit density particles with diameters >= 5[...] should be inhaled rapidly.\r\n\r\nThe 1.1[...] deposition patterns and efficiencies were significantly different for unsteady and steady inhalations at the same time-averaged flow rates, and similar conclusions should be valid for all respirable particles. Therefore, steady flow can not be used in lung models to accurately estimate deposition in the real lung.\r\n\r\nResults from the diffusion subrange can be used to estimate local transfer rates of pollutant gases in lung airways, gases and fat molecules at bifurcations in blood vessels, and heat and mass in other flow systems." }, { "name": "Benzer, Theodore I.", "degree": "PhD", "year": "1974", "title": "Investigations on the Tetrodotoxin Binding Component from Electrically Excitable Tissue", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09282005-082018", "creators": [ { "name": { "family": "Benzer", "given": "Theodore I." }, "id": "Benzer-Theodore-I", "display_name": "Benzer, Theodore I." } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3B26-2G75", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nTetrodotoxin from the Japanese puffer fish was labelled with tritium and purified from the crude mixture obtained. The interaction between the purified [[...]]-tetrodotoxin and membrane suspensions from the olfactory nerve of the long-nosed garfish was investigated using equilibrium dialysis. Tetrodotoxin was shown to bind to membrane suspensions with a dissociation constant [...]. The nerve preparation binds 43 picomoles of [[...]]-tetrodotoxin per gm of wet tissue at saturating toxin concentrations. Using various hydrolytic enzymes, the binding component was shown to be a protein embedded in a phospholipid environment. The binding is inhibited below pH 4.0 and is not stable towards heat. Tetrodotoxin binding is not inhibited by the local anaesthetic procaine.\r\n\r\nThe tetrodotoxin binding component from garfish olfactory nerve membranes was solubilized using the nonionic detergent Triton X-100. Tetrodotoxin binds to the solubilized component with a dissociation constant [...] and under saturating conditions [...] moles of tetrodotoxin are bound per milligram of solubilized protein. Upon solubilization the toxin binding component becomes much less stable towards heat, chemical modification and enzymatic degradation. Sucrose gradient velocity sedimentation yields an S value of 9.2 for the extracted binding component and from gel filtration data the binding component appears to be slightly larger than [...].\r\n\r\nTetrodotoxin binding to membrane fragments of the electric organ of Electrophorus electricus was measured and found to be [...] moles of the toxin per gram of wet tissue at saturating conditions with a dissociation constant of [...]. Calcium ions at millimolar concentrations were found to inhibit toxin binding to the membrane fragments. The tetrodotoxin binding component was solubilized with the nonionic detergent Lubrol-PX and a convenient assay was developed for measuring the toxin binding to detergent extracts using gel filtration in the centrifuge to separate bound toxin from free toxin. This assay was used to investigate the problem of the stability of the tetrodotoxin binding component in the detergent extract.\r\n\r\nTwo derivatives of tetrodotoxin were covalently linked to Sepharose-2B in an attempt to synthesize an affinity resin for purification of the tetrodotoxin binding component. It was found that the columns did not display properties which would make them useful since they effected only a minor purification of the binding component with low yields of activity." }, { "name": "Bobrowicz, Frank Wilhelm", "degree": "PhD", "year": "1974", "title": "Investigations of Spin-Eigenfunction Correlated Wavefunctions", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechETD:etd-09272005-143127", "creators": [ { "name": { "family": "Bobrowicz", "given": "Frank Wilhelm" }, "id": "Bobrowicz-Frank-Wilhelm", "display_name": "Bobrowicz, Frank Wilhelm" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2XSV-1F12", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I\r\n\r\nGeneralized Valence-Bond descriptions for the low-lying [...], [...], and [...] states of CH are presented. These wavefunctions are found to behave properly at all internuclear distances, giving a clear and consistent physical picture of formation of these molecules from their constituent atoms.\r\n\r\nPart II\r\n\r\nA procedure for calculating Spin-Eigenfunction Configuration Interaction matrices utilizing the U matrices which form the irreducible representations of [...] is presented. In addition, an improved determinant method is summarized. By combining both of these U-matrix and Determinant methods, it has been possible to formulate a practical and yet highly efficient procedure for generating such CI matrices.\r\n\r\nPart III\r\n\r\nEven for relatively simple Hartree-Fock (HF) or Perfect-Pairing Generalized Valence-Bond (PPGVB) many-electron wavefunctions, self-consistent calculations can be prohibitively expensive for, many chemically interesting systems. Considerable effort has been devoted toward developing highly efficient computational techniques for solving for such wavefunctions. The results of this research, as embodied in the GVBTWO program, have made such calculations on relatively large systems a practical reality.\r\n\r\nPart IV\r\n\r\nThe Generalized Valence-Bond (GVB) wavefunction has had considerable success in describing chemical reactions and molecular structure. Unfortunately, this method can only be applied to systems involving a few electrons. The Perfect-Pairing approximation to GVB (PPGVB) greatly simplifies the situation and is found to adequately describe the low-lying states of many molecules. However, in describing chemical reactions the restrictions of PPGVB are quite serious. The Strongly Orthogonal approximation (SOGVB) described here overcomes this problem by allowing the orbitals to recouple while still retaining the simplifying orbital restrictions of PPGVB. This intermediate method correctly describes many chemical reactions and is practical for treating relatively large systems." }, { "name": "Chen, Wen Hsiung", "degree": "PhD", "year": "1974", "title": "Estimation of Parameters in Partial Differential Equations: with Applications to Petroleum Reservoir Description", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252005-143807", "creators": [ { "name": { "family": "Chen", "given": "Wen Hsiung" }, "id": "Chen-Wen-Hsiung", "display_name": "Chen, Wen Hsiung" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6XF8-F790", "abstract": "The determination of parameters in dynamical systems, on the basis of noisy experimental data, is called the parameter estimation problem or inverse problem. In this dissertation, several methods for parameter estimation are derived for systems governed by partial differential equations, so-called distributed parameter systems.\r\n\r\nThe first class of problems, investigated in Chapter II, is that in which the parameters to be estimated are constants. This class of problems is important for it includes most cases of practical interest. Techniques based on gradient optimization, quasilinearization, and collocation methods are developed. A method of determining confidence intervals for parameter estimates is presented, a method which enables one to design experiments (and measurements) that lead to the best estimates of the parameters. The effectiveness of these methods for estimating constant parameters is illustrated through the estimation of the diffusivity in the heat equation, the estimation of the activation energy for a single reaction from dynamic plug flow reactor data, and the estimation of the permeabilities in a two-region reservoir model. The numerical results also show the advantage of using data taken at optimally chosen measurement locations to estimate the parameters.\r\n\r\nMany physical systems contain spatially varying parameters, for example, the permeability distribution in a petroleum reservoir model. In Chapter III, two approaches are presented for the estimation of spatially varying parameters. The first is a method of steepest descent based on consideration of the unknown parameter vector as a control vector. The second is based on treating the parameter as an additional state vector and employing least square filtering. The key feature of the former method is that the parameters are considered as continuous functions of position rather than as constant in a certain number of spatial regions. This technique may offer significant savings in computing time over conventional gradient optimization methods, such as steepest descent and Gauss-Newton in which the parameters are considered as uniform in a certain number of zones. Two examples are presented to illustrate the use of the method and its comparison to other algorithms.\r\n\r\nIn certain cases, the location of the boundary of a system may not be known, such as the boundary of a petroleum reservoir. In the case of oil reservoirs it is very important to be able to estimate the area and shape (or the location of the boundary) of a reservoir so that the production policies can be optimized. A method based on the variation of a functional defined on a variable region is developed in Chapter IV. The computational applications of this method are illustrated in determining the locations of the boundaries of a one-dimensional and a two-dimensional petroleum reservoir." }, { "name": "Clarke, Thomas Carl", "degree": "PhD", "year": "1974", "title": "I. Investigations on the Mechanism of Thermal Decomposition of l-Pyrazolines. II. The Stereochemistry of Solvolytic Displacement and Intramolecular Nucleophilic Substitution by a Double Bond at a Vinyl Center", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142005-153023", "creators": [ { "name": { "family": "Clarke", "given": "Thomas Carl" }, "id": "Clarke-Thomas-Carl", "display_name": "Clarke, Thomas Carl" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CY15-8E04", "abstract": "I. Two mechanisms have been proposed to account for the net single inversion of stereochemistry observed in the pyrolysis of 3,5-dialkyl-1-pyrazolines. The first, involving initial cleavage of both C-N bonds and formation of a [pi]-cyclopropane intermediate, predicts completely racemic singly inverted product on pyrolysis of an optically active pyrazoline. The sequential C-N bond cleavage proposed in the second mechanism predicts that, to the extent that the rates of initial cleavage of the two ON bonds are different, some optical activity should be observed in the singly inverted product. In order to resolve this problem, the pyrolysis of (+)-(3R,5R)-trans-3-ethyl-5-methyl-1-pyrazoline was undertaken. Flow pyrolysis of this pyrazoline at 292\u00b0 and atmospheric pressure led to 71% cis-1-ethyl-2-methylcyclopropane, 27% trans-1-ethyl-2-methylcyclopropane and minor amounts of olefin product. The cis cyclopropane was formed with 0.8% retention of optical purity while the trans product showed 23% retention of optically purity. Correlation of these results with the pyrolyses of this pyrazoline specifically deuterated at C3 and C5 will allow a distinction between the two mechanistic possibilities. This work is currently in progress.\r\n\r\nII. In order to determine the stereochemistry of solvolytic displacement and intramolecular nucleophilic substitution by a remote double bond at a vinyl center, the synthesis and solvolysis in trifluoroethanol of (Z)- and (E)-3-methyl-2,6-heptadien-2-yl trifluoro-methanesulfonate were undertaken. In addition to 3-methyl-1,2,6-heptatriene and the products of solvolytic displacement, four cyclized trifluoroethyl ether products were formed. These four products were also generated in the trifluoroethanolysis of 1,2-dimethyl-1-cyclohexen-4-yl tosylate. Net inversion of stereochemistry was observed in both the solvolytic displacement and cyclization processes in the vinyl triflates. Solvolysis of (Z)- and (E)-3-methyl-2-hepten-2-yl trifluoro-methanesulfonate also resulted in net single inversion in the vinyl trifluoroethyl ether products. These results are explained in terms of competitive attack on the initially formed ion pairs and on free vinyl cation intermediates." }, { "name": "Cowman, Charles Dane", "degree": "PhD", "year": "1974", "title": "An Investigation of the Electronic Structures of Transition Metal Complexes By Single Crystal Polarized Spectroscopy", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252005-091128", "creators": [ { "name": { "family": "Cowman", "given": "Charles Dane" }, "id": "Cowman-Charles-Dane", "display_name": "Cowman, Charles Dane" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3FCT-A075", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA technique for growing thin film single crystals using tetra-n-butylammonium as a cation is detailed. The polarizations of both ligand field and charge transfer transitions were measured at 5[degrees]K for a number of transition metal monomeric and dimeric species. The polarized spectra for the [...] square planar complexes [...] and [...] confirm the [...] nature of the charge transfer bands. Spin orbit coupling was found to be important. The d orbital ordering [...] was found. The absorption spectra of the planar chlorobridged species [...] and [...] were found to exhibit anomalously large intensities for the spin-forbidden bands in the in-plane direction perpendicular to the metal-metal axis. The observed splitting of the lowest spin allowed d-d transition confirms the existence of metal-metal interaction. The ligand field absorption spectra of the square pyramidal [...] and [...] species are dominated by the equatorial allowed [...], dyz transition. Progressions of the totally symmetric metal-nitrogen stretch are observed on the transition. The observation of an axial polarized double progression of the metal-halogen symmetric stretch requires the inclusion of spin orbit coupling. The d orbital ordering [...] is identical to that in vanadyl ion. The [...] transition in the quadruply bonded [...] and [...]. species has been positively identified by the MCD and polarization data in the [...] complexes, compared to the polarization of this band in the lower symmetry species [...]. Progressions of the totally symmetric metal-metal stretch characterize the band envelope. The related [...] and [...] species also contain an analogous temperature independent band. The applicability of the molecular orbital scheme proposed by Cotton was confirmed. The polarized spectra of the [...] anion suggest a [...] structure related to the [...] complex. The polarization of the absorption bands of [...] were distinctly different; this species is known to have a [...] confacial bioctahedral structure." }, { "name": "Eagar, Robert Gouldman", "degree": "PhD", "year": "1974", "title": "Mechanism of Action of Coenzyme B\u2081\u2082 : I. Mechanism of Action of Coenzyme B\u2081\u2082. Hydrogen Transfer in the Isomerization of \u03b2-Methylaspartate to Glutamate. II. Kinetic Studies of 3-Fluoro-1,2-Propanediol, a New Substance for Dioldehydrase. III. Reaction of 5'-Deoxyinosylcobalamen with Propanediol Dehydrase. IV. Adenosine Deaminase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10252005-111340", "creators": [ { "name": { "family": "Eagar", "given": "Robert Gouldman" }, "id": "Eagar-Robert-Gouldman", "display_name": "Eagar, Robert Gouldman" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WKKX-RB26", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I. Use of a mixture of non- and tetradeutero-beta-methylaspartate with coenzyme B12 dependent beta-methylaspartate-glutamate mutase has shown that the hydrogen that migrates becomes one of three equivalent hydrogens during the reaction. Kinetic isotope effects suggest that cleavage of the bond in the substrate from carbon to that hydrogen which migrates is an important component of the rate determining step. The evidence also supports the existence of an intermediate which can partition with similar probabilities to beta-methylaspartate or to glutamate. Some possible mechanistic implications of these findings are discussed.\r\n\r\nPART II. The mechanism and the kinetics of the action of diol dehydrase on 3-fluoro-1,2-propanediol, a new substrate for diol dehydrase, were examined. The results of this study lead to a reexamination of the kinetic behavior of the natural substrate, 1,2-propanediol, with diol dehydrase. The [...] values of (S)-, (RS)-, and (R)-3-fluoro-1,2-propanediol were found to be 340[...], 128[...], and 104[...] respectively, compared to 368[...], 250[...], and 191[...], for the corresponding isomers of 1,2-propanediol. A modification of the existing analytical procedure for the determination of aldehyde was necessary in order to measure the values of Km for these substrates. Km values for (S)-, (RS)-, and (R)-3-fluoro-1,2-propanediol were found to be [...], [...], and [...] respectively. For (R)-, (RS)-, and (S)-1,2-propanediol, Km values were measured at [...], [...], and [...] respectively.\r\n\r\nThese results show that the (R)- and (S)- isomers of both substrates exhibit simple competitive behavior for the active site in the racemic mixture, and that both the (R)- and (S)- isomers of the substrate pass through a similar transition state in the enzyme catalyzed conversion to aldehyde.\r\n\r\nPART III. The reactivity of 5'-deoxyinosylcobalamin in the propanediol dehydrase reaction was examined. This coenzyme B12 analogue showed no coenzyme activity in the diol dehydrase reaction. 5'-Deoxyinosylcobalamin was found to inhibit the activity of coenzyme B12 although it bound less efficiently than the natural coenzyme by a factor of 100. Previously reported experiments regarding the release of 5'-deoxyinosine by this system were shown to be inconclusive.\r\n\r\nPART IV. The kinetic behavior of 5'-deoxyadenosine in the adenosine deaminase reaction has been examined. The low catalytic rate and inefficient binding observed for this substrate suggest that the 5'-hydroxyl is very important to both catalysis and binding of ribosyladenines. In spite of the low catalytic rate and the poor binding, adenosine deaminase was used to effectively synthesize 5'-deoxyinosine from 5'-deoxyadenosine." }, { "name": "Ellern, James Bernard", "degree": "PhD", "year": "1974", "title": "I. Synthetic Studies on Tertiary Vinylogous Amides and Related Compounds. II. Cobalt(II) Chloride Complexes of Tertiary Vinylogous Amides and Related Ligands", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10132005-080720", "creators": [ { "name": { "family": "Ellern", "given": "James Bernard" }, "id": "Ellern-James-Bernard", "display_name": "Ellern, James Bernard" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0R6K-3R44", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nTertiary vinylogous amides, both open-chain and cyclic, were prepared by several routes with a view toward their use as ligands for metal ions. It is shown that the thermodynamically preferred isomer (functionality trans) is the exclusive product in the open chain case. A new convenient synthesis of [beta]-aminobutenones is described.\r\n\r\nIn contrast to previous studies, it was found that activated vinylidene chlorides (AVDC's) with [alpha]-hydrogen (Cl2C=CH-L, L = carbonyl function or cyano), react with certain secondary amines to give acetylenes, [...], either as intermediates or final products except with L = CHO. The mechanism of this reaction is discussed. A simple synthesis of 3,3-dichloropropenoic acid and its conversion to several functional derivatives are described. A case is presented for rotational isomerism in four [beta,beta]-dichlorovinyl carbonyl compounds.\r\n\r\nNuclear magnetic resonance and infrared spectral correlations were made for the compounds prepared. In particular, it is shown that nmr spectroscopy allows ready distinction of piperidino vinylogous ureas from the isomeric acyl ketenaminals of this amine.\r\n\r\nSynthesis and partial characterization of complexes of some of the above polarized ethylenes and acetylenes with cobalt(II) chloride are reported. The polarized ethylenes behave somewhat like tertiary amides as ligands; in two cases, different forms of complex with same ligand were found. The \"push-pull\" acetylenes form 1:1 complexes in which the triple bond absorption(s) of the ligand is absent. The possible implications of this result are discussed." }, { "name": "Feigenson, Gerald W.", "degree": "PhD", "year": "1974", "title": "Nuclear Magnetic Relaxation Studies of Lecithin Bilayers", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142005-110429", "creators": [ { "name": { "family": "Feigenson", "given": "Gerald W." }, "id": "Feigenson-Gerald-W", "display_name": "Feigenson, Gerald W." } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5YTJ-1M54", "abstract": "In an effort to elucidate the state of molecular motion in aqueous lecithin systems, the nuclear magnetic relaxation properties of unsonicated lecithin crystal and liquid crystal phases have been investigated. The presence of a narrow component in the nmr spectrum of aqueous lamellar lecithin crystals is taken to indicate a significant degree of motion of the lecithin methyl groups in this solid phase. Also in the crystal state of lecithin, nmr linewidth measurements, together with thermal analysis experiments appear to indicate that a structural rearrangement of either the lecithin or the bound water takes place, which is not accompanied by an increase in molecular mobility. Delayed Fourier Transform and wide-line nmr experiments show that at the crystal -> liquid crystal (bilayer) phase transition temperature, the lecithin choline methyl, terminal methyl, and hydrocarbon chain methylene protons are all simultaneously mobilized. A previously noted field dependence of the proton magnetic resonance linewidth of aqueous lecithin bilayers is shown to be accounted for by the chemical shift differences among the various kinds of protons. Spin lattice relaxation rates have been measured for these protons as a function of temperature and frequency, and these data have been interpreted in terms of models for the segmental motion of the choline head groups and the hydrocarbon chains. The influence of spin diffusion on the relaxation behavior of the various protons is also discussed." }, { "name": "Frank, Steven Neil", "degree": "PhD", "year": "1974", "title": "Investigations of the Binding of Some Azido-, Isocyano-, and Isothiocyanatochromium(III) and Azidocobalt(III) Complexes with Heavy Metal Ions and Mercury Electrodes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10132005-083002", "creators": [ { "name": { "family": "Frank", "given": "Steven Neil" }, "id": "Frank-Steven-Neil", "display_name": "Frank, Steven Neil" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/H0WX-5123", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. -- The reactions of [...], [...], and [...] with [...] and [...] to form binuclear and trinuclear adducts have been investigated. Equilibrium quotients evaluated include: [...]; [...]; [...]; [...]. Electrochemical reduction of the heavy metal adducts was utilized to generate a variety of the unstable isocyanochromium(III) isomers at mercury electrodes. No adsorptive binding of any of these complexes to the surface of the mercury electrodes could be detected. Possible reasons for the contrasting behavior displayed by the (nonadsorbing) isocyanochromium(III) and (strongly adsorbing) isothiocyanato chromium (III) complexes are examined.\r\n\r\nPart II. -- The adsorption at mercury electrodes of a number of azido- and thiocyanatochromium(III) and azidocobalt(III) complexes has been measured with chronocoulometry. Apparent attractive interactions between adsorbed molecules were observed for the thiocyanato-complexes at some coverages. Several possible explanations are advanced to account for this behavior. A correlation between the amounts of adsorption and the ligand field stabilization energies (LFSE) of the complexes was observed. This correlation is discussed in terms of an increase in the LFSE when the complexes bind with the electrode." }, { "name": "Geoffroy, Gregory Lynn", "degree": "PhD", "year": "1974", "title": "An Investigation of the Photochemical and Excited State Properties of Selected Second and Third Row Transition Metal Complexes", "advisor": "Hammond, George Simms; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10132005-154007", "creators": [ { "name": { "family": "Geoffroy", "given": "Gregory Lynn" }, "id": "Geoffroy-Gregory-Lynn", "display_name": "Geoffroy, Gregory Lynn" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5KPA-2F87", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe photochemical properties of several different types of 2nd and 3rd row transition metal complexes are discussed. Complexes of the type [...] have been prepared and characterized by electronic and infrared absorption spectral measurements. The complexes are readily prepared by thermal anation reactions of [[...]], the aquo complexes being formed by uv irradiation of acidic solutions of [...]. The lowest energy electronic absorption band in the [...] complexes is assigned to the ligand field transition [...], whereas in [...] both [...] and [...] absorptions are observed. The position of the [...] transition establishes the order of decreasing ligand field strength of X as [...] for both Rh(III) and Ir(III) complexes. Halide-to-metal charge transfer bands are observed for [...] complexes with X = [...] and [...].\r\n\r\nUltraviolet irradiation of H2 and O2 adducts of [...], [...], [...], and [...] has been found to induce reductive-elimination of molecular hydrogen and oxygen and regeneration of the square-planar complexes. The reactions occur in argon purged solutions and in frozen EPA solutions of the adducts at 77[degrees]K.\r\n\r\nAbsorption and emission spectra for the square planar complexes [...] and [...] have been measured in the solid state and in frozen EPA [ethyl ether-isopentane-ethyl alcohol (5:5:2)] solution at 77[degrees]K. Of the four complexes, only [...] fails to luminesce in the solid state at room temperature. At 77[degrees]K in EPA the emission maxima fall in the range 16.8-18.4[...], and the emission lifetimes are between 8.2 and 20.8 [...]; [...] exhibits an unusually sharp, strongly overlapping emission/absorption system, with an emission quantum yield of 0.93 \u00b1 0.07 It is suggested that in the Ir(I) cases emission occurs from a square planar [...] charge transfer state of [...] symmetry. The fact that the emission maxima of the two Rh(I) complexes are both red-shifted by about 4000 [...] from the lowest absorption peak is discussed in terms of an admixture of ligand field character in the primarily [...] emitting state, which could give rise to a distortion of the RhP4 core towards tetrahedral geometry. The absorption and emission spectra of several other Rh(I) complexes are also briefly discussed.\r\n\r\nIrradiation of [...] in CH3CN results in cleavage of the Re2 quadruple bond and formation of monomeric Re(III) products. The primary photoproduct is [...], and this species can be further photolyzed in CH3CN to give [...]. The quantum yield of disappearance of [...] upon irradiation at 313 nm was found to be 0.017 \u00b1 0.005. [...] is also the primary photoproduct under 254 nm irradiation. Irradiation of [...] in CH3CN with a He-Ne laser (632.8 nm) does not lead to reaction, indicating that the excited state derived from the [...] transition is not photoactive. Cleavage of the Re2 unit is observed, however, when solutions are irradiated at 366 nm.\r\n" }, { "name": "Grunthaner, Frank John", "degree": "PhD", "year": "1974", "title": "Electronic Structure, Surface Reactivity and Site Analysis of Transition Metal Complexes and Metalloproteins by X-Ray Photoelectron Spectroscopy", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10282005-125333", "creators": [ { "name": { "family": "Grunthaner", "given": "Frank John" }, "id": "Grunthaner-Frank-John", "display_name": "Grunthaner, Frank John" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/28F0-T511", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nHigh resolution x-ray photoelectron core level spectra for a variety of transition metal complexes and metalloproteins are presented and related to questions of surface reactivity, electronic structure and metal ion valency. Core level spectra of VOSO4, VB2, V2O3, V2O5, V, VN, Na3VO4, B2O3, B, H3BO3, [...], Au, Laccase, Stellacyanin, Plastocyanin, Hemocyanin, Spinach Ferredoxin, High Potential Iron Protein, [...], [...], [...], [...], [...], [...], [...], [...], [...], [...] are reported.\r\n\r\nElectron binding energies correlated by internal referencing are tabulated for the species studied.\r\n\r\nCharging effects in insulating chemical species are quantified and used to examine the electronic and chemical properties of the compounds studied. It is demonstrated that charge neutralization in electron spectroscopy is primarily due to capture of secondary electrons in the sample chamber with average kinetic energies below 6 eV.\r\n\r\nData handling methods for noise removal based on Fourier methods are presented. Treatment of the observed photoelectron line shape is given and spectral deconvolution is employed in data analysis.\r\n\r\nPassivation reactions on vanadium diboride in carboxylic acid attack are attributed to the formation of surface vanadium oxides. Quantitative aspects of the electron spectra are developed, together with observed charging phenomenon, to show the unperturbed observation of adsorbed species on catalytic vanadium oxides.\r\n\r\nThe valency of copper in Laccase is studied by means of new copper sulfo-complexes and the well-defined proteins Stellacyanin and Plastocyanin. Type 1 and Type 2 copper is observed and Type 3 copper is described by a [...] model. Oxyhemocyanin is also studied and assigned in terms of a cupric model.\r\n\r\nThe [...] cluster complex is examined and the mercaptyl and sulfido sulfurs are assigned. Only one iron state is observed, [...], supporting the delocalized model of this species. It is suggested that the oxidized and reduced cluster species can be stabilized in the electron spectrometer. By comparison of the photoelectron spectra, the cluster complex is shown to be a reasonable model for 2-Fe and 4-Fe Ferredoxins and a discussion of the spectral differences is given.\r\n\r\nThe experimental parameters necessary for the successful study of metalloproteins by photoelectron spectroscopy are developed in terms of elemental sensitivity, decomposition profiling, photoreduction, energy reference standards, sample preparation and thermal effects." }, { "name": "Gupta, Amitava", "degree": "PhD", "year": "1974", "title": "I. Radical Recombination in Solvent Cages. II. Quenching of Excited States of Aromatic Molecules Through Exciplex Formation. III. Magnetic Field Effect on Triplet-Triplet Energy Transfer Processes", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10132005-092659", "creators": [ { "name": { "family": "Gupta", "given": "Amitava" }, "id": "Gupta-Amitava", "display_name": "Gupta, Amitava" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7BCX-J566", "abstract": "The first section describes experiments on radical recombination rates. From the temperature and solvent dependence of quantities such as escape efficiency from primary solvent cages we deduced that the activation energy of recombination of radical pairs inside the primary cage is zero in all solvents. Some previous data on recombination rates were reinterpreted accordingly, and then we focused our attention on intersystem crossing in radical pairs. Cage efficiencies were determined in a magnetic field relative to zero field values and the significance of these results discussed.\r\n\r\nThe second section describes experiments designed to explore the mechanism of bimolecular quenching processes. Naphthalene fluorescence was quenched by trans-[beta]-ethyl styrene and it was found that this quenching process induces intersystem crossing in naphthalene. The same quencher was used to quench naphthalene triplets and it was observed that a substantial amount of energy wastage (quenching without electronic energy transfer to the quencher) occurs in solvents other than benzene.\r\n\r\nEnergy wastage was also found in quenching of acetophenone triplets by sterically hindered olefins. We obtained kinetic evidence that olefins quench acetophenone triplets through the formation of triplet exciplexes and we estimated its lifetime for the olefin cis-2,2-dimethyl-3-hexene.\r\n\r\nThe third section relates observations that bimolecular ratios of triplet-triplet energy transfer are affected by application of a magnetic field. Efforts were made to further study this field effect using deuterated quenchers and quenchee. A hypothesis has been put forward to explain our data. Other hypotheses have been critically evaluated." }, { "name": "Holwerda, Robert Alan", "degree": "PhD", "year": "1974", "title": "Kinetic Studies of the Reduction of Rhus vernicifera Laccase", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07152021-180805930", "creators": [ { "name": { "family": "Holwerda", "given": "Robert Alan" }, "id": "Holwerda-Robert-Alan", "display_name": "Holwerda, Robert Alan" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k0xx-5286", "abstract": "Anaerobic stopped flow kinetic studies of the reactions of hydroquinone, Fe(CN)64-, and Fe(EDTA)2- with Rhus vernicifera laccase have been performed with the objective of elucidating the mechanisms by which the three enzymatic copper sites are reduced.
\r\n\r\nSecond order rate constants characterizing the hydroquinone reduction of laccase Type 1 and Type 3 copper sites at 25.6\u00b0, pH 7.0, \u03bc = 0.1 (phosphate) are 325 and 457 M-1 sec-1, respectively. All of the experimental evidence points to the involvement of a common intermediate in the reduction mechanisms of these two functional units, and pH dependence results indicate that the phenolate monoanion HQ- is the active reductant interacting with the metalloprotein in the shared slow step. A requirement for penetration of HQ- into the first coordination sphere of Type 2 Cu(II) is strongly suggested by pH 6.0 fluoride inhibition results, and activation parameters (Type 1: \u0394H\u2021 = 15.0 kcal/mole, \u0394S\u2021 = +13 cal/mol-deg; Type 3: \u0394H\u2021 = 13.6 kcal/mole, \u0394S\u2021 = +15 cal/mol-deg; pH 7.0, \u03bc = 0.1) are compatible with rate-limiting reduction of an essentially axial copper(II) species.
\r\n\r\nDecolorization of the intense peak with maximum at 405 nm characteristic of the Type 2 Cu(II)-N3- laccase derivative is first order in [N3-] , zeroth order in [hydroquinone], suggesting that azide bridging is involved in an intramolecular Type 1 Cu(I) to Type 2 Cu(II) electron transfer step. Attack at the Type 2 copper is not a prerequisite to reduction of the Type 1 site in the laccase-azide complex, but the reactivity of the \"blue\" copper is considerably altered from that in the native enzyme.
\r\n\r\nFerrocyanide reduces laccase by a mechanism much different than that preferred by hydroquinone. The reduction rates of the Type 1 and Type 3 sites are identical (k = 42 M-1 sec-1, 25\u00b0, pH 7.0, \u03bc = 0.1; \u0394H\u2021 = 18.4 kcal/mole, \u0394S\u2021 = +10 cal/mol-deg), and only three electron equivalents are transferred to the metalloprotein anaerobically. The Type 2 copper atom is not reduced by Fe(CN)64-. Ionic strength and pH dependence studies suggest that electrostatic factors direct Fe(CN)64- to its initial attack site. At least one histidine residue appears to be involved in outer-sphere complex formation between laccase and the highly anionic reducing agent. The rate-limiting step for ferrocyanide reduction of laccase is reversible; calculations based on the forward and reverse rate constants indicate that the \"blue\" copper is probably the initial attack site preferred by ferrocyanide. The unusually high activation enthalpy for the reduction of laccase \"blue\" copper by Fe(CN)64- is attributed to the inaccesibility of this site to direct attack by external reducing agents.
\r\n\r\nPreliminary experiments with Fe(EDTA)2- as reductant have shown that the laccase \"blue\" copper site is reduced over 1000 times slower than that of stellacyanin (k = 2.31 x 102 M-1 sec-1 (laccase), 4.2 x 105 M-1 sec-1 (stellacyanin); 25.1\u00b0, pH 6.0, \u03bc = 0.5). Activation parameters for the reduction of laccase Type 1 copper by Fe(EDTA)2- are: \u0394H\u2021 =13.0 kcal/mole, \u0394S\u2021 = -4 cal/mol-deg; pH 7.0, \u03bc = 0.1.
" }, { "name": "Hsu, Ming-Ta", "degree": "PhD", "year": "1974", "title": "I. Electron Microscope Heteroduplex Analysis of DNA Sequences in F-Prime Factors. II. Electron Microscope Studies of \u03bb and Mu Prophages. III. An Electron Microscope Study of Sindbis Virus RNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-213025015", "creators": [ { "name": { "family": "Hsu", "given": "Ming-Ta" }, "id": "Hsu-Ming-Ta", "display_name": "Hsu, Ming-Ta" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/c22c-kg15", "abstract": "This thesis is composed of three parts. Part I is concerned with studies of the DNA sequences of several F-prime factors and the sequence relations among them using electron microscope heteroduplex methods. It was found that the DNA sequence of the F factor can be roughly divided into three regions: 1) a region about one-fourth of the molecule which is concerned with the fertility functions of the F factor. 2) a region about one-third of the molecule which is rich in A+T sequence and contains the sequences used to interact with the bacterial chromosome for the integration or excision of F factor DNA. J) a region which contains the genes for autonomous replication and female phage resistance and the structural element for conjugal transfer.
\r\n\r\nThe structure of the bacterial DNA carried in several classical episomes, F100, F152, F8 and some of their derivatives was studied extensively. Bacterial markers between fep and uvrB were analyzed both genetically and physically. A method was developed to reconstruct the original episomes from their deletion variants. The results confirm the history that F100 and F152 were derived from the same Hfr. The formation of a new episome, F80, from F8 suggested that there is a hot spot in the E. coli chromosome for the recombination with F sequence between 93.2 and 94.5/0.0F.
\r\n\r\nIn part II, the structures of \u03bb and Mu prophages and Mu phage DNA were studied. The \u03bb prophage carried in an F-prime factor was found by electron microscope heteroduplex analysis to be circularly permuted relative to the vegetative viral DNA. On the other hand, Mu prophage DNA was shown to be collinear with the viral DNA. The integrated Mu prophage DNA was used as a marker for physical mapping of bacterial genes in E. coli.
\r\n\r\nSequence heterogeneity in Mu phage and prophage DNA's was also studied. The G loop heterogeneity was found to be present in both phage and prophage DNA.'s and was shown to be due to sequence inversion. The heterogeneous split ends sequences were found to be absent in the several prophages studied.
\r\n\r\nPart III contains an electron microscope study of viral RNA of Sindbis virus and a method for mapping poly A sequences in RNA molecules. Under weak denaturing conditions Sindbis virus RNA appears in circular form with a double stranded \"handle\" of about 250 nucleotides long. This implies that Sindbis RNA contains complementary\r\nsequences at or near the ends of the molecule.
\r\n\r\nA technique using glyoxal as a denaturing agent for mapping polyA sequences in RNA was developed. Glyoxal attaches to guanine base irreversibly and thus removes the secondary structure of RNA without inhibiting the renaturation capacity of polyA sequences in the molecule. A polyA sequence was found at or near one end of Sindbis\r\nRNA by this method.
" }, { "name": "Hunkapiller, Michael W.", "degree": "PhD", "year": "1974", "title": "Nuclear Magnetic Resonance Studies of the Catalytic Mechanism of Proteolytic Enzymes: I. Ionization Behavior of the Histidine Residue in the Catalytic Triad Of \u03b1-Lytic Protease : Implications for the Catalytic Mechanism of Serine Proteases. II. Ionization Behavior of Enzymic and Inhibitor Groups in the Tetrahedral Adduct Between \u03b1 -Lytic Protease and a Peptide Aldehyde. III. Kinetics Of Pepsin-Catalyzed Hydrolysis Of N-Tri-Fluoroacetyl Amino Acids", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11072003-091804", "creators": [ { "name": { "family": "Hunkapiller", "given": "Michael W." }, "id": "Hunkapiller-Michael-W", "display_name": "Hunkapiller, Michael W." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WCV5-S044", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I \r\n\r\nSelective [superscript 13]C enrichment of C-2 of the single histidine residue of the serine protease [alpha]-lytic protease has allowed direct study of the Asp-His-Ser catalytic triad by magnetic resonance techniques. Both the chemical shift of C-2 and the coupling between C-2 and its directly bonded hydrogen have been observed as a function of pH. The results indicate that only below pH 3.3 does the histidine imidazole ring become protonated and only above pH 6.7 does the aspartic acid residue lose a proton to generate a carboxylate anion. Over the pH range 3.3-6.7, the catalytic triad contains a neutral aspartic acid and neutral histidine residue--not the ionized forms hitherto assumed. This interpretation of the ionization characteristics of the catalytic triad leads to a proposed catalytic mechanism which avoids any requirement for unfavorable charge separation in the transition state. The histidine residue plays two roles: (i) it provides insulation between water and the buried carboxylate anion, thus ensuring the latter a hydrophobic environment, and (ii) it provides a relay for net proton transfer from serine hydroxyl to carboxylate anion. The aspartate anion acts as the ultimate base which holds a proton during catalysis. An anionic, rather than a neutral, base both avoids the necessity of charge separation and, by giving the catalytic locus an overall negative charge, assists preferential expulsion of product relative to substrate from the active site. Relaxation measurements (T[subscript 1], T[subscript 2], and nuclear Overhauser enhancement) indicate that, over the pH range of enzymic activity, the histidine residue is held rigidly within the protein.\r\n\r\nPART II\r\n\r\nMagnetic resonance techniques have been used to study ionization behavior of enzymic and inhibitor moieties in the tetrahedral adduct (hemiacetal) formed between [alpha]-lytic protease and a peptide aldehyde, N-Ac-L-Ala-L-Pro-L-alaninal. Chemical shift, coupling constant, and relaxation measurements of [superscript 13]C-enriched C-2 of the catalytic histidine residue indicate that at pH > 6.25 the complex contains neutral aspartic acid, neutral histidine, and negatively charged inhibitor. Below pH 6.25, both the inhibitor oxyanion and the histidine become protonated in a cooperative ionization process which forces the histidine from its rigidly-held position as a member of the catalytic triad into a solution-like environment. This behavior by a complex thought to resemble the transition state for serine protease-catalyzed hydrolysis of ester and amide substrates supports proposals for a catalytic mechanism which involves a minimum of charge separation in the transition state. It also attests to the power of the intricate hydrogen-bonding network (previously observed in x-ray diffraction studies) to stabilize an otherwise high-energy intermediate and thereby achieve catalysis.\r\n\r\nPART III\r\n\r\nThe acidic gastric proteases, pepsin and gastricsin, have been found to catalyze hydrolysis of several N-trifluoroacetyl-L-amino acids with aromatic side chains. This catalytic activity is lost when they are chemically modified so as to inactivate their proteolytic activity. Magnetic resonance techniques were used to follow the porcine pepsin-catalyzed hydrolysis of N-trifluoroacetyl L-phenylalanine in the pH range 1.7-5.4. This study revealed that non-productive binding strongly influences the observed kinetic parameters and that productive enzyme-substrate binding requires an anionic substrate (pK[subscript a] 2.8) and an undissociated group (pK[subscript a] 3.7) on the free enzyme. Binding is also affected by ionization of a group on the free enzyme with a pK[subscript a] near 4.8. A kinetic isotope effect [...] has been observed for the reaction which suggests that proton transfer is involved in the rate-limiting step. A new mechanism--one involving three carboxylic acid groups on the enzyme and an intermediate in which the amino moiety is noncovalently held by the enzyme after release of the acyl moiety--is proposed to explain these and previous observations on catalysis by pepsin." }, { "name": "Hurley, John Neal", "degree": "Masters", "year": "1974", "title": "The Preparation and Properties of Large Lecithin Bilayer Vesicles", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132009-091109533", "creators": [ { "name": { "family": "Hurley", "given": "John Neal" }, "id": "Hurley-John-Neal", "display_name": "Hurley, John Neal" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M7HY-MS72", "abstract": "Sonicated lecithin vesicles of an \"average\" diameter of 1200 \u00c5 were prepared. PMR studies show a higher phase transition temperature than that found for small (300 - 500 \u00c5) vesicles. Osmotic pressure collapses the vesicle but does not change the PMR linewidth. This differs from the effect found in small vesicles. Upon addition of a cyclic polyether (cyclohexyl-15-crown-5) to a solution of large vesicles, the water diffusion rate is found to increase by a factor of 5 to 10. The internal water volume also increases significantly, suggesting that the crown compound is incorporated into the bilayer.\r\n" }, { "name": "Karnicky, Joseph Francis", "degree": "PhD", "year": "1974", "title": "Determination of the Argon Intermolecular Pair Potential from Distribution Functions Measured by X-Ray Diffraction from Fluid Argon", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07212021-212145639", "creators": [ { "name": { "family": "Karnicky", "given": "Joseph Francis" }, "id": "Karnicky-Joseph-Francis", "display_name": "Karnicky, Joseph Francis" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/htpg-c668", "abstract": "X-ray diffraction experiments were carried out on fluid argon at a temperature of -100\u00b0C and densities of .0824 g/cm3, .1331 g/cm3, .2087 g/cm3, and .3111 g/cm3. The measurements of the state at .2087 g/cm3 were repeated to establish reproducibility. The methods used to obtain the experimental quantities and to subsequently analyze the data included significant improvements over previous investigations.
\r\n\r\nThe data from each experiment at the three higher densities were analyzed to obtain a set of structure factors which were Fourier transformed to obtain sets of direct correlation functions and radial distribution functions. The Percus-Yevick equation was applied to these distribution functions to obtain the effective intermolecular potential from each experiment. These potentials were corrected for three-body effects to give four estimates of the argon pair potential, and a final estimate which is the precision weighted average of the four seperate estimates.
\r\n\r\nThe characteristics of these potentials, with error limits determined by a perturbation analysis of the uncertainties in the experimental quantities, are:
\r\n\r\nstate 1- n = .2087 g/cm3, \u03c3 = 3.401 \u00b1 .038 A\u00b0, \u2208 = 143.2 \u00b1 10.2 \u00b0K, rmin = 3.89 \u00b1 .09 A\u00b0.
\r\n\r\nstate 1R- n = .2087 g/cm3, \u03c3 = 3.402 \u00b1 .035 A\u00b0, \u2208 = 149.9 \u00b1 10.2 \u00b0K, rmin = 3.87 \u00b1 .07 A\u00b0.
\r\n\r\nstate 2- n = .3111 g/cm3, \u03c3 = 3.375 \u00b1 .0233 A\u00b0, \u2208 = 146.6 \u00b1 6.8 \u00b0K, rmin = 3.87 \u00b1.05 A\u00b0.
\r\n\r\nstate 3- n = .1331 g/cm3, \u03c3 = 3.379 \u00b1 .050 A\u00b0, \u2208 = 145.1 \u00b1 16.0 \u00b0K, rmin = 3.83 \u00b1 .13 A\u00b0.
\r\n\r\naverage u(r)- \u03c3 = 3.389 \u00b1 .015 A\u00b0, \u2208 = 146.3 \u00b1 4.9 \u00b0K rmin = 3.86 \u00b1 .05 A\u00b0.
\r\n\r\nPhysical quantities were calculated from the average potential and agreed with the experimental values for the second virial coefficient of argon and the vibrational transition energies of the argon dimer, as well as the theoretical long range dispersion potential.
\r\n\r\nThe range of densities studied was not large enough to allow direct determination of three-body forces. Methods are suggested whereby information about nonadditive forces could be derived from the combination of the results of these experiments with the results of previous x-ray experiments or with third virial coefficient data.
" }, { "name": "Kowalski, Conrad John", "degree": "PhD", "year": "1974", "title": "Part I. Efforts Directed Towards the Total Synthesis of Shionone. Part II. Conversion of Estrone to Androst-4-En-3-One: A New Method for Activating the C-9 and C-10 Positions of Estrogenic Steroids for Substitution", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162014-113619903", "creators": [ { "name": { "family": "Kowalski", "given": "Conrad John" }, "id": "Kowalski-Conrad-John", "display_name": "Kowalski, Conrad John" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XM7S-7224", "abstract": "Part I: An approach to the total synthesis of the triterpene shionone is described, which proceeds through the tetracyclic ketone i. The shionone side chain has been attached to this key intermediate in 5 steps, affording the olefin 2 in 29% yield. A method for the stereo-specific introduction of the angular methyl group at C-5 of shionone has been developed on a model system. The attempted utilization of this method to convert olefin 2 into shionone is described.
\r\n\r\nPart II: A method has been developed for activating the C-9 and C-10\r\npositions of estrogenic steroids for substitution. Estrone has been\r\nconverted to 4\u03b2,5\u03b2-epoxy-10\u03b2-hydroxyestr-3-one; cleavage of this\r\nepoxyketone using an Eschenmoser procedure, and subsequent modification\r\nof the product afforded 4-seco-9-estren-3,5-dione 3-ethylene acetal.\r\nThis versatile intermediate, suitable for substitution at the 9 and/or\r\n10 position, was converted to androst-4-ene-3-one by known procedures.
\r\n" }, { "name": "Langhoff, Charles Anderson", "degree": "PhD", "year": "1974", "title": "A Generalized Theory of Radiationless Transitions", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:06302021-163308263", "creators": [ { "name": { "family": "Langhoff", "given": "Charles Anderson" }, "id": "Langhoff-Charles-Anderson", "display_name": "Langhoff, Charles Anderson" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ea20-gq57", "abstract": "The problem of radiationless transitions in polyatomic molecules has been much discussed in recent years. Most attention has been focused on the large energy gap or statistical limit case where the lineshape is Lorentzian and the emission decay exponential. The weighted density of states is assumed to be constant with energy. The broad band approximation, which states that the exciting light uniformly and coherently excites the entire molecular resonance, is standardly employed. The cases of intermediate energy gap have not been extensively investigated. Also, the effect of a finite bandwidth excitation light has only been formally treated. The generalizations proposed here allow the weighted density function to assume general energy dependence. Using the techniques of scattering theory, we are able to present exact formulas for the spectrum and the emission decay which must be evaluated numerically. This enables a more thorough treatment of the intermediate energy gap case where the density is expected to be \"line-like\". The spectral line shapes become very complex and in no way resemble a Lorentzian. The emission decay curves are correspondingly complex showing quantum beat effects. The ability to detect these quantum beats is also discussed. Also, the excitation band is allowed to have finite width (and, of necessity, a finite time duration). The width and positioning of the excitation band has a dramatic effect on the emission decay. The above generalizations also lead to a new interpretation of the lifetimes of some intermediate case molecules such as NO2, SO2, and CS2. Finally, we apply the formal results to the calculation of the second singlet spectrum of naphthalene in various mixed crystal hosts. We are able to get virtually exact fits to the spectrum using our simple formulas Also, we compute some emission decay curves and compare these curves with some measured gas phase emission curves.
" }, { "name": "Levin, George Benjamin", "degree": "PhD", "year": "1974", "title": "The Generalized Valence Bond Description of the Pi Electron States of Conjugated Molecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-154826608", "creators": [ { "name": { "family": "Levin", "given": "George Benjamin" }, "id": "Levin-George-Benjamin", "display_name": "Levin, George Benjamin" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/n2qd-5z12", "abstract": "Using the generalized valence bond (GVB) wave function, the pi electron systems of ethylene, allyl cation, allyl radical, s-trans-1,3- butadiene and benzene were examined. The results were in good agreement with full configuration interaction calculations demonstrating the quantitative accuracy of the GVB method. The GVB description of the valence states systems includes a description of resonance and provides a rigorous quantum mechanical description of resonance in terms of spin couplings. It was found that the resonance stabilization energy is due to two effects, delocalization of orbitals onto additional centers while still maintaining their basically localized nature, and spin coupling optimization in a manner identical to the valence bond description of resonance.
\r\n\r\nIt was found that the GVB wave function imposed restrictions upon the orbitals of excited states. To remove these restrictions the GVB wave function was generalized by including a spatial projection operator. The GVB(SP) wave function imposes no restrictions upon individual orbitals and represents the most general independent particle wave function as yet presented. The GVB(SP) method was used to examine allyl radical and butadiene. All states were described by localized orbitals and energies were in excellent agreement with configuration interaction results. A molecules-in-molecules model using ethylene pi electron states was found to provide a qualitative description of all the states of allyl radical and butadiene examined.
\r\n" }, { "name": "Live, David Harris", "degree": "PhD", "year": "1974", "title": "The Interaction of Cations with Cyclic Ethers", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03222021-225134007", "creators": [ { "name": { "family": "Live", "given": "David Harris" }, "id": "Live-David-Harris", "display_name": "Live, David Harris" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kq1b-vg86", "abstract": "Proton and carbon nuclear magnetic resonance (NMR) have been used to aid in the understanding of solution structure, cation, anion and solvent interactions, and structural aspects of cation specificities of \"crown\" cyclic polyethers. Investigations were made in water, water-acetone, acetone and chloroform as a function of cation concentration and of anion. Using the effects of the aromatic residues on the molecules we have studied, we have been able to assign the proton and carbon spectra. From the vicinal proton-proton coupling, the electrostatic effect of cation and anion on the proton NMR, and the structural sensitivity of the carbon NMR, we have obtained results on the interaction of Na+, K+, Cs+ and Ba+2 with Benzo 18 Crown 6, Dibenzo 18 Crown 6 and Dibenzo 30 Crown 10. Analysis of the cation induced shifts has enabled us in some cases to examine the cation binding as a function of solvent.
\r\n\r\nThe complexes of Benzo 18 Crown 6 and Dibenzo 18 Crown 6 have the same structures in the various solvents as found in the crystal for DB18CR6. However, the solution conformation of the uncomplexed molecules differs from that in the crystal. The K+, Cs+ and Ba+2 complexes of Dibenzo 30 Crown 10 in solution, have the same configuration reported for the K+ complex in the crystal. The Na+ complex does not, and we have proposed an alternate structure. The solvation sphere of a cation is completely removed when it is complexed to the latter crown ether, which is not the case for the 18 membered rings.
" }, { "name": "McMahon, Terrance Brian", "degree": "PhD", "year": "1974", "title": "Trapped Ion Cyclotron Resonance Studies of Ion-Molecule Reactions", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01222009-092248", "creators": [ { "name": { "family": "McMahon", "given": "Terrance Brian" }, "id": "McMahon-Terrance-Brian", "display_name": "McMahon, Terrance Brian" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BJCA-7136", "abstract": "Techniques and instrumentation have been developed which permit trapping of ions in the source region of an ion cyclotron resonance cell. These techniques have been used to determined rates of ion-molecule reactions and to observe gas phase ion-molecule equilibria.\r\n\r\nThe rate constants of a number of symmetric charge exchange and proton transfer reactions in simple molecules have been determined and related to theoretical models of ion-molecule reaction. In addition, the role of a symmetric reaction in competition with exothermic reaction channels has been discussed.\r\n\r\nThe rates of symmetric proton and deuteron transfer in a number of simple alkyl alcohols and amines have also been obtained. These reactions have been related to de-excitation mechanisms of excited ions.\r\n\r\nGas phase ion-molecule equilibria have been examined to obtain substituent effects on such properties as gas phase basicity, acidity and carbonium ion stabilities.\r\n\r\nFinally, the ion-molecule reactions of a cyclic ether, trimethylene oxide, have been examined to illustrate the wide range of information available through ion cyclotron resonance experiments." }, { "name": "Mohr, Lawrence Henry", "degree": "Masters", "year": "1974", "title": "\u03b1-Secondary Tritium Isotope Effects in the Hydrolysis of Glycopyranosides of N-Acetyl-D-Glucosamine", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292010-085354161", "creators": [ { "name": { "family": "Mohr", "given": "Lawrence Henry" }, "id": "Mohr-Lawrence-Henry", "display_name": "Mohr, Lawrence Henry" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6EZB-BP10", "abstract": "Part I. Secondary tritium isotope effects were used to study the aqueous hydrolysis of a series of \u03b1 and \u03b2-glycopyranosides of N-acetyl-D-glucosamine. The magnitude of the secondary tritium isotope effects, and their dependence on the structure of the aglycone, are\r\ncompatible with the carbonium ion mechanism suggested for the specific acid catalysis of these compounds by Piszkiewicz and Bruice (1, 2, 3). The secondary tritium isotope effect determined for the spontaneous hydrolysis of the p-nitropheny1-2-acetamido-2-deoxy-\u03b2-D-glucopyrano-\r\nside is not consistent with an intramolecular, nucleophilic displacement mechanism. A mechanism involving the equilibrium formation of a carbonium ion-anion pair is proposed. The relevance of these model studies to hydrolysis of oligosaccharides of N-acetyl-D-glucosamine by \r\nlysozyme is discussed.\r\n\r\nPart II. Secondary tritium isotope effects are also used to study the enzymatic hydrolysis of two \u03b2-aryl\r\nglycopyranosides of N-acetyl-D-glucosamine by \u03b2-N-acetyl-D-glucosaminidase isolated from jack bean meal. The results obtained indicate a transition state for reaction \r\nprocessing less carbonium ion character than the corresponding hydrolysis catalyzed by aqueous acid or lysozyme. A mechanism involving anchimeric assistance by the acetamido group on the substrate is proposed.\r\n" }, { "name": "Nourse, James Gregory", "degree": "PhD", "year": "1974", "title": "I. Carbon-13 Nuclear Magnetic Resonance Spectroscopy of Erythromycin Derivatives. II. Algebraic Chemistry", "advisor": "Roberts, John D.; Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06152021-231651716", "creators": [ { "name": { "family": "Nourse", "given": "James Gregory" }, "id": "Nourse-James-Gregory", "display_name": "Nourse, James Gregory" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." }, { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0vg4-h136", "abstract": "I. Carbon-13 Nuclear-Magnetic Resonance Spectroscopy of Erythromycin Derivatives
\r\n\r\nCMR spectra were taken and assigned for a series of erythromycin derivatives. Interpretation was based on known effects on cmr spectra and conformational changes among the derivatives. While the results were consistent with a gross conformational homogeneity, some subtle differences were observed. Proposals were made concerning the conformational differences between erythromycin A and Band among the series of aglycones. A conformation was proposed for 5,6-dideoxy-5-oxoerythronolide B consistent with cmr and pmr results. It was also proposed that in the natural antibiotics the desosamine side-chain sugar is free to swing around to the side of the aglycone ring, while the cladinose side-chain sugar is relatively fixed. The results suggested and were consistent with this situation. In this series it appeared that cmr was most useful in ascertaining intramolecular hydrogen bonding and orientation of and around carbonyls. Diagnostic usefulness for the various ketal structures was also suggested. The results of an enriched propionate feeding experiment confirmed the propionate biosynthesis hypothesis and gave direct evidence for the origin of the individual aglycone carbons.
\r\n\r\nII. Algebraic Chemistry
\r\n\r\nSeveral mathematical-chemical problems were treated and general considerations discussed.
\r\n\r\nIt was shown that the Polya method could be used to count stereoisomers in systems with chiral ligands. An iterative procedure was given to determine the distribution and symmetry of all isomers possible in any given system. An extension of the method was made to count possible one-step substitution reactions in benzene systems.
\r\n\r\nThe algebraic nature of the synthetic design problem was discussed, based on some simple concepts from algebraic topology. It was shown that the symmetry group of a chemical structure relevant to the synthetic design problem can be considerably larger than the usual point group. Examples of this group were constructed along with some methods for taking advantage of this symmetry in hypothetical cases.
\r\n\r\nA complete algebraic description of pseudochirality was given. It was shown that pseudochirality results when a structure lacks a particular kind of symmetry based on the point group and operations which invert configurations of chiral ligands. Other related forms of stereoisomerism were similarly described. A derivation of the possible pseudochirality groups based on the usual point groups was given.
\r\n\r\nThe treatment of through-space orbital interactions given by Goldstein and Hoffmann was described abstractly and extended to reaction problems. A ribbon topology was assigned a homomorphism from a group of mode change operations to a group of interaction change operations. The concept of topologically equivalent transition state geometries was shown to correspond to group isomorphisms. The action of the mode. change group on a dynamic symmetry group for 1,5-hexadiene was given which interchanged allowed and forbidden reactions. It was suggested that the existence of allowed and forbidden reactions could be considered as a symmetry of a chemical structure.
\r\n\r\nThe applicability of concepts of categorical algebra to biological, physical and chemical problems was discussed. Basic categorical concepts were discussed and it was shown that the center. and inner automorphism groups are functorial constructions on the subcategory of Grp including only epi arrows. General features of application of categorical concepts outside pure mathematics were compared. The functorial nature of the problems treated in earlier sections was discussed. The similarity between isomerization of triaryl methanes and tris-metal chelates observed by Gust and Mislow was expressed as an isomorphism of the dynamic symmetry groups. The use of groupoids in problems of isomerizations between different geometric forms was demonstrated. It was shown that groupoids can be considered as representations of wreath products. A dynamic symmetry group for cyclobutene-butadiene interconversions was derived.
" }, { "name": "Reynolds, Steven Diggs", "degree": "PhD", "year": "1974", "title": "Mathematical Modeling of Photochemical Air Pollution", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152021-211653038", "creators": [ { "name": { "family": "Reynolds", "given": "Steven Diggs" }, "id": "Reynolds-Steven-Diggs", "display_name": "Reynolds, Steven Diggs" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/dx1x-j848", "abstract": "A model is presented for predicting the dynamic behavior of both inert and chemically reacting air pollutants in an urban atmosphere. Pollutants of interest include carbon monoxide, nitric oxide, nitrogen dioxide, ozone, and high and low reactivity hydrocarbons. The model is developed for a general urban area and then applied to the Los Angeles airshed. To evaluate the model, six smoggy days occurring in Los Angeles in 1969 are simulated followed by a comparison of the predictions with the numerous air quality measurements reported by the local air pollution control agencies. In addition, since evaluation of emission control strategies is an important potential use of the model, simulation results are also given demonstrating the possible impact on air quality in the Los Angeles area resulting from implementation of the U.S. Environmental Protection Agency's control strategy for the South Coast Air Basin proposed in July of 1973.
\r\n\r\nThe governing equations of the model are based on the general mass conservation relationships for a chemically reactive species in a three-dimensional, turbulent atmospheric boundary layer. These equations are solved independently of the coupled Navier-Stokes and energy equations; meteorological parameters in the model are estimated from measured wind and mixing depth data. Reaction rate expressions for the reacting species are derived from a concise, fifteen step kinetic mechanism describing the important chemical reactions that take place in the atmosphere. A detailed discussion is included of the treatment of the winds and temperature inversion in the Los Angeles area.
\r\n\r\nSince pollutant emissions are an essential input to the model, a general model and comprehensive inventory of contaminant emissions for Los Angeles is presented. Considered in this study are the spatial and temporal distribution of emissions from motor vehicles, aircraft, and fixed sources (including power plants, refineries, etc.).
\r\n\r\nBecause of the nonlinear nature of the chemical kinetics, the governing equations themselves are nonlinear. Thus, a finite difference scheme based on the method of fractional steps is developed to solve the equations. A detailed exposition of all difference equations and their manner of solution is given.
\r\n\r\nAs mentioned previously, an evaluation study of the model is performed by making extensive comparisons of predictions and measurements for Los Angeles. It is found that local pollutant sources near monitoring stations can hamper the comparison of spatially averaged predictions with point measurements. In an effort to account for sub-grid scale effects, a \"microscale\" model is developed to predict the concentration elevation observed at a monitoring site caused by local sources, such as traffic on nearby streets and freeways. In general, it is found that the model predicts pollutant concentrations reasonably well considering the complexity of the problem and the uncertainty in many of the parameters in the model.
\r\n\r\nFinally, possible future applications of the model are discussed, including the short range forecast of pollutant concentrations (say up to a few days in the future) and the evaluation of the impact of regional planning decisions and emission control strategies on air quality. To gain experience in applying the model to evaluate emission control strategies, simulations of the Los Angeles region are performed using an emission inventory based on control measures proposed by EPA for the region in 1977. The model results indicate that ozone concentrations will be reduced. substantially from 1969 levels; however, definitive statements with regard to air quality in 1977 must await further refinement of the model and better understanding of the effects of the various proposed control strategies on pollutant emissions.
" }, { "name": "Rosenberg, Robert Charles", "degree": "PhD", "year": "1974", "title": "Spectral and Magnetic Studies of Metallocarboxypeptidase A's", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07132021-182715013", "creators": [ { "name": { "family": "Rosenberg", "given": "Robert Charles" }, "id": "Rosenberg-Robert-Charles", "display_name": "Rosenberg, Robert Charles" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4peh-5f16", "abstract": "Spectral and magnetic studies on the cobalt(II), nickel(II), and copper(II) derivatives of the zinc containing metalloenzyme carboxypeptidase A (CPA) are reported and discussed.
\r\n\r\nThe absorption spectrum and magnetic moment of Co(II)-CPA are shown to be consistent with a five coordinate metal structure by comparison to the spectra and magnetic moments of a large number of pseudo-tetrahedral and five coordinate cobalt(II) complexes. The usefulness of magnetic susceptibility data in assigning coordination number for high-spin cobalt(II) metalloenzyme systems is demonstrated.
\r\n\r\nThe absorption spectrum and magnetic moment of Ni(II)-CPA are consistent only with an octahedral ground state geometry. The effect of substrate and inhibitor on the spectrum of Ni(II)-CPA was studied.
\r\n\r\nThe absorption and EPR spectra of Cu(II)-CPA were also investigated. A significant pseudo-tetrahedral distortion from planar coordination geometry is indicated for this derivative. The interaction of Cu(II)-CPA and the inhibitor sodium B-phenylpropionate was also studied.
\r\n\r\nThe results of these studies and especially those of Ni (II)-C PA do not agree with the predictions of the entatic state hypothesis.
" }, { "name": "Russ, Guston Price, III", "degree": "PhD", "year": "1974", "title": "Neutron Stratigraphy In the Lunar Regolith", "advisor": "Burnett, Donald S.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05292008-130623", "creators": [ { "name": { "family": "Russ", "given": "Guston Price, III" }, "id": "Russ-Guston-Price-III", "display_name": "Russ, Guston Price, III" } ], "advisors": [ { "name": { "family": "Burnett", "given": "Donald S." }, "id": "Burnett-D-S", "orcid": "0000-0001-9521-8675", "role": "advisor", "display_name": "Burnett, Donald S." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DEP4-KJ41", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nDifferences in the isotopic composition of Gd and Sm among lunar samples collected during the Apollo 11, 12, 14, 15, and 16 and Luna 16 missions have been measured by high precision mass spectrometry. These differences (up to 1.9% in [...]Gd/[...]Gd and 2.0% in [...]Sm/[...]Sm) can be attributed unambiguously to low energy neutron capture reactions and correspond to neutron fluences as high as 10[...] n/cm[...] (E < 0.18 eV). For the Apollo 16 samples, enrichments are reported for the [...]Gd/[...]Gd ratio which appear to be due to neutron capture by [...]Eu. The measured ratio of the number of neutrons captured per atom by [...]Sm to the number captured per atom by [...]Gd indicates that the low energy lunar neutron spectrum is in reasonable agreement with that calculated by Lingenfelter, Canfield, and Hampel but that the lunar spectrum is somewhat harder. A synthesis of all the available lunar neutron capture data for [...]Gd, [...]Gd,\t[...]Sm, [...]Eu, [...]Co, [...]Br, [...]Br, [...]Ba, [...]W, [...]U, [...]U, and [...]Ca indicates that only the [...]W and [...]U data are incompatible with the LCH neutron spectrum and flux.\r\n\r\nBased on the LCH neutron flux, the neutron fluences, [...], determined for the lunar soils are all lower than would be expected for materials mixed in the upper few meters of the regolith for > 3 x 10[...] yr. In terms of a uniform mixing model the measured neutron fluences imply that the depth of the regolith is between 10 and 14 m at all of the Apollo sites studied. These are greater than the depths implied from cratering theory. The [...]Xe/[...] ratios for the soils indicate that they have been well mixed to a depth of > 200 g/cm[...]. Detailed fluence studies in the Apollo 12 double core show that these materials could not have been undisturbed for > 10[...] yr. The upper layers of the Apollo 15 and 16 drill stems also imply mixing on this time scale. However, the Apollo 15 drill stem has a smooth peak in the fluence at a depth of ~ 190 g/cm[...]. From the magnitude of this peak, it can be concluded that below a depth of ~ 75 g/cm[...] these materials have been undisturbed for at least 400 my. The fluence profile in the Apollo 16 drill stem is more complicated but indicates an area where material has been accumulating for several hundred million years.\r\n\r\nA model is presented for the depth dependence of the ratio of [...]Xe produced by neutron capture on [...]Ba to [...]Xe produced by spallation reactions on Ba. Effective exposure depths are calculated for 24 rocks from Apollo 11 and 12. Detailed irradiation histories are presented for rocks 10017, 14310, and 15595. An erosion rate for Hadley Rille of ~1 cm/my is calculated from the neutron fluence of rock 15595.\r\n\r\nFrom Gd and Sm isotopic measurements it is shown that the Norton County meteorite has been exposed to a neutron flux with a spectrum compatible with that predicted by the LCH calculations. The neutron fluence to which our sample of Norton County has been exposed is 1.2 x 10[...] n/cm[...]. No neutron produced effects were observed in the isotopic composition of Gd from a bulk sample of the Allende meteorite." }, { "name": "Schmidt, Charles Frederick, Jr.", "degree": "PhD", "year": "1974", "title": "Nuclear Spin-Lattice Relaxation Studies", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06242021-224248892", "creators": [ { "name": { "family": "Schmidt", "given": "Charles Frederick, Jr." }, "id": "Schmidt-Charles-Frederick", "display_name": "Schmidt, Charles Frederick, Jr." } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d4e7-j132", "abstract": "In order to study and better understand the microdynamic behavior of liquids, the nuclear spin-lattice relaxation rate has been measured and calculated for fluorine-19 in trifluoroacetic acid, and calculated for carbon-13 in toluene, carbondisulfide, benzene, methyl iodide, acetonitrile, and n-decane.
\r\n\r\nFor fluorine in trifluoroacetic acid it is shown that the relaxation is controlled by the spin-internal-rotation interaction.
\r\n\r\nSpin-internal-rotation coupling is also shown to be important for carbon-13 relaxation of the methyl carbon of toluene, although intramolecular dipolar coupling also makes a significant contribution.
\r\n\r\nFor carbon disulfide, it is shown that while the anisotropic chemical shift mechanism will contribute to the relaxation rate at superconducting magnetic fields, the spin-rotation interaction provides the dominant mechanism.
\r\n\r\nFor benzene, it is shown that motion about the C6 symmetry axis can best be described using the inertial model. Intramolecular dipolar coupling is seen to be more important than spin-rotation coupling.
\r\n\r\nFor methyl iodide and acetonitrile, it is shown that a description in which the motion is taken to be highly anisotropic gives good agreement with experiment.
\r\n\r\nIn Part III, a description of the internal rotation for molecules containing alkane chains is given using the Rotational Isomeric State Approximation. The dynamics of the rotation implied by this model are analyzed, and the results are used to calculate carbon-13 spin-lattice relaxation rates for the methylene carbons. The model appears to be successful in predicting the relaxation time differences for the carbons at the methyl end of n-decanol.
" }, { "name": "Schweizer, Albert Edward, Jr.", "degree": "PhD", "year": "1974", "title": "Studies of Some Inorganic Reaction Mechanisms", "advisor": "Gray, Harry B.; Bercaw, John E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02082021-221037462", "creators": [ { "name": { "family": "Schweizer", "given": "Albert Edward, Jr." }, "id": "Schweizer-Albert-Edward", "display_name": "Schweizer, Albert Edward, Jr." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Bercaw", "given": "John E." }, "id": "Bercaw-J-E", "role": "advisor", "display_name": "Bercaw, John E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/75es-0c18", "abstract": "Part I
\r\n\r\nThe compound dihydridotetrakis (diethylphenylphosphonite)-iron(II) is known to undergo rapid rearrangement in solution. Considerable discussion has been presented to formulate a mechanism for this rearrangement. This discussion is based on a rearrangement between cis and trans dihydride isomers of octahedral stereochemistry. We present here some experimental evidence which shows the identification of one isomer (as the trans dihydride) is incorrect and also that the changes that occur are more complicated than the earlier workers proposed. Infrared, Raman, and very low temperature 1H n. m. r. spectra of both the iron and ruthenium compounds are used to construct a different picture of this system. We identify three distinct reactions or rearrangements that are occurring and offer some proposals for the structures of the isomers. A non-classical six-coordinate structure based on a tetrahedral skeleton of phosphorus atoms about the central metal is considered the most reasonable identification of the non-cis isomer.
\r\n\r\nPart II
\r\n\r\nNitric oxide undergoes many reactions to form transition metal nitrosyls of varying geometry. Under very special conditions, it then continues to react to form a species with nitrogen to nitrogen bonds. We have studied one of these reactions in detail: First, to establish the stoichiometry of the reaction exactly and second, to gain some insight into the mechanism of the dimerization step.
\r\n\r\nThere is an initial rapid reaction of an ammoniacal Co(II) solution and NO with the stoichiometry one NO per cobalt(II). The NO pressure dependence of the ratio NO to cobalt is given experimentally. A qualitative proposal is made to explain this dependence, but we are still searching for a quantitative description.
\r\n\r\nThere is a much slower reaction that consumes additional nitric oxide, producing N2O and nitrite ions. If the initial cobalt(II) concentration is high, an additional product is obtained, the \u03bc-hyponitrito bis(pentaammine cobalt(III)) ion, usually precipitated as the nitrate. The yield of the dimeric cation as a function of concentration, anion, and temperature are given. A proposal of a linkage isomerization of an unstable dimer of pentaamminenitrosyl cobalt(III) is offered to explain the experimental observations.
\r\n\r\nPart III
\r\n\r\nThe decomposition of nitric oxide to elements in the gas phase is a thermodynamically favored reaction that is very slow at low temperatures (below 1000\u00b0K). Some catalysts are known for this reaction carried out in a heterogeneous reactor. Work has been performed jointly with the chemical engineering faculty to try to understand the reaction over one of the known catalysts. The rate limiting factor is shown to be the strong inhibition by the product oxygen rather than any intrinsically slow reaction of NO. An interpretation of both our results and the results of another group is offered in terms of a unimolecular decomposition on a surface.
" }, { "name": "Seiter, Charles Harrington", "degree": "PhD", "year": "1974", "title": "Nuclear Magnetic Resonance Linewidth Studies of Model Membranes", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082021-230959216", "creators": [ { "name": { "family": "Seiter", "given": "Charles Harrington" }, "id": "Seiter-Charles-Harrington", "display_name": "Seiter, Charles Harrington" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bmyt-e427", "abstract": "The possible applications of magnetic resonance spectroscopy to current problems in membrane biophysics are surveyed with a particular view to the use of newer Fourier transform and multipulse techniques. Two contributions to this field are presented. The first contribution describes a Fourier transform filtering technique which removes the broad proton magnetic resonance (pmr) lines characteristic of cell membranes and unsonicated lipid bilayers to allow observation of methyl proton and other sharp resonance peaks. The interaction of valinomycin with lipid bilayers is monitored by this method, and the valinomycin is found to interact primarily with the polar choline head groups of the lecithin molecules in the bilayer. The second contribution analyzes the pmr linewidths of sonicated and unsonicated bilayers by the stochastic linewidth method of P. W. Anderson. It is found that the local packing of lipid chains in sonicated vesicles is significantly less orderly than the local packing in unsonicated bilayers. It is also shown that the sharp methyl resonances observed in pmr spectra of unsonicated bilayers correspond to the central spike characteristic of the methyl rotor dipolar powder spectrum in solids, and that this powder spectrum is only partially averaged by the restricted molecular motions available to lipids in unsonicated bilayers. Finally, a Waugh multipulse spectrum of unsonicated bilayers is used to establish kink formation on a timescale of 10-7 sec as the chief mode of local molecular motion for protons on lipid hydrocarbon chains in unsonicated systems, as compared to trans-gauche bond rotations on a timescale of 5 x 10-9 sec or faster as the mode of local motion of protons in sonicated vesicles. The value of these two systems as model membranes is discussed in the light of these motional results.
" }, { "name": "Sharda, Satish Chander", "degree": "PhD", "year": "1974", "title": "I. A New Elastic Potential Function for Rubbers. II. Thermoelastic Behavior of Rubbers", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252004-145531", "creators": [ { "name": { "family": "Sharda", "given": "Satish Chander" }, "id": "Sharda-Satish-Chander", "display_name": "Sharda, Satish Chander" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NYF8-8467", "abstract": "The internal energy and the entropy components of the elastic restoring force in rubbers were determined for natural rubber up to an extension ratio of about 3.0. Four different experimental measurements were necessary to determine these components: (1) the force-temperature coefficient at constant temperature and length; (2) the force-pressure coefficient at constant temperature and length; (3) the thermal expansion coefficient at constant length; and (4) the isothermal compressibility at constant length. The force-temperature and the force-pressure coefficients were functions of strain whereas the expansion coefficients and the isothermal compressibilities were independent of strain. These measurements gave an internal energy contribution of 23% for natural rubber independent of the strain over the range of extensions studied.\r\n\r\nTo describe the thermal as well as the elastic behavior of rubbers a new phenomenological description of elastomers based on a generalized measure of strain was developed. The incompressible form of the strain energy function correctly described the elastic data on various elastomers (natural rubber, styrene-butadiene rubber, chlorinated ethylene-propylene copolymer rubber) in both homogeneous and non-homogeneous deformation fields. For a given rubber the same set of parameters fitted the data in simple tension, simple compression, equal biaxial tension and pure shear up to the point of rupture.\r\n\r\nThe compressible form of the strain energy function also described the thermoelastic data on natural rubber. The thermoelastic data on chlorinated ethylene-propylene copolymer rubber, taken out of the literature, were also predicted. From the new strain energy function it was possible to determine the interchain interactions. For natural rubber the interchain energy effects were found to be small (4%) as compared to the intrachain energy effects.\r\n\r\nThe experimental results on natural rubber established the range of validity of the statistical mechanical (molecular) and the continuum mechanical (phenomenological) theories. The temperature coefficient of the unperturbed dimensions of natural rubber determined from the internal energy component of the force yielded the conformational energies associated with the cis-polyisoprene chain." }, { "name": "Sherfinski, James Stanley", "degree": "PhD", "year": "1974", "title": "A Structural Analysis of Three Arabinosylpyrimidines", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042021-210930114", "creators": [ { "name": { "family": "Sherfinski", "given": "James Stanley" }, "id": "Sherfinski-James-Stanley", "display_name": "Sherfinski, James Stanley" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vc0r-8820", "abstract": "The crystal structures of three arabinosylpyrimidines are presented. Crystals of 1-\u03b2-D-arabinofuranosylcytosine hydrochloride are monoclinic, space group P21, with cell dimensions a = 6.540(2) \u00c5, b = 15.260(2) \u00c5, c = 6.758(3) \u00c5, and \u03b2 = 117.68(3)o; Z = 2. The original structure solution was by Patterson-Fourier techniques; a second method of solution is presented which takes advantage of the chloride ion being an anomalous scatterer in a centrosymmetric array. Full-matrix least-squares refinement yielded a final R index of 0.022 for 2490 data; the estimated positional standard deviation of a carbon atom is 0.002 \u00c5. The cation is in the gauche-trans and C(2')-endo conformations; the glycosidic torsion angle \u00d8cn is 26.7\u00b0, Using the anomalous scattering of Cl-, O, and N in CuK\u221d radiation, the absolute configuration of the sugar ring was determined,
\r\n\r\nThe compound 1-\u03b2-D-arabinofuranosyluracil crystallizes in the orthorhombic space group P212121 with cell dimensions a = 6.888(2) \u00c5, b = 20.973(5) \u00c5, c = 6.826(3) \u00c5, and Z = 4. Solution was again by Patterson methods, and the structure was refined by full-matrix least squares to a final R index of 0.030 for 2034 counter-collected data (\u03bb(CuK\u221d) = 1.5418\u00c5). The estimated positional standard deviation of a carbon atom is 0,002 \u00c5, The absolute configuration of this molecule was also established, this time using only O and N as anomalous scatterers. The sugar is in the C(2')-endo, gauche-gauche conformation which is stabilized by an intramolecular 0(2')...0(5') hydrogen bond. The glycosidic torsion angle is 35.0\u00b0.
\r\n\r\nThe nucleotide 1-\u03b2-D-arabinofuranosylcytosine-5'monophosphate crystallizes from water in space group P212121 as the trihydrate; there are four formula units per unit cell of dimensions a = 17.531(3) \u00c5, b = 18.252(4) \u00c5, c = 4.816(1)\u00c5. Initial solution attempts centered on interpreting a projection Patterson map calculated with Beevers-Lipson strips and film data. Ultimately the structure solution was accomplished utilizing information from both a three-dimensional Patterson map and a direct methods solution in which no enantiomorph discrimination had been done. Least squares refinement was halted at R = 0.046 for 1859 diffractometer data; the estimated standard deviation in 0 the position of a carbon atom is 0.004 \u00c5. The absolute configuration of the arabinose was determined utilyzing the anomalous scattering properties of P, O, and N in CuK\u221d. radiation. The sugar is in the C(3')-endo, gauche-gauche conformation; the glycosidic torsion angle is 30.7\u00b0.
\r\n\r\nFor the three nucleotides and nucleosides studied, the glycosidic torsion angle is restricted to a very narrow range of values, whereas three quite different sugar conformations are exhibited. The results indicate that arabinofuranosylpyrimidines can with little effort conform to the same geometrical descriptions calculated for ribo- and deoxyribofuranosylpyrimidines in double-helical nucleic acid structures.
" }, { "name": "Smith, Lois Elaine Hodgson", "degree": "PhD", "year": "1974", "title": "Studies on the Catalytic Mechanism of Lysozyme", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07182023-183123737", "creators": [ { "name": { "family": "Smith", "given": "Lois Elaine Hodgson" }, "id": "Smith-Lois-Elaine-Hodgson", "display_name": "Smith, Lois Elaine Hodgson" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vvkx-7t08", "abstract": "Secondary \u03b1-tritium kinetic isotope effects have been utilized to \r\nprobe the nature of the transition state in the lysozyme catalyzed hydrolysis of chitotriose. A general synthesis of specifically labeled chitin oligomers (in particular 1,1',1\"-\u00b3H-chitotriose, the substrate used in these studies) is described. Injection of Drosophila melanogaster larvae with labeled N-acetyl-D-glucosamine yields chitin, which can be hydrolyzed to give a range of chitin oligomers from chitobiose to chitoheptose. The value of kH/kTobtained for the lysozyme catalyzed hydrolysis of chitotriose was found to be 1.19. This result indicates very considerable carbonium ion character in the transition \r\nstate, and thus the mechanistic alternatives for lysozyme hydrolysis become distinguishable.
\r\n\r\nThere is evidence for the existence of a stabilized intermediate formed after the production of the carbonium ion in a post-rate limiting step. Three alternatives exist for this stabilized intermediate:
\r\n1) a carbonium ion stabilized to some degree by asp 52 (an ion pair)
\r\n2) an acylal formed with asp 52 (a covalent intermediate )
\r\n3) an oxazoline
\r\nSubstrates of the form NAG-GLU- NO\u2082 have been found to undergo lysozyme catalyzed transglycosylation. Since these substrates are cleaved specifically between GLU and the aglycone, the possibility of an oxazoline intermediate can be eliminated.
A study of the variation with pH of the ratio transfer / transfer + hydrolysis for lysozyme has yielded the titration curve of a group of pKa~6.5. This has been assigned to glu 35. Because its pKa is unchanged from that in the unbound enzyme, the possibility of a highly charged intermediate can be eliminated. Therefore the stabilized intermediate must be an acylal or a tight ion pair.
" }, { "name": "Trust, Ronald Irving", "degree": "PhD", "year": "1974", "title": "Approaches to the Synthesis of d,l-Alnusenone via Non-Enzymic, Biogenetic-Like Polyolefin Cyclizations", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01292007-151243", "creators": [ { "name": { "family": "Trust", "given": "Ronald Irving" }, "id": "Trust-Ronald-Irving", "display_name": "Trust, Ronald Irving" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BD4H-E898", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nSeveral 4-methyl-4-polyalkenyl-2-cyclohexenols were synthesized in the hope that their acid-promoted cyclizations would yield polycyclic compounds in which the first two ring junctures formed would have a cis,anti,trans backbone, a procedure which is well precedented in the literature. Compounds of this stereochemistry bear a structural relationship to the pentacyclic triterpenes alnusenone and friedelin, thus offering a possible route to these and other triterpenoid compounds. Consequently, the model compounds 58 and 82 were synthesized. Their cyclizations in formic acid yielded complex mixtures of products with varying degrees of cyclization. Using stannic chloride as cation initiator in dichloromethane, these two alcohols cyclized to afford good yields of tricyclic products with high degrees of stereoselectivity. The structure of the tricyclic olefin 68, formed in 32% yield from alcohol 58, is believed to be that shown based on fact that the first three centers formed must be in a cis,anti relationship in order for cyclization to occur, and that the fourth center is trans to the third by previous analogies and by spectral data. Absolute confirmation of the structure is pending the results of an x-ray analysis. The structures of the olefins 109 and 110, formed in 62% yield from the alcohol 82, were confirmed by alternate synthesis of their hydrogenation product. Based on the results of these model studies, alcohol 51 was synthesized, and its cyclization was studied in hopes of obtaining the pentacyclic olefin 50. A compound with spectroscopic data consistant with the structure of 50 was isolated on brief treatment with stannic chloride in dichioromethane. Unfortunately, the yield was only 12%. In order to establish the structure of the pentacyclic olefin as 50, a sequence of reactions was devised to transform the olefin into the pentacyclic ether D-6. The required two carbon atoms were introduced via an eight-step sequence, affording the pentacyclic aldehyde 191 in 6.5% yield from olefin 50. Attempts to deoxygenate the carbonyl oxygen were unsuccessful. The structure of the olefin is believed to be 50 on the basis of its nmr spectrum, which shows an angular methyl group at 1.05 ppm, assigned to the methyl at C6-b, since it would lie in plane of the C-11,12 double bond. The other stereochemically possible product is the trans,anti,cis,anti,cis olefin 204. In addition to being an unlikely product on mechanistic grounds, the structure of this olefin would place the C-6b[...] out of the plane of the double bond, thereby placing its chemical shift at higher field.\r\n\r\nThe yield and selectivity in the cyclization reaction appears to decrease as the number of alkyl substituents on the internal double bonds is increased. This is explained on the basis of the stronger interactions that would develop in the transition states in the substituted cases, as opposed to those with a lesser degree of olefin substitution.\r\n\r\nIn a related study the cyclopentenol 194 was cyclized with stannic chloride to afford a 37% yield of the pentacyclic olefin 195 which was successfully transformed into a known compound, the enone D-4. Like the ether D-6, D-4 was used previously as an intermediate in the first total synthesis of alnusenone (Ireland and Welch, 1970). Successful transformation of olefin 195 into enone D-4 served to confirm the structure of and also constituted another formal total synthesis of alnusenone." }, { "name": "Beranek, William, Jr.", "degree": "PhD", "year": "1973", "title": "Investigation of the Catalytic Mechanism of Lysozyme using Substrate Analogs", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06292018-110142577", "creators": [ { "name": { "family": "Beranek", "given": "William, Jr." }, "id": "Beranek-William", "display_name": "Beranek, William, Jr." } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/H0X0-M137", "abstract": "The catalytic mechanism of hen egg-white lysozyme is investigated by comparing the rate of hydrolysis of the trifluoro-Nacetyl analog of chitohexose to that of chitohexose. Since the binding properties of the two hexasaccharides are shown to be similar, differences observed in the rates of hydrolysis of the two oligosaccharides are discussed in terms of recent model studies for and mechanistic studies of lysozyme hydrolysis.
\r\n\r\nThe role of distortion in the catalytic mechanism is investigated by comparing the kinetic parameters of the lysozyme-catalyzed hydrolysis of a xylose substrate analog with that of a glucose substrate analog.
" }, { "name": "Bertolucci, Michael Dean", "degree": "PhD", "year": "1973", "title": "Investigations on the Crystal and Vibrational Structures of Sym-Trifluorobenzene, Sym-Trideuterotrifluorobenzene and Hexafluorobenzene at Low Temperatures", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122019-112405134", "creators": [ { "name": { "family": "Bertolucci", "given": "Michael Dean" }, "id": "Bertolucci-Michael-Dean", "display_name": "Bertolucci, Michael Dean" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gtz1-j092", "abstract": "The investigations on the low temperature crystallographic and spectroscopic properties of sym-trifluorobenzene and hexafluorobenzene have been divided into three logical sections. The first section, headed by a paper submitted for publication in the Journal of Applied Crystallography, reports the established crystallographic parameters required for the theoretical interpretations in sections two and three. Section two consists entirely of two papers to be submitted to the Journal of Molecular Spectroscopy. They describe the vibrational structures of 1, 3, 5 C6F3H3, 1, 3, 5 C6F3D3 and C6F6. These papers establish for the first time complete vibrational assignments for these molecules in their vapor, liquid and crystalline phases. The last section, which is concluded by a paper to be submitted to Chemical Physics Letters, represents the culmination of efforts expended in the previous sections. Here, the partial analysis of the vibronic contributions observed in the vapor phase 1A'1 \u2192 1A'2 transition in 1, 3, 5 C6F3D3 is used to verify previous unpublished work on the protonated isomer. These results form the basis from which the singlet-singlet absorption spectra of 1, 3, 5 C6F3H3 and 1, 3, 5 C6F3D3 at 4.2 \u00b0K were analyzed.
" }, { "name": "Blumenstein, Michael", "degree": "PhD", "year": "1973", "title": "I. \u00b3\u00b9P and \u00b9\u00b3C Nuclear Magnetic Resonance Studies of Nicotinamide Adenine Denucleotide and Related Compounds. II. \u00b9\u2079F Nuclear Magnetic Resonance Studies of Rabbit Muscle Glyceraldehyde-3-Phosphate Dehydrogenase Covalently Labeled with a Trifluoromethyl Group", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122019-135233564", "creators": [ { "name": { "family": "Blumenstein", "given": "Michael" }, "id": "Blumenstein-Michael", "display_name": "Blumenstein, Michael" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0XYM-Z897", "abstract": "The 31P spectra of the reduced and oxidized forms of nicotinamide adenine dinucleotides as well as several related mono- and dinucleotides have been obtained and analyzed. From the spectral differences between the reduced and oxidized nucleotides, as well as from the determination of the pKa values of the phosphate group in the mononucleotides, it is postulated that in the oxidized nucleotides there is an electrostatic interaction between the positively charged nitrogen of the pyridine ring and a negatively charged oxygen of the diphosphate backbone.
\r\n\r\nThe natural abundance 13C spectra of nicotinamide adenine dinucleotide and related compounds have been recorded and assigned. These spectra yielded further evidence for the nicotinamide-phosphate interaction in oxidized nucleotides. Small effects on the 13C spectra were observed upon changes in pH or nucleotide concentration.
\r\n\r\nRabbit muscle glyceraldehyde-3-phosphate dehydrogenase has been reacted with bromotrifluoroacetone, leading to a modified protein containing a trifluoromethyl group at each of its four active site cysteines. Addition of NAD+ or NADH caused changes in the 19F spectrum arising from the bound trifluoromethyl group. Also changes in pH affected the 19F spectrum. At high pH, two resonances were observed, leading to the conclusion that the enzyme, which is composed of four subunits having identical amino acid sequences, exists as an \u03b12\u03b12' protein. The chemical shift changes observed in this study (up to 19 parts per million) are considerably larger than those previously observed in 19F nuclear magnetic resonance studies of proteins.
\r\n\r\nMeasurements of the spin-spin and spin-lattice relaxation times of the enzyme bound trifluoromethyl group have been performed. It has been shown that the bound label has very little mobility, and interacts with solvent protons, as well as protons on other residues of the protein.
" }, { "name": "Carhart, Raymond Edgar", "degree": "PhD", "year": "1973", "title": "A Detailed Theoretical Study of the Difluoromethane Molecule", "advisor": "Roberts, John D.; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:03042011-095512877", "creators": [ { "name": { "family": "Carhart", "given": "Raymond Edgar" }, "id": "Carhart-Raymond-Edgar", "display_name": "Carhart, Raymond Edgar" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0SRB-RQ87", "abstract": "The first chapter describes our theoretical investigation of\r\nthe potential energy surface of the difluoromethane molecule. The\r\nHartree-Fock (HF) method, with a 73/3 gaussian basis contracted\r\nto the double-zeta level, was used, and in many cases, CNOO/2\r\ncalculations were included for comparison.\r\n\r\nThe optimum HF geometry is found to be closer to experiment\r\nthan that reported by other workers using a minimum (STO-3G)\r\nbasis set, but it appears that our more flexible basis does little to\r\nimprove the computed general harmonic force constants, the complete\r\nset of which is considered. The stretching constants are found to be\r\nin error by +20% to +35%, the bending constants by -4% to +45%.\r\nIn comparison with HF, the CNOO/2 method grossly overestimates\r\nthe stretching constants, but mimics rather well the bending and\r\ninteraction constants.\r\n\r\nThe theoretical (HF) normal modes and observed vibration\r\nfrequencies are combined to give a set of semi-empirical force\r\nconstants (SEFC's) which are used to predict the vibration frequencies\r\nof the deuterated difluoromethanes. The synthesis and IR spectrum\r\nanalysis of these compounds is described, and the SEFC predictions\r\nare found to be superior to ones appearing previously in the literature.\r\n\r\nThe Urey-Bradley potential (UBP) model, with 1/r^6 steric\r\nterms, is fit to the HF constants and SEFC's. A comparison of the\r\ntwo UBP models indicates that the HF method consistently over\r\nestimates all parameters but the F-F steric term, which it underestimates.\r\n\r\nAnharmonicity in the angular coordinates for large molecular\r\ndistortions is investigated, and it is found that CNOO/2 mimics HF\r\nquite well, except that CNOO/2 under estimates the anharmonicity\r\nwhen the fluorines are quite close together. The UBP model derived\r\nfrom the HF force constants is found to account for most of the\r\nanharmonicity in the HF energy variation.\r\n\r\nThe second chapter describes our investigation of the electronic\r\nstructure of difluoromethane. The HF method, with the basis set\r\ndiscussed above, and certain configuration-interaction methods, were\r\nused.\r\n\r\nThe localized (HF) molecular orbitals (LMO's) were obtained\r\nfor the equilibrium geometry using a new, quadratically convergent\r\napproach which is useful for cases in which convergence of the\r\nEdmiston-Ruedenberg \"two-by-two\" method is slow. The LMO's are\r\nexamined in detail, and several methods are used to show that the\r\nfluorine lone pairs are delocalized toward carbon, a delocalization\r\nwhich represents an important stabilization in the molecule. It is\r\nnoted that this effect, which is most pronounced for lone pairs lying\r\nin the F-C-F plane, may be the molecular-orbital equivalent of the\r\n\"double bond-no bond\" resonance of valence-bond theory.\r\n\r\nAn analysis of the LMO's for distorted geometries indicates\r\nthat the \"orbital following\" concept does not apply to difluoromethane\r\nas the F-C-F angle is altered.\r\n\r\nAn economical approximation to the generalized valence-bond\r\n(GVB) method is developed and is used to give a more detailed picture\r\nof the electron pairs in the molecule. The GVB-like pairs are\r\nlocalized, but in this case the localization is a result of the variation\r\nprinciple rather than a physically meaningless localization criterion.\r\nThey are used to define (in an apprOXimate fashion) \"naturally\"\r\nlocalized Hartree- Fock orbitals (NLMO's) qualitatively similar to\r\nthe LMO's.\r\n\r\nAn analysis of the NLMO's supports the conclusions drawn\r\nfrom the LMO analysis concerning lone-pair delocalization and\r\n\"orbital following\".\r\n" }, { "name": "Carroll, Felix Alvin", "degree": "PhD", "year": "1973", "title": "Studies of Photochemical and Photophysical Processes: I. The Photochemistry of 3-Methyl-1-Phenoxybut-2-Ene. II. The Role of Charge Transfer Interactions in the Quenching of 1,4-Dimethoxybenzene Fluorescence. III. A New Method for\r\nthe Determination of Intersystem Crossing Quantum Yields", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02102009-101143", "creators": [ { "name": { "family": "Carroll", "given": "Felix Alvin" }, "id": "Carroll-Felix-Alvin", "display_name": "Carroll, Felix Alvin" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WSAF-0X70", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I: The photochemical reactions 3-methyl-I -phenoxybut-2-ene [(8)] have been investigated in solution and in the gas phase. Irradiation of [8] results in the formation of phenol [(9)], 3-methy1-3-phenoxybutene[(10)], 1-(2-hydroxypheny1)-3-methylbut-2-ene [(11)], 1-(4 -hydroxypheny1)-3-methylbut-2-ene [(12)], 3-(2-hydroxyphenyl)-3-methylbutene [(13)], and 3-(4-hydroxyphenyl)-3-methylbutene [(14)]. Formation of [10-14] in the gas phase is efficiently quenched by nitric oxide. The results suggest that all products are formed by a dissociation-radical recombination mechanism and that none are formed by concerted processes. The absorption spectrum of [8] and its quantum yields of photochemical reaction and fluorescence are used to estimate the rates of the processes which deactivate its lowest-lying excited singlet state. The results suggest that O-C bond homolysis need not occur via intersystem crossing from an S[subscript 1](\u03c0,\u03c0*) to a [superscript 3]\u03c3(C-O) state. Fragmentation to radicals, and perhaps nonradiative decay without chemical reaction, probably involves excitation to high vibrational levels of the C-O bond. Weak electronic interaction between the aromatic and olefinic chromophores may also be important.\r\n\r\nPART II: The fluorescence of 1,4-dimethoxybenzene (DMB) in acetonitrile is quenched by a number of organic compounds having lowest-lying excited singlets higher in energy than that of DMB. The rate constants show a structure-reactivity pattern which implicates charge transfer as an integral process, but they do not agree qualitatively with rate constants predicted from a kinetic formulation involving the intermediacy of radical ion pairs. The results suggest that charge transfer provides the binding energy of the exciplex, while the internal conversion of electronic excitation involves a vibronic mechanism which depends primarily on the type of quencher (organic chloride, acetate, or mesylate) and not on its reduction potential.\r\n\r\nPART III: A method is described for the determination of intersystem crossing quantum yields which is especially useful for benzene derivatives. The experimental procedure involves measurement of relative fluorescence intensities of the aromatic compound and relative yields of isomerization of a \"triplet counter\" in solutions with varying concentrations of a heavy atom fluorescence quencher such as xenon. Intersystem crossing quantum yields for anisole, mesitylene, and toluene in isooctane solution are 0.74, 0.60, and 0.52, respectively.\r\n" }, { "name": "Chow, Louise Tsi", "degree": "PhD", "year": "1973", "title": "Genetic Sequences by Electron Microscopy", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02072018-084611335", "creators": [ { "name": { "family": "Chow", "given": "Louise Tsi" }, "id": "Chow-Louise-Tsi", "display_name": "Chow, Louise Tsi" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YNNT-V341", "abstract": "Part I: Sequence homology between the DNA molecules of the \r\ntwo temperate Bacillus subtilis bacteriophages, SPO2 and \u00d8 105,\r\nhas been mapped by electron microcope observation of heteroduplexes.\r\nThere is a region of partial homology covering about 14 % of the\r\ngenome (3.8 x 106 daltons) close to the center of the heteroduplex\r\nmolecule, flanked by completely non-homologous regions of lengths\r\nabout 1.2 x 107 and 1.0 x 107 daltons on the two sides. Within the\r\ncentral homologous region there is a characteristic pattern of duplex \r\nregions and single-strand loops. The amount of duplex decreases as \r\nthe denaturing power of Ue solvent used for preparing the electron \r\nmicroscope grids increases; this indicates that the DNA molecules\r\nof the two phages are only partially homologous w ithin the homology \r\nregion. The heteroduplex patterns show that there are no completely \r\nhomologous nor completely non-homologous gene size sequences within \r\nthe central region of partial homology. Since the phages are sero\u00adlogically \r\nrelated, we conclude that the antigenic determinants for serological \r\ncross-reactivity in the phage tails are coded for by genes in the central \r\nregion of homology. This conclusion is consistent with available genetic \r\ndata. Comparison of genetic and physical data indi\u00adcates that the genes \r\nfor DNA synthesis and for clear plaque formation in the two phages are \r\nnon-homologous. The molecuiar weights of SPO2 DNA and \u00d8 105 DNA are both\t\r\ncalculated as 26.3 (\u00b1 0.3) x 106 daltons, from length measurements \r\nrelative to \u00d8x 174 RF II DNA. Both DNA's have cohesive ends and are capable \r\nof reversible cycli\u00adzation the joined ends dissociate more readily that \r\ndo those of \u03bb DNA. Our physical studies show that each phage DNA consists \r\nof a unique linear sequence and is not circularly permuted, in agreement with \r\nthe conclusion from genetic studies that both phage maps are linear.
\r\n\r\nPart II: Circular duplex structures of the correct length are \r\nobserved in the electron microscope in hybridization mixture of \r\nlysogen DNA and mature phage DNA for the case of the temperate \r\nBacillus subtilis SPO2. This result shows that the sequence order\r\nof the prophage is a circular per mutation of that of the mature phage. \r\nBy making heteroduplexes of prophage DNA with that of the SPO2 \r\ndeletion mutants R90 and S25, the att site of the phage has been\r\nmapped at 61.2 \u00b1 0.6 % from one end of the mature phage DNA,\r\nwhich has a length of 38,600 base-pairs. In the same coordinate \r\nsystem, the R90 deletion extends from 58.9 \u00b1 0.7 to 66.8 \u00b1 0.8 % \r\non the SPO2 chromosome whereas the S25 deletion extends from\r\n63.2 \u00b1 0.6 to 66.9 \u00b1 0.7 % In similar experiments with lysogen and\r\nmature phage DNA's of the temperate B. subtilis phage, \u00d8 105, no \r\ncircular structures were seen. This result shows that the sequence \r\norder in the prophage and the phage are collinear, without circular \r\npermutaion. Short duplex segments, of length 4830 \u00b1 250 base pairs, \r\nwith two single-strand arms at each end are seen at a low frequency \r\nafter denaturation and renaturation of B. sublitis DNA. Several lines \r\nof ecidence support the hy pothesis that these duplex segments are\r\nformed by out-of-register renaturation of the 16s+23s ribosomal \r\nRNA genes (rDNA) of B. subtilis. They are of the correct length. \r\nTheir formation is inhibited if homologous but not if heterologous\r\nribosomal RNA is added to the hybridization mixture. The frequency \r\nof occurrence of the duplex structures is consistent with the rDNA\r\nhypothesis. Heteroduplex molecules are seen with two or three rDNA \r\nduplex segments separated by single-strand substitution loops with \r\nspecific lengths for each of the two single-strand arms of any one \r\nloop. On the basis these structures, linkage groups containing\t7\r\nto 9 rDNA sets (each set containing one 16s and one 23s rDNA gene) \r\nseparated by spacer DNA's are proposed. The evidence indicates\r\nthat if 5s rDNA is present in the set it is located near one end to \r\ngive a gene order 16s-23s-5s. All of the 16s rDNA genes are \r\nlinked to 23s rDNA and vice versa with little or no spacer DNA \r\nbetween a 16s and a 23s sequence. The spacer DNA between 23s \r\nand 5s must also be short. The propnage SPO2 bacterial att \r\nsite maps at a distance 6200 bases away from a 16s+23s rDNA set \r\nwhich is itself separated by a very short spacer (less than \r\n600 bases) from a second rDNA set.
\r\n\r\nPart III: The genetic sequences of seventeen different \u03bbdv's \r\nobtained Dr. D.E. Berg have been mapped on \u03bb DNA by the elec\u00adtron \r\nmicroscope heteroduplex method. The physical results are\r\nin agreement with the genetic analyses of the contents of the \u03bbdv's. \r\nDifferent \u03bbdv's exist predominantly either as monomers, or as \r\ndimers, or as trimers in recA- carrier cells. Higher order \r\noli\u00adgomers are also found in all\u03bb \u03bbdv preparations, Most of the \u03bbdv's \r\noriginated from \u03bb phage carrying the nin deletion are observed to \r\ncontain inverted partial duplications (and are called amphimers).\r\nThat is, the \u03bbdv's carry a duplication of all or some of the sequences \r\nin an inverted order on the same strand. There are four types \r\nof inverted repeat structures: (1) complete inversion and duplication,\r\n(2) partial inversion and duplication with a long (5.7 % of \u03bb+) non\u00ad-\r\ninverted, non-duplicated (or unique) sequence on the left end \r\ncovering the immunity region (oriented according to the \u03bb map), (3) \r\npartial inversion and duplication with a long (5.1 %) and a short\r\n(2.2 %) unique sequence on the left and the tight ends respectively,\r\n(4) partial inversion and duplication with a very short (<0.7 %) \r\nunique sequence on the right end of the \u03bbdv's near the nin deletion. \r\nWhen the closed circular molecules of these inverted \u03bbdv's are \r\nnicked lightly, denatured by alkali, and then reneutralized, the\r\ncomplementary sequences on the same DNA strand \"snap back\" \r\nto form double-stranded linear molecules. The unique sequences,\r\nif any, appear as single-stranded loops at one or both ends when \r\nthe above treated DNA preparations are mounted by the formamide \r\ntechnique. Lambda phage that does not carry the nin deletion does \r\nnot produce \u03bbdv's with inverted repeats. Denaturation of the open \r\ncircular molecules of these non-inverted \u03bbdv's generates, as \r\nexpected, only single-stranded circular and single-stranded linear \r\nmolecules when mounted by the formamide technique. The nin \r\ndeletion is believed to have caused somehow the formation of the\r\n\u03bbdv's containing inverted repeats. The left end points of many \u03bbdv's \r\nmap around 73 % on the \u03bb map while the right boundaries of many\r\n\u03bbdv's map in the vicinity of the nin deletion which extends from\r\n83.8 to 89 .6 % on \u03bb+, indicative of two regions of high \r\nrecombination frequency.
" }, { "name": "Gammon, Kenneth Lee", "degree": "PhD", "year": "1973", "title": "Nuclear Magnetic Resonance Studies of \u03b1-Chymotrypsin: I. NMR Studies of the Binding of Small Molecule Inhibitors to \u03b1-Chymotrypsin. II. NMR Studies of the Interaction of N-TFA-D-Tryptophan Semicarbazide with \u03b1-Chymotrypsin. III. \u00b9\u00b3C-NMR Studies of Methylated \u03b1-Chymotrypsin. IV. NMR Studies of Acylated Chymotrypsins", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052018-102944228", "creators": [ { "name": { "family": "Gammon", "given": "Kenneth Lee" }, "id": "Gammon-Kenneth-Lee", "display_name": "Gammon, Kenneth Lee" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XXJX-AD69", "abstract": "Part I
\r\n\r\nMagnetic resonance studies of the interaction of N-trifluoro-acetyl-D-(and L-)p-fluorophenylalanine\r\nand N-trifluoro-acetyl-D-(and L-)tryptophan with \u03b1-chymotrypsin have been carried out at\r\npH 5.0-8.0. The effect of enzyme oligomerization and competitive\r\ninhibition have been quantitatively accounted for. The trifluoro-\r\nacetyl group of the D-isomer of both inhibitors is directed toward\r\nthe active site of the enzyme, while that of the L-isomers is\r\ndirected toward Ser 214. The aromatic side chain of all inhibitors\r\nresides in the hydrophobic specificity pocket of the enzyme.\r\nIonization of a group on the free enzyme with pKa of 6.6\r\n(presumably His 57) leads to a sharp decrease in binding affinity\r\nof the enzyme for anionic inhibitor molecules.
\r\n\r\n\r\nPart II
\r\n\r\n\r\nNuclear magnetic resonance studies of the binding of\r\nN-trifluoroacetyl-D-tryptophan semicarbazide at pH 5.0-9.0 have \r\nbeen carried out. Ionization of a group on the free enzyme\r\n(tenatively assigned to His 40) causes a nine-fold increase in the\r\nenzyme-inhibitor dissociation constant. Neutralization of His 57\r\naffects only the chemical shift of the bound inhibitor molecule.
\r\n\r\n\r\nPart III
\r\n\r\n\r\nCarbon -13 nuclear magnetic resonance studies of methylated\r\n\u03b1-chymotrypsin have been carried out. Selective enrichment of the\r\nmodifying methyl group allows assignment of this resonance. The\r\npH-dependent shift of the methyl group has been measured and\r\nindicates a pKa of 6.75. The direction of the shift upon \r\nionization (30 Hz downfield) indicates that this ionization is \r\naccompanied by a conformational change.
\r\n" }, { "name": "Guberman, Steven Lawrence", "degree": "PhD", "year": "1973", "title": "I. Projected G1 wavefunctions for He\u2082. II. Localized wavefunctions for H\u2082O, OH, and O", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222009-105738617", "creators": [ { "name": { "family": "Guberman", "given": "Steven Lawrence" }, "id": "Guberman-Steven-Lawrence", "display_name": "Guberman, Steven Lawrence" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TA01-KS50", "abstract": "I. The low-lying excited states of He_2 have been examined using projected Generalized Valence Bond wavefunctions. Two types of interactions are shown to be important in understanding the anomalous maxima \r\nand the general shapes of the curves. The interaction between core orbitals on opposite centers is important at small R whereas at large R the dominant interaction is between core and Rydberg orbitals on opposite centers. The latter effect is expressible in terms of the exchange kinetic energy and arises from the repulsion between singlet coupled pairs of orbitals. This is described simply in terms of the shapes of the Rydberg orbitals. The results in general agree favorably with experiment where such comparison can be made.\r\n\r\nII. Localized wavefunctions obtained from applying an external localization criterion to orbitals resulting from the GF method are reported for H_2O, OH, and 0. The shapes and angles between the orbitals \r\nare described in some detail. It is shown that the resulting GF orbitals change in a chemically reasonable manner as we proceed from 0 to OH to H_2O.\r\n" }, { "name": "G\u00fclari, Erdogan", "degree": "PhD", "year": "1973", "title": "A Laser Light Scattering Study of Transport and Critical Phenomena", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09072018-113523680", "creators": [ { "name": { "family": "G\u00fclari", "given": "Erdogan" }, "id": "G\u00fclari-Erdogan", "display_name": "G\u00fclari, Erdogan" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6YQH-1T42", "abstract": "The intensity and Rayleigh linewidth have been measured as a function of temperature and scattering angle for light scattered by concentration fluctuations near the\r\ncritical point of the binary liquid system 2,6-lutidine-water.
\r\n\r\nFrom the intensity data it is found that \u03b3 = 1.26 \u00b1 0.02 and \u03bd = 0.61 \u00b1 0.07. From the linewidth data the mutual diffusion coefficients were calculated as a function of\r\ntemperature. It is found that the diffusion coefficient decreases as the critical point is approached. The behavior of the linewidth as a function of k\u2208 was compared\r\nwith the Kawasaki theory without the nonlocal viscosity and vertex corrections. General agreement with some systematic deviations is observed.
\r\n\r\nThe shear viscosity anomaly in the same system was also studied in detail by measuring the shear viscosities as a function of temperature near the critical point.\r\nResults of analyses indicate that the viscosity is at most weakly divergent, with an exponent \u00f8 \u2243 \u00b10.001.
\r\n\r\nLight scattering techniques have been employed to measure the mutual diffusion coefficient D as a function of concentration in ten binary mixtures and the thermal\r\ndiffusivity \u03c7 in nine pure liquids and one binary mixture. The diffusion coefficient was also measured at one or two concentrations for four binary mixtures. The values obtained are in excellent agreement with the available literature data determined by more classical methods. Under most circumstances light scattering is found to offer\r\na fast and accurate way of determining \u03c7 and D.
\r\n\r\nThe turbidity \u03c4 and the decay rate \u0393 of the density fluctuations have been measured as a function of temperature on the critical isochore of ethane near the critical\r\npoint.
\r\n\r\nFrom the turbidity data absolute values of isothermal compressibilities and correlation lengths were calculated. The isothermal compressibility KT and the correlation length \u2208 are found to behave as:
\r\n\r\nKT = 1.24 \u00b1 0.11 x 10-3(\u0394T/Tc)-1.225 \u00b1 0.02atm-1
\r\n\r\n\u2208 = 1.64 \u00b1 0.20 (\u0394T/Tc)-0.664 \u00b1 0.02 \u00c5.
\r\n\r\nFrom the \u0393 data thermal diffusivities, thermal conductivities and excess thermal conductivities were calculated as a function of temperature. It is found that the thermal\r\ndiffusivity does not exhibit a simple power law behavior whereas the excess thermal conductivity does with an exponent of \u03c8 = 0.605 \u00b1 0.02. The singular part of the decay\r\nrate \u0393s, was compared with the Kawasaki expression with the nonlocal viscosity correction. It is observed that the nonlocal viscosity correction together with the vertex and the correlation function corrections improve the agreement between the theory and the experiment.
\r\n\r\nThe results for the isothermal compressibility, the thermal conductivity and the excess thermal conductivity are in very good agreement with the available literature\r\ndata.
\r\n" }, { "name": "G\u00fclari, Esin Cetegen", "degree": "PhD", "year": "1973", "title": "A Study of Critical Phenomena in Krypton", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09192018-095409363", "creators": [ { "name": { "family": "G\u00fclari", "given": "Esin Cetegen" }, "id": "G\u00fclari-Esin-Cetegen", "display_name": "G\u00fclari, Esin Cetegen" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/NNTS-KJ75", "abstract": "A detailed experimental study of equilibrium critical phenomena in krypton was made. Using the method of angle of minimum deviation the refractive index was measured along the coexistence curve, along 16 isotherms above and along 11 isotherms below the critical temperature. The range of the temperature measurements in terms of t the reduced temperature difference from Tc was -6.8 x 10-2 \u2266 t \u2266 -5.7 x 10-5 and 3.8 x 10-5 \u2266 t \u2266 4.8 10-2. The measurements were planned so that the region very near the critical point was covered in most detail. The refractive index was related to the density through the Lorentz-Lorenz relation.
\r\n\r\nAfter proper weight assignment, the data were analyzed in terms of the asymptotic power laws. The following values of the critical parameters, exponents and coefficients were determined: Tc = 209.286 \u00b1 0.010\u00b0K, Pc = 54.213 \u00b1 0.003 atm., LLc = 0.070588 \u00b1 0.000006, \u03b2 = 0.3571 \u00b1 0.0008, B = 1.840 \u00b1 0.001 \u03b3 = 1.182 \u00b1 0.008, \u0393 = 0.0835 \u00b1 0.0011; \u03b3G\u2019 =1.15 \u00b1 0.01, \u0393G\u2019 = 0.021 \u00b1 0.001, \u03b3L\u2019 = 1.13 \u00b1 0.01, \u0393L\u2019 = 0.025 \u00b1 0.001; \u03b4 = 4.25 \u00b1 0.25. The law of the rectilinear diameter was obeyed with its slope = 0.0918 \u00b1 0.0004.
\r\n\r\nThe reduced chemical potential differences and the reduced density differences were calculated. The chemical potential was observed to show antisymmetry for\r\n-2 x 10-3 \u2266 t < 4.8 x 10-2 and -0.3 < \u0394LL < 0.3. The data in this range were analyzed using Widom's equation of state and the closed-form(29) of h(x). The proposed equation was found to fit the experimental data very well.
\r\n\r\nThe predictions of the linear model(32) were also checked and were observed to be consistent with the experimental results.
\r\n" }, { "name": "Harris, Daniel Charles", "degree": "PhD", "year": "1973", "title": "More Fun Than Anything", "advisor": "Rossman, George Robert; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10232017-110825526", "creators": [ { "name": { "family": "Harris", "given": "Daniel Charles" }, "id": "Harris-Daniel-Charles", "display_name": "Harris, Daniel Charles" } ], "advisors": [ { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-G-R", "role": "advisor", "display_name": "Rossman, George Robert" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XBQW-9V06", "abstract": "An exhaustive study of piddling cyclopropenium salts is described.\r\nThis includes synthesis, characterization and the study of ligand
\r\n\r\n(See PDF)
\r\n\r\nsubstitution reactions of the M2Cl62- anions. The electronic absorption\r\nspectra and vibrational spectra are interpreted. A normal coordinate \r\nanalysis of the M2Cl62- anions are reported. Startling counterion effects\r\nin ligand substitution reactions in CH2Cl2 solvent were observed.
\r\n\r\n\r\nThe transformation M-M \u2192 M-H-M+, in which a metal-metal\r\nbond is protonated by strong acid, has been studied in several organomettalic\r\nsystems. Electronic spectra are tentatively interpreted in\r\nterms of three-center two-electron M-H-M bonding. The stretching\r\nvibrations associated with a W-H-W bridge are assigned. Infrared\r\nspectra indicate the presence of isomeric protonated species for\r\nseveral iron compounds. Base strength determination indicates that\r\nthe replacement of Fe by Ru or replacement of CO by P(OCH3)3 both\r\nincrease the basicity of [(\u03c0-C5H5)Fe(CO)2]2 by at least 2-3 orders of magnitude.
\r\n\r\nAncillary chapters deal with the present state of \u03c0-cyclopropenium \r\nchemistry, predictions about the infrared spectra of \u03c0-cyclopropenium \r\ncomplexes and an original technique for graphical display of the con\u00adcentrations \r\nof the various species present during an acid-base titra\u00adtion in \r\nacetic acid. A brief description of my advanced placement \r\nfreshman chemistry course is included.
\r\n" }, { "name": "Hecht, Thomas Arnold", "degree": "PhD", "year": "1973", "title": "Development of a Generalized Kinetic Mechanism for Photochemical Smog", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08172018-124115870", "creators": [ { "name": { "family": "Hecht", "given": "Thomas Arnold" }, "id": "Hecht-Thomas-Arnold", "display_name": "Hecht, Thomas Arnold" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NEJT-CW55", "abstract": "In this dissertation a generalized kinetic mechanism for photochemical smog is formulated and validated. There are two basic objectives for pursuing this work. First, kinetic mechanisms are a critical component of airshed simulation models whose uses include the evaluation of alternative control strategies for photochemical smog. Second, kinetic mechanisms provide a means of understanding the chemistry of smog formation. In addition to developing the kinetic mechanism, extensive consideration is given here to further experimental studies of the kinetics of elementary reactions and to procedural aspects of smog chamber experiments which will aid in reducing uncertainty in future mathematical simulation studies.
\r\n\r\nThe most important feature of the kinetic mechanism which 1s presented in Chapter I lies in its general nature; that is, the mechanism has been written so as to be applicable to a large number of hydrocarbons -- and, ultimately, the entire atmospheric hydrocarbon mix -- rather than just a specific hydrocarbon such as propylene. The rationale for the lumping procedure is described in detail. By design the resultant mechanism takes advantage of the general features typical of smog formation to maintain at a minimum the number of reactions and species included while at the same time retaining a high degree of detail, especially as concerns the chemistry of the inorganic species. In essence a careful balance between compactness of form and accuracy of prediction is sought. The mechanism is then validated using n-butane-NOx, propylene-NOx, and n-butane-propylene-\r\nNOx smog chamber data at 13 different sets of initial reactant concentrations and a wide variety of hydrocarbon to NOx ratios.
\r\n\r\nSeveral sources of potential uncertainty in the predictions of the mechanism are discussed. Of these the two most serious -- and the two most amenable to correction -- are gaps in our knowledge of rate constants and mechanisms of key elementary reactions and effects related to smog chamber systems which either alter or incorrectly monitor the course of smog formation in controlled experimenta1 studies. These sources of uncertainty along with recommendations for future studies to minimize them are the topics of Chapters II and III.
\r\n" }, { "name": "Helgeson, Norman Lewis", "degree": "PhD", "year": "1973", "title": "I. Latent Heat of Vaporization of Propane. II. Partial and Total Heats of Vaporization for the N-Propane/N-Decane Mixture", "advisor": "Pings, Cornelius J.; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272018-112734108", "creators": [ { "name": { "family": "Helgeson", "given": "Norman Lewis" }, "id": "Helgeson-Norman-Lewis", "display_name": "Helgeson, Norman Lewis" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/GPGR-N481", "abstract": "Experimental measurements are reported for total and partial heats-of-vaporization for the n-propane/n-decane system. Results are given for the 100, 130 and 160\u00b0F. isotherms and cover the entire composition range. It is shown that the temperature and concentration gradients which develop within the system during the vaporization process may, in some cases, cause a significant (~0.4%) deviation in the calculated results. A method is provided for introducing a correction for this effect. Based on the partial heat-of-vaporization of n-propane, heats-of-mixing for the liquid solution are calculated. The results are in qualitative agreement with predictions from theories for n-alkane liquid mixtures.
" }, { "name": "Huestis, David Lee", "degree": "PhD", "year": "1973", "title": "I. The Projected GI Method and the Excited States of H\u2082. II. A Superposition Principle for Siegert Resonant States", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052009-132233582", "creators": [ { "name": { "family": "Huestis", "given": "David Lee" }, "id": "Huestis-David-Lee", "display_name": "Huestis, David Lee" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zqek-hg39", "abstract": "The simplest orbital wavefunction that adequately describes the dissociation of the excited states of homonuclear diatomic molecules must involve a spatial symmetry projection operator. The use of such a wavefunction has been developed in detail and applied to the excited states of the hydrogen molecule. It was found that the advantages of an independent-particle description are enhanced considerably by spatial projection. The low-lying \u03a3 states of H_2 are explained unambiguously and convincingly in terms of orbital character based on the model of the one-electron heteronuclear diatomics.\r\n\r\nRecent experimental work in electron impact spectroscopy has illustrated that short-lived negative-ion resonances must play an important role. In an attempt to show that such resonances form a natural and complete characterization of the scattering process, the properties of the resonant states defined by Siegert have been investigated. In specific, a superposition principle for Siegert states was found, which provides a complete description of any quantum mechanical event involving a potential of finite range.\r\n" }, { "name": "Kelsey, Donald Ross", "degree": "PhD", "year": "1973", "title": "I. Studies on Cycloproply-Stabilized Vinyl Cation Intermediates. II. Molecular Orbital Calculations on Cationic Intermediates and Displacement Reactions. III. On the Complexation of NMR Lanthanide Shift Reagents with Organic Substrates", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09072018-101527022", "creators": [ { "name": { "family": "Kelsey", "given": "Donald Ross" }, "id": "Kelsey-Donald-Ross", "display_name": "Kelsey, Donald Ross" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QV6K-J118", "abstract": "I. The heterogeneous and homogeneous silver-catalyzed acetolyses of E- and Z-1-cyclopropyl-1-iodopropene (1E and 1Z, R = methyl), E- and Z-1,2-dicyclopropylethylene (1E and 1Z, R = cyclopropyl), E- and Z-1-cyclopropyl-3-ethyl-1-iodopentene (1E and 1Z, R = 3-pentyl), and 1-iodo-3,4-hexadiene (4) are examined in detail. The acetate product distributions reveal small, but important, contributions of heterogeneous catalysis, clearly show overall net inversion of geometry in the formation of the corresponding vinyl acetates under homogeneous conditions, and reveal selectivity in the cyclopropyl ring-opening rearrangements of the intermediate vinyl cations. The results are consistent with the intervention of non-equilibrated ion-pair intermediates which undergo both some solvent trapping and ring-opening rearrangement with net inversion and dissociation to linear, sp-hybridized vinyl cations. It is also found that the steric\r\neffects of the \u03b2-alkyl substituents R are important in determining the extent of ion-pair contribution. The product distributions are also highly dependent upon the R substituent, with the ratio of vinyl acetates to rearranged cyclobutyl-type acetates decreasing as R changes from hydrogen, to 3-pentyl, to methyl, to cyclopropyl. It is shown that this is consistent with the conjugative electron-releasing ability of R in stabilizing the transition state for rearrangement of the vinyl cations, whereas the initial ionizations of the vinyl iodides (Z isomers) qualitatively depend upon the inductive electronic properties of R. Other electronic and steric effects of substituent R are discussed.
\r\n\r\nIt is also shown that 1E and 1Z, R = cyclopropyl, with deuterium label in the \u03b2-cyclopropyl ring, undergo reaction with no isotopic scrambling, indicating the absence (< 0.2%) of 1,2-hydride shift across the double bond in the 1,2 dicyclopropylvinyl cation. A similar result (< 1% rearrangement) is found for the 1,2-dicyclopropylethyl cation. These results are discussed in terms of \u03c3-delocalization of the cyclopropyl rings adjacent to the cationic centers.
\r\n\r\nII. This part has been published in full, see D.R. Kelsey and R.G. Bergman, Journal of the American Chemical Society, 93, 1953 (1971).
\r\n\r\nIII. An explicit treatment of the complexation equilibrium between organic substrates and the lanthanide nmr shift reagents is developed. It is shown that for a single equilibrium, plots of the observed shifts of two substrate protons, i and j, against one another must be linear with slopes that reflect the ratios (\u0394maxi/\u0394maxj) of the chemical shifts in the bound complex. This \"internal standard proton\" method is applied to sixteen vinyl and eleven allyl acetates using the acetoxy methyl protons as standard and Eu(fod)3 shift reagent. Characteristic slopes are obtained which depend upon the stereochemical relationships to the reference group. The method is shown to be a valuable and reliable means of establishing substrate structures even for isomeric mixtures, since impurities and concentrations have little effect.
\r\n\r\nIt is shown that at large ratios of substrate to reagent concentrations, St/Et, a plot of reciprocal observed shift, 1/\u0394obsd, against the total substrate concentration, St, should be linear if a 1:1 stoichiometry obtains. The plots of the data for representative substrates (allyl acetate, isopropenyl acetate, 2-butanone, tetrahydrofuran, 2-propanol, and dimethyl sulfoxide) with Eu(fod)3 show excellent linearity and estimated bound chemical shifts, \u0394max, and equilibrium constants, K, are obtained. The results for dimethyl sulfoxide suggest that the major complex stoichiometry is 1:1 at room temperature, even though the literature data suggest formation of a 2:1 (DMSO: Eu(fod)3) complex at low temperatures. It is observed that the limiting observed shifts, \u0394lim, obtained at high Et/St ratios are generally less than the \u0394max values. This and other observations are discussed in terms of non-ideal solution behavior at high reagent concentrations. A bibliography of 240 references is included.
" }, { "name": "Kyan, Chwan Pein", "degree": "PhD", "year": "1973", "title": "Determination of Optimal Air Pollution Control Strategies", "advisor": "Seinfeld, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122019-165102707", "creators": [ { "name": { "family": "Kyan", "given": "Chwan Pein" }, "id": "Kyan-Chwan-Pein", "display_name": "Kyan, Chwan Pein" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "orcid": "0000-0003-1344-4068", "role": "advisor", "display_name": "Seinfeld, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/H6WX-2303", "abstract": "One of the important environmental problems facing urban officials today is the selection and enforcement of air pollutant emission control measures. These measures take two forms: long-term controls (multi-year legislation, such as the Federal new car emission standards through 1976) and short-term controls (action taken over a period of hours to days to avoid an air pollution episode). What is required for each form of control is a methodology for the systematic determination of the \"best\" strategy from among all those possible. In this thesis, a general theoretical framework for the determination of optimal air pollution control strategies is presented for both long-term and real-time controls.
\r\n\r\nFor the long-term control problem, it is assumed that emission control procedures are changed on a year-to-year basis. The problem considered is to determine the set of control measures that minimizes the total cost of control while maintaining specified levels of air quality each year. It is assumed that an airshed model exists which is capable of predicting pollutant concentrations as a function of source emissions in the airshed. Both single-year and multi-year problems are treated. Computational methods are developed based on mathematical programming techniques. The theory and computational methods developed are applied to the evaluation of long-term air pollution control strategies for the Los Angeles basin. Optimal strategies for the control of carbon monoxide, nitrogen dioxide and ozone for 1973 to 1975 in the Los Angeles basin have been obtained.
\r\n\r\nThe problem of determining real-time (short-term) air pollution control strategies for an urban airshed is posed as selecting those control measures from among all possible such that air quality is maintained at a certain level over a given time period and the total control imposed is a minimum. The real-time control is based on meteorological predictions made over a several hour to several day period. A computational algorithm is developed for solving the class of control problems that result.
\r\n\r\nTypical control measures include restrictions on the number of motor vehicles allowed on a freeway, reduced operation of power plants, and substitution of low emission fuel (e.g. natural gas) for high emission fuel (e.g. coal) in power plants. The control strategy is assumed to be enforced over a certain period, say, one hour, based on meteorological predictions made at the beginning of the period. The strategy for each time period could be determined by an air pollution control agency by means of a computer implementing the algorithm presented. The theory is applied to a hypothetical study of implementation of the optimal control on September 29, 1969 in the Los Angeles basin.
" }, { "name": "Macmurchie, Donald David", "degree": "PhD", "year": "1973", "title": "Conformational Aspects of Valinomycin by \u00b9H and \u00b9\u00b3C Nuclear Magnetic Resonance", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032012-161933043", "creators": [ { "name": { "family": "Macmurchie", "given": "Donald David" }, "id": "Macmurchie-Donald-David", "display_name": "Macmurchie, Donald David" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AA4Y-Z215", "abstract": "The conformation of valinomycin and its complex with\r\npotassium ion has been investigated by spectroscopic means\r\nand a plausible structure for the complex has been put forward.\r\nThe essential features of the complex structure are consistent\r\nwith the spectral data and the conformation in the crystal state.\r\nInconsistencies between the spectral observations and crystal\r\nstructure analysis of non-complexing valinomycin may be resolved\r\nif a rapid conformation equilibrium in solution is postulated; evidence\r\nfor this process is discussed. The characteristics of valinomycin\r\nare compatible with an independent mechanism of ion transport." }, { "name": "Meister, John Joseph", "degree": "PhD", "year": "1973", "title": "Bifunctionate Solutions to the Schr\u00f6dinger Equation for Reactive, Three-Atom, Colinear Encounters", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312018-092115580", "creators": [ { "name": { "family": "Meister", "given": "John Joseph" }, "id": "Meister-John-Joseph", "display_name": "Meister, John Joseph" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fhwd-vj37", "abstract": "Two methods for solving the Schr\u00f6dinger equation for one\r\ndimensional, three atom, electronically adiabatic, reactive\r\ncollisions have been investigated. The first bifunctionate method\r\nwas proposed by Diestler in 1969. It solves for vibrational\r\nexcitation probabilities by expanding two parts of the total\r\nsolution to the scattering problem in eigenfunctions of the\r\nunperturbed diatoms. These diatoms are the target and product\r\ndiatoms in the reactive encounter. This formalism allows the\r\neigenfunction series representation of the total solution to decay\r\nto zero in the interaction region of the reaction. Proposition\r\n1 shows that this decay process is indicative of a failure in\r\nDiestler's method which renders its solutions invalid.
\r\n\r\nA technique proposed as a means of solving the equations \r\ngoverning nuclear collisions was also investigated. This\r\nformalism, called the Method of Subtracted Asymptotics, has \r\nbeen shown to be an application of the general mechanism of \r\neigenfunction expansion to the scattering problem. Because of \r\nanalysis problems induced by the extensive eigenfunction series \r\ndemanded by this method, the Method of Subtracted Asymptotics \r\nis not an efficient or practical manner of solving the scattering \r\nproblem. This method is treated in part 2 of this work.
\r\n\r\nTests used to varify the numerical accuracy of several \r\nstudies of the Method of Subtracted Asymptotics required the \r\nvalues of several special functions on the complex plane. To\r\nmeet these needs, algorithms which compute the value of a \r\ncomplex number raised to a complex power, the Gamma \r\nfunction, the Digamma function and the Hyper geometric function \r\nwere prepared. These algorithms are discussed and presented \r\nin part 1 of this thesis.
" }, { "name": "Melius, Carl Frederick", "degree": "PhD", "year": "1973", "title": "I. A Theoretical Investigation of the Charge Transfer Process in Alkali-Atom Alkali-Ion Collisions. II. Ab Initio Effective Potentials for Use in Molecular Calculations", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202009-152551437", "creators": [ { "name": { "family": "Melius", "given": "Carl Frederick" }, "id": "Melius-Carl-Frederick", "display_name": "Melius, Carl Frederick" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8YKN-Z171", "abstract": "PART I. The charge transfer processes occurring in collisions of alkali atoms with alkali ions have been studied theoretically using the molecular wavefunction approach. In Part A, we discuss the coupling process between electronic states as exemplified in collisions of Li + Na^+ and Na + Li^+. We find that the total transition process can be decomposed into a succession of simple two-state transition processes. The \u03a3-\u03a3 two-state process can be described by a three-step process involving a coupling region, an uncoupled phase changing region, and a decoupling region. On the other hand, in the molecular wavefunction formulation, the \u03a3- II two-state transition involves a continuous coupling process. The resulting transition probabilities for \u03a3-II coupling differs from \u03a3- \u03a3 coupling leading to different cross sections. In Part B, the molecular wavefunction approach is used to calculate the charge transfer cross sections of alkali-atoms and alkali-ions involving Li, Na, and K.\r\n\r\nPART II. We have investigated the method of effective potentials in replacing the core electrons in molecular calculations. The effective potential method has been formulated in a way which will simplify computations while preserving ab initio quality results. The effective potential is expressed in an analytic form which represents the actual ab initio non-local potential (as defined by the matrix elements for a given basis set). Furthermore, this analytic form permits efficient computations of the effective potential integrals by incorporating the properties of Gaussian basis functions. To minimize the number of basis functions required in the molecular calculations, we define a new ab initio effective potential derived from a modified IMF orbital whose core character has been removed. The effective potential method as formulated becomes a very strong but reliable tool in attempting calculations on very large molecules.\r\n" }, { "name": "Miasek, Peter George", "degree": "PhD", "year": "1973", "title": "Trapped Ion Studies of Ion-Molecule Reactions", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312018-133321152", "creators": [ { "name": { "family": "Miasek", "given": "Peter George" }, "id": "Miasek-Peter-George", "display_name": "Miasek, Peter George" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/T9WX-ZR66", "abstract": "Ion-molecule reactions have been studied using a novel high pressure mass\r\nspectrometer employing crossed electric and magnetic fields for ion trapping.\r\nThese studies have been supplemented by ones undertaken using trapped-ion ion\r\ncyclotron resonance (ICR) spectrometry.
\r\n\r\n\r\nReaction rate constants at low ion energies have been measured in many\r\nsystems, and compare favourably with results of other studies. Correlations\r\nof measured rates with theoretical models have characterized certain \r\nfeatures of ion-neutral collision processes. Comparisons between chemically\r\nsimilar systems have also provided information about these encounters.
\r\n\r\n\r\nInternal excitation of reactant ions has been shown to induce\r\nthermodynamically disallowed reactions. Evidence suggesting the\r\nparticipation of vibrationally excited ions reacting at different rates\r\nthan their ground state counterparts is presented.
\r\n\r\n\r\nThe formation and lifetimes of excited intermediates in ethylene and\r\nmethanol has been investigated in detail. Relative rates of collisional\r\nstabilization of (C5H9+)* by inert gases have been\r\ndetermined and compared with similar processes in neutral systems. Stabilization\r\nof (C5H9+)* by ethylene itself exhibits \r\ndifferent characteristics than those of inert gases.
\r\n\r\n\r\nThe equilibrium constant of a reversible ion-molecule reaction has been measured\r\nat two temperatures and used to determine the enthalpy and entropy change\r\nfor the process.
\r\n\r\n\r\nThe rates of various thermoneutral proton and charge-transfer reactions have\r\nbeen measured using trapped ion-ion ejection ICR spectrometry. This has enabled a \r\ndetailed characterization of the collisional phenomena in these systems.
\r\n\r\n\r\nThe kinetic energy distribution of CH3+ arising from ionization\r\nof methyl halides has been determined using ICR spectrometry and photoionization\r\nspectroscopy. Inferences about the nature of the dissociative states are presented.
" }, { "name": "Miskowski, Vincent Mark", "degree": "PhD", "year": "1973", "title": "Electronic Structure of Metal Ion-Dioxygen Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022018-101456398", "creators": [ { "name": { "family": "Miskowski", "given": "Vincent Mark" }, "id": "Miskowski-Vincent-Mark", "display_name": "Miskowski, Vincent Mark" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZFYP-9D77", "abstract": "The electronic structures of cobalt complexes containing\r\nO2 units as ligands have been investigated, primarily by electronic\r\nspectroscopy. Various cobalt complexes containing, the structural\r\nunits present in the O2 complexes were investigated, and a\r\nsystematic and self-consistent classification of their ligand field\r\nelectronic transitions, charge-transfer electronic transitions, and\r\nexcited state reactivities developed, which provided a basis for \r\nunderstanding the O2 complexes.
\r\n\r\n\r\nThe O2 complexes investigated were all found to contain\r\nlow-spin d6 cobalt (III) central metal ions, by spectroscopic criteria,\r\nand either peroxide or superoxide ligands. The O2n- ligands have\r\npositions in the spectrochemical series between those of ammonia\r\nand water, and have characteristic charge-transfer transitions in\r\ntheir complexes, superoxide complexes showing low energy metal-to-ligand\r\ntransitions, while both superoxide and peroxide complexes\r\nshow characteristic ligand-to-metal transitions in the UV.\r\nExtensive comparisons were made to O2 complexes of other\r\nmetal ions, and the binding of dioxygen to metal ions concluded\r\nto be oxidative addition in general. Autoxidation of metal ions and\r\nthe structures and properties of oxymetalloproteins have been\r\nconsidered in the light of these results, and the formulation of\r\naddition of O2 to Cu(I) and Fe(II) as one- and two-electron oxidative\r\naddition, respectively, is discussed.
" }, { "name": "Mohr, Douglas Crane", "degree": "PhD", "year": "1973", "title": "Study of the Possibility of the Detection of Fluorescent Dyes by Cathodoluminescence in the Scanning Electron Microscope and Partial Denaturation Maps of Lambda DNA using Methylmercuric Hydroxide", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052018-145823945", "creators": [ { "name": { "family": "Mohr", "given": "Douglas Crane" }, "id": "Mohr-Douglas-Crane", "display_name": "Mohr, Douglas Crane" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1F4Q-0K50", "abstract": "Part I. The possibilities of using ethidium \r\nbromide, quinacrine hydrochloride, and dansyl chloride \r\nas cathodoluminescent stains for scanning electron\r\nmicroscopy have been investigated. Nucleic acid specimens\r\nstained with the dyes gave best results when they were\r\nembedded in frozen glycerol and examined at liquid\r\nnitrogen temperature. Under these conditions, the\r\nexcitation cross section for ethidium bromide is about\r\n0.5 A2 and the destruction cross section 5 A2. The\r\nother dyes were destroyed quite rapidly.
\r\n\r\nEven under the best conditions, the minimum amount\r\nof ethidium bromide detectable by cathodoluminescence is\r\nabout the same as detectable by fluorescence microscopy.
\r\n\r\nPart II. Methylmercuric hydroxide preferentially\r\nreacts with thymine. This reaction disrupts the Watson-Crick\r\nbase pairing, the mercurated regions appearing as\r\nloops in the electron microscope. Lambda DNA has been\r\npartially denatured by methylmercuric hydroxide and\r\nmounted for electron microscopy by the basic film\r\ntechnique.
\r\n\r\nThe results indicate that there are four regions\r\nwhich readily denature, located on one side of the lambda\r\ngenome. This result is in agreement with other thermal\r\nand alkaline partial denaturation data.
" }, { "name": "Morton, Thomas Hellman", "degree": "PhD", "year": "1973", "title": "Organic Reactions in the Gas Phase: Part I. The Thermal Rearrangement of 3,3-Dimethylcyclopropene. Part II. Interaction of Remote Functional Groups in the Ion Chemistry of Bifunctional Ethers", "advisor": "Bergman, Robert G.; Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312018-114130193", "creators": [ { "name": { "family": "Morton", "given": "Thomas Hellman" }, "id": "Morton-Thomas-Hellman", "display_name": "Morton, Thomas Hellman" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "co-advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0b6f-h333", "abstract": "PART I: The Thermal Rearrangement of 3, 3-Dimethylcyclopropene
\r\n\r\nThe thermal rearrangement of 3, 3-dimethylcyclopropene was\r\ninvestigated by entering the energy surface for the reaction by two \r\nroutes:\tthermal isomerization of the cyclopropene and pyrolysis \r\nof a diazo compound precursor, 3-methyl-1-diazo-2-butene. The\r\nproducts from both reactions are identical; however the proportions \r\nvary greatly. Greater than 95% of the product from the diazo compound \r\nis the cyclopropene, and the remainder of the product is\r\nisoprene and isopropylacetylene in a 5:2 ratio, with trace gem-dimethyl\u00adallene.\t\r\nThe products from isomerization of the cyclopropene are isopropylacetylene, \r\nisoprene, and gem-dimethylallene in a ratio of\r\n500:50:1. From these data it is concluded that two intermediates\r\nexist for the isomerization, gem-dimethylvinylcarbene, (CH3)2C=CH CH,\r\nand a 90\u00b0 rotamer, designated as a diradical, (CH3)2\u010aCH=\u010aH.\r\nRelative rates of interconversion and cyclization and an energy surface are \r\ndetermined and the results are compared with Huckel and CNDO/2 \r\ncalculations on vinylcarbene.
\r\n\r\n\r\nPART II. Interaction of Remote Functional Groups in the Ion Chemistry of Bifunctional Ethers
\r\n\r\n\r\nAn Ion Cyclotron Resonance examination of bifunctional ethers of \r\nthe form CH3O(CH2)nOR, where n = 1 - 6 and R = H, CH3, or C2H5,\r\nreveals a large number of mass spectral processes and ion-molecule\r\nreactions in which the interaction of remote functional groups plays a\r\nprominent role.\tChainlength effects are particularly pronounced:\r\n6-member cyclic intermediates are inf erred in rarrangements of odd\u00ad electron species, \r\nwhile larger cycles appear pref erred in rearrange\u00adments of \r\nmany even electron species.
" }, { "name": "Quina, Frank Herbert", "degree": "PhD", "year": "1973", "title": "Photophysical Studies: I. Singlet Quenching in Naphthalene-Conjugated Diene Bichromophores. II. Fluorescence of Aromatic Hydrocarbon-Tertiary Amine Bichromophores. III. Intersystem Crossing in the Methyl Benzenes", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:07202018-143432826", "creators": [ { "name": { "family": "Quina", "given": "Frank Herbert" }, "id": "Quina-Frank-Herbert", "display_name": "Quina, Frank Herbert" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zq65-sd49", "abstract": "Part I describes the synthesis, photochemistry, and fluorescence of several naphthalene-conjugated diene bichromophores. The data for these systems and for suitable reference systems are used to discuss and develop models for the bimolecular singlet quenching phenomenon.
\r\n\r\nPart II describes the synthesis and fluorescence of several aromatic hydrocarbon-tertiary amine bichromophores. The fluorescence properties of these systems are related to the accessibility of various conformations and possible configurational requirements of amine singlet quenching are discussed.
\r\n\r\nPart III reports the results of a systematic study of intersystem crossing in the methyl benzenes. Along with measured singlet lifetimes and literature values for the fluorescence quantum yields, these data allow evaluation of the rate constants for deactivation of the first excited singlet state of the methyl benzenes in degassed cyclohaxane solution. A qualitative dependence of the intersystem crossing rates on the sym\u00admetry of methyl substitution is found and mechanisms involving inter\u00adsystem crossing to the second triplet state are proposed to account for this result. Non-radiative decay of the first excite singlet state via pathways other than fluorescence and intersystem crossing is found to be a significant process for all of the methyl benzenes except p-xylene.
" }, { "name": "Ridge, Douglas Poll", "degree": "PhD", "year": "1973", "title": "I. Studies of Collision Broadening of Ion Cyclotron Resonance Lineshapes. II. Studies of the Gas Phase Ion Chemistry of Fluoroethanes ", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232018-123515101", "creators": [ { "name": { "family": "Ridge", "given": "Douglas Poll" }, "id": "Ridge-Douglas-Poll", "display_name": "Ridge, Douglas Poll" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FMJE-KV22", "abstract": "In Section I theoretical calculations of gas phase ion mobilities are reviewed. The results of measurements of ion cyclotron resonance linewidths of ions in methane and ions in hydrogen are presented. The relationship between ion mobilities, collision frequencies and ion cyclotron resonance linewidths is reviewed. The results of the linewidth measurements are compared with DC mobility measurements and theoretical calculations of the mobility. The results of previous ion cyclotron resonance linewidth measurements are in serious disagreement with DC mobility measurements. The results of the present study, however, agree well with recent mobility measurements. Except for H+ and H3+; in hydrogen the results of the linewidth measurements are consistent with the theory of Mason and Schamp which is based on a three term 12-6.-4 ion molecule interaction potential. It is concluded that weak chemical bonding occurs between hydrocarbon ions and methane and that the anisotropy of the H2 molecule plays a significant role in determining the cyclotron resonance linewidths of ions in hydrogen. The parameters which determine the 12-6-4 potentials which best characterize the interaction between the ion-neutral pairs studied are estimated. It is concluded that the interaction of H+ and H3+ with H2 are too energetic to be adequately represented by a 12-6-4 potential. Measurements of the linewidths of Na+ ions in the C3H6O isomers are found to increase linearly with dipole moment in quantitative agreement with a simple model. The implications of this result are discussed.
\r\n\r\nIn Section II a series of fluoride transfer reactions between fluoroalkyl cations and fluoroalkanes in the gas phase are described. In one case (CH3CHF+ + CH3CF3 \u2192 CH3CF+2 + CH3CHF+2) equilibrium is observed so that a free energy change can be assigned from the final ratio of the ionic products. From this result and from observations of competitive fluoride transfer reactions in mixtures of fluoroalkanes a sequence of fluoride affinities of fluoroalkyl cations is deduced (the fluoride affinity of R+ is -\u0394H for the reaction R+ + F- \u2192 RF). Including the results of previous studies the sequence in order of decreasing fluoride affinities is C2F+5 > CF+3 > CH+3 > CH2F+ > CHF+2 > CHF2CHF+ > CH2FCHF+ > CH3CF+2 > CH3CHF+ > C2H+5. The effects of fluorine substituents on ethyl cation stability are discussed. A simple electrostatic model is proposed to account for the destabilization of fluoroethyl cations by \u03b2 fluorine substituents.
\r\n\r\nThe base induced elimination of HX from alkyl halides (RX) in the gas phase is proposed and its observation reported. The reaction CH3O- + C2H5F \u2192 CH3OHF- + C2H4 is shown by isotopic labelling and kinetic studies to be a based induced 1,2 elimination. Analogous reactions are observed between CH3O- and CH3CHF2, CH3CF3, CH2FCHF2, and CHF2CHF2. It also appears that F- reacts with fluoroethanes in an analogous way. Other substrates from which bases appear to eliminate HX are \u03b2-chloroethanol, ethylene bromohydrin and CH3CC13. Proton transfer between fluoroethanes and CH3O- is also observed. The fluoroethyl anions formed transfer F- to the parent fluoroethanes. The thermochemical consequences of the observed reactions with regard to the binding in species of the type XHY- and with regard to the electron affinities of the fluoroethyl anions are discussed.
\r\n" }, { "name": "Rose, John Brandt", "degree": "PhD", "year": "1973", "title": "I. Application of the Equations-of-Motion Method to the Excited States of N\u2082, CO, and C\u2082H\u2084. II. Applicability of SCF Theory to Some Open-Shell States of CO, N\u2082, and O\u2082", "advisor": "Vinograd, Jerome Rubin; McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252018-120348724", "creators": [ { "name": { "family": "Rose", "given": "John Brandt" }, "id": "Rose-John-Brandt", "display_name": "Rose, John Brandt" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M243-0H55", "abstract": "In Part I various low-lying electronic states of N2, CO, and ethylene are studied by the equations-of-motion-method. This approach attempts to describe excitation processes directly, without solving Schroedinger's equation separately for the excited and ground states. It reduces to a matrix eigenvalue problem in a space of single particle-hole excitations, and the effect of double excitations is determined by perturbation theory.
\r\n\r\nUsing extensive Gaussian basis sets, excitation energies and oscillator strengths are obtained for nine states of CO and eleven states of N2 at the equilibrium geometry. The typical error in frequency is about five per cent relative to experiment. Calculated oscillator strengths are also very good since the total intensity must very nearly satisfy the energy weighted sum rule. Results for ethylene show that the V state is a valence state but is more diffuse than the T state and ground state.
\r\n\r\nPotential energy curves are constructed for all these states by solving the equations at a few points with slightly smaller basis sets. The theory is appropriate as long as the Hartree Fock approximation is a good one for the ground state -- within about thirty per cent of equilibrium. The \u03a3+ states of N2 and CO are most interesting because questions about perturbation and pre-dissociation can be answered.
\r\n\r\nPart II describes open shell SCF calculations for some diatomic molecules. By working with the real functions \u03c0x and \u03c0y instead of \u03c0+ and \u03c0-, the SCF Hamiltonians for the \u03a3 states of the configurations (\u03c0u)3(\u03c0g), (\u03c0u)3(\u03c0g)3,and (1\u03c0)3(2\u03c0) of diatomic molecules can be expressed in terms of Coulomb and exchange operators only. With these results, conventional SCF programs can solve for the wavefunctions of many interesting states of N2, O2, and CO, e.g., the B 3\u03a3-u state of O2. For many states, the SCF results are in good agreement with experiment. However, SCF theory runs into serious trouble if electron correlation is important in determining the relative locations of excited states.
\r\n" }, { "name": "Runyan, Charles Carroll", "degree": "Masters", "year": "1973", "title": "Studies of Matrix-Isolation Spectra in Solid Hydrogen", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-113436579", "creators": [ { "name": { "family": "Runyan", "given": "Charles Carroll" }, "id": "Runyan-Charles-Carroll", "display_name": "Runyan, Charles Carroll" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/01VE-B736", "abstract": "Studies into the spectral features produced by atomic \r\nand molecular systems isolated in solid hydrogen have\r\nbeen undertaken to elucidate the nature of the interaction \r\nbetween the isolated species and the surrounding matrix. \r\nThe absorption properties of matrix-isolated calcium are \r\ninvestigated to seek an understanding of the diffuse \r\ncharacteristics of absorption spectra perceived in stellar \r\nradiation that traverses interstellar dust clouds. The \r\nfine structural features of the A^1B_(2u) \u2013 X^1A(1g) transition of \r\nbenzene isolated in hydrogen are examined for their\r\nbearing on the extremely sharp lines exhibited by benzene \r\nin all light matrices.\r\n\r\n The impure hydrogen samples are prepared for absorption \r\ninvestigations by depositing hydrogen and calcium or benzene \r\nonto a window cooled to 2\u00b0K. Besides the spectra of the \r\nabove two systems isolated in hydrogen, the absorption\r\nsignals of benzene in solid deuterium and of perdeuterobenzene \r\nin both solid hydrogen and solid deuterium are also presented. \r\nFurthermore, changes in the benzene fine structure that\r\nresult from the reduction of the ortho/para ratio of the \r\nsolid hydrogen medium are provided.\r\n\r\n Because these studies have not been carried to completion, \r\nextensive detail in experimental procedures is supplied and\r\na brief analysis of the shifts and shapes of the observed \r\nabsorption lines offers thoughts for further research.\r\n" }, { "name": "Sheetz, Michael Patrick", "degree": "PhD", "year": "1973", "title": "Proton Magnetic Resonance Studies of Membrane Systems. I. Effect of Sonication and Osmotic Pressure on the Structure of the Lecithin Bilayer. II. PMR study of the Human Erythrocyte Membrane upon Perturbation.", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07202018-112502895", "creators": [ { "name": { "family": "Sheetz", "given": "Michael Patrick" }, "id": "Sheetz-Michael-Patrick", "display_name": "Sheetz, Michael Patrick" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZPAB-K217", "abstract": "I. Effect of Sonication and Osmotic Pressure on the Structure of the Lecithin Bilayer
\r\n\r\nThe properties of dipalmitoyl lecithin vesicles of varying sizes have been compared employing proton and 31P nmr spectroscopy and dilatometry. These studies indicate that small vesicles of about 250 \u00c5 in diameter are inherently disordered and that the well-known spectral differences generally observed for vesicles of different curvatures, such as lecithin multilayers and sonicated bilayers, arise from variations in the molecular packing of phospholipid molecules in the bilayer phase. Upon further perturbation of the membrane by an external osmotic pressure spectral changes were noted which were consistent with the expected changes in molecular packing. It was also noted that the structural rigidity of the bilayer appeared to change upon melting.
\r\n\r\nII. PMR Study of the Human Erythrocyte Membrane upon Perturbation
\r\n\r\nAn analysis of the pmr spectra of human erythrocyte membranes has been made in terms of the membrane components. The spectrum at 75\u00b0 was assigned to 20% of the membrane proteins, 20% of the choline methyl groups of the phospholipids, and the acetamide groups of the sugars. Changes in the pmr spectra were noted when the membranes were altered by either protein solubilization or membrane fragmentation. The choline methyl signal was found to be particularly sensitive to the state of the membranes. Certain proteins were found to be released from the membranes at high temperatures and this phenomenon was dependent upon the pH and the solvent, as well as the presence of certain ions in solution. The amount of proteins solubilized, however, was significantly less than that observed by the high-resolution pmr method. The effect of certain divalent ions was particularly striking. The presence of more than 5 x 10-4 M Mg2+, for example, was sufficient to stabilize the proteins in the membrane and eliminate the high-resolution pmr signal.
\r\n\r\nB. cereus and Cl. perfringens phospholipase C treatments were found to have quite different effects on human erythrocyte membranes from the pmr spectra of the treated membranes. These differences are explained in terms of the properties of the unreacted lipids left by the two enzymes.
\r\n" }, { "name": "Weigel, John Mitchell", "degree": "Masters", "year": "1973", "title": "Photoionization ion cyclotron resonance spectroscopy: a study of three C\u2083H\u2086O isomers", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062010-110530214", "creators": [ { "name": { "family": "Weigel", "given": "John Mitchell" }, "id": "Weigel-John-Mitchell", "display_name": "Weigel, John Mitchell" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/J7Q1-6293", "abstract": "Photoionization ion cyclotron resonance (pi-icr) spectroscopy is described in detail. The construction and use of rare gas resonance line lamps employing LiF windows is described, with principle emphasis on the argon resonance line lamp that produces photons of 11.62 and \r\n11.83 eV. Calculations of the number density and single resonance signal intensity are made for primary, secondary, and tertiary ions, and the low pressure lineshape calculated for an unreactive primary ion.\r\n\r\nThe ion chemistry of propanal, acetone, and propylene oxide (empirical formula C_3H_6O) is investigated using pi-icr with the argon resonance line lamp. The major reaction sequence in propanal and acetone is parent ion producing protonated parent ion, which condenses with the parent \r\nneutral to produce the proton bound dimer. This is also the reaction sequence in ethylene oxide. In propylene oxide, however, the parent ion relative abundance is esentially constant from 10^(-6) to 10^(-4) torr. The fragment ion of mass 43 is the predominant primary ion at the argon resonance lines, and reacts to form ions of mass 41, 57, and 59. Double resonance is used to determine the reaction sequence of the major ions. At 10^(-4) torr, there is less than 2% of the proton bound dimer in propylene oxide, while in acetone or propanal the proton bound dimer is the major\r\nproduct ion. Preliminary photolysis results on propylene oxide suggest a chain process is involved converting propylene oxide to propanal." }, { "name": "Bell, Robert Alan", "degree": "Masters", "year": "1972", "title": "A. The Crystal Structure of 9-Methyl Guanine Hydrochloride Monohydrate. B. Preliminary Studies on [C\u2082\u2087H\u2085\u2086N\u2082Cl]\u207a\u2022[H\u2081\u2083O\u2086]\u207a\u20222 Cl\u207b : a Bicyclic Diammonium Ion Containing a Caged Chloride", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282010-145750496", "creators": [ { "name": { "family": "Bell", "given": "Robert Alan" }, "id": "Bell-Robert-Alan", "display_name": "Bell, Robert Alan" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GCQS-GP30", "abstract": "The structure of 9-Methyl Guanine HC1 Monohydrate, \r\nC_6H_8N_5OC1\u2022H_2O, has been determined by single crystal x-ray analysis. The whitish salt crystallizes in the monoclinic space group P2_1/c with unit cell dimensions a = 5.324(2), b = 11. 236(15) c = 15.533(10) and \u03b2 = 96.11(3)\u00b0. There are four molecules in the unit cell and thus, one in the asymmetric unit. The measured density of 1.581 gm cm^(-3) is in close agreement with the calculated values of 1.578 gm cm^(-3). Three-dimensional intensity data were collected on a Datex-automated General Electric diffractometer using CoK\u03b1 radiation. The structure was \r\ndetermined by Patterson and Fourier methods and refined by \r\nFourier and least squares techniques to a final R index of 0.067 for 1224 reflections.\r\n\r\nThe molecules crystallize in slightly buckled planes \r\nwhich are parallel to and lie half way between the 104 plane of the unit cell. They are hydrogen bonded to chloride ions and water molecules between the planes and to each other within the plane. The water molecules and the chloride ions form staggered columns perpendicular to the molecular planes. The six hydrogen bonds, N(10A)-H\u2022\u2022\u2022N(3B), N(10A)-H\u2022\u2022\u2022O(2) N(1A)-H\u2022\u2022\u2022Cl^-, N(7A)-H\u2022\u2022\u2022Cl^-, O(2)-H(9)\u2022\u2022\u2022Cl^-, and O(2)-H(10)\u2022\u2022\u2022Cl^- are respectively 3.072, 2.828, 3.294, 3.191, 3.257, and 3.125 \u00c5 in length. The molecular planes are 3.17 and 3.33 \u00c5 apart.\r\n" }, { "name": "Betts, Timothy Charles", "degree": "PhD", "year": "1972", "title": "Rydberg States of Diatomic and Polyatomic Molecules Using Model Potentials", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012016-131612760", "creators": [ { "name": { "family": "Betts", "given": "Timothy Charles" }, "id": "Betts-Timothy-Charles", "display_name": "Betts, Timothy Charles" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JP17-7677", "abstract": "A simple model potential is used to calculate Rydberg series for the molecules: nitrogen, oxygen, nitric oxide, carbon monoxide, carbon dioxide, nitrogen dioxide, nitrous oxide, acetylene, formaldehyde, formic acid, diazomethane, ketene, ethylene, allene, acetaldehyde, propyne, acrolein, dimethyl ether, 1, 3-butadiene, 2-butene, and benzene. The model potential for a molecule is taken as the sum of atomic potentials, which are calibrated to atomic data and contain no further parameters. Our results agree with experimentally measured values to within 5-10% in all cases. The results of these calculations are applied to many unresolved problems connected with the above molecules. Some of the more notable of these problems are the reassignment of states in carbon monoxide, the first ionization potential of nitrogen dioxide, the interpretation of the V state in ethylene, and the mystery bands in substituted ethylenes, the identification of the R and R\u2019 series in benzene and the determination of the orbital scheme in benzene from electron impact data.
\r\n\r\n" }, { "name": "Blint, Richard Joseph", "degree": "PhD", "year": "1972", "title": "I. Orbital Interpretation and Properties of the X\u00b9\u03a3\u207a, a\u00b3\u220f, A\u00b9\u220f and \u00b3\u03a3\u207a States of BH. II. Gas Phase Reactions of Fluoromethyl Cations with Ethylene and Benzene", "advisor": "Goddard, William A., III; Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282009-093808296", "creators": [ { "name": { "family": "Blint", "given": "Richard Joseph" }, "id": "Blint-Richard-Joseph", "display_name": "Blint, Richard Joseph" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KJ13-G054", "abstract": "\"Ab initio\" calculations have been carried out on the states of BH(\u03c71\u03a3+, a3\u03a0, A1\u03a0, and 3\u03a3+) which dissociate to the ground states of B and H. The application of the Gl method (which is a special case of the GI method) was extended to handle five- and six-electron systems, and this method along with SOGI, CI and the GVB method was used to investigate the BH states. The effect of restricting the orbitals of the wave-function to be basis functions for the irreducible representations of the spatial symmetry group leads to noncontinuous changes in the orbitals as a function of internuclear distance. And further it is noted that the removal of this restriction on the atomic wavefunction of boron leads to simple predictions of the forms of the wavefunctions, geometries of the molecules and characteristics of the potential curves for the BHN molecules. On the basis of this the potential curves for the a3\u03a0 and\r\nA1\u03a0 states are correctly predicted to have humps and the 2A1 and 2B1 states of BH2 are predicted to be bent and linear, respectively. Molecular properties for many of these wavefunctions have been calculated and correlated with changes in the orbitals as a function of internuclear distance.
\r\n\r\nGas phase reactions and properties of fluoromethyl cations have been investigated using the techniques of ion cyclotron resonance spectroscopy (icr). Fluoride transfer reactions between substituted methyl cations are observed to be rapid and permit the determination of relative fluoride ion affinities, defined as the negative of the enthalpy change for the reaction CHNF+3-N + F- \u2192 CHNF4-N. By combining available thermochemical data and our experimental results the following order for the fluoride affinities of the methyl cations is constructed: CF+3 (256.3 kcal/mole) > CH+3 (252.0 kcal/mole) > CH2F+ (243.6 kcal/mole) > CF2H+ (242.8 kcal/mole). A measurement of the equilibrium constant for the reaction (CF2H+ + CH2F2 \u21cc CH2F+ + CF3H) between the latter two ions has permitted their relative fluoride ion affinities to be accurately determined. Fluoride ion affinities are a means of determining carbonium ion stabilities.
\r\n\r\nWith the general goal of understanding reactions involving electrophillic addition to \u03c0-systems the reactions of the fluoromethyl cations with ethylene, ethylene-d4 and benzene-d6 were investigated. The important process in each case involves addition of the fluoromethyl cation to the substrate to form a chemically activated intermediate which decomposes with loss of HF or H2. Rate constants for the reactions of the fluoromethyl cations with ethylene were determined using icr trapped ion techniques. In conjunction with ion ejection double resonance, product distributions for the reactions involving ethylene-d4 and benzene-d6 have been determined. Only in the case of the reactions of fluoromethyl cations with benzene-d6 is the possibility of a distinctive reaction mechanism revealed from the isotopic product distributions.
\r\n" }, { "name": "Chan, Emmy Tong", "degree": "Masters", "year": "1972", "title": "The Pyrimidine Oligonucleotide Analysis of Mitochondrial DNA from HeLa Cells", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282010-143422774", "creators": [ { "name": { "family": "Chan", "given": "Emmy Tong" }, "id": "Chan-Emmy-Tong", "display_name": "Chan, Emmy Tong" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HAE6-XA94", "abstract": "A pyrimidine cluster analysis of the light strand of HeLa mitochondrial DNA has been undertaken. The major difficulties in this attempt to obtain the pyrimidine oligonucleotide distribution in mitochondrial DNA are the limited amount of material available and the multistep procedure which may incur losses of DNA material as well as complications leading to irreproducible results.\r\n\r\nTo overcome the scarcity of material, the sensitivity of isotopic labelling is enhanced by using the enzyme 5'-OH-polynucleotide kinase to attach a radioactive phosphate to the end of each oligonucleotide. The fingerprinting procedure is adapted to the microgram level of DNA material by thin layer displacement chromatography.\r\n\r\nThe complications involved by multiple enzyme reactions have been solved by varying one parameter at a time. As a result of eight experiments, the conditions for a successful pyrimidine oligonucleotide analysis have been outlined." }, { "name": "Cohen, Robert Edward", "degree": "PhD", "year": "1972", "title": "Dynamic Mechanical Properties of Block Copolymer Blends: A Study of the Effects of Terminal Chains in Elastomeric Materials", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03292004-152803", "creators": [ { "name": { "family": "Cohen", "given": "Robert Edward" }, "id": "Cohen-Robert-Edward", "display_name": "Cohen, Robert Edward" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/J0FN-DS74", "abstract": "Blends of well characterized polystyrene-polybutadiene SB diblock and polybutadiene continuous SBS triblock copolymers provide rubbery network systems with controlled amounts of terminal chains of known molecular weight. Such systems also provide quantitative information on the concentrations of trapped and untrapped chain entanglements which is not available in conventional elastomers. Three different SB diblocks were synthesized using homogeneous anionic polymerization techniques. These diblocks were blended in various-amounts with a single research grade SBS triblock to form three series of samples for mechanical testing.\r\n\r\nThe mechanical properties of these materials were studied (1) in free oscillation at about 0.2 Hz over a temperature range from -150?C to 100?C, and (2) in dynamic uniaxial compression from 0.1 to 1000 Hz at various temperatures between -87 and 85?C.\r\n\r\nThe effect of terminal chains on the mechanical properties depends upon their length and concentration in the network. The terminal chains act as a diluent, lowering the storage modulus in the rubbery region. Above a critical molecular weight, the untrapped entanglements provided by the terminal chains can be coupled into a temporary stress-bearing portion of the network; the amount of entanglement coupling is dependent upon temperature. Several low frequency viscoelastic mechanisms appeared as a result of entanglement slippage, and their effect was enhanced as terminal chain content increased. At very high frequencies in the glassy and transition regions the presence of terminal chains had no effect on the mechanical behavior.\r\n\r\nThe various mechanisms associated with the terminal chains have been incorporated into a mathematical model whose parameters are given in terms of the structural and compositional features of an entanglement network. The model successfully predicts the level and the location of the low frequency mechanical response for the various materials studied here." }, { "name": "D'Amore, Michael Brian", "degree": "PhD", "year": "1972", "title": "Bicyclo[3.2.0]Hepta-1,4,6-Triene: Synthesis, Thermal Rearrangement, and Anion Formation", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04042016-112239738", "creators": [ { "name": { "family": "D'Amore", "given": "Michael Brian" }, "id": "D'Amore-Michael-Brian", "display_name": "D'Amore, Michael Brian" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HJ5M-D411", "abstract": "In order to determine the properties of the bicycloheptatrienyl anion (Ia) (predicted to be conjugatively stabilized by H\u00fcckel Molecular Orbital Theory) the neutral precursor, bicyclo[3. 2. 0] hepta-1, 4, 6-triene (I) was prepared by the following route.
\r\n\r\nReaction of I with potassium-t-butoxide, potassium, or lithium dicyclohexylamide gave anion Ia in very low yield. Reprotonation of I was found to occur solely at the 1 or 5 position to give triene II, isolated as to its dimers.
\r\n\r\nA study of the acidity of I and of other conjugated hydrocarbons by means of ion cyclotron resonance spectroscopy resulted in determination of the following order of relative acidities:
\r\n\r\nH2S \u02c3 C5H6 \u02c3 CH3NO2 \u02c3 1, 4- C5H8 \u02c3 I \u02c3 C2H5OH \u02c3 H2O;\r\ncyclo-C7H8 \u02c3 C2 H5OH; \u0444CH3 \u02c3 CH3OH
\r\n\r\nIn addition, limits for the proton affinities of the conjugate bases were determined:
\r\n\r\n350 kcal/mole \u02c2 PA(C5 H5-) \u02c2 360 kcal/mole
\r\n\r\n362 kcal/mole \u02c2 PA(C5H7-, Ia, cyclo-C7H7-) \u02c2 377 kcal/mole PA(\u0444CH2-) \u02c2 385 kcal/mole
\r\n\r\nGas phase kinetics of the trans-XVIII to I transformation gave the following activation parameters: Ea = 43.0 kcal/mole, log A = 15.53 and \u2206S\u01c2 (220\u00b0) = 9.6 cu. The results were interpreted as indicating initial 1,2 bond cleavage to give the 1,3-diradical which closed to I. Similar studies on cis-XVIII gave results consistent with a surface component to the reaction (Ea = 22.7 kcal/mole; log A = 9.23, \u2206S\u01c2 (119\u00b0) = -18.9 eu).
\r\n\r\nThe low pressure (0.01 to 1 torr) pyrolysis of trans-XVIII gave in addition to I, fulvenallene (LV), ethynylcyclopentadiene (LVI) and heptafulvalene (LVII). The relative ratios of the C7H6 isomers were found to be dependent upon temperature and pressure, higher relative pressure and lower temperatures favoring formation of I. The results were found to be consistent with the intermediacy of vibrationally excited I and subsequent reaction to give LV and LVI.
\r\n\r\n" }, { "name": "Dea, Phoebe Kin-Kin", "degree": "PhD", "year": "1972", "title": "The Nature of the Intramolecular Hydrogen-Bond in the Enol Tautomer of 2,4-Pentanedione", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02032005-155729", "creators": [ { "name": { "family": "Dea", "given": "Phoebe Kin-Kin" }, "id": "Dea-Phoebe-Kin-Kin", "display_name": "Dea, Phoebe Kin-Kin" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WST8-CK73", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe nature of the intramolecular hydrogen bond in the enol tautomer of 2,4-pentanedione has been studied in detail using high resolution proton, deuteron and [...] magnetic resonance spectroscopy. An unusually large deuterium isotope effect on the chemical shift of the bridge hydrogen has been observed. This unexpected result, together with the observation of a pronounced temperature dependence for both the bridge proton and deuteron resonances, as well as a temperature dependence of the carbonyl resonances, suggest that two states with different chemical shifts for the bridge hydrogen are involved in rapid equilibrium and that the anomalous deuterium isotope effect has its origin in the effect of deuterium substitution on the energy separation between these states. The results of a least-squares analysis of the OH and the OD temperature data in terms of a two-state model indicate that the energy separation for the proton and deuterated systems in the two states are [...] and [...]; but essentially identical chemical shifts were obtained for the OH proton as for the OD deuteron in each state (-14.15 and -10.10 ppm from the enol methyl group respectively).\r\n\r\nIt is proposed that these states correspond to the symmetric and asymmetric structures of the intramoleculax hydrogen bond. Results of our CNDO/2 calculations on the enol tautomer have indicated that these two structures have quite similar energies. In particular, it is suggested that the potential function associated with the vibrational motion of the bridge hydrogen is symmetric double minimum in nature when the donor-acceptor vibration (symmetric stretch) is in its zeroth vibrational state and the potential function becomes asymmetric when the symmetric stretch is excited by one or more vibrational quanta. By exciting the symmetric [...] stretch, we expect a charge shift in the [...] system which can alter the effective potential function for the bridge hydrogen. The [...] transition of the symmetric stretch is observed at [...] in the Raman spectrum of the normal compound and [...] in the deuterated molecule. This difference of [...] in the energy separation of the ground and first excited vibrational states of the symmetric stretch would be expected to give rise to the large deuterium isotope effect observed in our magnetic resonance experiments." }, { "name": "Eaton, David Fielder", "degree": "PhD", "year": "1972", "title": "I. Synthesis and Decomposition of Several 2,3-Diazabicyclo[3.1.0]Hex-2-Enes. II. Wavelength Effects in Piperylene Photoisomerization", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02112009-145526", "creators": [ { "name": { "family": "Eaton", "given": "David Fielder" }, "id": "Eaton-David-Fielder", "display_name": "Eaton, David Fielder" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p0z8-6a02", "abstract": "Part I: The synthesis and characterization of several methyl substituted 2,3-diazabicyclo[3.1.0]hex-2-enes are described. The thermal and photochemical decomposition of stereochemically labeled pyrazolines has been shown to afford mixtures of hydrocarbon products with a high degree of stereoselectivity. The nature of the products from exo- and endo-4-exo-6-dimethy1-2,3-diazabicyclo-[3.1.0]hex-2-ene suggests that carbene intermediates are formed, and multiple mechanisms for decomposition are proposed to account for the observation that the product distributions obtained are temperature dependent. A formal 1, 3-dipolar cycloreversion to afford an acyclic diazo compound, which decomposes to a carbene under the reaction conditions, is proposed to compete with formation of diradical intermediates.\r\n\r\nPart II: Initial quantum yields of trans\u2014>cis and cis\u2014>trans isomerization of trans- and cis-1, 3-pentadiene have been determined in pentane solutions for four excitation wavelengths in the range 236-254 nm. The photoisomerization efficiency was found to decrease markedly when high energy excitation was employed. Analysis of the data suggests that contributions of s-cis conformations may only be important for 254 nm excitation and that the bulk of the diminution in isomerization quantum yield as the initial excited state energy content is increased must be accounted for in terms of enhanced radiationless decay probabilities. Several possible mechanisms are discussed." }, { "name": "Gutschick, Vincent Peter", "degree": "PhD", "year": "1972", "title": "1. Ultrasonic Studies of Binary Liquid Structure in the Critical Region. Theory and Experiment for the 2,6-Lutidine/Water System. 2. Hartree-Fock Calculations of Electric Polarizabilities of Some Simple Atoms and Molecules, and Their Practicality. 3. Calculation of Vibrational Transition Probabilities in Collinear Atom-Diatom and Diatom-Diatom Collisions with Lennard-Jones Interaction", "advisor": "Pings, Cornelius J.; McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112016-103207668", "creators": [ { "name": { "family": "Gutschick", "given": "Vincent Peter" }, "id": "Gutschick-Vincent-Peter", "display_name": "Gutschick, Vincent Peter" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B8K2-V070", "abstract": "Part 1. Many interesting visual and mechanical phenomena occur in the critical region of fluids, both for the gas-liquid and liquid-liquid transitions. The precise thermodynamic and transport behavior here has some broad consequences for the molecular theory of liquids. Previous studies in this laboratory on a liquid-liquid critical mixture via ultrasonics supported a basically classical analysis of fluid behavior by M. Fixman (e. g., the free energy is assumed analytic in intensive variables in the thermodynamics)--at least when the fluid is not too close to critical. A breakdown in classical concepts is evidenced close to critical, in some well-defined ways. We have studied herein a liquid-liquid critical system of complementary nature (possessing a lower critical mixing or consolute temperature) to all previous mixtures, to look for new qualitative critical behavior. We did not find such new behavior in the ultrasonic absorption ascribable to the critical fluctuations, but we did find extra absorption due to chemical processes (yet these are related to the mixing behavior generating the lower consolute point). We rederived, corrected, and extended Fixman's analysis to interpret our experimental results in these more complex circumstances. The entire account of theory and experiment is prefaced by an extensive introduction recounting the general status of liquid state theory. The introduction provides a context for our present work, and also points out problems deserving attention. Interest in these problems was stimulated by this work but also by work in Part 3.
\r\n\r\nPart 2. Among variational theories of electronic structure, the Hartree-Fock theory has proved particularly valuable for a practical understanding of such properties as chemical binding, electric multipole moments, and X-ray scattering intensity. It also provides the most tractable method of calculating first-order properties under external or internal one-electron perturbations, either developed explicitly in orders of perturbation theory or in the fully self-consistent method. The accuracy and consistency of first-order properties are poorer than those of zero-order properties, but this is most often due to the use of explicit approximations in solving the perturbed equations, or to inadequacy of the variational basis in size or composition. We have calculated the electric polarizabilities of H2, He, Li, Be, LiH, and N2 by Hartree-Fock theory, using exact perturbation theory or the fully self-consistent method, as dictated by convenience. By careful studies on total basis set composition, we obtained good approximations to limiting Hartree-Fock values of polarizabilities with bases of reasonable size. The values for all species, and for each direction in the molecular cases, are within 8% of experiment, or of best theoretical values in the absence of the former. Our results support the use of unadorned Hartree-Pock theory for static polarizabilities needed in interpreting electron-molecule scattering data, collision-induced light scattering experiments, and other phenomena involving experimentally inaccessible polarizabilities.
\r\n\r\nPart 3. Numerical integration of the close-coupled scattering equations has been carried out to obtain vibrational transition probabilities for some models of the electronically adiabatic H2-H2 collision. All the models use a Lennard-Jones interaction potential between nearest atoms in the collision partners. We have analyzed the results for some insight into the vibrational excitation process in its dependence on the energy of collision, the nature of the vibrational binding potential, and other factors. We conclude also that replacement of earlier, simpler models of the interaction potential by the Lennard-Jones form adds very little realism for all the complication it introduces. A brief introduction precedes the presentation of our work and places it in the context of attempts to understand the collisional activation process in chemical reactions as well as some other chemical dynamics.
\r\n\r\n" }, { "name": "Hay, Philip Jeffrey", "degree": "PhD", "year": "1972", "title": "I. The Generalized Valence Bond Theory of Electronic Structure. II. An Orbital Interpretation of Superexchange in Antiferromagnetic Insulators", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11042009-080816954", "creators": [ { "name": { "family": "Hay", "given": "Philip Jeffrey" }, "id": "Hay-Philip-Jeffrey", "display_name": "Hay, Philip Jeffrey" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D2P6-BA46", "abstract": "Part I: A discussion is given of the generalized valence bond (GVB) method--a multi-configuration approach to electronic structure that combines a valence bond interpretation with the self-consistent techniques of Hartree-Fock theory. Ab initio calculations on simple hydrocarbons give improved descriptions of bonding in terms of localized C-C and C-H bonds. The nine lowest states of the ozone molecule are treated by GVB and configuration interaction techniques and an assignment of the spectrum of O_3 is made. A metastable excited singlet state with an equilateral geometry and an energy 1.5 eV above the ground state is discovered.\r\nThe calculated energy barrier of 60.5 kcal for the cis-trans isomerization of cyclopropane is in good agreement with the experimental value of 64.2 kcal. No barrier to ring closure is found in the trimethylene biradical in contrast to commonly accepted biradical mechanisms. The ^1A_1 state of CH_2 is calculated to be 0.50 eV (11. 5 kcal) above the ground ^3B_1 state. The ^1B_1 \u2190 ^1A_1, transition\u2014calculated to be 1. 40 eV--agrees with the lowest observed ^1B_1 \u2190 ^1A_1 band and suggests a reinterpretation of this as a 0-0 band. A new ^1A_1 state at 3.2 eV is also discussed. Good values of the barrier to internal rotation in ethane and of the dissociation energy of O_2 are obtained.\r\n\r\nPart II: An orbital interpretation of superexchange suggests that anti-ferromagnetism arises from increased metal-metal overlap due to the ligand orbitals. A theoretical value of the exchange parameter from ab initio calculations on the Ni^(++)-F^- -Ni^(++) \"molecule\" is 10% of the experimental value in KNiF_3.\r\n" }, { "name": "Hsu, George Chi", "degree": "PhD", "year": "1972", "title": "Estimation of Catalyst Activity Profiles and Deactivation Parameters from Reactor Operating Data with Applications to Naphtha Reforming", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182016-100200035", "creators": [ { "name": { "family": "Hsu", "given": "George Chi" }, "id": "Hsu-George-Chi", "display_name": "Hsu, George Chi" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9RNN-8952", "abstract": "Techniques are developed for estimating activity profiles in fixed bed reactors and catalyst deactivation parameters from operating reactor data. These techniques are applicable, in general, to most industrial catalytic processes. The catalytic reforming of naphthas is taken as a broad example to illustrate the estimation schemes and to signify the physical meaning of the kinetic parameters of the estimation equations. The work is described in two parts. Part I deals with the modeling of kinetic rate expressions and the derivation of the working equations for estimation. Part II concentrates on developing various estimation techniques.
\r\n\r\nPart I: The reactions used to describe naphtha reforming are dehydrogenation and dehydroisomerization of cycloparaffins; isomerization, dehydrocyclization and hydrocracking of paraffins; and the catalyst deactivation reactions, namely coking on alumina sites and sintering of platinum crystallites. The rate expressions for the above reactions are formulated, and the effects of transport limitations on the overall reaction rates are discussed in the appendices. Moreover, various types of interaction between the metallic and acidic active centers of reforming catalysts are discussed as characterizing the different types of reforming reactions.
\r\n\r\nPart II: In catalytic reactor operation, the activity distribution along the reactor determines the kinetics of the main reaction and is needed for predicting the effect of changes in the feed state and the operating conditions on the reactor output. In the case of a monofunctional catalyst and of bifunctional catalysts in limiting conditions, the cumulative activity is sufficient for predicting steady\r\nreactor output. The estimation of this cumulative activity can be carried out easily from measurements at the reactor exit. For a general bifunctional catalytic system, the detailed activity distribution is needed for describing the reactor operation, and some approximation must be made to obtain practicable estimation schemes. This is accomplished by parametrization techniques using measurements at a few\r\npoints along the reactor. Such parametrization techniques are illustrated numerically with a simplified model of naphtha reforming.
\r\n\r\nTo determine long term catalyst utilization and regeneration policies, it is necessary to estimate catalyst deactivation parameters from the the current operating data. For a first order deactivation model with a monofunctional catalyst or with a bifunctional catalyst in special limiting circumstances, analytical techniques are presented to transform the partial differential equations to ordinary differential equations which admit more feasible estimation schemes. Numerical examples include the catalytic oxidation of butene to butadiene and a simplified model of naphtha reforming. For a general bifunctional system or in the case of a monofunctional catalyst subject to general power law deactivation, the estimation can only be accomplished approximately. The basic feature of an appropriate estimation scheme involves approximating the activity profile by certain polynomials and then estimating the deactivation parameters from the integrated form of the deactivation equation by regression techniques. Different bifunctional systems must be treated by different estimation algorithms, which are illustrated by several cases of naphtha reforming with different feed or catalyst composition.
\r\n\r\n" }, { "name": "Huestis, Wray Hughes", "degree": "PhD", "year": "1972", "title": "Nuclear Magnetic Resonance Studies of Protein Conformation. I. Ribonuclease S. II. Hemoglobin", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182016-091216066", "creators": [ { "name": { "family": "Huestis", "given": "Wray Hughes" }, "id": "Huestis-Wray-Hughes", "display_name": "Huestis, Wray Hughes" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "biology" ], "doi": "10.7907/JZKA-C327", "abstract": "Fluorine nuclear magnetic resonance techniques have been used to study conformational processes in two proteins labeled specifically in strategic regions with covalently attached fluorinated molecules. In ribonuclease S, the \u03f5-amino groups of lysines 1 and 7 were trifluoroacetylated without diminishing enzymatic activity. As inhibitors bound to the enzyme, changes in orientation of the\r\npeptide segment containing the trifluoroacetyl groups were detected in the nuclear magnetic resonance spectrum. pH Titration of one of the histidines in the active site produced a reversal of the conformational process.
\r\n\r\nHemoglobin was trifluoroacetonylated at the reactive cysteine 93 of each \u03b2 chain. The nuclear magnetic resonance spectrum of the fluorine moiety reflected changes in the equilibrium position of the \u03b2 chain carboxy terminus upon binding of heme ligands and allosteric effectors. The chemical shift positions observed in deoxy- and methemoglobin were pH dependent, undergoing an abnormally steep\r\napparent titration which was not observed in hemoglobin from which histidine \u03b2 146 had been removed enzymatically. The abnormal sharpness of these pH dependent processes is probably due to interactions between several ionizing groups.
\r\n\r\nThe carbon monoxide binding process was studied by concurrent observation of the visible and nuclear magnetic resonance spectra of trifluoroacetonylated hemoglobin at fractional ligand saturations throughout the range 0-1.0. Comparison of the ligand binding process observed in these two ways yields evidence for a specific order of ligand binding. The sequence of events is sensitive\r\nto the pH and organic phosphate concentration of the medium, demonstrating the delicately balanced control system produced by interactions between the hemoglobin subunits and the effectors.
\r\n\r\n" }, { "name": "Hunt, William James", "degree": "PhD", "year": "1972", "title": "Electronic Wavefunctions for Small Molecules", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122009-074130644", "creators": [ { "name": { "family": "Hunt", "given": "William James" }, "id": "Hunt-William-James", "display_name": "Hunt, William James" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/F5KA-3M29", "abstract": "PART I. A simple variationally-based method for calculating electronic wavefunctions of excited states, the improved virtual orbital (IVO) method, is developed in this work. Calculations are presented for H_2O, O_2, CO, and N_2. While the IVO method gives limited accuracy in the treatment of valence excited states, the description of Rydberg states is very useful. For O_2 the theoretical prediction of 8.70 eV (v' = 2) for the transition from the ^3\u03a3^-_g ground state to the ^3\u03c0_g (1\u03c0_g \u2192 3s\u03c3_g) Rydberg state facilitated discovery of this transition in electron impact spectra at 8.65 eV (v' = 2).\r\n\r\nPART II. The N, T, and V states of ethylene have been studied with the Hartree-Foci (H-F) and configuration interaction (CI) techniques as a function of C-C bond distance and the twist angle between methylene groups. The calculated rotational barrier for the N state is 67.2 Kcal/mole, in good agreement with the experimentally derived activation energy of 65 Kcal/mole for cis-trans isomerization of 1,2di-deutero ethylene. The maximum in the N state curve lies 1.4 Kcal/mole above the minimum of the triplet state (T) curve. Both H-F end CI calculations show that the V state of planar ethylene has a more extended charge distribution than the T state. This charge distribution contracts as the methylene groups are twisted from the -planar geometry. Correlation terms included in the CI calculations contract the charge distribution considerably from its H-F size. A modified Franck-Condon Principle for internal rotation suggests that the maximum absorption observed experimentally does not correspond to vertical excitation for the N \u2192 V transition. \r\n\r\nPART III. A Generalized Valence Bond method combining the computational tractability of the usual MO-SCF approach with the conceptual advantages of a valence bond picture is proposed. The GVB method has been applied to calculation of potential curves for CH_2 in the ^3B_1, ^1A_1, and ^1B_1 states. These calculations predict that the ^3B_1 curve may cross the ^1A_1 curve near the minimum for the^1A_1 state. A study of the ring opening of cycloprooane predicts a barrier height of 61 Kcal/mole for cis-trans isomerization, in good agreement with the experimentally determined activation energy of 65 Kcal/mole for 1,2 di-deutero cyclopropene. An investigation of diatomic hydrides and fluorides in the GVB picture gives a consistent view of the energy levels and one-electron energies of these molecules.\r\n" }, { "name": "Kahn, Luis Ricardo", "degree": "PhD", "year": "1972", "title": "I. Ab-Initio Effective Potentials for Use in Molecular Calculations. II. The Sternheimer Correction, Perturbation Theory and Approximate Wavefunctions. III. The Theoretical Determination of the Li\u2082 B\u00b9\u03a0u Potential Energy Curve", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202009-150548056", "creators": [ { "name": { "family": "Kahn", "given": "Luis Ricardo" }, "id": "Kahn-Luis-Ricardo", "display_name": "Kahn, Luis Ricardo" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P3JP-H317", "abstract": "Part I: We have investigated the efficacy of ab-initio effective potentials in replacing the core electrons of atoms for use in molecular calculations. The effective potentials are obtained from ab initio GI calculations on atoms and are unique and local. We find that the use of these effective potentials to replace the core orbitals of such molecules as LiH, Li_2, BH, or LiH_2, leads to wavefunctions in excellent agreement with all-electron ab-initio results. The use of such effective potentials should allow ab-initio quality wavefunctions to be obtained for systems too large for the ab-initio consideration of all the electrons.\r\n\r\nPart II: We have investigated the Sternheimer correction for the calculation of the nuclear quadrupole coupling constants and its relation to the approximate nature of the zero-order wave- function. The first-order perturbed Hartree-Fock equations, and some approximations to them, are solved for the 2^2P state of Li, and the resulting Sternheimer type corrections are compared with Sternheimeris approximate calculations and with results from non-perturbation theory approaches.\r\n\r\nPART III: The Li_2 B^1\u03c0_u potential energy curve has been calculated with a Multi-Configuration SCF (MCSCF) wavefunction. Several different types of wavefunctions and basis sets have been examined and their accuracy determined. The most accurate wavefunction used predicts a binding energy of 0.3015 e.V. (84% of the experimental value of 0.362 e.V.), and predicts a potential hump of 0.0724 e.V. with its maximum in the vicinity of 10.6 Bohr. It is argued that the theoretical value of the hump is an upper bound to the experimental value.\r\n" }, { "name": "Kim, Jungsuh Park", "degree": "PhD", "year": "1972", "title": "Studies on T-Even Bacteriophage DNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022016-133803954", "creators": [ { "name": { "family": "Kim", "given": "Jungsuh Park" }, "id": "Kim-Jungsuh-Park", "display_name": "Kim, Jungsuh Park" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XYBG-3K08", "abstract": "Part I. The regions of sequence homology and non-homology between the DNA molecules of T2, T4, and T6 have been mapped by the electron microscopic heteroduplex method. The heteroduplex maps have been oriented with respect to the T4 genetic map. They show characteristic, reproducible patterns of substitution and deletion loops. All heteroduplex molecules show more than 85% homology. Some of the loop patterns in T2/T4 heteroduplexes are similar to those in T4/T6.
\r\n\r\nWe find that the rII, the lysozyme and ac genes, the D region, and gene 52 are homologous in T2, T4, and T6. Genes 43 and 47 are probably homologous between T2 and T4. The region of greatest homology is that bearing the late genes. The host range region, which comprises a part of gene 37 and all of gene 38, is heterologous\r\nin T2, T4, and T6. The remainder of gene 37 is partially homologous in the T2/T4 heteroduplex (Beckendorf, Kim and Lielausis, 1972) but it is heterologous in T4/T6 and in T2/T6. Some of the tRNA genes are homologous and some are not. The internal protein genes in general seem to be non-homologous.
\r\n\r\nThe molecular lengths of the T-even DNAs are the same within the limit of experimental error; their calculated molecular weights are correspondingly different due to unequal glucosylation. The size of the T2 genome is smaller than that of T4 or T6, but the terminally repetitious region in T2 is larger. There is a length distribution of the terminal repetition for any one phage DNA, indicating a variability in length of the DNA molecules packaged within the phage.
\r\n\r\nPart II. E. coli cells infected with phage strains carrying extensive deletions encompassing the gene for the phage ser-tRNA are missing the phage tRNAs normally present in wild type infected cells. By DNA-RNA hybridization we have demonstrated that the DNA complementary to the missing tRNAs is also absent in such deletion mutants. Thus the genes for these tRNAs must be clustered\r\nin the same region of the genome as the ser-tRNA gene. Physical mapping of several deletions of the ser-tRNA and lysozyme genes, by examination of heteroduplex DNA in the electron microscope, has enabled us to locate the cluster, to define its maximum size, and to order a few of the tRNA genes within it. That such deletions can be isolated indicates that the phage-specific tRNAs from this cluster are dispensable.
\r\n\r\nPart III. Genes 37 and 38 between closely related phages T2 and T4 have been compared by genetic, biochemical, and hetero-duplex studies. Homologous, partially homologous and non-homologous regions of the gene 37 have been mapped. The host range determinant which interacts with the gene 38 product is identified.
\r\n\r\nPart IV. A population of double-stranded \u00d8X-RF DNA molecules carrying a deletion of about 9% of the wild-type DNA has been discovered in a sample cultivated under conditions where the phage lysozyme gene is nonessential. The structures of deleted monomers, dimers, and trimers have been studied by the electron microscope heteroduplex method. The dimers and trimers are shown to be head-to-tail repeats of the deleted monomers. Some interesting examples of the dynamical phenomenon of branch migration in vitro have been observed in heteroduplexes of deleted dimer and trimer strands with undeleted wild-type monomer viral strands.
\r\n\r\n\r\n" }, { "name": "Kindergan, Michael Braun", "degree": "Masters", "year": "1972", "title": "Kinetic and Spectral Resolution of Two Components of Delayed Emission from Chlorella pyrenoidosa", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-134919845", "creators": [ { "name": { "family": "Kindergan", "given": "Michael Braun" }, "id": "Kindergan-Michael-Braun", "display_name": "Kindergan, Michael Braun" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VH7K-PQ20", "abstract": "1. Decay kinetics of delayed emission from Chlorella pyrenoidosa have been determined with a higher degree of precision than has previously been possible. The decay in the msec-to-sec interval after excitation can be represented accurately by the sum of two exponential decays--a \"fast component\" whose intensity- dependent lifetime ranges between 3 msec and 10 msec and a \"slow component\" whose lifetime ranges between 170 msec and 215 msec.\r\n\r\n2. The slow component can be isolated by monitoring the emission at 685 nm for long times (> 30 msec) after high or low intensity excitation, or at any time in the msec to sec interval following low intensity (< 0.9 mW/cm^2) excitation. Saturation of the slow component occurs in the low intensity region where oxygen evolution is linear with light intensity. The temperature sensitivity of the slow component indicates involvement of an enzymatic and/or diffusion-limited process.\r\n\r\n3. The emission spectrum of the fast component is identical to the fluorescence emission spectrum of the cells, with a peak at 685 nm and a shoulder between 710 and 730 nm. The intensity of the fast component parallels the reduction of System 2 electron acceptors and reaches a maximum level when photochemistry is light saturated. This fact was established by simultaneous measurements of oxygen evolution and delayed emission.\r\n\r\n4. The fast component can be selectively inhibited by 3(3, 4-dichlorophenyl)-1, 1-dimethylurea, heat or ultraviolet irradiation. The slow component can be selectively inhibited by hydroxylamine or low temperatures.\r\n\r\n5. Possible mechanisms resulting in fast and slow component delayed emission are discussed in view of the experimental results.\r\n" }, { "name": "Kirstein, Bruce Edward", "degree": "PhD", "year": "1972", "title": "The Structure of Liquid Argon as Determined by X-Ray Diffraction", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292016-140637476", "creators": [ { "name": { "family": "Kirstein", "given": "Bruce Edward" }, "id": "Kirstein-Bruce-Edward", "display_name": "Kirstein, Bruce Edward" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/88K0-V473", "abstract": "X-ray diffraction measurements and subsequent data analyses have been carried out on liquid argon at five states in the density range of 0.91 to 1.135 gm/cc and temperature range of 127 to 143\u00b0K. Duplicate measurements were made on all states. These data yielded radial distribution and direct correlation functions which were then used to compute the pair potential using the Percus-Yevick equation. The potential minima are in the range of -105 to -120\u00b0K and appear to substantiate current theoretical estimates of the effective pair potential in the presence of a weak three-body force.
\r\n\r\nThe data analysis procedure used was new and does not distinguish between the coherent and incoherent absorption factors for the cell scattering which were essentially equal. With this simplification, the argon scattering estimate was compared to the gas scattering estimate on the laboratory frame of reference and the two estimates coincided, indicating the data normalized. The argon scattering on the laboratory frame of reference was examined for the existence of the peaks in the structure factor and the existence of an observable third peak was considered doubtful.
\r\n\r\nNumerical studies of the effect of truncation, normalization, the subsidiary peak phenomenon in the radial distribution function, uncertainties in the low angle data relative to errors in the direct correlation function and the distortion phenomenon are presented.
\r\n\r\nThe distortion phenomenon for this experiment explains why the Mikolaj-Pings argon data yielded pair potential well depths from the Percus-Yevick equation that were too shallow and an apparent slope with respect to density that was too steep compared to theoretical estimates.
\r\n\r\nThe data presented for each measurement are: empty cell and cell plus argon intensity, absorption factors, argon intensity, smoothed argon intensity, smoothed argon intensity corrected for distortion, structure factor, radial distribution function, direct correlation function and the pair potential from the Percus-Yevick equation.
\r\n\r\n" }, { "name": "Kreishman, George Paul", "degree": "PhD", "year": "1972", "title": "Proton Magnetic Resonance Studies of Ribonucleic Acid Complexes: I. Complexes of Biological Bases and Oligonucleotides with RNA. II. Template Recognition and the Degeneracy of the Genetic Code", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022016-112630640", "creators": [ { "name": { "family": "Kreishman", "given": "George Paul" }, "id": "Kreishman-George-Paul", "display_name": "Kreishman, George Paul" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8MW5-JQ49", "abstract": "Part I. Complexes of Biological Bases and Oligonucleotides with RNA
\r\n\r\nThe physical nature of complexes of several biological bases and oligonucleotides with single-stranded ribonucleic acids have been studied by high resolution proton magnetic resonance spectroscopy. The importance of various forces in the stabilization of these complexes is also discussed.
\r\n\r\nPrevious work has shown that purine forms an intercalated complex with single-stranded nucleic acids. This complex formation led to severe and stereospecific broadening of the purine resonances. From the field dependence of the linewidths, T1 measurements of the purine protons and nuclear Overhauser enhancement experiments, the mechanism for the line broadening was ascertained to be dipole-dipole interactions between the purine protons and the ribose protons of the nucleic acid.
\r\n\r\nThe interactions of ethidium bromide (EB) with several RNA residues have been studied. EB forms vertically stacked aggregates with itself as well as with uridine, 3'-uridine monophosphate and 5'-uridine monophosphate and forms an intercalated complex with\r\nuridylyl (3' \u2192 5') uridine and polyuridylic acid (poly U). The geometry of EB in the intercalated complex has also been determined.
\r\n\r\nThe effect of chain length of oligo-A-nucleotides on their mode of interaction with poly U in D20 at neutral pD have also been studied. Below room temperatures, ApA and ApApA form a rigid triple-stranded complex involving a stoichiometry of one adenine to two uracil bases, presumably via specific adenine-uracil base pairing and cooperative base stacking of the adenine bases. While no evidence was obtained for the interaction of ApA with poly U above room temperature, ApApA exhibited complex formation of a 1:1 nature with poly U by forming Watson-Crick base pairs. The thermodynamics of these systems are discussed.
\r\n\r\nPart II. Template Recognition and the Degeneracy of the Genetic Code
\r\n\r\nThe interaction of ApApG and poly U was studied as a model system for the codon-anticodon interaction of tRNA and mRNA in vivo. ApApG was shown to interact with poly U below ~20\u00b0C. The interaction was of a 1:1 nature which exhibited the Hoogsteen bonding scheme. The three bases of ApApG are in an anti conformation and the guanosine base appears to be in the lactim tautomeric form in the complex.
\r\n\r\nDue to the inadequacies of previous models for the degeneracy of the genetic code in explaining the observed interactions of ApApG with poly U, the \"tautomeric doublet\" model is proposed as a possible explanation of the degenerate interactions of tRNA with mRNA during protein synthesis in vivo.
\r\n\r\n" }, { "name": "Ladner, Robert Charles", "degree": "PhD", "year": "1972", "title": "Independent-Particle Potential-Energy Surfaces for Chemical Reactions", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:07092010-164234058", "creators": [ { "name": { "family": "Ladner", "given": "Robert Charles" }, "id": "Ladner-Robert-Charles", "display_name": "Ladner, Robert Charles" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4FTW-PJ83", "abstract": "A new independent-particle method, the spin-coupling optimized GI (SOGI) method is described. This method removes many of the restrictions of the Hartree-Fock (HF), valence bond (VB), and GI methods. This method is applied to the two reactive systems of linear H_3 and linear LiH_2. The results of the H_3 calculations are carefully compared with CI results. The shapes of the potential energy surfaces (PES\u2019s) are explained in terms of the SOGI orbitals. Finally, the SOGI method is applied to the excited states of H_3, both linear and nonlinear." }, { "name": "Lee, Chi-Yu Gregory", "degree": "PhD", "year": "1972", "title": "Tautomerism of Nucleic Acid Bases and PMR Studies of Histones. I. Proton Magnetic Resonance Studies of Tautomerism of Nucleic Acid Bases. II. Proton Magnetic Resonance Studies of Histones and a DNA-Histone Complex. III. Nuclear Magnetic Resonance Studies of Ribonuclease A-Inhibitor Interactions and Nucleotide Conformations", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06132025-173756611", "creators": [ { "name": { "family": "Lee", "given": "Chi-Yu Gregory" }, "id": "Lee-Chi-Yu-Gregory", "display_name": "Lee, Chi-Yu Gregory" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jtd2-ac90", "abstract": "PART I. Proton Magnetic Resonance Studies\r\nof Tautomerism of Nucleic Acid Bases
\r\n\r\n1. Cytosine. It has long been noted that the H5 proton\r\nof cytosine and its related derivatives exhibits unusually\r\nbroad resonances in the pmr spectrum under certain conditions\r\nof temperature and solution pD. We have examined\r\nthis phenomenon as a function of temperature, concentration,\r\nand solution pD as well as the external magnetic\r\nfield, and have shown that the linebroadening arises\r\nfrom chemical exchange between the amino and imino\r\ntautomers of the cytosine base. The observation of sharp\r\nH5 resonances in cytosine derivatives existing in only\r\nthe amino or imino tautomeric structure supports this\r\ninterpretation. This tautomeric exchange was found to be\r\ncatalyzed by OD- as well as the solvent molecules (D20).\r\nAnalysis of the temperature and pD dependences of the H5\r\nlinewidth for 5'-CMP led to the following rate law at 30\u00b0C:
\r\n\r\n- (d A/dt) f = 1.2 x 1010 [OD- [A] + 1.2 [D20] [A], (Msec-1)
\r\n\r\nwhere [A] represents the major tautomeric species of 5'-CMP.\r\nActivation energies of 3.5 kcal/mole and 7.8 kcal/mole were\r\nobtained for the OD- and D20 catalyzed steps respectively.\r\nThe imino tautomer was estimated to be present to the\r\nextent of 15 \u00b1 3% at room temperature in neutral aqueous\r\nsolution.
\r\n\r\n2. Guanine. It has long been noted that the H3 proton of\r\nguanosine and its related derivatives exhibits unusually\r\nbroad resonances in the pmr spectra under certain conditions\r\nof temperature and pD. We have examined this\r\nphenomenon as a function of temperature, concentration,\r\nand solution pD, as well as the external magnetic field,\r\nand have shown that the linebroadening arises from\r\nchemical exchange between the lactam and lactim tautomers\r\nof the guanine base. The observation of sharp H8 resonances\r\nin guanine derivatives where the guanine base is frozen\r\nin only the lactam and lactim tautomeric structure\r\nsupports this interpretation. This tautomeric exchange\r\nwas found to be catalyzed by OD- and the solvent (D20).\r\nAnalysis of the temperature and pD dependence of the H8\r\nlinewidth for 2'-GMP led to the following rate law at\r\n30\u00b0c:
\r\n\r\n- (d A/dt) f = 1.7 x 109 [OD- [A] + 0.7 [D20] [A], (Msec-1
\r\n\r\nwhere A represents the major tautomeric species of 2'-GMP.\r\nActivation energies of 7 kcal/mole and 13 kcal/mole\r\nwere deduced for the OD- and D20 catalyzed steps respectively.\r\nThe minor lactim tautomer was estimated to be\r\npresent to the extent of 16 \u00b1 3% at room temperature in\r\nneutral aqueous solution.
\r\n\r\nIn most guanosine derivatives, with the notable\r\nexception of 2'-GMP, the Hg linewidth was also found to\r\nbe strongly concentration dependent over the pD range\r\n3 to 6. This concentration dependence has been interpreted\r\nin terms of the effect of intermolecular association\r\non the lactam-lactim tautomeric equilibrium. Analysis\r\nof the data in terms of a rapid equilibrium involving\r\nthe monomer, a hydrogen-bonded tetramer and stacked\r\naggregates of this tetramer yielded a tetramer formation\r\nconstant of(2.5 \u00b1 0.5)x 107 M-3 and a tetramer stacking\r\nor association constant of 40 \u00b1 10M-1 in the case of\r\n5'-GMP.
\r\n\r\nPART II. Proton Magnetic Resonance Studies of Histones\r\nand A DNA-Hostone Complex.
\r\n\r\n1. Solution Properties of Nucleoproteins - Histone I and\r\nHistone IIbI. The 220 MHz high resolution proton\r\nmagnetic resonance (pmr) spectra of histone I and histone\r\nIIbl have been examined as a function of histone concentration,\r\nsalt concentration as well as solution pD. The\r\nconcentration studies of both histone I and histone IIbl\r\nrevealed exclusively monomer-dimer equilibria in the\r\npresence or the absence of salt. The increase in the\r\ndimer formation of the proteins is attributed to the\r\ncounter ion binding upon the addition of salt which results\r\nin shielding of the long range electrostatic repulsion\r\nand facilitating the hydrophobic interactions between the\r\nmolecules. Changes in moles of the counter ion \u0394Vx and\r\nwater \u0394Vw bound to each mole of histones upon the\r\ncomplex formation were determined experimentally. Temperature\r\nstudies of histone I and histone IIbl indicate that\r\nin the presence of salt, the entropy change for the dimer\r\nformation of these proteins, AS becomes more positive\r\nthan that in the absence of salt.
\r\n\r\n2 . Proton Magnetic Resonance Studies of the DNA-Histone\r\nI Complex. The DNA-histone I complex prepared by a\r\ncontinuous salt gradient dialysis was studied by high\r\nresolution proton magnetic resonance spectroscopy at\r\nvarious temperatures. It was concluded that about 15 to\r\n20% of the side chain protons of the amino acid residues\r\nof the complexed histone I can be observed in the pmr\r\nspectra, and histone I in the complex is not removed from\r\nDNA when the latter is thermally denatured. The spectral\r\nbehaviors of histone I when mixed directly with DNA or\r\npoly U were examined at various temperatures for the\r\npurpose of comparison. Possible structural models of\r\nthis DNA-histone I reconstituted complex are presented on\r\nthe basis of our experimental observations.
\r\n\r\nPART III. Nuclear Magnetic Resonance Studies\r\nof Ribonuclease A Inhibitor Interactions\r\nand Nucleotide Conformations.
\r\n\r\n1. A 31P NMR Study of Interactions of Ribonuclease A and\r\nits Inhibitor. The association between ribonuclease\r\nA and its product inhibitor uridine-3'-monophosphate has\r\nbeen studied by 3lp nmr spectroscopy. Analysis of\r\nchemical shifts and the linewidths of the 31 resonance\r\nof the inhibitor over a wide range of enzyme concentrations\r\nyielded the apparent dissociation rate constant 3200 \u00b1\r\n300 sec-1 at 32\u00b0C for the enzyme-inhibitor complex and an\r\nactivation energy of 3.5 \u00b1 1.0 kcal/mole for this process.\r\nThe chemical shift data suggest that the phosphate group\r\nof this inhibitor is simultaneously bound to two positively\r\ncharged amino acid residues at the active site of the\r\nenzyme.
\r\n\r\n2. A Proton Magnetic Resonance Study of the Effects of pH\r\non Nucleosides and Nucleotides in Aqueous Solution.\r\nExperimentally it was observed that JH1 -H2 of some\r\nguanine nucleosides and nucleotides varies with pD of\r\nthe solution. This phenomenon was interpreted on the\r\nbasis of the ring-base interactions due to the protonation\r\nof the guanine base at low pD's. From the results of the\r\nconformational analysis of these guanine derivatives, it\r\nwas concluded that guanosine and 3'-GMP and 5'-GMP exist.\r\npredominantly in syn conformation when the guanine base is\r\nprotonated at low pD's, while the anti conformation is\r\nstill preferable at high pD's when the base is neutral.
" }, { "name": "Lim, Hong Sup", "degree": "PhD", "year": "1972", "title": "Chemical and Electrochemical Investigations of Cobalt Cyanide and Ruthenium Ammine Complexes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022016-145740021", "creators": [ { "name": { "family": "Lim", "given": "Hong Sup" }, "id": "Lim-Hong-Sup", "display_name": "Lim, Hong Sup" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PKKN-JV68", "abstract": "Part I.
\r\n\r\nThe stoichiometry and kinetics of the reaction between Co(CN5H3- and HgX2 (X = CN, OH) have been investigated. The products of the reaction are two new complexes, [(NC)5Co-HgX]3- and [(NC)5Co-Hg-Co(CN)5]6-, whose spectra are reported. The kinetic measurements produced a value for the forward rate constant of the reaction Co(CN)5H3- + OH- k1/k-1 Co(CN)54- +H2O, k1 = (9.7 \u00b1 0.8) x 10-2 M-1 sec-1 at 24\u00b0C, and an equilibrium constant for the reaction K = 10-6 M-1.
\r\n\r\nPart II.
\r\n\r\nUnusually large and sharp \"adsorption waves\" appear in cyclic voltammograms of Co(CN)53- and several cobalt(III) pentacyano complexes at stationary mercury electrodes. The nature of the adsorbed species and the reasons for the absence of the adsorption waves in polarograms taken with a d.m.e. have been examined. The data are compatible with the adsorption, in all cases, of a coordinatively unsaturated cobalt(II) complex, Co(CN)42-, by means of a cobalt-mercury bond. When the resulting adsorbed complex is reduced, a series of subsequent chemical and electrode reactions is initiated in which three faradays of charge are consumed for each mole of adsorbed complex. The adsorption of the anionic complex strongly retards the reduction of other negatively charged complexes.
\r\n\r\nPart III.
\r\n\r\nA number of formal redox potentials for RuIII (NH3)5L + e = RuII (NH3)5L and RuIII(NH3)4L2 + e = RuII (NH3)4L2 (where L is various ligands) has been measured by cyclic voltammetry, potentiometry, and polarography and are discussed in terms of the properties of the ligands, such as \u03c0-accepting capability. Reduction of coordinated pyrazine in the complexes, Ru(NH3)5 Pz2+, cis- and trans-Ru(NH3)4Pz22+, on a mercury electrode has been observed. The behavior of this reduction in various acidity of the solution as well as the reoxidation of the reduction products are discussed.
\r\n" }, { "name": "McGinty, David Jackson", "degree": "PhD", "year": "1972", "title": "Vapor Phase Homogeneous Nucleation and the Thermodynamic Properties of Small Clusters of Argon Atoms", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142005-153958", "creators": [ { "name": { "family": "McGinty", "given": "David Jackson" }, "id": "McGinty-David-Jackson", "display_name": "McGinty, David Jackson" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CSNR-SG47", "abstract": "Two methods have been developed for calculating the thermodynamic properties of the small clusters of atoms believed important in the phenomenon of vapor phase homogeneous nucleation. Clusters of up to 100 argon atoms have been considered. The interactions among atoms are represented by the Lennard-Jones pairwise additive potential function and all degrees of freedom are explicitly included.\r\n\r\nIn the first method, the microcrystal model is used and the independent-cluster partition function is evaluated in the same way as one would evaluate that for a polyatomic molecule in the simplest approximation: the harmonic, rigid-rotator, and perfect-gas approximations are used to calculate the vibrational, rotational, and translational contributions to the partition function. The steady-state rate of formation of nuclei as a function of degree of supersaturation has been calculated and is found to have a behavior similar to that expected from the classical, \"liquid-drop\" model.\r\n\r\nThe importance of using several stable configurations of a cluster in calculating its properties from the microcrystal model is examined in detail. It is shown that the single-configuration approximation that has been used extensively in recent work can lead to serious errors. Methods for selecting configurations that will minimize these errors are suggested.\r\n\r\nIn the second method, molecular dynamics computer simulation calculations are used. In these calculations the classical equations of motion for the atoms in a cluster are numerically integrated to yield time records of the atomic position and velocity coordinates. Values of the independent-cluster thermodynamic functions are calculated from these coordinate data and are compared with those obtained from the microcrystal model. The comparison indicates surprising agreement for values of the Gibbs free energy of formation. The transition between \"solid-like\" and \"fluid-like\" diffusion in the clusters occurs gradually; no semblance of a phase transition is noted. The radial variation of density indicates that nearly all ther atoms of a cluster exist in the \"surface\" region; the radial distribution of potential energy indicates that the environment inside the clusters is quite different from that inside the bulk liquid or solid phases.\r\n\r\nThe largest error in the molecular dynamics results is statistical errror in the temperature. An expression for this error has been derived in terms of the kinetic-energy autocorrelation function. We have shown that this and other correlation functions can be computed from the molecular dynamics data very rapidly using a method based on the Fast Fourier Transform.\r\n\r\nFinally, several very fundamental problems have been discovered in the classical, liquid-drop theory of nucleation. These problems a discussed in the context of a rigorous approach to nucleation theory that is based on the Frenkel-Band theory of noninteracting physical clusters." }, { "name": "Morrison, Paul Frederick", "degree": "PhD", "year": "1972", "title": "The X-Ray Scattering Behavior of Molecular Fluids", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06062016-090735912", "creators": [ { "name": { "family": "Morrison", "given": "Paul Frederick" }, "id": "Morrison-Paul-Frederick", "display_name": "Morrison, Paul Frederick" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R17M-GP28", "abstract": "The Steele-Pecora equation describing the x-ray scattering behavior of molecular fluids has been investigated. Several molecular scattering factor coefficients, molecular distribution functions for chlorine according to the Percus-Yevick theory,and intensity functions for chlorine have been evaluated using orthonormal expansion methods.
\r\n\r\nMolecular scattering factors for H2, N2, LiH, and HF have been obtained as spherical harmonic expansions. The coefficients of the expansions and corresponding gas scattering intensities have been evaluated using both the molecular orbital and isolated atom approaches, and significant differences have been found to exist between the two methods. Chlorine scattering factor coefficients were calculated for the isolated atom approximation only. Expressions for the two-centered Gaussian scattering integral coefficients were derived, and the harmonic expansion technique was shown to be a practical method of calculation.
\r\n\r\nThe Percus-Yevick equation was solved for chlorine by an extension of the Hankel transform method of Chen and Steele. Chlorine was represented by an appropriate two-centered Lennard -Jones potential, the \u03c3-and \u025b parameters having been determined from second virial data. Higher order expansions of f(R1R2), C(R1R2), and H(R1R2) were used here than in previous work as well as a more complete representation of the product of two harmonic series. Pair correlation functions were obtained over the density range \u03c1* = 0.1 to 1.2 for T* = 0.75, 1.00, and 1.30. It was concluded that the first two expansion coefficients of f(R1R2), C(R1R2), and H(R1R2) were sufficient to obtain accurate pair correlation functions over this range of states. For certain states, use of the more complete product expression reduced the error in g000 by several percent. Evidence for a chlorine critical point was obtained in the vicinity of (\u03c1*,T*) = (0.65, 0.70).
\r\n\r\nA version of the Steele-Pecora equation suitable for use with diatomic molecules was derived. Substitution of the chlorine scattering factor coefficients and Percus-Yevick distribution functions into this equation led to the determination of total scattered intensity functions expressed as sums of gas scattering, spherical, and angular intensity contributions. The angular contributions were shown to be experimentally significant in the regions of the first and second peaks at high densities (\u03c1*1.2). Temperature was shown to have only a slight effect on total intensity. g000, g200, and g220 were found to be the principal contributors to the intensity.
\r\n" }, { "name": "Mortola, Albert Patrick", "degree": "PhD", "year": "1972", "title": "Bonding in Transition Metal Compounds", "advisor": "Goddard, William A., III; Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-083723341", "creators": [ { "name": { "family": "Mortola", "given": "Albert Patrick" }, "id": "Mortola-Albert-Patrick", "display_name": "Mortola, Albert Patrick" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" }, { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FJ5R-XJ04", "abstract": "The values of the Hartree-Fock (HF) and Generalized Valence Bond (GVB) Theories of molecular structure are considered by theoretical investigations of the MnO_4^-, TiO, TiCO, and TiCO^+ molecules. Results of these calculations are used in determining the nature of the bonding in these compounds. From the ideas generated, extensions are made to other oxygen and carbonyl transition metal compounds. The conclusion is reached that GVB theory provides more information but is limited to small model compounds. In larger, real compounds, HF theory must be used." }, { "name": "Smith, Joseph Harold", "degree": "PhD", "year": "1972", "title": "Rheology of Concentrated Suspensions of Spheres", "advisor": "Cokelet, Giles R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07122016-160559951", "creators": [ { "name": { "family": "Smith", "given": "Joseph Harold" }, "id": "Smith-Joseph-Harold", "display_name": "Smith, Joseph Harold" } ], "advisors": [ { "name": { "family": "Cokelet", "given": "Giles R." }, "id": "Cokelet-Giles-R", "role": "advisor", "display_name": "Cokelet, Giles R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/D5BC-R506", "abstract": "The effects of concentration and composition upon the rheological properties of concentrated monomodal, bimodal, and trimodal suspensions of neutrally buoyant rigid spheres in Newtonian fluids were experimentally determined. Isothermal flow curves were calculated from torque measurements made with a Gilinson-Dauwalter-Merrill concentric cylinder viscometer with a stationary inner cylinder, a diameter ratio of 1.08, and a gap of 1.5 mm at as many as ten distinct shear rates between 0.06 and 100. inverse seconds. Median sphere diameters were 26, 61, 125, 183, and 221 microns. End effects were determined by a two bob technique, and smooth and artificially roughened cylinders were used to determine wall effects.
\r\n\r\nMonomodal suspensions were found to be power law fluids with strictly Newtonian flow properties at concentrations of 35 volume percent of solids or less, but exhibiting dilatancy at concentrations above 40 volume percent of solids. Relative viscosities and a value of the Mooney self-crowding factor \u03bbii, are reported for monomodal suspensions with concentrations between 20 and 40 volume percent of solids, and the power law parameters are reported for monomodal suspensions with concentrations between 40 and 52 volume percent of solids.
\r\n\r\nBimodal suspensions were found to be power law fluids with strictly Newtonian flow properties in the range of total concentrations up to the onset of dilatancy at total concentrations near 60 volume percent of solids for compositions at which the relative viscosity was minimized. The Mooney bimodal crowding factors, \u03bbij, were determined at nine diameter ratios between 0.12 and 0.68.
\r\n\r\nTrimodal suspensions with size ratios 0.14, 0.33, 1, at a total concentration of 45 volume percent of solids were found to be Newtonian fluids. The relative viscosities of these trimodal suspensions were found to be greater at all compositions than the minimum relative viscosity of an equally concentrated bimodal suspension of spheres with a size ratio of 0.14.
\r\n\r\nThe experimental results were discussed in terms of previous investigations and of the principal theoretical results appearing in the literature. Additional work was recommended in order to define the limits of Newtonian flow and the power law parameters for bimodal and trimodal suspensions as a function of size ratio, composition, and concentration. The approximate location of the anticipated minimum in relative viscosity as a function of trimodal composition was discussed.
\r\n" }, { "name": "Strumpf, Hal Jeffry", "degree": "PhD", "year": "1972", "title": "The Viscosity of Fluids in the Critical Region", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062016-112046701", "creators": [ { "name": { "family": "Strumpf", "given": "Hal Jeffry" }, "id": "Strumpf-Hal-Jeffry", "display_name": "Strumpf, Hal Jeffry" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1FYM-6N97", "abstract": "The viscosity of xenon has been measured along ten isochores and the viscosity of ethane has been measured along five isochores in the region of the gas-liquid critical point. The viscometer was a specially cut quartz cylinder, which was excited into a torsionally oscillating mode upon application of an alternating voltage. The\r\ncylinder, oscillating in this manner, generated a viscous wave when immersed in a fluid. The viscous wave caused an impedance loading on the quartz which changed its resonant resistance and frequency. This change in resonant properties can be related to the viscosity-density product of the fluid.
\r\n\r\nThe resonant properties of the quartz crystal were measured by connecting the crystal to the unknown arm of a Wheatstone bridge circuit, modified so as to measure parallel resistance and capacitance. The crystal was driven by a very stable frequency generator, and the circuit was tuned using an oscilloscope as a null detector.
\r\n\r\nThe crystal was enclosed in a high pressure stainless steel cell and placed in a water thermostat which controlled temperature to \u00b1 0.001\u00b0C. The temperature was measured with a calibrated platinum resistance thermometer. The density was determined by a gravimetric technique.
\r\n\r\nThe viscosities exhibit an \"anomalous\" increase as the critical temperature is approached along an isochore of close to critical density. The anomaly is consistent with a logarithmic divergence of the form:
\r\n\r\n\u2206\u019e = A log \u025b + \u0299
\r\n\r\nwhere \u2206\u019e is the anomalous viscosity, \u025b is the reduced temperature difference from critical, and A and \u0299 are constants. The possibility of an exponential divergence or a cusp-type finite limit for viscosity is not precluded, however.
\r\n\r\nThe critical temperatures and densities have been determined by visual observations. For xenon, Tc = 16.627 \u00b1 0.005\u00b0C, \u03c1c = 1.11 \u00b1 0.01 g/cm3 ; for ethane, Tc = 32.218 \u00b1 0.005\u00b0C, \u03c1c = 0.2055 \u00b1 0.002 g/cm3. The temperatures are stated with respect to the 1968 International Practical Temperature Scale.
\r\n\r\n" }, { "name": "Tilley, Jefferson Wright", "degree": "PhD", "year": "1972", "title": "Investigations Directed Toward the Total Synthesis of Shionone", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292025-151007913", "creators": [ { "name": { "family": "Tilley", "given": "Jefferson Wright" }, "id": "Tilley-Jefferson-Wright", "display_name": "Tilley, Jefferson Wright" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/em00-jn68", "abstract": "An approach to the total synthesis of the tetracyclic\r\ntriterpene shionone i is described. The key intermediate \r\nii was prepared in 17 steps (3.0% overall yield) from 2-methyl-\r\n1,3-cyclohexanedione. Generation of the essential trans,\r\ndisubstituted C/D ring fusion of ii was accomplished via\r\nthe stereospecific formation and cleavage of a fused methoxy-\r\ncyclopropane system. An additional 12 steps served to convert\r\nthe ketone ii into the ketal-ketone iii (12.5%) which\r\nrequires only addition of the side chain to complete the\r\ntotal synthesis.
\r\n\r\nSee abstract in PDF for figures i,ii and iii
" }, { "name": "Trus, Benes Louis", "degree": "PhD", "year": "1972", "title": "The Crystal Structures of Some Biologically Interesting Molecules", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:06162025-214748648", "creators": [ { "name": { "family": "Trus", "given": "Benes Louis" }, "id": "Trus-Benes-Louis", "display_name": "Trus, Benes Louis" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h9p8-e526", "abstract": "I. Crystals of 1-methylcytosine hydrochloride,\r\nC5H8N30+\u00b7Cl-, are monoclinic, space group P21/n, with\r\na = 6.695(3), b = 32.30(2), c = 6.912(2) \u00c5, \u03b2 = 104.22\u00b0.\r\nThere are eight formula units per cell, and hence two\r\nper asymmetric unit. Data were collected on an automated\r\ndiffractometer; the structural parameters were refined to\r\nan R index of 0.055 for 2609 reflections. Standard\r\nC> deviations in the bond distances are about 0.004 \u00c5.
\r\n\r\nBond distances in the two structurally distinct\r\nmolecules are in statistical agreement. The environments\r\nof both molecules are closely parallel; features of the\r\nstructure include layers of molecules joined by N-H\u00b7\u00b7\u00b70\r\nand N-H\u00b7\u00b7\u00b7Cl- hydrogen bonds, relatively short C-H\u00b7\u00b7\u00b70\r\ninteractions, and close meshing of methyl groups.
\r\n\r\nII. Crystals of lumiflavin-bisnaphthalene-2,3-diol,\r\nC13H12N402,2C10H8O2, are moloclinic, space group P21/c\r\nwith a = 20.78(2), b = 7.24(1), c = 20.15(2) \u00c5 and \u03b2 =\r\n116.19 \u00b1 0.04\u00b0 [\u03bb(Cu-K\u03b1) = 1.5418 \u00c5]. There are four\r\ncomplexes in the unit cell. Data were collected at Tulane\r\nUniversity on an automatic diffractometer, the structure\r\nwas solved at Caltech using direct methods, and the\r\nparameters returned to Tulane for final refinement.
\r\n\r\nThis is the first molecular complex of the physiologically\r\nactive neutral form of isoalloxazine studied.\r\nEach flavin is sandwiched between two napthalene molecules\r\nwith extensive overlap but a moderately large spacing\r\n(3.44 \u00c5).
\r\n\r\nIII. Crystals of thiabendazole, C10H7N3S, are orthorhombic,\r\nspace group Pbca, with a = 17.052(7), b = 10.998(4),\r\nand c = 10.030(8) \u00c5. There are eight formula units per\r\ncell. Data were collected on an automatic diffractometer;\r\nthe structural parameters were refined to an R index of\r\n0.066 for 1805 reflections. Standard deviations in bond\r\nlengths are about 0,006 \u00c5 for bonds involving carbon and\r\nnitrogen and about 0.003 \u00c5 for bonds involving sulfur.
\r\n\r\nThe two ring systems are approximately planar 9 but\r\ntwisted by 9\u00b055' with respect to each other. The C-C\r\nbond connecting\u00b7the two ring systems is 1.442 \u00c5.\r\nIV and V Crystals of the title compounds were obtained\r\nas intermediates in the syntheses of the terpenes alnusenone\r\nand shinone. The X-ray crystal structures were used to\r\nconfirm the similar stereo chemistry of these compounds.\r\nThe decahydro-ethoxy-methoxy-trimethylpycene (called\r\nPatrone 3) crystallizes in space group Pbca with eight\r\nmolecules per unit cell. The cell dimensions are a =\r\n7,094(2), b = 11.823(1), and c = 54.973 (5).The decahydromethoxy-\r\noxo-trimethvlchrysene (CHRY) crystallizes in\r\nspace group Pna21 with four molecules in the unit cell.\r\nThe cell parameters are a = 29.922(4), b = 7.757(1), and\r\nc = 7.630(4) \u00c5.
\r\n\r\nBoth molecules are rather flat except for the methyl\r\ngroups. The packing is determined largely by van der Waal\r\ninteractions. Both molecules exhibited the configuration\r\nexpected from the syntheses.
" }, { "name": "Wagner, Albert Fordyce", "degree": "PhD", "year": "1972", "title": "1. The Classification of Exact Quantum Methods for Nonreactive Scattering. 2. Quantum Mechanical Calculations of Rotational-Vibrational Scattering in Homonuclear Diatom-Atom Collisions. 3. The Effect of the Potential Well on Vibrational Scattering and the Validity of SSH Theory", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042017-113526294", "creators": [ { "name": { "family": "Wagner", "given": "Albert Fordyce" }, "id": "Wagner-Albert-Fordyce", "display_name": "Wagner, Albert Fordyce" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wtpc-sy44", "abstract": "Part 1. The exact quantum methods for the cal\u00adculation \r\nof nonreactive scattering are classified. The \r\nclassification is based on the essential characteristics \r\nof methods, not their detailed technical aspects. As a \r\nresult the potential efficiency of each class of methods \r\ncan be determined. Methods derived from differential \r\nformalism (time-independent and time-dependent Schroe\u00addinger \r\nequations) and from integral formalism (Lippmann\u00ad-Schwinger \r\nequation) are reviewed.\tThe most efficient class of differential\t\r\nmethods are found to be time\u00ad independent perturbation \r\npropagation channel methods. Integral and differential methods \r\nare found to be very similar. There seems to be no room for \r\nany further dra\u00admatic improvements in exact nonreactive \r\nquantum methods.
\r\n\r\n\r\nPart 2. Most calculations of the vibrational \r\nscattering of diatom-atom collisions use the breathing \r\nsphere approximation (BSA) of orientation-averaging the \r\nintermolecular potential. The resulting angularly sym\u00admetric \r\npotential cannot cause rotational scattering. We \r\ndetermine the error introduced by the BSA into observables \r\nof the vibrational scattering of low-energy homonuclear \r\ndiatom-atom collisions by comparing two quantum mechanical \r\ncalculations, one with the BSA and the other with the full \r\nangularly asymmetric intermolecular potential. For rea\u00adsons \r\nof economy the rotational scattering of the second \r\ncalculation is restricted by the use of special incomplete\r\nchannel sets in the expansion of the scattering wavefunction.\r\nThree representative collision systems are studied: H2-A,\r\nO2-He, I2-He. From our calculations we reach two\t\u00ad\r\nconclusions. First, the BSA can be used to analyze accurately \r\nexperimental measurements of vibrational scattering. Sec\u00adond, \r\nmeasurements most sensitive to the symmetric part of the \r\nintermolecular potential are, in order, elastic cross \r\nsections, inelastic cross sections and inelastic differen\u00adtial \r\ncross sections.\tElastic differential cross sections are sensitive \r\nto the potential only if the collision is \"sticky\", with scattering \r\nover a wide range of angles; I2-He is such a collision.\t\r\nOtherwise the potential sensitivity of elastic differential cross \r\nsections is con\u00adcentrated in the experimentally difficult region \r\nof very small angle scattering.
\r\n\r\n\r\nPart 3. The vibrational deexcitation probability,\r\nP10, is calculated quantum mechanically over a large \r\nener\u00adgy range for models of three collision systems: O2-O2,\r\nCl2-Cl2, and Br2-Br2. The vibrational \r\ndeexcitation cross section, \u03c310, is similarly calculated for the Cl2-Cl2 \r\nmodel. P10 and \u03c310 are obtained for the Lennard-Jones \r\nintermolecular potential and three otl1er \"well-less\" potentials \r\ndesigned to duplicate the scattering of the Lennard-Jones potential. \r\nThe results emphasize the adiabatic na\u00adture of potentials with wells \r\nand indicate that the acceler\u00adation approximation for the effect \r\nof the well is not valid. The curves of P10 and \u03c310\r\nas a function of initial translational energy are used to obtain exact collision numbers.\r\nThese numbers are compared to the results of SSH theory.\r\nSSH theory is found to predict collision numbers with\r\nreasonable accuracy except at low temperatures. SSH theory\r\nis also not suitable for analyzing experimental collision\r\nnumbers for the well depth potential parameter.
\r\n\r\n\r\n" }, { "name": "Webb, John Mark", "degree": "PhD", "year": "1972", "title": "Structural Studies of Some Polynuclear Iron Proteins", "advisor": "Gray, Harry B.; Saltman, Paul David", "url": "https://resolver.caltech.edu/CaltechETD:etd-02042005-105229", "creators": [ { "name": { "family": "Webb", "given": "John Mark" }, "id": "Webb-John-Mark", "display_name": "Webb, John Mark" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Saltman", "given": "Paul David" }, "id": "Saltman-P-D", "role": "advisor", "display_name": "Saltman, Paul David" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SJD3-AV69", "abstract": "The coordination structure and electronic configuration of iron(III) bound in a polynuclear fashion to a number of proteins have been investigated by a variety of physical methods. These have included the temperature dependence of the magnetic susceptibility, electron spin resonance spectroscopy, electronic absorption spectroscopy at low temperatures, vibrational spectroscopy, X-ray analysis, Mossbauer spectroscopy down to helium temperature, and electron spectroscopy for chemical analysis (ESCA). The proteins investigated included the iron transport protein transferrin, the phosphoglycoprotein phosvitin, the gastric juice glycoprotein gastroferrin, and the two iron storage proteins ferritin and hemosiderin. On the basis of the results obtained by these techniques the structural relationship of the iron to the protein and to other iron atoms present in the polynuclear complex was clarified. Structural models for these relationships were proposed for the proteins listed. The implications of these results for the biological role of iron have been considered." }, { "name": "Wilson, John Howard", "degree": "PhD", "year": "1972", "title": "Bacteriophage T4 Transfer RNA", "advisor": "Wood, William B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12042017-133901070", "creators": [ { "name": { "family": "Wilson", "given": "John Howard" }, "id": "Wilson-John-Howard", "display_name": "Wilson, John Howard" } ], "advisors": [ { "name": { "family": "Wood", "given": "William B." }, "id": "Wood-William-B", "role": "advisor", "display_name": "Wood, William B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/8JM5-QP49", "abstract": "Two T4-coded nonsense suppressors, psu+a and psu+b, have been\r\nisolated and characterized. Both were isolated as pseudo-wild type\r\nrevertants of phage strains which carry multiple amber mutations.\r\npsu+a is an amber suppressor which occurs at a frequency of 10-11 to \r\n10-12 and is indistinguishable from wild type phage in its growth\r\non both B and K strains of E. coli bacteria. psu+b may be either an amber\r\nor on an ochre suppressor which occurs at a frequency of 10-7 - 10-10 and\r\nmakes small plaques on B strains but grows very poorly or not at all\r\non K strains. Phage with the characteristics of psu+a occure in populations\r\nof psu+b phage at a frequency of 10-4. Both suppressors insert\r\nserine in response to the amber codon at an efficiency of about 45%.\r\npsu+a and psu+b map less than 0.3 map units apart and are located between genes e and 57 about 8 map units from gene e. On the basis of their \r\ninitial frequencies of appearance and the frequency of psu+b mutation to\r\npsu+a, we speculate that psu+a is derived from the wild type ser-tRNA by two base changes in the anticodon and that psu+b is a one-base-change\r\nintermediate.
\r\n\r\n151 independent suppressor-negative derivatives of psu+b phage have\r\nbeen isolated and characterized. They fall into two complementation \r\ngroups. One, designated mb (modifier of psu+b phenotype), is unlinked to\r\npsu+b and has been located about 10 map units from rII. The second\r\ngroup, designated psu+b, is made up of deletions and single base changes\r\nwhich affect sites within 0.2 map units of the original mutation. Those\r\npsu-b mutants which still contain the original mutation, psub, have been\r\nmapped relative to psub and each other by a series of two-factor and\r\nintragenic three-factor crosses. 32P-labeles tRNA from mb, psu-b and\r\nwild type infected cells have been compared by polyacrylamide gel electrophoresis. \r\nIn mb-infected cells several of the tRNA species are missing, while in psu-b-infected cells only the ser-tRNA is clearly absent. These studies suggest there are only two phage genes which are\r\nessential for the production of functional ser-tRNA. One is the structural gene for the ser-tRNA\r\nand the second plays an undefined role which affects several tRNAs.
\r\n\r\n\r\nE. coli cells infected with phage strains carrying a large deletion\r\nof gene e or gene psu+b, are missing most if not all of the phage tRNAs\r\nnormally present in wild type infected cells. By DNA-RNA hybridization\r\nwe have demonstrated that the DNA corresponding to the missing tRNAs is\r\nabsent. Thus the genes for these tRNAs must be clustered in the same\r\nregion of the genome as the ser-tRNA gene. We have been able to locate\r\nand to define a maximum size for the cluster by physically mapping the\r\ndeletions of genes e and psu+b by examination of heteroduplex DNA in the\r\nelectron microscope. That such deletions can be isolated indicates that the\r\nphage-specific tRNAs from this cluster are dispensable.
" }, { "name": "Wolcott, Robert Gordon", "degree": "PhD", "year": "1972", "title": "Investigations on the Acetylcholine Receptor", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06272025-153546793", "creators": [ { "name": { "family": "Wolcott", "given": "Robert Gordon" }, "id": "Wolcott-Robert-Gordon", "display_name": "Wolcott, Robert Gordon" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kq2g-6z40", "abstract": "Investigations directed toward isolation of the acetylcholine\r\nreceptor demonstrated that low molecular weight cholinergic ligands\r\nlack sufficient specificity for use as receptor labels. However,\r\na-bungarotoxin, a neurotoxin from B. multicinctus, proved to have\r\nthe desired characteristics of specificity and irreversibility of\r\nbinding. Chemical and physiological characterization of the purified\r\ntoxin revealed that a homogeneous species of ~8000 MW was obtained,\r\nand that the iodinated derivative was physiologically and antigenically\r\nidentical to the native protein.
\r\n\r\nThe radioiodide-labeled toxin was used as a specific,\r\nirreversible label and showed that the membrane of E. electricus\r\nelectric tissue contained a unique toxin-binding substance which could\r\nbe extracted by Triton X-100. The toxin complex had a molecular\r\nweight of ~2.5 x 105 by density gradient centrifugation and a pI ~ 5.1;\r\nuniqueness was suggested by the symmetry of the electrofocused\r\npeak. The toxin-binding component was enzymatically and chemically\r\ncharacterized as a protein with a membrane-supplied phospholipid\r\nrequirement which could also be supplied by Triton X-100 when the\r\nlatter was used to solubilize the protein. PCMB treatment of the\r\nTriton extract suggested involvement of a sulfhydryl group in toxin\r\nbinding; this group was insensitive to mild oxidation.
" }, { "name": "Wrighton, Mark Stephen", "degree": "PhD", "year": "1972", "title": "Photoprocesses in Metal Containing Molecules", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202004-113658", "creators": [ { "name": { "family": "Wrighton", "given": "Mark Stephen" }, "id": "Wrighton-Mark-Stephen", "orcid": "0000-0002-5127-2677", "display_name": "Wrighton, Mark Stephen" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vty0-hp05", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nRecent results obtained in the area of transition metal photochemistry are presented. Previous developments in this field are included. The two introductory chapters deal with structure, bonding, and electronic absorption spectroscopy of transition metal complexes. The remaining six chapters deal with pathways for decay of electronically excited states: radiative decay, nonradiative decay, electronic energy transfer, redox photochemistry, photosubstitution, and photoreactions of the coordinated ligands.\r\n\r\nHighlights of this work include new convincing evidence for assigning the low lying transitions in [...] metal carbonyls as ligand field excitations; the first definitive study of luminescence phenomena of metal carbonyls; a study of the nonradiative decay of metal carbonyl excited states with the conclusion that specific ligands can dominate the process of nonradiative decay; the first correlation of the quenching activity of a transition metal complex and its electronic properties; intramolecular energy transfer studies where one chromophore is a transition metal complex; data showing that the direct formation of CO(II) occurs via photolysis of some disubstituted cyanocobaltate(III) complexes; presentation of an associative type mechanism for the photoaquation of [...]; a description of a set of considerations (Wrighton-Gray rules) to predict and interpret photo substitution reactions; and a discussion of the photoreactivity of alkenes, dienes, and stilbenes when coordinated to Cr(0), Mo(0) or W(0).\r\n" }, { "name": "Wu, Shyue Yuan", "degree": "PhD", "year": "1972", "title": "Study of Equilibrium Critical Phenomena in Fluid Argon", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212017-114310188", "creators": [ { "name": { "family": "Wu", "given": "Shyue Yuan" }, "id": "Wu-Shyue-Yuan", "display_name": "Wu, Shyue Yuan" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z20H-HM70", "abstract": "The refractive index of fluid argon was measured by using\r\nthe method of angle of minimum deviation for \u03bbNa = 5893\u00c5. The\r\nmeasurements were carried out along the coexistence curve and along \r\nfourteen single phase isotherms from 150.7\u00b0 to 163\u00b0K at pressures from\r\n40 to 90 atmospheres.
\r\n\r\nThe Lorentz-Lorenz relation was used to relate the refractive\r\nindex data to the densities and subsequently to find the isothermal\r\ncompressibilities along the singla phase isotherms. Following the law\r\nof rectilinear diameter and the simple power laws for critical\r\nexponents, the values of the critical temperature and exponents for\r\nargon were found to be Tc = 150.725\u00b0 \u00b1 0.010\u00b0K, \u03b2 = 0.3574 \u00b1 0.0027,\r\nand \u03b3 = 1.170 \u00b1 0.013. Also values of nc = 1.08611 and\r\nPc = 47.983 atm were determined. These values agree well with\r\nothers reported for argon. Comparison of the values of \u03b2 and \u03b3\r\nwith those predicted by the classical theory and the three-dimensional\r\nlattice gas model suggests that the latter gives a better description\r\nof the critical behavior of fluid argon.
\r\n\r\nAnalysis of the reduced chemical potential differences, computed\r\nfrom the refractive index data along the singla phase isotherms,\r\nhas been made by using the scaled equation of state first proposed by\r\nWidom. Reasonable values Tc and \u03b3 were obtained when the\r\nvalue of \u03b2 determined above was used.
" }, { "name": "Abel, Roger Henry", "degree": "PhD", "year": "1971", "title": "Electrode Kinetic Studies Using a Computerized Data Acquisition and Analysis System", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03092018-170506721", "creators": [ { "name": { "family": "Abel", "given": "Roger Henry" }, "id": "Abel-Roger-Henry", "display_name": "Abel, Roger Henry" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "chair", "display_name": "Kuppermann, Aron" }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "member", "display_name": "Chan, Sunney I." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." } ], "option_major": [ "chemistry" ], "doi": "10.7907/HT2Z-3059", "abstract": "The first section of this dissertation introduces the basic concepts that are necessary for the quantitative description of electrode kinetics. The refinements and corrections in the rate equation that are due to a detailed model of the electrical double layer, and to the potential step relaxation technique are introduced and discussed.
\r\n\r\nA discussion of the non-linear statistical analysis techniques that are necessary for a rigorous analysis of rate equation is presented in the second section. The estimates of the precision of the desired parameters obtained by using statistical methods can be used as a measure of the efficiency of an experiment. Their use as measures of \"kinetic information density\" is developed and illustrated by comparing charge and current measurement in the potential step technique. Previous approaches to the subject of \"kinetic information density\" are discussed and compared to the results from statistical analysis.
\r\n\r\nThe third section describes the computerized data acquisition and analysis system that was designed and used for the study of electrode kinetics.
\r\n\r\nThe final section presents the results of the kinetic studies undertaken on the Zn+2/Zn(Hg) system in 1 F NaNO3, 1 F NaClO4, and 1 F NaCl supporting electrolytes. Ensemble averaging is used in these studies to increase precision and its values is illustrated.
\r\n\r\nThe results that are obtained for the rate constants in the various supporting electrolytes are compared and it is shown that the rates are comparable in NaNO3 and NaClO4 supporting electrolytes but significantly greater in 1 F NaCl. These results are compared with results of previous investigators and the quality of the results of this thesis are compared to those of previous investigators.
" }, { "name": "Barbee, James Henry", "degree": "PhD", "year": "1971", "title": "The Flow of Human Blood Through Capillary Tubes with Inside Diameters Between 8.7 and 221 Microns", "advisor": "Cokelet, Giles R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10182017-151706373", "creators": [ { "name": { "family": "Barbee", "given": "James Henry" }, "id": "Barbee-James-Henry", "display_name": "Barbee, James Henry" } ], "advisors": [ { "name": { "family": "Cokelet", "given": "Giles R." }, "id": "Cokelet-Giles-R", "role": "advisor", "display_name": "Cokelet, Giles R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3RKR-TH95", "abstract": "The purpose of this study was to investigate the pressure drop\u00ad \r\nflow rate behavior of normal human blood flowing through small \r\ncapil\u00adlary tubes. A sensitive pressure transducer was used to measure the \r\npressure gradient along an experimental tube when various red cell \r\nsuspensions passed through glass and plastic capillary tubes. \r\nIn particular, the effect of capillary tube diameter on the rheological \r\nproperties of blood was observed for capillary tube diameters from\r\n8 to 221 microns.
\r\n\r\nFor tubes of 221 microns and smaller, it was found that the \r\nhematocrit (volume fraction of red cells in a blood sample) of the \r\nblood flowing through a capillary tube is less than the hematocrit \r\nof the blood in the feed reservoir. The tube hematocrit decreases \r\nlinearly with the logarithm of the tube diameter at constant feed \r\nreservoir hematocrit and for a given diameter tube, increases lin\u00adearly \r\nwith the feed reservoir hematocrit.
\r\n\r\nAn equation was developed from data taken in an 811-micron ID \r\ntube that allows the shear stress-shear rate relation to be predicted \r\nfrom the tube diameter, tube hematocrit, and the temperature.
\r\n\r\nIt was found that the rheological properties of blood can be \r\naccurately predicted from the equation developed if the average \r\nhematocrit inside the capillary tube is used as the correct hematocrit \r\nparameter. A surprising result found is that fluid properties \r\ncan be predicted for blood flow through a 29-micron ID tube; in such \r\na tube, the equation of motion may not be valid because the \"continu\u00adous \r\nfluid\" assumption is not valid. Blood flow data were taken at\r\n98.6\u00b0F as well as 73.5\u00b0F. Blood heated to 111\u00b0F and then cooled to\r\n96.6\u00b0F was also investigated.
\r\n\r\nBlood flow through 15- and 9-micron ID capillaries was in\u00advestigated. \r\nBlood exhibits no yield stress in a 15-micron ID tube \r\nbecause rouleaux formation cannot restrict the flow as it does in \r\nlarger tubes.
\r\n\r\nAn increased yield stress was found in a 9-micron ID tube. \r\nThe measured shear stress was only slightly larger (for a given U) \r\nthan predicted by the continuum model in both the 15- and 9-micron \r\nID capillary tubes.
" }, { "name": "Bernstein, Paula K.", "degree": "PhD", "year": "1971", "title": "Electronic Structure of Complexes of the Ligand O-Phenylenebisdimethylarsine", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12062017-085349488", "creators": [ { "name": { "family": "Bernstein", "given": "Paula K." }, "id": "Bernstein-Paula-K", "display_name": "Bernstein, Paula K." } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xyq9-hp49", "abstract": "Various studies have been carried out to elucidate the detailed\r\nelectronic structure of the unusual spin doublet complex\r\n[Ni(diars)2X2]Y (X = Cl, Br, -NCS; Y = CL, Br, -NCS, ClO4-). An\r\nX-ray crystallographic study has been done which confirmed its\r\ncoordination number of six. U.v. and visible spectra have been taken\r\nof it and of other closely related cobalt and nickel complexes. Assignments\r\nfor the charge transfer and ligand field spectra are suggested.\r\nESR studies have been done in solution, powder, and single crystal\r\nto extract the components of the ligand superhyperfine splitting\r\ntensors. A semi-quantitative MO scheme, consistent with these\r\ntensor values, has been used to explain some of the unusual properties\r\nof this complex.
\r\n\r\n\r\nWe have concluded from these studies that the energy level\r\nordering in Ni(diarsine)2X2+ is x2 - y- < xz, yz < z2 < xy\r\nand that the ground state is 2Ag. The ground state is highly delocalized, consisting\r\nof approximately 50% ligand character distributed over all six ligands.\r\nThe tipping of the benzene rings and the distortion of the axial ligands\r\npermits an admixture of chlorine px orbitals into the ground state \r\nmolecular orbital which serves to further stabilize this system.
" }, { "name": "Betts, Jeanette Asay", "degree": "PhD", "year": "1971", "title": "Reaction of Monoenergetic Deuterium Atoms with Hydrogen and Monoenergetic Hydrogen Atoms with Per-Deutero Methane", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282018-135019156", "creators": [ { "name": { "family": "Betts", "given": "Jeanette Asay" }, "id": "Betts-Jeanette-Asay", "display_name": "Betts, Jeanette Asay" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8E5X-D717", "abstract": "Mixtures of DBr-H2, DI-H2 and HBr-CD4 were photolyzed\r\nwith monochromatic light. Thirteen different wavelengths\r\nwere used in the DBr-H2, DI-H2 systems yielding deuterium\r\natoms with initial laboratory energies ranging from 0.6 to\r\n3.0 eV. We were able to obtain the integral reaction yield
\r\n\r\nAH + D2 = k1/k1 + k2
\r\n\r\nwhere k1 and k2 are effective bimolecular rate coefficients\r\nfor the process:
\r\n\r\nD* + H2 \u2192 DH + H (1)
\r\nD* + H2 \u2192 D + H2 (2)
\r\n\r\nThese processes describe rates of reaction and thermalization\r\nwhich accompany the injection of monoenergetic atoms into\r\nthermal H2 gas. We were also able to obtain the integral\r\nreaction yield for the H + CD4 system at five wavelengths\r\nwith initial H atom laboratory energies ranging from 1.15 to\r\n3.0 eV.
\r\n\r\nFor both the D + H2 and H + CD4 systems we were able\r\nto show that the integral reaction yield is a monotonically\r\nincreasing function of energy over the energy ranges scanned.\r\nFor D + H2 a ranged from 0 at about 0.6 eV to 0.66 at 2.86 eV\r\ninitial laboratory energy while for H + CD4 A ranged from\r\n0.015 at 1.15 eV to 0.040 at 3.0 eV initial laboratory energy.\r\nThere is an order of magnitude difference between the integral\r\nreaction yields for H + CD4 and either D + H2 or H + D2.\r\nThese differences were attributed to the greater probability\r\nof inelastic collisions occuring in the H + CD4 system than\r\nin the D + H2 or H + D2 systems. Finally, we were able to\r\nshow how reaction cross sections can be extracted from the\r\nexperimental integral reaction yield using a steady state\r\nBoltzmann equation.
\r\n\r\nWe were also able to measure the abstraction fraction a\r\nfor the reaction of H with DX (X = Br, I). The results were\r\na(DBr) = 0.99 \u00b1 0.03 and a (DI) = 0.97 \u00b1 0.05.
\r\n\r\nFinally, using the integral reaction yield versus energy\r\nplot for D + H2 plus additional DI-H2, DI-He experiments we\r\nwere able to determine the fraction f of iodine atoms\r\nproduced in the excited 2P1/2 state in the photolysis of DI\r\nat 4 wavelengths. The results are f(2800\u00c5) = -0.08 \u00b1 0.27,\r\nf(2537\u00c5) = 0.46 \u00b1 0.05, f(2400\u00c5) = 0.60 \u00b1 0.07 and f(2138\u00c5) = 0.33 \u00b1 0.1.
\r\n" }, { "name": "Blumenthal, Alan Brian", "degree": "PhD", "year": "1971", "title": "Studies on Drosophila Phenol Oxidase", "advisor": "Mitchell, Herschel K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02022018-142752792", "creators": [ { "name": { "family": "Blumenthal", "given": "Alan Brian" }, "id": "Blumenthal-Alan-Brian", "display_name": "Blumenthal, Alan Brian" } ], "advisors": [ { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "advisor", "display_name": "Mitchell, Herschel K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/EG3S-V883", "abstract": "Phenol oxidase is the enzyme responsible for hardening \r\nand pigmentation of insect cuticle. The cuticular phenol \r\noxidase is not extractable, thus unavailable for biochemical \r\nstudies. The properties and composition of the enzyme, produced \r\nin vitro from extracts of late third instar Drosophila larvae, \r\nwere investigated to elucidate its in vivo function.
\r\n\r\n\r\nConditions for in vitro activation and isolation of the \r\nenzyme were studied in detail. The conditions of activation \r\naffect both the aggregation state and the density of the \r\nresulting phenol oxidase. The enzyme was isolated from the \r\nactivation extract by centrifugation on sucrose gradients.
\r\n\r\n\r\nThe active phenol oxidase is an insoluble, lipoprotein \r\ncomplex which can be partially separated into a tyrosinase \r\nand a dihydroxy phenol oxidase. The complex is largely \r\ndissociated by strong protein denaturing agents, though some \r\ncovalent cross linking is indicated. Analysis of the \r\ndissociated complex by SDS acrylamide gel electrophoresis \r\nshows a large number of protein bands. The significance of \r\nthese bands is discussed in relation to the purity of the \r\nphenol oxidase and expected subunit composition.
\r\n\r\n\r\nThe effects of denaturing agents, urea and sodium \r\ndeoxycholate, on the phenol oxidase indicate a complex \r\nrelationship between enzyme structure and activity.\t\r\nA tenta\u00adtive structural model for the phenol oxidase \r\ncomplex is\r\nproposed.
\r\n\r\nThe characteristics of in vitro phenol oxidase are \r\ndiscussed with regard to possible regulation of in vivo \r\nfunction.
\r\n\r\n" }, { "name": "Bowman, Ray Douglas", "degree": "PhD", "year": "1971", "title": "Hydrodynamic Shear Breakage of Native DNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012018-135717308", "creators": [ { "name": { "family": "Bowman", "given": "Ray Douglas" }, "id": "Bowman-Ray-Douglas", "display_name": "Bowman, Ray Douglas" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5f4m-ns78", "abstract": "Shear breakage is the process by which high molecular weight\r\npolymers are broken one or more times by shear stress generated in\r\nliquid velocity gradients. This thesis is a kinetic study of the \r\nbreakage of native DNA from the coliphage \u03bbb2b5c (contour length 12.8 \u00b5)\r\nin dilute aqueous solution. Breakage of this DNA is produced by flow\r\nthrough a capillary. In all our experiments, each DNA molecule\r\nbreaks only once to form two approximately half-sized molecules.\r\nThe shear stress required to induce breakage is about 103 dynes/cm2.\r\nWe find that the kinetics of breakage are first order and that the first\r\norder rate constant is a function of the fifteenth power of the shear\r\ngradient at 25\u00b0C. The shear stress required to produce breakage at\r\na particular rate increases linearly with DNA concentration over the\r\nrange 0.05 \u00b5g DNA/ml to 7.5 \u00b5g DNA/ml. We observe a very large\r\ntemperature coefficient for the breakage rate which arises from the\r\neffect of temperature on the viscosity of the DNA solution. This\r\nresult indicates that the rate limiting step for DNA shear breakage is\r\nthe speed at which random coil DNA unfolds to an extended configuration\r\nwhen it enters the capillary's liquid velocity gradient. We\r\ndiscuss a kinetic model and a simple theoretical model which have\r\nproperties similar to those observed experimentally.\r\n" }, { "name": "Bruckner, Joseph Robert", "degree": "Masters", "year": "1971", "title": "A Study of the Preparation of Tricyclo[4,1,0,0\u00b3,\u2077]heptane and the 6-Halofulvenes", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202010-094744901", "creators": [ { "name": { "family": "Bruckner", "given": "Joseph Robert" }, "id": "Bruckner-Joseph-Robert", "display_name": "Bruckner, Joseph Robert" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QQX0-NP82", "abstract": "Part I:
\r\nThe literature synthesis, with some modifications, of tricyclo[ 4, 1, 0, 03,7]heptane was undertaken. While considerable difficulty was encountered in the final reaction involving a sodium borohydride reduction, far more successful results were obtained when lithium aluminum hydride was used instead as the reducing agent. The hydrocarbon can be stereospecifically deuterated at various points in the reaction sequence and once labeled, can be pyrolyzed and its products studied to determine the extent of orbital symmetry restrictions on the pyrolytic rearrangement process.
Part II:
\r\nIn efforts to produce the mono- and diadducts of dichloro- and dibromocarbene to cyclopentadiene, it was found that the respective 6-halofulvenes were being produced instead. Depending upon the conditions used, varying amounts of halobenzene and 1, 1-dihalo-2, 2- dimethylcyclopropane could be produced as other major reaction products. The fulvenes were obtained in best yield using haloform as the dihalocarbene precursor and potassium tert-butoxide as the base. Ethyl trichloroacetate and phenyl (bromodichloromethyl) mercury were also used with various bases to generate dichlorocarbene, but these methods were unsuccessful in producing the 6-chlorofulvene.
A method was developed for measuring the self-diffusion\r\ncoefficient of solutes in agar gel suspensions of red cells. The\r\npurpose was to investigate the influence of the red cell on the\r\ndiffusion of ions which are important in blood solute transport.
\r\n\r\nThe capillary diffusion method was employed. The diffusion\r\ncoefficient was calculated from the initial and final concentration\r\nof tracer in the capillary. The results are discussed\r\nin terms of a modified Maxwell equation for the average conductivity\r\nin a granular medium in which a discontinuous boundary\r\ncondition is employed to account for the observed partition\r\ncoefficients.
\r\n\r\nThe results indicate the ration of the diffusivity of solute\r\nin the red cell suspension to that in the suspending medium\r\nvaries considerably with the ion. This ratio is greater for \r\nsodium than for chloride over the range of red cell volume\r\nfractions investigated. An augmented diffusional mechanism\r\nfor bicarbonate appears to exist in the red cell suspension.\r\nDepleting the intracellular ATP has little effect on the diffusion\r\nof sodium in the red cell suspension.
" }, { "name": "Clarke, Mildred Allen", "degree": "Masters", "year": "1971", "title": "Studies Leading to Iodine-Tagged Crosslinked Polybutadiene", "advisor": "Tschoegl, Nicholas W.; Rembaum, Alan", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222010-090826127", "creators": [ { "name": { "family": "Clarke", "given": "Mildred Allen" }, "id": "Clarke-Mildred-Allen", "display_name": "Clarke, Mildred Allen" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "co-advisor", "display_name": "Tschoegl, Nicholas W." }, { "name": { "family": "Rembaum", "given": "Alan" }, "id": "Rembaum-A", "role": "co-advisor", "display_name": "Rembaum, Alan" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7951-NC71", "abstract": "Work leading to the synthesis of uniformly crosslinked poly-butadiene with iodine tags at both ends of a small percentage of the crosslinking chains is described. The following reactions have been investigated: conversion of dibromopolybutadiene to diiodopolybutadiene; conversion of dihydroxypolybutadiene to polybutadiene diisocyanate; chain extension of polybutadiene diisocyanate with\r\n3-dirnethylamino-1, 2-propane-diol to form a linear polybutadiene with pendant dimethylamino groups (PBPA); crosslinking of the PBPA by quaternization of the amine groups with diiodopolybutadiene; and formation of \r\nthe amine salt of PBPA by treatment with hydrochloric acid.\r\n\r\nMechanical properties of PBPA, its HC1 salt, and the cross-linked polybutadiene were determined by free torsional oscillation. Salt formation apparently leads to pseudo-crosslinking of the polymer by association of the ionic groups, so that the polymer exhibits elastomeric behavior between -30\u00b0 and 40\u00b0C. Crosslinking of PBPA by\r\nquaternization of the amine groups with diiodopolybutadiene extends the elastic region to 130\u00b0C, where creep begins due to degradation of the polymer.\r\n" }, { "name": "Crawford, Jane Ellen", "degree": "PhD", "year": "1971", "title": "I. Proton Magnetic Resonance of Polynucleotides and Transfer RNA. II. Electron Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03072016-134037436", "creators": [ { "name": { "family": "Crawford", "given": "Jane Ellen" }, "id": "Crawford-Jane-Ellen", "display_name": "Crawford, Jane Ellen" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YV85-RX30", "abstract": "Part I. Proton Magnetic Resonance of Polynucleotides and Transfer RNA.
\r\n\r\nProton magnetic resonance was used to follow the temperature dependent intramolecular stacking of the bases in the polynucleotides of adenine and cytosine. Analysis of the results on the basis of a two state stacked-unstacked model yielded values of -4.5 kcal/mole and -9.5 kcal/mole for the enthalpies of stacking in polyadenylic and polycytidylic acid, respectively.
\r\n\r\nThe interaction of purine with these molecules was also studied by pmr. Analysis of these results and the comparison of the thermal unstacking of polynucleotides and short chain nucleotides indicates that the bases contained in stacks within the long chain poly nucleotides are, on the average, closer together than the bases contained in stacks in the short chain nucleotides.
\r\n\r\nTemperature and purine studies were also carried out with an aqueous solution of formylmethionine transfer ribonucleic acid. Comparison of these results with the results of similar experiments with the homopolynucleotides of adenine, cytosine and uracil indicate\r\nthat the purine is probably intercalating into loop regions of the molecule.
\r\n\r\nThe solvent denaturation of phenylalanine transfer ribonucleic acid was followed by pmr. In a solvent mixture containing 83 volume per cent dimethylsulf oxide and 17 per cent deuterium oxide, the tRNA molecule is rendered quite flexible. It is possible to resolve resonances of protons on the common bases and on certain modified bases.
\r\n\r\nPart II. Electron Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile.
\r\n\r\nThe electron paramagnetic resonance spectra of three Mn+2 complexes, [Mn(CH3CN)6]+2, [MnCl4]-2, and [MnBr4]-2, in acetonitrile were studied in detail. The objective of this study was to relate changes in the effective spin Hamiltonian parameters and the resonance\r\nline widths to the structure of these molecular complexes as well as to dynamical processes in solution.
\r\n\r\nOf the three systems studied, the results obtained from the [Mn(CH3CN)6]+2 system were the most straight-forward to interpret. Resonance broadening attributable to manganese spin-spin dipolar interactions was observed as the manganese concentration was increased.
\r\n\r\nIn the [MnCl4]-2 system, solvent fluctuations and dynamical ion-pairing appear to be significant in determining electron spin relaxation.
\r\n\r\nIn the [MnBr4]-2 system, solvent fluctuations, ion-pairing, and Br- ligand exchange provide the principal means of electron spin relaxation. It was also found that the spin relaxation in this system is dependent upon the field strength and is directly related to the manganese concentration. A relaxation theory based on a two state collisional model was developed to account for the observed behavior.
" }, { "name": "Dawson, Daniel Joseph", "degree": "PhD", "year": "1971", "title": "I. An Investigation of the Utility of the Claisen Rearrangement in Angular Methylation as Illustrated by the Synthesis of 1-Valeranone. II. The Total Synthesis of the Pentacyclic Triterpene dl-Germanicol", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282018-114652372", "creators": [ { "name": { "family": "Dawson", "given": "Daniel Joseph" }, "id": "Dawson-Daniel-Joseph", "display_name": "Dawson, Daniel Joseph" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A7NX-WW98", "abstract": "I. A new method of angular methylation was developed\r\nin a synthesis of 1-valeranone. This Claisen rearrangement--\r\ndecarbonylation procedure was further investigated on the\r\nsubstrate cholest-4-en-3\u03b2-o1.
\r\n\r\nII. The synthesis of the pentacyclic triterpene\r\ndl-germanicol is described.
" }, { "name": "Erb, Judith Louise", "degree": "Masters", "year": "1971", "title": "Studies on the Feasibility of Isolating the Acetyl Choline Receptor by Means of Affinity Chromatography", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-151021376", "creators": [ { "name": { "family": "Erb", "given": "Judith Louise" }, "id": "Erb-Judith-Louise", "display_name": "Erb, Judith Louise" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RBRP-RY38", "abstract": "Feasibility studies were conducted on the isolation of the acetyl choline receptor by means of affinity chromatography. Sepharose resins bearing acetyl choline receptor binding materials of at various distances from the backbone of the resin and of varying degrees of substitution were treated with extracts from electric eel organ, washed free of non-binding materials and the material bound to the column extracted by various means. Extracts from the column were studied for purity, binding to decamethonium and \u03b1-bungarotoxin, and presence or absence of acetyl cholinesterase or choline acetylase activity. Although material possessing the proper characteristics was extracted from some of the resins, electrophoretic purity was not obtained." }, { "name": "Fesko, Donald George", "degree": "PhD", "year": "1971", "title": "Time-Temperature Superposition for Block Copolymers", "advisor": "Tschoegl, Nicholas W.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04122004-145357", "creators": [ { "name": { "family": "Fesko", "given": "Donald George" }, "id": "Fesko-Donald-George", "display_name": "Fesko, Donald George" } ], "advisors": [ { "name": { "family": "Tschoegl", "given": "Nicholas W." }, "id": "Tschoegl-N-W", "role": "advisor", "display_name": "Tschoegl, Nicholas W." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RQDJ-8F02", "abstract": "The proposition is made that simple time-temperature superposition should not be valid for block copolymers exhibiting multiple mechanical transitions; and an explanation of the time temperature behavior, which is more consistent with the behavior of the individual phases, is presented in terms of an equivalent mechanical model. Based on this model, a method for generating time-temperature shifts, which depend on the experimental time as well as temperature, is developed. This method can easily be extended to any mechanical model and should be valid for polymer composites in general.\r\n\r\nThe storage and loss compliances of three benzene cast polystyrene/l,4-polybutadiene/polystyrene triblock copolymers with different compositions were measured between -85 and 90[degrees]C over a frequency range from 0.1 to 1000 Hz. The measurements suggest the presence of four relaxation processes. Two, the polystyrene and polybutadiene glass transitions, are treated according to the method of time-temperature superposition referred to above. Anomalous behavior appearing between the two glass transitions is attributed primarily to a temperature dependent interlayer between the two phases and can be treated as a compositional change in the composite. Entanglement slippage in the rubbery matrix also contributes to the total relaxation.\r\n\r\nThe apparatus used for these experiments is an extensively modified model of the Miles shear generator. This improved version offers large experimental frequency and temperature operating ranges." }, { "name": "Hwang, Myung Kyu", "degree": "PhD", "year": "1971", "title": "Estimation and Control of Stochastic Chemical Systems", "advisor": "Seinfeld, John H.; Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05252018-085149423", "creators": [ { "name": { "family": "Hwang", "given": "Myung Kyu" }, "id": "Hwang-Myung-Kyu", "display_name": "Hwang, Myung Kyu" } ], "advisors": [ { "name": { "family": "Seinfeld", "given": "John H." }, "id": "Seinfeld-J-H", "role": "advisor", "display_name": "Seinfeld, John H." }, { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/BG3X-F787", "abstract": "Chapter II
\r\n\r\nThe control of nonlinear lumped-parameter systems is \r\nconsidered with unknown random inputs and measurement noise. \r\nA scheme is developed whereby a nonlinear filter is included \r\nin the control loop to improve system performance. Pure \r\ntime delays in the control loop are also examined. A computational \r\nexample is presented for the proportional control on temperature \r\nof a CSTR subject to random disturbances, applying a nonlinear least \r\nsquare filter.
\r\n\r\nChapter III
\r\n\r\nLeast square filtering and interpolation algorithms are derived \r\nfor states and parameters in nonlinear distributed systems with unknown \r\nadditive volume, boundary and observation noises, and with volume and \r\nboundary dynamical inputs governed by stochastic ordinary differential \r\nequations. Observations are assumed to be made continuously in time at \r\ncontinuous or discrete spatial locations. Two methods are presented\r\nfor derivation of the filter. One is the limiting procedure of the \r\nfinite dimensional description of partial differential equation systems \r\nalong the spatial axis, applying known filter equations in ordinary \r\ndifferential equation systems. The other is to define a least square \r\nestimation criterion and convert the estimation problem into an optimal \r\ncontrol problem, using extended invariant imbedding technique in\r\npartial differential equations. As an example, the derived filter is \r\nused to estimate the state and parameter in a nonlinear hyperbolic system \r\ndescribing a tubular plug flow chemical reactor. Also a heat\r\nconduction problem is studied with the filtering and interpolation \r\nalgorithms.
\r\n\r\nChapter IV
\r\n\r\nNew necessary and sufficient conditions are presented for the \r\nobservability of systems described by nonlinear ordinary differential \r\nequations with nonlinear observations. The conditions are based on \r\nextension of the necessary and sufficient conditions for observability \r\nof time-varying linear systems to the linearized trajectory of the \r\nnonlinear system. The result is that the local observability of \r\nany initial condition can be readily determined, and the observability \r\nof the entire initial domain can be computed. The observability of \r\ncon\u00adstant parameters appearing in the differential equations is also \r\nconsidered.
" }, { "name": "Kowalski, Conrad John", "degree": "Masters", "year": "1971", "title": "Total Synthesis of a Key Intermediate for the Triterpene Shionone", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302010-151038761", "creators": [ { "name": { "family": "Kowalski", "given": "Conrad John" }, "id": "Kowalski-Conrad-John", "display_name": "Kowalski, Conrad John" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JG81-R503", "abstract": "Total synthesis of a key intermediate, in a synthetic scheme \r\naimed at the tetracyclic triterpene Shionone, has been accomplished by two closely related routes." }, { "name": "Lai, Fang Shyong", "degree": "Masters", "year": "1971", "title": "Lagrangian Models of the Dispersion of Airborne Chemically Reacting Contaminants", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:12082017-140901455", "creators": [ { "name": { "family": "Lai", "given": "Fang Shyong" }, "id": "Lai-Fang-Shyong", "display_name": "Lai, Fang Shyong" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9HBZ-SW15", "abstract": "The present work attempts to obtain a mathematical model for generation and dispersion of photochemical smog. A simplified kinetic model which is proposed by Friedlander and Seinfeld (1969), is presented for the photochemical smog reactions. To take into account the effect of atmospheric mixing processes on the chemical reactions, the Lagrangian similarity hypothesis for the diffusion of non-reactive components is extended to reacting species. The concept of a variable volume batch reactor model (VVBR) is applied in the study of the formation of photochemical smog. The critical value, [h/bu*]cr. where h is the source height, b constant and u* friction velocity, for the onset of photochemical smog is found.
\r\n\r\nCalculations based on the simplified kinetic model and the applications of the Lagrangian similarity hypothesis are given for a nonlinear, second order chemical reaction. Finally, determination of the probability density function of the pollutant is given for the non-reacting case.
" }, { "name": "Lee, Chi-Yu Gregory", "degree": "Masters", "year": "1971", "title": "The Tautomeric Exchange of Nucleic Acid Bases", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042010-094013118", "creators": [ { "name": { "family": "Lee", "given": "Chi-Yu Gregory" }, "id": "Lee-Chi-Yu-Gregory", "display_name": "Lee, Chi-Yu Gregory" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TDW7-S132", "abstract": "[Part 1]. For a series of PMR studies of cytidine and related compounds in D\u2082O solution at various pD, it was observed that the H\u2085 resonances of cytosine base are broad in some of these compounds at pD 4-7, while those of H\u2086 are not. We proposed that there is chemical exchange between two tautomeric forms of cytosine base to give rise to broadening of spectra. This chemical exchange was found to be catalyzed by both solvent (D\u2082O)and hydroxyl (OD\u207b) ion present in solution. The observation of sharp resonances in certain cytidine derivatives having only one possible \r\ntautomeric structure supports this proposal. Temperature study of H\u2085 resonances at different pD was used to investigate the kinetics of this exchange reaction. The percentage of its minor tautomer was estimated as 10 \u00b1 2% in neutral aqueous solution and its life time is about 10\u207b\u00b3 sec at room temperature. The activation energy of this tautomeric exchange is 7.5 \u00b1 0. 5 kcal/mole. for D\u2082O catalysis and 2.5 \u00b1 0.5 kcal/mole for OD\u207b catalysis. The relation between tautomeric exchange of nucleic acids and genetic mutation is also discussed.
\r\n\r\n[Part 2]. From the PMR study of guanosine and its related compounds at different pD, temperature and concentrations, it was observed that H\u2088 resonances of guanine base in some of these compounds are unusually broad over a wide pD range (from 2 to 8) in aqueous solutions. This phenomenon is explained in terms of the effects of base pairing, stacking and tautomeric exchange between the 1 and 6 positions of guanine base. The observation of sharp resonance of H\u2088 of\r\n1-methyl guanosine having only one possible tautomeric structure supports that there exists minor tautomer of this base. This tautomeric exchange is catalyzed either by solvent (D\u2082O), base (OD\u207b) or pairing of base. The percentage of minor tautomer and the activation energy of the exchange are also estimated from the kinetic analysis.
" }, { "name": "Leonard, Jack Edward", "degree": "PhD", "year": "1971", "title": "I. Studies in Isomerism: Permutations, Point Group Symmetries, and Isomer Counting. II. Studies in the Photochemistry of Coumarin and Certain Coumarin Derivatives", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112018-091948944", "creators": [ { "name": { "family": "Leonard", "given": "Jack Edward" }, "id": "Leonard-Jack-Edward", "display_name": "Leonard, Jack Edward" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0WGY-7455", "abstract": "PART I
\r\n\r\nPolya's group theoretical method for calculating the permutation isomers of a rigid molecular framework is extended to certain nonrigid systems. Symmetry operators are defined which allow the high symmetry of freely rotating, rapidly inverting, or ring-flipping molecules to be handled by group theoretical methods.
\r\n\r\nIn the second portion of this discussion the effect of chiral ligands on the number of possible permutation isomers is discussed and a number of unusual possible meso compounds are presented.
\r\n\r\nPART II
\r\n\r\nThe unusually high rate of energy dissipation in coumarin is discussed. In the raman spectrum of ultraviolet irradiated coumarin at 98\u00b0K evidence is found for the formation of an oxabicyclobutane derivative via the rearrangement:
\r\n\r\n[Diagram included in scanned thesis' abstract, p. iv.]
\r\n\r\nBands at 875 and 1231 cm-1 in the raman spectrum appear to arise from the oxabicyclobutane. When coumarin (or N-alkyl o-coumaramides) is irradiated in amine solution, N,N'-dialkyl-o-tyrosine amide derivatives are formed. This is a new pathway to o-tyrosine derivatives, but its generality is not known.
\r\n" }, { "name": "Meyer, James Wilfred", "degree": "PhD", "year": "1971", "title": "Photolyses of Phenyl Esters", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02102009-081424", "creators": [ { "name": { "family": "Meyer", "given": "James Wilfred" }, "id": "Meyer-James-Wilfred", "display_name": "Meyer, James Wilfred" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S1DE-KS63", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe photochemical reactions of phenyl esters have been studied in both solution and gas phases. The irradiation of phenyl esters in the gas phase with ultraviolet light results in their photolyses. The photolysis of phenyl acetate in the vapor phase produces mainly phenol with lesser amounts of [...] and [...]-cresols and [...] and [...]-hydroxy dipheny1 ethers. In addition to these compounds, [...]-benzoquinone was also isolated, however it is believed to be formed from the secondary photolysis of ga-hydroxydiphenyl ether. These products are explained with a mechanism involving the photolysis of phenyl acetate into phenoxy and aryl radicals followed by decarbonylation of the acy1 radical to give carbon monoxide and methyl radicals. The reactions of methyl and phenoxy radicals produce the observed products. Although attempts at scavenging the acyl radical failed, the detection of products from the decomposition of butyry1 radicals in the irradiations of phenyl [...]-butYrate indicates a simi1ar mechanism is operating in solution. These results are taken to indicate that the photo-Fries Rearrangement results from the cage recombination of phenoxy and acyl radicals rather than by means of a molecular rearrangement. The quantum yields of phenyl benzoate were measured in ether: [...]. The emission spectra of several different phenyl esters were recorded and discussed in terms of the excited state leading to reaction.\r\n\r\nThe irradiations of 1-butanethio1 in solution and [...]-hYdroxYacetophenone in the vapor phase were brieflY studied. 1-Butanethio1 gives hydrogen sulfide, butyldisulfide and dibutyl sulfide. Irradiations of [...]-hydroxyacetophenone appears to give phenol at low pressures and salicy1aidehyde at about 1000 mmHg." }, { "name": "Muchmore, David Charles", "degree": "PhD", "year": "1971", "title": "A Study of the Reductive Cleavage of Vinyl and Alkyl Phosphoryl Esters", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082018-123126359", "creators": [ { "name": { "family": "Muchmore", "given": "David Charles" }, "id": "Muchmore-David-Charles", "display_name": "Muchmore, David Charles" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0Z8V-FK18", "abstract": "A number of alcohols and enolate anions were deoxygenated by reduction of the corresponding diethylphosphate or tetramethyl-phosphorodiamidate esters. Lithium-amine solutions were successful reducing agents in most cases, and, in addition, tetramethyl-phosphorodiamidate esters were cleaved by the adduct of lithium and biphenyl in tetrahydrofuran.
" }, { "name": "Noe, Eric Arden", "degree": "PhD", "year": "1971", "title": "Conformational Study of Some Fluorine-Labeled Cyclic Compounds by Nuclear Magnetic Resonance Spectroscopy: I. 1,1-Difluorocyclodecane and 3,3-Difluoro-Trans-Cyclodecene. II. \u03b3,\u03b3-Difluoro-\u03b5-Caprolactone and \u03b3,\u03b3-Difluoro-\u03b5-Caprolactam", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082018-113949436", "creators": [ { "name": { "family": "Noe", "given": "Eric Arden" }, "id": "Noe-Eric-Arden", "display_name": "Noe, Eric Arden" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/08XX-JE96", "abstract": "Low-temperature fluorine magnetic resonance spectroscopy has been used to investigate the conformational equilibration of four cyclic gem-fluorides. Ring inversion in 1,1-difluorocyclodecane was stopped on the nmr time scale by -164\u00b0, and an activation energy of 7.0 kcal/mole was determined for this process. The spectra were interpreted in terms of the boat-chair-boat conformation. Changes in the spectra of 3,3-difluoro-trans-cyclodecene occurred continuously over a wide range of temperature, from above ambient temperature to about -140\u00b0. The free energy of activation for the first process, which is nearly stopped on the nmr time scale by -30\u00b0, was 12.4 kcal/mole at 2.8\u00b0. Activation parameters were not calculated for the changes which took place at lower temperatures. At -148\u00b0, two conformations were present in a ratio of 85:15, and other conformations may be present in smaller amounts.
\r\n\r\nThe activation energy for inversion of \u03b3,\u03b3-difluoro-\u03b5-caprolactone was 12.4 kcal/mole, and the free energy of activation for this process was 10.0 kcal/mole at -53\u00b0. The spectra indicate that the compound exists in the chair conformation, and the activation parameters provide information about the barrier to cis-trans isomerization of esters. The free energy of activation for \u03b3,\u03b3 difluoro-\u03b5-caprolactam was 10.4 kcal/mole at -53\u00b0. The lactam also prefers the chair conformation.
\r\n" }, { "name": "O'Brien, Edward Francis", "degree": "Masters", "year": "1971", "title": "Studies on the Microscopic Motion of a Diatomic in a Monatomic Solvent", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112010-155239731", "creators": [ { "name": { "family": "O'Brien", "given": "Edward Francis" }, "id": "O'Brien-Edward-Francis", "display_name": "O'Brien, Edward Francis" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JH9Y-QR36", "abstract": "The microscopic motion of a diatomic in a monatomic solvent has been studied using the molecular dynamics method and a model of Lennard-Jones spheres for the monatomics and two such spheres joined by a rigid bond for the diatomic. Data were generated by computer for three systems, each at the same density but varying in temperature. From these data autocorrelation functions were calculated for the following random quantities of the motion of the diatomic: orientation of the diatomic, velocity of its center of mass angular velocity and momentum, mean square displacement of its center of mass and the forces on the diatomic bond. Infrared and Raman band shapes and NMR relaxation times were determined from the above correlation functions.\r\n\r\nThe decay times of the correlation functions were found to be in the range of 0.25 to 2.5 x 10^(-12) sec. The band shapes were symmetrical and their bandwidth change reflects the change in inhonaogeneous broadening with respect to temperature. The NMR, relaxation times also behave correctly with respect to temperature and indicate which of the relaxation mechanisms studied is dominant.\r\n\r\nFurther studies are proposed to determine the reason for the discrepancies between the above calculated quantities and those quantities obtained from experimental data.\r\n" }, { "name": "O'Keefe, Patricia Marie", "degree": "PhD", "year": "1971", "title": "The Applications of the GI Method to Incorporation of Many-Body Effects in Metals; The Band Structure and Resolution of Several Anomalous Properties of Lithium Metal", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132010-113849886", "creators": [ { "name": { "family": "O'Keefe", "given": "Patricia Marie" }, "id": "O'Keefe-Patricia-Marie", "display_name": "O'Keefe, Patricia Marie" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QN5M-CW17", "abstract": "A new approach to studying the electronic energy band structure on solids has been developed and calculations are reported for lithium metal. This framework, the GI method, leads to one-electron orbitals which in general are singly occupied, have no orthogonality constraints, are no longer required to have the full symmetry of the system, and lead to a description which is valid at all internuclear distances. Yet they still retain an independent particle interpretation.
\r\n\r\nIn the application to solids, similar considerations apply. It is found that, for the alkalis, the resulting one-electron conduction orbitals can be taken to be Bloch functions for a smaller symmetry group than the bcc symmetry of the lattice. Thus, the resulting Brillouin zone (BZ) is smaller than that in Hartree-Fock (HF), and gaps can occur at the Fermi surface where none were previously permitted. For lithium these gaps are found to be sufficiently small so that many of the expected properties are not significantly affected and the resulting Fermi surface is found to be quite spherical in good agreement with, for example, position annihilation results. However, for such properties as the high field transverse magneto resistance, the soft X-ray emission spectrum, the optical absorption spectrum, the thermoelectric power, and the Hall coefficient, striking alterations in the description are obtained which lead to an appealing explanation of many of the anomalous properties of the alkalis, and seem to be in at least qualitative agreement with the experimental observations. The Mott paradox is also resolved; the metal is found to change continuously from a conductor to an insulator as the system is dilated.
" }, { "name": "Ottesen, David Keith", "degree": "PhD", "year": "1971", "title": "The Vibrational and Electronic Spectrum, and the Potential Field of Various Manganese Carbonyl Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202017-154553422", "creators": [ { "name": { "family": "Ottesen", "given": "David Keith" }, "id": "Ottesen-David-Keith", "display_name": "Ottesen, David Keith" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xbxd-q624", "abstract": "I. The infra-red and Raman spectra of Mn(CO)5Br as\r\nboth solid and CH2Cl2 solution from 50 to 2150 cm-1\r\nare presented for the normal isotopic compound, and\r\nthe 13CO and C18O substituted molecules. The observed \r\nbands are assigned, and the force constants and compliance\r\nconstants of a general quadratic potential field\r\nare calculated using the FG method of Wilson, Decius,\r\nand Cross.
\r\n\r\nII. The infra-red and Raman spectra of both Mn2(12CO)10\r\nand Mn2(13CO)10 as solids and in CH2Cl2\r\nsolutions from 50 to 2150 cm-1 are presented and are assigned. Potential\r\nconstants are calculated using values transferred\r\nfrom the Mn(CO)5Br calculations. Special attention is\r\npaid to splitting interactions across the Mn--Mn bond\r\nand to the Mn--Mn stretching potential constants.
\r\n\r\nIII. Raman intensities and the electronic absorption spectrum\r\nof M(CO)5Xn- compounds are presented and discussed.
" }, { "name": "Parsons, Stanley Monroe", "degree": "PhD", "year": "1971", "title": "The Catalytic Site of Lysozyme", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052018-084556110", "creators": [ { "name": { "family": "Parsons", "given": "Stanley Monroe" }, "id": "Parsons-Stanley-Monroe", "display_name": "Parsons, Stanley Monroe" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P8Q0-TK36", "abstract": "Proton magnetic resonance techniques have used to study the \r\nassociation of simple cyclohexane derivatives to the primary binding \r\nsubsite of lysozyme in solution. The results agree in detail with \r\ncrystallographic deductions about the nature of the important binding \r\ninteractions in subsite C.
\r\n\r\nA reagent new to protein modification studies, triethyloxonium \r\nfluoroborate, has been shown to selectively esterify carboxyl groups \r\nunder mild aqueous conditions. Two single ethylesters of lysozyme \r\nwere isolated chromatographically in good yield and were characterized.\t\r\nOne is enzymatically active and reverts to lysozyme under neutral \r\nconditions. The other is enzymatically inactive but still binds \r\nthe inhibitor chitotriose. This inactive ester was identified as \r\noccurring at aspartic acid residue 52 by \u03b1-chymotryptic digestion of\r\nthe oxidized derivative and direct observation of the \u03b2-ethyl aspartate \r\nreleased from the modified peptide by carboxypeptidase.
\r\n\r\nDifference pH titrations of the Asp 52 ester vs. the native \r\nlysozyme show a difference in proton uptake due to one group over \r\nthe pH range 3 to 9. The titration of glutamic acid residue 35 in the \r\nderivative is perturbed, though, and from the shape of the difference \r\ntitration curve the ionization behavior of Asp 52 and Glu 35 in native \r\nlysozyme and of Glu 35' in the derivative can be determined. Four \r\nmicroscopic constants for the interacting Asp 52-Glu 35 system\r\nconsidered as a dibasic acid are calculated for each difference curve.\r\nThe macroscopic pK of Asp 52 is 4.5 and that of Glu 35 is 5.9 in\r\n0.15 M KCl at 25\u00b0 C. The ionization of Asp 52 is very dependent on \r\nthe ionic strength of the solution in going from 0.02 M to 0.50 M KCl \r\nand it is shown that Asp 52 is in an environment only somewhat less \r\nhydrophobic than that of Glu 35. The heats of ionization determined \r\nover the temperature range 1.6\u00b0 to 40\u00b0 give an observed \u0394H equal to\r\n3.5 kcal/mole for Asp 52 and 2.9 kcal/mole for Glu 35. When these \r\nvalues are corrected for charge interactions in an approximate way \r\nthey become more normal. The corrected value for Asp 52 can be \r\ninterpreted in a manner consistent with hydrogen bonding to Asn 46 \r\nand Asn 59.
\r\n\r\nLysozyme inhibitors and small substrates are found not to \r\nperturb the ionization of Asp 52. The macroscopic pK of Glu 35 \r\nincreases to 6.5 when binding subsites A through D are filled.\t\r\nThe pK of Glu 35 exhibits a dramatic shift to 8-8.5 in the presence of the \r\nhigh molecular weight substrate glycol chitin. In addition, the pK of \r\nAsp 101 is determined to be about 4.1 in free lysozyme, about 3.9 \r\nwhen subsite B is filled, and about 3.7 when subsite A is filled.\r\nThese hydrogen bond mediated pK changes do not occur in the \r\nderivative and apparently require a precise binding orientation.
\r\n\r\n\r\n\r\n" }, { "name": "Prestegard, James Harold", "degree": "PhD", "year": "1971", "title": "Proton Magnetic Resonance Studies of Biologically Significant Molecules: I. Cation-Binding Properties of Nonactin. II. Salt Effects on Nucleotide Conformation", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04052018-112424721", "creators": [ { "name": { "family": "Prestegard", "given": "James Harold" }, "id": "Prestegard-James-Harold", "display_name": "Prestegard, James Harold" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/G186-PD07", "abstract": "Part I. Cation-Binding Properties of Nonactin.
\r\n\r\nIn an effort to elucidate the cation specificity of\r\ncertain macrocyclic antibiotics in metabolic behavior, the \r\nnature of the binding of K+, Na+ and Cs+ ions to the\r\nmacrotetrolide nonactin and the molecular structure of the nonactin\r\ncomplexes have been investigated by 220 MHz proton\r\nmagnetic resonance spectroscopy. Studies were made in dry \r\nacetone and in an acetone-water mixture as a function of \r\nvarying perchlorate salt concentrations. Salt-induced \r\nchemical shifts were observed for all the nonactin protons,\r\nexcept H2 and H21, with accompanying changes in the vicinal\r\ncoupling constants between the H2 and H3 protons and between\r\nthe H5 and H6-H6, protons. Analysis of the salt-induced\r\nshifts yielded apparent formation constants for each of the \r\nions in both solvent systems. The results indicate that all \r\nthree ions bind to nonactin with equally high affinity in\r\ndry acetone, but that in wet acetone the binding constants \r\nare preferentially reduced making the potassium complex \r\nhighly favored. It is shown that in wet acetone the alkali \r\nion must be stripped of its hydration shell prior to its \r\naccomodation in the nonactin cavity j and hence we surmise \r\nthat differences in hydration energies for the various ions \r\nmust contribute significantly to the ion selective behavior \r\nof nonactin. Analysis of limiting chemical shifts and\r\ncoupling constants also indicates that the nonactin mole\u00adcule \r\nundergoes sizable conformation changes on complex formation, \r\nbut that the complexes formed, all spherical with a nonsolvated ion \r\nat their center, differ little in exterior geometry. These results \r\nare interpreted in terms of their implications on a simple \r\nmodel for ion transport in a biological membrane.
\r\n\r\nPart II: Salt Effects on Nucleotide Conformation.
\r\n\r\nAqueous solutions of uracil, uridine, deoxyuridine, \r\nuridine 3'-monophosphate (3'-UMP), and uridine 5'-monophos\u00adphate \r\n(5'-UMP) have been investigated by proton magnetic resonance \r\nspectroscopy as a function of electrolyte concen\u00adtration. The \r\naddition of a \"solvent-structure breaking\"\r\nsalt such as Mg (ClO4)2 or NaClO4 to solutions of the \r\nnucleo\u00adsides and nucleotides was found to result in significant\r\nupfield shifts of the uracil H6 resonance. In the cases of uridine and 5'-UMP, \r\nthese salt-induced shifts were accom\u00adpanied by a decrease in the \r\nribose H1,-H2, coupling constant,\r\nand in the case of 5'-UMP, significant changes in certain \r\nintramolecular nuclear Overhauser effects were observed. \r\nThese observations are interpreted in terms of a salt\u00ad \r\ninduced conformation change, involving the orientation of the \r\nuracil base about the glycosidic bond and the puckering of the \r\nfuranose ring. In view of apparent correlation be\u00adtween the \r\nsalt-induced shifts of the uracil H6 resonance\r\nand the \"solvent-structure breaking\" properties of the salt, \r\nit is proposed that the addition of salt modifies the sol\u00advent \r\nstructure of the solution, which in turn can affect\r\nthe average orientation of the base about the glycosidic \r\nbond. The ribose conformation change is considered to be a \r\nsecondary effect resulting from nonbonded interactions be\u00adtween \r\nthe base and furanose moieties and occurring only to\r\nan extent commensurate with the rigidity of the ribose ring, \r\nCalculations based on current theories describing the roles of \r\nthe solvent in hydrophobic bonding are given in support of these \r\nconclusions.
\r\n\r\n" }, { "name": "Ravimohan, Arakali L.", "degree": "PhD", "year": "1971", "title": "I. Experimental Tests on the Positive Column of Pure Rare Gases and their Binary Mixtures. II. Kinetics of Hydrocarbon Reactions in the Positive Column of D.C. and Pulsed D.C. Discharges", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312016-105048485", "creators": [ { "name": { "family": "Ravimohan", "given": "Arakali L." }, "id": "Ravimohan-Arakali-L", "display_name": "Ravimohan, Arakali L." } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HEZA-FD75", "abstract": "Part I:
\r\nA TM011 microwave cavity was used to measure the radially averaged electron density n\u00afe and the electron-neutral collision frequency \u03bden in d.c. glow discharge positive columns of pure rare gases and their binary mixtures. Electric field E was measured by measuring the floating potential across pairs of probes in the plasma. The pure gases studied were He, Ne and Ar at pressures of 1-8 torr and discharge currents I of 5-20 mA. The calculated values of the electron drift velocity vd in He and Ne are substantially lower than the Bradbury and Nielson drift tube values, indicating substantial ionization via metastables in the range of p and I investigated. Discharges in He-Ar and He-Ne mixtures at p = 2-5 torr and I = 15 mA exhibit time and space dependent values of n\u00afe, \u03bden due to the effect of cataphoresis. The results indicate that the Shair and Remer model is a reasonable description of the phenomenon of cataphoresis in these mixtures where the impurity (Ar or Ne) content is in the range of 2-20%.
\r\n\r\nPart II:
\r\nBy employing a positive column flow reactor with low residence times (< 100 msec) in d.c. discharges with low currents (< 5 mA), it is possible to convert up to 5% of the feed methane into ethane, ethylene and hydrogen with negligible formation of solid and liquid products. The percent methane in the argon or helium feed Co affects the product distribution, with good selectivity for Co > 5%. Average steady-state electron densities in the discharge were simultaneously measured by perturbation of the resonance of a TM010 microwave cavity.\r\nA pulsed d.c. discharge enabled the residence time to be effectively reduced even further. The pulsed discharge experiments were conducted at 3-9 torr with pulse durations ~ 1 msec and pulse intervals of 20-50 msec. Pulse current was measured as a function of time with a current probe. The TM010 cavity was used to obtain transient electron densities in the discharge, which varied between 109 and 1010 electrons/cm3.
\r\n\r\nThe kinetic results are consistent with a free radical mechanism with electron-impact dissociation as the initiating step. Derived values of the integrated cross-section for CH4 + e \u2192\u03b1 CH3 + H + e and CH4 + e \u2192 \u03b2\r\n CH2 + H2 + e are in the range 3.6 - 15.5 x 10-11cm3sec-1, and that for C2H4 + e \u2192\u03b3 C2H2 + H2 + e is ~ 9 x 10-10cm3sec-1. \u03b1 and\r\n\u03b2 fall with Co in the range 4.0 - 12.6%, indicating a shift of the electron energy distribution function fe(\u03b5) to lower values of \u03b5. Calculations are presented for the case of H2 dissociation to illustrate the strong effect of the tail end of fe(\u03b5) on the rate of chemical reaction.
\r\n" }, { "name": "Rossman, George Robert", "degree": "PhD", "year": "1971", "title": "I. The Heptacyanomolybdate(III) Ion: Spectroscopic and Magnetic Properties and Chemical Reactivity. II. Spectroscopic and Magnetic Studies of Monomeric and Dimeric d\u2075 Systems. III. Spectroscopic and Magnetic Studies of Polymeric Oxo- and Hydroxobridged Systems", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12202016-092448657", "creators": [ { "name": { "family": "Rossman", "given": "George Robert" }, "id": "Rossman-George-Robert", "orcid": "0000-0002-4571-6884", "display_name": "Rossman, George Robert" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JZTQ-Q938", "abstract": "Heptacyanomolybdate(III), isolated as the potassium salt, K4Mo(CN)7 \u00b7 2H2O has been studied by infrared, raman, ESR, magnetic susceptibility, optical spectral, and x-ray techniques. Solutions of the ion have been identified as having a seven-coordinate pentagonal bipyramidal structure, while the structure in the solid potassium salt has been proposed to be a capped trigonal prism. The anhydrous potassium salt, K4Mo(CN)7, and the hydrated cesium salt, Cs4Mo(CN)7 \u00b7 xH2O also assume the pentagonal bi pyramidal geometry. The molecule is chemically reactive, combining readily in solution with oxygen to form [Mo(CN)7OH2]4- and with halogens to form products which when isolated are waxy and presumably polymeric.
\r\n\r\nOptical spectra have been obtained for four-, five-, six-, and seven-coordinate manganese(II) and iron(III) compounds. These are used as a basis of comparison for interpretation of the detailed optical and magnetic data obtained on the oxobridged iron(III) dimer enH2[(FeHEDT A)2O] \u00b7 6H2O.
\r\n\r\nThe occurrence of simultaneous pair electronic excitations in the dimer is described, and evaluation of the relative merits of the spin-coupling and molecular orbital models for oxobridged dimers is presented. A dihydroxobridged ferric dimer is described as well as a series of dialkoxobridged iron(m) and aluminum dimers derived from metal acetylacetonate and dipivaloylmetane complexes. The extent of antiferromagnetic coupling between the two iron atoms in the dihydroxo- and the dialkoxobridged iron dimers has been found to be nearly identical through variable temperature magnetic susceptibility studies. The magnetic and infrared studies are extended to include a variety of metal oxides, oxy-hydroxides, and natural and synthetic minerals which have various forms of oxo- and hydroxobridging. The OH infrared bands are identified and in some instances, the LN2 temperature positions of the band are compared to the room temperature position. Ferritin models and ferritin micelles are compared to these iron polymers, and the similarity of the infrared spectrum of ferric hydroxide to ferritin micelles is discussed.
" }, { "name": "Salzman, Paul Klenett", "degree": "PhD", "year": "1971", "title": "A Theory for the Hugoniot of Condensed Media", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04172018-113351900", "creators": [ { "name": { "family": "Salzman", "given": "Paul Klenett" }, "id": "Salzman-Paul-Klenett", "display_name": "Salzman, Paul Klenett" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7nnp-4m89", "abstract": "A shock model is developed that leads to an analytical expression \r\nfor the Hugoniot of condensed media. In the analysis the final \r\nstate is selected to coincide with the end of the shock transition so \r\nthat the total energy change across the shock front is evaluated from \r\nchanges in configurational energy only using an n-6 pair potential\r\n(shown to be valid for all n > 0) and a given lattice structure.\r\nThermal energy changes are ignored because the dwell time of the molecules \r\nin the shock transition region is less than the thermal relaxation \r\ntime. The total energy change is equated to the Hugoniot energy \r\nchange in the Rankine-Hugoniot conservation relations. This together \r\nwith the assumption of linear compression across the shock transition \r\ngives the desired expression for the Hugoniot.
\r\n\r\nIn the \"weak form\" (WF) solution the Hugoniot depends on molecular \r\n(atomic) weight M and initial density \u03c1o as well as the\r\ncollision diameter \u03c3, depth of the potential well \u03b5 and repulsive \r\nexponent n of the pair potential. Extrapolation of this solution, \r\nunder certain conditions, yields an expression for the sound velocity\r\nUo dependent on M, \u03b5 and n. In the \"strong form\" (SF) solution\r\nthe Hugoniot depends only on Uo and n.
\r\n\r\nThe shock data for 13 liquids and 23 metals are compiled and a \r\nselection process used to eliminate poor data and data affected by \r\nphase transitions. Using \u03c3 from the literature and \u03b5 from a melting \r\npoint correlation, the WF solution Hugoniot is applied to the \r\nliquids and the \"best\" values of n determined using numerical fitting \r\ntechniques. Excellent fits are obtained with values of n from\r\n6.2 to 11.7. A common value of 9.2 is found to fit the shock data for \r\nargon at four different initial states.\tFailure of the theory is\r\nnoted only for (di-)ethyl ether and water. The results are generally \r\nconcluded to support the validity of the shock model. Values of\tn \r\nfor argon, mercury and nitrogen compare favorably with values reported \r\nin the literature. The WF solution does not yield accurate values of\r\nUo.
\r\n\r\nThe SF solution is expanded in Taylor series to eliminate\r\nsingularities and applied to the shock data for 10 fcc and 13 bcc\r\nmetals and the \"best\" values of n determined. For the fcc metals\r\nexcellent fits are found for values of n from 4.0 to 6.3. Based on\r\nthe \"pseudo-atom\" concept, it is concluded that metals have \"softer\"\r\npotentials than liquids. The results for the fcc metals are concluded\r\nto generally support the validity of the shock model. For the bcc\r\nmetals excellent fits are found for n = 0.1 to 4.6 and it is concluded\r\nthat bcc metals are \"softer\" than fcc metals. Since \u03c3 is \"not\r\ndefined\" for all n < 3 it is speculated that the Hugoniot might not\r\nbe \"well defined\" in these cases. The theory is found to be not\r\napplicable to Cs and Ba. The values of n found for Cu, Al and Pb\r\nagree well with values in the literature. The n for metals are found\r\nto roughly correlate with the Gr\u00fcneisen coefficient \u03b3.
\r\n\r\nThe major assumption of the theory, that the transition region\r\nis \"sufficiently thin,\" is analyzed and found to be reasonable. The\r\nmean number of molecular layers in the transition region is ~ 7 and\r\nthe mean residence time ~ 2 x 10-12sec. In addition the n-6 potential\r\nis judged to be adequate for the present study.
\r\n\r\nThe SF solution Hugoniot is shown to be compatible with the\r\nclassical linear U-\u00b5 relation (U = A + Bu) when x-1 \u00ab 1. Values of\r\nthe slope B from experimental data are found to agree closely with\r\nthe derived relation B \u2243 (n + 5)/6 for the corresponding metals.\r\nRecommendations for further studies with liquids, fcc and bcc metals\r\nare made, including an evaluation of an explicit expression generally relating\r\nthe pair potential to the shock data.
\r\n\r\nIn several subsidiary studies a new method of computing \r\ntemperatures along the Hugoniot is found, two statistical approaches to\r\nthe definition of \"nearest neighbor distance\" and its use as a measure\r\nof liquid structure are developed and the effect of phase transitions\r\non the shock model is determined.
\r\n" }, { "name": "Sherrod, Shelby Allen", "degree": "PhD", "year": "1971", "title": "I. Structure and Reactions of the l-Cyclopropyvinyl Cation. II. Interaction of the Face of a Cyclopropane Ring with Positively Charged Carbon", "advisor": "Bergman, Robert G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182018-155138346", "creators": [ { "name": { "family": "Sherrod", "given": "Shelby Allen" }, "id": "Sherrod-Shelby-Allen", "display_name": "Sherrod, Shelby Allen" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Robert G." }, "id": "Bergman-R-G", "role": "advisor", "display_name": "Bergman, Robert G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9A8S-1W54", "abstract": "I. Structure and Reactions of the 1-Cyclopropyvinyl Cation
\r\n\r\nThe unusual solvolytic reactivity of cyclopropylcar\u00adbinyl derivatives suggested that cyclopropyl substitution should stabilize vinyl cations; accordingly, it has been shown that 1-cyclopropylvinyl iodide ionizes readily under solvolytic conditions, with or without silver catalysis.\r\nComparative kinetic measurements show that the cyclopropyl\r\ngroup enhances the uncatalyzed solvolysis rate by a factor greater than 1.2 x 103, apparently by delocalizing the incipient positive charge. The major products result from reactions of the 1-cyclopropylvinyl cation with solvent, but partial rearrangement of this intermediate to the 2-methyl-enecyclobutyl cation occurs in acetic acid. The enthalpy of activation for this rearrangement exceeds that required for solvent trapping by 2.2 kcal/mol. A small yield of 3,4-pentadien-l-yl acetate may involve rearrangement to the 3,4-pentadien-l-yl cation. Comparative product studies show that 1-cyclopropylvinyl cation is also the major intermediate in the solvolysis of 3,4-pentadien-l-yl derivatives but is not involved in solvolyses of 2-methylenecyclobutyl or\r\n1-cyclobutenylcarbinyl halides.\tThere appears to be a difference between the 2-methylenecyclobutyl cation resulting from rearrangement and that obtained on direct solvolysis.
\r\n\r\nII. Interaction of the Face of a Cyclopropane Ring with Positively Charged Carbon
\r\n\r\nIn order to evaluate the nature of the title interaction,\r\nthe solvolytic reactivities of 4-tricyclyl, 1-apocamphyl,\r\nand 1-methyl-4-tr icyclo[2.2.2.02.6]octyl derivatives were compared. Solvolysis of the trifluoromethanesulfonates (triflates) in 60% aqueous ethanol (buffered) provided good first-order kinetic and Arrhenius data. Extrapolated to 25\u00b0 the relative rates for these substrates (in the order given above) are 1.0, 2.84 x 104, and 5.45 x 107. In\r\neach case, product studies showed that no rearrangement\r\ntook place, and incorporation of 18O-in 4-tricyclenol on solvolysis of 4-tricyclyl triflate in isotopically enriched medium showed that even under the most forcing conditions, carbon-oxygen rather than sulfur-oxygen bond cleavage was occurring. Since the rate data are well rationalized by semiempirical calculations that consider only relative strain energies, interaction of an incipient carbonium ion with the face of a cyclopropane ring apparently affords no significant stabilization.
\r\n\r\n" }, { "name": "Sohn, Youn Soo", "degree": "PhD", "year": "1971", "title": "Electronic Structures of Metallocene Complexes. I. Electronic Structure of Metallocenes. Optical Spectroscopic Study of Metallocene Complexes. II. Magnetic Susceptibility Study of the Ferricenium Ion. III. Synthesis and Characterization of Several Oxidation Products of Ruthenocene", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262017-114444994", "creators": [ { "name": { "family": "Sohn", "given": "Youn Soo" }, "id": "Sohn-Youn-Soo", "display_name": "Sohn, Youn Soo" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/pg0q-y417", "abstract": "I. ELECTRONIC STRUCTURE OF METALLOCENES
\r\n\r\nThe electronic absorption spectra of various low-spin d5\r\nand d6 metallocene complexes have been studied in different \r\nenvironments (glasses,\tKBr pellets, and single crystals) and as a\r\nfunction of temperature. Ferrocene, phenylferrocene, ruthenocene, \r\nand cobalticenium ion were selected in the d6 study and several\r\nferricenium, n-butylferricenium, and 1,1' -di-n-butylferricenium \r\nsalts were examined in the d5 case.\tThe electronic spectra of\r\nferrocene and phenylferrocene single crystals at 4.2\u00b0K clearly \r\nindicate that the bands at 22,700 cm-1 and 22,400 cm-1, respectively, \r\nconsist of two electronic transitions each. The corresponding band \r\nsystems in ruthenocene and cobalticenium ion also exhibit asymmetry \r\nat 77 \u00b0K. Ligand field theory has been successfully applied to the \r\nabove d6 metallocenes, utilizing the three observed spin-allowed d-d \r\nabsorption band positions. Emission of ruthenocene has been observed \r\nat 23,300 cm-1 and discussed in conjunction with the \r\nreported ferrocene emission. The visible absorption spectra of the \r\nvarious ferricenium complexes show a low-energy charge transfer \r\ntransition (16,200 cm-1 in the unsubstituted ion). Ring substitution \r\nand temperature effects have been used to assign this band to the \r\nligand-to-metal 2E2g \u2192 2E1u\r\ntransition. The vibrational structure observed for this band at 77\u00b0K appears \r\nas a doubled progression of the lowest energy a1g vibration.\tThe doubling has been attributed to\r\nsplitting of the 2E1u excited state. Detailed assignments of this\r\nvibrational structure are given for [Fe(cp)2]PF6 and\r\n[Fe(cp)2](CCl3CO2H)3. The intense charge transfer band of\r\nferrocene(~ 50,000 cm-1), as well as the corresponding bands in the\r\nother d6 metallocenes, have been assigned as ligand-to-metal transitions.\r\nA similar assignment has been proposed for the three\r\nstrong (f \u2248 0.1) bands observed in the ferricenium ultraviolet absorption spectrum.
\r\n\r\n\r\nII. MAGNETIC SUSCEPTIBILITY STUDY OF THE FERRICENIUM ION
\r\n\r\nThe ground electronic state [2E2g(a1g)2(e2g)3] of the\r\nferricenium ion has been further characterized by a variable-temperature (40-300\u00b0K) magnetic susceptibility \r\nstudy of nine ferricenium and two analogous Fe(III) dicarbollide (1,2-B9C2H112- state. Solvent and counter ion effects on the magnetic properties of the ferricenium\r\nion are appreciable.
\r\n\r\nIII. SYNTHESIS AND CHARACTERIZATION OF SEVERAL OXIDATION PRODUCTS OF RUTHENOCENE
\r\n\r\nAttempts to prepare ruthenicenium salts have resulted in \r\nthe synthesis and characterization of several interesting ruthenocene\r\nderivatives. Contrary to a previous report, electrochemical oxidation\r\nof ruthenocene employing a mercury anode yields the mercury-bridged dimer\r\n[(cp)2Ru-Hg-Ru(cp)2](ClO4)2. Analytical, infrared,\r\nRaman, and electronic absorption spectral data were utilized in\r\nassigning the molecular structure. In particular, a Raman band at\r\n110 cm-1 was assigned to the symmetrical Ru-Hg-Ru stretching\r\nmode. Preliminary X-ray crystallographic data for the hexafluorophosphate salt,\r\nwhich was obtained by anion exchange, are in agreement\r\nwith the above dimeric formulation. Chemical oxidation of\r\nruthenocene by iodine and bromine gives [Ru(cp)2I]I3 and\r\n[Ru(cp)2Br]Br3, respectively, as indicated by analytical and\r\nspectral data.
\r\n\r\n\r\n\r\n" }, { "name": "Strickland, Alan Douglas", "degree": "Masters", "year": "1971", "title": "Studies on Transition Metal Porphines and Phthalocyanines", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112009-150339244", "creators": [ { "name": { "family": "Strickland", "given": "Alan Douglas" }, "id": "Strickland-Alan-Douglas", "display_name": "Strickland, Alan Douglas" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SYPY-BS46", "abstract": "Model systems for heme were constructed using three different compounds. The tetrasulfophthalocyanine transition metal derivatives were studied and rejected due to problems with the purification procedure. Transition metal derivatives of tetrapyridyl porphine were studied and rejected due to problems in the synthesis and low concentrations of the chemical in solution. Finally, the transition metal derivatives of tetraphenyl porphine were studied and spectral data were obtained.\r\n\r\nThe spectral data indicate that Fe(II)TPP is stable in the presence of oxygen. A photochemical reaction does occur, however, which appears to change the Fe(II)TPP to Fe(III)TPP.\r\n\r\nOther facts were also found. The ZnTPP is found to undergo a photochemical reaction similar to the one for Fe(II)TPP. The MnTPP appears to have already changed oxidation state upon synthesis.\r\n\r\nThe data suggest that TPP is a possible system for studying the interaction of heme and oxygen. The TPyP system might be even better if the problems with synthesis could be solved since its water solubility should solve the problem due to a low concentration.\r\n" }, { "name": "Surratt, Grover Timothy", "degree": "Masters", "year": "1971", "title": "The Minimum Kinetic Energy Orbital and the Band Structure of Sodium", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-111816149", "creators": [ { "name": { "family": "Surratt", "given": "Grover Timothy" }, "id": "Surratt-Grover-Timothy", "display_name": "Surratt, Grover Timothy" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "orcid": "0000-0003-0097-5716", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2665-JE74", "abstract": "For calculations on molecules and solids it has proven \r\nuseful to replace the various core electrons with a pseudo-potential. The most common method for doing this, that of \r\nPhillips andKleinman, suffers from the disadvantage that\r\nthe pseudopotential obtained is not unique. It has previously \r\nbeen shown, however, th t the non-uniqueness problem can be \r\nresolved by the use of ab-initio GI orbitals as the basis\r\nfor the potential. Such potentials have proven quite \r\nsatisfactory in replacing the core electrons in molecular and \r\nsolid-state calculations. Unfortunately, systems of ten or \r\nmore electrons are not accessible to GI, so that the approach \r\ncannot be used for sodium, for example.\r\n\r\n We have examined the GI orbitals and effective potentials \r\nfor Li, Be+, B++ and compared these orbitals and potentials \r\nwith those obtained from the usual Hartree-Fock formalism,\r\nbut employing an extra condition on the orbitals to ensure \r\nuniqueness. It was found that a condition suggested (but \r\napparently never tried) by Cohen and Heine, that the Hartree-Fock core orbitals be allowed to mix with the valence\r\norbital in such a way as to minimize the kinetic energy, \r\nproduced orbitals and potentials nearly identical to those \r\nfrom the GI method.\r\n\r\n We then employed this method to obtain local potentials \r\nfor the ^2S, ^2P and ^2D states of sodium.. These potentials \r\nwere found to reproduce the spectrum of sodium quite well.\r\nThese potentials were then used to study the energy levels \r\nof sodium metal at the high symmetry points in the Brillouin \r\nzone, employing the GI band structure formalism.\r\n" }, { "name": "Titus, Donald Dean", "degree": "PhD", "year": "1971", "title": "Structural Studies of Diethylphenylphosphonite-Transition Metal Complexes", "advisor": "Gray, Harry B.; Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232017-162818079", "creators": [ { "name": { "family": "Titus", "given": "Donald Dean" }, "id": "Titus-Donald-Dean", "display_name": "Titus, Donald Dean" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." }, { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/G8JJ-JX74", "abstract": "The synthesis and spectral properties of several\r\ntetrakis (diethylphenylphosphonite) transition metal complexes\r\nare reported.
\r\n\r\n\r\nThe crystal structures of the hydrido complexes\r\nH2Fe((C6H5)P(OC2H5)2)4 and HCo((C6H5)P(OC2H5)2)4 have been\r\ndetermined. The phosphorus ligands are disposed nearly\r\ntetrahedrally about the metal atoms, with the hydrogen\r\nligands occupying faces of the tetrahedra.
\r\n\r\n\r\nInfrared and n.m.r. studies of the hydrido complexes\r\nin methylcyclohexane solution indicate that the molecules are \r\nstereochemically non-rigid. The classical coordination\r\nstructures used in discussing rearrangements of five-\r\nand six-coordinate complexes (octahedron, square pyramid,\r\nand trigonal bipyramid) are found to be inadequate in the \r\ndiscussion of the present complexes. A structure based\r\non a tetrahedral skeleton of phosphorus atoms is presented\r\nas an alternative.
" }, { "name": "Treitel, Irving Marvin", "degree": "PhD", "year": "1971", "title": "Electronic Structures of Ligand Bridged Ruthenium and Cobalt Binuclear Complexes", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12012017-104324366", "creators": [ { "name": { "family": "Treitel", "given": "Irving Marvin" }, "id": "Treitel-Irving-Marvin", "display_name": "Treitel, Irving Marvin" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "orcid": "0000-0002-7937-7876", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1K1S-M151", "abstract": "Bridged superoxo and peroxodecaamminedicobalt complexes\r\nhave been investigated using electronic room and low temperature\r\nspectroscopy. Assignments for these spectra have been proposed.\r\nThe most important feature in the superoxo spectra is a low energy\r\nmetal ligand, Co \u2192 O2-, charge transfer transition of moderate \r\nintensity. Both the superoxide and peroxide ions have been assigned\r\npositions in the spectrochemical series. The Dq of superoxide is \r\nvery close to ammonia, while the Dq of peroxied is between NCS-\r\nand H2O. These results have been used to eliminate Fe(III) - O2-\r\nas possible model for oxyhemoglobin.
\r\n\r\n\r\nCyano bridged dicobalt and mixed iron-cobalt dimers have \r\nbeen looked at, and their spectra assigned as simple super-positions\r\nof their component parts.
\r\n\r\n\r\nA series of 4+, 5+ and 6+ \u00b5-pyrazinedecaamminediruthenium\r\ncompounds have been investigated. Magnetic susceptibilities of the \r\n5+ and 6+ compounds were measured and analyzed, assuming a\r\ntetragonally distorted d5 ion. Values for the tetragonal field,\r\ndelocalization, and spin-orbit coupling parameters have been\r\nobtained. The 5+ compound gives an ESR signal at room temperature,\r\na result not usually obtained for d5 Ru(III) salts.
\r\n\r\n\r\nElectronic spectra were looked at for the ruthenium pyrazine\r\ndimers. The interesting 1570 nm band was found to be temperature\r\nindependent, indicating an orbitally allowed transition. The origin\r\nof this band is discussed. A molecular orbital description of these\r\ncompounds is suggested. The near IR transition is explained as a\r\nb3u (xz + xz) \u2192 b2g (xz - xz) d-d transition. The applicability of the\r\nMarcus Hush theory of electron transfer to the 5+ cation is discussed.
\r\n\r\n\r\nThe crystal structure of \u00b5-nitrogendecaamminediruthemium(II)\r\nwas determined. The Ru-N-N-Ru linkage is linear, and the N-N\r\ndistance was found to be 1.124 \u00c5, - only slightly longer than that\r\nin free nitrogen. An approximate molecular orbital scheme is\r\ngiven which assumes back donation of electrons from ruthenium d\r\norbitals to the \u03c0*N2 orbital.
" }, { "name": "Upholt, William Boyce", "degree": "PhD", "year": "1971", "title": "Properties of Closed Circular DNA", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:11302017-114639809", "creators": [ { "name": { "family": "Upholt", "given": "William Boyce" }, "id": "Upholt-William-Boyce", "display_name": "Upholt, William Boyce" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YGXW-1222", "abstract": "A method for the measurement of the superhelix density, \u03c30, of\r\na closed circular DNA from separation between fluorescent buoyant\r\nbands of nicked and closed circular forms in an ethidium bromide-CsCl\r\nequilibrium gradient is presented. Nicked and closed circular DNA's\r\nare banded together in a gradient formed by centrifuging a CsCl solution\r\nof density 1.56 gm/ml. containing 330 \u00b5g/ml ethidium bromide at\r\n20\u00b0C for 48 hours in the preparative ultracentrifuge. The separation\r\nbetween the bands, normalized by the separation between the nicked\r\nand closed circular forms of a DNA of known superhelix density, is\r\nshown to be linearly related to the difference in superhelix density\r\nbetween the DNA's of known and unknown superhelix densities according\r\nto the equation
\r\n\r\n\r\n\u0394\u03c30 = (0.115 \u00b1 0.005)(\u03a9c - 1)
\r\n\r\nwhere
\r\n\r\n\r\n\u0394\u03c30 = \u03c30 - \u03c30* and \u03a9c = \u0394r/\u0394r* r/r (v1\u03b8*-1)2/(v1\u03b8-1)2
\r\n\r\n\r\n\u0394r is the separation between the bands, r is the average distance of\r\nthe two bands from the center of rotation, \u03b8 is the buoyant density of\r\nthe DNA and v1 is the partial specific volume of water. The asterisk\r\nrefers to the reference DNA. A molecular weight dependence of the \r\nintercept is seen when \u03bbb2b5c DNA (molecular weight 25 x 106) is banded\r\nagainst a SV40 DNA (3 x 106 standard. The relationship was obtained\r\nby measuring the separations for DNA's whose superhelix densities\r\nwere determined by sedimentation velocity-dye titrations. Native\r\nSV40 viral DNA with a superhelix density of -0.039 was used as a\r\nstandard in all cases. DNA's with altered superhelix densities were\r\nprepared by closing nicked circular DNA's with polynucleotide ligase\r\nunder various conditions.
\r\n\r\nTen closed SV40 DNA's with superhelix densities ranging from\r\n-0.007 to -0.085 have been prepared. This family of DNA's has been \r\nused to examine the effects of superhelix density on the sedimentation \r\nvelocity behavior of closed SV40 DNA. The sedimentation coefficient \r\nincreases as the absolute value of the superhelix density rises\tfrom a \r\nlow value to 0.019, then decreases to a local minimum at 0.035 and \r\nfinally increases steadily as |\u03c30| rises to 0.085.
\r\n\r\n\r\nThe sedimentation velocity-ethidium bromide titrations of these\r\nDNA's have been converted from the primary s020,* versus c data, in\r\nwhich s020,* is the standard sedimentation coefficient still uncorrected\r\nfor the buoyant effect of bound ethidium chloride and c is the free\r\nethidium bromide concentration, to the more meaningful s020,w versus\r\n\u03c30 form, with the aid of coefficients in the expression for the free\r\nenergy of superhelix formation. The resultant curves form a family\r\nthat is approximately superimposable on the curve for s020,w versus \r\n\u03c30 in the absence of ethidium bromide.
\r\n\r\n\r\nThe dependence of the sedimentation coefficient of selected SV40\r\nDNA's upon ionic strength, the nature of the cation, and temperature is\r\nconsistent with the previously reported effects of these variables on the\r\nrotation angle of the base pairs along the helix axis.
\r\n\r\n\r\nSeparations between open and closed circular DNA's in buoyant\r\nCsCl gradients containing the ethidium bromide analogue, propidium\r\ndi-diodide, are shown to be 1.8 times larger than in ethidium bromide.
" }, { "name": "Wyatt, Robert Howard", "degree": "Masters", "year": "1971", "title": "Acidity, Basicity, and Ion-Molecule Reactions of Arsine in the Gas Phase by Ion Cyclotron Resonance Spectroscopy", "advisor": "Beauchamp, Jesse L.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082010-073342301", "creators": [ { "name": { "family": "Wyatt", "given": "Robert Howard" }, "id": "Wyatt-Robert-Howard", "display_name": "Wyatt, Robert Howard" } ], "advisors": [ { "name": { "family": "Beauchamp", "given": "Jesse L." }, "id": "Beauchamp-J-L", "role": "advisor", "display_name": "Beauchamp, Jesse L." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CNW1-W685", "abstract": "The ion-molecule reactions of arsine, both pure and in binary mixtures with several other molecules, have been investigated by ion cyclotron resonance spectroscopy. Reaction pathways, product distributions, and rate constants have been determined for the ion-molecule reactions for both positive and, to a lesser extent, negative ions. Arsine fragment ions condense with neutral AsH_3 to generate product ions containing two and, on further reaction, three atoms of arsenic. In the process of condensation, one or two molecules of H_2 are expelled. The formation of AsH_4^+ occurs from AsH_3^+ which does not undergo condensation reactions to any significant extent. Where possible, thermochemical data have been determined, including the gas phase acidity, PA(AsH_2^-) = 356 \u00b1 6 kcal/mole, and basicity, PA(AsH_3) = 175 \u00b1 5 kcal/mole, of AsH_3. Observation of gas phase nucleophilic displacement reactions involving AsH_3 as a nucleophile have allowed limits to be placed on the basicity of AsH_3 toward a soft acid, CH_3^+. The implications of these results are discussed and the ion-molecule reactions of AsH_3 are compared with those of other hydrides.\r\n" }, { "name": "Bell, Karl Ammon", "degree": "Masters", "year": "1970", "title": "Theory of Particle Deposition by Inertial Forces at Bifurcations in the Human Respiratory Tract", "advisor": "Lees, Lester; Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05172018-084339801", "creators": [ { "name": { "family": "Bell", "given": "Karl Ammon" }, "id": "Bell-Karl-Ammon", "display_name": "Bell, Karl Ammon" } ], "advisors": [ { "name": { "family": "Lees", "given": "Lester" }, "id": "Lees-L", "role": "advisor", "display_name": "Lees, Lester" }, { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XVNX-TN65", "abstract": "The prediction of lung disease development in man from\r\naerosol particles and the medical justification for subsequent \r\ncontrol of particulate atmospheric pollutants requires specific\r\nknowledge of the rate and location of the aerosol deposition\r\nin the lungs. A theoretical development is presented to\r\nnumerically predict the rate and location of aerosol deposition\r\nby impaction at the wedge walls in a model of a lung bifurcation.\r\nTwo limiting flow cases, steady potential flow and steady\r\nlaminar boundary layer flow, are analyzed and found to\r\nrepresent upper and lower bounds of limited experimental deposition\r\ndata for one-micron particle obtained from a lung apparatus\r\nsimulating normal inhalations.
\r\n\r\nNumerical deposition results for 20, 10, 5, 4, 3, 2,\r\nand 1 micron particles in steady potential flow show\r\ndeposition fluxes to be functions of Stokes number and also\r\nthe local air velocity distribution along the wedge. Boundary\r\nlayer deposition results for the same particle are found to\r\ncorrespond to the first few data points of the steady potential\r\ncase, however no boundary layer deposition occurs beyond a\r\nfew particle diameters along the wedge.
" }, { "name": "Blakemore, James Edwin", "degree": "PhD", "year": "1970", "title": "The Pyrolysis and Partial Oxidation of N-Butane", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182011-091224731", "creators": [ { "name": { "family": "Blakemore", "given": "James Edwin" }, "id": "Blakemore-James-Edwin", "display_name": "Blakemore, James Edwin" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/TR7H-V189", "abstract": "A gas-chromatograph network capable of the analysis of possible products in the gas-phase pyrolysis, oxidative pyrolysis, and partial oxidation of n-butane was developed. Low-molecular-weight paraffins, olefins, alcohols, esters, aldehydes, ketones, organic acids, carbon oxides, fixed gases, and water could be identified and measured in the parts-per-mi1lion range of product mixtures. \r\n\r\nThe pyrolysis of n-butane was examined in tubular-flow, gold microreactors having lengths of twelve inches and an inside diameter of 0.0625 inch. Partial pressures of butane were varied from 0.5 to 12 psia, with the total pressure being maintained at fifteen psia by use of an argon diluent. Conversions of butane were less than 2.5 per cent. The overall rate of reaction of the butane was accurately described by kinetics of three-halves order. An average activation energy of 65 kcal mole^(-1) was observed. Approximately equal molar quantities of methane and propylene were observed in the products. Formation of ethane, ethylene, and hydrogen varied with temperature and concentration of butane. The pyrolysis varied only slightly in untreated and in acid-treated reactors. \r\n\r\nThe influence of trace quantities of oxygen on moderate-temperature (500 to 600\u00b0C) pyrolysis of butane was investigated using gold microreactors having lengths of twelve inches and inside diameters of 0.0625 and 0.125 inch. Partial pressures of butane from one to twelve psia were used, with the total pressure being maintained at fifteen psia. Oxygen, present from 7 to 800 parts-per-million in the reactants, inhibited the overall pyrolysis rate and increased the olefin content of the product mixture which was predominantly paraffins and olefins. \r\n\r\nThe investigation of the oxidative dehydrogenation of n-butane was also examined from 460 to 595\u00b0C. Concentration of oxygen in the reactants was varied from 0.04 to 1.0 per cent by volume. At the lower temperatures, isomers of butene, 1,3-butadiene, water, and carbon dioxide comprised over 97 per cent of the products. At higher temperatures, formation of the cracked products of the pyrolysis increased. The overall rate of the disappearance of n-butane was correlated on the basis of a power-law expression of three-halves order with respect to the butane and one-half order with respect to oxygen. The Arrhenius activation energy of the overall dehydrogenation of n-butane was 23.1 kcal mole^(-1) compared to a value of 65 kcal mole^(-1) for the pyrolysis. \r\n\r\nThe partial oxidation of n-butane to oxygenated-organic products was totally suppressed at temperatures of 400 and 440\u00b0C for contact times of 20 seconds and less.\r\n" }, { "name": "Burland, Donald Maxwell", "degree": "PhD", "year": "1970", "title": "Spectroscopic Investigations of Inter- and Intramolecular Processes in Crystalline Benzene", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:07212015-114219783", "creators": [ { "name": { "family": "Burland", "given": "Donald Maxwell" }, "id": "Burland-Donald-Maxwell", "display_name": "Burland, Donald Maxwell" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6T3J-3019", "abstract": "I. Introductory Remarks
\r\nA brief discussion of the overall organization of the thesis is presented along with a discussion of the relationship between this thesis and previous work on the spectroscopic properties of benzene.
\r\nII. Radiationless Transitions and Line broadening
\r\nRadiationless rates have been calculated for the 3B1u\u21921A1g transitions of benzene and perdeuterobenzene as well as for the 1B2u\u21921A1g transition of benzene. The rates were calculated using a model that considers the radiationless transition as a tunneling process between two multi-demensional potential surfaces and assuming both harmonic and anharmonic vibrational potentials. Whenever possible experimental parameters were used in the calculation. To this end we have obtained experimental values for the anharmonicities of the carbon-carbon and carbon-hydrogen vibrations and the size of the lowest triplet state of benzene. The use of the breakdown of the Born-Oppenheimer approximation in describing radiationless transitions is critically examined and it is concluded that Herzberg-Teller vibronic coupling is 100 times more efficient at inducing radiationless transitions.
\r\nThe results of the radiationless transition rate calculation are used to calculate line broadening in several of the excited electronic states of benzene. The calculated line broadening in all cases is in qualitative agreement with experimental line widths.
\r\nIII. 3B1u\u21901A1g Absorption Spectra
\r\nThe 3B1u\u21901A1g absorption spectra of C6H6 and C6D6 at 4.2\u02daK have been obtained at high resolution using the phosphorescence photoexcitation method. The spectrum exhibits very clear evidence of a pseudo-Jahn-Teller distortion of the normally hexagonal benzene molecule upon excitation to the triplet state. Factor group splitting of the 0 \u2013 0 and 0 \u2013 0 + v exciton bands have also been observed. The position of the mean of the 0 \u2013 0 exciton band of C6H6 when compared to the phosphorescence origin of a C6H6 guest in a C6D6 host crystal indicates that the \u201cstatic\u201d intermolecular interactions between guest and hose are different for C6H6 and C6D6. Further investigation of this difference using the currently accepted theory of isotopic mixed crystals indicates that there is a 2cm-1 shift of the ideal mixed crystal level per hot deuterium atom. This shift is observed for both the singlet and triplet states of benzene.
\r\nIV. 3E1u\u21901A1g, Absorption Spectra
\r\nThe 3E1u\u21901A1g absorption spectra of C6H6 and C6D6 at 4.2\u02daK have been obtained using the phosphorescence photoexcitation technique. In both cases the spectrum is broad and structureless as would be expected from the line broadening calculations.
\r\n" }, { "name": "Cooke, Robert Sanderson", "degree": "PhD", "year": "1970", "title": "The Naphthalene Sensitized Photoracemization of Sulfoxides", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:04192011-132638953", "creators": [ { "name": { "family": "Cooke", "given": "Robert Sanderson" }, "id": "Cooke-Robert-Sanderson", "display_name": "Cooke, Robert Sanderson" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AYK6-7Q95", "abstract": "The sensitized photoracemization of alkyl aryl sulfoxides has been shown to result from energy transfer from the singlet state of naphthalene. The possibility of exothermic electronic energy transfer has been ruled out on the basis of spectroscopic data. It is postulated that an exciplex is reversibly formed from an excited singlet state naphthalene molecule and a ground state molecule of the sulfoxide. This excited complex then undergoes radiationless decay converting electronic energy to vibrational energy partitioned between the two components of the exciplex. Enough vibrational energy appears in the aryl sulfinyl center to effect thermal pyramidal inversion with high efficiency. Steric and electronic effects on the rates of fluorescence quenching or of photoracemization are small.\r\n" }, { "name": "Davis, Ronald Wayne", "degree": "PhD", "year": "1970", "title": "A Study of the Base Sequence Arrangements in DNA by Electron Microscopy", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09212004-105308", "creators": [ { "name": { "family": "Davis", "given": "Ronald Wayne" }, "id": "Davis-Ronald-Wayne", "display_name": "Davis, Ronald Wayne" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1QZW-ZP91", "abstract": "The study of base sequence arrangements in DNA molecules was accomplished by coupling electron microscopy (EM) with DNA hybridization. Modifications of the basic protein film technique were used. EM methods for examining both double-stranded and single-stranded DNA were used.
\r\n\r\nMany EM studies have a tendency to be rather descriptive in nature. However, it has been my aim to approach problems from a more quantitative aspect. The major problem in quantitative EM of DNA is length fluctuations. It was discovered that the standard deviation in the length of a homogeneous sample of DNA molecules is directly proportional to the square root of the length.
\r\n\r\nAn EM method was developed for determining the size and location of deletion mutations and substitutions in the \u03bb bacteriophage DNA. Heteroduplexes with one strand from the wild type and one strand from the mutant were formed by renaturation. The location of the nonhomology regions can be accurately mapped. A number of mutants were selected that are unable to integrate and by EM studies of the heteroduplexes it was discovered that there is a specific site in the \u03bb DNA (0.574 from the left end) and a specific site in the E. coli DNA where the integration takes place. It was also shown that this specific site in \u03bb DNA would not form stable base pairing with the specific site in the E. coli DNA. This means that the two sites have a base sequence similarity of less than 10 base pairs. A physical gene map of the left arm of the \u03bb DNA molecule was constructed by comparing the physical and genetic location of a large number of mutations.
\r\n\r\nThe DNA isolated from a defective lysogenic phage of E. coli 15 was studied. After induction there is a closed circular DNA in vivo. However, the DNA is packaged as a linear molecule in the phage head. The mature linear DNA is 7.5% longer than the in vivo closed circular DNA. This was found to be because the mature linear DNA is both terminally repetitious (TR) and circularly permuted. Circular molecules are obtained by denaturing and renaturing the linear molecules. These in vitro circular molecules have two single-stranded DNA branches, each equal in length to the TR. The amount of the TR was found to be slightly heterogeneous. Therefore, the amount of linear DNA that is packaged in the phage head is slightly variable and there is no mechanism for packaging exactly the same amount of DNA.
\r\n\r\nThe mitochondria of human leukemic leukocytes contain covalently closed circular DNA molecules of twice the molecular weight found in mitochondria of normal leukocytes. Heteroduplexes containing one dimer length strand and two complementary monomer length strands were formed by renaturation. These heteroduplex DNA molecules appear as figure eights. They were carefully examined for DNA substitutions or deletions but none were found. Therefore, the dimer molecule is composed of exactly two monomer molecules.
\r\n\r\nEM studies of the SV40 DNA showed that it is heterogeneous in length. From heteroduplex studies it was learned that this DNA is heterogeneous in base sequence as well. About half of the self-renatured molecules contained non-homology regions. The size (up to 1/2 the molecule) and the number of non-homology regions varied considerably. Unique classes of heteroduplex molecules could not be found and no reasonable conclusions could be given for the nature or origin of the heterogeneity.
\r\n\r\nThe replicating intermediates in the in vivo synthesis of \u00d8X174 DNA were studied. The single-stranded DNA is synthesized from a double-stranded template as a linear molecule. The replicating intermediate appears as a double-stranded circular molecule with a linear single-stranded branch attached to the circle. The linear branch was never found to be longer than the mature circular DNA and is presumably released after one round of replication on the template and then cyclized by an as yet undetermined means.
\r\n\r\nRNA was synthesized on T\u2087 DNA in vitro. The resulting RNA-RNA polymerase-DNA complex was visualized in the EM. By synchronizing initiation and mapping the location of the RNA at various times it was discovered that synthesis is always initiated close to one unique end, and thus, presumably at a unique site. At one min there is one PNA per DNA. At high RNA polymerase concentrations, closely spaced sequential initiations occur from the one active initiation site. The rate of propagation was measured as about 45 bases/sec.
" }, { "name": "Dunning, Thomas Harold, Jr", "degree": "PhD", "year": "1970", "title": "The Excitation Operator Method and the Valence Excited States of Ethylene", "advisor": "McKoy, Basil Vincent; Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272010-083324433", "creators": [ { "name": { "family": "Dunning", "given": "Thomas Harold, Jr" }, "id": "Dunning-Thomas-Harold, Jr", "display_name": "Dunning, Thomas Harold, Jr" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RJ3Z-DE73", "abstract": " The problem of describing the electronic excited states of an atomic or molecular system can be reduced to one of finding a form for an operator A^+(E) such that it satisfies the following equation:\r\n\r\n[\u0124, A^+(E)] | 0> = \u0394E A^+(E) | 0>.\r\n\r\nFour approximations to the excitation operator, A^+(E), have been considered: (a) the single transition approximation, corresponding to excitation into virtual orbitals, (b) the improved single transition approximation which allows for the self-consistent field adjustment of the virtual orbital, (c) the Tamm-Dancoff approximation, corresponding to selective configuration interaction in the excited state and (d) the random-phase approximation which attempts to take into account correlation in both ground and excited states.\r\n\r\n Analyzing the excitation operator method in terms of the approximations to the excitation operator listed above, we found that the correlation does not always enter in the ground and excited states in a particularly balanced manner and that self-consistent field changes in the core are neglected. In addition, the strong \"mixing\" of certain doubly excited configurations into the ground state wavefunction, such as (\u03c0*\u03b1\u03c0*\u03b2) in ethylene, is shown to lead to a number of problems in the random-phase approximation, e.g., an instability in the triplet equations.\r\n\r\n The excitation operator approach is illustrated by ab initio calculations on a number of valence excited states of the ethylene molecule. These calculations indicate that the lowest singlet \u03c0\u2192\u03c0* state of ethylene is not a valence state as previously assumed, but that it is significantly more diffuse, e.g., in the improved single transition approximation thePart I
\r\nA study of the thermal reaction of water vapor and parts-per-million concentrations of nitrogen dioxide was carried out at ambient temperature and at atmospheric pressure. Nitric oxide and nitric acid vapor were the principal products. The initial rate of disappearance of nitrogen dioxide was first order with respect to water vapor and second order with respect to nitrogen dioxide. An initial third-order rate constant of 5.5 (\u00b1 0.29) x 104 liter2 mole-2 sec-1 was found at 25\u02daC. The rate of reaction decreased with increasing temperature. In the temperature range of 25\u02daC to 50\u02daC, an activation energy of -978 (\u00b1 20) calories was found.
\r\nThe reaction did not go to completion. From measurements as the reaction approached equilibrium, the free energy of nitric acid vapor was calculated. This value was -18.58 (\u00b1 0.04) kilocalories at 25\u02daC.
\r\nThe initial rate of reaction was unaffected by the presence of oxygen and was retarded by the presence of nitric oxide. There were no appreciable effects due to the surface of the reactor. Nitric oxide and nitrogen dioxide were monitored by gas chromatography during the reaction.
\r\nPart II
\r\nThe air oxidation of nitric oxide, and the oxidation of nitric oxide in the presence of water vapor, were studied in a glass reactor at ambient temperatures and at atmospheric pressure. The concentration of nitric oxide was less than 100 parts-per-million. The concentration of nitrogen dioxide was monitored by gas chromatography during the reaction.
\r\nFor the dry oxidation, the third-order rate constant was 1.46 (\u00b1 0.03) x 104 liter2 mole-2 sec-1 at 25\u02daC. The activation energy, obtained from measurements between 25\u02daC and 50\u02daC, was -1.197 (\u00b10.02) kilocalories.
\r\nThe presence of water vapor during the oxidation caused the formation of nitrous acid vapor when nitric oxide, nitrogen dioxide and water vapor combined. By measuring the difference between the concentrations of nitrogen dioxide during the wet and dry oxidations, the rate of formation of nitrous acid vapor was found. The third-order rate constant for the formation of nitrous acid vapor was equal to 1.5 (\u00b1 0.5) x 105 liter2 mole-2 sec-1 at 40\u02daC. The reaction rate did not change measurably when the temperature was increased to 50\u02daC. The formation of nitric acid vapor was prevented by keeping the concentration of nitrogen dioxide low.
\r\nSurface effects were appreciable for the wet tests. Below 35\u02daC, the rate of appearance of nitrogen dioxide increased with increasing surface. Above 40\u02daC, the effect of surface was small.
\r\n" }, { "name": "Fehder, Paul Lee", "degree": "PhD", "year": "1970", "title": "A Molecular Dynamics Study of the Microscopic Properties of Simple Dense Fluids", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:07312015-091400303", "creators": [ { "name": { "family": "Fehder", "given": "Paul Lee" }, "id": "Fehder-Paul-Lee", "display_name": "Fehder, Paul Lee" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EGRF-VD09", "abstract": "The microscopic properties of a two-dimensional model dense\r\nfluid of Lennard-Jones disks have been studied using the so-called\r\n\"molecular dynamics\" method. Analyses of the computer-generated\r\nsimulation data in terms of \"conventional\" thermodynamic and distribution\r\nfunctions verify the physical validity of the model and the simulation\r\ntechnique.
\r\n\r\nThe radial distribution functions g(r) computed from the simulation\r\ndata exhibit several subsidiary features rather similar to those\r\nappearing in some of the g(r) functions obtained by X-ray and thermal\r\nneutron diffraction measurements on real simple liquids. In the case of\r\nthe model fluid, these \"anomalous\" features are thought to reflect the\r\nexistence of two or more alternative configurations for local ordering.
\r\n\r\nGraphical display techniques have been used extensively to provide\r\nsome intuitive insight into the various microscopic phenomena\r\noccurring in the model. For example, \"snapshots\" of the instantaneous\r\nsystem configurations for different times show that the \"excess\" area\r\nallotted to the fluid is collected into relatively large, irregular, and\r\nsurprisingly persistent \"holes\". Plots of the particle trajectories over\r\nintervals of 2.0 to 6.0 x 10-12 sec indicate that the mechanism for diffusion\r\nin the dense model fluid is \"cooperative\" in nature, and that\r\nextensive diffusive migration is generally restricted to groups of\r\nparticles in the vicinity of a hole.
\r\n\r\nA quantitative analysis of diffusion in the model fluid shows that\r\nthe cooperative mechanism is not inconsistent with the statistical\r\npredictions of existing theories of singlet, or self-diffusion in liquids.\r\nThe relative diffusion of proximate particles is, however, found to be\r\nretarded by short-range dynamic correlations associated with the\r\ncooperative mechanism--a result of some importance from the standpoint\r\nof bimolecular reaction kinetics in solution.
\r\n\r\nA new, semi-empirical treatment for relative diffusion in\r\nliquids is developed, and is shown to reproduce the relative diffusion\r\nphenomena observed in the model fluid quite accurately. When incorporated\r\ninto the standard Smoluchowski theory of diffusion-controlled\r\nreaction kinetics, the more exact treatment of relative diffusion is\r\nfound to lower the predicted rate of reaction appreciably.
\r\n\r\nFinally, an entirely new approach to an understanding of the\r\nliquid state is suggested. Our experience in dealing with the simulation\r\ndata--and especially, graphical displays of the simulation data--has\r\nled us to conclude that many of the more frustrating scientific problems\r\ninvolving the liquid state would be simplified considerably, were it possible\r\nto describe the microscopic structures characteristic of liquids\r\nin a concise and precise manner. To this end, we propose that the\r\ndevelopment of a formal language of partially-ordered structures be\r\ninvestigated.
" }, { "name": "Firkins, John Lionel", "degree": "PhD", "year": "1970", "title": "Norbornenyl- and Nortricyclyl Free Radicals", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302015-142129886", "creators": [ { "name": { "family": "Firkins", "given": "John Lionel" }, "id": "Firkins-John-Lionel", "display_name": "Firkins, John Lionel" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JFE9-5888", "abstract": "The number, symmetry, and product-forming capabilities of\r\nthe intermediates in the photoinitiated reductions of endo- and exo-5-\r\nbromonorbornene and 2-bromonortricyclene with tri-n-butyltin\r\nhydride at temperatures between -10\u00b0 and 22\u00b0 were investigated.
\r\n\r\nThree mechanisms were evaluated:
\r\n1. The 5-norbornenyl- and 2-nortricyclyl radicals isomerize\r\nreversibly with the former producing nortricyclene by\r\nabstraction of hydrogen from tri-n-butyltin hydride.
\r\n2. The 5-norbornenyl- and 2-nortricyclyl radicals isomerize\r\nreversibly, but some norbornene can be formed from the\r\n2-nortricyclyl radical or some nortricyclene can be formed\r\nfrom the 5-norbornenyl radical by abstraction of hydrogen.
\r\n3. There is intervention of a \"bridged\" radical which may be\r\nfor med reversibly or irreversibly from the 5-norbornenyl- and\r\n2-nortricyclyl radicals.
Within small error limits, the ratios of norbornene to\r\nnortricyclene as a function of the concentration of tri-n-butyltin\r\nhydride are consistent with the first mechanism.
\r\n\r\nIn the reductions with tri-n-butyltin deuteride, primary\r\ndeuterium isotope effects of 2. 3 and 2. 1 for the abstraction of\r\ndeuterium by the 2-nortricyclyl- and 5-norbornenyl radicals,\r\nrespectively, were found. The primary deuterium isotope effects\r\nwere invariant with the concentration of tri-n-butyltin deuteride,\r\nalthough the ratios of norbornene to nortricyclene changed appreciably\r\nover this range. This is consistent with the first mechanism, and can\r\naccommodate the formation of either product from more than one\r\nintermediate only if the primary kinetic deuterium isotope effects are\r\nnearly equal for all reactions leading to the single product.
\r\n\r\nThe reduction of endo-5-bromonorbornene-5, 6, 6-d3 with\r\ntri-n-butyltin hydride or tri-n-butyltin deuteride leads to both\r\nunrearranged and rearranged norbornenes. The ratios of unrearranged\r\nto rearranged norbornene require that the 5-norbornenyl-5, 6, 6-d3\r\nradical isomerize to an intermediate with the symmetry expected of a\r\nnortricyclyl free radical. The results are consistent with mechanism\r\n1, but imply a surprising normal secondary kinetic deuterium isotope\r\neffect of about 1.25 for the abstraction of hydrogen by the 5-norbornenyl-\r\n5, 6, 6-d3 radical.
\r\n\r\nApproximate calculations show that there does not appear to be\r\nany substantial difference in the stabilities of the 5-norbornenyl and\r\n2-nortricyclyl radicals.
\r\n\r\nAlthough the results can not exclude a small contribution by a\r\nmechanism other than mechanism 1, no such contribution is required\r\nto adequately explain the results.
\r\n\r\n\r\n\r\n\r\n\r\n" }, { "name": "Frank, Robert", "degree": "Masters", "year": "1970", "title": "Theoretical correlation of the geometry and magnetic hyperfine splittings of the methyl radical", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302010-075156671", "creators": [ { "name": { "family": "Frank", "given": "Robert" }, "id": "Frank-R", "display_name": "Frank, Robert" } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5YF2-J383", "abstract": "Spin densities at carbon and hydrogen are calculated at several out of plane angles of the methyl radical. Comparison with temperature dependent ESR studies indicate that the GF method describes the variation adequately while Hartree-Fock, Unrestricted Hartree-Fock, and Valence-Bond treatments do not." }, { "name": "Hamilton, Edwin John, Jr", "degree": "PhD", "year": "1970", "title": "I. Free Radical Reaction Rates by Electron Paramagnetic Resonance. II. Termination Rates of Substituted Benzophenone Ketyl Radicals in Alkanes", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092009-085516", "creators": [ { "name": { "family": "Hamilton", "given": "Edwin John, Jr" }, "id": "Hamilton-Edwin-John-Jr", "display_name": "Hamilton, Edwin John, Jr" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X55V-R661", "abstract": "PART I: A general method for the measurement of absolute rate constants for the termination of photochemically produced organic free radicals in solution has been developed. Radicals are generated in the cavity of an EPR spectrometer by high intensity UT irradiation of a suitable sample; an EPR spectrum is obtained from the steady-state concentration of intermediate radicals. The (second-order) decay of the EPR signal with time is followed after irradiation is abruptly stopped by mechanical means. Many such decay curves are averaged by computer. From the averaged decay curve plus a measurement of the steady-state radical concentration (by electronic double integration), absolute rate constants for radical termination are obtained. Rate constants as fast as diffusion-controlled may be determined by this technique.
\r\n\r\nPART II: Using the flash photolysis technique, the self-termination rate constants of benzophenone ketyl, 4, 4'-dichlorobenzophenone ketyl, and 4, 4'-dimethoxybenzophenone ketyl radicals were measured in a series of eight alkanes. These rate constants were all at least about 0.5 times, but clearly less than, the corresponding theoretical diffusion-controlled rate constants. Rate variations with solvent were satisfactorily accounted for by the theory of the effect of diffusion coefficient on an observed bimolecular rate constant. There was no significant rate variation with ketyl radical. Thus, the widely different self-termination rate constants of the above ketyl radicals that have been measured in other solvents are due to substituent-dependent solvent effects. In benzene, these substituent effects may be due to charge-transfer complexing between radical and solvent.
" }, { "name": "Hoffman, Donald Richard", "degree": "PhD", "year": "1970", "title": "Model Systems for the Study of Drug Hypersensitivity", "advisor": "Campbell, Dan Hampton", "url": "https://resolver.caltech.edu/CaltechTHESIS:08052015-131911954", "creators": [ { "name": { "family": "Hoffman", "given": "Donald Richard" }, "id": "Hoffman-Donald-Richard", "display_name": "Hoffman, Donald Richard" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3JJM-Z756", "abstract": "I. It was not possible to produce anti-tetracycline antibody in\r\nlaboratory animals by any of the methods tried. Tetracycline\r\nprotein conjugates were prepared and characterized. It was shown\r\nthat previous reports of the detection of anti-tetracycline antibody\r\nby in vitro-methods were in error. Tetracycline precipitates\r\nnon-specifically with serum proteins. The anaphylactic reaction\r\nreported was the result of misinterpretation, since the observations\r\nwere inconsistent with the known mechanism of anaphylaxis and\r\nthe supposed antibody would not sensitize guinea pig skin. The\r\nhemagglutination reaction was not reproducible and was extremely\r\nsensitive to minute amounts of microbial contamination. Both\r\nfree tetracyclines and the conjugates were found to be poor\r\nantigens.
\r\n\r\nII. Anti-aspiryl antibodies were produced in rabbits using 3\r\nprotein carriers. The method of inhibition of precipitation was used\r\nto determine the specificity of the antibody produced. \u03b5-Aminocaproate\r\nwas found to be the most effective inhibitor of the haptens tested,\r\nindicating that the combining hapten of the protein is \u03b5-aspiryl-lysyl.\r\nFree aspirin and salicylates were poor inhibitors and did not combine\r\nwith the antibody to a significant extent. The ortho group was found\r\nto participate in the binding to antibody. The average binding\r\nconstants were measured.
\r\n\r\nNormal rabbit serum was acetylated by aspirin under in vitro\r\nconditions, which are similar to physiological conditions. The extent\r\nof acetylation was determined by immunochemical tests. The\r\nacetylated serum proteins were shown to be potent antigens in rabbits.\r\nIt was also shown that aspiryl proteins were partially acetylated. The\r\nrelation of these results to human aspirin intolerance is discussed.
\r\n\r\nIII. Aspirin did not induce contact sensitivity in guinea pigs when\r\nthey were immunized by techniques that induce sensitivity with other\r\nreactive compounds. The acetylation mechanism is not relevant to\r\nthis type of hypersensitivity, since sensitivity is not produced by potent\r\nacetylating agents like acetyl chloride and acetic anhydride. Aspiryl\r\nchloride, a totally artificial system, is a good sensitizer. Its\r\nspecificity was examined.
\r\n\r\nIV. Protein conjugates were prepared with p-aminosalicylic acid\r\nand various carriers using azo, carbodiimide and mixed anhydride\r\ncoupling. These antigens were injected into rabbits and guinea pigs\r\nand no anti-hapten IgG or IgM response was obtained. Delayed\r\nhypersensitivity was produced in guinea pigs by immunization with\r\nthe conjugates, and its specificity was determined. Guinea pigs were\r\nnot sensitized by either injections or topical application of p-amino-salicylic\r\nacid or p-aminosalicylate.
" }, { "name": "Hong, Hwei-Kwan", "degree": "PhD", "year": "1970", "title": "I. The Electronic States of Heavily-doped Molecular Crystals -- Naphthalene: I. Theoretical. II. Experimental. II. Lowest Singlet and Triplet Excited States of Pyrazine", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:09012015-081452587", "creators": [ { "name": { "family": "Hong", "given": "Hwei-Kwan" }, "id": "Hong-Hwei-Kwan", "display_name": "Hong, Hwei-Kwan" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fwyp-yw14", "abstract": "PART I
\r\n\r\nThe energy spectrum of heavily-doped molecular crystals was treated in the Green\u2019s function formulation. The mixed crystal Green\u2019s function was obtained by averaging over all possible impurity distributions. The resulting Green\u2019s function, which takes the form of an infinite perturbation expansion, was further approximated by a closed form suitable for numerical calculations. The density-of-states functions and optical spectra for binary mixtures of normal naphthalene and deuterated naphthalene were calculated using the pure crystal density-of-state functions. The results showed that when the trap depth is large, two separate energy bands persist, but when the trap depth is small only a single band exists. Furthermore, in the former case it was found that the intensities of the outer Davydov bands are enhanced whereas the inner bands are weakened. Comparisons with previous theoretical calculations and experimental results are also made.
\r\n\r\nPART II
\r\n\r\nThe energy states and optical spectra of heavily-doped mixed crystals are investigated. Studies are made for the following binary systems: (1) naphthalene-h8 and d8, (2) naphthalene--h8 and \u03b1d4, and (3) naphthalene--h8 and \u03b2d1, corresponding to strong, medium and weak perturbations. In addition to ordinary absorption spectra at 4\u02daK, band-to-band transitions at both 4\u02daK and 77\u02daK are also analyzed with emphasis on their relations to cooperative excitation and overall density-of-states functions for mixed crystals. It is found that the theoretical calculations presented in a previous paper agree generally with experiments except for cluster states observed in system (1) at lower guest concentrations. These features are discussed semi-quantitatively. As to the intermolecular interaction parameters, it is found that experimental results compare favorably with calculations based on experimental density-of-states functions but not with those based on octopole interactions or charge-transfer interactions. Previous experimental results of Sheka and the theoretical model of Broude and Rashba are also compared with present investigations.
\r\n\r\nPART III
\r\nThe phosphorescence, fluorescence and absorption spectra of pyrazine-h4 and d4 have been obtained at 4\u02daK in a benzene matrix. For comparison, those of the isotopically mixed crystal pyrazine-h4 in d4 were also taken. All these spectra show extremely sharp and well-resolved lines and reveal detailed vibronic structure.
\r\nThe analysis of the weak fluorescence spectrum resolves the long-disputed question of whether one or two transitions are involved in the near-ultraviolet absorption of pyrazine. The \u201cmirror-image relationship\u201d between absorption and emission shows that the lowest singlet state is an allowed transition, properly designated as 1B3u \u2190 1A1g. The forbidden component 1B2g, predicted by both \u201cexciton\u201d and MO theories to be below the allowed component, must lie higher. Its exact location still remains uncertain.
\r\nThe phosphorescence spectrum when compared with the excitation phosphorescence spectra, indicates that the lowest triplet state is also symmetry allowed, showing a strong 0-0 band and a \u201cmirror-image relationship\u201d between absorption and emission. In accordance with previous work, the triplet state is designated as 3B3u.
\r\nThe vibronic structure of the phosphorescence spectrum is very complicated. Previous work on the analysis of this spectrum all concluded that a long progression of v6a exists. Under the high resolution attainable in our work, the supposed v6a progression proves to have a composite triplet structure, starting from the second member of the progression. Not only is the v9a hydrogen-bending mode present as shown by the appearance of the C-D bending mode in the d4 spectrum, but a band of 1207 cm-1 in the pyrazine in benzene system and 1231 cm-1 in the mixed crystal system is also observed. This band is assigned as 2v6b and of a1g symmetry. Its anonymously strong intensity in the phosphorescence spectrum is interpreted as due to the Fermi resonance with the 2v6a and v9a band.
\r\nTo help resolve the present controversy over the crystal phosphorescence spectrum of pyrazine, detailed vibrational analyses of the emission spectra were made. The fluorescence spectrum has essentially the same vibronic structure as the phosphorescence spectrum.
\r\n\r\n\r\n" }, { "name": "Hyman, Richard Walter", "degree": "PhD", "year": "1970", "title": "On the Interaction of Actinomycin and DNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08122015-102840138", "creators": [ { "name": { "family": "Hyman", "given": "Richard Walter" }, "id": "Hyman-Richard-Walter", "display_name": "Hyman, Richard Walter" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RJRA-PV20", "abstract": "Experiments have been accomplished that (a) further define the nature of the strong, G-containing DNA binding sites for actinomycin D (AMD), and (b) quantitate the in vitro inhibition of E. coli RNA polymerase\r\nactivity by T7 DNA-bound AMD.
\r\n\r\nTwenty-five to forty percent of the G's of crab dAT are disallowed\r\nas strong AMD binding sites. The G's are measured to be \r\nrandomly distributed, and, therefore, this datum cannot be explained\r\non the basis of steric interference alone. Poly dAC:TG binds as much\r\nAMD and as strongly as any natural DNA, so the hypothesis that the\r\nunique strong AMD binding sites are G and a neighboring purine is\r\nincorrect. The datum can be explained on the basis of both steric\r\ninterference and the fact that TGA is a disallowed sequence for strong\r\nAMD binding.
\r\n\r\nUsing carefully defined in vitro conditions, there is one RNA\r\nsynthesized per T7 DNA by E. coli RNA polymerase. The rate of the\r\nRNA polymerase-catalyzed reaction conforms to the equation\r\n\r\n1/rate = 1/kA(ATP) + 1/KG(GTP) + 1/KC(CTP) + 1/KU(UTP)\r\n\r\nT7 DNA-bound AMD has only modest effects on initiation and termination\r\nof the polymerase-catalyzed reaction, but a large inhibitory effect\r\non propagation. In the presence of bound AMD, kG and kC are decreased,\r\nwhereas kA and kU are unaffected. These facts are interpreted to mean that on the microscopic level, on the average, the rates of incorporation of ATP and UTP are the same in the absence or\r\npresence of bound AMD, but that the rates of incorporation of GTP and\r\nCTP are decreased in the presence of AMD.
\r\n" }, { "name": "Jacobson, Richard Norman", "degree": "PhD", "year": "1970", "title": "Forced Convection Film Boiling of Subcooled Water Around a Sphere", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072015-152422673", "creators": [ { "name": { "family": "Jacobson", "given": "Richard Norman" }, "id": "Jacobson-Richard-Norman", "display_name": "Jacobson, Richard Norman" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0Z9T-2181", "abstract": "An experimental investigation was made of forced convection film\r\nboiling of subcooled water around a sphere at atmospheric pressure.\r\nThe water was sufficiently cool that the vapor condensed before leaving\r\nthe film with the result that no vapor bubbles left the film. The experimental\r\nruns were made using inductively heated spheres at temperatures\r\nabove 740\u00b0C. and using inlet water temperatures between\r\n15\u00b0C. and 27\u00b0C. The spheres used had diameters of 1/2 inch, 9/16\r\ninch, and 3/8 inch and were supported by the liquid flow. Reynolds\r\nnumbers between 60 and 700 were used.
\r\n\r\nAnalysis of the collected non-condensables indicated that oxygen\r\nand nitrogen dissolved in the water accumulated within the vapor film\r\nand that hetrogeneous chemical reactions occurred at the sphere\r\nsurface. An iron-steam reaction resulted in more than 20% by volume\r\nhydrogen in the film at wall temperatures above 900\u00b0C. At temperatures\r\nnear 1100\u00b0C. more than 80% by volume of the film was composed\r\nof hydrogen. It was found that gold plating of the sphere could eliminate\r\nthis reaction.
\r\n\r\nMaterial and energy balances were used to derive equations which\r\nmay be used to predict the overall average heat transfer coefficients\r\nfor subcooled film boiling around a sphere. These equations include\r\nthe effect of dissolved gases in the water. Equations also were derived\r\nwhich may be used to predict the composition of the film for\r\ncases in which an equilibrium exists between the dissolved gases and\r\nthe gases in the film.
\r\n\r\nThe derived equations were compared to the experimental results.\r\nIt was found that a correlation existed between the Nusselt number\r\nfor heat transfer from the vapor-liquid interface into the liquid and\r\nthe Reynolds number, liquid Prandtl number product. In addition,\r\nit was found that the percentage of dissolved oxygen removed during\r\nthe film boiling could be predicted to within 10%.
" }, { "name": "Lee, Chong Sung", "degree": "PhD", "year": "1970", "title": "I. Studies on Bacteriophage DNA's and Minicircular DNA's in M. lysodeikticus and E. coli 15. II. Flow Dichroism of DNA Solutions", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08102015-160156690", "creators": [ { "name": { "family": "Lee", "given": "Chong Sung" }, "id": "Lee-Chong-Sung", "display_name": "Lee, Chong Sung" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K05B-3W74", "abstract": "Part I
\r\n\r\nChapter 1.....A physicochemical study of the DNA molecules\r\nfrom the three bacteriophages, N1, N5, and N6, which infect the bacterium,\r\nM. lysodeikticus, has been made. The molecular weights, as measured\r\nby both electron microscopy and sedimentation velocity, are 23 x 106\r\nfor N5 DNA and 31 x 106 for N1 and N6 DNA's. All three DNA's are capable\r\nof thermally reversible cyclization. N1 and N6 DNA's have identical\r\nor very similar base sequences as judged by membrane filter hybridization\r\nand by electron microscope heteroduplex studies. They have identical\r\nor similar cohesive ends. These results are in accord with the close\r\nbiological relation between N1 and N6 phages. N5 DNA is not closely\r\nrelated to N1 or N6 DNA. The denaturation Tm of all three DNA's is the\r\nsame and corresponds to a (GC) content of 70%. However, the buoyant\r\ndensities in CsCl of Nl and N6 DNA's are lower than expected,\r\ncorresponding to predicted GC contents of 64 and 67%. The buoyant\r\ndensities in Cs2SO4 are also somewhat anomalous. The buoyant density\r\nanomalies are probably due to the presence of odd bases. However, direct\r\nbase composition analysis of N1 DNA by anion exchange chromatography\r\nconfirms a GC content of 70%, and, in the elution system used, no peaks\r\ndue to odd bases are present.
\r\n\r\nChapter 2.....A covalently closed circular DNA form has been\r\nobserved as an intracellular form during both productive and abortive\r\ninfection processes in M. lysodeikticus. This species has been isolated\r\nby the method of CsC1-ethidium bromide centrifugation and examined with\r\nan electron microscope.
\r\n\r\nChapter 3.....A minute circular DNA has been discovered as\r\na homogeneous population in M. lysodeikticus. Its length and molecular\r\nweight as determined by electron microscopy are 0.445 \u03bc and 0.88 x 106\r\ndaltons respectively. There is about one minicircle per bacterium.
\r\n\r\nChapter 4.....Several strains of E. coli 15 harbor a prophage.\r\nViral growth can be induced by exposing the host to mitomycin C or to\r\nuv irradiation. The coliphage 15 particles from E. coli 15 and E, coli\r\n15 T- appear as normal phage with head and tail structure; the particles\r\nfrom E. coli 15 TAU are tailless. The complete particles exert a\r\ncolicinogenic activity on E.coli 15 and 15 T-, the tailless particles\r\ndo not. No host for a productive viral infection has been found and the\r\nphage may be defective. The properties of the DNA of the virus have\r\nbeen studied, mainly by electron microscopy. After induction but before\r\nlysis, a closed circular DNA with a contour length of about 11.9 \u03bc is\r\nfound in the bacterium; the mature phage DNA is a linear duplex and\r\n7.5% longer than the intracellular circular form. This suggests the\r\nhypothesis that the mature phage DNA is terminally repetitious and\r\ncircularly permuted. The hypothesis was confirmed by observing that\r\ndenaturation and renaturation of the mature phage DNA produce circular\r\nduplexes with two single-stranded branches corresponding to the terminal\r\nrepetition. The contour length of the mature phage DNA was measured\r\nrelative to \u03c6X RFII DNA and \u03bb DNA; the calculated molecular weight is\r\n27 x 106. The length of the single-stranded terminal repetition was\r\ncompared to the length of \u03c6X 174 DNA under conditions where single-stranded\r\nDNA is seen in an extended form in electron micrographs. The length of\r\nthe terminal repetition is found to be 7.4% of the length of the nonrepetitious\r\npart of the coliphage 15 DNA. The number of base pairs in\r\nthe terminal repetition is variable in different molecules, with a fractional\r\nstandard deviation of 0.18 of the average number in the terminal\r\nrepetition. A new phenomenon termed \"branch migration\" has been discovered\r\nin renatured circular molecules; it results in forked branches, with\r\ntwo emerging single strands, at the position of the terminal repetition.\r\nThe distribution of branch separations between the two terminal\r\nrepetitions in the population of renatured circular molecules was studied.\r\nThe observed distribution suggests that there is an excluded volume\r\neffect in the renaturation of a population of circularly permuted molecules\r\nsuch that strands with close beginning points preferentially\r\nrenature with each other. This selective renaturation and the phenomenon\r\nof branch migration both affect the distribution of branch separations;\r\nthe observed distribution does not contradict the hypothesis of a\r\nrandom distribution of beginning points around the chromosome.
\r\n\r\nChapter 5....Some physicochemical studies on the minicircular\r\nDNA species in E. coli 15 (0.670 \u03bc, 1.47 x 106 daltons) have been made.\r\nElectron microscopic observations showed multimeric forms of the minicircle\r\nwhich amount to 5% of total DNA species and also showed presumably\r\nreplicating forms of the minicircle. A renaturation kinetic study\r\nshowed that the minicircle is a unique DNA species in its size and base\r\nsequence. A study on the minicircle replication has been made under\r\ncondition in which host DNA synthesis is synchronized. Despite\r\nexperimental uncertainties involved, it seems that the minicircle replication\r\nis random and the number of the minicircles increases\r\ncontinuously throughout a generation of the host, regardless of host\r\nDNA synchronization.
\r\n\r\nPart II
\r\n\r\nThe flow dichroism of dilute DNA solutions (A260\u22480.1) has been\r\nstudied in a Couette-type apparatus with the outer cylinder rotating\r\nand with the light path parallel to the cylinder axis. Shear gradients\r\nin the range of 5-160 sec.-1 were studied. The DNA samples were whole,\r\n\"half,\" and \"quarter\" molecules of T4 bacteriophage DNA, and linear\r\nand circular \u03bbb2b5c DNA. For the linear molecules, the fractional\r\nflow dichroism is a linear function of molecular weight. The dichroism\r\nfor linear A DNA is about 1.8 that of the circular molecule. For a given\r\nDNA, the dichroism is an approximately linear function of shear gradient,\r\nbut with a slight upward curvature at low values of G, and some trend\r\ntoward saturation at larger values of G. The fractional dichroism\r\nincreases as the supporting electrolyte concentration decreases.
" }, { "name": "Lee, Jo Woong", "degree": "PhD", "year": "1970", "title": "Spin-Internal-Rotation Interaction and Relaxation of Nuclear Spin on an Internal Rotor", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07142025-171837407", "creators": [ { "name": { "family": "Lee", "given": "Jo Woong" }, "id": "Lee-Jo-Woong", "display_name": "Lee, Jo Woong" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "orcid": "0000-0002-5348-2723", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nfsr-k733", "abstract": "A magnetic nucleus located on an internal top can interact with\r\nthe magnetic fields arising from the internal rotation as well as overall\r\nmolecular rotation. The coupling Hamiltonian for this kind of magnetic\r\nnuclei has been derived following the method of Van Vleck for the spin-rotation\r\ninteraction in rigid molecules. It is shown that the\r\nHamiltonian for this problem may be written
\r\n\r\n(See PDF for equation)
\r\n\r\nwhere the first term is the ordinary spin-rotation interaction and the\r\nsecond term arises from the spin-internal-rotation coupling. When the\r\ninternal rotation is very fast compared with the overall rotation, it is\r\nshown that the effective spin-rotation Hamiltonian takes the approximate\r\nform
\r\n\r\n(See PDF for equation)
\r\n\r\nwhere (See PDF for equation) is the effective spin-rotation coupling tensor,\r\nand D(j)\u03b1 is a constant.
\r\n\r\nOn the basis of this coupling model, an analytic expression of\r\nT1 , the spin-lattice relaxation time, for 19F spins in \u0278-CF3-type molecules\r\nhas been derived and the effect of an internal barrier is discussed.
\r\n\r\nA physical model of molecular rotation in \u0278-CF3-type molecules\r\nin their liquid state is proposed and temperature dependence of 19F\r\nspin-lattice relaxation time is explained in terms of this model.
\r\n\r\nIt seems that the rotation of the internal top (-CF3) about its\r\nsymmetry axis is inertial while rotations of the entire molecule can be\r\ndescribed better by the diffusion model.
\r\n\r\nThus, the temperature dependence of the internal rotation is\r\nlikely to be different from that for the end-over-end rotation of entire\r\nmolecule. Burke has successfully shown that the temperature dependence\r\nof fluorine spin-lattice relaxation time in benzotrifluoride can\r\nbe interpreted in terms of the above model.
\r\n\r\nA more complete and quantitative theory of the nuclear spin\r\nrelaxation via the spin-rotation interaction in the presence of internal\r\nrotation is developed and Hubbard's treatment is generalized for non-spherical\r\nmolecules with internal rotors.
" }, { "name": "Lindgren, Robert Gary", "degree": "PhD", "year": "1970", "title": "Theory of the Positive Column of a Gas Discharge", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062015-144055650", "creators": [ { "name": { "family": "Lindgren", "given": "Robert Gary" }, "id": "Lindgren-Robert-Gary", "display_name": "Lindgren, Robert Gary" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/B4W0-ST96", "abstract": "An attempt is made to provide a theoretical explanation of the effect of the positive column on the voltage-current characteristic of a glow or an arc discharge. Such theories have been developed before, and all are based on balancing the production and loss of charged particles and accounting for the energy supplied to the plasma by the applied electric field. Differences among the theories arise from the approximations and omissions made in selecting processes that affect the particle and energy balances. This work is primarily concerned with the deviation from the ambipolar description of the positive column caused by space charge, electron-ion volume recombination, and temperature inhomogeneities.
\r\n\r\nThe presentation is divided into three parts, the first of which involved the derivation of the final macroscopic equations from kinetic theory. The final equations are obtained by taking the first three moments of the Boltzmann equation for each of the three species in the plasma. Although the method used and the equations obtained are not novel, the derivation is carried out in detail in order to appraise the validity of numerous approximations and to justify the use of data from other sources. The equations are applied to a molecular hydrogen discharge contained between parallel walls. The applied electric field is parallel to the walls, and the dependent variables\u2014electron and ion flux to the walls, electron and ion densities, transverse electric field, and gas temperature\u2014vary only in the direction perpendicular to the walls. The mathematical description is given by a sixth-order nonlinear two-point boundary value problem which contains the applied field as a parameter. The amount of neutral gas and its temperature at the walls are held fixed, and the relation between the applied field and the electron density at the center of the discharge is obtained in the process of solving the problem. This relation corresponds to that between current and voltage and is used to interpret the effect of space charge, recombination, and temperature inhomogeneities on the voltage-current characteristic of the discharge.
\r\n\r\nThe complete solution of the equations is impractical both numerically and analytically, and in Part II the gas temperature is assumed uniform so as to focus on the combined effects of space charge and recombination. The terms representing these effects are treated as perturbations to equations that would otherwise describe the ambipolar situation. However, the term representing space charge is not negligible in a thin boundary layer or sheath near the walls, and consequently the perturbation problem is singular. Separate solutions must be obtained in the sheath and in the main region of the discharge, and the relation between the electron density and the applied field is not determined until these solutions are matched.
\r\n\r\nIn Part III the electron and ion densities are assumed equal, and the complicated space-charge calculation is thereby replaced by the ambipolar description. Recombination and temperature inhomogeneities are both important at high values of the electron density. However, the formulation of the problem permits a comparison of the relative effects, and temperature inhomogeneities are shown to be important at lower values of the electron density than recombination. The equations are solved by a direct numerical integration and by treating the term representing temperature inhomogeneities as a perturbation.
\r\n\r\nThe conclusions reached in the study are primarily concerned with the association of the relation between electron density and axial field with the voltage-current characteristic. It is known that the effect of space charge can account for the subnormal glow discharge and that the normal glow corresponds to a close approach to an ambipolar situation. The effect of temperature inhomogeneities helps explain the decreasing characteristic of the arc, and the effect of recombination is not expected to appear except at very high electron densities.
\r\n" }, { "name": "Lynds, Lahmer", "degree": "PhD", "year": "1970", "title": "I. Electron Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile. II. Nuclear Spin Relaxation Studies of Manganese (II) Complexes in Acetonitrile", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08132015-143344768", "creators": [ { "name": { "family": "Lynds", "given": "Lahmer" }, "id": "Lynds-Lahmer", "display_name": "Lynds, Lahmer" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/H07H-XD45", "abstract": "Magnetic resonance techniques have given us a powerful means for investigating dynamical processes in gases, liquids and solids. Dynamical effects manifest themselves in both resonance line shifts and linewidths, and, accordingly, require detailed analyses to extract desired information. The success of a magnetic resonance experiment depends critically on relaxation mechanisms to maintain thermal equilibrium between spin states. Consequently, there must be an interaction between the excited spin states and their immediate molecular environment which promote changes in spin orientation while excess magnetic energy is coupled into other degrees of freedom by non-radiative processes. This is well known as spin-lattice relaxation. Certain dynamical processes cause fluctuations in the spin state energy levels leading to spin-spin relaxation and, here again, the environment at the molecular level plays a significant role in the magnitude of interaction. Relatively few electron spin relaxation studies of solutions have been conducted and the present work is addressed toward the extension of our knowledge in this area and the retrieval of dynamical information from line shape analyses on a time scale comparable to diffusion controlled phenomena.
\r\nSpecifically, the electron spin relaxation of three Mn+23d5 complexes, Mn(CH3CN)6+2, MnCl4-2 in acetonitrile has been studied in considerable detail. The effective spin Hamiltonian constants were carefully evaluated under a wide range of experimental conditions. Resonance widths of these Mn+2 complexes were studied in the presence of various excess ligand ions and as a function of concentration, viscosity, temperature and frequency (X-band, ~9.5 \u050c Hz and K-band, ~35 \u050c Hz).
\r\nA number of interesting conclusions were drawn from these studies. For the Et4NCl-4-2 system several relaxation mechanisms leading to resonance broadening were observed. One source appears to arise through spin-orbit interactions caused by modulation of the ligand field resulting from transient distortions of the complex imparted by solvent fluctuations in the immediate surroundings of the paramagnetic ion. An additional spin relaxation was assigned to the formation of ion pairs [Et4N+\u2026MnCl4-2] and it was possible to estimate the dissociation constant for this specie in acetonitrile.
\r\nThe Bu4NBr-MnBr4-2 study was considerably more interesting. As in the former case, solvent fluctuations and ion-pairing of the paramagnetic complex [Bu4N+\u2026MnBr4-2] provide significant relaxation for the electronic spin system. Most interesting, without doubt, is the onset of a new relaxation mechanism leading to resonance broadening which is best interpreted as chemical exchange. Thus, assuming that resonance widths were simply governed by electron spin state lifetimes, we were able to extract dynamical information from an interaction in which the initial and final states are the same
\r\n\r\nMnBr4-2 + Br- = MnBr4-2 + Br-.
\r\n\r\nThe bimolecular rate constants were obtained at six different temperatures and their magnitudes suggested that the exchange is probably diffusion controlled with essentially a zero energy of activation. The most important source of spin relaxation in this system stems directly from dipolar interactions between the manganese 3d5 electrons. Moreover, the dipolar broadening is strongly frequency dependent indicating a deviation between the transverse and longitudinal relaxation times. We are led to the conclusion that the 3d5 spin states of ion-paired MnBr4-2 are significantly correlated so that dynamical processes are also entering the picture. It was possible to estimate the correlation time, Td, characterizing this dynamical process.
\r\n\r\nIn Part II we study nuclear magnetic relaxation of bromine ions in the MnBr4-2-Bu4NBr-acetonitrile system. Essentially we monitor the 79Br and 81Br linewidths in response to the [MnBr4-2]/[Br-] ratio with the express purpose of supporting our contention that exchange is occurring between \"free\" bromine ions in the solvent and bromine in the first coordination sphere of the paramagnetic anion. The complexity of the system elicited a two-part study: (1) the linewidth behavior of Bu4NBr in anhydrous CH3CN in the absence of MnBr4-2 and\r\n(2) in the presence of MnBr4-2. It was concluded in study (1) that dynamical association, Bu4NBr k1= Bu4N+ + Br-, was modulating field-gradient interactions at frequencies high enough to provide an estimation of the unimolecular rate constant, k1. A comparison of the two isotopic bromine linewidth-mole fraction results led to the conclusion that quadrupole interactions provided the dominant relaxation mechanism. In study (2) the \"residual\" bromine linewidths for both 79Br and 81Br are clearly controlled by quadrupole interactions which appear to be modulated by very rapid dynamical processes other than molecular reorientation. We conclude that the \"residual\" linewidth has its origin in chemical exchange and that bromine nuclei exchange rapidly between a \"free\" solvated ion and the paramagnetic complex, MnBr4-2.
\r\n" }, { "name": "Mog, David Michael", "degree": "PhD", "year": "1970", "title": "Mechanistic Studies of a Model Reaction for Enzymatic Hydroxylation", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08182015-100458662", "creators": [ { "name": { "family": "Mog", "given": "David Michael" }, "id": "Mog-David-Michael", "display_name": "Mog, David Michael" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RTHJ-0E62", "abstract": "A study has been made of the reaction mechanism of a model system for enzymatic hydroxylation. The results of a kinetic study of the hydroxylation of 2-hydroxyazobenzene derivatives by cupric ion and hydrogen peroxide are presented. An investigation of kinetic orders indicates that hydroxylation proceeds by way of a coordinated intermediate complex consisting of cupric ion and the mono anions of 2-hydroxyazobenzene and hydrogen peroxide. Studies with deuterated substrate showed the absence of a primary kinetic isotope effect and no evidence of an NIH shift. The effect of substituents on the formation of intermediate complexes and the overall rate of hydroxylation was studied quantitatively in aqueous solution. The combined results indicate that the hydroxylation step is only slightly influenced by ring substitution. The substituent effect is interpreted in terms of reaction by a radical path or a concerted mechanism in which the formation of ionic intermediates is avoided. The reaction mechanism is discussed as a model for enzymatic hydroxylation.
" }, { "name": "Penner, Thomas Lorne", "degree": "PhD", "year": "1970", "title": "Ions and Excitations in Organic Radiation Chemistry. I. The Gamma Radiation Induced Reactions of 1,3-Cyclohexadiene. II. The Radiation Induced Isomerization of 1,2-Diphenylpropene in Cyclohexane", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02182009-112539", "creators": [ { "name": { "family": "Penner", "given": "Thomas Lorne" }, "id": "Penner-Thomas-Lorne", "display_name": "Penner, Thomas Lorne" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jfmj-rs86", "abstract": "PART I: Irradiation of 1,3-cyclohexadiene with \u03b3 rays leads to dimerization, either in benzene solution or in the neat liquid. Relative amounts of the products vary widely with reaction conditions but the composition of the mixtures can be expressed as consisting of variable amounts of two groups. One set of products corresponds to those formed in thermal dimerization and the other has the distribution found in photodimerization induced by triplet sensitizers. Formation of the \"thermal\" dimers is inhibited by 2-propanol, a cation scavenger, and promoted by electron scavengers, so a cationic mechanism is postulated. The other, \"photo\" dimers,are presumably formed from triplet diene. Ring cleavage to give 1,3, 5-hexatriene is also observed and attributed to an excited singlet state of 1,3-cyclohexadiene. Since ring opening is not affected by electron scavengers whereas \"photo\" dimers are quenched, it is inferred that excited singlets are formed in primary excitation processes and that triplets are largely produced by charge neutralization. In benzene solution charge and excitation transfer from the solvent are involved in the production of diene products. A chain dimerization also seems to be present in benzene solution.\r\n\r\nPART II: The cis and trans isomers of 1,2-diphenylpropene are isomerized in cyclohexane by irradiation of solutions with \u03b3 radiation. At low solute concentrations both isomers appear to react through the triplet state of the 1,2-diphenylpropene which is formed by charge neutralization. At higher alkene concentrations and especially at low radiation doses a cationic chain reaction contributes to cis\u2192trans isomerization. The value for isomerization of the trans isomer at high solute concentration gives a G for solute triplet of 4.4." }, { "name": "Petersson, George Arthur", "degree": "PhD", "year": "1970", "title": "Filtering N.M.R. Spectra", "advisor": "McLachlan, Andrew D.; McKoy, Basil Vincent; Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08252015-093052674", "creators": [ { "name": { "family": "Petersson", "given": "George Arthur" }, "id": "Petersson-George-Arthur", "display_name": "Petersson, George Arthur" } ], "advisors": [ { "name": { "family": "McLachlan", "given": "Andrew D." }, "id": "McLachlan-A-D", "role": "advisor", "display_name": "McLachlan, Andrew D." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b9m3-qs59", "abstract": "Methods of filtering an n.m.r. spectrum which can improve the resolution by as much as a factor of ten are examined. They include linear filters based upon an information theory approach and non-linear filters based upon a statistical approach. The appropriate filter is determined by the nature of the problem. Once programmed on a digital computer they are both simple to use.
\r\n\r\nThese filters are applied to some examples from 13C and 15N n.m.r. spectra.
" }, { "name": "Preer, James Randolph", "degree": "PhD", "year": "1970", "title": "Electronic Structure in Five-Coordinate Complexes of Nickel(II) with Heavy Donor Ligands", "advisor": "Gray, Harry B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09082015-093220306", "creators": [ { "name": { "family": "Preer", "given": "James Randolph" }, "id": "Preer-James-Randolph", "display_name": "Preer, James Randolph" } ], "advisors": [ { "name": { "family": "Gray", "given": "Harry B." }, "id": "Gray-H-B", "role": "advisor", "display_name": "Gray, Harry B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xfdt-p976", "abstract": "I.
\r\n\r\nVarious studies designed to elucidate the electronic structure of the arsenic donor ligand, o-phenylenebisdimethylarsine (diarsine), have been carried out. The electronic spectrum of diarsine has been measured at 300 and 77\u02daK. Electronic spectra of the molecular complexes of various substituted organoarsines and phosphines with tetracyanoethylene have been measured and used to estimate the relative ionization potentials of these molecules.
\r\n\r\nUv photolysis of arsines in frozen solution (96\u02daK) has yielded thermally labile, paramagnetic products. These include the molecular cations of the photolyzed compounds. The species (diars)+ exhibits hyper-fine splitting due to two equivalent 75As(I=3/2) nuclei. Resonances due to secondary products are reported and assignments discussed.
\r\n\r\nEvidence is presented for the involvement of d-orbitals in the bonding of arsines. In (diars)+ there is mixing of arsenic \u201clone-pair\u201d orbitals with benzene ring \u03c0-orbitals.
\r\n\r\nII.
\r\n\r\nDetailed electronic spectral measurements at 300 and 77\u02daK have been carried out on five-coordinate complexes of low-spin nickel(II), including complexes of both trigonal bipyramidal (TBP) and square pyramidal (SPY) geometry. TBP complexes are of the form NiLX+ (X=halide or cyanide,
\r\n\r\nL = Q\u01ad(CH2)3As(CH3)2]3 or
\r\n\r\nP [hexagon - Q'CH3] , Q = P, As,
\r\n\r\nQ\u2019=S, Se).
\r\n\r\n\r\nThe electronic spectra of these compounds exhibit a novel feature at low temperature. The first ligand field band, which is asymmetric in the room temperature solution spectrum, is considerably more symmetrical at 77\u02daK. This effect is interpreted in terms of changes in the structure of the complex.
\r\n\r\nThe SPY complexes are of the form Ni(diars)2Xz (X=CL, Br, CNS, CN, thiourea, NO2, As). On the basis of the spectral results, the d-level ordering is concluded to be xy \u02c2 xz, yz \u02c2 z2 \u02c2\u02c2 x2 - y2. Central to this interpretation is identification of the symmetry-allowed 1A1 \u2192 1E (xz, yz \u2192 x2 - y2) transition. This assignment was facilitated by the low temperature measurements.
\r\n\r\nAn assignment of the charge-transfer spectra of the five-coordinate complexes is reported, and electronic spectral criteria for distinguishing the two limiting geometries are discussed.
\r\n" }, { "name": "Priestley, Eldon Bruce", "degree": "PhD", "year": "1970", "title": "I. A Study of the Dynamics of Triplet Excitons in Molecular Crystals. II. An Investigation of Delayed Emission from Chlorella pyrenoidosa", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272015-141947872", "creators": [ { "name": { "family": "Priestley", "given": "Eldon Bruce" }, "id": "Priestley-Eldon-Bruce", "display_name": "Priestley, Eldon Bruce" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/J3KT-FD46", "abstract": "I. PREAMBLE AND SCOPE
\r\n\r\nBrief introductory remarks, together with a definition of the scope of the material discussed in the thesis, are given.
\r\n\r\nII. A STUDY OF THE DYNAMICS OF TRIPLET EXCITONS IN MOLECULAR CRYSTALS
\r\n\r\nPhosphorescence spectra of pure crystalline naphthalene at room temperature and at 77\u02da K are presented. The lifetime of the lowest triplet 3B1u state of the crystal is determined from measurements of the time-dependence of the phosphorescence decay after termination of the excitation light. The fact that this lifetime is considerably shorter in the pure crystal at room temperature than in isotopic mixed crystals at 4.2\u02da K is discussed, with special importance being attached to the mobility of triplet excitons in the pure crystal.
\r\n\r\nExcitation spectra of the delayed fluorescence and phosphorescence from crystalline naphthalene and anthracene are also presented. The equation governing the time- and spatial-dependence of the triplet exciton concentration in the crystal is discussed, along with several approximate equations obtained from the general equation under certain simplifying assumptions. The influence of triplet exciton diffusion on the observed excitation spectra and the possibility of using the latter to investigate the former is also considered. Calculations of the delayed fluorescence and phosphorescence excitation spectra of crystalline naphthalene are described.
\r\n\r\nA search for absorption of additional light quanta by triplet excitons in naphthalene and anthracene crystals failed to produce any evidence for the phenomenon. This apparent absence of triplet-triplet absorption in pure crystals is attributed to a low steady-state triplet concentration, due to processes like triplet-triplet annihilation, resulting in an absorption too weak to be detected with the apparatus used in the experiments. A comparison of triplet-triplet absorption by naphthalene in a glass at 77\u02da K with that by naphthalene-h8 in naphthalene-d8 at 4.2\u02da K is given. A broad absorption in the isotopic mixed crystal triplet-triplet spectrum has been tentatively interpreted in terms of coupling between the guest 3B1u state and the conduction band and charge-transfer states of the host crystal.
\r\n\r\nIII. AN INVESTIGATION OF DELAYED LIGHT EMISSION FROM Chlorella Pyrenoidosa
\r\n\r\nAn apparatus capable of measuring emission lifetimes in the range 5 X 10-9 sec to 6 X 10-3 sec is described in detail. A cw argon ion laser beam, interrupted periodically by means of an electro-optic shutter, serves as the excitation source. Rapid sampling techniques coupled with signal averaging and digital data acquisition comprise the sensitive detection and readout portion of the apparatus. The capabilities of the equipment are adequately demonstrated by the results of a determination of the fluorescence lifetime of 5, 6, 11, 12-tetraphenyl-naphthacene in benzene solution at room temperature. Details of numerical methods used in the final data reduction are also described.
\r\n\r\nThe results of preliminary measurements of delayed light emission from Chlorella Pyrenoidosa in the range 10-3 sec to 1 sec are presented. Effects on the emission of an inhibitor and of variations in the excitation light intensity have been investigated. Kinetic analysis of the emission decay curves obtained under these various experimental conditions indicate that in the millisecond-to-second time interval the decay is adequately described by the sum of two first-order decay processes. The values of the time constants of these processes appear to be sensitive both to added inhibitor and to excitation light intensity.
\r\n" }, { "name": "Remer, Donald Sherwood", "degree": "PhD", "year": "1970", "title": "The Separation of Atomic and Molecular Gases from Helium by Cataphoresis", "advisor": "Shair, Fredrick H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032015-135156772", "creators": [ { "name": { "family": "Remer", "given": "Donald Sherwood" }, "id": "Remer-Donald-Sherwood", "display_name": "Remer, Donald Sherwood" } ], "advisors": [ { "name": { "family": "Shair", "given": "Fredrick H." }, "id": "Shair-F-H", "role": "advisor", "display_name": "Shair, Fredrick H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/e8fd-be69", "abstract": "The cataphoretic purification of helium was investigated for binary mixtures of He with Ar, Ne, N2, O2, CO, and CO2 in DC glow discharge. An experimental technique was developed to continuously measure the composition in the anode end-bulb without sample withdrawal. Discharge currents ranged from 10 ma to 100 ma. Total gas pressure ranged from 2 torr to 9 torr. Initial compositions of the minority component in He ranged from 1.2 mole percent to 7.5 mole percent.
\r\n\r\nThe cataphoretic separation of Ar and Ne from He was found to be in agreement with previous investigators. The cataphoretic separation of N2, O2, and CO from He was found to be similar to noble gas systems in that the steady-state separation improved with (1) increasing discharge current, (2) increasing gas pressure, and (3) decreasing initial composition of the minority component. In the He-CO2 mixture, the CO2 dissociated to CO plus O2. The fraction of CO2 dissociated was directly proportional to the current and pressure and independent of initial composition.
\r\n\r\nThe experimental results for the separation of Ar, Ne, N2, O2, and CO from He were interpreted in the framework of a recently proposed theoretical model involving an electrostatic Peclet number. In the model the electric field was assumed to be constant. This assumption was checked experimentally and the maximum variation in electric field was 35% in time and 30% in position. Consequently, the assumption of constant electric field introduced no more than 55% variation in the electrostatic Peclet number during a separation.
\r\n\r\nTo aid in the design of new cataphoretic systems, the following design criteria were developed and tested in detail: (1) electric field independent of discharge current, (2) electric field directly proportional to total pressure, (3) ion fraction of impurity directly proportional to discharge current, and (4) ion fraction of impurity independent of total pressure. Although these assumptions are approximate, they enabled the steady-state concentration profile to be predicted to within 25% for 75% of the data. The theoretical model was also tested with respect to the characteristic time associated with transient cataphoresis. Over 80% of the data was within a factor of two of the calculated characteristic times.
\r\n\r\nThe electrostatic Peclet number ranged in value from 0.13 to 4.33. Back-calculated ion fractions of the impurity component ranged in value from 4.8x10-6 to 178x10-6.
\r\n" }, { "name": "Sharp, Louis James, IV", "degree": "PhD", "year": "1970", "title": "The Photoreactions of N-Methyl-2-Pyridone", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02272009-095718", "creators": [ { "name": { "family": "Sharp", "given": "Louis James, IV" }, "id": "Sharp-Louis-James-IV", "display_name": "Sharp, Louis James, IV" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RK5J-7E32", "abstract": "In studying the photochemistry of N-methyl-2- pyridone, four products were observed. Besides the previously known dimer and bicyclic monomer, two new dimers were isolated.\r\n\r\nThe quantum yields of product formation were measured, and it was found that only one intermediate was involved. From sensitization and quenching experiments, the lowest excited singlet state appears to be that intermediate although a highly reactive, ground state isomer cannot be ruled out. Some spectroscopic evidence for this isomer is given." }, { "name": "Smith, Ronald Lee", "degree": "PhD", "year": "1970", "title": "Joule-Thomson Coefficients of Propane and N-Butane", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272015-130752874", "creators": [ { "name": { "family": "Smith", "given": "Ronald Lee" }, "id": "Smith-Ronald-Lee", "display_name": "Smith, Ronald Lee" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1TJD-R369", "abstract": "Experimental Joule-Thomson measurements were made on gaseous propane at temperatures from 100 to 280\u02daF and at pressures from 8 to 66 psia. Joule-Thomson measurements were also made on gaseous n-butane at temperatures from 100 to 280\u02da and at pressures from 8 to 42 psia. For propane, the values of these measurements ranged from 0.07986\u02daF/psi at 280\u02daF and 8.01 psia to 0.19685\u02daF/psi at 100\u02daF and 66.15 psia. For n-butane, the values ranged from 0.11031\u02daF/psi at 280\u02daF and 9.36 psia to 0.30141\u02daF/psi at 100\u02daF and 41.02 psia. The experimental values have a maximum error of 1.5 percent.
\r\n\r\nFor n-butane, the measurements of this study did not agree with previous Joule-Thomson measurements made in the Laboratory in 1935. The application of a thermal-transfer correction to the previous experimental measurements would cause the two sets of data to agree. Calculated values of the Joule-Thomson coefficient from other types of p-v-t data did agree with the present measurements for n-butane.
\r\n\r\nThe apparatus used to measure the experimental Joule-Thomson coefficients had a radial-flow porous thimble and was operated at pressure changes between 2.3 and 8.6 psi. The major difference between this and other Joule-Thomson apparatus was its larger weight rates of flow (up to 6 pounds per hour) at atmospheric pressure. The flow rate was shown to have an appreciable effect on non-isenthalpic Joule-Thomson measurements.
\r\n\r\nPhotographic materials on pages 79-81 are essential and will not reproduced clearly on Xerox copies. Photographic copies should be ordered.
\r\n" }, { "name": "Trifunac, Natalia Pisker", "degree": "PhD", "year": "1970", "title": "Photochemical Cis-Trans Isomerization of \u03b2-Stytylferrocene", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312015-100258588", "creators": [ { "name": { "family": "Trifunac", "given": "Natalia Pisker" }, "id": "Trifunac-Natalia-Pisker", "display_name": "Trifunac, Natalia Pisker" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/09YE-YV13", "abstract": "The effect of metal atoms on photochemical transformations\r\nhas been investigated by studies of the cis-trans isomerization of\r\n\u03b2-styrylferrocene.
\r\n\r\nThe photostationary state lies entirely on the side of the trans\r\nisomer in the cases of direct irradiation at 3130 \u00c5 or at 3660 \u00c5. The\r\nquantum yield at 3130 \u00c5 is 0.00650 and does not vary with concentration.\r\nIn the presence of benzophenon as sensitizer the quantum yield\r\nis 0.00540. On the other hand, the quantum yield for direct irradiation \r\nat 3660 \u00c5 decreases with increasing concentration of cis \u03b2-\r\nstyrylferrocene varying from 0.00365 to 0.00198.
\r\n\r\n\r\nThese results lead to the suggestion that the isomerization takes\r\nplace from a triplet state of \u03b2-styrylferrocene which probably has\r\nhigher energy than the lowest triplet; reaction from the third triplet\r\nseems most likely.
" }, { "name": "Truhlar, Donald Gene", "degree": "PhD", "year": "1970", "title": "Quantum Mechanical Calculations for Rearrangement Collisions of Electrons, Atoms, and Molecules", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-01082009-135357", "creators": [ { "name": { "family": "Truhlar", "given": "Donald Gene" }, "id": "Truhlar-Donald-Gene", "orcid": "0000-0002-7742-7294", "display_name": "Truhlar, Donald Gene" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/488E-2Y91", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nQuantum mechanical calculations are presented of approximate scattering cross sections for elastic and inelastic collisions, including rearrangements, for several processes involving electrons, hydrogen (H), helium (He), and potassium (K) atoms, and hydrogen (H[subscript 2]) and hydrogen halide (HX) molecules. In addition to their interest in terms of the processes themselves, the results are intercompared and compared with previous experimental and theoretical results in such a way as to provide tests of the general usefulness of the various methods used.\r\n\r\nElectron scattering is treated using the Born, polarized Born, and Vainshtein-Presnyakov-Sobelman approximations for the direct scattering and thirteen different methods for the exchange scattering. The transitions treated are 1s-1s, 1s-2s, and 2s-2s in H, 1 [\u2026]S - 2 [\u2026]P, 1 [\u2026]S - 3 [\u2026]P, and 1 [\u2026]S- 2 [\u2026]S in He, and elastic scattering and rovibrational excitation of the ground state of H[subscript 1]. Most emphasis is placed on impact energies less than about 100 eV but higher energies are also treated. We draw conclusions concerning the accuracy of the various methods for treating the exchange scattering and for calculating integral cross sections and the angular dependences of differential cross sections for small and medium scattering angles. A version of the distorted wave approximation which should often be useful is presented. Some of the results and discussions for scattering off H and for excitation of the 2 [\u2026]P state of He have been presented in two articles and a long abstract which are summarized and referred to in the text.\r\n\r\nThe statistical phase space theory of Light, Pechukas, and Nikitin is used to calculate cross sections and rate constants for the reactions H + HX (including two isotopes of H) and K + HC1. The H + HX calculations presented here supplement those already published. The probability of reaction is studied as a function of the incident translational energy and impact parameter and the internal states of the products. A generalized nonstatistical phase space theory is presented which is adiabatic in one limit and equivalent to the statistical theory of Light, Pechukas, and Nikitin in another. Some sample calculations using the new theory on H + HBr reactions are also given.\r\n\r\nWe present numerical solutions of the three-body Schroedinger equation for the collinear H + H[subscript 2] and D + D[subscript 2] chemical reactions on an assumed potential energy surface. The parametrized analytic surface is based on the calculations of Shavitt and coworkers and is thought to be the most accurate surface available. Calculations are performed in one mathematical dimension by the conservation-of-vibrational-energy and vibrational-adiabaticity models. Calculations are presented in two mathematical dimensions which are essentially exact for the collinear collision. The calculations include vibrationally excited reactants and products. The calculations are compared and their relation to and implications for the usual tunneling approximations are discussed.\r\n" }, { "name": "Van, Shui Pong", "degree": "PhD", "year": "1970", "title": "Exciplexes in Fluorescence Quenching of Aromatic Hydrocarbons by Tertiary Aliphatic Amines", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032015-150910276", "creators": [ { "name": { "family": "Van", "given": "Shui Pong" }, "id": "Van-Shui-Pong", "display_name": "Van, Shui Pong" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/x2hs-6j63", "abstract": "Strong quenching of the fluorescence of aromatic hydrocarbons by tertiary aliphatic amines has been observed in solution at room temperature. Accompanying the fluorescence quenching of aromatic hydrocarbons, an anomalous emission is observed. This new emission is very broad, structureless and red-shifted from the original hydrocarbon fluorescence.
\r\n\r\nKinetic studies indicate that this anomalous emission is due to an exciplex formed by an aromatic hydrocarbon molecule in its lowest excited singlet state with an amine molecule. The fluorescence quenching of the aromatic hydrocarbons is due to the depopulation of excited hydrocarbon molecules by the formation of exciplexes, with subsequent de-excitation of exciplexes by either radiative or non-radiative processes.
\r\n\r\nAnalysis of rate constants shows the electron-transfer nature of the exciplex. Through the study of the effects on the frequencies of exciplex emissions of substituents on the hydrocarbons, it is concluded that partial electron transfer from the amine molecule to the aromatic hydrocarbon molecule in its lowest excited singlet state occurs in the formation of exciplex. Solvent effects on the exciplex emission frequencies further demonstrate the polar nature of the exciplex.
\r\n\r\nA model based on this electron-transfer nature of exciplex is proposed and proves satisfactory in interpreting the exciplex emission phenomenon in the fluorescence quenching of aromatic hydrocarbons by tertiary aliphatic amines.
\r\n" }, { "name": "Wamser, Carl Christian", "degree": "PhD", "year": "1970", "title": "I. Photochemical Studies on Phenoxy Radical. II. The Photoreaction of Michler's Ketone with Benzophenone", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02272009-093235", "creators": [ { "name": { "family": "Wamser", "given": "Carl Christian" }, "id": "Wamser-Carl-Christian", "display_name": "Wamser, Carl Christian" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/390h-jd89", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. Photochemical studies of phenoxy radical: \r\nPhenoxy radical was generated by flash photolysis of aqueous phenol. The ultraviolet-visible absorption spectrum of phenoxy radical was obtained. Decay kinetics for the bimolecular disappearance of phenoxy radical led to a second order rate constant of k[...] = 1.2 \u00b1 0.1 x [...] sec[...]. In these solution-phase flash photolysis studies, no evidence was obtained for further decomposition of phenoxy radical. Molecular orbital symmetry correlations demonstrate that the conversion of phenoxy radical to cyclopentadienyl radical and carbon monoxide is symmetry-allowed from the ground state and symmetry-forbidden from the excited state of phenoxy radical.\r\n\r\nII. The photorecation of Michler's ketone with benzophenone:\r\nMichler's ketone (4,4'-bis[dimethylamino]benzophenone) undergoes a photoreaction with benzophenone in 2-propanol to give photoproduct I with moderate quantum efficiency. This product arises from the coupling of benzophenone [...] ketyl radical with the corresponding radical derived from Michler's ketone. Each of these photointermediates was characterized by the absorption spectra and decay kinetics obtained from flash photolysis studies. The key mechanistic step must be transfer of hydrogen from the triplet state of Michler's ketone to benzophenone, and is without precedent in photochemistry. A triplet \"exciplex\" is postulated to lead to the hydrogen transfer." }, { "name": "Wilson, Charles Woodrow, Jr.", "degree": "PhD", "year": "1970", "title": "Molecular Stability and the H\u2082 + D\u2082 \u2192 2HD Four Center Exchange Reaction Surface", "advisor": "Goddard, William A., III", "url": "https://resolver.caltech.edu/CaltechTHESIS:11192009-140720848", "creators": [ { "name": { "family": "Wilson", "given": "Charles Woodrow, Jr." }, "id": "Wilson-Charles-Woodrow", "display_name": "Wilson, Charles Woodrow, Jr." } ], "advisors": [ { "name": { "family": "Goddard", "given": "William A., III" }, "id": "Goddard-W-A-III", "role": "advisor", "display_name": "Goddard, William A., III" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PE87-HJ15", "abstract": "Partitions of the energy of the spin-coupling optimized GI wavefunctions of small systems are examined to isolate the factor responsible for chemical binding. One term, the contragradience energy, is found to dominate the binding energy in all cases. The magnitude of the contragradience energy is found to be insensitive to self-consistency effects; this property is used to extend the results to molecules too large for self-consistent calculation. Resonance, rotational barriers and the concept of a bond region are discussed in terms of the contragradience energy.\r\n\r\nCalculations of the reaction surface for the H_2 + D_2 \u2192 2HD four-center exchange reaction are examined in terms of the contra-gradience energy.\r\n" }, { "name": "Winter, Nicholas Wilhelm", "degree": "PhD", "year": "1970", "title": "I. Numerical Solution of Exact Pair Equations. II. Numerical Solution of First-Order Pair Equations", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:09112015-100730009", "creators": [ { "name": { "family": "Winter", "given": "Nicholas Wilhelm" }, "id": "Winter-Nicholas-Wilhelm", "display_name": "Winter, Nicholas Wilhelm" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DCXZ-TX32", "abstract": "Part I
\r\n\r\nNumerical solutions to the S-limit equations for the helium ground\r\nstate and excited triplet state and the hydride ion ground state are obtained\r\nwith the second and fourth difference approximations. The\r\nresults for the ground states are superior to previously reported values.\r\nThe coupled equations resulting from the partial wave expansion of the\r\nexact helium atom wavefunction were solved giving accurate S-, P-, D-, F-,\r\nand G-limits. The G-limit is -2.90351 a.u. compared to the exact\r\nvalue of the energy of -2.90372 a.u.
\r\n\r\nPart II
\r\n\r\nThe pair functions which determine the exact first-order wavefunction\r\nfor the ground state of the three-electron atom are found with\r\nthe matrix finite difference method. The second- and third-order\r\nenergies for the (1s1s)1S, (1s2s)3S, and (1s2s)1S states of the two-electron\r\natom are presented along with contour and perspective plots\r\nof the pair functions. The total energy for the three-electron atom\r\nwith a nuclear charge Z is found to be\r\nE(Z) = -1.125\u2022Z2 +1.022805\u2022Z-0.408138-0.025515\u2022(1/Z)+O(1/Z2)a.u.
" }, { "name": "Aung, Soe", "degree": "PhD", "year": "1969", "title": "Part I. Approximate Hartree-Fock Wavefunctions, One-Electron Properties, and Electronic Structure of the Water Molecule. Part II. Perturbation-Variational Calculation of the Nuclear Spin-Spin Isotropic\r\nCoupling Constant in HD", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042016-113458282", "creators": [ { "name": { "family": "Aung", "given": "Soe" }, "id": "Aung-Soe", "display_name": "Aung, Soe" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WC0F-N163", "abstract": "Part I
\r\n\r\nSeveral approximate Hartree-Fock SCF wavefunctions for the ground electronic state of the water molecule have been obtained using an increasing number of multicenter s, p, and d Slater-type atomic orbitals as basis sets. The predicted charge distribution has been extensively tested at each stage by calculating the electric dipole moment, molecular quadrupole moment, diamagnetic shielding, Hellmann-Feynman forces, and electric field gradients at both the hydrogen and the oxygen nuclei. It was found that a carefully optimized minimal basis set suffices to describe the electronic charge distribution adequately except in the vicinity of the oxygen nucleus. Our calculations indicate, for example, that the correct prediction of the field gradient at this nucleus requires a more flexible linear combination of p-orbitals centered on this nucleus than that in the minimal basis set. Theoretical values for the molecular octopole moment components are also reported.
\r\n\r\nPart II
\r\n\r\nThe perturbation-variational theory of R. M. Pitzer for nuclear spin-spin coupling constants is applied to the HD molecule. The zero-order molecular orbital is described in terms of a single 1s Slater-type basis function centered on each nucleus. The first-order molecular orbital is expressed in terms of these two functions plus one singular basis function each of the types e-r/r and e-r ln r centered on one of the nuclei. The new kinds of molecular integrals were evaluated to high accuracy using numerical and analytical means. The value of the HD spin-spin coupling constant calculated with this near-minimal set of basis functions is JHD = +96.6 cps. This represents an improvement over the previous calculated value of +120 cps obtained without using the logarithmic basis function but is still considerably off in magnitude compared with the experimental measurement of JHD = +43 0 \u00b1 0.5 cps.
\r\n" }, { "name": "Baldwin, Steven Worth", "degree": "PhD", "year": "1969", "title": "Studies Directed Toward the Total Synthesis of Germanicol", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252016-111724271", "creators": [ { "name": { "family": "Baldwin", "given": "Steven Worth" }, "id": "Baldwin-Steven-Worth", "display_name": "Baldwin, Steven Worth" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R8K1-QY22", "abstract": "An approach to the synthesis of the pentacyclic triterpene germanicol is discussed." }, { "name": "Bangerter, Benedict William", "degree": "PhD", "year": "1969", "title": "Studies of Dinucleoside Monophosphates and Monomer-Polynucleotide Interactions by Proton Magnetic Resonance", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252016-091430836", "creators": [ { "name": { "family": "Bangerter", "given": "Benedict William" }, "id": "Bangerter-Benedict-William", "display_name": "Bangerter, Benedict William" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7Y0A-NF90", "abstract": "The nature of the intra- and intermolecular base-stacking interactions involving several dinucleoside monophosphates in aqueous solution have been investigated by proton magnetic resonance spectrosocopy, and this method has been applied to a study of the interaction of polyuridylic acid with purine and adenosine monomers.
\r\n\r\nThe pmr spectra of adenylyl (3' \u2192 5') cytidine (ApC) and cytidylyl (3' \u2192 5') adenosine (CpA) have been studied as a function of concentration and temperature. The results of these studies indicate that the intramolecular base-stacking interactions between the adenine and cytosine bases of these dinucleoside monophosphates are rather strong, and that the stacking tendencies are comparable for the two sequence isomers. The chemical shifts of the cytosine H5 and adenine H2 protons, and their variations with temperature, were shown to be consistent with stacked conformations in which both bases of the dinucleoside monophosphates are preferentially oriented in the anti conformation as in similar dApdC, and dCpdA (dA = deoxyadenosine; dC = deoxycytidine) segments in double helical DNA. The intramolecular stacking interaction was found to have a pronounced effect on the conformations of the ribose moieties, and these conformational changes are discussed. The concentration studies indicate extensive self-association of these dinucleoside monophosphates, and analysis of the concentration data facilitated determination of the dimerization constant for the association process as well as the nature of the intermolecular complexes.
\r\n\r\nThe dependence of the ribose conformation upon the extent of intramolecular base-stacking was used to demonstrate that the base-base interaction in cytidylyl (3' \u2192 5') cytidine (CpC) is rather strong, while there appears to be little interaction between the two uracil bases of uridylyl (3' \u2192 5') uridine (UpU).
\r\n\r\nStudies of the binding of purine to several ribose and deoxyribose dinucleoside monophosphates show that the mode of interaction is base-stacking, and evidence for the formation of a purine-dinucleoside monophosphate intercalated complex is presented. The purine proton resonances are markedly broadened in this complex, and estimates of the purine linewidths in the complex and the equilibrium constant for purine intercalation are obtained.
\r\n\r\nA study of the interaction of unsubstitued purine with polyuridylic acid at 29\u00b0C by pmr indicated that purine binds to the uracil bases of the polymer by base-stacking. The severe broadening of the purine proton resonances observed provides strong evidence for the intercalation of purine between adjacent uracil bases of poly U. This interaction does not result in a more rigid or ordered structure for the polymer.
\r\n\r\nInvestigation of the interaction between adenosine and polyuridylic acid revealed two modes of interaction between the monomer and the polymer, depending on the temperature. At temperatures above 26\u00b0C or so, monomeric adenosine binds to poly U by noncooperative A-U base stacking. Below this temperature, a rigid triple-stranded 1A:2U complex is formed, presumably via cooperative hydrogen-bonding as has previously been reported.
\r\n\r\nThese results clearly illustrate the importance of base-stacking in non-specific interactions between bases, nucleosides and nucleotides, and also reveal the important role of the base-stacking interactions in cooperatively for med structures involving specific base-pairing where both types of interaction are possible.
\r\n" }, { "name": "Barker, John Roger", "degree": "PhD", "year": "1969", "title": "The Pyrolysis of n-Butane", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:01112016-152926399", "creators": [ { "name": { "family": "Barker", "given": "John Roger" }, "id": "Barker-John-Roger", "display_name": "Barker, John Roger" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4QG7-JQ66", "abstract": "A study of the pyrolysis of n-butane was carried out using an all-gold tubular reactor. The initial rate of decomposition of the n-butane was of 1.50-order with respect to the partial pressure of the n-butane. A free radical mechanism, similar to that originally proposed by Rice, accounted satisfactorily for the distribution of products. Oxygen was rigorously excluded from the pyrolysis gases. The surfaces of the gold reactor had been acid-treated to remove oxide impurities. Some preliminary experiments were performed in the partial oxidation of n-butane." }, { "name": "Burke, Thomas Edmund", "degree": "PhD", "year": "1969", "title": "F\u00b9\u2079 Nuclear Spin Lattice Relaxation in Liquids", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142002-155051", "creators": [ { "name": { "family": "Burke", "given": "Thomas Edmund" }, "id": "Burke-Thomas-Edmund", "display_name": "Burke, Thomas Edmund" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q5X7-KP46", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA magnetic nucleus located on an internal rotor is coupled not only to the rotational magnetic field generated by the end-over-end rotation of the molecule but also to the magnetic field produced by the internal rotation of the top relative to the frame. Although the importance of the nuclear-spin-internal-rotation coupling as a nuclear spin-lattice relaxation mechanism has been established, the nature of the stochastic processes which modulate the interaction and are thereby responsible for the coupling between the nuclear spin system and the lattice has yet to be determined.\r\n\r\nIn order to elucidate the nature of the dynamical processes that provide the coupling between the nuclear spins and the lattice, both the temperature and viscosity dependence of the fluorine spin-lattice relaxation times for benzotrifluoride have been examined. The viscosity dependence of the fluorine spin-lattice relaxation times for hexafluorobutyne-2 has also been investigated.\r\n\r\nIt is concluded that the rotational magnetic fields generated by overall and internal rotation are fluctuating independently and that each field is described by a distinct correlation time. It is also concluded that, contrary to previous proposals, the nuclear-spin-internal-rotation interaction contributes significantly to the spin-lattice relaxation of the methyl group protons in molecules such as toluene.\r\n\r\nThe effect of solvents on the relaxation of rigid molecules has also been investigated. The fluorine spin-lattice relaxation times of CF[subscript 3]CH[subscript 2]C1, CF[subscript 3]CH[subscript 2]Br, CF[subscript 3]CH[subscript 2]I, and CF[subscript 3]CC1[subscript 3] have been measured as a function of concentration in various solvents, both polar and non-polar. The intramolecular contributions to relaxation, arising from the intramolecular dipolar and spin--overall-rotation interactions, were analyzed in terms of various correlation time models. It is found that the Hill[superscript 1] model for molecular reorientation provides the only satisfactory explanation for all the results; it is also found that, in general, the efficacy of the Hill model is dependent upon the mutual viscosity." }, { "name": "Chia, Wu-sun", "degree": "PhD", "year": "1969", "title": "Part I. Convective Thermal Transfer in a Steady, Nearly Uniform Flow of Air Between Parallel Plates. Part II. A Study of Organ-Pipe Combustion Oscillations of Premixed Gases in a Combustor with Variable Length at Atmospheric Pressure", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-140720", "creators": [ { "name": { "family": "Chia", "given": "Wu-sun" }, "id": "Chia-Wu-sun", "display_name": "Chia, Wu-sun" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DMCW-1391", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPART I\r\n\r\nMeasurements of the total viscosity and total conductivity were made as a function of position and Reynolds number for the flow of air between two parallel plates with a separation of approximately 0.75 in. The temperature of the upper plate was 103.0[degrees]F and that of the lower plate 70.0[degrees]F. The investigations were carried out at Reynolds numbers from 40,000 to 100,000 and were in good agreement with earlier data obtained at Reynolds numbers up to 40,000. The results obtained indicate little change in the total Prandtl number with increasing Reynolds number from the value of the molecular Prandtl number.\r\n\r\nPART II\r\n\r\nThe effect of varying the length of the combustor upon the frequency and the amplitude of the organ-pipe oscillations has been investigated in a cylindrical combustor 3.836 in. in diameter and approximately 162 in. in length. Measurements of the perturbations in pressure were made in a premixed flame of air and natural gas at a mixture ratio of about 90 per cent stoichiometric. Results indicate some discontinuous variations in frequency, along with the presence of some quiet regions, as the length of the combustor is systematically changed. A driving mechanism of the combustion oscillation is proposed and is examined in the light of Rayleigh's criterion. The calculated results based upon this driving mechanism turn out to be in good agreement with the experimental data." }, { "name": "Chu, Frank I-Chien", "degree": "PhD", "year": "1969", "title": "Investigations on Some Diffusion Problems in Rarefied Gases", "advisor": "Gavalas, George R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-143841", "creators": [ { "name": { "family": "Chu", "given": "Frank I-Chien" }, "id": "Chu-Frank-I-Chien", "display_name": "Chu, Frank I-Chien" } ], "advisors": [ { "name": { "family": "Gavalas", "given": "George R." }, "id": "Gavalas-G-R", "role": "advisor", "display_name": "Gavalas, George R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/SAKW-WA48", "abstract": "This is a theoretical study of diffusion problems in transitional rarefied gases with surface dissociation and recombination reactions. The method of composite solution, which is a simplified version of the exact composite expansion theory with similarity to the mean free path method, has proved to be very successful.\r\n\r\nBoth the methods of Lester Lees and of composite solution have been used to solve the problem of simultaneous heat and mass transfer of a partially dissociated diatomic gas of transitional rarefaction from a hot fine wire to a surrounding cylinder. We have employed a sticking probability to describe the dissociation reaction of the diatomic gas at the wire but have used continuum type boundary conditions at the outer cylinder. We have also assumed a small total temperature variation and a small mole fraction of the dissociated atoms. The results obtained by both methods are identical and agree very well with the existing formulas in many limiting cases.\r\n\r\nOwing to its simplicity, the method of composite solution was applied to the problem of a subsonic viscous flow past a sphere for small Mach number but arbitrary Knudsen number. This problem was considered both as a prerequisite for the investigation of mass transfer from a sphere to a stream of gas mixtures and as a means to acquire familiarity with the matching procedures. The result for the drag force agrees with the known formulas in both the free molecular flow limit and the continuum limit. The agreement with experimental data in the transitional flow regimes is less satisfactory.\r\n\r\nThe method of composite solution was then applied to the problem of mass transfer from a sphere to a partially dissociated diatomic gas. Surface recombination reaction was assumed to take place at the sphere while the flow conditions were the same as those in the previous problem. Small mole fraction of the dissociated atoms was also assumed, with the implication of a uniform temperature field. The concentration and flux of the dissociated atoms were found in terms of the sticking probability of the recombination reaction.\r\n\r\nThe problem of simultaneous diffusion and reaction of dissociated atoms in the interior of a sphere is also very interesting and practically important. We have studied the special case of a very fast reaction where the concentration of atoms at the surface of the sphere is given. A new method of solving this unsteady state diffusion problem with moving boundary was proposed and has proved to be more advantageous than the existing ones.\r\n\r\nFinally, the sticking probabilities employed in the previous problems were obtained for various mechanisms of dissociation and recombination reactions. These sticking probabilities turn out to be constant over a wide range of Knudsen number and vanish in the continuum limit." }, { "name": "Dahlquist, Frederick Willis", "degree": "PhD", "year": "1969", "title": "The Binding and Catalytic Properties of Lysozyme", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01292016-143302044", "creators": [ { "name": { "family": "Dahlquist", "given": "Frederick Willis" }, "id": "Dahlquist-Frederick-Willis", "display_name": "Dahlquist, Frederick Willis" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WEXB-9D59", "abstract": "The binding and catalytic properties of hen's egg white lysozyme have been studied by a variety of techniques. These studies show that the enzyme has three contiguous binding subsites, A, B, and C. The application of nuclear magnetic resonance (NMR) spectroscopy to probe the binding environment of several saccharides to lysozyme has demonstrated that the reducing end sugar rings of chitotriose, chitobiose and the \u03b2-form of N-acetylglucosamine all bind in subsite C. The central sugar ring of chitotriose and the sugar ring at the nonreducing end of chitobiose were found to bind in subsite B, while the nonreducing end sugar residue of chitotriose occupied subsite A. The dynamics of the binding process has also been investigated by NMR. The formation rate constant of chitobiose--and chitotriose-enzyme complexes were found to be about 4 X 10-6 M-1 sec-1 with small activation energies.
\r\n\r\nThe stereochemical path of the lysozyme catalyzed hydrolysis of glycosidic bonds has been shown to proceed with at least 99.7% retention of configuration at C-1 of the sugar. The lysozyme catalyzed hydrolysis of glucosidic bonds has been shown to be largely carbonium ion in character by virtue of the \u03b1-deuterium kinetic isotope effect (kH/kD = 1.11) observed for the reaction. It is probable that the mechanism of action of the enzyme involves a carbonium ion intermediate which is stereospecifically quenched by solvent. However, acetamido group participation cannot be ruled out for natural substrates.
\r\n" }, { "name": "Davis, Allyn Merrill", "degree": "PhD", "year": "1969", "title": "The Rate and Mechanism of the Partial Oxidation of Acetaldehyde by PPM Concentrations of Nitrogen Dioxide", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012016-095046535", "creators": [ { "name": { "family": "Davis", "given": "Allyn Merrill" }, "id": "Davis-Allyn-Merrill", "display_name": "Davis, Allyn Merrill" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DC6G-XN83", "abstract": "The thermal reaction between nitrogen dioxide and acetaldehyde in the gas phase was investigated at room temperature and atmospheric pressure. The initial rate of disappearance of nitrogen dioxide was 1.00 \u00b1 0.03 order with respect to nitrogen dioxide and 1.00 \u00b1 0.07 order with respect to acetaldehyde. An initial second order rate constant of (8.596 \u00b1 0.189) x 10-3 1.mole-1 sec-1 was obtained at 22.0 \u00b1 0.1 \u00b0C and a total pressure of one atmosphere. The activation energy of the reaction was 12,900 cal/mole in the temperature range between 22\u00b0C and 122\u00b0C.
\r\n\r\nThe products of the reaction were nitric oxide, carbon dioxide, methyl nitrite, nitromethane and a trace amount of trans-dimeric nitrosomethane. The addition of nitric oxide increased the rate of formation of nitromethane and decreased the rate of formation of methyl nitrite. There were no measurable surface effects due to the addition of glass wool or glass beads to the reactor.
\r\n\r\nReactants and products were analyzed by gas chromatography. A mechanism was proposed incorporating the principal features of the reaction.
\r\n" }, { "name": "Dence, Joseph Bernard", "degree": "PhD", "year": "1969", "title": "I. Efforts Toward the Synthesis of Aliphatic Iodonium Salts. II. Fluorine-19 Nuclear Magnetic Resonance Spectroscopy of Cyclic and Bicyclic Systems", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012016-113113097", "creators": [ { "name": { "family": "Dence", "given": "Joseph Bernard" }, "id": "Dence-Joseph-Bernard", "display_name": "Dence, Joseph Bernard" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2qcy-bg06", "abstract": "The synthesis of iodonium salts of the general formula [C6H5IR]+X-, where R is an alkyl group and x- is a stabilizing anion, was attempted. For the choice of R three groups were selected, whose derivatives are known to be sluggish in SN1 and SN2 substitutions: cyclopropyl, 7, 7 -dimethyl-1-norbornyl, and 9 -triptycyl. The synthetic routes followed along classical lines which have been exploited in recent years by Beringer and students. Ultimately, the object of the present study was to study the reactions of the above salts with nucleophiles. In none of the three cases, however, was it possible to isolate a stable salt. A thermodynamic argument suggests that this must be due to kinetic instability rather than thermodynamic instability. Only iodocyclopropane and 1-iodoapocamphane formed isolable iododichlorides.
\r\n\r\nSeveral methylated 2, 2-difluoronorbornanes were prepared with the intent of correlating fluorine -19 chemical shifts with geometric features in a rigid system. The effect of a methyl group on the shielding of a \u03b2 -fluorine is dependent upon the dihedral angle; the maximum effect (an upfield shift of the resonance) occurs at 0\u00b0 and 180\u00b0, whereas almost no effect is felt at a dihedral angle of 120\u00b0. The effect of a methyl group on a \u03b3 -fluorine is to strongly shift the resonance downfield when fluorine and methyl group are in a 1, 3 - diaxial-like relationship. Molecular orbital calculations of fluorine shielding in a variety of molecules were carried out using the formalism developed by Pople; the results are, at best, in modest agreement with experiment.
\r\n" }, { "name": "Desai, Satish Vithal", "degree": "PhD", "year": "1969", "title": "I. Thermodynamic and Kinetic Behavior of an Argon Plasma Jet. II. Decomposition of Nitric Oxide between 1300-1750\u00b0K in an Argon Plasma", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222016-153354943", "creators": [ { "name": { "family": "Desai", "given": "Satish Vithal" }, "id": "Desai-Satish-Vithal", "display_name": "Desai, Satish Vithal" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZDNV-X816", "abstract": "In the first part of the study, an RF coupled, atmospheric pressure, laminar plasma jet of argon was investigated for thermodynamic equilibrium and some rate processes.
\r\n\r\nImproved values of transition probabilities for 17 lines of argon I were developed from known values for 7 lines. The effect of inhomogeneity of the source was pointed out.
\r\n\r\nThe temperatures, T, and the electron densities, ne , were determined spectroscopically from the population densities of the higher excited states assuming the Saha-Boltzmann relationship to be valid for these states. The axial velocities, vz, were measured by tracing the paths of particles of boron nitride using a three-dimentional mapping technique. The above quantities varied in the following ranges: 1012 \u02c2 ne \u02c2 1015 particles/cm3, 3500 \u02c2 T \u02c2 11000 \u00b0K, and 200 \u02c2 vz \u02c2 1200 cm/sec.
\r\n\r\nThe absence of excitation equilibrium for the lower excitation population including the ground state under certain conditions of T and ne was established and the departure from equilibrium was examined quantitatively. The ground state was shown to be highly underpopulated for the decaying plasma.
\r\n\r\nRates of recombination between electrons and ions were obtained by solving the steady-state equation of continuity for electrons. The observed rates were consistent with a dissociative-molecular ion mechanism with a steady-state\r\nassumption for the molecular ions.
\r\n\r\nIn the second part of the study, decomposition of NO was studied in the plasma at lower temperatures. The mole fractions of NO denoted by xNO were determined gas-chromatographically and varied between 0.0012 \u02c2 xNO \u02c2 0.0055. The temperatures were measured pyrometrically and varied between 1300 \u02c2 T \u02c2 1750\u00b0K. The observed rates of decomposition were orders of magnitude greater than those obtained by the previous workers under purely thermal reaction conditions. The overall activation energy was about 9 kcal/g mol which was considerably lower than the value under thermal conditions. The effect of excess nitrogen was to reduce the rate of decomposition of NO and to increase the order of the reaction with respect to NO from 1.33 to 1.85. The observed rates were consistent with a chain mechanism in which atomic nitrogen and oxygen act as chain carriers. The increased rates of decomposition and the reduced activation energy in the presence of the plasma could be explained on the basis of the observed large amount of atomic nitrogen which was probably formed as the result of reactions between excited atoms and ions of argon and the molecular nitrogen.
\r\n\r\n" }, { "name": "Gillham, Robert Allen", "degree": "PhD", "year": "1969", "title": "Alkylation of Ketones with 3-Bromomethyl-l, 2-Benzisothiazoles", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222016-113055066", "creators": [ { "name": { "family": "Gillham", "given": "Robert Allen" }, "id": "Gillham-Robert-Allen", "display_name": "Gillham, Robert Allen" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M56P-Z605", "abstract": "The synthesis of 3-bromomethyl-1,2-benzisothiazole and its 5- and 7-methoxy derivatives has been accomplished. In alkylation reactions, these bromides were found to behave much like benzylic bromides; and in this respect they have been used successfully to alkylate strongly basic enolates, thus introducing a latent \u03b2-phenylethyl moiety in situations where \u03b2-phenylethyl bromide and phenacyl bromide give at best poor yields of alkylated product. In several cases, degradative procedures have been devised to remove the heteroatoms from the benzisothiazoyl system to provide the actual \u03b2-phenylethyl fragment; however, no generally applicable degradative method has yet been developed.\r\n" }, { "name": "Grand, Paul Sheldon", "degree": "PhD", "year": "1969", "title": "The Structural Elucidation of a Proposed Intermediate in the Stereoselective Synthesis of dl-Desoxypodocarpic Acid", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222016-105427770", "creators": [ { "name": { "family": "Grand", "given": "Paul Sheldon" }, "id": "Grand-Paul-Sheldon", "display_name": "Grand, Paul Sheldon" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YBB4-6J75", "abstract": "The hydroxyketone C-3, an intermediate in the stereo-selective total synthesis of dl-Desoxypodocarpic acid (ii), has been shown by both degradative and synthetic pathways to rearrange in the presence of base to diosphenol E-1 (5-isoabietic acid series). The exact spatial arrangements of the systems represented by formulas C-3 and E-1 have been investigated (as the p-bromobenzoates) by single-crystal X-ray diffraction analyses. The hydroxyketone F-1, the proposed intermediate in the rearrangement, has been synthesized. Its conversion to diosphenol E-1 has been studied, and a single-crystal analysis of the p-bromobenzoate derivative has been performed. The initially desired diosphenol C-6 has been prepared, and has been shown to be stable to the potassium t-butoxide rearrangement conditions. Oxidative cleavage of diosphenol E-1 and subsequent cyclization with the aid of polyphosphoric acid has been shown to lead to keto acid I-2 (benzobicyclo [3.3.1] nonane series) rather than keto acid H-2 (5-isoabietic acid series).
\r\n\r\n" }, { "name": "Hanson, David Marvin", "degree": "PhD", "year": "1969", "title": "Energy States and Intermolecular Integrations in Molecular Aggregates--Crystalline Naphthalene", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022017-101853292", "creators": [ { "name": { "family": "Hanson", "given": "David Marvin" }, "id": "Hanson-David-Marvin", "display_name": "Hanson, David Marvin" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4GN0-9K47", "abstract": "The stationary states of condensed systems such as crystals\r\nare characterized by energy bands. These energy bands are described\r\nby a dispersion relation and a density function. Within the Frenkel\r\ntight-binding method, the physical quantities that determine the band\r\nstructure are the intermolecular resonance interactions.
\r\n\r\nThe density functions for the first excited singlet states of\r\ncrystalline benzene and naphthalene are determined experimentally\r\nfrom spectral data involving band \u2194 band transitions. The experimental\r\nresults are not in complete agreement with a transition\r\noctopole model for the intermolecular interactions.
\r\n\r\n\r\nMixed molecular crystals provide theoretically and experimentally\r\ntractable systems for studying the properties of molecular\r\naggregates. This knowledge is basic to understanding the liquid and\r\nbiological states and may in the future be of significant technological\r\nimportance. Spectroscopic observations on isotopic mixed crystals\r\nof naphthalene are made to determine the energy of the crystal states\r\nthat correlate with the 1B2u state of the free naphthalene molecule.\r\nThe spectral data for the dilute crystals are interpreted in terms of\r\na one-particle Green's function and are consistent with the band\r\nstructure as observed in band \u2194 band transitions. The transition\r\nenergies of guest levels disagree with a model involving configuration\r\ninteraction with charge transfer states. New theoretical models are\r\nsuggested, and the data available for evaluating these models are\r\noutlined.
\r\n\r\n\r\nVery high resolution spectra at 4.2 \u00b0K reveal fine structure in\r\nthe 1B2u \u2190 1Ag and 3BIu \u2192 1Ag electromc trans1t10ns of the naphthalene\r\nmixed crystals. Some of the structure corresponds to the resonance\r\nsplitting of pairs of guest molecules in the host lattice. In the Frenkel\r\ntight-binding approximation, this structure gives directly the intermolecular\r\nexcitation transfer matrix elements responsible for the\r\nexciton mobilities and the energy band structures.
\r\n\r\n\r\nOptical spectra of 13CC5H6-C6H6 mixed crystals show that the\r\nshallow impurity 13CC5H6 shifts the 1B2u factor group components by\r\n2 cm-1 and increases the linewidth by 5 cm-1 in going from 6% to 50%\r\n13CC5H6. The effect is explained qualitatively by an extension of the\r\nFrenkel exciton theory to the mixed crystal system.
\r\n\r\n\r\nExciton structure in the two lowest ungerade triplet states of\r\ncrystalline naphthalene is reported. For the lowest state the calculated \r\nsplitting of 40 cm-1 is in good agreement with the experimental\r\nresult.
\r\n\r\n\r\nThe Raman scattering tensor for each vibrational mode is\r\ndetermined by polarized Raman scattering from oriented single\r\ncrystals. The experimental data when compared with the\r\nphosphorescence spectrum of the C10H8 - C10D8 mixed crystal allow\r\nunambiguous vibrational assignments to be made and provide a\r\nmeasure of the intermolecular interactions in the crystal. It is\r\nfound that the crystal effects on the gerade vibrations are small.\r\nFrequency shifts are 2-4 cm-1; exciton splittings are less than\r\n1 cm-1; and intensities are described qualitatively by the oriented\r\ngas model.
" }, { "name": "Hudson, Bruce Samuel", "degree": "Masters", "year": "1969", "title": "Studies of Circular and Catenated Circular DNA", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-114048109", "creators": [ { "name": { "family": "Hudson", "given": "Bruce Samuel" }, "id": "Hudson-Bruce-Samuel", "display_name": "Hudson, Bruce Samuel" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1JDD-AM72", "abstract": "No abstract." }, { "name": "Hudson, Mary Suzanne Speck", "degree": "Masters", "year": "1969", "title": "Applications of a Method for the Analyses of Many-Electron Wavefunctions", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032010-093742868", "creators": [ { "name": { "family": "Hudson", "given": "Mary Suzanne Speck" }, "id": "Hudson-Mary-Suzanne-Speck", "display_name": "Hudson, Mary Suzanne Speck" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/99MP-BR64", "abstract": "We show how the method of successive partial orthogonalizations can be used to obtain approximate Hartree-Fock (HF) pair functions directly from the hydrogenic pair functions. The method is more practical than accurate but with the explicit Z-dependence of the bar -nuclei pair functions just eleven such pair functions are needed to obtain an approximate HF pair function by this method for any pair of orbitals in any first row atom. We use the same method of analysis to extract HF orbitals directly from suitable trial functions for the He-He system at several internuclear distances and and also for the auto-ionizing 2s^2 2p^2 states of helium. This approach avoids a separate variational calculation for the HF wave function and furthermore it provides approximate HF pair functions for these auto-ionizing states." }, { "name": "Larsen, Alvin Henry", "degree": "PhD", "year": "1969", "title": "I. Combinatorial Theory of Nonlinear Graphs, Applied to the Virial Equation of State. II. Chemical Thermodynamics of Open Systems", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08312006-091634", "creators": [ { "name": { "family": "Larsen", "given": "Alvin Henry" }, "id": "Larsen-Alvin-Henry", "display_name": "Larsen, Alvin Henry" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/SCDN-4B19", "abstract": "PART I:
\r\n\r\nBy extension of the concept of a linear graph, as a topological configuration of vertexes with lines (2-bonds) connecting certain pairs of them, a nonlinear graph is defined to include also associations of certain triplets of the vertexes, or 3-bonds, representable by topological \"areas\" of triangles; quadruplets, or 4-bonds, by \"volumes\" of tetrahedra; etc. The configurational part of the partition function, including nonadditivity effects or three-body and higher interactions in the potential energy of a configuration of molecules, may be expanded as a sum of integrals over products of cluster functions, corresponding to a sum of nonlinear graphs. Certain special types of graphs, called trees and stars, figure prominently in the combinatorial analysis. The nth virial coefficient corresponds to the sum of all stars on n vertexes. Since topologically equivalent graphs correspond to integrals which yield the same result upon integration, the nth virial coefficient corresponds also to the sum of all topologically distinct stars on n vertexes, each multiplied by the appropriate combinatorial coefficient.
\r\n\r\nDevelopment of the combinatorial theory for nonlinear graphs, trees, and stars proceeds similarly to that forlinear graphs. An explicit formula for counting nonlinear graphs on distinguishable vertexes is obtained, and generating functions relate the numbers of graphs to the numbers of corresponding nonlinear trees and stars. A novel term, the cycle function, is defined; the triplet cycle function, for 3-bonds, is derived; and cycle functions are used in generalizing Polya's theorem to apply to nonlinear graphs with more than one type of bond present. A theorem is thus obtained which solves the problem of counting nonlinear graphs on indistinguishable vertexes, and a relationship between generating functions permits the number of corresponding trees to be calculated. All of these techniques are extended to apply to multicomponent systems and to rooted graphs and trees. Then the problem of counting stars on indistinguishable or multicomponent vertexes is solved by a systematic procedure. The numbers of such stars are also closely approximated by a simple formula. Including 2- and 3-bonds only, the number of distinct stars on n = 3 indistinguishable vertexes is 5; for n = 4, there are 72 topologically distinct stars; and for n = 5, 10,346.
\r\n\r\nBecause of the rapidly increasing number and complexity of the calculations, a practical limit for actual calculations involving any nonadditivity effects for a pure substance is the fourth virial coefficient. For multicomponent systems, the numbers of topologically distinct stars are always greater than for systems of a single component; hence even more compelling reasons would then be necessary to justify calculation of the fourth virial coefficient including three-body nonadditivity effects.
\r\n\r\nPART II:
\r\n\r\nGeneral thermodynamic expressions for partial derivatives of extent of reaction with respect to external composition perturbations by a single species, for multicomponent, multiple-reaction systems constrained to paths of chemical equilibrium under various conditions, are obtained as the solution of a set of simultaneous, linear algebraic equations. The corresponding heat and temperature effects follow immediately. Derivatives of the extent of reaction are evaluated for ideal solutions. For multicomponent composition perturbations, the derivatives result from a linear combination of those for perturbations by a single species, each weighted by the net mole fraction of the given species in the streams crossing the boundary. Possible applications of the thermodynamic expressions include behavior of open systems under externally introduced composition perturbations, error analysis, and optimization of yield.
" }, { "name": "McFarland, James Thomas", "degree": "PhD", "year": "1969", "title": "Part I. The Structure of 1,2-Dimethylnorbornyl Cation. Part II. The Relative Stabilities of Some Tertiary Aliphatic Cations", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03292017-092122515", "creators": [ { "name": { "family": "McFarland", "given": "James Thomas" }, "id": "McFarland-James-Thomas", "display_name": "McFarland, James Thomas" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NJST-QK11", "abstract": "Part I.
\r\n\r\nThe pmr spectrum of 1,2-dimethylnorbornyl cation\r\nindicates that the Wagner-Meerwein rearrangement is rapid\r\non the nmr time scale at -100\u00b0 C. Furthermore the protons\r\nat C-6 are deshielded by 1.3 ppm with respect to the\r\nprotons at C-5. This is consistent with the nonclassical\r\nstructure for this cation.
\r\n\r\nPart II.
\r\n\r\nMixtures of organic chlorides have been forced to\r\ncompete for less than one equivalent of antimony penta-fluoride\r\nin order to judge relative cation stabilities.\r\nThe results indicate no stabilization of 2,3,3-trimethyl-\r\n2-butyl cation by methyl bridging. However methylene\r\nbridging seems to stabilize 1,2-dimethylnorbornyl cation.\r\nThe qualitative order of cation stabilities measured by\r\nthis method is not always the same as that measured by\r\nsolvolysis experiments.
" }, { "name": "Metzger, Robert Melville", "degree": "PhD", "year": "1969", "title": "Crystal Coulomb Energies: I. Organic Donor-Acceptor Complexes - a Review. II. Classical Ewald Calculations of the Coulomb Binding Energy of Four Donor-Acceptor Crystals and Wurster's Blue Perchlorate. III. A Rapid-Convergence Quantum-Mechanical Formalism for Crystal Electronic Energies", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03172014-093730629", "creators": [ { "name": { "family": "Metzger", "given": "Robert Melville" }, "id": "Metzger-Robert-Melville", "display_name": "Metzger, Robert Melville" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VD9B-K107", "abstract": "Chapter I
\r\n\r\nTheories for organic donor-acceptor (DA) complexes in\r\nsolution and in the solid state are reviewed, and compared with\r\nthe available experimental data. As shown by McConnell et al. (Proc.\r\nNatl. Acad. Sci. U.S., 53, 46-50 (1965)), the DA crystals fall\r\ninto two classes, the holoionic class with a fully or almost\r\nfully ionic ground state, and the nonionic class with little or\r\nno ionic character. If the total lattice binding energy 2\u03b51\r\n(per DA pair) gained in ionizing a DA lattice exceeds the cost\r\n2\u03b5o of ionizing each DA pair, \u03b51 + \u03b5o less than 0, then the lattice is\r\nholoionic. The charge-transfer (CT) band in crystals and in\r\nsolution can be explained, following Mulliken, by a second-order\r\nmixing of states, or by any theory that makes the CT transition\r\nstrongly allowed, and yet due to a small change in the ground\r\nstate of the non-interacting components D and A (or D+ and A-).\r\nThe magnetic properties of the DA crystals are discussed.
\r\n\r\nChapter II
\r\n\r\nA computer program, EWALD, was written to calculate by the\r\nEwald fast-convergence method the crystal Coulomb binding energy\r\nEC due to classical monopole-monopole interactions for crystals\r\nof any symmetry. The precision of EC values obtained is high:\r\nthe uncertainties, estimated by the effect on EC of changing the\r\nEwald convergence parameter \u03b7, ranged from \u00b1 0.00002 eV to\r\n\u00b1 0.01 eV in the worst case. The charge distribution for organic\r\nions was idealized as fractional point charges localized at the\r\ncrystallographic atomic positions: these charges were chosen\r\nfrom available theoretical and experimental estimates. The\r\nuncertainty in EC due to different charge distribution models is\r\ntypically \u00b1 0.1 eV (\u00b1 3%): thus, even the simple H\u00fcckel model\r\ncan give decent results.
\r\n\r\nEC for Wurster's Blue Perchl orate is -4.1 eV/molecule: the\r\ncrystal is stable under the binding provided by direct Coulomb\r\ninteractions. EC for N-Methylphenazinium Tetracyanoquino-\r\ndimethanide is 0.1 eV: exchange Coulomb interactions, which cannot\r\nbe estimated classically, must provide the necessary binding.
\r\n\r\nEWALD was also used to test the McConnell classification\r\nof DA crystals. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para-\r\nphenylenediamine: 7,7,8,8-Tetracyanoquinodimethan) EC = -4.0\r\neV while 2\u03b5o = 4.65 eV: clearly, exchange forces must provide\r\nthe balance. For the holoionic (1:1)-(N,N,N',N'-Tetramethyl-para-\r\nphenylenediamine:para-Chloranil) EC = -4.4 eV, while 2\u03b5o = 5.0 eV:\r\nagain EC falls short of 2\u03b51. As a Gedankenexperiment, two nonionic\r\ncrystals were assumed to be ionized: for (1:1)-(Hexamethyl-\r\nbenzene:para-Chloranil) EC = -4.5 eV, 2\u03b5o = 6.6 eV; for (1:1)-\r\n(Napthalene:Tetracyanoethylene) EC = -4.3 eV, 2\u03b5o = 6.5 eV. Thus,\r\nexchange energies in these nonionic crystals must not exceed 1 eV.
\r\n\r\nChapter III
\r\n\r\nA rapid-convergence quantum-mechanical formalism is\r\nderived to calculate the electronic energy of an arbitrary\r\nmolecular (or molecular-ion) crystal: this provides estimates of\r\ncrystal binding energies which include the exchange Coulomb inter-\r\nactions. Previously obtained LCAO-MO wavefunctions for the\r\nisolated molecule(s) (\"unit cell spin-orbitals\") provide the\r\nstarting-point. Bloch's theorem is used to construct \"crystal\r\nspin-orbitals\". Overlap between the unit cell orbitals localized\r\nin different unit cells is neglected, or is eliminated by L\u00f6wdin\r\northogonalization. Then simple formulas for the total kinetic\r\nenergy Q^(XT)_\u03bb, nuclear attraction [\u03bb/\u03bb]XT, direct Coulomb [\u03bb\u03bb/\u03bb'\u03bb']XT\r\nand exchange Coulomb [\u03bb\u03bb'/\u03bb'\u03bb]XT integrals are obtained, and\r\ndirect-space brute-force expansions in atomic wavefunctions are\r\ngiven. Fourier series are obtained for [\u03bb/\u03bb]XT, [\u03bb\u03bb/\u03bb'\u03bb']XT, and\r\n[\u03bb\u03bb/\u03bb'\u03bb]XT with the help of the convolution theorem; the Fourier\r\ncoefficients require the evaluation of Silverstone's two-center\r\nFourier transform integrals. If the short-range interactions are\r\ncalculated by brute-force integrations in direct space, and the\r\nlong-range effects are summed in Fourier space, then rapid convergence\r\nis possible for [\u03bb/\u03bb]XT, [\u03bb\u03bb/\u03bb'\u03bb']XT and [\u03bb\u03bb'/\u03bb'\u03bb]XT.\r\nThis is achieved, as in the Ewald method, by modifying each\r\natomic wavefunction by a \"Gaussian convergence acceleration\r\nfactor\", and evaluating separately in direct and in Fourier space\r\nappropriate portions of [\u03bb/\u03bb]XT, etc., where some of the portions\r\ncontain the Gaussian factor.
\r\n\r\n\r\n\r\n" }, { "name": "Morrison, Malcolm Cameron", "degree": "PhD", "year": "1969", "title": "I. The Effects of Variations in Certain Parameters Upon the Efficiency of In Vivo Hemodialysis with a Kiil Dialyzer. II. Interfacial Structure of Concurrent Air-Water Flow in a Two-Inch Diameter Horizontal Tube", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302014-141243233", "creators": [ { "name": { "family": "Morrison", "given": "Malcolm Cameron" }, "id": "Morrison-Malcolm-Cameron", "display_name": "Morrison, Malcolm Cameron" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9ERD-DM13", "abstract": "Part I
\r\n\r\nRegression analyses are performed on in vivo hemodialysis data\r\nfor the transfer of creatinine, urea, uric acid and inorganic phosphate\r\nto determine the effects of variations in certain parameters on the\r\nefficiency of dialysis with a Kiil dialyzer. In calculating the mass\r\ntransfer rates across the membrane, the effects of cell-plasma mass\r\ntransfer kinetics are considered. The concept of the effective permeability\r\ncoefficient for the red cell membrane is introduced to\r\naccount for these effects. A discussion of the consequences of neglecting\r\ncell-plasma kinetics, as has been done to date in the literature, is\r\npresented.
\r\n\r\nA physical model for the Kiil dialyzer is presented in order to\r\ncalculate the available membrane area for mass transfer, the linear\r\nblood and dialysate velocities, and other variables. The equations\r\nused to determine the independent variables of the regression analyses\r\nare presented. The potential dependent variables in the analyses are\r\ndiscussed.
\r\n\r\nRegression analyses were carried out considering overall mass-transfer\r\ncoefficients, dialysances, relative dialysances, and relative\r\npermeabilities for each substance as the dependent variables. The\r\nindependent variables were linear blood velocity, linear dialysate\r\nvelocity, the pressure difference across the membrane, the elapsed\r\ntime of dialysis, the blood hematocrit, and the arterial plasma\r\nconcentrations of each substance transferred. The resulting correlations\r\nare tabulated, presented graphically, and discussed. The implications\r\nof these correlations are discussed from the viewpoint of a research\r\ninvestigator and from the viewpoint of patient treatment.
\r\n\r\nRecommendations for further experimental work are presented.
\r\nPart II
\r\n\r\nThe interfacial structure of concurrent air-water flow in\r\na two-inch diameter horizontal tube in the wavy flow regime has\r\nbeen measured using resistance wave gages. The median water\r\ndepth, r.m.s. wave height, wave frequency, extrema frequency,\r\nand wave velocity have been measured as functions of air and water\r\nflow rates. Reynolds numbers, Froude numbers, Weber numbers, and\r\nbulk velocities for each phase may be calculated from these measurements. \r\nNo theory for wave formation and propagation available\r\nin the literature was sufficient to describe these results.
\r\n\r\nThe water surface level distribution generally is not adequately\r\nrepresented as a stationary Gaussian process. Five types\r\nof deviation from the Gaussian process function were noted\r\nin this work. The presence of the tube walls and the relatively\r\nlarge interfacial shear stresses precludes the use of simple\r\nstatistical analyses to describe the interfacial structure. A\r\ndetailed study of the behavior of individual fluid elements near\r\nthe interface may be necessary to describe adequately wavy two-phase\r\nflow in systems similar to the one used in this work.
\r\n" }, { "name": "Murayama, Stanley Tetsu", "degree": "PhD", "year": "1969", "title": "I. Synthesis of dl-cis-Tetrahydroeremophilone. II. Studies on Systems Free from Angular Strain", "advisor": "Brown, Morris", "url": "https://resolver.caltech.edu/CaltechTHESIS:03232017-140452739", "creators": [ { "name": { "family": "Murayama", "given": "Stanley Tetsu" }, "id": "Murayama-Stanley-Tetsu", "display_name": "Murayama, Stanley Tetsu" } ], "advisors": [ { "name": { "family": "Brown", "given": "Morris" }, "id": "Brown-Morris", "role": "advisor", "display_name": "Brown, Morris" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EF19-GE34", "abstract": "I. The total synthesis of racemic cis-tetrahydroeremophilone (17) has been achieved. The key feature of the synthesis was a solvolytic cyclization that proceeded through a symmetrical cation 41 and gave rise to two major products, one of which had the stereochemistry required for the synthesis of tetrahydroeremophilone.
\r\n\r\nII. Attempts on the synthesis of the alcohol 1 have been investigated in three related reaction sequences (Schemes 1, 4, 5, and 6). Although none of the reaction sequences gave the desired alcohol 1 that was intended for use in a solvolysis study, an unexpected product, the keto acetate 48, resulted in one sequence and afforded adamantanone (44) upon chromatography on alumina.
\r\n\r\n" }, { "name": "Nelson, James Henry", "degree": "PhD", "year": "1969", "title": "Studies of the Conformational Properties of Dinucleoside Monophosphates and Oligoribonucleotides by Proton Magnetic Resonance", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03232017-153915578", "creators": [ { "name": { "family": "Nelson", "given": "James Henry" }, "id": "Nelson-James-Henry", "display_name": "Nelson, James Henry" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3XNW-2X84", "abstract": "The structural and conformational properties of several dinucleoside\r\nmonophosphates and oligonucleotides in aqueous solution have\r\nbeen studied by proton magnetic resonance spectroscopy. Specifically,\r\nthe role of intramolecular base-stacking interactions and other intramolecular\r\nforces in the determination of the conformational properties\r\nof these molecules has been investigated; and the results of these\r\nstudies are discussed in relation to the structural properties of biologically\r\nsignificant nucleic acids.
\r\n\r\nThe proton magnetic resonance spectrum of adenylyl-(3'\u21925')-adenosine\r\n(ApA) was studied as a function of concentration, temperature,\r\nsolution pH, and concentration of added purine. The results of\r\nthese studies indicate that the stacking interaction between the two\r\nadenine rings in ApA is relatively strong and that the adenine rings are\r\nstacked with each of the bases preferentially oriented in the anti conformation\r\nas in a similar dApdA (dA = deoxyadenosine) segment in\r\ndouble helical DNA. In the concentration studies, ApA was found to\r\nself-associate extensively in aqueous solution via vertical stacking of\r\nthe planar bases. The purine-binding studies indicate that ApA-purine\r\ncomplexes are formed via purine-adenine base-stacking and evidence\r\nwas obtained for the formation of a purine-intercalated dinucleotide\r\ncomplex in neutral solution.
\r\n\r\nSimilar proton magnetic resonance studies of adenylyl-(3'\u21925')-guanosine\r\n(ApG) and guanylyl-(3'\u21925')-adenosine (GpA) indicate that each\r\nof these dinucleotides is strongly stacked intramole cularly at 30\u00b0 and\r\nneutral pH with the bases preferentially oriented in the anti conformation.\r\nThe base-stacking interaction in these molecule s is somewhat\r\nweaker than the adenine-adenine base-stacking in ApA. These studies\r\nalso provided information concerning conformational changes which\r\noccur in the ribose rings of the dinucleotides as a result of changes in\r\nthe intramolecular base-stacking; and this phenomenon is discussed in\r\ndetail.
\r\n\r\nThe concentration dependence of the proton magnetic resonance\r\nspectra of adenylyl-(3'\u21925')-uridine (ApU) and uridylyl-(3'\u21925')-\r\nadenosine (UpA) has been used to determine the mode of self-association\r\nof these dinucleotides and the dimerization equilibrium constant of the\r\nself-association process. The binding of 6-methylpurine to ApU was\r\nused in additional studies of the nature of purine-dinucleotide complexes\r\nand the effect of complex formation on the spectra of these molecules.
\r\n\r\nFinally, the intramolecular base-stacking inte ractions in ApApA\r\nand ApApApA were shown to be comparable to those in ApA. The study\r\nof these molecules indicates that each assumes a molecular configuration\r\nsimilar to an analagous segment of double helical DNA.
\r\n\r\nThe results of these studies explicitly demonstrate the importance\r\nof base-stacking interactions in determining the conformational\r\nproperties of nucleic acids and their derivatives in aqueous solution.
" }, { "name": "Parr, Christopher Alan", "degree": "PhD", "year": "1969", "title": "Classical Dynamics of Triatomic Systems: I. Dynamics of Energized Harmonic Molecules. II. Dynamics of Energized Anharmonic Molecules. III. The H + DX Reactions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-04122007-082248", "creators": [ { "name": { "family": "Parr", "given": "Christopher Alan" }, "id": "Parr-Christopher-Alan", "display_name": "Parr, Christopher Alan" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NDDH-1D34", "abstract": "Part I. Dynamics of Energized Harmonic Molecules:
\r\n\r\nThe classical equations of motion of some bent triatomic harmonic molecular models are integrated numerically to investigate the assumptions underlying contemporary theories of unimolecular reaction rates. The small vibration and weak coupling approximations are shown to be inadequate for energies near dissociation, but reaction frequencies, based upon a modification of the former approximation, are seen to be in good agreement with the model's actual reaction frequencies. The effects of rotation upon intramolecular energy exchange are shown to be non-negligible. The effects of bond anharmonicity were not included in this paper.
\r\n\r\nPart II. Dynamics of Energized Anharmonic Molecules:
\r\n\r\nThe classical equations of motion of two anharmonic bent triatomic molecular models are integrated numerically. It is found that at dissociative energies, the intramolecular energy transfer rate is the frequency with which any two bonds compress. The normal mode description of the motion is observed to be entirely inadequate. Molecular lifetimes are shown to be unstable to small perturbations in the initial conditions for the molecular trajectory. This instability may imply gross differences in the classical and quantal lifetimes of energized molecules.
\r\n\r\nPart III. The H + DX Reactions:
\r\n\r\nA Sato surface, free of spurious wells, is proposed for the reaction H + DBr. The abstraction fraction, the ratio of abstraction to total reaction rate, is shown to have similar large temperature dependence from activated complex theory that is found from classical trajectory results. The latter yield broad product energy distributions and reaction cross sections which peak (at ~ 1 eV relative energies) at 3 and 13 aO2 for abstraction and exchange, respectively.
" }, { "name": "Rathjen, Nancy Katherine", "degree": "Masters", "year": "1969", "title": "An Investigation of the System Cr(III)/Cr(II) by Digital Polarography, at Different Cr(III) Concentrations, at Varying pH, and in Different Supporting Electrolytes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05042010-123622070", "creators": [ { "name": { "family": "Rathjen", "given": "Nancy Katherine" }, "id": "Rathjen-Nancy-Katherine", "display_name": "Rathjen, Nancy Katherine" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N5V3-H153", "abstract": "One of the implications of Marcus theory of electron transfer is that d, the electrochemical transfer coefficient, would not be constant, but would be a function of potential. Recent work has tended to confirm this implication.\r\n\r\nTo examine this possible potential-dependence d, the system Cr(III)/Cr(II) was investigated by digital polarography, at different Cr(III) concentrations, at varying pH, and in different supporting electrolytes. Most of the resulting rate data do suggest a potential-dependence of d.\r\n\r\nApparent heats of activation were obtained for three of the supporting electrolytes investigated, and from these a calculation was made of the magnitude of the potential-dependence predicted by Marcus theory. There was little correlation between the magnitude of the potential-dependence predicted by Marcus theory, and that actually found.\r\n" }, { "name": "Rice, James Kinsey", "degree": "PhD", "year": "1969", "title": "Low Energy, High Resolution, Variable Angle, Electron Impact Spectroscopy", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechETD:etd-09272002-155546", "creators": [ { "name": { "family": "Rice", "given": "James Kinsey" }, "id": "Rice-James-Kinsey", "display_name": "Rice, James Kinsey" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/36HJ-RS93", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA low-energy, variable angle, high-resolution, electron-impact spectrometer has been designed, constructed, and put into operation. Its performance is discussed and is found to compare favorably with that of similar instruments [...].\r\n\r\nThe differential scattering cross sections (DCS) for the electron-impact excitation of helium and five molecules [(N2, CO, H2, C2H2, and C2H4)] have been measured as a function of incident electron kinetic energy (from about 20 to 60 eV) and scattering angle (from about -30[degrees] to +80[degrees]) with a resolution of 0.04 to 0.15 eV. These studies included the observation of twenty-nine electronically excited states, including 12 singlet [...] triplet transitions.\r\n\r\nComparisons of these results with presently available theoretical predictions have indicated the inadequacy of the latter. In addition, a theoretical calculation of the exchange excitation of ethylene [...] by electron-impact is carried out via the Ochkur-Rudge, approximation [...] and is compared with experiment.\r\n\r\nThe vibrational structure within several electronic bands has been resolved, and the relative vibrational intensities have been compared with optical and calculated relative Franck-Condon factors. Discrepancies, due to underlying forbidden transitions, have been noted in [H2], acetylene, and ethylene.\r\n\r\nSome general \"spectroscopic rules\" for the identification of spin-forbidden excitations observed by electron-impact are presented. These rules are derived from an examination of the angular dependencies of the differential cross sections for twenty-six known transitions. On this basis, one state in [N2 (...)] has been unequivocally identified as a triplet, and two previously unknown low-lying triplet states in [C2H2] at 5.2 eV and 6.1 eV have been detected and characterized." }, { "name": "Schaefer, Phillip Cuthbert", "degree": "PhD", "year": "1969", "title": "Squalene Cyclization", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10032002-124237", "creators": [ { "name": { "family": "Schaefer", "given": "Phillip Cuthbert" }, "id": "Schaefer-Phillip-Cuthbert", "display_name": "Schaefer, Phillip Cuthbert" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GV74-NT60", "abstract": "It has been observed that the proton, which is located at C-14 in squalene or C-13 in the \"presterol cation,\" migrates less than 10% of the time (with a confidence level of 74%) to C-20 in lanosterol, and therefore 90% of the time (with a confidence level of 74%) to C-17 in lanosterol. If enzymatically controlled reactions are stereospecific, then at C-13/C17/C-20 in the \"presterol cation,\" there are two sequential 1, 2-migrations during the backbone rearrangement to form lanosterol. A theoretical interpretation of this observation, which reflects on the stereochemistry of the C-18/C-19 double bond of squalene just prior to cyclization, is presented.
\r\n\r\nA theoretical discussion of the minimal requirements for binding squalene-2, 3-oxide to an enzyme in order to obtain complete stereochemical control over the product is presented.
\r\n" }, { "name": "Smelser, Stephen Chester", "degree": "PhD", "year": "1969", "title": "An X-Ray Diffraction Study of the Structure of Argon in the Dense Liquid Region", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022017-150552931", "creators": [ { "name": { "family": "Smelser", "given": "Stephen Chester" }, "id": "Smelser-Stephen-Chester", "display_name": "Smelser, Stephen Chester" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/YYW1-T338", "abstract": "X-ray diffraction measurements were made on argon at six\r\nstates in the general liquid region below the critical pressure at\r\ndensities between 0.910 to 1.261 gm/cc and at temperatures between\r\n108 to 143 \u00b0K. The intensity patterns exhibited three distinct\r\nmaxima at s values of 1.91 \u00b1 .02, 3.68 \u00b1 .06 and 5.43 \u00b1 .16 \u00c5 -1.\r\nThe intensity patterns were Fourier transformed to the net radial\r\ndistribution function and the direct correlation function. The\r\nfunctions, 4\u03c0r2\u03c1h(r), showed 3 maxima at low densities and 4 at the\r\nhigh densities at values of r of 3.85 \u00b1 0.05, 7.29 \u00b1 .10, 10.75 \u00b1 .45\r\nand 14.1 \u00b1 .5 \u00c5. A subsidiary maximum between the first and second\r\nmain peaks was observed to increase in prominence and disappear\r\nsystematically as the density increased. It was not noticeably\r\nevident at either the lowest or highest density. The first zero of\r\nthe direct correlation function was at an r value of 3.34 \u00b1 .03 \u00c5,\r\nwhereas the first maximum was at 3.78 \u00b1 .06 \u00c5. Unlike previous\r\ndeterminations of C(r) in this laboratory, the direct correlation\r\nfunction exhibited secondary features on the shoulder of the main peak.\r\nAt the highest density the direct correlation function goes negative\r\nnear 6 \u00c5. The intermolecular potential function was calculated from\r\nthe data using the Percus-Yevick equation. At the lowest density the\r\npotential predicted in this way closely resembled the Lennard-Jones\r\n12-6 potential for argon. However, the well-depths of these predicted\r\npotentials diminished rapidly with increasing density and decreasing\r\ntemperature from 118.0 \u00b0K at \u03c1 = .910 to 68.6 \u00b0K at \u03c1 = 1.261 gm/cc.\r\nComparisons of the direct correlation function and the radial\r\ndistribution function with analytic predictions based on the Lennard-Jones\r\npotential and the P-Y equation indicated internal consistency\r\nat the lower densities. A comparison of the experimental radial\r\ndistribution function at the highest density, with one calculated\r\nby molecular dynamics, indicated substantial agreement.\r\n\r\n" }, { "name": "Tsai, Shirley Shieu-lang Cheng", "degree": "PhD", "year": "1969", "title": "I. Phosphorescence and the True Lifetime of Triplet States in Fluid Solutions. II. Why is Condensed Oxygen Blue?", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:02192016-140307419", "creators": [ { "name": { "family": "Tsai", "given": "Shirley Shieu-lang Cheng" }, "id": "Tsai-Shirley-Shieu-lang-Cheng", "display_name": "Tsai, Shirley Shieu-lang Cheng" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5KQV-4R78", "abstract": "I. PHOSPHORESCENCE AND THE TRUE LIFETIME OF TRIPLET\r\nSTATES IN FLUID SOLUTIONS
\r\n\r\nPhosphorescence has been observed in a highly purified fluid solution of naphthalene in 3-methylpentane (3-MP). The phosphorescence lifetime of C10H8 in 3-MP at -45 \u00b0C was found to be 0.49 \u00b1 0.07 sec, while that of C10D8 under identical conditions is 0.64 \u00b1 0.07 sec. At this temperature 3-MP has the same viscosity (0.65 centipoise) as that of benzene at room temperature. It is believed that even these long lifetimes are dominated by impurity quenching mechanisms. Therefore it seems that the radiationless decay times of the lowest triplet states of simple aromatic hydrocarbons in liquid solutions are sensibly the same as those in the solid phase. A slight dependence of the phosphorescence lifetime on solvent viscosity was observed in the temperature region, -60\u00b0 to -18\u00b0C. This has been attributed to the diffusion-controlled quenching of the triplet state by residual impurity, perhaps oxygen. Bimolecular depopulation of the triplet state was found to be of major importance over a large part of the triplet decay.
\r\n\r\nThe lifetime of triplet C10H8 at room temperature was also measured in highly purified benzene by means of both phosphorescence and triplet-triplet absorption. The lifetime was estimated to be at least ten times shorter than that in 3-MP. This is believed to be due not only to residual impurities in the solvent but also to small amounts of impurities produced through unavoidable irradiation by the excitation source. In agreement with this idea, lifetime shortening caused by intense flashes of light is readily observed. This latter result suggests that experiments employing flash lamp techniques are not suitable for these kinds of studies.
\r\n\r\nThe theory of radiationless transitions, based on Robinson's theory, is briefly outlined. A simple theoretical model which is derived from Fano's autoionization gives identical result.
\r\n\r\nIl. WHY IS CONDENSED OXYGEN BLUE?
\r\n\r\nThe blue color of oxygen is mostly derived from double transitions. This paper presents a theoretical calculation of the intensity of the double transition (a 1\u0394g) (a 1\u0394g)\u2190(X 3\u03a3g-) (X 3\u03a3g-), using a model based on a pair of oxygen molecules at a fixed separation of 3.81 \u00c5. The intensity enhancement is assumed to be derived from the mixing (a 1\u0394g) (a 1\u0394g) ~~~ (X 3\u03a3g-) (X 3\u03a3u-) and (a 1\u0394g) (1\u0394u) ~~~ (X 3\u03a3g-) (X 3\u03a3g-). Matrix elements for these interactions are calculated using a \u03c0-electron approximation for the pair system. Good molecular wavefunctions are used for all but the perturbing (B 3\u03a3u-) state, which is approximated in terms of ground state orbitals. The largest contribution to the matrix elements arises from large intramolecular terms multiplied by intermolecular overlap integrals. The strength of interaction depends not only on the intermolecular separation of the two oxygen molecules, but also as expected on the relative orientation. Matrix elements are calculated for different orientations, and the angular dependence is fit to an analytical expression. The theory therefore not only predicts an intensity dependence on density but also one on phase at constant density. Agreement between theory and available experimental results is satisfactory considering the nature of the approximation, and indicates the essential validity of the overall approach to this interesting intensity enhancement problem.
\r\n\r\n\r\n" }, { "name": "Weinzierl, Jon Edward", "degree": "PhD", "year": "1969", "title": "I. The 3.7 \u00c5 Crystal Structure of Horse Heart Ferricytochrome C. II. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing", "advisor": "Dickerson, Richard E.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252016-155336507", "creators": [ { "name": { "family": "Weinzierl", "given": "Jon Edward" }, "id": "Weinzierl-Jon-Edward", "display_name": "Weinzierl, Jon Edward" } ], "advisors": [ { "name": { "family": "Dickerson", "given": "Richard E." }, "id": "Dickerson-Richard-E", "role": "advisor", "display_name": "Dickerson, Richard E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TX4H-5788", "abstract": "I. The 3.7 \u00c5 Crystal Structure of Horse Heart Ferricytochrome C.
\r\n\r\nThe crystal structure of horse heart ferricytochrome c has been determined to a resolution of 3.7 \u00c5 using the multiple isomorphous replacement technique. Two isomorphous derivatives were used in the analysis, leading to a map with a mean figure of merit of 0.458. The quality of the resulting map was extremely high, even though the derivative data did not appear to be of high quality.
\r\n\r\nAlthough it was impossible to fit the known amino acid sequence to the calculated structure in an unambiguous way, many important features of the molecule could still be determined from the 3.7 \u00c5 electron density map. Among these was the fact that cytochrome c contains little or no \u03b1-helix. The polypeptide chain appears to be wound about the heme group in such a way as to form a loosely packed hydrophobic core in the molecule.
\r\n\r\nThe heme group is located in a cleft on the molecule with one edge exposed to the solvent. The fifth coordinating ligand is His 18 and the sixth coordinating ligand is probably neither His 26 nor His 33.
\r\n\r\nThe high resolution analysis of cytochrome c is now in progress and should be completed within the next year.
\r\n\r\nII. The Application of the Karle-Hauptman Tangent Formula to Protein Phasing.
\r\n\r\nThe Karle-Hauptman tangent formula has been shown to be applicable to the refinement of previously determined protein phases. Tests were made with both the cytochrome c data from Part I and a theoretical structure based on the myoglobin molecule. The refinement process was found to be highly dependent upon the manner in which the tangent formula was applied. Iterative procedures did not work well, at least at low resolution.
\r\n\r\nThe tangent formula worked very well in selecting the true phase from the two possible phase choices resulting from a single isomorphous replacement phase analysis. The only restriction on this application is that the heavy atoms form a non-centric cluster in the unit cell.
\r\n\r\nPages 156 through 284 in this Thesis consist of previously published papers relating to the above two sections. References to these papers can be found on page 155.
" }, { "name": "Winokur, Melvin", "degree": "PhD", "year": "1969", "title": "I. Configurational Stability and Redistribution Equilibria in Organomagnesium Compounds. II. Redistribution Equilibria in Organocadmium Compounds", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222016-080339846", "creators": [ { "name": { "family": "Winokur", "given": "Melvin" }, "id": "Winokur-Melvin", "display_name": "Winokur, Melvin" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3WWJ-ZC46", "abstract": "I. CONFIGURATIONAL STABILITY AND REDISTRIBUTION EQUILIBRIA IN ORGANOMAGNESIUM COMPOUNDS
\r\n\r\nThe dependence of the rate of inversion of a dialkylmagnesium compound on the solvent has been studied.
\r\n\r\nExamination of the temperature dependence of the nuclear magnetic resonance spectrum of 1-phenyl-2-propylmagnesium bromide in diethyl ether solution indicates that inversion of configuration at the methylene group of this Grignard reagent occurs with an approximate rate of 2 sec-1 at room temperature. This is the first example of a rapid inversion rate in a secondary Grignard reagent.
\r\n\r\nThe rates of exchange of alkyl groups between dineopentylmagnesium and di-s-butylmagnesium, bis-(2-methylbutyl)-magnesium and bis-(4, 4-dimethyl-2-pentyl)-magnesium respectively in diethyl ether solution were found to be fast on the nmr time scale. However, the alkyl group exchange rate was found to be slow in a diethyl ether solution of dineopentylmagnesium and bis-(2-methylbutyl)-magnesium containing N, N, N', N'-tetramethylethylenediamine. The unsymmetrical species neopentyl-2-methylbutyl-magnesium was observed at room temperature in the nmr spectrum of the solution containing the diamine.
\r\n\r\nII. REDISTRIBUTION EQUILIBRIA IN ORGANOCADMIUM COMPOUNDS
\r\n\r\nThe exchange of methyl groups in dimethylcadmium has been studied by nuclear magnetic resonance spectroscopy. Activation parameters for the methyl group exchange have been measured for a neat sample and for a solution in tetrahydrofuran. The exchange is faster in the basic solvent tetrahydrofuran relative to the neat sample and in tetrahydrofuran solution is retarded by the solvating agent N, N, N\u2019, N\u2019-tetramethylethylenediamine and greatly increased by cadmium bromide. The addition of methanol to a solution of dimethylcadmium in tetrahydrofuran appears to have very little effect on the rate of exchange. The exchange was found to proceed with retention of configuration. The rate-limiting step for the exchange of methyl groups in a basic solvent appears to be the dissociation of coordinating solvent from dimethylcadmium.
\r\n\r\nThe equilibrium between methylcadmium bromide, dimethylcadmium and cadmium bromide in tetrahydrofuran solution has also been studied. At room temperature the interconversion of the species is very fast on the nmr time scale but at -100\u00b0 distinct absorptions for methylcadmium bromide and imethylcadmium are observed.
\r\n\r\nThe species ethylmethylcadmium has been observed in the nmr spectrum.
\r\n\r\nThe rate of exchange of vinyl groups in a solution of divinylcadmium in tetrahydrofuran has been found to be fast on the nmr time scale.
\r\n" }, { "name": "Bauer, William Robert", "degree": "PhD", "year": "1968", "title": "I. The Structure and Properties of Closed Circular Duplex DNA. II. Chemically Interacting Systems at Equilibrium in a Buoyant Density Gradient", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182016-124256042", "creators": [ { "name": { "family": "Bauer", "given": "William Robert" }, "id": "Bauer-William-Robert", "display_name": "Bauer, William Robert" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0v4z-sg21", "abstract": "I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 \u00b5g/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 \u00b5g/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, \u03c4, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.
\r\n\r\nThe free energy of superhelix formation is calculated as a function of \u03c4 from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 \u00c5 and 135 \u00c5, respectively.
\r\n\r\nA buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.
\r\n\r\nII. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.
\r\n" }, { "name": "Bernstein, Elliot R.", "degree": "PhD", "year": "1968", "title": "I. Site Effects and Exciton Structure in Molecular Crystals - Benzene. II. The First and Second Triplet States of Solid Benzene", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142016-085928606", "creators": [ { "name": { "family": "Bernstein", "given": "Elliot R." }, "id": "Bernstein-Elliot-R", "display_name": "Bernstein, Elliot R." } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PMT5-3V95", "abstract": "The effect of intermolecular coupling in molecular energy levels (electronic and vibrational) has been investigated in neat and isotopic mixed crystals of benzene. In the isotopic mixed crystals of C6H6, C6H5D, m-C6H4D2, p-C6H4D2, sym-C6H3D3, C6D5H, and C6D6 in either a C6H6 or C6D6 host, the following phenomena have been observed and interpreted in terms of a refined Frenkel exciton theory: a) Site shifts; b) site group splittings of the degenerate ground state vibrations of C6H6, C6D6, and sym-C6H3D3; c) the orientational effect for the isotopes without a trigonal axis in both the 1B2u electronic state and the ground state vibrations; d) intrasite Fermi resonance between molecular fundamentals due to the reduced symmetry of the crystal site; and e) intermolecular or intersite Fermi resonance between nearly degenerate states of the host and guest molecules. In the neat crystal experiments on the ground state vibrations it was possible to observe many of these phenomena in conjunction with and in addition to the exciton structure.
\r\n\r\nTo theoretically interpret these diverse experimental data, the concepts of interchange symmetry, the ideal mixed crystal, and site wave functions have been developed and are presented in detail. In the interpretation of the exciton data the relative signs of the intermolecular coupling constants have been emphasized, and in the limit of the ideal mixed crystal a technique is discussed for locating the exciton band center or unobserved exciton components. A differentiation between static and dynamic interactions is made in the Frenkel limit which enables the concepts of site effects and exciton coupling to be sharpened. It is thus possible to treat the crystal induced effects in such a fashion as to make their similarities and differences quite apparent.
\r\n\r\nA calculation of the ground state vibrational phenomena (site shifts and splittings, orientational effects, and exciton structure) and of the crystal lattice modes has been carried out for these systems. This calculation serves as a test of the approximations of first order Frenkel theory and the atom-atom, pair wise interaction model for the intermolecular potentials. The general form of the potential employed was V(r) = Be-Cr - A/r6 ; the force constants were obtained from the potential by assuming the atoms were undergoing simple harmonic motion.
\r\n\r\nIn part II the location and identification of the benzene first and second triplet states (3B1u and 3E1u) is given.
\r\n\r\n" }, { "name": "Borders, Charles LaMonte", "degree": "PhD", "year": "1968", "title": "I. Purification and Partial Characterization of Testicular Hyaluronidase. II. Mechanistic Studies of Human Lysozyme", "advisor": "Raftery, Michael A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262002-152327", "creators": [ { "name": { "family": "Borders", "given": "Charles LaMonte" }, "id": "Borders-Charles-LaMonte", "display_name": "Borders, Charles LaMonte" } ], "advisors": [ { "name": { "family": "Raftery", "given": "Michael A." }, "id": "Raftery-M-A", "role": "advisor", "display_name": "Raftery, Michael A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7RZ0-5W42", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I\r\nA new method is presented for the purification of testicular hyaluronidase involving ion exchange chromatography followed by gel filtration on Sephadex G-75. A highly purified hyaluronidase preparation has been obtained which contains 45,000 N. F. activity units per mg dry weight and which migrates as a single component on polyacrylamide gel electrophoresis at pH 4.3. The amino acid composition has been determined, and the enzyme has been shown to be a glycoprotein containing 5.00% mannose and 2.17% glucosamine (expressed as N-acetylglucosamine). The molecular weight of the purified hyaluronidase has been determined to be 61,000 by gel filtration methods. This value is in contrast to a molecular weight of 126,000 for the crude enzyme, as determined by similar techniques. A glycopeptide has been isolated from the purified hyaluronidase after total enzymatic digestion of the reduced carboxymethylated enzyme. This glycopeptide was shown to have molecular weight of approximately 1,600, and to have a composition of (mannose)7(glucosamine)2(asp)1. The amino acid involved in the protein-carbohydrate linkage is thus aspartic acid.\r\n\r\nPART II\r\nIt has been shown that when human lysozyme catalyzed glycosidic bond cleavage of chitobiose is carried out in the presence of methanol, transglycosylation occurs with production of methyl-N-acetyl-[beta]-D-glucosaminide. Thus, retention of configuration occurs at the anomeric carbon of the disaccharide substrate during catalysis and eliminates the possibility of a single displacement mechanism for the enzyme. Use has been made of this transglycosylation reaction to enzymatically synthesize oligomeric p-nitrophenyl-[beta]-D-glucosaminides from chitin oligosaccharides, p-nitrophenyl-N-acetyl-[beta]-D-glucosaminide, and human lysozyme. Such saccharides serve as substrates for human lysozyme with release of p-nitrophenol. Similar synthesis of oligosaccharides from chitin oligomers, p-nitrophenyl-[beta]-D-glucoside, and human lysozyme has been carried out. Since human lysozyme effects hydrolysis of the glucosidic bonds in such oligosaccharides, a mechanism involving anchimeric assistance of an N-acetyl group has been eliminated. Similar enzymatic synthesis and hydrolysis of oligosaccharide substrates from chitin oligomers and p-nitrophenyl-2-deoxty-[beta]-D-glucoside has eliminated a mechanism involving acetamido or C-2 oxyanion participation by substrate due to general base catalysis by the enzyme. Only two closely related possibilities remain to explain the mechanistic pathway of substrate during catalysis by human lysozyme.\r\n\r\nThe hydrolysis of chitobiose, chitotriose, and chitotetraose by human lysozyme under different sets of conditions has also been investigated. It was found that this enzyme could be distinguished from hen lysozyme by the product distributions obtained for hydrolysis by the two enzymes under identical reaction conditions.\r\n\r\nThe hydrolysis of p-nitrophenyl-[beta]-D-chitobioside by human lysozyme was shown to follow Michaelis-Menton kinetics, with K[subscript M] = 2.6 x 10[^-2] M and k[subscript cat] = 6.8 x 10[^-5] mole x sec[^-1] x (mole enzyme)[^-1]." }, { "name": "Cole, Ronald Sinclair", "degree": "PhD", "year": "1968", "title": "Part One. Photodimerizations of Coumarin. Part Two. Asymmetric Induction During Energy Transfer", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-01222008-114929", "creators": [ { "name": { "family": "Cole", "given": "Ronald Sinclair" }, "id": "Cole-Ronald-Sinclair", "display_name": "Cole, Ronald Sinclair" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KEEE-B108", "abstract": "Part I:
\r\n\r\nStudies on the mechanism of the photodimerizations of coumarin are reported. Trans coumarin photodimers are shown to result from excited triplet coumarin. It seems likely that an intermediate triplet-ground state complex precedes a biradical intermediate which closes to trans-dicoumarin. This dimer, formedby benzophenone sensitization is also produced by direct irradiation in benzene. Here coumarin has a low intersystem crossing yield of 2.2 x 10\u207b\u00b2. We account for 98% of the absorbed quanta by a photocleavage of coumarin singlets, competing with the other modes of unimolecular decay. No evidence supporting singlet self quenching was found. Singlet energy transfer from benzophenone to coumarin occurs by emission-reabsorption. The low efficiency of the latter process makes it insignificant compared to competing mechanisms.
\r\n\r\n\r\nPart II:
\r\n\r\nStudies on the detailed mechanism of an energy transfer are reported. Optically active photosensitizers induce optical activity into trans-1,2-diphenylcyclopropane, II, while effecting the trans \u2192 cis isomerization. The asymmetric induction is shown to result from differing rates of energy transfer to the two optical isomer of trans-II. A rather large steric effect operative during energy transfer is thus demonstrated. Quenching studies indicate that the reaction occurs by a singlet mechanism resulting in production of 1,3 -diphenyltrimethylene. The intermediate apparently has the same decays paths as that generated by triplet energy transfer to II. The asymmetric induction results from a number of sensitizers are useful in constructing a probable transition state for this energy transfer reaction.
" }, { "name": "Colson, Steven Douglas", "degree": "PhD", "year": "1968", "title": "Excitons in Crystalline Benzene", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122002-100424", "creators": [ { "name": { "family": "Colson", "given": "Steven Douglas" }, "id": "Colson-Steven-Douglas", "display_name": "Colson, Steven Douglas" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B02E-Q937", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. Experimental procedure\r\n\r\nThe spectrographs and excitation sources used to study the absorption and emission spectra of crystalline benzene are described and their relative merits discussed.\r\n\r\nA new purification method is also described. This method, in which the benzene is vacuum refluxed over an ~100[degree]C cesium mirror, can be used in conjunction with zone refining techniques to reduce the spectroscopic impurity level to ~10[superscript -6] mole percent. Also see Part III in this regard.\r\n\r\nA modified Bridgman type crystal growing technique that is used to produce high quality, low temperature crystals is described in detail. The development of these experimental techniques was essential to the success of the experiments described in Parts II and III.\r\n\r\nPart II. Singlet Exciton Band Structure of Crystalline Benzene\r\n\r\nThe Frenkel theory for localized excitations in molecular crystals is redeveloped and extended for the case of benzene to lay a consistent theoretical framework for the interpretation of pure and mixed crystal spectra. Three types of dipole selection rules are proved for [...] transitions in a restricted Frenkel limit. They are: 1) [delta][...] =0; 2) general selection rules based on interchange symmetry; and 3) the [...] selection rule for centrosymmetric crystals. These are particularly important in the interpretation of exciton band [...] exciton band transitions. Furthermore, the interchange group and ideal mixed crystal concepts are introduced to provide a clear, precise definition of the static and dynamic contributions to the energy of the crystal states. Emphasis is placed upon the relative signs and magnitudes of the dynamic coupling constants rather than on crystal splittings since these constants give directly the anisotropy of the resonance interactions in the crystal.\r\n\r\nExperimental data from the absorption and emission spectra of the [superscript 1]B[subscript 2u] state of pure and isotopic mixed benzene crystals are also presented. From these data it can be concluded that the line shapes and transition energies are very sensitive to the effects of crystal strain. Exciton band [...] exciton band transition line shapes are interpreted in terms of the density of states function of the [superscript 1]B[subscript 2u] exciton band. This experimental function is found to be inconsistent with that predicted from the data obtained from the variation of energy denominators method of analysis of this exciton band by Nieman and Robinson. The variation of energy denominators method is investigated with more extensive and improved experiments. It is found to be inappropriate for the study of the [superscript 1]B[subscript 2u] state of crystalline benzene, and these new experiments lead to a different interpretation of this band. The resonance coupling constants obtained from this new interpretation are used to calculate the density of states function for a crystal of 32,000 molecules. This calculated function is in excellent agreement with that obtained from the exciton band [...] exciton band transition line shapes. Exciton band [...] exciton band transitions involving the lowest singlet of crystalline naphthalene are also reported and discussed.\r\n\r\nPart III. Triplet excitons in Crystalline Benzene: Location of the First and Second Triplets; Phosphoresence and Trap - Trap Energy Transfer in Isotopic mixed Crystals.\r\n\r\nThe first and second triplets of solid benzene are observed using O[subscript 2] and NO perturbation techniques. The absorption spectra of long benzene crystals of ultrahigh spectroscopic purity are discussed in terms of the unperturbed transition to the second triplet state.\r\n\r\nThe phosphorescence spectrum of isotopic mixed benzene crystals is analyzed with special emphasis being placed on the effects of the static crystal field. The fluorescence and absorption spectra are used to supplement this analysis.\r\n\r\nThe phosporescence and fluorescence spectra of three component isotopic mixed benzene crystals are studied as a function of guest concentration, excitation lamp intensity, and, temperature. Some very interesting effects are observed at high lamp intensities and interpreted in terms of triplet - triplet annihilation of trapped excitation. Triplet excitation is found to be transferred between two different traps which are not more than ~20 [angstroms] apart in this system." }, { "name": "Diestler, Dennis Jon", "degree": "PhD", "year": "1968", "title": "I. Quantum Mechanics of One-Dimensional Two-Particle Models. II. A Quantum Mechanical Treatment of Inelastic Collisions", "advisor": "McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:12142015-085217224", "creators": [ { "name": { "family": "Diestler", "given": "Dennis Jon" }, "id": "Diestler-Dennis-Jon", "display_name": "Diestler, Dennis Jon" } ], "advisors": [ { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/70MF-3B21", "abstract": "Part I
\r\n\r\nSolutions of Schr\u00f6dinger\u2019s equation for system of two particles bound in various stationary one-dimensional potential wells and repelling each other with a Coulomb force are obtained by the method of finite differences. The general properties of such systems are worked out in detail for the case of two electrons in an infinite square well. For small well widths (1-10 a.u.) the energy levels lie above those of the noninteresting particle model by as much as a factor of 4, although excitation energies are only half again as great. The analytical form of the solutions is obtained and it is shown that every eigenstate is doubly degenerate due to the \u201cpathological\u201d nature of the one-dimensional Coulomb potential. This degeneracy is verified numerically by the finite-difference method. The properties of the square-well system are compared with those of the free-electron and hard-sphere models; perturbation and variational treatments are also carried out using the hard-sphere Hamiltonian as a zeroth-order approximation. The lowest several finite-difference eigenvalues converge from below with decreasing mesh size to energies below those of the \u201cbest\u201d linear variational function consisting of hard-sphere eigenfunctions. The finite-difference solutions in general yield expectation values and matrix elements as accurate as those obtained using the \u201cbest\u201d variational function.
\r\n\r\nThe system of two electrons in a parabolic well is also treated by finite differences. In this system it is possible to separate the center-of-mass motion and hence to effect a considerable numerical simplification. It is shown that the pathological one-dimensional Coulomb potential gives rise to doubly degenerate eigenstates for the parabolic well in exactly the same manner as for the infinite square well.
\r\n\r\nPart II
\r\n\r\nA general method of treating inelastic collisions quantum mechanically is developed and applied to several one-dimensional models. The formalism is first developed for nonreactive \u201cvibrational\u201d excitations of a bound system by an incident free particle. It is then extended to treat simple exchange reactions of the form A + BC \u2192AB + C. The method consists essentially of finding a set of linearly independent solutions of the Schr\u00f6dinger equation such that each solution of the set satisfies a distinct, yet arbitrary boundary condition specified in the asymptotic region. These linearly independent solutions are then combined to form a total scattering wavefunction having the correct asymptotic form. The method of finite differences is used to determine the linearly independent functions.
\r\n\r\nThe theory is applied to the impulsive collision of a free particle with a particle bound in (1) an infinite square well and (2) a parabolic well. Calculated transition probabilities agree well with previously obtained values.
\r\n\r\nSeveral models for the exchange reaction involving three identical particles are also treated: (1) infinite-square-well potential surface, in which all three particles interact as hard spheres and each two-particle subsystem (i.e. BC and AB) is bound by an attractive infinite-square-well potential; (2) truncated parabolic potential surface, in which the two-particle subsystems are bound by a harmonic oscillator potential which becomes infinite for interparticle separations greater than a certain value; (3) parabolic (untruncated) surface. Although there are no published values with which to compare our reaction probabilities, several independent checks on internal consistency indicate that the results are reliable.
\r\n" }, { "name": "Evans, David Albert", "degree": "PhD", "year": "1968", "title": "A Stereoselective Approach Toward the Synthesis of Some Pentacyclic Triterpenes", "advisor": "Ireland, Robert E.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06042004-103447", "creators": [ { "name": { "family": "Evans", "given": "David Albert" }, "id": "Evans-David-Albert", "display_name": "Evans, David Albert" } ], "advisors": [ { "name": { "family": "Ireland", "given": "Robert E." }, "id": "Ireland-R-E", "role": "advisor", "display_name": "Ireland, Robert E." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XJ7P-FH24", "abstract": "An approach to the synthesis of pentacyclic triterpenes of the friedelin type has been outlined, and the synthesis of pentacyclic intermediates related to this approach has been accomplished.\r\n" }, { "name": "Halgren, Thomas Arthur", "degree": "PhD", "year": "1968", "title": "Nature of the Radical Intermediates in a Substituted Cyclopropylcarbinyl--Allylcarbinyl System", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12142015-100545207", "creators": [ { "name": { "family": "Halgren", "given": "Thomas Arthur" }, "id": "Halgren-Thomas-Arthur", "display_name": "Halgren, Thomas Arthur" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a5tm-n775", "abstract": "We have sought to determine the nature of the free-radical precursors to ring-opened hydrocarbon 5 and ring-closed hydrocarbon 6. Reasonable alternative formulations involve the postulation of hydrogen abstraction (a) by a pair of rapidly equilibrating classical radicals (the ring-opened allylcarbinyl-type radical 3 and the ring-closed cyclopropylcarbinyl-type 4), or (b) by a nonclassical radical such as homoallylic radical 7.
\r\n\r\n[Figure not reproduced.]
\r\n\r\nEntry to the radical system is gained via degassed thermal decomposition of peresters having the ring-opened and the ring-closed structures. The ratio of 6:5 is essentially independent of the hydrogen donor concentration for decomposition of the former at 125\u00b0 in the presence of triethyltin hydrdride. A deuterium labeling study showed that the \u03b1 and \u03b2 methylene groups in 3 (or the equivalent) are rapidly interchanged under these conditions.
\r\n\r\nExistence of two (or more) product-forming intermediates is indicated (a) by dependence of the ratio 6:5 on the tin hydride concentration for decomposition of the ring-closed perester at 10 and 35\u00b0, and (b) by formation of cage products having largely or wholly the structure (ring-opened or ring-closed) of the starting perester.
\r\n\r\nRelative rates of hydrogen abstraction by 3 could be inferred by comparison of ratios of rate constants for hydrogen abstraction and ortho-ring cyclization:
\r\n\r\n[Figure not reproduced.]
\r\n\r\nAt 100\u00b0 values of ka/kr are 0.14 for hydrogen abstraction from 1,4-cyclohexadiene and 7 for abstraction from triethyltin hydride. The ratio 6:5 at the same temperature is ~0.0035 for hydrogen abstraction from 1,4-cyclohexadiene, ~0.078 for abstraction from the tin hydride, and \u2265 5 for abstraction from cyclohexadienyl radicals. These data indicate that abstraction of hydrogen from triethyltin hydride is more rapid than from 1,4-cyclohexadiene by a factor of ~1000 for 4, but only ~50 for 3.
\r\n\r\nMeasurements of product ratios at several temperatures allowed the construction of an approximate energy-level scheme. A major inference is that isomerization of 3 to 4 is exothermic by 8 \u00b1 3 kcal/mole, in good agreement with expectations based on bond dissociation energies. Absolute rate-constant estimates are also given.
\r\n\r\nThe results are nicely compatible with a classical-radical mechanism, but attempted interpretation in terms of a nonclassical radical precursor of product ratios formed even from equilibrated radical intermediates leads, it is argued, to serious difficulties.
\r\n\r\nThe roles played by hydrogen abstraction from 1,4,-cyclohexadiene and from the derived cyclohexadienyl radicals were probed by fitting observed ratios of 6:5 and 5:10 in the sense of least-squares to expressions derived for a complex mechanistic scheme. Some 30 to 40 measurements on each product ratio, obtained under a variety of experimental conditions, could be fit with an average deviation of ~6%. Significant systematic deviations were found, but these could largely be redressed by assuming (a) that the rate constant for reaction of 4 with cyclohexadienyl radical is inversely proportional to the viscosity of the medium (i.e., is diffusion-controlled), and (b) that ka/kr for hydrogen abstraction from 1,4-cyclohexadiene depends slightly on the composition of the medium. An average deviation of 4.4% was thereby attained.
\r\n\r\nDegassed thermal decomposition of the ring-opened perester in the presence of the triethyltin hydride occurs primarily by attack on perester of triethyltin radicals, presumably at the \u2013O-O- bond, even at 0.01 M tin hydride at 100 and 125\u00b0. Tin ester and tin ether are apparently formed in closely similar amounts under these conditions, but the tin ester predominates at room temperature in the companion air-induced decomposition, indicating that attack on perester to give the tin ether requires an activation energy approximately 5 kcal/mole in excess of that for the formation of tin ester.
\r\n" }, { "name": "Hyndman, Harry Lester", "degree": "PhD", "year": "1968", "title": "The Excited State Geometry of Conjugated Dienes and Characterization of a Quantum Chain-Transfer Mechanism of Energy Transfer", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092009-090005", "creators": [ { "name": { "family": "Hyndman", "given": "Harry Lester" }, "id": "Hyndman-Harry-Lester", "display_name": "Hyndman, Harry Lester" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9q2h-7591", "abstract": "An investigation has been carried out to determine whether the geometry corresponding to the lowest lying triplet state of conjugated dienes is in the form of a 1, 4-biradical system or an allyl-methylene system (a \"1, 2-biradical\"). This has been done by measuring the various quantum yields for cis-trans isomerization of these dienes and comparing the results with certain previously conceived empirical standards and to the criteria imposed by the proposed mechanism.
\r\n\r\nDuring the course of this investigation, a novel and very interesting phenomenon was uncovered. It appears that a quantum-chain mechanism, heretofore unreported for this type of system, is in operation in at least the early stages of the photoisomerization process. Characterization of such a mechanism and the chain propagating species has been carried out.
\r\n" }, { "name": "Lam, Ernest Yee Yeung", "degree": "PhD", "year": "1968", "title": "I. Photodimerization of Cyclohexenone. II. Radiation Chemistry of Benzophenone in Cyclohexene Solution", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092009-140344", "creators": [ { "name": { "family": "Lam", "given": "Ernest Yee Yeung" }, "id": "Lam-Ernest-Yee-Yeung", "display_name": "Lam, Ernest Yee Yeung" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6SGH-K335", "abstract": "PART I:\tThe photodimerization of cyclohexenone has been studied in the neat liquid and in solvents. Although four products can be detected, 1 and 2 predominate under all conditions. The reaction can be ensitized by benzophenone, thioxanthone, acetophenone, and naphthalene. The enone was used as a sensitizer for the cis- trans isomerization of three pairs of isomeric olefins and the response was used to estimate the triplet excitation energy of the enone as 61 \u00b1 1 kcal per mole. Dimerization can be quenched by addition of piperylene. Most evidence points to a triplet mechanism for the reaction. However, the ratio of 1 to 2 varies with reaction conditions and the quantum yield does not show the expected variation with enone concentration. These phenomena are attributed to solvent effects, rather than to a change of mechanism.
\r\n\r\n[See thesis for Illustration]
\r\n\r\nPART II: Gamma-irradiation of benzophenone in cyclohexene solution produced 3,3'-dicyclohexenyl and cyclohexenyldiphenylcarbinol as main products. The reaction was quenched by phenyl disulfide and to a less extent by chloroform. It was not significantly affected by 2-propanol. Naphthalene also acted as a quencher. The reaction probably involved the cleavage of the allylic C-H bond of cyclohexene to a cyclohexenyl radical and a hydrogen atom. Benzophenone effectively took up the hydrogen atom to give a ketyl radical. The main cross product, cyclohexenyldiphenylcarbinol, resulted from a combination of the ketyl radical with the cyclohexenyl radical.
\r\n\r\nQuenching by naphthalene was taken to be an indication that excited states of cyclohexene played an important role, probably as a precursor of cyclohexenyl radical. This was supported by the fact that gamma-irradiation or cis- or trans-2,3-diphenylpropenes in cyclohexene solution resulted in isomerization. That benzophenone did not act as an energy sink in cyclohexene was probably due to inefficient energy transfer from an excited cyclohexene triplet to benzophenone.
\r\n" }, { "name": "Lin, Leroy Chi-tsun", "degree": "PhD", "year": "1968", "title": "I. The Crystal Structure of Potassium Bis-(Tricyanovinyl) Amine. II. Nuclear Magnetic Resonance Studies of Alkali Halide Solutions. III. Elucidation of the Intramolecular Hydrogen Bond in Acetylacetone by the Deuterium Isotope Effect on the Chemical Shift of the Bridge Hydrogen", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechTHESIS:12212015-083027456", "creators": [ { "name": { "family": "Lin", "given": "Leroy Chi-tsun" }, "id": "Lin-Leroy-Chi-tsun", "display_name": "Lin, Leroy Chi-tsun" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/125N-CX62", "abstract": "Part I
\r\n\r\nPotassium bis-(tricyanovinyl) amine, K+N[C(CN)=C(CN)2]2-, crystallizes in the monoclinic system with the space group Cc and lattice constants, a = 13.346 \u00b1 0.003 \u00c5, c = 8.992 \u00b1 0.003 \u00c5, B = 114.42 \u00b1 0.02\u00b0, and Z = 4. Three dimensional intensity data were collected by layers perpendicular to b* and c* axes. The crystal structure was refined by the least squares method with anisotropic temperature factor to an R value of 0.064.
\r\n\r\nThe average carbon-carbon and carbon-nitrogen bond distances in \u2013C-C\u039eN are 1.441 \u00b1 0.016 \u00c5 and 1.146 \u00b1 0.014 \u00c5 respectively. The bis-(tricyanovinyl) amine anion is approximately planar. The coordination number of the potassium ion is eight with bond distances from 2.890 \u00c5 to 3.408 \u00c5. The bond angle C-N-C of the amine nitrogen is 132.4 \u00b1 1.9\u00b0. Among six cyano groups in the molecule, two of them are bent by what appear to be significant amounts (5.0\u00b0 and 7.2\u00b0). The remaining four are linear within the experimental error. The bending can probably be explained by molecular packing forces in the crystals.
\r\n\r\nPart II
\r\n\r\nThe nuclear magnetic resonance of 81Br and 127I in aqueous solutions were studied. The cation-halide ion interactions were studied by studying the effect of the Li+, Na+, K+, Mg++, Cs+ upon the line width of the halide ions. The solvent-halide ion interactions were studied by studying the effects of methanol, acetonitrile, and acetone upon the line width of 81Br and 127I in the aqueous solutions. It was found that the viscosity plays a very important role upon the halide ions line width. There is no specific cation-halide ion interaction for those ions such as Mg++, Di+, Na+, and K+, whereas the Cs+ - halide ion interaction is strong. The effect of organic solvents upon the halide ion line width in aqueous solutions is in the order acetone \u02c3 acetonitrile \u02c3 methanol. It is suggested that halide ions do form some stable complex with the solvent molecules and the reason Cs+ can replace one of the ligands in the solvent-halide ion complex.
\r\n\r\nPart III
\r\n\r\nAn unusually large isotope effect on the bridge hydrogen chemical shift of the enol form of pentanedione-2, 4(acetylacetone) and 3-methylpentanedione-2, 4 has been observed. An attempt has been made to interpret this effect. It is suggested from the deuterium isotope effect studies, temperature dependence of the bridge hydrogen chemical shift studies, IR studies in the OH, OD, and C=O stretch regions, and the HMO calculations, that there may probably be two structures for the enol form of acetylacetone. The difference between these two structures arises mainly from the electronic structure of the \u03c0-system. The relative population of these two structures at various temperatures for normal acetylacetone and at room temperature for the deuterated acetylacetone were calculated.
\r\n" }, { "name": "Magnuson, James Andrew", "degree": "PhD", "year": "1968", "title": "I. The Effect of N,N,N',N'-Tetramethylethylenediamine on the Schlenk Equilibrium. II. The Nature of the Di-Grignard Reagent", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12182015-155008048", "creators": [ { "name": { "family": "Magnuson", "given": "James Andrew" }, "id": "Magnuson-James-Andrew", "display_name": "Magnuson, James Andrew" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0CT8-7385", "abstract": "I. The influence of N,N,N\u2019,N\u2019-tetramethylethylenediamine on the Schlenk equilibrium
\r\n\r\nThe equilibrium between ethylmagnesium bromide, diethylmagnesium, and magnesium bromide has been studied by nuclear magnetic resonance spectroscopy. The interconversion of the species is very fast on the nmr time scale, and only an averaged spectrum is observed for the ethyl species. When N,N,N\u2019,N\u2019-tetramethylethylenediamine is added to solutions of these reagents in tetrahydrofuran, the rate of interconversion is reduced. At temperatures near -50\u00b0, two ethylmagnesium species have been observed. These are attributed to the different ethyl groups in ethylmagnesium bromide and diethylmagnesium, two of the species involved in the Schlenk equilibrium of Grignard reagents.
\r\n\r\nII. The nature of di-Grignard reagents
\r\n\r\nDi-Grignard reagents have been examined by nuclear magnetic resonance spectroscopy in an attempt to prove that dialkylmagnesium reagents are in equilibrium with alkylmagnesium halides. The di-Grignard reagents of compounds such as 1,4-dibromobutane have been investigated. The dialkylmagnesium form of this di-Grignard reagent can exist as an intramolecular cyclic species, tetramethylene-magnesium. This cyclic form would give an nmr spectrum different from that of the classical alkylmagnesium halide di-Grignard reagent. In dimethyl ether-tetrahydrofuran solutions of di-Grignard reagents containing N N,N,N\u2019,N\u2019-Tetramethylethylenediamine, evidence has been found for the existence of an intramolecular dialkylmagnesium species. This species is rapidly equilibrating with other forms, but at low temperatures, the rates of interconversion are reduced. Two species can be seen in the nmr spectrum at -50\u00b0. One is the cyclic species; the other is an open form.
\r\n\r\nInversion of the carbon at the carbon-magnesium bond in di-Grignard reagents has also been studied. This process is much faster than in corresponding monofunctional Grignard reagents.
\r\n" }, { "name": "Miller, William Walter", "degree": "PhD", "year": "1968", "title": "Part I. Coenzyme B\u2081\u2082 as a Hydroformylation-Type Catalyst. Part II. Mechanisms of Hydrogen Transfer in the Methylmalonyl Coenzyme A Mutase Reaction", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12182015-145538579", "creators": [ { "name": { "family": "Miller", "given": "William Walter" }, "id": "Miller-William-Walter", "display_name": "Miller, William Walter" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BBKP-QT89", "abstract": "Part I
\r\n\r\nThe mechanism of the hydroformylation reaction was studied. Using cobalt deuterotetracarbonyl and 1-pentene as substrates, the first step in the reaction, addition of cobalt tetracarbonyl to an olefin, was shown to be reversible.
\r\n\r\nPart II
\r\n\r\nThe role of coenzyme B12 in the isomerization of methylmalonyl coenzyme A to succinyl coenzyme A by methylmalonyl coenzyme A mutase was studied. The reaction was allowed to proceed to partial completion using a mixture of methylmalonyl coenzyme A and 4, 4, 4-tri-2H-methylmalonyl coenzyme A as substrate. The deuterium distribution in the product, succinyl coenzyme A, was shown to best fit a model in which hydrogen is transferred from C-4 of methylmalonyl coenzyme A to C-5\u2019 of the adenosyl moiety of coenzyme B12 in the rate determining step. The three hydrogens at the 5\u2019-adenosyl position of the coenzyme B12 intermediate are then able to become enzymatically equivalent before hydrogen is transferred from the coenzyme B12 intermediate to form succinyl coenzyme A.
\r\n" }, { "name": "Riley, Merle Eugene", "degree": "PhD", "year": "1968", "title": "Energy Transfer in Molecular Collisions", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042016-101919332", "creators": [ { "name": { "family": "Riley", "given": "Merle Eugene" }, "id": "Riley-Merle-Eugene", "display_name": "Riley, Merle Eugene" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/76fq-q631", "abstract": "Two general, numerically exact, quantum mechanical methods have been developed for the calculation of energy transfer in molecular collisions. The methods do not treat electronic transitions because of the exchange symmetry of the electrons. All interactions between the atoms in the system are written as potential energies.
\r\n\r\nThe first method is a matrix generalization of the invariant imbedding procedure, 17, 20 adapted for multi-channel collision processes. The second method is based on a direct integration of the matrix Schr\u00f6dinger equation, with a re-orthogonalization transform applied during the integration.
\r\n\r\nBoth methods have been applied to a collinear collision model for two diatoms, interacting via a repulsive exponential potential. Two major studies were performed. The first was to determine the energy dependence of the transition probabilities for an H2 on the H2 model system. Transitions are possible between translational energy and vibrational energy, and from vibrational modes of one H2 to the other H2. The second study was to determine the variation of vibrational energy transfer probability with differences in natural frequency of two diatoms similar to N2.
\r\n\r\nComparisons were made to previous approximate analytical solutions of this same problem. For translational to vibrational energy transfer, the previous approximations were not adequate. For vibrational to vibrational energy transfer of one vibrational quantum, the approximations were quite good.
\r\n" }, { "name": "Shugarman, Arnold Louis", "degree": "PhD", "year": "1968", "title": "I. Autoxidation of Manganese(II) \u03b2-Diketonates. II. Synthesis of Dipivaloylmethane Chelates of Manganese(II)", "advisor": "Schaefer, William P.; Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-111115", "creators": [ { "name": { "family": "Shugarman", "given": "Arnold Louis" }, "id": "Shugarman-Arnold-Louis", "display_name": "Shugarman, Arnold Louis" } ], "advisors": [ { "name": { "family": "Schaefer", "given": "William P." }, "id": "Schaefer-W-P", "role": "advisor", "display_name": "Schaefer, William P." }, { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MA2A-TC68", "abstract": "NOTE: Text and symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I.\r\n\r\nThe oxidation of several manganese(II) [beta]-diketonates by molecular oxygen has been studied in benzene and ethanol with the goals of elucidating the mechanisms and understanding the influence of ligand structure on the reactivities of the chelates.\r\n\r\nAutoxidation of bis(acetylacetonato)diaquomanganese(II) in benzene follows a two-term rate law which can be interpreted in terms of an uncatalyzed bimolecular reaction and an acetylacetone-catalyzed reaction of manganese(II) complex and oxygen. Excess acetylacetone inhibits autoxidation of the manganese(II) chelates in ethanol, suggesting that a key step is formation of a bond between metal and molecular oxygen. Kinetic studies in ethanol are complicated by autoxidation of [beta]-diketone coordinated to the manganese(III) product and competition between manganese(II) and manganese(III) for available ligand.\r\n\r\nThe ligand bound to manganese(II) strongly influences the reactivity of the compound towards oxygen. A factor of 10[superscript 3] was observed between the rates of autoxidation of bis(ethylacetoacetato)-manganese(II) and bis(3methylacetylacetonato)manganese(II). Results have been interpreted in terms of steric, resonance, and inductive effects.\r\n\r\nManganese [beta]-diketonates catalyze the autoxidation of several organic cosubstrates. Catalytic behavior falls into three classes in which manganese is predominantly divalent, trivalent, or in between the two extremes. Formation of a ternary complex of substrate, manganese, and oxygen is consistent with the limited data available.\r\n\r\nPart II.\r\n\r\nSynthesis of bis(dipivaloylmethanato)manganese(II), Mn(DPM)[subscript 2], was attempted in aqueous acetone and methanol solution. A bis compound, Mn(DPM)[subscript 2](H[subscript 2]O)[subscript 2], was prepared in aqueous acetone. The compound is octahedral, unlike the DPM chelates of other first-row transition metals, which suggests that steric factors alone do not control the geometry of these compounds. The product obtained from methanol solution contains bridging methoxy ligands and is probably a dimer, [Mn(DPM)(OCH)[subscript 3])][subscript 2]." }, { "name": "Stephenson, Leonard Merriman, Jr.", "degree": "PhD", "year": "1968", "title": "The Mechanism and Effect of the Quenching of Aromatic Hydrocarbon Singlet Excited States by Conjugated Dienes", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-121558", "creators": [ { "name": { "family": "Stephenson", "given": "Leonard Merriman, Jr." }, "id": "Stephenson-Leonard-Merriman", "display_name": "Stephenson, Leonard Merriman, Jr." } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3X2N-X015", "abstract": "Strong and rather specific quenching of fluorescence of aromatic hydrocarbons by conjugated dienes has been observed in solution at room temperature, despite the fact that the first excited singlet states of dienes lie considerably higher than those of the aromatic hydrocarbons involved. A study of various substituent effects on the quenching rates has been carried out and attempts have been made to ascertain those effects important in determining these rates and the stability of the (presumed) excited complex. A model based on delocalization of excitation energy through virtual states of the diene is proposed and is successful in rationalizing the correlation found between diene singlet state energies and quenching rates. The model will allow qualitative estimation of the effect of diene structure on quenching rates and will predict the susceptibility of various aromatic hydrocarbon singlets to diene quenching.\r\n\r\nThe quenching has been shown to be noneffective in producing diene excited states or in inducing any appreciable change in the diene or aromatic hydrocarbon. It is concluded, therefore, that dienes quench, by acting as specific catalysts for the nonradiative decay of aromatic hydrocarbon singlets." }, { "name": "Teague, Richard King", "degree": "PhD", "year": "1968", "title": "The Refractive Index and the Lorentz-Lorenz Function of Fluid Argon", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10042002-145820", "creators": [ { "name": { "family": "Teague", "given": "Richard King" }, "id": "Teague-Richard-King", "display_name": "Teague, Richard King" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZM82-EZ50", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe refractive index, for [gamma][subscript Na]=5893 [angstroms], of dense fluid argon was measured by the determination of the angle of minimum deviation. The study covered states from 133 to 173[degrees]K for pressures 20 to 100 atm. The density data of J. Levelt were used to calculate values of the Lorentz-Lorenz function for these states.\r\n\r\nA prism cell with 1/4\" diameter sapphire windows in a cryostat was used to contain the sample. The cell temperature was measured to ?0.015[degrees]K and controlled to ?0.001[degrees]K. The pressure was measured with a gage calibrated against a dead weight tester to ?0.06%.\r\n\r\nIn a detailed study of the critical region the Lorentz-Lorenz function was used to find the difference between coexisting gas-liquid densities, and the critical coefficient resulting from this work is [Beta]=0.361. The critical temperature was varied to find the best fit of the experimental data to a linear equation for the critical coefficient; the value, T[subscript C]=150.704[degrees]K, is significantly different from the accepted value, 150.86[degrees]K. Values of n[subscript C]=1.0859 and P[subscript C]=48.18 atm. were also determined. The measurements on the coexistence curve outside the critical region yielded an average gas value of (L-L)[subscript G]=4.152 cc/mole. The average liquid value is 4.213 cc/mole. There are no indications of an anomalous value at the critical point. The values of L-L on the eight isotherms between 133 and 173[degrees]K show a sharp peak near the critical point, 2.1% maximum, but this is within the experimental uncertainty." }, { "name": "Tinti, Dino Sabatino", "degree": "PhD", "year": "1968", "title": "I. Spectroscopic Evidence for Slow Vibrational Relaxation in Excited Electronic States of Diatomics in Rare Gas Solids. II. Static Crystal Field Effects in the Electronic Spectra of Isotopically Mixed Benzene Crystals", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182014-134017900", "creators": [ { "name": { "family": "Tinti", "given": "Dino Sabatino" }, "id": "Tinti-Dino-Sabatino", "display_name": "Tinti, Dino Sabatino" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q9F2-8F38", "abstract": "Part I
\r\n\r\nStudies of vibrational relaxation in excited electronic states of\r\nsimple diatomic molecules trapped in solid rare-gas matrices at low\r\ntemperatures are reported. The relaxation is investigated by\r\nmonitoring the emission intensity from vibrational levels of the\r\nexcited electronic state to vibrational levels of the ground electronic\r\nstate. The emission was in all cases excited by bombardment of the\r\ndoped rare-gas solid with X-rays.
\r\n\r\nThe diatomics studied and the band systems seen are: N2,\r\nVegard-Kaplan and Second Positive systems; O2, Herzberg system;\r\nOH and OD, A 2\u03a3+ - X2IIi system. The latter has been investigated\r\nonly in solid Ne, where both emission and absorption spectra were\r\nrecorded; observed fine structure has been partly interpreted in\r\nterms of slightly perturbed rotational motion in the solid. For N2,\r\nOH, and OD emission occurred from v' > 0, establishing a vibrational\r\nrelaxation time in the excited electronic state of the order, of longer\r\nthan, the electronic radiative lifetime. The relative emission intensity\r\nand decay times for different v' progressions in the Vegard-Kaplan\r\nsystem are found to depend on the rare-gas host and the N2 concentration,\r\nbut are independent of temperature in the range 1.7\u00b0K to 30\u00b0K.
\r\n\r\nPart II
\r\n\r\nStatic crystal field effects on the absorption, fluorescence, and\r\nphosphorescence spectra of isotopically mixed benzene crystals were\r\ninvestigated. Evidence is presented which demonstrate that in the\r\ncrystal the ground, lowest excited singlet, and lowest triplet states of\r\nthe guest deviate from hexagonal symmetry. The deviation appears\r\nlargest in the lowest triplet state and may be due to an intrinsic\r\ninstability of the 3B1u state. High resolution absorption and phospho-\r\nrescence spectra are reported and analyzed in terms of site-splitting\r\nof degenerate vibrations and orientational effects. The guest phosphorescence\r\nlifetime for various benzene isotopes in C6D6 and sym-C6H3D3\r\nhosts is presented and discussed.
\r\n" }, { "name": "Vesley, George Francis", "degree": "PhD", "year": "1968", "title": "Complications in the Systematic Study of Photochemical Mechanisms", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192009-135529", "creators": [ { "name": { "family": "Vesley", "given": "George Francis" }, "id": "Vesley-George-Francis", "display_name": "Vesley, George Francis" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/v6eb-y708", "abstract": "The rate constants for energy transfer have been measured by flash spectroscopic techniques. These results show that 1,3-cyclohexadiene undergoes a nonvertical transition when low energy sensitizers are used.
\r\n\r\nThe quantum yields for the high energy sensitized dimerization of 1,3-cyclohexadiene are consistant with the simple mechanism proposed.
\r\n\r\nThe use of 1,2-benzanthracene, a low energy sensitizer, to sensitize the dimerization of 1,3-cyclohexadiene has been studied in detail. The results show that in addition to energy transfer from donor to acceptor, other steps such as reversible energy transfer, adduct formation, singlet quenching of aromatic hydrocarbons by dienes and sensitizer-sensitizer interactions are important.
\r\n" }, { "name": "Wei, Pax Samuel Pin", "degree": "PhD", "year": "1968", "title": "Determination of Electronic Energy Levels of Molecules by 90\u00b0 Low Energy Electron Scattering", "advisor": "Kuppermann, Aron", "url": "https://resolver.caltech.edu/CaltechTHESIS:01112016-083235093", "creators": [ { "name": { "family": "Wei", "given": "Pax Samuel Pin" }, "id": "Wei-Pax-Samuel-Pin", "display_name": "Wei, Pax Samuel Pin" } ], "advisors": [ { "name": { "family": "Kuppermann", "given": "Aron" }, "id": "Kuppermann-A", "role": "advisor", "display_name": "Kuppermann, Aron" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/T6F4-S527", "abstract": "A review of the theory of electron scattering indicates that low incident beam energies and large scattering angles are the favorable conditions for the observation of optically forbidden transitions in atoms and molecules.
\r\n\r\nAn apparatus capable of yielding electron impact spectra at 90\u00b0 with incident electron beam energies between 30 and 50 electron volts is described. The resolution of the instrument is about 1 electron volt.
\r\n\r\nImpact spectra of thirteen molecules have been obtained. Known forbidden transitions to the helium 23S, the hydrogen b3\u01a9+u, the nitrogen A3\u01a9+u, B3\u03c0g, a\u2019\u03c0g, and C3\u03c0u, the carbon monoxide a3\u03c0, the ethylene \u1fb63B1u, and the benzene \u1fb63B1u states from the corresponding ground states have been observed.
\r\n\r\nIn addition, singlet-triplet vertical transitions in acetylene, propyne, propadiene, norbornadiene and quadricyclene, peaking at 5.9, 5.9, 4.5, 3.8, and 4.0 ev (\u00b10.2 ev), respectively, have been observed and assigned for the first time.
\r\n" }, { "name": "Weigert, Frank Julian", "degree": "PhD", "year": "1968", "title": "Carbon-13 Magnetic Resonance Spectroscopy", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042016-132544422", "creators": [ { "name": { "family": "Weigert", "given": "Frank Julian" }, "id": "Weigert-Frank-Julian", "display_name": "Weigert, Frank Julian" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2KB0-DB51", "abstract": "High-resolution, natural-abundance 13C spectra have been obtained from a wide variety of organic compounds; 13C chemical shifts and coupling constants have been correlated with other molecular properties.
\r\n\r\nGeminal and vicinal, carbon-proton couplings in benzene and the five- and six-membered aromatic heterocycles have been related to the corresponding proton-proton couplings in substituted ethylenes. The carbon-proton coupling constants in benzene are JCCH = + 1.0, JCCCH = +7.4 and JCCCH = -1.1 Hz. Extended H\u00fcckel wavefunctions are uniformly poor in explaining the long-range, carbon-proton couplings in aromatic systems.
\r\n\r\nCouplings between carbon and elements other than hydrogen have been observed in proton decoupled 13C spectra. All of the carbons in fluorobenzene and 1-fluoronaphthalene, but only six of the carbons in 2-fluoronaphthalene are coupled to the fluorine. One-bond, carbon-phosphorus coupling in trialkylphosphines is negative, while one-bond, carbon-phosphorus coupling in tetra-alkylphosphonium ions is positive. Atoms which do not use hybrid orbitals to form bonds to carbon (F, P(III), Se, Te) may have negative, one-bond coupling constants because of the failure of the average energy approximation. One-bond couplings between carbon and carbon, silicon, tin, lead and mercury appear to be explainable in terms of an effective nuclear charge and the s-bond order of the metal. Couplings between carbon and nitrogen and phosphorus (IV) have significant negative contributions to the Fermi contact coupling expression, though, within one series, correlations with s-bond order may be valid. Carbon-carbon coupling in cyclopropane derivatives (10-15 Hz) is consistent with a high degree of p character in the interior orbitals. Some two- and three-bond carbon-carbon coupling constants have also been observed.
\r\n\r\nSubstituent effects of hydroxyl groups on the 13C chemical shifts of continuous-chain alkanes depend both on steric and electronic factors. The hydroxyl substituent effects in the long-chain, primary alcohols are \u03b1 = -48.3, \u03b2 = -10.2, and \u03b3 = +6.0 ppm. The upfield \u03b3 effect is attributed to steric crowding in the gauche conformations. Additivity of the hydroxyl and carbonyl and alkyl substituent effects in alkyl-substituted cyclohexanols and cyclohexanones has been demonstrated.
\r\n\r\n\r\n" }, { "name": "Coyne, Lelia Mary", "degree": "PhD", "year": "1967", "title": "Photosensitized Cis-Trans Isomerization of 2, 3-Diphenylbutene-2. Investigation of Anomalous Sensitizers for Substituted Stilbene Isomerizations", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122015-145521569", "creators": [ { "name": { "family": "Coyne", "given": "Lelia Mary" }, "id": "Coyne-Lelia-Mary", "display_name": "Coyne, Lelia Mary" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8kds-1d07", "abstract": "The behavior of the photosensitized cis-trans isomerization of 2,3-diphenylbutene-2 was studied as a function of sensitizer energy by previously established methods. In addition, certain sensitizers for which parameters other than energy transfer are operative in inducting isomerizations, were studied in more detail. Sensitization of various stilbenes and substituted stilbenes by triphenylene is discussed in terms of excited state complex formation with stilbene. Sensitization by quinones, halogen-containing aromatics and 1,2-diketones is discussed in terms of attack by photolytically produced free radicals, either by addition to and elimination from the double bond, or in the cases of 1,2-diphenylpropene and 2,3-diphenylbutene-2, by hydrogen abstraction from one of the methyl groups and reversible abstraction by the allylic radical to produce cis-trans isomerized substrate and the structurally isomerized products, 2,3-diphenylpropene and 2,3-diphenylbutene-1.
" }, { "name": "Dannenberg, Joseph Jay", "degree": "PhD", "year": "1967", "title": "I. Nuclear Magnetic Resonance Analysis of Ferrocenylcarbonium Ion. II. Ferrocene Catalyzed Photochemistry", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11232015-095956061", "creators": [ { "name": { "family": "Dannenberg", "given": "Joseph Jay" }, "id": "Dannenberg-Jospeh-Jay", "display_name": "Dannenberg, Joseph Jay" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/q6jv-7q59", "abstract": "I. Nuclear magnetic resonance spectra of appropriately substituted ferrocenylcarbonium ions reveal the \u03b1-protons of the substituted ring to be more shielded than \u03b2-protons. The observation is discussed in terms of various models proposed for the ferrocenylcarbonium ion and is found to support a model in which the iron is bonded to all six carbona of the substituted ring.
\r\n\r\nII. Ferrocene catalyzes the photoisomerization of the piperylenes and the photodimerization of isoprene. Our results suggest a mechanism in which a complex of ferrocene and diene is excited to its second singlet state which dissociates to a triplet-state ferrocene molecule and a triplet-state diene molecule. The triplet-state diene, then, proceeds to isomerize or attack ground-state diene to form dimers.
\r\n" }, { "name": "Dubin, Alan Sander", "degree": "PhD", "year": "1967", "title": "I. Nuclear Spin-Internal-Rotation Coupling. II. Fluorine Spin-Rotation Interaction and Magnetic Shielding in\r\nFluorobenzene", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11232015-132330206", "creators": [ { "name": { "family": "Dubin", "given": "Alan Sander" }, "id": "Dubin-Alan-Sander", "display_name": "Dubin, Alan Sander" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BQRF-JJ35", "abstract": "Part I.
\r\nThe interaction of a nuclear magnetic moment situated on an internal top with the magnetic fields produced by the internal as well as overall molecular rotation has been derived following the method of Van Vleck for the spin-rotation interaction in rigid molecules. It is shown that the Hamiltonian for this problem may be written
\r\nHSR = \u1fd9 \u00b7 M \u00b7 \u0134 + \u1fd9 \u00b7 M\u201d \u00b7 \u0134\u201d
\r\nWhere the first term is the ordinary spin-rotation interaction and the second term arises from the spin-internal-rotation coupling.
\r\nThe F19 nuclear spin-lattice relaxation time (T1) of benzotrifluoride and several chemically substituted benzotrifluorides, have been measured both neat and in solution, at room temperature by pulsed nuclear magnetic resonance. From these experimental results it is concluded that in benzotrifluoride the internal rotation is crucial to the spin relaxation of the fluorines and that the dominant relaxation mechanism is the fluctuating spin-internal-rotation interaction.
\r\nPart II.
\r\nThe radiofrequency spectrum corresponding to the reorientation of the F19 nuclear moment in flurobenzene has been studied by the molecular beam magnetic resonance method. A molecular beam apparatus with an electron bombardment detector was used in the experiments. The F19 resonance is a composite spectrum with contributions from many rotational states and is not resolved. A detailed analysis of the resonance line shape and width by the method of moments led to the following diagonal components of the fluorine spin-rotational tensor in the principal inertial axis system of the molecule:
\r\nF/Caa = -1.0 \u00b1 0.5 kHz
\r\nF/Cbb = -2.7 \u00b1 0.2 kHz
\r\nF/Ccc = -1.9 \u00b1 0.1 kHz
\r\nFrom these interaction constants, the paramagnetic contribution to the F19 nuclear shielding in C6H5F was determined to be -284 \u00b1 ppm. It was further concluded that the F19 nucleus in this molecule is more shielded when the applied magnetic field is directed along the C-F bond axis. The anisotropy of the magnetic shielding tensor, \u03c3\u201d - \u03c3\u22a5, is +160 \u00b1 30 ppm.
\r\n" }, { "name": "Fung, Bing-Man", "degree": "PhD", "year": "1967", "title": "I. Study of Hydrogen Bonding by Infrared Spectroscopy and Nuclear Magnetic Resonance. II. Electron Paramagnetic Resonance of Mn(II) Complexes in Acetonitrile", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122002-131924", "creators": [ { "name": { "family": "Fung", "given": "Bing-Man" }, "id": "Fung-Bing-Man", "display_name": "Fung, Bing-Man" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/38M4-4C81", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPart I.\r\n\r\n\r\nThe infrared and near infrared spectra of acetic acid, d [subscript 3-] acetic acid, acetic acid-d, formic acid, d-formic acid, formic acid-d, HOD and methanol have been studied in several organic solvents. The solvents used were acetone, acetonitrile, dimethylsulfoxide, dioxane, tetrahydrofuran and their perdeuterated analogues. The spectra were characterized on the basis of the formation of 1-1 hydrogen bonded complexes between the proton donors and the solvent molecules. A one-dimensional double minimum potential function was developed and then calculated for each hydrogen bonded complex. The principles of treating the problem in a more complete way, namely, including the interaction between the A-H vibration and the A-B vibration in the complex A-H...B, were outlined.\r\n\r\nThe nuclear magnetic resonance of the hydroxyl proton of acetic acid dissolved in acetone, dimethylsulfoxide, dioxane and tetrahydrofuran has been investigated. The results are discussed in terms of the equilibria between the acid monomer, the acid dimer and the acid-solvent complex in dilute solutions of acid. The equilibrium constant for each system and the hydroxyl proton chemical shift for the hydrogen bonded complexes were obtained.\r\n\r\nThe infrared and near infrared spectra and the nuclear magnetic resonance of the hydrogen biacetate anion have been studied. Potential curve, equilibrium constant and proton chemical shift for this species were calculated.\r\n\r\nPart II.\r\n\r\nElectron paramagnetic resonance for Mn(II) was studied in the systems Mn(ClO[subscript4])[subscript 2] in acetonitrile. The g value and hyperfine interaction constant were determined for the complexes Mn(CH[subscript 3]CN)[subscript 6][superscript ++], MnCl[subscript 4][superscript=], MnBr[subscript 4][superscript=]. Computer-simulated e.s.r. spectra were obtained and compared with the experimental spectra." }, { "name": "Galley, William Claude", "degree": "PhD", "year": "1967", "title": "Triplet Energy Delocalization in Polynucleotide-Acridine Complexes", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09172002-162743", "creators": [ { "name": { "family": "Galley", "given": "William Claude" }, "id": "Galley-William-Claude", "display_name": "Galley, William Claude" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QTHP-8Y47", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nTransfer of triplet electronic excitation energy from the purine and/or pyrimidine moities of native DNA and adenine polynucleotides to the acridine dye 9-aminoacridine has been demonstrated at 77 [degrees] K. The occurrence of such transfers indicates that there is pi electron overlap between the purine and/or pyrimidine bases and the dye bound to the polymer.\r\n\r\nThe acridine dye has then been used as a trap for the polymer triplet excitation energy. The polymer to dye dependence of the base to dye transfer efficiency indicates that triplet energy is delocalized in native DNA and adenine polynucleotides. Kinetic studies provide evidence that the pathlength for triplet energy transfer in native DNA is determined by trapping within the polymer rather than by diffusion.\r\n\r\nDelayed fluorescence from the dye bound to DNA has been observed and its origin in the triplet state of the polymer has been confirmed at high polymer to dye ratios. In addition it has been shown that delayed fluorescence can arise from triplet-triplet annihilation between dyes at low polymer to dye ratios." }, { "name": "Galloway, Terry Randolph", "degree": "PhD", "year": "1967", "title": "A Study on the Mechanism of Molecular Transport with Systems of Gaseous Paraffins and of Convective Transport from Single Cylinders, Single Spheres, and Arrays of Spheres into Turbulently Flowing Streams", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182002-074117", "creators": [ { "name": { "family": "Galloway", "given": "Terry Randolph" }, "id": "Galloway-Terry-Randolph", "display_name": "Galloway, Terry Randolph" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/G08F-3042", "abstract": "PART I.
\r\n\r\nIntermolecular pair potential functions for the Leonard-Jones ∞-6, 12-6, and 9-6 form, and of the three parameter forms of Morse and of Kihara for a spherical core, were used to fit new gas phase viscosity data at low pressure for the normal paraffins through n-decane. The intermolecular force parameters were obtained and found to be unique for the Morse and Kihara potentials. All potential models underestimated the temperature dependence of the viscosity, but the Kihara was found to be superior with deviations of several percent.
\r\n\r\nThe Eucken relation for predicting the gas phase thermal conductivities of gaseous paraffins at low pressure proved to 18% low. Configurational thermal conductivities were calculated from experimental data, and a new form of conductivity excess above the configurational value was developed which produced a quantitative relationship to the heat capacity excess. This relation was compared with a number of theories and found to be in agreement, and it predicted the paraffin data within 4.9%.
\r\n\r\nBinary diffusion coefficient data were compiled and found to be in agreement with theoretical predictions, within the large experimental uncertainties associated with the data. Existing methods of prediction of viscosity and conductivity for binary mixtures of similar species were found to be inadequate for dissimilar systems and a more adequate but simple theoretical relation was shown to apply. Also the importance of the dense gas corrections involved in high pressure gas phase viscosities and conductivities are discussed.
\r\n\r\nPART II.
\r\n\r\nSimilarity solutions of the Blasius form to the problem of flow around a circular cylinder and sphere at moderately high Reynolds numbers were obtained for the general case of variable Prandtl (or Schmidt) groups. A dimensionless ratio referred to as the Fr\u00f6ssling group\" was obtained from these solutions which proved to be most useful in understanding the mechanism of transport from bluff bodies into turbulently flowing streams and into separated wake-flows. Quantitive experimental results were obtained for the influence of the level of turbulence in the main stream and effects of separation on the convective heat and mass transfer from cylinders and spheres. The Reynolds number was varied from 2,600 to 86,000 and free-stream turbulence from 0.013 to 0.25. These results were correlated in terms of the Fr\u00f6ssling group and compared with available experimental data within 7.7% for cylinders and 8.8% for spheres.
\r\n\r\nThe local Fr\u00f6ssling group was found to be proportional to the product of the turbulence level and the square root of the Reynolds number in the laminar flow region and increased strongly with Reynolds number in the wake. The local effects of turbulence were uniform from 35% increases at the forward stagnation. The point of separation was strongly delayed by turbulence. The transition to supercritical flow was established from the heat transfer measurements and found to agree with drag measurements. The local pressure coefficient was measured with a small pitot tube in the surface, and remained as unity at the forward stagnation point, independent of turbulence variations, and was altered only slightly near and following separation by varying Reynolds number and turbulence during subcritical conditions. The dependence of the position of separation upon Reynolds number and free-stream turbulence level was established quantitatively.
\r\n\r\nPART III.
\r\n\r\nThe mechanism of local transport in regular packed arrays of uniform spheres was studied in the light of boundary layer theory and the established behavior from bluff bodies. Local measurements were made with a movable calorimeter on the surface of a sphere placed in a rhombohedral No. 6 array. The effective local velocity and turbulence level within the array were determined. This model was found to predict available data in packed, distended, and fluidized beds of all shaped particles within 9.8%, and 12% for columns irrigated with liquid.
\r\n\r\nElectrostatic reproductions of photography on pp. 132,136, 220-221, 297-299, 308, 310, 368, 374, 376, 379, and 388 are not adequate.
\r\n\r\n" }, { "name": "Hoffman, Brian Mark", "degree": "PhD", "year": "1967", "title": "Interactions Between Molecules and Superconductors", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182002-132853", "creators": [ { "name": { "family": "Hoffman", "given": "Brian Mark" }, "id": "Hoffman-Brian-Mark", "orcid": "0000-0002-3100-0746", "display_name": "Hoffman, Brian Mark" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VMY9-GQ09", "abstract": "Recently, the possibility has been raised that interactions favorable to superconductivity might occur in molecules. Although most molecules or molecular aggregates are not even potentially superconducting, it has occurred to us that molecules can be coupled to metals through various kinds of bonds, and that such systems may then have interesting superconducting properties. Our approach to the preparation of such systems involves the deposition of selected molecules on thin metal films.
\r\n\r\nWe first present a discussion of the theory of superconductivity, including a review of some of the interaction mechanisms appropriate to molecules. The experimental apparatus is described. Our results are then reported and discussed. We have found compounds that increase the superconducting transition temperature and critical current of thin vanadium films, as well as others which decrease them, and we have found that the sign of this effect can be correlated in a simple way with the electronic structure of the molecules. The nature of these effects is partially clarified by comparison to similar experiments with indium films.
" }, { "name": "Hubbard, Arthur Thornton", "degree": "PhD", "year": "1967", "title": "Electrochemistry in Thin Layers of Solution", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202002-110337", "creators": [ { "name": { "family": "Hubbard", "given": "Arthur Thornton" }, "id": "Hubbard-Arthur-Thornton", "display_name": "Hubbard, Arthur Thornton" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SXRN-PW80", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nNew electrodes for electrochemistry in thin layers of solution have been constructed which are easier to use and give more reproducible data than previous designs. The theory of voltammetry, chronopotentiometry and chronocoulometry in thin layers is derived and verified for simple systems using these electrodes. The particular advantages of the thin layer approach for study of systems in which adsorption of the reactants can occur and for elucidation of the stoichiometry of complicated reactions have been exploited in the present work.\r\n\r\nThe extent of adsorption of the I[subscript 2] - I[superscript -], CoY[superscript -] - CoY[superscript -2] and FeY[superscript -] - FeY[superscript -2] couples (H[subscript 4]Y = ethylenediaminetetraacetic acid) at platinum electrodes has been determined. About 2 x 10[superscript -9] mole/cm.[superscript 2] of iodide ion or 2 x 10[superscript -9] mole/cm.[superscript 2] of iodide were shown to be adsorbed in a non-electroactive state. An additional 1 x 10[superscript -9] mole/cm[superscript 2] of iodine but no iodide was adsorbed in an electroactive state. About 3.1 x 10[superscript -10] mole/cm[superscript 2] of CoY[superscript -] or 4.7 x 10[superscript -10] mole/cm[superscript 2] of CoY[superscript -2] are adsorbed at bright platinum electrodes. No adsorption of FeY[superscript -] or FeY[superscript -2] was detected.\r\n\r\nThe stoichiometry of the electrochemical oxidation of PtCl[subscript 4][superscript -2], PtBr[subscript 4][superscript -2] and PtI[subscript 4][superscript -2], and of the electrochemical reduction of PtCl[subscript 6][superscript -2], PtBr[subscript 6][superscript -2] and PtI[subscript 6][superscript -2] and their hydrolysis products has been examined. The effect of acidity and halide concentration on these reactions was investigated. The reduction of PtCl[subscript 6][superscript -2] leads to PtCl[subscript 4][superscript -2] in solutions containing sufficient acid or chloride, but proceeds directly to platinum metal in neutral, chloride-free solutions. The reduction of PtBr[subscript 6][superscript -2] yields PtBr[subscript 4][superscript -2] in 1 F bromide solutions, but proceeds to the metal in either acid or neutral bromide-free solutions. The oxidation of PtCl[subscript 4][superscript -2] in 1 F chloride solutions appears to give a mixture of PtCl[subscript 6][superscript -2] and Pt(OH)[subscript 2]Cl[subscript 4][superscript -2] , whereas the oxidation of PtBr[subscript 4][superscript -2] in 1 F bromide solutions gives simply PtBr[subscript 6][superscript -2]. The products of hydrolysis of PtCl[subscript 6][superscript -2] and PtBr[subscript 6][superscript -2] are more readily reduced than are the parent complexes." }, { "name": "Itzkowitz, Martin Stanley", "degree": "PhD", "year": "1967", "title": "A Theoretical Study of the Electron Spin Resonance Spectra of Nitroxide Free Radicals", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09132002-115317", "creators": [ { "name": { "family": "Itzkowitz", "given": "Martin Stanley" }, "id": "Itzkowitz-Martin-Stanley", "display_name": "Itzkowitz, Martin Stanley" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EA9P-5Z37", "abstract": "We are concerned with the electron spin resonance spectra of nitroxide free radicals in various molecular environments. These radicals may be described as a single electron interacting anisotropically with an external field and a nitrogen nucleus of spin one. We use both exact and approximate solutions to the hamiltonian to simulate spectra from oriented samples. We then perform the orientation averages to obtain theoretical spectra from polycrystalline samples. We consider the effects of molecular motion on the system, and develop a Monte Carlo scheme to evaluate the spectrum for a variety of molecular tumbling rates. The theoretical spectra so computed are compared with experimental spectra taken in solutions of varying rotational correlation time; excellent agreement is obtained. We use the Monte Carlo calculation to estimate the rotational correlation time for the molecule in solution." }, { "name": "Iwamasa, Robert Tomatsu", "degree": "PhD", "year": "1967", "title": "A Study of the Polarization of Water and Methanol by Various Diamagnetic Ions in an Aprotic Solvent", "advisor": "Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09132002-123257", "creators": [ { "name": { "family": "Iwamasa", "given": "Robert Tomatsu" }, "id": "Iwamasa-Robert-Tomatsu", "display_name": "Iwamasa, Robert Tomatsu" } ], "advisors": [ { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hdzp-5312", "abstract": "Part I. Proton Magnetic Resonance Studies on the Polarization of Water and Methanol by NaClO[subscript 4], LiClO[subscript 4], Mg(ClO[subscript 4])[subscript 2], Et[subscript 4]NClO[subscript 4], Bu[subscript 4]NI, Et[subscript 4]NBr, and Et[subscript 4]NCl in an Aprotic Solvent.\r\n\r\n The polarization of water by NaClO[subscript 4], LiClO[subscript 4], Mg(ClO[subscript 4])[subscript 2], Et[subscript 4]NClO[subscript 4], Bu[subscript 4]NI, Et[subscript 4]NBr, and Et[subscript 4]NCl in acetone and acetonitrile has been investigated by studying the variation in the chemical shift of the water protons as a function of the salt and water concentration. The effects of cation solvation were obtained from the perchlorate salts since Et[subscript 4]NClO[subscript 4] showed no effect on the water resonance. The effects of anion polarization were obtained from the tetraalkylammonium salts.\r\n\r\n The chemical shifts at low salt and low water concentration are analyzed. Information on solvation constants and the chemical shifts of the solvated ion-water complex are reported and discussed. The results indicate the expected dependence on ion size and charge as well as on the solvent.\r\n\r\n Similar studies on the methanol molecule were made using acetonitrile as solvent. These studies have indicated that only one proton of the water molecules is complexed in the anion-water complex.\r\n\r\n The experimentally-determined polarization shifts of the OH proton in the various ion complexes of water and methanol are discussed in terms of the electric field and neighbor magnetic anisotropy effect.\r\n\r\nPart II. Infrared Spectroscopic Studies on the Influence of NaClO[subscript 4], LiClO[subscript 4], Mg(ClO[subscript 4])[subscript 2], Et[subscript 4]NClO[subscript 4], Bu[subscript 4]NI, Et[subscript 4]NBr, and Et[subscript 4]NCl on the OH Stretching Frequency of Water and Methanol in Acetonitrile.\r\n\r\n The effects of NaClO[subscript 4], LiClO[subscript 4], Mg(ClO[subscript 4])[subscript 2], Et[subscript 4]NClO[subscript 4], Bu[subscript 4]NI, Et[subscript 4]NBr, and Et[subscript 4]NCl on the OH stretching frequency for H[subscript 2]0 and CH[subscript 3]OH and on the OD stretching frequency of D[subscript 2]0 and CD[subscript 3]OH in acetonitrile have been investigated. This work was undertaken to supplement the proton magnetic resonance studies reported in Part I. The various complex bands attributed to the various solvated complexes have been assigned and interpreted in terms of the symmetry and the structure of the solvated ion complex.\r\n\r\nPart III. Infrared and Proton Magnetic Resonance Studies on the Polarization of Water and Methanol by Nat, LiI, and LiBr in an Aprotic Solvent.\r\n\r\n In Parts I and II, a study of the polarization of water and methanol in an aprotic solvent by various diamagnetic salts was reported for the case where the polarization is dominated by one ion. In the more general case, the polarization of water or methanol by diamagnetic salts can be effected by both cation and anion. In this part, the results of some infrared and proton magnetic resonance studies on the polarization of water and methanol by NaI, LiI, and LiBr in an aprotic solvent are reported.\r\n\r\n The infrared spectrum of the OH stretching and OD stretching vibration for the various ion complexes of water and methanol is characterized by the appearance of several bands. An attempt has been made towards the assignment and interpretation of the complex bands. The proton chemical shifts for the water resonance are also discussed and analyzed in terms of several possible ion water or methanol complexes." }, { "name": "Jones, Janet Gretchen", "degree": "PhD", "year": "1967", "title": "Ligand Bridging in the Oxidation of Chromium(II) at Mercury Electrodes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232002-120547", "creators": [ { "name": { "family": "Jones", "given": "Janet Gretchen" }, "id": "Jones-Janet-Gretchen", "display_name": "Jones, Janet Gretchen" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2cg1-tr65", "abstract": "Controlled potential electrolysis and electrochemical relaxation techniques have been used to investigate the mechanism of oxidation of chromium(II) at mercury electrodes in the presence of chloride, bromide, and iodide. It is shown that the major path for the oxidation is through a bridged activated complex of the type Hg---X--Cr.\r\n\r\nKinetic parameters have been determined for the bromide-dependent path and the halide-independent path. Equations have been derived to predict from kinetic data the product distribution between two competing reactions.\r\n\r\nIt is suggested that the activated complex is formed with halide adsorbed on the electrode surface.\r\n\r\nThe limitations of chronopotentiometry at hanging mercury drop electrodes have been investigated and corrections are given for spherical diffusion effects at times greater than 0.1 sec. It is demonstrated that reverse current chronopotentiometry under these conditions is a qualitatively unreliable technique." }, { "name": "Komai, Ralph Yutaka", "degree": "Masters", "year": "1967", "title": "A Study of the Effect of Viscosity on the Resolution of Bands in the Preparative Ultracentrifuge", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-090546085", "creators": [ { "name": { "family": "Komai", "given": "Ralph Yutaka" }, "id": "Komai-Ralph-Yutaka", "display_name": "Komai, Ralph Yutaka" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/570A-N634", "abstract": "Band velocity experiments in the preparative ultracentrifuge are usually performed in a linear density gradient established by mixing a 5% and a 20% sucrose solution. This stabilizing density gradient introduces a significant viscosity gradient which in turn may effect the resolving power of the sedimentation velocity experiment. The fast components travel on the average through more viscous solutions than do the slow components.\r\n\r\nIn this investigation the effect of viscosity gradients \r\nwas examined by experiments in which density stability was \r\nachieved by using a cesium chloride density gradient and the viscosity was independently controlled by introducing a uniform sucrose concentration or a positive or negative sucrose gradient in the cesium chloride gradient.\r\n\r\nExperiments performed with a mixture of tritiated thymidine labeled polyoma DNA components I, II, and III showed \r\nthat the separation of band maxima increased as the direction of the viscosity gradient was changed from positive to zero to negative with respect to field. On the other hand the band widths increased in the same order. The resolution in terms of the separation between the bands divided by the sum of the band widths was clearly lowest with the negative viscosity gradient and was approximately the same for the positive and zero viscosity gradients." }, { "name": "Lauer, George", "degree": "PhD", "year": "1967", "title": "I. Characterization of the Anodically Formed Oxide Film on Platinum Electrodes. II. Development of Electrochemical Instrumentation", "advisor": "Anson, Fred C.; Osteryoung, Robert A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262002-120406", "creators": [ { "name": { "family": "Lauer", "given": "George" }, "id": "Lauer-George", "display_name": "Lauer, George" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Osteryoung", "given": "Robert A." }, "id": "Osteryoung-R-A", "role": "advisor", "display_name": "Osteryoung, Robert A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9hyg-5140", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nThe oxygen containing film formed at anodically polarized platinum electrodes in oxyacid solutions has been characterized. By making use of a thin layer electrode it is shown that the film is composed of Pt(II) and Pt(IV) oxides. This was proven by oxidizing the electrodes, and then stripping the oxides with acidic chloride solution and then analyzing, coulometrically, the platinum chlorides in solution. It is shown that the discrepancy between anodic charge passed during oxidation and the cathodic charge passed during reduction is due to Pt(IV) oxide which is not reducible at potentials anodic of the hydrogen evolution reaction.\r\n\r\nThe oxides decompose slowly in formal sulfuric acid to form hydrogen peroxide and platinum; elevated temperatures accelerate the decomposition. A correlation is drawn between the presence of Pt(IV) on the surface of the electrode and \"activation\" of the electrode. It is concluded that the cause of activation is irreducible oxide.\r\n\r\nA standard electrode free of oxides can be obtained by immersion in 1 F H2SO4 at 100[degrees] C. It is proposed that such pretreatment is an excellent point of departure for further investigations with platinum electrodes.\r\n\r\nIt is shown that ozone is evolved in sulfuric and perchloric acids at potentials more positive than 1.3 volts with respect to the saturated calomel electrode. The evolved ozone is reduced at 1.1 volts.\r\n\r\nIn the second portion the use of operational amplifiers in electrochemical control and measurement instrumentation is discussed, and the simplified theory is presented. The design and construction of a multi-purpose electrochemical control instrument is discussed and a complete set of construction instructions is given. The last section considers the use of a small general purpose digital computer as an on-line digital data acquisition instrument. The interfacing and the logical circuitry required to perform electrochemical experiments with such a computer are described." }, { "name": "Lu, Chien-Shih", "degree": "PhD", "year": "1967", "title": "A Thermodynamic Study of Multiple Reaction Systems At and Near Equilibrium", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10012002-101446", "creators": [ { "name": { "family": "Lu", "given": "Chien-Shih" }, "id": "Lu-Chien-Shih", "display_name": "Lu, Chien-Shih" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pjnw-bc68", "abstract": "The near-equilibrium dynamic behavior of a homogeneous batch chemical reactor in which only one reaction occurs has been studied. The system has been analyzed thermodynamically and kinetically near equilibrium. The equations obtained have been linearized and then solved by means of Laplace transform techniques. The derivation for isobaric case has been presented in detail. The solutions for other cases, which include isothermal, isochoric, and adiabatic, have also been given. One numerical application indicates that the linearized equations can be useful even for protracted time intervals providing the forcing function is sufficiently small.\r\n\r\nA general expression for the displacement of extent of reactions and mole fractions for multiple reaction systems near equilibrium has been derived. The displacement of extent of reactions for a two-reaction system which obeys ideal solution laws under isobaric condition has also been given. A numerical example has been worked out. The result agrees with the one obtained by brute force approach.\r\n\r\nThe condition for a multiple reaction system to obey LeChatelier's theorem is derived. It is shown that for the system to obey the theorem the matrix composed of Onsager phenomenological coefficients must be positive definite.\r\n\r\nExpressions for the initial distribution of reactants required to maximize a desired product or to suppress an undesired product of a system of chemical reactions proceeding toward equilibrium have been derived. The system consists of R independent reactions and behaves as an ideal solution. It is assumed that the initial feed contains only the reactants and no inerts are present. Three different cases have been considered. They are isothermal-isobaric, isothermal-isochoric and adiabatic-isobaric. The expressions are implicit and complex so that no direct conclusion can be deduced. However, a numerical example (methane-steam system) shows that the effect of initial feed on the distribution of the final product is significant and deserves attention." }, { "name": "Moses, Francis Guy", "degree": "PhD", "year": "1967", "title": "I. The Thermolysis of Acetyl Peroxide. and II. The Photosensitized Decomposition of Acetyl Peroxide in Solution", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10022002-083657", "creators": [ { "name": { "family": "Moses", "given": "Francis Guy" }, "id": "Moses-Francis-Guy", "display_name": "Moses, Francis Guy" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0whd-rp13", "abstract": "Part I.
\r\nThe mechanism of the thermal decomposition of acetyl peroxide has been reinvestigated. The intermediacy of acetoxyl radicals has been demonstrated by a scavenging technique and evidence is presented which strongly suggests that the rate constant for acetoxyl radical decarboxylation is of the order of 2 x 10[superscript 9] sec.[superscript -1]. A primary process involving mainly simple 0_0 bond scission followed by acetoxyl radical decarboxylation at a rate competitive with diffusive separation of the radicals satisfies the results quite consistently.
Part II.
\r\nThe photosensitized decomposition of acetyl peroxide by certain aromatic hydrocarbons and ketone has been studied. The evidence suggests that the extent of \"primary\" decarboxylation is a function of the triplet state energy of sensitizer. A second major mode of destruction of peroxide appears to be operative in the decompositions sensitized by ketones. Mechanisms are suggested to explain these processes.
I. The synthesis of conformationally stable carbohydrates by use of the dialdehyde cyclization method of Baer and Fischer has been investigated. The synthesis of two new 3-C-alkyl-3-aminoaldohexose derivatives was achieved and the full structure elucidation of one of these compounds, methyl 3-isopropyl-3-amino-3-deoxy-[alpha]-D-gulopyranoside hydrochloride, has been accomplished.
\r\n\r\nII. A study of the stereoselective synthesis of compounds related to eremophilone by use of the Michael reaction has been performed and the synthesis of compounds stereochemically related to eremophilone has been accomplished.
\r\n" }, { "name": "Schmidt, Donald Emil, Jr.", "degree": "PhD", "year": "1967", "title": "Part I. \u03b1-Secondary Isotope Effects on the Reaction Catalyzed by the Enzyme Fumarase. Part II. Salt Effects on the Enzyme Fumarase", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10042002-125501", "creators": [ { "name": { "family": "Schmidt", "given": "Donald Emil, Jr." }, "id": "Schmidt-Donald-Emil", "display_name": "Schmidt, Donald Emil, Jr." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D85P-2N72", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPART I\r\n\r\nThe [alpha]-secondary isotope effect of L-malic-2-T-1, 4-C[superscript 14] acid on the reaction catalyzed by fumarase was determined. Evidence was presented which indicated that the reaction proceeded by formation of a carbonium ion in a rate-determining state at C-2 which possesses little sp[superscript 2] character.\r\n\r\nPART II\r\n\r\nThe effects of sodium bromide and sodium phosphate at pH 7.3 and 27[degrees] were determined. A partial kinetic and mechanistic scheme has been developed to explain these effects.\r\n\r\n" }, { "name": "Shim, Sang Chul", "degree": "PhD", "year": "1967", "title": "Part One. Photochemical Cis\u21ccTrans Isomerization of \u03b2-Styrylnaphthalene. Part Two. Photochemistry of N-Methyl-4-Pyridone and N-Methyllutidone", "advisor": "Hammond, George Simms; Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072002-103918", "creators": [ { "name": { "family": "Shim", "given": "Sang Chul" }, "id": "Shim-Sang-Chul", "display_name": "Shim, Sang Chul" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" }, { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/aym7-2k91", "abstract": "PART ONE.
\r\n\r\nPhotochemical cis\u21cctrans isomerization of \u03b2-styrylnaphthalene is studied by direct irradiation with light of various wavelengths and irradiation in the presence of sensitizers. A very unusual \"negative\" wavelength effect on quantum yields of trans\u2192cis isomerization by direct irradiation is observed. The interpretation of this observation is presented in terms of multiple conformers of electronically excited states which are not interconvertible. The study of fluorescence spectra confirms the interpretation. Sensitizers transfer triplet energy quite efficiently to \u03b2-styrylnaphthalene. However, benzophenone whose triplet energy is considered to be high transfers triplet excitation preferentially to the cis isomer. Quenching constants, both kqc and kqt, were expected to be diffusion controlled. However, the study of the photostationary states and quantum yields of sensitized isomerization indicates the opposite for the benzophenone. A significant quantum waste is observed and interpreted in terms of localization of excitation in the naphthalene chromophore. The effect was far more pronounced in direct isomerization perhaps because the excited singlets are shorter lived than triplets made by energy transfer. Definitely a singlet mechanism is involved, perhaps in conjunction with other mechanisms, in direct isomerization. This is confirmed by the studies of quantum yields, photostationar y states, and side reactions. The studies of solvent effect and concentration effect on quantum yields in direct isomerization are also presented. 60Co \u03b3-ray radiolysis of \u03b2-styrylnaphthalene in benzene indicates that the triplet mechanism is responsible for the isomerization of \u03b2-styrylnaphthalene in the radiolysis of benzene solution. The detailed study of G values and radiostationary states are presented with the discussions of the nature of the reaction. The implications of above studies in the study of other photoreactions are presented.
\r\n\r\nPART TWO.
\r\n\r\nThe photochemistry of the model compounds for pyrimidine bases, N-methyl-4-pyridone and N-methyllutidone, is reported. Spectroscopic and chemical studies on the irradiations of these compounds in aqueous solutions indicate that the hydration occurs at the \u03b1-position and leads to ring opening. The products obtained from ring opening undergo some unknown reactions, perhaps photo-oxidations and polymerizations.
\r\n\r\n" }, { "name": "Smith, Stephen Charles", "degree": "Masters", "year": "1967", "title": "Analysis and Interpretation of the Fluorine N.M.R. Spectrum of 1,3-Dimethoxy-1,1,2,3,3-Pentafluoropropane", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072010-114932724", "creators": [ { "name": { "family": "Smith", "given": "Stephen Charles" }, "id": "Smith-Stephen-Charles", "display_name": "Smith, Stephen Charles" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0Z2N-CM78", "abstract": "A variety of physical techniques including infrared, micro\u00adwave and Raman spectrocopies and dipole measurements have been used to study conformational preferences and restricted rotation in aliphatic compounds. N. m. r. spectra are now of recognized utility in studies of this sort (1, 2, 3, 4).
\r\n\r\nThis thesis is concerned with a study of the n. m. r. spectrum of 1, 3-dimethoxy-1, 1, 2, 3, 3-pentafluoropropane (I) and presents information about the propensities for conformational preferences in alkyl fluoroalkyl ethers.
" }, { "name": "Steadman, Vivian Louise", "degree": "Masters", "year": "1967", "title": "Some Factors Which Affect the Spin Densitites of Protons, with Particular Emphasis on the \u03b2-Protons of Cyclobutenyl", "advisor": "McLachlan, Andrew D.; McKoy, Basil Vincent", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-160004325", "creators": [ { "name": { "family": "Steadman", "given": "Vivian Louise" }, "id": "Steadman-Vivian-Louise", "display_name": "Steadman, Vivian Louise" } ], "advisors": [ { "name": { "family": "McLachlan", "given": "Andrew D." }, "id": "McLachlan-A-D", "role": "advisor", "display_name": "McLachlan, Andrew D." }, { "name": { "family": "McKoy", "given": "Basil Vincent" }, "id": "McKoy-B-V", "role": "advisor", "display_name": "McKoy, Basil Vincent" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6S0F-1650", "abstract": "Both first-order and variational valence bond calculations were made to estimate the ESR hyperfine splittings of the \u03b2-protons of cyclobutenyl. The ESR spectrum of the radical has not been obtained; but on the basis of these calculations, it is anticipated that the \u03b2-proton splittings will be large and in the range 42g to 101g. The first-order results indicate considerably larger splittings than the variational calculation; this situation was shown to be in marked contrast with another valence bond calculation on a free radical containing \u03b2-protons. Possible inequality in the \u03b2-proton splittings of cyclobutenyl at low temperatures was also discussed.\r\n\r\nThe dependence of the spin densities of \u03b2-protons on \u03c0-electron excitation energies (in appropriate free radicals) was discovered and was shown to reduce the size of the \u03b2-proton hyperfine splittings. The agreement with experiment was satisfactory.\r\n\r\nThe transformation between the vector-coupling states for an eight electron system and its canonical states was obtained. The canonical states were found to be especially amenable to computer computations, involving the non-overlap, empirical valence bond theory.\r\n\r\nThe reasons for the suitability of the use of vector-coupling functions in configuration interaction in the valence bond theory were discussed. A case was presented in which it appeared desirable to distribute the antisymmetrical spatial components of the ground-state\r\nwave function somewhat differently in space than that of the symmetrical spatial components.\r\n\r\nAn anomaly in the ESR spectra of irradiated benzene was deduced from theoretical considerations." }, { "name": "Wetmur, James Gerard", "degree": "PhD", "year": "1967", "title": "Studies on the Kinetics of Renaturation of DNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232002-113015", "creators": [ { "name": { "family": "Wetmur", "given": "James Gerard" }, "id": "Wetmur-James-Gerard", "display_name": "Wetmur, James Gerard" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YB2H-T758", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nA temperature jump system is described for studying fast DNA renaturation reactions. The reaction is found to be second order as seen in the time course of the reaction and in the concentration dependence of the rate. The stepwise base-pairing model of Saunders and Ross is extended to allow varying DNA base composition. Rate constants calculated with this model are compared with experimental rate constants at varying temperatures.\r\n\r\nT4 and T7 DNAs were fragmented by various procedures. The molecular weight of denatured DNA was determined by alkaline sedimentation. For a given DNA, fragmented into different molecular weights, the rate of renaturation is found to be proportional to the square root of the molecular weight. The rate of renaturation of DNA was measured in sucrose, glycerol, ethylene glycol and sodium perchlorate solutions. The melting temperature of DNA is changed by different amounts in each solvent. Nevertheless, the rate constant multiplied by the viscosity and divided by the renaturation temperature is found to be a constant. Thus, the rate determining step must be hydrodynamically limited.\r\n\r\nThe complexity of the DNA of an organism is defined as the total DNA complement of the organism. The rates of renaturation of SV40, T7, Nl, T4, E coli and Ascites tumor DNA (non-repeated sequences) are inversely proportional to the complexity. After complexity correction, the rate of renaturation is found to depend slightly on the GC content of the DNA. The stepwise renaturation model predicts this result.\r\n\r\nA method is described for positively staining electron microscope grids prepared by the method of Kleinschmidt and Zahn.\r\n\r\nSome properties of N1 DNA are described. The DNA has a buoyant density corresponding to 64% GC, a molecular weight of 33 X 10[^6]and the property of reversible cyclization like lambdoid phage DNAs." }, { "name": "Beineke, Thomas Andrew", "degree": "PhD", "year": "1966", "title": "I. The Crystal Structure of a New Dimer of Triphenylfluorocyclobutadiene. II. A Low Temperature Refinement of the Cyanuric Triazide Structure", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172015-153545633", "creators": [ { "name": { "family": "Beineke", "given": "Thomas Andrew" }, "id": "Beineke-Thomas-Andrew", "display_name": "Beineke, Thomas Andrew" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5R0B-0W61", "abstract": "I. The Crystal Structure of a New Dimer of Triphenylfluorocyclobutadiene
\r\n\r\nThe crystal structure of thermal isomer of the \u201chead-to-head\u201d dimer of triphenylfluorocyclobutadiene was determined by the direct method. The \u03a32 relationship involving the low angle reflections with the largest E\u2019s were found and solved for the signs by the symbolic method of Zachariasen. The structure was seen in the electron density map and the E-map, and was refined antisotropically by the method of least squares. The residual R was 0.065.
\r\n\r\nThe structure is a gem-difluorohexaphenyldihydropentalene. All of the phenyl groups are planar as it is the cyclopentadiene ring of the dihydropentalene skeleton. Overcrowding at the position of the flourines causes some deviations from the normal bond angles in the cyclopentene ring.
\r\n\r\nThe list of observed and calculated structure factors on pages 32-34 will not be legible on the microfilm. Photographic copies may be obtained from the California Institute of Technology.
\r\n\r\nII. A Low Temperature Refinement of the Cyanuric Triazide Structure
\r\n\r\nThe structure of cyanuric triazide was refined anisotropically by the method of least squares. Three-dimensional intensity data, which has been collected photographically with MoK\u03b1 radiation at -110\u02daC, were used in the refinement. The residual R was reduced to 0.081.
\r\n\r\nThe structure is completely planar, and there is no significant bond alternation in the cyanuric ring. The packing of the molecules causes the azide groups to deviate from linearity by 8 degrees.
\r\n" }, { "name": "Brueckner, David Armstrong", "degree": "Masters", "year": "1966", "title": "Studies in enzyme crystallography", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062010-111323235", "creators": [ { "name": { "family": "Brueckner", "given": "David Armstrong" }, "id": "Brueckner-D-A", "display_name": "Brueckner, David Armstrong" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/W06N-8494", "abstract": "This thesis presents X-ray crystallographic research on chymotrypsin and lysozyme. Seven crystal types of chymotrypsin were identified -- five for the first time. The seven crystal types appear to be different packings of two conformations of the same molecule.\r\n\r\nOne crystal type of lysozyme was studied. From Patterson projections of crystals diffused with PtI_6^= ions, the x, y, and z coordinates for these ions were determined. After one least squares refinement of these coordinates, the agreement factor between calculated and observed contributions of the PtI_6^= ions was 0.34 for 108 hkO and hOl reflections. Using these coordinates, an hkO and an hOl Fourier projection were prepared.\r\n\r\nX and y coordinates for the heavy atoms in lysozyme crystals diffused with UO_2^(++) ions, WO_4^= ions, HgI_4^= ions, HgCl_2, ThCl_4, and p-ClHg\u0444SO_3H were determined from Patterson and Fourier projections.\r\n" }, { "name": "Chen, Shiou-Shan", "degree": "PhD", "year": "1966", "title": "Mass Transfer from a Cylinder to an Air Stream in Axisyrnmetrical Flow (an Experimental Study)", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09102015-141338965", "creators": [ { "name": { "family": "Chen", "given": "Shiou-Shan" }, "id": "Chen-Shiou-Shan", "display_name": "Chen, Shiou-Shan" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8V6K-1R36", "abstract": "Mass transfer from wetted surfaces on one-inch cylinders with unwetted approach sections was studied experimentally by means of the evaporation of n-octane and n-heptane into an air stream in axisymmetrical flow, for Reynolds numbers from 5,000 to 310,000. A transition from the laminar to the turbulent boundary layer was observed to occur at Reynolds numbers from 10,000 to 15,000. The results were expressed in terms of the Sherwood number as a function of the Reynolds number, the Schmidt number, and the ratio of the unwetted approach length to the total length. Empirical formulas were obtained for both laminar and turbulent regimes. The rates of mass transfer obtained were higher than theoretical and experimental results obtained by previous investigators for mass and heat transfer from flat plates.
" }, { "name": "Christensen, Charles Richard", "degree": "PhD", "year": "1966", "title": "I. Chronopotentiometry in Thin Layers of Solution. II. Application of Thin Layer Chronopotentiometry to Kinetic Studies. III. Proton Spin Relaxation in Hydrogen Deuteride", "advisor": "Anson, Fred C.; Chan, Sunney I.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12012011-093412038", "creators": [ { "name": { "family": "Christensen", "given": "Charles Richard" }, "id": "Christensen-Charles-Richard", "display_name": "Christensen, Charles Richard" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Chan", "given": "Sunney I." }, "id": "Chan-S-I", "role": "advisor", "display_name": "Chan, Sunney I." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5XJ1-PF05", "abstract": "Part I:
\r\n\r\n\r\nThe theory of chronopotentiometry of an electroactive species confined in a thin layer of solution next to the electrode is presented. The potential-time and transition time relationships are verified for the reduction of iron(III) in 1F perchloric acid for solution layer\r\nthicknesses from 2 X 10^(-3) to 1 X 10^(-2) cm . The technique is shown to be especially useful for studying irreversible systems that give poor diffusion\r\nchronopotentiograms and for determining the number of electrons transferred in electrochemical reactions. Application of the technique to the oxidation of N,N-dimethyl-p-phenylenediamine in 1F sulfuric acid\r\nis demonstrated.
\r\n\r\nPart II:
\r\n\r\nA chronopotentiometric procedure is described for studying the rates of chemical reactions that occur subsequent to the electrochemical generation of a species that is confined in a thin layer of solution next to an electrode. The theory is verified for the hydrolysis of\r\np-benzoquinoneimine , and the technique is shown to be especially useful for the study of reactions too slow to be investigated conveniently by other voltammetric methods. Applicability of the technique to the study of ligand exchange reactions is demonstrated.
\r\n\r\nPart III:
\r\n\r\nThe HD proton spin-lattice relaxation time T_1 has been measured in pure HD and in mixtures with eight other gases as a function of composition at room temperature. Probabilities per collision for \u0394 m_J transitions are determined from the Schwinger relation and compared\r\nwith the values for pure H_2 and H_2 in the same gases. The differences are interpreted in terms of the displacement of the HD center of mass from the charge center of the molecule, and show up in a way correlated with the strengths of the interactions. With the assumptions that \u0394 J\r\ntransitions do not contribute to the nuclear spin relaxation and that the isotropic part of the H_2 intermolecular interaction is described by the Lennard-Jones potential, it is found that the Bloom-Oppenheim\r\ntheory does not explain the large difference in relaxation times for HD and H_2. A method of testing the form of isotropic intermolecular potential functions is proposed.
\r\n" }, { "name": "Couch, Harold Thompson", "degree": "PhD", "year": "1966", "title": "Part I. Latent Heat of Vaporization of N-Decane. Part II. Heat and Mass Transfer from a Cylinder in a Turbulent Air Stream - Sherwood and Fr\u00f6ssling Numbers as a Function of Free Stream Reynolds Number and Turbulence Level and Reynolds Number", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09142015-094917910", "creators": [ { "name": { "family": "Couch", "given": "Harold Thompson" }, "id": "Couch-Harold-Thompson", "display_name": "Couch, Harold Thompson" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/RHDM-SZ46", "abstract": "Part I
\r\n\r\nThe latent heat of vaporization of n-decane is measured calorimetrically at temperatures between 160\u00b0 and 340\u00b0F. The internal energy change upon vaporization, and the specific volume of the vapor at its dew point are calculated from these data and are included in this work. The measurements are in excellent agreement with available data at 77\u00b0 and also at 345\u00b0F, and are presented in graphical and tabular form.
\r\n\r\nPart II
\r\n\r\nSimultaneous material and energy transport from a one-inch adiabatic porous cylinder is studied as a function of free stream Reynolds Number and turbulence level. Experimental data is presented for Reynolds Numbers between 1600 and 15,000 based on the cylinder diameter, and for apparent turbulence levels between 1.3 and 25.0 per cent. n-heptane and n-octane are the evaporating fluids used in this investigation.
\r\n\r\nGross Sherwood Numbers are calculated from the data and are in substantial agreement with existing correlations of the results of other workers. The Sherwood Numbers, characterizing mass transfer rates, increase approximately as the 0.55 power of the\r\nReynolds Number. At a free stream Reynolds Number of 3700 the\r\nSherwood Number showed a 40% increase as the apparent turbulence level of the free stream was raised from 1.3 to 25 per cent.
\r\n\r\nWithin the uncertainties involved in the diffusion coefficients used for n-heptane and n-octane, the Sherwood Numbers are comparable for both materials. A dimensionless Fr\u00f6ssling Number is computed which characterizes either heat or mass transfer rates for cylinders on a comparable basis. The calculated Fr\u00f6ssling Numbers based on mass transfer measurements are in substantial agreement with Fr\u00f6ssling Numbers calculated from the data of other workers in heat transfer.
\r\n" }, { "name": "DeBoer, Charles David", "degree": "PhD", "year": "1966", "title": "Part I. Thermal Rearrangements of Small Ring Hydrocarbons. Part II. Photosensitized Rearrangements of Small Ring Hydrocarbons - Nonvertical Energy Transfer", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092009-135708", "creators": [ { "name": { "family": "DeBoer", "given": "Charles David" }, "id": "DeBoer-Charles-David", "display_name": "DeBoer, Charles David" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ffvv-9988", "abstract": "PART I
\r\n\r\nThe thermal rearrangements of cis- and trans-1, 2-divinylcyclobutane, cis- and trans-8-vinylbicyclo(4, 2, 0)-2-octene, trans1, 2-dimethy1-1, 2-divinylcyclobutane and trans-1-isopropeny1-2- methyl-2-vinylcyclobutane have been studied in detail. The kinetic parameters indicate that the rearrangements of the cis isomers occur by way of a concerted transition state while the trans isomers rearrange through a diradical intermediate. Optically active trans-1, 2-divinylcyclobutane undergoes racemization as well as rearrangement, and produces 4-vinylcyclohexene having a trace of residual optical activity. Consequently we infer that the rates of ring closure in the intermediate are of the same order of magnitude as the rates of internal rotation about single bonds.
\r\n\r\nWe have also studied the rates for the reversible isomerization of cis- and trans-1, 2-diphenylcyclopropane. Here the concerted mechanism is not possible for the cis isomer; both isomers appear to go through a diradical intermediate.
\r\n\r\nPART II
\r\n\r\nWe have observed the reversible photosensitized isomerization of cis- and trans-1, 2-diphenylcyclopropane. In contrast to the direct irradiation of diphenylcyclopropane, which gives several products, the sensitized reaction is very clean, giving only cis-trans isomerization. Comparison of the product ratios from the photosensitized decomposition of 3, 5-dipheny1-1-pyrazoline with the intercepts of Stern-Volmer plots for the sensitized isomerization of diphenylcyclopropane indicates that the same rotationally equilibrated species, 1, 3-diphenyltrimethylene, is produced in both cases. Apparently the triplet state of the diradical undergoes cis-trans equilibration before ring closure, while the singlet state, produced by either thermal decomposition or direct irradiation of the pyrazoline, does not. We infer from this that the rate of spin inversion is slower than the rate of internal rotation.
\r\n\r\nThe quantum yields for the reaction with many different sensitizers were measured, and the rate constants for the energy transfer step calculated from these. These rate constants show an approximate correlation with the triplet energy of the sensitizer.
" }, { "name": "Glazer, Edward Stanley", "degree": "PhD", "year": "1966", "title": "Applications of Nuclear Magnetic Resonance Spectroscopy to the Study of Medium-Sized Rings: I. Conformational Properties of Cycloheptane. II. Conformational Properties of Cyclo\u00f6ctane", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09242015-150926803", "creators": [ { "name": { "family": "Glazer", "given": "Edward Stanley" }, "id": "Glazer-Edward-Stanley", "display_name": "Glazer, Edward Stanley" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3V4M-PW36", "abstract": "Conformational equilibrium in medium-sized rings has been investigated by the temperature variation of the fluorine-19 n.m.r. spectra of 1, 1-difluorocycloalkanes and various substituted derivatives of them. Inversion has been found to be fast on the n.m.r. time scale at -180\u02da for 1, 1-difluorocycloheptane, but slow for 1, 1-difluoro-4, 4-dimethylcycloheptane at -150\u02da. At low temperature, the latter compound affords a single AB pattern with a chemical-shift difference of 841 cps. which has been interpreted in terms of the twist-chair conformation with the methyl groups on the axis position and the fluorine atoms in the 4-position. At room temperature, the n.m.r. spectrum of 1, 1-difluoro-4-t-butylcycloheptane affords an AB pattern with a chemical-shift difference of 185 cps. The presence of distinct trans and gauche couplings from the adjacent hydrogens has been interpreted to suggest the existence of a single predominant form, the twist chair with the fluorine atoms on the axis position.
\r\n\r\nInvestigation of 1, 1-difluorocyclo\u00f6ctane and 1, 1, 4, 4-tetrafluorocyclo\u00f6ctane has led to the detection of two kinetic processes both having activation energies of 8-10 kcal./mole but quite different A values. In light of these results eleven different conformations of cyclo\u00f6ctane along with a detailed description of the ways in which they may be interconverted are discussed. An interpretation involving the twist-boat conformation rapidly equilibrating through the saddle and the parallel-boat forms at room temperature is compatible with the results.
\r\n" }, { "name": "Herkstroeter, William George", "degree": "PhD", "year": "1966", "title": "Kinetic Studies of Energy Transfer to the Geometric Isomers of Stilbene and 1,2-Diphenylpropene by Kinetic Spectrophotometry", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182002-115322", "creators": [ { "name": { "family": "Herkstroeter", "given": "William George" }, "id": "Herkstroeter-William-George", "display_name": "Herkstroeter, William George" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5q92-f570", "abstract": "The rate constants for triplet energy transfer from a series of photosensitizers to the cis and trans isomers of stilbene and 1,2-diphenylpropene in benzene solution at room temperature have been measured by kinetic spectrophotometry. A plot of rate constants vs. triplet excitation energies of the sensitizers shows that there is a smooth transition from diffusion controlled to immeasurably small rates. Even when the triplet of the sensitizer is appreciably less energetic than the spectroscopic triplet of the acceptor, energy transfer takes place. In accord with previous work in these laboratories, this observation is interpreted in terms of non-vertical excitation in which the acceptor is excited to a triplet having lower energy and different geometry than the spectroscopic triplet. By contrast, dibenzcycloheptenol, selected as an isoenergetic and rigid model for cis-stilbene, accepts triplet energy less efficiently than cis-stilbene from a sensitizer having less than the spectroscopic triplet energy of these molecules. Evidence that 2, 4, 6-triisopropyl-4'-methoxybenzophenone transfers triplet energy to cis- and trans-stilbene at a reduced rate because of steric hindrance indicates that factors other than the relative triplet energies of sensitizer and acceptor can be important in the process of energy transfer." }, { "name": "Holmquist, Walter Richard", "degree": "PhD", "year": "1966", "title": "The Origin, Partial Structure, and Properties of Hemoglobin A\u2081\ua700", "advisor": "Schroeder, Walter Adolph", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182002-134944", "creators": [ { "name": { "family": "Holmquist", "given": "Walter Richard" }, "id": "Holmquist-Walter-ichard", "display_name": "Holmquist, Walter Richard" } ], "advisors": [ { "name": { "family": "Schroeder", "given": "Walter Adolph" }, "id": "Schroeder-W-A", "role": "advisor", "display_name": "Schroeder, Walter Adolph" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3J9E-MW80", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nHemoglobin A(Ic) is a minor hemoglobin component of normal adult humans and comprises approximately 5% of the total hemoglobin. This thesis describes the in vitro biosynthesis of A(Ic) and the chemical properties and structure of this component and its degradation products.\r\n\r\nA(Ic) was found to be biosynthesized concurrently with hemoglobin A, which is the major component (80-90%) in normal adult hemoglobin. A(Ic) is thus a normal constituent of all red cells, irrespective of their physiological age.\r\n\r\nChemically, A(Ic) is the condensation product--a Schiff base--between one molecule of hemoglobin A and one molecule of a ketone or aldehyde R==O. The point of linkage of R==O to hemoglobin A is the N-terminus of one of the two [beta] chains. Other than this, no difference has been found between the primary amino acid sequence of the [alpha] and [beta] chains of hemoglobin A(Ic) and A.\r\n\r\nThe ketone or aldehyde R==O has a molecular weight of approximately 281, is not an aromatic aldehyde, is not a steroid, and does not contain phosphorus, carbohydrates or amino acids. Esterified nonketo acyl groups of less than five carbon atoms are absent. It is probable, but not certain, that R==O does not contain nitrogen and that it does not contain any free carboxyl groups.\r\n\r\nMethods are described for isolating A(Ic) as well as smaller peptides which contain the blocking group R such as R=val-his. The use and construction of a large (10 x 100-cm) chromatographic column for the preparative isolation of minor hemoglobin components is described. This column is rather unique and should find applications in the isolation of other biological compounds. Certain other isolation procedures which are described in the thesis, such as the purification of peptides on cellulose phosphate, have not been previously described.\r\n\r\nFinally several miscellaneous theoretical aspects of the thesis are of interest. These include the theory of self-hybridization experiments, a theoretical treatment of protein biosynthesis which includes a method for correcting the experimental data for nonconstant ribosomal activity and for interconversions of the protein of interest to other proteins during the biosynthesis. A practical method for calculating ionization constants from paper electrophoretic data is also given.\r\n\r\nPhotographic materials on pp. 25, and 46 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered." }, { "name": "Hultgren, Glen Owen", "degree": "PhD", "year": "1966", "title": "A Theory of the Annulenes", "advisor": "Pitzer, Russell M.; McLachlan, Andrew D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202002-141107", "creators": [ { "name": { "family": "Hultgren", "given": "Glen Owen" }, "id": "Hultgren-Glen-Owen", "display_name": "Hultgren, Glen Owen" } ], "advisors": [ { "name": { "family": "Pitzer", "given": "Russell M." }, "id": "Pitzer-R-M", "role": "advisor", "display_name": "Pitzer, Russell M." }, { "name": { "family": "McLachlan", "given": "Andrew D." }, "id": "McLachlan-A-D", "role": "advisor", "display_name": "McLachlan, Andrew D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AAK2-Y031", "abstract": "It has been proposed that large annulenes have alternation of bond length. The height of the annulene singlet transition energies has been cited as evidence for bond alternation.\r\n\r\nThis thesis shows that the mechanism of bond alternation is inadequate to reproduce the experimental spectrum of the annulenes. I am able to explain the height of the annulene singlet transitions by the use of the alternant molecular orbital method.\r\n\r\nIt appears that simple MO methods and even limited C.I. treatments seriously underestimate the energy depression of the ground state through electron correlation.\r\n\r\nIt is shown that the tendency towards bond length alternation exhibited by the simple MO method is an artifact of this method, and should not be taken seriously. Some of the limitations of the AMO method are examined and it is shown how the AMO method may be extended to sigma as well as pi electron" }, { "name": "Lingane, Peter James", "degree": "PhD", "year": "1966", "title": "I. Chronoamperometry and Chronopotentiometry with Unshielded, Circular, Planar Electrodes. II. Applications of Potential Step Chronocoulometry. III. Faradaic Integration of the Diffuse Double Layer", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11292011-085122446", "creators": [ { "name": { "family": "Lingane", "given": "Peter James" }, "id": "Lingane-Peter-James", "display_name": "Lingane, Peter James" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S5G2-TP76", "abstract": "The first portion of this dissertation demonstrates both theoretically and experimentally that the chronoamperometric and chronopotentiometric\r\nconstants obtained with unshielded, circular, planar electrodes are of the form
\r\n\r\n[...]
\r\n\r\nHigher order terms appear to be unimportant under normal experimental conditions (1,2).
\r\n\r\nThe second portion presents the results of detailed calculations of \"working tables\" for double potential step chronocoulometry applied to the study of first-order chemical reactions of the form\r\n\r\n
[...]
\r\n\r\nwhere Y is non-electroactive. The double potential step chronocoulometric technique is applied to the study of the Ti(m)-hydroxylamine reaction (3) and it is shown that the previously determined value of the Arrhenius energy is inexplicably too small by a factor of two. A new\r\ntechnique for the estimation of the electrochemical parameters of electrode reactions from potential step data is developed (4) and it is shown that this technique eliminates the need for a short- or a long-time approximation.\r\n\r\nThe final sections discuss the results of chronopotentiometric and chronocoulometric experiments conducted in the presence of \"insufficient\"\r\nsupporting electrolyte. It is shown that the observed chronopotentiometric E-t curves should be distorted by the sum of \"liquid junction\" and \"iR_u\" voltages. Doublet chronopotentiometric waves are observed for the reduction of certain transition metals. The measured\r\nchronopotentiometric constant increases at high current densities and this is interpreted in terms of the reaction of electroactive material in the diffuse layer. It is shown that the residual uncompensated resistance in solutions of low concentrations of supporting electrolyte introduces sufficiently large uncertainties in the potential step chrono- coulometric Q-t^\u00bd intercepts as to invalidate this technique under these conditions.
\r\n\r\nA least-squares analysis of chronopotentiometric data for the estimation of adsorption statistics according to three common models is described and the listing of a suitable Fortran IV computer program is included.
\r\n\r\nExtensive tables are calculated for the amount of a doubly charged ion in the diffuse double layer as a function of the concentration of the singly charged indifferent electrolyte.
\r\n\r\n\r\n(1) Anal. Chem., 36, 1723 (1964).
\r\n\r\n(2) J. Phys. Chem. , 68, 3821 (1964).
\r\n\r\n(3) J. Electroanal. Chem., in press (1966).
\r\n\r\n(4) J. Electroanal. Chem. , 10, 284 (1965).
\r\n" }, { "name": "Neil, Gary Lawrence", "degree": "PhD", "year": "1966", "title": "The Structural Specificity of \u03b1-Chymotrypsin. I. Polypeptides as Substrates. II. N-Acylated Peptide Esters as Substrates. III. Some Reactive Esters of N-Acylated Amino Acids as Substrates", "advisor": "Hammond, George Simms; Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292015-113737929", "creators": [ { "name": { "family": "Neil", "given": "Gary Lawrence" }, "id": "Neil-Gary-Lawrence", "display_name": "Neil, Gary Lawrence" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" }, { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MHTA-3S12", "abstract": "The structural specificity of \u03b1-chymotrypsin for polypeptides and denatured proteins has been examined. The primary specificity of the enzyme for these natural substrates is shown to closely correspond to that observed for model substrates. A pattern of secondary specificity is proposed.
\r\n\r\nA series of N-acetylated peptide esters of varying length have been evaluated as substrates of \u03b1-chymotrypsin. The results are interpreted in terms of proposed specificity theories.
\r\n\r\nThe \u03b1-chymotrypsin-catalyzed hydrolyses of a number of N-acetylated dipeptide methyl esters were studied. The results are interpreted in terms of the available specificity theories and are compared with results obtained in the study of polypeptide substrates. The importance of non-productive binding in determining the kinetic parameters of these substrates is discussed. A partial model of the locus of the active site which interacts with the R\u20191CONH- group of a substrate of the form R\u20191CONHCHR2COR\u20193 is proposed.
\r\n\r\nFinally, some reactive esters of N-acetylated amino acids have been evaluated as substrates of \u03b1-chymotrypsin. Their reactivity and stereo-chemical behavior are discussed in terms of the specificity theories available. The importance of a binding interaction between the carboxyl function of the substrate and the enzyme is suggested by the results obtained.
\r\n" }, { "name": "Ohlenbusch, Heiko Herbert Emil Walter", "degree": "PhD", "year": "1966", "title": "Part I. Electric Birefringence Studies of Deoxyribonucleic Acids. Part II. Selective Dissociation of Nucleohistone Complexes", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10052015-092714954", "creators": [ { "name": { "family": "Ohlenbusch", "given": "Heiko Herbert Emil Walter" }, "id": "Ohlenbusch-Heiko-Herbert-Emil-Walter", "display_name": "Ohlenbusch, Heiko Herbert Emil Walter" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GA9Z-6S65", "abstract": "Part I
\r\nThe electric birefringence of dilute DNA solutions has been studied in considerable detail and on a large number of samples, but no new and reliable information was discovered concerning the tertiary structure of DNA. The large number of variables which effect the birefringence results is discussed and suggestions are made for further work on the subject.
\r\nThe DNA molecules have been aligned in a rapidly alternating (10 to 20 kc/sec) square wave field confirming that the orientation mechanism is that of counterion polarization. A simple empirical relation between the steady state birefringence, \u0394nst, and the square of the electric field, E, has been found: \u0394nst = E2/(a E2 + b), where a = 1/\u0394ns and b = (E2/\u0394nst)E\u2192o. \u0394ns is the birefringence extrapolated to infinite field strength.
\r\nThe molecules show a distribution of relaxation times from 10-4 to 0.2 sec, which is consistent with expectations for flexible coil molecules. The birefringence and the relaxation times decrease with increasing salt concentrations. They also depend on the field strength and pulse duration in a rather non-reproducible manner, which may be due in part to changes in the composition of the solution or in the molecular structure of the DNA (other than denaturation). Further progress depends on the development of some control over these effects.
\r\nPart II
\r\nThe specificity of the dissociation of reconstituted and native deoxyribonucleohistones (DNH) by monovalent salt solutions has been investigated. A novel zone ultracentrifugation method is used in which the DNH is sedimented as a zone through a preformed salt gradient, superimposed on a stabilizing D2O (sucrose) density gradient. The results, obtained by scanning the quartz sedimentation tubes in a spectrophotometer, were verified by the conventional, preparative sedimentation technique. Procedures are discussed for the detection of microgram quantities of histones, since low concentrations must be used to prevent excessive aggregation of the DNH.
\r\nThe data show that major histone fractions are selectively dissociated from DNH by increasing salt concentrations: Lysine rich histone (H I) dissociates gradually between 0.1 and 0.3 F, slightly lysine rich histone (H II) dissociates as a narrow band between 0.35 and 0.5 F, and arginine rich histone (H III, H IV) dissociates gradually above 0.5 F NaClO4.
\r\nThe activity of the partially dissociated, native DNH in sustaining RNA synthesis, their mobility and their unusual heat denaturation and renaturation behavior are described. The two-step melting behavior of the material indicates that the histones are non-randomly distributed along the DNA, but the implications are that the uncovered regions are not of gene-size length.
\r\n" }, { "name": "Olivera, Baldomero Marquez", "degree": "PhD", "year": "1966", "title": "The Interactions of Basic Proteins and DNA : I. Electrophoresis of the Nucleic Acids. II. The Cytochrome C/DNA Complex. III. Studies of the Electrophoresis and Melting Behavior of Nucleohistones. IV. The Dissociation of Histone from Calf Thymus Chromatin", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10012015-160718695", "creators": [ { "name": { "family": "Olivera", "given": "Baldomero Marquez" }, "id": "Olivera-Baldomero-Marquez", "display_name": "Olivera, Baldomero Marquez" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6NP0-3K17", "abstract": "I. ELECTROPHORESIS OF THE NUCLEIC ACIDS
\r\nA zone electrophoresis apparatus using ultraviolet optics has been constructed to study nucleic acids at concentrations less than 0.004%. Native DNA has a mobility about 15% higher than denatured DNA over a range of conditions. Otherwise, the electrophoretic mobility is independent of molecular weight, base composition or source. DNA mobilities change in the expected way with pH but the fractional change in mobility is less than the calculated change in charge. A small decrease in mobility accompanies an increase in ionic strength. RNA\u2019s from various sources have mobilities slightly lower than denatured DNA except for s-RNA which travels slightly faster. The important considerations governing the mobility of nucleic acids appear to be the nature of the hydrodynamic segment, and the binding of counterions. The differences between electrophoresis and sedimentation stem from the fact that all random coil polyelectrolytes are fundamentally free draining in electrophoresis.
\r\nII. THE CYTOCHROME C/DNA COMPLEX
\r\nThe basic protein, cytochrome c, has been complexed to DNA. Up to a cytochrome:DNA mass ratio of 2, a single type of complex is formed. Dissociation of this complex occurs between 0.05F and 0.1F NaCl. The complexing of cytochrome to DNA causes a slight increase in the melting temperature of the DNA, and a reduction of the electrophoretic mobility proportional to the decrease in net charge. Above a cytochrome:DNA mass ratio of 2.5, a different type of complex is formed. The results suggest that complexes such as are formed in the Kleinschmidt technique of electron microscopy would not exist in bulk solution and are exclusively film phenomena.
\r\nIII. STUDIES OF THE ELECTROPHORESIS AND MELTING BEHAVIOUR OF NUCLEOHISTONES
\r\nElectrophoresis studies on reconstituted nucleohistones indicate that the electrophoretic mobility for these complexes is a function of the net charge of the complex. The mobility is therefore dependent on the charge density of the histone complexing the DNA, as well as on the histone/DNA ratio. It is found that the different histones affect the transition from native to denatured DNA in different ways. It appears that histone I is exchanging quite rapidly between DNA molecules in 0.01 F salt, while histone II is irreversibly bound. Histone III-IV enhances the capacity of non-strand separated denatured DNA to reanneal. Studies on native nucleoproteins indicate that there are no gene-sized uncomplexed DNA regions in any preparations studied.
\r\nIV. THE DISSOCIATION OF HISTONE FROM CALF THYMUS CROMATIN
\r\nCalf thymus nucleoprotein was treated with varying concentrations of NaCl. The identity of the histones associated and dissociated from the DNA at each salt concentration was determined by gel electrophoresis. It was found that there is no appreciable histone dissociation below 0.4 F NaCl. The lysine rich histones dissociate between 0.4 and 0.5 F NaCl. Their dissociation is accompanies by a marked increase in the solubility of the chromatin. The moderately lysine rich histones dissociate mainly between 0.8 and 1.1 F NaCl. There are two arginine rich histone components: the first dissociates between 0.8 F and 1.1 F NaCl, but the second class is the very last to be dissociated from the DNA (dissociation beginning at 1.0 F NaCl). By 2.0 F NaCl, essentially all the histones are dissociated.
\r\nThe properties of the extracted nucleoprotein were studied. The electrophoretic mobility increases and the melting temperature decreases as more histones are dissociated from the DNA. A comparison with the dissociation of histones from DNA in NaClO4 shows that to dissociate the same class of histones, the concentration of NaCl required is twice that of NaClO4.
\r\n" }, { "name": "Riggs, Arthur Dale", "degree": "PhD", "year": "1966", "title": "Part I. Studies on Mycoplasm gallisepticum. Part II. Autoradiography of Chromosomal DNA Fibers from Chinese Hamster Cells", "advisor": "Mitchell, Herschel K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08252008-095724", "creators": [ { "name": { "family": "Riggs", "given": "Arthur Dale" }, "id": "Riggs-Arthur-Dale", "display_name": "Riggs, Arthur Dale" } ], "advisors": [ { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "advisor", "display_name": "Mitchell, Herschel K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/P60E-AW11", "abstract": "Part I:
\r\n\r\nThe cell size, DNA content, and chromosome size and structure of Mycoplasma gallisepticum A5969 was studied. After calibrating a phase microscope with polystyrene latex spheres of known diameter, it was determined that the average cell volume in the living state is only 36 \u00b1 9 x 10-15 cm3, which is equivalent to the volume of a sphere 0.40 \u00b1 0.04 \u03bc in diameter.
\r\n\r\nBy a DNA determination method based on analysis for thymine, the DNA content of M. gallisepticum was found to be 4.0 \u00b1 0.6% of the dry weight. The DNA per colony forming unit was found to be 300 x 106 daltons. For these experiments, the cells were harvested by centrifugation. The results of later experiments, in which the cells were directly precipitated from a broth culture by the addition of trichloroacetic acid (TCA), suggested that there had been DNA loss during the centrifugation steps of the earlier experiments and that the DNA per clone forming unit is 1,200 \u00b1 200 x 106 daltons.
\r\n\r\nThe Cairns autoradiographic technique was used to visualize the chromosome of M. gallisepticum. The DNA autoradiograms seen indicated that its chromosome is 630 \u00b1 150 \u03bc long. This corresponds to 1,200 \u00b1 300 x 10106 daltons of DNA. The DNA autoradiograms often showed \"replication forks\" and were sometimes circular.
\r\n\r\nThe Kleinschmidt technique was also used to provide evidence on the size and structure of the chromosome of M. gallisepticum. Tangles of DNA were found that were very similar to those obtained from bacteria. The total length of DNA in the tangles indicated that the chromosome of M. gallisepticum is 500 \u00b1 200 \u03bc long, a value that supports the estimate obtained by autoradiography.
\r\n\r\nPart II:
\r\n\r\nLinear DNA autoradiograms were found when the Cairns technique was applied to Chinese hamster cells. At least 6% of these autoradiograms are more than 0.8 mm long - roughly the size of the E. coli chromosome and considerably longer than previously reported DNA fibers from higher organisms. Some rare autoradiograms are as long as 1.6 - 1.8 mm. The implications of these results in terms of models of chromosome structure are discussed.
\r\n" }, { "name": "Urey, John Clayton", "degree": "PhD", "year": "1966", "title": "Enzyme Induction in Neurospora crassa", "advisor": "Horowitz, Norman Harold", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262015-082758473", "creators": [ { "name": { "family": "Urey", "given": "John Clayton" }, "id": "Urey-John-Clayton", "display_name": "Urey, John Clayton" } ], "advisors": [ { "name": { "family": "Horowitz", "given": "Norman Harold" }, "id": "Horowitz-N-H", "role": "advisor", "display_name": "Horowitz, Norman Harold" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/MBMA-NM23", "abstract": "I. Studies on Nicotinamide Adenine Dinucleotide Glycohydrase (NADase)
\r\nNADase, like tyrosinase and L-amino acid oxidase, is not present in two day old cultures of wild type Neurospora, but it is coinduced with those two enzymes during starvation in phosphate buffer. The induction of NADase, like tyrosinase, is inhibited by puromycin. The induction of all three enzymes is inhibited by actinomycin D. These results suggest that NADase is synthesized de novo during induction as has been shown directly for tyrosinase. NADase induction differs in being inhibited by certain amino acids.
\r\nThe tyrosinaseless mutant ty-1 contains a non-dialyzable, heat labile inhibitor of NADase. A new mutant, P110A, synthesizes NADase and L-amino acid oxidase while growing. A second strain, pe, fl;cot, makes NADase while growing. Both strains can be induced to make the other enzymes. These two strains prove that the control of these three enzymes is divisible. The strain P110A makes NADase even when grown in the presence of Tween 80. The synthesis of both NADase and L-amino acid oxidase by P110A is suppressed by complete medium. The theory of control of the synthesis of the enzymes is discussed.
\r\nII. Studies with EDTA
\r\nNeurospora tyrosinase contains copper but, unlike other phenol oxidases, this copper has never been removed reversibly. It was thought that the apo-enzyme might be made in vivo in the absence of copper. Therefore cultures were treated with EDTA to remove copper before the enzyme was induced. Although no apo-tyrosinase was detected, new information on the induction process was obtained.
\r\nA treatment of Neurospora with 0.5% EDTA pH 7, inhibits the subsequent induction during starvation in phosphate buffer of tyrosinase, L-amino acid oxidase and NADase. The inhibition of tyrosinase and L-amino acid oxidase induction is completely reversed by adding 5 x 10-5M CaCl2, 5 x 10-4M CuSO4, and a mixture of L-amino acids (2 x 10-3M each) to the buffer. Tyrosinase induction is also fully restored by 5 x 10-4M CaCl2 and amino acids. As yet NADase has been only partially restored.
\r\nThe copper probably acts by sequestering EDTA left in the mycelium and may be replaced by nickel. The EDTA apparently removes some calcium from the mycelium, which the added calcium replaces. Magnesium cannot replace calcium. The amino acids probably replace endogenous amino acids lost to the buffer after the EDTA treatment.
\r\nThe EDTA treatment also increases permeability, thereby increasing the sensitivity of induction to inhibition by actinomycin D and allowing cell contents to be lost to the induction buffer. EDTA treatment also inhibits the uptake of exogenous amino acids and their incorporation into proteins.
\r\nThe lag period that precedes the first appearance of tyrosinase is demonstrated to be a separate dynamic phase of induction. It requires oxygen. It is inhibited by EDTA, but can be completed after EDTA treatment in the presence of 5 x 10-5M CaCl2 alone, although no tyrosinase is synthesized under these conditions.
\r\nThe time course of induction has an early exponential phase suggesting an autocatalytic mechanism of induction.
\r\nThe mode of action of EDTA, the process of induction and the kinetics of induction are discussed.
\r\n" }, { "name": "Valentine, Donald Herman", "degree": "PhD", "year": "1966", "title": "Part One. Thermal and Photosensitized Dimerizations of 1,3-Cyclohexadiene. Part Two. Photosensitized Isomerization of Stilbene: Further Studies", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232002-104139", "creators": [ { "name": { "family": "Valentine", "given": "Donald Herman" }, "id": "Valentine-Donald-Herman", "display_name": "Valentine, Donald Herman" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8qsr-dn54", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart One\r\n\r\nThermal dimerization of 1, 3-cyclohexadiene gives 4:1 mixtures of endo and exo tricyclo[6.2.2.0(^2,7)]dodeca-4, 9-diene, 1 and 2. Photosensitized dimerization of cyclohexadiene gives 90% yields of three products in about 3:1:1 ratio. The major photodimer was shown in two ways to be trans-cis-trans-tricyclo[6.4.0.0(^2,7)]dodeca-3, 11-diene, 3. One of the minor photodimers was shown to be exo-dicyclohexadiene, 2; the other photodimer was assigned the structure cis-cis-cis-tricyclo[6.4.0.0(^2,7)]dodeca-3,11-diene,4. Photodimerization of 2-cyclohexenone and its photoaddition to cyclohexene are described. The mechanism of the photosensitized dimerization of cyclohexadiene is considered. Quantum yields for the sensitized dimerization are lower than the expected value by varying factors depending upon the particular sensitizer. This effect is interpreted in terms of formation of a sensitizer triple t-cyclohexadiene complex which can break apart either to yield sensitizer ground state plus diene triplet or the ground states of both species. The photoaddition of sensitizers to cyclohexadiene is discussed; it is concluded that in some cases at least the diene triplet is the reactive intermediate leading to sensitizer-diene adducts. Thermal rearrangements of the dicyclohexadienes are studied. At higher temperatures, 3 rearranges smoothly to give 1 as the only product, and 4 rearranges to give 2. Surprisingly, various catalysts are able to effect the reverse conversions at and below room temperature. Kinetic studies of these rearrangements are described as are heat of combustion measurements which show that the cyclobutanes 3 and 4 are less stable than the thermal dimers 1 and 2. A discussion of the significance of these results is also given. \r\n\r\nPart Two\r\n\r\nReinvestigation of the Hammond-Saltiel description of the photosensitized isomerization of the stilbenes is reported. Most of the gross features of their theory are confirmed but many changes in detail are required by new data. Greater than 5 kcal/mole exothermicity in the energy transfer step is not, as previously reported, sufficient to insure that the process rate is diffusion controlled. A discussion of the meaning of a diffusion controlled process is given. Various factors are considered as possible sources of inefficiency in exothermic energy transfer. Quantum yield measurements for sensitized stilbene isomerization show there is only very limited wastage of quanta. Transfer of energy from sensitizers with triplet energies below 62 kcal/mole to the stilbenes and especially to cis-stilbene is governed not only by the sensitizer triplet energy but also by other factors which are characteristic of the sensitizer. These effects are discussed in terms of energy transfer to cis-stilbene via an intermediate complex of sensitizer triplet and stilbene. Results with sensitizers containing bromine indicate that these substances cause stilbene isomerization by light induced liberation of bromine atoms and not, in general, by electronic energy transfer. This finding casts doubt on some of the evidence adduced in support of nonvertical energy transfer to cis-stilbene. The nature and reactions of stilbene triplets are discussed with special reference to reversible energy transfer to trans-stilbene, azulene quenching effects and self quenching due to trans-stilbene. The implications of this study in the study of other photosensitized reactions are presented." }, { "name": "Wang, Chiu-sen", "degree": "PhD", "year": "1966", "title": "A mathematical study of the particle size distribution of coagulating disperse systems\r\n\r\nA Mathematical Study of the Particle Size Distribution of Coagulating Disperse Systems", "advisor": "Friedlander, Sheldon K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232002-110824", "creators": [ { "name": { "family": "Wang", "given": "Chiu-sen" }, "id": "Wang-Chiu-sen", "display_name": "Wang, Chiu-sen" } ], "advisors": [ { "name": { "family": "Friedlander", "given": "Sheldon K." }, "id": "Friedlander-S-K", "role": "advisor", "display_name": "Friedlander, Sheldon K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/QYDE-A565", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe behavior of the particle size distribution of coagulating dispersions is studied theoretically. If the collision frequency factor is a homogeneous function of particle volume, the partial integro-differential equation describing the coagulation kinetics can be transformed into an ordinary integro-differential equation by a similarity transformation originally proposed by Friedlander. The solution to the resulting equation, called the self-preserving spectrum, is determined for three different collision mechanisms: (1) constant collision frequency factor, (2) Brownian motion, and (3) simultaneous Brownian motion and shear flow, in which the shear rate decreases with time in a particular way. The results of this study indicate that the shape of the self-preserving spectrum is greatly influenced by the collision mechanism.\r\n\r\nIf a slip correction for the particle drag is taken into consideration, the coagulation equation for Brownian motion cannot be reduced to an ordinary integro-differential equation. However, the coagulation equation can be written in terms of a reduced size spectrum, By assuming that the reduced size spectrum varies slowly with time, a family of \"quasi-self-preserving\" spectra are obtained for various values of a parameter [?] which is a function of the mean free path of the fluid, the total volume concentration and the total number concentration of particles.\r\n\r\nThe self-preserving hypothesis concerning the particle size distribution is proved to be true for the case of constant collision frequency factor. For Brownian coagulation, arguments are presented to support the hypothesis.\r\n\r\nIn the cases which are worked out, it is assumed that the particles are uncharged and spherical in shape and that their density is conserved in the coagulation process.\r\n" }, { "name": "Adams, Kenneth Hoyt", "degree": "PhD", "year": "1965", "title": "Dislocation Mobility and Density in Zinc Single Crystals", "advisor": "Vreeland, Thad; Wood, David Shotwell", "url": "https://resolver.caltech.edu/CaltechETD:etd-09102002-095733", "creators": [ { "name": { "family": "Adams", "given": "Kenneth Hoyt" }, "id": "Adams-Kenneth-Hoyt", "display_name": "Adams, Kenneth Hoyt" } ], "advisors": [ { "name": { "family": "Vreeland", "given": "Thad" }, "id": "Vreeland-T", "role": "advisor", "display_name": "Vreeland, Thad" }, { "name": { "family": "Wood", "given": "David Shotwell" }, "id": "Wood-D-S", "role": "advisor", "display_name": "Wood, David Shotwell" } ], "committee": [ { "name": { "family": "Vreeland", "given": "Thad" }, "id": "Vreeland-T", "role": "chair", "display_name": "Vreeland, Thad" }, { "name": { "family": "Buffington", "given": "Francis Stephan" }, "id": "Buffington-F-S", "role": "member", "display_name": "Buffington, Francis Stephan" }, { "name": { "family": "Clark", "given": "Donald S." }, "id": "Clark-D-S", "role": "member", "display_name": "Clark, Donald S." }, { "name": { "family": "Duwez", "given": "Pol E." }, "id": "Duwez-P-E", "role": "member", "display_name": "Duwez, Pol E." }, { "name": { "family": "Housner", "given": "George W." }, "id": "Housner-G-W", "role": "member", "display_name": "Housner, George W." }, { "name": { "family": "Wood", "given": "David Shotwell" }, "id": "Wood-D-S", "role": "member", "display_name": "Wood, David Shotwell" } ], "option_major": [ "matsci" ], "doi": "10.7907/SYCE-8B03", "abstract": "Experimental measurements of dislocation mobility and density, and the strain-rate sensitivity of the flow stress have been made on 99.999 per cent pure zinc crystals. Dislocation density and the strain-rate sensitivity of the flow stress were also measured on zone refined crystals and crystals containing 0.0025 and 0.02 wt per cent aluminum. Dislocation mobilities in the 1120 {0001} (basal), and 1213 {1212} (nonbasal) slip systems were measured by observing slip band growth produced by load pulses of controlled amplitude and duration. The results of the experimental measurements of dislocation mobility are discussed in relation to current theories. A comparison of the strain-rate sensitivity and the mobility measurements shows that a significant change in the density of roving dislocations is associated with a change in strain-rate. This change in density has generally been ignored by previous investigators. A dislocation model is proposed to explain the observed strain-rate sensitivity.
\r\n\r\nObservations were also made of the change of substructure and in particular the change of nonbasal dislocation density accompanying impurity additions of aluminum to the zinc. The effect of the aluminum on the basal stress-strain behavior is explained in terms of changes in nonbasal dislocation density which determines the separation distance of attractive and repulsive junctions between basal and nonbasal dislocations. The onset of basal slip is associated with the breaking of attractive junctions.
\r\n\r\nThe change in basal dislocation density produced by plastic shear strain is shown to obey the relation \u0394\u03c1 = C\u0b6ap1/3, and is independent of purity. A markedly different relation is indicated for the nonbasal dislocation density vs. strain. These results are explained by a significant difference in the average glide distance of dislocations in the basal and nonbasal slip systems.
" }, { "name": "Caputi, Roger William", "degree": "PhD", "year": "1965", "title": "Studies of Liquid Mercury and Liquid Mercury-Gallium Systems by X-Ray Diffraction", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09102002-145935", "creators": [ { "name": { "family": "Caputi", "given": "Roger William" }, "id": "Caputi-Roger-William", "display_name": "Caputi, Roger William" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HZ5D-3G89", "abstract": "The purpose of this study was to determine the radial distribution of pure mercury and mercury-gallium mixtures by xray diffraction. Work was also done to resolve the problem of whether microdroplets of the solute metal existed in the solvent metal of the mercury-gallium system or whether the mercury-gallium mixtures were true solutions.
\r\n\r\nThe experimental system used a reflection geometry from a horizontal free surface of the liquid metals. A silver x-ray tube was used in conjunction with a scintillation detector and pulse height analyzer. Data points were taken over an S range of approximately 1.6Å-1 to 17Å-1.
\r\n\r\nThree samples were run at 0°, 30° and 50° C. The compositions of the three samples were pure mercury, 0.9658 mole froction of mercury, and 0.0197 mole fraction of mercury.
\r\n\r\nThe peak positions of the final radial distribution functions for all samples showed no significant change over the temperature range used. The average positions of the first and second peaks of the mercury curves were 3.01Å and 5.80Å respectively. The coordination numbers for mercury as determined by the symmetrical curve method were 7.5, 7.3, and 7.0 atoms for the 0°, 30° and 50° C runs respectively.
\r\n\r\nThe final results indicated that both samples of mercury-gallium were true solutions.
" }, { "name": "Duchamp, David James", "degree": "PhD", "year": "1965", "title": "l. The Crystal Structure of Trimesic Acid. II. Topics in Crystallographic Calculations", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192015-081930753", "creators": [ { "name": { "family": "Duchamp", "given": "David James" }, "id": "Duchamp-David-James", "display_name": "Duchamp, David James" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JGPC-Y356", "abstract": "I. Trimesic acid (1, 3, 5-benzenetricarboxylic acid) crystallizes\r\nwith a monoclinic unit cell of dimensions a = 26.52 A, b = 16.42 A,\r\nc = 26.55 A, and \u03b2 = 91.53\u00b0 with 48 molecules /unit cell. Extinctions\r\nindicated a space group of Cc or C2/c; a satisfactory\r\nstructure was obtained in the latter with 6 molecules/asymmetric\r\nunit - C54O36H36 with a formula weight of 1261 g. Of approximately\r\n12,000 independent reflections within the CuK\u03b1 sphere, intensities\r\nof 11,563 were recorded visually from equi-inclination Weissenberg\r\nphotographs.
\r\n\r\nThe structure was solved by packing considerations aided by\r\nmolecular transforms and two- and three-dimensional Patterson\r\nfunctions. Hydrogen positions were found on difference maps. A\r\ntotal of 978 parameters were refined by least squares; these included\r\nhydrogen parameters and anisotropic temperature factors for the C\r\nand O atoms. The final R factor was 0.0675; the final \"goodness of\r\nfit\" was 1.49. All calculations were carried out on the Caltech IBM\r\n7040-7094 computer using the CRYRM Crystallographic Computing\r\nSystem.
\r\n\r\nThe six independent molecules fall into two groups of three\r\nnearly parallel molecules. All molecules are connected by carboxylto-\r\ncarboxyl hydrogen bond pairs to form a continuous array of sixmolecule\r\nrings with a chicken-wire appearance. These arrays bend\r\nto assume two orientations, forming pleated sheets. Arrays in different\r\norientations interpenetrate - three molecules in one orientation\r\npassing through the holes of three parallel arrays in the alternate\r\norientation - to produce a completely interlocking network. One\r\nthird of the carboxyl hydrogen atoms were found to be disordered.
\r\n\r\nII. Optical transforms as related to x-ray diffraction patterns are\r\ndiscussed with reference to the theory of Fraunhofer diffraction.
\r\n\r\nThe use of a systems approach in crystallographic computing\r\nis discussed with special emphasis on the way in which this has been\r\ndone at the California Institute of Technology.
\r\n\r\nAn efficient manner of calculating Fourier and Patterson maps\r\non a digital computer is presented. Expressions for the calculation of\r\nto-scale maps for standard sections and for general-plane sections are\r\ndeveloped; space-group-specific expressions in a form suitable for\r\ncomputers are given for all space groups except the hexagonal ones.
\r\n\r\nExpressions for the calculation of settings for an Eulerian-cradle\r\ndiffractometer are developed for both the general triclinic case\r\nand the orthogonal case.
\r\n\r\nPhotographic materials on pp. 4, 6, 10, and 20 are essential\r\nand will not reproduce clearly on Xerox copies. Photographic copies\r\nshould be ordered.
" }, { "name": "Dyroff, David Ray", "degree": "PhD", "year": "1965", "title": "The Crystal Structure of Sodium Triphosphate Hexahydrate", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechETD:etd-03262003-155847", "creators": [ { "name": { "family": "Dyroff", "given": "David Ray" }, "id": "Dyroff-David-Ray", "display_name": "Dyroff, David Ray" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FT3A-YQ66", "abstract": "The crystal structure of sodium triphosphate hexahydrate was determined by X-ray crystallographic methods. The crystals are triclinic with two Na5P3O10.6H2O per unit cell in space group P\u03a4. The structure of the anion was determined much more accurately than in other triphosphate structures done previously, and the unexpectedly large difference in length of the two types of P-O chain bond was confirmed. The P-O-P angle was 123.5\u00b0, which is closer than the previously reported values to what is observed in other kinds of phosphates. Sodium coordination is fivefold and sixfold. An unusual feature of the hydrogen bonding is that two of the phosphate oxygen atoms accept four hydrogen bonds each. Several macroscopic properties of the crystals are explained in terms of the crystal structure." }, { "name": "Fisch, Michael Hamilton", "degree": "PhD", "year": "1965", "title": "The Photochemistry of Santonin in Aprotic Solvent: Part l. Photoproducts. Part II. Mechanism", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02182003-102952", "creators": [ { "name": { "family": "Fisch", "given": "Michael Hamilton" }, "id": "Fisch-Michael-Hamilton", "display_name": "Fisch, Michael Hamilton" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5EQE-4M55", "abstract": "Irradiation of santonin in aprotic solvents, e. g. benzene or dioxane, gives rise only to lumisantonin, but further irradiation of lumisantonin then leads to no fewer than four new photoproducts which will be designated mazdasantonin, H, B, and J. The further photoconversion of these compounds, although considerably less striking than that of lumisantonin, has also been studied in a qualitative way.\r\n\r\nStudies of the singlet or triplet nature of these reactions provides evidence for triplet paths in the conversion of one isomer to another and in the subsequent dimerization of mazdasantonin. Thus, triplet states appear to play an important role in photochemistry even in simple isomerizations which quenching data show to be very fast and to have rates in the range of normal singlet reactions.\r\n" }, { "name": "Foster, James Norman", "degree": "PhD", "year": "1965", "title": "I. The Electrochemistry of Certain Metal Cations in Pyrophosphate Media. II. A Theoretical Study of Chronopotentiometry and Chronoamperometry at\r\nUnshielded Electrodes. III. Determination of Cobalt by Constant Current Coulometry", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04092003-115642", "creators": [ { "name": { "family": "Foster", "given": "James Norman" }, "id": "Foster-James-Norman", "display_name": "Foster, James Norman" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9AHN-A311", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn Part I results are reported for the electrolytical reduction of iron(III), copper(II), lead(II), zinc(II), and cadmium(II) in sodium pyrophosphate media. In the cases of iron(III) and copper(II), reduction in neutral and basic pyrophosphate media is irreversible. However, if a pyrophosphate ligand is dissociated from the metal complex, a species is obtained that is reversibly reduced. In the case of iron(III) in the region 4 < pH < 6, loss of a hydrogen pyrophosphate ligand results in a species that is reversibly reduced. The dissociation constant is 2.8 x 10[superscript -3], the rate constant for dissociation of the ligand is 24 sec.[superscript -1], and the rate constant for association is 8.5 x 10[superscript 3] M[superscript -1]sec.[superscript -1]. In the case of copper(II) the loss of a sodium pyrophosphate ligand yields a species that is reversibly reduced. The dissociation constant is 3.2 x 10[superscript -3], the rate constant for dissociation of the ligand is 19 sec.[superscript -1], and the rate constant for association is 5.9 x 10 [superscript 3] M[superscript -1]sec.[superscript -1]. These constants were determined by chronopotentiometry.\r\n\r\nThe reduction of zinc(II) is irreversible in neutral pyrophosphate media; however, this irreversibility is not due to a slow chemical reaction. The reduction of lead(II) is not reversible in neutral pyrophosphate media, but this reduction is not sufficiently irreversible to allow the mechanism of the reduction to be studied by polarography or chronopotentiometry.\r\n\r\nReduction of cadmium(II) was studied by polarography, but no quantitative results were obtained.\r\n\r\nIn Part II equations for the product [...] and the product [...] are derived for the cases of chronopotentiometry and chronoamperometry, respectively, at an unshielded electrode. The equations for an annular electrode or radius r are [...] For a rectangular electrode with dimensions b and c the above equations are valid if the quantity bc/(b+c) is substituted for the variable r.\r\n\r\nIn Part III a method is described by which cobalt may be determined with a relative error of less than 0.1%. In this method triscarbonatocobaltate(III) oxidizes iodide to iodine. Arsenic(III) is added to reduce the iodine and coulometrically generated iodine is employed to titrate excess arsenic(III).\r\n" }, { "name": "Frosch, Robert Peter", "degree": "PhD", "year": "1965", "title": "I. The Emission and Absorption Spectra of Some Simple Molecules Trapped in Solid Rare Gases. II. Theory of Electronic Relaxation in the Solid Phase", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-04102003-103306", "creators": [ { "name": { "family": "Frosch", "given": "Robert Peter" }, "id": "Frosch-Robert-Peter", "display_name": "Frosch, Robert Peter" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0F5C-F303", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nThis thesis consists of two parts. The first part describes a study of the spectral properties of simple molecules trapped in liquid helium-cooled rare gas matrices and the equipment used in these studies. Measurements have been made of the phosphorescence lifetimes of C[subscript 6]H[subscript 6], C[subscript 6]D[subscript 6], C[subscript 10]H[subscript 8], and C[subscript 10]D[subscript 8] in at least one of the following solids: Ar, Kr, and Xe. The a[superscript 4]II [...] X[superscript 2]II and the B[superscript 2]II [...] X[superscript 2]II transitions of NO have been excited in Ar and Kr using x rays, and the resulting spectra measured and interpreted. The radiative lifetime of the NO quartet state has been measured in Ne, Ar, and Kr and found to be 156, 93, and 35 msec, respectively, in these solvents.\r\n\r\nC[subscript 2]H[subscript 2] and C[subscript 2]D[subscript 2] have been deposited in Ar, Kr, and Xe and submitted to x-ray damage. The well-known Swan bands of C[subscript 2] have been observed in both emission and absorption. Both the upper and lower states of the Swan system have [Delta]G values in the solid more than 10% greater than the gas phase values. In addition two new C[subscript 2] band systems with 0-0 bands in Ar at 22973 and 19619 cm[superscript -1], respectively, and with a common lower state have been tentatively identified. These systems apparently have not been reported in the gas phase. A transient system has been seen in the emission of a deposit of C[subscript 2]H[subscript 2] in Kr that may be due to HC[subscript 2]. Another series observed when C[subscript 2]H[subscript 2] is deposited in either Kr or Xe is apparently diacetylene phosphorescence.\r\n\r\nThe second part of this thesis presents a theory of electronic relaxation in solid media. The theory indicates that rates of electronic relaxation in solids depend in an important way on the electronic coupling between initial and final states and on the vibrational overlap between initial and final states. The theory has been successful in explaining the effect of deuterium substitution and the heavy atom effect on relaxation rates. Only a small temperature effect is predicted.\r\n" }, { "name": "Graue, Dennis Jerome", "degree": "PhD", "year": "1965", "title": "I. A Numerical Method for Smoothing Thermodynamic Data. II. Diffusion Coefficients in Binary Hydrocarbon Liquids. III. Correlation of Diffusion Coefficients of Liquid Hydrocarbons", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02192003-104147", "creators": [ { "name": { "family": "Graue", "given": "Dennis Jerome" }, "id": "Graue-Dennis-Jerome", "display_name": "Graue, Dennis Jerome" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/V1DZ-TR47", "abstract": "I. A numerical method was developed for smoothing thermodynamic data with a digital computer. As a feasibility study, data on specific volume and enthalpy from the skeleton tables of the Sixth International Conference on the Properties of Steam and from the tables of Keenan and Keyes were smoothed and interpolated. Orthogonal polynomials of temperature and pressure were used as the smoothing functions. In order to maintain thermodynamic onsistency between the smoothed values of the two thermodynamic properties, Lagrange multipliers were used in conjunction with least squares techniques to accomplish the curve fitting. Excellent agreement was obtained between tabulated and smoothed values of the above properties and their derivatives except near the critical region where data were sparse. The method is recommended for the smoothing of the above and other thermodynamic properties which may be subject to consistency restrictions.\r\n\r\nII. Data on the Chapman-Cowling diffusion coefficients of liquid hydrocarbons were expressed analytically in terms of the physical properties of the liquid phase and the nature of the components. The weight fraction of the light component, temperature, and the molecular weight of the heavy component served satisfactorily as independent variables to describe the recent data of Sage for binary hydrocarbon systems. The results permit the calculation of the Chapman-Cowling diffusion coefficients in the liquid phase for saturated hydrocarbons from methane through n-decane.\r\n\r\nIII. The above data were used in the testing and formulation of correlations of diffusion coefficients of binary liquid mixtures. The correlation methods which were tested were the following: empirical, rate process theory, hole theory, and kinetic theory. The hole theory was inadequate for describing the available data on mutual diffusion; accurate empirical and rate-process expressions were developed for calculating Chapman-Cowling diffusion coefficients for binary mixtures of methane and ethane with heavier hydrocarbons through n-decane and a heavier \"white oil;\" although the expressions which were tested from kinetic theory did not predict correctly the dependence of the data on temperature and composition, they presented good approximations and appeared to be a promising area for future development." }, { "name": "Griffith, O. Hayes", "degree": "PhD", "year": "1965", "title": "Electron Spin Resonance of Several Molecules in the Solid State", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02102003-103751", "creators": [ { "name": { "family": "Griffith", "given": "O. Hayes" }, "id": "Griffith-O-Hayes", "display_name": "Griffith, O. Hayes" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5W0W-AZ49", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nSingle crystals of ester-urea, ketone-urea, and ether-urea inclusion compounds were X-irradiated and investigated by electron spin resonance. Eleven inclusion compounds formed between urea and the straight-chain alkyl esters yielded radicals of the type [...]. The [alpha] and [beta] proton coupling constants of two radicals were studied over the temperature range 352?K to 7?K. The splittings caused by the alcohol (R') protons were resolved in many cases. Information regarding the structure of the inclusion compounds was obtained. The long-lived radical [...] was detected in all six ketone-urea crystals. The spin density in the 2p orbital adjacent to the carbonyl group is 0.81 [plus or minus].04. The ether radicals were of the type [...] and the spin density on the carbon atom is approximately 0.70 [plus or minus].08. The ketone radical and ether radical spin distributions obtained from the [pi]-electron theory are in qualitative agreement with the experimental spin distributions. In addition, single crystals of fumaric acid-urea were X-irradiated and studied by electron spin resonance. The dominant radical [...] in this case is formed by addition of a hydrogen atom (rather than by removal of a hydrogen atom, as above). The fumaric acid-urea crystal is not a hexagonal inclusion compound. The major orientations of the radical were determined with respect to the external crystal morphology.\r\n\r\nElectron spin resonance studies of the triplet state of pyrene and triplet exciton states in ion radical salts are also briefly reported. The approximate g values and zero field parameters for pyrene in a fluorene matrix at 100[degrees]K are g[subscript xx] = 2.0033, g[subscript yy] = 2.0026, g[subscript zz] = 2.0033, D(xy)/hc = [plus or minus] 0.0806 cm[superscript -1], D(z)/hc = [plus or minus] 0.0810 cm[superscript -1], and E/hc = [plus or minus] 0.0182 cm[superscript -1]. The estimated errors in the g values, D, and E are [plus or minus] 0.005, [plus or minus] 0.0012, and [plus or minus] 0.0009, respectively. The relation between triplet excitons and magnetically dilute radicals in the [...] and [...] ion radical salts was investigated. The temperature dependent broadening of the radical line is apparently caused by an exciton-radical exchange interaction. At 77?K the exciton line width is proportional to the free radical impurity line width, which suggests that unresolved nuclear hyperfine interactions contribute greatly to the exciton line width at this temperature." }, { "name": "Hardham, William Morgan", "degree": "PhD", "year": "1965", "title": "Some Photochemistry of Maleic Anhydride: the Addition to Benzene and the Dimerization", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-02182003-110831", "creators": [ { "name": { "family": "Hardham", "given": "William Morgan" }, "id": "Hardham-William-Morgan", "display_name": "Hardham, William Morgan" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/g5sc-av21", "abstract": "The detailed mechanism of the sensitized and unsensitized addition of maleic anhydride (MA) to benzene has been determined. By suitable quenching studies on both additions and use of a variety of sensitizers a triplet mechanism has been established. Studies of the variation of initial quantum yield with concentration of reactants showed the benzene and MA effects to be independent. This information, together with the fact that the benzene-MA charge transfer complex is a better quencher of benzophenone triplets than free MA by a factor of 13 led by elimination to the following mechanism. Energy transfer or direct absorption leads to the triplet state of the complex which can decay to a cyclohexadiene-like intermediate or dissociate to triplet MA and benzene. The major energy loss in the sequence comes from decay of MA triplets before they recombine with benzene. Competition between Diels-Alder addition of MA and dissociation of the intermediate provides the other energy loss and the MA concentration effect.
\r\n\r\nBy comparison of the rates of energy transfer from three ketones to MA or the complex determined by photo reduction or flash photolytic techniques and from the phosphorescence spectrum of MA we calculate that the triplet state of the complex is ~2 kcal./mole lower than that of MA.
" }, { "name": "Hwang, Kwang-chou", "degree": "PhD", "year": "1965", "title": "A Mathematical Study of the Transient Behavior of a Fixed-Bed Catalytic Reactor", "advisor": "Longwell, Paul A.; Seagrave, Richard C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202002-143911", "creators": [ { "name": { "family": "Hwang", "given": "Kwang-chou" }, "id": "Hwang-Kwang-chou", "display_name": "Hwang, Kwang-chou" } ], "advisors": [ { "name": { "family": "Longwell", "given": "Paul A." }, "id": "Longwell-P-A", "role": "advisor", "display_name": "Longwell, Paul A." }, { "name": { "family": "Seagrave", "given": "Richard C." }, "id": "Seagrave-R-C", "role": "advisor", "display_name": "Seagrave, Richard C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/s4x7-2k68", "abstract": "Partial differential equations describing the transient behavior of a non-adiabatic fixed-bed catalytic reactor are derived with a minimum of simplifying assumptions. These equations axe applied to predict the transient behavior of a reactor for the oxidation of SO2 taking into account the behavior of both the fluid stream and the associated catalyst pellets.
\r\n\r\nStability analyses of the numerical methods of solving the equations are presented in great detail, as the methods of analyses available in the literature are inadequate for the complicated system of equations encountered. A special study is made of the effects on stability of various methods of handling the nonlinear source terms in the equations. Some of the schemes proposed in the literature are found to be subject to severe stability criteria.
\r\n\r\nA method of obtaining a rigorous solution is devised. The method is always stable, and the use of varying time increment size is allowable. A rigorous solution takes only a few minutes of computer time with an IBM-7094 computer.
\r\n\r\nTo investigate the effects of various limiting assumptions, three problems are studied using the rigorous method and also with methods employing various assumptions. These problems are the start-up, the loss of cooling with subsequent restoration, and the response of the exit concentration to a sinusoidal concentration forcing function at the entrance. For the system investigated, the effects of using an \"effectiveness factor\" model, neglecting radial changes, and neglecting the axial diffusion and axial velocity variations are found to be not large. The neglecting of reverse reactions, or the use of an average effectiveness factor throughout the whole reactor causes significant errors.
\r\n\r\nA simplified method, which for the system studied, gives a reasonably good approximation to the true solution, is used to investigate problems in the optimization and control of the reactor. The frequency response of the exit temperature to a sinusoidal forcing upon the optimum wall temperature is found to be equivalent to that of a phase lag network frequently used in regulating systems.
\r\n\r\nLimitations to the applicability of the simplified method are discussed.
" }, { "name": "Jensen, Ronald Harry", "degree": "PhD", "year": "1965", "title": "Complexes of Silver (I) with Nucleic Acids", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242003-090009", "creators": [ { "name": { "family": "Jensen", "given": "Ronald Harry" }, "id": "Jensen-Ronald-Harry", "display_name": "Jensen, Ronald Harry" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7V9M-6D68", "abstract": "The equilibrium properties of the Ag (I) complexes of DNA have been studied potentiometrically and spectrophotometrically at ionic strength of 0.1 M (NaC10[subscript 4]) and at pH's from 5.6 to 8.0. There are at least two different complexes which form at low silver ion concentrations. The strength of association of one complex (type I binding) is pH independent. The type I complexing reaction releases no protons from the DNA. A second complex (type II binding) is stronger at high pH. This complexing causes the release of approximately one proton per Ag (I) bound.\r\n\r\nDNA which is rich in GC binds Ag (I) more strongly than does AT rich DNA. However, at pH's between 5.6 and 8.0 more protons are released from AT-rich DNA's.\r\n\r\nIt is proposed that the first complex (type I) involves only GC base pairs, with silver (I) adding to the sigma electrons of a ring nitrogen or interacting with the pi electrons. In the second complex (type II), Ag (I) replaces an N-1 (purine) to N-3 (pyrimidine) hydrogen bond, thus displacing one proton.\r\n\r\nThe complexing behavior of various polynucleotides, nucleotides and substituted purines was studied, and the DNA complexes are discussed in the light of these results.\r\n\r\nA cesium sulfate equilibrium density gradient ultracentrifugation technique has been developed in which buoyant density differences between different DNA's are generated by the specific formation of their Ag (I) complexes. When Ag (I) is bound to the extent of one silver ion per DNA base pair, the buoyant density of either native or denatured DNA increases by about .17 g/cc.\r\n\r\nCompetition experiments in which Ag (I) was added to a mixture of two different DNA's resulted in specific binding of the Ag (I) by one of the DNA species. At equilibrium in the ultracentrifuge two widely separated DNA bands were observed. The buoyant density difference between these bands corresponded to the difference in Ag (I) binding by the two species of DNA.\r\n\r\nA survey was done of various useful preparative separations based on this technique. One such preparative separation has been accomplished, and the separated components have been characterized." }, { "name": "Keyser, Leon Frank", "degree": "PhD", "year": "1965", "title": "I. Infrared Spectra of Monomeric and Polymeric HCL and DCL in Solid Krypton and Xenon. II. Infrared Spectra of NH\u2082 and ND\u2082 Produced by Photolysis and X-Radiolysis of Ammonia in Solid Krypton. III. Ultraviolet Spectra of CH Produced by X-Radiolysis of Methane in Solid Argon", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-04142003-163123", "creators": [ { "name": { "family": "Keyser", "given": "Leon Frank" }, "id": "Keyser-Leon-Frank", "display_name": "Keyser, Leon Frank" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/735D-4Q28", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPART I\r\n\r\nThe construction and operation of a low temperature infrared cell is described; the cell is capable of maintaining temperatures between 7 and 50[degrees]K while in the light beam of a Beckman IR-7 spectrophotometer.\r\n\r\nInfrared spectra of HC1 and DC1 at 0.2 to 2% concentrations in solid krypton and xenon are reported. Fine structure in the region of the (1-0) vibrational transitions of HC1 and DCl is assigned to monomeric and polymeric species of HC1 and DC1.\r\n\r\nThe monomer lines are assigned to vibration-rotation transitions of HC1 and DCl. In krypton the R(0) transition of HC1 occurs at 2872.7, R(1) at 2887, P(1) at 2837.4, and Q(0) at 2852.8 cm[superscript-1]. The R(0) transition of DC1 in krypton occurs at 2078.9, R(1) at 2089, P(1) at 2058, and Q(0) at 2067.5 cm[superscript-1]. In xenon the R(0) transition of HC1 occurs at 2858.2, R(1) at 2872, P(1) at 2825.5, and Q(0) at 2837.8 cm[superscript-1]. The R(0) transition of DC1 in xenon occurs at 2069, R(1) at 2075, P(1) at 2047 and Q(0) at 2058 cm[superscript -1].\r\n\r\nBesides a J-independent band origin shift with respect to the gas phase frequencies of -31 cm[superscript-1] in krypton and -44 cm[superscript -1] in xenon, the rotational levels of HCl exhibit J-dependent perturbations of 5 to 10 cm[superscript -1]. The band origin shift of DC1 is -23 cm[superscript-1] in krypton and -33 cm[superscript-1] in xenon; the J-dependent perturbations of the DC1 rotational levels lie between 1 and 3 cm[superscript -1]. Hindered rotation and libration of HC1 and DCl in the rare gas crystals are not suitable descriptions of the J-dependent perturbations. A model based on the interaction of the rotational motion with the localized translational motion of HC1 and DCl at substitutional sites in the rare gas crystals is used to interpret the J-dependent perturbations. The translational frequencies of HC1 and DC1 and the strength of the translation-rotation interaction are treated as parameters. The values of the translational frequencies which give the best fit to the observed rotational spacings are 36 cm[superscript -1] in xenon, 57 cm[superscript -1] in krypton, and 31 cm[superscript-1] in argon. The strength of the translation-rotation interaction as measured by the distance between the center of mass and the center of electrical symmetry in the molecule is 0.13 [...] for HCl and 0.096 [...] for DC1.\r\n\r\nA mechanism for the induction of a Q branch in the vibration-rotation spectra of monomeric HC1 and DCl in the solid rare gases is discussed.\r\n\r\nThe vibrational spectra of polymeric HC1 and DC1 are discussed in terms of dimeric and trimeric aggregates.\r\n\r\nPART II\r\n\r\nThe photolysis of ammonia in solid krypton with 1849 [...] light or with X radiation gives rise to new absorption maxima at 1521, 1114, 1289, and 1280 cm[superscript -1] in the infrared. The line at 1521 cm[superscript -1] is assigned to the previously unobserved bending mode of the NHZ radical. Experiments with isotopic ammonia show that the bending mode of NDZ occurs at 1106 cm[superscript -1] in solid krypton.\r\n\r\nPART III\r\n\r\nThe CH radical is produced by X-radiolysis of methane in solid argon and krypton. The radiolysis mechanism is discussed in terms of energy transfer from the rare gas lattice to methane." }, { "name": "Kwok, Joel", "degree": "PhD", "year": "1965", "title": "I. Spectroscopic Observation of Discrete Sites in Simple Liquids. II. Infrared Intensity Perturbations of Hydrogen Halide Fundamentals in Liquid Xenon. III. Molecular Motion of HCI in Solid Rare Gas Matrices", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:10092014-095106324", "creators": [ { "name": { "family": "Kwok", "given": "Joel" }, "id": "Kwok-Joel", "display_name": "Kwok, Joel" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gs5f-7s38", "abstract": "Part I
\r\nThe spectrum of dissolved mercury atoms in simple liquids has been shown to be capable of revealing information concerning local structures in these liquids.
Part II
\r\nInfrared intensity perturbations in simple solutions have been shown to involve more detailed interaction than just dielectric polarization. No correlation has been found between frequency shifts and\r\nintensity enhancements.
Part III
\r\nEvidence for perturbed rotation of HCl in rare gas matrices has been found. The magnitude of the barrier to rotation is concluded to be of order of 30 cm\u207b\u00b9.
The temperature dependence of the geminal fluorine-fluorine chemical-shift differences in a variety of unsymmetrically substituted cyclobutanes has been interpreted in terms of a classical equilibrium between axial and equatorial conformations, for which free energy differences have been calculated. The absence of this effect for cyclobutenes and cyclobutanones indicates that these systems are nearly planar. The angle of puckering of 1,1-difluoro-3phenylcyclobutane has been calculated by the dipole-moment method to be about 27\u00b0. The observation of substantial temperature variations of the vicinal hydrogen-fluorine coupling constants is consistent with the presence of an equilibrium between conformers. The magnitude of these couplings as a function of the dihedral angle appears to follow a relationship similar to that described by Karplus for proton-proton coupling constants.
\r\n\r\nNitrogen-15 magnetic resonance spectroscopy has been investigated for the first time. The absolute magnitude of the chemical shift and its variation with protonation have been interpreted in terms of the predominance of the paramagnetic term in the shielding expression. A correlation between the energy of the n \u2192 \u03c0* transition and the magnitude of the chemical shift is considered. An empirical relationship between the hybridization of nitrogen and the coupling between directly bonded nitrogen-15 and hydrogen is derived, and the limitations are discussed. Contributions to the coupling from orbital motion are invoked in order to explain the significant deviation of the coupling in ketimines from the behavior predicted by this relationship. The temperature dependence of the proton spectrum of nitrogen-15-labeled ketimines is interpreted as resulting from a degenerate, bimolecular exchange of the imine protons. Separate geometrical isomers of an imine unsubstituted at nitrogen s-butylphenylketimine are observed for the first time.
" }, { "name": "Lamola, Angelo Anthony", "degree": "PhD", "year": "1965", "title": "Part I. Radiationless Transitions in Organic Systems: Determination of Intersystem Crossing Yields in Fluid Solution. Part II. Intramolecular Energy Transfer Between Non-Conjugated Chromophores in Some Model Compounds", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262002-115009", "creators": [ { "name": { "family": "Lamola", "given": "Angelo Anthony" }, "id": "Lamola-Angelo-Anthony", "display_name": "Lamola, Angelo Anthony" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "chair", "display_name": "Hammond, George Simms" }, { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "member", "display_name": "McConnell, Harden M." }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "member", "display_name": "Robinson, G. Wilse" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b837-bk69", "abstract": "PART I
\r\n\r\nThe efficiency of reaching the lowest triplet state after excitation into low excited singlet levels was determined for benzene, naphthalene, and other polycyclic aromatic hydrocarbons as well as for a number of carbonyl compounds and amines in fluid solution at room temperature. The determinations were accomplished by a chemical method in which the compound in question is used as a photosensitizer for the cis-trans isomerization of suitable olefins. Conditions are such that olefin molecules quench all triplet sensitizer molecules; the olefins subsequently undergo geometric (cis\u21cctrans) isomerization. The details of the isomerization reaction are known and a simple determination of the quantum yield for the sensitized isomerization leads directly to the quantum yield of sensitizer triplets.
\r\n\r\nFrom the data, intersystem crossing rates are estimated, as well as efficiencies and rates of radiationless triplet-to-ground-state transitions. Some information concerning the mode and importance of radiationless first-excited-state-to-ground-state transitions is also included, as well as a discussion of the results in terms of present theoretical treatments of radiationless transitions.
\r\n\r\nPART II
\r\n\r\nIntramolecular transfer of both singlet and triplet electronic excitation in the Leermakers' Compounds, 4-(1-naphthylmethyl) -benzophenone (LI), 1-(1-naphthyl)-2-(4-benzoylphenyl)ethane (LII), and 1-(1-naphthyl)-3-(4benzoylphenyl)propane (LIII) occurs and has been studied in some detail. In addition to emission spectroscopy, chemical methods for detecting, characterizing, and counting molecules in triplet states were employed.
\r\n\r\nIn all three compounds, totally efficient transfer of triplet excitation from the benzophenone groups to the naphthalene moieties occurs, and at nearly the same fast rate (k > 10\u00b9\u2070 sec\u207b\u00b9).
\r\n\r\nTransfer of singlet excitation from the naphthalene moiety to the benzophenone group is about 90% efficient in LI, 75% efficient in LII, and 85% efficient in LIII. The rate of the singlet energy transfer (k ~ 10\u2077 - 10\u2078 sec\u207b\u00b9) are much slower than the rate of the triplet excitation transfer. The fluorescent emissions from the Leermakers' Compounds exhibit a quite different spectrum than that from 1-methylnaphthalene, and significant bathochromic and hyperchromic effects are noted in the absorption spectra of the compounds. The nature of singlet excitation transfer in the Leermakers' Compounds is quite complex, and large stereochemical effects no doubt exist. A discussion of the results in terms of the several presently accepted mechanisms for electronic energy transfer is included
" }, { "name": "Levenberg, Milton Irwin", "degree": "PhD", "year": "1965", "title": "I. Preliminary Studies of the Chain-Transfer Constant of Methylferrocene. II. Protonation of Metallocenes. III. An Analysis of the N.M.R. Spectra of Substituted Ferrocenes. IV. Experimental and Theoretical Studies of the Charge Distribution on the Ferrocenyl Carbinyl Carbonium Ion", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09272002-144907", "creators": [ { "name": { "family": "Levenberg", "given": "Milton Irwin" }, "id": "Levenberg-Milton-Irwin", "display_name": "Levenberg, Milton Irwin" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EGD5-Z205", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPART I:\r\n\r\nStyrene monomer containing various concentrations of methylferrocene was allowed to polymerize at 70?C. The average molecular weight of the resulting polystyrene was determined, and the chain transfer constant of methylferrocene then calculated. The constant was found to be 0.7 x 10[superscript -4], indicating some contribution to the stability of the methyl free radical by the ferrocenyl group.\r\n\r\nThe reactivity of methylferrocene to free radical attack is discussed, and the copolymerization of methylferrocene with styrene is considered.\r\n\r\nPART II:\r\n\r\nThe n. m. r. spectra of ferrocene, ruthenocene, and osmocene in boron trifluoride monohydrate have been studied. Accurate measurements of relative peak areas and positions are reported. The species responsible for the n.m.r. spectra are discussed.\r\n\r\nPART III:\r\n\r\nA detailed analysis of the n. m. r. spectra of a series of alkylacetylferrocenes in a variety of solvents has been carried out. This has allowed a determination of the coupling constants between the various protons in these substances. For protons attached to the same ring, the following values are generally observed: J[subscript 23] ~ 2.5 cps and J[subscript 24] ~ 1.3 cps. The magnetic anisotropy of the carbonyl group in 2-acetyl-1, 1'-trimethylene ferrocene is also discussed.\r\n\r\nPART IV:\r\n\r\nThe existence of the stable ferrocenylcarbinyl carbonium ion has been demonstrated by freezing point depression measurements in concentrated sulfuric acid. The n. m. r. spectrum of the carbonium ion has been observed and the chemical shifts of its protons relative to those of methylferrocene have been measured. The factors influencing the proton chemical shifts are discussed.\r\n\r\nTechniques of molecular orbital calculations applicable to ferrocenyl systems are discussed and the results of a series of molecular orbital calculations on the ferrocenylcarbinyl carbonium ion are presented. The chemical shifts of the protons on the carbonium ion are predicted from the molecular orbital calculations, and the predictions are compared with the experimentally measured chemical shifts. The agreement is not as good as could be desired." }, { "name": "Liebling, Gerald Richard", "degree": "PhD", "year": "1965", "title": "I. Study of Molecular Orbital Degeneracy in C\u2085H\u2085. II. The Crystal and Molecular Structure of Cyclopentadiene", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09302002-122910", "creators": [ { "name": { "family": "Liebling", "given": "Gerald Richard" }, "id": "Liebling-Gerald-Richard", "display_name": "Liebling, Gerald Richard" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KEZ8-7539", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPart I. The paramagnetic resonance of the cyclopentadienyl radical C5H5 has been observed in a single oriented crystal of cyclopentadiene at temperatures ranging from 25[degrees]K to 150[degrees]K. The spectra are of two types, high-temperature and low-temperature spectra, with the transition occurring reversibly between 70[degrees]K and 120[degrees]K. The high temperature spectra consist of six equally spaced lines with a splitting of 6.2 gauss and can be accounted for in terms of a uniform spin distribution around the ring and rapid reorientation of the ring in its plane. The low-temperature spectra are slightly anisotropic and can be reasonably well accounted for by a distorted C5H5 radical with a nonuniform spin distribution undergoing rapid reorientation in its molecular plane. \r\n\r\nPart II. The crystal structure of cyclopentadiene, C5H6, has been determined from X-ray diffraction photographs made at about -150[degrees]C. The crystals are monoclinic, space group P2[subscript 1]/n, with cell dimensions [...]. Intensities of 70 reflections recorded on four zero-level precession photographs were estimated visually and used in a least-squares refinement of the atomic coordinates. The final R factor for these reflections is 0.10.\r\n\r\nThe five-membered ring of carbon atoms is planar; the values for the bond distances are in close agreement with those previously determined by electron diffraction techniques.\r\n\r\nABSTRACTS OF PROPOSITIONS\r\n\r\nProposition 1: A method of constructing semiconductor devices that would operate at very low temperatures is proposed.\r\n\r\nProposition 2: It is proposed that the EPR spectra of x-irradiated trimesic acid be studied for the possibility of observing an aromatic sigma radical.\r\n\r\nProposition 3: Several experiments are proposed that would elucidate the mechanism of carbene addition across a double bond.\r\n\r\nProposition 4: It is proposed that attenuated total reflection spectroscopy can be very useful for studying electrode processes in electrochemical reactions.\r\n\r\nProposition 5: Several EPR experiments are proposed." }, { "name": "Liu, Robert Shing-Hei", "degree": "PhD", "year": "1965", "title": "Photosensitized Reactions of Conjugated Ddienes", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10012002-095952", "creators": [ { "name": { "family": "Liu", "given": "Robert Shing-Hei" }, "id": "Liu-Robert-Shing-Hei", "display_name": "Liu, Robert Shing-Hei" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0BHB-7E68", "abstract": "Conjugated dienes are shown to undergo photosensitized dimerization reaction, photosensitized cross addition reaction, and photosensitized inter- or intramolecular addition to olefins. Structures of isoprene, piperylenes, 2, 3dimethylbutadiene dimers, butadiene-1, 3-cyclohexadiene, 1, 3-cyclohexadiene-cyclopentene cross adducts, and myrcene photoisomers have been assigned (some in parts). The mechanism of the dimerization reaction, which is closely related to the other reactions, has been studied in detail with isoprene as the representative system. It was found that in order to explain the results consistently, several postulates are necessarily invoked. They include the non-interconvertible stereoisomeric triplets of conjugated diene, the unusual stable nuclei configuration of diene triplets, new assignments of the O-O components of singlet-triplet transition of dienes, and \"nonvertical\" energy transfer from sensitizer to diene molecules. Evidence is presented in support of the mechanism in which only one diene triplet is involved in such a bimolecular reaction." }, { "name": "Mikolaj, Paul George", "degree": "PhD", "year": "1965", "title": "An X-Ray Diffraction Study of the Structure of Fluid Argon", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10012002-162731", "creators": [ { "name": { "family": "Mikolaj", "given": "Paul George" }, "id": "Mikolaj-Paul-George", "display_name": "Mikolaj, Paul George" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/BYAA-0S21", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAtomic radial distribution functions of fluid argon have been determined from experimental x-ray diffraction measurements at 13 different thermodynamic states. These states, forming a temperature-density grid in the critical region, include isotherms of -130[degrees]C, -125[degrees]C, -120[degrees]C, -110[degrees]C and isochores (in gm/cc) of 0.982, 0.910, 0.780, 0.536 (the critical density), and 0.280 (argon vapor).\r\n\r\nMo radiation, monochromated by a Zr filter and PHS set for 50% [...] transmission, was used in a Debye-Scherrer type geometry and was detected with a NaI scintillation counter. A narrow incident beam was used to partially irradiate the argon sample which was confined in a cylindrical cell constructed from sintered beryllium powder. A calibration experiment, performed with a vitreous SiO2 sample, established the validity of the experimental method and the data processing techniques.\r\n\r\nThe structural features in the x-ray diffraction patterns were found to depend predominantly on the bulk density of the argon sample and were relatively insensitive to the sample temperature. Except for the low density states, the intensity patterns showed three clearly defined peaks at [...], [...], and [...] The height of the main intensity peak was linear with the bulk sample density and the main peak broadened slightly with increasing temperature.\r\n\r\nThe radial atomic density functions, [...], had three maxima for the high density states and only a single well defined maximum for the vapor state. Their radial positions were relatively constant and were located at [...], and [...]. The height of these maxima was approximately linear with the bulk sample density and was independent of the sample temperature. The first coordination number showed a simple dependence on the argon density, varying from 6.0 atoms at the highest density to 2.1 atoms at the vapor state. Values of the radial electronic density functions are also reported.\r\n\r\nThe first maximum in the atomic radial distribution function, g(r), was found to be independent of both the temperature and the bulk sample density. The average height of this maximum was 1.97 and its average radial position was [...]. No abrupt changes or discontinuities were observed in g(r) as the critical state was approached. A subsidiary maximum, appearing at [...], reported in the previous x-ray studies of argon is shown to be spurious. Tables are presented of the estimated g(r) values and also of the smooth x-ray intensity patterns.\r\n\r\n" }, { "name": "Morrison, Milton Edward", "degree": "PhD", "year": "1965", "title": "I. The Rate and Mechanism of the Air Oxidation of Parts-Per-Million Concentrations of Nitric Oxide. II. The Quantitative Determination of Parts-per-Million Quantities of Nitrogen Dioxide in Nitrogen, Oxygen, and up to 75 p.p.m. of Nitric Oxide by Electron-Capture Detection in Gas Chromatography", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232004-114631", "creators": [ { "name": { "family": "Morrison", "given": "Milton Edward" }, "id": "Morrison-Milton-Edward", "display_name": "Morrison, Milton Edward" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/12M9-RH51", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I\r\n\r\nA study of the air oxidation of parts-per-million (p.p.m.) concentrations of nitric oxide was carried out in a constant-volume, batch reactor. The initial concentration of nitric oxide was varied from 2 to 75 p.p.m. while the oxygen concentration ranged from 3 x 10[^4] to 25 x 10[^4] p.p.m. The rate of the reaction was measured in the ambient temperature region from 17 to 37[degrees]C and at a pressure of one atmosphere. Gas analyses were made by means of chromatography.\r\n\r\nThe initial order of the oxidation reaction in the absence of nitrogen dioxide was 2.00 [plus or minus] 0.09 for nitric oxide and 0.97 [plus or minus] 0.11 for oxygen. From initial rate data at 26.5[degrees]C, a third-order rate constant of (1.297 [plus or minus] 0.051) x [...] was obtained. There were no measurable surface effects due to the Pyrex reaction vessel, but the addition of nitrogen dioxide did increase the initial oxidation rate. The initial third-order rate constant in the absence of nitrogen dioxide exhibited a small negative activation energy.\r\n\r\nA mechanism was proposed which involved six reactions with NO3, N2O3, and N2O5 as intermediates. When the rate equation which resulted from that mechanism for the oxidation of nitric oxide was integrated, the standard deviation of the predicted concentration of nitric oxide from the experimental data in the range from 2 to 75 p.p.m. of nitric oxide was 1.6 p.p.m.\r\n\r\nPart II\r\n\r\nA gas chromatograph was developed for the quantitative analysis of gas mixtures containing nitrogen dioxide at concentrations from 0.5 to 75 p.p.m. in nitrogen, less than 25 x 10[^4] p.p.m. of oxygen, and up to 75 p.p.m. of nitric oxide. The chromatography column consisted of powdered Teflon, Fluoropak 80, which had been coated with a methyl silicone oil, SF-96. A parallel-plane electron-capture detector when operated in the pulse mode was found to be the most sensitive chromatography device available for the detection of nitrogen dioxide. The analysis was accurate to an absolute deviation of 3.4 percent, with a standard deviation of 1.3 p.p.m. in the concentration range from 3 to 75 p.p.m. of nitrogen dioxide when oxygen was present to the extent of 25 percent by volume in nitrogen. The detection limit for the method was 0.5 p.p.m. of nitrogen dioxide.\r\n\r\nStudies were carried out to determine the optimum properties and operating conditions for the chromatography column. The parameters that affected the sensitivity of the electron-capture detector were examined. These included temperature, flow rate, cell geometry, size of tritium source, voltage, and the means of applying this potential to the cell.\r\n\r\nPhotographic materials on pp. 87, 88, 154, 155, 157, 158, 159 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered." }, { "name": "Mukatis, Werner Alfred", "degree": "PhD", "year": "1965", "title": "Variation of the Conformation of the Active Site of \u03b1-Chymotrypsin: I. Hydrogen Ion Concentration Studies. II. Electrolyte Concentration Studies", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232004-141835", "creators": [ { "name": { "family": "Mukatis", "given": "Werner Alfred" }, "id": "Mukatis-Werner-Alfred", "display_name": "Mukatis, Werner Alfred" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SZB4-EM75", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe initial velocities of [alpha]-chymotrypsin-catalyzed hydrolyses of acylated amino acid esters follow the rate law [...] when the only variables are initial substrate and enzyme concentration. In the above equation, [...] is the initial velocity, [...] and [...] are initial enzyme and substrate concentration, respectively, and [...] and [...] are a pair of experimentally determined kinetic parameters. Factors such as temperature, ionic strength, hydrogen-ion concentration, structure of substrate, etc., affect the values of [...] and [...].\r\n\r\nVariation in the kinetic parameters [...],[...], and [...] for selected substrates and variations in the ratios of the parameters [...],[...]and [...] for selected pairs of substrates are studied as functions of hydrogen-ion concentration and concentration of added electrolyte.\r\n\r\nThe results are discussed in terms of possible changes in conformation of the active site of [alpha]-chymotrypsin with changing hydrogenion concentration and concentration of added electrolyte." }, { "name": "Nebeker, Eugene Byrd", "degree": "PhD", "year": "1965", "title": "Thermodynamic Study of Coupled Chemical Reactions", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01122004-145535", "creators": [ { "name": { "family": "Nebeker", "given": "Eugene Byrd" }, "id": "Nebeker-Eugene-Byrd", "display_name": "Nebeker, Eugene Byrd" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HTEW-XR80", "abstract": "To investigate the principles of Non-Equilibrium Thermodynamics, an experimental and theoretical study of a chemical reacting system is made. Nitric oxide, iodine, chlorine, iodine monochloride, and nitrosyl chloride in the gas phase are the macroscopic chemical species which comprise this system.\r\n\r\nThe system displays a coupling behavior which is uncommon to chemical reacting systems. However, this behavior may be useful in explaining some biological phenomena. The observed coupling effect results in a phenomenological coefficient matrix which is not diagonal.\r\n\r\nNone of the macroscopic derivations of the Onsager reciprocity relations which are examined appear to be generally applicable. However, a limited derivation is proposed which not only identifies the phenomenological coefficients in the linear rate laws for chemical reacting systems but also indicates the validity of the Onsager relations. Linear transformations of the fluxes and forces which diagonalize or destroy the symmetry of the phenomenological coefficient matrix are not applicable to a chemical reacting system.\r\n\r\nPhotometric methods are used to experimentally determine the reaction velocities and chemical affinities of this system. The phenomenon of coupling is definitely exhibited by this system, as shown by the existence of the coupling coefficients, L[subscript 12] and L[subscript 21], and by the presence of a negative AV product. The applicability of linear phenomenological rate laws and also rate laws which include quadratic terms are investigated. The linear rate laws are better approximations as the system approaches equilibrium and may be useful at appreciable distances from equilibrium in certain cases. A conclusive test of the Onsager reciprocity relations could not be made." }, { "name": "Nieman, George Carroll", "degree": "PhD", "year": "1965", "title": "Triplet Exciton phenomena in Benzene Crystals", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-04172003-162535", "creators": [ { "name": { "family": "Nieman", "given": "George Carroll" }, "id": "Nieman-George-Carroll", "display_name": "Nieman, George Carroll" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FR70-V452", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nVarious aspects of the triplet exciton problem are investigated. By studying three-component isotopic mixed crystals of benzene it is shown that trap-to-trap triplet excitation migration is very rapid compared to singlet excitation migration. The closely related phenomenon of triplet-triplet annihilation is also discussed. Triplet-triplet annihilation accounts for the production of delayed fluorescence in molecular crystals and for the quenching of all phosphorescence from pure crystals of n-electron molecules.\r\n\r\nBy studying the small quasiresonance shifts introduced in the C[subscript 6]H[subscript 6] phosphorescence by changing the degree of deuteration of the benzene host crystal, the nearest neighbor \"pairwise\" triplet exciton matrix element ([beta]) for benzene is determined to be 12[...]1 cm[superscript -1]. This compares very well with the rough value of 9 cm[superscript -1] determined from excitation transfer studies and is only slightly less than that (18 cm[superscript -1] found for the singlet exciton interaction. These investigations also imply a new interpretation of the factor group splitting of the first singlet-singlet transition in crystalline benzene.\r\n\r\nOptical evidence is presented which shows that benzene in its lowest triplet state is not a regular hexagon. Rather detailed phosphorescence spectra of various deuterated benzenes are also presented." }, { "name": "Nugent, Maurice Joseph", "degree": "PhD", "year": "1965", "title": "Part I. \u03b2-Ferrocenylalkyl Carbonium Ions. Part II. The Stereospecific Syntheses of the Exo and Endo Isomers of \u03b1-Hydroxymethyl-I, 2-Tetramethyleneferrocene", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01152004-112000", "creators": [ { "name": { "family": "Nugent", "given": "Maurice Joseph" }, "id": "Nugent-Maurice-Joseph", "display_name": "Nugent, Maurice Joseph" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8FWY-7415", "abstract": "Part I. The solvolysis mechanism of [Beta]-ferrocenylalkyl tosylates is discussed. Evidence is presented which shows that solvolysis occurs with preferential participation of the interannular electrons of the ferrocene moiety leading to intermediate formation of very stable carbonium ions. The products resulting from these solvolysis reactions demonstrate that these carbonium ions exhibit features expected for both ferrocenyl ring-bridged and iron-stabilized intermediates. The stereochemistry of solvolysis of (-)-1-ferrocenyl-2propyl-p-toluenesulfonate has also been examined and found to occur with complete retention of configuration.
\r\n\r\nPart II. The stereospecific syntheses of the exo and endo isomers of [alpha]-hydroxymethyl-1,2-tetramethyleneferrocene is described.
" }, { "name": "Peterson, Roger L.", "degree": "PhD", "year": "1965", "title": "The Alpha-Chymotrypsin-Catalyzed Hydrolyses of Derivatives of N-Acetyl-L-Phenylalanine Methyl Ester and Methyl Hippurate", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01262004-141645", "creators": [ { "name": { "family": "Peterson", "given": "Roger L." }, "id": "Peterson-Roger-L", "display_name": "Peterson, Roger L." } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4HRY-XZ68", "abstract": "N-Acetyl-L-phenylalanine methyl ester and 23 of its derivatives (all substituted at the phenyl ring of the parent compound) have been evaluated as substrates of [alpha]-chymotrypsin. The results are interpreted in terms of a model of the active site of the enzyme. An elaboration of the model for the locus of the active site where the side chains of the amino acid derivatives are bound is offered.\r\n\r\nThe rates of the [alpha]-chymotrypsin-catalyzed hydrolyses of N-acetyl-N-methyl-L-tyrosine methyl ester and of methyl parahydroxyhydrocinnamate were evaluated. Comparisons among the kinetic constants for these reactions and for the [alpha]-chymotrypsin-catalyzed hydrolyses of N-acetyl-L-tyrosine methyl ester are made. The effect of the structural modifications of the acetylamino group of N-acetyl-L-tyrosine methyl ester on the kinetic constants of its [alpha]-chymotrypsin-catalyzed reaction are again interpreted in terms of a model of the active site of [alpha]-chymotrypsin.\r\n\r\nFinally, four derivatives of methyl hippurate were evaluated as substrates of [alpha]-chymotrypsin. Two other derivatives of methyl hippurate were reversible competitive inhibitors of [alpha]-chymotrypsin. All six were substituted on the benzene ring of the benzoylamino group. The results are compatible with the proposal that the benzamido groups of methyl hippurate derivatives interact with the same locus of the enzymatic active site as do the side chains of derivatives of N-acetyl-L-phenylalanine methyl ester." }, { "name": "Roth, Dana Lincoln", "degree": "Masters", "year": "1965", "title": "Charge-Transfer Association in Enzyme Inhibition", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052010-095701928", "creators": [ { "name": { "family": "Roth", "given": "Dana Lincoln" }, "id": "Roth-Dana-Lincoln", "display_name": "Roth, Dana Lincoln" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DPPB-6X75", "abstract": "Attempts to determine if charge-transfer bonding forces are involved in enzyme inhibition by gas chromatographic and spectral methods were, in general, unsuccessful.
\r\n\r\nDirect spectral evidence of formation of the \u03b2-naphthoquino-linium cation in the presence of the enzyme, \u03b1-chymotrypsin, has been shown.
" }, { "name": "Servis, Kenneth L.", "degree": "PhD", "year": "1965", "title": "I. The Formolysis of Allylcarbinyl Tosylates. II. Studies of Fluoroalkadienes by Nuclear Magnetic Resonance Spectroscopy. III. The Dissociation Constants of Methyl Alkyl Ketone Cyanohydrins", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01212004-111546", "creators": [ { "name": { "family": "Servis", "given": "Kenneth L." }, "id": "Servis-Kenneth-L", "display_name": "Servis, Kenneth L." } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VRRZ-1Q11", "abstract": "Allylcarbinyl tosylate was found to solvolyze in 98% formic acid 3.7 times faster than n-butyl tosylate. Changes in the rate ratio with nucleophilicity of the solvent suggest different mechanisms for these solvolyses. The formolysis products of allylcarbinyl tosylate, when corrected for secondary rearrangements, were found to be virtually identical with those from cyclobutyl tosylate. Deuterium-labeling experiments indicated complete scrambling of the methylene groups in the ring-closed products. These results are interpreted in terms of formation of bicyclobutonium ion intermediates. The rate acceleration for formolysis obtained upon methyl substitution in the 3- and 4-positions and phenyl substitution in the 4-position have been measured and found to be as large as 4500 for the 4,4-dimethyl substituted allylcarbinyl tosylate. The nature of the initial solvolytic transition state is discussed; the results are shown to be inconsistent with formation of classical carbonium ion intermediates.\r\n\r\n1,1,4,4-Tetrafluoro-1,3-butadiene has been shown by dipole moment studies to exist in the s-trans conformation. The F19-F19 spin-spin coupling constants for this compound were found to be very similar to those of bis-4,5(difluoromethylene)-cyclohexene and perfluoro-1,2-dimethylenecyclobutane. These results are discussed in terms of the mechanism of fluorine-fluorine spin-spin coupling.\r\n\r\nThe dissociation constants of a series of methyl alkyl ketone cyanohydrins have been measured by nuclear magnetic resonance spectroscopy. The heats of solution of the ketones and the cyanohydrins in methanol have been measured. The effect of alkyl groups on the heats of solution have been shown to be unimportant in determining the observed dissociation constants of the cyanohydrins of these ketones." }, { "name": "Soos, Zolta\u0301n Ge\u0301za", "degree": "PhD", "year": "1965", "title": "I. Theory of the Linear Heisenberg Antiferromagnet. II. Phonon Effects in Triplet Exciton Theory", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01272004-105953", "creators": [ { "name": { "family": "Soos", "given": "Zolta\u0301n Ge\u0301za" }, "id": "Soos-Zolta\u0301n-Ge\u0301za", "display_name": "Soos, Zolta\u0301n Ge\u0301za" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8NTG-SP91", "abstract": "NOTE: Tect or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I\r\n\r\nIn the Heisenberg model, the hamiltonian describing a linear array of tightly-bound electrons that are exchangecoupled to their neighbors is [...], where [...] is the alternation parameter, [...] is the electron spin on the jth site, and J > 0 (antiferromagnetic coupling). The solutions of the one-dimensional antiferromagnet are studied by transforming to pseudo-spin operators similar to those used by Anderson in superconductivity theory. In a self-consistent molecular-field approximation, the ground state energy, the excitation spectrum, and the coherence between antiparallel spins are found for arbitrary [...] and temperature. At 0[degrees]K, the solutions agree with or improve upon previous calculations of the properties of the regular ([...]) or the alternating ([...]) antiferromagnet. For T > 0, good agreement is found with the experimental paramagnetic susceptibilities of organic crystals whose spin properties may be represented by a regular or an alternating antiferromagnet. The temperature dependence of the excitation energies agrees with the observed behavior of the singles-triplet energy gap in triplet exciton systems. The high temperature and weak alternation extension of triplet exciton theory is presented.\r\n\r\nPART II\r\n\r\nCertain organic crystals consist of linear chains of antiferromagnetically-coupled, tightly-bound electrons; their EPR (electron paramagnetic resonance) properties are discussed in terms of triplet excitons. We consider a deformable lattice and investigate the influence of phonons on triplet excitons. For low exciton density (i.e., at low temperature) the excitons, on account of the phonons, are localized and diffusional; they resemble chargeless polarons in the strong-coupling limit. A general expression for the rate, and its temperature dependence, of an exciton process in a phonon bath at thermal equilibrium is found. In particular, we obtain the diffusion constant for exciton motion, the activation energy for diffusion, and the rates of exciton creation and annihilation; we estimate these parameters for Wurster's blue perchlorate. Even at 0[degrees]K, diffusional excitons are mobile enough to account for the absence of hyperfine structure in the EPR spectra. Modifications, due to the phonons, of the parameters of the effective exciton hamiltonian are obtained and a spin-independent, phonon-coupled repulsion between excitons is rederived." }, { "name": "Woodward, Joe William", "degree": "PhD", "year": "1965", "title": "A Study of the Effects of Dislocation Density and Crystal Orientation on the Kinetics of the Catalyzed Oxidation of Ethylene over a Single Crystal of Silver", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-02102004-111444", "creators": [ { "name": { "family": "Woodward", "given": "Joe William" }, "id": "Woodward-Joe-William", "display_name": "Woodward, Joe William" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/G7TT-6X89", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA study of the effects of dislocation density and crystal orientation on the kinetics of the catalyzed oxidation of ethylene over a single crystal of silver was carried out in a continuous-flow microreactor. The reactor was constructed so the reacting gas stream contacted only gold surfaces and the surface of the silver crystal. A high-sensitivity gas chromatograph was developed and calibrated for the analysis of the exhaust gas from the reactor. The effect of diffusion to and from the catalyst surface on the observed kinetics was determined by solution of the partial differential equations which described diffusion and flow in the reactor geometry.\r\n\r\nTests of the reactor indicated ethylene oxide was oxidized on the gold surfaces. The rate was independent of the ethylene oxide concentration and had an apparent activation energy of 9.0 ? 1.3 Kcal./gm. mole. The rate of production of carbon dioxide from the oxidation of 0 ethylene oxide at 260 [degrees] C with 80% oxygen in feed gas and a pressure of 740 mm was 2.1 X 10[^-8] gm. moles/min. [centimeter squared].\r\n\r\nThe gold surface was also active for the oxidation of ethylene With a feed of 20% ethylene and 80% oxygen at 260[degrees] C and a pressure of 740 mm, the rate of production of carbon dioxide was 2. 8 X 10[^-8] gm. moles/min. [centimeter squared] with an apparent activation energy of 26.0 ? 4.0 Kcal ./gm . mole.\r\n\r\nA feed composition of approximately 20% ethylene and 80% oxygen was used for all reactor runs with silver crystals, and the temperature was varied from 250 to 350 [degrees] C to determine the effects of dislocation density and crystal orientation on the temperature dependence of the reaction rate. No significant differences were observed in the rates of production of carbon dioxide on non-strained crystals with (100), (110), and (111) crystal planes parallel to the surface. In addition no significant differences were observed in the rates of production of carbon dioxide on crystals with (100), (110), and (111) planes parallel to the surface which had been strained 0.8% by rolling parallel to the axis at 45[degree] increments around the circumference of the crystals. An apparent activation energy of 23.1 ? 1.8 Kcal./gm. mole was obtained for the strained and non-strained crystals, but the rate decreased from 6. 3 x 10[^-8] gm. moles/min. centimeter squared for the non-strained crystals to 3. 2 x l0[^-8] gm. moles/min. centimeter squared for the strained crystals, with a feed of 20% ethylene and 80% oxygen at 260 [degrees] C and 740 mm pressure.\r\n\r\nThe results of chemical etching of the crystal surfaces to reveal dislocations were not considered conclusive, but if a one-to-one correspondence between etch pits and dislocations is assumed, then the dislocation density increased about 40% with the 0.8% strain. As a result it was concluded that the dislocations did not act as active sites for the oxidation of ethylene to carbon dioxide but interfered with the oxidation reaction in some manner.\r\n\r\nPhotographic materials on pp. 79-87 are essential and will not reproduce clearly on Xerox copies. Photographic copies should be ordered." }, { "name": "Cuffel, Robert Fredrick", "degree": "PhD", "year": "1964", "title": "Part I. Latent Heat of Vaporization of 1-Pentene. Part II. Thermal Transfer from a Small Wire in Isothermal and\r\nNonisothermal Boundary Flows about a Cylinder", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122002-122032", "creators": [ { "name": { "family": "Cuffel", "given": "Robert Fredrick" }, "id": "Cuffel-Robert-Fredrick", "display_name": "Cuffel, Robert Fredrick" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HD4W-8F71", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nPart I\r\n\r\nThe enthalpy change upon vaporization of 1-pentene was experimentally determined by calorimetric measurements at temperatures between 100 [degrees] and 280 [degrees] F. The results are in good agreement with available data at the lower temperatures and are presented in graphical and tabular form.\r\n\r\nPart II.\r\n\r\nThe heat transfer from a one-mil platinum wire was measured in isothermal and nonisothermal boundary flows about a one-inch copper cylinder. The flow of the 100[degrees] F air stream was normal to the 100 [degree] and 160 [degree] F cylinder at a Reynolds number of 3500. The measured wire Nusselt numbers and smoothed values at a wire temperature loading of 50 [degrees] F are presented as a function of the position within the forward half of the flow about the cylinder for these two cases. For both cases, Nusselt numbers predicted from calculated velocity distributions gave reasonable agreement with the measured values at distances greater than ten wire-diameters from the surface of the cylinder.\r\n\r\nXerox copies of the photographic material on page 36 are adequate for reproduction." }, { "name": "Grocki, John James", "degree": "Masters", "year": "1964", "title": "Nuclear Magnetic Resonance Studies of Solvent Effect on the Molecular Structure of Some Aryl and Alkyl Ethers", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-141753551", "creators": [ { "name": { "family": "Grocki", "given": "John James" }, "id": "Grocki-John-James", "display_name": "Grocki, John James" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4FAK-TX66", "abstract": "The nuclear magnetic resonance spectra of several substituted benzyl ethers containing a center of asymmetry reveals that in certain solvents the methylene protons of the ether are magnetically nonequivalent. Further investigation shows that the magnitude of this effect is related to the dielectric constant of the solvent.\r\n\r\nFrom this information a structure for the molecule in solution is postulated, and the observed magnetic nonequivalence of the protons is explained on the basis of steric and electronic effects.\r\n" }, { "name": "Honeywell, Wallace Irving", "degree": "PhD", "year": "1964", "title": "X-Ray Diffraction Studies of Dense Fluids", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09182002-140103", "creators": [ { "name": { "family": "Honeywell", "given": "Wallace Irving" }, "id": "Honeywell-Wallace-Irving", "display_name": "Honeywell, Wallace Irving" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/E2BS-WS38", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nRadial distribution functions supply useful information for the investigation of the structure of liquids. An x-ray cryostat and supporting equipment have been developed for determination of these functions experimentally. The apparatus has been tested on confined fluids at pressures up to 2000 psia and temperatures to 77 [degrees] K. Although a cylindrical beryllium sample cell is currently used in a geometry of the Debye-Scherrer type, the equipment is adaptable to parafocusing methods and to a wide variety of cell configurations. Except for self-absorption in the sample and cell, absorption of the incident and scattered x rays is less than 1%.\r\n\r\nThe cryostat and supporting equipment maintain automatic temperature control to ?0.006[degrees] C. The sample temperature is measured to ?0.05[degrees] C with a miniature platinum resistance element placed directly in the sample fluid; temperature homogeniety of the irradiated sample is better than 0.003[degrees] C.\r\n\r\nThe sample pressure is transmitted through a steel diaphragm to an oil system where it is measured to 1:10,000 on a pressure balance of the dead weight variety. A pressure transducer incorporating the diaphragm is used to balance the sample and oil pressures. The transducer has a sensitivity of 3.27 volts per differential psi.\r\n\r\nThe analysis of x-ray diffraction data from highly absorbing samples is extended to include losses of incoherent scattering in the sample and cell and in the detection system. Methods for treating incident or scattered beams with nonuniform intensities are also presented. The scattering geometry represents an optimum choice for highly absorbing samples in cylindrical cells. The sample position is determined experimentally to within 0. 001 in.\r\n\r\nX-ray diffraction measurements made with molybdenum radiation are presented for liquid argon at -130.00[degrees]C for the densities 0.9098, 0.9818, and 1.0052 gm/[cubic centimeter]. Scintillation detection was employed; monochromatization was effected with [beta] filtering and pulse height selection. Radial distribution functions are derived from the intensity curves for data to S=9[Angstroms][superscript -1)]. The coordination numbers and shell distances show good agreement with previous work at a nearby state, but suggest the possibility of systematic error in the older data." }, { "name": "Huisman, Johannes", "degree": "PhD", "year": "1964", "title": "I. Latent Heat of Vaporization of n-Hexane. II. Volumetric and Latent Heat of Vaporization Measurements for Trans-2-Butene. III. Partial Enthalpy Change upon Vaporization for n-Butane in the n-Butane-n-Decane System", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09202002-140514", "creators": [ { "name": { "family": "Huisman", "given": "Johannes" }, "id": "Huisman-Johannes", "display_name": "Huisman, Johannes" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/GW1B-B786", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nI. The enthalpy change upon vaporization of n-hexane was experimentally determined by calorimetric measurements at temperatures between 100[degrees] and 340[degrees]F. The results are presented in tabular and graphical form. Good agreement is indicated with the limited data available.\r\n\r\nII. The specific volumes of the liquid and dense phase of trans-2-butene were measured at pressures up to 5000 pounds per square inch in the temperature interval between 40[degrees] and 400[degrees]F. The latent heat of vaporization was determined from calorimetric measurements at temperatures between 100[degrees] and 250[degrees]F. The results are presented in graphical and tabular form together with comparisons with earlier published data.\r\n\r\nIII. The enthalpy change upon vaporization, often referred to as the differential latent heat of vaporization, has been measured for the n-butane-n-decane system by calorimetric techniques. The measurements covered the complete composition range in the temperature interval between 100[degrees] and 340[degrees]F. The partial enthalpy change upon vaporization for n-butane was determined by applying a correction for the presence of small amounts of n-decane in the vapor. The partial internal energy change upon vaporization for n-butane was also computed. The results are presented in graphical and tabular form. A general thermodynamic analysis for withdrawal or addition of material to an isochoric vessel containing coexisting phases of a multi-component system is presented" }, { "name": "Jones, Noel Duane", "degree": "PhD", "year": "1964", "title": "The Crystal Structures of Several Organic Compounds. I. \u03b1-Keto-1, 1'-Trimethyleneferrocene. II. The Chloranil-Hexamethylbenzene Complex, a Refinement. III. Two Phenazine Derivatives from Pseudomonas aureofaciens", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechETD:etd-09252002-115411", "creators": [ { "name": { "family": "Jones", "given": "Noel Duane" }, "id": "Jones-Noel-Duane", "display_name": "Jones, Noel Duane" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TMB9-4198", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. The three-dimensional crystal structure of a [alpha]-keto-1,1'-trimethyleneferrocene has been determined by X-ray diffraction analysis. This compound crystallizes in the centrosymmetric monoclinic space group [...]. The unit cell contains four molecules and has the dimensions a = [...] and b = [...] and [?]. The structure was solved from the locations of the iron-iron vectors in the (001) Patterson projection and was refined in both two and three-dimensions by the method of least-squares. The final reliability factor, R, was 0. 067. The dihedral angle between the best planes through the two nearly planar cyclopentadienyl rings is about 9. 8?. The average ring carbon-carbon bond is [...] and the average iron-ring bond is [...]. The principal thermal motion is a vibration of the entire molecule in a direction roughly parallel to the [...] axis.\r\n\r\nII. The crystal structure of the chloranil-hexamethylbenzene complex, as first reported by Harding and Wallwork [Acta Cryst., 8, 787 (1955)], has been refined in order to show that their data are consistent with a more reasonable structure than that proposed by them. The molecular dimensions of the refined structure show no significant deviations from the expected values. In addition, the molecules are nearly planar.\r\n\r\nIII. The crystal structures of two phenazine derivatives from extracts of Pseudomonas aureofaciens have been determined. The first of these, 1-phenazinecarboxylic acid, has been solved and refined in two dimensions. The molecular structure of the other derivative, 2-hydroxy-1-phenazinecarboxylic acid, was unknown at the time this work was begun. It has been solved in three dimensions and partially refined by the method of least-squares.\r\n\r\n1-Phenazinecarboxylic acid crystallizes in the space group [...] with four molecules in the monoclinic unit cell. The lattice constants are [...] and [...]. The structure was solved from the weighted hk0 reciprocal lattice net and from the (001) Patterson map. The molecule is tilted 20-25[degrees] with respect to the (001) plane and is internally hydrogen bonded. The principal thermal vibration is a torsion motion about an axis which passes through the center ring of the phenazine nucleus.\r\n\r\n2-Hydroxy-1-phenazinecarboxylic acid also crystallizes in the space group [...] with four molecules in a unit cell which has the dimensions [...] and [...]. This structure was solved from the weighted [...] reciprocal lattice net and from the (010) Patterson vector map. The average ring carbon-carbon bond length, calculated from the partially refined positional parameters, is [...] and the average carbon-nitrogen bond length is [...]. The molecules lie parallel and coplanar in \"ribbons\" which are stacked normal to the [...] axis and very nearly parallel to the (012) plane. The hydroxyl hydrogen atom is internally bonded to the carboxyl group and the carboxyl hydrogen atom possibly forms a \"bifurcated\" bond, being bonded both intra- and intermolecularly." }, { "name": "Kover, Warner Bruce", "degree": "PhD", "year": "1964", "title": "Carbonium Ion Intermediates from Allylcarbinyl and Cyclopropylcarbinyl Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09252002-143022", "creators": [ { "name": { "family": "Kover", "given": "Warner Bruce" }, "id": "Kover-Warner-Bruce", "display_name": "Kover, Warner Bruce" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3Q9Z-7H69", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe products of the amine-nitrous acid reaction of ([alpha]-methylallyl)-carbinylamine were determined. The deamination of dideutero-([beta]-methylallyl)-carbinylamine was found to yield apparently unrearranged dideutero-([beta]-methylallyl)-carbinol and 1-methylcyclobutanol with > 97% of the deuterium in the 3-position. The deamination of dideutero-([alpha]-methylallyl)-carbinylamine was found to yield methylallylcarbinol with 78% of the deuterium in the [alpha]-methylene position and (2-methylcyclopropyl)-carbinol with 66% of the deuterium on the cyclopropyl ring. The deamination of dideutero-(2-methylcyclopropyl)-carbinylamine was found to yield methylallylcarbinol with 74% of the deuterium in the vinyl methylene position and (2-methylcyclopropyl)-carbinol with 85% of the deuterium on the carbinyl carbon.\r\n\r\nThese results are discussed in terms of various intermediates. It is concluded that the experimental evidence appears to require interpretation in terms of the equilibrating nonclassical bicyclobutonium and homoallylic carbonium ions." }, { "name": "Leif, Robert Cary", "degree": "PhD", "year": "1964", "title": "The Distribution of Buoyant Density of Human Erythrocytes in Bovine Albumin Solutions", "advisor": "Vinograd, Jerome Rubin; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-09262002-124229", "creators": [ { "name": { "family": "Leif", "given": "Robert Cary" }, "id": "Leif-Robert-Cary", "display_name": "Leif, Robert Cary" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/T2HY-3G14", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nA procedure for preparing and fractionating linear density gradients of bovine serum albumin is described. Reproducible buoyant density distributions of human erythrocytes in these gradients were obtained and individual fractions could be rebanded. The average buoyant density of erythrocytes from four individuals was 1.0808 [plus or minus] 0.0004 g. cm.[superscript -3]; the average density from a fifth individual was 0.0028 g. cm.[superscript -3] greater. The entire buoyant density distribution shifts with salt content; the erythrocytes behave as \"perfect\" osmometers. Salt gradients predictably spread or narrow the distribution, and may be used to increase the resolving power of the density gradient.\r\n\r\nRabbit erythrocytes pulse-labeled with Fe[superscript 59] first appear at the light edge of the distribution, and the mean progresses linearly with time through the distribution. The width of the distribution of labeled cells also increases with time.\r\n\r\nA study with the Coulter-Counter Model B of cell volumes in the buoyant density fractions showed that the mean cell volumes on the lighter side remained constant, while on the dense side the mean cell volume decreases. This decrease, if regarded as a water loss, does not quantitatively account for the increase in density.\r\n\r\nMicroscopic examination of the individual fractions of the buoyant density distribution show that the cells do not appear to be damaged by the manipulations, and that cells in the denser fractions are significantly less biconcave than the average cell. The reticulocytes concentrate in the lighter fractions, but do not clearly separate from the erythrocytes. It is proposed that the buoyant density be regarded as an index of the physiological condition of the erythrocyte. A summary discussion of the aging of the erythrocyte is given." }, { "name": "McDowell, Edward Rae Held", "degree": "PhD", "year": "1964", "title": "Transient Heat Transfer in Solids", "advisor": "Longwell, Paul A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10222002-102244", "creators": [ { "name": { "family": "McDowell", "given": "Edward Rae Held" }, "id": "McDowell-Edward-Rae-Held", "display_name": "McDowell, Edward Rae Held" } ], "advisors": [ { "name": { "family": "Longwell", "given": "Paul A." }, "id": "Longwell-P-A", "role": "advisor", "display_name": "Longwell, Paul A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0HDZ-WB26", "abstract": "The accuracy of approximate calculations of transient temperature distributions in solids is studied, emphasizing easily applied methods for both irregular and regular solids with a heat-transfer coefficient boundary condition. General stability criteria are shown which are easily found and used, and which apply for regular or asymmetric networks.\r\n\r\nAnalytic solutions of the one-dimensional partial difference equation are found by z-transforms. A. method with points located half an increment inside the surface gives the most accurate solutions. A graphical method is shown analytically to give approximations of engineering accuracy. A procedure is also presented for finding the differencing parameters which give a solution of a specified accuracy with the minimum calculations.\r\n\r\nTransient temperature distributions of satisfactory accuracy can be calculated for irregular solids using a relatively coarse network, by locating points that describe the boundary a short distance within, rather than on, the boundary, and by making the interior network as regular as possible." }, { "name": "Merkl, Arthur William", "degree": "PhD", "year": "1964", "title": "I. Spectrometer for Zero-Field Spin Resonance. II. Triplet Exciton Spin Resonance in Zero Field", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10182002-091245", "creators": [ { "name": { "family": "Merkl", "given": "Arthur William" }, "id": "Merkl-Arthur-William", "display_name": "Merkl, Arthur William" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZKQX-9R12", "abstract": "[No Abstract Submitted.]" }, { "name": "Olson, Edwin Soland", "degree": "PhD", "year": "1964", "title": "I. The Structure of the Orange Pigment from Pseudomonas aureofaciens. II. The Biogenesis of Strychnine. III. Beckmann Fission of a \u03b3-Keto Oxime", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10092002-153828", "creators": [ { "name": { "family": "Olson", "given": "Edwin Soland" }, "id": "Olson-Edwin-Soland", "display_name": "Olson, Edwin Soland" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/V3CJ-7176", "abstract": "PART I. \r\n\r\nThe structure of the orange pigment from Pseudomonas aureofaciens was investigated and found to be 1-carboxy-2-hydroxyphenazine. A degradation product, 1-methyl-2-methoxyphenazine, was shown to be identical to a synthetic sample.\r\n\r\nPART II.\r\n\r\nThe biogenesis of the indole alkaloid, strychnine, was studied by administration of C[superscript 14] labelled precursors to Strychnos nus-vomica plants and degradations of the radioactive strychnine isolated from the plants. The results indicate an acetate origin for the non-tryptophan portion and a formate origin for the \"berberine bridge\" carbon of strychnine.\r\n\r\nPART III.\r\n\r\nA Beckmann fission of the tosylate of the [gamma]-keto oxime, 3-acetoxylanostane-7, 11-dione-7-oxime, was carried out with sodium t-butoxide, and the expected cleavage of ring B and formation of a nitrile and unsaturated ketone occurred." }, { "name": "Rapp, James Ray", "degree": "PhD", "year": "1964", "title": "I. Stereospecificity in alpha-Chymotrypsin-Catalyzed Reactions. II. The Structural Specificity of alpha-Chymotrypsin: Some New Substrates.\r\nIII. A Further Study of Monofunctional Aromatic Inhibitors of alpha-Chymotrypsin", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10212002-113251", "creators": [ { "name": { "family": "Rapp", "given": "James Ray" }, "id": "Rapp-James-Ray", "display_name": "Rapp, James Ray" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QBMD-X884", "abstract": "A series of acylated glycine, D and L-alanine methyl esters have been evaluated as substrates for alpha-chymotrypsin. These results are correlated with a theory concerning the stereospecificity of the enzyme.\r\n\r\nThe effect on the kinetic constants of reducing an aromatic substrate to its hydroaromatic counterpart is studied. Two classes of substrates are distinguished, one in which the ring is in the side chain and the other where the ring is part of the acylamido group. \r\n\r\nSeveral analogues of known substrates are examined and their relationship and importance to the general picture of the specificity of alpha-chymotrypsin are discussed.\r\n\r\nA series of simple aromatic inhibitors of alpha-chymotrypsin were examined. Concomitantly, the combined effect of two inhibitors on alpha-chymotrypsin-catalyzed hydrolyses is discussed." }, { "name": "Rodriguez, Sergio Enrique", "degree": "PhD", "year": "1964", "title": "X-Ray Diffraction Studies of Stable and Supercooled Liquid Gallium", "advisor": "Pings, Cornelius J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09272002-162252", "creators": [ { "name": { "family": "Rodriguez", "given": "Sergio Enrique" }, "id": "Rodriguez-Sergio-Enrique", "display_name": "Rodriguez, Sergio Enrique" } ], "advisors": [ { "name": { "family": "Pings", "given": "Cornelius J." }, "id": "Pings-C-J", "role": "advisor", "display_name": "Pings, Cornelius J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZDWW-TW72", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nX-ray diffraction studies of stable and supercooled liquid gallium (m.p. 29.8[degrees]C.) between 0 and 50[degrees]C. show no important dependence of internal structure on temperature. Atomic radial distribution functions were determined for 0, 10, 20, 29.5, 30, 40, and 50[degrees] from diffraction data to S=11[...]. Diffraction data was obtained in reflection geometry with Ag K-alpha radiation, scintillation counter, and pulse-height analyzer. The sample was contained in a sealed plastic cell with transparent walls. A supporting assembly provided temperature control within 0.1[degrees]C. and a transparent plastic X-ray window which permitted visual inspection of the sample surface. Arguments are presented in favor of normalizing scattered intensities to independent scattered intensity at high S values. The method of inversion is based on a single, piecewise polynomial approximation to the scattering function i(S) for each temperature." }, { "name": "Rosen, Allan Joseph", "degree": "PhD", "year": "1964", "title": "Studies of Cyclopropylcarbinyl-Allylcarbinyl Free Radicals", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10012002-153114", "creators": [ { "name": { "family": "Rosen", "given": "Allan Joseph" }, "id": "Rosen-Allan-Joseph", "display_name": "Rosen, Allan Joseph" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A61A-Z940", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe di-t-butyl peroxide-initiated decarbonylations of cyclopropylacetaldehyde and dimethylcyclopropylacetaldehyde in the presence of benzyl mercaptan have been carried out and the chain-transfer constants of neopentane, n-butane, 2,3-dimethylbutane, methylcyclopropane, and isopropylcyclopropane with styrene at 79.1[degrees] have been determined in an attempt to ascertain the nature and number of the intermediates involved in interconversions of certain cyclopropylcarbinyl and allylcarbinyl derivatives in free-radical reactions. These interconversions are shown to be reversible. It is concluded that the nonclassical homoallyl radical and the classical allylcarbinyl radical are the intermediates involved in the free-radical interconversion of the cyclopropylcarbinyl and allylcarbinyl skeletons. No evidence is found for the existence of a nonclassical dimethylhomoallyl radical; the classical dimethylcyclopropylcarbinyl and ([gamma, gamma]-dimethylallyl)-carbinyl radicals are probably the only intermediates involved in the free-radical interconversion of the dimethylcyclopropylcarbinyl and ([gamma, gamma]-dimethylallyl)-carbinyl skeletons." }, { "name": "Saltiel, Jack", "degree": "PhD", "year": "1964", "title": "Photoisomerization of the Stilbenes: an Application of Chemical Spectroscopy", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-10032002-121819", "creators": [ { "name": { "family": "Saltiel", "given": "Jack" }, "id": "Saltiel-Jack", "display_name": "Saltiel, Jack" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4BXD-4D28", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nFormation and quenching of stilbene triplet states by means of energy transfer is used in an attempt to elucidate the mechanism of [cis-trans] photoisomerization in this system.\r\n\r\nIt is found that the [cis-trans] ratios attained at the photostationary state in the presence of sensitizers map a \"chemical spectrum\" when plotted against the triplet state energies of the sensitizers. This spectrum is interpreted by assuming that stilbene triplet states can be produced by vertical or nonvertical energy transfer from the lowest triplet states of the sensitizers. A consistent picture is presented to account for the effect of sensitizer or quencher concentration on the stilbene photostationary states.\r\n\r\nEvidence is presented which strongly supports the hypothesis that stilbene isomerization induced by direct absorption of light proceeds by way of the lowest triplet states." }, { "name": "Shah, Usha", "degree": "Masters", "year": "1964", "title": "\u03b1-Carbonium Ion Stabilization in Derivatives of Cyclopentadienylmanganese Tricarbonyl", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032010-131343121", "creators": [ { "name": { "family": "Shah", "given": "Usha" }, "id": "Shah-Usha", "display_name": "Shah, Usha" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GQ3E-6784", "abstract": "A study has been made of the solvolyses of some acetoxy and trifluoroacetoxy compounds of cyclopentadienylmanganese tricarbonyl and of benzene. Also, a study of some addition reactions to the double bond of vinyl cyclopentadienylmanganese tricarbonyl has been made. Both studies show that an \u03b1-cyclopentadienylmanganese tricarbonyl carbonium ion is less stable than an \u03b1-ferrocenylcarbonium ion, but more stable than an \r\n\u03b1-phenylcarbonium ion.\r\n" }, { "name": "Silverstone, Harris Julian", "degree": "PhD", "year": "1964", "title": "A Theoretical Study of the Electron Spin Resonance Spectra of Cycloheptatrienyl", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10082002-103423", "creators": [ { "name": { "family": "Silverstone", "given": "Harris Julian" }, "id": "Silverstone-Harris-Julian", "display_name": "Silverstone, Harris Julian" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DF27-YB41", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\nThe ESR spectra of the cycloheptatrienyl radical (CHT) have been studied theoretically, and the orbital degeneracy of the ground state of CHT has been decisively confirmed. The static Jahn-Teller effect and out-of-plane puckering do not occur. The spin densities have been calculated according to the prescriptions of the simple Huckel, approximate UHFLCAO-MO, Pariser-Parr and valence bond theories. The modifications of the dynamic Jahn-Teller effect and of the unusually strong coupling between the CHT molecule and the lattice through the crystal field have been discussed. The hyperfine structure of the high temperature spectra in naphthalene has been quantitatively explained, and the hyperfine structure of the low temperature spectra in naphthalene has been semi-quantitatively explained. The pi-electron contribution to the spectroscopic splitting factor, g[subscript z, subscript z], has been estimated and shown to account for the low temperature polycrystalline g-factors. The role of the spin-orbit interaction in inducing spin-lattice relaxation has been examined in the light of the strong lattice-CHT coupling." }, { "name": "Thomas, Donal Diepen", "degree": "PhD", "year": "1964", "title": "I. The Magnetic Resonance of Triplet Excitons in Solid Free Radicals. II. A Zero Field Magnetic Resonance Spectrometer", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05142003-150740", "creators": [ { "name": { "family": "Thomas", "given": "Donal Diepen" }, "id": "Thomas-Donal-Diepen", "display_name": "Thomas, Donal Diepen" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8SSP-8R37", "abstract": "Part I.
\r\n\r\nThe magnetic resonance of triplet excitons in solid free radicals has been studied in both zero magnetic field and a high magnetic field. A discussion of the spin Hamiltonian for triplet excitons in zero field and high field is presented. Calculations of the second moment of the exciton resonances is given and compared for the two cases. The fine-structure splittings of triplet excitons in Wurster's blue perchlorate in a high magnetic field and in (0\u2083AsCH\u2083\u207a (TCNQ)\u2082\u207b in zero field have been determined and their temperature dependence is discussed. The temperature dependence of the line width is also given.
Part II.
\r\n\r\nA zero field magnetic resonance spectrometer has been constructed for use in the 10 - 100 Mc/sec frequency range. A marginal oscillator and bidirectional square wave field modulation are used.
Part I
\r\n\r\nThe Configurational Stability of Primary Grignard Reagents
\r\n\r\nExamination of the temperature dependence of the nuclear magnetic resonance spectrum of 3,3-dimethylbutylmagnesium chloride in diethyl ether solution indicates that inversion of configuration at the methylene group of this Grignard reagent occurs with an approximate rate of 10 sec.\u207b\u00b9 at room temperature. The dependence of the rate of inversion on solvent and on the structure of the Grignard reagent is discussed in terms of possible mechanisms for the inversion.
\r\n\r\nPart II
\r\n\r\nApplications of Nuclear Magnetic Resonance Spectroscopy to the Study of Molecular Asymmetry
\r\n\r\nThe methylene protons of 1-phenylethyl benzyl ether are magnetically non-equivalent and display an AB-type nuclear magnetic resonance spectrum. The variation in the spectrum of this compound and in the spectra of other structurally similar ethers with solvent indicates that the principal contribution to the magnetic non-equivalence of the methylene protons originates in the magnetic anisotropy of the phenyl group bonded directly to the methylene group. It is suggested that the solvent dependence of these spectra reflects changes in the populations of the possible rotational conformations open to the molecule.
" }, { "name": "Wirth, Thomas Henry", "degree": "PhD", "year": "1964", "title": "Mercury-Amine Complexes and Aromatic Mercurials: a Study of Compounds Containing Mercury-Nitrogen and Mercury-Carbon Bonds in Aqueous Solution", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11052002-161025", "creators": [ { "name": { "family": "Wirth", "given": "Thomas Henry" }, "id": "Wirth-Thomas-Henry", "display_name": "Wirth, Thomas Henry" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2P2A-GE19", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe Hg(II) complexes of aniline, guanidine, and ammonia have been studied potentiometrically in aqueous solution with a mercury electrode. The stability of the HgR[subscript 2][superscript ++] complexes of these compounds correlates well with their basicities. An RHgOH[superscript +] complex (R = guanidine) has been identified potentiometrically and its stability determined.\r\n\r\nPotentiometric evidence for the existence of a 1: 1 Hg(I)-aniline complex was confirmed spectrophotometrically. The complex is less stable than the corresponding complex of Hg(II). No 2: 1 complex (Hg[subscript 2] L[subscript 2][superscript ++]) was observed.\r\n\r\nThe 1: 1 complexes of aniline and para-mercurated aniline with Hg(II) were studied spectrophotometrically. Cationic, ring mercurated anilines bind Hg(II) strongly; no decrease in complex stability occurs as -Hg[superscript +] groups are added to the aromatic ring. Complexes of Hg(II) with mercurated anilines exhibit a unique ultraviolet absorption band at 330-335 m[mu] in aqueous solution.\r\n\r\nSlow but pronounced spectral changes occur in aqueous Hg(C1O[subscript 4])[subscript2]-HC1O[subscript 4] solutions containing small amounts of [psi]NH[subscript 3C1O[subscript 4] which are allowed to stand. These changes have been interpreted in terms of mercuration of the aniline and the formation of Hg(II) complexes with the products.\r\n\r\nSingle crystals of an explosive Hg(II)-aniline compound C[subscript 6]NH[subscript 3]Hg[subscript 3](C1O[subscript 4)[subscript 2] [...] 4H[subscript 2]O have been prepared.\r\n\r\nEquilibrium in the mercuration of benzene and p-methoxy anisole has been studied at room temperature in aqueous HC1O[subscript 4]NaC1O[subscript 4] solution in the presence of excess organic. An analytical procedure utilizing the U.V. absorption of the HgC1[subscript 4][superscript =] complex was used. The equilibrium quotient of the reaction C[subscript 6]H[subscript 6] + Hg[superscript ++] = C[subscript 6H[subscript 5]Hg[superscript +] +H [superscript +] lies in the range 70-500." }, { "name": "Wood, David Eldon", "degree": "PhD", "year": "1964", "title": "I. Electron Spin Resonance of Cycloheptatrienyl. II. Auxiliary Apparatus", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062002-152348", "creators": [ { "name": { "family": "Wood", "given": "David Eldon" }, "id": "Wood-David-Eldon", "display_name": "Wood, David Eldon" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QX4Y-W142", "abstract": "Part I. The ESR spectra of cycloheptatrienyl (CHT) in several crystalline environments at temperatures ranging from 1.5[degrees] to 300[degrees]K and the methods of sample preparation are described in detail.\r\n\r\nThe observed spectra are classified as:\r\n\r\n(a) High-temperature spectra--eight equally spaced lines with splittings of 3.7 to 4 gauss and intensity ratios 1:7:21:35:35:21:7:1.\r\n\r\n(b) Low-temperature spectra-highly anisotropic and different for each environment. \r\n\r\nThe transitions between (a) and (b) are abrupt, and the transition temperatures are different for each environment.\r\n\r\nCHT is a planar regular heptagon with an orbitally degenerate ground state. This degeneracy can be removed by a crystalline electric field. The wave functions, after the degeneracy has been removed, are determined by the crystal field. The Jahn-Teller distortion of the ring and the spin-orbit interaction are probably less than 1 cm[superscript -1].\r\n\r\nPart II. The low-temperature ESR system used in the study of CHT is described in detail. A simple and effective zone refiner for organic compounds is described.\r\n\r\nAbstract of propositions\r\n\r\n1. An extremely versatile low-temperature ESR system is described in detail.\r\n\r\n2. The vapor phase photolysis of cyclopropene to produce cyclopropenyl radical (C[subscript 3]H[subscript 3]) for study by ESR is proposed.\r\n\r\n3. An experiment to measure the pi-electron spin-orbit interaction in CHT is proposed.\r\n\r\n4. It is proposed that magnetic rotation spectroscopy be used to search for the second and third triplet states of benzene.\r\n\r\n5. Bitropyl-thiourea inclusion compound is proposed as a novel triplet exciton system." }, { "name": "Atkinson, Thomas Vincent, Jr.", "degree": "Bachelors", "year": "1963", "title": "pK's of Nucleic Acid Components as a Function of Temperature", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122026-224322797", "creators": [ { "name": { "family": "Atkinson", "given": "Thomas Vincent, Jr." }, "id": "Atkinson-Thomas-Vincent", "display_name": "Atkinson, Thomas Vincent, Jr." } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s176-y927", "abstract": "The pK's of the -N1H- groups for the several deoxynucleic\r\nacid components have been studied as a function of temperature.\r\nFrom this the \u25b3\u0124's for the ionizations are obtained. The components\r\nstudied were thymidine, thymidylic acid, deoxyguanosine, and\r\ndeoxyguanylic acid (5').
" }, { "name": "Baldwin, John Edwin", "degree": "PhD", "year": "1963", "title": "Part I. Mechanism of the Thermal Isomerization of 2-Norbomene-5,6-Endodicarboxylic Anhydride. Part II. The Aldoketene Dimer Rearrangement", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052005-154306", "creators": [ { "name": { "family": "Baldwin", "given": "John Edwin" }, "id": "Baldwin-John-Edwin", "display_name": "Baldwin, John Edwin" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/83K8-TP73", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I\r\n \r\nThe Diels-Alder adduct of cyclopentadiene and maleic anhydride, 2-norbornene-5,6-endo-dicarboxylic anhydride, may be rearranged thermally to its exo-isomer. This isomerization is known to occur in part through an internal mechanistic pathway. In order to study the mechanism of this rearrangement, an attempt was made to synthesize 2-norbornene-5,6-endo-dicarboxylic anhydride stereospecifically labeled with carbon-14 in one carboxyl group, rearrange this material under conditions favoring the internal pathway, and degrade the exo-anhydride in a stereospecific fashion, measuring the carbon-14 activities of each carbonyl group separately.\r\n\r\nThree synthetic approaches to the stereo specifically labeled endo-anhydride, through the intermediates ethyl cis-[...]-cyanoacrylate, (-)-menthyl hydrogen maleate, and (-)-menthoxymalealdehydic acid, have not been successful. Rearrangement of the endo-anhydride in the presence of tetracyanoethylene gave exo-anhydride from the internal mechanism and 2,2,3,3-tetracyanonorborn-5-ene from the external process. Degradation of 2-norbornene-5,6-exo-dicarboxylic anhydride by hydrogenation and reaction with (-)-menthol gave two diasteromeric (-)-menthyl hydrogen 2,3-exo-norbornanedicarboxylates, whose absolute configurations were established by degradation of one to an optically active 2-exo-norbornanecarboxylic acid.\r\n\r\n2,3-Endo-norbornanedicarboxylic anhydride was rearranged to its exo-isomer when heated to 250\u00ba for 18 hours.\r\n\r\nPART II\r\n\r\nThe neutral phenylketene dimer has been synthesized, identified as 3-hydroxy-2,4-diphenyl-3-butenoic lactone, reduced to [...],[...]-diphenylbutyric acid, and rearranged with base to an acidic isomer, tentatively postulated to be 2,4-diphenylcyclobutanedione or 2,4-diphenylcyclobutenolone.\r\n\r\nStructural assignments for neutral methylketene dimer, acidic methylketene dimer, 3,5-dimethyl-6-ethylpyronone, 3,5-diphenyl-4-hydroxy-6-benzylpyrone, and 3,5-dimethyl-4-hydroxy-6-ethylpyrone have been confirmed or corrected." }, { "name": "Barker, David Lowell", "degree": "Bachelors", "year": "1963", "title": "The Crystal Structure of Anhydrous Cytosine", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132026-150504639", "creators": [ { "name": { "family": "Barker", "given": "David Lowell" }, "id": "Barker-David-Lowell", "display_name": "Barker, David Lowell" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sm37-gr24", "abstract": "The crystal structure of anhydrous cytosine has been\r\ndetermined and refined by analysis of complete three-dimensional\r\ncopper X-radiation data. The crystals are orthorhombic with\r\nspace group P212121; the unit-cell dimensions are a = 13.041 \u00c5,\r\nb = 9.494 \u00c5, c = 3.815 \u00c5. Refinement of the positional parameters\r\nfor all 13 atoms and of the individual anisotropic temperature\r\nfactors of the eight heavier atoms was by the method of least\r\nsquares. For the 608 observed reflections of non-zero weight,\r\nthe final R factor is 0.061.
\r\n\r\nThe molecule is found to exist in the amino form with a\r\nhydrogen atom bonded to N1 and none to N3 The amino nitrogen\r\nparticipates in two hydrogen bonds to carbonyl oxygens of other\r\nmolecules. These bonds have relatively long lengths of 2.98 and\r\n3.03 \u00c5. N1 hydrogen bonds to N3 of a neighboring molecule at a\r\ndistance of 2.84 \u00c5.
" }, { "name": "Booth, Frank Bliss", "degree": "PhD", "year": "1963", "title": "I. Electron Magnetic Resonance Studies on Irradiated Single Crystals of Sebacic Acid. II. Rate of Electron Exchange Between Dip-Anisyl Nitrogen Oxide Molecules by Electron Paramagnetic Resonance", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02292012-111329527", "creators": [ { "name": { "family": "Booth", "given": "Frank Bliss" }, "id": "Booth-Frank-Bliss", "display_name": "Booth, Frank Bliss" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3KR4-E339", "abstract": "Part I
\r\n\r\nThe electron magnetic resonance spectrum of freshly x - ray\r\ndamaged single crystals of sebacic acid shows that two radical species,\r\nI and II, are produced, the spectrum of I about twice as intense as\r\nthat of II. Upon illumination of a damaged crystal with ultraviolet\r\nlight, radical II is destroyed, leaving I unaffected. Analysis of the\r\nmagnetic hyper fine spectrum of such a \"bleached\" crystal identifies\r\nI as HOOC\u010aH(CH_2)_7COOH and shows that I is oriented within experimental error in the same way in the crystal lattice as the undamaged\r\nmolecule. The \u03c3 proton and \u03c0 proton hyperfine interactions with the\r\nunpaired spin are measured for I and are found to be consistent with\r\nthose values observed for similar radicals formed in other irradiated\r\ndicarboxylic acids . Radical II is not identified but is judged to be\r\nstructurally similar to I, primarily because of the observed and\r\ndeduced similarities between the spectra of I and II. A damaged\r\ncrystal which has been heat treated has a spectrum interpretable in\r\nterms of three radicals, I, III, and IV. The evidence is that radical\r\nII is the precursor of III and IV. Several models for III and IV are\r\noffered, which invoke fractional spin densities to account for the\r\nobserved small hyperfine splittings. Arguments are advanced that\r\nfavor IV being (\u2022OOC)(CH_2)_8COOH. Radical III may be HOOCCHCH=CH(CH_2)_6COOH or an ionized species as (O=CHCHC+/H)(CH_2)_5COOH.
\r\n\r\nPart II
\r\n\r\nThe line shape of the EPR spectrum of di-p-anisyl nitrogen\r\noxide (DANO) in CHC1_3 was studied over a range of concentrations\r\n(0.006-0.F) so chosen to show the transition from the hyperfine\r\ntriplet spectrum (arising from the hyperfine contact interaction of the\r\nelectron spin with the nitrogen nucleus) to the exchange narrowed\r\nsingle line spectrum as the concentration of free radical increases.\r\nThe observed change of line shape with concentration agreed well\r\nwith that predicted by the modified Bloch equations which allow for\r\nspin magnetization exchange. The rate of electron exchange between\r\nmolecules of DANO was calculated to be 7.5 x 10^9 liter mole ^(-1) sec ^(-1) \r\nat room temperature. The lifetimes of the electron spin state with respect to exchange ranged from 3 x 10 ^(-8) sec to 1 x 10 ^(-9) sec.
\r\n" }, { "name": "Bopp, Thomas Theodore", "degree": "Bachelors", "year": "1963", "title": "The Interaction of T-4 Phage Particles and Mercuric Ion", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132026-151632161", "creators": [ { "name": { "family": "Bopp", "given": "Thomas Theodore" }, "id": "Bopp-Thomas-Theodore", "display_name": "Bopp, Thomas Theodore" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/z73j-4r52", "abstract": "The interaction of T-4 phage particles and mercuric ion \r\nhas been studied by ultraviolet spectrophotometry. The changes\r\nin the ultraviolet absorption spectrum upon the addition of\r\nHg(II) are very similar to the changes observed by Yamane\r\nand Davidson and others for free DNA." }, { "name": "Chesebro, Bruce Wilcox", "degree": "Bachelors", "year": "1963", "title": "A Quantitative Assay of Polyoma Virus Mediated Neoplastic Transformation of Cells in Vitro", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132026-163637415", "creators": [ { "name": { "family": "Chesebro", "given": "Bruce Wilcox" }, "id": "Chesebro-Bruce-Wilcox", "display_name": "Chesebro, Bruce Wilcox" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fd2k-fp37", "abstract": "No abstract." }, { "name": "Clovis, James Stanley", "degree": "PhD", "year": "1963", "title": "The Mechanism of the Benzidine Rearrangement. Part I. The Rearrangement of p-Hydrazotoluene. Part II. The Rearrangement of m-Hydrazoaniline", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042013-085236180", "creators": [ { "name": { "family": "Clovis", "given": "James Stanley" }, "id": "Clovis-James-Stanley", "display_name": "Clovis, James Stanley" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E47T-2V77", "abstract": "Part I
\r\n \r\nA number of unsuccessful experiments were carried out in\r\nan attempt to show that the benzidine rearrangement proceeds through intermediate cation radicals. The rearrangement of p-hydrazo- toluene (HzT), which has been reported to give rise to p-toluidine, p-azotoluene, and 2-amino-4, 5'-dimethyldiphenylamine (an o-semidine) in a 2:1:2 weight ratio, was extensively investigated.
\r\n\r\nAttempts to initiate polymerization by intermediates formed during the rearrangement of HzT (and hydrazobenzene) failed. The product solution that was obtained after all of the HzT had reacted was found to oxidize N,N,N',N' tetramethyl-p-phenylenediamine to Wurster's Blue . The kinetics of this oxidation were investigated.
\r\n\r\nThe composition of the mixture of products obtained from\r\nHzT was re-examined by the technique of isotope dilution. The results showed that p-toluidine, p-azotoluene, and the o-semidine account for only 90% of starting material and are actually formed in a 3:2:4 weight ratio. An additional product (or products) must account for 10% of the reac tion of HzT.
\r\n\r\nRadioactive HzT was rearranged in the presence of a number of added compounds. The presence of hydrazobenzene was found to reduce the yield of p-azotoluene, but not to alter the formation of p-toluidine and the o-semidine. These results show that p-azotoluene is formed by an intermolecular process, while the remaining products probably originate from intramolecular paths.
\r\n\r\nThe rearrangement of p,p'-ditrideuteromethylhydrazobenzene-4,4'-C^(14) was investigated and found to be unaffected by the presence\r\nof the deuterium.
\r\n\r\nAn unknown compound was isolated in very small quantities from the product mixture obtained from the rearrangement of HzT. This compound was in the form of an oil and was only partially characterized.
\r\n\r\nA possible explanation for the formation of the 10% of unknown product is that it arises from coupling of the para carbon atoms of HzT.
\r\n\r\nPart II
\r\n\r\nThe rearrangement of m-hydrazoaniline (HzA) to 2,2'-di -\r\naminobenzidine has been investigated. The reaction rate exhibits an inverse dependence upon hydrogen ion. As HzA is a diacidic base, the observed rate law requires that the transition state of the rearrangement involve a monoconjugate acid of HzA.
\r\n\r\nHzA-N^(15)H-N^(15)H- was prepared and rearranged at four acid concentrations, three of which were within the concentration range used to determine the acid dependence of the rearrangement. The N^(15) content of the o-amino groups of the resulting benzidine was found to increase as the acidity of the rearrangement solutions was increased. In terms of coupling reactions the results showed that the extent of ortho coupling that occurred in the formation of the benzidine varied from approximately 35% at the lowest acid concentration to 44% at the highest. As only one hydrogen is involved in the transition state of the rearrangement, a metastable intermediate must be formed which can either collapse to product or be attacked\r\nby a second proton. The results are consistent with a mechanism which involves initial heterolysis of the N-N bond to give Dewar's \"n-complex.\" This complex can either collapse to product or can be attacked by proton to form a pair of cation radicals which will also collapse to product.
\r\n\r\nStarting material was recovered after a rearrangement had proceeded to 50% completion and the N^(15) content of the hydrazo linkage was found to be unchanged.
\r\n" }, { "name": "Counsell, Ronald Keith", "degree": "Bachelors", "year": "1963", "title": "Isomerization of Piperylene the Dependence on the Concentration of Sensitizer", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:05132026-171656270", "creators": [ { "name": { "family": "Counsell", "given": "Ronald Keith" }, "id": "Counsell-Ronald-Keith", "display_name": "Counsell, Ronald Keith" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2may-d875", "abstract": "The data support the idea that the physical transfer of energy from\r\ncertain sensitizers to piperylene is a reversible process. That similar\r\nbehavior was observed for 2-acetonaphthone and fluorenone suggests either\r\nthat in these cases the quenching process is so exothermic that the controlling\r\nfactor is the decay processes of piperylene triplets; or that as\r\nEt of the sensitizer changes from 53 kcal. to 60 kcal. all four excited\r\npiperylene configurations are important. The observed behavior for benzil\r\nmight be attributed to incomplete data, but perhaps the photostationary\r\nstates of this compound should be studied more closely." }, { "name": "Foss, Robert Paul", "degree": "PhD", "year": "1963", "title": "The Mechanism of Triplet-Energy Transfer in Solution: the Quenching of Excited-State Benzophenone by Transition-Metal Chelates", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-03252009-151617", "creators": [ { "name": { "family": "Foss", "given": "Robert Paul" }, "id": "Foss-Robert-Paul", "display_name": "Foss, Robert Paul" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/16RT-DR28", "abstract": "The quenching of triplet-state benzophenone by transition-metal chelates of acetylacetone, dipivaloylmethane and dibenzoylmethane is studied in detail. Compounds with both diamagnetic and paramagnetic ground state configurations and with square planar and octahedral structural configurations are used in this investigation.\r\n\r\nThe most extensively studied chelates are the octahedrally complexed acetylacetonate and dipivaloylmethide complexes of iron, chromium, cobalt and aluminum. Detailed molecular orbital calculations considering the \u03c0-orbital interaction between the ligand \u03c0-orbital system and the d-atomic orbitals centered on the metal atom are performed on these chelates. The calculated spectra of the chelates agree well with the observed.\r\n\r\nQuenching experiments show no correlation between the paramagnetic susceptibility of the chelates and their quenching efficiency. Furthermore, no correlation between quenching efficiencies and the energies of the low energy ligand field transitions is observed. A correlation is obtained, however, between the quenching efficiencies of the chelates and the calculated and observed \u03c0-\u03c0* transition energies. A steric effect, introduced by the ligands, is observed between corresponding sets of dipivaloylmethide and acetylacetonate chelates. Both the energy correlation and the steric effect may be explained by a general mechanism for triplet energy transfer in solution which is given in this thesis.\r\n\r\nQuenching of singlet benzophenone by the dibenzoylmethide chelates of iron and chromium is also observed. A possible explanation of these results is given." }, { "name": "Fritchie, Charles Julius", "degree": "PhD", "year": "1963", "title": "The Crystal and Molecular of a Dimer of a Cyclobutadiene Derivative. The Crystal Structure of BIS-(2-Bromopyridine)-Dodecahydrodecaborane", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232012-084021160", "creators": [ { "name": { "family": "Fritchie", "given": "Charles Julius" }, "id": "Fritchie-Charles-Julius", "display_name": "Fritchie, Charles Julius" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0JNR-XX66", "abstract": "I. The crystal and molecular structures of a dimer of a cyclobutadiene derivative.
\r\nThe molecular structure of this compound, previously suggested by other chemical work, has been conclusively established. Bond lengths and angles within the tricyclooctadiene skeleton were established with a precision exceeding that of any other study of a substituted cyclobutane and of any save one study of a substituted cyclobutene. Lengthening of the average C-C single and double bond in a C_4 ring is confirmed, and a shortening of the average external bond is also found. All bonds are normal (considering the above effects) except a C-C single bond in the configuration F-C-C-F, which is found to be 1.500 \u00b1 0.009 \u00c5 rather than the expected 1.58 \u00c5. The difference is attributed to change in the carbon hybridization state by the presence of the fluorine atoms.
\r\n\r\nThe cyclobutane ring is accurately planar, but the two cyclobutene rings are slightly folded, with dihedral angles of 177\u00b0 and 178\u00b0 between the two halves. This folding is probably due to steric crowding within the molecule. The angles between the mean planes of the three rings, fused in a stairstep arrangement, are 113.3\u00b0 and 113.7\u00b0.
\r\n\r\nII. The crystal structure of BIS (2-bromopyridine)-dodecahydrodecaborane.
\r\n\r\nThe crystal structure of this compound has been determined, all atoms including hydrogen being located by examination of Patterson syntheses and use of the heavy atom technique. The compound has the same borohydride skeleton within experimental error as diacetonitrile-dodecahydrodescaborane, the first of the B_(10)H_(12)R_2 compounds with R an electron donor to be studied crystallographically. The B-B bond distances in the borohydride radical differ from those in the parent compound, B_(10)H_(14), and the positions of bridge hydrogens attached to borone 5 through 10 in B_(10)H_(14) are changed. There are two hydrogen bridges in the B_(10)H_(12)R_2 compounds, compared with four in B_(10)H_(14). Bond distances in the bromopyridine ligands are unchanged by attachment to the borohydride skeleton, but some angles are slightly abnormal. The abnormalities can be explained in terms of intramolecular steric repulsion.
\r\n\r\n" }, { "name": "Hall, David Warren", "degree": "PhD", "year": "1963", "title": "I. Electrophilic Substitution Reactions of Some Substituted Ferrocenes. II. The Effects of Heteroannular Substituents on the Rates of Solvolyses of Methylferrocenylcarbinyl Acetates; a Comparison with Substituent Effects in Other Reactions of Ferrocene", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182012-093046041", "creators": [ { "name": { "family": "Hall", "given": "David Warren" }, "id": "Hall-David-Warren", "display_name": "Hall, David Warren" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D0MY-K780", "abstract": "Part I. The directive effects of substituents in ferrocene have been\r\ninvestigated by means of Friedel-Crafts acetylation studies. It was\r\ndemonstrated that the effect of an alkoxycarbonylamino group is comparable to that of an alkyl group in the acetylation of \r\n1,1'-disubstituted ferrocenes. Contrary to expectations, acetylation of acetamide- and alkoxycarbonylaminoferrocenes gave chiefly the heteroannular isomers. Only small amounts of the 1, 2-isomers were formed; no 1,3-isomers were isolated.
\r\n\r\nThe iodine in iodoferrocene was replaced by hydrogen under the\r\nconditions of the Friedel-Crafts reaction. Bromo- and chloroferrocenes were readily acetylated; only heteroannularly substituted isomers were formed.
\r\n\r\nPart II. The nature of the transmission of substituent effects from one cyclopentadienyl ring of ferrocene to a reaction center on the other ring was investigated by means of solvolyses studies on heteroannularly substituted methylferrocenylcarbinyl acetates. The evidence indicates that inductive or field effects predominate, and that resonance interactions play at most a minor role.
\r\n\r\nSubstituents possessing unshared pairs of electrons can\r\napparently undergo nucleophilic participation with the central iron\r\natom. This interaction very likely requires that the ring bearing the substituent be shifted or tilted in the transition state so that the substituent can be sufficiently close to the iron atom.
\r\n\r\nA linear relationship has been shown to exist between substituent\r\neffects in all side-chain reactions of ferrocene reported to\r\ndate and the reversible quarter-wave oxidation potentials of the\r\nappropriately substituted ferrocenes.
\r\n" }, { "name": "Hamilton, Carole Lois", "degree": "PhD", "year": "1963", "title": "I. An Investigation of Rearrangement in 2-Phenylethyl Organometallic Compounds. II. Skeletal Interconversion in AIIylcarbinyl Cyclopropylcarbinyl and Cyclobutyl Grignard Reagents", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142012-092542581", "creators": [ { "name": { "family": "Hamilton", "given": "Carole Lois" }, "id": "Hamilton-Carole-Lois", "display_name": "Hamilton, Carole Lois" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D4XP-HN97", "abstract": "I. An investigation of rearrangement in 2-phenylethyl organometallic compounds.\r\nThe Grignard reagent formed by 2-phenylethyl-l-14C chloride has been shown not to undergo significant isotope-position rearrangement. Attempts to prepare 2-phenylethyllithium are discussed.
\r\n\r\nII. Skeletal interconversion in allylcarbinyl, cyclo-propylcarbinyl and cyclobutyl Grignard reagents.\r\nThe Grignard reagents have been prepared from allylcarbinyl, cyclopropylcarbinyl, and cyclobutyl chlorides in the presence of proton donors, and rearrangement of all three skeletons has been observed. It has been established that allylcarbinylmagnesium chloride exists in equilibrium with cyclopropylcarbinylmagnesium chloride, the former being very much favored. Evidence for the existence of a non-classical homoallyl free radical is presented.
" }, { "name": "Kessel, James W.", "degree": "PhD", "year": "1963", "title": "Part I. The Isolation and Structure of Two Alkaloids from Tabemaemontana rupicola. Part II. The Structure of Necrosamine", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04242012-131610899", "creators": [ { "name": { "family": "Kessel", "given": "James W." }, "id": "Kessel-J-W", "display_name": "Kessel, James W." } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CRDM-RN71", "abstract": "Part I
\r\n\r\nTwo alkaloids have been isolated from the leaves and twigs of Tabernaemontana rupicola, a South American shrub. Physical and chemical data indicate that one of these alkaloids, named rupicoline, is 18\u2013carbomethoxyiboluteine, a pseudoindoxyl compound closely related to the alkaloid voacangine. The second alkaloid, named montanine, is believed to be 18-carbomethoxy-20-hydroxyiboluteine.\r\nHowever, attempts to prove this structure for\r\nmontanine by converting some of this alkaloid to rupicoline were unsuccessful. Experiments were also conducted which suggest that these alkaloids are not artifacts of the isolation procedure.
\r\n\r\nPart II
\r\n\r\nNecrosamine, a base isolated from an Escherichia coli\r\nlipopolysaccharide causing the regression of an experimental mouse tumor, yields, when oxidized with periodate and permanganate, n-butyric acid. Necrosamine is therefore an isomer of 4, 5-diaminoeicosane. Several attempts were made to resolve synthetic 4, 5-diaminoeicosane. These were unsuccessful as were\r\nattempts to prepare a derivative of necrosamine with a detectable optical rotation.
" }, { "name": "King, Donald Menford", "degree": "PhD", "year": "1963", "title": "I. A Kinetic Study of the Reaction Between Thioacetamide and Hydrazine. II. The Iodometric Determination of Peroxydisulfate. III. Effect of Surface Oxidation and Platinization on the Behavior of Platinum Electrodes", "advisor": "Anson, Fred C.; Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04202012-154932323", "creators": [ { "name": { "family": "King", "given": "Donald Menford" }, "id": "King-Donald-Menford", "display_name": "King, Donald Menford" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." }, { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZW53-M845", "abstract": "Part I.
\r\n\r\nHydrazine reacts with thioacetamine to produce hydrogen sulfide. This reaction is first order with respect to both thioacetamide and hydrazine and is both specific and general acid catalyzed. Rapid precipitation of metal sulfides can be obtained in solutions of pH 4-6 with the thioacetamide hydrazine combination.
\r\n\r\nPart II.
\r\n\r\nRate measurements were made of the catalytic effects of copper and iron salts on the rate of the peroxydisulfate iodide reaction. The optimum conditions for the iodometric determination of peroxydisulfate have been established on the basis of these measurements.
\r\n\r\nPart III.
\r\n\r\nThe electroreduction of vanadium (V) and iodate investigated chronopotentiometrically with platinum electrodes subjected to a variety of pretreatment procedures. It was shown that platinization of the electrode resulting from the reduction of the platinum oxide film increases the reversibility of the electrode.
\r\n\r\n" }, { "name": "Kwiram, Alvin L.", "degree": "PhD", "year": "1963", "title": "I. A Chemical Application of Electron-Nuclear Double Resonance. II. Auxiliary Equipment", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042006-080059", "creators": [ { "name": { "family": "Kwiram", "given": "Alvin L." }, "id": "Kwiram-Alvin-L", "display_name": "Kwiram, Alvin L." } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "chair", "display_name": "McConnell, Harden M." }, { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "member", "display_name": "Robinson, G. Wilse" }, { "name": { "family": "Sturdivant", "given": "James-Homes" }, "id": "Sturdivant-J-H", "role": "co-chair", "display_name": "Sturdivant, James-Homes" }, { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "member", "display_name": "Roberts, John D." }, { "name": { "family": "Mead", "given": "Carver" }, "id": "Mead-C-A", "orcid": "0000-0003-4051-0462", "role": "member", "display_name": "Mead, Carver" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9S5C-NB53", "abstract": "Part I:
\r\n\r\nThe technique of electron-nuclear double resonance (ENDOR) is applied to the study of the hyperfine interactions in one (A) of the two radicals formed by x-irradiating single crystals of glutaric acid. It is shown that the other radical (B) can be destroyed with u.v. irradiation. Complete hyperfine tensors based on the EMR data are calculated for the A radical using an iterative procedure which is also prescribed. Comparing this data with the ENDOR measurements reveals an appreciable orientations disorder of the radicals as well as temperature dependent splitting. Small hyperfine interactions not resolvable in EMR spectra are observable via ENDOR. The experimental development is described in some detail.
Part II:
\r\n\r\nA low temperature EMR system which permits in situ u.v. irradiation is described. The TE011 microwave cavity, which operates at room temperature, accommodates the helium cold finger along the cavities' axis of symmetry.
I. The general theory of the irreversible thermodynamics of chemically reacting systems interacting with radiation is developed. From this, a limit to the efficiency of photochemical processes is derived, and this is compared with approximate experimental efficiencies of published researches, which are found to be considerably lower.
\r\n\r\nII. A general cluster method of obtaining approximations to ensemble averages of functions depending on coordinates and/or momenta at a single time is derived, starting with a method, due to Mazo and Zemach, valid only for short-range forces, and proceeding to a method capable of treating systems of particles with long and short-range potentials, such as ionic solutions.
\r\n\r\nIII. Approaches to the time evolution of distribution functions and to time-correlation functions are discussed. A general perturbation series approach to time-correlation functions through the exponential Liouville operator is derived, and this is applied to the calculation of the first-order correction to a Fokker-Planck friction constant and to first and second-order corrections to a momentum autocorrelation function.
" }, { "name": "Neuman, Robert Canute", "degree": "PhD", "year": "1963", "title": "I. A Nuclear Magnetic Resonance Study on Amidinium Ions in Solution. II. The Kinetics of the Thermal Decomposition of Azobisisobutyramidines and their Salts in Solution", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022012-081124156", "creators": [ { "name": { "family": "Neuman", "given": "Robert Canute" }, "id": "Neuman-Robert Canute", "display_name": "Neuman, Robert Canute" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P23A-ND76", "abstract": "Part I
\r\n \r\nN. m. r. spectra of unsubstituted and symmetrically substituted aliphatic amidinium salts in dimethyl sulioxide or water demonstrate the presence of hindered internal rotation about the C_(CN)-N bonds in the amidinium groups. The kinetics of nitrogen-proton exchange in dilute aqueous add and sulfuric acid-water mixtures, containing amidinium salts, have been studied by the n. m. r. method and compared with proton exchange reactions of ammonium ions in similar media. The nature of the nitrogen-proton magnetic resonance signals of amidinium salts is discussed in terms of current theory concerning the effect of the ^(14)N nucleus on magnetic resonance characteristics of bonded hydrogen atoms.
\r\n\r\nPart II
\r\n\r\nRates of the thermal decomposition of two aliphatic azo-bis-amidines, and their first and second conjugate acids, have been determined. The rate of decomposition of the first and second conjugate acids for each azo-amidine are quite similar, but much greater than those of the corresponding neutral azo-amidines. The efficiencies of radical production of the neutral azo-amidines are only slightly less than those of the second conjugate acids, indicating that the \"cage effect\" may be only slightly influenced by electrostatic repulsive interactions between geminate radicals. The synthesis of a new aliphatic azo-nitrile is described.
\r\n" }, { "name": "Patel, Dinshaw Jehangir", "degree": "Masters", "year": "1963", "title": "Nuclear Magnetic Resonance Spectroscopy Cyclopropane Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04302010-094941787", "creators": [ { "name": { "family": "Patel", "given": "Dinshaw Jehangir" }, "id": "Patel-Dinshaw-Jehangir", "display_name": "Patel, Dinshaw Jehangir" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MXFQ-9281", "abstract": "Chemical shifts and coupling constants have been determined from the analysis of proton nuclear magnetic resonance spectra for a series of cyclopropane derivatives . The geminal and vicinal cyclopropyl couplings have opposite signs. Additional ^(13)C-H coupling constants have been obtained for cyclopropanes which support the conclusion that the hybridization in cyclopropanes is close to sp^2. The chemical shifts for several cyclopropanes seem consistent with a ring-current effect." }, { "name": "Peterson, James Macon", "degree": "PhD", "year": "1963", "title": "I. Remarks on the Archibald Technique for Determining Molecular Weights in the Ultracentrifuge. II. The Hydrodynamic Alignment of Rod-like Molecules in Centrifugal Fields", "advisor": "Mazo, Robert M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262012-145551769", "creators": [ { "name": { "family": "Peterson", "given": "James Macon" }, "id": "Peterson-James-Macon", "display_name": "Peterson, James Macon" } ], "advisors": [ { "name": { "family": "Mazo", "given": "Robert M." }, "id": "Mazo-R-M", "role": "advisor", "display_name": "Mazo, Robert M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VZXF-V320", "abstract": "I. The theoretical validity of the linear extrapolation of concentration gradient usually used in Archibald measurements of molecular weights is discussed.
\r\n\r\nII. Intrinsic and concentration-dependent hydrodynamic alignment of rod-like molecules are considered in an attempt to explain the observed increased sedimentation coefficients with field and concentration. An entropy mechanism is also discussed.
\r\n" }, { "name": "Russell, Charles Dyer", "degree": "PhD", "year": "1963", "title": "Chronopotentiometry in Acetonitrile : Oxidation of Substituted Acetates and Substituted Ferrocenes at Platinum Electrodes", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01102013-143610560", "creators": [ { "name": { "family": "Russell", "given": "Charles Dyer" }, "id": "Russell-Charles-Dyer", "display_name": "Russell, Charles Dyer" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZJJE-MQ70", "abstract": "Chronopotentiometry was used to study electrode reactions in acetonitrile\r\nsolutions Evidence is presented for the formation of an oxide film on platinum\r\nelectrodes in acetonitrile by reaction with traces of moisture. Oxygen dissolved\r\nin acetonitrile solutions of tetraethylammonium perchlorate is reduced to\r\nperoxide at the platinum electrode, although it is not reduced in solutions of\r\nalkali perchlorates. The potential-limiting background reactions in\r\ntetraethylammonium perchlorate solutions were investigated by current-reverse\r\nchronopotentiometry.
\r\n\r\nOxidation of acetate ion in acetonitrile gave 91 \u00b1 6% current yield of carbon\r\ndioxide and 77 \u00b1 3% ethane. Acetic acid does not react below the anodic background\r\npotential. Oxidation of substituted acetates was studied chronopotentiometrically\r\nbut traces of moisture in the solution were found to react simultaneously at the\r\nelectrode and seriously interfere. Water is not oxidized below the background\r\npotential in the absence of carboxylate ion.
\r\n\r\nOxidation potentials for a series of substituted ferrocenes were measured\r\nchronopotentiometrically and evidence was found for a new type of neighboring\r\ngroup interaction between the iron in ferrocinium ion and oxygen, nitrogen, or\r\nhalogen in the ring position. The same substitutuents did not interact in the\r\nalpha position.
\r\n\r\nA computer program was written for the calculation of kinetic data from\r\ntotally irreversible chronopotentiometric waves and used to evaluate graphical\r\nmethods previously proposed. New graphical and algebraic methods were also\r\nevaluated. These methods were applied to the determination of rate constants\r\nfor the reduction of iodate ion at mercury in aqueous sodium hydroxide solution.
" }, { "name": "Sternlicht, Himan", "degree": "PhD", "year": "1963", "title": "I. The Electron Spin Resonance Line Shape of a Polycrystalline Radical. II. Paramagnetic Excitons in Molecular Crystals", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12302004-143339", "creators": [ { "name": { "family": "Sternlicht", "given": "Himan" }, "id": "Sternlicht-Himan", "display_name": "Sternlicht, Himan" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FW4P-9Q59", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I:\r\n\r\nElectron spin resonance spectra of polycrystalline radicals are complicated by the anisotropic dipolar magnetic interactions between the unpaired electron and the nuclear spins. Although general expressions in the form of multiple integrals can be derived for the polycrystalline line shapes, their complicated nature makes closed form evaluations very difficult to do except in certain limiting cases.\r\n\r\nWe derive a theorem which enables us to calculate the polycrystalline line shape of an arbitrary polynuclear radical when the external magnetic field is larger than the internal dipolar fields. Our results are applied to polyconjugated hydrocarbons radicals. We find that we can explain a fact heretofore not well understood: namely, the polycrystalline spectra of such radicals can be remarkably similar to those obtained from the liquid state, despite the fact that significant anisotropic dipolar interactions are present in the solid state but not in the liquid.\r\n\r\nPART II:\r\n\r\nThe possibility of using electron spin resonance to study paramagnetic excited electronic states of aromatic crystals is explored. Two limiting cases, are considered: On the one hand, the excitation energy moves from molecule to molecule by a diffusion process; on the other, the triplet excitation is described by a Frenkel wave exciton. In either case intermolecular propagation of the triplet excitation is assumed to proceed through virtual triplet ionization states.\r\n\r\nA. The theory of the spin resonance of triplet wave excitons is developed in some detail. It is shown that large Davydov splittings between the exciton bands require that there be only a weak dependence of the ESR spectra on the [...] vector of the exciton wave, except when [...] is near regions of band degeneracies. Band degeneracies arise from time-reversal symmetry in benzene, naphthalene, and coronene crystals and occur on boundary planes of the first Brillouin zone. A spin Hamiltonian is calculated for these three aromatic crystals for most [...] vectors which are far removed from regions of band degeneracy. Two-line spectra (with no hyperfine structure), representing an average over the molecular sites in the unit cell, are obtained. Scattering of the exciton wave by lattice perturbations can be a mechanism for spin lattice relaxation.\r\n\r\nB. The ESR line shape is correlated with the characteristic time, [...], for a diffusing triplet exciton to undergo a random walk between the nontranslatory neighbors of a two site unit cell. A general expression for the line shape is derived by time dependent perturbation treatment. This expression is valid for (1) sufficiently large transfer rates [...]; (2) for all transfer rates provided that significant differences between the spin Hamiltonians of the nontranslatory neighbors only occur to first and second order. Wave and diffusional triplet exciton spectra are compared." }, { "name": "Stewart, Robert Farrell", "degree": "PhD", "year": "1963", "title": "Polarized Absorption Spectra of Purines and Pyrimidines", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302012-085345824", "creators": [ { "name": { "family": "Stewart", "given": "Robert Farrell" }, "id": "Stewart-Robert-Farrell", "display_name": "Stewart, Robert Farrell" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y85T-DN22", "abstract": "The polarized absorption spectra for single crystals of 1-methylthymine and 9-methyladenine and hydrogen-bonded complex of the two have been determined. A \r\nmicrospectro-photometer was constructed to carry out these measurements. A technique for preparing thin sections of the single crystals with thicknesses down to 10^(-5) cm has been developed. Special attention has been given to intensity determinations for the several ultraviolet absorption spectra." }, { "name": "Turro, Nicholas John", "degree": "PhD", "year": "1963", "title": "Part I. Photosensitized Isomerization. Part II. Photosensitized Dimerization", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechETD:etd-07162004-111757", "creators": [ { "name": { "family": "Turro", "given": "Nicholas John" }, "id": "Turro-Nicholas-John", "display_name": "Turro, Nicholas John" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y47D-AH86", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\ncis[...]trans isomerization of the piperylenes (1,3-pentadienes), the 1,2-dichloroethylenes, and the 2-pentenes occurs in the presence of photosensitizers, mainly carbonyl compounds. The results form a coherent pattern if it is assumed that the key step is transfer of triplet excitation, which occurs on every collision between carbonyl triplets and a second molecule provided that transfer is exothermic. Endothermic transfers may occur but only with reduced efficiency.\r\n\r\nButadiene, cyclopentadiene, and cyclohexadiene are dimerized by irradiation in the presence of various photosensitizers. The relative yields of butadiene dimers are dependent upon the photosensitizer employed; however, the relative yields of cyclic diene dimers shows no corresponding dependence. The results are consistent with the assumption that energy transfer to the two conformers of butadiene produces two stereoisomeric, non-interconvertible triplets." }, { "name": "Ulery, Harris E.", "degree": "PhD", "year": "1963", "title": "I. Acid Catalyzed Reactions of 1,5-Epoxyolefins. II. The Alkylative Cyclization of 1,5-Hexadiene. III. The Acid Catalyzed Cyclizations of Cis/Cis-and Trans,Trans-2,6-Octadiene. IV. The Infrared Spectra of Cyclobutane Compounds", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10092012-081052816", "creators": [ { "name": { "family": "Ulery", "given": "Harris E." }, "id": "Ulery-Harris-E", "display_name": "Ulery, Harris E." } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DH79-9M97", "abstract": "I. The acid catalyzed reactions of certain 1,5-epoxyolefins
\r\n\r\nThe monoxides of a number of 1,5-dienes were prepared and\r\ntreated with a variety of acidic reagents known to induce cyclization\r\nof the parent diolefins. In all cases the major reaction observed was\r\nthe isomerization of the epoxide to a carbonyl function. No cyclic\r\nproducts were observed. These results are discussed in terms of\r\nthe general requirements for cyclization.
\r\n\r\nII. The alkylative cyclization of 1,5-hexadiene
\r\n\r\nThe alkylation of 1,5 -hexadiene with t-butyl chloride in the\r\npresence of aluminum trichloride was studied. The major monomeric\r\nreaction products were cyclic, and both the t-butylcyclohexane and\r\nneopentylcyclopentane skeletons were identified among them. Formation of the latter ring system appeared to be slightly favored over\r\nformation of the six-membered ring. This preference is undoubtedly\r\ndue to both steric and electronic factors.
\r\n\r\nIII. The acid catalyzed cyclization of cis, cis- and trans, trans-2,6-octadiene
\r\n\r\nBoth cis, cis- and trans, trans-2, 6-octadiene were cyclized in\r\na mixture of formic and sulfuric acids . While the cis, cis-diene gave\r\nboth 2^t, 3^c-dimethylcyclohexyl^c formate and its C-1 epimer in a ratio\r\nof approximately 15: 1, the trans, trans-diene yielded only the former\r\nepimer. When cyclization was induced in deuterated acid, the trans,\r\ntrans-diene gave 2^t, 3^c-dlmethyl-4-deuterocyclohexyl^c formate, while\r\nthe cis, cis-isomer produced the C-4 epimer. These results indicate\r\nthe existence of a sterically controlled reaction pathway. In the\r\ncyclization of the cis, cis-diene, this control is partially lost due to\r\nhighly unfavorable conformational effects. Further, these results show\r\nunambiguously that the diene has assumed the quasi-chair conformation\r\nat the time of ring closure.
\r\n\r\nIncidental to this work the isomers of 2,3-dimethylcyclohexanol\r\nand 2,3-dimethylcyclohexanone were identified and characterized.
\r\n\r\nIV. The infrared spectra of cyclobutane compounds
\r\n\r\nIn an attempt to locate possible characteristic frequencies of\r\nthe C_4-ring, the infrared spectra of 191 cyclobutane derivatives have\r\nbeen examined. The most useful correlations appear to be a band near\r\n1235 cm.^(-1) for cyclobutane compounds with at least one ring methylene\r\ngroup, and a band near 915 cm.^(-1) for mono- and 1,1-disubstituted\r\ncyclobutanes. Less frequently a band is found close to 750 cm.^(-1).
\r\n\r\nIn addition, a novel application of a computer technique is proposed,\r\nwhich may be of some value in the analysis of large numbers of\r\nspectra.
" }, { "name": "Vasi\u013cevskis, J\u0101nis", "degree": "PhD", "year": "1963", "title": "Studies of the Metal Ion Complexes of Purines and Pyrimidines by Electrophoresis and Other Methods", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162012-070830184", "creators": [ { "name": { "family": "Vasi\u013cevskis", "given": "J\u0101nis" }, "id": "Vasilevskis-J\u0101nis", "display_name": "Vasi\u013cevskis, J\u0101nis" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y9PS-DG32", "abstract": "A density-gradient-stabilized electrophoresis apparatus has been designed and built.
\r\n\r\nSpectrophotometric and electrophoretic measurements are used to investigate the hydrogen ion, mercuric ion, and methylmercuric ion complexes of purine and pyrimidine derivatives. The results are used to infer the charge of the complexes.
\r\n\r\nThe problem of determining the charge of an ion from its mobility and diffusion coefficient is also considered.
\r\n" }, { "name": "Wang, Yui Loong", "degree": "PhD", "year": "1963", "title": "One. Thermal Decomposition of n-Butane. Two. Flow in Entrance Section of Parallel Plates", "advisor": "Corcoran, William Harrison; Longwell, Paul A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11062012-155050999", "creators": [ { "name": { "family": "Wang", "given": "Yui Loong" }, "id": "Wang-Yui-Loong", "display_name": "Wang, Yui Loong" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Longwell", "given": "Paul A." }, "id": "Longwell-P-A", "role": "advisor", "display_name": "Longwell, Paul A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/FGRQ-9X11", "abstract": "Part One
\r\n\r\nThe thermal decomposition of n-butane was investigated in a\r\nflow reactor at a pressure of 1 atm, in a temperature range of\r\n460\u00b0 to 560\u00b0C, and at low conversion levels, i.e. 0.06 - 0.68%\r\nfor the 460\u00b0 runs, 0.5 - 2.3% for the 510\u00b0 runs, and 3.5 to\r\n8.2% for the 560\u00b0C runs. Temperature, velocity, and concentration\r\nprofiles at the exit end of the reactor were measured\r\nto study the effects of energy, momentum, and mass transports\r\non chemical reaction. It was found after analysis of data\r\nthat the reactor could be treated as an isothermal reactor\r\nwith plug flow under the prevailing operating conditions.
\r\n\r\nTwo rate expressions were determined for the reaction; one\r\ncorresponding to a first-order and the other to a second-order\r\nrate. They are
\r\n\r\nFirst-order rate = 3.34 x 10^(12) e -54,600/RT (C_4H_(10) lb/ft^3 sec
\r\n\r\nSecond-order rate = 2.55 x 10^(14) e -56,800/RT (C_4H_(10)^2 lb/ft^3 sec
\r\n\r\nThese two expressions equally well represent the experimental\r\ndata.
\r\n\r\nOn the basis of the products formed and the rates observed, a\r\nRice-type, free-radical mechanism was proposed for the thermal\r\ndecomposition of n-butane. The mechanism, which is presented\r\nin the section on correlation of data, quantitatively describes\r\nthe reaction. One major feature of the mechanism is the consideration\r\nof secondary reactions at very low conversions.
\r\n\r\nPart Two
\r\n\r\nFlow of an incompressible fluid at the entrance section of\r\nparallel plates under isothermal, laminar conditions was investigated\r\nby solving the two-dimensional Navier-Stokes\r\nequations numerically. The Navier-Stokes equations were transformed\r\ninto finite-difference equations in terms of stream\r\nfunctions \u03c8 and vorticities \u03c9 with a technique developed by\r\nde G. Allen. The finite-difference equations were then\r\nsolved by an iterative procedure on digital computers. From\r\nthe solution, point velocities and pressure gradients were\r\ncomputed.
\r\n\r\nTwo cases were studied, both with a Reynolds number of 300.\r\nCase I had a flat velocity distribution at the entrance to the\r\nplates. Case II assumed that potential-flow conditions existed\r\nonly far upstream from the entrance. For both cases, large\r\nvelocity and pressure gradients were found near the leading\r\nedges of the plates, although they were comparatively smaller\r\nin Case II. Also the velocity profiles for small distances\r\nfrom the entrance were found to be slightly concave in the\r\ncentral portion between the plates.
\r\n\r\nSchlichting and others have solved the boundary layer equation\r\nfor Case I. Their solutions agree well with the present work\r\nat large distances from the entrance but deviate considerably\r\nnear the leading edges as the boundary-layer equation does\r\nnot describe the behavior of fluid flow near singular points.
" }, { "name": "Webb, Ned Conder", "degree": "PhD", "year": "1963", "title": "Determinations of the Crystal Structures of Bis-Indenylruthenium and of Two So-Called \u03b3-Brass Type Compounds. I. Bis-Indenylruthenium. II. \"Ni\u2085Cd\u2082\u2081\". III. \"Ni\u2085Zn\u2082\u2081\"", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102012-084202445", "creators": [ { "name": { "family": "Webb", "given": "Ned Conder" }, "id": "Webb-Ned-Conder", "display_name": "Webb, Ned Conder" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GB4N-K224", "abstract": "I. The crystal and molecular structure of bis-indenylruthenium\r\nwas determined by X-ray crystallographic methods. Crystals of\r\nbis-indenylruthenium are monoclinic with four molecules per unit\r\ncell in space group P2_(1/a). The indenyl groups are in the eclipsed\r\nconfiguration, and the ruthenium atom is midway between the two\r\nfive-membered rings. Within experimental error, the molecule has\r\nmm symmetry, and the planar indenyl groups are parallel. The\r\naverage Ru-C bond distance is 2.193 \u00c5, but the ruthenium atom is\r\nslightly displaced toward the carbon atoms in position 2.
\r\n\r\nII and III. The procedures as well as the results of the investigation of the crystal structures of \"Ni_(5)Cd_(21)\" and \"Ni_(5)Zn_(21)\" are described. These compounds have been believed to have crystal structures very closely related to that of \u03b3 brass. This investigation has shown that the actual atomic arrangements in these compounds are considerably more complicated than was generally assumed. The structures were found to differ drastically from that of \u03b3 brass.
" }, { "name": "Beach, William Frederick", "degree": "PhD", "year": "1962", "title": "The Structure and Biogenesis of Nidulin", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282011-084657541", "creators": [ { "name": { "family": "Beach", "given": "William Frederick" }, "id": "Beach-William-Frederick", "display_name": "Beach, William Frederick" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3RME-0Q76", "abstract": "The structure of nidulin, the major metabolic product of\r\nAspergillus nidulans, is demonstrated beyond reasonable doubt to be that which was set forth recently by other workers. In support of the structure, a xanthene was isolated and characterized. It was also discovered that nidulin suffered a remarkably facile dechlorination\r\nin the presence of hydrobromic acid and red phosphorous.\r\n\r\nPreliminary tracer experiments with labelled acetate were\r\nperformed, and the expected pattern of incorporation was observed. Isoleucine was likewise shown to be incorporated into nidulin. A possible biogenesis for nidulin is discussed which points the way for future research.\r\n" }, { "name": "Carter, Robert Everett", "degree": "PhD", "year": "1962", "title": "I. The Biogenesis of Phenazine Pigments. II. \u03b2-Ferrocenyl Carbonium Ions. III. Chemical Shift and \u03c0-Electron Densities", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292011-081826791", "creators": [ { "name": { "family": "Carter", "given": "Robert Everett" }, "id": "Carter-Robert-Everett", "display_name": "Carter, Robert Everett" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "biology", "chemistry" ], "doi": "10.7907/GM3C-6N32", "abstract": "Part I:\r\nThe biogenesis of phenazine pigments in bacteria has been studied by the use of radioactive substrates. The results indicate that the pigment of Pseudomonas chlororaphis originates in the dimerization of precursors derived from anthranilic acid. The structures of all the other known phenazine pigments are compatible with such a derivation.
\r\n\r\nPart II:\r\n\u03b2-Ferrocenyl carbonium ions have been studied in solvolytic experiments with \u03b2-ferrocenyl ethyl and \u03b2-ferrocenylisopropyl tosylates. A deuterium-labelling\r\nexperiment with the ethyl compound indicates the absence of\r\ncyclopentadienyl ring participation. The isotope effect in the solvolysis (in 80% acetone) of \u03b2-ferrocenylethyl-a,a-d_2 tosylate was determined. The racemization of optically active \u03b2-ferrocenylisopropyl tosylate in 60% acetone at pH 6.9 is discussed; it is suggested that the racemization\r\nmay come about through a special iron-carbon interaction which leads to a symmetrical carbonium ion. A simple diagram of a \u03b2-ferrocenyl carbonium ion stabilized by iron participation is presented and discussed to scrutinize the plausibility of such participation.
\r\n\r\nPart III:\r\nThe use of the equation \u03b4 = \u03c0 which relates the chemical shift (\u03b4) of an aromatic proton to the excess \u03c0-electron density q on the carbon to which the proton is attached is discussed and illustrated by examples from the current literature.
\r\n" }, { "name": "Dove, William Franklin", "degree": "PhD", "year": "1962", "title": "The Helix-Coil Transition in DNA: Effects of the Interactions with Small-Ion and of the Composition of DNA", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282011-100303520", "creators": [ { "name": { "family": "Dove", "given": "William Franklin" }, "id": "Dove-William-Franklin", "display_name": "Dove, William Franklin" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SYPJ-C611", "abstract": "We have studied the effects of ion binding and DNA composition on the helix-coil denaturation of the DNA macromolecule. Among the systems studied, none gave a marked increase in the composition dependence of the denaturation conditions, an increase which would\r\nallow extensive fractionation of a compositionally disperse DNA sample.\r\n\r\nThe binding of protons to DNA is extensive even before hyperchromicity and irreversible changes in intrinsic viscosity are observed, and includes protonation of the cytosine heterocycle. It is intriguing that this cytosine protonation seems to require the breaking of hydrogen\r\nbonds in the Watson-Crick structure.\r\n\r\nThe binding of Mg^(++), Co^(++), or Ag^+ at low ionic strengths markedly stabilizes the helical conformation. We have evaluated the extent to which high concentrations of Na^+ ion reduce the binding of Mg^(++) and H^+ ions.\r\n\r\nBroad transitions are observed at low ionic strengths of Na^+ ion, and in the presence of the equivalent ratios r=0.2 Ag^+, r=0.5 Co^(++), or r=0.5 Mg^(++). In the latter two cases, this broadening maybe due to the selective binding of cations to native DNA, but the broadening observed at low Na^+ concentrations may be due to a change in Zimm's parameters \u03c3_o and/or \u03c3_j.\r\n\r\nThe inactivation of the transforming ability of pneumococcal\r\nDNA for three characteristics was studied at 0.1 and 3x10^(-4) ionic strengths. Differences in denaturation temperature were observed which could not be correlated with the compositions deduced by Rolfe and Ephrussi-Taylor from density differences. At low ionic strengths, extremely broad inactivation curves were observed, and can be explained by the renaturation made possible by the existence of short helical regions in low ionic strength denaturations." }, { "name": "Foran, Bernard", "degree": "Masters", "year": "1962", "title": "Some Optical Spectra Studies of the Rare Earth Atom Samarium in Inert Gas Matrices at 4.2\u00b0K", "advisor": "Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-114413285", "creators": [ { "name": { "family": "Foran", "given": "Bernard" }, "id": "Foran-Bernard", "display_name": "Foran, Bernard" } ], "advisors": [ { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0R9G-EA66", "abstract": "The optical spectrum of samarium atoms trapped in matrices of argon and krypton at 4.2\u00b0K was examined. A simple basis for interpretation of the results is presented, in which the matrix perturbation is applied to the free atom in some quantum state of total angular momentum J.\r\n\r\nThe spectra can be correlated with the published data for SmI, but the complexity of the results, particularly in argon, make a detailed interpretation difficult. Some exceptionally sharp triplets with small splittings are considered to be derived from levels of the excited 4f^55d6s^2 configuration, none of which has previously been identified. Fluorescence was observed, corresponding to transitions from an excited state to the ^7F_1 and ^7F_2 levels of the ground state." }, { "name": "Garwood, Donald Charles", "degree": "PhD", "year": "1962", "title": "I. Electrophilic aromatic substitution of metallocenes. II. Stereochemistry of halogen addition to 4-t-butylcyclohexene. III. Lithium aluminum hydride reduction of cis-2,6-dimethylcyclohexanone.\r\n\r\nI. Electrophilic Aromatic Substitution of Metallocenes. II. Stereochemistry of Halogen Addition to 4-t-Butylcyclohexene. III. Lithium Aluminum Hydride Reduction of CIS-2,6-DimethyIcyclohexanone", "advisor": "Richards, John H.; Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192011-155709631", "creators": [ { "name": { "family": "Garwood", "given": "Donald Charles" }, "id": "Garwood-Donald-Charles", "display_name": "Garwood, Donald Charles" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." }, { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1BRD-QP23", "abstract": "Part I.\r\n\r\nThe mechanism of electrophilic substitution of metallocenes\r\nwas investigated by the competitive acetylation of\r\nferrocene and ruthenocene and of ferrocene and l,l'-diethylferrocene. Solvolyses of \u03c9 -ferrocenylalkyl p-bromobenzenesulfonates did not show any significant aryl participation. These results lead to the hypothesis that direct interaction between the metal and the electrophile is of great importance in electrophilic substitution reactions f metallocenes.\r\n\r\nPart II.\r\n\r\nThe bromination and chlorination of 4-t-butylcyclohexene\r\nhave been shown to produce diequatorial dihalides\r\nas well as diaxial dihalides. The amount of diequatorial\r\ndichloride produced increases with solvent polarity. The\r\nresults are explained in terms of two competing mechanisms,\r\nthe classical, planar trans-addition and a carbonium ion\r\nprocess which increases in importance in the more polar\r\nsolvents.\r\n\r\nPart III.\r\n\r\nLithium aluminum hydride reduction of cis-2,6-dimethylcyclohexanone gave only 14% of the 2(e), 6(e) -dimethyl- l(e)-cyclohexanol. This is in striking contrast to other results for lithium aluminum hydride reductions. Two equatorial groups adjacent to a reaction center on a\r\ncyclohexane ring thus cause an especially severe steric\r\nhindrance at that center.\r\n" }, { "name": "Greenough, Ralph Clive", "degree": "PhD", "year": "1962", "title": "I. Distribution of Antimony (ill) Between Hydrochloric Acid and Isopropyl Ether. II. The Infrared Spectra and Probable Structures of Some Nitrogen-Sulfur Compounds", "advisor": "Swift, Ernest H.; Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292011-093334190", "creators": [ { "name": { "family": "Greenough", "given": "Ralph Clive" }, "id": "Greenough-Ralph-Clive", "display_name": "Greenough, Ralph Clive" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." }, { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JXNV-AK83", "abstract": "Antimony (III) was extracted by isopropyl ether from solutions of HCl, HCl-HCl0_4, and HCl-NaCl. The ether and acid layers were analyzed for antimony (III) and chloride. On the basis of the variation of the distribution ratios with the aqueous HCl concentrations a model of the species of antimony (III) present in the HCl solution was\r\nconstructed. The following constants relating the species to one another were calculated.\r\n\r\nK_(2-3) = [SbCl_3] a_(H_2O / [SbCl_2OH] a^2_(HCl) = 0.145\r\nK_(3-4) = [SbCl^-_4] / [SbCl_3] a_(HCl) = 0.34\r\nD_2 = [SbCl_2OH] _e / [SbCL_2OH] _a = 0.0080\r\nD_3 = [SbCl_3] _e / [SbCl_3] _a = 0.062\r\n\r\nSpectrophotometric measurements on antimony (III) in acid and ether solutions indicated the presence of a hydrate of SbCl_3 in the acid. Reasonable agreement was found between the results predicted by the model and the experimental values of the solubility of Sb_40_5Cl_2 in HCl, the\r\npotential of the antimony (III) - antimony (V) half cell in HCl, and the catalytic effect of antimony (III) on the hydrolysis of SbCl^-_6.\r\n\r\nThe infrared spectra of the products of fluorinations of N_4S_4 were taken. CCl_4, CFCl_3, SO_2, SOF_2, SF_4, SF_6 and SiF_4 were identified as components of the mixture. Bands of four unknown compounds were found. Compound A with bands at 1375 and 644 cm^(-1) was identified as SNF on the\r\nbasis of its instability and infrared spectrum. Compound B was identified as NSF_3 since it was not decomposed by heating nor was capable of being further fluorinated. The envelopes of the 1520, 819, and 774 cm^(-1) bands indicate that it is a symmetric rotor. Compound C with bands at 1340 and 1160 cm^(-1) was unidentified. Compound D with bands at 1340 and 1160 cm^(-1) was at first thought to be NSF but a force constant calculation led to an unreasonable structure. It is still unidentified.\r\n\r\nAn approximate normal coordinate treatment of SNF led to k_(NS) = 10.4 millidynes/A and k_(NF) = 2.3 millidynes/A. These values indicate that the N-F bonding has considerable ionic character. Approximate force constants for NSF_3 were calculated and were found to correspond to the NSF_3\r\nstructure with normal single and triple bonds.\r\n\r\nNo evidence was found for the existence of Glemser's SN_2F_2. His erroneous results could be explained by the presence of SO_2, SOF_2, and SF_4 as impurities in his product of the N_4S_4 fluorination.\r\n" }, { "name": "Hobey, William David", "degree": "PhD", "year": "1962", "title": "Vibronic Interactions in Conjugated Systems", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232011-100758499", "creators": [ { "name": { "family": "Hobey", "given": "William David" }, "id": "Hobey-William-David", "display_name": "Hobey, William David" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ATND-5V97", "abstract": "A. It is first shown how the ordinary Born-Oppenheimer approximation for separating nuclear and electron motions in a molecule can be adapted to degenerate electronic states. Semi-empirical molecular orbital theory is then used to examine Jahn-Teller distortions in the ground states of conjugated hydrocarbon radicals. Numerical predictions are made for cyclic polyenes radicals and the mononegative ions of coronene and triphenylene. It is concluded that, except in the cyclic polyenes C_(4x) H_(4x), x = 0, 1, 2..., the barriers between \"stable\" distorted molecular configurations are negligible and that a dynamical coupling of nuclear and electronic motions exists in these radicals.\r\n\r\nB. It has been suggested in the literature that certain anomalies in the electronic spectra of coronene and triphenylene mononegative ions are due to Jahn- Teller distortions. The methods of the thesis are adapted to the Pariser and Parr molecular orbital scheme and\r\nbenzene negative ion is treated in detail as a model for these systems. It is concluded that the Jahn-Teller effect cannot be responsible for the observed anomalies. The intensity of the ^1A_(1g) \u2192 ^1B_(1u) transition in benzene is calculated mainly as a test of the theory which is\r\nfound to be adequate.\r\n\r\nC. A theoretical treatment of the pseudo-Jahn-Teller effect is presented and shows that several types of behavior arise.\r\nThe ^1B_(1u) state of benzene undergoes a pseudo-Jahn-Teller interaction and a detailed calculation shows the state suffers a significant decrease in its e_(2g) CC stretching force constant, but is not permanently\r\ndistorted. The ^1E_(1u) level of benzene does not experience a simple Jahn-Teller effect, but in addition to the pseudo-Jahn-Teller effect has a Jahn-Teller effect due to two electron perturbations. These perturbations result in changes in both bond lengths and valence angles, the changes being small and leading to a dynamical coupling." }, { "name": "Howden, Merlin E. H.", "degree": "PhD", "year": "1962", "title": "I. Carbonion- and Free Radical-Type Rearrangements in Homoallylic Systems. II. Nuclear Magnetic Resonance in Cyclopropanes", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08162011-081910216", "creators": [ { "name": { "family": "Howden", "given": "Merlin E. H." }, "id": "Howden-Merlin-E-H", "display_name": "Howden, Merlin E. H." } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/J9CT-A176", "abstract": "I. A study was made of the Grignard and free-radical reactions of vinyl-and phenyl-substituted allyl-carbinyl derivatives. Cyclopropylcarbinyl products were obtained in both types of reactions for the ([...]-vinylallyl)-carbinyl and ([...], [...]-diphenylallyl)-carbinyl systems, and evidence was obtained bearing on the intermediates involved\r\nin some of these rearrangements.
\r\n\r\nII. Analysis of the nuclear magnetic resonance spectra of a number of cyclopropanes yielded data in the form of spin-spin coupling constants and chemical shifts. This information was correlated with existing theories on molecular structure and on the electronic structure of\r\ncyclopropanes. The chemical shifts for several cyclopropane hydrocarbons were interpreted in part in terms of a cyclopropane ring current effect.
\r\n" }, { "name": "Ifft, James Brown", "degree": "PhD", "year": "1962", "title": "A Quantitative Examination of the Buoyant Behavior of Macromolecules of Known Molecular Weight in a Density Gradient at Equilibrium in the Ultracentrifuge", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:08182011-091559077", "creators": [ { "name": { "family": "Ifft", "given": "James Brown" }, "id": "Ifft-James-Brown", "display_name": "Ifft, James Brown" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VKXK-ZC50", "abstract": "The quantitative aspects of the method of sedimentation\r\nequilibrium in a density gradient with a purified protein of\r\nknown molecular weight have been examined.\r\n\r\nIn order to quantitatively evaluate the results of\r\ndensity gradient experiments, the density distribution and\r\nthe density gradient in the salt solution at equilibrium in\r\nthe ultracentrifuge must be known. Calculations based on\r\nthermodynamic data were made to determine these quantities.\r\nThe results of this work are given in Part I.\r\n\r\nBecause of the large hydrostatic pressures encountered\r\nduring centrifugation, it was necessary to evaluate the effects of pressure on the results. In Part II, an experimental investigation of the changes in banding position of deoxyribonucleic acid (DNAY and tobacco mosaic virus (TMV) with pressure was made. A useful quantity involving the compressibilities of the solution and of the solvated macromolecule was obtained. The results agree with the thermodynamic theory presented.\r\n\r\n\r\nAn experimental investigation of bovine serum mercaptalbumin\r\n(BMA) in a variety of salt solutions was carried out.\r\nPart III presents the experimental techniques and the methods of calculation for such experiments. The net hydration of BMA was determined solely from the ultracentrifuge results. The extent of anion binding was independently determined to obtain the net hydration of the protein-salt complex and the density gradient required to calculate the solvated molecular weight.\r\n" }, { "name": "Kennicott, Phillip Ray", "degree": "PhD", "year": "1962", "title": "Studies in Infrared Spectroscopy", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:08122011-112725761", "creators": [ { "name": { "family": "Kennicott", "given": "Phillip Ray" }, "id": "Kennicott-Phillip-Ray", "display_name": "Kennicott, Phillip Ray" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/40GV-PH75", "abstract": "The modernization of a vacuum grating infrared spectrometer is described. Experiments using this spectrometer on N-methyl formamide in the vapor phase are described, and the results are interpreted in terms of the position, shape, and intensity change with temperature of the vibration bands of this substance. It is concluded that N-methyl formamide exists in two isomeric forms in the vapor phase. The less abundant form is the cis isomer which lies 1.4 kcal. above the trans isomer.
\r\n\r\nAn echelle-type grating used with this spectrometer is shown to have an unusually wide and flat efficiency curve. This is ascribed to a scattering phenomenon in which both faces of a groove participate. Mathematical analyses based on both the Kirchhoff theory and on the Rayleigh theory are shown to predict the broad region of high efficiency for this grating.
\r\n\r\nAn amplifier which is intended to be used with a novel double-beam ratio detection system is described.
\r\n" }, { "name": "Kozicki, William", "degree": "PhD", "year": "1962", "title": "I. Enthalpy Change upon Vaporization of the Hydrocarbons n-Pentane, Cyclohexane and 1-Butane. II. Evaluations of Diffusion Coefficients for the Methane-n-Butane System Based on Gradients in Thermodynamic State Properties", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10042005-130821", "creators": [ { "name": { "family": "Kozicki", "given": "William" }, "id": "Kozicki-William", "display_name": "Kozicki, William" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9385-4112", "abstract": "I. An experimental investigation was made of the enthalpy change upon vaporization of three hydrocarbons in the pure state. The hydrocarbons studied were n-pentane, cyclohexane and 1-butene. Direct calorimetric determinations of the enthalpy change were carried out at 30\u00b0 temperature intervals in the temperature range 100\u00b0F. up to 310\u00b0F. and at pressures in the range 3-250 lb. per sq. in. abs. The experimental data was smoothed and interpolated utilizing residual techniques. Critically chosen values of the enthalpy change upon vaporization of n-pentane, cyclohexane and 1-butene are presented at even temperature increments of 10\u00b0F. The data extrapolated to 77\u00b0F. is in excellent agreement with selected values at 77\u00b0F. reported by Rossini which were measured at the National Bureau of Standards.\r\n\r\nII. Evaluations were made of the phenomenological coefficient and the diffusion coefficients based on gradients in the chemical potential and fugacity for methane diffusing in the liquid phase of the methanen-butane system. Values of these coefficients are presented at six pressures evenly spaced in the pressure range 250-1500 lb. per sq. in. at each of the temperatures 100\u00b0, 160\u00b0 and 220\u00b0F. The evaluated coefficients are marked functions of the state of the phase." }, { "name": "Leermakers, Peter Anthony", "degree": "PhD", "year": "1962", "title": "Part I. Chemistry of Low Energy \u03c0-\u03c0* Triplet States. The Photoproduction of I-Naphthaldehyde and 2-Acetonaphthone. Part II. Triplet-Triplet Energy Transfer in Solution", "advisor": "Hammond, George Simms; Robinson, G. Wilse", "url": "https://resolver.caltech.edu/CaltechETD:etd-02112009-095624", "creators": [ { "name": { "family": "Leermakers", "given": "Peter Anthony" }, "id": "Leermakers-Peter-Anthony", "display_name": "Leermakers, Peter Anthony" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" }, { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "advisor", "display_name": "Robinson, G. Wilse" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K0A0-AY90", "abstract": "Part I: Photoreduction of 1-naphthaldehyde and 2-acetonaphthone has been accomplished by the use of tributylstannane as a hydrogen donor. Rate constants for hydrogen abstraction and thermal deactivation of the excited species have been estimated. The \u03c0-\u03c0* triplet states of the two carbonyl compounds are responsible for the hydrogen abstraction reaction. The naphthoyl compounds do not undergo photoreduction by secondary alcohols. Their low reactivity is attributed to the fact that the \u03c0-\u03c0* rather than the n-\u03c0* triplet is involved. Carbonyl compounds that are easily photoreduced have the n-\u03c0* configuration in their lowest triplets.\r\n\r\nPart II: The phenomenon of energy transfer between triplet states of molecules in solution has been investigated. Two methods have been employed in this investigation. The first involves the photosensitized cis-trans isomerization of piperylene. Aromatic carbonyl compounds were used as sensitizers. The trans/cis ratio in the photostationary state was related to the energy of the lowest triplet state of the sensitizer.\r\n\r\nThe second method involved the study of the effects of quenchers on the quantum yield in the photoreduction of benzophenone by benzhydrol. Many of the quenchers were found to have about the same efficiency. It was concluded that the energy transfer (quenching) reaction is probably diffusion controlled." }, { "name": "Lutz, Raymond Paul", "degree": "PhD", "year": "1962", "title": "Part I. Mechanism of the Rearrangement of Fenchone. Part II. Mechanism of the Diels-Alder Reaction", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08032011-144903807", "creators": [ { "name": { "family": "Lutz", "given": "Raymond Paul" }, "id": "Lutz-Raymond- Paul", "display_name": "Lutz, Raymond Paul" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0GDS-G649", "abstract": "Part I: \r\nThe rearrangement of fenchone (1,3,3-trimethylbicyclo[ 2.2.1]-heptan-2-one) to 3,4-dimethylacetophenone has been carried out using a sample labeled with carbon-14 in the methyl groups of the 3-position. In concentrated sulfuric acid at 90\u00b0, 96% of the reaction takes the following course:\r\n\r\n[\u2026]
\r\n\r\nPart II: \r\nOptically active methacrolein dimer, labeled with deuterium at the aldehyde hydrogen, rearranges thermally with complete retention of optical activity to the isomer in which the deuterium is shifted to the vinyl position on the ring. The rearrangement is accompanied by \r\n\r\n[\u2026]
\r\n\r\nsubstantial competitive formation of methacrolein by a Diels\u2013Alder dissociation, lending support to the presumption that this and analogous isomerizations represent partial reverse Diels-Alder reactions. The results rule out the intervention of a linear intermediate in the Diels-Alder reaction of methacrolein, and make it unlikely that similar intermediates are involved in other Diels-Alder reactions.
\r\n" }, { "name": "Lyon, Alexander Newell", "degree": "Bachelors", "year": "1962", "title": "Hydrogen Bonding in Ferrocenyl Alcohols", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122026-204408694", "creators": [ { "name": { "family": "Lyon", "given": "Alexander Newell" }, "id": "Lyon-Alexander-Newell", "display_name": "Lyon, Alexander Newell" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qfq4-dt10", "abstract": "Spectral evidence has been found which indicates that \u221d-hydroxy\r\nferrocenyl alcohols may form hydrogen bonds directly with the iron atom.\r\nInvestigations are now in progress of the isomerization of the exo and of\r\nthe endo forms of \u221d-hydroxy-1,2-tetram.ethylene ferrocene toward the\r\nequilibrium mixture, using aluminum isopropoxide in isopropanol plus a\r\ntrace of acetone as the isomerizing agent. Preliminary results indicate\r\nthe equilibrium ratio of endo isomer to exo to be roughly 3:1 (75% endo;\r\n25% exo)." }, { "name": "Marr, Harold Everett, III", "degree": "Bachelors", "year": "1962", "title": "Unit Cell Determination of Silver Azide", "advisor": "Marsh, Richard Edward; Stanford, Richard Henry", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122026-210833370", "creators": [ { "name": { "family": "Marr", "given": "Harold Everett, III" }, "id": "Marr-Harold-Everett-III", "display_name": "Marr, Harold Everett, III" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "Stanford", "given": "Richard Henry" }, "id": "Stanford-Richard-Henry", "role": "advisor", "display_name": "Stanford, Richard Henry" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5s8w-7625", "abstract": "No abstract." }, { "name": "Millard, Hugh Thompson, Jr.", "degree": "PhD", "year": "1962", "title": "I. A Procedure for the Analysis of Polonium-210 and Lead-210 in Rocks. II. A Characterization of the Meteorite Flux at the Earth's Orbit", "advisor": "Brown, Harrison", "url": "https://resolver.caltech.edu/CaltechTHESIS:08232011-094813077", "creators": [ { "name": { "family": "Millard", "given": "Hugh Thompson, Jr." }, "id": "Millard-Hugh-Thompson", "display_name": "Millard, Hugh Thompson, Jr." } ], "advisors": [ { "name": { "family": "Brown", "given": "Harrison" }, "id": "Brown-Harrison", "role": "advisor", "display_name": "Brown, Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WEPX-9Q33", "abstract": "Part I. A method for the analysis of polonium-210 (138.4 day\r\nhalf-life) and lead-212 (10.6 hour half-life) in rocks has\r\nbeen studied. The procedure involves dissolution of the\r\nsample and addition of 10 mg. lead carrier. The polonium\r\nis separated by spontaneous electrodeposition on a silverfoil disk at room temperature from a 0.5F HCl medium containing 0.05F hydrazine and the alpha-activity from the\r\npolonium-210 measured, with a scintillation counter. Sodium\r\ntartrate is added to the solution remaining from the polonium deposition, the pH raised to 4.7, and the lead-212 deposited with the lead carrier on a second silver-foil disk. The yield of lead is determined gravimetrically and the decaying alpha-activity supported by the lead-212 observed with the scintillation counter. The procedure has been calibrated by using minerals which had been analyzed for lead-210 and thorium-232 by other methods. The effects of temperature, volume, and inhibiting ions on the yield and rate of deposition of polonium were also studied. The procedure was tried on a synthetic uraninite-thorite mixture and on the zircon from the Pacoima Canyon pegmatite. The results indicate that extreme care must be taken to get all material into solution and to avoid high temperatures during fusion of the sample. The weight equivalent uranium found from the polonium-210 analysis on the zircon agreed with the mass spectrometric value for the uranium content to 3.3%.\r\n\r\nPart II. A study has been conducted in order to better characterize the meteorite flux at the earth's orbit with respect to type, mass, direction, and magnitude. A survey of the meteorite data was made by placing the information on punch cards and sorting these cards according to various categories. On the basis of the year of fall, it was noted that the achondrites were more abundant than the irons from 1850 to 1870 and that the reverse was true from 1890 and 1910. No enstatite chondrites fell prior to the 1860's and a large number of this type fell during 1930. A chi-squared test applied to the monthly patterns of fall indicates that the distributions for the veined-hypersthene chondrites, the veined-white hypersthene chondrites, the achondrites, and the howarditic achondrites were those least likely to be\r\nrandom, suggesting that these types may travel in definite\r\norbits. As for the direction of the flux, the hourly patterns are heavily biased toward the daylight hours with no 6:00 maximum as in the case of sporadic meteors. The\r\nachondrites display an interesting bimodal distribution\r\nduring the daylight hours. The magnitude of the flux shows\r\nsignificant variations with year among which the decrease\r\nsince 1940 appears to be most important. The functional\r\nrelationship between the rate of meteorite recovery and\r\nthe rural population density has been investigated and an\r\naverage value of 1.0 meteorite/10^6 sq. km.-year found for\r\nthe total flux, R_o, arriving at the bottom of the atmosphere for the period 1810 to 1950.\r\n" }, { "name": "Mitchell, Gary Francis", "degree": "Bachelors", "year": "1962", "title": "Complexing of Guanylic Acid with Silver", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122026-214935177", "creators": [ { "name": { "family": "Mitchell", "given": "Gary Francis" }, "id": "Mitchell-Gary-Francis", "display_name": "Mitchell, Gary Francis" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4kyx-8881", "abstract": "The complexing of deoxyguanylic acid with silver ion has been\r\nstudied by potentiometric determinations of silver binding, pH-stat\r\nproton release measurements, and ultraviolet spectrophotometry.
\r\n\r\nThe stepwise equilibria
\r\n\r\n3 Ag+ + 2 GH \u21cc Ag3G2H++ + H+ K32
\r\n\r\nAg3G2H++ + Ag+ \u21cc Ag4G++ + H+ K132
\r\n\r\nfit the data fairly well, and are proposed as a tentative explanation,\r\nalthough the exclusive occurrence of these reactions has not been\r\nconclusively proved.
" }, { "name": "Rapaport, Seymour Alvin", "degree": "Masters", "year": "1962", "title": "I. Determination of the Quantum Yield of Thymidine Dinucleoside Irradiated by Ultra-Violet Light. II. Studies on the Inactivation by Ultra-Violet light of T\u2084D Bacteriophage Containing 5-Bromodesoxyuridine Substituted DNA", "advisor": "Delbruck, Max; Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05112010-154607309", "creators": [ { "name": { "family": "Rapaport", "given": "Seymour Alvin" }, "id": "Rapaport-Seymour-Alvin", "display_name": "Rapaport, Seymour Alvin" } ], "advisors": [ { "name": { "family": "Delbruck", "given": "Max" }, "id": "Delbr\u00fcck-M", "role": "advisor", "display_name": "Delbruck, Max" }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/V4NH-KB09", "abstract": "It has been found that when frozen thymine solutions are irradiated by ultra-violet light a photoreversible steady state is formed between thymine and a thymine diner. The suggestion has been made that such photoreversible chemical reactions might be involved in the photoreactivable mutations that occur upon irradiation of viruses with ultra-violet light. In order to give further credence to this thymine dinucleoside, TpT, was prepared and irradiated by ultra-violet light as described in Part I. A wavelength dependent photosteady state was found tobe established by this, and the quantum yield of the reaction of TpT to its photoproduct determined. The existence of this steady state and the magnitude of the quantum yield (0.002) support the supposition that similar reactions may cause the photoreversible mutations in viral DNA.\r\n\r\nPart II describes the determination of the action spectrum of in activation of plaque forming ability of T_4 bacteriophages grown in the presence of the thymidine analogue 5-bromodesoxyuridine (5-BD). Under these conditions 5-BD is substituted intothe DNA in place of thymidine. Such substituted DNA has been found to have increased sensitivity to UV light at 254 m\u03bc. The action spectrum was determined to more precisely define this increase in sensitivity and to obtain additional information regarding the UV inactivation of DNA. It was found that 5-BD substituted T_4 was uniformly more sensitive to UV than unsubstituted T_4; this effect was most striking in the 302 to 334 m\u03bc region where a factor of increased sensitivity up to 500 to 1000 times was noted. Furthermore, unlike unsubstituted T_4, killing of 5-BD substituted T_4 was found to follow \"one hit\" kinetics. The action spectrum indicated that 5-BD was directly involved in the initial steps of inactivation and was compatible with the possibility of transfer of absorbed light energy along the polynucleotide chain." }, { "name": "Takahashi, Masaaki", "degree": "Masters", "year": "1962", "title": "Nuclear Magnetic Resonance Studies of Some 1,1-Difluoro-3-Phenylcyclobutane Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062010-112117806", "creators": [ { "name": { "family": "Takahashi", "given": "Masaaki" }, "id": "Takahashi-Masaaki", "display_name": "Takahashi, Masaaki" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/481A-5Q94", "abstract": "1-Difluoro-2, 2-dichloro-3-methy1-3-phenylcyclobutane has been prepared by the cycloacidition of a-methylstyrene to 1,1-difluoro2, 2-dichloroethylene. A 2 cps long-range H-F spin-spin coupling has been observed over five consecutive saturated bonds in 1,1-difluoro2, 2-dichloro-3-methyl-3-phenylcyclobutane, involving one of the fluorines at the 1-position and the protons of the 3-methyl group. Analysis of the spectrum and that of the stereospecifically labeled 4-deutero derivatives suggest that the fluorine involved is the one cis to the methyl group.\r\n\r\nThe n. m. r. studies of 1,1-difluoro-3-bromo-3-phenylcyclobutane which was obtained by bromination of 1,1-difluoro-3-phenylcyclobutane with N-bromosuccinimide indicate that this molecule has on the average a more nearly planar cyclobutane ring than that of 1,1- difluoro-2, 2-dichloro-3-methyl-3-phenylcyclobutane. The four protons of the 2- Etna 4-positions are nearly magnetically equivalent, so that the spectrum of this compound is almost that of an ABX_4 system rather than an ABX_2Y_2 system. The theoretical calculations suggest that the chemical shift difference between X and Y is on the order of 1-2 cps. The chemical shift difference between the fluorines decreases in 1,1-difluoro-2, 2-dichloro-3-methy1-3-phenylcyclobutane and 1,1- difluoro-3-bromo-3-phenylcyclobutane with increasing temperature, suggesting that rapid ring-inversion is taking place. " }, { "name": "Venezian, Emilio Cesare", "degree": "PhD", "year": "1962", "title": "Part I. Temperature Gradients in Turbulent Gas Streams Effect of Viscous Dissipation on the Evaluation of Total Conductivity. Part II. Thermal Transfer from Small Wires in the Boundary Flow about a Cylinder", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192011-105606734", "creators": [ { "name": { "family": "Venezian", "given": "Emilio Cesare" }, "id": "Venezian-Emilio-Cesare", "display_name": "Venezian, Emilio Cesare" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/W00C-BC43", "abstract": "Part I. \r\nValues of the total conductivity for air in turbulent flow were originally reported without regard to effects of viscous dissipation. The reported values were corrected for such effects by utilizing measurements taken at the time of the original investigation. The total conductivity obtained by taking into account dissipation effects was found to be independent of the average temperature gradient with which measurements were made.\r\n\r\nPart II.\r\nThe heat transfer characteristics from a 0.001-inch diameter\r\nplatinum wire in the boundary flow about a 1-inch copper cylinder were measured at Reynolds numbers, based on the cylinder diameter of about 1750, 3500 and 7100. The results are presented in terms of the Nusselt number for the wire as a function of position for the three Reynolds numbers investigated. Comparison of the measured Nusselt numbers with values predicted from calculated velocity distributions\r\nindicate that, in the vicinity of the cylinder wall, the Nusselt number is not a unique function of the Reynolds number based on the wire diameter.\r\n" }, { "name": "Wulff, Daniel Lewis", "degree": "PhD", "year": "1962", "title": "On Nucleic Acid Photochemistry", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08182011-150313553", "creators": [ { "name": { "family": "Wulff", "given": "Daniel Lewis" }, "id": "Wulff-Daniel-Lewis", "display_name": "Wulff, Daniel Lewis" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ENS3-PQ39", "abstract": "I. Frozen aqueous solutions of thymine and N, N'-dimethylthymine have been irradiated at 2537 \u00c5 to yield two dimers from N,N'-dimethylthymine and a single dimer from thymine. In all cases irradiation of the dimer in liquid aqueous solution at 2537 \u00c5 causes reversion to the monomer. One of the photodimers obtained from N,N'-dimethylthymine is identical to a product obtained by exhaustively N\u2013methylating the single photodimer obtained from thymine. Nuclear magnetic resonance and ultraviolet absorption data support a structure containing a cyclobutane ring.\r\n\r\nII. Action spectra for formation of thymine dimer in E. coli\r\nDNA have been taken. The initial quantum yield is not strongly dependent on wavelength. The ratio of thymine dimer to thymine in the photo-stationary state is much more dependent on wavelength. At the 235 m\u00b5 photo steady state 1.7% of the thymine is present as dimer. This shifts\r\nto 6.5% at 254 m\u00b5 and to 20% at 275 m\u00b5. While the change in the position of the photosteady state with wavelength fails to fit a simple model, the data do indicate that not all thymines are capable of participating in dimer formation.\r\n\r\nIII. Irradiation of ultraviolet irradiated DNA with photoreactivating light (370 m\u00b5) in the presence of an extract from baker's yeast containing photoreactivating enzyme causes the disappearance of thymine photodimer. The agent causing thymine photodimer to disappear is heat\r\nlabile. These results suggest that the molecular basis of photoreactivation of biological damage to microorganisms is the reconversion of thymine photodimer to thymine.\r\n" }, { "name": "Abrash, Henry Ivan", "degree": "PhD", "year": "1961", "title": "I. Steric and Electrostatic Repulsions in the Inhibition of \u03b1-Chymotrypsin Catalysed Hydrolyses by Indole Derivatives. II. Steric Requirements for Substrates of \u03b1-Chymotrypsin", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03202006-085153", "creators": [ { "name": { "family": "Abrash", "given": "Henry Ivan" }, "id": "Abrash-Henry-Ivan", "display_name": "Abrash, Henry Ivan" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "chair", "display_name": "Roberts, John D." }, { "name": { "family": "Buchman", "given": "Edwin R." }, "id": "Buchman-E-R", "role": "member", "display_name": "Buchman, Edwin R." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Dean", "given": "Richard A." }, "id": "Dean-Richard-A", "role": "member", "display_name": "Dean, Richard A." }, { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "member", "display_name": "Niemann, Carl G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/YTFM-K212", "abstract": "The enzyme-inhibitor dissociation constants, i.e., KI's, were evaluated for the six isomeric pairs of C-substituted indolecarboxylate ions and carboxamides. The variation of KI with the position and nature of the substituent indicates that the enzyme-indole complex exhibits a high degree of steric hindrance near the 4 position of the indole ring and electrostatic repulsion due to a negative group near the indole nitrogen.
\r\n\r\nThe synthesis of D,L-\u03b2,\u03b2-dimethylphenylalanine was modified by use of air oxidation of 4, 6-di-(\u03b1,\u03b1-dimethylbenzyl)pyrogallol to 3,5-di-(\u03b1,\u03b1-dimethylbenzyl)coumalic acid and permanganate oxidation of this product to obtain \u03b1-keto-\u03b2-phenylisovaleric acid. The by-products of the air oxidation were investigated.
\r\n\r\nD,L-2,6-Dimethyltyrosine, a previously unreported amino acid, and several of its derivatives were synthesized.
\r\n\r\nStudies on the rates of \u03b1-chymotrypsin catalysed hydrolyses of N-acetyl-D,L-t-leucine methyl ester, N-acetyl-D,L-\u03b2,\u03b2;-dimethyl-phenylalanine methyl ester and N-acetyl-D,L-2,6-dimethyltyrosine methyl ester indicate the presence of a strong \u03b2 steric effect.
\r\n\r\nMethods of resolution of D,L-\u03b2,\u03b2-dimethylphenylalanine and D,L-2,6-dimethyltyrosine derivatives were investigated.
\r\n\r\nMethyl indole-2-carboxylate is not a substrate of \u03b1-chymotrypsin.
\r\n" }, { "name": "Albert, Norman Edward", "degree": "PhD", "year": "1961", "title": "Infrared Absorption Associated with Strong Hydrogen Bonds", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechETD:etd-03232006-153024", "creators": [ { "name": { "family": "Albert", "given": "Norman Edward" }, "id": "Albert-Norman-Edward", "display_name": "Albert, Norman Edward" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "chair", "display_name": "Davidson, Norman R." }, { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "member", "display_name": "Anson, Fred C." }, { "name": { "family": "Badger", "given": "Richard M." }, "id": "Badger-R-M", "role": "member", "display_name": "Badger, Richard M." }, { "name": { "family": "King", "given": "Robert Burnett" }, "id": "King-R-B", "role": "member", "display_name": "King, Robert Burnett" }, { "name": { "family": "Robinson", "given": "G. Wilse" }, "id": "Robinson-G-W", "role": "member", "display_name": "Robinson, G. Wilse" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JACR-N881", "abstract": "The hydrogen bond systems in potassium hydrogen fluoride, acetamide hemihydrochloride, nickel dimethylglyoxime, potassium hydrogen bis-phenylacetate and maleic acid were studied via infrared spectroscopy between 5000 cm-1 and 400 cm-1. Each compound was studied in detail by the potassium bromide pressed disc technique.
\r\n\r\nThe infrared active fundamentals of the bifluoride ion were found to be shifted from the values reported for the pure, crystalline compound. Integral absorption intensities of the two infrared active fundamentals in the KBr solid solution were evaluated and interpreted in terms of the effective charge motion.
\r\n\r\nSpectra of acetamide hemihydrochloride, nickel dimethylglyoxime and potassium hydrogen bis-phenylacetate exhibited unusual features: an intense, extremely broad background absorption between 2000 cm-1 and 400 cm-1 and a deep \"window\" in the broad background. Maleic acid, however, was found to give a normal, well-behaved spectrum. These unusual features have been interpreted in terms of the symmetry of the hydrogen bond and the complexity of the hydrogen bonded molecules. The broad background is regarded as the superposition of several hydrogen bond vibrational modes, each of which is anharmonically coupled with low frequency intermolecular vibrational modes. The \"windows\" have been explained on the basis of a special perturbation between certain vibrational energy levels of the hydrogen bond modes and the molecular group modes in a small fraction of the molecules; in a majority of the molecules the perturbation is either absent or is very weak. It is suggested that these features are characteristic of short symmetric hydrogen bonds in complex molecules.
" }, { "name": "Almond, Harold Russell", "degree": "PhD", "year": "1961", "title": "I. The Consequences of Systematic Error in Enzyme Kinetics. II. L-Tyrosyl-L-Tyrosine Derivatives for the Detection of Transpeptidation in \u03b1-Chymotrypsin-Catalyzed Hydrolyses. III. The Interaction of \u03b1-Methyl-\u03b1-Acylamino Acids with \u03b1-Chymotrypsin. IV. The Apparent Ionization Constants of a Series of Phenylalanine Derivatives", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03272006-084330", "creators": [ { "name": { "family": "Almond", "given": "Harold Russell" }, "id": "Almond-Harold-Russell", "display_name": "Almond, Harold Russell" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GJ3M-A585", "abstract": "The consequences of systematic error in enzyme kinetics were investigated. Systematic error in substrate blank, enzyme blank, velocity determination, substrate concentration and the Beer-Lambert relationship was considered. The advisability of using weighting procedures in the presence of systematic error was questioned.
\r\n\r\nL-Tyrosyl-L-tyrosine methyl ester, amide, hydrazide and hydroxamide were prepared in order to detect transpeptidation in alpha-chymotrypsin-catalyzed hydrolyses. The reaction products from the hydrolyses of the corresponding L-tyrosine derivatives were found to contain only negligible amounts of transpeptidation products except for L-tyrosinhydroxamide which gave some L-tyrosyl-L-tyrosine. alpha- and beta-chymotrypsin were qualitatively the same with respect to these reactions.
\r\n\r\nThe N-acetyl methyl esters of alpha-methylphenylalanine, alpha-methyltyrosine and alpha-methyl-beta-(2-naphthyl)-alanine were synthsized and resolved. These esters are good competitive inhibitors of alpha-chymotrypsin. N-acetyl-(-) alpha-methyl-beta-(2-naphthyl)-alanine is a slowly hydrolyzed substrate of this enzyme. The inactivity of these esters toward alpha-chymotrypsin-catalyzed hydrolysis is a consequence of their inability to react further after complexing with the enzyme.
\r\n\r\nThe pK'a values of the alpha-ammonium groups of D,L-phenylalanine amide, thioamide, amidoxime, hydrazide, methyl ester and hydroxamide were determined. Comparison of these pK'avalues with some for corresponding glycine derivatives shows the former to be 0.59 \u00b1 .04 pK units lower. The infrared spectra of these phenylalanine derivatives were determined in KBr.
" }, { "name": "Berger, Stuart Brooke", "degree": "PhD", "year": "1961", "title": "Part I. Rates of Paramagnetic Pulse Reactions by Nuclear Magnetic Resonance. Part II. The Electron Paramagnetic Resonance Spectrum of Gas Phase \u00b9\u2074N\u00b9\u20760\u2082 and its Pressure Dependence", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03302006-112606", "creators": [ { "name": { "family": "Berger", "given": "Stuart Brooke" }, "id": "Berger-Stuart-Brooke", "display_name": "Berger, Stuart Brooke" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NTDW-4N34", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I of this thesis concerns the classically derived theory of the effect on the nuclear magnetic resonance line width and shape of a species which has a nucleus under investigation and is involved in an electron exchange reaction. The result is that the pseudo-first order reaction rate constant is added, under certain conditions, directly onto the no electron exchange line width of the species investigated, thereby increasing that line width. A reprint of a published article is included.\r\n\r\nPart II of this thesis concerns the investigation of the gas phase E.P.R. spectrum of nitrogen 14, oxygen-16 at a total pressure of 0.65 millimeters of mercury to 1.3 atmospheres. A many lined spectrum is recorded at low pressures which upon increase of pressure loses intensity in the portion away from the center of the spectrum and gains intensity in the central region, especially in three positions. Upon further increase in pressure the many lines broaden into a triplet at the three positions cited which continues to broaden with increase of pressure, eventually forming a singlet. This singlet continues to broaden with increase in pressure. A linear relation between line width and pressure is approached at the intermediate to high end of the pressure range investigated. The data is consistent with the assignment of a Fermi contact interaction equal to 131 Mcps and a spin-rotation interaction equal to 73 Mcps. The comparison to the theory of the electronic distribution of NO2 and to the work done on the NO2 E.P.R. spectrum in liquid CS2 and CCl4 in the argon matrix is discussed. The broadening is interpreted in terms of the spin-rotation and spin-spin coupling (spin-lattice interaction) and collision theory. A treatment of the overlapping of three spectral lines at [...] and [...] is given." }, { "name": "Farrar, Grover Louis", "degree": "PhD", "year": "1961", "title": "Part I. cis- and trans-l,2-Diaminocyclohexanes. Part II. A Study of the Tertiary Amine Precursors of Pirylene", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechETD:etd-03282006-131742", "creators": [ { "name": { "family": "Farrar", "given": "Grover Louis" }, "id": "Farrar-Grover-Louis", "display_name": "Farrar, Grover Louis" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/F20M-YA16", "abstract": "PART I: cis- and trans-1,2-Diaminocyclohexanes:\r\n\r\nWork initiated in these laboratories by Reims and Buchman on the stereospecific conversion of cis- and trans-cyclohexane-1,2-dicarboxylic acids to the corresponding diamines has been extended. cis- and trans-1,2-Diaminocyclohexanes have been characterized by measurements of densities, refractive indices, acid constants and melting points and by preparations of both side-chain and cyclic derivatives.\r\n\r\nPART II: A study of the tertiary amine precursors of pirylene:\r\n\r\nThe observation of Sargent, Buchman and Farquhar, that the Hofmann degradation of N,N-dimethyl-[alpha]-bromomethylpyrrolidinium bromide does not give a single C7H13N amine, but a mixture of isomeric tertiary amines has been confirmed. The components of the C7H13N amine mixture have been identified as follows:\r\n\r\n(1) 1-dimethylamino-4-pentyne\r\n\r\n(2) 1-dimethylamino-2,4-pentadiene\r\n\r\n(3) 1-dimethylamino-3,4-pentadiene\r\n\r\n(4) 1-dimethylamino-3-pentyne\r\n\r\n(5) 1-dimethylamino-1,3-pentadiene.\r\n\r\nComponents (2), (4) and (5) have been isolated and characterized. Components (1) and (3) were detected by infrared spectroscopy.\r\n\r\nA probable course of formation of the C7H13N amine mixture from N,N-dimethyl-[alpha]-bromomethylpyrrolidinium bromide is discussed." }, { "name": "Giuliano, Concetto Richard", "degree": "PhD", "year": "1961", "title": "I. Carbon-Thirteen Interactions in the Electron Resonance of Oriented Organic Radicals. II. Rate of Electron Transfer between Vanadium (V) and Vanadium (IV) by Nuclear Magnetic Resonance", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03142006-133845", "creators": [ { "name": { "family": "Giuliano", "given": "Concetto Richard" }, "id": "Giuliano-Concetto-Richard", "display_name": "Giuliano, Concetto Richard" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9424-YJ98", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I consists of the measurement of the angular dependence of the anisotropic C13 hyperfine interactions in the radical [...]. The above radical is formed when perdeutero malonic acid is subjected to x-ray damage. The deuterated radical's EPR spectra are compared with those of the protonated radical. In addition it was possible, because of the large anisotropy in the C13 interaction, to identify and determine the orientation of another radical formed. The second radical is [...] (or [...]) and is found to have two orientations in the crystal lattice.\r\n\r\nIn Part II the rate of electron transfer between vanadium (IV) and vanadium (V) is determined by [...] nuclear resonance line broadening. The rate of transfer was found to be first order in vanadium (IV) and second order in vanadium (V). The rate constant for the exchange reaction in 6.5 F acid solution is k= 1.5 x 10(6) [...]." }, { "name": "Hearst, John Eugene", "degree": "PhD", "year": "1961", "title": "Ultracentrifuge Studies on Deoxyribonucleic Acid and Tobacco Mosaic Virus. I. The Effect of Angular Velocity on the Sedimentation Velocity Behavior of DNA and TMV. II. The Three Component Theory of Sedimentation Equilibrium in a Density Gradient and the Hydration of DNA. III. The Effects of Pressure on the Buoyant Behavior of DNA and TMV in a Density Gradient at Equilibrium", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechETD:etd-04072006-090550", "creators": [ { "name": { "family": "Hearst", "given": "John Eugene" }, "id": "Hearst-John-Eugene", "display_name": "Hearst, John Eugene" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FWYT-4782", "abstract": "Part 1 - A dependence of sedimentation coefficient and sedimentation boundary shape upon the angular velocity of the ultracentrifuge has been observed for T-4 bacteriophage deoxyribonucleic acid (DNA), E. coli DNA, and tobacco mosaic virus. The effects resulting from extrapolation of high-speed data are discussed along with possible causes of the phenomenon.\r\n\r\nPart 2 - T-4 bacteriophage DNA is renatured by slow dialysis of a sodium citrate buffer solution into a solution of DNA in formamide. The first step in the renaturation appears to require the formation of approximately fifty percent of the possible hydrogen bonds.\r\n\r\nPart 3 - The dependence of the buoyant density of DNA on the presence of a second cation is studied and a theory presented. The system enables one to evaluate a relative binding constant of the two cations to DNA.\r\n\r\nPart 4 - The theory of density gradient sedimentation equilibrium including the effects of solvation is presented. The correction terms necessary for the evaluation of an anhydrous molecular weight are shown to be experimentally available. DNA is observed to have a large hydration parameter which is strongly dependent on water activity.\r\n\r\nPart 5 - The theory for the effect of pressure on the density gradient in a concentrated salt solution is presented. The effect of pressure on the buoyant density of DNA and tobacco mosaic virus is measured and found to be a linear function of pressure.\r\n\r\nPart 6 - The apparent molecular weight of T-4 bacteriophage DNA is evaluated using the density gradient sedimentation equilibrium theory presented in Parts 4 and 5. The DNA appears to have density heterogeneity." }, { "name": "Hill, Elgin Alexander", "degree": "PhD", "year": "1961", "title": "Stabilization of Carbonium Ions in the Vicinity of Metallocene Nuclei", "advisor": "Richards, John H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-111842", "creators": [ { "name": { "family": "Hill", "given": "Elgin Alexander" }, "id": "Hill-Elgin-Alexander", "display_name": "Hill, Elgin Alexander" } ], "advisors": [ { "name": { "family": "Richards", "given": "John H." }, "id": "Richards-J-H", "role": "advisor", "display_name": "Richards, John H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RPVG-GP20", "abstract": "A remarkable stabilization imparted to a carbonium ion by an adjacent metallocene nucleus has been demonstrated by a solvolytic study of substituted metallocenylcarbinyl acetates. The solvolysis mechanism has be shown to be to be an uncatalyzed alkl-oxygen fission of the neutral ester by a study of the hydrolysis under a variety of conditions and by determination of the products from the ethanolyses. Participation of the metal in the solvolyses by direct bonding between the metal and the incipient carbonium ion center is indicated by the effects of simple substituents by the effect of joining the rings by a three-carbon bridge, by the solvolysis of the acetate vinylogous to methylferrocenylcarbinyl acetate and by the stereochemistry of the solvolyses of derivatives with substitution in the 2-position of the ferrocene nucleus. A plausible molecular orbital model for such participation has been suggested in qualitative terms.\r\n\r\nSpectra of the ferrocene derivatives prepared in this study are correlated and discussed. Evidence is presented which demonstrates intramolecular hydrogen bonding to the metal atom in substituted metallocenylcarbinols, and which indicates that the rings of l,l'- trimethyleneferrocene are tilted." }, { "name": "Hybl, Albert", "degree": "PhD", "year": "1961", "title": "I. The Crystal Structures of Mono- and the Two Dimethylureas. II. The Determination and Use of Crystallographic Parameters", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-101757", "creators": [ { "name": { "family": "Hybl", "given": "Albert" }, "id": "Hybl-Albert", "display_name": "Hybl, Albert" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MCYS-5G51", "abstract": "Part I:\tThe crystal structures of mono-, and the two dimethylureas were determined by x-ray crystallographic methods. The positional and anisotropic temperature parameters of all heavy atoms were refined by the method of least-squares. All of the hydrogen atoms bonded to the amide nitrogen atoms were found in difference map sections computed in the planes of the molecules. Preferred orientations were found for the two methyl groups on N,N-dimethylurea, but the methyl groups in N-methylurea and N, N'-dimethylurea appear to be rotating. The preferred methyl orientations are neither the perfectly staggered nor eclipsed arrangements and appear to depend, in part, on the manner of packing of the molecules to form hydrogen bonded chains in the crystal.\r\n\r\nThe average bond distances were found to be: C=0, 1.253 A; c1-N (carbonyl C), 1.336 A and C2-N (methyl group C), 1.447 A. The partial double bond character is calculated to be 40% for the C=O bond and 30% for the C1-N bonds. The methyl groups appear to make little change in the contributions of the resonance structures to the hybrid structure. The average out of plane distance for the heavy atoms is 0.02 A, the maximum being 0.05 A.\r\n\r\nThe various types and configurations of cis- and trans-amide hydrogen bonds are reviewed and classified by the type of hydrogen bonded chain structure formed.\r\n\r\nPart II: Expressions employable for the calculation of structure factors and their derivatives for any orthorhombic space group are developed. Complementing this work is a general description of the least-squares method as used to determine a parameter set. Several methods for the conversion of a parameter set into more perceptible quantities, such as interatomic distances, bond angles, planarity of groups of atoms, magnitudes and direction cosines of the principal axes of the vibrational ellipsoids of each atom and the rigid body representation of the thermal displacements and vibrations, are reviewed." }, { "name": "Jones, Richard Theodore", "degree": "PhD", "year": "1961", "title": "Chromatographic and Chemical Studies of Some Abnormal Human Hemoglobins and of Some Minor Hemoglobin Components", "advisor": "Schroeder, Walter Adolph; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142006-133108", "creators": [ { "name": { "family": "Jones", "given": "Richard Theodore" }, "id": "Jones-Richard-Theodore", "display_name": "Jones, Richard Theodore" } ], "advisors": [ { "name": { "family": "Schroeder", "given": "Walter Adolph" }, "id": "Schroeder-W-A", "role": "advisor", "display_name": "Schroeder, Walter Adolph" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6S0R-AP08", "abstract": "Major and minor components in hemoglobins A, C, D, F, H, and S were detected and compared with one another by chromatography on IRC-50 resin. A procedure utilizing radioactive hemoglobins was developed for differentiating two hemoglobins with very similar chromatographic movements.\r\n\r\nChemical studies including amino acid composition, N-terminal sequence analysis, peptide pattern analysis of tryptic hydrolysates, ultraviolet spectroscopy, and subunit hybridization were carried out on several of the components which were isolated by chromatography. Conclusions about the polypeptide chains present in each components were drawn from these studies. Molecular formulas in terms of the number and kind of polypeptide chains were deduced for some of the components.\r\n\r\nAs well as yielding information about the chemical structure of hemoglobin F and the two abnormal components associated with thalassemia hemoglobin H, subunit hybridizations of these hemoglobins and hemoglobin A indicated that the rate of the hybridization reaction is slow and that there is non-random recombination of the subunits of these hemoglobins." }, { "name": "Kiefer, Edgar Francis", "degree": "PhD", "year": "1961", "title": "Synthesis and Solvolytic Reactivity of Unsaturated Cyclobutyl Bromides", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04112006-152145", "creators": [ { "name": { "family": "Kiefer", "given": "Edgar Francis" }, "id": "Kiefer-Edgar-Francis", "display_name": "Kiefer, Edgar Francis" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KS0P-Y690", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIn order to study the effect of unsaturation electrons at the 3-position of a cyclobutyl carbonium ion, 3-methylenecyclo-butyl bromide and 1-methyl-l-bromocyclobut-2-ene have been synthesized and their rates of solvolysis in aqueous ethanol determined and correlated with the solvolytic rates of a series of analogous bromides.\r\n\r\nThe synthesis of 3-methylenecyclobutanol, the precursor of 3-methylenecyclobutyl bromide, was accomplished by two independent schemes, both utilizing the cycloaddition reaction of allene and an activated olefin. Allene and vinyl benzoate afforded small yields of 3-methylenecyclobutyl benzoate, which liberated the alcohol on reduction. 3-Methylenecyclobutanecarbonitrile, obtained in good yield from allene and acrylonitrile by a published procedure, was converted to 3-methylenecyclobutylamine by hydrolysis followed by Curtius degradation. 3-Methylenecyclobutanol was obtained from the amine by nitrous acid deamination. 3-Methyl-3-bromocyclobutene was synthesized by dehydrobromination of 3-methyl-enecyclobutyl bromide, followed by low-temperature addition of one mole of hydrogen bromide.\r\n\r\nThe rate of solvolysis of 3-methylenecyclobutyl bromide in aqueous ethanol was found to be appreciably slower than the value predicted from simple molecular orbital theory by assigning a small resonance integral between the 1- and 3-positions in the carbonium ion intermediate. It is concluded that \"homoallylic resonance\" is hindered in this system because the planar structure requires inefficient [...]-type overlap of the p-orbitals at the 1- and 3-positions, instead of the [...]-type orbital overlap which contributes to the startling rate enhancement observed elsewhere in the solvolysis of anti-7-norbornenyl derivatives, for example. Cross-ring interaction is considered to be of some importance in the methylcyclobutenyl carbonium ion, although the solvolysis rate data in this case permit a wide range of interpretation." }, { "name": "Laidlaw, William George", "degree": "Masters", "year": "1961", "title": "I. Linearization Methods for Systems not at Chemical Equilibrium. II. Equilibrium Pressures and Phase Compositions for Non-Ideal Mixtures", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05072010-075038096", "creators": [ { "name": { "family": "Laidlaw", "given": "William George" }, "id": "Laidlaw-William-George", "display_name": "Laidlaw, William George" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CF3P-3866", "abstract": "No abstract." }, { "name": "Mather, William Brewster", "degree": "PhD", "year": "1961", "title": "Coulometric-Acidemetric Titrations and Related Studies in Acetic Acid-Acetic Anhydride Solutions", "advisor": "Anson, Fred C.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-104755", "creators": [ { "name": { "family": "Mather", "given": "William Brewster" }, "id": "Mather-William-Brewster", "display_name": "Mather, William Brewster" } ], "advisors": [ { "name": { "family": "Anson", "given": "Fred C." }, "id": "Anson-F-C", "role": "advisor", "display_name": "Anson, Fred C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4X11-3S02", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I: \r\n\r\nA coulometric titration of bases is described in which the supporting electrolyte consists of a sodium perchlorate solution in acetic anhydride, containing a small amount of acetic acid. A number of inorganic bases (sodium acetate, potassium hydrogen phthalate, sodium fluoride, sodium chloride, sodium nitrate and sodium sulfate have been titrated in this solvent with accuracies of \u00b10.2%. Perchloric acid is generated with 100% efficiency with a mercury anode. The end point is determined potentiometrically.\r\n\r\nApplication of this coulometric technique has been made to the determination of fluoride ion. Most anions other than perchlorrate display basic character in this solvent and were titrated with the fluoride. The titration has been applied to the determination of the total base in mixtures of fluoride with sulfate, chloride and nitrate. In some instances two end points can be observed with binary mixtures, so that analysis for each component is possible. An example is a mixture of fluoride and chloride.\r\n\r\nPart II:\r\n\r\nAn investigation of reactions occurring at and around platinum electrodes, both anode and cathode, in the electrolysis of a solution of 0.1 VF sodium perchlorate in acetic anhydride, which contains a small amount of acetic acid (0.1 VF), is described. Chronopotentiometric techniques have been extensively employed in these studies.\r\n\r\nThe cathode reaction is the reduction of the small amount of acetic acid present in the acetic anhydride solution. The reduction products are hydrogen and acetate ion: [...].\r\n\r\nThe anode reaction is probably the oxidation of acetic acid or acetic anhydride to form hydrogen ions or acetylium ions: [...].\r\n\r\nThe acetylium ions condense rapidly with the solvent to form slightly dissociated products: [...].\r\n\r\nFurther condensations to higher, very slightly dissociated products occur. These higher condensation products, in the protonated form, are such weak acids that they do not react with sodium acetate in the acetic anhydride solution. Thus, hydrogen ions are effectively lost from the solution. Coulometric-acidimetric titrations of bases, performed with hydrogen ions generated at a platinum anode in acetic anhydride, were unsuccessful because of this loss of hydrogen ions.\r\n\r\nAn appendix is included in which attention is drawn to the very reducing potentials attainable in acetic anhydride. From preliminary experiments it appears that sodium ion is more easily reduced than the acetic anhydride solvent." }, { "name": "Montgomery, Lawrence Kernan", "degree": "PhD", "year": "1961", "title": "Substitution Reactions Occurring via the Elimination-Addition Mechanism. Part 1. The Reactions of 1-Chlorocyclopentene and 1-Bromocyclobutene with Phenyllithium. Part II. The Coupling Reaction of Phenyllithium and Cyclopropyl Chloride and the Action\r\nof Strong Bases on 1-Bromoadamantane", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04182006-090002", "creators": [ { "name": { "family": "Montgomery", "given": "Lawrence Kernan" }, "id": "Montgomery-Lawrence-Kernan", "display_name": "Montgomery, Lawrence Kernan" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5BGQ-MG47", "abstract": "PART I:\r\n\r\nPhenyllithium and 1-chlorocyclopentene couple at 150\u00b0 to give 1-phenylcyclopentene in 30% yield. The mechanism of this reaction was investigated by reacting phenyllithium and 1-chlorocyclopentene-1-14C under similar conditions. Extensive rearrangement of the 14C label occurred; 1 phenylcyclopentene-x-14C was formed with 48.9%, 36.2%, and 14.9% of the 14C distributed among the 1-, 2-, and 5-positions, respectively. The coupling reaction proceeds by way of the elimination-addition mechanism with the intervention of an intermediate possessing the symmetry properties of cyclopentyne. The 14.9% of 1-phenylcyclopentene-5-14C most probably arises from a phenyllithium-induced allylic rearrangement of the double bond of the first-formed 1-phenylcyclopentene-2-14C. Alternative substitution mechanisms are discussed.\r\n\r\nPiperidine catalyzes the coupling reaction of phenyllithium and 1-chlorocyclopentene. The catalysis is similar in magnitude to that observed for the coupling of phenyllithium and aryl halides.\r\n\r\nThe reaction of 1-bromocyclobutene and phenyllithium has been studied at temperatures from 42-135\u00b0. Phenylacetylene and cyclobutene are formed as reaction products, but no 1-phenylcyclobutene was observed. The mechanism of this unusual phenylacetylene-forming fragmentation reaction has been investigated, and several possible mechanistic courses have been ruled out.\r\n\r\nPART II:\r\n\r\nPhenyllithium and cyclopropyl chloride couple under mild conditions to give phenylcyclopropane in low yield. The poor nucleophilicity of phenyllithium and the known reluctance of cyclopropyl derivatives to undergo typical unimolecular (SN1) and bimolecular (SN2) nucleophilic substitution reactions make it doubtful that the substitution proceeds by either of these courses. The possibility that substitution occurs via the elimination-addition mechanism was investigated briefly, but experimental difficulties prevented a unique interpretation of the results.\r\n\r\nBridgehead halides are known to be inert to nucleophilic substitution reactions. The possibility that substitution reactions of bridgehead halides might be achieved by way of elimination-addition is very interesting, since this mechanistic route would require the formation of an intermediate in violation of Bredts rule. 1-Bromoadamantane did not react with potassium amide in liquid ammonia but was converted to adamantane by potassium piperidide in refluxing piperidine." }, { "name": "Nordlander, John Eric", "degree": "PhD", "year": "1961", "title": "Studies of Grignard Reagent Rearrangements by Means of Nuclear Magnetic Resonance Spectroscopy. I. The Structure of Allylic Grignard Reagents. II. The Interconversion of Cyclopropylcarbinyl and Allylcarbinyl Grignard Reagents", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04112011-151419797", "creators": [ { "name": { "family": "Nordlander", "given": "John Eric" }, "id": "Nordlander-John-Eric", "display_name": "Nordlander, John Eric" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XS2P-1R78", "abstract": "I. The structure of allylic Grignard reagents:\r\n\r\nThe nuclear magnetic resonance (n.m.r.) spectra of several simple allylic Grignard reagents in diethyl ether solution, of benzylmagnesium chloride in ether, and of diallylmagnesium and dibutenylmagnesium in dioxane have been investigated. The results for the simple allylic systems are best interpreted in terms of an extremely mobile tautomeric exchange of magnesium between allylic positions, whereas the conventional structure is indicated for the benzyl Grignard reagent. The results are related to the rearrangements known to occur in the Grignard reactions of allylic halides.\r\n\r\nII. The interconversion of cyclopropylcarbinyl and allylcarbinyl Grignard reagents:\r\nThe Grignard reagent, in ether solution, from either cyclo-propylcarbinyl chloride or allylcarbinyl chloride has been shown by its n.m.r. spectrum to possess the allylcarbinyl structure. Nortricyclcylchloride and exo- or endo-5-dehydronorbornyl chloride also give a common Grignard reagent, whose n.m.r. spectrum seems best fitted to the nortricyclyl structure. The results explain the products formed in the Grignard reactions of these sets of isomeric halides. They are also discussed with respect to the recently discovered interchange between the 1- and 2-positions in allylcarbinylmagnesium halides.\r\n" }, { "name": "Panar, Manuel", "degree": "PhD", "year": "1961", "title": "The Elimination-Addition Mechanism of Nucleophilic Aromatic Substitution", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04122011-082331600", "creators": [ { "name": { "family": "Panar", "given": "Manuel" }, "id": "Panar-Manuel", "display_name": "Panar, Manuel" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5JAK-A186", "abstract": "Part I: The elimination-addition (benzyne) mechanism postulated for nucleophilic substitutions of non-activated halobenzenes provided the first coherent explanation of the rearrangements which frequently accompany these reactions. However, several less likely alternative mechanisms were able to explain the available data. These alternatives have been disproven by the finding that the amination of iodobenzene-l-^(14)C-2,4,6-^2H_3 gives the same extend of ^(14)C rearrangement in the resulting aniline as does iodobenzene-l-^(14)C.\r\nPart II: Substituent effects in aminations of halobenzenes have been explained by inductive control of both the direction of formulation of benzyne and the manner of addition of the nucleophile to the reactive benzyne bond. Although the intermediacy of benzyne in non-rearranging aminations of halobenzenes having electron-withdrawing substituents in the 3-position has been rationalized, the possibility of direct displacement remained. The intermediacy of benzyne has been confirmed by a determination of the isotope effect in reactions of 3-bromoanisole-2,4,6-^2H_3.\r\nPart III: While leaving groups such as non-activated halogens react with amide ion in liquid ammonia via a benzyne intermediate, others react entirely or primarily via direct substitution. In order to obtain needed data on the leaving group characteristics which lead to benzyne formation, attempts have been made to find further non-activated substituted benzenes which react with amide ion.\r\n\r\nPart IV: While all alternatives to the elimination-addition mechanism for amination of non-activated halobenzenes have been disproven one cannot rule out the possibility that benzyne exists as a c_6H_4-complex with halide ion or metal ion. In order to demonstrate the ability of benzyne to exist as a stable C_6H_4 hydrocarbon it would be desirable to pass benzyne through the vapor-phase. Several experiments of this nature have been attempted.\r\n" }, { "name": "Rolfe, Ronald Efrom", "degree": "PhD", "year": "1961", "title": "I. The Relative Homogeneity of Microbial Desoxyribonucleic Acid. II. The Molecular Arrangement of the Conserved Subunits of the Desoxyribonucleic Acid of Escherichia coli", "advisor": "Meselson, Matthew S.; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132011-072837251", "creators": [ { "name": { "family": "Rolfe", "given": "Ronald Efrom" }, "id": "Rolfe-Ronald-Efrom", "display_name": "Rolfe, Ronald Efrom" } ], "advisors": [ { "name": { "family": "Meselson", "given": "Matthew S." }, "id": "Meselson-M-S", "role": "advisor", "display_name": "Meselson, Matthew S." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CBDY-KV20", "abstract": "I. The buoyant density of DNA in a CsCl-density gradient has been shown to depend on its nucleotide composition. The linear relationship has been used to study the distribution of nucleotide compositions among the DNA molecules isolated from a single microbial species. Each microbial DNA has been shown to be unusually homogeneous relative to the range of compositions found for DNA isolated from different species. The relevance of these findings to current views of the function of DNA in biological systems is discussed.\r\n\r\nII. The molecular arrangement of the conserved subunits of E. coli DNA has been investigated by examining molecular fragments of hybrid ^(13)C, ^(15)N E. coli DNA. Two extreme models for the arrangement of subunits, the side-to \u2013side model, and the end-to-end model, were considered. Predictions regarding CsCl-density-gradient distribution for fragments of hybrid DNA were developed for each model. These predictions were based on a theoretical analysis, but utilized pertinent experimental data obtained from a study of unlabelled E. coli DNA. Comparison of theory with experiment indicated that the end-to-end model is incorrect, and set an upper limit to the amount of fully labeled fragments released when hybrid DNA is sonicated.\r\n" }, { "name": "Schuster, David Israel", "degree": "PhD", "year": "1961", "title": "Synthesis and Free Radical Decarbonylation of Some Small-Ring Aldehydes", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132011-073827678", "creators": [ { "name": { "family": "Schuster", "given": "David Israel" }, "id": "Schuster-David-Israel", "orcid": "0000-0002-8989-1801", "display_name": "Schuster, David Israel" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZCMA-XQ70", "abstract": "A number of small-ring radicals have been generated by peroxide-initiated decarbonylation of the appropriate aldehydes, neat and in diphenyl ether, and that extent of rearrangement in these reactions has been determined in each cases. The results are compared with known examples of free radical rearrangements and with rearrangements which occur in carbonium ion reactions in the same small-ring systems. The results are found to be in accord with the predictions of simple molecular orbital (L.C.A.O) theory.
\r\n\r\nNo decarbonylation of cyclopropanecarboxaldehyde was observed. 1-Methyl- and 1-phenylcyclopropanecaroxaldehyde gave exclusively methyl- and phenylcyclopropane, respectively, on decarbonylation. Cyclobutanecarboxaldehyde, cyclopropylacetaldehyde and dimethyl-cyclopropylacetaldehyde afforded exclusively cyclobutane, 1-butene and 2-methyl-2-pentene, respectively, on decarbonylation. A mixture of 2-methyl-2-pentene and isopropylcyclopropane was obtained on decarbonylation of dimethylcycloprpylacetaldehyde in benzyl mercaptan.
\r\n\r\nThe possible role of \"non-classical\" homoallylic radical intermediates in the free radical reactions of cyclopropylcarbinyl derivatives is discussed. A decision could not be made on the basis of available evidence between mechanisms involving classical and \"non-classical\" radical intermediates in these reactions. The evidence does suggest that \"non-classical\" bicyclobutonium radical intermediates are not important in these reactions.
\r\n\r\nThe methods of synthesis of the small-ring aldehydes in this study are presented and discussed.
\r\n" }, { "name": "Tunder, Richard Steve", "degree": "Masters", "year": "1961", "title": "Development of a Competitive Technique for the Comparison of Strong Oxidation Inhibitors", "advisor": "Hammond, George Simms", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062010-142421533", "creators": [ { "name": { "family": "Tunder", "given": "Richard Steve" }, "id": "Tunder-Richard-Steve", "display_name": "Tunder, Richard Steve" } ], "advisors": [ { "name": { "family": "Hammond", "given": "George Simms" }, "id": "Hammond-G-S", "role": "advisor", "display_name": "Hammond, George Simms" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FZ6G-N196", "abstract": "The mechanism of the inhibited chain oxidation of \r\ncumene has been carefully investigated in previous studies.\r\nA competitive technique for determining relative efficiencies of strong inhibitors was to be tried in this study. Such a study might extend and verify work of a similar nature on weaker inhibitors. However the relative efficiencies determined were not constant. They varied because of possible side reactions of N,N'-dipheny1-p-phenylenediamine, the inhibitor chosen as a standard. For the same reason variation of the initial concentration of the standard inhibitor caused slight unexpected deviations in the results.\r\n\r\nHydroquinones were found to reduce N,N'-diphenyl-p-quinonimine, the oxidation product of the standard inhibitor, back to the inhibitor while stopping chains at the same time. As in previous studies, the strength of an inhibitor was found to increase with increasing ortho steric hindrance as well as with increasing electron density in the aromatic ring. Initiator concentration was found to be first order with respect to termination rate as would be expected in a chain reaction in which an inhibitor molecule stops two radical chains. The oxidation product formed from a phenolic inhibitor was found not to affect the standard inhibitor." }, { "name": "Vogel, Martin", "degree": "PhD", "year": "1961", "title": "Stereochemical Study of CycIopropylcarbinyl Derivatives in Carbonium-lon Reactions", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04132011-075059835", "creators": [ { "name": { "family": "Vogel", "given": "Martin" }, "id": "Vogel-Martin", "display_name": "Vogel, Martin" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7H4C-6W65", "abstract": "Cyclopropylmethylcarbinylamine and cyclopropylmethylcarbinol\r\nwere resolved and their configurations related.\r\nThe former was deaminated with aqueous nitrous acid to give\r\nthe latter with 0-4% net inversion of configuration. The\r\nsolvolyses of several N-methyl-4-alkoxypyridinium salts\r\nwere investigated. Solvolysis rates for N-methyl-4-\r\n(cyclopropylcarbinyloxy)-pyridinium iodide and perchlorate\r\nin water and in 80% ethanol and of N-methyl-4-(cyclopropylmethy1carbinyloxy)-pyridinium iodide in water were measured. The first-order rate constant for the hydrolysis of N-methyl-4-(cyclopropylmethylcarbinyloxy)-pyridinium iodide at 30\u00b0 was calculated to be 6 x 10^3 times that of N-methyl-4-(cyclopropylcarbinyloxy)-pyridinium iodide. The hydrolysis of optically active N-methyl-4-(cyclopropylmethylcarbinyloxy)-pyridinium iodide produced cyclopropylmethylcarbinol with 4.4 \u00b1 1.5% inversion of configuration.\r\n\r\nThe stereochemistry of the deamination of cyclopropylmethylcarbinylamine and of the hydrolysis of N-methyl-4-(cyclopropylroethylcarbinyloxy)-pyridinium iodide and the ratio of rate constants for the cyclopropylroethylcarbinyl and cyclopropylcarbinyl pyridinium salts are discussed with respect to the possible intervention of non-classical carbonium-ion intermediates in these reactions.\r\n" }, { "name": "Wallace, Frederic Andrew", "degree": "Masters", "year": "1961", "title": "pH Titration Studies of the Acid Denaturation of Calf Thymus Deoxyribosenucleic Acid", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212010-142614826", "creators": [ { "name": { "family": "Wallace", "given": "Frederic Andrew" }, "id": "Wallace-Frederic-Andrew", "display_name": "Wallace, Frederic Andrew" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MME6-8038", "abstract": "The acid denaturation of calf thymus deoxyribosenucleic acid (DNA) has been studied both by PH and \r\nspectrophotometric titration in the temperature range \r\n10 - 30\u00b0C and at ionic strengths 0.1 F and 0.5 F. The \r\nnumber of hydrogen ions bound by the DNA at any given \r\npH increased with increasing temperature and decreased \r\nwith increasing ionic strength. The number bound at \r\nany given pH was greater after denaturation. A model \r\nfor acid denaturation is proposed. The site of protonation of cytosine is discussed.\r\n" }, { "name": "Dearman, Henry Hursell", "degree": "PhD", "year": "1960", "title": "I. Studies of the Spin Distribution in Aromatic Radicals. II. Electron Resonance Studies of Some Sandwich Compounds", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03142006-142740", "creators": [ { "name": { "family": "Dearman", "given": "Henry Hursell" }, "id": "Dearman-Henry-Hursell", "display_name": "Dearman, Henry Hursell" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CA5W-J786", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I: Studies of the Spin Distributions in Aromatic Radicals. \r\n\r\nIt is shown that if conventional molecular orbital theory is extended in such a way as to include electron correlation, according to the proposal of Lowdin, negative spin density is predicted at unstarred positions of odd alternant hydrocarbon radicals. However, it is found that Lowdin's suggested method of alternant orbitals is not a sufficiently good approximation to the ground state of an even alternant hydrocarbon ion for the effects of electron correlation on the [...] electron spin density to be estimated. As a check of the validity of this approximate wave function for the radicals, the method of alternant orbitals function for the allyl radical is developed and commpared numerically with the results of a [...] configuration calculation.\r\n\r\nCalculation of spin densities by simple valence bond theory is described for several odd alternant radicals. For the perinaphthenyl and trivinylmethyl radicals, the secular equation is solved and the ground state eigenvector is derived. Normalization gives the coefficients of the various structures for the benzyl, [alpha]-methylnaphthanyl and [beta]-methylnaphthanyl radicals from the coefficient ratios given by Pauling and Wheland.\r\n\r\nEquations are derived which relate the [...] electron spin density at an atom in the [...] molecular framework in that hyperfine coupling constant due to the atom itself. Previously, McConnell and Chesnut have shown that there is a linear relation between the proton coupling constant and the [...] electron spin density at the adjacent carbon atom in [...] molecular radicals. In the case of the coupling constant of the carbon atom itself, for instance, it is shown that the relation is also a linear one, but the spin density at any neighbor atom must be included. It is concluded that negative spin density at a neighbor results in \"donation\" of spin density to the atom in question and to the observation of an abnormally large coupling constant. Estimation of the necessary constants for C13 is carried out semi-empirically in a simple way.\r\n\r\nPart II. Electron Resonance studies of Some Sandwich Compounds. \r\n\r\nESR signals from pure polycrystalline nickelocene and cobaltocene are observed at liquid temperature. Although little information of a quantitive nature can be obtained from a powder spectrum, comparison with the predictions of Robertson is made whenever possible. The ESR spectrum of vanadocene as a substitutional impurity in a single crystal of ferrocene at room temperature is measured. The angular dependence of the absorption peaks is interpreted using the spin Hamiltonian given by Schulz-Du Bois for the isoelectronic ion, Cr+3. This analysis allows the evaluation of the splitting of the ground quartet which is present in the zero magnetic field, [...] = 50 Kmc." }, { "name": "Helman, William Phillip", "degree": "Masters", "year": "1960", "title": "Absorption and Dispersion of Sound in Reacting and Relaxing Fluids", "advisor": "Mazo, Robert M.; Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222010-093442090", "creators": [ { "name": { "family": "Helman", "given": "William Phillip" }, "id": "Helman-William-Phillip", "display_name": "Helman, William Phillip" } ], "advisors": [ { "name": { "family": "Mazo", "given": "Robert M." }, "id": "Mazo-R-M", "role": "advisor", "display_name": "Mazo, Robert M." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DW69-PB79", "abstract": "The hydrodynamic equations for a chemically reacting and internally relaxing fluid are obtained in a suitable form, and, are then used to find the dispertion and absorption of plane infinitesimal sound waves, Only the case of no viscosity, heat conduction, and diffusion is considered. It is shown that the interference effects between relaxation processes are not, in general, negligible compared to the relaxation effects themselves. A specific example, that of oxygen gas at 2500\u00b0 K is considered giving an idea of the relative magnitudes of the several effects which are involved.\r\n" }, { "name": "Hutchinson, William Day", "degree": "PhD", "year": "1960", "title": "Physical Chemical Studies of Reactions of Human Hemoglobins", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechETD:etd-12202005-152231", "creators": [ { "name": { "family": "Hutchinson", "given": "William Day" }, "id": "Hutchinson-William-Day", "display_name": "Hutchinson, William Day" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6QAM-0X37", "abstract": "The molecular dissociation of the derivatives, carbonmonoxy-, oxy-, ferro-, and ferri-, of normal adult hemoglobin has been studied at a pH of five. Of these derivatives, ferrohemoglobin is least dissociated while ferrihemoglobin is most extensively dissociated at a given concentration. The apparent dissociation constants have been calculated and related to the acid dissociation of the \"theme-linked\" acid groups of these derivatives.\r\n\r\nHemoglobins labelled with Carbon-14 have been prepared. Using C14 labels on one hemoglobin, the exchange of molecular subunits has been studied after dissociation of mixtures of normal adult and sickle cell hemoglobins at acid and alkaline pH. Hemoglobin \"hybrids\", in which one type of subunit is radioactive and the other not, have been formed and isolated. These hybrids have been used in the identification of the polypeptide chain in which the anomaly occurs in sickle cell hemoglobin. This anomaly was found to occur in the [beta] chains. The kinetics of the [alpha] chain exchange between the two hemoglobins has been studied at alkaline pH. Presumptive evidence of the mode of dissociation at this pH has been obtained. Preliminary investigations are reported on the isolation of hemoglobin hybrids in which only the chains are radioactive.\r\n\r\nSpectral data for several derivatives of hemoglobin have been related to a recently adopted standard. The use of the ferroversenate ion in forming ferrohemoglobin from oxyhemoglobin is reported." }, { "name": "Kurtz, Abraham Nathan", "degree": "PhD", "year": "1960", "title": "I. Structural Analogs of Typical Substrates of Alpha-Chymotrypsin. II. l-Acetyl-2-[L-Tyrosyl] Hydrazine: an Inhibitor of Alpha-Chymotrypsin. Ill. Binuclear Aromatics as Inhibitors of Alpha-Chymotrypsin Catalyzed Hydrolyses. IV. Applicability of the pH-Stat to Alpha-Chymotrypsin Catalyzed Hydrolyses that Produce a Buffer", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06302006-085322", "creators": [ { "name": { "family": "Kurtz", "given": "Abraham Nathan" }, "id": "Kurtz-Abraham-Nathan", "display_name": "Kurtz, Abraham Nathan" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8C7N-4Z18", "abstract": "Substitution of a nitrogen atom in place of the C-H group that occurs at the asymmetric center of typical substrates of alpha-chymotrypsin results in the complete loss of the ability of the enzyme to catalyze the hydrolysis of the carboethoxy or carboxamido group. However, the nitrogen-substituted analogs, which otherwise possess all of the remaining significant structural entities of typical substrates, function as inhibitors of alpha-chymotrypsin catalyzed hydrolyses but in general show less affinity for the enzyme than do the analogous C-H containing substrates.\r\n\r\nIt has been found that l-acetyl-2-[L-tyrosyl] hydrazine is a reversible inhibitor of alpha-chymotrypsin catalyzed hydrolyses with unusual affinity for the enzyme. At pH 7.9 the enzyme inhibitor constant was found to have a value of KI = 0.074 x 10(-3)M, which shows that this substance associates reversibly with alpha-chymotrypsin at the active site to a greater extent than any other known substrate or reversible inhibitor.\r\n\r\nPreliminary results, based upon inhibition studies, indicate that alpha-chymotrypsin possesses a greater affinity for the naphthalene function than for the indole function.\r\n\r\nA study of the applicability of the pH-stat to alpha-chymotrypsin catalyzed hydrolyses that produce a buffer showed that the reliability was a function of the buffer capacity. Amides gave poor results; hydrazides gave good or fair results, one of which contradicted a literature value, and a hydroxamide gave excellent results." }, { "name": "Moore, Carleton Bryant", "degree": "PhD", "year": "1960", "title": "I. Kinetics of the Reactions of Silver, Lead and Thallium with Thioacetamide. II. The Distribution of Barium, Titanium, Manganese, Iron, Nickel and Cobalt in Stony Meteorites", "advisor": "Swift, Ernest H.; Brown, Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-06302006-091438", "creators": [ { "name": { "family": "Moore", "given": "Carleton Bryant" }, "id": "Moore-Carleton-Bryant", "display_name": "Moore, Carleton Bryant" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." }, { "name": { "family": "Brown", "given": "Harrison" }, "id": "Brown-Harrison", "role": "advisor", "display_name": "Brown, Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/W8C0-E784", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe precipitation of silver from acid solutions by thioacetamide at 60\u00b0C was investigated. Below pH 2 the reaction takes place predominantly by the hydrolysis of thioacetamide to form hydrogen sulfide. Above pH 2 a direct reaction between the silver and thioacetamide has a significant effect. The direct reaction rate equation was found to be\t[...]. At 60\u00b0C in a malonic acid - 0.1 VF sodium hydrogen malonate buffer k\" is 8.6 x 10(-7) mole 7/2 liter 7/2 minute(-1).\r\n\r\nThe presence of chloride ion inhibits the rate of direct reaction between lead and thioacetamide. The reaction is first order with respect to PbCl+ and about 50% slower than with Pb++ at 90\u00b0.\r\n\r\nThallous sulfide is precipitated by thioacetamide by both hydrolysis and direct reactions. The direct reaction is second order with respect to thallium, first order with respect to thioacetamide and probably inverse half order with respect to hydrogen ion.\r\n\r\nThe concentrations of barium, manganese and titanium have been determined spectrographically in 94 stony meteorites. There appear to be four barium concentration groups with median barium concentrations of 5, 10, 25 and 150 ppm. For the falls the average concentrations of manganese and titanium are 0.260 \u00b1 0.028% and 0.064 \u00b1 0.008%. For the finds the manganese content is 0.235 \u00b1 0.023% and the titanium content is 0.059 \u00b1 0.007%. The presence of grouping in chondrites has been confirmed by X-ray fluorescence spectroscopic analysis." }, { "name": "Porterfield, William Wendell", "degree": "Masters", "year": "1960", "title": "Some Electron Paramagnetic Resonance Studies of Bis-Cyclopentadienyl Vanadium", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04232010-114434337", "creators": [ { "name": { "family": "Porterfield", "given": "William Wendell" }, "id": "Porterfield-William-Wendell", "display_name": "Porterfield, William Wendell" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7D95-T093", "abstract": "Section I: \r\nBis-cyclopentadienyl vanadium was examined by electron paramagnetic resonance (EPR) in dilute benzene solution (1). Vanadium nuclear hyperfine splittings equal to 77 Mc centered at g=2.00 were found, providing experimental evidence that the unpaired electrons occupy orbitals with a very small amount of s character. The orbital ground state is shown to be a singlet. It follows that one of the three unpaired electrons must occupy an orbital of a_(1g) symmetry, the other two orbitals of e_g symmetry, and that the g factor is nearly isotropic.\r\nEPR spectra taken of an oxidized solution show hyperfine structure 210 Mc wide at g=1.99, indicating the possible presence of bis-cyclopentadienyl vanadyl, V0(C_5H_5)_2.\r\nSection II: \r\nEPR spectra were taken of a dilute single crystal of bis-cyclopentadienyl vanadium in ferrocene and the angular dependence of the spectra studied. The spectral lines changed from g^e\u22432 at a position with H_0 approximately parallel to the molecular symmetry axis to g^e=3.77 with\r\nH_0 perpendicular to this axis, where h\u03bd=g^e\u03b2H. This angular dependence indicates a zero-field energy level splitting of 47.0 kMc or 1.57 cm^(-1). The bis-cyclopentadienyl vanadium was synthesized by a process originated by Wilkinson (2) but some minor changes were found desirable in product recovery.\r\n" }, { "name": "Robertson, Richard Earl", "degree": "PhD", "year": "1960", "title": "I. Isotropic Nuclear Resonance Shifts. II. The Magnetic Resonance Properties of Some Sandwich Molecules", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07062006-083552", "creators": [ { "name": { "family": "Robertson", "given": "Richard Earl" }, "id": "Robertson-Richard-Earl", "display_name": "Robertson, Richard Earl" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B5YD-3B43", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nIsotropic Nuclear Resonance Shifts:\r\n\r\nIt is shown that isotropic or average nuclear resonance shifts for a nucleus in a paramagnetic molecule in solution, and in a polycrystalline solid, can be used to distinguish between Fermi contact and \"pseudo contact\" contributions to isotropic nuclear hyperfine interactions. The pseudo contact interaction is that isotropic hyperfine coupling which arises from the combined effects of (electron-spin)-(nuclear-spin) coupling, (electron-orbit)-(nuclear-spin) coupling, and electron spin-orbit interaction. When the magnetic hyperfine interaction between the electronic moment and nuclear spin is approximated by a point dipolar interaction, and the isotropic hyperfine interaction is exclusively pseudo contact, then the isotropic nuclear shift in a polycrystalline solid exceeds the solution shift by the factor [...]/[...] where [...] and [...] are the spectroscopic splitting factors parallel and perpendicular to the molecular symmetry axis. Isotropic shifts due to the Fermi contact interaction are the same for both solid state and solution cases.\r\n\r\nThe Magnetic Resonance Properties of Some Sandwich Molecules:\r\n\r\nUsing the results of the two models as a first orientation the results of the magnetic susceptibility experiments (i.e., the observed deviation from spin only values) are used to choose appropriate arrangements for the three low-lying one-electrons in calculating the fine structure. The fine structure is considered for both when the Jahn-Teller effect splits a degenerate orbital ground state and when spin-orbit interaction splits the orbital ground state without the Jann-Teller distortion. However, it is found that the Jahn-teller effect operates when appropriate in all the molecules and ions with the possible exception of [...]. Expressions are given for the g-factors and zero-field splittings, although the lack of knowledge as to the values of many of the parameters precluded numerical estimates in most cases.\r\n\r\nHyperfine structure is considered although not in much detail. Cognizance is taken of the fact the \"exchange polarization\", which results from paramagnetism of the ion causing the [alpha] and [beta] spins in the [...], [...], and [...] configurations to be in slightly different orbitals, leads to negative hyperfine coupling coefficients while unpaired electrons being in orbitals having s-character leads to a positive coupling coefficient." }, { "name": "Sakaida, Roy Ryosuke", "degree": "PhD", "year": "1960", "title": "I. A Study of the Catalytic Decomposition of Nitric Oxide. II. A Chromatographic Apparatus and Technique for the Analysis of Nitric Oxide in Nitrogen. III. Kinetics and Mechanism of the Air Oxidation of the Dithionite Ion (S\u20820\u2084\u207c) in Aqueous Solution", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-07112006-080753", "creators": [ { "name": { "family": "Sakaida", "given": "Roy Ryosuke" }, "id": "Sakaida-Roy-Ryosuke", "display_name": "Sakaida, Roy Ryosuke" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "chair", "display_name": "Corcoran, William Harrison" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "member", "display_name": "Sage, Bruce H." }, { "name": { "family": "Longwell", "given": "Paul A." }, "id": "Longwell-P-A", "role": "member", "display_name": "Longwell, Paul A." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "member", "display_name": "Lacey, William Noble" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VQEV-BW35", "abstract": "Part I:\tThe study of the catalytic decomposition of nitric oxide at a concentration of 0.5% by volume in nitrogen was conducted over a packed bed in a tubular flow reactor. The packed bed was in the form of alumina pellets impregnated with 0.1% by weight of platinum oxide and 3.0% by weight of nickel oxide. Tests which were conducted at pressures of 1 to 15 atm and temperatures of 800 to 1000\u00b0F showed that the rate is second-order with respect to the nitric oxide and is retarded by the adsorption of atomic oxygen on the surface of the catalyst.\r\n\r\nPart II: In conjunction with the decomposition studies, a gas chromatographic technique for the analysis of nitric oxide at a concentration of less than 0.5% by volume in nitrogen was developed. The chromatograph column with a length of 8 ft contained silica gel and was operated in a temperature range of 65 to 85\u00b0C. Helium was used as the carrier gas, and the eluted components were measured by means of a thermal conductivity cell with dual thermistors.\r\n\r\nPart III: A study of the air oxidation of sodium dithionite in aqueous solution was made. A mechanism was proposed in which the SO2- freeradical ion was the reactive intermediate. The rate of oxidation was found to be half-order with respect to the dithionite ion and first-order with respect to molecular oxygen." }, { "name": "Schoomer, Bertrand Alva", "degree": "PhD", "year": "1960", "title": "I. The Crystal Structure of Cyclohex-1-enylcyclobutenedione. II. The Crystal Structure of 3,6-dimethylpiperazine-2,5-dione. III. Programs for the Burroughs Model 205 Computer", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechETD:etd-07142006-084404", "creators": [ { "name": { "family": "Schoomer", "given": "Bertrand Alva" }, "id": "Schoomer-Bertrand-Alva", "display_name": "Schoomer, Bertrand Alva" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/W46M-W507", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe crystal structure of cyclohex-l-enylcyclobutenedione has been determined by x-ray diffraction techniques. Complete three-dimensional intensity data were collected about each of two axes using [...] radiation. A trial structure was evolved which proved to be correct. This structure was refined both in projection and in three dimensions by conventional Fourier and least-squares methods. During the last several cycles of refinement six thermal parameters and three positional parameters for each of the twelve heavy atoms were optimized. An unusually long carbon-carbon bond distance [...] has been found; this result is not inconsistent with purely chemical properties of the compound.\r\n\r\nThe crystal structure of 3,6-dimethylpiperazine-2,5-dione has been investigated by means of x-ray diffraction methods. Three-dimensional intensity data have been collected and a trial structure has been evolved. This trial structure seems to be the only structure which affords a suitable hydrogen-bonding scheme and molecular packing. Moreover, it is in agreement with the very distinctive crystalline habit and cleavage of the compound. Apparently because of difficulties in scaling the data, however, the very large number of refinements which were attempted all failed to converge. Consequently, work on this compound has been stopped temporarily until sufficient additional information has been collected to allow all of the intensity data to be put onto a common scale.\r\n\r\nA number of programs of general crystallographic interest have been coded for the Burroughs electronic digital computer, model 205. A brief description of these programs is given." }, { "name": "Taylor, Raymond Leonard", "degree": "PhD", "year": "1960", "title": "I. A Study of Vibrational Relaxation in Carbon Monoxide by Shock-Waves and Infra-Red Emission. II. A Study of the Effect of a Resonant Transfer of Energy on the Vibrational Relaxation of Gas Mixtures", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07242006-152841", "creators": [ { "name": { "family": "Taylor", "given": "Raymond Leonard" }, "id": "Taylor-Raymond-Leonard", "display_name": "Taylor, Raymond Leonard" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/61Z9-2S65", "abstract": "I: Pure CO gas was rapidly heated by the passage of a shock wave, and the vibrational relaxation time determined from measurements of the time history of the intensity of the 1st overtone transition at 2.35[microns]. The relaxation time was measured over a temperature range of 1400-3000\u00b0K and at pressures from 1 1/2 - 4 atmospheres. At 1400\u00b0K and 1 atm. a value of 650 \u00b1 50 [micro]sec. was obtained. A large impurity effect was discovered and is believed to be caused by traces of water vapor.\r\n\r\nII: The effect of an efficient, near-resonant exchange of vibration energy between O2 and N2 molecules on the vibration relaxation behavior was investigated. The near-resonant and non-resonant vibrations transition probabilities were estimated from current theory. It was shown that the resonant process can provide a catalytic path for the rapid vibrational relaxation of the slower component (N2). The hypothetical calculations are compared with experiment, and\tinterpretation of the \"impurity effect\" of H2O is given in terms of a resonant process." }, { "name": "Thompson, Don Dean", "degree": "PhD", "year": "1960", "title": "I. Molecular Transfer of Non-Equilibrium Nuclear Spin Magnetization. II. Electron Resonance of an Organic Free Radical in Zero Field", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07052006-130411", "creators": [ { "name": { "family": "Thompson", "given": "Don Dean" }, "id": "Thompson-Don-Dean", "display_name": "Thompson, Don Dean" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/073X-P405", "abstract": "Part I contains a new magnetic resonance technique that has been developed to measure rates of fast molecular processes. The method involves the experimental introduction of a nonequilibrium nuclear magnetization in one system, A, and the subsequent measurement of the rate at which rapid molecular processes transfer this nonequilibrium magnetization to a second system, B. Systems A and B may correspond to different chemical sites in a molecule that give rise to a chemical shift, or to sites that are distinct because of electron coupled spin-spin interaction. This technique has been applied to determinations of the rate of proton exchange between ammonium ions in aqueous solution.\r\n\r\nPart II contains a description of a theoretical and experimental investigation of zero field electron spin resonance of malonic acid radicals produced by X-irradiation at room temperature. The radicals produced in a single crystal are oriented in a specific manner. The theory involved predicts six lines of equal intensity, except for a very small Boltzmann factor. Some of these transitions have been found experimentally in a small modulation field at 77\u00b0K. The electron is presumed to \"precess\" in the field of the proton; however, the energy levels cannot be explained classically. A detailed account of the experimental apparatus is given." }, { "name": "Yamane, Tetsuo", "degree": "PhD", "year": "1960", "title": "I. Complexes of Mercury (I) with Polyphosphate and Dicarboxylate Anions and Mercury (II) Pyrophosphate Complexes. II. The Interaction of Mercuric Chloride with Deoxyribonucleic Acid", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202006-091354", "creators": [ { "name": { "family": "Yamane", "given": "Tetsuo" }, "id": "Yamane-Tetsuo", "display_name": "Yamane, Tetsuo" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/D5YM-BF81", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\n\r\nPart I: It has been discovered that mercurous mercury forms complexes with pyrophosphate, tripolyphosphate, oxalate, [...]-dimethylmalonate, and succinate. These complexes are stable towards disproportionation to mercury (II) complexes and mercury. If L(-q) is the anion, the principal complexes are Hg2L2(-2q+2) and Hg2(OH)L(-q+1). The formation constants were determined from the potential of a mercury-mercurous electrode in ligand solutions. Theory and experiment agree that mercurous complexes of ligands (such as NH3 and CN-) which form strong covalent bonds to mercury are unstable towards disproportionation to give mercuric complexes but \"ionic\" chelating ligands can form stable mercurous complexes.\r\n\r\nThe mercury (II) pyrophosphate complex was studied from the potential of a Pt electrode in Hg2(I), Hg(II), pyrophosphate solutions at pH 7-10. The principal species is Hg(OH)(P2O7)(-3), with a formation constant of (2.8\u00b10.6)10(17)M-2.\r\n\r\nPart II: The interaction of mercury (II) with DNA was studied. The formation of the DNA-Hg(II) complex is reversible according to spectrophotometric, viscometric, and biological criteria. Based on the ultraviolet absorption spectra and on the number of protons liberated from DNA during complexation, the binding sites of Hg(II) to DNA are discussed." }, { "name": "Bromberg, J. Philip", "degree": "Masters", "year": "1959", "title": "Experiments in Nuclear Magnetic Resonance", "advisor": "McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242009-075328528", "creators": [ { "name": { "family": "Bromberg", "given": "J. Philip" }, "id": "Bromberg-J-Philip", "display_name": "Bromberg, J. Philip" } ], "advisors": [ { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/F20V-N746", "abstract": "I. Proton and cobalt resonances were observed in single crystals of Co(NH_2CH_2CH_2NH_2)_3Cl_3 ^3H_2_O. The cobalt spectrum consists of a maximum of seven lines whose separation follows a (3cos^2\u03b8 \u2013 1) dependence quite closely where \u03b8 is the angle between the c-axis of the crystal and H_o. The spectrum is fully explained on the basis of quadrupole interaction. Two sets of doublets were found for the proton resonances; an inner, very narrow set following a dependence similar to the cobalt resonance, and a pair of outer broad peaks which overlap the sharp peaks. The narrowness of the central peaks is attributed to internal rotation of one of the proton bearing groups.\r\n\r\nII. A summary is given of various high resolution spectra of compounds related to phosphine.\r\n" }, { "name": "Engleman, Rolf", "degree": "PhD", "year": "1959", "title": "On the Recombination Rate of Iodine Atoms in the Presence of Various Gases", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02062006-102644", "creators": [ { "name": { "family": "Engleman", "given": "Rolf" }, "id": "Engleman-Rolf", "display_name": "Engleman, Rolf" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Wulf", "given": "Oliver Reynolds" }, "id": "Wulf-O-R", "role": "chair", "display_name": "Wulf, Oliver Reynolds" }, { "name": { "family": "Buchman", "given": "Edwin R." }, "id": "Buchman-E-R", "role": "member", "display_name": "Buchman, Edwin R." }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Lauritsen", "given": "Thomas" }, "id": "Lauritsen-T", "role": "member", "display_name": "Lauritsen, Thomas" }, { "name": { "family": "Mazo", "given": "Robert Marc" }, "id": "Mazo-R-M", "role": "member", "display_name": "Mazo, Robert Marc" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KAVE-WG75", "abstract": "The rate of iodine atom recombination in the presence of various gases has been studied by the flash photolysis technique. The temperature dependence of the rate constant has been determined for recombination in helium, hydrogen, benzene, and methyl iodide. The negative temperature dependences are fitted by the form, k∝1/Tn, where n(He) = 0.80, n(H2 = 1.48, n(C6H6 = 2.53, and n(CH3I = 3.24.
\r\n\r\nThe iodine atom recombination rate constant was also measured at 50\u00b0C. for ethyl iodide, hydrogen iodide, carbon monoxide, and nitric oxide. The rate constants relative to helium at 50\u00b0C. are:
\r\n
\r\nHe 1.00 C2H5I 179.
\r\nH2 3.33 NI 21.1
\r\nC6H6 61.1 CO 4.07
\r\nCH3I 88.8 NO >1.4 x 104
\r\n
\r\nNitric oxide appears to be a very efficient third body gas and only a lower limit on the rate constant could be established.
Calculations have been made for some possible mechanisms of iodine atom recombination. A classical three body collision model is proposed for atom recombinations. The classical equations of motion were programmed to be solved numerically on a digital computer and some trajectories were examined.
" }, { "name": "Gordon, Thomas Pascoe", "degree": "PhD", "year": "1959", "title": "I. Studies in the Chemistry of Sodium Dithionite. II. A pH Study of the alpha-Chymotrypsin Catalysed Hydrolysis of Methyl Hippurate", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02012006-154755", "creators": [ { "name": { "family": "Gordon", "given": "Thomas Pascoe" }, "id": "Gordon-Thomas-Pascoe", "display_name": "Gordon, Thomas Pascoe" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JPWX-NF92", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. The kinetics of the air oxidation of sodium dithionite in alkaline solution suggest the transfer of an electron from [...] radical-ions, which are in equilibrium with [...] ions, to molecular oxygen in the rate determining step.\r\n\r\nElectron paramagnetic resonance experiments confirm the presence of [...] radical-ions in equilibrium with [...] ions in solution.\r\n\r\nElectrolytic reduction of sulfurous acid solutions at constant potential in the range -0.7v to -0.9v produces dithionite at constant current efficiency.\r\n\r\nThermal decomposition of dithionite solutions occurs slowly at first, apparently by a free radical mechanism, and then rapidly, indicating a degenerate chain-branching mechanism.\r\n\r\nPart II. The results of a pH study of the [alpha]-chymotrypsin catalysed hydrolysis of methyl hippurate at three different added salt concentrations are consistent with the postulation of ionizing groups at the active site of the enzyme with [...] values 6.9 +/- 0.1 and 8.6 +/- 0.1. Important interactions of added salt and hydrogen ion concentrations are not indicated.\r\n\r\nHippuric acid and L-tryptophan are shown to be competitive inhibitors.\r\n\r\nThe development of a negative charge at or near the active site of the enzyme above pH 8 is confirmed." }, { "name": "Kalvinskas, John Joseph", "degree": "PhD", "year": "1959", "title": "The Partial Oxidation of n-Butane", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172006-085228", "creators": [ { "name": { "family": "Kalvinskas", "given": "John Joseph" }, "id": "Kalvinskas-John-Joseph", "display_name": "Kalvinskas, John Joseph" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z5WH-WZ51", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe study of the partial oxidation of n-butane was carried out in a porcelain reactor having an inside diameter of 1 inch, and an adjustable length from 0 to 30 inches. The tube was equipped with traverse gear to allow measurement of both temperature and velocity gradients across the outlet section. Electric heaters were mounted on the wall of the reactor tube for obtaining the desired reaction temperatures. Supplementary to the reactor, equipment was provided to meter and preheat the butane and oxygen. A gas chromatograph was developed to provide analysis of the expected product gases, namely CH4, C2H6, C2H4, C3H6, C3H8, C4H8, C4H10, CO, CO2, H2, H2O, AND O2. The composition of the product stream from the reactor was correlated with the reaction variables of time, temperature, and inlet oxygen composition by means of a multiple regression analysis. Also, by the same technique, the degree of conversion of butane was studied on the basis of assumed rate equations.\r\n\r\nThe reaction rate data for the n-butane oxidation were correlated on the basis of the following rate equation: [...]. A minimum reaction rate for the oxidation of n-butane was observed at [...].\r\n\r\nThe thermal decomposition data were found to correlate best on the basis of the following second order rate equation: [...].\r\n\r\nThe application of the rate equations for the partial oxidation and the thermal decomposition of n-butane is restricted to the range of the experimental investigation, namely one atmosphere, 360\u00b0-760\u00b0C and 0-25% inlet oxygen concentration.\r\n\r\nThe correlation of the product distribution data by means of the multiple regression analysis is represented graphically as moles of component formed per 100 moles of butane feed versus inlet oxygen concentrations for several parametric values of retention time and temperature over the range of conditions investigated." }, { "name": "Manatt, Stanley Lawrence", "degree": "PhD", "year": "1959", "title": "Part I. 3-Phenylcyclobut-2-enone and 3-Phenylcyclobutanone Derivatives. Part II. Calculation of the Delocalization Energies of Some Small-ring Systems Employing the Simple Molecular Orbital Treatment", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172006-102844", "creators": [ { "name": { "family": "Manatt", "given": "Stanley Lawrence" }, "id": "Manatt-Stanley-Lawrence", "display_name": "Manatt, Stanley Lawrence" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1JFX-G176", "abstract": "Part I:\r\n\r\nCatalytic hydrogenation of either 1,1-difluoro-2,2dichloro-3-phenylcyclobutene or 1,1-difluoro-2,2-dichloro-3-phenylcyclobutane gives 1,1-difluoro-3-phenylcyclobutane. Bromination of this compound with N-bromosuccinimide followed by dehydrobromination with one mole of ethanolic potassium hydroxide gives good yields of 1,1-difluoro-3-phenylcyclobut-2-ene. Careful hydrolysis of this material with concentrated sulfuric acid gives 3-phenylcyclobut-2-enone. Treatment of 3-phenylcyclobut-2-enone with dilute aqueous sodium hydroxide opens the ring to give benzoylacetone. Ring-opening of 3-phenylcyclobut-2-enone in acetic acid gives [beta]-methyl-cinnamic acid. Reduction of 3-phenylcyclobut-2-enone by sodium borohydride in methanol gives 3-phenylcyclobut-2-enol.\r\n\r\nThe reaction of phosphorus pentachioride with several 3-phenylcyclobut-2-enones was found to give good yields of gem-dichlorides. Concentrated sulfuric acid hydrolysis of these gem-dichlorides in most cases regenerated the corresponding 3-phenylcyclobut-2-enone.\r\n\r\nCatalytic reduction of 2-chloro-3-phenylcyclobut-2-enone gives 3-phenylcyclobutanone. The reduction of this ketone by several reagents is described. Reduction of 2-chloro-3-phenylcyclobut-2-enone by sodium borohydride in methanol gives 2-chloro-3-phenylcyclobut-2-enol. Catalytic hydrogenation of this alcohol gives cis-3-phenylcyclobutanol.\r\n\r\nThe rates of the acid-catalyzed hydrolysis in \"80%\" acetone-water, of the 4-nitrobenzoates of cinnamyl alcohol, methylstyrylcarbinol, cyclobutanol, cis- and trans-3-phenyl-cyclobutanol, 2-chloro-3-phenylcyclobut-2-enol, and 3-phenylcyclobut-2-enol, are described. The importance of 1,3-interaction in the 3-phenylcyclobut-2-enyl carbonium ion is discussed. It has been concluded that the acid-catalyzed hydrolysis of 4-nitrobenzoate esters is not a satisfactory means of studying relative carbonium ion stabilities.\r\n\r\nPart II: \r\n\r\nThe simple molecular orbital method (LCAO) has been used to calculate the electron delocalization energies of number of small-ring compounds in order to see which might be predicted to be reasonably stable on theoretical grounds. Included are a number of phenyl-substituted cyclobutadienes, benzocyclobutadienes, cyclobutadienoquinones, cyclobutenes, cyclobutenones, methylenecyclopropenes, cyclopropenones, phenyl-substituted cyclopropenyl cations, and several miscellaneous cyclobutenyl cations. The qualitative significance of the results is discussed." }, { "name": "McGriff, Richard Bernard", "degree": "Masters", "year": "1959", "title": "The Synthesis of 1-Keto-3-Carbomethoxy-1,2,3,4-Tetrahydroisequinoline", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05102010-153156629", "creators": [ { "name": { "family": "McGriff", "given": "Richard Bernard" }, "id": "McGriff-Richard-Bernard", "display_name": "McGriff, Richard Bernard" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B06Z-W247", "abstract": "The preparation of 1-keto-3-carbomethoxy-1,2,3,4-tetrahydroisequinoline byt wo routes is described. The first involves hydrolysis of the adduct of a-bromo-o-tolunitrile and acetamidomalinicester to 1-keto-3-carboxy-1,2,3,4-tetrahydroisequinoline. Esterification of this acid yields the desired ester. The second route involves the condensation of phenylalanine with formaldehyde to form 3-carboxy-1,2,3,4-tetrahydroisequinoline. The benzoyle derivative of this compounds is smoothly oxidized by cold permanganate to N-benzoyl (o-carboxyphenyl) alanine, wich is convert by acid hydrolysis to 1-keto-3-carboxy-1,2,3,4-tetrahydroisequinoline and benzoic acid. Preliminary experiments show that 1-keto-3-carboxy-1,2,3,4-tetrahydroisequinoline is hydrolyzed by a-chymotrypsin, and indicate that both forms are hydrolyzed,albeit at differing rates." }, { "name": "McKay, Richard Alan", "degree": "PhD", "year": "1959", "title": "I. Measurement of the Latent Heat of Vaporization of Lighter Hydrocarbons - Values for Normal Octane. II. Volumetric and Phase Behavior in the Ethane-Propene System", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172006-102234", "creators": [ { "name": { "family": "McKay", "given": "Richard Alan" }, "id": "McKay-Richard-Alan", "display_name": "McKay, Richard Alan" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/049T-H779", "abstract": "Part I: A calorimeter, originally built to measure the heat capacities of liquids at temperatures from 100 to 400\u00b0F and at pressures up to 1000 pounds per square inch, was modified to extend its utility to include the measurement of latent heats of vaporization of liquids over the same range of conditions. A description of the apparatus and of the procedure used for determining experimentally the heat of vaporization is presented in detail.\r\n\r\nExperimentally determined values of the latent heat of vaporization of n-octane at temperatures from 100 to 340\u00b0F are presented. The results at the lower temperatures agree with the measurements of the National Bureau of Standards within 0.09 per cent. At the higher temperatures the results are within 2 per cent of the values calculated from volumetric and phase behavior data.\r\n\r\nPart II: The molal volumes of three mixtures of ethane and propene were measured at pressures up to 10,000 pounds per square inch in the temperature interval between 10 and 400\u00b0F. The compositions of the coexisting phases were established throughout the two-phase region of this system at temperatures from 10 to 160\u00b0F." }, { "name": "Rinker, Robert Gene", "degree": "PhD", "year": "1959", "title": "I. Studies in the Chemistry of Sodium Dithionite. Il. A Preliminary Study of the Catalyzed Addition of Hydrogen Chloride to Vinyl Chloride in a Stirred Reactor", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172006-104009", "creators": [ { "name": { "family": "Rinker", "given": "Robert Gene" }, "id": "Rinker-Robert-Gene", "display_name": "Rinker, Robert Gene" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/VS2K-BE10", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I: Rate studies of the air oxidation and thermal decomposition of aqueous sodium dithionite, Na2S2O4, were conducted. These experiments were supplemented by studies of the electron-paramagnetic-resonance properties and the electrolytic formation of dithionite.
\r\n\r\nIn the air-oxidation experiments, the overall rate was observed to have half-order dependence on the dithionite concentration and a first-order dependence on molecular oxygen concentration. This could be explained mechanistically on the basis of an instantaneous equilibrium reaction between dithionite and the [...] radical ion.
\r\n\r\nThe results of the EPR studies confirmed the presence of [...] and established the existence of equilibrium between the free radical and dithionite.
\r\n\r\nThe electrolytic production of dithionite from a bisulfite solution gave current efficiencies of 75% but did not show conclusively that the reduction was either a one- or two-electron transfer process.
\r\n\r\nIn the thermal decomposition studies, the overall rate showed a 3/2-order dependence on dithionite concentration and a half-order dependence on hydrogen ion concentration. A mechanism involving [...] or a protonated form of the radical in a reaction with the dimer appeared to fit the observed facts.
\r\n\r\nPart II: A preliminary rate study of the catalyzed addition-reaction between HCl and vinyl chloride was conducted in a continuous-flow stirred reactor. Gas-phase chromatography was used in the analysis of the chemical constituents.
\r\n\r\nThe rate data for the primary reaction appeared to fit, at least empirically, a second-order rate law with respect to the forward reaction.
\r\n\r\nIn addition to the primary reaction, fouling of the catalyst, ZnCl2, was also observed, but the decreasing conversion as a function of catalyst-exposure time reached an asymptotic value greater than zero. This indicated that the catalyst fouling was an irreversible dual-site mechanism.
\r\n\r\nThe fact that 1,1 dichloroethane was formed exclusively in the primary reaction eliminated the possibility of a free-radical reaction. Because of the relatively low rate of reaction, even in the presence of a catalyst, the addition probably occurred by a four-center-type mechanism.
" }, { "name": "Sharts, Clay Marcus", "degree": "PhD", "year": "1959", "title": "Some Fluorinated Cyclobutenes and their Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02232006-152633", "creators": [ { "name": { "family": "Sharts", "given": "Clay Marcus" }, "id": "Sharts-Clay-Marcus", "display_name": "Sharts, Clay Marcus" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1VHF-D738", "abstract": "Cyclobutene structures were established for the cycloaddition products of 1-ethynylcyclohex-l-ene with trifluorochloroethylene or difluorodichloroethylene. The orientations of the addends were in accord with theories developed previously.\r\n\r\nHydrolysis of the fluorinated cyclobutenes with sulfuric acid gave halogen-substituted cyclohex1encyclobutenones as well as cyclohex-1-enylcyclobutadienoquinone. Some halide displace merit reactions of the adducts were found to give, in general, products corresponding to reaction by SN2 mechanisms. Trifluro-2-chlaro-3-(cyclox-1-enyl)-cyclobutene gave Dials-Alder adducts with maleic anhydride and dicarbethoxyacetylene. 1,1-Difluoro-2,4-dicloro-3-(cyclohex-1-enyl)-cyclobutene with triethylamine underwent dehydrohalogenation and afforded, by means of an unusual rearrangements, 2-fluoro-1,3-dichloro-5,6,7,8-tetrahydronaphthalene.\r\n\r\nThe nuclear magnetic resonance (NMR) spectra of the fluorinated cyclobutenes and cyclobutenones showed spectra which were anomalous in terms of simple NMR theory but which could be explained by assumption of cross-ring spin-spin coupling between hydrogen and fluorine." }, { "name": "Silver, Marc Stamm", "degree": "PhD", "year": "1959", "title": "Intermediates in Carbonium Ion Reactions of Methyl-Substituted Cyclopropylcarbinyl Cyclobutyl and Allylcarbinyl Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172006-092624", "creators": [ { "name": { "family": "Silver", "given": "Marc Stamm" }, "id": "Silver-Marc-Stamm", "display_name": "Silver, Marc Stamm" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PZ7V-9K90", "abstract": "The products of the nitrous acidination of 2-methylcyclobutylamine, 3-methylcyclobutylamine, 2-methylcyclopropylcarbinylamine, cyclopropylmethylcarbinylamine, allylmethylcarbinylamine and crotylcarbinylamine have been determined. In addition, studies on the rates of solvolysis of suitable derivatives of the same carbon skeleton have been carried out. The experimental data are reminiscent of those reported for the reactions of unsubstituted cyclobutyl, cyclopropylcarbinyl and allylcarbinyl compounds and are interpreted in terms of cationic intermediates closely related to those proposed for the latter substances. In the present case, the intermediates are most reasonably represented as three non-classical, unsymmetrical, non-equivalent pyramidal ions, \"bicyclobutonium\" ions." }, { "name": "Smith, Darwin Waldron", "degree": "PhD", "year": "1959", "title": "Some Electron Diffraction Studies: I. Electron Diffraction Studies of Some Heavy Metal Hexafluorides. II. The Molecular Structure of Gaseous N\u2082O\u2084. Ill. Applications of the Method of Least Squares in Electron Diffraction Investigations", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02132006-132126", "creators": [ { "name": { "family": "Smith", "given": "Darwin Waldron" }, "id": "Smith-Darwin-Waldron", "display_name": "Smith, Darwin Waldron" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A9G6-3H34", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. An electron diffraction investigation has been made by the sector-microphotometer method of WF6, OsF6, IrF6, UF6, NpF6 and PuF6. The photographs of all these compounds exhibit a phase shift anomaly which gives rise to apparently assymetric structures, the anomaly setting in at smaller angles [...] of scattering for the heavier molecules and at smaller values of q = (40/[...])sin [...]/2 the greater the electron wavelength. There is good evidence for the symmetrical octahedral structure of all the compounds. The metal-fluorine distances were found to be (in Angstrom units) l.833(W-F), l.831(Os-F), l.830(Ir-F), 1.996(U-F), l.981(Np-F), and l.971(Pu-F).\r\n\r\nPart II. An electron diffraction molecular structure determination of gaseous N2O4 has shown that the N-O distance, the N-N distance, and the ONO bond angle are 1.177 A, 1.752 A, and 134.8\u00b0 respectively. The molecule is planar, which is surprising in view of the long N-N bond.\r\n\r\nPart III. A structure refinement procedure, which was applied to the above compounds, has been programmed for the Burroughs 205 computer. It involves the fitting of a theoretical intensity curve to the experimental one." }, { "name": "Wolf, John Peter", "degree": "PhD", "year": "1959", "title": "I. The Alpha-Chymotrypsin-Catalyzed and Base-Catalyzed Hydrolysis of Some Substituted Glycine Esters and Related Compounds. II. The Nature and Properties of the Enzyme-Substrate Complex Produced under Conditions of Very High Substrate Concentrations. III. A Hypothesis Concerning Alpha-Chymotrypsin-Substrate Complexes", "advisor": "Niemann, Carl G.; Metcalf, Robert Lee", "url": "https://resolver.caltech.edu/CaltechETD:etd-02212006-134559", "creators": [ { "name": { "family": "Wolf", "given": "John Peter" }, "id": "Wolf-John-Peter", "display_name": "Wolf, John Peter" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." }, { "name": { "family": "Metcalf", "given": "Robert Lee" }, "id": "Metcalf-R-L", "role": "advisor", "display_name": "Metcalf, Robert Lee" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KPJF-0G56", "abstract": "A series of substituted glycogen esters have been evaluated as substrates for [alpha]-chymotrypsin. The second order base-catalyzed hydrolysis constants for these compounds have also been determined.\r\n\r\nFour substrates for [alpha]-chymotrypsin have been found to exhibit unusual kinetic behavior at very high concentrations in the presence of [alpha]-chymotrypsin. It has been shown that these data can be the result of two molecules of substrate combining with each enzyme active site.\r\n\r\nA hypothesis concerning the enzyme-substrate complex is offered which helps to correlate the data given in this work." }, { "name": "Bowersox, David Frederic", "degree": "PhD", "year": "1958", "title": "Potentiometric and Coulmetric Studies and the Mechanisms of the Precipitation of Metal Sulfides from Acid Solutions by Thioacetamide", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-095819", "creators": [ { "name": { "family": "Bowersox", "given": "David Frederic" }, "id": "Bowersox-David-Frederic", "display_name": "Bowersox, David Frederic" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/C5X1-V153", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe standard potential of the half cell [...] has been measured in cells with negligible liquid junction potentials. The value calculated at 25[degrees]C. in solutions 0.2 to 4.0 volume formal in perchloric acid is -0.711 volt; the value for a hypothetical half cell 1 molal in iodine is -0.625 volt. The constant for the reaction [...] was calculated from solubility measurements to be 0.87.\r\n\r\nConditions under which electrolytically generated chlorine can be employed for the coulometric titration of iodide to iodine monocyanide have been determined. Titrations in the presence of bromide were made. One to three mg. of iodide were determined with an accuracy of 0.1%.\r\n\r\nThe conditions were determined under which tetrapositive lead can be generated quantitatively. The determination of lead(IV) with electrolytically generated iron(II) was proved feasible. In confirmatory titrations with ferrous ion an accuracy of 0.1% was attained in the determination of quantitles of lead(IV) in the range from 0.25 to 1.50 microgram. This showed the feasibility of alternately generating lead(IV) and iron(II) in a coulometric cell, that is, the use of the lead-iron system as dual intermediates.\r\n\r\nAttempts to titrate glycols with excess lead(IV) were not successful because the reaction of glycols with lead(IV) was slow and incomplete when the reactants were present in low concentrations.\r\n\r\nThe precipitation of cadmium as sulfide from acid solutions by thioacetamide has been studied. In solutions having pH values of 2 or less the rate of precipitation is controlled by the rate of hydrolysis of the thioacetamide to give hydrogen sulfide, and is first order with respect to the hydrogen ion and to the thioacetamide concentrations.\r\n\r\nIn solutions having pH values from 6.3 to 3.3 a direct reaction occurs in which the rate of cadmium sulfide precipitation is first order with respect to the hydrogen ion concentration. The velocity constant for the expression [...] is [...] in 0.15 M sodium formate solution. The energy of activation for this reaction was calculated to be 20.8 kcal. per mole.\r\n\r\nThe rate of precipitation of cadmium as sulfide from acid solutions by thioacetamide in this pH range is slower in the presence of chloride. At a pH of 4.0 this effect has been quantitatively studied at 25[degrees] and 90[degrees]C. with chloride concentrations from [...]. The data obtained conforms to the rate expression [...] where [...] and [...] are [...] and [...] [...] mole[...] min[...], respectively, at 90[degrees]C. The validity of these proposed constants was checked by the calculation of an equilibrium constant for the reaction [...] at each chloride concentration by the use of these constants. The value of this constant is [...] mole, per liter at 90[degrees]C.\r\n\r\nThe precipitation of nickel sulfide by thioacetamide has been studied in solutions in which the hydrogen ion concentration was maintained at values from [...]. Rate measurements have shown that the precipitation reaction conforms to the expression for the direct reaction [...] where the velocity constant is [...] at 90[degrees]C. Nickel sulfide was precipitated by the direct reaction with thioacetamide at hydrogen ion concentrations at which precipitation by hydrogen sulfide is not possible. The energy of activation for the reaction was calculated to be 20.8 kcal. per mole. Precipitation by the hydrolysis of thioacetamide was not observed.\r\n\r\nThe effectiveness of the separation of lead(II) and cadmium(II) from nickel(II) by the use of thioacetamide in solutions at 90[degrees]C. has also been studied. It was found that nickel sulfide was formed only by the direct reaction shown above. The precipitation of nickel sulfide was independent of the concentration of lead(II) or of cadmium(II), or of the amount of hydrogen sulfide in the reaction solution. It was found that the quantity of nickel sulfide which precipitated with the lead or cadmium sulfide was insignificant under certain conditions, and that an effective separation can be made.\r\n\r\nRate measurements were made to determine the mechanisms of the precipitation of zinc sulfide from acid solutions by thioacetamide. Two mechanisms, similar to those found for lead and cadmium, were observed.\r\n\r\nIn solutions having pH values of 1 or 2, the rate of precipitation of zinc sulfide is first order with respect to both the thioacetamide and hydrogen ion concentrations. The second order velocity constant for this reaction was found to be [...] at 90[degrees}C., the same value as that reported for cadmium and lead.\r\n\r\nIn solutions having pH values from 6.3 to 2.5 the precipitation is first order with respect to both the thioacetamide and the zinc(II) concentrations and inversely half order with respect to the hydrogen ion concentration. The velocity constant for the expression\t[...] was found to be [...] in solutions 0.30 M in sodium formate, and the energy of activation for the reaction was calculated to be 20.1 kcal. per mole. This type of precipitation is similar to that observed for lead, cadmium, and nickel in the same pH range. The value of the energy of activation is almost equal to those calculated for the precipitation of cadmium and nickel.\r\n\r\nSeparations of lead(II) from zinc(II) by the precipitation of lead sulfide from solutions 0.3 M in hydrogen ion and 0.6 M in chloride were made with thioacetamide or hydrogen sulfide at 90[degrees]C. The two methods were comparable in effectiveness." }, { "name": "Bush, Warren Van Ness", "degree": "PhD", "year": "1958", "title": "A Study of the Boron Trifluoride Complexes of Some Carotenoid Hydrocarbons and the Products of their Hydrolytic and Alcoholytic Cleavage", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-100851", "creators": [ { "name": { "family": "Bush", "given": "Warren Van Ness" }, "id": "Bush-Warren-Van-Ness", "display_name": "Bush, Warren Van Ness" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N1HM-3215", "abstract": "Formation of a deeply-colored [alpha]-carotene - boron trifluoride complex, by means of boron trifluoride etherate, and subsequent hydrolysis of the complex result mainly in the formation of 4-hydroxy-[alpha]-carotene, indicating that, under the conditions applied, only the [beta]-ionone end of the complex is reactive; ethanolysis gave the corresponding ethoxy derivative. The structures of these two compounds and some of the other reaction products were clarified. On this basis the structure of the BF3-complex has also been established, and a mechanism for its hydrolysis and alcoholysis was postulated. The length of the resonating system within the proposed complex is consistent with the observed deep blue color.\r\n\r\nLycopene and [gamma]-carotene were studied along similar lines. The observed formation of 5,6-dihydroxy-5,6-dihydrolycopene by hydrolysis of the lycopene complex can be explained by means of a structure and a hydrolysis mechanism both similar to those of the [alpha]-carotene complex.\r\n\r\nThe formation of 4-hydroxy-[gamma]-carotene by hydrolysis of the [gamma]-carotene complex is in accordance with an analogous structure and hydrolysis mechanism. The [beta]-ionone end of the [gamma]-carotene complex appears to be more reactive than the [psi]-ionone end.\r\n\r\nThe cis-trans isomerization of 4-hydroxy-, 4-keto-, and 4-ethoxy-[alpha]-carotene as well as 5,6-dihydroxy-5,6-dihydrolycopene was studied." }, { "name": "Chesnut, Donald Blair", "degree": "PhD", "year": "1958", "title": "An X-Ray Diffraction Study of the Crystal Structure of Cyclopropane Carbohydrazide. II. A Theory of Isotropic Hyperfine Interactions in \u03c0-Electron Radicals", "advisor": "Marsh, Richard Edward; McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-133003", "creators": [ { "name": { "family": "Chesnut", "given": "Donald Blair" }, "id": "Chesnut-Donald-Blair", "display_name": "Chesnut, Donald Blair" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" }, { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M4K6-BK57", "abstract": "NOTE: Text or symbols not renderable in plain ASCII arre indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. The crystal structure of cyclopropanecarbohydrazide has been determined and refined using Fourier and least-squares methods. The crystals are monoclinic with [...] and [...]; the space group is [...], and there are four molecules in the unit cell. The molecules are held together by chains of NH [...] O hydrogen bonds running parallel to the b axis and by a network of weak NH [...] N bonds running along the twofold screw axes which relate the terminal nitrogen atoms. The value of [...] for the C-C distance between the cyclopropane and carbonyl groups suggests the presence of a fairly strong conjugative effect.\r\n\r\nII. Indirect proton hyperfine interactions in [pi]-electron radicals are first discussed in terms of a hypothetical C H fragment which holds one unpaired [pi]-electron and two [sigma]-C H bonding electrons. Molecular orbital theory and valence bond theory yield almost identical results for the unpaired electron density at the proton due to exchange coupling between the [pi]-electron and the [sigma]-electrons. The unpaired electron spin density at the proton tends to be antiparallel to the average spin of the [pi]-electrons, and this leads to a negative proton hyperfine coupling constant.\r\n\r\nThis theory of indirect hyperfine interaction in the C H fragment is generalized to the case of polyatomic [pi]-election radical systems - e.g., large planar aromatic radicals. In making this generalization there is introduced an unpaired [pi]-electron spin density operator [...], where N refers to carbon atom N . Molecular orbital theory without configuration interaction gives zero order spin densities [...] which are either positive or zero. If [...] is positive, the calculated proton N hyperfine coupling constant is negative, and negative paramagnetic proton nuclear resonance shifts are predicted in such cases.\r\n\r\nCertain aromatic radicals (e.g., odd-alternate aromatics) contain one or more carbon atoms [...] for which the zero order spin density is exactly zero, [...]. In such cases [pi]-[pi] configuration interaction gives rise to a first order density at atoms [...], [...], which may be positive or negative, leading to negative or positive hyperfine couplings of the protons [...].\r\n\r\nA previously proposed linear relation between the hyperfine splitting due to proton N, [...], and the unpaired spin density at N, [...] is derived using molecular orbital theory without [pi]-[pi] configuration interaction, assuming the [sigma]-[pi] coupling to be first order. It is shown that even when the effects of [pi]-[pi] configuration interaction are included in the calculations, the above simple linear relation is still exact, provided the [pi]-[pi] configuration interaction is treated as a first order perturbation on the [pi]-part of the wave functions and one assumes the excitation energies of the [sigma]-[pi] excited states to be approximately the same." }, { "name": "Claus, Albert Charles", "degree": "PhD", "year": "1958", "title": "The lntermetallic Compounds in the Silver-Strontium System and their Crystal Structures", "advisor": "Bergman, Gunnar B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09232004-133238", "creators": [ { "name": { "family": "Claus", "given": "Albert Charles" }, "id": "Claus-Albert-Charles", "display_name": "Claus, Albert Charles" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Gunnar B." }, "id": "Bergman-Gunnar-B", "role": "advisor", "display_name": "Bergman, Gunnar B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XNZ7-WX84", "abstract": "Four congruently melting intermetallic compounds with the compositions Ag4Sr, Ag5Sr3, AgSr, and Ag2Sr3 respectively have been reported to exist in the silver-strontium system. In the present investigations the crystal structures of all four compounds were studied by application of X-ray diffraction techniques. The first compound was found to have the quite common CaZn5 structure and the composition is Ag5Sr rather than Ag4Sr. The structure of the second compound has orthorhombic symmetry. It was not determined but there can hardly be any doubt that it is closely related to the C32 type (AlB2 structure) and that the composition of the compound is Ag2Sr and not Ag5Sr3. The third compound also has a structure of orthorhombic symmetry and is of a type not observed previously. The composition is correctly represented by the formula AgSr. The structure is partially disordered. The structure of the fourth compound was not determined in detail. It could, however be established that it is very closely related to the AgSr structure. The composition Ag2Sr3 could be neither confirmed nor rejected. The structure has orthorhombic symmetry." }, { "name": "Cole, Terry", "degree": "PhD", "year": "1958", "title": "Studies of Free Radicals at 4.2\u00b0K by Electron Paramagnetic Resonance", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09222004-134112", "creators": [ { "name": { "family": "Cole", "given": "Terry" }, "id": "Cole-Terry", "display_name": "Cole, Terry" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RRD7-HJ20", "abstract": "Electron paramagnetic resonance spectra have been observed from the products of gaseous microwave electric discharges frozen at 4.2[degrees]K. The gases investigated were N2 and NH3.
\r\n\r\nThe spectrum of the frozen nitrogen discharge products plainly indicates the presence of atomic nitrogen whose half life in the solid is greater than ten hours. Dilution of the nitrogen in an inert matrix of argon is found to cause considerable line broadening. When the nitrogen discharge products are passed over mercury prior to condensation, a complex spectrum of 11 lines is obtained.
\r\n\r\nThe spectrum of NH3 discharge products indicates the presence of atomic nitrogen and hydrogen. Data concerning the presence of NH and NH2 radicals are not conclusive.
\r\n\r\nA description of the apparatus and techniques developed for these experiments is included.
\r\n" }, { "name": "DeMore, William Bailey", "degree": "PhD", "year": "1958", "title": "Chemical Processes in Rigid Media at Low Temperatures", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-114343", "creators": [ { "name": { "family": "DeMore", "given": "William Bailey" }, "id": "DeMore-William-Bailey", "display_name": "DeMore, William Bailey" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZR35-PF54", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAn apparatus has been developed for studying chemical processes in rigid inert media at low temperatures (4.2[degrees]K, 20[degrees]K., or 77[degrees]K. The materials to be studied are deposited as a thin film on a cold surface by vacuum effusion. Infrared and visible-ultraviolet absorption spectroscopy were used for detection.\r\n\r\nThe CS molecule and the benzyl radical were isolated in hydrocarbon films at 77[degrees]K. CF2 and NO3 were trapped in films of nitrogen at 20[degrees]K. Visible-ultraviolet spectra of these species were obtained.\r\n\r\nThe photolysis of diazomethane in films of nitrogen at 20[degrees]K has been extensively studied. By adding various reactants to the films, evidence for the following reactions has been obtained: [...].\r\n\r\nOzone in nitrogen films is decomposed by ultraviolet light and some nitrous oxide is produced. This is attributed to the reaction [...], which is a hot atom reaction.\r\n\r\nIrradiation of mixtures of O3 and NO2 in nitrogen films yields NO3, N2O5, NO, and HNO3 (due to the presence of water). Irradiation of NO2 and O2 in nitrogen films yields O3 and NO.\r\n\r\nThe results obtained indicate that (1) hot atom or radical reactions occur in the film, and (2) photochemical fragments are energy-rich and may diffuse for a distance of at least a few molecular diameters in the rigid media." }, { "name": "Gordon, Derck Alexander", "degree": "PhD", "year": "1958", "title": "I. Measurement of Diamagnetic Anisotropy in Single Crystals. II. The Crystal Structure of Monomethylurea", "advisor": "Marsh, Richard Edward", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-143941", "creators": [ { "name": { "family": "Gordon", "given": "Derck Alexander" }, "id": "Gordon-Derck-Alexander", "display_name": "Gordon, Derck Alexander" } ], "advisors": [ { "name": { "family": "Marsh", "given": "Richard Edward" }, "id": "Marsh-R-E", "role": "advisor", "display_name": "Marsh, Richard Edward" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WHH0-JE78", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA method of determining the magnetic anisotropy of single crystals by measuring the torque exerted by a homogeneous magnetic field has been studied. Particular attention was paid to the overcoming of errors in the method of measurement, to the determination of the torsion constants of thin quartz fibers used as torque-measuring devices and to the method of mounting and orienting crystals for use in the investigation. It is believed that the newly devised procedures greatly increase the precision, accuracy and convenience of the measurements.\r\n\r\nMeasurements of diamagnetic anisotropy in crystals of several simple organic and inorganic compounds and in two protein samples were made and are discussed in terms of crystal and molecular structure.\r\n\r\nSome time was spent in an effort to determine the crystal structure of monomethylurea using X-ray diffraction data in the literature and a trial structure suggested by the results of diamagnetic anisotropy measurements. A serious error in the published data was discovered, necessitating the rejection of much of the work. The intensities of the[...] [...] and [...] diffraction maxima were redetermined, and some conclusions about the crystal structure were drawn. Sufficient work has not been done to permit assignment of parameters to the individual atoms." }, { "name": "Huffman, Robert Eugene", "degree": "PhD", "year": "1958", "title": "I. Kinetics of the Thermal Decomposition of Nitrogen Dioxide Behind Shock Waves. II. Kinetics of the Ferrous Ion-Oxygen Reaction in Sulfuric Acid Solution", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10072004-150337", "creators": [ { "name": { "family": "Huffman", "given": "Robert Eugene" }, "id": "Huffman-Robert-Eugene", "display_name": "Huffman, Robert Eugene" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/53F3-0D68", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nShock waves into argon containing a small amount of N02 have been used to study the kinetics of the thermal decomposition of nitrogen dioxide from 1100 to 2300[degrees]K. Mole fractions of N02 varied from 2.8 x 10[...] to 1.5 x 10[...]; the ratio argon/N02 varied from 5.6 to 350; the argon concentration varied by a factor of twenty; and the N02 concentration varied by a factor of ten. Under these conditions, the results indicate that two separate reaction mechanisms are operative. One path has the rate law [...] with [...] and is apparently the unimolecular decomposition of N02 at the second order limit. The other path has the rate law [...] with an activation energy of 22[plus or minus]6 kcal/mole. This path is believed to be the bimolecular decomposition of N02 first observed by Bodenstein. However, extrapolation of this mechanism to the shock tube temperatures gives results about eight times too low. The reason for this discrepancy is not known. One interpretation is that there is another bimolecular reaction path for the decomposition of N02. A good possibility for such a path is the bimolecular formation of N02, recently postulated by Ashmore and Levitt, and its subsequent rapid decomposition, either by reaction with N02 or by unimolecular dissociation into N02 and 0. This discrepancy has also recently been observed by Steinburg and Lyon in a concurrent investigation. However, the mechanism and conclusions of that study are not supported by the present investigation.\r\n\r\nPart II consists of a paper that has already been published on the kinetics of the ferrous ion-oxygen reaction in sulfuric acid solution.\r\n" }, { "name": "King, James", "degree": "PhD", "year": "1958", "title": "I. Magnetic resonance studies of paramagnetic solutions. II. Kinetics of the ferrous iron-oxygen reaction in acidic phosphate-pyrophosphate solutions\r\n\r\nI. Magnetic Resonance Studies in Paramagnetic Solutions. II. Kinetics of the Ferrous Iron-Oxygen Reaction in Acidic Phosphate-Pyrophosphate Solutions", "advisor": "Davidson, Norman R.; McConnell, Harden M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11012004-144834", "creators": [ { "name": { "family": "King", "given": "James" }, "id": "King-James", "display_name": "King, James" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." }, { "name": { "family": "McConnell", "given": "Harden M." }, "id": "McConnell-H-M", "role": "advisor", "display_name": "McConnell, Harden M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/266P-TV05", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe techniques of Nuclear Magnetic Resonance and Electron Paramagnetic Resonance have been used to study the interaction of electrons and nuclei in solution. Results of a study of the interaction between paramagnetic manganeous ions [...] and water molecules indicate that the abnormally large ratio of the proton relaxation times, [...], previously found in the system, can be essentially explained by an isotropic hyperfine interaction between the electrons and protons in the solution. When this interaction is destroyed by complexing the [...] with the hexadentate ligand, ethylenediaminetetraacetate [...], or with the tetradentate ligand, nitrilotriacetate [...], [...] is increased slightly and [...] is increased markedly, so that [...] = [...] and the ratio is unity as expected.\r\n\r\nAn isotropic hyperfine interaction is also found to exist in ferric fluoride solutions. The interaction between the electrons of the ferric ion and the fluoride nuclei produces characteristic resonance spectra for the different complexes in the system. From a study of the system, the existence in solution of the [...] complex is definitely established. A value for the dissociation constant of the complex is obtained and an upper limit is set for the rate of exchange of complexed and uncomplexed fluorides in the system. The amount of 2s - character of the [...] bond in the ferric fluoride complexes is also obtained.\r\n\r\nThe shifts, due to the magnetic susceptibility in the system are treated in Section IV. It is found that the shifts deviate from the values one would expect if the susceptibility in the system were isotropic. Both organic and inorganic systems are treated. The method used to measure these small shifts is also described.\r\n\r\nPart II consists of a published article on the oxygenation of ferrous ion in acidic phosphate-pyrophosphate solutions." }, { "name": "Kraus, Bernhard August", "degree": "Masters", "year": "1958", "title": "The Photoisomerization of Azobenzene at 77\u00b0K in a Rigid Solvent and at Room Temperature", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05032010-130844301", "creators": [ { "name": { "family": "Kraus", "given": "Bernhard August" }, "id": "Kraus-Bernhard-August", "display_name": "Kraus, Bernhard August" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RDAG-4773", "abstract": "The photoisomerization of azobenzene has been studied at room temperature in ethanol and P. Me.H., and at 77\u00b0K in a P.Me.H. rigid solvent. At room temperature, the photostationary state composition is 74% trans (and 26 % cis) in ethanol and 77 % trans in P.Me.H.; it is 98 % trans in P.Me.H. at 77\u00b0K. It has been shown that both the trans to cis and the cis to trans photoisomerizations occur in the rigid solvent at liquid nitrogen temperature.\r\n\r\nThe spectra and molar extinction coefficients have been determined at room temperature for trans azobenzene in ethanol and P.Me.H. Other spectra were taken of azobenzene: at the photostationary state, at room temperature in ethanol and P.Me.H., and at 77\u00b0K in P.Me.H.; at 77\u00b0K of 100 % and 77 % trans in P.Me.H.\r\n\r\nIt has been shown that the photoisomerization occurs more readily by irradiation in the visible, than in the ultraviolet region. A new low temperature cell has been designed and used.\r\n" }, { "name": "Mallory, Frank Bryant", "degree": "PhD", "year": "1958", "title": "I. Photochemical Reactions of Phenylcyclobutadienoquinone. II. Thermal Reactions of Phenylcyclobutadienoquinone in Methanol. III. The Photochemical Synthesis of Phenanthrenes", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01122006-092041", "creators": [ { "name": { "family": "Mallory", "given": "Frank Bryant" }, "id": "Mallory-Frank-Bryant", "display_name": "Mallory, Frank Bryant" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/HWRF-HZ38", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPART I: PHOTOCHEMICAL REACTIONS OF PHENYLCYCLOBUTADIENOQUINONE\r\n\r\nThe photolysis of phenylcyclobutadienoquinone in methanol gave dimethyl phenylsuccinate and a compound, [...] of unknown structure.\r\n\r\nPART II: THERMAL REACTIONS OF PHENYLCYCLOBUTADIENOQUINONE IN METHANOL\r\n\r\nThe thermal reaction of phenylcyclobutadienoquinone with methanol in a stainless steel bomb gave 2,4-dimethoxy-3-phenylcyclobutenone, 3-phenyl-4-hydroxy-4-methoxy-2-butenoic acid lactone and dimethyl phenylsuccinate.\r\n\r\nPART III: THE PHOTOCHEMICAL SYNTHESIS OF PHENANTHRENES\r\n\r\nThe photochemical reactions of tetraphenylethylene and trans-stilbene with dissolved oxygen in cyclohexane solutions gave 9,10-diphenylphenanthrene and phenanthrene, respectively." }, { "name": "Scardiglia, Franco", "degree": "PhD", "year": "1958", "title": "I. Reactions of Non-Activated Aryl Halides with Strong Basic and Nucleophilic Agents. II. Evidence for Cyclohexyne as an Intermediate in the Coupling Reaction of Phenyllithium with 1-Chlorocyclohexene. III. Reactions of Non-Activated Aryl Halides with Strong Bases at High Temperatures. IV. The Synthesis of Some Four-Membered Ring Compounds", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01132006-130643", "creators": [ { "name": { "family": "Scardiglia", "given": "Franco" }, "id": "Scardiglia-Franco", "display_name": "Scardiglia, Franco" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6HT7-ZC93", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. Previous studies have shown that non-activated aryl halides are aminated by alkali amides in liquid ammonia by the way of a benzyne intermediate. Nucleophilic substitution products are formed with some strong bases and aryl halides in liquid ammonia, provided alkali amides are present. A study of the mechanism and the scope of such reactions has been made. It has been shown that the first step is the formation of benzyne through reaction of alkali amide and aryl halide. The intermediate is then attacked competitively by the various nucleophilic species (including amide ion) present in solution. Thus, when o- and p-bromotoluene were treated with sodium phenylacetylide in liquid ammonia, the product contained, in addition to aromatic amines, approximately equimolar amounts of 2- and 3-methyldiphenylacetylene and 3- and 4-methyldiphenylacetylene respectively. Benzyne has been found to be attacked by good nucleophiles. The ease of attack of nucleophilic species cannot be directly correlated either with base strength or nucleophilicity as measured in simple [...] reactions.\r\n\r\nPart II. Cyclohexanone-2-[...] has been converted to l-phenylcyclohexene by way of 1,1-dichlorocyclohexane and 1-chlorocyclohexene. Oxidation of a benzenesulfenyl chloride derivative of 1-phenylcyclohexene gave benzoic acid which contained 23% of the radiocarbon present in 1-phenylcyclohexene. This is consistent with an elimination-addition mechanism, in which 1-chlorocyclohexene loses a molecule of hydrogen chloride to give cyclohexyne as a reaction intermediate.\r\n\r\nPart III. The reaction of p-chloro, p-bromo and p-iodotoluene with potassium anilide in refluxing aniline gave approximately equimolar mixtures of m- and p-tolylphenylamine. These product compositions are consistent with a benzyne (elimination-addition) mechanism.\r\n\r\nPart IV. l,l-Difiuoro-2-piperidino-3-phenyl-2-cyclobutene (I) has been obtained by treating 1,1,2-trifluoro-2-chloro-3-phenylcyclobutane with piperidine. Treatment of I with concentrated sulfuric acid gave 2-piperidino-3-phenyl-2-cyclobutenone." }, { "name": "Short, Wallace Walter", "degree": "PhD", "year": "1958", "title": "Part I. Heat Transfer Coefficients and Correction for Thermocouples in the Boundary Layer of a Sphere. Part II. Local Convective Heat Transfer from a Sphere. Part III. Thermal Transfer in Turbulent Gas Streams. Effect of Turbulence on Local Transport from Spheres", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202006-080929", "creators": [ { "name": { "family": "Short", "given": "Wallace Walter" }, "id": "Short-Wallace-Walter", "display_name": "Short, Wallace Walter" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6CZB-AW27", "abstract": "Part I:
\r\n\r\nThe deviation of thermocouple temperatures from the temperature of the fluid surrounding the junction as a result of conduction along the leads was studied. Measurements were made around a 1/2-inch heated sphere in the plane of the equator normal to a stream whose velocity was 16 feet per second. Point air temperatures in the boundary layer of the sphere were predicted from the indications of a 0.001-inch diameter thermocouple with wires of platinum and platinum alloyed with 10% rhodium. The method employed also determined the heat transfer coefficients for the thermocouple wire in the boundary layer. These local heat transfer coefficients are lower than those observed in a uniform stream whose velocity is equal to the local velocity in the boundary layer.
\r\n\r\nPart II:
\r\n\r\nThe local convective heat transfer from a heated sphere 0.5 inch in diameter was determined by means of temperature gradients measured in the boundary layer. Point temperatures were obtained in the boundary layer with a 0.001-inch diameter thermocouple mounted on a probe. The sphere was suspended in air streams at velocities of 4, 8, 16, and 32 feet per second and at a turbulence level of 0.013. Local Nusselt numbers were computed for seven positions around the sphere at Reynolds numbers between 800 and 7000.
\r\n\r\nPart III:
\r\n\r\nThe present investigation was undertaken because of the absence of data concerning the effect of level of turbulence upon local thermal transport from spheres. A series of measurements was made of the local thermal transport in the forward hemisphere and a part of the after hemisphere of a silver sphere 0.5 inch in diameter. The measurements were made in an air stream the longitudinal turbulence level of which was varied between 0.013 and 0.146 for Reynolds numbers up to 3600.
\r\n\r\nAt a turbulence level of 0.013 and a Reynolds number of 3600, the local heat transfer varied by a factor of seven around the sphere. Increasing the level of turbulence to 0.15 increased the over-all heat transfer 20 per cent. The local heat transfer varied by a factor of three at this high level of turbulence.
" }, { "name": "Vannier, Wilton Emile", "degree": "PhD", "year": "1958", "title": "I. House Dust Allergens. II. Experiments on the Distensibility of the Excised Rabbit Bladder", "advisor": "Campbell, Dan Hampton", "url": "https://resolver.caltech.edu/CaltechETD:etd-01262006-102957", "creators": [ { "name": { "family": "Vannier", "given": "Wilton Emile" }, "id": "Vannier-Wilton-Emile", "display_name": "Vannier, Wilton Emile" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TMHA-9268", "abstract": "Part I: \r\n\r\nThe problem of the nature of house dust allergens has been investigated by studying the chemical and physical properties of active fractions of aqueous dust extracts. The fractions consisted largely of a heterogeneous mixture of acidic polysaccharides and in lesser amounts a polypeptide component (2-30%), probably linked to the polysaccharides. The polysaccharides contained uronic acid (probably mostly glucuronic acid), D-glucose, D-mannose, D-galactose and L-rhamnose and lesser amounts of a number of pentoses. Nitrogen free active polysaccharide fractions have not been obtained. The most purified active fraction contained 0.4% nitrogen. The relation between the chemical and physical properties of the fractions and current ideas of the origin of the dust allergens was discussed.\r\n\r\nPart II:\r\n\r\nRabbit bladder stretching curves under constant pressure have been studied. A method, involving the use of eserine and acetylcholine, has been found to restretch the same bladder and obtain reproducible curves. The effect of temperature and epinephrine upon the bladder stretching curves was investigated." }, { "name": "Wilburn, Norman Patrick", "degree": "PhD", "year": "1958", "title": "Preliminary Studies in the Determination of the Volumetric Properties of Nitrogen Using a Ballistic Piston Apparatus", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232006-081105", "creators": [ { "name": { "family": "Wilburn", "given": "Norman Patrick" }, "id": "Wilburn-Norman-Patrick", "display_name": "Wilburn, Norman Patrick" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/9N7B-ZR75", "abstract": "A ballistic piston apparatus is described briefly. The instruments in the apparatus and the associated external measuring circuits are discussed in detail. The differential equations which describe the energy and material transport in the axially-collapsing cylindrical sample-gas chamber are derived and solved numerically. Compressibility factors are calculated for nitrogen gas employing data obtained from two tests made on the ballistic piston apparatus. Temperatures in this investigation range from 2300\u00b0 to 3300\u00b0 R, and pressures from 1000 to 6300 pounds per square inch absolute." }, { "name": "Wilson, David James", "degree": "PhD", "year": "1958", "title": "Part One. Further Investigation of Energy Transfer Processes in the Unimolecular Decomposition of Nitryl Chloride. Part Two. Decomposition of Nitrogen Pentoxide in the Presence of Nitric Oxide. (IV.) Effect of Noble Gases. Part Three. Theoretical Pre-Exponential Factors for Hydrogen Atom Abstraction Reactions. Part Four. Carbon Isotope Effect During Oxidation of Carbon Monoxide with Nitrogen Dioxide", "advisor": "Johnston, Harold S.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01272006-092440", "creators": [ { "name": { "family": "Wilson", "given": "David James" }, "id": "Wilson-David-James", "display_name": "Wilson, David James" } ], "advisors": [ { "name": { "family": "Johnston", "given": "Harold S." }, "id": "Johnston-H-S", "role": "advisor", "display_name": "Johnston, Harold S." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XPN5-F021", "abstract": "The unimolecular decomposition of nitryl chloride was investigated in the pressure range 10 to 500mm. and the temperature range 141 to 205\u00b0C. Relative efficiencies of foreign gases were found to vary slightly, if at all, over this range of conditions. The reaction was observed to be partially heterogeneous in the Pyrex reaction cell used. The results of this work are in agreement with those of Volpe and Cordes at low pressures and with those of Casaletto at high pressures. The discrepancies between the relative efficiencies obtained by Volpe and those obtained Schumacher and Sprenger are probably due to effects of heterogeneity in the work of Schumacher and Sprenger.\r\n\r\nThe data obtained in this work were interpreted in terms of the Lindemann mechanisms. Relative efficiencies were calculated by means of the Schwartz-Slavsky-Herzfeld theory and the Landau Teller theory; the latter theory gave results in qualitative agreement with the available experimental data.\r\n\r\nRelative efficiencies of the noble gases and of carbon tetrachloride for the decomposition of nitrogen pentoxide at 50\u00b0C in the pressure range 0.1 to 3.0 mm., are reported in Part Two of this thesis. It was found that deactivation of activated reactant molecules does not occur on every collision.\r\n\r\nPart Three of this thesis, \"Theoretical Pre-exponential Factors for Hydrogen Atom Abstraction Reactions,\" contains its own abstract. Pre-exponential factors were calculated by means of Eyring's activated complex theory for ten bimolecular reactions. Part Four of this thesis \"Carbon Isotope Effect during Oxidation of Carbon Monoxide with Nitrogen Dioxide,\" contains its own abstract.\r\n" }, { "name": "Applewhite, Thomas Hood", "degree": "PhD", "year": "1957", "title": "I. Thiocarbamate Studies. II. Preliminary Investigations of the alpha-Chymotrypsin Catalyzed Hydrolysis of Acylated Amino Acid Esters. III. The alpha-Chymotrypsin Catalyzed Hydrolysis of Methyl Hippurate and of Benzoyl-L-Valine Methyl Ester. IV. The Enzyme-Inhibitor Dissociation Constants of Some N-Acetyl Amino Acid N'-Methylamides", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07082004-132616", "creators": [ { "name": { "family": "Applewhite", "given": "Thomas Hood" }, "id": "Applewhite-Thomas-Hood", "display_name": "Applewhite, Thomas Hood" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/03FF-7N17", "abstract": "The known reactions of N,S-diphenylthiocarbamate were extended by studies of the effects of various reagents and conditions. The results are discussed in terms of previously suggested reaction mechanisms.\r\n\r\nThe mixed anhydrides between S-phenylthiocarbonylchloride and carboxylic acids were briefly investigated as preparative intermediates. Low yields of the expected products offset the utility of this method.\r\n\r\nThe non-reactivity of secondary amine S-phenylthiocarbamates was further demonstrated with N-pentamethylene-S-phenylthiocarbamate. The inert nature of this compound indicates that the effects are not due to steric hindrance.\r\n\r\nA brief investigation of the reactions of S-benzylthio- and 0-benzyl-N-phenylcarbamate suggest that they have little value as preparative intermediates as compared to the S- and 0-phenyl derivatives.\r\n\r\nSome S-phenylthiocarbamates of amino acid derivatives were prepared, and their use in a polymerization reaction and stepwise dipeptide synthesis is described. The results suggest that the various methods are not as elegant as indicated earlier.\r\n\r\nA recently developed automatic titration instrument was employed in a preliminary study of the [alpha]-chymotrypsin catalyzed hydrolysis of some acylated amino acid esters. A useable system was developed, and some preliminary results were obtained concerning techniques, data treatment, surface effects and steric effects in enzyme catalyzed reactions.\r\n\r\nThe kinetics of the [alpha]-chymotrypsin catalyzed hydrolysis of methyl hippurate were re-investigated. In addition, the enzyme-inhibitor dissociation constants of two competitive inhibitors were re-determined. The results are compared with values obtained earlier.\r\n\r\nBenzoyl-L-valine methyl ester, a new substrate for this enzyme, was studied in the catalyzed reaction employing the above techniques. Additional refinements in technique and errors in this system are discussed.\r\n\r\nA number of potential competitive inhibitors, the N-acetyl amino acid N'-methylamides, were synthesized and tested for inhibitory activity in the [alpha]-chymotrypsin catalyzed hydrolysis of methyl hippurate and benzoyl-L-valine methyl ester. The results indicate that, of the compounds studied, only those containing an aromatic residue have a measurable effect in the present systems." }, { "name": "Berndt, Alan Fredric", "degree": "PhD", "year": "1957", "title": "Some Molecular Structures by Electron and X-Ray Diffraction", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07012004-091059", "creators": [ { "name": { "family": "Berndt", "given": "Alan Fredric" }, "id": "Berndt-Alan-Fredric", "display_name": "Berndt, Alan Fredric" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X8RN-9G20", "abstract": "Two polycyclohydrocarbons, norbornane and the compound C12H14 of De Vries and Winstein, were investigated by electron diffraction. For both molecules the C-C bond was found to be lengthened from the normal value of 1.54 A. Bond strain calculations were made for both molecules.\r\n\r\nAn electron diffraction investigation of ferrocene confirmed the proposed sandwich structure. The following distances for a model with D5d symmetry were derived by the correlation method: Fe-C, 2.064 A; C-C, 1.440 A. Both models in which the rings were allowed to rotate with a small potential barrier and models in which the inter-ring C...C distances were assigned a moderately large vibrational temperature factor constant, with no rotation, were found to be consistent with the visual data.\r\n\r\nThe crystal structure of cyclopentadienyl manganese tricarbonyl was studied by X-ray diffraction. The crystal was treated as a heavy atom problem and three-dimensional methods were used. Anisotropic temperature factors were calculated from a difference Fourier synthesis. The positional parameters were refined by least squares. The Mn(CO)3 part of the molecule has nearly trigonal symmetry and the ring was found to be nearly planar. The packing of the molecules approximates a cubic closest packed array of spheres.\r\n\r\nCyclopentadienyl nickel nitrosyl was investigated by electron diffraction. The method of least squares was used in order to refine the parameters and to estimate the limits of error. Both models with a linear Ni-N-0 bond and models with a bent Ni-N-0 bond were found to be acceptable. Bond distances in metal carbonyls and related compounds are discussed." }, { "name": "Bixler, Robert L.", "degree": "PhD", "year": "1957", "title": "I. The Synthesis of Pyridine and Pyridine 1-Oxide Substituted Alanine Derivatives. II. Preliminary Investigations of Alpha-Chymotrypsin Catalyzed Hydrolyses of Acylated Amino Acid Esters at Low Enzyme Concentrations -- Studies of Surface Effects. Ill. The Synthesis and Rate of Acetolysis of 1-Bicyclo[2.2.11 Heptylmethyl Tosylate", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07012004-100202", "creators": [ { "name": { "family": "Bixler", "given": "Robert L." }, "id": "Bixler-Robert-L", "display_name": "Bixler, Robert L." } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8PDN-2835", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\t\t\t\t\t\r\nMethods for the preparation of pyridine and pyridine 1-oxide substituted alanines for use as substrates for the enzyme alpha-chymotrypsin were studied. As a consequence of this work, N-benzoyl-L-4-pyridylalanine 1-oxide methyl and ethyl esters, N-acetyl-DL-4-pyridylalanine 1-oxide methyl ester, and N-(nicotinyl 1-oxide)-L-phenylalanine methyl ester were prepared. The method for the synthesis of 4-pyridyl-alanine via a malonic ester condensation has been improved to the point where it is preparatively useful.\r\n\r\nIt has been demonstrated that the catalytic reduction of pyridine 1-oxides in water with a platinum catalyst is nonspecific, the pyridine and pyridine 1-oxide groups being reduced at comparable rates.\r\n\r\nA kinetic study of the effect of surface on alpha-chymotrypsin catalyzed hydrolyses of acylated amino acid esters was carried out. It was shown that there was no effect of surface on the kinetics, varying the surface by a factor of 3000. However, it was shown that serious losses of enzyme can occur during transfer operations at an enzyme to surface ratio of [...] or greater. The possibility of avoiding these losses of enzyme during transfer by adding a \"carrier\" for the enzyme, in the form of colloidal silica, was investigated, and shown to have promise. It was shown that the enzyme was adsorbed on colloidal silica.\r\n\r\nBicylo[2.2.1]hepty1methyl tosylate has been prepared, and its rate of acetolysis at 99[degrees]C. determined." }, { "name": "Bottini, Albert Thomas", "degree": "PhD", "year": "1957", "title": "I. Mechanisms for Liquid Phase Hydrolyses of Chlorobenzene and Halotoluenes. II. The Products from the Reaction of N-(2-Bromoallyl)-Ethylamine with Sodium Amide. III. The Nitrogen Inversion Frequency in Cyclic Imines. IV. The Nuclear Magnetic Resonance Spectrum of Feist's Acid", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07082004-142125", "creators": [ { "name": { "family": "Bottini", "given": "Albert Thomas" }, "id": "Bottini-Albert-Thomas", "display_name": "Bottini, Albert Thomas" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YXKG-ZT83", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. A study of the rearrangements which occur during the high temperature liquid phase hydrolyses of the halotoluenes has shown that the extent of rearrangement is a sensitive of temperature, base strength and the nature of the halogen. These hydrolyses involve either a benzyne (elimination-addition) mechanism, which gives both rearranged and unrearranged products, or an [...]-type mechanism. The [...]-type mechanism was found to be favored at lower temperatures, in the presence of weaker bases and with the more easily ionizable halogens. By suitable choice of conditions, one or the other reaction could be made to occur almost exclusively. Chlorobenzene-[...],with 4 M sodium hydroxide solution at 340[degrees], gave 58[plus or minus]1% [...] and [...], which indicates that under these conditions the benzyne mechanism predominates but is not the exclusive reaction path.\r\n\r\nPart II. The principal product obtained from N-(2-bromoallyl)-ethylamine and sodium amide in liquid ammonia has been shown to be N-ethylallenimine as proposed by Ettlinger and Kennedy rather than N-ethylallylideneamine. N-Ethylpropargylamine was also isolated in small yield from this reaction. N-Ethylpropargylamine was obtained in 71% yield by treatment of N-(2-chloroallyl)-ethylamine with potassium amide in liquid ammonia.\r\n\r\nPart III. The nuclear magnetic resonance spectra of derivatives of cyclic imines ranging in ring size from three to six were examined. The temperature dependent spectra of aziridine (ethylenimine) derivatives allowed an evaluation of the factors which affect the nitrogen inversion frequency. Conjugation with nitrogen and, generally to a lesser degree, bulkiness of the group attached to nitrogen increase the inversion frequency. Two groups attached to carbon on opposite sides of the imine ring also increase the inversion frequency. One, or two subtituents attached to the ring carbons in a cis manner essentially fix the configuration about nitrogen with the N-substituent trans to the other group (s). The inversion frequency is decreased in hydroxylic solvents due to stabilization of configuration by hydrogen bonding with nitrogen. The data obtained indicate that theoretically resolvable aziridines in which the asymmetric center is trivalent nitrogen are resolvable only at temperatures below -50[degrees]. The nitrogen inversion frequency in N-substituted azetidines (trimethylenimines) and larger-ring imines is too great to measure from nuclear magnetic resonance data at temperatures above -77[...].\r\n\r\nPart IV. The nuclear magnetic resonance spectrum of Feist's acid, as the sodium salt in a basic solution of deuterium oxide, was found to be consistent with the structure 3-methylene-1,2-trans-cyclopropanecarboxylic acid (I). It was discovered that the ring hydrogens undergo exchange with the solvent whereas the methylene hydrogens do not appear to exchange. These facts cast serious doubt on the possibility of a facile equilibration of I and 3-methyl-1,2-cyclopropenedicarboxylic acid (II). Structure II has been considered elsewhere to account for the ozonization product of esters of I. A mechanism that accounts for the formation of ethyl acetoxaloacetate in the ozonization of the diethylester of I has been developed.\r\n\r\nThe nuclear magnetic resonance spectrum of the reduction product of I was also studied. The ring hydrogens did not appear to undergo exchange with the solvent in a deuterium oxide solution of sodium deuteroxide." }, { "name": "Brady, William Thomas", "degree": "Masters", "year": "1957", "title": "The Synthesis of O-Methyl-N-Acetyl-L-Tyrosine", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04292010-095951946", "creators": [ { "name": { "family": "Brady", "given": "William Thomas" }, "id": "Brady-William-Thomas", "display_name": "Brady, William Thomas" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2XEN-8E12", "abstract": "An efficient method of preparing N-acetyl-L-tyrosine methyl ester is described. This compound has been converted to the optically pure O-methyl derivative by reaction with diazomethane. The saponification of N-acetyl-L-tyrosine methyl ester is a more convenient rout to N-acetyl-L-tyrosine than the direct acetylation of L-tyrosine. N-acetyl-L-tyrosine can be converted to optically pure O-methylN-acetyl-L-tyrosine via the Williamson synthesis. The preparation of several other derivatives of L- tyrosine is also described.\r\n" }, { "name": "Bunker, Don Louis", "degree": "PhD", "year": "1957", "title": "Flash Photolysis and the Recombination of Iodine Atoms", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07082004-142823", "creators": [ { "name": { "family": "Bunker", "given": "Don Louis" }, "id": "Bunker-Don-Louis", "display_name": "Bunker, Don Louis" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Q36G-BS81", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe rate of recombination of iodine atoms in the presence of argon has been redetermined by a flash photolysis technique. The measured rate constant agrees with results obtained by the same method in other laboratories. The recombination rate has also been measured at temperatures up to 548[degrees]K; these results are in accord with shock tube data and with other flash photolysis experiments. The rate is found to decrease slowly with increasing temperature, as about [...].\r\n\r\nIn experiments at temperatures between 300 [degrees]K and 493 [degrees]K n-butane has been employed as \"third body.\" It is found to be 13 times more efficient than argon at room temperature; this margin decreases as the temperature is raised. The third-body efficiencies of hydrogen and deuterium have been compared at 323 [degrees]K; they are equal.\r\n\r\nThe above experiments collectively lead to a determination of the rate of the recombination reaction involving I2 itself as third body. This reaction is about 600 times more rapid than that occurring with argon at room temperature, but rapidly becomes insignificant if the temperature is increased. From its temperature dependence [...] Kcal may be deduced for the reaction [...]." }, { "name": "Helfrey, Paul Francis", "degree": "PhD", "year": "1957", "title": "I. Preliminary Studies in the Application of a Ballistic Piston to Investigation of Chemical Reaction in the Nitrogen-Oxygen System. II. Isobaric Heat Capacities at Bubble Point of Pseudocumene and of n-Heptane", "advisor": "Corcoran, William Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-07212004-115113", "creators": [ { "name": { "family": "Helfrey", "given": "Paul Francis" }, "id": "Helfrey-Paul-Francis", "display_name": "Helfrey, Paul Francis" } ], "advisors": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-W-H", "role": "advisor", "display_name": "Corcoran, William Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0TX5-XZ31", "abstract": "An apparatus, in which gaseous samples may be subjected to rapid compression, is described. This \"ballistic piston\" offers a mechanically simple method of producing for a short time a very high temperature and pressure in a sample under study.\r\n\r\nThe results of preliminary studies on the nitrogen-oxygen system are presented. Appreciable yields of nitrogen dioxide, up to 3.3 mol per cent of the gas remaining after compression, were obtained. The conditions investigated involved calculated maximum temperatures as high as 13,000[degrees] R and maximum pressures up to 30,000 psi. The maximum temperature and pressure achieved in each run were calculated on the basis of fairly simple assumptions. An increase in the yield of NO2 with increasing maximum temperature and with increasing maximum pressure was noted.\r\n\r\nCoefficients for a second order rate equation were tested by comparing predicted yields based on the coefficients with the observed yields. In the temperature range above 3500[degrees] R rate coefficients not more than one-tenth as great as those obtained by extrapolation of existing data are indicated. The rate coefficients obtained are subject to much uncertainty because of the many simplifying assumptions made in treating the data. The results are discussed in the light of the limitations imposed by the assumptions.\r\n\r\nAs part of a long-term project for measurement of the heat capacities of hydrocarbons, the isobaric heat capacity at bubble point of 1,2,4,-trimethylbenzene (pseudocumene) was determined in the range 70-210[degrees] R. Using the same equipment, the same property was determined for n-heptane, a widely accepted standard for calorimetric work. The results are reported in a manuscript which includes results obtained by a later investigator on the project for 1,3,5-trimethyl-benzene." }, { "name": "Hutchinson, William Day", "degree": "Masters", "year": "1957", "title": "An Ultracentrifugal Study of the Dissociation of Human Carboxyhemoglobin", "advisor": "Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechTHESIS:04262010-094002832", "creators": [ { "name": { "family": "Hutchinson", "given": "William Day" }, "id": "Hutchinson-William-Day", "display_name": "Hutchinson, William Day" } ], "advisors": [ { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/W8JC-7T49", "abstract": "The dissociation of human carboxyhemoglobin has been investigated by means of sedimentation velocity measurements. Sedimentation studies on this protein have been extended to concentrations as low as 0.002% by the use of absorption optics. Hemoglobin was observed to dissociate increasingly as the pH was changed from 7 to 5. Apparent dissociation constants at each pH have been calculated. Values of the apparent specific volume of human carboxyhemoglobin have been found." }, { "name": "Kerr, Richard John", "degree": "PhD", "year": "1957", "title": "I. Investigations of the Alpha\u00b7Chymotrypsin Catalyzed Hydrolysis of Amino Acid Hydrazides. II. Synthesis of Amino Acid Derivatives. III. The Apparent Ionization Constants of a Series of Phenylalanine Derivatives", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202004-112555", "creators": [ { "name": { "family": "Kerr", "given": "Richard John" }, "id": "Kerr-Richard-John", "display_name": "Kerr, Richard John" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AXT0-NZ95", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe effect of variation in the concentration of tris-(hydroxymethyl)-aminomethane buffer systems upon the kinetic constants of the alpha-chymotrypsin catalyzed hydrolysis of nicotinyl-L-tyrosinhydrazide has been determined at pH 7.9 and 25.0[degrees]C. This study indicates a linear relationship between the logarithm of values of [...] and the square root of the ionic strength. It has been demonstrated, in the case of the hydrazide investigated, that the value of the Michaelis-Menten constant, [...], is independent of the variations applied.\r\n\r\nA confirmation of the activating influence of calcium ion has been made. An increase of approximately 75% in the initial velocity of the alpha-chymotrypsin catalyzed hydrolysis of nicotinyl-L-tyrosinhydrazide is noted upon the addition of [...] calcium ion to the reaction system.\r\n\r\nThe colorimetric determination of hydrazine employed to determine the extent of hydrolysis in the above cases has been reinvestigated.\r\n\r\nA reinvestigation of the kinetics of the alpha-chymotrypsin catalyzed hydrolysis of acetyl-L-tyrosinhydrazide utilizing improved procedures of analysis indicated above has been made. The possibility of observing product inhibition depending upon values of initial substrate concentration and [...] is discussed.\r\n\r\nThe preparation of acetyl-, benzoyl-, trifluoracetyl-, and methanesulfonyl-DL-phenylalanine salicylamide esters is described. Several attempts to synthesize the optically active esters are described. Reasons for racemization in the cases tried are briefly discussed.\r\n\r\nDuring the course of attempted dehydration procedures with polyphosphoric acid several interesting dehydrocyclination products are isolated and described.\r\n\r\nThe preparation of trifluoracetyl-L-phenylalanine anthranilamide is described.\r\n\r\nThe synthesis of acetyl-DL-phenylalanine glycolamide and acetyl-L-phenylalanine glycolamide are described.\r\n\r\nPreliminary investigations were conducted in the alpha-chymotrypsin catalyzed hydrolysis of the above compound.\r\n\r\nThe apparent ionization constants of the protonated amino group of a series of DL-phenylalanine derivatives have been determined. The expected differences in the pK of these derivatives due to changes in acid derivative were not realized except in the case of phenylalanine hydrazide. The use of an automatic pH titration and recording instrument is described." }, { "name": "Longwell, Paul Alan", "degree": "PhD", "year": "1957", "title": "Chemical Reactions of Methane and of n-Hexane in Ballistic Piston Apparatus", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08032004-142746", "creators": [ { "name": { "family": "Longwell", "given": "Paul Alan" }, "id": "Longwell-Paul-Alan", "display_name": "Longwell, Paul Alan" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/WXBB-8989", "abstract": "The results of ballistic piston tests on methane and on n-hexane are described. In the case of methane the calculated reaction temperatures are 2500 to 3500[degrees]R. and maximum pressure range up to 100,000 pounds per square inch. The distribution of reaction products and the amount of reaction are correlated with the reaction conditions. For n-hexane the products are correlated with reaction conditions and in addition reaction rate coefficients were obtained. The decomposition reaction was found to be of apparent one half order with a low apparent activation energy. The range of reaction, temperatures investigated for n-hexane was 1600-2800[degrees]R. with maximum pressures up to 115,000 pounds per sqaure inch.\r\n\r\nIn addition to the experimental results there are included derivations of the differential equations describing the behavior of the ballistic piston apparatus and solution of these equations for various conditions and assumptions. In order to obtain numerical solutions it was necessary to estimate the thermodynamic properties of gases at high pressures and temperatures. These are tabulated for 1500-20,000[degrees]R. for hydrogen, helium and nitrogen; for 1500-5000[degrees]R. for methane, and 1500-4000[degrees]R. for n-hexane. The range of pressures is 0-200,000 pounds per square inch in each case." }, { "name": "McHugh, James Paul", "degree": "PhD", "year": "1957", "title": "The Molecular Structures of Some Simple Olefins and Small Ring Compounds", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07152004-085833", "creators": [ { "name": { "family": "McHugh", "given": "James Paul" }, "id": "McHugh-James-Paul", "display_name": "McHugh, James Paul" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/68JC-HH51", "abstract": "The structures of three simple olefins and three small ring compounds containing double bonds have been determined by electron diffraction, and the results discussed in terms of hyperconjugation, rehybridization, strain, and intramolecular repulsions.\r\n\r\nIn Part I, the structures of propene, isobutene, and cis butene-2 are described. The single bonds in these molecules have a length of about 1.50 A, exhibiting about half the shortening found in single bonds adjacent to triple bonds.\r\n\r\nIn Part II, an attempt is made to calculate the intramolecular repulsive energy of the methyl groups in cis butene-2, using intermolecular force constants.\r\n\r\nParts III, IV, and V describe the structure determinations of methylenecyclopropane, 1,3-dimethylenecyclobutane, and 1-methyl-3-methylenecyclobutene. In each case, the single bonds adjacent to double bonds are found to be short.\r\n\r\nPart VI contains some further discussion of the factors which alter carbon-carbon single bond lengths." }, { "name": "Meselson, Matthew Stanley", "degree": "PhD", "year": "1957", "title": "I. Equilibrium Sedimentation of Macromolecules in Density Gradients with Application to the Study of Deoxyribonucleic Acid. II. The Crystal Structure of N, N'-Dimethyl Malonamide", "advisor": "Pasternak, Rafael A.; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-06102004-145206", "creators": [ { "name": { "family": "Meselson", "given": "Matthew Stanley" }, "id": "Meselson-Matthew-Stanley", "display_name": "Meselson, Matthew Stanley" } ], "advisors": [ { "name": { "family": "Pasternak", "given": "Rafael A." }, "id": "Pasternak-R-A", "role": "advisor", "display_name": "Pasternak, Rafael A." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5PJC-KZ44", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract in included in .pdf document.\r\n\r\n1. A method is presented for the study of the molecular weight and composition of macromolecules by observing in the ultracentrifuge their equilibrium distribution in a density gradient. The macromolecular material is centrifuged to near equilibrium in a solution of a low molecular weight solute. Under these conditions, sedimentation of the low molecular weight solute results in a continuous increase of density along the direction of the centrifugal field. The macromolecules collect in a band where their effective density is the same as that of the solution. Analysis of the shape and position of such bands yields information regarding molecular weight and composition. By this method, a deoxyribonucleic acid sample from bacteriophage is shown to be monodisperse with molecular weight [...]. Bacteriophage DNA containing 5-bromouracil instead of thymine has been prepared and found to differ considerably in effective density from normal DNA.\r\n\r\nII. The crystal structure of N,N'-dimethyl malonamide has been determined by two-dimensional methods. A type of weighted density projection has been devised which is especially suited to the refinement of projections complicated by atomic overlap. The crystal is monoclinic with space group [...]. A network of N-H...0 hydrogen bonds ties molecules into extended sheets parallel to the [...] plane. Although the configuration and dimensions found for the amide group conform quite closely to previous findings for related compounds, there is some indication of an especially large double bond character for the [...] bond." }, { "name": "Miller, Arthur", "degree": "PhD", "year": "1957", "title": "I. The Crystal Structure of the Intermetallic Compound Mg\u2081\u2082Ce. II. Reaction Products of \u03b3-Picoline and Iodine", "advisor": "Bergman, Gunnar B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-112016", "creators": [ { "name": { "family": "Miller", "given": "Arthur" }, "id": "Miller-Arthur", "display_name": "Miller, Arthur" } ], "advisors": [ { "name": { "family": "Bergman", "given": "Gunnar B." }, "id": "Bergman-Gunnar-B", "role": "advisor", "display_name": "Bergman, Gunnar B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B4C7-XS45", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I:\tThe structure of the intermetallic compound Mg12Ce has been investigated by x-ray diffraction methods. The diffraction photographs seem to indicate that the structure has hexagonal symmetry, but further considerations reveal that the true symmetry is orthorhombic, and that the space group is very probably [...]. The orthorhombic unit cell, with dimensions [...], [...], and [...], contains 156 atoms. The diffraction maxima with the Miller index 1 even can be indexed on the basis of a smaller pseudo-hexagonal unit cell containing only 13 atoms. In this subcell, the arrangement of the atoms is related to those found in the CaZn5 and TiBe12 structures.\r\n\r\nThe structure of the crystal is partially disordered in a complex fashion. A theory based on crystal growth has been devised which successfully accounts for the gross features of the disorder.\r\n\r\nPart II: Two distinct addition compounds, with formulas C12H14N2I2 and C6H7NI2 have been isolated from the reaction products of iodine and [gamma]-picoline. The second of these compounds is analogous to the well-known addition compound of pyridine and iodine. It has been of interest to determine whether the complexing forces between iodine and the organic base are sufficient to break the iodine-iodine covalent bond. X-ray radial distribution analyses showed that in the first compound the covalent bond had been broken, leading to an ionic structure, whereas in the second compound the covalent bond remained intact." }, { "name": "Nazarian, Girair Mihran", "degree": "PhD", "year": "1957", "title": "I. A Perturbation Theory of the Approach Toward Sedimentation Equilibrium in the Ultracentrifuge and an Analysis of a Proposed Fast Method for Reaching Equilibrium. II. The Detailed Interpretation of the Anomalous Electron Diffraction Photographs of Some Symmetrical Gas Molecules with the Aid of Complex Scattering Amplitudes", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07152004-093903", "creators": [ { "name": { "family": "Nazarian", "given": "Girair Mihran" }, "id": "Nazarian-Girair-Mihran", "display_name": "Nazarian, Girair Mihran" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2EQX-9P31", "abstract": "I. The transient concentration distribution in the ultracentrifuge is obtained in the form of a power series expansion in a small parameter by a perturbation treatment of the appropriate differential equation. The problem reduces in zero order to that of sedimentation in a constant gravitational field.\r\n\r\nThe theory is used for determining which initial step distributions lead to the fastest approach to equilibrium. The saving in time as compared to the conventional uniform initial distribution is also calculated.\r\n\r\nII. The neglect of a phase shift in the theory of scattering has been shown by Schomaker and Glauber to be the reason why electron diffraction investigations in the past led to distorted structures for certain molecules otherwise expected to be symmetrical. Complex scattering amplitudes for use in calculating theoretical intensity patterns are now available as a result of the work of Hoerni and Ibers. In the present investigation we reinterpret the diffraction photographs of a number of these molecules in terms of symmetrical structures. The bond lengths in these molecules are thus determined accurately. In addition, further confirmation is provided for the theory." }, { "name": "Nichols, William Burt", "degree": "PhD", "year": "1957", "title": "I. An Apparatus for the Measurement of Liquid Diffusion Coefficients. II. Supersaturation in Hydrocarbon Systems: (1) n-Pentane in the Liquid Phase; (2) Statistical Procedures for Supersaturation Data. III. Volumetric and Phase Behavior of Hydrocarbon Systems: (1) Hydrogen-n-Hexane; (2) n-Heptane", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07152004-104918", "creators": [ { "name": { "family": "Nichols", "given": "William Burt" }, "id": "Nichols-William-Burt", "display_name": "Nichols, William Burt" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/41FD-R190", "abstract": "I. An apparatus was constructed for the measurement of Fick diffusion coefficients in the liquid phase under steady state conditions at pressures up to 10,000 psi. and at temperatures from 40 to 460[degrees]F. The apparatus consists of a device for the feed of a gas at an accurately known rate, a diffusion cell, and a device identical to the feed equipment for the withdrawal of a gas. The details of construction are given and a tentative method of operation is discussed.\r\n\r\nII. 1. A limited number of measurements were made of the effect of the degree of supersaturation on the rate of bubble formation as shown by the time for the first bubble to form in liquid n-pentane. Data were taken at 160[degrees] and 280[degrees]F. in an isochoric cell and at 160[degrees]F. in an isobaric apparatus which is described. The results show that for a given degree of supersaturation the times of bubble formation are widely distributed and must be considered statistically.\r\n\r\nII. 2. A procedure for the treatment of supersaturation data is discussed which includes a derivation of a theoretical distribution function for the times of formation of the first bubbles, a regression analysis based on an elementary hypothesis for the dependence of the rate of bubble formation on the degree of supersaturation, and a study of several pertinent confidence intervals.\r\n\r\nIII. 1. The volumetric behavior of four mixtures of different composition in the binary system hydrogen-n-hexane was investigated at pressures up to 10,000 pounds per square inch for eight temperatures in the interval between 40 and 460[degrees]F. The composition of coexisting phases in the heterogeneous region was determined at seven temperatures from 40 to 400[degrees]F. and at pressures up to 10,000 pounds per square inch. The results are presented in tabular and graphical form.\r\n\r\nIII. 2. Prior work on n-heptane by other investigators was extended as a preliminary to the study of the binary system methane-n-heptane. The molal volume of n-heptane is reported in tabular and graphical form as a function of pressure up to 10,000 pounds per square inch at eight temperatures covering the range from 40 to 460[degrees]F." }, { "name": "Richter, George Neal", "degree": "PhD", "year": "1957", "title": "I. Thermal Conductivity of Nitrogen Dioxide in the Liquid Phase. II. Thermal Conductivity of Nitric Oxide. III. Viscosity of Nitrogen Dioxide and Nitrogen Dioxide-Nitric Oxide Mixtures", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05042006-132419", "creators": [ { "name": { "family": "Richter", "given": "George Neal" }, "id": "Richter-George-Neal", "display_name": "Richter, George Neal" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/QX3K-AB73", "abstract": "Part I: An apparatus has been constructed for the determination of the thermal conductivity of fluids. In this equipment the thermal flux between concentric spheres is measured. The apparatus has been used to measure the thermal conductivity of nitrogen dioxide in the liquid state at 40\u00b0, 100\u00b0, and 160\u00b0F., and at pressures up to 5000 pounds per square inch.\r\n\r\nPart II: The thermal conductivity of nitric oxide was measured at atmospheric pressure from 40\u00b0 to 400\u00b0F., and the variation of its thermal conductivity with pressure was observed at 40\u00b0, 220\u00b0, and 340\u00b0F. to a maximum pressure of 1400 pounds per square inch. At higher pressures the nitric oxide was found to undergo catalytic decomposition.\r\n\r\nPart III: A rolling ball viscometer was utilized to measure the viscosity of nitrogen dioxide and mixtures of nitrogen dioxide and nitric oxide. A temperature range of 400 to 280\u00b0F. was used at pressures from bubble point to 5000 pounds per square inch. Mixtures containing up to 20 weight per cent nitric oxide were studied." }, { "name": "Silvey, Franklin Clark", "degree": "Engineering Degree", "year": "1957", "title": "I. Supersaturation in Hydrocarbon Systems Methane-n-Decane. II. Supersaturation in Hydrocarbon Systems Methane-n-Decane Silica", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08092004-113527", "creators": [ { "name": { "family": "Silvey", "given": "Franklin Clark" }, "id": "Silvey-Franklin-Clark", "display_name": "Silvey, Franklin Clark" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2D0D-TV43", "abstract": "PART I\r\n\r\nAn understanding of the possible influence of supersaturated liquids upon the production and refining of petroleum is of industrial interest. Only limited information is available as to the influence of environment upon the duration of supersaturation for pure hydrocarbons and their mixtures.\r\n\r\nA number of measurements were made of the influence of strain upon the behavior of four mixtures of methane and n-decane at temperatures ranging from 70 [degrees] to 390[degrees] F. The mixtures exhibited equilibrium bubble-point pressures between 54 and 1048 pounds per square inch. The local strain was introduced by raising the temperature of a portion of the system above that of the remainder.\r\n\r\nThe formation of bubbles in such systems appears to be randomly distributed in time and its rate is nearly directly proportional to the volume of the phase. The results indicate markedly greater tendency for the persistence of supersaturation than obtained in a pure hydrocarbon but the probability of formation of a bubble under a given condition of strain decreased with an increase in mole fraction methane.\r\n\r\nPART II\r\n\r\nAn understanding of the influence of volume and surface effects upon the duration of supersaturation in hydrocarbon liquids is necessary to describe the behavior of liquids in a strained state. A very limited amount of information is available on the influence of surface and volume upon supersaturation in pure hydrocarbons.\r\n\r\nPreliminary information in this field was obtained using a mixture of methane and n-decane containing 0.2290 mole fraction methane at 220[degrees] F. The mixture exhibited an equilibrium bubble-point pressure at 220[degrees] F. of 949 pounds per square inch. These measurements were made in equipment in which the strain was introduced by raising the temperature of a portion of the system above that of the remainder.\r\n\r\nThe volume and surface area of the liquid phase under strain were varied by the introduction of silica crystals. The degree of supersaturation which may be realized in such systems was found to be nearly directly proportional to the volume of the phase. The data were insufficient in number to establish the effect of surface area on bubble formation." }, { "name": "Takei, William Junkichi", "degree": "PhD", "year": "1957", "title": "The Crystal Structures of Some Organic Compounds", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechETD:etd-08302004-154057", "creators": [ { "name": { "family": "Takei", "given": "William Junkichi" }, "id": "Takei-William-Junkichi", "display_name": "Takei, William Junkichi" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/E6PW-AB98", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe crystal structure of acetamide hemihydrochloride has been determined by x-ray diffraction techniques. Three dimensional data were utilized for obtaining the final parameters by least squares and Fourier synthesis refinement techniques with an average positional standard deviation of 0.009 A. The results for acetamide molecule show bond distances closer to those previously accepted than to those from the investigation of acetamide itself. There is a distance of 2.40 A between two oxygen atoms related by a center of symmetry. This has been interpreted as a hydrogen bond and as such would be the shortest such distance reported.\r\n\r\nPotassium dicyanoguanidine crystallizes in an orthorhombic space group, either Pbcm (centrosymmetric) or [...] (non-centrosymmetric). A structure has been determined conforming to Pbcm using least squares and generalized Fourier projections. The average positional standard deviation is 0.006 A for carbon and nitrogen. One of the C-N distances of the guanidine group is significantly shorter than the others. The two terminal NCN groups are not exactly linear, contrary what might be expected. Each potassium ion is surrounded by eight nitrogens in a distorted Archimedes antiprism.\r\n\r\nA study of the structure of the dimer phenylisocyanate was initiated but discontinued for reasons which are discussed.\r\n" }, { "name": "Thorson, Walter Rollier", "degree": "PhD", "year": "1957", "title": "Pressure Broadening in the Gamma-Bands of Nitric Oxide", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechETD:etd-09022004-134612", "creators": [ { "name": { "family": "Thorson", "given": "Walter Rollier" }, "id": "Thorson-Walter-Rollier", "display_name": "Thorson, Walter Rollier" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2KT8-P674", "abstract": "The pressure broadening in the [gamma]-bands of nitric oxide, which has been the subject of considerable controversy in the literature, has been studied quantitatively with the Cary Ultraviolet Spectrophotometer. The behavior of the optical density, as a function of total pressure and of the amount of gas in the path, has been investigated for the [gamma](1,0) and [gamma](0,0) bands. Both the nitric oxide self-broadening and the broadening by nitrogen were studied. The classical theory of Lorentz gives an adequate description of the effect. Curves of growth computed from a model of the spectrum near the band head of [gamma](0,0) have been used to analyze the pressure effect quantitatively. Without recourse to absolute intensity data it is not possible to do more than show that the collision diameter is less than 9 A. The recent measurements of intensity made by Weber and Penner permit the collision diameter to be estimated as 3.8 A. By this criterion the pressure broadening cannot be called \"abnormal.\"\r\n\r\nThe photographic work of Naude on the pressure effect has given support to the suggestion of a large pressure broadening. A photograph taken by him shows no fine structure at a pressure of 450 mm Hg, and this was attributed to a broadening of the lines into one another. A photograph taken in this laboratory under the same conditions is in strong disagreement with his results, showing very clear fine structure. There exists at present no other evidence on pressure broadening in the [gamma]-bands which cannot be harmonized with the interpretation given above. It may be concluded that there is no evidence from the pressure broadening effect for a pressure-induced predissociation in these bands of nitric oxide." }, { "name": "Wong, Chi-hsiang", "degree": "PhD", "year": "1957", "title": "The Study of a Crystal Structure by X-Ray Diffraction and Some Molecular Structures by Electron Diffraction", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-08172004-163006", "creators": [ { "name": { "family": "Wong", "given": "Chi-hsiang" }, "id": "Wong-Chi-hsiang", "display_name": "Wong, Chi-hsiang" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SE1Q-EG73", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe crystal structure of phenylcyclobutenedione has been investigated by the x-ray diffraction method. Three-dimensional techniques were used to deduce and to refine the trial structure. The space group is [...] with four molecules per unit cell.\r\n\r\nElectron diffraction photographs have been made of cuprous chloride vapor. A six-membered alternating ring model of the trimer molecule with [...] and very large amplitude of symmetric bending vibration seems plausible and is shown to be in agreement with the diffraction pattern.\r\n\r\nThe electron diffraction study of two light-heavy compounds [...] has verified the complex nature of the atomic scattering factors for electron diffraction. The bond lengths and bond angles of these two compounds are also determined.\r\n\r\nThe proposed structural formula of the polycyclohydrocarbon [...] (the 'cage') is consistent with the electron diffraction pattern. The average bond length was found to be longer than the normal C-C single bond length in both 'cage' and norbornane. A simple treatment based on a Hooke's law potential for bond stretchings and cross-ring repulsions gives pleasing agreement with the experimental result for the average bond lengths.\r\n" }, { "name": "Woods, William George", "degree": "PhD", "year": "1957", "title": "I. Homoconjugation in Some 7-Chloronorbornane Derivatives. II. Electrostatic Effects in Some 7-Chloronorbornane Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09222004-141146", "creators": [ { "name": { "family": "Woods", "given": "William George" }, "id": "Woods-William-George", "display_name": "Woods, William George" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RGMW-4B58", "abstract": "I. \r\n\r\nA review of carbonium-ion reactions of bornyl and norbornyl derivatives involving non-classical intermediates and a discussion of various \"homoallylic\" systems are given.\r\n\r\n7-Chloronorbornane and syn-7-chloronorbornene have been found to possess very unreactive chlorine under conditions where exo-norbornyl and cyclopentyl chloride solvolyze readily. In contrast, anti-7-chloronorbornene is quite reactive. The solvolysis of anti-7-chloronorbornene is probably facilitated through stabilization of the carbocationic transition state by electron delocalization analogous to that predicted theoretically for the cyclopropenyl cation. First-order molecular orbital and steric strain calculations provide support for this formulation.\r\n\r\nMolecular orbital calculations predict a substantial delocalization energy for the carbocation expected from the solvolysis of 7-chlorobicyclo[2.2.1]heptadiene. Several attempts to synthesize this chlorodiene are described.\r\n\r\nsyn-7-Chloro-endo-norbornyl p-toluenesulfonate has been prepared and its acetolysis rate determined. The relative magnitude of the first-order acetolysis rate constant is taken as further evidence for the substantial participation of a non-classical hydrogen-bridged cationic intermediate in the solvolysis of syn- and anti-7-chloro-exo-norbornyl p-toluenesulfonates.\r\n\r\nII. \r\n\r\nA review of theoretical and experimental efforts to evaluate the inductive and field effects of substituents on reactivity is presented.\r\n\r\nNuclear magnetic resonance spectroscopy has been used to determine the relative base strengths of very weak bases.\r\n\r\nThe rates of bromination of several substituted norcamphors are interpreted in terms of the steric and electrical effects of the substituents.\r\n\r\nThe ultraviolet spectra of a number of substituted norcamohor derivatives are rationalized in terms of the inductive and field effects of the substituents.\r\n\r\nSeveral substituted norcamphoroximes have been prepared and their relative acidities measured.\r\n" }, { "name": "Booman, Keith Albert", "degree": "PhD", "year": "1956", "title": "I. The Use of Numerical Methods in the Treatment of Data from Enzyme Kinetics Studies. II. The Effect of Enzyme Concentration on the Rate of a Reaction Catalyzed by Alpha-Chymotrypsin", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03182004-144601", "creators": [ { "name": { "family": "Booman", "given": "Keith Albert" }, "id": "Booman-Keith-Albert", "display_name": "Booman, Keith Albert" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6602-GW22", "abstract": "Three methods have been developed for handling data from enzyme kinetics studies. The first method, which involves the use of Simpson's rule, is applicable when Michaelis-Menten (21) kinetics obtain and has the advantage of a short calculation time. The second method, which involves approximation of the data by a set of orthogonal polynomials, is applicable when the reaction mechanism is either unknown or so complicated that the mathematical formulation is intractable. The third method applies when the Michaelis-Menten mechanism holds but the steady state approximation is invalid. Use is made of Simpson's rule and of numerical differentiation.\r\n\r\nThe effect of enzyme concentration in the alpha-chymotrypsin catalyzed hydrolysis of L-tryptophanhydroxamide has been studied. All the work was done at 25[degrees]C. at an ionic strength of either 0.15 M. or 0.30 M. The experiments covered the pH range of 6 to 8. The buffer from pH 6 to pH 7 was cacodylic acid. The buffer used at pH 8 was tris-(hydroxymethyl)-aminomethane.\r\n\r\nIt is shown that the effect of changing enzyme concentration is understandable in terms of a reversible dimerization of the enzyme which makes one active site of the two enzyme molecules involved unavailable for bonding to substrate. This effect decreases with increasing pH, becoming negligible at pH 8." }, { "name": "Bradbury, James Thomas", "degree": "Masters", "year": "1956", "title": "I. Development of Paper Electrophoresis Technique for Observation of Microgram Quantities of Protein. II. Electrophoretic and Ultra-Centrifugal Studies of Soluble Antigen-Antibody Complexes as a Method of Determining Antibody and Antigen Valences", "advisor": "Campbell, Dan Hampton; Vinograd, Jerome Rubin", "url": "https://resolver.caltech.edu/CaltechETD:etd-03182004-155047", "creators": [ { "name": { "family": "Bradbury", "given": "James Thomas" }, "id": "Bradbury-James-Thomas", "display_name": "Bradbury, James Thomas" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" }, { "name": { "family": "Vinograd", "given": "Jerome Rubin" }, "id": "Vinograd-J-R", "role": "advisor", "display_name": "Vinograd, Jerome Rubin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9CZJ-ZS08", "abstract": "Quantities of protein as small as five micrograms can be positively detected after electrophoresis on paper if strong adsorption to the paper, known as tailing, is prevented. Adding 0.1% gelatin to the buffer solution used to soak the paper is the simplest way to reduce tailing, and allows the conventional bromphenol blue stain to be used to locate the protein. A protein as nearly identical to the sample as possible eliminates tailing more completely than gelatin, and can be used if the sample can be located in a background of the other protein. Making the sample fluorescent under ultraviolet light by coupling 1-dimethylaminonaphthlalene-5-sulfonyl chloride to it before electrophoresis is an effective way to locate the sample in the presence of otherwise identical proteins. Oxidation of the paper with nitrogen dioxide to reduce tailing has been attempted, but the method has not been refined to a practical degree of effectiveness.\r\n\r\nPaper electrophoresis of BSA-rabbit anti-BSA complexes shows two zones attributed to the Ag2Ab and Ag3Ab2 complexes, in qualitative agreement with moving boundary electrophoresis and ultracentrifugation by Singer and Campbell. As a supplementary argument as to the identity of the complexes, a simple statistical theory is developed to show the relative proportions of different complexes to be expected from antigens and antibodies of given valences, or to show the valences of antigens and antibodies from the quantities of the different complexes formed. Using the ultracentrifugal data of Singer and Campbell in the theoretical equations limits the valence of the antibodies to a value close to two, and the valence of the BSA antigen to a value around five." }, { "name": "Butler, Eliot Andrew", "degree": "PhD", "year": "1956", "title": "Part I. A System of Elemental Analysis. Part ll. The Standard Potential of the Iodine-Iodine Monocyanide Half Cell. Part Ill. The Use of Thioacetamide for the Homogeneous Phase Precipitation of Inorganic Sulfides", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03182004-162239", "creators": [ { "name": { "family": "Butler", "given": "Eliot Andrew" }, "id": "Butler-Eliot-Andrew", "display_name": "Butler, Eliot Andrew" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2CC1-QR40", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA system of elemental analysis for pedagogical use has been developed. Non-metallic solids are fused with sodium hydroxide, sodium carbonate and sodium nitrate and the melt is treated with water to give a residue of the basic element oxides, hydroxides and carbonates, and a solution containing the amphoteric and acidic elements. Metallic solids are dissolved in nitric acid and the hot solution is treated with sodium chlorate. The solution is made alkaline with sodium hydroxide and the separation into groups is the same as is obtained by the fusion treatment. The procedures are capable of yielding semi-quantitative results and thus they permit approximate estimation of the elements.\r\n\r\nThe standard potential of the iodine-iodine monocyanide half cell has been determined. Measurements were made through the concentration ranges 0.2 to 4 F HClO4 and 0.06 to 0.3 F total cyanide and the value -0.6248 [plus or minus] 0.0026 v was obtained for the potential. The constant for the disproportionation of iodine in hydrocyanic acid solutions was determined by solubility measurements to be 0.870 [plus or minus] 0.009.\r\n\r\nThe hydrolysis of thioacetamide to acetamide and hydrogen sulfide in dilute acid solutions was found to be first order with respect to both thioacetamide and hydrogen ion concentrations; under the conditions of the experiments in this study only a small fraction of the acetamide formed was hydrolyzed to acetic acid and ammonia. The second order rate constant for the hydrolysis reaction was found to be 0.21 [plus or minus] 0.02 liter/mole minute at 90[degrees] C. The energy of activiation was determined and is 19.1 kcal mole through the temperature range from 60 [degrees] to 90 [degrees] C.\r\n\r\nThe precipitation of lead sulfide by thioacetamide was found to proceed through two distinct mechanisms depending upon the pH of the solution. At low pH the precipitation involves the hydrolysis of thioacetamide to give hydrogen sulfide which then reacts with the lead. At higher pH the rate of precipitation shows first order dependence upon both thioacetamide and lead ion concentrations and inverse half order dependence upon hydrogen ion concentration. The rate constant and energy of activation have been calculated to be 1.15 [plus or minus] 0.12 x 10[superscript -3] liter[superscript 1/2] mole[superscript -1/2] minute[superscript -1] and 15.5 kcal/mole respectively. A discussion of the analytical use of thioacetamide is presented." }, { "name": "Carter, Forrest Lee", "degree": "PhD", "year": "1956", "title": "Complexes of the cuprous halides with dialkyl acetylenes", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192004-144626", "creators": [ { "name": { "family": "Carter", "given": "Forrest Lee" }, "id": "Carter-Forrest-Lee", "display_name": "Carter, Forrest Lee" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y1D3-NM49", "abstract": "The complex formation of the disubstituted alkynes with cuprous halides has been investigated. No cuprous iodide-alkyne complexes have been observed. Many of the physical characteristics of the cuprous chloride-and cuprous bromide-alkyne crystalline complexes have been determined. These include the dissociation vapor pressures, the heats of dissociation, the compositions, their solubilities in excess ligand, and the densities and vapor pressures of their saturated solutions. In addition the vapor pressure lowering as a function of temperature for the saturated solution of the cuprous chloride 3-hexyne system has been investigated and compared with a theoretical model. A study of the vapor pressure lowering as a function of temperature for alkyne solutions of constant concentration for the cuprous chloride 2-butyne and cuprous chloride 2-pentyne systems suggests the presence of more than one complex species in solution.\r\n\r\nA preliminary investigation of the absorption spectra indicates that the cuprous halide-alkyne complexes are strongly absorbent in the infrared and the ultraviolet.\r\n\r\nThe unit cell and space group of the cuprous chloride-2-butyne complex are given." }, { "name": "Ghirardelli, Robert George", "degree": "PhD", "year": "1956", "title": "I. The Stereochemistry of the Opening of the Imine Ring with Various Reagents. II. The Attempted Reduction of Naturally Occurring Threonine to 3-Amino-2-Butanol", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03232004-104542", "creators": [ { "name": { "family": "Ghirardelli", "given": "Robert George" }, "id": "Ghirardelli-Robert-George", "display_name": "Ghirardelli, Robert George" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/AF4V-BN43", "abstract": "The 2,3-iminobutanes react with acetic acid to give products that are easily converted without isolation into 3-acetamido-2-acetoxybutanes. Comparisons of the latter with samples of known configuration demonstrate that ring opening occurs in a trans manner.\r\n\r\nAttempts to prepare 3-p-toluenesulfonamido-2-p-toluenesulfonoxybutane by reaction of 2,3-iminobutane with p-toluenesulfonic acid, followed by treatment with p-toluenesulfonyl chloride, have failed. Under mild conditions the ring is not attacked, and under strenuous conditions elimination of ammonia occurs.\r\n\r\nThe ring of the N-ethyl-2,3-iminobutanes, as well as that of the simple 2,3-iminobutanes, is opened by aqueous ammonia and ethylamine at elevated temperatures to give products which demonstrate that an inversion occurs. Many new imines, amino alcohols, and diamines have been synthesized. They are described, along with some of their derivatives.\r\n\r\nBoth DL- and naturally occurring threonine have been reduced to derivatives of the corresponding 2-amino-1,3-butanediols. Attempts to reduce the latter to derivatives of the 3-amino-2-butanols have not yet succeeded." }, { "name": "Goldish, Elihu", "degree": "PhD", "year": "1956", "title": "I. The Molecular Structures of Certain Organic Four-Membered Ring Compounds. II. The\r\nBaMg\u2089 Structure", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03232004-112451", "creators": [ { "name": { "family": "Goldish", "given": "Elihu" }, "id": "Goldish-Elihu", "display_name": "Goldish, Elihu" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DRDJ-XF36", "abstract": "Part I presents the results of electron diffraction investigations of some relatively simple four-membered organic ring compounds: trimethylene oxide, 3-methylenetrimethylene oxide, trimethylene sulfide, and cyclobutene. Discussion is given of the bond lengths in these and other small-ring molecules.\r\n\r\nIn a supplementary section are the results of an investigation of dimethyl selenide, which indicates a somewhat larger radius for selenium than is usually given, and preliminary results for decaborane.\r\n\r\nIn Part II the disordered BaMg9 structure is investigated and discussed. It can be described on the basis of a CaCu5-type structure in which about half the barium atoms are replaced by pairs of magnesium atoms." }, { "name": "Hsu, Nan-Teh", "degree": "PhD", "year": "1956", "title": "Part I. Local Convective Thermal Transfer from Spherical Surface. Part II. Temperature Gradients in Turbulent Gas Streams. Measurement of Temperature, Energy, and Pressure Gradients. III. Temperature Gradients in Turbulent Gas Streams. Behavior near Boundary in Two-Dimensional Flow", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03242004-110420", "creators": [ { "name": { "family": "Hsu", "given": "Nan-Teh" }, "id": "Hsu-Nan-Teh", "display_name": "Hsu, Nan-Teh" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/TSJN-KQ40", "abstract": "The local convective thermal transfer from a spherical surface in an air stream was experimentally investigated by measuring the temperature distribution in the air stream surrounding the sphere. The investigation was carried out in an air stream of known turbulence level at bulk velocities of 8 and 16 feet per second using two different half-inch spheres. The local thermal flux over the spherical surface was calculated from the detailed measurements of temperature distribution in the air close to the surface. These results are compared with available experimental results obtained at higher velocities with larger spheres.\r\n\r\nIn the forward region of the sphere from the stagnation point up to an angle of about 80[degrees], the experimental radial temperature distributions are correlated empirically in terms of the displacement thickness of the thermal boundary layer. Over this region the experimental and correlated results are compared in terms of the Nusselt and Reynolds numbers with the results of theoretical analyses based on the laminar boundary layer theory. There is satisfactory agreement with the theoretical results obtained by the method of Drake and the application of the solutions of Eckert.\r\n\r\nThe integrated values of thermal transfer are in agreement with the gross values obtained from simultaneous over-all measurements. There is also fair agreement between the integrated results and available published information on the gross thermal transfer from a sphere.\r\n\r\nA detailed knowledge of the distribution of temperature, thermal flux, and the pressure gradients associated with the turbulent flow of fluids is of importance in creating a background of experimental facts from which it is possible to predict the transfer characteristics for a particular physical situation.\r\n\r\nSpecial methods and equipment employed in the measurement and control of temperature and thermal flux in an investigation of thermal transfer in turbulent gas streams are described. Measurements of the thermal flux and the pressure gradient are presented as a function of the imposed temperature distribution and macroscopic flow rate. They extend from gross velocities of 10 to 90 feet per second and to average temperature gradients as high as 1000[degrees] F. per foot.\r\n\r\nThe results represent a contribution to the knowledge of the shear and the thermal flux associated with the nonisothermal flow of air between parallel plates. As expected, the thermal transfer coefficients for nonuniform transfer are larger than those obtained in this work under conditions of uniform transfer.\r\n\r\nThe region near the boundary of a turbulently flowing fluid accounts for the greater part of the resistance to thermal transfer to or from the stream. An understanding of the influence of conditions of flow upon the temperature distribution near the boundary of turbulently flowing streams is required in order to permit the recent advances in fluid mechanics to be applied to the prediction of thermal transfer in steady flow.\r\n\r\nThe detailed temperature distribution near the boundary of a turbulent air stream flowing between parallel plates was measured at gross velocities from 10 to 90 feet per second and for average temperature gradients as high as 1000[degrees] F. per foot. The corresponding value of thermal flux was determined directly, and from these primary measurements the temperature gradient and eddy conductivity were established as a function of flow conditions.\r\n\r\nThe eddy conductivity was correlated with the position in the stream and the gross conditions of flow. The measurements permit estimation of the thermal transfer to a turbulently flowing air stream in conduits of large radius to be made with accuracy adequate for some engineering purposes for a variety of uniform and nonuniform conditions of thermal transfer." }, { "name": "Humphrey, Floyd Bernard", "degree": "PhD", "year": "1956", "title": "Studies in Paramagnetic Resonance", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03242004-114132", "creators": [ { "name": { "family": "Humphrey", "given": "Floyd Bernard" }, "id": "Humphrey-Floyd-Bernard", "display_name": "Humphrey, Floyd Bernard" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/RGNN-0K54", "abstract": "A paramagnetic resonance spectrometer has been designed and constructed which is particularly adaptable to problems in the field of chemistry. It is a wide range, high resolution instrument suitable for investigating the spectrum of paramagnetic substances from g = 0.7 to g = 7.5 with resonance lines from a fraction of a gauss to 1000 gauss wide. Spectra can be observed at temperatures from room temperature to liquid helium temperature using single crystals, powders, or solutions as samples. The sensitivity is such that 10[superscript 15] paramagnetic atoms are needed per sample.\r\n\r\nThe spectrum of gadolinium ion in a micro-crystalline sample of ceric oxide has been investigated. The observed resonance line contained structure that could not be resolved with extreme magnetic dilution (100,000:1) low temperature (4.5[degrees]K) or both. An explanation for this structure is suggested. The value of g for the line was measured at two different magnetic field strengths, as was the zero field splitting. An anomalous shift in the direction of the free ion value of g was found when the field was changed from 3400 gauss to 8600 gauss.\r\n\r\nThe spectrum of manganous ion in a micro-crystalline sample of aragonite was observed at both 3400 gauss and 8600 gauss. An isotropic hyperfine structure of 6 lines was observed. A precise comparison between theory and experiment was made showing excellent agreement.\r\n\r\nWork on other compounds is also reported." }, { "name": "Jacobson, Norman Ford", "degree": "PhD", "year": "1956", "title": "Studies in the Measurement of Nuclear Radiations of Extremely Low Intensity - Carbon 14 Dating", "advisor": "Yost, Don M.; Neher, Henry Victor; Bacher, Robert F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03242004-143552", "creators": [ { "name": { "family": "Jacobson", "given": "Norman Ford" }, "id": "Jacobson-Norman-Ford", "display_name": "Jacobson, Norman Ford" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." }, { "name": { "family": "Neher", "given": "Henry Victor" }, "id": "Neher-H-V", "role": "advisor", "display_name": "Neher, Henry Victor" }, { "name": { "family": "Bacher", "given": "Robert F." }, "id": "Bacher-R-F", "role": "advisor", "display_name": "Bacher, Robert F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M68S-AP25", "abstract": "The technical details of a radiation measuring system based on a quartz torsion fiber electroscope and a pressurized ionization chamber are described. This equipment is designed to measure the radiation intensity from the carbon-14 contained in a sample introduced into the system as carbon dioxide. This system, including the shielding, is shown to be capable of measuring nuclear radiations of extremely low intensities, on the order of 1/200 of the normal laboratory background level, with a probable error of approximately l%. The background radiation intensity observed with the system including the shielding is also on the order of 1/200 of the normal laboratory background level. The nature of background radiation and its relation to the measurement of such low intensities is discussed. It is shown that the main limitation in accuracy, with the equipment described here, is due to cosmic ray bursts. It is also shown that the major source of background radiation is external to the equipment, being thus due to cosmic rays and/or local external gamma ray emitting material contamination. Although the evidence is not conclusive, the data indicates in addition that the cosmic rays are the major contributor to this background radiation. The main conclusion which may be drawn from these results is that the selection of an equipment location is very effective in reducing the level of background radiation, thus permitting the measurement of radiation fields of extremely low intensity. The final application of this equipment was to the well known carbon-14 dating method originated by W. F. Libby. Several samples of interest were dated and the results are given. Of particular interest, are the samples from the Santa Rosa Islands off the California Coast, concerning an Indian culture which existed there before Christ and after." }, { "name": "Mower, Howard Frederick", "degree": "PhD", "year": "1956", "title": "I. Studies on Mixed Anhydride Systems. II. Studies of the Alpha-Chymotrypsin Catalyzed Hydrolysis of Specific Substrates", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06162004-132607", "creators": [ { "name": { "family": "Mower", "given": "Howard Frederick" }, "id": "Mower-Howard-Frederick", "display_name": "Mower, Howard Frederick" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/031V-1769", "abstract": "The synthesis and purification of p-nitrobenzoic-acetic mixed anhydride, p-methoxybenzoic-acetic mixed anhydride and benzoic-acetic mixed anhydride is described. The thermodynamic constants for the disproportionation reaction have been determined. A mechanism for this reaction is discussed. Measurements of the interaction of acetic and benzoic acids with the acetic-benzoic anhydride system have been made.\r\n\r\nThe cleavage of the mixed anhydrides with nucleophilic agents is described.\r\n\r\nThe synthesis of the following compounds is described: N-trimethylacetyl-L-tyrosinhydrazide, N-dichloroacetyl-L-tyrosinhydrazide, N-formyl-L-tyrosinhydrazide, N-trichloroacetyl-L-tyrosinamide and N-acetyl-L-cysteic acid carboxylamide. The kinetic constants for the [alpha] chymotrypsin hydrolysis of these substances are reported." }, { "name": "Nathan, Robert", "degree": "PhD", "year": "1956", "title": "The Crystal Structures of Two Compounds: I. A Base Derived from Veatchine. II. \u03b1-Triglycine", "advisor": "Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechETD:etd-06162004-152918", "creators": [ { "name": { "family": "Nathan", "given": "Robert" }, "id": "Nathan-Robert", "display_name": "Nathan, Robert" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ERA8-0Z65", "abstract": "Organic chemists at the University of New Brunswick, while investigating the alkaloid veatchine derived from Garrya veatchii, had isolated a degradation product C16H15N which they believed to be a substituted phenanthridine. A sample was submitted to us for investigation by X-ray diffraction. Using the phenanthrene-like nucleus as a \"heavy atom\" it was possible to determine the substituents. Difference syntheses indicated that the skeleton is not a phenanthridine but an aza-phenanthrene. The final structure obtained is l-methyl-7-ethyl-3-aza-phenanthrene. At one time the chemists were planning to synthesize each of nineteen isomers considered by them to be possible, but all of them in fact incorrect; the X-ray analysis directed them to the correct structure.\r\n\r\nA desire to investigate the bond lengths and angles of a peptide group located between two other peptide groups prompted the investigations of alpha-triglycine. In the h01 projection all atoms are resolved. The molecule takes on the extended chain configuration, and is twisted only to an extent necessary to make fullest use of all possible hydrogen bonds. The present stage of refinement shows no particular conflict with those dimensions for polypeptide chains presented by Pauling and Cory.\r\n\r\nAnother approach to the phase problem through the intensity continuum is also described.\r\n" }, { "name": "Peterson, Paul Eugene", "degree": "PhD", "year": "1956", "title": "I. Reactions of Phthaloylamino Acids: Modification of the Carboxyl Group of Amino Acid Derivatives. II. Derivatives of Indole 3-Carboxylic Acid. III. Metal Ion Complexes of Amidoximes: the Inhibition of the Alpha-Chymotrypsin Catalyzed Hydrolysis of Nicotinyl-L-Tyrosine Hydrazide by L-\u03b1-Acetamido-\u03b2-Phenylpropionamidoxime", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08012025-222724812", "creators": [ { "name": { "family": "Peterson", "given": "Paul Eugene" }, "id": "Peterson-Paul-Eugene", "display_name": "Peterson, Paul Eugene" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qmaa-9v82", "abstract": "Various derivatives of \u03b1-phthalimido-\u03b2-phenylpropionic acid\r\nhave been synthesized. starting from phenylalanine. The derivatives\r\nhave a doubly bound nitrogen or sulfur atom in place of the carbonyl\r\noxygen atom. The goal of the work was to prepare similar derivatives\r\nof other acylamino acids for evaluation as substrates in studies of\r\n\u03b1-chymotrypsin catalyzed hydrolysis. This has been accomplished in\r\nthe case of the amidoximes, as exemplified by the preparation of\r\nL-\u03b1-acetamido-\u03b2-phenylpropionamidoxime. The preparation of this\r\ncompound was accomplished by the use of a new method for cleaving\r\nthe phthaloyl group, discovered during the present study. However,\r\nthe above compound was not hydrolyzed by \u03b1-chymotrypsin at pH values\r\nranging from five to nine.
\r\n\r\n3-Indolecarbonyl chloride has been prepared by an unusual\r\nmethod and used to acylate \u03b1-amino acid derivatives.
\r\n\r\nThe enzyme-inhibitor dissociation constant of \u03b1-chymotrypsin\r\nand L-\u03b1-acetamido-\u03b2-pheynylpropionamidoxime has been determined\r\nusing nicotinyl-L-tyrosine hydrazide as the substrate.
" }, { "name": "Petracek, Francis James", "degree": "PhD", "year": "1956", "title": "Conversions of \u03b2-Carotene and Some Related Polyenes to Keto and Hydroxy Derivatives by Means of N-Bromosuccinimide and Boron Trifluoride", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechETD:etd-06212004-154038", "creators": [ { "name": { "family": "Petracek", "given": "Francis James" }, "id": "Petracek-Francis-James", "display_name": "Petracek, Francis James" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N6EY-9G47", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe reaction of N-bromosuccinimide (NBS) with [beta]-carotene in alcohol-containing chloroform results mainly in the formation of 4-keto-[beta]-carotene, 4,4'-diketo-[beta]-carotene, and 4-keto-3',4'-dehydro-[beta]-carotene, Their structures were clarified by relating them to known carotenoids through partial synthetic or degradative schemes. In the course of this work, the following new carotenoids were also prepared: 4-keto-4'-hydroxy-[beta]-carotene, 4,4'-dihydroxy-[beta]-carotene, 4-hydroxy-3',4'-dehydro-[beta]-carotene and 4-keto-[alpha]-carotene.\r\n\r\nA reaction mechanism for the conversion of carotenes to ketones is proposed, based on pertinent experiments. The infrared and visible spectra of the new compounds are discussed, and the provitamin A2 effect of the 3,4-dehydro compounds has been demonstrated. Synthetic 4,4'-diketo-[beta]-carotene has been identified with canthaxanthin occurring in some fungi and algae.\r\n\r\nThe investigation of the products from the hydrolysis and ethanolysis of BF3-carotenoid complexes has been continued and extended: [beta]-carotene, [retro]-dehydrocarotene and 3,4-dehydro-[beta]-carotene have yielded 4-hydroxy-[beta]-carotene. From 3,4-dehydro-[alpha]-carotene 4-hydroxy-[alpha]-carotene was obtained. [retro]-Bisdehydrocarotene gave a new type of carotenoid, viz. 2-hydroxy-3,4-dehydro-[beta]-carotene.\r\n\r\nFrom anhydrovitamin A1 a new isomer of vitamin A1, viz. 4-hydroxy-axeropthene, was obtained.\r\n\r\nA photometric method for determining the partition coefficients of carotenoids was devised and tested on thirty-two compounds.\r\n" }, { "name": "Richter, Henry Leopold Jr.", "degree": "PhD", "year": "1956", "title": "l. Hindered Rotation in Solid Hexamminecobalt(III) Chloride. II. Automatic Coulometric Titrations Involving an Amperometric End Point", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-151115", "creators": [ { "name": { "family": "Richter", "given": "Henry Leopold Jr." }, "id": "Richter-Henry-Leopold", "display_name": "Richter, Henry Leopold Jr." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S0Y5-4A62", "abstract": "Part I: A study has been made of the unusual behavior that solid hexamminecobalt(III) chloride exhibits when examined by the technique of nuclear magnetic resonance absorption. From the examples of substances exhibiting similar behavior to this one, the conclusion is reached that some sort of internal motion is taking place within the solid. On the basis of the structure of the hexamminecobalt(III) ion, and from information gathered on related ions, it is postulated that the motion involved is the rotation of the whole complex ion in the crystal lattice. From a study of the nuclear magnetic resonance absorption line width for the protons in the complex ion as a function of temperature, the motion is described in terms of a rate process.
\r\n\r\nThe general theory of nuclear magnetic resonance is discussed, and in particular the application of this technique to the study of rate processes. The design and construction of a nuclear magnetic resonance spectrograph are described.
\r\n\r\nPart II: An instrument has been developed for automatic control of coulometric titrations employing the dual indicator electrode amperometric end point. The instrument is capable of detecting the end of the titration and stopping the generation, freeing the analyst of this task. The titration is stopped at a pre-set indicator current, either as a \"dead stop\" end point or as a preliminary operation to determining the exact end point by extrapolation of the post end point current to zero. The operation of the instrument on three different types of coulometric titrations is described.
\r\n" }, { "name": "Rubalcava, Hector", "degree": "PhD", "year": "1956", "title": "Part I. The Infrared Spectra and Structure of Cyanamide. Part II. The Infrared Spectra of Formamide, N,N-Dideuteroformamide, and N-Methylformamide", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechETD:etd-06242004-155629", "creators": [ { "name": { "family": "Rubalcava", "given": "Hector" }, "id": "Rubalcava-Hector", "display_name": "Rubalcava, Hector" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EN6S-9V80", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\t\t\t\t\t\r\nThe prismatic spectra of crystalline cyanamide and of methylene chloride solutions of cyanamide were obtained from 2 to 15 microns, and of gaseous cyanamide from 2 to 6.5 microns. High dispersion spectra in the three micron region were obtained for all these substances. The rotational structure of the antisymmetric NH2 stretching vibration shows an intensity alternation which implies that cyanamide has a planar structure, belongs to the symmetry point group [...], and has the structural formula H2NCN. Geometrical parameters of the NH2 group were obtained using the spacing of the rotational structure of the three micron band, together with a non-critical estimate of the mean value of the two smallest rotational constants, and the mean value of the NH2 stretching frequencies. The HNH angle is approximately 126[degrees], and the NH bond distance is 1.002[Angstroms]. A vibrational assignment was made with the aid of Raman data obtained by Kahovec and Kohlrausch. A normal coordinate analysis of the vibrations primarily involving the NCN stretching and the HNH scissors deformations was made. This analysis gave values, depending parametrically on the HNH bending force constant, of the CN stretching and interaction force constants. The forms of the normal modes of the three lowest frequency [...] vibrations for a plausible set of force constants was calculated, and applied to a discussion of the intensities of the absorptions of these vibrations. The high dispersion spectra of methylene chloride solutions of cyanamide showed no absorptions attributable to hydrogen-bonded polymers of cyanamide.\r\n\r\nThe spectra of HCONH2, HCOND2 and HCONHCH3 were obtained in the gas and in the liquid states. The three micron spectrum of HCONH2 gas was examined under high dispersion. These data together with the results obtained by Prof. R. M. Badger in a study of vibrating mechanical models, and by Dr. R. Newman in a study of the polarized spectrum of sodium formate have been the basis for an analysis of the vibrational spectra of the formamides. An explanation has been presented for the differences between the spectra of each substance in the gas and in the liquid states based on the effects of hydrogen bonding. The spectral data have been used to support the hypothesis that formamide is a planar molecule, and an estimate of 0.993[Angstroms] for the NH bond distance based on the value of the mean frequency of the NH2 stretching vibrations has been made. The rotational structure of the three micron high dispersion band has been analyzed, and a value for the difference of the large rotational constant and the average of the two smallest rotational constants has been found which agrees, within experimental error, with the microwave value." }, { "name": "Schott, Garry Lee", "degree": "PhD", "year": "1956", "title": "Chemical Studies in Shock Waves", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06282004-143746", "creators": [ { "name": { "family": "Schott", "given": "Garry Lee" }, "id": "Schott-Garry-Lee", "display_name": "Schott, Garry Lee" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TQXE-RK75", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nShock waves in argon bearing about one percent nitrogen pentoxide vapor have been used to initiate the rapid decomposition of N2O5 between 450[degrees] and 1100[degrees]. The important intermediate in the reaction is the nitrate radical, NO3, whose characteristic absorption bands in the green and red are known. These bands have been identified in flash absorption spectrograms, and quantitative photoelectric measurements of absorption by NO3 have followed its appearance and disappearance in the reaction mixture. Simultaneous measurements with violet light have recorded the production of NO2.\r\n\r\nThe first step in N2O5 decomposition is: [...]. Near 500[degrees]K, the forward rate and the equilibrium in this reaction have been measured. Above 600[degrees]K, the dissociation is rapid and complete, and the rates of the bimolecular decomposition reactions [...] and [...] have been measured. The contributions of these steps have been established by experiments in the presence of excess NO2. The reaction [...] is fast, and although NO2 is unstable with respect to NO and O2 above about 600[degrees]K, the stoichiometric reaction [...] has been observed in the short times of these experiments. The rate equations and the constants and energies measured agree very well with predictions based on mechanisms known at room temperature.\r\n\r\nTwo papers on the rate of dissociation of molecular iodine, by the present author and others, are included. The abstracts accompanying these papers are on pages 118 and 131." }, { "name": "Shlichta, Paul Joseph", "degree": "PhD", "year": "1956", "title": "I. The Preparation and Configuration of Levorotatory 4,5-Dimethyl-1,3-Dioxolane. II. Studies of Color Centers in Alkali Halide Crystals. III. A Structural Investigation of Strontium-Zinc System", "advisor": "Pauling, Linus; Lucas, Howard J.; Bergman, Gunnar B.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06282004-145527", "creators": [ { "name": { "family": "Shlichta", "given": "Paul Joseph" }, "id": "Shlichta-Paul-Joseph", "display_name": "Shlichta, Paul Joseph" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Bergman", "given": "Gunnar B." }, "id": "Bergman-Gunnar-B", "role": "advisor", "display_name": "Bergman, Gunnar B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NJ4T-FQ21", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI. The configuration of the formal of [...]-2,3-butanediol has been established unequivocally by reactions of the diol under basic conditions with methylene iodide, methylene chloride, and chloromethyl acetate. The products are optically active, are alike, and are the same as the one obtained in the acid-catalyzed reaction of the glycol with formaldehyde.\r\n\r\nII. The coloration of sodium chloride by white x-radiation has been separated into two distinct types. The intense color at the surface involves the creation of new anionic vacancies by longwave radiation; aggregate color centers result from optical or thermal bleaching. The less intense coloration throughout the crystal is due to the short-wave radiation; no new vacancies are created and no secondary coloration occurs. Plastic deformation does not affect the overall colorability but greatly enhances the secondary coloration effects. Tentative mechanisms for these processes are discussed.\r\n\r\nStudies of the secondary radiative coloration, the so-called colloidal band in additively colored crystals, and the color of blue rocksalt have led to the suggestion that these color centers are members of a continuous series of F center aggregates. The possibility of a true colloidal dispersion in additively colored sodium chloride has been investigated by comparison of these crystals with sodium chloride, known to contain colloidal copper.\r\n\r\nCrystals of sodium chloride have been grown containing heavy metal ion impurities. Spectrophotometric studies have been made of these crystals before and after radiative and additive coloration. The ultraviolet absorption bands in the uncolored crystals have been tentatively explained in terms of V centers. X-radiation and bleaching destroys some of the absorption bands and creates others.\r\n\r\nIII. An investigation of the strontium-zinc system, using x-ray diffraction techniques, has revealed four intermetallic phases. The compound SrZn13, previously reported elsewhere, has been confirmed with respect to composition and symmetry. The second phase, SrZn5, contains 24 atoms in its unit cell, is orthorhombic, and has been tentatively assigned the symmetry Pmnb. The third phase, SrZn2, is also orthorhombic, and has 12 atoms in a body centered unit cell. No single crystals of the fourth phase have been isolated, but the composition has been shown to correspond approximately to Sr3Zn2 or Sr4Zn3.\r\n\r\nThe structure of the [...] phase has been worked out in detail. It has the space group [...]-Imma, and corresponds to an orthorhombic distortion of the hexagonal magnesium boride structure." }, { "name": "Whiteker, Roy Archie", "degree": "PhD", "year": "1956", "title": "I. An Ion-Exchange Method for a Volumetric Determination of Sulfate. II. A Study of Iron(lII) Sulfate Complex Ions. III. A Sodium\r\nCoulometer. IV. A Sodium-Ion Glass Electrode", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-07162004-153912", "creators": [ { "name": { "family": "Whiteker", "given": "Roy Archie" }, "id": "Whiteker-Roy-Archie", "display_name": "Whiteker, Roy Archie" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YWA8-4962", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA procedure has been developed for a volumetric determination of sulfate in solutions containing iron(III), chloride, and bromide. A solution is passed through the hydrogen form of a cation exchange resin, the effluent is titrated for hydrogen and for halide ion, and the sulfate is calculated from these titrations. The procedure was successfully used for a determination of sulfur in a pyrite ore.\r\n\r\nThe complexing of iron(III) with sulfate was studied both spectrophotometrically and by an equilibrium ion-exchange distribution method. Association constants and extinction coefficients for the [...] and [...] complex ions were obtained from these studies.\r\n\r\nResistance measurements and a study of the effect of current flow were made on a redesigned sodium coulometer. A number of the liabilities inherent in a sodium coulometer were considered.\r\n\r\nA literature survey was made on the behavior of clay, ion-exchange, and glass membranes in solutions of various ionic species. Glass-membrane electrodes were prepared from four types of glass. The sodium-ion response of these electrodes in various buffer solutions was determined by following the change in potential of a glass-membrane electrode--buffer solution--calomel electrode system caused by varying the sodium-ion concentration of the solution. Resistance measurements were made on some of the glass membranes." }, { "name": "Applequist, Douglas Einar", "degree": "PhD", "year": "1955", "title": "Methylenecyclobutene and Related Substances", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11202003-141714", "creators": [ { "name": { "family": "Applequist", "given": "Douglas Einar" }, "id": "Applequist-Douglas-Einar", "display_name": "Applequist, Douglas Einar" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7N2P-TH64", "abstract": "Methylenecyclobutene was synthesized by a modification of the Willstatter cyclobutene synthesis, with the use of the Hofmann reaction to introduce the intracyclic double bond. A novel feature of the synthesis was the use of anthracene as a blocking group for the exocyclic double bond during the malonic-ester ring closure. 4,4-Dimethylmethylenecyclobutene was synthesized from pinene, and 3-phenylmethylenecyclobutene was obtained by condensation of allene and phenylacetylene.\r\n\r\nThe structures of the methylenecyclobutene dibromides and of the polymers formed by three different mechanisms were investigated. The results were shown to be consistent with the predictions of simple molecular orbital theory.\r\n\r\n3-Methylenetrimethylene oxide was synthesized and its structure investigated by electron diffraction.\r\n\r\nThe structures of the dibromides of methylenecyclobutane were determined and found to be consistent with a carbonium-ion mechanism for bromine addition." }, { "name": "Arcand, George Myron", "degree": "PhD", "year": "1955", "title": "I. Studies of the Distribution of Inorganic Substances Between Aqueous and Non-Aqueous Phases. II. Studies in Coulometric Analysis", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11212003-111738", "creators": [ { "name": { "family": "Arcand", "given": "George Myron" }, "id": "Arcand-George-Myron", "display_name": "Arcand, George Myron" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XM4H-9N36", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe distribution of arsenic (III) between aqueous HC1 solutions and [...] ether has been studied. Arsenic chloride species have been proposed, equilibrium constants have been calculated relating these species in the aqueous solutions, and distribution constants have been calculated for each species. The data from the distribution experiments have been correlated with solubility and electromotive force data taken from the literature.\r\n\r\nA partial study has been made of the distribution of ferric thiocyanate and of KSCN and NaSCN between aqueous solutions and tributyl phosphate. Sufficient data were taken to indicate that the distribution of the alkali thiocyanates is strongly dependent on the ionic strength of the aqueous solutions and that species of ferric thiocyanate other than (Fe(SCN)[subscript 3])[subscript x] are extracted by tributyl phosphate.\r\n\r\nA coulometric method for determining microgram quantities of bromate has been developed which made use of electrolytically generated cuprous copper as the intermediate. Optimum conditions for the titration were determined. Quantities of bromate ranging from 18 to 240 micrograms have been determined within 0.3 microgram.\r\n\r\nA coulometric method for the determination of ammonia has been developed which made use of electrolytically generated bromine in alkaline solutions as the intermediate. The effects of pH and of certain metal ions on the titration were studied. Quantities of ammonia ranging from 14 to 230 micrograms have been determined within 0.2 microgram." }, { "name": "Bernhard, Richard Allan", "degree": "PhD", "year": "1955", "title": "Studies on the Mode and Mechanism of Action of alpha-Chymotrypsin", "advisor": "Niemann, Carl G.; Bonner, James Frederick", "url": "https://resolver.caltech.edu/CaltechETD:etd-11212003-114338", "creators": [ { "name": { "family": "Bernhard", "given": "Richard Allan" }, "id": "Bernhard-Richard-Allan", "display_name": "Bernhard, Richard Allan" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." }, { "name": { "family": "Bonner", "given": "James Frederick" }, "id": "Bonner-J-F", "role": "co-advisor", "display_name": "Bonner, James Frederick" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CPFB-ZF49", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe enzyme-inhibitor dissociation constants, i. e. , K[subscript I] values, for alpha-chymotrypsin and two competitive inhibitors, indole-2-carboxylate and cinchoninamide, have been determined at pH 7. 9 and 25[degrees].\r\n\r\nA new colorimetric procedure for the determination of proteolytic activity employing the reaction of ninhydrin with ammonia has been developed.\r\n\r\nA study has been made of the effect of buffer species and ions upon the course of alpha-chymotrypsin catalyzed hydrolyses. It has been demonstrated for the case at hand that K[subscript S] is essentially independent of buffer species and ionic strength. The discrepancies between values of k[subscript 3], evaluated in the presence of THAM-HCl buffers and in the presence of phosphate buffers, appear to be due principally to the effects of the increased ionic strength of the phosphate buffers. A number of enzyme-inhibitor dissociation constants have been evaluated in different buffer systems. During the evaluation of K[Subscript I] values for anionic, bifunctional, competitive inhibitors of alpha-chymotrypsin, it was determined that the presence of phosphate buffers apparently increased the affinity of the enzyme for the inhibitor. A possible mechanism for this phenomenon has been proposed and has been supported by experimental observations.\r\n\r\nIt has been demonstrated that in a typical alpha-chymotrypsin catalyzed hydrolysis, the reaction proceeds in solution insofar as can be experimentally determined, and that wall effects are unimportant within the limits of experimental error.\r\n\r\nAn investigation has been made of the possible use of dilatometry as a means of following the course of enzyme catalyzed hydrolyses. A number of instruments have been developed and discussed. Some typical data have been experimentally determined and analyzed in the usual manner." }, { "name": "Britton, John Doyle", "degree": "PhD", "year": "1955", "title": "Shock Waves in Chemical Kinetics", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-11262003-143942", "creators": [ { "name": { "family": "Britton", "given": "John Doyle" }, "id": "Britton-John-Doyle", "display_name": "Britton, John Doyle" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y16V-VY27", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe rates of dissociation of I[subscript 2] in N[subscript 2] and CO[subscript 2], and Br[subscript 2] in A were measured at temperatures around 1300[degrees]K by heating room temperature mixtures by means of shock waves and observing the subsequent reactions. The rates of recombination of both I[subscript 2] and Br[subscript 2] were found to decrease with increasing temperature. The results, combined with room temperature measurements seemed to be best expressed in the form K[subscript R] = A exp([...]/RT). Attempts to measure the efficiency of I[subscript 2] or Br[subscript 2] molecules as third bodies for the recombination gave only rather wide limits to the possible values.\r\n\r\nThe experiments also showed that CO[subscript 2] is vibrationally relaxed at high temperatures in a time short compared to the reaction time of 20-200 microseconds. It was not possible to decide whether or not N[subscript 2] is vibrationally relaxed at this temperature in this short time.\r\n\r\nExtinction coefficients of I[subscript 2] and Br[subscript 2] were measured as a function of the temperature. They appeared to be dependent on the inert gas." }, { "name": "Clayton, Robert Norman", "degree": "PhD", "year": "1955", "title": "Variations in Oxygen Isotope Abundances in Rock Minerals", "advisor": "Epstein, Samuel", "url": "https://resolver.caltech.edu/CaltechETD:etd-11242003-105309", "creators": [ { "name": { "family": "Clayton", "given": "Robert Norman" }, "id": "Clayton-Robert-Norman", "display_name": "Clayton, Robert Norman" } ], "advisors": [ { "name": { "family": "Epstein", "given": "Samuel" }, "id": "Epstein-S", "role": "advisor", "display_name": "Epstein, Samuel" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SN3M-5S20", "abstract": "Analytical techniques for determination of oxygen isotope abundances in silicates and oxides have been investigated. The reduction of compounds with carbon at high temperatures gives reliable results only from a few important minerals, including quartz and iron oxides. Liberation of oxygen from compounds using fluorine has more wide-spread application, but is more susceptible to errors by contamination.\r\n\r\nOxygen isotope analyses have been made on nineteen natural samples of quartz and associated carbonates, and on seventeen samples of quartz and associated iron oxides. It has been found that, for suitable samples, the isotopic fractionation measured between two associated minerals can be used to fix the temperature at which the minerals crystallized.\r\n\r\nSeveral geological problems are discussed on the basis of the oxygen isotope data. In cases where the geological evidence is clear-cut, the conclusions from the isotope analyses are in complete agreement with those from geological reasoning." }, { "name": "Cox, Eugene Floyd", "degree": "PhD", "year": "1955", "title": "Carbonium Ion Rearrangements in Reactions of Cyclopropylcarbinyl and Cyclobutyl Derivatives", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042003-093721", "creators": [ { "name": { "family": "Cox", "given": "Eugene Floyd" }, "id": "Cox-Eugene-Floyd", "display_name": "Cox, Eugene Floyd" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NS0V-W084", "abstract": "1-Methylcyclopropylcarbinylamine and 1-methylcyclobutylamine on treatment with aqueous nitrous acid gave only 1-methylcyclobutanol, while [beta]-methylallylcarbinylamine gave predominantly [beta]-methylallylcarbinol and 1-methylcyclobutanol, with smaller amounts of of [alpha]-methyl-[beta]-methylallyl alcohol and [beta]-methyl-[gamma]-methylallyl alcohol and possibly 2-3% of 1-methylcyclopropylcarbinol. The 1-methylcyclobutanol from 1-methylcyclopropylcarbinyl-C[superscript 14]-amine contained only 2.6 of the total C[superscript 14]-activity in C-3. The corresponding reaction in acetic acid gave 1-methylcyclobutyl acetate with 3.1% of the C[superscript 14] in C-3.\r\n\r\n1-Methylcyclopropylcarbinyl chloride solvolyzes in 50% aqueous ethanol ca. 10 times faster than 1-methylcyclobutyl chloride and about as fast as t-butyl chloride.\r\n\r\nIt was concluded that the above carbonium-ion type reactions of 1-methylcyclobutyl and 1-methylcyclopropylcarbinyl derivatives are best accounted for by formation, as the important reaction intermediate, of an unsymmetrical, nonclassical carbonium ion, structurally similar to the classical 1-methylcyclobutyl cation." }, { "name": "Felsenfeld, Gary", "degree": "PhD", "year": "1955", "title": "Some Modifications and Applications of the Pauling Theory of Ferromagnetism", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-12032003-093700", "creators": [ { "name": { "family": "Felsenfeld", "given": "Gary" }, "id": "Felsenfeld-Gary", "display_name": "Felsenfeld, Gary" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XD9G-QV08", "abstract": "The Pauling theories of ferromagnetism and metal structure are discussed and compared with other theories. The results of Pauling are derived with the inclusion of previously neglected temperature effects. The metallic band structure assumed by Pauling is also modified and the modification is shown to lead to better agreement with the results of previous investigations.
\r\n\r\nThe ferromagnetic alloys are studied with the use of the Pauling theory. It is demonstrated that the simple theory is inadequate for the treatment of alloys, and an improved model is proposed. Calculations based upon this model provide qualitatively correct predictions of the behavior of the Curie temperature of many ferromagnetic alloys. Explanations of the abnormal behavior of the iron-vanadium and nickel-chromium alloys are offered.
\r\n\r\nThe effects of non-uniform electron distribution in ferromagnetic crystals are considered. An expression for the Curie temperature is derived. If reasonable values of the parameters which describe the non-uniformity are inserted in this expression, the result is an increase in the predicted Curie temperature of nickel and a decrease in that of iron, both of which are improvements. Some methods of estimating the values of the parameters are discussed.
\r\n\r\nIt is concluded that the Pauling theory, with appropriate modifications, will accurately describe ferromagnetic behavior.
" }, { "name": "Fort, Arthur W.", "degree": "PhD", "year": "1955", "title": "The Reaction of 3-Arylpropylamines with Nitrous Acid", "advisor": "Roberts, John D.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12122003-161659", "creators": [ { "name": { "family": "Fort", "given": "Arthur W." }, "id": "Fort-Arthur-W", "display_name": "Fort, Arthur W." } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PCT4-DB71", "abstract": "3-Phenylpropylamine-1-C\u00b9\u2074 reacts with nitrous acid in aqueous solution to give hydrocinnamyl alcohol, benzylmethylcarbinol and allylbenzene in the ratio 2.5:1.6:1.0. Under similar conditions, 3-(p-methoxyphenyl)-propylamine-1-C\u00b9\u2074 gives p-methoxyhydrocinnamyl alcohol, p-methoxybenzylmethylcarbinol\r\nand p-methoxyallylbenzene in the ratio 2.1:1.4:1.0. No evidence was found for the presence of other isomeric alcohols or olefins.
\r\n\r\nA sample of each product from 3-phenylpropylamine-1-C\u00b9\u2074 was oxidized to benzoic acid, which was found to be inactive in each case. Likewise, anisic acid obtained from each of the products from 3-(p-methoxyphenyl)- propylamine-1-C\u00b9\u2074 was found to be inactive.
\r\n\r\nThe number two carbon atom of each of the six products was shown to contain less than 0.5% of the total C\u00b9\u2074 activity of the product except in the case of benzylmethylcarbinol-C\u00b9\u2074, where the activity at C-2 was found to be 0-3%.
\r\n\r\nThese results eliminate the symmetrical carbonium ions having structures A and B as intermediates in the reactions studied.
\r\n\r\n[chemical formulae omitted]
" }, { "name": "Jennings, Robert Ross", "degree": "PhD", "year": "1955", "title": "I. The Kinetics of the Alpha-Chymotrypsin Catalyzed Hydrolysis of Acetyl-L-Hexahydrophenylalaninamide. II. The Influence of pH on the Kinetic Constants for Alpha-Chymotrypsin Catalyzed Reaction Involving Selected Substrates and Inhibitors. III. Genetic Studies in Neurospora crassa", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01132004-140522", "creators": [ { "name": { "family": "Jennings", "given": "Robert Ross" }, "id": "Jennings-Robert-Ross", "display_name": "Jennings, Robert Ross" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FRZ7-TZ35", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe kinetic constants for the alpha-chymotrypsin-catalyzed hydrolysis of acetyl-L-hexahydrophenylalaninamide have been determined at 25[degrees] and pH 7.9. This study indicates that aromaticity in the amino acid side chain is neither essential nor particularly helpful to the action of alpha-chymotrypsin. Some computational procedures are discussed.\r\n\r\nThe kinetic constants for the alpha-chymotrypsin-catalyzed hydrolyses of L-tyrosinhydroxamide and acetyl-L-tyrosinhydroxamide have been determined at 25[degrees] at several pH's. The inhibition constants of variously ionizing inhibitors have also been determined at several pH's. The observations are generally consistent with formulations based on the existence of differently protonated forms of the enzyme and enzyme-substrate complexes.\r\n\r\nPotentiometric titrations of sour hydroxamic acids reveal that the [...] values for these acids range from 9.0 to 9.5, and that these acids are mach weaker than previously believed.\r\n\r\nSome of the conditions necessary for the good expression of the phenotype dotted in Neurospora crassa have been determined. The linkage and centromere distance of the gene controlling tyrosinase thermostability in Neurospora crassa have been determined by genetic studies." }, { "name": "King, James", "degree": "Masters", "year": "1955", "title": "The Kinetics of the Oxygenation of Ferrous Ion in Phosphoric Acid Containing Pyrophosphate", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01072004-101648", "creators": [ { "name": { "family": "King", "given": "James" }, "id": "King-James", "display_name": "King, James" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9W2D-4P13", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\t\r\nThe kinetics of the ferrous-oxygen reaction in an acid solution containing phosphate and pyrophosphate has been investigated. The rate law at [...] is [...]. Sodium perchlorate is used to maintain the ionic strength at 1.0-l.1M. There is inhibition due to ferric ion. This phase of the reaction has not been investigated. It is believed that the inhibition is due to the insolubility of ferric pyrophosphate at high concentrations and to the formation of complexes at low concentrations. The following mechanism, suggested by Weiss, is consistent with the experimental results. [...]. The rate of the reaction is given by [...]. The phosphate and pyrophosphate species catalyse the reaction through complex ion formation." }, { "name": "Lutwack, Ralph", "degree": "PhD", "year": "1955", "title": "Studies on the Mode of Enzyme Catalysis and the Hydrolysis of Bis-P-Dimethylaminobenzalazine", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01262004-093505", "creators": [ { "name": { "family": "Lutwack", "given": "Ralph" }, "id": "Lutwack-Ralph", "display_name": "Lutwack, Ralph" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CA38-8B92", "abstract": "The alpha-chymotrypsin catalyzed hydrolysis of four L-tyrosinhydrazides at 25[degrees]C have been studied. The values of the kinetic constants K[subscript s] and k[subscript 3] for L-tyrosinhydrazide, acetyl L-tyrosinhydrazide, and nicotinyl L-tyrosinhydrazide have been evaluated by the usual procedure. The values of these constants for benzoyl L-tyrosinhydrazide have been obtained by the method of competitive hydrolysis.\r\n\r\nThe procedure for the quantitative determination of hydrazine by the reaction with p-dimethylaminobenzaldehyde to form the corresponding azine has been adapted to the study of the rate of the hydrolysis of alpha-amino acid hydrazides.\r\n\r\nThe rates of formation and of hydrolysis of bis p-dimethylaminobenzalazine have been studied under various conditions. The effects of dielectric constant, ionic strength, acid concentration, and temperature on the rate of hydrolysis have been investigated. The acid dissociation constants for p-dimethylaminobenzaldehyde in two distinct ethanol-water systems have been determined. The acid dissociation constants for the hydrazone and the azine of p-dimethylaminobenzaldehyde have been obtained. The value of the constant for the assumed aldehyde- hydrazine- hydrazone equilibrium has been calculated." }, { "name": "Manning, David Treadway", "degree": "PhD", "year": "1955", "title": "l. Some Studies in Enzyme Kinetics. II. The Oxidation of 3-Indoleacetic Acid by Plant Enzymes. III. The Synthesis of Some \u03b1-Alkyl \u03b1-Amino Acids and Their Derivatives", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01142004-142952", "creators": [ { "name": { "family": "Manning", "given": "David Treadway" }, "id": "Manning-David-Treadway", "display_name": "Manning, David Treadway" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PC3Z-A208", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe kinetics of the alpha-chymotrypsin catalyzed hydrolysis of N-carboethoxy-L-tyrosinamide have been determined in aqueous solution at 25[degrees]C and at both pH 7.9 and pH 8.2. The enzyme-inhibitor dissociation constants of N-carboethoxy-D-tyrosinamide, N-carboethoxy-D-tyrosinmethylamide, and N-carboethoxy-L-tyrosinmethylemide have been evaluated in aqueous solution at 25[degrees]C, the former at pH 7.9 and the latter two at pH 7.6. The L isomers of each enantiomorphic pair appear to have a greater affinity for the enzyme than do their respective D-isomers.\r\n\r\nAn investigation into the nature of the enzymatic oxidation products of 3-Indoleacetic acid (IAA) has been made. 3-Indolealdehyde, o-formamidoacetophenone, o-aminoacetophenone, and 4-hydroxyquinoline have been eliminated as possible major products of the reaction.\r\n\r\nA study of synthetic routes to the alpha-alkyl alpha-amino acids has been made. DL-alpha-Methlphenylalanine and DL-alpha-methyltyrosine have been synthesized. All attempts to resolve these compounds by enzymatic means have failed." }, { "name": "Marshall, Royal Richard", "degree": "PhD", "year": "1955", "title": "I. The Rate of Recombination of Iodine Atoms. II. Some Studies of the Trace Quantities of Lead, Uranium, and Thorium in Marine Carbonate Skeletons", "advisor": "Davidson, Norman R.; Patterson, Clair C.; Brown, Harrison", "url": "https://resolver.caltech.edu/CaltechETD:etd-01152004-092735", "creators": [ { "name": { "family": "Marshall", "given": "Royal Richard" }, "id": "Marshall-Royal-Richard", "display_name": "Marshall, Royal Richard" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." }, { "name": { "family": "Patterson", "given": "Clair C." }, "id": "Patterson-C-C", "role": "advisor", "display_name": "Patterson, Clair C." }, { "name": { "family": "Brown", "given": "Harrison" }, "id": "Brown-Harrison", "role": "advisor", "display_name": "Brown, Harrison" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KV4S-PC49", "abstract": "PART I.
\r\n\r\nThe rate constants for the homogeneous recombination of iodine atoms in the gas phase I+I+M \u2192 d[I\u2082]/d[I\u2082][M], have been measured for the gases M=A, n\u0332e\u0332o\u0332-C\u2085H\u2081\u2082 and n\u0332-C\u2085H\u2081\u2082 at room temperature. The rate constants are 4.2 (\u00b10.4) x 10\u2079, 58 (\u00b14) x 10\u2079, and 65 (\u00b16) x 10\u2079 liter\u00b2mole\u207b\u00b2sec\u207b\u00b9, respectively. In these experiments and those with iodine solutions, a short, intense pulse of light from a flash lamp dissociated 1-10% of the iodine molecules in a reaction cell. The photoelectric cell response to a light signal modulated with the change in the iodine atom concentration was amplified and used as the vertical deflection input of an oscilloscope. The oscilloscope trace, a direct indication of the subsequent recombination observed during periods from 0.0002 sec after the flash to as long as 0.01 sec, was recorded photographically.
\r\n\r\nThe rate constants for the recombination of iodine atoms in the liquids CCl\u2084 and n\u0332-C\u2087H\u2081\u2086, d[I\u2082]/d[I\u2082], were found to be at room temperature 0.7 (\u00b10.11) x 10\u00b9\u2070 and 2.2 (\u00b10.4) x 10\u00b9\u2070 liter mole\u207b\u00b9sec\u207b\u00b9, respectively. The primary quantum yields in the solutions were found to 0.19 (\u00b10.05) and 0.41 (\u00b10.26), respectively.
\r\n\r\nPART II.
\r\n\r\nA procedure is described for the chemical isolation from carbonates of microgram quantities of lead, uranium, and thorium suitable for mass spectrometric analyses. The concentration of lead in a Jurassic belemnite as well as a Mississippian Spirifer has been found to be less than 1 ppm while for Strombus gigas, a living species of gastropod, the value 0.19\u00b10.04 ppm was found. The uranium concentration in this gastropod was determined as 0.036\u00b10.002 ppm. The isotopic composition of the lead from the Strombus gigas has also been determined and is compared to other analyses of \"common\" lead.
" }, { "name": "Petersen, Donald Ralph", "degree": "PhD", "year": "1955", "title": "The Crystal Structure of Feist's Acid", "advisor": "Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202004-095607", "creators": [ { "name": { "family": "Petersen", "given": "Donald Ralph" }, "id": "Petersen-Donald-Ralph", "display_name": "Petersen, Donald Ralph" } ], "advisors": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SXC6-W012", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe crystal structure of Feist's acid, 1-methylenecyclopropane-trans-2,3-dicarboxylic acid, has been examined. The substance crystallizes in the triclinic system with space group [...]. Two enantiomorphous molecules of formula [...] are in the unit cell; the direct-cell constants are [...] and [...]. There is good cleavage at the face (010), and this is also the twinning plane.\r\n\r\nThe intensity data from equi-inclination Weissenberg photographs about each crystal axis were utilized in selecting and then refining a trial structure. Punched-card computing techniques were used to carry out least-squares refinements of atomic positions; two Fourier summations aided in final refinement. All refining work was based on full three-dimensional data.\r\n\r\nHydrogen bonds bind individual molecules into chains which extend in the [...] direction through the crystal. The methylene groups extended in the [...] direction form cogs on the chains, and two chains related by centers of symmetry are intermeshed closely." }, { "name": "Pings, Cornelius John", "degree": "PhD", "year": "1955", "title": "Part One. An Orthogonal Polynomial Equation of State. Part Two. Application of the Benedict Equation of State to the Methane-n-Pentane System. Part Three. Isobaric Heat Capacity at Bubble Point of n-Decane", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01202004-144113", "creators": [ { "name": { "family": "Pings", "given": "Cornelius John" }, "id": "Pings-Cornelius-John", "display_name": "Pings, Cornelius John" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/QSJF-1657", "abstract": "PART ONE\r\n\r\nAn equation of state has been developed which is a series expansion in orthogonal polynomials. The evaluation of coefficients by least squares methods is significantly simpler than for the case of a power series expansion. The values of the expansion coefficients are independent of the point of truncation of the series. Additional terms may be added to the equation without necessitating recomputation of existing coefficients. The Tchebichef and Gram polynomials were used.\r\n\r\nThe equation of state has been applied to propane for pressures up to 10,000 psia in the temperature interval 100[degrees] to 460[degrees] F. Terms involving eighth and higher powers of reciprocal molal volume were found not to contribute significantly to the description. The equation predicts volumetric behavior, phase behavior, thermodynamic properties, the critical state, and the second virial coefficient with an accuracy that is promising. Limited experience in application indicates that the equation is easier to handle with automatic digital computing equipment than is the Benedict equation of state.\r\n\r\nPART TWO\r\n\r\nValues of the coefficients for the Benedict equation of state were determined by least squares methods from experimental data for each of a series of mixtures of the methane-n-pentane system. In addition, values were obtained for the interaction constants for groupings of the Benedict coefficients corresponding to the second and third virial coefficients. Corresponding values of the interaction constants predicted by the methods suggested by Benedict are included for comparison. Measures of the accuracy of description for the interaction constants determined by the several different methods are reported.\r\n\r\nInteraction constants were evaluated by least squares methods for the methane-n-pentane system in the liquid and gas phases at pressures up to 5,000 pounds per square inch in the temperature interval between 100[degrees] and 460[degrees] F. The accuracy of description of the volumetric behavior was improved severalfold over that obtained with the constants calculated from the behavior of the components by the method suggested by Benedict. Such methods may prove useful in evaluating interaction constants for mixtures as a function of the characteristics of the system involved.\r\n\r\nPART THREE\r\n\r\nThe isobaric heat capacity at bubble point of n-decane was determined in the temperature interval 80[degrees] to 200[degrees] F. Measurements were made in the two-phase region utilizing a constant volume calorimeter. The energy required to change the temperature of the calorimeter and contents was determined for each of two quantities of n-decane. The effect of the gross heat capacity of the bomb was eliminated by considering the difference of these two sets of measurements. The two-phase isochoric measurements were transformed to values of the isobaric heat capacity at bubble point by applying a thermodynamic correction involving the volumetric properties of the gas and liquid phases and the heat capacity of the gas phase." }, { "name": "Sato, Kazuhiko", "degree": "PhD", "year": "1955", "title": "Part I. Effect of Shape on Evaporation of Drops of n-Heptane. Part ll. Thermal and Material Transport from Spheres into a Turbulently Flowing Air Stream. Part Ill. Temperature Gradients in Turbulent Gas Streams Recovery Factors in Steady, Uniform Flow", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01212004-095601", "creators": [ { "name": { "family": "Sato", "given": "Kazuhiko" }, "id": "Sato-Kazuhiko", "display_name": "Sato, Kazuhiko" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/QGB7-3769", "abstract": "I.\r\n\r\nMeasurements of the rate of evaporation of drops of varying shapes are required in order to determine the influence of such a variable on this important industrial transport process. Few data, if any, are available concerning the evaporation of drops of hydrocarbons.\r\n\r\nMeasurements were made of the evaporation of drops of n-heptane at air velocities from 2 to 8 feet per second, corresponding to Reynolds numbers as high as 200. The transport rate was established for drops under approximately 30 different conditions, and for each drop the shape, surface area, and volume were determined in detail. The measurements were made at an air temperature of 100[degrees] F. and at a low level of turbulence, with negligible radiant transfer to the drop. The temperature of the evaporating drop was measured with small thermocouples.\r\n\r\nThe results indicate a marked influence of the shape of the drop on its evaporating rate, and the Sherwood number was found to increase by as much as 30 percent for drops which deviate significantly from spherical forms. The present results, when reduced to the behavior of spheres, are in excellent agreement with the early measurements of Frossling and in fair agreement with those of Ranz and Marshall.\r\n\r\nII.\r\n\t\r\nAn investigation was made on the effect of turbulence level on the thermal and material transport from spherical surfaces in a turbulently flowing air stream. A high level of turbulence was produced at the location of the test sphere by inserting a perforated plate in the flowing air stream.\r\n\t\r\nMeasurements were made of the rate of heat flow from a polished silver sphere, 0.500 inch in diameter, at air velocities from 4 to 32 feet per second. The measurements were made at a bulk air temperature of 100[degrees] F.\r\n\t\r\nMeasurements were made of the rate of evaporation of n-hexane and n-heptane from a porous sphere, 0.500 inch in diameter, at air velocities from 2 to 35 feet per second. The measurements were made at bulk air temperatures of 85[degrees] f., 100[degrees] F. and 115[degrees] F.\r\n\t\r\nThe results indicate that the turbulence level in the flowing air stream has a marked influence on the magnitude of the transfer coefficients. It was found that, in an air stream flowing at a bulk velocity of 16 feet per second with a turbulence level of 13 per cent, the Nusselt number increased by 11 per cent over the value obtained in the undisturbed air stream. The Sherwood number was found to increase by 14 per cent under the same flow condition.\r\n\t\r\nThe data obtained in this investigation were compared where possible with published information of similar nature.\r\n\r\nIII.\r\n\r\nAt high velocities the temperature variation across a flowing stream is appreciable under steady conditions for fluids having a high Prandtl number. A knowledge of such temperature distributions within steady, uniform streams is needed in certain thermal transport calculations. This information is not readily available in the literature.\r\n\r\nBy utilizing available information concerning the dissipation of kinetic energy and the thermal transport in laminar turbulently flowing streams, expressions were derived for the temperature distribution in fluids flowing between infinite parallel plates and in circular conduits. The calculations included both adiabatic and isothermal conditions at the wall.\r\n\r\nThese expressions differ somewhat from the relationships which have been derived for the temberature distribution in fluids flowing along a plate in an infinite stream under isobaric conditions. Recovery factors are directly proportional to the Prandtl number and not to the square root of the Prandtl number as found for the case of isobaric flow. Only the value of the Prandtl number is required in order to establish the temperature distribution under known conditions of laminar flow, whereas supplemental information is required in order to determine the behavior in turbulent flow." }, { "name": "Semenow, Dorothy Ann", "degree": "PhD", "year": "1955", "title": "1. The Mechanism of Aminations of Halobenzenes. ll. Quantum Mechanical Calculations of Electrical Effects of Substituents in Para-substituted Anilines", "advisor": "Roberts, John D.; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-01212004-110215", "creators": [ { "name": { "family": "Semenow", "given": "Dorothy Ann" }, "id": "Semenow-Dorothy-Ann", "display_name": "Semenow, Dorothy Ann" } ], "advisors": [ { "name": { "family": "Roberts", "given": "John D." }, "id": "Roberts-J-D", "role": "advisor", "display_name": "Roberts, John D." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/C8SK-WN09", "abstract": "PART I. The Mechanism of Aminations of Halobenzenes.\r\n\r\nAn elimination-addition mechanism, probably involving a \"benzyne\" intermediate, was established for the rearrangements which often occur in the conversion of non-activated aryl halides to arylamines with metallic amides. The evidence for the \"benzyne\" intermediate was obtained through 14C-tracer studies of rearrangements with iodobenzene, experiments designed to determine the role of the hydrogen atom located ortho to the displaced halogen atom and studies of orientations in the reactions of substituted halobenzenes.\r\n\r\nPART II. Quantum Mechanical Calculations of Electrical Effects of Substituents in Para-substituted Anilines.\r\n\r\nCalculations made by the simple molecular orbital method indicated that the relative basicities of aromatic amino groups para to electron-attracting substituents provide a reasonable measure of the charge on C4." }, { "name": "Sly, William Glenn", "degree": "PhD", "year": "1955", "title": "I. The Crystal Structure of Oxamide. ll. The Crystal Structure of 15,15'-Dehydro-\u03b2-Carotene", "advisor": "Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechETD:etd-01262004-143104", "creators": [ { "name": { "family": "Sly", "given": "William Glenn" }, "id": "Sly-William-Glenn", "display_name": "Sly, William Glenn" } ], "advisors": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8GNV-3M53", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nI\r\n\r\nA two-dimensional trial structure has been determined for oxamide by means of a Patterson projection. The analysis, which was the reinvestigation of a previous preliminary survey that had reported a slightly wavy planar structure with a 1.65 [Angstrom] C-C bond, was interrupted by the publication of an apparently satisfactory structure by Romers. The present study and two recent publications are in agreement both as to the parameters and space group of the triclinic unit cell, and the configuration of the molecule. The oxamide molecules are centered and they are hydrogen bonded into an essentially planar sheet which is parallel to the almost perfect cleavage plane exhibited by the crystals. The dimensions indicate that the C-C bond is a pure single bond and that the C-N bond has about 50% double-bond character as a result of resonance in the amide group. Oxamide, like oxalic acid and a few other related substances, is planar although the C-C bond apparently has no double-bond character.\r\n\r\nII\r\n\r\nThe crystal structure of 15,15'-dehydrobetacarotene has been determined; this analysis represents the first conclusive study of any carotenoid. The analysis was accomplished through the use of a three-dimensional Patterson coupled with trial and error methods, and has been carried to a moderate state of refinement with Fourier projections, two-dimensional least squares, and a three-dimensional Fourier. The monoclinic unit cell has the parameters [...], [...], [...], and [...]; the space group is uniquely determined to be [...], which requires that the two molecules in the unit cell be centered. Except for the cyclohexene rings, the molecule is essentially plane with bond lengths and angles in general agreement with those predicted by theory and experiment. The chains are packed together almost unaffected by the cyclohexene rings. Each ring has the cis orientation about the single bond from ring to chain; the molecule is otherwise all trans. The molecules are efficiently packed, but the arrangement has resulted in a loss of resonance energy since the rings are not coplanar with the chain. The hypersymmetry of the molecules accounts for the deviation of the intensities from a normal statistical distribution.\r\n\r\nA brief discussion of some of the IBM techniques used in the refinement of this structure has been included in the appendix." }, { "name": "Viglierchio, David Richard", "degree": "PhD", "year": "1955", "title": "Investigations of Some Plant Wound Hormones", "advisor": "Haagen-Smit, Arie Jan", "url": "https://resolver.caltech.edu/CaltechETD:etd-01222004-111130", "creators": [ { "name": { "family": "Viglierchio", "given": "David Richard" }, "id": "Viglierchio-David-Richard", "display_name": "Viglierchio, David Richard" } ], "advisors": [ { "name": { "family": "Haagen-Smit", "given": "Arie Jan" }, "id": "Haagen-Smit-A-J", "role": "advisor", "display_name": "Haagen-Smit, Arie Jan" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "bioch" ], "doi": "10.7907/XXKJ-HW24", "abstract": "Research has shown that renewed cell division and growth may be induced in many mature living cells either by wounding or treating with an extract of certain tissue macerates. During the past decade there have been no publications in the field of wound hormones along the lines of Haberlandt (4) (5) or Bonner, English and Haagen-Smit (11-13). The latter authors isolated a natural wound hormone of beans, traumatic acid; the present investigation seeks to extend their work by the study of a wound hormone from another source. The modified Wehnelt test used as an assay in the earlier isolation work was adopted. Variety of beans but not environment was shown to influence the test. Of a number of natural products investigated for wound hormone activity, citrus products were found exceptionally active. From lemon peel infusion it was possible to prepare a very active concentrate. This concentrate could be subjected to catalytic hydrogenation without losing its activity. Pressed Valencia Orange Oil contains an active component which upon purification was found to be a mixture of unsaturated fatty acids. Preparations of pure linoleic and linolenic acids were found active as wound hormones. In lemon peel infusion there was a water soluble complement, which though inactive itself, was able to augment the activity not only of the wound hormone of lemon peel infusion but also those of orange oil, linoleic and linolenic acids. Several purified water soluble factors which enhanced the activity of wound hormones were found, the most effective being Coenzyme A and Cytochrome C. Several positional and geometrical isomers of linolenic acid were found only slightly active." }, { "name": "Burriss, William Louis", "degree": "Engineering Degree", "year": "1954", "title": "Evaporation from N-Heptane Drops in an Air Stream", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12012003-115944", "creators": [ { "name": { "family": "Burriss", "given": "William Louis" }, "id": "Burriss-William-Louis", "display_name": "Burriss, William Louis" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DGDS-SD18", "abstract": "The rates of heat and mass transfer from equilibrium non-spherical n-heptane drops in an air stream have been investigated. Two types of drops were produced, one wetting the supporting tube and another not wetting the supporting tube. The drops ranged from 0.005 to 0.008 ft in diameter. Measurements were made at bulk air velocities between 2 and 8 fps, with an air temperature of 100?F. A semi-empirical relation taking into account the deviation of drop shape from spherical leads to a satisfactory correlation of data with those obtained by other investigators for spherical drops." }, { "name": "Crosby, Donald Gibson", "degree": "PhD", "year": "1954", "title": "I. The Structures of Phytotoxic Compounds from Thamnosma Montana. II. The Action of Phytotoxic Compounds on Plants. III. Preparation and Reactions of S-Phenylthiolcarbamates. IV. Studies on the Synthesis of Actidione", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042003-095430", "creators": [ { "name": { "family": "Crosby", "given": "Donald Gibson" }, "id": "Crosby-Donald-Gibson", "display_name": "Crosby, Donald Gibson" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/T35B-D641", "abstract": "The chemistry of the three phytotoxic compounds isolated from Thamnosma montana by E.L. Bennett in 1949 has been studied, and two of the substances have been identified as the known furocoumarins isopimpinellin and byakangelicin. Degradation and partial synthesis of the third compound have shown that it is also a furocoumarin, and have indicated its probable structure.\r\n\r\nThe effects of several naturally-occurring phytotoxic substances on plants have been observed under controlled conditions, and have been compared with the effects noted in nature. The mechanism of the toxic action is still ambiguous.\r\n\r\nConvenient methods for the synthesis of S-substituted thiolcarbamates have been found, and the scope and limitations of their reactions with primary and secondary amines, amides, and hydrazines to produce ureas, acylureas, and semicarbazides, respectively, have been determined. The mechanism of the general reaction and its application to the identification of organic compounds also have been considered.\r\n\r\nAttempts have been made to synthesize the antibiotic substance \"Actidione\" by four different routes, and although this end has not been achieved, much groundwork has been laid for the eventual preparation of the compound." }, { "name": "Golding, Bert Henry", "degree": "Engineering Degree", "year": "1954", "title": "Volumetric Properties of Corrosive Gases", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-12152003-113452", "creators": [ { "name": { "family": "Golding", "given": "Bert Henry" }, "id": "Golding-Bert-Henry", "display_name": "Golding, Bert Henry" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/20FR-RP94", "abstract": "Part I: The volumetric behavior of nitrogen dioxide was determined experimentally at temperatures between 100 and 340?F for pressures up to 2000 pounds per square inch. The two-phase data are compared with the results obtained by other investigators. The measurements were made in a stainless steel cell of essentially constant volume, and the experimental apparatus is described.\r\n\r\nPart II: The volumetric behavior of nitric oxide was determined experimentally at temperatures between 40 and 220?F for pressures up to 2500 pounds per square inch. The measurements were made in a variable volume container of chrome-nickel stainless steel with mercury as the confining fluid. Reaction between the mercury and the nitric oxide was experienced at temperatures of 280?F and above.\r\n\r\nPart III: The volumetric behavior of six mixtures in the binary system nitric oxide - nitrogen dioxide was determined in an essentially constant volume apparatus over a temperature range from 10 to 340?F. The composition range was from 0 to 20 weight percent of nitric oxide, and the maximum pressure obtained was approximately 600 pounds per square inch.\r\n\r\nPart IV. The volumetric behavior of four mixtures in the binary system hydrogen sulfide - water was determined in an essentially constant volume apparatus over a temperature range from 10 to 340?F.\r\n\r\nPart V:\tThermodynamic properties of nitric oxide were calculated from the data presented in Part II of this thesis. Values of entropy, enthalpy, and of the ratio of fugacity to pressure are presented at temperatures of 40, 100, 160, and 220?F for pressures up to 2500 pounds per square inch.\r\n\r\nPart VI: Thermodynamic properties of nitrogen dioxide were calculated from the data presented in Part I of this thesis. Values of entropy, enthalpy, and of the ratio of fugacity to pressure are presented for the equilibrium material, the molecular weight of which is taken as that of nitrogen dioxide, at temperatures between 160 and 340?F for pressures up to 1000 pounds per square inch." }, { "name": "Hamilton, Walter Clark", "degree": "PhD", "year": "1954", "title": "I. The Crystal Structure of Dimethyl Phosphino-Borine Trimer. II. The Method of Least Squares in Electron Diffraction. III. Some Structural Studies by the Electron Diffraction by Gas Molecules", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12152003-090535", "creators": [ { "name": { "family": "Hamilton", "given": "Walter Clark" }, "id": "Hamilton-Walter-Clark", "display_name": "Hamilton, Walter Clark" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FCYP-NV05", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe crystal structure of dimethyl phosphino-borine trimer, [(CH[subscript 3][subscript 2]PBH[subscript 2][subscript 3], has been determined by analysis of its x-ray diffraction maxima. Use was made of a three-dimensional Patterson function, least squares on the structure factors, and a three-dimensional electron-density difference map. The space group is P[subscript nma]; the unit cell constants are a = 11.16 [angstroms], b = 13.16 [angstroms], and c = 10.53 [angstroms]. There are four molecules per unit cell. The molecule has a cyclohexane-like ring of alternating phosphorus and boron atoms, with two methyl groups attached to each phosphorus atom. It has a plane of symmetry, and the environment of each phosphorus atom is C[subscript 2v]. The following average structural parameters were found: [...].ome attention is given to the determination of temperature factors from the difference map and to fitting of atomic form factors by Gaussians. The R factor for the final structure is 0.169.\r\n\r\nThe advantages of the method of least squares, as contrasted to the usual correlation treatment, in electron diffraction investigations of molecular structure are outlined. Special attention is given to visual data and to the weighting of observations, including remarks on the use of a non-diagonal weight matrix and the derivation of weights from the goodness of fit, and to obtaining reliable estimates of error, and of error correlation, for the parameters.\r\n\t\t\r\nThe method of least squares has been applied to electron diffraction photographs of bicycloheptadiene, C[subscript 7]H[subscript 8], and bicyclo-octane, C[subscript 8]H[subscript 14]. In the case of bicyeloheptadiene, a simple valence-force potential function adequately explains the values found for the structural-parameters. The structure of difluoromethane has been reinvestigated by electron diffraction." }, { "name": "Hershman, Jerome Marshall", "degree": "Masters", "year": "1954", "title": "Preparation and Characterization by Streaming Birefringence of Sodium Desoxyribonucleate", "advisor": "Rich, Alexander", "url": "https://resolver.caltech.edu/CaltechETD:etd-05062003-095853", "creators": [ { "name": { "family": "Hershman", "given": "Jerome Marshall" }, "id": "Hershman-Jerome-Marshall", "display_name": "Hershman, Jerome Marshall" } ], "advisors": [ { "name": { "family": "Rich", "given": "Alexander" }, "id": "Rich-Alexander", "role": "advisor", "display_name": "Rich, Alexander" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8XHJ-5E14", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThree preparations of the sodium salt of desoxyribonucleic acid were isolated from calf thymus by a method expected to give minimal or no depolymerization. In addition, preparations were made from calf spleen and bull testis tissues.\r\n\r\nStreaming birefringence measurements indicate that the distributions of molecular length are identical in the calf thymus preparations. The apparent molecular lengths range from 7,500 to 11,500[...]. The sodium desoxyribonucleate from testis appeared to be significantly shorter; that from spleen was intermediate between thymus and testis. The distributions of molecular length of two calf thymus preparations isolated by N. Simmons were compared with those prepared here.\r\n\r\nSeveral explanations are put forth to explain the polydispersity and discrepancies between preparations." }, { "name": "Ibers, James Arthur", "degree": "PhD", "year": "1954", "title": "Studies in Electron and X-Ray Diffraction : I. The Structure of Oxygen Fluoride. II. The Failure of the Born Approximation -- the Calculation of Complex Atomic Scattering Amplitudes for Electron Diffraction. III. Some Calculations of Atomic Form Factors. IV. Structural Studies by X-Ray Diffraction", "advisor": "Schomaker, Verner F.; Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechETD:etd-12032003-104507", "creators": [ { "name": { "family": "Ibers", "given": "James Arthur" }, "id": "Ibers-James-Arthur", "orcid": "0000-0002-5418-3645", "display_name": "Ibers, James Arthur" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." }, { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6K8R-3A92", "abstract": "In Part I the determination of the structure of oxygen fluoride by the method of electron diffraction is described.\r\n\r\nIn Part II the calculation of complex atomic scattering amplitudes and their ease in electron diffraction is discussed. Section A provides an outline of the theory and a summary of the calculations which have been made. In Section B some experimental work, the failure of the Born approximation, and the early calculations are described. In Section C the calculation of complex atomic scattering amplitudes from the partial waves scattering theory and the WKB method is described in detail.\r\n\r\nIn Part III the calculations of atomic form factors for a few selected atoms from Hartree-Fock anal Hartree radial wave functions are described.\r\n\r\nIn Part IV some structural studies by x-ray diffraction are described. In particular, a determination of the unit cell and space group of tetrapyridinecopper (II) fluoborate is described. A determination of the structure of potassium fluotitanate is presented. Finally, the work to date on the structure of monoclinic ceric iodate is presented. Included in this presentation is a detailed discussion of the various I. B. M. procedures used in the reduction of the large number of intensity data." }, { "name": "Johnson, Kenneth Delford", "degree": "PhD", "year": "1954", "title": "I. The Inclusion of Monohaptenic Substances in Immune Aggregates. II. Heteroligating Antibody in Anti-Arsanilic Acid Sera", "advisor": "Campbell, Dan Hampton", "url": "https://resolver.caltech.edu/CaltechETD:etd-01152004-161441", "creators": [ { "name": { "family": "Johnson", "given": "Kenneth Delford" }, "id": "Johnson-Kenneth-Delford", "display_name": "Johnson, Kenneth Delford" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FZHV-AC28", "abstract": "I.\r\n\r\nMethods have been developed for the preparation and purification of iodinated haptens of the arsanilic acid series suitable for critical experiments on hapten binding in immune aggregates. Additional data are given on the preparation and properties of the solid immune adsorbents described by Lerman.\r\n\r\nThe inclusion of homologous monohaptenic substances in the aggregates formed between these solid adsorbents and homologous antibody has been studied under a variety of experimental conditions. The existence of such hapten binding has been clearly demonstrated, as has the inclusion of hapten in the immune precipitates formed between anti-RBG antibody and both azoprotein and polyhaptenic simple antigens. This demonstration has been interpreted as additional evidence in support of the theory of the bivalence of antibody.\r\n\r\nII\r\n\r\nThe Pauling theory of antibody synthesis predicts that among the antibody molecules synthesized in spatial contact with the stimulating antigen, there should be some molecules having the two binding sites directed against different antigenic determinants on the surface of the antigen. The existence of such heteroligating antibody molecules has not previously been demonstrated. Data presented here are interpreted as evidence for the existence of heteroligating antibody in the anti-RBG sera studied. These data are derived from experiments on (1) the loss of anti-bovine globulin activity on adsorbing anti-RBG sera with R-adsorbent, (2) the recovery of such activity in the eluates from the adsorbent, and (3) the inclusion of arsanilic acid haptens in precipitates formed between such sera and a native bovine globulin precipitating antigen." }, { "name": "Karplus, Martin", "degree": "PhD", "year": "1954", "title": "A Quantum-Mechanical Discussion of the Bifluoride Ion", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-01072004-094608", "creators": [ { "name": { "family": "Karplus", "given": "Martin" }, "id": "Karplus-Martin", "display_name": "Karplus, Martin" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EY65-WG09", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe variation method for obtaining approximate solutions to the Schrodinger equation is examined. It is demonstrated that one-electron orbitals can to employed in the construction of a convergent variation function. As special cases of the one-electron approach, the valence bond and molecular orbital methods are discused and compared.
\r\n\r\nVariation functions containing only a few terms are known to lead to incorrect results. The reasons for this failure are discussed. A semi-theoretical apnroach, which corrects some of the failings, is developed and tested on HF. Results in good agreement with experimental determinations of the energy and dipole moment are obtained. Application of the method to FHF\u207b leads to a value of 36.5 kcal for the energy of the reaction
\r\n\r\nF\u207b + HF \u2192 FHF\u207b
\r\n\r\nCalculation of the FHF\u207b wave function shows that the completely ionic structure (F\u207b H\u207a F\u207b) makes the largest contribution.
I. The eddy diffusivity and the eddy viscosity near the center of a pipe have been determined for the case of turbulent, cylindrically symmetric, steady, non-uniform flow*. The eddy properties were calculated from measurements of composition and velocity in a test section 36 in. long and 6 in. in diameter. Natural gas was introduced into a turbulent air stream through an annulus section 1/8 in. thick. Experiments were made at Reynolds numbers of 45,000 and 82,300. Both eddy properties were found to vary appreciably with distance downstream from the annulus. The eddy diffusivity varied much more than did the eddy viscosity, being less in some regions and much greater in others. However, there appeared to be no tendency for either eddy property to approach zero at the center of the channel. The results of the experiments are discussed and compared to the data of other workers.
\r\n\r\nIIA. The optical absorbance of the liquid phase of mixtures of nitric acid, nitrogen dioxide**, and water was measured at 32[degrees]F at wavelengths of 500 and 425m[...]. At the longer wavelength compositions containing 0.8 or more weight fraction nitric acid were studied. At the shorter wavelength the compositions were limited to a minimum weight fraction nitric acid of 0.93. The results indicate that the absorbance varies linearly with the weight fraction nitrogen dioxide at small concentrations of this component. The optical absorption appears to be a useful intensive property of the liquid phase to be employed as an aid in determining the composition of the ternary system.
\r\n \r\nIIB. Values of the optical absorbance of solutions of nitrogen dioxide in nitric acid were measured at 32[degrees]F and one atmosphere using light at a wave length of 425m[...]. The data obtained were applied in a study of the ionisation occurring in the solutions. The numerical solution of simultaneous equations based on equilibrium expressions indicated that in nitric acid solutions containing less than one weight per cent nitrogen dioxide the nitrogen dioxide is about 70 per cent dissociated into nitrosonium ([...]) and nitrate ([...]) ions whereas the nitric acid is about five per cent dissociated into nitronium ([...]) ions, nitrate ions, and water. Although the uncertainty is high, the order of magnitude of these values is correct.
\r\n\r\nIII. In aqueous solution, Na2S2O4, sometimes called sodium hydrosulfite but more correctly sodium dithionite, undergoes irreversible decomposition at a measurable rate to give NaHSO3, sodium bisulfate, and Na2S2O3, sodium thiosulfate, as products. Studies of this reaction with initial compositions in the range 0.01 - 0.10 F Na2S2O4 were made with the exclusion of air. A solution of Na2S2O4 alone decomposes in a fashion suggesting that a degenerate branching chain mechanism is involved. An apparent positive salt effect on the reaction rate results when NaCl is added to the solution. At values of the concentration of H[superscript+] above 10[superscript -3] moles per liter this decomposition is extremely rapid. Initial concentrations*** of the products of decomposition, NaHSO3 and Na2S2O3 less than the initial concentration of [...] catalyze the decomposition, indicating that it is autocatalytic in nature. Initial concentrations of [...] up to tenfold that of [...] markedly catalyze the decomposition.
\r\n\r\nHowever, in the presence of initial concentrations of NaHSO3 greater than the initial concentration of [...] the chain mechanism is overshadowed, and the reaction is first order with respect to both the species [...] and [...] and is independent of the initial concentration of [...] and of the concentration of H[superscript +] but is slightly dependent on the initial concentration of [...]. With only [...] and [...] added the reaction rate is greatly inhibited, and part of this effect may be attributed to the corresponding lowering of the concentration of [...].
\r\n\r\nIn the presence of initial concentrations of both Na2S2O3 and NaHSO3 which are equimolar or greater than the initial concentration of Na2S2O4 the reaction appears to be approximately first order with respect to the concentrations of the species [...], [...], and [...]. In the presence of both [...] and [...], however, the reaction rate is dependent on both the initial concentration of the H[superscript +] and the concentration of [...]. Superposed on these overall first order reactions is an inherent periodicity in the reaction rate. The bulk of the kinetics measurements were made at 60[degrees] C, although several measurements were made at 50[degrees] and 70[degrees] C to obtain the activation energy of the thermal decomposition reaction.
\r\n\r\nA few measurements were made at 50[degrees], 60[degrees], and 70[degrees] C of the rapid oxidation of 0.01 F Na2S2O4 in aqueous solution by air. This oxidation reaction appears to be first order with respect to the concentration of [...] and is inhibited in basic solutions. A modified analytical procedure employing methylene blue in a basic aqueous solution of methanol or acetone was used to determine Na2S2O4 in the presence of large quantities of other reducing agents.
\r\n\r\nIV. A method is described for determining amounts of chromium of the order of a few milligrams. Trivalent chromium is oxidized by fuming perchloric acid in the presence of a small amount of silver ion. The dichromate is then determined iodimetrically. For small amounts of chromium the method gives better results than do other methods listed in the literature. The method has not been tried for large amounts of chromium.
\r\n\r\n*Flow is defined as steady when the average velocity, temperature, and other properties of interest at a point do not change with time. Flow is defined as uniform when the derivatives with respect to x, the coordinate in the direction of flow, of velocity, temperature, and other properties of interest are zero. Uniform flow is theoretically unattainable but may be closely approached in practice.
\r\n\r\n**The term nitrogen dioxide is used to designate equilibrium mixtures of nitrogen dioxide and nitrogen tetroxide.
\r\n\r\n***Unless otherwise specified, concentrations refer to molar or formal concentrations.
" }, { "name": "Moore, Gordon Earle", "degree": "PhD", "year": "1954", "title": "I. Infra-Red Studies of Nitrous Acid, the Chloramines and Nitrogen Dioxide. II. Observations Concerning the Photochemical Decomposition of Nitric Oxide", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechETD:etd-01232004-112159", "creators": [ { "name": { "family": "Moore", "given": "Gordon Earle" }, "id": "Moore-Gordon-Earle", "display_name": "Moore, Gordon Earle" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K3MR-VX06", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document. \r\n\r\n1. The results of an investigation of the infra-red spectra of gaseous nitrous acid and deutero-nitrous acid in the region to 25? have been combined with previous data in the 1.4-15? region to make a complete vibrational assignment. Nitrous acid exists as a pair of rotational isomers which we believed to be the cis and trans forms, The cis form is of higher energy by 500 ? 250 calories mole[^-1]. From rotational constants and by comparison of force constants with those of molecules of known structure sets of structural parameters for both species have been obtained, from which conclusions are drawn regarding the electronic structure of nitrous acid. The barrier for hindered rotation of the hydrogen atom about the nitrogen-oxygen single bond has been approximated by a three-term series, which suggests a maximum barrier height of about 12 kcal. mole[^-1]. The standard entropy of an equilibrium mixture of cis and trans nitrous acids at 25[degrees] has been calculated to be 56.0 e.u., to be compared with 54.0 e.u., and 54.8 e.u. for the pure trans and cis isomers, respectively.\r\n\r\n2. The infra-red vibration spectra of gaseous NH2Cl, NHDCl, NHCl2 and NCl3 were investigated from 1.4 to 25?. Several fundamental vibrations were identified, and the large rotational constants were evaluated for NH2Cl, NHDCl and NHCl2. With the assistance of reasonable assumptions regarding other parameters these were used to calculate an H-N-Cl angle of 102[degrees] in NH2Cl and suggest that [?]Cl-N-1 =106[degrees] and [?]=1.76 [Angstrom] in NHCl2. These parameters are interpreted on the basis of simple electronic considerations.\r\n\r\n3. The infra-red spectrum of NO2 has been reinvestigated in the 1.4-3.4? region under high dispersion. The nine bands observed show resolvable rotational structure and the moments of inertia obtained, in conjunction with the large rotational constant from measurements of [?] by Wilson and Brown, yield the ground state parameters r[?] = 1.188? 0.004 [Angstrom] and [?]. The set of overtones and combinations observed together with [?] from Wilson and Brown allow one to determine a complete set of quadratic vibrational interaction constants. The frequencies of NO2 are [?]. An intensity alternation is observed in type A bands as is predicted by theory but which, as far as the author is aware, has not previously been observed in a similar case. An apparently abnormal interaction which is not adequately explained occurs between the vibrational levels [?] and [?] and likewise between [?] and [?].\r\n\r\n4. Section II describes briefly some experiments concerning the photochemical decomposition of nitric oxide. It was shown that absorption to the 0,0 and 1,0 [?] under conditions where these bands are pressure broadened leads to photochemical decomposition. Nitrogen was shown to effect the rate of decomposition only slightly when added to nitric oxide at 15 cm of Hg pressure. This decomposition is of interest because of its possible connection with the problem of the heat of dissociation of nitrogen." }, { "name": "Nevill, William Albert", "degree": "PhD", "year": "1954", "title": "Studies Relating to the Free Radical Chlorination of Cyclobutanecarboxylic Acids", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechETD:etd-12052003-092441", "creators": [ { "name": { "family": "Nevill", "given": "William Albert" }, "id": "Nevill-William-Albert", "display_name": "Nevill, William Albert" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/B3J7-0627", "abstract": "The halogenated cyclobutanecarboxylic acid are of importance in connection with projected syntheses of theoretically important cyclobutane derivatives.\r\n\r\nTo facilitate the direct synthesis of such compounds, the free radical chlorination of two simple models, cyclobutanecarboxylic acid and 1,1-cyclobutanedicarboxylic acid, has been investigated.\r\n\r\nNecessary to this study was the synthesis, by means indicative of structure, of 5 isomeric monochlorocyclobutanecarboxylic acids. A chromatographic method has been developed capable of effecting the separation of these isomers from a mixture.\r\n\r\nThe results obtained in this work are consistent with modern interpretations of organic chemistry theory and extend the scope of its application in the field of free radical chlorination to carboxyl-substituted carbocyclic systems." }, { "name": "Opfell, John Burton", "degree": "PhD", "year": "1954", "title": "A Detailed Study in the Application of the Benedict Equation to One-Component Systems", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232025-225306219", "creators": [ { "name": { "family": "Opfell", "given": "John Burton" }, "id": "Opfell-John-Burton", "display_name": "Opfell, John Burton" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/wpe6-g155", "abstract": "No abstract." }, { "name": "Rowley, John Keith", "degree": "PhD", "year": "1954", "title": "Coulometric and Amperometric Studies", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12082003-113012", "creators": [ { "name": { "family": "Rowley", "given": "John Keith" }, "id": "Rowley-John-Keith", "display_name": "Rowley, John Keith" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X71A-V450", "abstract": "The coulometric titration of thiosulfate with iodine has been investigated at different hydrogen ion concentrations. The applicability of this titration to the determination of oxidizing agents has been demonstrated by determining microgram quantities of ferric iron, chromate, and selenious acid.\r\n\r\nA modification of the Norris and Fay method for the volumetric determination of selenious acid has been compared to a proven, but less direct method.\r\n\r\nIt has been shown that tripositive antimony can be titrated in concentrated hydrochloric acid solutions more successfully with chlorine than with bromine. Evidence concerning the nature of the species of tripositive and pentapositive antimony existing hydrochloric acid solutions has been obtained amperometrically during the coulometric titrations in hydrochloric acid of tripositive antimony with bromine and chlorine, and of pentapositive antimony with cuprous copper.\r\n\r\nThe indicator currents obtained with an amperometric system during the reduction of iodate with cuprous copper and during the oxidation of iodide with both chlorine and ceric cerium have been investigated as functions of the hydrogen ion concentration, the chloride concentration, and the applied potential.\r\n\r\nA quantitative study of the amperometric system used for above measurements has been made. An equation has been derived which relates the indicator current to the applied potential and to the concentrations of electrode-reactive species in the solution. Experimental tests have been made on the ferrocyanide-ferricyanide half-cell. The amperometric end point is discussed." }, { "name": "Stottlemyer, Quayton Ray", "degree": "Masters", "year": "1954", "title": "Investigation of the Behavior of the Aqueous I\u2083\u207b-I\u2082-I\u207b System Following Intense Irradiation", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01272004-154020", "creators": [ { "name": { "family": "Stottlemyer", "given": "Quayton Ray" }, "id": "Stottlemyer-Quayton-Ray", "display_name": "Stottlemyer, Quayton Ray" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CSV2-DQ22", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nAcidified aqueous solutions containing [...], [...], and [...] have been irradiated by a high intensity flash lamp and the resulting change in the optical density of the solution has been observed spectrophotometrically as a function of time after the flash.\r\n\r\nImmediately following the flash, there is an increase in the optical density of the solution. This is attributed to the photochemical production of the diiodide ion, [...], by reaction (1) and/or reaction (2) and (3). [...] [...] [...].\r\n\r\nThe disappearance of the colored species, in about 1.5--8 milliseconds after the flash, has been found to be kinetically of the second order with respect to that species and has been explained in terms of the recombination of [...], principally by equation (4). [...] [...] [...].\r\n\r\nOn the basis of these assumptions, the value of [...] has been determined at wave lengths 365 mmu. and 435 mmu. for [...] ranging from [...] to [...] M. The experimental dependence of the rate of disappearance of [...] on [...] has been found to agree qualitatively with the theoretical equation: [...].\r\n\r\nThe calculated value of [...] has been found to vary with the wave length of the light used to observe the reaction as predicted by the equation: [...].\r\n\r\nThe presence of [...] in concentrations about [...] caused a slight increase in the value of [...], which was attributed to one or both of the reactions: [...] [...]. [...] in concentrations less than [...] appeared to decrease the rate of disappearance of [...]; for this anomalous effect no explanation is given.\r\n\r\nExperiments performed in which a large percentage of the light absorbed by [...] was cut off by filters produced correspondingly smaller phenomena but gave no conclusive evidence as to the relative proportion of [...] and [...] dissociated by the irradiation.\r\n\r\nAn extensive summary of data is presented." }, { "name": "Carter, Paul Richard", "degree": "PhD", "year": "1953", "title": "I. Kinetics of the Oxidation of Iron (II) by Bromine. II. Complex Ion Formation in the Systems Iron (III), Phosphoric Acid. III. Kinetics of the Oxidation of Ferrocyanide Ion by Bromine", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04222003-090120", "creators": [ { "name": { "family": "Carter", "given": "Paul Richard" }, "id": "Carter-Paul-Richard", "display_name": "Carter, Paul Richard" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PDTJ-FP82", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nThe kinetics of the oxidation of iron (II) by bromine has been studied spectrophotometrically. At (Br[...]) = 0.50 M, tribromide ion was found to be the reactive bromine species, while evidence for HOBr and Br[subscript 2] reacting with iron (II) was obtained at (Br[...]) [...] 10[superscript -3] M. A mechanism involving Br[...][subscript 2] is suggested, and the observed inhibition by iron (III) eliminates an alternative mechanism involving iron (IV) as an unstable intermediate. The catalytic effect of phosphoric acid was investigated.\r\n\r\nThe ultraviolet light absorption of iron (III) in phosphoric acid was studied. An attempt was made to determine the nature of the complex that is present. The presence of only one complex could not be verified.\r\n\r\nThe oxidation of ferrocyanide ion by bromine was found to proceed at a faster pace than the analogous oxidation of iron (II). Both molecular bromine and tribromide ion were found to react with ferrocyanide ion when (Br[...]) = 0.05 M. The reaction appeared to be first order with respect to bromine and ferrocyanide ion at H[superscript +] = 0.93 M, but was found to deviate from a simple second order behaviour when the hydrogen ion concentration was decreased to 0.50 M." }, { "name": "Helmkamp, George Kenneth", "degree": "PhD", "year": "1953", "title": "I. Stereochemistry of the Reaction of D(+)-2, 3-Epoxybutane with Alcohols. II. The Coordination Reaction Between Silver Ion and Alkynes. III. Some Relationships of Sterols to Plant Growth", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05082003-105201", "creators": [ { "name": { "family": "Helmkamp", "given": "George Kenneth" }, "id": "Helmkamp-George-Kenneth", "display_name": "Helmkamp, George Kenneth" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2VN2-KE23", "abstract": "PART I.\r\n\r\nThe reaction between D(+)-2,3-epoxybutane and alcohols is accompanied by a Walden inversion. The 3-methoxy-2-butanol prepared in this manner is an erythro-isomer, for meso-2,3-dimethoxybutane can be prepared from it by the Williamson synthesis. \r\n\r\nPART II.\r\n\r\nPermanganate oxidation under alkaline conditions has been employed as a method for the quantitative determination of aqueous solutions of 3-hexyne.\r\n\r\n3-Hexyne and several homologs (methyl groups in the 1-, 2- and 5-positions) have been synthesized. Argentation constants for these have been evaluated by means of their solubilities in aqueous solutions of silver ion at constant ionic strength. \r\n\r\nPART III.\r\n\r\nA survey has been made concerning the effect of various steroidal substances on growth of pea embryos. A strong inhibition was noted in the presence of testosterone. Estrone and saponins tended to enhance early growth." }, { "name": "Hogness, David Swenson", "degree": "PhD", "year": "1953", "title": "I. The Kinetics of the Alpha-Chymotrypsin Catalysed Hydrolysis of Acetyl-L-Tyrosinhydroxamide. II. Genetic Factors Influencing the Activity of Tryptophane Desmolase in Neurospora crassa", "advisor": "Niemann, Carl G.; Mitchell, Herschel K.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232003-104814", "creators": [ { "name": { "family": "Hogness", "given": "David Swenson" }, "id": "Hogness-David-Swenson", "display_name": "Hogness, David Swenson" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." }, { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "advisor", "display_name": "Mitchell, Herschel K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4Y9X-NZ51", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nFrom an analysis of the pH-activity curves of the systems alpha-chymotrypsin-acetyl-L-tyrosinamide and alpha-chymotrypsin-acetyl-L-tyrosinehydroxamide it has been concluded that in the latter system the active specific substrate is acetyl-L-tyrosinehydroxamide and not acetyl-L-tyrosinehydroxamate ion. At pH 7.6 and 25[degrees]C, in aqueous solutions 0.3 M with respect to the amine component of a tris-(hydroxy-methyl)-aminomethane-hydrochloric acid buffer, the kinetics of the alpha-chymotrypsin catalysed hydrolysis of acetyl-L-tyrosinehydroxamide have been found to be similar to those observed previously for this enzyme and specific substrates of the acylated alpha-amino acid type at pH 7.9 [plus or minus] 0.1 and 2.5[degrees]C in aqueous solutions 0.02 M with respect to the amine component of the same buffer system. Acetyl-D-tyrosine ethyl ester, acetyl-D-tyrosine hydrazide, acetyl-D-tyrosinehydroxamide and acetyl-D-tyrosinamide were found to be competitive inhibitors of the alpha-chymotrypsin catalysed hydrolysis of acetyl-L-tyrosinehydroxamide at pH 7.6 and 25[degrees]C, under the conditions previously specified, and from these and other data it was concluded that proteins, amides, esters, hydrazides and hydroxamides are hydrolysed at the same single active site on the enzyme.\r\n\r\nPreliminary to an examination of the effect of genetic factors on tryptophane desmolase activity in Neurospora, this enzyme was extracted from a reference strain and partially purified. The kinetics of this tryptophane desmolase system was investigated and the apparent K[subscript m] values of indole, L-serine and pyridoxal phosphate determined. No tryptophane desmolase activity could be found in a tryptophaneless mutant, C83. The tryptophane requirement of this mutant and the lack of tryptophane desmolase activity were found to be associated with the same single gene. The reversion of C83 to wild type under the influence of ultraviolet irradiation was studied, and it was shown that the C83 mutant can backmutate. The backmutant was found to contain a tryptophane desmolase system which could not be distinguished from the tryptophane desmolase from wild type on the basis of the kinetic criteria that were applied. A histidineless mutant, C84, was found to exert a control on the tryptophane desmolase activity of Neurospora. From a limited amount of evidence it was tentatively concluded that the histidine requirement and the alteration of the tryptophane desmolase activity are the effects of the same single gene in the C84 mutant." }, { "name": "Jenkins, Wilmer Atkinson, II", "degree": "PhD", "year": "1953", "title": "I. The Kinetics of the Exchange of Radioactive Hydrogen between Hypophosphorous Acid and Water. II. An Investigation of Some Aspects of the Chemistry of Hypophosphorous Acid and Thallous Hypophosphite. Ill. A New Assay Method for Tritiated Water", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04242003-090233", "creators": [ { "name": { "family": "Jenkins", "given": "Wilmer Atkinson, II" }, "id": "Jenkins-Wilmer-Atkinson", "display_name": "Jenkins, Wilmer Atkinson, II" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EAQE-MR88", "abstract": "The kinetics of the exchange of radioactive hydrogen between hypophosphorous acid and water have been studied in acid, neutral, and basic solution. In acid solution the kinetics of the exchange were found to be the same as the kinetics of the oxidation of hypophosphorous acid by certain oxidizing agents. The mechanism common to both of these reactions is formulated and discussed. The isotope effect found in acid solution is explained, and a general theory of isotope effects in exchange reactions is presented. Exchange was found to be extremely slow in neutral solution and a little faster in basic solution; the results in basic solution, however, were complicated by the decomposition of the hypophosphite ion.\r\n\r\nA new method for the purification of hypophosphorous acid is described.\r\n\r\nExperiments on the preparation and thermal stability of thallous hypophosphite were conducted. These experiments are presented and discussed, along with some data on the reaction of hypophosphorous acid with persulfate and dichromate.\r\n\r\nA new, rapid assay method for tritiated water, involving the use of solid samples and a windowless flow counter, is described." }, { "name": "Jones, Morton Edward", "degree": "PhD", "year": "1953", "title": "I. The Structures of Some Compounds of Boron. II. Some Other Structural Studies", "advisor": "Pauling, Linus; Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04242003-093103", "creators": [ { "name": { "family": "Jones", "given": "Morton Edward" }, "id": "Jones-Morton-Edward", "display_name": "Jones, Morton Edward" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BX25-TG82", "abstract": "Section I contains a description of the structural investigations of several compounds of boron, using electron diffraction and X-ray diffraction techniques. The structure of stable pentaborane has been determined and the interatomic distances and bond angles have been derived. The structure of tetraborane has been found and approximate values for the parameters are given. A possible model for unstable pentaborane has been found. A magnesium boride, MgB[subscript 2], has been prepared and shown to be isomorphous with AlB[subscript 2]. A beryllium boride of approximate composition Be[subscript 2]B has been prepared in impure form and shown to have a structure similar to CaF[subscript 2]. An unsuccessful attempt has been made to prepare the copper boride Cu[subscript3]B[subscript 2] that is reported in the literature.\r\n\r\nSection II contains a description of some other electron diffraction and X-ray diffraction investigations. The interatomic distances and bond angle in formyl fluoride have been determined. A partially successful study has been made of ozone. A reinvestigation of copper silicide has removed the major portion of an unpleasant random feature of the previous structure. A method has been devised for simplifying the calculation of theoretical intensity curves containing temperature factored terms." }, { "name": "Phillips, Robert Edward", "degree": "PhD", "year": "1953", "title": "Structural Studies on Febrifugine and Isofebrifugine. Alkaloids from Dichroa Febrifuga. Studies on 4-Quinazolones. Synthesis of Some 8-Aminoquinolines", "advisor": "Koepfli, Joseph Blake; Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122003-110549", "creators": [ { "name": { "family": "Phillips", "given": "Robert Edward" }, "id": "Phillips-Robert-Edward", "display_name": "Phillips, Robert Edward" } ], "advisors": [ { "name": { "family": "Koepfli", "given": "Joseph Blake" }, "id": "Koepfli-J-B", "role": "advisor", "display_name": "Koepfli, Joseph Blake" }, { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "co-advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QQS1-H154", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n \r\nStructural studies on two isomeric, antimalarial alkaloids, febrifugine and isofebrifugine, isolated from Dichroa febrifuga, have been continued. The basic structure of both alkaloids is proposed to be 3-[[Beta]-keto ?[gamma]-(3-hydroxy-2-piperidyl)propyl]-4-quinazalone, and the relationship of febrifugine and isofebrifugine to this structure is discussed.\r\n\r\nFebrifugine is shown to be polymorphic, and evidence is presented that the alkaloid [gamma]-dichroine, from Dichroa febrifuga, is not chemically distinct, but a mixture of two of the crystalline modifications of febrifugine.\r\n\r\nThe synthesis of some 3-substituted-4-quinazolones is described. These are shown to be unreactive to benzenesulfonyl chloride, while the parent substance, 4-quinazolone, forms 3-benzenesulfonyl-4-quinazolone. The structure of a hydrolysis product of the letter compound is proposed to be N-(N?-formyl-[?]-aminobenzoyl) benzenesulfonamide, and the synthesis of this and of some related compounds is described.\r\n\r\nThe synthesis of some 8-aminoquinolines related to isoplasmocid was carried out as part of a cooperative project to study to study their action on experimental poliomyelitis in monkeys. These compounds were tested elsewhere and found to be without specific activity." }, { "name": "Ramsey, William James", "degree": "PhD", "year": "1953", "title": "I. Praseodymium and Neodymium Complexes with 8-Quinolinol-5-Sulfonic Acid. II. Some Reactions of Nitrosyl Disulfonate Ion", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05082003-161950", "creators": [ { "name": { "family": "Ramsey", "given": "William James" }, "id": "Ramsey-William-James", "display_name": "Ramsey, William James" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DFPN-4K64", "abstract": "Stable complexes are formed between 8-quinolinol-5-sulfonic acid and praseodymium (III) and neodymium (III). There is no conclusive evidence for the existence, in solution, of complexes between that acid and praseodymium and neodymium in higher oxidation states than three.\r\n\r\nDry solid potassium nitrosyl disulfonate is stable indefinitely, but the moist solid decomposes quite rapidly. In acid solution, nitrosyl disulfonate ion undergoes autocatalytic decomposition. In the investigation of this decomposition it was discovered that the reaction between nitrosyl disulfonate and hydroxylamine monosulfonate ions is catalyzed by iron. The investigation of these two reactions, and particularly the kinetics of the latter reaction are described." }, { "name": "Robertson, Glenn David", "degree": "Engineering Degree", "year": "1953", "title": "Some Physico-Chemical Properties of the System Nitric Acid--Nitrogen Dioxide--Water. I. The Kinetics of the Thermal Decomposition of Nitric Acid in the Liquid Phase. II. Electrolytic Conductance of the Ternary System Nitric Acid--Nitrogen Dioxide--Water at 32\u00b0 F and Atmospheric Pressure", "advisor": "Mason, David Malcolm", "url": "https://resolver.caltech.edu/CaltechETD:etd-05092003-090250", "creators": [ { "name": { "family": "Robertson", "given": "Glenn David" }, "id": "Robertson-Glenn-David", "display_name": "Robertson, Glenn David" } ], "advisors": [ { "name": { "family": "Mason", "given": "David Malcolm" }, "id": "Mason-David-Malcolm", "role": "advisor", "display_name": "Mason, David Malcolm" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Z3QB-4Q13", "abstract": "Part I.\r\n\r\nThe investigation of the kinetics of the decomposition of the liquid phase of nitric acid has indicated that the reaction probably proceeds by way of the unimolecular decomposition of dinitrogen pentoxide which exists in the pure acid. The effects of several inorganic additives in suppressing the rate of decomposition are in agreement with the postulate involving dinitrogen pentoxide. The magnitude of the inhibition of the decomposition by various additives has been found to be insufficient to prevent the eventual attainment of high equilibrium pressures resulting from decomposition when nitric acid is stored in closed containers. The solubility of oxygen in fuming nitric acid has been determined for oxygen pressures up to 21 atmospheres in the temperature range between 35[degrees] and 70[degrees]C. Under these conditions, the solubility of oxygen was found to increase with an increase in temperature.\r\n\r\nPart II.\r\n\r\nThe electrolytic conductance of the system nitric acid--nitrogen dioxide--water in the liquid phase was measured at 0[degrees]C and a pressure of 1 atmosphere for compositions containing more than 0.80 weight fraction nitric acid. The conductance of the associated binary systems nitric acid--water and nitric acid--nitrogen dioxide has been measured over the entire range of compositions from 0 to 1.00 weight fraction nitric acid. The conductance measurements offer additional proof of the self-ionization of pure nitric acid and of the ionization of nitrogen dioxide dissolved in nitric acid." }, { "name": "Wallcave, Lawrence", "degree": "PhD", "year": "1953", "title": "The Stereochemistry of Dehydro-\u03b2-Carotene. Studies on the Interaction of Some Carotenoids with Boron Trifluoride and N-Bromosuccinimide. Provitamin A Activity of a C\u2084\u2082-Carotenoid", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechETD:etd-05092003-171754", "creators": [ { "name": { "family": "Wallcave", "given": "Lawrence" }, "id": "Wallcave-Lawrence", "display_name": "Wallcave, Lawrence" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0TZT-6C69", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nAn extensive study of the stereoisomerization of dehydro-[Beta]-carotene is presented. Two of the cis isomers have been isolated in crystalline form and described. The nature of \"isocarotene\" has been clarified.\r\n\r\nTreatment of [Beta]-carotene with boron trifluoride under defined conditions leads chiefly either to its stereoisomerization or chemical conversion. Two of the several conversion products have been crystallized; a third, exhibiting strong fluorescence in ultraviolet light is also described.\r\n\r\nThree new carotenoids, termed isocryptoxanthin, isocryptoxanthin methyl ether, and dimethoxy-[Beta]-carotene, formed by the addition of water or methanol to dehydro-[Beta]-carotene in the presence of boron trifluoride are described. The structures of the first two compounds have been determined; the location of the substituent groups in the third is, at present, uncertain.\r\n\r\nDehydro-[Beta]-carotene, bisdehydro-[Beta]-carotene, and anhydroeschscholtzxanthin have been isolated from the end products of the reaction of [Beta]-carotene with N-bromosuccinimide. Bisdehydro-[Beta]-carotene is a new carotenoid whose probable structure is discussed.\r\n\r\nThe considerable provitamin A potency of 16,16'-homo-[Beta]-carotene is discussed from the standpoint of its novel structural features." }, { "name": "Waugh, John Stewart", "degree": "PhD", "year": "1953", "title": "Line Profiles in Nuclear Magnetic Resonance Absorption", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-05122003-145444", "creators": [ { "name": { "family": "Waugh", "given": "John Stewart" }, "id": "Waugh-John-Stewart", "display_name": "Waugh, John Stewart" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MTG1-GV96", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nThe general theory of line shapes in nuclear magnetic resonance experiments is first outlined in some detail, and results important to the ensuing discussion are derived.\r\n\r\nA radiofrequency spectrometer has been assembled, and its design, construction, and operation are described.\r\n\r\nThe fine structure problem for collinear systems of three interacting spins is solved by application of perturbation theory. Application is then made to the special case represented by the bifluoride ion. Experimental determinations of the line shapes and mean square line widths are made for the proton and fluorine resonances in potassium bifluoride, and interpreted in terms of the configuration of the ion. The equilibrium position for the proton is found to be within ? 0.05 A.U. of the center of the ion axis. Similar experiments performed on sodium bifluoride are less conclusive, but limits are set on the possible configurations of the [...] ion in this salt.\r\n\r\nLine width studies have been made on a number of crystalline coordination complexes. It is found that the cobalt (III) hexammine ion possesses freedom of reorientation in the lattice, but that no such freedom exists in other related compounds which were studied.\r\n\r\nFinally, an attempt to determine the third proton configuration in phosphorous acid is briefly described." }, { "name": "Alder, Berni Julian", "degree": "PhD", "year": "1952", "title": "The Radial Distribution Function and the Thermodynamic Properties of Monatomic Liquids. A Statistical Mechanical Theory of the Coefficient of Thermal Conductivity of Monatomic Liquids", "advisor": "Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032017-141351791", "creators": [ { "name": { "family": "Alder", "given": "Berni Julian" }, "id": "Alder-Berni-Julian", "display_name": "Alder, Berni Julian" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "chair", "display_name": "Kirkwood, John Gamble" }, { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "member", "display_name": "Davidson, Norman R." }, { "name": { "family": "Epstein", "given": "Paul Sophus" }, "id": "Epstein-P-S", "role": "member", "display_name": "Epstein, Paul Sophus" }, { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "member", "display_name": "Niemann, Carl G." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "member", "display_name": "Pauling, Linus" } ], "option_major": [ "chemistry" ], "doi": "10.7907/22ER-1E05", "abstract": "A fluid consisting of molecules interacting with the Lennard-Jones intermolecular potential but with rigid cores is treated by the Kirkwood and the Born-Green statistical\u00ad mechanical formulations. The integral equation for the radial distribution function of this fluid is solved numeri\u00adcally by a series expansion of all temperature dependent quantities in the reciprocal of the temperature. The first three terms of this series for the radial distribution func\u00adtion have been evaluated over a wide range of densities for the Born-Green integral equation.
\r\n\r\nThe distribution functions so obtained have been used to calculate the equation of state, the excess internal energy, and the excess entropy of this fluid. The two phase region of this equation of state is determined. For reason\u00adable values of the parameters in the potential, these calcu\u00adlated quantities agree within 10% to 20% with experimental data available for argon.
\r\n\r\nAt one density a comparison between the Kirkwood and the Born-Green theories shows that the two formulations agree closely.
\r\n\r\nA molecular theory of the coefficient of heat conduc\u00adtivity of monatomic liquids is developed on the basis of the general theory of transport processes presented by Kirkwood in 1946. The coefficient is expressed in terms of the inter\u00admolecular force and the equilibrium radial distribution func\u00adtion. Substituting for these, respectively, the Lennard-Jones potential and a reasonable analytic approximation to the experimental radial distribution function, the product of the thermal conductivity and the friction constant has been eval\u00aduated, for liquid argon at 89\u00b0K. With a preliminary estimate of the friction constant, the value of the coefficient of thermal conductivity is then given.
" }, { "name": "Bettman, Max", "degree": "PhD", "year": "1952", "title": "The Determination of the Crystal Structure of Potassium Picrate", "advisor": "Hughes, Edward Wesley; Donohue, Jerry", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272017-100629593", "creators": [ { "name": { "family": "Bettman", "given": "Max" }, "id": "Bettman-Max", "display_name": "Bettman, Max" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" }, { "name": { "family": "Donohue", "given": "Jerry" }, "id": "Donohue-Jerry", "role": "advisor", "display_name": "Donohue, Jerry" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1S9K-H086", "abstract": "The crystal structure of potassium picrate has been\r\ndetermined and refined to a considerable degree of accuracy\r\nby means of x-ray diffraction techniques. Most of the \r\nrefinement was carried out by the use of least squares methods,\r\nby making use of about half of the three dimensional data\r\nobtainable from copper K\u03b1 radiation.
\r\n\r\n\r\nThe benzene ring of the picrate ion is nearly planar,\r\nthe deviation from planarity being within experimental error.\r\nThe para nitro group is twisted 6\u00b0 out of the plane of the\r\nbenzene ring, apparently due to ionic attraction of the\r\noxygen atoms to neighboring potassium ions. The ortho nitro\r\ngroups are twisted 27\u00b0 out of the plane of the benzene ring\r\ndue to steric hindrance between the phenol oxygen and its\r\ntwo nearest oxygen neighbors in the ortho nitro groups.\r\nChemical bonds of a given species, such as carbon-carbon\r\nbonds, show considerable variations in length. All these\r\nvariations are quite reasonable in the light of well known\r\nprinciples of structural chemistry.
\r\n\r\n\r\nThe packing of the structure seems to be largely \r\ndetermined by the ionic attraction between potassium ions and\r\nfive out of the seven oxygen atoms of each picrate ion.\r\nThere also exist some rather short van der Waals contacts\r\nbetween neighboring picrate ions.
" }, { "name": "Bulman, Norman", "degree": "PhD", "year": "1952", "title": "I. Hapten Inhibition Studies with a Series of Local Anesthetics Derived from Piperidino Alcohols. II. The Incorporation of C\u00b9\u2074-Carboxyl-Labeled Leucine by Serum Proteins", "advisor": "Campbell, Dan Hampton; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272017-105740469", "creators": [ { "name": { "family": "Bulman", "given": "Norman" }, "id": "Bulman-Norman", "display_name": "Bulman, Norman" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/S9G7-0786", "abstract": "Part I
\r\n\r\nRabbit antibodies specific for the 3-(2-methyl-piperidino)propyl-p-aminobenzoate group have been prepared and the inhibition of precipitation of these antibodies\r\nhas been studied. It was found that a series of local \r\nanesthetics derived from piperidino alcohols were effective\r\ninhibitors of precipitation in this system. Reasonable\r\nexplanations of the serological properties of these drugs\r\nhave been given but it has not been found possible to\r\nestablish any relation between their serological properties\r\nand their pharmacological properties.
\r\n\r\nPart II
\r\n\r\nC14-carboxyl-labeled leucine has been administered to\r\nimmunized rabbits. While receiving the labeled amino acid\r\nthey also received intravenous injections of different\r\nantibody solutions. It was found that the normal constituents\r\nof the serum incorporated the radioactivity to any marked\r\nextent or else did so only upon the loss of their specific\r\nantibody characteristics.
" }, { "name": "Carrington, Tucker", "degree": "PhD", "year": "1952", "title": "Photoelectric Observation of the Rate of Dissociation of Dinitrogen Tetroxide Behind a Shock Wave", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102017-110749047", "creators": [ { "name": { "family": "Carrington", "given": "Tucker" }, "id": "Carrington-Tucker", "display_name": "Carrington, Tucker" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/63P4-AF03", "abstract": "An experimental method has been developed in which\r\na shock wave is used to heat a gas by definite amount\r\nin a time short compared to the rate of adjustment of the\r\ngas to the new temperature. The rate of attainment of the\r\nnew thermal equilibrium is then followed photoelectrically.\r\nThe apparatus described here can be used to study reactions\r\nwith half times as short as 10-5 seconds.
\r\n\r\n\r\nBy this method the rate of dissociation of dinitrogen\r\ntetroxide in the presence of a large excess of nitrogen\r\nhas been studied over a 48 degree temperature range and\r\nwith an eight fold variation in total pressure. The results\r\nindicate that dissociation is a unimolecular reaction,\r\nnear its second order limit at one atmosphere pressure,\r\nand approaching a first order limit at higher pressures.
" }, { "name": "Ellman, George Leon", "degree": "PhD", "year": "1952", "title": "I. Phosphorus-Containing Compounds in Neurospora. II. Synthetic Substrates for Chymotrypsin", "advisor": "Mitchell, Herschel K.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10042017-093300451", "creators": [ { "name": { "family": "Ellman", "given": "George Leon" }, "id": "Ellman-George-Leon", "display_name": "Ellman, George Leon" } ], "advisors": [ { "name": { "family": "Mitchell", "given": "Herschel K." }, "id": "Mitchell-H-K", "role": "advisor", "display_name": "Mitchell, Herschel K." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/FZ0J-HB93", "abstract": "I. Phosphorus-containing Compounds in Neurospora
\r\n\r\nA paper chromatographic method is described for the\r\nseparation of the water soluble phosphorus compounds found in\r\ntissue extracts. Results with known compounds are given. The\r\nmethod has been applied to the separation of the phosphorus\r\ncompounds in extracts of Neurospora. The presence of the \r\nfollowing compounds is indicated: the adenosine phosphates,\r\n3-phosphoglycerate, glucose-1-phosphate, glucose-6-phosphate,\r\nand fructose-6-phosphate. The presence of at least one major\r\nunknown compound is also indicated. The significance of these\r\nresults is discussed.
\r\n\r\nModifications of the usual methods for the study of the\r\nphospholipids were also devised. The phospholipids were\r\nseparated into the lecithins and cephalins. The cephalins were\r\nconverted into the N-2,4-dinitrophenyl derivatives. These\r\nwere chromatographed on silicic acid-celite columns. The \r\nfractions collected were hydrolyzed. Titration of the fatty\r\nacids indicate the presence of some phospholipids which do not\r\ncorrespond to the classical formulae. Chromatography of the\r\nphosphate esters present in these hydrolyzates revealed \r\nglycerophosphate and one unknown phosphorus compound. Chromatography\r\nof the DNP-amines showed the presence of eight components.\r\nThe DNP derivatives of ammonia, ethanolamine, serine, and\r\n1-amino-2-methyl-2-propanol were identified. The techniques\r\nused and the significance of the results are discussed.
\r\n\r\nII. Synthetic Substrates for Chymotrypsin
\r\n\r\nA general synthesis of methyl acyl-phenylalanyl-anthranilates\r\nhas been devised. The acetyl derivative serves as a \r\nsubstrate for chymotrypsin. Methyl anthranilate is\r\nproduced when this compound is hydrolyzed and it is detected\r\nby its fluorescence. The succinyl and maleyl derivatives\r\nwere also prepared, but they are not hydrolyzed by the enzyme.\r\nThese results are discussed.
" }, { "name": "Fasman, Gerald David", "degree": "PhD", "year": "1952", "title": "Studies on: I. A Reinvestigation of the Kinetics of the Urease Catalyzed Hydrolysis of Urea. II. Attempted Purification of the Adrenocorticotropic Hormone. III. Instrumental Adsorption Analysis. IV. The Effect of the Diphenyl Hydantoin (Dilantin) on the Ether Narcosis in the Cat", "advisor": "Niemann, Carl G.; Van Harreveld, Anthonie", "url": "https://resolver.caltech.edu/CaltechTHESIS:11252020-221750765", "creators": [ { "name": { "family": "Fasman", "given": "Gerald David" }, "id": "Fasman-Gerald-David", "display_name": "Fasman, Gerald David" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." }, { "name": { "family": "Van Harreveld", "given": "Anthonie" }, "id": "Van-Harreveld-A", "role": "advisor", "display_name": "Van Harreveld, Anthonie" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/33yv-xf08", "abstract": "In an investigation of the factors operative in the urease-catalyzed hydrolysis of urea in aqueous solutions, buffered at pH 7.0 with sodium or potassium phosphate, it has been found that both of the buffer components participate in the hydrolytic reaction. The buffer anion apparently functions as an activator and the buffer cation as an inhibitor. Sodium phosphate buffer displays a greater inhibitory action in the urease-catalyzed hydrolysis of urea than does an equivalent concentration of potassium phosphate buffer. After dialysis of urease solutions the activity in the presence of organic-inorganic buffers, e.g., ethylenedianine phosphate, was found to be greater than that of the initial preparation. The order of activation of the enzyme for the investigated anions as their ehtylenedianine salts is citrate > phosphate > maleate > sulphate > chloride > acetate. The activity of the enzyme increases with increased concentrations of these buffers.
\r\n\r\nAttempted purifications of three samples of adrenocorticotropic hormone, RN 145, RN 146 and RN 147, resulted in the following conclusions. Paper chromatography revealed three components in RN 145, two in RN 146 with a possible third; and three in RN 147 with a possible fourth. Further work on sample RN 147 indicated five moieties by electrophoresis on paper, five with a possible sixth by dinitrophenylation and chromatography and a separation into five components by dialysis and fractional ammonium sulphate precipitation.
\r\n\r\nThe machine built for Instrumental Adsorption Analysis at the California Institute of Technology was put into operation. Successful separations of fatty acid mixtures and an isomeric cis-trans mixture were achieved. Attempted resolution of the adrenocorticotropic hormone indicated non-homogeneity.
\r\n\r\nThe administration of diphenyl hydantoin (dilantin) in a dose of fifty milligrams per kilogram bodyweight was observed to potentiate the narcotic effect of ether. It caused a forty percent decrease in blood ether concentration necessary to suppress the knee jerk of the cat. This supports the thesis that the depolarizing effects of ether and diphenyl hydantoin are additive and that depolarization is an important factor in the narcotic effect of ether on central conduction.
" }, { "name": "Ferington, Thomas Edwin", "degree": "Masters", "year": "1952", "title": "Observations on the Interaction of Ion Exchange Resins with Some Cupric Compounds", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10162017-102130831", "creators": [ { "name": { "family": "Ferington", "given": "Thomas Edwin" }, "id": "Ferington-Thomas-Edwin", "display_name": "Ferington, Thomas Edwin" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CMRX-8587", "abstract": "The interaction of the Sulfonic Acid Resin,\r\nNalcite HCR, with CuII halide solutions was studied\r\nin hope of obtaining dissociation constants for the complex \r\nions CuX+. The fact that CuX+ is absorbed by\r\nthe resin to an appreciable extent prevented the\r\nattainmnet of this goal. It was found in the case of\r\nCuF+ that the complex ion is absorbed even more strongly\r\nthan Cu++. The presence of a Cu++-F- complex\r\nwas indicated by spectrophotometric observations.
\r\n\r\nThe action of the carboxylic acid resin, IRC - 50\r\nwas studied in a column. It was found that the \r\nvolume of the resin in the Cu++ salt form depended\r\non the salt with which the resin was treated. In the\r\ncase of solutions of Cu(OAc)2 it was found that Cu(OAc)+\r\nwas taken into the resin as well as Cu++.
\r\n\r\nA titration curve for IRC - 50 with NaOH in\r\nsolutions of ionic strength one is given.
" }, { "name": "Fickett, Wildon", "degree": "PhD", "year": "1952", "title": "Walden Inversions Involving the Isomeric 2,3-Butanediamenes and Related Compounds. An Experimental Test of Kirkwood's Theory of Optical Rotatory Power. Zero-Point Vibrational Contributions to the Optical Activity of Isotopically Asymmetric Molecules", "advisor": "Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032017-114803981", "creators": [ { "name": { "family": "Fickett", "given": "Wildon" }, "id": "Fickett-Wildon", "display_name": "Fickett, Wildon" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YA4K-H648", "abstract": "It has been demonstrated that reaction of ammonia\r\nwith 1,2-dimethylethyleneimine is attended by single Walden\r\ninversion and that the analogous reaction of ammonia with\r\n2,3-epoxybutane very probably proceeds in the same way. This\r\nresult and other evidence have been used to assign configurations\r\nto the 3-amino-2-butanols and to draw certain conclusions\r\nabout the courses of the reactions in which they are\r\ninvolved.
\r\n\r\n\r\nOptically active 1,2-dichloropropane has been prepared\r\nand its relative configuration determined. Measurements of\r\nits optical rotatory power in different solvents and at \r\ndifferent temperatures permit an approximate determination of\r\nthe optical rotations of the two forms of the molecule \r\ncorresponding to the two lowest potential minima for internal\r\nrotation about the 1,2-carbon-carbon bond. These values are\r\ncompared with the results of a theoretical calculation; the\r\nresulting assignment of absolute configuration is consistent\r\nwith a previous result for 2,3-epoxybutane.
\r\n\r\n\r\nKirkwood's theory of optical rotation has been modified\r\nso as to take into account contributions arising from zero-point\r\nvibrational effects. The theory is used to calculate\r\nthe optical rotations of compounds of the type R1R2CHD. The\r\nresult for \u03b1-deuteroethylbenzene is found to be comparable\r\nin magnitude with an experimental value and consistent in\r\nsign with previous assignments of absolute configuration.
" }, { "name": "Foster, Robert Joseph", "degree": "PhD", "year": "1952", "title": "Monoacetylation of 2,4-Diamino-6-Nitrotoluene. Kinetic Studies with \u03b1-Chymotrypsin. Effect of Dilantin Upon Ether Narcosis in the Cat", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10052017-131007685", "creators": [ { "name": { "family": "Foster", "given": "Robert Joseph" }, "id": "Foster-Robert-Joseph", "display_name": "Foster, Robert Joseph" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K13Z-9D57", "abstract": "The structure of the monoacetyl derivative of 2,4-diamino-6-nitrotoluene \r\nformed by reaction with an equimolar quantity of \r\nacetic anhydride in dry acetone at room temperature has been \r\nshown to be 2-amino-4-acetamido-6-nitrotoluene.
\r\n\r\n\r\n\r\nThe kinetic constants for the enantiomorphic pair of\r\nacetyl-phecylalaninamides and \u03b1-chymotrypsin at 25\u00b0and pH 7.9 \r\nin aqueous solution have been determined. The relationships of \r\nthese constants with others determined for similar enantiomorphic \r\npairs is discussed. Equations for the competitive hydrol\u00adysis \r\nof two substrates at the same catalytically active site of\r\nan enzyme have been derived and have been tested experimentally.
\r\n\r\n\r\n\r\nThe kinetic constants for L-tyrosine-hydroxamide and\r\n\u03b1-chymotrypsin have been determined at pH 6.9 and 25\u00b0. With \r\nthis hydroxamide as substrate, the enzyme-inhibitor complex dis\u00adsociation \r\nconstants have been determined for a series of\r\ninhibitors at pH 6.9 and 25\u00b0. The differences between these\r\nconstants and those at pH 7.9 is discussed and the charge state \r\nof the catalytically active site is inferred.
\r\n\r\n\r\nThe effect of the anti-convulsant dilantin upon ether \r\nnarcosis in the cat has been determined and is discussed in its \r\nrelation to present theories of nervous propagation and narcosis.
\r\n" }, { "name": "Goldberg, Richard Jay", "degree": "PhD", "year": "1952", "title": "I. A Theory of Antibody-Antigen Reactions. Part II. The Light-Scattering Properties of an Antigen-Antibody Reaction. III. Light-Scattering Arising from Composition Fluctuations in Multi-Component Systems", "advisor": "Kirkwood, John Gamble; Campbell, Dan Hampton", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102017-140804348", "creators": [ { "name": { "family": "Goldberg", "given": "Richard Jay" }, "id": "Goldberg-Richard-Jay", "display_name": "Goldberg, Richard Jay" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" }, { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M3F7-H051", "abstract": "Part I describes a theory of antibody-antigen reactions\r\nemploying bivalent and univalent antibody molecules\r\nand multivalent antigen molecules. All species in a system\r\nof this kind are defined by a distribution function which\r\nhas been derived on the basis that the most probable distribution\r\nis the appropriate one. Some of the features of\r\nantibody-antigen reactions are discussed in the light of\r\nthis theory.
\r\n\r\n\r\nIn Part II experiments are described which measured\r\nthe increase in turbidity of an antibody-antigen system\r\nwith increasing time of reaction. It was found that the\r\nrate of aggregation of antibody and antigen molecules\r\ninto large aggregates is dependent on the composition\r\nof the system. The existence of soluble aggregates in\r\nthe antigen excess region is indicated.
\r\n\r\n\r\nA general theory of Rayleigh scattering due to\r\ncomposition fluctuations in multi-component systems has\r\nbeen developed with the aid of the grand canonical ensemble\r\nof Gibbs. It is found in Part III. The equation\r\ndeveloped contains previously neglected terms arising\r\nfrom thermodynamic interactions between solutes in systems\r\nof more than two components.
" }, { "name": "Koe, B. Kenneth", "degree": "PhD", "year": "1952", "title": "The Isolation and Study of Some Naturally Occurring Fluorescent Organic Compounds and Stereoisomerization of Prolycopene, Pro-\u03b3-Carotene, and Lycopene in Chickens and Hens", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202017-102618218", "creators": [ { "name": { "family": "Koe", "given": "B. Kenneth" }, "id": "Koe-B-Kenneth", "display_name": "Koe, B. Kenneth" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZT9Z-S931", "abstract": "A report on the detection, analysis, spectrum, and identification \r\nof several polycyclic aromatic hydrocarbons as lipoid-soluble, \r\nfluo\u00adrescent organic compounds occurring in certain marine invertebrates \r\n(barnacles) is presented. Crystalline preparations of these compounds \r\nhave been obtained from the intensely fluorescent zones resulting\r\nfrom chromatographic resolution of the crude barnacle extracts. These \r\nhydrocarbons include anthracene, phenanthrene, fluoranthene, chrysene,\r\n1,12-benzperylene, coronene, and the strongly active carcinogen, \r\n3,4-benzpyrene. Similar experiments carried out with the beach worm have \r\nrevealed only traces of polycyclic aromatic compounds. They have not \r\nbeen found in deep-sea mud samples or in some seaweeds tested. Some \r\nsuggestions are made as to the origin of these compounds in barnacles \r\n(and beach worms).
\r\n\r\n\r\nWhen polycis carotenoids are fed to chickens and hens over a \r\nperiod of several days, and the crude extracts of the different \r\ntissues, gut washings, and feces of these animals are submitted to \r\nchromatographic analysis, the pigments recovered are found to con\u00adsist \r\nof the unchanged starting compound and stereoisomerized forms. \r\nThis bio-stereoisomerization results in the formation of not only \r\nthe all-trans and neo-forms of the carotenoid administered but also \r\npolycis isomers, some of which possess more cis double bonds than \r\nthe starting material.
\r\n" }, { "name": "O'Brien, Joseph Lloyd", "degree": "PhD", "year": "1952", "title": "I. The Ionization of Amino Acids and Other Polyfunctional Organic Compounds in the Solvent Sulfuric Acid. II. Studies on the Chemistry of Azlactones. III. Miscellaneous Observations on Amino Acid Derivatives. IV. The Nodal Silver Stain: its Mechanism and Relation to the Potassium Loss of Isolated Nerve", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09292017-150042637", "creators": [ { "name": { "family": "O'Brien", "given": "Joseph Lloyd" }, "id": "O'Brien-Joseph-Lloyd", "display_name": "O'Brien, Joseph Lloyd" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/120A-V997", "abstract": "The ionization of thirty compounds, including amino\r\nacids, \u03b1-acylamino acids, amides and related compounds, in\r\nthe solvent sulfuric acid has been determined by cryoscopic\r\nmeasurements. The results for the aliphatic amino acids\r\nclearly illustrate the phenomenon of polybasic ionization\r\nin sulfuric acid and are also significant to the discussion\r\nof the mechanisms for certain acid-catalyzed reactions. Sulfuric\r\nacid is found to catalyze both the dehydrative cyclization\r\nof \u03b1-acylamino acids and the bimolecular elimination\r\nof hydrazine from benzhydrazide.
\r\n\r\n\r\nA sulfuric acid catalyzed Erlenmeyer synthesis is\r\ndescribed which gives an excellent yield of 2-phenyl-4-benzal-5-oxazolone,\r\nobtained as a mixture of the geometrical isomers.\r\nThe stereochemistry of this condensation is considered and it\r\nis suggested that sulfuric acid inhibits the mutarotation of\r\nthe intermediate addition product. The satisfactory yield with\r\nbenzoylsarcosine provides definitive evidence for the existence\r\nof an oxazolonium ion intermediate.
\r\n\r\n\r\nSeveral reactions of amino acid derivatives are described,\r\namong them the cleavage of benzenesulfonylglycine by acetyl\r\nchloride. The structure of the so-called anhydropeptides is\r\nconsidered and it is concluded that a 5-imidazolone structure\r\nis unlikely.
\r\n\r\n\r\nThe nodal silver stain is shown to be a vital stain. A\r\nmechanism for this stain is presented and shown to be similar\r\nto the process which probably causes the initial potassium loss\r\nof isolated nerve.
" }, { "name": "Rosser, Willis Andrew, Jr.", "degree": "Masters", "year": "1952", "title": "Hydrogen Bonding in Alcohols", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:10182017-132702543", "creators": [ { "name": { "family": "Rosser", "given": "Willis Andrew, Jr." }, "id": "Rosser-Willis-Andrew", "display_name": "Rosser, Willis Andrew, Jr." } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2S8Z-D418", "abstract": "It is usually assumed in optical absorption work \r\nthat the natural stretching frequency of the hydroxyl\r\ngroup in an alcohol is appreciably changed by hydrogen\r\nbonding. A survey of work relating to hydrogen bonding\r\nin alcohols favors this assumption. Moreover, it appears\r\nthat the deviation of alcohols in solvents such as carbon\r\ntetrachloride from Henry's law is primarily due to\r\nhydrogen bonding polymerization, the extent of such \r\ndeviation being the same for the lower aliphatic alcohols\r\nand phenol.
\r\n\r\nOptical transmission measurements on dilute solutions\r\nof methyl alcohol and of ethyl alcohol in carbon\r\ntetrachloride were used to determine for these alcohols the\r\ndimerization constants associated with the reaction.
\r\n\r\n\r\n2 ROH \u2192 (ROH)2
\r\n\r\n\r\nThese constants in turn were used in support of the \r\ncontention that the polymerization constants associated with\r\nthe reactions
\r\n\r\n(ROH)g-1 + ROH \u2192 (ROH)g
\r\n\r\nare not independent of g as has been assumed on occasion.
\r\n\r\nThe viscosity of solutions of alcohols in carbon\r\ntetrachloride is briefly discussed in a semi-quantitative\r\nmanner.
" }, { "name": "Sheehan, William Francis, Jr.", "degree": "PhD", "year": "1952", "title": "Studies in Molecular Structure and Valence State Energy", "advisor": "Pauling, Linus; Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10182017-141152372", "creators": [ { "name": { "family": "Sheehan", "given": "William Francis, Jr." }, "id": "Sheehan-William-Francis", "display_name": "Sheehan, William Francis, Jr." } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/708M-H162", "abstract": "The structures of six gaseous molecules, trifluoromethyl\u00adacetylene, \r\nperfluorobutyne-2, tetramethylsilane, tungsten \r\nhexacarbonyl, molybdenum hexacarbonyl, and osmium tetroxide, \r\nhave been determined from a study of their electron diffraction \r\npatterns by the visual correlation method employed in these \r\nLaboratories. An interpretation of the interesting features\r\nof the unusual structures of the hexacarbonyls and the tetroxide \r\nis given. This thesis concludes with a discussion of the \r\nenergies of the valence states of atoms as they exist in \r\ndiatomic molecules.\r\n" }, { "name": "Sherwin, Robert Mitchell", "degree": "Engineering Degree", "year": "1952", "title": "Momentum and Heat Transfer Studies. I. Transfer of Heat and Momentum in Uniform Turbulent Air Streams. II. Continuous Velocity Measurements by the Hot Wire Method", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10132017-134354937", "creators": [ { "name": { "family": "Sherwin", "given": "Robert Mitchell" }, "id": "Sherwin-Robert-Mitchell", "display_name": "Sherwin, Robert Mitchell" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HJ09-KX96", "abstract": "Part I
\r\n\r\nThe thermal flux has been measured across an air stream flowing \r\nin a uniform, two-dimensional manner between horizontal parallel \r\nplates at different temperatures. Reynolds numbers ranged from 9,800\r\nto 56,500. A macroscopic correlation shows the effect of turbulence \r\non the thermal transfer.
\r\n\r\n\r\nA revised correlation of total conductivity as a function \r\nof position is subsequently obtained by correcting previously deter\u00admined \r\nvalues of total conductivity. A similar correlation of the\r\ntotal viscosity with position is revised to allow for variation in\r\nthe pressure gradient with plate separation. The correlations fall \r\noff with increasing Reynolds number. The turbulent Prandtl numbers \r\nfor two tests by an earlier investigator are compared with those predicted \r\nfrom the ratio of the revised point correlations.
\r\n\r\n\r\nPart II
\r\n\r\nTwo hot-wire methods are described for determining continuously \r\nthe mean velocity as a function of position in a turbulently-flowing \r\nair stream. In the constant-resistance method the mean wire temperature \r\nis automatically controlled. In the constant-current method no \r\ncontrol is necessary. In exploratory measurements the total \r\nviscosities bridge the discontinuous gap which arises from the use of \r\nvon K\u00e1rm\u00e1n's expression at the boundary between the buffer layer and \r\nthe turbulent core. Thermal flux corresponding to a Nusselt number\r\nof 40 has no noticeable effect on the velocity profile.
" }, { "name": "Shoolery, James Nelson", "degree": "PhD", "year": "1952", "title": "Studies in Microwave Spectroscopy", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10112017-162852337", "creators": [ { "name": { "family": "Shoolery", "given": "James Nelson" }, "id": "Shoolery-James-Nelson", "display_name": "Shoolery, James Nelson" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N37Q-4C88", "abstract": "The theory of microwave spectroscopy is first presented in some detail.\r\nFollowing this, sources of errors in structure determinations based\r\non moment of inertia data are considered, and approximate equations for\r\nestimating their effects are derived.
\r\n\r\n\r\nA microwave spectroscope has been assembled and its design, construction,\r\nand operation are discussed. Microwave spectra in the region from\r\n20 to 25 kmc have been obtained for HN14C12O16, and DN14C12O16.\r\nA rotational constant obtained from an infrared study of HNCO by L. H. \r\nJones is combined with the microwave data to yield the interatomic distances\r\nand bond angle. High resolution studies of the spectra of HNCO \r\nand HNCS permit evaluation of their electric quadrupole coupling constants\r\nand qualitative deductions concerning their structures to be made. The\r\nmolecular species CF3-C\u2261C-H, CF3-C13\u2261C-H, CF3-C13\u2261-H, and CF3-C\u2261C-D have\r\nbeen observed to absorb in the microwave region, and from the frequencies\r\nof these absorptions the C\u2261C and C-H distances are determined. In addition,\r\nthe measured moments of inertia are employed to calculate consistent\r\nsets of the remaining three parameters in CF3-C\u2261C-H. The application\r\nof the electron diffraction data of W. F. Sheehan, Jr., to this problem\r\nto determine which set of parameters actually represents the structure is\r\ndescribed. Stark effect measurements are presented which determine the\r\ndipole moments of HN14C12O16 in three vibrational states and of DNCO, OCS,\r\nH2CO, CHF3, and CHF3-C\u2261C-H in their ground states. Finally, attempts to\r\nobtain microwave spectra for several other compounds are briefly described.
" }, { "name": "Waldron, Robert Douglas", "degree": "PhD", "year": "1952", "title": "The Vibrational Spectrum and Structure of Organic Crystals: Urea, Thiourea, Glycine", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:02292012-090540895", "creators": [ { "name": { "family": "Waldron", "given": "Robert Douglas" }, "id": "Waldron-Robert-Douglas", "display_name": "Waldron, Robert Douglas" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YKFT-HQ71", "abstract": "Investigations of the infra-red spectra of single crystals of urea, thiourea, glycine, and deuterium derivatives with polarized radiation are presented. The polarization measurements are of value in identifying the normal vibrations.
\r\n\r\nFor urea, evidence is presented that the molecular structure is entirely planar. Frequency assignments are made for 14 of the 18 fundamental vibrations tor urea and deutero-urea. A valence force calculation of the skeletal force constants is made. The isotope product rule is applied to the vibrations of 2 symmetry species.
\r\n\r\nFor thiourea, the spectrum is closely related to that of\r\nurea. Frequency assignments of fundamental vibrations are\r\nmade for 15 frequencies of thiourea and 12 frequencies of\r\ndeutero-thiourea. A valence force calculation of the skeletal force constants is made. The isotope product rule is used to calculate 2 of the unobserved frequencies of deutero-thiourea. Evidence is given in support of a planar or nearly planar molecular structure.
\r\n\r\nThe spectrum of glycine yields polarization data giving\r\nthe orientation of the transition moment of individual vibrations. This is applied to the analysis of the observed frequencies. The polarizations of the absorption bands associated with stretching vibrations of the NH^+_3 group are compatible with restricted rotation of that group about the C-N bond. The relation between vibrational frequency and hydrogen bonding is discussed. The use of partially deuterated glycine permits the study of the effects of individual hydrogen bonds on the frequency and band shape of ND stretching vibrations.
\r\n\r\nSome features of the polarization technique are used to\r\npredict group orientations in the l-leucine crystal.
" }, { "name": "Yakel, Harry L.", "degree": "PhD", "year": "1952", "title": "An Investigation of the Structures of Some Crystalline Peptides and the Synthetic Polypeptide Poly-\u03b3-Methyl-L-Glutamate", "advisor": "Hughes, Emlyn Willard; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:10052017-093432115", "creators": [ { "name": { "family": "Yakel", "given": "Harry L." }, "id": "Yakel-Harry-L", "display_name": "Yakel, Harry L." } ], "advisors": [ { "name": { "family": "Hughes", "given": "Emlyn Willard" }, "id": "Hughes-Emlyn-Willard", "role": "advisor", "display_name": "Hughes, Emlyn Willard" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JK0E-GS59", "abstract": "The unit cell dimensions and space groups of \u03b1-triglycine,\r\ntriglycine hydrate and NN'-diglycyl-L-cystine have been\r\ndetermined by X-ray methods. The complete structure\r\nof NN'-diglycyl-L-cystine has also been elucidated. The\r\nstructural nature of the \"disulfide bridge\", which forms a \r\npart of this molecule, is described. Bond lengths and angles\r\nare of the usual size found in previous peptide molecules,\r\nbut there are several weak hydrogen bonds particularly in\r\nthe amide groups of the molecule.
\r\n\r\nAn investigation of the fibrous synthetic polypeptide\r\npoly-\u03b3-methyl-L-glutamate is reported. X-ray diffraction\r\ndata from well oriented \u03b1 fibers of this substance have\r\nbeen indexed on the basis of a hexagonal cell. The\r\nintensities of the X-ray reflections for two layer lines have\r\nbeen interpreted using the 3.6 residue \u03b1-helix model proposed\r\nby Pauling and Corey. A resume of the data appears to \r\nsupport this model for the polypeptide chain in \r\npoly-\u03b3-methyl-L-glutamate.
" }, { "name": "Zwanzig, Robert Walter", "degree": "PhD", "year": "1952", "title": "Quantum Hydrodynamics. A Statistical Mechanical Theory of Light Scattering from Simple Non-Polar Fluids", "advisor": "Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202004-160131", "creators": [ { "name": { "family": "Zwanzig", "given": "Robert Walter" }, "id": "Zwanzig-Robert-Walter", "display_name": "Zwanzig, Robert Walter" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZJSM-HT46", "abstract": "The first part of this thesis is concerned with certain extensions of a formal technique devised by Wigner for handling problems in quantum statistical mechanics, especially to problems in quantum mechanical transport processes. The approach is to find the closest possible analogy between classical and quantum statistical mechanics, so that the extensive work in classical statistical mechanics can be utilized. This analogy is attained with the Wigner distribution function, with which averages of dynamical variables in quantum mechanics may be calculated by integrations in phase space. We will first state some basic properties of distribution functions in classical statistical mechanics, and then state the corresponding properties of the density matrix in quantum mechanics. We will define and discuss the Wigner distribution function, show that it has the desired averaging properties, and obtain the analogue of the Liouville equation satisfied by this function. We will derive the analogue of the Liouville equation in reduced phase space, and then obtain the equations of hydrodynamics from quantum statistical mechanics. This will lead to expressions for the stress tensor and heat current density in terms of singlet and pair distribution functions.
\r\n\r\nIn the second part of this thesis, the statistical mechanical theory of light scattering from fluids is developed. The model used consists of a collection of spherically symmetric, optically isotropic particles, which are capable of interacting both mechanically and electromagnetically. The effects of these interactions are included rigorously. This is done by using the radial distribution function for the spatial configuration of the particles, and the pair moment distribution function, which gives the dipole moment of a particle when it and another particle are fixed at specified positions, and the rest are averaged out. A chain of integral equations is set up, which is capable of giving the local field within the fluid. The index of refraction is then derived, with corrections to the Clausius-Mosotti formula. Finally, the light scattering cross section is obtained. This reduces to the result obtained with the Einstein-Smoluchowski theory in the proper limit, but contains corrections when the wavelength of the light is of the order of interparticle distances.
" }, { "name": "Auer, Peter Louis", "degree": "PhD", "year": "1951", "title": "Part I. The Kinetics and Mechanism of Addition of Hydrogen Chloride to 2,3-Dimethyl-Butadiene-1,3 in Systems of Aprotic Solvents. Part II. A Theory of Visco-Elastic Behavior and Flow Birefringence in Solutions of Rigid Rod-Like Macromolecules", "advisor": "Lucas, Howard J.; Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechTHESIS:07252025-165414380", "creators": [ { "name": { "family": "Auer", "given": "Peter Louis" }, "id": "Auer-Peter-Louis", "display_name": "Auer, Peter Louis" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "co-advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2nze-c217", "abstract": "The kinetics of addition of hydrogen chloride to 2,3-dimethyl-\r\nbutadiene-1,3 in systems of aprotic solvents has been investigated\r\nat 25\u00b0 and 35\u00b0C. The reaction of one molecule of hydrogen chloride\r\nwith one molecule of diene is reversible; the rate of the forward\r\nreaction is proportional to the first power of the diene concentration\r\nand the three halves power of the hydrogen chloride concentration,\r\nwhile the rate of the reverse reaction is proportional to the\r\nfirst power of the butene chloride concentration and to\r\nthe one half power of the hydrogen chloride concentration. In\r\na system of aprotic solvents the rate of addition is inversely\r\nproportional to the basicity of the reaction medium. A mechanism\r\nis proposed wherein the reacting species are a proton-diene\r\ncomplex and a hydrogen chloride molecule; thus, the addition of \r\nhydrogen chloride to conjugated dienes in aprotic solvents may\r\nbe viewed as a proton catalysed reaction.
\r\n\r\nThe general statistical mechanical theory of irreversible\r\nprocesses in solutions of macromolecules presented previously\r\nby John F. Kirkwood has been applied to solutions containing\r\nlarge rigid rod-like molecules. It has been found that orientational\r\nfactors previously neglected contribute significant terms\r\nto the real part of the shear viscosity coefficient and give\r\nrise to a rigidity modulus in the presence of periodic shear\r\nwaves. A simple theory of flow birefringence gives results\r\npreviously obtained by other investigators.
" }, { "name": "Bergman, B. Gunnar", "degree": "PhD", "year": "1951", "title": "I. A Structural Investigation of the Mercury-Tin System. II. The Determination of the Crystal Structure of the Sigma Phase by Application of X-Ray Diffraction Methods to This Phase in the Iron-Chromium and Iron-Molybdenum Systems", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-190750018", "creators": [ { "name": { "family": "Bergman", "given": "B. Gunnar" }, "id": "Bergman-B-Gunnar", "display_name": "Bergman, B. Gunnar" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1gn8-2a14", "abstract": "A study of the mercury-tin system has been made by the application of thermal analysis and x-ray powder methods in order to determine whether four hypothetical intermetallic compounds of the compositions HgSn\u2083\u2085, HgSn\u2081\u2087, HgSn\u2081\u2081 and HgSn\u2088 proposed by Professor Linus Pauling, exist. The thermal analysis did not indicate the presence of these compounds in equilibrium with the liquid phase. By x-ray powder\r\nmethods the occurrence of only two different phases was established, one of tetragonal structure and identical with that of white tin, and one of simple hexagonal structure as has been reported by previous workers. The four intermetallic compounds proposed by Professor Pauling do not seem to exist.
\r\n\r\nThe structure of the sigma phase in the iron-chromium system at 46.5 at. % chromium content has been successfully determined by the application of x-ray diffraction methods. The structure is of a type that has not been observed earlier in intermetallic compounds.
\r\n\r\nThe structure of the sigma phase in the iron-molybdenum system has also been investigated briefly and found to be of the same type as the iron-chromium sigma structure.
" }, { "name": "Berry, Virgil Jennings", "degree": "PhD", "year": "1951", "title": "Temperature and Velocity Distribution in Non-Uniform Turbulent Flow", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03192009-111248", "creators": [ { "name": { "family": "Berry", "given": "Virgil Jennings" }, "id": "Berry-Virgil-Jennings", "display_name": "Berry, Virgil Jennings" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/KVQC-DV23", "abstract": "As part of a series of investigations of the relative rates of transfer of heat and momentum in a turbulent air stream, measurements were made of temperature and air speed distributions in the wake of an 0.0318 inch diameter steel cylinder. The cylinder was electrically heated and was mounted transverse to a two-dimensional, turbulently flowing air stream. Vertical traverses were made at seven stations downstream from the cylinder at each of three bulk air speeds. The data are presented in both graphical and tabular form. Measurements were also made, of the rate of heat transfer from the cylinder as a function of average cylinder surface temperature.
\r\n\r\nThe analytical problem of predicting temperature and air speed profiles downstream from a heated cylinder is considered, and a number of simple correlations are derived. These correlations are shown to describe the data with accuracy, and are extended to the prediction of temperatures in the wake of a large heated cylinder and in-the wake of a heated sphere, and to the prediction of concentrations in a turbulent diffusion flame apparatus. Agreement with experiment is excellent.
\r\n\r\nAn electric analog computer was used to calculate temperature distributions in a uniformly flowing turbulent air stream for three different sets of temperature boundary conditions. The resulting profiles compare favorably with available experimental data.
" }, { "name": "Buck, Richard Pierson", "degree": "Masters", "year": "1951", "title": "Studies on the Use of Coulometric and Amperometric Analysis", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08092017-100407498", "creators": [ { "name": { "family": "Buck", "given": "Richard Pierson" }, "id": "Buck-Richard-Pierson", "display_name": "Buck, Richard Pierson" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QJZB-MY25", "abstract": "A coulometric titration is described in which unipositive\r\nthallium is oxidized to the tripositive state by electrolytically\r\ngenerated bromine or chlorine. The end-point is determined \r\namperometrically by measuring the current between\r\ntwo platinum electrodes with an impressed potential difference\r\nof 200 millivolts. Confirmatory analyses have shown an accuracy of 0.2% for 93\r\nto 200 microgram samples, and of 0.1%\r\nfor samples of from 200 to 1900 micrograms.
\r\n\r\nThe application of dual intermediates to secondary coulometric titrations\r\nwith an amperometric end point has been studied.\r\nCupric copper and bromide have been used for the alternate electrolytic \r\ngeneration of bromine and cuprous copper for the purpose of titrating\r\na substance exhibiting a slow rate of reaction with bromine.\r\nA procedure is described by which aniline has been titrated in\r\nquantities of from 13 to 280 micrograms with an average error without regard \r\nto sign of less than 0.4 micrograms.
\r\n\r\nA study has been made of the bromine-bromide diffusion current,\r\nthe effects of the concentrations of bromine, bromide\r\nand hydrogen ion; the minimum bromide ion concentration necessary\r\nto maintain generation of bromine with 100% current efficiency was determined.
\r\n\r\nStudies have been made of the diffusion-controlled currents observed when potential\r\ndifferences, less than the decomposition potential, are impressed upon two\r\nplatinized-platinum electrodes in solutions of hydrochloric acid which are 0.1 VF\r\nin potassium chloride and saturated with hydrogen gas. The effects of the \r\nelectrode size and material, the applied potential, and the presence of \r\noxygen and nitrogen gas are described.
" }, { "name": "Clarke, Donald Walter", "degree": "PhD", "year": "1951", "title": "I. Attempts to Isolate the Rh Antigen from Red Blood Cells. II. The Fractionation of an Anti-Rh Antiserum. III. A Comparison of the Vasoconstrictor Actions of Adrenaline and Noradrenaline", "advisor": "Campbell, Dan Hampton; Van Harreveld, Anthonie", "url": "https://resolver.caltech.edu/CaltechTHESIS:10052017-143320468", "creators": [ { "name": { "family": "Clarke", "given": "Donald Walter" }, "id": "Clarke-Donald-Walter", "display_name": "Clarke, Donald Walter" } ], "advisors": [ { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "advisor", "display_name": "Campbell, Dan Hampton" }, { "name": { "family": "Van Harreveld", "given": "Anthonie" }, "id": "Van-Harreveld-A", "role": "advisor", "display_name": "Van Harreveld, Anthonie" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VP6F-PS33", "abstract": "Part I
\r\n\r\nAttempts to obtain a substance with Rh antigenic \r\nactivity from human red blood cells are described. At \r\nfirst, some extractions of the cells using ethanol, \r\nmethanol, acetone, ether, dioxan, chloroform, and tol\u00aduene, \r\nunder different conditions, were performed.\r\nLater work involved treatment of the cells with aqueous \r\nreagents to degrade the cell wall, followed by attempts \r\nto obtain a purified, active extract by precipitation\r\nor solution. None of these methods yielded a pure, \r\nspecifically active Rh antigenic material.
\r\n\r\n\r\nPart II
\r\n\r\nThe fractionation of an anti-Rh serum by \r\nelectro\u00adphoresis-convection, and the immunologic \r\ncharacterization of these fractions, are described.\t\r\nEvidence is presented to show that certain anti-Rh \r\nantibodies may exist in globulin fractions other \r\nthan the \u03b3-globulin.
\r\n\r\n\r\nPart III
\r\n\r\n\r\nExperiments are described in which the vasoconstricting \r\nactions of adrenaline and of nor-adrenaline on rats were \r\ncompared. It was concluded that there was but little difference \r\nin their action in this respect. Other experiments indicated \r\nthat the administration of these drugs to lightly anaesthetized \r\nrabbits did not affect the metabolic rate of the subjects.
\r\n\r\n" }, { "name": "Cleland, George Horace", "degree": "PhD", "year": "1951", "title": "I. An Investigation of the Dakin-West Reaction. II. The Role of Peroxides in Mutagenesis", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062017-132951069", "creators": [ { "name": { "family": "Cleland", "given": "George Horace" }, "id": "Cleland-George-Horace", "display_name": "Cleland, George Horace" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A274-DG11", "abstract": "An investigation of the Dakin-West reaction has been\r\nmade, as a result of which the scope of the reaction has been \r\nextended in a number of ways.
\r\n\r\na. It has been found that a number of aliphatic, aromatic \r\nand heterocyclic acid anhydrides, acyl fluorides, and (with \r\nthe proper choice of catalysts) acid chlorides can be used in \r\nplace of acetic anhydride in the reaction. Several cyclic \r\nanhydrides of dibasic acids have been shown not to react; in\u00adconclusive \r\nresults were obtained with maleic anhydride.
\r\n\r\n\r\nb. The reaction has been shown not to depend on a specific \r\ncatalytic action of the pyridine structure, but to be cata\u00adlyzed \r\nalso by such bases as sodium acetate.
\r\n\r\nc. Several unusual \u03b1-amino acids have been shown to undergo \r\nthe reaction; conclusions have been drawn as to the failure of \r\nseveral other amino acids to react. It has been shown that \r\ndipeptides can be used in place of amino acids.
\r\n\r\nd. A mechanism for the reaction has been proposed, based\r\non evidence now available.
\r\n\r\ne. Observations have been made on side reactions of importance\r\nto the reaction; a method of utility for purifying the\r\nproducts of the reaction has been developed.
\r\n\r\nThe role of peroxides in mutagenesis has been investigated;\r\nseveral peroxides have proved to be effective for the\r\ninduction of mutations.
" }, { "name": "Deutsch, Daniel Harold", "degree": "PhD", "year": "1951", "title": "I. The Synthesis of Spiro(3,5)Nonane. II. The Presumed Synthesis of 1,3-Cyclobutanedicarboxylic Acid by Markownikoff and Krestownikoff. III. The Synthesis of Cis and Trans-1,3-Cyclobutanedicarboxylic Acids", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:10122017-111506286", "creators": [ { "name": { "family": "Deutsch", "given": "Daniel Harold" }, "id": "Deutsch-Daniel-Harold", "display_name": "Deutsch, Daniel Harold" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/K23E-7793", "abstract": "Spiro(3,5)nonane was prepared by methods indicative\r\nof structure.
\r\n\r\nThe historically The historically important acid reported in 1881 by \r\nMarkownikoff and Krestownikoff and assigned the structure \r\n1,3-cyclobutanedicarboxylic acid (a structure which has\r\nnever subsequently been questioned) was shown to be 1-methyl- \r\n1,2-cyclopropanedicarboxylic acid. The mechanism of the for\u00admation \r\nof the Markownikoff-Krestownikoff acid is discussed.
\r\n\r\nThe previously unknown cis- and trans-1,3-cyclobutane\u00ad-\r\ndicarboxylic acids were synthesized. After numerous unsuc\u00adcessful \r\nattempts the synthesis was achieved starting from \r\npentaerythritol. The reaction between the benzylidene der\u00adivative \r\nof 2,2-bis(bromomethyl)-1,3-propandiol and sodium\r\nmalonic ester gave a condensation product which\tafter hydrolysis\t\r\nand oxidation with nitric acid yielded 1,1,3,3-cyclobutanetetracarboxylic \r\nacid. On decarboxylation of the latter, \r\nthe desired acids were obtained.
\r\n" }, { "name": "Douglas, David Lewis", "degree": "PhD", "year": "1951", "title": "I. The Magnetic Susceptibility of Europium(III) and Europium(II) Ions and the Photochemical Reduction of Water by Europium(II) Ion. II. The Magnetic Susceptibility of Europium and Samarian Amalgams. III. Observations on the Chemistry of Europium. IV. Age Determination from Carbon-14 Content: Ionization Chamber Techniques. V. The Volume Change Due to Hydrogen Bonding of Methanol in Carbontetrachloride Solution", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08312017-152910390", "creators": [ { "name": { "family": "Douglas", "given": "David Lewis" }, "id": "Douglas-David-Lewis", "display_name": "Douglas, David Lewis" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9X7A-Y940", "abstract": "The discovery of the photchemical reduction of water by europium(II) ion is reported.\r\nBy use of a chemical actinometer for determining light intensities and a Gouy balance\r\nfor following the change in magnetic susceptibility overall quantum yields were\r\ndetermined to be about 0.2 for solutions 0.5 m. in HCl and 0.15 m. in EuCl2.\r\nA mechanism consistent with the experimental data is
\r\n\r\nEu(II)\u00b7H2O + hv = Eu(II)*\u00b7H2O
\r\n\r\nEu(II)*\u00b7H2O = Eu(III)aq + H + OH-aq
\r\n\r\nH + H+aq + Eu(II)aq = Eu(III)aq + H2
\r\n\r\nThe thermal reaction under these conditions was found to be relatively unimportant.
\r\n\r\n\r\nThe magnetic susceptibility of europium in its liquid amalgam was observed\r\nto be 8.09 \u00b1 0.03 Bohr magnetons and that of samarium in its liquid amalgam\r\nto be 2.31 \u00b1 0.05 Bohr magnetons.
\r\n\r\n\r\nIn a brief investigation europium(II) perchlorate was observed to be\r\nquite soluble in water and the solution stable as regards oxidation of\r\nthe europium. The preparation of europium(II) carbonate is discussed. The possible\r\nreduction of CO2 by the hydrogen atoms produced in the irradiation\r\nof Eu(II) solutions was investigated, negative results being obtained.
\r\n\r\n\r\nUsing an ionization chamber in conjunction with a very sensitive quartz fiber electroscope, the small amount of C14 present in \"living\" carbon was detected. The problem of background ionization observed in\r\nthe chambers was investigated in detail. Preliminary experiments to determine the suitability of the instruments for the measurement of the age of archeological specimens were carried out. The age of one specimen was observed to be about 3,500 years.
\r\n\r\n\r\nThe densities of dilute solutions of CH3OH in CC14 are reported. A\r\ncomparison of the partial molar volumes obtained therefrom with the mono\u00admer\r\n fraction of CH3OH determined by spectroscopic means leads to the \r\nconclusion that the average volume of the monomer is only 2% greater than that \r\nof the CH3OH in the polymers.\r\n
" }, { "name": "Goeddel, Walter Van Norman", "degree": "Masters", "year": "1951", "title": "An Investigation of the Manganese Indium System", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10162017-141948279", "creators": [ { "name": { "family": "Goeddel", "given": "Walter Van Norman" }, "id": "Goeddel-Walter-Van-Norman", "display_name": "Goeddel, Walter Van Norman" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CBKV-KJ81", "abstract": "A preliminary phase-equilibria study has been made of the\r\nmanganese-indium alloy system by means of thermal analysis\r\n(cooling curves) and metallographic studies (photomicrographs).\r\nFerromagnetism has been found to exist in alloys containing up\r\nto 70 atom percent manganese and has tentatively been attributed\r\nto the compound Mn2In. A phase diagram has been proposed, on\r\nthe basis of the data obtained, in which the indium rich portion\r\nof the system consists of indium plus Mn2In, while the manganese\r\nrich portion is made up of a manganese solid solution.\r\nAdditional experiments have been outlined to further identify\r\nthe nature and extent of the phases present. A new scheme of\r\nchemical analysis has been applied to the alloys with good success." }, { "name": "Jones, Llewellyn Hosford", "degree": "PhD", "year": "1951", "title": "Infrared Studies of Hydrogen Bonding of Methanol with Aromatic Hydrocarbons. Infrared Spectrum and Molecular Structure of Nitrous Acid. Infrared Spectra and Molecular Structure of Isocyanic Acid, and Isothiocyanic Acid", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:08112017-094705440", "creators": [ { "name": { "family": "Jones", "given": "Llewellyn Hosford" }, "id": "Jones-Llewellyn-Hosford", "display_name": "Jones, Llewellyn Hosford" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CAJ1-B520", "abstract": "Part I of this thesis presents the results of an investigation \r\nof hydrogen bonding of methanol with aromatic hydrocarbons.\r\nThe infrared spectra of methanol in various solvents\r\nindicate that the methanol molecules form weak hydrogen bonds\r\nwith aromatic hydrocarbons, probably at the center of the \r\naromatic ring.
\r\n\r\nPart II of this thesis presents the results of an investigation\r\nof the infrared spectrum of nitrous acid. The spectrum\r\nindicates that there are two isomeric forms of nitrous acid, a\r\ncis and a trans form. The rotational structure of the hydrogen\r\nstretching band of the cis form indicates that the O=N-O angle\r\nof cis nitrous acid is 113 \u00b1 2\u00b0. A normal coordinate treatment\r\nof HONO and DONO indicates that the strongest band in the spectrum\r\nout to fifteen microns is the overtone of the O=N-O bending\r\nvibration. On the basis of this treatment the frequencies \r\nof the five in plane vibrations of trans nitrous acid have been\r\nassigned as 3590, 1696, 1270, 825, and 413 cm-1.
\r\n\r\nIn Part III the results of an investigation of the infrared\r\nspectrum of isocyanic acid and isothiocyanic acid are presented.\r\nFor isocyanic acid the fundamental vibrational frequencies are\r\n3534, 2280, 1340, 779, 650, and 550 cm-1. The last\r\nfrequencies were obtained from combination bands. For isothiocyanic\r\nacid the fundamental vibrational frequencies are 3530, \r\n1972, 1000, 660, 616, and 543 cm-1. The last three were \r\nobtained from combination bands. From the rotational structure of the\r\nN-H stretching bands of these two molecules we have calculated\r\nthat the effective H-N-C angle in the ground vibrational state\r\nis 128\u00b019' \u00b1 40' for HNCO and 138\u00b040' \u00b1 1\u00b0 for HNCS.
" }, { "name": "Leroux, Pierre Jean", "degree": "PhD", "year": "1951", "title": "Kinetics and Stereochemistry of the Hydrolysis of Esters of Nitric, Sulfuric and p-Toluenesulfonic Acids", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10032017-105106793", "creators": [ { "name": { "family": "Leroux", "given": "Pierre Jean" }, "id": "Leroux-Pierre-Jean", "display_name": "Leroux, Pierre Jean" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SCPZ-H386", "abstract": "Unlike the hydrolysis of carboxylic esters or that of\r\nalkyl halides, the hydrolysis of esters derived from\r\noxygenated acids of nitrogen, phosphorus, sulfur and the \r\nhalogens has not been subjected to a systematic investigation.
\r\n\r\nThis work represents an attempt to clarify the\r\nmechanism operating in the hydrolysis of alkyl sulfonates,\r\nsulfates and nitrates.
\r\n\r\n2-Butanol and 2,3-butanediol were chosen as the alcoholic\r\nconstituents because they afforded easily obtainable\r\noptical isomers and also because of their intermediate\r\nposition as secondary alkyl derivatives.
\r\n\r\nThe study of the kinetics and stereochemistry of their\r\nhydrolysis has revealed that sec-butyl p-toluenesulfonate\r\nand sec-butyl nitrate resemble the secondary halides while\r\nsec-butyl hydrogen sulfate behaves much like the corresponding\r\ncarboxylic esters.
\r\n\r\nThe study of 3-hydroxy-sec-butyl hydrogen sulfate has\r\nafforded a reasonable explanation of the complex behavior\r\nof cyclic sulfate of 2,3-butanediol upon hydrolysis.
\r\n\r\nAn improvement in the synthesis of D(+)-sec-butyl bromide\r\nhas lead to the preparation of L(-)-sec-butyl nitrate\r\nwith a relatively high degree of optical activity.
\r\n\r\nFinally a new preparation of L(-)-2-butanol from D(-)-2,3-butanediol\r\nis described.
\r\n\r\n\r\n\r\n\r\n" }, { "name": "McConnell, Harden Marsdon", "degree": "PhD", "year": "1951", "title": "I. Investigation of Possible Interactions Between Thallium (I) and Thallium (III) in Solution and in the Crystalline Thallium Sesqui-Halides. II. Spectrophotometric Investigations of the Copper (II) Chloro-Complexes in Aqueous Solutions of Unit Ionic Strength. III. Optical Interaction Between the Chloro-Complexes of Copper (I) and Copper (II) in Solutions of Unit Ionic Strength. Interpretations of the Spectral Absorption of a Copper (I) - Copper (II) Dichloro-Complex. IV. Spectrophotometric Investigation of the Interaction Between Iron (II) and Iron (III) in Hydrochloric Acid Solutions", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06102004-141410", "creators": [ { "name": { "family": "McConnell", "given": "Harden Marsdon" }, "id": "McConnell-Harden-Marsdon", "display_name": "McConnell, Harden Marsdon" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M9F6-ZC83", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\t\t\t\t\t\r\n\r\nA radiochemical and spectrophotometric investigation of the interactions between thallium (I) and thallium (III) is used to show that the majority of the thallium (I) and thallium (III) atoms in the crystalline thallium sesquihalides do not occupy equivalent positions in the crystalline lattice and that there is no strong optical interaction between thallium (I) and thallium (III) in aqueous solutions containing perchlorate or chloride ion.\r\n\r\nThe absorption spectra of mixed solutions of copper (II) perchlorate, perchloric acid and hydrochloric acid at a constant ionic strength of 1.00 in the wavelength range 250-300 [...] are interpreted in terms of the equilibria, [...]. The equilibrium constants for these reactions are determined and the enthalpy of formation of [...] is estimated.\r\n\r\nThe non-additive light absorption in the 400-600 mp wavelength range of solutions maintained at unit ionic strength with perchloric acid and containing copper (I) and copper (II) and low concentrations of chloride ion, has been interpreted in terms of an \"interaction complex\", [...]. At higher chloride ion concentrations in solutions of the same ionic strength, interaction complexes of higher chloride coordination (but still containing only one copper (I) and one copper (II) in each complex) are important.\r\n\r\nTwo interpretations of the 400-600 [...] spectral absorption of [...] are advanced and discussed. At present no conclusions can be drawn as to which interpretation is to be preferred.\r\n\r\nThe light absorption in the 450-900 [...] wavelength range by mixed solutions of iron (II) and iron (III) in hydrochloric acid is interpreted as evidence for the formation of unstable but strongly absorbing interaction complexes, each interaction complex containing one atom of iron (II) and one atom of iron (III) and a number of coordinating chloride ligands. The light absorption by interaction complexes decreases with decreasing hydrochloric acid concentration and there is no interaction absorption by solutions containing [...] and no chloride ion.\r\n\r\nAbsorption spectra of iron (II) in solutions of varying hydrochloric acid concentration observed in the 700-900 [...] wavelength range are used to show the presence of iron (II) chloro-complexes." }, { "name": "Petracek, Francis James", "degree": "Masters", "year": "1951", "title": "A Study of Some Plant Carotenoids and of Certain Colorless Fluorescing Compounds of Marine Origin", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282025-183252396", "creators": [ { "name": { "family": "Petracek", "given": "Francis James" }, "id": "Petracek-Francis-James", "display_name": "Petracek, Francis James" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2ge3-te76", "abstract": "The sudden color change observed during the ripening\r\nof the Pyracantha gibbsi ynnanensis berries was investigated.\r\nIt was caused by the rapid formation of an anthocyanin, \r\nnot by the cis\u2192trans isomerization of a polycis\r\ncarotenoid.
\r\n\r\n30 gm. of all-trans lycopene were stereoisomerized by\r\nrefluxing in benzene, and the solutions were chromatographed\r\nto separate the very small amounts of polycis lycopenes that\r\nshould be present according to theoretical considerations.\r\nFour chromatographically separable pigments were isolated\r\nfrom the filtrate which would have contained any polycis\r\nlycopenes, but none of the four pigments belonged to the\r\nstereoisomerica lycopene sot.
\r\n\r\nThe carotenoid pigments and fluorescing substances\r\nextracted from several marine sources were isolated and\r\ninvestigated by chromatographic and spectroscopic methods.\r\nA provitamin D sterol was identified and isolated in an\r\nimpure form from one of these marine sources, the Thoracophelia \r\nmucronata.
" }, { "name": "Thomas, Dudley Watson", "degree": "PhD", "year": "1951", "title": "Studies on the Purification and Properties of L-Leucine. Studies on the Mode of Action of Trypsin and Chymotrypsin", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09272017-150651665", "creators": [ { "name": { "family": "Thomas", "given": "Dudley Watson" }, "id": "Thomas-Dudley-Watson", "display_name": "Thomas, Dudley Watson" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DKCB-ER97", "abstract": "A procedure for the preparation of L-leucine is described\r\nand certain physical properties, useful for establishing the \r\nidentity or purity, have been redetermined. The behavior of\r\nL-leucine in sulfuric acid and glacial acetic acid solutions\r\nhas been investigated.
\r\n\r\n\r\nPreliminary investigations of the tryptic hydrolosis of\r\nacetyl- and benzoyl-L-argininamide have been conducted. It\r\nwas found that aqueous trypsin solutions are quite unstable,\r\nand thus not ideally suited for kinetic studies. L-Arginine-methyl\r\nester was found to be rapidly split at pH 4.0, this\r\npH being far removed from the expected optimum (i.e. pH 7-8).
\r\n\r\n\r\nThe kinetics of the \u03b1-chymotrypsin catalyzed hydrolysis\r\nof acetyl- and nicotinyl-L-tyrosinamide has been investigated\r\nat 25\u00b0C. and pH 7.8-8.0. Suitable rate expressions \r\nhave been developed and the rate constants determined. The\r\neffect of various competitive inhibitors of \u03b1-chymotrypsin\r\nhas been measured, and conclusions have been drawn relative\r\nto structure and affinity for the enzyme. It has been shown\r\nthat the \u03b1-chymotryptic hydrolyses, so far investigated\r\nquantitatively, can be described in terms of the classical\r\nMichaelis-Menten enzyme-substrate complex theory.
" }, { "name": "Wood, William Wayne", "degree": "PhD", "year": "1951", "title": "Experimental and Theoretical Investigations on Optical Rotatory Power", "advisor": "Kirkwood, John Gamble; Schomaker, Verner", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102017-145355975", "creators": [ { "name": { "family": "Wood", "given": "William Wayne" }, "id": "Wood-William-Wayne", "display_name": "Wood, William Wayne" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" }, { "name": { "family": "Schomaker", "given": "Verner" }, "id": "Schomaker-V-F", "role": "co-advisor", "display_name": "Schomaker, Verner" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6J2M-7Q11", "abstract": "The optical rotatory power of a fluid system of molecules\r\nis calculated. The result is the same as obtained\r\nby previous investigators using similar but less \r\nsatisfactory arguments. Various means of calculating the\r\noptical activity of a substance are discussed, one previously\r\nused by Kirkwood being employed to discuss theoretically\r\nthe absolute configurations of trans-2,3-epoxybutane,\r\n1,2-dichloropropane and 1,2-dibromopropane. An experimental\r\ninvestigation of the molecular structure of 1,2-dichloropopane \r\nby electron diffraction methods is described." }, { "name": "Adams, Robert Train", "degree": "PhD", "year": "1950", "title": "I. The Synthesis of D- and L-Threo- and D- and L-Erythro-\u03b1-Amino-\u03b2-hydroxy-n-caproic Acids. II. Experiments on the Preparation of \u03b1-Aminoalkanesulfonamides. III. The Influence of Nerve Impulse Sequence on the Contractions of Different Crustacean Muscles", "advisor": "Niemann, Carl G.; Wiersma, Cornelius A. G", "url": "https://resolver.caltech.edu/CaltechTHESIS:08292019-160935347", "creators": [ { "name": { "family": "Adams", "given": "Robert Train" }, "id": "Adams-Robert-Train", "display_name": "Adams, Robert Train" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." }, { "name": { "family": "Wiersma", "given": "Cornelius A. G" }, "id": "Wiersma-C-A-G", "role": "advisor", "display_name": "Wiersma, Cornelius A. G" } ], "committee": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "chair", "display_name": "Niemann, Carl G." }, { "name": { "family": "Bates", "given": "Robert H." }, "id": "Bates-Robert-H", "role": "member", "display_name": "Bates, Robert H." }, { "name": { "family": "Buchman", "given": "Edwin R." }, "id": "Buchman-E-R", "role": "member", "display_name": "Buchman, Edwin R." }, { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "member", "display_name": "Lucas, Howard J." }, { "name": { "family": "Wiersma", "given": "Cornelis A. G." }, "id": "Wiersma-C-A-G", "role": "member", "display_name": "Wiersma, Cornelis A. G." } ], "option_major": [ "chemistry" ], "doi": "10.7907/BWFC-9S12", "abstract": "The preparation of each of the four optical isomers of \u03b1-amino-\u03b2-hydroxy-n-caproic acid is described. The configurations of the four optically active amino acids have been deduced on the basis of evidence obtained from the reactions of their N-benzoyl-O-methyl derivatives with p-toluidine in the presence of papain and evidence obtained by oxidative degradation of one of the active \u03b1-amino-\u03b2-hydroxy-n-caproic acids to an optically active \u03b1-hydroxyvaleric acid. The reduction of \u03b1-benzamido-\u03b2-methoxy-n-caproic acid with lithium aluminum hydride is described.
\r\n\r\nExperiments directed toward the synthesis of aminomethanesulfonamide and \u03b1-aminoethanesulfonamide are reported.
\r\n\r\nThe influence of nerve impulse sequence on the contractions of different crustacean muscles has been investigated by studying the effect of intercalating extra stimuli during stimulation at a low frequency and by studying the effect of changes in the pattern of the stimulating impulses. The effect of impulse-spacing on subsequent facilitation of the contraction has been examined. The results of these investigations are described. The significance of pattern-sensitivity in synaptic structures is discussed.
\r\n\r\n" }, { "name": "Blaker, Robert Hockman", "degree": "PhD", "year": "1950", "title": "Characterization of Nitrocellulose and Certain Other High Molecular Weight Substances Including Studies of the General Applicability of the Light Scattering Method", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:06302025-200842507", "creators": [ { "name": { "family": "Blaker", "given": "Robert Hockman" }, "id": "Blaker-Robert-Hockman", "display_name": "Blaker, Robert Hockman" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0gtm-cd81", "abstract": "A description is given of various instruments which have been\r\ndesigned and constructed. These include: a capillary viscometer for\r\nuse with volatile solvents; dynamic and static osmometers; a recording\r\napparatus for precipitation titration experiments; and instruments\r\nfor light; scattering experiments, including a photoelectric\r\nphotometer, a prism differential refractometer, and an angular scattering\r\ncamera.
\r\n\r\nOsmotic pressure and intrinsic viscosity measurements on solutions\r\nof nitrocellulose fractions were used to establish a new value of the\r\nStaudinger Constant, 9.39 \u00b7 10-3, for nitrocellulose dispersed in acetone\r\nat 25\u00b0 C. The suggestion is made that the value of the ratio of\r\nthe number average to the weight average molecular weight of a polymer\r\nvaries with the degree of molecular heterogeneity. The use of this\r\ncriterion indicates that nitrocellulose manufactured from wood pulp\r\nis distinctly more heterogeneous than that from cotton linters.
\r\n\r\nA technique has been developed for the estimation of the degree\r\nof molecular heterogeneity of nitrocellulose by means of precipitation\r\ntitration. The rate of precipitation in a solution is followed\r\nby measuring the decrease in light transmission. The method was\r\nfound to be useful in the characterization of artificial blends of\r\nnitrocellulose.
\r\n\r\nA detailed description is given of the technique for making\r\nlight scattering measurements on nitrocellulose solutions. Carbon disulfide \r\nis recommended as a light scattering standard. The values determined\r\nfor the absolute scattering power of carbon disulfide for\r\nlight of wave length 4358 \u00c5 and 5461 \u00c5 are, respectively, 15.1 \u00b7 10-5\r\nand 4.8 \u00b7 10-5.
\r\n\r\nLight scattering measurements on solutions of nitrocellulose\r\nfractions indicate that the molecule is relatively stiff, and is\r\nnearly fully extended up to a degree of polymorization of about 100.\r\nThe \"effective bond length\" is about 10 times the len6rth of the\r\nmonomer unit. The suggestion is made that the validity of the\r\nStaudinger viscosity relation for nitrocellulose is fortuitous and\r\nresults from the fact that t here is little change in the value of\r\n[\u019e]/z over a range of z which is usually encountered in nitrocellulose\r\nsamples.
\r\n\r\nThe interaction between nitrocellulose and the components of a\r\nbinary solvent has been studied by light scattering and the results\r\nhave been interpreted in terms of the recent Kirkwood-Goldberg theory.\r\nThe data indicate that there is considerable interaction between\r\nnitrocellulose and certain non-solvents; for example, water, ligroin,\r\nbutyl chloride.
\r\n\r\nAn investigation has been :made of the special problems involved\r\nin the application of the light scattering method to the study of\r\nprotein solutions, and a technique has been developed for making such\r\nmeasurements. The method has been used to establish the molecular\r\nweight of an antibody from rabbit serum.
\r\n\r\nA tentative value has been established for the molecular weight\r\nof a preparation of Blood Group A-specific substance on the basis of\r\nlight scattering and osmotic pressure data in conjunction with\r\nA. Pardee's viscosity and diffusion data.
\r\n\r\nA preliminary investigation has been made of the usefulness of\r\nthe light scattering method for the study of heat denaturation of\r\nserum proteins.
" }, { "name": "Brough, Harry Ward, Jr.", "degree": "Engineering Degree", "year": "1950", "title": "An Investigation of the Benedict Equation of State as a Means of Correlating Volumetric Data for Light Hydrocarbons", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07162025-182800937", "creators": [ { "name": { "family": "Brough", "given": "Harry Ward, Jr." }, "id": "Brough-Harry-Ward", "display_name": "Brough, Harry Ward, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6n8t-1k91", "abstract": "The problem of evaluating constants for the Benedict equation of state is discussed. It is concluded that a method must be found which is adaptable to high-speed digital computers and which is capable of precise analytical interpretation if the equation is to be made practical as a means of correlating data for mixtures of hydrocarbons.
\r\nA study has been made of the least squares criterion of best fit as a means of evaluating the Benedict constants from volumetric data alone. The necessary equations are presented and some analytical characteristics of the solution investigated. A procedure was developed for performing the calculations with commercial punched card equipment, and the results of two test calculations are presented. It is shown that a significantly better fit of volumetric data is possible that was obtained by Benedict. Computations are shown which indicate that the Benedict constants are determined by the experimentally observed behavior to four digits at most. Coefficients are presented for for an equation by means of which the least squares measure of the precision of fit may readily be calculated for any arbitrary values of the constant.
\r\nIt is concluded that the method used is suitable for digital-computer treatment and, as applied to volumetric data, gives both an improved fit and the desired precise interpretation of the fit
" }, { "name": "Burket, Stanley Campbell", "degree": "PhD", "year": "1950", "title": "The Relation Between the Infrared Spectra and Structure of Carbohydrates and Related Compounds", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:06242025-143842219", "creators": [ { "name": { "family": "Burket", "given": "Stanley Campbell" }, "id": "Burket-Stanley-Campbell", "display_name": "Burket, Stanley Campbell" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/eeq1-8d09", "abstract": "Historically the investigation reported in this thesis\r\nwas initiated as a study of the relation between the infrared\r\nspectra and structure of cellulose. It was soon found,\r\nhowever, that the large backlog of information about the\r\ninfrared spectra of related compounds which would naturally\r\nbe required in the study of such a complex substance was\r\nalmost entirely missing. Consequently the material presented \r\nin this thesis consists principally of a study of\r\nthe infrared spectra of simpler related compounds. The\r\nregion of the spectrum which we have discussed is that\r\nfrom 7.6 to about 13\u03bc.
\r\n\r\nThe compounds which we have studied are either pyranoid\r\ncarbohydrates or possess one or more of the following structural \r\nfeatures in common with them: (1) many hydroxyl\r\ngroups, (2) an oxygen-containing six-membered ring, (3) many\r\nhydroxyl groups attached to a six-membered ring. The infrared \r\nspectra of these compounds have been discussed on the\r\nbasis of the tentative assumption that each atom may be\r\nassigned a fixed fractional charge and that the infrared\r\nactivity of vibration may be estimated roughly by considering\r\ntheir forms.
\r\n\r\nThe glykitols (polyhydr1c acyclic alcohols), tetrahydropyran\r\nand p-dioxane, and some cyclitols (polyhydric\r\ncyclic alcohols) are discussed in Part II. By application\r\nof the assumptions mentioned above fairly complete vibrational \r\nassignments are made for the spectral region 7 to 12.5\u03bc\r\nfor ethylene glycol, tetrahydropyran and p-dioxane. Ethylene\r\nglycol is shown to have a staggered C2 structure rather\r\nthan the flat C2h trans structure, and new spectroscopic\r\narguments, based on the above assumptions, are advanced\r\nagainst the flat D2h and the C2v boat structures for p-dioxane\r\nand the corresponding structures for tetrahydropyran.
\r\n\r\nThe principal absorption bands of the cyclitols between \r\n8 and 13\u03bc are accounted for in terms of skeletal\r\nstretching vibrations only and it is inferred that this\r\nholds true for the sugars also. Scyllitol, the all-trans\r\ncyclohexanehexol, is shown to have. its hydroxyls in equatorial\r\nrather than polar positions.
\r\n\r\nIn Part III the sugars are discussed, and it is shown\r\nthat their structures are probably based on a somewhat\r\nstrained chair-type pyranose ring. A correlation has been\r\nobserved bet ween the intensity distribution. in the infrared\r\nspectral of the monosaccharides and the number of polar hydroxyls,\r\nassuming the hydoxymethyl group to be in an\r\nequatorial position. This correlation is quite good for the\r\nglucose oligosaccharides, but is not very useful for mixed\r\noligosaccharides.
\r\n\r\nThe infrared absorption spectra of animal cellulose,\r\ncellophane, starch, and some cellulose derivatives are presented\r\nin Part IV.
" }, { "name": "Conly, James Carroll", "degree": "PhD", "year": "1950", "title": "Spiro(3,3)heptane. The Hunsdiecker Degradation of Carboxylic Acids", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:06252025-005631461", "creators": [ { "name": { "family": "Conly", "given": "James Carroll" }, "id": "Conly-James-Carroll", "display_name": "Conly, James Carroll" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/yc45-qe31", "abstract": "A general method for the synthesis of polyspiranes containing cyclobutane rings is described. The method involves condensation of sodiomalonic esters with derivatives of trimethylene glycol to give cyclobutane-1,l-dicarboxylates, reduction of these esters with lithium aluminum hydride to the corresponding 1,1-dimethylol cyclobutane, and the use of this substituted trimethylene glycol tor a repetition of the cycle. By means of this series of reactions, spiro-(3,3)-heptane has been made.
\r\nThe degradation of silver salts of certain types of aliphatic oarboxylle acids with bromine has been investigated. Halogen-substituted acids were found to give results that were dependent upon the position of the halogen and the technique that was employed. Polycarboxylic acids, contrary to some previous reports, were found to undergo the reaction in fair yields, giving alkyl polybromides. The cyclobutane ring was found to be cleaved during the degradation if carried out as customarily described, but use of low temperature techniques gave cyclobutyl bromides in good yields. The mechanism of the reaction is the subject of some speculation, but its synthetic usefulness seems considerable.
" }, { "name": "Connolly, Thomas Joseph", "degree": "PhD", "year": "1950", "title": "I. Application of Digital Computer Techniques to the Calculation of Thermodynamic Properties of Hydrocarbon Systems. II. Isobaric Heat Capacities of N-Hexane, Methylcyclopentane and N-Octane at the Bubble Point", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07302025-223752277", "creators": [ { "name": { "family": "Connolly", "given": "Thomas Joseph" }, "id": "Connolly-Thomas-Joseph", "display_name": "Connolly, Thomas Joseph" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/yapz-fy69", "abstract": "I.
\r\n\r\nThe thermodynamic properties of mixtures of real substances\r\nmay be calculated rigorously from certain calorimetric or spectroscopic\r\nmeasurements on the components together with volumetric\r\nmeasurements on the mixtures. The practical impossibility of making\r\nsufficient volumetric measurements precludes application of such an\r\nanalysis to all mixtures of interest. One possible solution of this \r\nproblem is the use of an equation of state which satisfactorily \r\nrepresents the volumetric behavior of mixtures. Benedict, Webb, and\r\nRubin (9,10) met with considerable success in developing such an\r\nequation for mixtures of light hydrocarbons. These authors have\r\nproposed an equation of state and derived thermodynamic equations\r\nwhich give accurate predictions of properties of both homogeneous\r\nand heterogeneous hydrocarbon systems.
\r\n\r\nThese equations are quite complex and their solution a \r\nvery time-consuming operation when performed by conventional\r\ncomputational techniques. It was proposed that this difficulty could be\r\novercome by use of recently developed high-speed digital computers.\r\nAccordingly, an investigation has been made into the feasability of\r\nsolving the equations of Benedict et al on a punched card digital\r\ncomputer known as the Electronic Calculating Punch, Type 604, manufactured\r\nby the International Business Machines Corporation. The results of the\r\ninvestigation are reported in the first part of this thesis.\r\nThe development and application of digital techniques for \r\nthe calculation of thermodynamic properties of coexisting phases in\r\nlight hydrocarbon systems are discussed. A routine procedure for such\r\na calculation which may be completed in about one and one half\r\nhours is presented. Results of calculations on the methane-ethylene-ethane\r\nsystem and the methane-propane system are presented in\r\ngraphical and tabular form. Where possible, comparison is made with\r\nexperimental measurements.
\r\n\r\nII
\r\n\r\nThe isobaric heat capacity at bubble point has been determined\r\nat temperatures from 80\u00b0 to 200\u00b0 F. for n-hexane, methyl-cyclopentane,\r\nand n-octane. This quantity was calculated from directly measured values\r\nof the isochoric heat capacity in the two-phase region by the use\r\nof supplementary volumetric data. The latter were obtained from\r\nexperimental measurements, when available, or estimated from\r\nthe law of corresponding states. The results are presented\r\nin graphical and tabular form.
" }, { "name": "Craig, Roy Phillip", "degree": "Masters", "year": "1950", "title": "Radiochemical Investigation of the Kinetics of the Electron Exchange Between the Oxidation States of Tin", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06162025-180659877", "creators": [ { "name": { "family": "Craig", "given": "Roy Phillip" }, "id": "Craig-Roy-Phillip", "display_name": "Craig, Roy Phillip" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4e56-hq86", "abstract": "The kinetics of the electron exchange between SnII and SnIV\r\nin 10.0 f HCl have been investigated by the use of a \r\nradio-active tracer. It is found that the rate of exchange\r\nis proportional to the product of the SnII and SnIV concentrations.\r\nIn the HCl concentration range between 9.0 f and 11.0 f,\r\nthe exchange rate is found to be proportional to the 0.3 power of the HCl activity,\r\ngiving the empirical rate equation R = k [SnII] [SnIV] (HCl)0.3
\r\n\r\nRadio-active exchange experiments carried out at 0\u00b0 C.\r\nand at 25.2\u00b0C. show this exchange to have an activation\r\nenergy of 10.7 Kcal. per mole. The exchange is found to be\r\nhomogeneous.
\r\n\r\nIt is found that exposure of the SnII-SnIV solutions\r\nto illumination from a capillary Hg arc gives a marked photochemical\r\nincrease in the rate of electron exchange between\r\nthe two valence states.
\r\n\r\nPreliminary spectrophotometric investigations of cobalt-glycine\r\nsystems also have been made.
" }, { "name": "Dorsey, W. Smith, Jr.", "degree": "PhD", "year": "1950", "title": "I. Determination of an Acetylenic Hydrocarbon (3-Hexyne) in Carbon Tetrachloride and in Aqueous Solution. II. Complex Formation by the Carbon-Carbon Triple Bond", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112025-205818340", "creators": [ { "name": { "family": "Dorsey", "given": "W. Smith, Jr." }, "id": "Dorsey-W-Smith", "display_name": "Dorsey, W. Smith, Jr." } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7hb8-kt43", "abstract": "Using 3-hexyne, the method of Lucas and Pressman (1)\r\nfor determining acetylenic hydrocarbons by bromlnat1on with\r\na mercuric salt catalyst in the absence of light and oxygen\r\nwas studied in detail. Determinations of 3-hexyne in carbon\r\ntetrachloride solution yielded a two-phase system of considerable\r\ncomplexity, the rate of bromination being dependent upon\r\nseveral factors. From 99 to 102% of the 3-hexyne taken was\r\nfound in numerous runs, the average deviation being usually\r\nless than 1%. Determination of 3-hexyne in aqueous solutions\r\nyielded a more simple system but gave the same resu1ts if\r\noxygen was excluded from the solutions. The nature of the\r\noxygen interference was not established. Some evidence indicates\r\nthat the process involved is not true bromination, but\r\nrather some more complicated reaction-.
\r\n\r\nIt was found by a distribution method that 3-hexyne\r\ncomplexes with silver ion in aqueous solutions, but does not\r\ncomplex with bipositive cadmium, copper, nickel, cobalt, or\r\nzinc ions. A rapid reaction with mercuric salts precluded\r\nany conclusion about complexing. The evidence for cuprous\r\nchloride or for cuprous ion is inconclusive, but no complexing\r\nis indicated. Two silver ions complex stepwise with one molecule\r\nof 3-hexyne, the argentation constants being 19.1 and\r\n0.22 respectively. The interaction is much weaker than that\r\nof olefins, but several times stronger than that of the \r\naromatic hydrocarbons.
" }, { "name": "Farrington, Paul Stephen", "degree": "PhD", "year": "1950", "title": "I. Coulometric and Amperometric Methods of Analysis. II. Spectrophotometric Investigation of the Copper (II) Monobromo Complex. III. Determination of Carbon by Wet Combustion", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08052025-224132798", "creators": [ { "name": { "family": "Farrington", "given": "Paul Stephen" }, "id": "Farrington-Paul-Stephen", "display_name": "Farrington, Paul Stephen" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hka4-a051", "abstract": "The conditions under which electrolytically generated\r\nchlorine can be used for secondary coulometric titrations With\r\nan amperometric end point have been investigated. A procedure\r\nis described by which triposittve arsenic has been titrated in\r\nquantities of from 30 to 800 micrograms with an average error\r\nwithout regard to sign of less than 0.5 micrograms.
\r\n\r\nthe method proposed by Wooster (30) for calculating corrections \r\nfor the coulometric titration of iodide in hydrochloric\r\nacid has been studied. Data are presented to show that\r\nimproved methods of calculation give more accurate results.
\r\n\r\nFor the coulometric titration of iodide by means of electrolytically\r\ngenerated bromine perchloric acid may be substituted\r\nfor hydrochloric acid. The perchloric acid requires no\r\npurification and the titrations are just as accurate as those\r\nmade With hydrochloric acid.
\r\n\r\nA metallic bismuth micro-reductor has proven satisfactory\r\nfor quantitative reduct1on of ferric iron. Samples containing\r\n234 micrograms of iron have been reduced and titrated with\r\nelectrolytically generated ohloll\"1ne to an accuracy of better than\r\n1%. Iodine monochloride has also been used for the oxidation\r\nof ferrous iron. Recommendations are made for further\r\ninvestigation.
\r\n\r\nA combination of coulometric and amperometric techniques\r\nhas been used to determine a dissociation constant for iodine\r\nmonobromide and a constant for the oxidation-reduction equilibrium\r\ninvolving cupric copper and bromide ions. For the iodine-iodine\r\nmonobromide half-cell, data from this investigation\r\nyield a potential value of -0.92 volt as compared with a value\r\nof -0.88 volt obtained from the literature. On the other hand,\r\na potential value for the cupric-cuprous bromide half-cell calculated\r\nfrom this experimental data differed by 0.06 volt from\r\ndata found in the literature.
\r\n\r\nA study of the indicator currents caused by various oxidation\r\nstates of vanadium established the fact that tripositive\r\nand quadrapositive vanadium give rise to an indicator current.\r\nAlso, it was observed that a reducing agent capable of replacing\r\nhydrogen ion would probably be partially oxidized by the indicator\r\ncircuit; a special method would be required for the coulometric \r\ntitration of such a substance,
\r\n\r\nThe equilibrium constant for the formation of the monobromo\r\ncomplex of copper (II) was determined by means of a spectrophotometric\r\nmethod. In solutions of unit ionic strength the\r\nconstant was found to be 2.1 \u00b1 0.25.
\r\n\r\nFor the determination of carbon in organic solids and relatively\r\nnonvolatile liquids, a scheme has been devised to use\r\nthe Van Slyke-Folch combustion solution. An apparatus is described \r\nfor situations where a Van Slyke manometric apparatus\r\ncannot be provided. The results are accurate to \u00b1 0.05 mg of\r\ncarbon.
" }, { "name": "Grinstead, Robert Russell", "degree": "PhD", "year": "1950", "title": "I. The Ferromagnetic Alloy System Copper-Manganese-Indium. II. A Volumetric Method for the Determination of Indium", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06192025-005939368", "creators": [ { "name": { "family": "Grinstead", "given": "Robert Russell" }, "id": "Grinstead-Robert-Russell", "display_name": "Grinstead, Robert Russell" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vhza-a018", "abstract": "A phase-equilibria study of the copper-rich portion of the copper-magnase-indium system has been made, using thermal, microscopic, and magnetic measurements. The thermal data was obtained from cooling curves in the region of solidification, and melting-point contours are given. Microscopic data on the high- tempera.tu.re solid phases was obtained by annealing the alloys at temperatures just below the solidus, then quenching and observing them under the microscope. The magnetic work consisted of Curie point measurements on the alloys as originally prepared, after quenching, and after reannealing at 100\u00b0C. On the basis of these results, approximate locations of the [Formula. See abstract in scanned thesis for details] phase boundaries are given. Ferromagnetism has been found to exist over mo.st of the composition diagram.
\r\nAn attempt has been made to apply a known method for the volumetric determination of zinc to the determination of indium. The procedure consists of adding an excess of potassium iodide and potassium ferricyanide to a buffered solution of indium, and titrating the liberated iodine with sodium thiosulfate. Within very restricted ranges of concentration, results accurate to \u00b11% were obtained, but the method is not considered usable at present.
" }, { "name": "Itano, Harvey Akio", "degree": "PhD", "year": "1950", "title": "I. Contributions to the Study of Sickle Cell Hemoglobin. II. A Rapid Diagnostic Test for Sickle Cell Anemia", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-02222007-084824", "creators": [ { "name": { "family": "Itano", "given": "Harvey Akio" }, "id": "Itano-Harvey-Akio", "display_name": "Itano, Harvey Akio" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/J454-PF24", "abstract": "The red blood cells of individuals who have either sickle cell anemia or sicklemia possess the capacity to undergo reversible changes in shape in response to changes in the partial pressure of oxygen. When the oxygen pressure is lowered, these cells change their forms from the normal biconcave disk to crescent, holly wreath, and other forms. This process, known as sickling, occurs more readily in sickle cell anemia than in sicklemia. The evidence available at the time this investigation was begun indicated that the process of sickling might be intimately associated with the state and nature of the hemoglobin in the sickle cell erythrocyte. Electrophoretic investigations revealed a difference in net charge between the hemoglobins of normal individuals and sickle cell anemia individuals. The hemoglobin from the erythrocytes of sicklemic individuals was found to consist of two electrophoretic components, identifiable with sickle cell anemia hemoglobin and normal hemoglobin. The globins derived from these hemoglobins cannot be distinguished from each other on the basis of electrophoretic experiments. Titration studies on these hemoglobins failed to reveal any significant differences in number and type of ionizable groups. A rapid chemical method was developed for producing sickle cells by the use of sodium dithionite." }, { "name": "Jenkins, Rodman", "degree": "PhD", "year": "1950", "title": "Studies on Thermal and Material Transfer in Turbulent Flow: I. Problems in Turbulent Heat Transfer. II. An Attempt to Measure the Eddy Diffusivity in Uniform Turbulent Flow", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06132025-204353827", "creators": [ { "name": { "family": "Jenkins", "given": "Rodman" }, "id": "Jenkins-Rodman", "display_name": "Jenkins, Rodman" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2bgw-1606", "abstract": "I. A method of correlating experimental va1ues\r\nof the eddy viscosity in turbulent flow inside\r\ntubes and rectangular channels is described.\r\nA procedure for predicting the influence of\r\nphysical properties on the ratio of the eddy\r\neo11duetivity to the eddy viscosity is presented.\r\nThe values of the eddy conductivity obtained in\r\nthis manner have been used to predict rates of\r\nheat transfer inside tubes which check well with\r\nexperimental values.
\r\n\r\nII. A study of the evaporation of iodoform \r\ncontaining radioactive iodine is described. An\r\nattempt was made to measure the eddy diffusivity\r\nin a turbulent air stream through this study.\r\nThe use of radioactive materials for measuring\r\nsmall. concentrations of vapors in gaseous mixtures\r\nwas investigated. No measurements of\r\nconcentrations in turbulent air flow, and consequently,\r\nvalues of the eddy diffusivity were obtained.
" }, { "name": "Keilin, Bertram", "degree": "PhD", "year": "1950", "title": "Part I. The Adsorption of Capillary-Active Substances at the Dropping Mercury Electrode. Part II The Polarographic Analysis of Nitrite and of Nitrite-Nitrate Mixtures. Part III. An Electron Diffraction Investigation of the Structure of Some Organic Molecules: a) Some Cyclic Derivatives of Ethylene Glycol. b) Naphthalene and Anthracene", "advisor": "Schomaker, Verner F.; Pauling, Linus; Corey, Robert B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222024-192757047", "creators": [ { "name": { "family": "Keilin", "given": "Bertram" }, "id": "Keilin-Bertram", "display_name": "Keilin, Bertram" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "co-advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Corey", "given": "Robert B." }, "id": "Corey-R-B", "role": "co-advisor", "display_name": "Corey, Robert B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/afvs-3n49", "abstract": "Part I. The Adsorption of Capillary-Active Materials at the Dropping Mercury Electrode
\r\n\r\nIt has been found that the addition of a capillary-active substance to a solution which is to be analyzed at the dropping mercury electrode brings about a decrease in the diffusion current which passes as a result of the discharge of the reducible ion. Molecules of the capillary-active compound, adsorbed on the surface of the growing drop, appear to deactivate a portion of this electrode surface. As a result, some of the reducible ions or molecules which reach the electrode vicinity by diffusion do not actually reach the electrode surface, and the current which passes as a result of the reduction is consequently decreased. As the concentration of capillary-active material is increased, the diffusion current decreases to a limiting value which is apparently dependent upon the amount of surface still left free on the electrode after a monomolecular layer of material has been adsorbed. Experimental verification and theoretical consequences of the foregoing are described in Part I of this thesis.
\r\n\r\nPart II. The Polarographic Analysis of Nitrite and of Nitrite-Nitrate Mixtures
\r\n\r\nIt has been found that a solution containing both nitrate and nitrite ions can be analyzed for both constituents in two polarographic experiments. With one aliquot part, the diffusion current due to the two constituents in the original solution is measured. In another aliquot part, the nitrite present is quantitatively oxidized to nitrate, and the diffusion current of the resulting solution is measured as before. The two experiments provide sufficient data for determining the quantity of each ion in the solution. The oxidation of nitrite is conveniently carried out with hydrogen peroxide in acid solution and the excess peroxide is destroyed catalytically by manganese dioxide in basic solution.
\r\n\r\nPart III. An Electron Diffraction Investigation of the Structure of Some Organic Molecules
\r\n\r\na) Some Cyclic Derivatives of Ethylene Glycol
\r\n\r\nThe results of an electron diffraction investigation of some cyclic derivatives of ethylene glycol (chlorophosphite ester, sulfite ester, and acetal) confirm the configuration assigned by the organic\r\nchemist to these molecules. Non-planarity of the five-membered ring may be demonstrated only in the chlorophosphite ester, in which also there is found an abnormally long phosphorus-to-chlorine bond distance and a subnormally short phosphorus-to-oxygen bond distance. The covalent bond distances in the other molecules were shown to be normal but no conclusion could be drawn concerning the planarity or nonplanarity of the ring systems.
\r\n\r\nb) Naphthalene and Anthracene
\r\n\r\nIn an electron diffraction investigation of naphthalene, the average carbon-to-carbon bond distance has been found to be 1.397 \u00b1 0.02 \u00c5. The limits of error cannot be narrowed sufficiently to permit a definite choice to be made among the theoretical models proposed by various workers, but the configuration suggested by Penney and Coulson appears to be in best agreement with the observations.
\r\n\r\nIn anthracene, the mean carbon-to-carbon bond distance has been found to be 1.419 \u00b1 0.02 \u00c5. Although no statement of the limits of error for the individual distances could be made, it was concluded that the best model in the region investigated is different than that proposed by Robertson, in which the atoms lie at the corners of regular hexagons.
" }, { "name": "Koenig, Nathan Hart", "degree": "PhD", "year": "1950", "title": "Part I. The Distribution of Cyclohexene Between Carbon Tetrachloride and Aqueous Solutions of Acids and Salts. Part II. The Solubility of Some Nonpolar Organic Liquids in Water in Aqueous Solutions of Strong Acids, Alkali Salts, and Silver Nitrate. The Coordination of Silver Ion with Benzene. Part III. A Proposed Enium Nomenclature for Ionic Complexes Involving Carbon-Carbon Multiple Bonds", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:06162025-172908063", "creators": [ { "name": { "family": "Koenig", "given": "Nathan Hart" }, "id": "Koenig-Nathan-Hart", "display_name": "Koenig, Nathan Hart" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/evmw-7s52", "abstract": "It has been shown that cyclohexene distributed at 25\u00b0\r\nbetween carbon tetrachloride and dilute aqueous solutions\r\nis less soluble in aqueous solutions of alkali salts,\r\nhydrochloric acid, and sulfuric acid than in water, but is\r\nmore soluble in aqueous solutions of perchloric acid and\r\nnitric acid. Analysis of the data relative to general\r\nsalting effects indicates that if aqueous proton-olefin complexes\r\nexist, they are present only in very low concentration.
\r\n\r\nA new procedure, stripping analysis, has been employed\r\nto determine the solubility of benzene at 100\u00b0 and 25\u00b0, and\r\nof carbon tetrachloride and cyclohexane at 25\u00b0 in water and\r\nin aqueous solutions of strong acids, alkali salts, and silver\r\nnitrate. Each of the organic liquids is somewhat more soluble\r\nin 3 M perchloric acid than in water, and benzene is much\r\nmore soluble in 1 M silver nitrate than in water. Qualitative\r\ndata on the change of solubility, with temperature have been\r\nobtained by the cloudiness method. The combined solubility\r\ndata, together with related data for cyclohexene, are discussed\r\nin terms of the salting and complexing factors involved.
\r\n\r\nEquilibrium constants and heats of complex formation have\r\nbeen calculated for the coordination of silver ion with benzene.
\r\n\r\nThe nature of ionic complexes involving carbon-carbon\r\nmultiple bonds is discussed, and an enium nomenclature is\r\nproposed for such complexes because of their distinctive\r\ncharacter. The terms \"enium\" and \"onium\" are compared.
" }, { "name": "Lemaire, Henry", "degree": "PhD", "year": "1950", "title": "Addition to the Carbon-Carbon Triple Bond. The Reaction of Acetic Acid with 3-Hexyne", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-185511760", "creators": [ { "name": { "family": "Lemaire", "given": "Henry" }, "id": "Lemaire-Henry", "display_name": "Lemaire, Henry" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5g6h-b137", "abstract": "The mechanism of the mercury-catalyzed addition to the carbon-carbon triple bond has been investigated. Acetic acid was used as the solvent and one reactant. The other reactant was 3-hexyne. The course of the reaction was followed by bromine titration and by a special indicator method. The addition was found to take place in two discrete steps, forming 3-acetoxyhexene-3 and 3-hexanone.
\r\n\r\nThe rate of the initial reaction was determined for a range of initial concentrations of hexyne and the catalysts. When mercuric acetate and perchloric acid were used as the catalysts , the initial rates were found to be interpretable on the assumption that the reactive species was a 1 to 1 to 1 complex formed by the 3-hexyne, the mercuric acetate, and the perchloric acid. By means of indicator studies the existence of the 1 to 1 to 1 complex (probably a hexyne-mercuric monoacetate cation) was proved and its equilibrium constant measured.
\r\n\r\nThe indicator studies were extended to the measurement of the basicities of weak bases in acetic acid. A simple relationship was found between the observed ionization constant and the thermodynamic activity constant. New values were found for the basic strengths of dioxane, acetonitrile, p-toluene-sulfonamide, water, acetanilide, acetamide, and urea.
" }, { "name": "MacAllister, Robert V.", "degree": "PhD", "year": "1950", "title": "Studies in Carbohydrate and Amino Acid Chemistry", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06262025-175527294", "creators": [ { "name": { "family": "MacAllister", "given": "Robert V." }, "id": "MacAllister-Robert-V.", "display_name": "MacAllister, Robert V." } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/eejb-6z03", "abstract": "The optimum conditions for the colorimetric determination\r\nof hexoses by reaction with carbazole in hot sulfuric acid\r\nsolution have been determined, and a convenient procedure for\r\nthe analysis is described.
\r\n\r\nThe inhibition of the chymotrypsin catalyzed hydrolysis\r\nof N-acetyl-L-tyrosylglycinamide by equimolar quantities of its\r\nD antipode has been observed to be a function of the concentration \r\nof the DL mixture. The general features of the above\r\nsystem have been described, and an explanation has been advanced\r\nrelative to the lack of antipodal inhibition obtaining in the\r\ncase of N-benzoyl-DL-tyrosylglycinamide.
\r\n\r\nSeveral new tyrosine derivatives have been synthesized\r\nwhich have been used to show that the rate of the chymotrypsin\r\ncatalyzed hydrolysis of N-acyl-L-tyrosinamides is critically\r\ndependent upon the nature of the acyl group. The pertinent\r\nequilibrium and rate constants have been determined.
\r\n\r\nThe competitive nature of the inhibitory effect of\r\nN-acetyl-D-tyrosinamide on the enzymatic hydrolysis of N-acetyl-L-\r\ntyrosinamide has been demonstrated. An inhibitory effect by\r\nthe corresponding D ethyl ester is described.
\r\n\r\nA rapid and convenient method for the resolution of DL\r\ntyrosine has been devised.
\r\n\r\nThe hydrolysis of N-acetyl-L-tyrosinhydrazide by chymotrypsin\r\nhas been demonstrated.
" }, { "name": "Mason, John Latimer", "degree": "PhD", "year": "1950", "title": "Transfer of Heat and Momentum in Non-Uniform Turbulent Flow", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042003-104548", "creators": [ { "name": { "family": "Mason", "given": "John Latimer" }, "id": "Mason-John-Latimer", "display_name": "Mason, John Latimer" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/K0WE-SJ09", "abstract": "Determinations of pressure, temperature and velocity as functions of position in a non-uniform, steady, two dimensional, turbulently flowing air stream have been made under four different flow conditions.\r\n\r\nValues of the eddy viscosity and eddy conductivity have been calculated and compared to those obtained under conditions of uniform flow. Bulk temperatures have been computed and compared with those obtained from existing empirical correlations.\r\n\r\nThe general problem of predicting temperature and velocity fields in non-uniform flow is discussed. Previous theoretical work is compared with the experimental results of this work. The further research necessary to solve this problem for the case of fully developed turbulent flow is outlined.\r\n\r\nThe partial differential equation for heat transfer has been solved for one of the above four flow conditions by means of an electrical analogy. Use has been made of eddy conductivity data obtained for uniform flow. This work is evaluated in light of the accompanying experimental results, and plans for further analog work are outlined." }, { "name": "Page, Franklin, Jr.", "degree": "PhD", "year": "1950", "title": "Further Studies of the Analogy Between Fluid Friction and Heat Transfer in a Steady State, Two-Dimensional Turbulently Flowing Air Stream", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292025-204034656", "creators": [ { "name": { "family": "Page", "given": "Franklin, Jr." }, "id": "Page-Franklin-Jr", "display_name": "Page, Franklin, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/a343-3x41", "abstract": "Velocity and temperature distributions have been\r\nmeasured in a steady-state, two-dimensional, turbulently\r\nflowing air stream. These measurements have been\r\nmade both in an essentially isothermal stream and in\r\none upon which a temperature gradient had been imposed.\r\nThe heat flux and shear and the thermodynamic state of\r\nthe fluid were determined at the same positions in the\r\nair stream.
\r\n\r\nFrom these data, the eddy conductivity and eddy\r\nviscosity distributions were calculated for fifteen\r\ndifferent flow conditions.
\r\n\r\nThe results of the eddy property calculations\r\nhave been compared with eddy property distributions predicted\r\nby other investigators. The data have been\r\ncorrelated in a manner which appears to simplify prediction\r\nof eddy properties in other similar situat1ons.
" }, { "name": "Pinckard, James Howard", "degree": "PhD", "year": "1950", "title": "A Study of Some Naturally Occurring and Synthetic Cis-Trans Polyenes", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:06252025-223435637", "creators": [ { "name": { "family": "Pinckard", "given": "James Howard" }, "id": "Pinckard-James-Howard", "display_name": "Pinckard, James Howard" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/sbxe-af89", "abstract": "No abstract." }, { "name": "Schuch, Adam Frank", "degree": "PhD", "year": "1950", "title": "Studies in X-Ray Crystallography: I. The Allotropic Forms of Cerium. II. The Structure of Urea Oxalate", "advisor": "Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechTHESIS:07282025-203451269", "creators": [ { "name": { "family": "Schuch", "given": "Adam Frank" }, "id": "Schuch-Adam-Frank", "display_name": "Schuch, Adam Frank" } ], "advisors": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ck0c-vr70", "abstract": "I. The Allotropic Forms of Cerium
\r\n\r\nThe crystal structure of elementary cerium has been investigated\r\nby X-ray diffraction at temperatures from room temperature to that of\r\nliquid nitrogen. Despite a variety of heat treatments, I have been able\r\nto obtain at room temperature only a cubic closest-packed structure with\r\na0 = 5.139 Kx. No evidence could be found to confirm the existence of a\r\nhexagonal closest-packed structure.
\r\n\r\nWhen stresses are produced in cerium, aa for example by quenching\r\nfrom 250\u00b0C. or higher, and it is then rapidly cooled with liquid air, a\r\nnew form is obtained which also has the cubic closest-packed arrangement\r\nbut with a0 = 4.82 Kx. If the cerium is annealed or free of stresses then\r\nno allotropic change takes place.
\r\n\r\nIn the new structure it is believed that the 4f electron has moved\r\ninto hybridized 5d 6s orbitals to take part in bond formation. This experimental\r\nwork confirms in part the predictions of Tromba.
\r\n\r\nII. The Structure of Urea Oxalate
\r\n\r\nUrea oxalate crystallizes monoclinic prismatic, P 21/c, A1 = 5.218 \u00c5.,\r\nA2 = 12.404 \u00c5., A3 = 11.576 \u00c5., and \u03b2 = 143\u00b01'. There are two formula.\r\nweights per unit cell. The structure is a layer one with the molecules\r\nalmost parallel to (100). The layers are held together by van der Waals\r\nforces. There is no discrete urea oxalate molecule. Each layer is a\r\nnetwork of urea and oxalic acid molecules held together by hydrogen bonds.\r\nOne extremely short O - H \u00b7 O distance of 2.47 \u00c5. was found.
" }, { "name": "Soldate, Albert Mills", "degree": "PhD", "year": "1950", "title": "I. The Crystal Structures of Certain Intermetallic Compounds: (a) The Nature of the Bonds in the Iron Silicide FeSi and Related Crystals; (b) A Study of the Structure of the Intermediate Compounds MG\u2082Tl, Mg\u2082In, and Mg\u2082Ga. II. Metallic Valence and X-Ray Emission Fine Structure: a Discussion. III. Crystal Structures of Certain Inorganic Compounds: (a) Crystal Structure of Sodium Borohydride; (b) A Redetermination of the Structural Parameters in the Cubic Modification of Arsenious Oxide", "advisor": "Pauling, Linus; Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechTHESIS:06232025-183816561", "creators": [ { "name": { "family": "Soldate", "given": "Albert Mills" }, "id": "Soldate-Albert-Mills", "display_name": "Soldate, Albert Mills" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/82p4-ba49", "abstract": "Part I. Section (a)
\r\n\r\nThe structure of the iron silicide FeSi was determined by\r\nmeans of X-ray single-crystal photography. The previously reported\r\nstructure was verified. The structure is based upon the\r\nspace group T4 - P213 with ao = 4.489 \u00b1 0.005 \u00c5.\r\nFour iron and four silicon atoms are in the positions (xxx; x + \u00bd. \u00bd - x, x;)\r\nwith xFe = 0.1370 \u00b1 0.0020 and xSi = 0.842 \u00b1 0.004.
\r\n\r\nA detailed discussion of the structure was given in terms\r\nof the resonating-valence-bond theory developed by Professor\r\nPauling.
\r\n\r\nPart I. Section (b)
\r\n\r\nAn investigation of the structures of the intermetallic\r\ncompounds Mg2Tl, Mg2In, and Mg2Ga was made. The methods of X-ray single-crystal and powder photography were employed.\r\nThe structures of Mg2Tl end Mg2In are based upon the space\r\ngroup D33h - C62m with three molecules in a unit cell of\r\ndimensions ao = 8.068 \u00b1 0.005 \u00c5, co = 3.457 \u00b1 0.0007 \u00c5;\r\nao = 8.324 \u00b1 0.005 \u00c5, co = 3.457 \u00b1 0.0007 \u00c5, respectively. The\r\nthree thallium or indium a toms are in the positions
\r\n\r\n1: (a) 000,
\r\n\r\n2: (c) \u2153 \u2154 \u00bd; \u2154 \u2153 \u00bd.
\r\n\r\nThe six magnesium atoms are in the positions
\r\n\r\n3: (f) x100; 0x1o; x1x10
\r\n\r\n3: (g) x20\u00bd; 0x2\u00bd; x2x2\u00bd.
\r\n\r\nIn the case of Mg2Tl x1 = 0.3746 \u00b1 0.0028 and x2 = 0.2866 \u00b1 0.0038.\r\nIt was not possible to fix the parameters x1 and x2 accurately\r\nin the instance of Mg2In, but it is highly probable that they\r\ndo not differ greatly from the corresponding values of Mg2Tl in terms of the \r\nresonating-valence-bond theory(1),(2) was given and it was \r\nfound that the valences of the thallium atoms are larger than \r\nthat exhibited in the elementary substance.
\r\n\r\nThe structure of Mg2Ga is apparently similar to that of\r\nMg2Tl and Mg2In. The positions of the atoms, however, necessitate\r\na doubling of the unit cell dimension along the c axis. It was\r\nnot possible to determine the exact position of the atoms.
\r\n\r\nPart II.
\r\n\r\nA discussion is given of the relationship between metallic\r\nvalence and the fine structure of the X-ray emission bands\r\nof metals, alloys, and intermetallic compounds. The study of\r\nfine structure seems to offer a chance to gain valuable information\r\nconcerning metallic valences; there is, hov1ever,\r\na great need for more experimental information.
\r\n\r\nPart III. Section (a)
\r\n\r\nThe structure of sodium borohydride was investigated\r\nby means of X-ray powder photography and found to be based\r\non a face-centered cubic lattice. The unit cell of dimensions \r\nao = 6.151 \u00b1 0.009 kX contains four sodium and four\r\nboron atoms arranged in the following manner:
\r\n\r\n4 Na at ooo, o\u00bd\u00bd, \u00bdo\u00bd, \u00bd\u00bdo
\r\n\r\n4 B at \u00bd\u00bd\u00bd, \u00bdoo, o\u00bdo, oo\u00bd
\r\n\r\nIt is probable that the structure consists of tetrahedral\r\nBH-4 ions and Na+ ions. The dimensions of the ions\r\nwould permit oscillation or rotation of the BH-4 tetrahedra.
\r\n\r\nPart III. Section (b)
\r\n\r\nThe structural parameters of the cubic modification of\r\narsenious oxide have been redetermined by means of X-ray\r\npowder and single crystal photography and found to agree\r\nclosely with those reported by Almin and Westgren(5).
\r\n\r\nThe structure is based upon the packing of As406\r\nmolecules which have the same dimensions as those found for\r\nthe molecules of the gas(2),(12).
" }, { "name": "Sullivan, John Henry", "degree": "PhD", "year": "1950", "title": "Part I. Kinetics of the Vapor Phase Exchange of Radioactive Bromine Between Trichlorobromomethane and Bromine. Part II. Kinetics of the Forward and Reverse Reactions of the Vapor Phase Thermal Bromination of Chloroform. Part III. A Method of Estimating and Minimizing the Rate of a Radioactive Exchange Reaction", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06242025-212122769", "creators": [ { "name": { "family": "Sullivan", "given": "John Henry" }, "id": "Sullivan-John-Henry", "display_name": "Sullivan, John Henry" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nysr-5c25", "abstract": "The rate of the homogeneous vapor phase thermal radioactive\r\nexchange reaction
\r\n\r\nCBrCl3 + Br2* \u2192 exchange
\r\n\r\nand the rates of the forward and reverse reactions of the homogeneous \r\nvapor phase thermal bromination of chloroform
\r\n\r\nCHCl3 + Br2 \u21c4 CBrCl3 + HBr (A)
\r\n\r\nhave been measured in the temperature range 420-455\u00b0 K.
\r\n\r\nFor the bromination reaction a mechanism which is consistent\r\nwith all the experimental data is
\r\n\r\nBr2 \u21c4 2Br (d) (5)
\r\n\r\nBr + CHCl3 \u21c4 -CCl3 + HBr (1) (2)
\r\n\r\n-CCl3 + Br2 \u21c4 CBrCl3 + Br. (3) (4)
\r\n\r\nThe rate determining steps are (1) and (4). The rate of the\r\nexchange reaction is given by k0(CBrCl3)(Br) and the equation for\r\nthe rate determining constant k0 = k0(T) is identical to that\r\nfor k4 as a function of temperature. The exchange reaction\r\ntakes place, therefore, by the reaction sequence (d), (4), and (3).
\r\n\r\nThe activation energies of (1) and (4) imply that the CH\r\nbond in CHCl3 is weaker than that in CH4 by at least 6.6 kcal,\r\nand the CBr bond in CBrCl3 is weaker than that in CH3Br by at\r\nleast 11 kcal. The equilibrium constant K = (CBrCl3)(HBr)/\r\n(CHCl3)(Br2) is 1.96 at 442\u00b0 K; the heat of reaction (A) is\r\n-0.9(\u00b10.65) kcal.
\r\n\r\nIn a single exploratory experiment, it was observed that\r\nthe exchange reaction between bromine and trifluorobromomethane\r\nis much slower than that between bromine and trichlorobromomethane.
\r\n\r\nA method of estimating and minimizing the error of measurement of \r\nthe rate of a radioactive exchange reaction is given.
" }, { "name": "Tang, You-Chi", "degree": "PhD", "year": "1950", "title": "I. The Investigation of the Alloy System Lead-Thallium. II. The Investigation of the Crystal Structure of the Complex of Hexamethylenetetramine with Manganous Chloride", "advisor": "Pauling, Linus; Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechTHESIS:06082010-110159875", "creators": [ { "name": { "family": "Tang", "given": "You-Chi" }, "id": "Tang-You-Chi", "display_name": "Tang, You-Chi" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NVF2-SD16", "abstract": "Part I: The Investigation of the Alloy System Lead-Thallium.\r\n The lattice spacings for alloys in the lead phase of the \r\nsystem lead-thallium were accurately determined. The \r\nlattice-spacing-composition curve disagrees with that previously constructed \r\nby Olander on the basis of his fewer determinations. \r\nThe new curve indicated that ordered phases PbTl_3 and PbTlTl_6 \r\nprobably occur.\r\n\r\nPart II: The Investigation of the Crystal Structure of the Complex\r\n of Hexamethylenetetramine with Manganous Chloride.\r\n Suitable crystals of the complex of hexamethylenetetramine \r\nwith manganous chloride were grown in a 1:1 mixture of alcohol \r\nand acetone. By chemical analysis the composition was shown\r\nto correspond to the formula, 2(CH_2)6N_4\u2022MnCl_2\u20222H_20. The crystal \r\nhas a pseudo unit cell with a_1 = 11.80 \u00c5., a_2 = 22.00 \u00c5., a_3 =\r\n7.21 \u00c5., and Z = 4. The pseudo space group is C^9_(2v)-P2_1nb. A\r\nfew weak reflections indicate that the a_1 axis should be doubled, \r\nbut no account was taken of this in the present determination.\r\n\r\n A trial structure derived from steric considerations and the \r\nintensities of reflections h00 led to a satisfactory interpretation \r\nof the Patterson distribution function. The approximate structure based \r\non the Patterson syntheses was confirmed by the Fourier projections \r\n\u03c1(x) and \u03c1(y,x), and by calculation of structure factors for reflections \r\nh00 and Ok\u2113.\r\n\r\n The structure has the following important features. A manganese \r\natom lies on the common three-fold axis of two hexamethylenetetramine \r\nmolecules at the center of symmetry of a complex molecule, and the Mn-Cl \r\nbonds are approximately perpendicular to the Mn-N bonds. Both the Patterson \r\nsyntheses andthe Fourier projections indicate that two molecules of \r\nwater are present in each complex molecule, and the Mn-O bonds are \r\napproximately normal to the plane of the Mn-Cl and Mn-N bonds.\r\n" }, { "name": "Arrington, Charles Hammond, Jr.", "degree": "PhD", "year": "1949", "title": "Studies on the Structural Properties of Actin, Myosin, Actomyosin, and the Interaction with Adenosine Triphosphate", "advisor": "Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechTHESIS:06172025-215849671", "creators": [ { "name": { "family": "Arrington", "given": "Charles Hammond, Jr." }, "id": "Arrington-Charles-Hammond", "display_name": "Arrington, Charles Hammond, Jr." } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ec4g-jq61", "abstract": "The muscle proteins actin, myosin, and actomyosin have been investigated. Their electrophoretic behavior was examined. The molecular weights by light scattering and dissymmetry coefficients were also determined for each protein. From the last two quantities, it has been possible to show that the random coil is the best structure to assign to most of the proteins involved. Values of the root\r\nmean square separations of such random coils have been found.
\r\n\r\nThe effect of adenosinetriphosphate on these properties has been determined, and a mechanism proposed to account for the changes observed. The mechanism postulates the existence of an actomyosin complex of high molecular weight. This complex molecule dissociates in the presence of ATP, not into actin and myosin, but into complex molecules of smaller size. The experimental evidence for this mechanism is presented.
" }, { "name": "Bennett, Edward Leigh", "degree": "PhD", "year": "1949", "title": "I. Studies on the Synthesis, Resolution, and Properties of Some Fluorinated Amino Acids. II. Studies on Blood Group-A-Specific Substance. III. Systematic Qualitative Tests for Certain Acidic Elements in Organic Compounds. IV. Isolation of Compounds Toxic to Tomato Plants from Thamnosma montana", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08192025-204359745", "creators": [ { "name": { "family": "Bennett", "given": "Edward Leigh" }, "id": "Bennett-Edward-Leigh", "display_name": "Bennett, Edward Leigh" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/npzt-sm68", "abstract": "I. Syntheses are described of the following fluorinated amino acids: ortho-, meta-, and para-fluorophenylalanine, 2-fluoro-4-methoxy-phenylalanine and 2-fluorotyrosine.
\r\nThe apparent dissociation constants of the above mentioned phenylalanine derivatives have been determined by electrometric titration. The ultra-violet absorption spectra of the mono-fluorophenylalanines and fluorotyrosines have been obtained.
\r\nA study has been made of the factors influencing the asymmetric specificity of the papa.in catalyzed synthesis of amides.
\r\nThe attempted preparation of fluorocyclohexanol is described.
\r\nII. Studies on blood group A-specific substance have been made. These include a study of methods of isolation, a study of the electrophoretic properties of blood group A-specific substance, and a colorimetric method for the estimation of the activity of substances inhibiting the isoagglutination of blood group A-cells. Also the appearance of sheep cell lysins and human A-cell agglutinins in rabbits immunized with a partially purified blood group A-specific substance from hog gastric mucin has been observed.
\r\nIII. Qualitative tests for certain inorganic elements (and carbon) in organic compounds are described.
\r\nIV. A survey of desert shrubs for materials toxic to tomato seedlings grown in nutrient culture has been made. From Thamnosma montana three crystalline compounds toxic to tomato seedlings have been isolated.
" }, { "name": "Billheimer, John S.", "degree": "Engineering Degree", "year": "1949", "title": "The Generalized Phase Behavior of Paraffin-Tetralin-Bitumen Systems", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:06172025-221443684", "creators": [ { "name": { "family": "Billheimer", "given": "John S." }, "id": "Billheimer-John-S", "display_name": "Billheimer, John S." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7b1g-ka12", "abstract": "The addition of paraffin hydrocarbons to a solution of\r\nbitumen in tetralin will cause partial separation of the bitumen. Increasing the paraffin concentration will increase the separation of bitumen providing a second liquid phase characterized by high solvency for bitumen does not form. A maximum in the bitumen separation is thus obtained at the paraffin concentration corresponding to the formation of this second liquid phase. An increase in temperature generally results in a decreased separation of bitumen. These complex phase behaviors have been investigated for the addition of methane, n-pentane, and decane to a restricted bitumen-tetralin system." }, { "name": "Brown, Raymond Allen", "degree": "PhD", "year": "1949", "title": "The Fractionation of Serum Proteins by Electrophoresis-Convection", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05072007-104547", "creators": [ { "name": { "family": "Brown", "given": "Raymond Allen" }, "id": "Brown-Raymond-Allen", "display_name": "Brown, Raymond Allen" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/43QN-WP04", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nA new improved electrophoresis-convection apparatus for the fractionation of proteins is described. The potentialities of the apparatus are demonstrated in the partial separation of bovine serum proteins and in the sub-fractionation of bovine [...]-globulin, Fraction II obtained by alcohol-salt precipitation. A fraction containing 96% [...]-globulin has been isolated from bovine serum. Bovine [...]-globulin has been separated into eight fractions with mobilities ranging from -1.25x10(-5) to -2.25x10(-5) and isoelectric points extending from pH 7.31 to pH 5.74.\r\n\r\nAn extension of the theory of reversible boundary spreading in the electrophoresis of proteins is presented. The theory has been applied to the characterization of the [...]-globulin fractions." }, { "name": "Buff, Frank Paul", "degree": "PhD", "year": "1949", "title": "A Statistical Mechanical Theory of the Coefficients of Shear and Bulk Viscosity of Monatomic Liquids", "advisor": "Kirkwood, John Gamble", "url": "https://resolver.caltech.edu/CaltechTHESIS:06142025-203348846", "creators": [ { "name": { "family": "Buff", "given": "Frank Paul" }, "id": "Buff-Frank-Paul", "display_name": "Buff, Frank Paul" } ], "advisors": [ { "name": { "family": "Kirkwood", "given": "John Gamble" }, "id": "Kirkwood-J-G", "role": "advisor", "display_name": "Kirkwood, John Gamble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6vjk-v091", "abstract": "A detailed molecular theory of the coefficients of shear and bulk viscosity of monatomic liquids is developed on the basis of the general theory of transport processes proposed by Kirkwood. The coefficients are expressed explicitly in terms of the potential of intermolecular force and the perturbations in the pair number density produced by viscous fluid flow. These perturbations are obtained from the steady state solutions of an equation of forced diffusion, derived from the generalized Chandrasekhar equations determining the distribution functions of sets of one and two molecules. This procedure leads to a set of ordinary differential equations, which are solved in terms of the Whittaker confluent hypergeometric function by means of a reasonable analytic approximation to the experimental radial distribution function.
\r\nWith the use of the Lennard-Jones potential and the approximate radial distribution function, calculations of the coefficients of shear and bulk viscosity of liquid argon at 89\u00b0K and 1.2 atm. have been carried out. The theory leads explicitly to ratios of the coefficients to the friction constant of the theory of Brownian motion. With an estimate of the friction constant, a value of the shear viscosity of liquid argon in moderately good agreement with experiment is obtained.
" }, { "name": "Dickey, Frank Host", "degree": "PhD", "year": "1949", "title": "Walden Inversions Involving the Isomeric 2, 3-Butanediamines and Related Compounds. The Preparations of Specific Adsorbents. The Role of Peroxides in Mutagenesis", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032025-203113504", "creators": [ { "name": { "family": "Dickey", "given": "Frank Host" }, "id": "Dickey-Frank-Host", "display_name": "Dickey, Frank Host" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hrtf-ft37", "abstract": "It has been demonstrated that the reaction of ammonia\r\nwith 1,2-dimethylethyleneimine is attended by a single Walden\r\ninversion and that the analogous reaction of ammonia with\r\n2,3-epoxybutane very probably proceeds in the same way. This\r\nresult and other evidence have been used to assign configurations\r\nto the 3-amino-2-butanols and to draw certain conclusions\r\nabout the courses of reactions in which they are involved.
\r\n\r\nThe theory that adsorbents formed in the presence of\r\nforeign substances will acquire, as a result of this method\r\nof formation, specific affinities for such foreign substances\r\nhas been proposed. Its validity in a particular system\r\ninvolving silica gel and certain azo dyes has been demonstrated.
\r\n\r\nThe hypothesis that x-rays, ultra-violet light, and\r\nvarious compounds related to mustard gas produce gene mutations\r\nthrough the intermediate formation of peroxides has been investigated\r\nby testing the effects of various organic peroxides\r\non mutation rates. Several of these compounds have proved to\r\nbe effective for the induction of mutations and a continuation\r\nof these studies would hold promise of uncovering fundamental\r\ninformation about the nature of the mutation process.
" }, { "name": "Garner, Harold Karl", "degree": "PhD", "year": "1949", "title": "The Mechanisms of Some Reactions of Optically Active 2,3-Butanediol and its Derivatives", "advisor": "Lucas, Howard J.; Bonner, James Frederick", "url": "https://resolver.caltech.edu/CaltechTHESIS:06022025-183255549", "creators": [ { "name": { "family": "Garner", "given": "Harold Karl" }, "id": "Garner-Harold-Karl", "display_name": "Garner, Harold Karl" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Bonner", "given": "James Frederick" }, "id": "Bonner-J-F", "role": "advisor", "display_name": "Bonner, James Frederick" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fwfg-wr89", "abstract": "Dextrorotatory 2,3-epoxybutane has been shown to belong to the D\r\nfamily by a consideration of the mechanisms of the reactions involved in\r\nits preparation from D(-)-2,3-butanediol. Similar considerations show\r\ndextrorotatory erythro-3-chloro-2-butanol to belong to the L family. The\r\nlatter compound was oxidized by hypobromite to L(-)-\u03b1-chloropropionic\r\nacid, giving additional proof of its configuration.
\r\n\r\nThe stereochemical results of, (a) the acetolysis of the p-toluenesulfonates\r\nof D(-)-2,3-butanediol, and (b) the reactions of the optically\r\nactive erythro- and threo-3-iodo-2-butanols with the hydrohalic acids, can\r\nbe satisfactorily explained only by assuming neighboring group participation\r\nin the replacement process. This participation is by way of the\r\ncyclic intermediate ions, I and II respectively.
\r\n\r\nSee PDF of abstract for Figs. I and II.
\r\n\r\nA number of cyclic acetals and esters of D(-)-2,3-butanediol were prepared,\r\nnamely, the formal, acetal, carbonate, sulfite, sulfate, borate, and\r\nseveral phosphite derivatives. All of these behaved normally on hydrolysis\r\nexcept the sulfate, which gave the meso-glycol on acid hydrolysis, and the\r\nDL-glycol on basic hydrolysis.
\r\n\r\nThe effect of 3-acetyl-6-methoxybenzaldehyde in inhibiting the growth\r\nof tomato plants was reduced somewhat by removing the roots from the test\r\nplants. The compound was also shown to inhibit germination and root growth\r\nof tomato seedlings.
" }, { "name": "Goff, Gordon Henry", "degree": "Engineering Degree", "year": "1949", "title": "Volumetric and Phase Behavior of Propane 1-Butene System", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-083939402", "creators": [ { "name": { "family": "Goff", "given": "Gordon Henry" }, "id": "Goff-Gordon-Henry", "display_name": "Goff, Gordon Henry" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7cef-5r26", "abstract": "The volumetric behavior of an 81.739 mole % 1-butene mixture\r\nof propene and 1-butene was investigated at seven temperatures\r\nfrom 40\u00b0F to 280\u00b0F over a pressure range from about 40 pounds per\r\nsquare inch absolute to 10,000 pounds per square inch absolute. Tabulations\r\nof single-phase and two-phase data interpolated to even values\r\nof pressure are presented.
\r\n\r\nRevised volumetric data for three mixtures of propene and\r\n1-butene previously investigated by Farrington are presented in tabular\r\nform over similar ranges of temperature and pressure. Variations\r\nof actual volumetric behavior from ideal behavior are shown graphically\r\nfor the system.
\r\n\r\nThe compositions of bubble-point liquid and dew-point gas\r\nwere established experimentally throughout the two-phase region for\r\ntemperatures between 40\u00b0 and 280\u00b0F. Values of specific volume and composition\r\nfor coexisting liquid and gas phases are tabulated. Equilibrium\r\nconstants are given for propene and 1-butene. Properties for the critical\r\nregion are estimated.
" }, { "name": "Guthrie, George Boardman, Jr.", "degree": "PhD", "year": "1949", "title": "Part I. The Standard Entropies of Several Compounds. Part II. Theory of the Thermal Diffusion of Electrolytes in a Clusius Column. Part III. A Study of the Structure of Sulphur-Monochloride by Electron Diffraction. Part IV. A Study of Factors in the Design and Use of an Electron Diffraction Camera", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06072025-131648172", "creators": [ { "name": { "family": "Guthrie", "given": "George Boardman, Jr." }, "id": "Guthrie-George-Boardman", "display_name": "Guthrie, George Boardman, Jr." } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h7z1-1k75", "abstract": "The standard entropies of isopentane, ethyl benzene, azelaic acid\r\nand sebacic acid have been determined by the method of the third law of\r\nthermodynamics. An anomalous hysteresis in the heat capacity of isopentane\r\nreported by Aston et al. was not found. A transition was found in\r\nsebacic acid crystals and is discussed.
\r\n\r\nA theory is presented which accounts approximately for the apparently\r\nanomalous difference, between the thermal diffusion coefficients of the\r\nions of an electrolyte in the presence and in the absence of other \r\nelectrolytes.
\r\n\r\nThe structure of sulfur monochloride has been redetermined by electron\r\ndiffraction. The molecule was found to have an extended structure.\r\nThe parameters have been determined and are reported.
\r\n\r\nThe theoretical expression for the scattering of electrons by gases\r\nis altered by a camera of finite dimensions. An approximate theory of\r\nthe alteration in terms of the camera dimensions (and electron lens parameters)\r\nhas been developed. An expression for the effect of multiple\r\nscattering has been obtained.
" }, { "name": "Harmon, Kent Midgley", "degree": "PhD", "year": "1949", "title": "Studies on: The Specific Activity and Inhibition of Urease; Trypsin and Chymotrypsin Catalyzed Hydrolysis of Simple Peptides; Isomeric Transitions of Radioactive Tellurium", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08142025-170954622", "creators": [ { "name": { "family": "Harmon", "given": "Kent Midgley" }, "id": "Harmon-Kent-Midgley", "display_name": "Harmon, Kent Midgley" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "abstract": "It has been observed that the specific activity of\r\nurease in solutions containing hydrogen sulfide, or cysteine,\r\nand expressed in terms of arbitrary. units of urease activity\r\nper unit weight of enzyme taken as protein nitrogen is dependent~\r\nwithin limits, upon the apparent enzyme concentration.\r\nThe Michaelis constants of several urease preparations have\r\nbeen determined at 25\u00b0 and pH 7.0 under conditions minimizing\r\nthe above noted phenomenon.
\r\n\r\nIt has been observed that urease is competitively inhibited\r\nby phosphate, but not by maleate or glycine buffers.\r\nThe effects of several substituted ureas upon the kinetics of\r\nthe urease-catalyzed hydrolysis of urea have been compared.
\r\n\r\nIt has been observed that although the trypsin-catalyzed\r\nhydrolysis of benzoyl-1-arginineamide is apparently\r\nfirst order with respect to substrate, the first order rate\r\nconstant is dependent upon the initial substrate concentration.\r\nSimilar results have been obtained in a study of the\r\nhydrolysis, by chymotrypsin, of N-acetyl-1-tyrosylglycineamide,\r\nand possible explanations for the two cases have been\r\nadvanced. Inhibition of chymotrypsin by N-acetyl-d-tyrosyl-glycineamide\r\nhas been observed.
\r\n\r\nUnsuccessful attempts have been made to obtain proof\r\nof a proposed mechanism for the chemical changes which accompany\r\nthe isomeric transition of Te127-129. Further information\r\nregarding the nature of these changes has been obtained.
" }, { "name": "Leroux, Pierre Jean", "degree": "Masters", "year": "1949", "title": "Studies on the Rate of Hydrolysis of Sec-Butyl P-Toluenesulfonate", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09092025-003348891", "creators": [ { "name": { "family": "Leroux", "given": "Pierre Jean" }, "id": "Leroux-Pierre-Jean", "display_name": "Leroux, Pierre Jean" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7j05-b860", "abstract": "The rate of hydrolysis of sec-butyl p-toluenesulfonate has been investigated in different solvent mixtures of acetone and water and dioxane and water.
\r\nThe mechanism of the hydrolysis of this ester, which is similar to the secondary alkyl halides, is situated on the border line between the unimolecular dissociation and the bimolecular displacement.
\r\nIt has been found that the rate is proportional to a certain function of the dielectric strength of the solvent but that the proportionality factor is much larger when the solvating power of the medium is high.
\r\nBy studying the ionic strength effect, the so called \"mass law effect\", and the hydroxyl ion influence on the rate, one has come to the conclusion that both un1molecular and bimolecular mechanisms are involved in this hydrolysis.
\r\nFor low values of the dielectric constant of the medium, the bimolecular mechanism seems to be present to the larger extent while for high values of this function the unimolecular dissociation is predominant.
" }, { "name": "Mason, David Malcolm", "degree": "PhD", "year": "1949", "title": "Temperature and Velocity Distribution in the Wake of a Heated Cylinder", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06242004-092715", "creators": [ { "name": { "family": "Mason", "given": "David Malcolm" }, "id": "Mason-David-Malcolm", "display_name": "Mason, David Malcolm" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/QYBZ-YV67", "abstract": "Detailed measurements of the temperature and velocity distribution in the two-dimensional wake of a heated cylinder are presented. Measurements of the temperature distribution on the surface of the cylinder for various rates of heat dissipation are also included, and these data are correlated in the form of dimensionless parameters. The cylinder was 12.15 inches long and 0.190 inch in outside diameter and was placed midway between the upper and lower parallel walls of a horizontal conduit of rectangular cross section through which air flowed normal to the cylinder. The walls, which were spaced 0.75 inch apart, were independently maintained at desired temperatures. In one series of measurements of the temperature and velocity distribution in the wake the rate of heat dissipation from the cylinder was maintained at a constant value of 5.42 watts per inch length of the cylinder for Reynolds numbers of 4,270, 7,630, 15,200, and 26,900 based on the free cross-section area of the conduit. In another series of measurements at a Reynolds number of 15,200 the rate of heat dissipation from the cylinder was maintained at 1.70 watts per inch and 3.20 watts per inch. In each of the above cases the temperature of the walls of the conduit was maintained at 100\u00b0F, identical to the bulk temperature of the entering air. In addition measurements at a Reynolds number of 15,200 were made with the entering air at a temperature of 100\u00b0F, the upper wall at 130\u00b0F, the lower wall at 70\u00b0F, and a rate heat dissipation of about 5.43 watts per inch. Point values of temperature and velocity were obtained as a function of position in the wake of the cylinder. From these data values of eddy conductivity and eddy viscosity were calculated. Analysis of the data on the basis of Prandtl's momentum transfer theory and Taylor's vorticity transfer theory is included. The results are given in tabular form, and a number of graphical presentations of the data are included." }, { "name": "Maun, Eugene Kingery", "degree": "PhD", "year": "1949", "title": "I. The Iodometric Determination of Zinc. II. Investigations in the Chemistry of Rhenium", "advisor": "Davidson, Norman R.; Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06032025-181307069", "creators": [ { "name": { "family": "Maun", "given": "Eugene Kingery" }, "id": "Maun-Eugene-Kingery", "display_name": "Maun, Eugene Kingery" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." }, { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/t88x-1113", "abstract": "Part I describes a study of the iodometric determination\r\nof zinc. The equilibrium of the ferricyanide-ferrocyanide\r\nand iod1de-iodine couples is shifted far to the right by zinc\r\nion, which precipitates ferrocyanide and hence causes iodine\r\nliberation. Conditions based on this principle were developed\r\nfor a rapid, accurate titration of zinc.
\r\n\r\nThe results of a series of investigations of the reactions\r\nof oxidation states of rhenium in aqueous solution\r\nare presented in Part II. These reactions were studied by\r\nspectrophotometric and analytical experiments for the states\r\nReVII, ReV, ReIV, ReI, and R-I.
\r\n\r\nReV was formed rapidly in a light green solution by\r\naddition of 1 or 2 equivalents of stannous chloride to\r\nsolutions of perrhenic acid, HReO4 , in 4 F hydrochloric\r\nacid; this oxidation state has been previously reported,\r\nSimilarly, yellow-brown ReIV was verified as the product\r\nwith further addition of stannous chloride. Brown ReIV\r\nprepared from hydrochloric acid with rhenium dioxide had\r\nreactivity similar to the stannous chloride preparations,\r\nbut yellow-green ReIV Cl=6 was very resistant against a wide\r\nvariety of oxidizing agents.
\r\n\r\nIt was confirmed that Re-I was formed by treatment of\r\ndilute solutions of perrhenic acid, in hydrochloric acid,\r\nby amalgamated zinc. Oxidation of Re-I by HReO4 or O2 formed\r\nfirst brown Re+I and then yellow Re . Titration of Re-I\r\nwith CuII gave Re+I and copper metal.
" }, { "name": "Mirza, Rafat", "degree": "Masters", "year": "1949", "title": "Some Synthetical Experiments with 4-Quinazolone", "advisor": "Koepfli, Joseph Blake", "url": "https://resolver.caltech.edu/CaltechTHESIS:06172025-224633884", "creators": [ { "name": { "family": "Mirza", "given": "Rafat" }, "id": "Mirza-Rafat", "display_name": "Mirza, Rafat" } ], "advisors": [ { "name": { "family": "Koepfli", "given": "Joseph Blake" }, "id": "Koepfli-J-B", "role": "advisor", "display_name": "Koepfli, Joseph Blake" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1kmx-c424", "abstract": "An exceedingly labile compound has been isolated by the\r\ndirect acetylation of 4-quinazolone. The same compound was obtained by reacting silver acetate and 4-chlorquinazoline. Attempts to prepare 3-acetyl-4-quinaazolone by the oxidation of 3-acetyl-3, 4-dihydroquinazoline were not successful, and only 4-quinazolone was isolated as the oxidation product.
\r\nAttempts to attach the alkylaminoalkyl side chains to 4-quinazolone showed that such secondary amines undergo self condensation rather than react with 4-quinazolone. However, it was possible to introduce a dialkylaminoalkyl side chain, and 3-(diethylaminoethyl)-4-quinazolone has been synthesized and is being tested for possible antimalarial activity.
\r\n3-Acetonyl-4-quinazolone gave a well defined crystalline\r\nsolid with diethylamine under the conditions of the Mannich reaction. The analysis of this compound did not agree with the values for the expected compound, and the structure has not been elucidated.
" }, { "name": "Monroe, Emmett Paul", "degree": "Masters", "year": "1949", "title": "I. Derivatives of Spiro (3,3) Heptanetetra Carboxylic Acid. II. Attempted New Synthesis of Cis-2 Butene-1, 4-Diol", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechETD:etd-02122009-093328", "creators": [ { "name": { "family": "Monroe", "given": "Emmett Paul" }, "id": "Monroe-Emmett-Paul", "display_name": "Monroe, Emmett Paul" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/VB67-1R54", "abstract": "I. DERIVATIVES OF SPIRO(3,3) HEPTANETETRACARBOXYLIC ACID:\r\n\r\nThe isolation of the isoamyl ester of spiroheptanetetra-carboxylic acid, prepared by the condensation of sodiomalonic ester with pentaerythrityl tetrabromide in isoamyl alcohol is reported. The synthetic method is that of Fecht as modified by Backer and Schurink. Pentaerythrityl benzenesulfonate is substituted for the bromide in the reaction with the malonic ester, but the yield is found to be much poorer. Attempts to prepare the ethyl ester of spiroheptanetetracarboxylic acid by using pentaerythrityl benzenesulfonate in ethyl alcohol solvent, and pentaerythrityl bromide in excess malonate and xylene solvents are described. These experiments did not produce a practical synthesis of the ethyl ester.\r\n\r\nThe unsuccessful attempt to reduce the isoamyl ester of spiroheptanetetracarboxylic acid with lithium aluminum hydride is described.\r\n\r\nII. ATTEMPTED NEW SYNTHESIS OF CIS-2-BUTENE-,4-DIOL:\r\n\r\nA synthesis of cis-2-butene-1,4-diol by the reduction of maleic anhydride with lithium aluminum hydride is attempted. Two experiments are described, one of which employs an aqueous system in the isolation of the product, the other a non-aqueous system. No amount of any consequence of the diol was obtained. A discussion of lithium aluminum hydride as a reducing agent is included.\r\n" }, { "name": "Nevenzel, Judd Cuthbert", "degree": "PhD", "year": "1949", "title": "I. The Apparent Acid Dissociation Constants of Phenylalanine and Some of its Nuclearly Substituted Derivatives. II. The Isolation of Sphingosine from Bovine Spinal Cord. III. The Ultraviolet Absorption of Some O-Benzoyl Compounds", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-210235284", "creators": [ { "name": { "family": "Nevenzel", "given": "Judd Cuthbert" }, "id": "Nevenzel-Judd-Cuthbert", "display_name": "Nevenzel, Judd Cuthbert" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "role": "member", "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gshw-sd89", "abstract": "I. Apparent dissociation constants for the following compounds were determined by electrometric titration or ultraviolet spectroscopy: phenylalanine, ortho-, meta-, and parachloro-phenylalanines, para-sulfamido-phenylalanine, benzene sulfonamide, toluene sulfonamide, and methane sulfonamide.
\r\n\r\nII. The basic hydrolysis of sphingolipids to obtain sphingosine and psychosine was investigated, using both liquid ammonia and anhydrous hydrazine. Dilituric acid was found to be an excellent reagent for the precipitation of the sphingosine bases. The presence of dihydrosphingosine in bovine spinal cord was confirmed by isolation of the tribenzoyl derivative. The ultraviolet light extinction curve of this derivative was determined in ethanol.
\r\n\r\nIII. The ultraviolet light extinction curves of methyl benzoate, \"n-Octadecyl\" benzoate, d, 1-di benzoyl n-octadecandiol-1,2, and benzoic anhydride were determined in hexane and those of the first and third compounds in ethanol.
" }, { "name": "Ordway, Fred Delancy, Jr.", "degree": "PhD", "year": "1949", "title": "Studies in X-ray Crystallography : I. Calcium Chloride Hexahydrate. II. Hexamethylene Tetramine Complexes with Metal Halides", "advisor": "Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechTHESIS:06012025-103610682", "creators": [ { "name": { "family": "Ordway", "given": "Fred Delancy, Jr." }, "id": "Ordway-Fred-Ordway", "display_name": "Ordway, Fred Delancy, Jr." } ], "advisors": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/15v1-gm05", "abstract": "I. The crystal structure of calcium chloride hexahydrate has been\r\ndetermined by means of Patterson syntheses and stereochemical consideration\r\nof the atomic positions allowed by possible space groups. The parameters\r\nwere determined from peaks in the Patterson syntheses, which were well\r\nresolved.
\r\n\r\nThis determination confirms the conclusions of Jensen (7,8), who used\r\na method of successive Fourier syntheses to arrive at the structure of the\r\nalkaline earth hexahydrates and to obtain approximate parameters for\r\nstrontium chloride hexahydrate, but did not refine these parameters.
\r\n\r\nThe results of this investigation were as follows:
\r\n\r\nSpace group: D23-C321
\r\n\r\nUnit cell: a = 7.80 \u00c5., c = 3.95 \u00c5.; contains one molecule
\r\n\r\nCaCl2\u00b76H2O.
\r\n\r\nAtomic positions: Ca at 1(a) 0 0 0;
\r\n\r\nCl at 2(d) \u2153 \u2154 z, \u2154 \u2153 z, z = 0.576
\r\n\r\n0I at 3(e) x 00, 0 x 0, x x 0, x = 0.313
\r\n\r\n0II at 3 (f) x 0 \u00bd , 0 x \u00bd, x x \u00bd, x = -0.218
\r\n\r\nThe bonding within the crystal is discussed in the light of the\r\nobserved interatomic distances.
\r\n\r\nII. The structures of certain complexes of metal halides with\r\nhexamethylene tetramine, C6H12N4, have been investigated.
\r\n\r\nThe compound SnCl4\u00b74C6H12N4 and the isomorphous TiCl4\u00b74C6H12N4 have\r\nspace group C53v-R3m. The triply primitive hexagonal unit cell has\r\na = c = 8.95 \u00c5. It contains three hexamethylene tetramine molecules and\r\nthree chlorine atoms. The centers of the hexamethylene tetramines and of\r\nthe chlorines form two interpenetrating rhombohedral lattices, separated\r\nby half the rhombohedral body diagonal. The tin atoms are probably\r\ndistributed randomly among the gaps between the larger atoms.
\r\n\r\nthe compounds MnCl2\u00b72C6H12N4 and 2\u00b72C6H12N4 give powder\r\nphotographs considerably different from each other. The former has Laue\r\nsymmetry D2h, a = 11.86 \u00c5., b = 21.92 \u00c5., c = 7.23 \u00c5. The lattice is\r\nprimitive. There is no glide plane normal to a, but possibly an n\r\nglide normal to b and probably a b glide normal to c.
\r\n\r\nA complex of hexamethylene tetramine with SnCl2 gave the same powder\r\npattern as SnCl4\u00b74C6H12N4. A compound with SbCl3 gave the same pattern\r\nwith a few additional lines. The formulas of the complexes are reported\r\n(7) to be SnCl2\u00b72C6H12N4 and SbCl3\u00b73C6H12N4.
\r\n\r\nThe main factors determining the structures of these compounds seem\r\nto be packing of the anions with hexamethylene tetramine molecules and\r\ninteractions among the letter as in crystals of the pure compound .
" }, { "name": "Pfeiffer, Heinz Gerhard", "degree": "PhD", "year": "1949", "title": "An X-Ray Diffraction Investigation of Silver Azide and Boric Oxide and an Electron Diffraction Investigation of Some Three-Membered Rings and Some Halogenated Methanes", "advisor": "Hughes, Edward Wesley; Schomaker, Verner F.; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:05202025-153449195", "creators": [ { "name": { "family": "Pfeiffer", "given": "Heinz Gerhard" }, "id": "Pfeiffer-Heinz-Gerhard", "display_name": "Pfeiffer, Heinz Gerhard" } ], "advisors": [ { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qrgh-1m86", "abstract": "Sections I and II report the X-ray diffraction\r\ninvestigations of silver azide and boric oxide. Silver azide\r\ncrystallizes in a body-centered orthorhombic structure. The\r\nspace group is Ibam with four molecules in the unit cell.\r\nThe silver atoms are in (a), the central nitrogens in(~),\r\nand the end nitrogens in (j) with x = 0.156 and -y: 0.369.\r\nA new type of part cell projection is developed. Boric\r\noxide crystallizes in a hexagonal structure with three\r\nmolecules in the unit cell, ao = 4.320 Kx., co = 8.139 Kx.\r\nEach boron has three bonded oxygen neighbors at a distance\r\nof 1.35 \u00c5 and coplanar with the boron.
\r\n\r\nSections III and IV report electron diffraction\r\ninvestigations of some three-membered rings and some halogenated\r\nmethanes. The HCH bond angles of cyclopropane are\r\nabout 116\u00b0, the C-H distance 1.10 Kx., and the C-C distance\r\n1.515 Kx. The other three-membered rings...ethylene imine,\r\nethylene oxide, ethylene sulfide, and N-methyl ethylene\r\nimine...have HCH angles of 116\u00b0 and all other distances close\r\nto the sum of the covalent radii. The halogenated methanes...\r\ndifluorobromomethane, trifluorobromomethane, trichlorobromomethane,\r\nand difluorodibromomethane...have bond angles close\r\nto tetrahedral; the only significant deviation is the FCBr\r\nangle of 110.5\u00b0 in trifluorobromomethane. The bond lengths in\r\nthese compounds are close to the sum of the covalent radii\r\nwith the exception of the C-Br in difluorodibromomethane\r\n(1.925 Kx.) and in trifluorobromomethane (1.89 Kx.).
" }, { "name": "Rosicky, Fred George", "degree": "Masters", "year": "1949", "title": "An Improved Synthesis of 2-Nitro-6-Aminotoluene", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09242025-191121445", "creators": [ { "name": { "family": "Rosicky", "given": "Fred George" }, "id": "Rosicky-Fred-George", "display_name": "Rosicky, Fred George" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8nyx-ge59", "abstract": "Aromatic fluorides have been prepared and known for a long time (1), but not much work has been done with them until comparatively recently when they have assumed considerable importance as starting materials for the preparation of fluorinated \u221d-amino acids. A considerable number of fluorinated \u221d-amino acids have been prepared. during the past fifteen years, chiefly fluorine derivatives of phenylalanine (2), tyrosine (3,4,5,6,7), and thyronine (5,8).
\r\n\r\nFluorine derivatives of tryptophane have to date not been described in the literature. The compound 2-nitro-6-fluorotoluene was desired as a starting material later to be used in an attempt to synthesize a r1uorine derivative of tryptophane; hence this work was undertaken in an effort to achieve an improved synthesis of the nitrofluorotoluene.
" }, { "name": "Schlinger, Warren Gleason", "degree": "PhD", "year": "1949", "title": "Thermodynamic and Mass Transfer Studies: I. An Apparatus to Determine the Volumetric Behavior of Nitrogen Oxides. II. Isobaric Heat Capacity of I-Butane and I-Pentene\r\nat Bubble Point. III. Mass Transfer in a Turbulent Air Stream", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-09082006-130754", "creators": [ { "name": { "family": "Schlinger", "given": "Warren Gleason" }, "id": "Schlinger-Warren-Gleason", "display_name": "Schlinger, Warren Gleason" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/C9TS-8280", "abstract": "Part I: An apparatus was designed and constructed to determine the volumetric behavior of a number of corrosive fluids at pressures up to 10,000 pounds per square inch and temperatures ranging from -30\u00b0 to 360\u00b0F. Photographic illustrations of the equipment are included and the operation and calibration procedures discussed. Some measurements of the volumetric behavior of nitrogen dioxide are presented in graphical and tabular form.
\r\n \r\nPart II: The isobaric heat capacity at bubble point of 1-butene and 1-pentene was determined at temperatures from 90 to 200\u00b0F. These measurements were carried out in the two-phase region in a constant-volume adiabatic calorimeter. The isobaric heat capacity at bubble point was calculated from the directly measured isochoric values by the use of supplementary volumetric data. The latter data were obtained experimentally for 1-butene and were estimated from the law of corresponding states for 1-pentene. The results are presented in graphical and tabular form.
\r\n\r\nPart III: Values of the eddy diffusivity were determined for turbulently flowing coaxial streams of natural gas and air. The primary measurements included the composition and velocity as a function of radial position and distance from the point at which mixing of the coaxial streams began. The investigations were carried out at gross velocities of 25, 50, and 100 feet per second in a working section 4 inches in diameter and 8 feet in length. The air and natural gas entered the working section at substantially the same relative gross velocities in the case of each set of measurements. Experimental results and derived values of the eddy diffusivity are presented and a method of predicting the composition pattern is discussed.
" }, { "name": "Showell, John Sheldon", "degree": "Masters", "year": "1949", "title": "Studies on the Kinetics of the Addition of Acetic Acid to Isobutene", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172025-021803490", "creators": [ { "name": { "family": "Showell", "given": "John Sheldon" }, "id": "Showell-John-Sheldon", "display_name": "Showell, John Sheldon" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5kmx-0d09", "abstract": "The kinetics of the addition of acetic acid to isobutene with anhydrous and water-containing acetic acid as the\r\nsolvent were studied. The rate was determined by following the changing unsaturation with bromine. The reaction was found to be sensitive to the presence of water, tertiary butyl alcohol being the principal product, when water was present and no polymerization was observed. Under anhydrous conditions the tertiary butyl acetate was formed and the isobutene was observed to polymerize. The kinetics of the anhydrous reaction were theoretically treated quantitatively and the rate step was shown to be the addition of the proton to the isobutene. The water containing conditions were studied, but could not be quantitatively interpreted due to the complex equilibrium system set up, the results were however interpreted qualitatively. The concept of the carbonium ion intermediate of Whitmore was shown to be consistent with the esterification and t he polymerization reaction." }, { "name": "Vaughan, Philip Alfred", "degree": "PhD", "year": "1949", "title": "I. Preparation and Description of Some Derivatives of Molybdenum Dichloride. II. Structure Determination of Complex Molecules or Ions by X-Ray Diffraction by Solutions", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:08182025-175127143", "creators": [ { "name": { "family": "Vaughan", "given": "Philip Alfred" }, "id": "Vaughan-Philip-Alfred", "display_name": "Vaughan, Philip Alfred" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "abstract": "See thesis PDF for abstract." }, { "name": "Wayne, Lowell Grant", "degree": "PhD", "year": "1949", "title": "Kinetics of the Gas Phase Reaction Between Nitric Oxide, Nitrogen Dioxide and Water Vapor", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062025-161436410", "creators": [ { "name": { "family": "Wayne", "given": "Lowell Grant" }, "id": "Wayne-Lowell-Grant", "display_name": "Wayne, Lowell Grant" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a5q4-vg59", "abstract": "Using the absorption of light by nitrogen dioxide\r\nas a measure of its concentration, the rate of the reaction\r\nNO2 + NO + H2O(g) = 2HNO2O(g) has been measured\r\nover a five-fold range of water vapor and nitrogen dioxide\r\nconcentrations, with nitric oxide greatly in excess.\r\nChanges in light intensity were detected by means\r\nof an electron-multiplier phototube and recorded by\r\nphotographing the screen of cathode-ray oscilloscope.\r\nHalf-times as short as 0.014 sec. were observed. The\r\nreaction rate was found to depend more strongly upon \r\nthe concentration of water vapor than upon that of nitrogen\r\ndioxide and to be kinetically consistent with a\r\nmechanism involving termolecular collisions.
\r\n\r\nAn incidental results of the study, the equilibrium\r\nconstant of the above reaction has been calculated\r\nand its order of magnitude experimentally confirmed,\r\nand a lower limit has been fixed for the rate of \r\ndissociation of nitrogen sesquioxide.
" }, { "name": "Wilson, Mathew Kent", "degree": "PhD", "year": "1949", "title": "I. A Reinvestigation of the Vibration Spectra of Several Triatomic Molecules. II. The Infrared Spectrum and Configuration of Hydrogen Persulfide. III. Some Observations on the Spectrum of \"Sulfur Monoxide\"", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-220418464", "creators": [ { "name": { "family": "Wilson", "given": "Mathew Kent" }, "id": "Wilson-Mathew-Kent", "display_name": "Wilson, Mathew Kent" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dpf4-d440", "abstract": "The vibration spectra and molecular configuration of ozone and nitrogen dioxide have been the subject of considerable controversy. Part I of this thesis is a comparative study of the positions, relative intensities, and temperature dependence of the infrared absorption bands in the region 1.5-15 \u00b5 of ozone, nitrogen dioxide, oxygen fluoride, and sulfur dioxide.
\r\n\r\nThe ozone band at 705 cm\u207b\u00b9 is not temperature sensitive and, therefore, is not a difference band as was once postulated. The relative intensity of the ozone band at 2100 cm\u207b\u00b9 is about that expected for a combination or overtone band and, therefore, this band need not be considered as a fundamental on the basis of intensity. A previously unreported band was found for ozone and has been shown to be the fundamental \u03bd\u2081. A new assignment of fundamentals has been given which agrees with the positions, intensities, and contours of the observed ozone bands. In agreement with the electron diffraction results, this assignment requires an obtuse model for ozone. However, the rotational spacing observed in the perpendicular bands is only about one-half that calculated for the model found by electron diffraction.
\r\n\r\nThe symmetric valence vibration, \u03bd\u2081, for nitrogen dioxide previously had been unreported in the infrared, and conflicting assignments had been proposed for the observed nitrogen dioxide bands. By examining the spectrum of the nitrogen dioxide - nitrogen tetroxide system at 25\u00b0 and 200\u00b0 C, it was possible to locate the missing fundamental and to show that several of the bands previously ascribed to nitrogen dioxide are in reality nitrogen tetroxide bands. The symmetric valence vibration of nitrogen dioxide was found near 1306 cm\u207b\u00b9 which is in good agreement with the value of 1320 cm\u207b\u00b9 reported from measurements upon the temperature-sensitive ultra,-violet bands. The rotational. spacing observed in \u03bd\u2084 for nitrogen dioxide is much smaller than that required by the molecular structure as determined by electron diffraction. If the existence of two identical overlapping bands is assumed, the spectroscopic and electron diffraction data can be reconciled. No explanation for the occurrence of two such overlapping bands can be given at this time.
\r\n\r\nMany of the bands previously assigned to oxygen fluoride have been shown to be due to an impurity, presumably carbon tetrafluoride. A new assignment of fundamentals has been given which accounts satisfactorily for the observed oxygen fluoride bands.
\r\n\r\nThe apex angle decreases in the series, nitrogen dioxide - ozone - oxygen fluoride. It was observed that the values of \u03bd\u2083/\u03bd\u2081, and the bond constant, K\u2081, also decrease while the interaction constant, K\u2081\u2082, increases. The value for the ozone bond constant seemed remarkably low in comparison with the value obtained for sulfur dioxide, but has now been shown to be intermediate between the bond constants of the more closely similar molecules, nitrogen dioxide and oxygen fluoride.
\r\n\r\nHeretofore the evidence has not been conclusive in support of either the plane symmetric or symmetric 90\u00b0 model for nitrogen tetroxide. By new considerations involving the occurrence and frequencies of the N-O vibrations in nitrogen dioxide and nitrogen tetroxide, it has been possible to indicate that very probably the planes determined by the two NO\u2082 groups in nitrogen tetroxide are at 90\u00b0 to each other.
\r\n\r\nPart II of this thesis is an investigation of the vibration spectrum of hydrogen persulfide and the rotational. analysis of the band at 2\u00b5. Since only one near-perpendicular type band and no near-parallel band could be investigated under high resolution, only the small moment of inertia was experimentally determined for\r\nthe hydrogen persulfide molecule. Assuming a non-linear, non-planar (C\u2082) structure, it has been found that when the S-S distance, S-H distance, and S-S-H angle are allowed to vary within their range of probable values as inferred from the structures of similar molecules, the angle between the two S-S-H planes may be as small as 10\u00b0 but no larger than 75\u00b0 if the calculated least moment of inertia is to agree with observation. The maximum possible angle for hydrogen persulfide is somewhat smaller than the most probable angle in hydrogen peroxide.
\r\n\r\nThe carrier of the absorption spectrum observed in a mixture of sulfur vapor and sulfur dioxide which has been passed through an electric discharge has variously been described as SO, S\u2082O\u2082 , and S\u2082\u2260. The final part of the thesis describes several experiments undertaken in an attempt to identify the substance responsible for this\r\nspectrum. It was shown conclusively that oxygen is needed for the production of the spectrum, but that the absorption spectrum was not observed under conditions which yielded the SO bands strongly in emission. Although the necessity for the presence of oxygen appears to rule out S\u2082\u2260 as the carrier, no decision could be made\r\nregarding the actual carrier of the spectrum.
" }, { "name": "Auerbach, Charles Edward", "degree": "Engineering Degree", "year": "1948", "title": "Isobaric Heat Capacity at Bubble Point of Four Hydrocarbons", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04072025-205212965", "creators": [ { "name": { "family": "Auerbach", "given": "Charles Edward" }, "id": "Auerbach-Charles-Edward", "display_name": "Auerbach, Charles Edward" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/a9jy-ta81", "abstract": "The isobaric heat capacity of the bubble-point liquid was determined\r\nfor propene at temperatures from 80\u00b0 to 160\u00b0F, and for neohexane,\r\ncyclohexane, and iso-octane in the temperature range from 80\u00b0 to 200\u00b0F.\r\nAn equation for obtaining the isobaric heat capacity has been derived\r\nwhich employs volumetric correction terms applied to the heat capacity\r\nof the substance as measured in an isochoric adiabatic calorimeter. The\r\nresults are presented in both graphical and tabular form." }, { "name": "Billman, Glenn Wagner", "degree": "PhD", "year": "1948", "title": "I. The Transfer of Energy from a Heated Cylinder to a Turbulently Flowing Air Stream. II. The Diffusion of Energy in the Wake of a Heated Cylinder Exposed to a Turbulently Flowing Air Stream", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04142025-222515372", "creators": [ { "name": { "family": "Billman", "given": "Glenn Wagner" }, "id": "Billman-Glenn-Wagner", "display_name": "Billman, Glenn Wagner" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/zvsd-9021", "abstract": "An experimental apparatus is described which was designed to\r\naccomplish:
\r\n\r\n(1) The production of a stable, two-dimensional, turbulently\r\nflowing air stream, and
\r\n\r\n(2) The measurement of temperature and velocity distributions\r\nassociated with the thermal transfer of energy from heated bodies to\r\nthe turbulent air stream.
\r\n\r\nParticular emphasis is placed upon design details of the apparatus\r\nwhich are unique.
\r\n\r\nExperimental data are presented for measurements of:
\r\n\r\n(1) The transfer of energy from a heated cylinder to the turbulent\r\nair stream
\r\n\r\n(2) The diffusion of energy in the wake of a heated cylinder.\r\nThese data are analyzed and the results presented in numerical and\r\ngraphical form. The data are compared, where possible, with published\r\ndata of a similar nature.
" }, { "name": "Brockman, John A., Jr.", "degree": "PhD", "year": "1948", "title": "I and II. Studies on Dichroa Febrifuga. III. A Method for Estimating Chloride. IV. Studies on Cambarus Clarkii", "advisor": "Koepfli, Joseph Blake; Lucas, Howard J.; Wiersma, Cornelius A. G", "url": "https://resolver.caltech.edu/CaltechTHESIS:05062025-212625604", "creators": [ { "name": { "family": "Brockman", "given": "John A., Jr." }, "id": "Brockman-John-A", "display_name": "Brockman, John A., Jr." } ], "advisors": [ { "name": { "family": "Koepfli", "given": "Joseph Blake" }, "id": "Koepfli-J-B", "role": "advisor", "display_name": "Koepfli, Joseph Blake" }, { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Wiersma", "given": "Cornelius A. G" }, "id": "Wiersma-C-A-G", "role": "advisor", "display_name": "Wiersma, Cornelius A. G" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k2bc-dx13", "abstract": "No abstract." }, { "name": "Browne, Charles Idol", "degree": "Masters", "year": "1948", "title": "Spectrophotometric and Radiochemical Investigation of the Interaction Between the Oxidation States of Tin in Aqueous Solution", "advisor": "Davidson, Norman R.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05162025-181639771", "creators": [ { "name": { "family": "Browne", "given": "Charles Idol" }, "id": "Browne-Charles-Idol", "display_name": "Browne, Charles Idol" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rn6j-5f45", "abstract": "The spectrophotometry and radioactive exchange of\r\nSnII and SnIV in hydrochloric acid have been investigated.\r\nIt is found that mixtures of SnII and SnIV in hydrochloric\r\nacid exhibit anomalous absorption of ultra-violet light\r\nand that with the extent of this anomalous absorption is\r\nproportional to the product of the SnII and SnIV concentrations,\r\nimplying absorption by a dimeric complex of\r\nSnII and SnIV.
\r\n\r\nIt is found that SnII and SnIV exchange radioactivity\r\nmoderately slowly (half-exchange time about 7 min.) in 9N\r\nhydrochloric acid. The extent of exchange upon immediate\r\nseparation after mixing is about 17%, which is\r\neither a function of the separation method or an indication\r\nthat only certain chloride complexes of tin exchange.
\r\n\r\nIt is found that CuI and CuII exhibit interaction\r\nabsorption in 6N HCl
" }, { "name": "Corcoran, William Harrison", "degree": "PhD", "year": "1948", "title": "Temperature Gradients in Turbulent Air Streams. Thermodynamics Properties of Methane at Low Temperature", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12042003-091303", "creators": [ { "name": { "family": "Corcoran", "given": "William Harrison" }, "id": "Corcoran-William-Harrison", "display_name": "Corcoran, William Harrison" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/JYDC-RZ04", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nEquipment is described that was used in making velocity and temperature measurements at various points within an air stream flowing in a smooth, rectangular channel 0.675 inch in height, 12 3/8 inches in width, and 162 inches in length. The aspect ratio of the channel was such that flow along the center line was essentially two-dimensional. In addition to equipment for velocity and temperature measurements, means were provided for establishing the thermal flux from the upper wall of the channel into the flowing air stream.\r\n\r\nThe apparatus was applied to a research problem concerned with the analogy between momentum transfer and heat transfer. Steady state, two-dimensional flow of air was attained at the downstream portion of the channel. Observations were made in the Reynolds number range of 18,000 to 48,000. The experimental data were examined on the basis of heat and momentum transfer equations whose basic forms were first suggested by Osborne Reynolds. It was found that in the turbulent core the coefficient of eddy conductivity for heat was practically constant and approximately 1.3 times the coefficient of eddy viscosity.\r\n\r\nThermodynamic properties of methane were computed using values of [...] and the compressibility factor Z obtained from experimental measurements, and theoretical information for heat capacities at zero pressure. Data are tabulated for the temperature range from 70 to -230[degrees]F and the pressure range from zero to 1400 pounds per square inch. A temperature-entropy diagram of methane in this low temperature region is presented." }, { "name": "Farrington, Paul Stephen", "degree": "Engineering Degree", "year": "1948", "title": "Volumetric Behavior of Propene and Three Mixtures of Propene and l-Butene", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172025-030633581", "creators": [ { "name": { "family": "Farrington", "given": "Paul Stephen" }, "id": "Farrington-Paul-Stephen", "display_name": "Farrington, Paul Stephen" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/k5r4-tb84", "abstract": "The volumetric behavior of propene was investigated at temperatures from 40\u00b0 to 460\u00b0 F. and pressures from 10,000 pounds per square inch absolute to values well below vapor pressure at 40\u00b0 F. The results are tabulated and are compared graphically with the data of other investigators.
\r\nThree mixtures of propene and 1-butene were subjected to volumetric study at temperatures from 40\u00b0 to 280\u00b0 F. in the pressure range from 10,000 to about 100 pounds per square inch absolute. The results are tabulated separately for the single-phase and two-phase regions pf each mixture.\r\nVariations of actual behavior from that of ideal solutions\r\nare shown graphically.
" }, { "name": "George, Joseph Doyle", "degree": "Masters", "year": "1948", "title": "Kinetics of the Acid-Catalyzed Hydrolysis of Amine Disulfonate Ion. The Third Ionization Constant of Amine Disulfonic Acid", "advisor": "Davidson, Norman R.; Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06042025-200212097", "creators": [ { "name": { "family": "George", "given": "Joseph Doyle" }, "id": "George-Joseph-Doyle", "display_name": "George, Joseph Doyle" } ], "advisors": [ { "name": { "family": "Davidson", "given": "Norman R." }, "id": "Davidson-N-R", "role": "advisor", "display_name": "Davidson, Norman R." }, { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bdxy-bd03", "abstract": "The rate of the acid-catalyzed hydrolysis of amine\r\ndisulfonate ion, HN(SO3)=2, in water solution has been\r\nthoroughly studied over the temperature range 25-45\u00b0 C.\r\nThe effect of varying the concentration of reactants, the\r\neffect of ionic strength (neutral salt effect), and the\r\neffect of temperature have been studied. All results at\r\nconstant ionic strength confirm the rate equation
\r\n\r\n- d(HN(SO3)=2)/dt = k(H+)(SO3)=2)
\r\n\r\nif the equilibrium between sulfate ion and hydrogen ion is\r\ntaken into account. The uncatalyzed hydrolysis was found\r\nto have an undetectable rate compared to the rate of the\r\ncatalyzed reaction.
\r\n\r\nThe variation of the rate constant with ionic strength\r\nimplies that the charge product of the ions involved in the\r\nrate determining reaction is -2.
\r\n\r\nThe internal energy of activation, \u0394E\u2260, was found to\r\nbe 23.5 \u00b1 1 Kcal., and the entropy of activation, \u0394S\u2260, was\r\nfound to be +7.2 \u00b1 1.5 e.u. for the reaction at zero\r\nionic strength.
\r\n\r\nA mechanism involving an activated complex of amine\r\ndisulfonate ion and hydronium ion may be invoked to explain\r\nthese results.
\r\n\r\nIn addition, the ionization function (classical ionization\r\nconstant) for the equilibrium
\r\n\r\nHN(SO3)=2) = H+ + N(SO3)=2)
\r\n\r\nwas measured in a sodium chloride solution at an ionic\r\nstrength of 1.00 at 25\u00b0 C. It was found that
\r\n\r\n(H+)N(SO3)=2)/HN(SO3)=2) = 3.2 x 10-9.
" }, { "name": "Glanville, James William", "degree": "Engineering Degree", "year": "1948", "title": "Volumetric Behavior of Benzene, Propane and Four Mixtures of these Substances", "advisor": "Lacey, William Noble; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10262004-153802", "creators": [ { "name": { "family": "Glanville", "given": "James William" }, "id": "Glanville-James-William", "display_name": "Glanville, James William" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DNCC-4G10", "abstract": "The volumetric behavior of benzene and of propane was investigated over a pressure range from vapor pressure to 10,000 pounds per square inch absolute and a temperature range from 100 to 4600[degrees] F. The results of these studies are presented in tabular form.\r\n\r\nThe volumetric behavior of four mixtures of benzene and propane was investigated at temperatures from 100 to 4600[degrees] F. in the pressure range from substantially below bubble point to 10,000 pounds per square inch absolute. The single phase and two-phase data are presented in separate tabulations for each mixture. Deviations of the mixtures from the behavior of ideal solutions are shown graphically.\r\n" }, { "name": "Hayward, Philip", "degree": "PhD", "year": "1948", "title": "Kinetics of the Reaction of Iodate Ion with Hypophosphorous Acid", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09302025-215138856", "creators": [ { "name": { "family": "Hayward", "given": "Philip" }, "id": "Hayward-Philip", "display_name": "Hayward, Philip" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/epfx-ve54", "abstract": "The hypothesis that a normal and an active form of hypophosphorous acid coexist in aqueous solution, and that the conversion of the normal to the active form can be a rate-determining step in its reactions, is supported by a study of the kinetics of its reaction with iodate ion.
\r\n\r\nThe rate law [Formula. See abstract in scanned thesis for details] is found to be in agreement with observation, the best values of the constants at 30\u00b0 being 9.7 moles-1 1 hr-1 for k1 and 0.44 for k2 /k3. The respective activation energies are 17 kcal. and 4.5 kcal.
\r\n\r\nIt is probable that the iodate ion reacts with the active form of hypophosphorous acid at a much lower rate than do other substances conforming to this rate law. No evidence could be detected for a reaction involving the hypophosphite ion.
\r\n\r\nThe addition of small amounts of n-propanol to the reaction mixtures is found to be helpful, in that some side reactions are thereby suppressed.
" }, { "name": "Hedberg, Kenneth Wayne", "degree": "PhD", "year": "1948", "title": "Part I. Investigations of the Mechanism and Kinetics of the Formation of Malchite Green Dye. A. Mechanism of the Oxidation of Leuco Malachite Green. B. Kinetics of the Conversion of Malachite Green Carbinol to Dye. Part II. Determination of some Molecular Structures by the Method of Electron Diffraction. A. Adamantane. B. 1,3,5,7,-Cyclooctatetraene. Part III. The Molecular Structure of Arsenobenzene. Determination of the Unit Cell and Space Group of the Crystal", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-01312005-160036", "creators": [ { "name": { "family": "Hedberg", "given": "Kenneth Wayne" }, "id": "Hedberg-Kenneth-Wayne", "display_name": "Hedberg, Kenneth Wayne" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/52FH-Y603", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I. Investigations of the mechanism and kinetics of the formation of malachite green dye.\r\n\r\nA. Mechanism of the oxidation of leuco malachite green.\r\n\r\nThe oxidation of leuco malachite green to malachite green dye is commonly considered to take place through the formation of malachite green carbinol: [...]. The present study shows that malachite green carbinol cannot be an intermediate in this process. The proof rests on the observation that the oxidation of leuco malachite green to dye occurs at a much more rapid rate than that at which malachite green carbinol is dehydrated to dye.\r\n\r\nIt is suggested that this result is evidence that the oxidation of ethanol does not take place through the formation of a gem-diol as intermediate.\r\n\r\nB. Kinetics of the conversion of malachite green carbinol to dye.\r\n\r\nThe kinetics of the conversion of malachite green carbinol to dye have been studied in solutions of ionic strength approximately 2.84 over the pH range 2.5 - 4.9. The rate constants representing the rate of approach to equilibrium are first order with respect to carbinol and have the values 15.8, 13.4, 6.2, 8.7, 21.4 and 20.4 x [...] [...] at pH 4.88, 4.69, 4.08, 2.98, 2.25, and 1.65, respectively.\r\n\r\nAn attempt is made to account for the observed minimum in the curve which results when these values of the constant for the approach to equilibrium are plotted against pH.\r\n\t\t\r\nPart II. Determination of sole molecular structures by the method of electron diffraction.\r\n\r\nA. Adamantane.\r\n\r\nAn investigation of the structure of adamantane by electron diffraction has led to the following results for the structural parameters: [...], [...],[...]. (assumed), [...] (assumed) The molecular symmetry [...] was assumed. These results are in agreement with results obtained from x-ray diffraction studies of the crystal.\r\n\r\nB. 1,3,5,7, - cyclooctatetraene.\r\n\r\nThe structure of cyclooctatetraene is of great theoretical importance to chemists because of the relationship between this molecule and the benzene molecule. From an earlier electron diffraction investigation of cyclooctatetraene it was concluded that all C - C bonded distances were equal and that the molecule has the symmetry [...]. This result is in complete disagreement with preliminary results from an x-ray diffraction investigation currently in progress in another laboratory; these results indicate cyclooctatetraene to have two different C - C bonded distances and the molecular symmetry [...].\r\n\r\nThe results of our electron diffraction investigation show that cyclooctatetraene has two C - C bonded distances, which are about equal to the normal double bond distance and to the conjugated single bond distance. The molecule has the symmetry [...] \"tub\" in agreement with the result from x-ray diffraction.\r\n\r\nThe positions of the double bonds in the molecule cannot be placed from the electron diffraction data; two different regions of parameter combinations, depending upon the position of the double bonds, give acceptable models. It is possible to make a choice between these regions, however, based upon considerations of strains induced by rotation about the double bond. The structural parameters for the best model in the chosen region are: [...] (assumed), and C - H = 1.098, (assumed).\r\n\r\nPart III. The molecular structure of arsenobenzene determination of the space group and unit cell.\r\n\r\nThe molecular formula of arsenobenzene is commonly written as [...] although the true molecular formula is unknown. Determinations of the molecular weight of this substance indicate from 2 to 6 of the [...] units to be combined in solution. It was hoped that a determination of the space group and unit cell of the crystal would yield useful information regarding the structure of the molecule.\r\n\r\nA tentative unit cell was determined from layer line measurements made from rotation photographs, and verified by a symmetrical Laue photograph. The arsenobenzene crystal was found to be monoclinic; and to contain 12 [...] units per cell. Accurate values of the lattice constants were obtained from oscillation photographs. These values are [...]. With the aid of Weissenberg photographs the probable space group of the crystal was determined to be [...].\r\n\r\nThe space group and unit cell of arsenobenzene together with considerations based on the chemistry of arsenic allow interesting deductions to be made regarding the molecules of this substance. One molecule may consist of 2,3, or 6 [...] units, giving 6,4, or 2 molecules per unit cell, respectively, There is, however, considerable qualitative evidence which indicates that discrete molecules of arsenobenzene do not exist in the crystal, and that instead the arsenic atoms are bonded together in infinite chains probably parallel to the monoclinic axis." }, { "name": "Holzman, George", "degree": "PhD", "year": "1948", "title": "Studies on Blood Group A Substance", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05302025-184553880", "creators": [ { "name": { "family": "Holzman", "given": "George" }, "id": "Holzman-George", "display_name": "Holzman, George" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/c6fv-2w05", "abstract": "A study has been made of the isolation of blood group\r\nA-substance from various sources with the aim of ascertaining\r\nthe relative efficacy of procedures in concentrating A-substance.\r\nPreparations of A-substance were isolated from hog gastric mucin,\r\nhog gastric mucose, pepsin, human erythrocytes and stromata, and\r\npseudomucinous ovarian cyst fluids according to procedures previously\r\ndescribed. This has afforded a direct comparison of the\r\nprocedures and products obtained.
\r\n\r\nIn order to facilitate the examination of the activities\r\nof fractions obtained in isolation procedures, a color test was\r\ndeveloped which under certain conditions can be used to predict\r\nserological potencies. The carbazole reaction for the estimation\r\nof hexoses in polysaccharides was also reinvestigated and an improved\r\nprocedure developed.
\r\n\r\nThe preparation of A-substance from hog mucin was studied\r\nin detail by means of electrodialysis and alcohol fractionation\r\nand with the aid of a number of criteria of fractionation including\r\nserological potency, elementary analyses, analyses for a few sugars\r\nand amino acids, and ultraviolet absorption spectra. Spectrophotometric\r\nanalyses have also led to the separation of highly potent,\r\nelectrophoretically homogeneous, preparations into two distinct\r\nfractions differing strikingly in their solubility at low ionic\r\nstrength and low pH. The more active insoluble component was inhomogeneous,\r\nhowever, by electrophoresis, solubility, particle size studies,\r\nand serological specificity.
\r\n\r\nA preliminary investigation of the nature of the alkaline\r\ndecomposition of A-substance and of some of the products so formed\r\nwas made.
\r\n\r\nThe diurnal variation in the carbon dioxide content of the\r\nextractable gases of leaves of Bryophyllum fedtschenkoi was\r\nmeasured; results were not decisive in testing a hypothesis concerning\r\nthe mechanism of diurnal acid production of succulents.
" }, { "name": "Hoyer, Horst Walter", "degree": "Masters", "year": "1948", "title": "Studies on the Diamagnetic Anisotropy of Crystals", "advisor": "Pauling, Linus; Hughes, Edward Wesley", "url": "https://resolver.caltech.edu/CaltechTHESIS:04062025-023517312", "creators": [ { "name": { "family": "Hoyer", "given": "Horst Walter" }, "id": "Hoyer-Horst-Walter", "display_name": "Hoyer, Horst Walter" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Hughes", "given": "Edward Wesley" }, "id": "Hughes-Edward-Wesley", "role": "advisor", "display_name": "Hughes, Edward Wesley" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wje8-nt24", "abstract": "Apparatus for the measurement of magnetic anisotropy has been constructed. It is based upon a method first developed by Krishnan in which the torsional force due to the twist on a fine quartz fiber is used to measure the couple acting on the crystal resulting from its anisotropy. By this means the diamagnetic anisotropy of iodoform, arsenic triiodide and potassium chloroplatinite were measured. The results obtained with the last named compound indicated the presence of ferromagnetic impurities. A table of the diamagnetic anisotropy of organic compounds measured to January 1948 has been compiled.
" }, { "name": "Johnston, Harold Sledge", "degree": "PhD", "year": "1948", "title": "Part I. The Kinetics of the Fast Reaction Between Ozone and Nitrogen Dioxide. Part II. A Mechanism for the Formation of Red Phosphorous from White Phosphorus in Solution", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262004-153834", "creators": [ { "name": { "family": "Johnston", "given": "Harold Sledge" }, "id": "Johnston-Harold-Sledge", "display_name": "Johnston, Harold Sledge" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P40Q-X050", "abstract": "NOTE: Text or symbols not renderable in plain ASCII are indicated by [...]. Abstract is included in .pdf document.\r\n\r\nPart I.\r\n\r\n1. A system has been designed and constructed which will mix two gaseous reactants, isolate them in a reaction cell, and follow the entire course of the reaction photoelectrically in one-tenth of a second. The output of the photoelectric tube is recorded by a time-exposure photograph of the screen of an oscilloscope.\r\n\r\n2. The kinetics of the fast reaction between ozone and nitrogen dioxide mas studied over a ten-fold range of each reactant. The rate law was found to be [...] over the entire course of the reaction. As expected from the speed of the reaction, the energy of activation was found to be low, 6.4 kilocalories per mole. A simple two-step mechanism is proposed to account for the observations.\r\n\r\nPart II.\r\n\r\n1. In an effort to obtain information about the mechanism of the formation of red phosphorus from white phosphorus in a solution of phosphorus tribromide, a radioactive tracer study was made of that system. Tentative explanations are advanced for certain features of the process.\r\n\r\n2. A great variety of colors of polymerized phosphorus were observed in this study, and correlations between presumed size and color are discussed." }, { "name": "Meier, Dale Joseph", "degree": "Masters", "year": "1948", "title": "Studies on the Use of Coulometric and Amperometric Analysis", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04082025-212811851", "creators": [ { "name": { "family": "Meier", "given": "Dale Joseph" }, "id": "Meier-Dale-Joseph", "display_name": "Meier, Dale Joseph" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/53yb-sn68", "abstract": "I. The coulometric determination of chromates and\r\nvanadates by means of electrolytically generated\r\ncuprous ion has been investigated. For samples\r\nof chromate larger than 170 micrograms, the error\r\nin the determination was less than 0.1 percent.\r\nThe presence of oxygen has been shown to give a\r\npositive error of about 0.5 percent when determining\r\nvanadates. When oxygen was excluded, the\r\nerror in determining 750 micrograms was less than\r\n0.15 percent.
\r\n\r\nII. The use of electrolytically generated argentic\r\nsilver for the determination of manganous ion,\r\ncerous ion and arsenious acid has been investigated\r\nand has been shown to be impractical because of the\r\nslow rate of oxidation by the argentic silver.
\r\n\r\nIII. The determination of Bromine Numbers with electrolytically\r\ngenerated bromine has been investigated.\r\nFor olefins which rapidly add bromine, the use of a\r\n50 percent acetic acid solution of sodium bromide as\r\nthe titration medium has been shown to give good\r\nresults. A means has been proposed for the electrolytic\r\ndetermination of Bromine Numbers for slowly\r\nreacting olefins.
\r\n\r\nIV. An amperometric method for determining the formal\r\npotential of the reaction 2 Cu+++7Br- = 2CuBr2-+Br3-\r\nhas been investigated. The formal potential was\r\nfound to be -.384 v. for solutions 0.017 formal in\r\ncupric ion, 0.44 formal in bromide ion, an 0.7 formal\r\nin sulfuric acid.
" }, { "name": "Winniford, Robert Stanley", "degree": "Masters", "year": "1948", "title": "I. The Synthesis of Methylenecyclobutane from Pentaerythrityl Chloride. II. The Attempted Synthesis of Cyclobutane. III. A Reinvestigation of the Synthesis of Spiroheptanedicarboxylic Acid", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechETD:etd-10062005-083407", "creators": [ { "name": { "family": "Winniford", "given": "Robert Stanley" }, "id": "Winniford-Robert-Stanley", "display_name": "Winniford, Robert Stanley" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZMYX-Z369", "abstract": "I. The Synthesis of Methylenecyclobutane from Pentaerythrityl Chloride\r\n\r\nA new method for preparing methylenecyclobutane is described in which the starting material is pentaerythrityl tetrachloride. Pentaerythrityl chloride is dechlorinated by zinc dust in the presence of sodium iodide and sodium carbonate, using as solvent either diethylene glycol or acetamide. Reasonable yields are obtained.\r\n\r\nII. The Attempted Synthesis of Cyclobutane\r\n\r\nA synthesis of cyclobutanone through treatment of the methylenecyclobutane-nitrogen trioxide addition compound, with alcoholic potassium hydroxide is not successful.\r\n\r\nThe oxidation of methylenecyclobutane dibromide with potassium permanganate does not yield cyclobutanone.\r\n\r\nIII. A Reinvestigation of the Synthesis of Spiroheptanedicarboxylic Acid\r\n\r\nAn experiment is described in which two mols of malonic ester are condensed with one mol of pentaerythrityl chloride to form spiroheptanetetracarboxylic acid ester. The tetra acid is decarboxylated by heat to afford the dicarboxylic acid. The procedure is a modification of that described in the literature, whereby spiroheptanedicarboxylic acid is prepared from pentaerythrityl bromide.\r\n\r\nA parallel experiment in which pentaerythrityl bromide is condensed with malonic ester is also described.\r\n\r\nThe yields are low in each case." }, { "name": "Brown, Raymond Allen", "degree": "Masters", "year": "1947", "title": "The Formal Potential of the Antimonous-Antimonic Couple in Hydrochloric Acid and a Method for the Determination of Tripositive Antimony", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10052005-162608", "creators": [ { "name": { "family": "Brown", "given": "Raymond Allen" }, "id": "Brown-Raymond-Allen", "display_name": "Brown, Raymond Allen" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MQYW-D781", "abstract": "1. The antimonous-antimonic half cell formal potential has been found to be -0.746 in 3.5 weight formal HC1, -0.784 in 4.5 weight formal HC1, and -0.818 in 6.0 weight formal HC1 when the total antimony concentration is 3.20x10(-2) weight formal.
\r\n\r\n2. The dependence of the formal potential upon total antimony concentration and the ratio Sb(+III)/Sb(+V) has been studied.
\r\n\r\n3. Tripositive antimony has been determined in quantities ranging from 10 to 1,500 micrograms by coulometric titration in hydrochloric acid solutions containing bromide with electrolytically generated bromine using an amperometric end point.
" }, { "name": "Donohue, Jerry", "degree": "PhD", "year": "1947", "title": "Studies of the Representation of Interatomic Distances in Molecules and Crystal as Sum of Atomic Radii", "advisor": "Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112015-134546938", "creators": [ { "name": { "family": "Donohue", "given": "Jerry" }, "id": "Donohue-Jerry", "display_name": "Donohue, Jerry" } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3NAA-ZA17", "abstract": "The electron diffraction investigation of the following compounds has been carried out: sulfur, sulfur nitride, realgar, arsenic trisulfide, spiropentane, dimethyltrisulfide, cis and trans lewisite, methylal, and ethylene glycol.
\r\nThe crystal structures of the following salts have been determined by x-ray diffraction: silver molybdateand hydrazinium dichloride.
\r\nSuggested revisions of the covalent radii for B, Si, P, Ge, As, Sn, Sb, and Pb have been made, and values for the covalent radii of Al, Ga, In, Ti, and Bi have been proposed.
\r\nThe Schomaker-Stevenson revision of the additivity rule for single covalent bond distances has been used in conjunction with the revised radii. Agreement with experiment is in general better with the revised radii than with the former radii and additivity.
\r\nThe principle of ionic bond character in addition to that present in a normal covalent bond has been applied to the observed structures of numerous molecules. It leads to a method of interpretation which is at least as consistent as the theory of multiple bond formation.
\r\nThe revision of the additivity rule has been extended to double bonds. An encouraging beginning along these lines has been made, but additional experimental data are needed for clarification.
\r\n" }, { "name": "Hammock, Edward Woodrow", "degree": "Masters", "year": "1947", "title": "Part I. Iodometric Determination of Copper. Section I. The Use of Thiocyanate. Section II. The Use of Sulfate-Hydrogen Sulfate Buffers. Part II. The Use of Iodine Monochloride End-Point for the Titration of Antimony Using Ceric Sulfate, Potassium Permanganate and Potassium Iodate Solutions. Part III. The Use of Iodine Monochloride as an Indicator in the Titration of Thiocyanate with Permanganate, Iodate and Ceric Sulfate. Part IV. The Distribution of Thallium Between Isopropyl Ether and Hydrochloric Acid", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:05052025-230344625", "creators": [ { "name": { "family": "Hammock", "given": "Edward Woodrow" }, "id": "Hammock-Edward-Woodrow", "display_name": "Hammock, Edward Woodrow" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4ykb-rz18", "abstract": "I. This part of the thesis reports a study of some of the limitations\r\nencountered in the iodometric determination of copper. The sulfate-hydrogen\r\nsulfate buffer was introduced for this determination. The permissible pH\r\nrange for this buffer was found to be from about O.5 to 3. It was found\r\nthat the \"oxygen error\" was not noticeable even at the lower limits of this\r\nrange and the end-points were stable enough for a normal titration. Chlorides\r\nand nitrates do not cause serious errors. The procedure using the sulfate\r\nbuffers and thiocyanate was tested against pure copper and copper alloys\r\nwhich contain interfering constituents. The results show that the percentage\r\ndifference from the theoretical is less than one part per thousand.
\r\n\r\nThe effect of adding thiocyanate at various points during the titration,\r\nthe amount required, and the necessity of using pure thiocyanate\r\nwere studied and reported. A study of the difference of the iodide and thiocyanate\r\nend-points was made. It was observed that a small excess of thiosulfate\r\ncould be back titrated. Several wetting agents as well as shellac were\r\ntried in an attempt to protect the cuprous iodide during this back titration.
\r\n\r\nII. A study has been made of the titration of antimony with permanganate,\r\neerie sulfate, and iodate solutions, using the iodine monochloride as\r\nthe indicator. The oxidizing solutions were standardized against Bureau of\r\nStandards arsenious oxide by two methods which agreed within one part per\r\nthousand. In the analysis of an antimony ore, the amount of antimony found\r\nwas about three parts per thousand too high of that present.
\r\n\r\nIII. A study of the titration of thiocyanate has been made in which\r\npermanganate, iodate and eerie sulfate were used as the oxidizing agents,\r\nand iodine monochloride used as the indicator. Results show that iodate\r\ntitration gives results within one part per thousand, the permanganate\r\ntitration within three parts per thousand, and eerie sulfate titration was\r\nnot satisfactory. Potassium thiocyanate can be used as a primary standard.
\r\n\r\nIV. This report is a progress report on the study of the distribution\r\nof thallium between isopropyl ether and hydrochloric acid solution. The\r\nmethod for purifying the ether and the method of the analyzing the ether\r\nand water layers is given. There is not sufficient data to draw any definite\r\nconclusions as to the distribution curve nor the extracted species.
" }, { "name": "Mislow, Kurt Martin", "degree": "PhD", "year": "1947", "title": "I. The Synthesis of Potential Antimaterials. Some 2-Substituted 8-(3-Diethylaminopropylaminol)-Quinolines. II. Isomorphism in Relation to Serological Specificity. III. A Study of the Hammick Reaction", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142004-140844", "creators": [ { "name": { "family": "Mislow", "given": "Kurt Martin" }, "id": "Mislow-Kurt-Martin", "display_name": "Mislow, Kurt Martin" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/60T0-BG46", "abstract": "No Abstract Submitted." }, { "name": "Naiditch, Sam", "degree": "PhD", "year": "1947", "title": "I. Rate and Mechanism of the Hydrolysis of the Hydroxylamine Disulfonate Ion. II. The Low Voltage Electrically Exploded Wire", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282025-185303011", "creators": [ { "name": { "family": "Naiditch", "given": "Sam" }, "id": "Naiditch-Sam", "display_name": "Naiditch, Sam" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wne4-hb77", "abstract": "No abstract." }, { "name": "Pardee, Arthur Beck", "degree": "PhD", "year": "1947", "title": "I. The Degree of Association of Some Simple Antigens. II. The Reactions of Synthetic Antigens with Specifically Purified Antibodies. III. The Size and Shape of Molecules of \"A\" Substance from Hog Gastric Mucin", "advisor": "Swingle, Stanley Morse; Campbell, Ian; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-06212004-111231", "creators": [ { "name": { "family": "Pardee", "given": "Arthur Beck" }, "id": "Pardee-Arthur-Beck", "display_name": "Pardee, Arthur Beck" } ], "advisors": [ { "name": { "family": "Swingle", "given": "Stanley Morse" }, "id": "Swingle-S-M", "role": "advisor", "display_name": "Swingle, Stanley Morse" }, { "name": { "family": "Campbell", "given": "Ian" }, "id": "Campbell-I", "role": "co-advisor", "display_name": "Campbell, Ian" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "co-advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9RYM-GG08", "abstract": "No abstract." }, { "name": "Scully, Charles Norman", "degree": "Masters", "year": "1947", "title": "The Chemistry of the 1,3,2 Dioxaphospholanes and Related Compounds", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012025-175442003", "creators": [ { "name": { "family": "Scully", "given": "Charles Norman" }, "id": "Scully-Charles-Norman", "display_name": "Scully, Charles Norman" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b7qb-j098", "abstract": "No abstract." }, { "name": "Shoemaker, David Powell", "degree": "PhD", "year": "1947", "title": "I. An Attempt to Prepare Antibodies to Histamine In Vitro. II. An Investigation of a Possible Method for Preparing Large Single Crystals of Aluminum Orthophosphate. III. Investigations of the Crystal Structures of Amino Acids by X-Ray Diffraction: A. An Investigation of the Space-Group and Lattice Constants of dl-Serine. B. An Investigation of the Crystal Structure of \u2113-Threonine", "advisor": "Pauling, Linus; Corey, Robert B.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04222025-154900081", "creators": [ { "name": { "family": "Shoemaker", "given": "David Powell" }, "id": "Shoemaker-David-Powell", "display_name": "Shoemaker, David Powell" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Corey", "given": "Robert B." }, "id": "Corey-R-B", "role": "advisor", "display_name": "Corey, Robert B." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a036-nq76", "abstract": "No abstract." }, { "name": "Thomas, Dudley Watson", "degree": "Masters", "year": "1947", "title": "The Synthesis of Some Aromatic Sulfonic Acids and a Procedure for the Purification of L(-) Leucine", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03282025-212522311", "creators": [ { "name": { "family": "Thomas", "given": "Dudley Watson" }, "id": "Thomas-Dudley-Watson", "display_name": "Thomas, Dudley Watson" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ap96-ct83", "abstract": "No abstract." }, { "name": "Thompson, Russell Albert, Jr.", "degree": "Engineering Degree", "year": "1947", "title": "Phase Behavior of Propane and Propene Hydrates", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012025-183309950", "creators": [ { "name": { "family": "Thompson", "given": "Russell Albert, Jr." }, "id": "Thompson-Russell-Albert", "display_name": "Thompson, Russell Albert, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/rxjk-nq88", "abstract": "The compositions of propane, propene, and propane-propene\r\nhydrates varied from 5 to 15 mols of water per mol of\r\nhydrocarbon. No appreciable separation of the propene from the\r\npropane was found between the excess liquid hydrocarbon phase\r\nand the hydrate phase. These facts represent the results of\r\ntwenty experiments at 400 psia and 33 - 39\u00b0 F.
\r\n\r\nWhile the variations in apparent compositions are over\r\none hundred times the experimental error as demonstrated by\r\nmaterial balances, no theoretical explanation is offered to\r\ninterpret this behavior.
" }, { "name": "Trueblood, Kenneth Nyitray", "degree": "PhD", "year": "1947", "title": "I. The Coordination of Silver Ion with Ethylene and Propylene. II. The Development of a Chromatographic-Spectrophotometric Method for the Isolation and Estimation of Minor Impurities in RDX. III. An Experimental Study of Chromatography on Silicic Acid-Celite Columns. IV. A Method for the Study of the Absorption Spectra of Adsorbed Compounds", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04212004-161329", "creators": [ { "name": { "family": "Trueblood", "given": "Kenneth Nyitray" }, "id": "Trueblood-Kenneth-Nyitray", "display_name": "Trueblood, Kenneth Nyitray" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BFBP-3E86", "abstract": "No Abstract ." }, { "name": "Wooster, Warren Scriver", "degree": "Masters", "year": "1947", "title": "The Coulometric Titration of Iodide with Electrolytically Generated Bromine Using an Amperometric Endpoint", "advisor": "Swift, Ernest H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012025-165751766", "creators": [ { "name": { "family": "Wooster", "given": "Warren Scriver" }, "id": "Wooster-Warren-Scriver", "display_name": "Wooster, Warren Scriver" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0pc3-me36", "abstract": "No abstract." }, { "name": "Gilman, Theodore Silkman", "degree": "Masters", "year": "1946", "title": "The Study of Nitrocellulose Solutions by Light Scattering Measurements", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232025-180526666", "creators": [ { "name": { "family": "Gilman", "given": "Theodore Silkman" }, "id": "Gilman-Theodore-Silkman", "display_name": "Gilman, Theodore Silkman" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/78w8-vm82", "abstract": "No abstract." }, { "name": "Hall, Luther Axtell Richard", "degree": "Masters", "year": "1946", "title": "Hapten Inhibition of Precipitation of Antisera Homologous to the o-, m-, and p-Azobenoic Acid Groups", "advisor": "Pressman, David", "url": "https://resolver.caltech.edu/CaltechTHESIS:05022025-184306892", "creators": [ { "name": { "family": "Hall", "given": "Luther Axtell Richard" }, "id": "Hall-Luther-Axtell-Richard", "display_name": "Hall, Luther Axtell Richard" } ], "advisors": [ { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "role": "advisor", "display_name": "Pressman, David" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1k41-bj64", "abstract": "No abstract." }, { "name": "Howton, David Ronald", "degree": "PhD", "year": "1946", "title": "The Synthesis of Potential Antimalarials. I. 1,3-Dimethylpiperidone-4. II. Application of the Darzens-Claisen Reaction to a \u03b2-Dialkylaminoketone. III. 6'-Methoxyrubanol-9. IV. Synthesis of Some 2-Phenylquinolyl-4-\u03b1-Piperidylcarbinols. V. 2,6-Diphenylpyridyl-4-di-n-butylaminomethylcarbinol. VI. Preparation and Reduction of 9-Picolinylanthracene. VII. Preparation and Reduction of \u03b1-Phenacylpyridine. A New Guinea-Pig Test for Relaxin Activity.", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:06092025-221024740", "creators": [ { "name": { "family": "Howton", "given": "David Ronald" }, "id": "Howton-David-Ronald", "display_name": "Howton, David Ronald" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/y07y-vt13", "abstract": "No abstract." }, { "name": "Lipscomb, William Nunn", "degree": "PhD", "year": "1946", "title": "I. Electron Diffraction Investigations of Vanadium Tetrachloride, Dimethylketene Dimer, Tetrachloroethylene, and Trichloroethylene. II. The Crystal Structure of Methylammonium Chloride", "advisor": "Pauling, Linus; Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-10142002-160250", "creators": [ { "name": { "family": "Lipscomb", "given": "William Nunn" }, "id": "Lipscomb-William-Nunn", "display_name": "Lipscomb, William Nunn" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TGA8-ST30", "abstract": "No abstract." }, { "name": "Mitchell, Fern Wood, Jr.", "degree": "Masters", "year": "1946", "title": "The Reaction Steps in the Conversion of 2,3-Di-p-Toluenesulfonoxybutane to 2,3-Diacetoxybutane", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182025-220746373", "creators": [ { "name": { "family": "Mitchell", "given": "Fern Wood, Jr." }, "id": "Mitchell-Fern-Wood", "display_name": "Mitchell, Fern Wood, Jr." } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/r83p-vm58", "abstract": "No abstract." }, { "name": "O'Gorman, John Michael", "degree": "PhD", "year": "1946", "title": "I. The Rate of Hydration of Methyl Vinyl Ketone. II. The Hydrolysis of Optically Active 2-Octanol Acetal. III. Electron Diffraction Investigation of the Structures of Certain Organic Compounds", "advisor": "Lucas, Howard J.; Schomaker, Verner F.", "url": "https://resolver.caltech.edu/CaltechTHESIS:04212025-184622066", "creators": [ { "name": { "family": "O'Gorman", "given": "John Michael" }, "id": "O'Gorman-John-Michael", "display_name": "O'Gorman, John Michael" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3vqx-n657", "abstract": "No abstract." }, { "name": "Rapport, Maurice M.", "degree": "PhD", "year": "1946", "title": "I. The Synthesis of Potential Antimalarials : A. Carbinolamines Related to Quinine, B. Sulfonamides. II. The Resolution of 3-Fluoro-Dl-Tyrosine, and the Determination of the Acute Toxicity of the Optically Active Isomers. III. The Synthesis of P-Arsono-Dl-Phenylalanine. IV. A Study of the Proteins in Some Invertebrate Body Fluids", "advisor": "Koepfli, Joseph Blake", "url": "https://resolver.caltech.edu/CaltechETD:etd-09122006-084203", "creators": [ { "name": { "family": "Rapport", "given": "Maurice M." }, "id": "Rapport-Maurice-M", "display_name": "Rapport, Maurice M." } ], "advisors": [ { "name": { "family": "Koepfli", "given": "Joseph Blake" }, "id": "Koepfli-J-B", "role": "advisor", "display_name": "Koepfli, Joseph Blake" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/EP9A-CG71", "abstract": "Part I: The synthesis of two series of compounds, benzenesulfonanilides and carbinolamines related to quinine, are described. These compounds were prepared as potential antimalarials.
\r\n\r\nPart II: The enzymatic resolution of N-benzoyl 3-fluoro-dl-tyrosine and the preparation of 3-fluoro-D- and L-tyrosine are described. A study of the acute toxicity of the optical isomers is also reported.
\r\n\r\nPart III: The synthesis of p-arsono-N-acetylphenylalanine is described.
\r\n\r\nPart IV: The chemical fractionation of the protein constituents of Panulirus Interruptus (spiny lobster) blood was repeated, and an electrophoretic study of the fractions, confirming the presence of at least three separate proteins, is described. Preliminary fractionations of the body fluids of Cancer Anthonyi (crab), Stichopus Californicus (sea cucumber), and Halitotis Fulgens (green abalone) are also reported.
" }, { "name": "Sease, John William", "degree": "PhD", "year": "1946", "title": "I. Some Irreversible Conversions of Lutein at Elevated Temperatures. II. Investigation of the Effect of Globulin Depletion on Antibody Production in Rabbits", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282025-165204735", "creators": [ { "name": { "family": "Sease", "given": "John William" }, "id": "Sease-John-William", "display_name": "Sease, John William" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p7zh-r891", "abstract": "No abstract." }, { "name": "Senear, Allen Eugene", "degree": "PhD", "year": "1946", "title": "The Synthesis of Potential Antimalarials: I. Analogues of Pantothenic Acid. II. N\u00b9-Phenylsulfanilamides. III. Sulfonamidopyrimidines. IV. Quinolinemethanols Related to Quinine", "advisor": "Koepfli, Joseph Blake; Campbell, Dan Hampton", "url": "https://resolver.caltech.edu/CaltechTHESIS:04182025-222026361", "creators": [ { "name": { "family": "Senear", "given": "Allen Eugene" }, "id": "Senear-Allen-Eugene", "display_name": "Senear, Allen Eugene" } ], "advisors": [ { "name": { "family": "Koepfli", "given": "Joseph Blake" }, "id": "Koepfli-J-B", "role": "advisor", "display_name": "Koepfli, Joseph Blake" }, { "name": { "family": "Campbell", "given": "Dan Hampton" }, "id": "Campbell-D-H", "role": "co-advisor", "display_name": "Campbell, Dan Hampton" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gr2p-1187", "abstract": "Soon after the start of the war with Japan in 1941 it became apparent that one of the most pressing medical problems facing the United States was the control of malaria. The early conquests by Japan in the Dutch East Indies interfered with the use of quinine for the control of this disease, since the major world production centers of the alkaloid were under enemy control. At the same time it was obvious that much of the fighting would take place in highly malarial regions, especially in the South Pacific Ocean.
\r\n\r\nThe synthetic drugs which were available for use against malaria were relatively new and untried. Atebrin was very promising but there were various unpleasant effects attending its use, and it was not certain that it could completely replace quinine. Plasmochin, although extremely active, was of little use as a general drug, due to its great toxicity. Neither of these drugs, nor for that matter quinine itself, acted as a causal prophylactic, a property which would have been extremely desirable in a drug.
\r\n\r\nIn this emergency the Committee on Medical Research of the Office of Scientific Research and Development sponsored a large program of research on malaria. One branch of this program was concerned with testing a large number of drugs for possible antimalarial activity, in the hope of finding new classes of active compounds, of discovering more active members of classes of known activity, and possibly of finding a causal prophylactic. To assist this phase of the program the Survey on Antimalarial Drugs was set up to test the available compounds. Most of the drugs tested were examined for activity against avian malaria, although certain compounds which showed exceptional promise were tried out in human malaria. The two tests used most frequently were for activity against P. lophurae in ducks, and against P. gallinaceum in\r\nchicks.
\r\n\r\nMany of the drugs which were pasted in this program were compounds immediately available, from the shelves of chemical manufacturers, pharmaceutical houses, etc. In addition a great deal of work in synthetic organic chemistry was sponsored to provide new drugs for testing. This thesis describes a number of syntheses carried out by the author between September 1942 and December 1945, working under a contract between the Office of Scientific Research and Development and the California Institute of Technology. This project waw under the direction of Dr. Joseph B. Koepfli.
\r\n\r\nBeing carried out as part of a war research program, this work differs in several respects from the type of work usually described in a thesis. Since the primary object was to prepare the desired compounds as quickly as possible in a given quantity, it was not always necessary to examine reactions critically for conditions of maximum yield and ease of working. If a reaction took place with a low yield, it was often quicker to carry it out several times than to try to find conditions under which the yield might be improved. In several cases interesting side reactions were not iced; these were ignored unless the by-products formed seemed to have a direct bearing on the problem at hand.
\r\n\r\nIn addition the work often took on a cooperative aspect, with several members of the project working simultaneously on the same problem and even, on occasion, on the same reaction. In so far as possible I have endeavored to acknowledge assistance with particular problems in the body of this report.
\r\n\r\nThe details of the pharmacological action of the compounds whose preparation is described are not discussed. It is the intention of the Survey on Antimalarial Drugs to publish a monograph in which the activities of all the compounds tested will be given. The number designated by SN given following the compounds in this thesis is the number by which these compounds will be designated in the report of the Survey.
" }, { "name": "Shand, Wiliam, Jr.", "degree": "PhD", "year": "1946", "title": "Part I. Some Investigations of Molecular Structures by the Electron Diffraction Method. Part II. On the Ultraviolet Absorption Spectrum of Ozone", "advisor": "Schomaker, Verner F.; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122025-214739895", "creators": [ { "name": { "family": "Shand", "given": "Wiliam, Jr." }, "id": "Shand-Wiliam", "display_name": "Shand, Wiliam, Jr." } ], "advisors": [ { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "advisor", "display_name": "Schomaker, Verner F." }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jx27-6t41", "abstract": "No abstract." }, { "name": "Bryden, John H.", "degree": "Masters", "year": "1945", "title": "Inhibition of the Precipitin Reaction by Optically Active Haptens and by Derivatives of the Homologous Hapten", "advisor": "Pressman, David", "url": "https://resolver.caltech.edu/CaltechTHESIS:03272025-212241957", "creators": [ { "name": { "family": "Bryden", "given": "John H." }, "id": "Bryden-John-H", "display_name": "Bryden, John H." } ], "advisors": [ { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "role": "advisor", "display_name": "Pressman, David" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qq08-w397", "abstract": "The work described in this thesis is part of a program of investigation of immunological reactions being carried out at the California Institute of Technology by Drs. Linus Pauling, David Pressman, Dan H. Campbell, and others. Part I consists largely of the results reported in Paper X of the series \"The Serological Properties of Simple Substances\", published in the Journal of the American Chemical Society.
\r\n\r\nThe phenomenon of hapten inhibition was discovered by Landsteiner, when, to explain the f act that no precipitation occurred with an excess of test azoprotein, he postulated that a reaction did occur between the antibodies and the specific groups of the test antigen, but the products were soluble. A similar effect should be expected if molecules of the simple hapten were present in the solution; i.e., the amount of precipitate formed with optimum amounts of antiserum and antigen should be much less with hapten present than with antiserum and antigen alone. This effect was observed by Landsteiner.
\r\n\r\nIt was also found. that simple compounds having a structure closely similar to that of the homologous hapten would inhibit the precipitation, though to a lesser degree. This fact has been utilized in this investigation as described in Part I, using d- and \u2113-N-(\u03b1-methylbenzyl) succinamic acid, a derivative of N-benzylsuccinamic acid which closely resembles the homologous hapten, succinanilic acid. The affect of various substituents in various positions on the molecule of the homologous hapten is described in Part II.
" }, { "name": "Keilin, Bertram", "degree": "Masters", "year": "1945", "title": "I. The Attempted Synthesis of Cyclobutane from Tetramethylene Dibromide. II. Attempted New Syntheses of 1,3 Cyclobutane Dicarboxylic Acid. III. The Synthesis of Ortho and Meta Arsanilic Acid", "advisor": "Buchman, Edwin Raphael; Pressman, David", "url": "https://resolver.caltech.edu/CaltechTHESIS:04282025-201213151", "creators": [ { "name": { "family": "Keilin", "given": "Bertram" }, "id": "Keilin-Bertram", "display_name": "Keilin, Bertram" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" }, { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "role": "advisor", "display_name": "Pressman, David" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ehs6-rt06", "abstract": "No abstract." }, { "name": "Seneker, James Albert", "degree": "Masters", "year": "1945", "title": "The Preparation of Cinchoninic Acids and Related Compounds", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:04162025-230307879", "creators": [ { "name": { "family": "Seneker", "given": "James Albert" }, "id": "Seneker-James-Albert", "display_name": "Seneker, James Albert" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bb4y-j481", "abstract": "No abstract." }, { "name": "Escue, Richard Byrd, Jr.", "degree": "PhD", "year": "1944", "title": "I. The Provitamin A Content of American Whole Wheat Flour and Whole Wheat Bread. II. Isolation of Prolycopene and Pro-\u03b3-Carotene from Evonymus Fortunei. III. The Stereochemistry of Methylbixin", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:04152025-155718379", "creators": [ { "name": { "family": "Escue", "given": "Richard Byrd, Jr." }, "id": "Escue-Richard-Byrd", "display_name": "Escue, Richard Byrd, Jr." } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3yep-5p05", "abstract": "A chromatographic investigation of the carotenoid pigments\r\nof whole wheat flour has been made to establish its pro~\r\nvitamin A activity. While xanthophyll (lutein) was found to\r\npredominate, 0.02 to 0.06 milligrams of \u03b2-carotene was detected\r\nin a kilogram of flour and its identity was established\r\nby the mixed chromatogram method. Whole wheat bread was found\r\nto be even poorer in carotene. Investigations of rye flour\r\nand bread gave essentially the same qualitative and quantitative\r\nresults.
\r\n\r\nFrom one kilogram of the ripe seeds of Evonymus fortunei\r\nRehd., 11 milli-grams of prolycopene and 0.5 milligrams of \r\npro-\u03b3-carotene have been isolated.
\r\n\r\nTwo new stereoisomers of methylbixin have been obtained\r\nin crystalline form and a third has been observed in solution.\r\nVarious isomerization procedures have been tried on the four\r\ncrystalline materials and the interconversion of these isomers\r\nhas been demonstrated. A consideration of the absorption data\r\nhas been used to assign tentative configurations to the four\r\nprincipal members isolated from the methylbixin set of stereoisomers.
" }, { "name": "Golding, David Roy Vincent", "degree": "PhD", "year": "1944", "title": "I. The Heat Capacity, Heats of Transition, Fusion and Vaporization, Vapor Pressure and Entropy of 1, 1, 1, Trifluoroethane. II. Synthesis of Potential Antimalarials and Related Compounds", "advisor": "Buchman, Edwin Raphael; Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03282025-213401864", "creators": [ { "name": { "family": "Golding", "given": "David Roy Vincent" }, "id": "Golding-David-Roy-Vincent", "display_name": "Golding, David Roy Vincent" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" }, { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/he2n-hb33", "abstract": "Part of the low temperature calorimetric research program\r\nof this laboratory has been the careful detennination of the\r\nentropy of simple compounds in which hindered rotation about\r\nsingle bonds would be expected and for which straightforward\r\nand reliable statistical mechanical calculations can be made. Of the compounds available, ethane and similar molecules with two symmetrical groups on a common axis seem best suited for study both because of their convenient boiling points and because their configurations and normal frequencies can be readily determined. The existence of a barrier of about 3000 cal/mole hindering internal rotation in ethane was established by Kemp and Pitzer and Kistiakowsky, Lacher and Stitt." }, { "name": "Grossberg, Allan Louis", "degree": "Masters", "year": "1944", "title": "Precipitin and Hapten Inhibition Reactions in Serological Systems Involving Simple Chemical Substances of Known Constitution", "advisor": "Pauling, Linus; Pressman, David", "url": "https://resolver.caltech.edu/CaltechTHESIS:04022025-184440823", "creators": [ { "name": { "family": "Grossberg", "given": "Allan Louis" }, "id": "Grossberg-Allan-Louis", "display_name": "Grossberg, Allan Louis" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "role": "advisor", "display_name": "Pressman, David" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jqt2-xs50", "abstract": "No abstract." }, { "name": "Martin, Don Stanley", "degree": "PhD", "year": "1944", "title": "Investigations of the Removal of the Toxic Gases, Arsine and Phosgene, from Gas-Air Mixtures by Impregnated Charcoals, Using the Radioactive Indicator Method", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12192007-093234", "creators": [ { "name": { "family": "Martin", "given": "Don Stanley" }, "id": "Martin-Don-Stanley", "display_name": "Martin, Don Stanley" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/J4FA-ZA04", "abstract": "No abstract submitted.\r\n\r\n" }, { "name": "Sargent, Herbert", "degree": "PhD", "year": "1944", "title": "I. The Constitution of Naphthenic Acids. II. Heterocyclic Nitrogen and Sulfur Studies. III. The Structure of Pirylene", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:04122025-010458038", "creators": [ { "name": { "family": "Sargent", "given": "Herbert" }, "id": "Sargent-Herbert", "display_name": "Sargent, Herbert" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b94m-8w06", "abstract": "The preparation of 4-methyl-5-(hydroxymethyl)-thiazole by several different methods has been investigated. It may conveniently be obtained by a two-step synthesis starting from chloroacetone.
\r\nThe thiamin analog was prepared from 4-methyl-5 (hydroxymethyl)-thiazole and found to be completely devoid of vitamin activity when tested with Phycomyces Blakesleeanus and with rats.
\r\nThe effects of acetyl choline, histamine, atropine and adrenaline on the long muscles of the Sea Cucumber and on lobster intestine were investigated.
\r\nLobsters can be passively and actively sensitized to ovalbumen and upon anaphylaxis a substance is given off into their blood stream that causes guinea pig small intestine to contract. This substance could very well be histamine.
" }, { "name": "Waser, J\u00fcrg", "degree": "PhD", "year": "1944", "title": "I. A Survey of Structure Determinations of Organic Molecules by Diffraction Methods. II. An Electron Diffraction Investigation of Biphenylene. III. The Crystal Structure of Biphenylene. IV. On Arsenomethane. V. On the Radial Distribution Method in Electron Diffraction", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-08202007-110657", "creators": [ { "name": { "family": "Waser", "given": "J\u00fcrg" }, "id": "Waser-J\u00fcrg", "display_name": "Waser, J\u00fcrg" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/G9WG-4K63", "abstract": "No abstract ." }, { "name": "Felbeck, George Theodore", "degree": "PhD", "year": "1943", "title": "The Rate of Thermal Diffusion in Mixtures of Carbon Dioxide and Hydrogen", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:01242017-150443602", "creators": [ { "name": { "family": "Felbeck", "given": "George Theodore" }, "id": "Felbeck-George-Theodore", "display_name": "Felbeck, George Theodore" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1901-1751", "abstract": "An equation is derived for the time rate\r\nof change of composition of a binary gas mixture\r\nof initially uniform composition by thermal diffusion\r\nin an apparatus consisting of two chambers,\r\none above the other, connected by a straight tube.\r\nThe upper chamber is held at a given constant high\r\ntemperature and the lower chamber at a given constant\r\nlower temperature.
\r\n\r\nUsing the thermal conductivity method of\r\nanalysis the rate of change of composition in\r\nthe lower chamber has been measured for carbon\r\ndioxide-hydrogen mixtures for various compositions,\r\npressures and higher temperatures.
\r\n\r\nFrom the experimental results and the derived\r\nequation, values are determined for the\r\nthermal diffusion coefficient, the ordinary or\r\nconcentration diffusion coefficient and the\r\ntemperature exponent for these coefficients.
\r\n\r\n\r\n " }, { "name": "Lemmon, Richard Millington", "degree": "Masters", "year": "1943", "title": "Contributions to the Stereochemistry of Cryptoxanthin and Zeaxanthin", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:03062024-211843082", "creators": [ { "name": { "family": "Lemmon", "given": "Richard Millington" }, "id": "Lemmon-Richard-Millington", "display_name": "Lemmon, Richard Millington" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bbt8-2m16", "abstract": "[Summary]
\r\n\r\n1. The stereoisomerization of cryptoxanthin was studied under the\r\ninfluence of iodine catalysis at room temperature, melting the crystals,\r\nrefluxing and irradiation. Two new stereoisomers of cryptoxanthin were\r\ndetected, one of which, neo-cryptoxanthin U, is adsorbed above all-trans-cryptoxanthin\r\non the Tswett column.
\r\n\r\n2. Molecular extinction curves were taken in the region from 320 to\r\n380 m\u00b5. for all-trans-cryptoxanthin, three of its stereoisomers, and the\r\ncryptoxanthin iodine-catalyzed equilibrium mixture of stereoisomers.
\r\n\r\n3. The stereoisomerization of zeaxanthin was studied under the influence\r\nof melting the crystals, refluxing and irradiation. Three new\r\nstereoisomers of zeaxanthin were detected, two of which appear below all-trans-\r\nzeaxanthin on the Tswett column.
" }, { "name": "McNeely, William Harold", "degree": "PhD", "year": "1943", "title": "I. Contribution to the Stereochemistry of Stilbenes by Application of Chromatographic Methods. II. Separation of Some Cis- and Trans-Oximes by Means of the Chromatographic Brush Method. III. Chromatographic Isolation of Homopterocarpin and Vanillin from Red Sandalwood. IV. Model Experiments Directed Toward the Synthesis of Quinine", "advisor": "Zechmeister, Laszlo; Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012017-104146897", "creators": [ { "name": { "family": "McNeely", "given": "William Harold" }, "id": "McNeely-William-Harold", "display_name": "McNeely, William Harold" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" }, { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R6H2-GN02", "abstract": "Part I.
\r\n\r\nThe chromatographic brush method, with permanganate as brush reagent, \r\nhas been used for the detection, separation and estimation of the\r\ncis- and trans-forms of stilbene, p-methylstilbene and p-methoxystilbene.\r\nIn a mixture composed of two stereoisomeric compounds, 1-2% of either form\r\ncan be detected. The method can be used for the study of the interconversion\r\nof stilbene cis- and trans-isomers. Fluorescent contaminants can\r\nbe removed by chromatography in ultraviolet light.
\r\n\r\nPart II.
\r\n\r\nThe chromatographic brush method, with an ammoniacal copper solution\r\nas color reagent, has been used for the detection and separation of\r\ncis- and trans-benzoin and anisoin oximes on Neutrol Filtrol columns.\r\nIn a mixture composed of two stereoisoraers, 1-2% of either form can be\r\nrapidly detected in the presence of the other. Some data concerning the\r\ninterconversion of stereoisomeric oximes is given, and the influence of\r\nthe adsorbent on the cis-trans shift is discussed.
\r\n\r\nPart III.
\r\n\r\nA preliminary chromatographic investigation of some colorless\r\nconstituents of red sandalwood has been carried out. The chromatographic\r\nisolation and purification of homopterocarpin and vanillin \r\nis described
\r\n\r\nPart IV.
\r\n\r\nModel experiments directed towards the synthesis of quinine\r\nhave been carried out.
" }, { "name": "Pardee, Arthur Beck", "degree": "Masters", "year": "1943", "title": "Hapten Inhibition of Precipitation of Antisera Specific to the p-Azophenylarsonic Acid Group, the p-(p-Azophenylazo) Phenylarsonic Acid Group, and the p-Azophenylmeylarsinic Acid Group", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:03192025-182405303", "creators": [ { "name": { "family": "Pardee", "given": "Arthur Beck" }, "id": "Pardee-Arthur-Beck", "display_name": "Pardee, Arthur Beck" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ga0t-gq17", "abstract": "No abstract." }, { "name": "Schroeder, Walter Adolph", "degree": "PhD", "year": "1943", "title": "Studies of \u03b3-Carotene and Related Carotenoids: I. \u03b3-Carotene. II. Pro-\u03b3-Carotene. III. Gazaniaxanthin. IV. Micro-Determinations of the Isopropylidene Group in Carotenoids", "advisor": "Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:03142025-023952435", "creators": [ { "name": { "family": "Schroeder", "given": "Walter Adolph" }, "id": "Schroeder-Walter-Adolph", "display_name": "Schroeder, Walter Adolph" } ], "advisors": [ { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ftdt-0v09", "abstract": "A series of investigations have been carried out with \u03b3-carotene and related carotenoids.
\r\nIn \u201cmonkey flowers\u201d (Mimulus longiflorus) a carotenoid occurs which apparently differs only in melting point from \u03b3 -carotene described \"by Kuhn and Brockmann. The available evidence indicates that this compound is indeed \u03b3-carotene but the cause of the melting point difference remains anomalous.
\r\nA new carotenoid, the second of its type, possessing four to five cis double bonds in the molecule has been isolated from the fruit of Butia capitata and Pyracantha angustifolia and its properties described. The compound, a hydrocarbon, has been termed pro- \u03b3 -carotene because of its relation to \u03b3 -carotene. Its most remarkable property is the almost instantaneous change in the spectrum upon treatment with iodine. The change is caused by the formation of a mixture of stereoisomors of the carotenoid, in which the all trans form predominates but in which the pro-carotenoid is absent. The stereoisomerization of pro-\u03b3-carotene under the influence of several catalysts and experimental conditions has been studied chromatographically.
\r\nExperiments with gazaniaxanthin, discovered by Schor in the flowers of Gazania rigens, have indicated that this carotenoid is dihydro-rubixanthin. The stereoisomerization of the compound has been studied but the chromatographic separation of the stereoisomers is extremely difficult. The spectral curve of the substance exhibits the \u201ccis peak\" phenomenon on isomerization.
\r\n\r\nIsopropylidene determinations by ozonolysis have been carried out with a number of carotenoids. Gazaniaxanthin, which probably possesses an isopropyl group, behaves as if about 0.9 \u201cisopropylidene\u201d group were present while \u03b2-carotene seemingly possesses 0.3 \u201cisopropylidene.\u201d These results have been correlated with the fact that the method is known to indicate the presence of some \u201cisopropylidene\u201d when an isopropyl group is present.
" }, { "name": "Swingle, Stanley Morse", "degree": "PhD", "year": "1943", "title": "Part I. Electron Diffraction Investigations of the Structures of Some Fifth Group Halides and of Quinine. Part II. Precipitation Reactions Between Antibodies and Benzoic Acid Derivatives. Part III. The Construction and Operation of a Tiselius Electrophoresis Apparatus", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:03132025-204054395", "creators": [ { "name": { "family": "Swingle", "given": "Stanley Morse" }, "id": "Swingle-Stanley-Morse", "display_name": "Swingle, Stanley Morse" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/55xs-a959", "abstract": "No abstract." }, { "name": "Wagner, Charles Daniel", "degree": "PhD", "year": "1943", "title": "I. An Attempt to Determine the Absolute Configurations of \u03b1-D-Glucose and \u03b2-d-Glucose. II. The Synthesis of dl-1,2-Octadecanediol and Several of its Homologues. III. The Relation of Chemical Structure to Thyroxine-Like Activity; The Role of the Side-Chain and the Hydroxyl", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-180543872", "creators": [ { "name": { "family": "Wagner", "given": "Charles Daniel" }, "id": "Wagner-Charles-Daniel", "display_name": "Wagner, Charles Daniel" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/570p-vw67", "abstract": "[No Abstract]" }, { "name": "Cooley, Robert Alonzo", "degree": "PhD", "year": "1942", "title": "Applications of Isotopes to Chemical Problems", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282025-030335813", "creators": [ { "name": { "family": "Cooley", "given": "Robert Alonzo" }, "id": "Cooley-Robert-Alonzo", "display_name": "Cooley, Robert Alonzo" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4z8b-7161", "abstract": "In the first part of this thesis is described research in nuclear physics on radioactive isotopes of barium, cesium, and bismuth. Isotopes of barium and cesium were chemically identified and their properties were determined.
\r\n\r\nThe second part consists of studies of exchange reactions involving the following radioactive elements: sulfur, phosphorus, bromine, iodine, and vanadium. Rate of reaction measurements were made. The kinetics of the exchanges were considered, and interpretation of the exchanges in terms of the structure and nature of the reactants was made where possible.
\r\n\r\nThe solution of a problem for the National Defense Research Committee, which is of a confidential nature, is submitted as the third part of this thesis.
\r\n\r\nThe fourth part contains miscellaneous studies. The structural parameters of thionyl bromide were determined by electron diffraction experiments. Experience was gained in rare earth inorganic chemistry by preparative work and observations on the very interesting bivalent state of europium.
" }, { "name": "Mead, James Franklyn", "degree": "PhD", "year": "1942", "title": "I. The Benzylation of Carbohydrates. II. The Preparation of Fluorinated Analogues of Tyrosine and Thyronine. III. The Preparation of Isomers and Analogues of Thyroxine with Relation to a Proposed Hypothesis of the Relationship Between Structure and Thyroxine-Like Activity. IV. A Carotenoid from Bovine Spinal Cord. V. Studies on the Structure of Sphingosine. VI. The Length Muscles of the Holothurians (a Summary)", "advisor": "Niemann, Carl G.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10062017-104405641", "creators": [ { "name": { "family": "Mead", "given": "James Franklyn" }, "id": "Mead-James-Franklyn", "display_name": "Mead, James Franklyn" } ], "advisors": [ { "name": { "family": "Niemann", "given": "Carl G." }, "id": "Niemann-C-G", "role": "advisor", "display_name": "Niemann, Carl G." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MND7-0F42", "abstract": "Part I
\r\n\r\n\r\nA new method for the determination of the structure of \r\npolysaccharides has been proposed. A method for the benzylation of\r\nsugars has been found, since the benzylation of the polysaccharides\r\nis necessary as the first step in the proposed method.
\r\n\r\n\r\nPart II
\r\n\r\n\r\nIn connection with the physiological action of organic fluorine\r\ncompounds, a number of fluorinated amino acids have been prepared.\r\nThe synthesis of 3-fluoro-dl-tyrosine, 3-fluoro-5-iodo-dl-tyrosine,\r\n3-fluoro-dl-phenlalanine, 3'-fluoro-dl-thyronine, 3'-fluoro-3,5-\r\ndiiodo-dl-thyronine and 3'-fluoro-5'-iodo-3,5-diiodo-dl-thyronine\r\nhas been described.
\r\n\r\n\r\nIn connection with the synthesis of 3,5-difluoro-dl-thyronine,\r\nthe preparation of the necessary starting materials has been\r\ndescribed.
\r\n\r\n\r\nPart III
\r\n\r\n\r\nThe synthesis of dl-3,5-diiodo-4-(3',5'diiodo-2'-hydroxy-phenoxy)-phenylalanine,\r\nan isomer of thyroxine, is described. This \r\ncompound is physiologically active, the activity being approximately\r\none twenty-fifth of that of dl-thyroxine. This finding is in accordance\r\nwith a prediction relating thyroxine-like activity to chemical structure.
\r\n\r\n\r\nThe attempted synthesis of dl-diiodo-4-(3',5'-diiodo-4'-\r\naminophenoxy)-phenylalanine is described.
\r\n\r\n\r\nPart IV
\r\n\r\nThe separation of the carotenoid, \u03b2-carotene, from bovine\r\nspinal cord is described.
\r\n\r\n\r\nPart V
\r\n\r\n\r\nThe separation of large amounts of cerebrodise-sphinogomylin\r\nfraction from bovine spinal cord is described. The separation of\r\nsphingosine and sphingosine derivatives, and reactions proposed to\r\nlead to a determination of the structure of sphingosine are given.
" }, { "name": "Baumgarten, Werner", "degree": "PhD", "year": "1941", "title": "I. The Reduction of Tartaric Acid. II. The Heats of Combustion of Anhydrous Oxalic Acid, Malonic Acid, dl-Malic Acid, Glutaric Acid, Adipic Acid, Azelaic Acid and Sebacic Acid", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112025-190035731", "creators": [ { "name": { "family": "Baumgarten", "given": "Werner" }, "id": "Baumgarten-Werner", "display_name": "Baumgarten, Werner" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/h6tg-a563", "abstract": "No abstract." }, { "name": "Burcik, Emil Joseph", "degree": "PhD", "year": "1941", "title": "Heat Capacity of Gases by the Adiabatic Expansion Method", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02112025-212518614", "creators": [ { "name": { "family": "Burcik", "given": "Emil Joseph" }, "id": "Burcik-Emil-Joseph", "display_name": "Burcik, Emil Joseph" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fjb0-rt16", "abstract": "The theory of adiabatic expansions is given and an apparatus for\r\nthe measurement of gaseous heat capacities by this method is described.\r\nAs here applied the method is relative, involving a comparison with a\r\nstandard gas, nitrogen. The heat capacities of oxygen, carbon dioxide,\r\nboron trifluoride, cyanogen, sulfur dioxide, ethylene, difluorodichloromethane,\r\nfluorotrichloromethane, sulfuryl fluoride, and phosphorus trifluoride\r\nfound at temperatures ranging from 0\u00b0 to 57\u00b0 are compared with\r\nthose reported by earlier investigators and with those derived from molecular\r\ndata. In general the agreement is good to within 0.5%, but for\r\nsulfur dioxide and phosphorus trifluoride there are discrepancies between\r\nthe observed and calculated values of about 3% and 8%, respectively.\r\nThe difficulty with sulfur dioxide may possibly arise from an error in\r\nthe equation of state, but the phosphorus trifluoride discrepancy stands\r\nquite without explanation." }, { "name": "Farquhar, John Percival", "degree": "Masters", "year": "1941", "title": "An Investigation of the Synthesis of \"Pirylene\"", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:02102025-185855030", "creators": [ { "name": { "family": "Farquhar", "given": "John Percival" }, "id": "Farquhar-John-Percival", "display_name": "Farquhar, John Percival" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zgmr-qz28", "abstract": "No abstract." }, { "name": "Fischer, James Rodney", "degree": "Masters", "year": "1941", "title": "The Preparation of Methylene Cyclobutane and Methyl \u0394' Cyclobutane", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:02102025-210337743", "creators": [ { "name": { "family": "Fischer", "given": "James Rodney" }, "id": "Fischer-James-Rodney", "display_name": "Fischer, James Rodney" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mdp4-fq82", "abstract": "No abstract." }, { "name": "Rasmussen, Robert Severin", "degree": "PhD", "year": "1941", "title": "I. Studies of Some Absorption Spectra in the Photographic Infrared. II. Studies of the Hydrogen Bond. III. The Raman Spectra of CCl\u2082F-CClF\u2082 and CClF\u2082-CClF\u2082", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:03122025-214929725", "creators": [ { "name": { "family": "Rasmussen", "given": "Robert Severin" }, "id": "Rasmussen-Robert-Severin", "display_name": "Rasmussen, Robert Severin" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/216h-k397", "abstract": "Absorption of formaldehyde and difluoro-methane under low dispersion in the photographic infra-red region is described, and approximate vibrational assignments made. An attempt was made to study some of the bands of difluoro-methane under high dispersion, but does not yield much information. The C-H band of formic acid monomer photographed under high dispersion is discussed. It has the same rotational structure as the 0-E bands. The small moment of inertia is calculated. for the third C-H vibrational state, and the band origin located.
" }, { "name": "Rogers, Max Tofield", "degree": "PhD", "year": "1941", "title": "I. The Crystal Structures of Iodic Acid and of Potassium Oxyfluoiodate, and the Redetermination of the Parameters in Potassium Difluoride and Ammonium Bifluoride. II. The Internuclear Distance in the Fluorine Molecule and the Electron Diffraction Investigation of Tellurium Dibromide. III. The Determination of the Magnetic Anisotropy of Crystals", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03112025-165720350", "creators": [ { "name": { "family": "Rogers", "given": "Max Tofield" }, "id": "Rogers-Max-Tofield", "display_name": "Rogers, Max Tofield" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zfqp-wg97", "abstract": "No abstract." }, { "name": "Rundle, Robert Eugene", "degree": "PhD", "year": "1941", "title": "I. The Crystal Structures of Trimethyl Platinum Chloride and Tetramethyl Platinum. II. The Electron Diffraction Investigation of Dimethyl Sulfone, Dimethyl Sulfoxide, and Trimethyl Amine Oxide. III. The Heat Capacity and Entropy of Arsenic Trifluoride", "advisor": "Sturdivant, James Holmes", "url": "https://resolver.caltech.edu/CaltechTHESIS:02232025-005122458", "creators": [ { "name": { "family": "Rundle", "given": "Robert Eugene" }, "id": "Rundle-Robert-Eugene", "display_name": "Rundle, Robert Eugene" } ], "advisors": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-J-H", "role": "advisor", "display_name": "Sturdivant, James Holmes" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5ytm-8s13", "abstract": "All reported structures of tetravalent platinum compounds have involved octahedral coordination about platinum. Presumably, however, tetravalent platinum is capable of forming d2sp tetrahedral bonds, and the organo-platinum compounds, tetramethyl platinum and hexamethyl diplatinum, prepared by Gilman and Lichtenwalter were expected to have this configuration. In order to establish their structure and., if possible, to determine the tetrahedral radius of platinum, the X-ray study of these compounds was undertaken.
\r\nIt early became necessary, however, to alter the plan of this research. Isolated tetrahedral molecules in the required number could not be packed into the observed unit cell of tetramethyl platinum. In addition the observed intensities, together with space group considerations, led to two non-equivalent sets of positions for the platinum atoms with identical structure factors. Finally, the scattering of the methyl groups was nearly negligible relative to ths.t of the platinum atoms. As a result neither chemical reasoning nor X-ray data permitted further progress. Fortunately some incomplete observations of Cox and Webster led to the discovery that trimethyl platinum chloride has a structure similar to that of tetramethyl platinum. In the structure of trimethyl platinum chloride the chlorine atoms could be located with some accuracy, and the platinum arrangement could be determined uniquely. This latter structure determination will therefore be discussed before the presentation of the results on tetramethyl platinum.
" }, { "name": "Russell, Horace, Jr.", "degree": "PhD", "year": "1941", "title": "Some Molecular Data from Raman Spectra, Electron Diffraction and Low Temperature Colorimetry", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282025-000015219", "creators": [ { "name": { "family": "Russell", "given": "Horace, Jr." }, "id": "Russell-Horace-Jr.", "display_name": "Russell, Horace, Jr." } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cv71-j597", "abstract": "No abstract." }, { "name": "Schlatter, Maurice Jay", "degree": "PhD", "year": "1941", "title": "I. The Isomeric 2,3-Epoxypentanes and 2-Pentanes. The Extent to Which Mixtures of Diastereomers are Formed in Reactions of Some Pentane Compounds. II. The Preparation of Cyclopropane. III. The Thermal Decomposition of Trans-1,2-Cyclobutane-Bis(Trimethylammonium) Hydroxide", "advisor": "Buchman, Edwin Raphael", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282025-211013383", "creators": [ { "name": { "family": "Schlatter", "given": "Maurice Jay" }, "id": "Schlatter-Maurice-Jay", "display_name": "Schlatter, Maurice Jay" } ], "advisors": [ { "name": { "family": "Buchman", "given": "Edwin Raphael" }, "id": "Buchman-E-R", "role": "advisor", "display_name": "Buchman, Edwin Raphael" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9txa-0p49", "abstract": "No abstract." }, { "name": "Spitzer, Ralph William", "degree": "PhD", "year": "1941", "title": "I. Thermal Data on Some Cyclic Hydrocarbons. II. The Electron Diffraction Investigation of Molecular Structure of Silicon Tetrabromide, Tribromosilane and Difluorodibromosilane", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-09102004-145749", "creators": [ { "name": { "family": "Spitzer", "given": "Ralph William" }, "id": "Spitzer-Ralph-William", "display_name": "Spitzer, Ralph William" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JF44-NK50", "abstract": "No Abstract Submitted." }, { "name": "Stewart, William Thomas", "degree": "PhD", "year": "1941", "title": "I. The Rate of Hydration of beta-Methylcrotonaldehyde; the Equilibrium between beta-Methylcrotonaldehyde and beta-Hydroxyisovaleraldehyde in Dilute Aqueous Solution. II. Esters of Alginic Acid. III. Oxidation of Alginic Acid by Periodic Acid. IV. A Chromatographic Study of Lignite", "advisor": "Lucas, Howard J.; Zechmeister, Laszlo", "url": "https://resolver.caltech.edu/CaltechTHESIS:03042025-233656031", "creators": [ { "name": { "family": "Stewart", "given": "William Thomas" }, "id": "Stewart-William-Thomas", "display_name": "Stewart, William Thomas" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." }, { "name": { "family": "Zechmeister", "given": "Laszlo" }, "id": "Zechmeister-L", "role": "advisor", "display_name": "Zechmeister, Laszlo" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hjh4-g938", "abstract": "This study is one of a series1,2,3,4,5 undertaken to determine the effect of various substituents on the heat of hydration of the ethylenic double bond. Data have been collected in an endeavor to correlate structural effects with hydration and dehydration reaction velocities, activation energies and heats of hydration.
\r\n\r\nSince the heats of hydration of crotonaldehyde3, crotonic acid4 and \u03b2-methylcrotonic acid5 have been determined, it was desirable to study the hydration of \u03b2-methylcrotonaldehyde and its equilibrium with \u03b2-hydroxyisovaleraldehyde. No reference has been found regarding the hydration of \u03b2-methylcrotonaldehyde nor has the hydrated compound, \u03b2-hydroxyisovaleraldehyde, been reported in the literature.
\r\n\r\nThe heat of hydration was conveniently determined from equilibria between the hydrated and dehydrated compounds in dilute aqueous nitric acid at several different temperatures. Activation energies were obtained from the equilibrium and kinetic constants of the hydration and dehydration reactions.
" }, { "name": "Wahrhaftig, Austin Levy", "degree": "PhD", "year": "1941", "title": "The Absorption Spectrum of Chlorine Fluoride in the Region \u03bb\u03bb4650-5200A. The Electron Diffraction Investigation of Chlorine Fluoride and Chlorine Trifluoride", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10312023-173840321", "creators": [ { "name": { "family": "Wahrhaftig", "given": "Austin Levy" }, "id": "Wahrhaftig-Austin-Levy", "display_name": "Wahrhaftig, Austin Levy" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jm8w-mj73", "abstract": "[No Abstract]" }, { "name": "Carter, Robert-Trissel", "degree": "Bachelors", "year": "1940", "title": "The Phase Behavior of the Methane-Propane-N-Pentane System", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:01042025-030856648", "creators": [ { "name": { "family": "Carter", "given": "Robert-Trissel" }, "id": "Carter-Robert-Trissel", "display_name": "Carter, Robert-Trissel" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/f0mm-3b35", "abstract": "The composition of the coexisting gas and liquid phases in the ternary system consisting of methane, propane, and normal pentane was determined at 100\u00b0 F. and at pressures of 200, 500, 1000, 1500, and 2000 pounds per square inch. From these data the values of equilibrium constants for methane, propane, and pentane were calculated.
\r\nThe actual phase behavior of the ternary system is compared to the phase behavior predicted from Raoult's Law and to the predictions made from a correlation of previously available data.
" }, { "name": "Dekker, Albert Ono", "degree": "PhD", "year": "1940", "title": "The Kinetics of Selected Chemical Reactions", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012025-021940281", "creators": [ { "name": { "family": "Dekker", "given": "Albert Ono" }, "id": "Dekker-Albert-Ono", "display_name": "Dekker, Albert Ono" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/790m-hn87", "abstract": "PART I
\r\n\r\nThe Oxidation of Ascorbic Acid by Oxygen with Cupric Ion as Catalyst
\r\n\r\nThe initial rate of the reaction was found to be directly proportional to the concentrations of cupric ion and ascorbic acid and inversely proportional to the square of the hydrogen ion concentration. These facts have been explained by the assumption that in the initial stages the ascorbate ion is oxidized by the cupric ion to an ion with a semiquinone-like structure, which is rapidly oxidized by oxygen to dehydroascorbic acid. The cupric ion concentration is maintained constant through oxidation by oxygen of the cuprous ion formed. An observed increase in the specific reaction rate during the course of the reaction is attributed to the accumulation of hydrogen peroxide formed through oxidation of cuprous ion by oxygen.
\r\n\r\nIt was found that in the absence of oxygen an equilibrium involving ascorbic acid and cupric ion as well as dehydroascorbic acid, cuprous ion, and hydrogen ion, is apparently attained. However, the results of some of the numerous experiments carried out in an attempt to measure the equilibrium cast some doubt on the reliability of the equilibrium constants determined.
\r\n\r\nPART II
\r\n\r\nThe- Photochemical Formation of Sulfuryl Chloride from Sulfur\u00b7 Dioxide and Chlorine
\r\n\r\nIt was found that the photochemical formation of sulfuryl chloride from sulfur dioxide and chlorine proceeds at an immeasurably slow rate when the gases are dry. It was, however, found that if the vessel walls are wet with pure sulfuric acid the formation of sulfuryl chloride takes place at a slow but measurable rate. The effect of moisture on the rate, which had been observed by earlier workers, is explained in terms of the effect of the sulfuric acid produced by the reaction of water with chlorine and sulfur dioxide. Stationary states for the photochemical reaction are compared with the thermal equilibria.
\r\n\r\nPART III
\r\n\r\nThe Thermal Isomerization of Dimethyl Maleate Catalyzed by Iodine
\r\n\r\nRates of isomerization of dimethyl maleate in cyclohexane solution and employing iodine as a catalyst were measured. Although these rates fluctuated to a considerable extent, the kinetics appear to be compatible with an iodine atom catalysis plus a catalysis or inhibition due to some as yet undetermined factor.
" }, { "name": "Doescher, Russell Nimtz", "degree": "PhD", "year": "1940", "title": "The Heat Capacities and Entropy of Dimethyl Sulphide and of Fluorotrichloromethane. The Preparation of Boron Trichloride", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:12082024-125122031", "creators": [ { "name": { "family": "Doescher", "given": "Russell Nimtz" }, "id": "Doescher-Russell-Nimtz", "display_name": "Doescher, Russell Nimtz" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/23zx-q159", "abstract": "No abstract." }, { "name": "Gould, Clark Webster, Jr.", "degree": "Masters", "year": "1940", "title": "Stereochemical Relationships of the Isomeric 3 Chloro 2 Butanols and the 2,-3-Dichlorobutanes", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12082024-135314029", "creators": [ { "name": { "family": "Gould", "given": "Clark Webster, Jr." }, "id": "Gould-Clark-Webster", "display_name": "Gould, Clark Webster, Jr." } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/px28-mz96", "abstract": "No abstract." }, { "name": "Heegaard, Erik Vilhelm", "degree": "Masters", "year": "1940", "title": "Studies on the Relation Between Intake and Urinary Excretion of Thiamin in Normal Man", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01212025-223602853", "creators": [ { "name": { "family": "Heegaard", "given": "Erik Vilhelm" }, "id": "Heegaard-Erik-Vilhelm", "display_name": "Heegaard, Erik Vilhelm" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/23wg-vy77", "abstract": "No abstract." }, { "name": "Howell, William Jasper, Jr.", "degree": "Masters", "year": "1940", "title": "The Electron Diffraction Investigation of Difluorodibromosilane", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:12162024-192243872", "creators": [ { "name": { "family": "Howell", "given": "William Jasper, Jr." }, "id": "Howell-William-Jasper", "display_name": "Howell, William Jasper, Jr." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qaq8-fs39", "abstract": "The electron diffraction investigations of the halides of the fourth, fifth, and sixth group elements (1) have shown many interatomic distances to be shorter than those given by Pauling and Huggins\u2019 table of empirical covalent bond radii (2), representing the distances between atoms in pure single bonds in the elements and in other bonds that have considerable ionic character. In the silicon fluorides, which are usually written formally as containing four t-wo-electron bonds, large shortenings occur, and in SiF4, in which the interatomic distance is 5% less than that corresponding to a pure double bond, the explanation of anomalous shortenings applied by Brockway to the fluorochloromethanes (3) breaks down. This laboratory\r\nhas undertaken careful electron diffraction studies of substances showing these unexpected shortenings in the hope that improved explanations may result from a larger accumulation of data. At present, for example, some explanations require postulating sets of resonance structures which altogether give to the atoms reversed orders of electronegativities which disagree with values obtained from electric moments and ionic resonance energies.
" }, { "name": "Lu Valle, James Ellis", "degree": "PhD", "year": "1940", "title": "An Electron-Diffraction Investigation of Several Unsaturated Conjugated Molecules", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-04272004-162550", "creators": [ { "name": { "family": "Lu Valle", "given": "James Ellis" }, "id": "Lu-Valle-James-Ellis", "display_name": "Lu Valle, James Ellis" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "chair", "display_name": "Pauling, Linus" }, { "name": { "family": "Schomaker", "given": "Verner F." }, "id": "Schomaker-V-F", "role": "member", "display_name": "Schomaker, Verner F." }, { "name": { "family": "Stevenson", "given": "David P." }, "id": "Stevenson-D-P", "role": "member", "display_name": "Stevenson, David P." } ], "option_major": [ "chemistry" ], "doi": "10.7907/XRRJ-7H19", "abstract": "[Summary]\r\n\r\nThe electron-diffraction investigation of formaldehyde, glyoxal, dimethylgloxal, oxalyl chloride, and vinyl ether has shown that the conjugating power of two carbon-oxygen double bonds is of the same magnitude as the conjugating power of two carbon-carbon double bonds. The criterion for the magnitude of the conjugating power is the decrease in the carbon-carbon single bond distance. The carbon-carbon single bond distance in glyoxal and dimethylgloxal is 1.47\u00c5 (lg), and the carbon-carbon single bond distance in butadiene and cyclopentadiene is 1.46\u00c5 (lh). These distances are the same within the experimental error of the determination.
\r\n\r\nThe investigation of formaldehyde (li) gave a reliable value of the carbon-oxygen double bond distance of 1.21\u00c5.
\r\n\r\nIn oxalyl chloride the carbon-carbon bond distance is only 1.50\u00c5 instead of 1.47\u00c5 as in glyoxal and dimethylgloxal (lg). The carbon-chlorine bond distance in the. same molecule is 1.72\u00c5, a shortening of of 0.04\u00c5. The value of 1.50\u00c5 may be explained by the competition of a free electron pair on the chlorine atom with the carbon-carbon single bond for the carbon-oxygen double bond.
\r\n\r\nIn vinyl ether a bond shortening of only 0.02\u00c5 in each bond or 0.04\u00c5 total shortening is reported. The shortening may be summed in this molecule as the heat of hydrogenation data(10) show that the amount of resonance in vinyl ether is the same as in ethyl vinyl ether. The shortening is due to the resonance between a tree electron pair on the oxygen atom and the two carbon-carbon double bonds. This shortening is less than that shown by the chloroethylenes(3) but the difference in electronegativity of chlorine and oxygen may well explain this fact.
\r\n\r\nThe molecules glyoxal, dimethylgloxal, oxalyl chloride and vinyl ether are all found to be coplanar and trans with the exception of oxalyl chloride in which the (COCl) groups are rotated 17\u00b0 from the trans position. The potential barrier restricting rotation in the first three molecules was found to be greater than five kcals. and it is indicated that the potential curve for oxalyl chloride will show a double minimum. No estimate was made at the potential barrier in vinyl ether.
" }, { "name": "Moore, Robert Sydney", "degree": "Masters", "year": "1940", "title": "The Association of Silver Ion with Cis and Trans Isomers", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122024-213633196", "creators": [ { "name": { "family": "Moore", "given": "Robert Sydney" }, "id": "Moore-Robert-Sydney", "display_name": "Moore, Robert Sydney" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ef8q-9k62", "abstract": "No abstract." }, { "name": "Pressman, David", "degree": "PhD", "year": "1940", "title": "The Hydration of Crotonic Acid and \u03b2, \u03b2-Dimethylacrylic Acid", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01132025-235049188", "creators": [ { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "display_name": "Pressman, David" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/p9jn-a073", "abstract": "No abstract." }, { "name": "Redemann, C. Ernst", "degree": "PhD", "year": "1940", "title": "I. A Study of the Chemistry Leading to Probable Structures for Cyameluric Acid and Some Related Compounds. II. The Diliturates of Some Physiologically Important Bases", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032025-210830379", "creators": [ { "name": { "family": "Redemann", "given": "C. Ernst" }, "id": "Redemann-C-Ernst", "display_name": "Redemann, C. Ernst" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/mdgr-fq10", "abstract": "Recently the question of the structure of cyameluric and hydromelonic acids has been reopened by Pauling and Sturdivant. It is rather surprising that cyameluric acid and related compounds, for example melon, melam, melem, and hydromelonic acid, should have received so little attention at the hands of organic chemists. With the exception of a limited amount of work by E. C. Franklin and students, the problems in this field have been neglected for many years. Since most of these compounds are insoluble both in organic solvents and in water, show neither melting nor boiling points, are inert chemically with the exception that they undergo hydrolytic cleavage, and do not yield derivatives which are readily identified, it is probable that the reasons for this neglect bear some relation to their physical and chemical properties
" }, { "name": "Russell, Charles Daniel, Jr.", "degree": "Masters", "year": "1940", "title": "Magnetochemical Structural Investigations with Particular Reference to Hemoglobin Equilibria and Compound Formation", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:01132025-221915071", "creators": [ { "name": { "family": "Russell", "given": "Charles Daniel, Jr." }, "id": "Russell-Charles-Daniel", "display_name": "Russell, Charles Daniel, Jr." } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6014-2d85", "abstract": "No abstract." }, { "name": "Beeson, Carrol Menefee", "degree": "PhD", "year": "1939", "title": "I. The Equilibrium Dissociation and Thermodynamic Constants of Nitrosyl Chloride - Comparison with Spectroscopic Data. II. The Diamagnetism of Gaseous Nitrosyl Chloride. III. The Thermodynamic Constants of Bromine Chloride. The Equilibrium Reaction Between Nitric Oxide, Bromine, Chlorine, Nitrosyl Bromide and Chloride and Bromine Chloride.", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11202024-222842843", "creators": [ { "name": { "family": "Beeson", "given": "Carrol Menefee" }, "id": "Beeson-Carrol-Menefee", "display_name": "Beeson, Carrol Menefee" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/tcbc-dm96", "abstract": "No abstract." }, { "name": "Cardwell, William Thomas, Jr.", "degree": "Masters", "year": "1939", "title": "Some Properties of the Glass Electrode, Including: The Determination of the Nature of the Asymmetry Potential, The Determination of the Effects of Aging in 0.1 N HCl and 0.1 N KOH, A New Approach to the Theory of the Glass Electrode", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12162024-215157917", "creators": [ { "name": { "family": "Cardwell", "given": "William Thomas, Jr." }, "id": "Cardwell-William-Thomas", "display_name": "Cardwell, William Thomas, Jr." } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/eerx-3896", "abstract": "No abstract." }, { "name": "Gullekson, Ellsworth Eugene", "degree": "Masters", "year": "1939", "title": "Some Fundamental Properties of Asphalts", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12112024-234645502", "creators": [ { "name": { "family": "Gullekson", "given": "Ellsworth Eugene" }, "id": "Gullekson-Ellsworth-Eugene", "display_name": "Gullekson, Ellsworth Eugene" } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/mkd6-4x08", "abstract": "No abstract." }, { "name": "Hepner, Franklin Ross", "degree": "Masters", "year": "1939", "title": "Coordination Complexes of the Mercuric Ion with Cyclohexene", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102024-211142242", "creators": [ { "name": { "family": "Hepner", "given": "Franklin Ross" }, "id": "Hepner-Franklin-Ross", "display_name": "Hepner, Franklin Ross" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6x1m-2793", "abstract": "No abstract." }, { "name": "Hinds, George Putnam, Jr.", "degree": "Masters", "year": "1939", "title": "Volumetric Behavior of Liquid Mixtures of Propane and n-Pentane", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:12122024-234649297", "creators": [ { "name": { "family": "Hinds", "given": "George Putnam, Jr." }, "id": "Hinds-George-Putnam", "display_name": "Hinds, George Putnam, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/egvm-qc39", "abstract": "No abstract." }, { "name": "Lavender, Harrison Morton, Jr.", "degree": "Masters", "year": "1939", "title": "The Pressure-Volume-Temperature Relations for the Methane-Decane System in the Liquid and Two-Phase Regions", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:12032024-210703408", "creators": [ { "name": { "family": "Lavender", "given": "Harrison Morton, Jr." }, "id": "Lavender-Harrison-Morton", "display_name": "Lavender, Harrison Morton, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/py65-zq39", "abstract": "No abstract." }, { "name": "Smith, Max F.", "degree": "Masters", "year": "1939", "title": "Cation Errors of the Glass Electrode at High Temperatures", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01022025-222404716", "creators": [ { "name": { "family": "Smith", "given": "Max F." }, "id": "Smith-Max-F", "display_name": "Smith, Max F." } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/af6j-8893", "abstract": "No abstract." }, { "name": "Stosick, Arthur James", "degree": "PhD", "year": "1939", "title": "I. Molecular Structure Investigations. II. A Theory of Molecular Compounds", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032025-215224287", "creators": [ { "name": { "family": "Stosick", "given": "Arthur James" }, "id": "Stosick-Arthur-James", "display_name": "Stosick, Arthur James" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/g401-yz91", "abstract": "No abstract." }, { "name": "Wald, George, Jr.", "degree": "Masters", "year": "1939", "title": "The Phase Behavior of the Methane-Propane-Pentane System", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:01072025-181637917", "creators": [ { "name": { "family": "Wald", "given": "George, Jr." }, "id": "Wald-George", "display_name": "Wald, George, Jr." } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3kym-qy27", "abstract": "The compositions of the coexisting phases in the methane-n-pentane\r\nsystem for a pressure range from atmospheric to 2500\r\npounds per square inch at temperature of 100\u00b07F., 160\u00b0F. and 220\u00b0F.\r\nwere studied. Coupling these determinations with data from other \r\nsources, gas-liquid equilibrium constants of methane and pentane as\r\nwell as dew point specific volumes were calculated.
\r\n\r\nThe composition of coexisting phases in the methane, propane-n-pentane \r\nsystem for a temperature of 100\u00b0F. and pressures of 200,\r\n500, 1000, 1500, 2000 pounds per square inch in a range of ratios\r\nof propane to n-pentane from 0.05 to 1 was studied. From these data,\r\nvalues for the equilibrium constants of methane, propane and pentane\r\nwere calculated.
" }, { "name": "Wilson, John Norton", "degree": "PhD", "year": "1939", "title": "Studies in Chemical Kinetics", "advisor": "Dickinson, Roscoe Gilkey; Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:01032025-232452716", "creators": [ { "name": { "family": "Wilson", "given": "John Norton" }, "id": "Wilson-John-Norton", "display_name": "Wilson, John Norton" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" }, { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ryw6-gc28", "abstract": "No abstract." }, { "name": "Wood, Reuben Esselstyn", "degree": "PhD", "year": "1939", "title": "Kinetic Studies of the Thermal Iodine-Catalyzed Isomerization of Cis-and Trans-Dichlorethylene in Several Solvents", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:05222024-214213318", "creators": [ { "name": { "family": "Wood", "given": "Reuben Esselstyn" }, "id": "Wood-Reuben-Esselstyn", "display_name": "Wood, Reuben Esselstyn" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jpj1-4818", "abstract": "An investigation of the thermal iodine-catalyzed isomerization\r\nof cis- and trans-dichlorethylene was carried out. The reaction cisC2H2Cl2 and \u2192 transC2H2Cl2 its reverse were studied in solutions in dichlorethylene, benzene, and cyclohexane, at different temperatures, and with different concentrations of iodine and dichlorethylene.
\r\n\r\nThe following differential rate expression is in accord with the kinetic\r\ndata for all the solutions studied:
\r\n\r\nd(C)/dt = [k K(T) + (C)]
\r\n\r\nin which equation k is a rate constant depending on iodine concentration
\r\n\r\nK is the equilibrium constant (cisC2H2Cl2/transC2H2Cl2
\r\n\r\nC and T are respectively cis- and trans-dichlorethylene
\r\n\r\nthe concentrations are expressed in mol fractions
\r\n\r\nIn 10 mol percent solutions of C2H2Cl2 in benzene, over the temperature range studied (140\u00b0 to 160\u00b0 for k, 150\u00b0 and 185\u00b0 for K)
\r\n\r\nk/\u221a(I2) = 1.30 x 1015 e-15650/T K = .617 e580/T
\r\n\r\nwhen the time is expressed in hours.
\r\n\r\nIn the other solvents the values of the numerical constants in these expressions were only slightly changed.
\r\n\r\nThe mechanism following is proposed as probable for the reaction:
\r\n\r\nI2 \u21c4 2I I + C \u21c4 CI
\r\nCI \u21c4 TI TI \u21c4 T + I
\r\n\r\nFor the estimation of the composition of the solutions\r\ncontaining the two dichlorethylene isomers a dielectric-constant\r\nmeasuring apparatus was built. With this apparatus curves relating\r\ndielectric constant to composition were obtained for several liquid systems.
" }, { "name": "Zumwalt, Lloyd Robert", "degree": "PhD", "year": "1939", "title": "Studies of the Infrared Spectra of Unsymmetrical Molecules", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01062025-234118673", "creators": [ { "name": { "family": "Zumwalt", "given": "Lloyd Robert" }, "id": "Zumwalt-Lloyd-Robert", "display_name": "Zumwalt, Lloyd Robert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4nt1-c125", "abstract": "No abstract." }, { "name": "Axelrod, Joseph", "degree": "Masters", "year": "1938", "title": "Crystal Structure of Tripotassium Cuprocyanide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182024-180405592", "creators": [ { "name": { "family": "Axelrod", "given": "Joseph" }, "id": "Axelrod-Joseph", "display_name": "Axelrod, Joseph" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/y1s0-5g15", "abstract": "No abstract." }, { "name": "Elliott, Norman", "degree": "PhD", "year": "1938", "title": "I. Electromotive Force Measurements in Liquid Ammonia. II. Determination of the Structure of Crystals and Molecules by the Diffraction of X-Rays and Electrons and by Magnetic Measurements", "advisor": "Pauling, Linus; Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12022024-183107813", "creators": [ { "name": { "family": "Elliott", "given": "Norman" }, "id": "Elliott-Norman", "display_name": "Elliott, Norman" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" }, { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/b5pk-tj96", "abstract": "No abstract." }, { "name": "Evans, Harry Dean", "degree": "Masters", "year": "1938", "title": "Calorimetric Measurement of Latent Heats of Vaporization of Propane and Normal Pentane and Some Thermodynamic Properties of Normal Pentane", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:11252024-214704859", "creators": [ { "name": { "family": "Evans", "given": "Harry Dean" }, "id": "Evans-Harry-Dean", "display_name": "Evans, Harry Dean" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4gpy-yp06", "abstract": "Measurements of the latent heat of vaporization of\r\npropane and normal pentane were made with an adiabatic\r\nbomb calorimeter. The temperature range for propane was from\r\n103.4\u00b0 F. to 163.2\u00b0 F. Normal pentane measurements were\r\nfrom 103.7 to 200\u00b0 Fahrenheit. A description of the\r\napparatus and the method of calculation will be found in\r\npart 1 of this paper.
\r\n\r\nIn the second section of this paper some of the thermodynamic \r\nproperties of n-pentane in the superheated gas\r\nregion were calculated. Included in this section are\r\ntabulated values of entropy, enthalpy, residual volume, and\r\nheat capacity.
" }, { "name": "Eyster, Eugene Henderson", "degree": "PhD", "year": "1938", "title": "Photographic Investigations in Molecular Spectroscopy", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:03262013-141554986", "creators": [ { "name": { "family": "Eyster", "given": "Eugene Henderson" }, "id": "Eyster-Eugene-Henderson", "display_name": "Eyster, Eugene Henderson" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z375-JT29", "abstract": "The determination of the energy levels and the probabilities of\r\ntransition between them, by the formal analysis of observed electronic,\r\nvibrational, and rotational band structures, forms the direct goal of all\r\ninvestigations of molecular spectra, but the significance of such data lies\r\nin the possibility of relating them theoretically to more concrete properties\r\nof molecules and the radiation field. From the well developed\r\nelectronic spectra of diatomic molecules, it has been possible, with the\r\naid of the non-relativistic quantum mechanics, to obtain accurate moments\r\nof inertia, molecular potential functions, electronic structures, and\r\ndetailed information concerning the coupling of spin and orbital angular\r\nmonenta with the angular momentum of nuclear rotation. The silicon\r\nfluori1e molecule has been investigated in this laboratory, and is found\r\nto emit bands whose vibrational and rotational structures can be analyzed \r\nin this detailed fashion.
\r\n\r\nLike silicon fluoride, however, the great majority of diatomic\r\nmolecules are formed only under the unusual conditions of electrical\r\ndischarge, or in high temperature furnaces, so that although their\r\nspectra are of great theoretical interest, the chemist is eager to\r\nproceed to a study of polyatomic molecules, in the hope that their more\r\npractically interesting structures might also be determined with the\r\naccuracy and assurance which characterize the spectroscopic determinations\r\nof the constants of diatomic molecules. Some progress has been made in\r\nthe determination of molecule potential functions from the vibrational\r\nterm values deduced from Raman and infrared spectra, but in no case can\r\nthe calculations be carried out with great generality, since the number\r\nof known term values is always small compared with the total number\r\nof potential constants in even so restricted a potential function as\r\nthe simple quadratic type. For the determination of nuclear configurations\r\nand bond distances, however, a knowledge of the rotational terms\r\nis required. The spectra of about twelve of the simpler polyatomic \r\nmolecules have been subjected to rotational analyses, and a number of\r\nbond distances are known with considerable accuracy, yet the number of\r\nmolecules whose rotational fine structure has been resolved even with\r\nthe most powerful instruments is small. Consequently, it was felt\r\ndesirable to investigate the spectra of a number of other promising\r\npolyatomic molecules, with the purpose of carrying out complete\r\nrotational analyses of all resolvable bands, and ascertaining the value\r\nof the unresolved band envelopes in determining the structures of such\r\nmolecules, in the cases in which resolution is no longer possible.\r\nAlthough many of the compounds investigated absorbed too feebly to be\r\nphotographed under high dispersion with the present infrared sensitizations,\r\nthe location and relative intensities of their bands, determined\r\nby low dispersion measurements, will be reported in the hope that these\r\ncompounds may be reinvestigated in the future with improved techniques.
\r\n" }, { "name": "Garner, Clifford Symes", "degree": "PhD", "year": "1938", "title": "I. A. The Oxidation Potential of Cerous-Ceric Salts in Aqueous Nitric Acid Solution. B. The Oxidation Potential of Thallous-Thallic Salts in Aqueous Nitric Acid Solution. II. An Attempt to Determine the Electrode Potential and Raman Spectrum of Fluorine. The Entropy of Fluorine. III. A. The Construction of a Low Temperature Vacuum Calorimeter. B. The Heat Capacity of Monofluorotrichloromethane from 60\u00b0K to its Boiling Point. Its Heat of Fusion, Heat of Vaporization, Vapor Pressure and Entropy", "advisor": "Yost, Don M.; Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01142025-192537228", "creators": [ { "name": { "family": "Garner", "given": "Clifford Symes" }, "id": "Garner-Clifford-Symes", "display_name": "Garner, Clifford Symes" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." }, { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jzs3-pj92", "abstract": "I. A. Potential measurements made at 25 and 0\u00b0C on cells of the type
\r\n\r\nPt + H2(p atm.), HClO4(c'), {HNO3(c) + CeIV (c2)/CeIII (c1)}, Pt
\r\n\r\ngive the value 1.6093 \u00b1 0.0007 volts for the formal cerous-ceric\r\noxidation potential at 25\u00b0C, substantially independent of the\r\nnitric acid concentration in the range 0.5 to 2f.
\r\n\r\nThe decrease in free energy, heat content and entropy at 25\u00b0C\r\nfound for the reaction
\r\n\r\nCeIV(1f) + E-I = CeIII(1f)
\r\n\r\nin nitric acid 0.5 to 2f are, respectively, 37,120 cal., 34, 970 cal.\r\nand -7.2 cal./deg.
\r\n\r\nEvidence is discussed for nitrate complex ions of both cerous\r\nand ceric ions in nitric acid.
\r\n\r\nB. Measurements on cells of a similar type involving thallium\r\nsalts give 1.2302 \u00b1 0.0007 volts for the formal thallous-thallic\r\noxidation potential at 25\u00b0C, independent in the range 0.5 to 2f\r\nof the concentration of nitric acid.
\r\n\r\nFor the reaction T1III(1f) + 2E-I = T1I(1f)
\r\n\r\nin nitric acid 0.5 to 2f the decrease in free energy, heat content\r\nand entropy at 25\u00b0C were found to be 56,800 cal., 30,700 cal. and\r\n-87.6 cal./deg., respectively.
\r\n\r\nII. An attempt to experimentally determine the electrode potential\r\nof fluorine met with failure because of non-reproducibility.
\r\n\r\nNo Raman lines due to fluorine could be discovered when plates \r\nwere exposed up to four hours to the light of a mercury arc\r\nscattered by liquid fluorine in a quarts container.
\r\n\r\nThe value 48.6 cal./deg./mole has been calculated for the\r\nstandard virtual entropy of fluorine from the internuclear distance\r\nand Badger's Rule. The calorimetric data of Kanda lead to a value \r\nwhich has been shown to be too low.
\r\n\r\nIII. A. A vacuum calorimeter has been constructed for the determination\r\nof heat capacities of condensed gases from 60\u00b0K room temperature.\r\nDescriptions of it, the manometer, electrical circuits and instruments,\r\nand of the establishment of a temperature scale are given.
\r\n\r\nB. The heat capacity of crystalline CCl3F has been measured from\r\n60\u00b0K to its melting point (162.54 \u00b1 0.05\u00b0K), and the heat capacity\r\nof the liquid determined from the melting point to the boiling point.
\r\n\r\nThe heat fusion at the melting point has been determined as\r\n1641.8 \u00b1 3.2 cal./mole.
\r\n\r\nThe vapor pressure of the liquid was determined over the pressure\r\nrange 5 to 72 cm. Hg; the observations can be represented by the equation:
\r\n\r\nlog10 P (int. cm Hg) = -1610.04/T + 8.21671 - 0.0030743 T/
\r\n\r\nFrom this equation the normal boiling point is calculated to be\r\n296.88 \u00b1 0.05\u00b0K, and the heat of vaporization at the boiling point\r\nto be 5905 \u00b1 30 cal./mole after a Berthelot correction of -220\r\ncal./mole is made. The Trouton's constant is then 19.89.
\r\n\r\nAn extrapolation of the heat capacity to the absolute zero gives\r\n71.92 \u00b1 1.5 cal./deg./mole for the standard virtual entropy of the\r\nideal CCl3F gas. This value is 2.2 cal./deg./mole lower than the\r\n\"spectroscopic\" value.
" }, { "name": "Hatcher, John Burton", "degree": "Masters", "year": "1938", "title": "Rates of Absorption and Description of Butane in Crystal Oil and Some Considerations in the Circulation of Diffusion Constants", "advisor": "Lacey, William Noble; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12032024-183651455", "creators": [ { "name": { "family": "Hatcher", "given": "John Burton" }, "id": "Hatcher-John-Burton", "display_name": "Hatcher, John Burton" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/grzk-a017", "abstract": "No abstract." }, { "name": "Lassettre, Edwin Nichols", "degree": "PhD", "year": "1938", "title": "Part I. The Interpretation of Freezing Point Lowering Data in Terms of Polymerization. The Hydrogen Bond and Association. A Comparative Method of Measuring Vapor Pressure Lowering with Application to Solutions of Phenol in Benzene. Part II. The Raman Spectra of Carbon and Silicon Tetraflourides. The Raman Spectra of Boron Triflouride, Trichloride, and Tribromide. The Effect of the Boron Isotopes", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:12132024-232121041", "creators": [ { "name": { "family": "Lassettre", "given": "Edwin Nichols" }, "id": "Lassettre-Edwin-Nichols", "display_name": "Lassettre, Edwin Nichols" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/m9d5-sb37", "abstract": "In the course of reviewing data on molecular weights in solution, a new method of calculating equilibrium constants was discovered which throws considerable light upon the behavior of polymerized compounds in various solvents. This method and a few applications are described in the following paper." }, { "name": "L\u00e9vy, Henri Arthur", "degree": "PhD", "year": "1938", "title": "The Calculation of Second Order Polarization Energies in Atoms. The Molecular Structures of the Bromoethanes, Boron Trimethyl, and Three Boron Trihalides", "advisor": "Brockway, Lawrence Olin", "url": "https://resolver.caltech.edu/CaltechTHESIS:11242024-020308455", "creators": [ { "name": { "family": "L\u00e9vy", "given": "Henri Arthur" }, "id": "L\u00e9vy-Henri-Arthur", "display_name": "L\u00e9vy, Henri Arthur" } ], "advisors": [ { "name": { "family": "Brockway", "given": "Lawrence Olin" }, "id": "Brockway-L-O", "role": "advisor", "display_name": "Brockway, Lawrence Olin" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4tgm-q502", "abstract": "The development of the quantum mechanics made possible a systematic attack on many problems of atomic energy. The problem of polarization in an external field is one to which the approximation methods of quantum mechanics are applicable, since in cases of interest the external field is small compared to internal atomic forces. Indeed, the first use to which Schrod1nger1 put his newly developed first order perturbation theory was the treatment of the first order Stark effect in atomic hydrogen. A second order perturbation theory was developed independently by Epstein2 , Wentzel3 , and Waller4 and applied to the second order Stark effect in hydrogen. Other treatments of hydrogen and more complex atoms in a uniform field followed, notably by Buckingham5 , who applied the variation method to the problem.
\r\n\r\nThe more complex problem of polarization in a nonhomogeneous field has received relatively little attention. Th. Neugebauer6 has given an approximate treatment of ion deformation in binary crystals, but he was not concerned with the energy effect of the deformation.
\r\n\r\nInasmuch as an ion in an ionic crystal is subject to a complex electric field arising from the distribution of positive and negative charges in its environment, knowledge of the theory of atomic polarization in non-uniform fields is essential to a complete understanding of crystal lattice energies. It 1s with this application primarily in mind that the following treatment is undertaken.
\r\n\r\nThe method to be followed in the subsequent calculation is first to carry through as rigorous as possible a treatment for an electron in an hydrogen-like orbital, then to generalize the result by substituting an effective nuclear charge for the true nuclear charge. This method is, to be sure, an approximate one, since it assumes that the field about one electron due to the rest is central, a condition obviously not fulfilled.
\r\n\r\nThe expression for the hydrogen-like 'atom will be obtained by application of a general perturbation theory7 which is capable of giving results which are exact (for the hydrogen-like atom) to second-order terms in the parameters describing the field. However, since filled-shell ions are of primary interest, simplifications will be made which, while not affecting the results for filled-shell ions, will destroy the rigor of the treatment for hydrogen.
" }, { "name": "Nellis, Donald Charles", "degree": "Masters", "year": "1938", "title": "The Pressure-Volume-Temperature Relationships of Propane", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12102024-214146715", "creators": [ { "name": { "family": "Nellis", "given": "Donald Charles" }, "id": "Nellis-Donald-Charles", "display_name": "Nellis, Donald Charles" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0vyq-6m71", "abstract": "No abstract." }, { "name": "Nysewander, Cecil Wright", "degree": "Masters", "year": "1938", "title": "Phase Equilibria in the Propane-Butane System", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:11252024-191022116", "creators": [ { "name": { "family": "Nysewander", "given": "Cecil Wright" }, "id": "Nysewander-Cecil-Wright", "display_name": "Nysewander, Cecil Wright" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/77pd-9657", "abstract": "No abstract." }, { "name": "Osborne, Darrell Wayne", "degree": "PhD", "year": "1938", "title": "The Raman Spectrum Heat Capacities from 60 to 297\u00b0K., Heat of Fusion, Vapor-Pressures and Entropy of Monofluorotrichloromethane", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11272024-170748854", "creators": [ { "name": { "family": "Osborne", "given": "Darrell Wayne" }, "id": "Osborne-Darrell-Wayne", "display_name": "Osborne, Darrell Wayne" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ba3g-ms21", "abstract": "No abstract." }, { "name": "Palmer, Kenneth James", "degree": "PhD", "year": "1938", "title": "Electron Diffraction Investigation of the Structure of Gas Molecules", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312025-033006515", "creators": [ { "name": { "family": "Palmer", "given": "Kenneth James" }, "id": "Palmer-Kenneth-James", "display_name": "Palmer, Kenneth James" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1ggw-5611", "abstract": "In the year 1931 Wierl published a paper in which he gave the results of an investigation of the molecular structures of some twenty compounds in which high velocity electrons were diffracted by the respective compounds in the gaseous state. Since that time electron diffraction by gas molecules has come to be recognized as a powerful tool for the study of molecular structure, and today the structures of approximately two hundred compounds have been determined by this method.
\r\n\r\nSince the molecules of most compounds which have a fairly high vapor pressure at a temperature in the neighborhood of 300\u00b0 C possess covalent bonds, the electron diffraction method is an excellent way of determining the covalent radii of atoms, and of studying the variations in interatomic distances due to differences in bond type and to differences in environment. The results of such studies have demonstrated the usefulness of assigning radii to atoms and have also led to empirical relations, for example that connecting bond distance and bond type, which enable one to predict with considerable accuracy the interatomic distances in many compounds. The reliability of these predictions has been adequately confirmed for compounds containing first row elements, in particular organic compounds. This is due to the comparative simplicity of the carbon atom as compared with atoms lying outside the first row of the periodic table. However, further study will no doubt lead to the discovery of more embracing relations, which will enable one to predict, not only distances, but also angles for all\r\nsimple molecules. It is hoped that the results of the investigation reported in the first part of this thesis will prove to be a step in this direction.
\r\n\r\nThe second part gives the results of an investigation of the structures of the dimeric molecules aluminum chloride, bromide, and iodide. In the third part the structure of selenium dioxide is reported. The fourth part is concerned with the effect of the benzene ring on the C-Cl distance in seven of the chlorobenzenes, end in the fifth and last part of this thesis the structure of nitrosyl chloride and nitrosyl bromide e.re discussed.
" }, { "name": "Schomaker, Verner", "degree": "PhD", "year": "1938", "title": "I. Modifications of the Radial Distribution Method of Interpretation of Electron Diffraction Photographs of Gas Molecules. II. The Electron Diffraction Investigation of the Structure of Benzene, Pyridine, Pyrazine, Butadine, Cyclopentadiene, Furan, Pyrrole, and Theophene", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102003-115316", "creators": [ { "name": { "family": "Schomaker", "given": "Verner" }, "id": "Schomaker-Verner", "display_name": "Schomaker, Verner" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PP7Z-VY74", "abstract": "No abstract." }, { "name": "Winstein, Saul", "degree": "PhD", "year": "1938", "title": "I. The Hydration of Crotonaldehyde. II. The Coordination of Silver Ion With Unsaturated Molecules. III. Stereochemical Relationships in the Conversion of Acetates to Bromides", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04092004-093654", "creators": [ { "name": { "family": "Winstein", "given": "Saul" }, "id": "Winstein-Saul", "display_name": "Winstein, Saul" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/310Z-S824", "abstract": "I. The hydration of crotoaldehyde and the dehydration of aIdol in dilute aqueous solutions of acids are first order with respect to the organic compound and to the acid. Energies of activaton for hydration and dehydration are 18.23 and 24.48 kcal., respectively. Equilibrium is reached when 47% of the crotonaldehyde has been converted to aldol at 25\u00b0 and 39% at 35\u00b0.
\r\n\r\nII. Complex formation between silver ion and a variety of unsaturated molecules in aqueous solution has been studied and equilibrium constants for the reactions of formation of several kinds of complex ions have been determined. A structure is proposed for the olefin-siver ion complex, and trends in equilibrium constants are explained in terms of steric and resonance effects.
\r\n\r\nIII. The occurance of an odd number of inversions in the transformation of 2,3-diacetoxybutane to 2,3-dibrombutane has been confirmed. 1,2-Diacetoxycyclohexane fails to give 1,2-dibromcyclohexane on treatment with aqueous fuming hydrobromic acid. 2-Acetoxyoctane on treatment with fuming hydrobromic acid gives a bromide of preponderantly inverted configuration, but the retention of optical purity is only 67%.
\r\n" }, { "name": "Lotzkar, Harry", "degree": "Masters", "year": "1937", "title": "The Thermal Cis-Transisomerization of Cinnamic Acid Catalyzed by Iodine", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:03182025-211218731", "creators": [ { "name": { "family": "Lotzkar", "given": "Harry" }, "id": "Lotzkar-Harry", "display_name": "Lotzkar, Harry" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/53cg-va67", "abstract": "In this investigation, a study was made of the kinetics and mechanism suggested by the kinetics of the iodine-catalyzed thermal conversion of cis-cinnamic acid to trans-cinnamic acid. Berthoud and Urech studied the kinetics of the iodine-sensitized photo-chemical conversion of cis-cinnamic acid to trans-cinnamic acid and proposed a mechanism for it. They found that the reaction rate is given by
\r\n[Equation. See abstract in scanned thesis for details]
\r\nThey suggested the following mechanism for the photochemical conversion:
\r\nI2 + h\u2713 \u2192 2I
\r\nC + I \u2192 CI
\r\nCI \u2192 TI
\r\nTI \u2192 T + I
\r\n2I \u2192 I2
\r\nwhere C and T denote cis-cinnamic acid and trans-cinnamic acid, resp. Structurally, the conversion is represented as follows:
\r\n\r\n[Formula. See abstract in scanned thesis for details]
" }, { "name": "Pressman, David", "degree": "Bachelors", "year": "1937", "title": "The Effect of Mercury on the Quantitative Bromination of Unsaturated Compounds", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11212024-010003826", "creators": [ { "name": { "family": "Pressman", "given": "David" }, "id": "Pressman-David", "display_name": "Pressman, David" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qa31-qw92", "abstract": "It has been shown that the simple bromide, bromate procedure for the determination of unsaturation is unsatisfactory for triple bonded compounds. Davis, Crandall and Hibee (1) have pointed out that in the case of acetylene, interference is due to the presence of oxygen. Quantitative bromination can be achieved by carrying out the reaction \u00b7n an oxygen free system (evacuated). The authors / also pointed out that the bromination of acetylene is catalysed by aluminum, nickel and mercury salts. Frieman, Kennedy and Lucas (2) have definitely shown that the use of a mercuric sulfate catalyst in the bromination of a sulfuric acid solution of acetylene yields theoretical results, each mole of acetylene adding two moles of bromine. Mulliken and Wakeman (3) attempted to determine liquid alkynes by bromination and obtained low results. The purpose of the work presented in this thesis is to find a general method f or the quantitative bromination of unsaturated compounds by studying:
\r\n(a) The bromination of different triple bonded compounds.
\r\n(b) The effect of mercuric sulfate on these brominations.
\r\n(c) The effect of mercury upon the bromination of double bonded compounds, both those easily and those difficultly brominated in the absence of mercury.
\r\n(d) The effect of 1 oxygen and peroxides on these systems.
" }, { "name": "Vermeulen, Theodore", "degree": "Masters", "year": "1937", "title": "Calorimetric Measurements of Some Hydrocarbons", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052024-220419432", "creators": [ { "name": { "family": "Vermeulen", "given": "Theodore" }, "id": "Vermeulen-Theodore", "display_name": "Vermeulen, Theodore" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/bbv4-2x12", "abstract": "No abstract." }, { "name": "Anderson, Thomas Foxen", "degree": "PhD", "year": "1936", "title": "Ein Neues Drehprismenverfahren zur Photographischen Ermittlung der Dispersion, and Applications of Raman Spectra to Chemistry", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012024-203800967", "creators": [ { "name": { "family": "Anderson", "given": "Thomas Foxen" }, "id": "Anderson-Thomas-Foxen", "display_name": "Anderson, Thomas Foxen" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/07vb-w743", "abstract": "I. Ein Drehprismenverfahren zur Ermittlung der Dispersion
\r\n\r\nAn inexpensive ultraviolet spectrograph using concave\r\nmirrors instead of lenses is described. After trial determinations\r\nof the known dispersion of quartz and KCl, the instrument\r\nwas used to determine the dispersion of CsCl to\r\n2265\u00c5. Refractive index results are good to one unit in the\r\nfourth decimal place.
\r\n\r\nII. Applications of Raman Spectra to Chemistry
\r\n\r\nA. The Raman Spectra and Molecular Constants of Phosphorus\r\nTrifluoride and Phosphine.
\r\n\r\nThe Raman frequencies of PF3 and PH3 are reported\r\ntogether with the molecular constants and entropies of PH3, \r\nPF3, PCl3, AsF3, and AsCl3. From these data \u0394F298\r\nis calculated for PH3 and PCl3 together with S*298 for P(s, white).
\r\n\r\nB. The Entropy of Phosphorus.
\r\n\r\nA more accurate value of S*298 for P(s, white) is\r\ncalculated using recent electron diffraction and Raman\r\nspectrum results for P4. This leads to a more accurate value\r\nof \u0394F298 for PCl3
\r\n\r\nC. The Raman Spectrum of Arsenic Trichloride.
\r\n\r\nIt is pointed out that the assignment of frequencies\r\nof AsCl3 made in an article by Brodskii and Sack is contradicted\r\nby polarization experiments. From this is follows \r\nthat a central force treatment alone does not suffice for \r\nthe treatment of the AsCl3 type of molecule as Brodskii and \r\nSack assert.
\r\n\r\nD. The Raman Spectrum of Deuterium.
\r\n\r\nThe Raman spectrum of D2 is reported. From the\r\nfrequencies of the two rotation lines and the one vibration \r\nline observed it is concluded that the potential function\r\nfor D2 is the same as that for H2. This suggests that M-D\r\npotential functions are equal to those for M-H.
\r\n\r\nE. The Raman Spectrum of Tetraethyl Silane. Vibrational Resonance in Tetraalkyls.
\r\n\r\nThe Raman Spectrum of Si(C2H3)4 is reported. The\r\npresence of extra lines in its spectrum and in the spectra\r\nof other tetraalkyls is ascribed to vibrational resonance\r\nbetween various modes of vibration of the tetrahedral\r\nmolecule. Quantum mechanical treatments of the effects are \r\ngiven in some detail.
" }, { "name": "Beach, John Youngs", "degree": "PhD", "year": "1936", "title": "Application of Quantum Mechanics to Molecular Structure. Electron Diffraction Investigation of the Structure of Gas Molecules, and the Dependence of Interatomic Distance on Single Bond-Double Bound Resonance", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:11022024-090738724", "creators": [ { "name": { "family": "Beach", "given": "John Youngs" }, "id": "Beach-John-Youngs", "display_name": "Beach, John Youngs" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nyk7-yk34", "abstract": "No abstract." }, { "name": "Davies, James Allman", "degree": "Masters", "year": "1936", "title": "The Thermodynamic Properties of an Ethane Crystal Oil Mixture", "advisor": "Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232008-153555", "creators": [ { "name": { "family": "Davies", "given": "James Allman" }, "id": "Davies-James-Allman", "display_name": "Davies, James Allman" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/WN7F-W289", "abstract": "No abstract." }, { "name": "Deahl, Thomas Jay", "degree": "Masters", "year": "1936", "title": "The Oxidation Potential of Cobaltous-Cobaltic Salts in Nitric Acid Solution", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232008-095756", "creators": [ { "name": { "family": "Deahl", "given": "Thomas Jay" }, "id": "Deahl-Thomas-Jay", "display_name": "Deahl, Thomas Jay" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BGPA-XC19", "abstract": "No abstract." }, { "name": "Dunn, Clarence Lincoln", "degree": "PhD", "year": "1936", "title": "I. The Oxidation State of Argentic Salts in Acid Solution. II. The Mercury Sensitized Photoreaction Between Ammonia and Oxygen. III. The Photochemical Decomposition of Hydrogen Selenide", "advisor": "Noyes, Arthur A.; Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02052025-164415074", "creators": [ { "name": { "family": "Dunn", "given": "Clarence Lincoln" }, "id": "Dunn-Clarence-Lincoln", "display_name": "Dunn, Clarence Lincoln" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." }, { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d1s7-gs24", "abstract": "I. THE OXIDATION STATE OF ARGENTIC SALTS IN ACID SOLUTION
\r\n\r\nThe argentic salt produced in solution by\r\noxidizing with ozone argentous nitrate dissolved in\r\nconcentrated nitric acid at 0\u00b0C. is shown to contain\r\nthe silver almost entirely in the bipositive form. One\r\nof the three independent methods used involves the determination\r\nof the magnetic moment of the argentic silver\r\nion. A value of 1.98 Bohr magnetons is found for its\r\nmagnetic moment.
\r\n\r\nII. THE MERCURY SENSITIZED PHOTO-REACTION BETWEEN AMMONIA AND OXYGEN
\r\n\r\nExperiments which were made in two different\r\nreaction vessels give evidence of a surface reaction. The\r\ncontradictory results of two former pairs of investigators\r\nare discussed and the present results are shown to be in\r\naccord with both previous pieces of work.
\r\n\r\nIII. THE PHOTOCHEMICAL DECOMPOSITION OF HYDROGEN SELENIDE
\r\n\r\nThe results are given of a study of the photodecomposition\r\nof hydrogen selenide at a series of pressures\r\nfrom 8 to 60 mm. A unit quantum yield was found,\r\nconstant over this pressure range. A mechanism for\r\nthe decomposition is offered.
" }, { "name": "Harker, David", "degree": "PhD", "year": "1936", "title": "The Application of the Three Dimensional Patterson Method and the Crystal Structures of Proustite, Ag\u2083AsS\u2083, and Pyrargyrite, Ag\u2083SbS\u2083", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:03312025-223924929", "creators": [ { "name": { "family": "Harker", "given": "David" }, "id": "Harker-David", "display_name": "Harker, David" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7x7x-cv79", "abstract": "It is shown that the three dimensional Patterson method can be so\r\nsimplified by the use of the symmetry properties of the crystal under consideration\r\nthat its use in determining the positions of atoms in crystals is\r\npracticable. This method is then used to determine the positions of the\r\nheavy atoms in proustite, Ag3AsS3. The positions of the sulfur atoms are\r\nfound by the use of the covalent atomic radii and assumptions concerning\r\nbond directions. The structure so derived is found to be compatible with\r\nthe observed data. Proustite is found to contain pyramidal AsS3 groups\r\nand silver atoms forming two bonds to sulfur in almost opposed directions.\r\nPyrargyrite, Ag3SbS3, is found to have almost the same structure as proustite.\r\nThe analytical statement of the structures is as follows:--
\r\n\r\nThe space group C63v - R3c, is common to both proustite and pyrargyrite.\r\nThe special positions of C63v are (in hexagonal axes)
\r\n\r\n2a) 0,0,z; 0,0,\u00bd+z
\r\n\r\n6b) x,y,z; y,x-y,z; y-x,x,z;
\r\n\r\ny,x,\u00bd+z; x,x-y,\u00bd+z; y-x,y,\u00bd+z;
\r\n\r\nand positions derived from these by the operations of the rhombohedral lattice.\r\nThe parameter values are:--
\r\n\r\nProustite
\r\n\r\nao = 10.74 \u00c5, co = 8.64 \u00c5
\r\n\r\n2As in 2a) ZAs = 0.000
\r\n\r\n6Ag in 6B) xAg = 0.246
\r\n\r\nyAg = 0.298
\r\n\r\nzAg = 0.235
\r\n\r\n6S in 6b) xS = 0.220
\r\n\r\nyS = 0.095
\r\n\r\nzS = 0.385
\r\n\r\nPyrargyrite
\r\n\r\nao = 11.04 \u00c5, co = 8.71 \u00c5
\r\n\r\n2Sb in 2a) ZSb = 0.000
\r\n\r\n6Ag in 6B) xAg = 0.250
\r\n\r\nyAg = 0.305
\r\n\r\nzAg = 0.210
\r\n\r\nxS = 0.220
\r\n\r\nyS = 0.105
\r\n\r\nzS = 0.355
" }, { "name": "Inman, Byron Noll", "degree": "Masters", "year": "1936", "title": "The Viscosities for Hydrocarbon Systems. The Effect of Composition and Pressure Upon the Viscosity for a Three Component Hydrocarbon System", "advisor": "Sage, Bruce H.; Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:11072024-190004643", "creators": [ { "name": { "family": "Inman", "given": "Byron Noll" }, "id": "Inman-Byron-Noll", "display_name": "Inman, Byron Noll" } ], "advisors": [ { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." }, { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/mqe2-r454", "abstract": "No abstract." }, { "name": "Kennedy, Edwin Russell", "degree": "PhD", "year": "1936", "title": "I. The Decomposition of Di-Ortho-Tolyliodonium Iodide. II. Joule-Thomson Coefficients of Some Hydrocarbon Gases. III. The Hydration of Acetylene", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11052024-233822488", "creators": [ { "name": { "family": "Kennedy", "given": "Edwin Russell" }, "id": "Kennedy-Edwin-Russell", "display_name": "Kennedy, Edwin Russell" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rhbj-8a17", "abstract": "I. The Decomposition of Di-Orthotolyliodonium Iodide
\r\n\r\nNo abstract
\r\n\r\nII. Joule-Thomson Coefficients of Some Hydrocarbon Gases
\r\n\r\nIn determining the thermal properties of hydrocarbons\r\nin the gaseous region the Joule-Thomson coefficient is\r\na powerful tool when known as a function of the state. The\r\npurpose of the present paper is to describe an apparatus developed\r\nto measure this property, to report upon the data\r\nobtained for propane, and to outline the usefulness of this\r\nmeasurement in thermal calculations.
\r\n\r\nIII. The Hydration of Acetylene
\r\n\r\nAn analytical method for the determination of acetylene\r\nin aqueous solution is described together with tests to\r\nascertain its validity. Rates of homogeneous reaction were\r\nexperimentally determined for the mercuric sulfate catalysed\r\nhydration of acetylene in sulfuric acid solution. The dependence\r\nof rate upon acetylene and mercuric sulfate is established\r\nand the effect of acetaldehyde is discussed.
" }, { "name": "Larsen, Delmar H.", "degree": "Masters", "year": "1936", "title": "Photochemical Intermittency and the Photochlorination of Tetrachloroethylene in Carbon Tetrachloride Solution", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:04012025-153556923", "creators": [ { "name": { "family": "Larsen", "given": "Delmar H." }, "id": "Larsen-Delmar-H", "display_name": "Larsen, Delmar H." } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/qndx-yz67", "abstract": "No abstract." }, { "name": "McCullough, James Douglas", "degree": "PhD", "year": "1936", "title": "I. A Study of the Allotropes of Selenium. II. Evidence for Existence of a Selenium-Iodine Compound. III. An Attempt to Reproduce the Allison Magneto-Optic Effect. IV. The Crystal Structure of Potassium Chlorosmate and Potassium Bromosmate", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11072024-231343892", "creators": [ { "name": { "family": "McCullough", "given": "James Douglas" }, "id": "McCullough-James-Douglas", "display_name": "McCullough, James Douglas" } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/z4wx-2g84", "abstract": "I.
\r\n\r\nA new vacuum-vaporization method for determination\r\nof transition temperatures, due to Dr. A. O. Beckman,\r\nhas been tested and proven to be all right by means of the\r\nmercuric iodide transition at 127\u00b0 .
\r\n\r\nThis method shows an apparent transition between\r\na red micro-crystalline form of selenium and the hexagonal\r\nform at a temperature of 74-75\u00b0C.
\r\n\r\nThe relative stability of the three crystalline\r\nforms of selenium at 25\u00b0 has been definitely established as:
\r\n\r\n(1.) hexagonal selenium (most stable).
\r\n\r\n(2.) \u03b1 - monoclinic selenium.
\r\n\r\n(3.) \u03b2 - monoclinic selenium (least stable).
\r\n\r\nII.
\r\n\r\nEvidence quoted in the literature which supposedly\r\ndisproves compound formation between iodine and selenium in\r\nno case prohibits the possibility of a highly dissociated\r\ncompound.
\r\n\r\nAbsorption spectra were photographed which give\r\nstrong evidence favoring a selenium-iodine compound in\r\nsolution.
\r\n\r\nQuantitative measurements on the equilibrium\r\nbetween selenium and iodine 1n ethylene bromide and carbon\r\ntetrachloride indicate a compound of formula Se2I2, and\r\npossibly SeI4 also.
\r\n\r\nIII.
\r\n\r\nThe Magneto-optic Apparatus was set up according to\r\nthe directions given by Allison in his numerous publications.\r\nThe broad minima attributed to the solvent could be located\r\nas described, but no minima of the sharp type due to isotopes\r\nof the positive ions were observed.
\r\n\r\nIV.
\r\n\r\nWith the aid of Laue and oscillation photographs,\r\npotassium chlorosmate and potassium bromosmate have been shown\r\nto have the ammonium chloroplatinate structure. The edge of\r\nthe unit cube was found to be 9.729 \u00b1 0.02 \u00c5 for potassium\r\nchlorosmate and 10.30 \u00b1 0.03 \u00c5 for potassium bromosmate. The\r\nhalogen parameters were found to be 0.243 \u00b1 0.002 and 0.244 \u00b1 0.001\r\nrespectively. These values give an osmium-chlorine separation\r\nof 2.36 \u00b1 0.02 \u00c5 and an osmium-bromine separation of 2.51 \u00b1 0.01\r\n\u00c5 in the complexes. Subtracting the normal electron-pair bond\r\nradius for the halogen in each case, the octahedral electron\r\npair bond radius for quadrivalent osmium is found to be 1.37 \u00b1\r\n0.02 \u00c5 in K2OsCl6 and 1.37 \u00b1 0.01 \u00c5 in K2OsBr6.
" }, { "name": "Mendenhall, William Rees", "degree": "Masters", "year": "1936", "title": "Studies of Some Properties of Hydrocarbons", "advisor": "Lacey, William Noble; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11132024-183212993", "creators": [ { "name": { "family": "Mendenhall", "given": "William Rees" }, "id": "Mendenhall-William-Rees", "display_name": "Mendenhall, William Rees" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/g0ff-aq67", "abstract": "No abstract." }, { "name": "Skinner, Davis Ayres", "degree": "Masters", "year": "1936", "title": "Butadiene from the Pyrolysis of 2,3-Dichlorobutane", "advisor": "Lacey, William Noble; Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:12052017-105033167", "creators": [ { "name": { "family": "Skinner", "given": "Davis Ayres" }, "id": "Skinner-Davis-Ayres", "display_name": "Skinner, Davis Ayres" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "co-advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZX4V-1K10", "abstract": "Summary:
\r\n\r\n1. A satisfactory laboratory apparatus and method for\r\npreparing butadiene from 2,3-dichlorobutane, by\r\npassing over BaCl2 on pumice, at temperatures\r\nranging from 500-600\u00b0C., has been described.
\r\n\r\n2. An analytical method for the products is developed\r\nusing maleic anhydride to absorb butadiene, 87 percent\r\nsulfuric acid for butenes, and fractional distillation\r\nfor the separation of chlorobutenes from the butadiene.
\r\n\r\n3. Butadiene, chlorobutene, butene, lower hydrocarbons,\r\nand hydrochloric acid have been shown to result from \r\nthe pyrolysis of 2,3-dichlorobutane over BaCl2.
\r\n\r\n4. Conditions are described for obtaining yield, of\r\nbutadiene as high as 57.6% and optimum conditions\r\nare predicted. The higher yields here obtained\r\nexceeding those found in the literature, for this \r\npyrolysis.
" }, { "name": "Stitt, Fred Beals", "degree": "PhD", "year": "1936", "title": "I. Raman Spectra of Some Silicon Compounds. II. Kinetics of Oxidized Silver Solutions", "advisor": "Swift, Ernest H.; Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11182024-223402858", "creators": [ { "name": { "family": "Stitt", "given": "Fred Beals" }, "id": "Stitt-Fred-Beals", "display_name": "Stitt, Fred Beals" } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." }, { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kkz8-ch15", "abstract": "I. Raman Spectra of Some Silicon Compounds.
\r\n\r\nSiH4 : Two lines were observed in the gas and liquid. With the\r\nhelp of infra-red data a complete assignments made for the vibrational\r\nspectrum of silane.
\r\n\r\nSi2H6(g) and Si2Cl6(l) : Three lines were observed in Si2H6(g)\r\nand some fourteen in Si2Cl6(l). Polarization measurements on the\r\nstronger lines of Si2Cl6 were made by a convenient method which is\r\ndescribed.
\r\n\r\nFrom a consideration of the relations among the modes of\r\nvibration of similar molecules having different symmetry, the analysis\r\nof the observed lines is facilitated by a knowledge of the assignments\r\nof the fundamental frequencies of SiH4, HSiCl3, and BrSiCl3.\r\nA definite assignment is made for the three observed lines Si2H6 is made and\r\nsome evidence is presented for the existence of internal rotation \r\nin this molecule at room temperature.
\r\n\r\nII. Kinetics of Oxidized Silver Solutions.
\r\n\r\nThe behavior of a number of reducing agents toward nitric\r\nacid solutions of agentic silver and of ozone has been observed.\r\nArgentic solutions may be reduced quantitatively by titration with\r\nany of a number of reducing agents using the disappearance of the \r\nargentic color as end point.
\r\n\r\nThe rate of oxidation by ozone of nitric acid solutions of \r\nsilver nitrate and the rate of decomposition of these oxidized solutions\r\nhas been studied using suitable technique and method of analysis. The \r\nreduction rate is found to fit the differential equation
\r\n\r\n- d(Ag++)2/dt = k2 d(Ag++)2/(Ag+) + k4 (Ag++)4/(Ag+) (4)
\r\n\r\nindicating simultaneous occurrence of two slow reactions. (The oxidized\r\nsilver is assumed to be principally in the divalent state.)
\r\n\r\nThe oxidation rate is found to fit the equation
\r\n\r\nd(Ag++)/dt = ko (Ag+)(O3) - reduction rate (10)
\r\n\r\nThe steady state reached on prolonged oxidation by ozone of \r\nnitric acid solutions of silver nitrate is shown to correspond approximately\r\nto the point where d(Ag++)/dt = 0 in equation 10 with the \r\nreduction rate given by equation 4.
\r\n\r\nEquilibrium between three valence states of silver is postulated,\r\nprobably according to the equation
\r\n\r\nAgO+ + Ag+ + 2 H+ = 2 Ag++ + H2O. (2)
\r\n\r\nThe oxidation mechanism is probably
\r\n\r\nAgO+ + H2O = Ag++ H2O2
\r\n\r\ncombined with equation 2.
\r\n\r\nThe fourth order reduction reaction may be
\r\n\r\nH2O + 2 Ag++ + AgO+ = 3 Ag+ + O2 + 2 H+.
" }, { "name": "Welge, Henry John", "degree": "PhD", "year": "1936", "title": "New Light on the Nature of the Photodecomposition of Ammonia", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:11112024-190339770", "creators": [ { "name": { "family": "Welge", "given": "Henry John" }, "id": "Welge-Henry-John", "display_name": "Welge, Henry John" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/54xx-8p67", "abstract": "No abstract." }, { "name": "Backus, Harrison Stout", "degree": "Masters", "year": "1935", "title": "Specific Heats of Some Hydrocarbon Solutions", "advisor": "Lacey, William Noble; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222024-211548740", "creators": [ { "name": { "family": "Backus", "given": "Harrison Stout" }, "id": "Backus-Harrison-Stout", "display_name": "Backus, Harrison Stout" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/r6xy-6p78", "abstract": "No abstract." }, { "name": "Bertram, Edward Austen", "degree": "Masters", "year": "1935", "title": "The Rate of Solution of Methane in a Hydrocarbon Oil Held in the Pores of Sand", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072024-163108746", "creators": [ { "name": { "family": "Bertram", "given": "Edward Austen" }, "id": "Bertram-Edward-Austen", "display_name": "Bertram, Edward Austen" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/4zm6-na51", "abstract": "No abstract." }, { "name": "Blair, Charles Melvin", "degree": "PhD", "year": "1935", "title": "I. The Thermodynamic Constants of Iodine Monochloride, Iodine Monobromide and Bromine Monochloride in Carbon Tetrachloride Solutions. II. The Equilibrium Between Nitric Oxide, Bromine and Nitrosyl Bromide. III. The Infra-Red Emission Spectrum of Bunsen Type Flame", "advisor": "Yost, Don M.; Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:10072024-211304431", "creators": [ { "name": { "family": "Blair", "given": "Charles Melvin" }, "id": "Blair-Charles-Melvin", "display_name": "Blair, Charles Melvin" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." }, { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/anms-r326", "abstract": "No abstract." }, { "name": "Bonner, Lyman Gaylord", "degree": "PhD", "year": "1935", "title": "I. The Vibrational Spectrum of Water Vapor. II. An Analysis of the Vibrational Spectrum of Ethylene", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:10042024-224650227", "creators": [ { "name": { "family": "Bonner", "given": "Lyman Gaylord" }, "id": "Bonner-Lyman-Gaylord", "display_name": "Bonner, Lyman Gaylord" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/d65m-js48", "abstract": "No abstract." }, { "name": "Carrico, James Leon", "degree": "PhD", "year": "1935", "title": "Photochemical Reactions Involving the Double Bond Between Carbon Atoms. I. The Photochlorination and the Chlorine-Sensitized Photo-Oxidation of Gaseous Tetrachloroethylene. II. The Bromine-Sensitized Photodecomposition of Gaseous Dibromotetrachloroethane", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:11122024-220037716", "creators": [ { "name": { "family": "Carrico", "given": "James Leon" }, "id": "Carrico-James-Leon", "display_name": "Carrico, James Leon" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/s0bt-z735", "abstract": "The express purpose of the work to be presented was to determine, in so far as possible, the products formed, the intermediates formed, the factors controlling the rate and the mechanism involved in the addition reaction of oxygen, on the one hand, and the addition of chlorine, on the other, at the double bond between the two carbon atoms of tetrachloroethylene, C2 Cl4. Interest was centered, perhaps, on the intricacies of the oxidation, and still is.
\r\n\r\nIn attempting to study the bromine addition at the double bond of tetrachloroethylene, experimental facilities accentuated the study of the elimination of two bromine atoms from dibromotetrachloroethane, C2 Cl4 Br2, and the accompanying double bond formation between two carbon atoms rather than the addition reaction study. It was highly probable that a study of the elimination of two halogen atoms from two adjacent carbon atoms would elucidate the processes involved in the addition of the two halogen atoms to the adjacent carbon atoms.
\r\n\r\nTo be more explicit concerning the intermediate compounds involved, it was desirable to establish evidence for or against the existence of a Cl3 or a Br3 molecule postulated as a transient intermediate by certain investigators.
" }, { "name": "Coryell, Charles Dubois", "degree": "PhD", "year": "1935", "title": "The Reduction Potential of Pentavalent Vanadium to Vanadyl Ion in Hydrochloric Acid Solutions. Fluoresenzversuch AnOrganische Daempfe, Besonders Aceton. Studies of the Nature and Reactions of Oxidized Silver Compounds, Especially in Nitric Acid", "advisor": "Noyes, Arthur A.; Scheibe, G\u00fcnter", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312011-113455408", "creators": [ { "name": { "family": "Coryell", "given": "Charles Dubois" }, "id": "Coryell-Charles-Dubois", "display_name": "Coryell, Charles Dubois" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." }, { "name": { "family": "Scheibe", "given": "G\u00fcnter" }, "id": "Scheibe-G\u00fcnter", "role": "advisor", "display_name": "Scheibe, G\u00fcnter" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A37S-KX50", "abstract": "I:
\r\n\r\nA series of measurements of the electromotive force of half-cells made up of solutions of V2O5 and VOCl2 in excess HCl against calomel half cells in HCl of the same strength,for which there were negligible liquid junctions, is presented. The acid concentration was varied from 0.01012 to 2.146 M. The observed potentials were corrected for calomel cell and for other concentrations as per the following assumed reaction:
\r\nVO++ + 2 H2O == HVO3 + 3 H+ E-.
\r\nValues of E0 so obtained decreased with decreasing acid concentration. This decrease was correlated with complex formation ( V(OH)+4, etc.) noted in increased solubility of freshly precipitated HVO3 in HCl as measured. The potential in molal HCl is -1.0216 Volts, corresponding to a free energy decrease of +23,572 cal. when 1/2 H2 reduces a pentavalent atom of vanadium (irrespective of nature) in 1.00 M HC1. From the temperature coefficient of the cell, the heat content increase for the same reaction was found to be -29,350 cal.
II:
\r\n\r\nExperiments carried out in the Physico-chemical Institute of the Technische Hochschule M\u00fcnchen in searching for a discrete fluorescence spectrum of acetone vapor are given. A detailed description of the apparatus for studying flowing gases at various pressures is included, as well as a study of benzene fluorescence which was used to standardize technique and test the sensitivity of the methods. Long illuminations of acetone vapor at various pressures with powerful Al sparks gave no fluorescence, although the line 1862 \u00c5 was absorbed. A mercury arc produced in short time three continua in the visible, two of which were already known, but no line spectrum. Conditions were found with Tesla excitation in which output of light was good but little CO was formed in decomposition. Nine hours exposure yielded only the continua mentioned. Preliminary work was done on methyl iodide.
III:
\r\n\r\nThe analytical chemistry of bivalent silver solutions is discussed, especially the exact TlNO3 method and the rapid Cr(NO3)3 method. Conditions prevailing in anodic oxidation are outlined, as well as a convenient method for preparation of solution. The main work deals with the complicated kinetics of oxidation of water by argentic silver at 25\u00b0 and at 0\u00b0. The rate of decomposition of the argentic silver solution may be represented at constant acid by the equation:
\r\n -d(Ag++)/dt = k2(Ag++2/(Ag+) + k4(Ag++4/(Ag+)
\r\n where k2 varies roughly inversely as the square of the hydrogen ion concentration and is not greatly decreased by increasing ionic strength while k_4 falls off very rapidly with increasing acid and ionic strength. The mechanism seems to involve tervalent silver. From existent data the free energies of formation at 0\u00b0 C. of the following are calculated: Ag++, Ag2O3, AgO, Ag2O, O3, H2O and Ag+, and a number of equilibria involving them are predicted and discussed.
Crystals of potassium chloroplatinate, studied by means\r\nof spectral and Laue photographs, are shown to have the potassium\r\nchlorostannate structure with d100 = 9.73 \u00c5 and u = 0.240 = 0.005.\r\nThe reported value of u = 0.16 is shown to be incorrect, and the\r\ntheoretical treatment of Jones and Dent which supported this latter\r\nvalue is thereby deprived of its supposed agreement with experiment.
\r\n\r\nThe parameters in diaspora are redetermined, and the\r\nstructure is discussed from the standpoint of the coordination\r\ntheory. The existence and location of hydrogen bonds in the\r\nstructure are established, and representative formulas are proposed.
\r\n\r\nThe unit of structure, space group symmetry, and detailed\r\natomic arrangements of lepidocrocite are determined from x-ray\r\ndata, and the existence and location of hydrogen bonds in the\r\nstructure are established from considerations of interatomic distances. \r\nThe relationship between the diaspore and lepidocrocite\r\nstructures is discussed from the standpoint of the coordination theory,\r\nand found to depend on two alternative ways of satisfying the\r\nelectrostatic valence rule.
" }, { "name": "Gross, Siegfried Theodore", "degree": "Masters", "year": "1935", "title": "The Raman Spectra of Some Volatile Fluorides", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10292024-153525943", "creators": [ { "name": { "family": "Gross", "given": "Siegfried Theodore" }, "id": "Gross-Siegfried-Theodore", "display_name": "Gross, Siegfried Theodore" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wdvh-m211", "abstract": "No abstract." }, { "name": "Medlin, William Virgil", "degree": "PhD", "year": "1935", "title": "Interatomic Distances from X-Ray Power Photographs. The Crystal Structure of Mercuric Tellurate", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:10162024-164410269", "creators": [ { "name": { "family": "Medlin", "given": "William Virgil" }, "id": "Medlin-William-Virgil", "display_name": "Medlin, William Virgil" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/dsry-rp97", "abstract": "The Fourier series is discussed as a method\r\nfor obtaining directly the arrangement of atoms within\r\na crystal, and difficulties in this method are\r\npointed out. A recently developed treatment of x-ray\r\npowder photographs giving interatomic distances is\r\ntested on various substances and found to be\r\nsatisfactory when applied to compounds c011taining\r\nrelatively few heavy atoms- in reasonably simple\r\narrangement. Crystalline diphyenyliodonium iodide is\r\nshown to have an ionic bond between the iodine atoms.\r\nThe sulfur bond angle 1ti orpiment is measured, and\r\ngreat similarity is found to exist between the\r\nstructures of orpiment and realgar. The arsenic-sulfur\r\ndistance in sodium sulfantimonate is found to be\r\nsmaller than that predicted by the table of radii or\r\nPauling and Huggins. A short discussion is given of\r\nthe difficulties encountered in applying this method.
\r\n\r\nOn the basis of an incomplete investigation\r\ninto the crystal structure or mercuric tellurate, Hg3TeO6,\r\nthe TeO6 group is shown to exist as a unit here as in\r\ntelluric acid, with a shape that is nearly regularly\r\noctahedral. The unit cell size is found, and a\r\ndetermination of the space group is made.
" }, { "name": "Nies, Nelson Perry", "degree": "Masters", "year": "1935", "title": "The Effect of the Wave Length on the Photochemical Decomposition of Ethylene Iodide in Carbon Tetrachloride Solution", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:10102024-174620263", "creators": [ { "name": { "family": "Nies", "given": "Nelson Perry" }, "id": "Nies-Nelson-Perry", "display_name": "Nies, Nelson Perry" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/e8jg-kq17", "abstract": "No abstract." }, { "name": "Prater, Arthur Nicolas", "degree": "PhD", "year": "1935", "title": "The Isomeric 2-Pentenes. The Reaction Between Oxygen and 2-Butene", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10302024-221544079", "creators": [ { "name": { "family": "Prater", "given": "Arthur Nicolas" }, "id": "Prater-Arthur-Nicolas", "display_name": "Prater, Arthur Nicolas" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bexf-gg83", "abstract": "No abstract." }, { "name": "Simmons, Norwood Lee", "degree": "Masters", "year": "1935", "title": "The Mercury-Sensitized Photochemical Decomposition of Arsine", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012024-145403091", "creators": [ { "name": { "family": "Simmons", "given": "Norwood Lee" }, "id": "Simmons-Norwood-Lee", "display_name": "Simmons, Norwood Lee" } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/rhqt-7h26", "abstract": "No abstract." }, { "name": "Wilson, Chester Eugene", "degree": "PhD", "year": "1935", "title": "The Relationship Between the Isomeric 2-Butenes and the 2,3-Butanediols", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:11012024-160852756", "creators": [ { "name": { "family": "Wilson", "given": "Chester Eugene" }, "id": "Wilson-Chester-Eugene", "display_name": "Wilson, Chester Eugene" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/90f4-ep68", "abstract": "No abstract." }, { "name": "Dickinson, Bernard Neil", "degree": "PhD", "year": "1934", "title": "The Crystal Structure of Tetramminopalladous Chloride. The Crystal Structure of Potassium Bromoselenite. The Normal State of the Hydrogen Molecule-Ion", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:01252017-083837484", "creators": [ { "name": { "family": "Dickinson", "given": "Bernard Neil" }, "id": "Dickinson-Bernard-Neil", "display_name": "Dickinson, Bernard Neil" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A597-FY24", "abstract": "An investigation of the crystal structure of tetramminopalladous chloride has considerable interest because of Werner's contention that compounds containing bivalent\r\npalladium (or platinum) possess a planar configuration\r\nconsisting of four groups coordinated about the central\r\npalladium atom. The correctness of this assumption has\r\nbeen verified in the case of potassium chloroplatinite\r\nand palladite by the x-ray studies of Dickinson (1).\r\nPauling (2) has shown theoretically that the bivalent\r\ntransitional elements platinum, palladium, and nickel can\r\nform bonds directed toward the corners of a square. Recently\r\nCox (3) has reported that tetramminoplatinous\r\nchloride, Pt(NH3)4Cl2\u00b7H2O, is in accord with Werner's viewpoint and has a structure closely similar to that of\r\npotassium chloroplatinite. The determination of the\r\nstructure of tetramminopalladous chloride was undertaken\r\nto test Werner's assumption for a cation containing bivalent\r\npalladium. This palladium compound might reasonably\r\nbe expected to have the same structure as Pt(NH3)4Cl2\u00b7H2O;\r\nit is shown in this paper that the structure is closely\r\nrelated to the potassium chloroplatinite structure but\r\nis based on a unit containing two molecules instead of\r\none as reported by Cox for the platinum compound.
\r\n\r\nTetramminopalladous chloride forms pale yellow\r\ntetragonal needles from a solution of diamminopalladous\r\nchloride in aqueous ammonia. In most cases the crystals\r\nwe prepared developed prism faces belonging only to {110}.
\r\n\r\n" }, { "name": "Doescher, Russell Nimtz", "degree": "Masters", "year": "1934", "title": "The Magnetic Susceptibilities of the Metal Ketyls", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09182024-174614735", "creators": [ { "name": { "family": "Doescher", "given": "Russell Nimtz" }, "id": "Doescher-Russell-Nimtz", "display_name": "Doescher, Russell Nimtz" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3rap-7h11", "abstract": "No abstract." }, { "name": "Eberz, William Ferdinand", "degree": "PhD", "year": "1934", "title": "The Hydration of Isobutene. I. The Hydration Rate of Isobutene in Dilute Nitric Acid. II. The Free Energy of Hydration of Isobutene. III. The Hydration of Isobutene in the Presence of Silver Nitrate", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:03232017-083732057", "creators": [ { "name": { "family": "Eberz", "given": "William Ferdinand" }, "id": "Eberz-William-Ferdinand", "display_name": "Eberz, William Ferdinand" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/0CTT-0W94", "abstract": "The three articles contained in this thesis describe\r\nthe investigation of the hydration of isobutene.
\r\n\r\nIn the first paper the rates of hydration of\r\nisobutene were measured in dilute nitric acid solutions\r\nboth with and without other ions present to observe possible\r\ncatalytic effects.
\r\n\r\nIn the second paper the equilibrium of the hydration\r\nreaction in aqueous solution was determined and, by means\r\nof additional data, the standard free energy change and\r\nchange in heat content of the reaction were calculated.
\r\n\r\nIn the third part the hydration in the presence of\r\nsilver ion was investigated and the role of this metal in\r\nthe reaction was elucidated.
" }, { "name": "Frieman, Rubin Harold", "degree": "Masters", "year": "1934", "title": "I. Oxonium Compound Formation by Alcohol in Aqueous Solution. II. The Hydration of Acetylene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02082017-133402744", "creators": [ { "name": { "family": "Frieman", "given": "Rubin Harold" }, "id": "Frieman-Rubin-Harold", "display_name": "Frieman, Rubin Harold" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YBHJ-YH98", "abstract": "Part I
\r\n\r\n1. The distribution of alcohol between benzene and\r\naqueous solutions of (1) sulfuric acid, (2) sodium sulfate,\r\nand (3) mixtures of perchloric acid and sodium perchlorate\r\nhas been studied.
\r\n\r\n2. Apparent values of equilibrium constants for the\r\nformation of oxonium salts in aqueous solutions have been\r\ncalculated.
\r\n\r\nPart II
\r\n\r\n\r\n1. It has been established that oxygen exerts an\r\ninhibiting effect in the formation of the complex compounds \r\nof mercury which catalyze the hydration of acetylene.
\r\n\r\n2. The hydration of acetylene has been shown to\r\nbe of first order with respect to acetylene.
\r\n\r\n3. The conditions for the rapid determination of\r\nacetylene in the presence of oxygen by the bromate-bromide \r\nmethod have been determined.
\r\n\r\n\r\n\r\n" }, { "name": "Hill, Earl S.", "degree": "PhD", "year": "1934", "title": "The Rate of Solution of Methane and Propane in Hydrocarbon Oils", "advisor": "Lacey, William Noble; Sage, Bruce H.", "url": "https://resolver.caltech.edu/CaltechTHESIS:02222018-150308842", "creators": [ { "name": { "family": "Hill", "given": "Earl S." }, "id": "Hill-Earl-S", "display_name": "Hill, Earl S." } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" }, { "name": { "family": "Sage", "given": "Bruce H." }, "id": "Sage-B-H", "role": "co-advisor", "display_name": "Sage, Bruce H." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Y3Z0-0Z59", "abstract": "The apparatus used for determination of the rate of solution\r\nof hydrocarbon gases in hydrocarbon oils by Pomeroy, Scudder,\r\nand Stapp has been improved so that consistent results reproducible\r\nwithin 3% can be obtained. Methane and propane gases with over 99%\r\npurity have been prepared. The coefficients for the rate of solution\r\nof methane in 16 oils, varying in viscosity from 0.21 to 99 centipoises,\r\nincluding 6 crude oils, at 86\u00b0F (30\u00b0C) and 300 lbs./sq.in. (20 atm.)\r\nwere measured. The equilibrium concentration of methane in the oil\r\nhas been correlated with the density of the original oil. The effect\r\nof temperature on the diffusion coefficient for methane was studied\r\nwith 2 crudes and 2 refined oils over the range from 86\u00b0F to 140\u00b0F (60\u00b0C).\r\nA logarithmic correlation of the diffusion constant for methane over\r\nthis temperature range has been made with the viscosity of the original\r\noil and the temperature.
\r\n\r\nThe rate of solution of propane in kerosene, and in spray\r\noil over a temperature range of 96\u00b0F to 140\u00b0F was determined up to 67%\r\nof the vapor pressure of liquid propane. The equilibrium concentration\r\nin mol fraction of propane in the liquid was found to be a linear function\r\nof the percent of the vapor pressure of liquid propane. The effect on the\r\ndiffusion coefficient of the expansion of the liquid due to solution\r\nof gas was calculated and found to be small. The diffusion coefficient\r\nfor the highly soluble gas, propane, was found to be a linear function\r\nof the concentration of propane in the liquid and the temperature,\r\nwith a variation in the diffusion coefficient of about five-fold.
\r\n" }, { "name": "Hooper, Duncan-Leverich", "degree": "Masters", "year": "1934", "title": "The Wagner Turbidimeter as an Instrument for the Determination of Specific Surface and Particle-Size Distribution of Portland Cement. An Instrument for the Measurement of the Thermal Conductivity of Water, and for the Investigation of Phenomena in Heat Transfer in the Liquid and at the Liquid-Solid Boundary", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:10162024-011149839", "creators": [ { "name": { "family": "Hooper", "given": "Duncan-Leverich" }, "id": "Hooper-Duncan-Leverich", "display_name": "Hooper, Duncan-Leverich" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jve9-ps32", "abstract": "The Wagner Turbidimeter has given promise of being a suitable instrument for use in the determination of the surface exposed by the particles in samples of Portland cement. Since the extent of this surface is an important factor in controlling or predicting the behavior of cements in the production of concrete, a simple but accurate method for its determination is highly desirable in connection with investigations and acceptance tests.
\r\n\r\nThe purpose of the present investigation was to make a critical study of the advantages and short-comings of this instrument and to recommend modifications of apparatus or procedure which might improve its performance. The various steps in the procedure and the possible sources of uncertainty and error in the results have been examined in detail.
\r\n\r\nSeveral modifications of the apparatus have been found beneficial and numerous changes in the procedure to be used have been found essential for obtaining satisfactory results. With the suggested improvements, the instrument appears to offer a reasonably satisfactory method for routine\r\ntests of specific surface (usually expressed as square centimeters of surface per gram of cement), and also for approximation of the distribution of the sizes of the particles of the cement.
\r\n\r\nAlthough the results are not entirely accurate and reproducible, they are within useful limits and the instrument is recommended for use in acceptance test work on specific surface measurement, until a more accurate method, utilizing instruments of reasonable cost and with simple operating procedure has been developed. For research or investigational purposes, where cements of varying chemical and physical characteristics (including optical properties) are -being studied, it is believed that the turbidimeter method may not be sufficiently accurate and should not be depended upon, unless special precautions are observed and great care taken in the work.
" }, { "name": "Kennedy, Edwin Russell", "degree": "Masters", "year": "1934", "title": "The Decomposition of Di-o-Tolyliodonium Iodide", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09202024-181837097", "creators": [ { "name": { "family": "Kennedy", "given": "Edwin Russell" }, "id": "Kennedy-Edwin-Russell", "display_name": "Kennedy, Edwin Russell" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/7da9-yc49", "abstract": "No abstract." }, { "name": "Liu, Yun-Pu", "degree": "PhD", "year": "1934", "title": "The Hydration Rate of Trimethyl Ethylene in Different Acids. The Nitration of Para-Cresol and of Para-Cresyl Carbonate in the Presence of Sulfuric Acid. The Preparation of Crystalline Lactic Acid", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09262024-224119974", "creators": [ { "name": { "family": "Liu", "given": "Yun-Pu" }, "id": "Liu-Yun-Pu", "display_name": "Liu, Yun-Pu" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3p2t-6a54", "abstract": "The hydration of trimethyl-ethylene is effected by different\r\nacids. At constant ionic strength the rate is first order with respect\r\nto both pentene concentration and the nitric acid concentration.\r\nThe rate at a given acid concentration is increased on the addition of\r\npotassium nitrate. Other acids were used alone as follows: hydrochloric,\r\nperchloric, hydrobromic, dithionic, p-toluene-sulfuric, picric,\r\nsulfuric, oxalic and acetic. Strong acids give not much different rates.\r\nThe dibasic acids like sulfuric and oxalic have mostly their first hydrogen\r\nion effect on the rate of hydration. Dithionic acid shows its\r\nsecond hydrogen ion effect.
\r\n\r\nNitration of p-cresol and p-cresyl carbonate have been carried\r\nout in the presence of sulfuric acid. It was found in the case of\r\np-cresol that the ortho directive power of the hydroxyl group decreased\r\nas sulfuric acid increased, and that more and more of the entering nitro\r\ngroup took up a position meta to the hydroxyl. In the case of p-cresyl\r\ncarbonate, increase in the amount of sulfuric acid likewise increased\r\nthe meta-ortho ratio. This change in directive power is ascribed to\r\nthe salt-forming property of the oxygen atom of p-cresol and p-cresyl\r\ncarbonate.
\r\n\r\nSeveral methods have been worked out for obtaining optically\r\nactive lactic acid (both isomers) from a commercial aqueous syrup. One\r\nof the methods consists of fractional distillation followed by fractional\r\ncrystallization from a mixture of equal volumes of ethyl and isopropyl\r\nethers. This process effects a good separation of the active isomer \u2113(+)\r\nfrom the d\u2113- form. The active acids were also prepared by way of their\r\nzinc ammonium salts obtained by resolution of the commercial syrup. It\r\nwas also found that when zinc ammonium d(-) lactate was mixed with\r\na large quantity of the double salts of the d\u2113 acid, the active acid\r\ncould be separated out by warming up to 55\u00b0. Some of the properties\r\nof the crystalline acids were described.
" }, { "name": "Myers, Albert Edward", "degree": "PhD", "year": "1934", "title": "A Study of the Photosensitized Decomposition of Gaseous Hydrogen Azide", "advisor": "Beckman, Arnold O.", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282024-174817161", "creators": [ { "name": { "family": "Myers", "given": "Albert Edward" }, "id": "Myers-Albert-Edward", "display_name": "Myers, Albert Edward" } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zga4-d968", "abstract": "No abstract." }, { "name": "Offner, Franklin Faller", "degree": "Masters", "year": "1934", "title": "A Determination of the Parameter for Hauerite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09222017-164814870", "creators": [ { "name": { "family": "Offner", "given": "Franklin Faller" }, "id": "Offner-Franklin-Faller", "display_name": "Offner, Franklin Faller" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TKAX-JE95", "abstract": "In Part I, after a discussion of covalency and covalent radii, a brief review of the work of Bragg on pyrite, and Ewald and Friedrich on pyrite and hauerite, with an evaluation of accuracy, is given. The Laue method for crystal analysis is described, and the theory outlined.
\r\n\r\nPart II is devoted to the description of a new parameter determination for hauerite carried out by the writer. As a result of this determination, the parameter has been fixed at u = 0.4012 \u00b1 0.0004, giving a covalent sulfur radius of 1.043 \u00c5.
" }, { "name": "Sage, Bruce Hornbrook", "degree": "PhD", "year": "1934", "title": "Studies of Thermal and Physical Properties of Hydrocarbons", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-01122004-095420", "creators": [ { "name": { "family": "Sage", "given": "Bruce Hornbrook" }, "id": "Sage-Bruce-Hornbrook", "display_name": "Sage, Bruce Hornbrook" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3SFC-Y308", "abstract": "The work reported in this thesis was carried out during the last three years at the California Institute of Technology as part of Research Project 37 of the American Petroleum Institute. The general purpose of the investigation is the study of the fundamental properties of hydrocarbon mixtures which control their retention in underground formations.
\r\n\r\nThe work of earlier investigators had indicated that rather large changes in the physical properties from those observed at atmospheric pressure took place when natural hydrocarbon mixtures were at equilibrium under the pressures and temperatures found in many natural reservoirs. As the physical properties such as viscosity, density, etc. have a large effect on the retention of the oil in a natural reservoir, a study of the more important of them was undertaken by the American Petroleum Institute. The work of Project 37 has been restricted to measurements of the composition, rate of solution, density, change in volume, specific heat, viscosity of hydrocarbon mixtures as a function of pressure and temperature. The derived thermal properties are of interest in the determination of the available energy of a natural reservoir.
\r\n\r\nThe work reported in this thesis consists of a description of the apparatus used in the general study of the physical properties of hydrocarbon mixtures under equilibrium conditions, and of complete equilibrium data on the system composed of methane and propane, and of complete pressure-volume-temperature and thermal data on pure propane. Both studies covered most of the pressure and temperature ranges encountered in underground formations.
" }, { "name": "Schaafsma, Jan Gerard", "degree": "Masters", "year": "1934", "title": "Some Studies on the Thermodynamic Relations in Multi-Component Systems", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09242024-152737146", "creators": [ { "name": { "family": "Schaafsma", "given": "Jan Gerard" }, "id": "Schaafsma-Jan-Gerard", "display_name": "Schaafsma, Jan Gerard" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8s06-q590", "abstract": "No abstract." }, { "name": "Steffens, Carsten Conover", "degree": "PhD", "year": "1934", "title": "I. The Measurement of Small, Commercial-Frequency, Alternating Potentials. II. The Normal Frequencies of Vibration for Systems of Point Particles Having Tetrahedral and Octahedral Symmetry", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:12132024-234623984", "creators": [ { "name": { "family": "Steffens", "given": "Carsten Conover" }, "id": "Steffens-Carste-Conover", "display_name": "Steffens, Carsten Conover" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/8bqt-cz98", "abstract": "A mechanical rectifier for use at commercial frequencies has been constructed. Accidental electromotive forces have been so far eliminated that it can be used with a sensitive direct current\r\ngalvanometer as a detecting instrument. Four galvanometers have been tried and the results are described. With the most sensitive galvanometers used, the sensitivities of the system at 50 cycles\r\nwere 0.05 microvolts (without the critical damping resistance) and 0.00004 microamperes.
\r\n\r\nThe use of a vibration galvanometer and of the mechanical rectifier with a low-frequency vacuum-tube amplifier has been investigated. An input potential 0.001 of that corresponding to\r\nthe noise level of the amplifier can be detected. This combination is then about 100 times as sensitive as an amplifier with the same noise level used with a telephone receiver.
" }, { "name": "Stirton, Robert Ingersoll", "degree": "PhD", "year": "1934", "title": "Some Factors Affecting the Efficiency of Copper Deposition from Leaching Solutions Rich in Iron", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:10282024-222816833", "creators": [ { "name": { "family": "Stirton", "given": "Robert Ingersoll" }, "id": "Stirton-Robert-Ingersoll", "display_name": "Stirton, Robert Ingersoll" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/21ga-g322", "abstract": "Experimental work is described serving to identify eleven\r\nvariable factors influencing the efficiency of operation of electrolytic\r\ncells operating with copper cathodes and lead anodes and fed with solutions\r\ncontaining relatively high concentrations of copper, iron, aluminum\r\nand sulfuric acid.
\r\n\r\nResults are given constituting a systematic investigation of\r\nthe effect on anode and cathode efficiencies of three of these variables,\r\nand some work has been done on the effect of a fourth.
\r\n\r\nIt is found that increasing temperature results in decreasing\r\ncathode efficiency with very little effect on the net anode efficiency.
\r\n\r\nIt is found that increasing concentration of ferrous iron results\r\nin marked increase in net anode efficiencies and relatively small\r\ndecreases in cathode efficiencies until a concentration of 19 grams per\r\nliter is reached. Further increase of ferrous iron results in marked\r\nincrease in the cathode efficiency but also in pronounced decrease in\r\nthe net anode efficiency.
\r\n\r\nIt is found that increasing the concentration of ferric iron\r\nresults in decreasing both cathode and net anode efficiencies. \r\nInvestigation of this variable was not complete.
\r\n\r\nIt is found that increasing concentration of aluminum results\r\nin marked increase in cathode efficiency after a poorly defined lower\r\nlimit is passed. Small increases in the net anode efficiency with increasing\r\naluminum concentration are found, the maximum gain being recorded\r\nat approximately the lower limit of concentration which has appreciable\r\neffect on the cathode efficiency.
\r\n\r\nThe use of the glass electrode to determine the pH of the solution\r\nhas been investigated and further work on the effect of varying aluconcentration\r\ninvolving pH control thru use of the glass electrode is outlined.
" }, { "name": "Barton, Robert C.", "degree": "PhD", "year": "1933", "title": "Studies of Various Methods for the Separation of the Common Elements into Groups. The Activity Coefficients of Hydrochloric Acid in Solutions Containing Sodium Dithionate Perchloric Acid", "advisor": "Swift, Ernest H.; Bates, Stuart Jeffery", "url": "https://resolver.caltech.edu/CaltechTHESIS:10212024-182807074", "creators": [ { "name": { "family": "Barton", "given": "Robert C." }, "id": "Barton-Robert-C", "display_name": "Barton, Robert C." } ], "advisors": [ { "name": { "family": "Swift", "given": "Ernest H." }, "id": "Swift-E-H", "role": "advisor", "display_name": "Swift, Ernest H." }, { "name": { "family": "Bates", "given": "Stuart Jeffery" }, "id": "Bates-Stuart-Jeffery", "role": "advisor", "display_name": "Bates, Stuart Jeffery" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/gqdr-yw32", "abstract": "Studies of Various Methods for the Separation of the\r\nCommon Elements into Groups
\r\n\r\nI. Data are presented for the separation of chromium, aluminum\r\nand iron from manganese, nickel, cobalt and zinc by the various modifications\r\nof the ammonia separation. Under the best possible conditions\r\nit was found that the separation of nickel, cobalt and zinc from chromium.\r\nand aluminum was unsatisfactory for quantitative work although the Ardagh\r\nmodification of the method improved the aluminum separations.
\r\n\r\nII. An experimental study of the separation of manganese, iron,\r\ncobalt and nickel from aluminum, chromium and zinc by means of sodium\r\nhydroxide and peroxide has been made. The separations are unsatisfactory\r\nquantitatively.
\r\n\r\nIII. It has been found that zinc, cobalt, nickel and iron (the Zinc\r\nGroup} can be separated from aluminum, chromium and manganese (the Aluminum\r\nGroup} by precipitation with hydrogen sulfide from a solution having\r\na controlled excess of sodium hydrocarbonate and sufficient oxalate\r\nto prevent the precipitation of aluminum and chromium. The separations\r\nare very satisfactory quantitatively.
\r\n\r\nThe Activity Coefficients of Hydrochloric Acid in Solutions\r\nContaining Sodium Dithionate and Perchloric Acid.
\r\n\r\nThe effects of added sodium dithionate and added perchloric\r\nacid upon the activity coefficients of hydrochloric acid in aqueous\r\nsolution were determined at 25\u00b0C up to an ionic strength somewhat\r\ngreater than unity.
" }, { "name": "Brockway, Lawrence Olin", "degree": "PhD", "year": "1933", "title": "Electron Diffraction and the Molecular Structure of Gases. The Crystal Structure of Chalcopyrite", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:10142024-222455831", "creators": [ { "name": { "family": "Brockway", "given": "Lawrence Olin" }, "id": "Brockway-Lawrence-Olin", "display_name": "Brockway, Lawrence Olin" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/c9xm-jv17", "abstract": "An apparatus has been developed for the study of the\r\nmolecular structure of gases by the electron diffraction method.\r\nA number of improved features in the construction are described.
\r\n\r\nThe method has been applied to an investigation of the\r\nresonance among the possible electronic structures of the Lewis\r\ntype and also of the atomic configurations in certain molecules.
\r\n\r\nDiacetylene and cyanogen are found to be linear, contrary\r\nto a published report of evidence for a model with 150\u00b0 bond angles.
\r\n\r\nMethyl azide is found to have a linear azide group. The\r\nring model which has been proposed is shown to be eliminated. The\r\nring model for carbon suboxide has also been eliminated in favor of\r\na linear model.
\r\n\r\nChlorine dioxide shows evidence for the existence of the\r\nthree-electron bond, and this fact explains its lack of tendency to\r\npolymerize to Cl2O4.
\r\n\r\nThe hexafluoride of sulfur, selenium and tellurium are\r\nfound to have structures which may be represented by a regular octahedron\r\nwith six atoms at the corners surrounding the central atom.
\r\n\r\nThe interatomic distances for all of the above compounds\r\nare reported.
\r\n\r\nThe crystal structure of chalcopyrite has been re-investigated\r\nand the correct structure is reported.
" }, { "name": "Hultgren, Ralph Raymond", "degree": "PhD", "year": "1933", "title": "I. The Spark-in-Flame Method of Spectrographic Analysis. II. Equivalent Chemical Bonds Formed by s, p and d Eigenfunctions. III. The Crystal Structure of Sulvanite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012017-150349623", "creators": [ { "name": { "family": "Hultgren", "given": "Ralph Raymond" }, "id": "Hultgren-Ralph-Raymond", "display_name": "Hultgren, Ralph Raymond" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2PRM-8Q37", "abstract": "No abstract." }, { "name": "Kircher, Charles Edmund Jr.", "degree": "Masters", "year": "1933", "title": "Solubility of Natural Gas in Various Crude Oils and Preparation of Pure Methane from Natural Gas", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:05122017-093006165", "creators": [ { "name": { "family": "Kircher", "given": "Charles Edmund Jr." }, "id": "Kircher-Charles-Edmund-Jr.", "display_name": "Kircher, Charles Edmund Jr." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/FWDP-HK80", "abstract": "The work reported in this paper is a continuation of experiments begun and carried out by B.H. Sage, and described in his thesis for the Masters degree C.I.T. 1931. The object of the research was to determine as quantitatively as possible the solubility of natural gas in various crude oils, as it was known that by dissolving natural gas in crude oil, the physical properties of the oil could be changed in such a way as to make possible greater recovery of the crude oil from the underground formation. As pointed out by Mr. Sage, the solubility figures presented in his thesis had to be arrived\r\nat by a method of approximation as he was then not experimentally able to measure the change in liquid volume resulting from dissolved gas. In order to make possible more accurate calculation of gas solubility, apparatus was designed and installed for directly measuring the change in volume of the crude oil which occurred as a result of dissolved gas. Other changes were made in the equipment as first set up by Mr. Sage, which were designed to increase accuracy and speed in carrying out the experiments. These changes will be discussed in the main body of this report.\r\n" }, { "name": "Lewis, William Bradley", "degree": "PhD", "year": "1933", "title": "Dissociation Constants of Para Substituted Benzoic Acids in Alcoholic Solutions", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282017-141954872", "creators": [ { "name": { "family": "Lewis", "given": "William Bradley" }, "id": "Lewis-William-Bradley", "display_name": "Lewis, William Bradley" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/N64X-D109", "abstract": "The dissociation constants for benzoic and p-chlorobenzoic\r\nacids were measured in aqueous solution, and the constants for benzoic,\r\np-chlorobenzoic, p-bromobenzoic, p-iodobenzoic, p-toluic, p-ethyl\r\nbenzoic, and p-cuminic acids were measured in 80% alcoholic solutions\r\nby means of a quinhydrone electrode.
\r\n\r\nA description of the electrode, and the vacuum tube amplifying\r\ncircuit used in connection with the potantiometer, is given.
\r\n\r\nThe synthesis of p-toluic, p-ethyl benzoic, and p-cmninic\r\nacids is described.
" }, { "name": "Lyons, Ernest Herbert, Jr.", "degree": "Masters", "year": "1933", "title": "The Photo-Oxidation of Carbon Tetrachloride", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:02282017-090332720", "creators": [ { "name": { "family": "Lyons", "given": "Ernest Herbert, Jr." }, "id": "Lyons-Ernest-Herbert-Jr.", "display_name": "Lyons, Ernest Herbert, Jr." } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ZC4V-5J32", "abstract": "1. It has been shown that carbon tetrachloride\r\nis not decomposed by light of wavelength 2537\r\n\u00e5ngstroms.
\r\n\r\n2. It has been shown that light of wavelength\r\n2537 \u00e5ngstroms produces an oxidation of carbon\r\ntetrachloride according to the reaction
\r\n\r\nCCl4 + \u00bdO2 \u2192 COCl2 + Cl2\r\n\r\nIt has been shown that one molecule of carbon\r\ntetrachloride is decomposed per quantum of light\r\nabsorbed. A possible mechanism for this reaction\r\nhas been given.
\r\n\r\n3. The difficulty of purifying carbon\r\ntetrachloride for photochemical work has been\r\npointed out.
\r\n\r\n4. Evidence suggesting a photochemical \r\nhydrolysis of carbon tetrachloride has been\r\ngiven.
\r\n\r\n" }, { "name": "Prater, Arthur Nickolas", "degree": "Masters", "year": "1933", "title": "The Reaction Between Oxygen and 2-Butene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:03012017-102431032", "creators": [ { "name": { "family": "Prater", "given": "Arthur Nickolas" }, "id": "Prater-Arthur-Nickolas", "display_name": "Prater, Arthur Nickolas" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NNVD-0F26", "abstract": "2-Butene has been found to react with oxygen at temperatures\r\nof 375\u00b0 to 500\u00b0. At the higher temperatures, polymerization as well as\r\noxidation takes place. The products of the reaction which have been\r\nidentified are acetaldehyde, glyoxal and/or glycollic aldehyde,\r\n1,3-butadiene, acid, peroxide and an olefin oxide. The simplest explanation of the reactions occurring involve both hydroxylation and peroxide formation as primary products." }, { "name": "Rose, Robert Selden", "degree": "PhD", "year": "1933", "title": "I. The Catalytic Decomposition of n-Butyl Alcohol. The Equilibrium Between the Three Normal Butenes. II. The Use of Crotonaldehyde in the Synthesis of Lepidine", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09182024-222036257", "creators": [ { "name": { "family": "Rose", "given": "Robert Selden" }, "id": "Rose-Robert-Selden", "display_name": "Rose, Robert Selden" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/72bp-qf22", "abstract": "I.
\r\n\r\nn-Butyl alcohol has been dehydrated at 350-450\u00b0 with\r\nvarious catalysts. Soda lime, sodium aluminate and sodium hydroxide\r\nare without effect. Kaolin, tungsten oxide on asbestos and thorium\r\noxide on asbestos, give good results. The compositions of the butene\r\nmixtures so obtained have been determined.
\r\n\r\nl-Butene and 2-butene respectively have been passed over\r\npumice stone impregnated with phosphoric acid at 350, 400 and 500\u00b0.\r\nEquilibrium has been reached at 350 and 400\u00b0, and equilibrium \r\nconstants and free energies have been calculated for the reactions:
\r\n\r\n(1) l-butene \u21c4 trans 2-butene
\r\n\r\n(2) l-butene \u21c4 cis 2-butene
\r\n\r\n(3) trans 2-butene \u21c4 cis 2-butene
\r\n\r\nII.
\r\n\r\nThe synthesis of lepidine has been attempted in three ways,\r\nusing crotonaldehyde as a starting material:
\r\n\r\n(1) By preparing an aldehyde-ammonia from B-phenyl butyracetal\r\nand ammonia, followed by ring closure with the use of AlCl3.
\r\n\r\n(2) By the condensation of aniline with B-chlor butyracetal.
\r\n\r\n(3) By ring closure of B-phenyl butyric bromamide, with the \r\nuse of AlCl3.
\r\n\r\nA new compound, B-phenyl butyric bromamide has been prepared.
\r\n\r\nA new method for the preparation in good yield of B-phenyl\r\nbutyric acid has been outlined.
" }, { "name": "Urmston, Joseph Winchester", "degree": "PhD", "year": "1933", "title": "I. The Separation of the Two Types of Iodine Molecule and the Photochemical Reaction of Gaseous Iodine with Hexene. II. The Photochemical Reaction Between Bromine Vapor and Platinum", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:02012017-144036059", "creators": [ { "name": { "family": "Urmston", "given": "Joseph Winchester" }, "id": "Urmston-Joseph-Winchester", "display_name": "Urmston, Joseph Winchester" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5K53-GX81", "abstract": "No abstract." }, { "name": "Wilson, Chester Eugene", "degree": "Masters", "year": "1933", "title": "Chlorohydrins and Oxides of the Isomeric-2-Butenes", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:01302017-152800940", "creators": [ { "name": { "family": "Wilson", "given": "Chester Eugene" }, "id": "Wilson-Chester-Eugene", "display_name": "Wilson, Chester Eugene" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BCPN-QV04", "abstract": "1. A method is given for the preparation of 2-butene chlorohydrin by the addition of acetic acid to a mixture of calcium hypochlorite and butene at -10\u00b0C.
\r\n\r\n2. A convenient method is given for the preparation of large amounts of butene oxide by dropping butene chlorohydrin on hot concentrated potassium hydroxide solution.
\r\n\r\n3. The fractional distillation of the isomeric chlorohydrins of the 2-butenes is described.
\r\n\r\n4. The fractional distillation of the isomeric 2-butene oxides is described.
\r\n\r\n5. The physical properties of the fractions of 2-butene chlorohydrin and of the fractions of 2-butene oxide are given.
\r\n\r\n6. The approximate values are given for the hydrolysis rate of the two fractions of 2-butene chlorohydrin.
" }, { "name": "Wilson, Edgar Bright", "degree": "PhD", "year": "1933", "title": "Wave Functions for Simple Atoms", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202004-102922", "creators": [ { "name": { "family": "Wilson", "given": "Edgar Bright" }, "id": "Wilson-Edgar-Bright", "display_name": "Wilson, Edgar Bright" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/SJ1R-RT13", "abstract": "This thesis is a review of the methods which have been used to apply the Schrodinger equation to the problem of atomic structure, an important problem to chemists because it precedes any similar treatment of molecules and valence. Original work includes computations on helium, lithium, and beryllium, together with iso-electronic ions. The Thomas-Fermi statistical atom, the Hartree method of the self-consistent field, Pauling's and Slater's sets of screening constants, and the variation principle are discussed and estimates of their applicability made, Hydrogen, helium, lithium, and beryllium are individually treated and tables showing the results of many investigators included. In the case of lithium the new results give an ionization potential in very close agreement with experiment while the new work on beryllium is a slight but not satisfactory improvement over previous results. The Appendix lists tables of integrals used in the computations.\r\n" }, { "name": "Brass, Philip Davis", "degree": "PhD", "year": "1932", "title": "I. Experiments on the Rate of Dissociation of Nitrogen Tetroxide. II. The Thermodynamic Constants of Bromine Chloride. III. The Dissociation of Nitrosyl Bromide", "advisor": "Tolman, Richard Chace; Yost, Don M.; Ramsberger, Herman C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09132024-180948190", "creators": [ { "name": { "family": "Brass", "given": "Philip Davis" }, "id": "Brass-Philip-Davis", "display_name": "Brass, Philip Davis" } ], "advisors": [ { "name": { "family": "Tolman", "given": "Richard Chace" }, "id": "Tolman-R-C", "role": "advisor", "display_name": "Tolman, Richard Chace" }, { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." }, { "name": { "family": "Ramsberger", "given": "Herman C." }, "id": "Ramsberger-Herman-C", "role": "advisor", "display_name": "Ramsberger, Herman C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nyqx-8w32", "abstract": "No abstract." }, { "name": "Ellis, Emory Leon", "degree": "Masters", "year": "1932", "title": "The Rate of Decomposition of Ethyl Hypochlorite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262004-144509", "creators": [ { "name": { "family": "Ellis", "given": "Emory Leon" }, "id": "Ellis-Emory-Leon", "display_name": "Ellis, Emory Leon" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3DTD-RK20", "abstract": "No Abstract." }, { "name": "Gunderson, Norman Robert", "degree": "Masters", "year": "1932", "title": "Losses of Sulphur from the Sulphate Paper Pulp Process", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172024-215758337", "creators": [ { "name": { "family": "Gunderson", "given": "Norman Robert" }, "id": "Gunderson-Norman-Robert", "display_name": "Gunderson, Norman Robert" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/pfqn-0q59", "abstract": "No abstract." }, { "name": "Hoard, James Lynn", "degree": "PhD", "year": "1932", "title": "I. The Crystal Structure of Potassium Silver Cyanide. II. An X-Ray Examination of the 12-Molybdophosphates and Related Compounds. III. The Crystal Structure of Cadmium Chloride", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:09182024-170700357", "creators": [ { "name": { "family": "Hoard", "given": "James Lynn" }, "id": "Hoard-James-Lynn", "display_name": "Hoard, James Lynn" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kd0j-7p10", "abstract": "No abstract." }, { "name": "Launer, Herbert Franz", "degree": "Masters", "year": "1932", "title": "The Kinetics of the Reaction between Potassium Permanganate and Oxalic Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09112024-214755981", "creators": [ { "name": { "family": "Launer", "given": "Herbert Franz" }, "id": "Launer-Herbert-Franz", "display_name": "Launer, Herbert Franz" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/879d-f064", "abstract": "No abstract." }, { "name": "Leermakers, John Andrew", "degree": "PhD", "year": "1932", "title": "I. The Thermal Decomposition of Dimethyl-Triazene. A Homogenous Unimolecular Reaction. II. The Gas Phase Equilibrium between Methyl Nitrite, Hydrogen Chloride, Methyl Alcohol, and Nitrosyl Chloride. The Absorption of Nitrosyl Chloride. III. The Chlorine Photosensitized Oxidation of Tetra-Chloroethylene in Carbon Tetrachloride Solution", "advisor": "Ramsberger, Herman C.; Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:01312025-031607632", "creators": [ { "name": { "family": "Leermakers", "given": "John Andrew" }, "id": "Leermakers-John-Andrew", "display_name": "Leermakers, John Andrew" } ], "advisors": [ { "name": { "family": "Ramsberger", "given": "Herman C." }, "id": "Ramsberger-Herman-C", "role": "advisor", "display_name": "Ramsberger, Herman C." }, { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hsx5-9321", "abstract": "During the past four years a considerable amount of experimental data has given support to certain theories of unimolecular reaction velocity which postulate that activation occurs by kinetic theory collisions. The rate of production of activated molecules by collisions is a second order process but if only a very small fraction of those molecules which become activated decompose spontaneously the rate of decomposition is first order. At sufficiently low pressures collisions can no longer maintain the Maxwell Boltzmann quota of activated molecules; consequently the rate falls off until finally at still lower pressures the rate approaches the rate of activation and is second order.
\r\nNow that the rate of decomposition of nitrogen pentoxide has at last also been shown to decrease at very low pressures, every example of a homogeneous unimolecular reaction shows such a decrease or else theory does not require it in the pressure range studied.
\r\nWe have now studied the decomposition of dimethyl-triazene and find that this reaction also is first order at high pressures but falls off in rate at pressures below about one centimeter. Rate measurements have been made at temperatures from 200 to 230\u00b0 and at pressures from 0.02 to 8.0 cm. of mercury.
" }, { "name": "Morris, Ross Elliott", "degree": "Masters", "year": "1932", "title": "The Reaction between Oxygen and 2-Butene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09112024-183709851", "creators": [ { "name": { "family": "Morris", "given": "Ross Elliott" }, "id": "Morris-Ross-Elliott", "display_name": "Morris, Ross Elliott" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/b8c7-6y32", "abstract": "No abstract." }, { "name": "Murdoch, Philip Griffis", "degree": "PhD", "year": "1932", "title": "I. The Activity of Hydrochloric Acid in the Presence of a Unibivalent Salt. II. The Dissociation Constant of Bromide Chloride at Room Temperature. III. A Method for Deriving Photochemical Reaction Mechanisms of Certain Types from Observed Reaction Rates", "advisor": "Bates, Stuart Jeffery; Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:09172024-180906590", "creators": [ { "name": { "family": "Murdoch", "given": "Philip Griffis" }, "id": "Murdoch-Philip-Griffis", "display_name": "Murdoch, Philip Griffis" } ], "advisors": [ { "name": { "family": "Bates", "given": "Stuart Jeffery" }, "id": "Bates-Stuart-Jeffery", "role": "advisor", "display_name": "Bates, Stuart Jeffery" }, { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/aewy-z275", "abstract": "No abstract." }, { "name": "Robinson, Roger Theophilus", "degree": "Masters", "year": "1932", "title": "An Investigation of the Characteristics of Dennisite and its Components", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09112024-222645094", "creators": [ { "name": { "family": "Robinson", "given": "Roger Theophilus" }, "id": "Robinson-Roger-Theophilus", "display_name": "Robinson, Roger Theophilus" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8y4q-7n17", "abstract": "No abstract." }, { "name": "Sherman, Jack Henry", "degree": "PhD", "year": "1932", "title": "I. The Calculation of Atomic Scattering Factors. II. The Crystal Structure of the Micas", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:09122024-200600537", "creators": [ { "name": { "family": "Sherman", "given": "Jack Henry" }, "id": "Sherman-Jack-Henry", "display_name": "Sherman, Jack Henry" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vgx7-n716", "abstract": "No abstract." }, { "name": "Waddington, Guy", "degree": "PhD", "year": "1932", "title": "I. The Kinetics of the Thermal Decomposition of Trichlor Methyl Chlorformate. II. The Interpretation of the Thermal Decomposition of Nitrous Oxide. III. The Thermal Chlorination of Chloroform", "advisor": "Ramsberger, Herman C.", "url": "https://resolver.caltech.edu/CaltechTHESIS:09122024-201158392", "creators": [ { "name": { "family": "Waddington", "given": "Guy" }, "id": "Waddington-Guy", "display_name": "Waddington, Guy" } ], "advisors": [ { "name": { "family": "Ramsberger", "given": "Herman C." }, "id": "Ramsberger-Herman-C", "role": "advisor", "display_name": "Ramsberger, Herman C." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/bas7-3p40", "abstract": "No abstract." }, { "name": "Welge, Henry", "degree": "Masters", "year": "1932", "title": "The Hydration of Iso-Butylene to Tertiary Butyl Alcohol", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09122024-153530269", "creators": [ { "name": { "family": "Welge", "given": "Henry" }, "id": "Welge-Henry", "display_name": "Welge, Henry" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ny6a-0d95", "abstract": "No abstract." }, { "name": "Hill, Earl S.", "degree": "Masters", "year": "1931", "title": "Diffusion of Hydrocarbon Gases into Oils and Oil Sands", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262024-215224028", "creators": [ { "name": { "family": "Hill", "given": "Earl S." }, "id": "Hill-Earl-S", "display_name": "Hill, Earl S." } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ee00-6h79", "abstract": "No abstract." }, { "name": "Hoeppel, Raymond Winfield", "degree": "Masters", "year": "1931", "title": "Denitrification of Chuquicamata Copper Solutions", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032024-210245990", "creators": [ { "name": { "family": "Hoeppel", "given": "Raymond Winfield" }, "id": "Hoeppel-Raymond-Winfield", "display_name": "Hoeppel, Raymond Winfield" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/sc6j-cf26", "abstract": "No abstract." }, { "name": "Jeffreys, Cecil Edward Pruitt", "degree": "PhD", "year": "1931", "title": "Photochemical Reactions in Non-Aqueous Solutions : I. The Photochemical Formation of Chlorine Dioxide from Chlorine Monoxide in Carbon Tetrachloride Solution. II. The Photochemical Reaction of Iodine with Cyclohexene in Benzene Solution", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062024-180839937", "creators": [ { "name": { "family": "Jeffreys", "given": "Cecil Edward Pruitt" }, "id": "Jeffreys-Cecil-Edward-Pruitt", "display_name": "Jeffreys, Cecil Edward Pruitt" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/beqn-x303", "abstract": "No abstract." }, { "name": "Pomeroy, Richard Durant", "degree": "PhD", "year": "1931", "title": "The Diffusion of Gases in Oils", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09092024-201722610", "creators": [ { "name": { "family": "Pomeroy", "given": "Richard Durant" }, "id": "Pomeroy-Richard-Durant", "display_name": "Pomeroy, Richard Durant" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/wzc0-3m08", "abstract": "No abstract." }, { "name": "Ravitz, Sol Frederick", "degree": "PhD", "year": "1931", "title": "A. Photochemical Reactions Involving Tri-Iodine Ion. B. The Photochemical Reaction between Iodine Monochloride and Hydrogen", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:09092024-210528692", "creators": [ { "name": { "family": "Ravitz", "given": "Sol Frederick" }, "id": "Ravitz-Sol-Frederick", "display_name": "Ravitz, Sol Frederick" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xxeg-5247", "abstract": "No abstract." }, { "name": "Sage, Bruce Hornbrook", "degree": "Masters", "year": "1931", "title": "The Determination of the Solubility of Natural Gases in Crude Oils", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062024-154506775", "creators": [ { "name": { "family": "Sage", "given": "Bruce Hornbrook" }, "id": "Sage-Bruce-Hornbrook", "display_name": "Sage, Bruce Hornbrook" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0xt4-mr86", "abstract": "No abstract." }, { "name": "Shirley, Howard Emerson", "degree": "Masters", "year": "1931", "title": "The Progress of the Reactions in a Portland Cement Kiln, and A Method for the Production of Anhydrous Sodium Sulfate", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062024-185453476", "creators": [ { "name": { "family": "Shirley", "given": "Howard Emerson" }, "id": "Shirley-Howard-Emerson", "display_name": "Shirley, Howard Emerson" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vzj2-x573", "abstract": "No abstract." }, { "name": "Wenner, Ralph Richter", "degree": "PhD", "year": "1931", "title": "The Photochemical Decomposition of Hydrazine", "advisor": "Beckman, Arnold O.; Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechTHESIS:09062024-171104247", "creators": [ { "name": { "family": "Wenner", "given": "Ralph Richter" }, "id": "Ralph-Richter-Wenner", "display_name": "Wenner, Ralph Richter" } ], "advisors": [ { "name": { "family": "Beckman", "given": "Arnold O." }, "id": "Beckman-Arnold-O", "role": "advisor", "display_name": "Beckman, Arnold O." }, { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hjtw-a149", "abstract": "No abstract." }, { "name": "Woo, Sho-Chow", "degree": "PhD", "year": "1931", "title": "I. Potentiometric Determination of Iridium. II. Reduction Potential of Quadrivalent to Trivalent Iridium in Hydrochloric Acid Solution. III. The Absorption Spectra Structure and Dissociation Energies of the Gaseous Halogen Cyanides", "advisor": "Badger, Richard McLean", "url": "https://resolver.caltech.edu/CaltechTHESIS:09052024-151417377", "creators": [ { "name": { "family": "Woo", "given": "Sho-Chow" }, "id": "Woo-Sho-Chow", "display_name": "Woo, Sho-Chow" } ], "advisors": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-R-M", "role": "advisor", "display_name": "Badger, Richard McLean" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/86hm-mc28", "abstract": "No abstract." }, { "name": "Brantley, Lee Reed", "degree": "PhD", "year": "1930", "title": "High Temperature Equilibria", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08202024-224826900", "creators": [ { "name": { "family": "Brantley", "given": "Lee Reed" }, "id": "Brantley-Lee-Reed", "display_name": "Brantley, Lee Reed" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/hwky-r736", "abstract": "No abstract." }, { "name": "McRae, Daniel Brent", "degree": "PhD", "year": "1930", "title": "Investigations on the Reflection and Transmission Characteristics of Photographic Plates", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272024-185548335", "creators": [ { "name": { "family": "McRae", "given": "Daniel Brent" }, "id": "McRae-Daniel-Brent", "display_name": "McRae, Daniel Brent" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/994m-ar08", "abstract": "A method is described for measuring the reflection and\r\ntransmission of light by a photographic plate under conditions similar\r\nto those met in the ordinary use of the plate. The essential features\r\nof the work are the use of photographic methods of measurement and the\r\ndevelopment of a null method of working which eliminates from the discussion\r\nthe characteristic curve of the plate the degree of development\r\nor contrast, and which requires as a final step only a single\r\nmeasurement of the transmission of an optical wedge at some chosen\r\npoint.
\r\n\r\nA complete series of measurements was carried thru on several\r\nboxes of Eastman 40 plates, all of the same emulsion number. The\r\nmeasurements were made using white, blue, green and red light.
\r\n\r\nIt was found that for blue light the plate reflected 25%,\r\ntransmitted 9%, and absorbed 66%. The reflection and transmission\r\nlosses increased rapidly with increasing wavelength. The effect of\r\nexposure time on reflection and transmission was investigated and\r\nno change was found in these factors over considerably greater lengths\r\nof time than any of the exposures used in this work.
" }, { "name": "Pohl, Wadsworth Egmont", "degree": "Masters", "year": "1930", "title": "Studies on the Drying of Sugar Pine Lumber", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08272024-214529660", "creators": [ { "name": { "family": "Pohl", "given": "Wadsworth Egmont" }, "id": "Pohl-Wadsworth-Egmont", "display_name": "Pohl, Wadsworth Egmont" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/j4pa-kg61", "abstract": "No abstract." }, { "name": "Scoville, Loren P.", "degree": "Masters", "year": "1930", "title": "Experimental Studies of Oil Flow through Sands", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262024-210019529", "creators": [ { "name": { "family": "Scoville", "given": "Loren P." }, "id": "Scoville-Loren-P.", "display_name": "Scoville, Loren P." } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/byrq-2c70", "abstract": "No abstract." }, { "name": "Stapp, Frederick Pearce", "degree": "Masters", "year": "1930", "title": "The Rate of Diffusion of Methane in Liquid Hydrocarbons", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:09032024-184023419", "creators": [ { "name": { "family": "Stapp", "given": "Frederick Pearce" }, "id": "Stapp-Frederick-Pearce", "display_name": "Stapp, Frederick Pearce" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/jg9v-v519", "abstract": "No abstract." }, { "name": "Stenzel, Richard Werner", "degree": "Masters", "year": "1930", "title": "The Heat of Wetting of Silica Gel by Petroleum Hydrocarbons", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08262024-204024746", "creators": [ { "name": { "family": "Stenzel", "given": "Richard Werner" }, "id": "Stenzel-Richard-Werner", "display_name": "Stenzel, Richard Werner" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5fgq-2s27", "abstract": "No abstract." }, { "name": "Sturdivant, James Holmes", "degree": "PhD", "year": "1930", "title": "The Structure of the Ionic Crystals Brookite and Columbite", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-12012003-084446", "creators": [ { "name": { "family": "Sturdivant", "given": "James Holmes" }, "id": "Sturdivant-James-Holmes", "display_name": "Sturdivant, James Holmes" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/ANRX-9P07", "abstract": "No abstract." }, { "name": "Urmston, Joseph Winchester", "degree": "Masters", "year": "1930", "title": "Activity of Hydrochloric Acid in the Presence of Added Salts", "advisor": "Bates, Stuart Jeffery", "url": "https://resolver.caltech.edu/CaltechTHESIS:02272024-214831724", "creators": [ { "name": { "family": "Urmston", "given": "Joseph Winchester" }, "id": "Urmston-Joseph-Winchester", "display_name": "Urmston, Joseph Winchester" } ], "advisors": [ { "name": { "family": "Bates", "given": "Stuart Jeffery" }, "id": "Bates-Stuart-Jeffery", "role": "advisor", "display_name": "Bates, Stuart Jeffery" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3609-3p39", "abstract": "[Summary] The effect of added salts without a common ion upon the\r\nactivity of hydrochloric acid has been determined by measurements\r\nof the electromotive force of cells of the type
\r\n\r\nH2, HCl c1m + NaClO4 c2m, AgCl+Ag,
\r\n\r\nwhere e1 = 0.25 m, 0.1 m, 0.05 m and 0.005 m, and for values of \r\nc1 + c2 up to 1 m.
\r\n\r\nSimilar cells substituting KClO4 for NaClO4 were investigated \r\nover a concentration range which, however, was rather restricted due to \r\nthe limited solubility of potassium perchlorate.
\r\n\r\nThe results show that the activity coefficient of hydrochloric \r\nacid in the presence of the added salts without a common ion is, at \r\nsimilar ionic strengths, somewhat less than that of the pure acid, that \r\nis at a fixed concentration of acid the activity goes thru a minimum \r\nwith increasing ionic strength and then increases in a manner which is \r\nroughly similar to that observed for pure acid solutions.
\r\n\r\nThe ion attraction theory is discussed qualitatively. In \r\ndilute solutions it undoubtedly accounts for the facts upon a relatively \r\nsimple physical basis, but its extension to more concentrated solutions \r\nresulting in a two constant equation and the application of this to mixtures \r\nof electrolytes is probably largely empirical in nature.
\r\n\r\nThe fact that the activity coefficient of hydrochloric acid \r\nin its own pure solution, and in solution in the presence of a salt without a \r\ncommon ion including solutions which contain no acid, and whose \r\nproperties therefore depend entirely upon those of the added salt goes \r\nthru a minimum. with increasing ionic strength shows that this electrolyte \r\nis very readily \"salted out\". This behaviour is probably associated \r\nwith the unique structure of the hydrogen ion in that it has no electron \r\norbits to be deformed in the strong electrical field prevailing \r\nin concentrated solutions.
\r\n\r\nThe principle of linear variation of logo \u03b1 with the concentration\r\nof acid at constant total molality applies to mixtures of \r\nthe acid and sodium perchlorate in dilute solutions, but does not \r\nhold at concentrations from 0.25 m. to 1.0 m. In this last respect \r\nthe behaviour is different from that observed when a chloride is the \r\nadded salt.
\r\n\r\nThe results of this investigation are discussed in terms of \r\nthe effect of added salt upon the solubility of hydrochloric acid and \r\nits change in solubility with added salt is compared at similar initial \r\nsolubilities with those of thallous chloride and potassium perchlorate. \r\nFor hydrochloric acid in the presence of an added salt \r\nwithout a common ion, a solubility curve of a new type is disclosed, \r\nin that its solubility increases to a maximum and then decreases as \r\nthe concentration of added salt is increased.
" }, { "name": "Wellman, Homer Bigelow", "degree": "PhD", "year": "1930", "title": "The Equilibrium Between Bivalent and Quadrivalent Palladium and Chlorine in Hydrochloric Acid Solution", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10222018-160642927", "creators": [ { "name": { "family": "Wellman", "given": "Homer Bigelow" }, "id": "Wellman-Homer-Bigelow", "display_name": "Wellman, Homer Bigelow" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WPKP-CF15", "abstract": "[Introduction]
\r\n\r\nThe equilibrium between palladous and palladic chlorides and chlorine in hydrochloric acid solution seems not to have been previously measured, and no physico-chemical studies have been made as to the state in which bivalent and quadrivalent palladium exist in chloride solutions. It is well known, however, that from such solutions salts of the types R2Pd-Cl4 and R2PdCl6 separate, and it is probable that in such solutions the palladium exists mainly or wholly in the form of the corresponding ions PdCl4-- and PdCl6--. In that case the equilibrium to be here considered would be expressed by the simple equation: PdCl4-- + Cl2 = PdCl6--.
\r\n\r\n[...]
" }, { "name": "Dillon, Robert Troutman", "degree": "PhD", "year": "1929", "title": "Researches on the Normal Butenes", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-03222005-100208", "creators": [ { "name": { "family": "Dillon", "given": "Robert Troutman" }, "id": "Dillon-Robert-Troutman", "display_name": "Dillon, Robert Troutman" }, { "name": { "family": "Young", "given": "William Gould" }, "id": "Young-William-Gould", "display_name": "Young, William Gould" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/9TNB-D116", "abstract": "No abstract." }, { "name": "Hincke, William Berrard", "degree": "PhD", "year": "1929", "title": "Equilibrium Between Aluminum Carbide and Nitrogen at High Temperature", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08152024-202623799", "creators": [ { "name": { "family": "Hincke", "given": "William Berrard" }, "id": "Hincke-William-Berrard", "display_name": "Hincke, William Berrard" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6990-w486", "abstract": "No abstract." }, { "name": "Kirschman, H. Darwin", "degree": "PhD", "year": "1929", "title": "Analytical Studies by Potentiometric Methods", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08212024-164714071", "creators": [ { "name": { "family": "Kirschman", "given": "H. Darwin" }, "id": "Kirschman-H-Darwin", "display_name": "Kirschman, H. Darwin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cr30-6a70", "abstract": "No abstract." }, { "name": "Baxter, Warren Phelps", "degree": "PhD", "year": "1928", "title": "Activation of Molecular Hydrogen by Electron Impact. Quantum Yield in the Photochemical Decomposition of Nitrogen Dioxide. Mechanism of the Photochemical Decomposition of Nitrogen Pentoxide", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252005-131836", "creators": [ { "name": { "family": "Baxter", "given": "Warren Phelps" }, "id": "Baxter-Warren-Phelps", "display_name": "Baxter, Warren Phelps" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KEEQ-CB73", "abstract": "No abstract." }, { "name": "Dalton, Robert Hennah", "degree": "PhD", "year": "1928", "title": "Activation of Molecular Hydrogen by Electron Impact. Velocity Distribution of Electrons Issuing from Small Holes. Activation of Gases by Electron Impact", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-091511", "creators": [ { "name": { "family": "Dalton", "given": "Robert Hennah" }, "id": "Dalton-Robert-Hennah", "display_name": "Dalton, Robert Hennah" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/1K4P-YQ61", "abstract": "No abstract." }, { "name": "Nordberg, Martin Emery", "degree": "PhD", "year": "1928", "title": "The Decomposition of Ozone-Nitrogen Pentoxide Mixtures", "advisor": "Tolman, Richard Chace", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252005-153549", "creators": [ { "name": { "family": "Nordberg", "given": "Martin Emery" }, "id": "Nordberg-Martin-Emery", "display_name": "Nordberg, Martin Emery" } ], "advisors": [ { "name": { "family": "Tolman", "given": "Richard Chace" }, "id": "Tolman-R-C", "role": "advisor", "display_name": "Tolman, Richard Chace" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JATY-HG31", "abstract": "No abstract." }, { "name": "Preble, Bennett", "degree": "Bachelors", "year": "1928", "title": "The Suitability of Some California Grown Eucalypts for Paper Pulp", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-03102005-102313", "creators": [ { "name": { "family": "Preble", "given": "Bennett" }, "id": "Preble-Bennett", "display_name": "Preble, Bennett" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/R013-E503", "abstract": "Pulp and paper men in recent years have taken much interest in the development of new species to take the place of the rapidly disappearing supplies of the softwoods which are at present so necessary to the industry. In 1922, the latest year for which figures are available, seventy-seven percent of the wood used for pulp in the United States was either spruce, fir or hemlock. As much as fifty-five percent of the pulpwood was from a single group of conifers, the spruces. With this concentration on a small number of species, it is not surprising that it is now becoming increasingly important to find ways in which other woods can be used economically in place of the conifers. The western hemlock, now used so extensively in the Pacific Northwest, was formerly held to be unsuitable for pulp manufacture and is a good example of the adaptation of a new species. Douglas Fir is another wood which is just now beginning to be used. A recent bulletin issued by the U.S. Dept. of Agriculture gives the results of tests made at the Forest Products Laboratory in Madison, Wisconsin, on some ninety-four American woods. The pulping tests were made by the four commercial processes now in general use. A large percentage of the woods were those known as hardwoods. The pulp and paper industry in 1922 used 790,000 cords of hardwoods and about 4,750,000 cords of softwoods." }, { "name": "Scudder, Nathan Frost", "degree": "Masters", "year": "1928", "title": "Further Studies Toward the Prevention of Brown Stain in Sugar Pine Lumber", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-03072005-130729", "creators": [ { "name": { "family": "Scudder", "given": "Nathan Frost" }, "id": "Scudder-Nathan-Frost", "display_name": "Scudder, Nathan Frost" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/NFF4-VX56", "abstract": "Since this report is a continuation of the work described by Mr. Steinour in his thesis, and rightly should accompany that thesis, the reader is referred directly to it for a description of the nature of the problem, the existing knowledge pertaining to it before Mr. Steinour started his work, and the facts concerning the stain and means of preventing it that he discovered. The experimental method he developed for making small scale kiln drying experiments was followed exactly in every detail, including the use of the same drying oven and instruments, and the same assumptions in calculating the data taken, so that the results described herein should be entirely comparable." }, { "name": "Steinour, Harold Heiges", "degree": "PhD", "year": "1928", "title": "The Potential of Inert Electrons in Sulfurous Acid Solution", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-02232005-154106", "creators": [ { "name": { "family": "Steinour", "given": "Harold Heiges" }, "id": "Steinour-Harold-Heiges", "display_name": "Steinour, Harold Heiges" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/M3NF-MT71", "abstract": "Certain reducing substances, such as sulfurous acid, formic acid, or oxalic acid, show in their chemical behavior a much smaller reducing power than that calculated from the free-energy changes attending their conversion into their ordinary oxidation products, sulfuric acid or carbon dioxide and water. This fact is especially pronounced in the case of sulfurous acid, where a fairly definite electrode-potential (about -0.4 volts) results, which is in much better agreement with its known chemical behavior than is the potential (-0.14 volts) calculated for the conversion of SO2 (1 atm.) to SO4= (1 m.)
\r\n\r\nThe probable nature of the electrode process has been considered by Carter and James. In view of the apparent discrepancy with the calculated sulfite-sulfate potential, they considered the observed potential to be due to the tendency of the sulfur dioxide to be reduced rather than oxidized, an assumption which is also justified by its chemical behavior, which will be discussed later. Since experiments in which sulfur was added to the electrode vessel did not improve the constancy or reproducibility of the potential (which varied over 0.05 volts), they concluded that the sulfur was without effect, and that an intermediate reduction-product of sulfurous acid was concerned, which their experiments on the cathodic reduction in acid solution led them to believe was hydrosulfurous acid, H2S2O4.
\r\n\r\nThe present work is a further contribution to the interpretation of this sulfur dioxide potential. It is concerned chiefly with the potentials exhibited at a platinized platinum electrode in a half-cell containing sulfur dioxide in acid solution under various conditions of concentration, temperature, and agitation, and in the presence of certain other substances.
" }, { "name": "Ure, William", "degree": "PhD", "year": "1928", "title": "A Test of the Radiation Hypothesis of Chemical Reaction", "advisor": "Tolman, Richard Chace", "url": "https://resolver.caltech.edu/CaltechETD:etd-02282005-092521", "creators": [ { "name": { "family": "Ure", "given": "William" }, "id": "Ure-William", "display_name": "Ure, William" } ], "advisors": [ { "name": { "family": "Tolman", "given": "Richard Chace" }, "id": "Tolman-R-C", "role": "advisor", "display_name": "Tolman, Richard Chace" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/CDKJ-6283", "abstract": "The viewpoint that thermal unimolecular reactions are to be considered as photochemical reactions with the activating frequencies lying in the infra-red region should be susceptible of experimental test by subjecting a system to radiation from an outside source, and determining whether or not the thermal reaction rate is thereby increased. The difficulties in such an experiment arise from two sources. First, there is the necessity of obtaining a high intensity of infra-red radiation, without at the same time raising the temperature of the reacting substance to such a point that the normal thermal rate is the preponderating effect. In the second place, the extreme opacity of almost all substances to all but the shortest of infra-red rays makes it difficult to find a window that will permit a high intensity over the wide range of frequencies which may be important in activating the molecules. For, since we do not know in what part of the infra-red spectrum the activating frequencies might lie, a conclusive test of the hypothesis should involve the use of all frequencies which are present to an appreciable extent in a hohlraum at the thermal reacting temperature." }, { "name": "Bilicke, Albert Constant", "degree": "Masters", "year": "1927", "title": "The Space-Group and Molecular Symmetry of Beta-Benzenehexabromide and Hexachloride", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12092004-113152", "creators": [ { "name": { "family": "Bilicke", "given": "Albert Constant" }, "id": "Bilicke-Albert-Constant", "display_name": "Bilicke, Albert Constant" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KRQ9-E936", "abstract": "The small crystallographic symmetry of most organic compounds has limited the determination of their structures by crystal-structure researches. Yet many problems of structural organic chemistry can be so answered. We have determined the space-group and molecular symmetry of \u03b2-benzene hexabromide and hexachloride, and have obtained information of value in the interpretation of the geometrical isomerism of these compounds.
\r\n\r\nBoth benzene hexabromide, C6H6Br6 and benzene hexacholoride, C6H6Cl6, crystallize in two modifications differing markedly in physical properties. The monoclinic forms, designated alpha, have been assigned the \"trans\" configuration. The \"cis\" or beta modification of the hexabromide crystallizes in the cubic system, while the hexachloride has been reported to form hexagonal crystals which are pseudocubic. Our investigation has been restricted to the beta forms.
\r\n" }, { "name": "Datin, Richard Clyde", "degree": "Bachelors", "year": "1927", "title": "The Bromination of Para-Cresol in the Presence of Strong Acids", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-130128", "creators": [ { "name": { "family": "Datin", "given": "Richard Clyde" }, "id": "Datin-Richard-Clyde", "display_name": "Datin, Richard Clyde" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/93SS-KP67", "abstract": "The purpose of this work has been to determine whether or not the formation of an oxonium compound of a cresol would change the directing influence of the hydroxyl group.\r\n" }, { "name": "Ewing, Frederick Junior", "degree": "Bachelors", "year": "1927", "title": "Investigation on the Possibility of Differential Reduction from the Standpoint of Oxidation-Reduction Potentials", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102004-141151", "creators": [ { "name": { "family": "Ewing", "given": "Frederick Junior" }, "id": "Ewing-Frederick-Junior", "display_name": "Ewing, Frederick Junior" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/JSKE-7E31", "abstract": "No abstract." }, { "name": "Pomeroy, Richard Durant", "degree": "Masters", "year": "1927", "title": "Use of Adsorbents in Natural Gas Analysis", "advisor": "Millikan, Robert Andrews", "url": "https://resolver.caltech.edu/CaltechETD:etd-12272004-135856", "creators": [ { "name": { "family": "Pomeroy", "given": "Richard Durant" }, "id": "Pomeroy-Richard-Durant", "display_name": "Pomeroy, Richard Durant" }, { "name": { "family": "Campbell", "given": "John Stuart" }, "id": "Campbell-John-Stuart", "display_name": "Campbell, John Stuart" } ], "advisors": [ { "name": { "family": "Millikan", "given": "Robert Andrews" }, "id": "Millikan-R-A", "role": "advisor", "display_name": "Millikan, Robert Andrews" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5GP7-C585", "abstract": "No abstract. " }, { "name": "Schultz, Murray Navarre", "degree": "Bachelors", "year": "1927", "title": "The Sulfonation of Ortho Toluidine and the Preparation of Sodium 6-Chloro-5-Nitro-Meta-Tolene Sulfonate", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-133814", "creators": [ { "name": { "family": "Schultz", "given": "Murray Navarre" }, "id": "Schultz-Murray-Navarre", "display_name": "Schultz, Murray Navarre" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/7QT9-YD51", "abstract": "No abstract.\r\n\r\n" }, { "name": "Stone, Donald Stuart", "degree": "Bachelors", "year": "1927", "title": "The Catalytic Effect of Osmium Tetroxide on the Oxidation of Hydrazine by Potassium Chlorate", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-140817", "creators": [ { "name": { "family": "Stone", "given": "Donald Stuart" }, "id": "Stone-Donald-Stuart", "display_name": "Stone, Donald Stuart" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/0HWT-WM67", "abstract": "No abstract." }, { "name": "Thompson, Donald Raw", "degree": "Bachelors", "year": "1927", "title": "The Preparation of 2 Heptanol and Investigations into Methods for the Preparation of Alpha Napthylisocyanate as Preliminary Syntheses for the Determination of the Properties of the Urethanes of Four Isomeric Heptyl Alcohols", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-143231", "creators": [ { "name": { "family": "Thompson", "given": "Donald Raw" }, "id": "Thompson-Donald-Raw", "display_name": "Thompson, Donald Raw" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/BXR2-1T52", "abstract": "No abstract." }, { "name": "Winegarden, Howard Merlin", "degree": "Masters", "year": "1927", "title": "The Determination of Carbon Dioxide in Fermenting Mixtures. Co-Zymase: a Study of Purification Methods", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12272004-144412", "creators": [ { "name": { "family": "Winegarden", "given": "Howard Merlin" }, "id": "Winegarden-Howard-Merlin", "display_name": "Winegarden, Howard Merlin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/R7YV-A670", "abstract": "No abstract." }, { "name": "Alles, Gordon Albert", "degree": "PhD", "year": "1926", "title": "The Comparative Physiological Action of Some Derivatives Of Guanidine", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11022004-113158", "creators": [ { "name": { "family": "Alles", "given": "Gordon Albert" }, "id": "Alles-Gordon-Albert", "display_name": "Alles, Gordon Albert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X65Z-KB54", "abstract": "Guanidine, methylguanidine and asymmetric dimethylguanidine are of extended biological interest. Guanidine itself has been isolated as a nitrogenous constituent of some plants, [1,2] while methyl and dimethyl guanidine probably play a part in intermediary nitrogen metabolism and have been isolated as physiological constituents in the urine of the dog, horse and man. [3,4,5].
\r\n\r\nPathologically these compounds have considerable interest from many points of view. Koch [6] found methylguanidine in the urine of parathyroidectomized dogs and later reported the presence of guanidine, symmetric and asymmetric dimethylguanidine, choline, neurine and histamine. [7] Henderson [8] reports that with such dogs there is a decreased muscular content of substances containing guanidine complex. Burns and Sharpe [9] carefully determined the guanidine and methylguanidine in the blood of animals after parathyroidectomy and found a marked increase of these substances, together with an increase of these bases in the urine, as had been reported by Koch. Paton and Findlay [10] showed that the symptoms of tetania parathyreopriva are identical with those produced by the administration of guanidine and methylguanidine, and Watanabe [11] has shown that the injection of guanidine causes hypoglucemia, calcium decrease in the blood, phosphate retention and acidosis similar to the metabolic changes occurring after parathyroidectomy. Burns and Sharpe [9] found an increased content of guanidine and methylguanidine in the urine of children with idiopathic tetany and Findlay and Sharpe [12] and Nattrass and Sharpe [13] found an increased excretion of dimethylguanidine. Methylguanidine has been isolated from the faeces of children with idiopathic tetany.
\r\n\r\nMajor [15] believes that there is a possible relationship between metabolism and hypertension in man. Fairly large quantities of methylguanidine are reported to occur in the urine of animals killed by anaphylactic shock or by burning, according to Heyde [16,17] and it has been suggested that the poison produced by shock may be the methylguanidine elaborated by the toxicogenic destruction of protein. Heyde reported [16] that methylguanidine poisoning in gunea-pigs and rabbits showed a marked similarity to anaphylactic shock, but F\u00fchner [18] using rabbits and Loewitt [19] using guinea-pigs were not able to observe any marked lung action when using a synthetic methylguanidine.
\r\n\r\nGuanidine and especially methylguanidine have been shown to be active in decreasing the poisonous action of protein split-products by Weichardt and Schwenk. [20] Similar to this is the observation of Burns that methylguanidine protects sensitized animals from toxic doses of antigenic protein. The possible relationship of the guanidines to epilepsy, epidemic encephalitis and various protein intoxications has been discussed in the literature.
\r\n\r\nBecause of the widespread interest regarding the physiological activity of guanidine, its methyl and asymmetric dimethyl derivatives, it seemed that a study of the relation between chemical constitution and certain physiological actions of several guanidine derivatives would be desirable. Pharmacological studies have been made by previous workers with the following derivatives [22,23]; guanidine, methylguanidine, asymmetric dimethylguanidine, dicyandiamidine, glycocyamine, creatine and agmatine. These studies in the case of guanidine, methylguanidine and dimethylguanidine have fairly completely covered their general physiological action, but little attempt has been made to carefully compare their relative physiological activity. For the study of the derivatives prepared in this work it was decided that careful observations of their blood pressure and respiratory effects, together with toxicity determinations would offer the best comparisons of their relative physiological activity.
\r\n\r\nThe glucemic effect of these derivatives was also investigated as it seemed probable that a variation in chemical constitution might produce a substance having a hypoglucemic activity much greater than that of guanidine itself. [11] Such a fact would be of considerable importance with regard to speculations concerning a possible chemical constitution of insulin.
" }, { "name": "Ball, Alpheus M.", "degree": "Bachelors", "year": "1926", "title": "A Method for the Manufacture of Phosphate Fertilizer", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12092004-110048", "creators": [ { "name": { "family": "Ball", "given": "Alpheus M." }, "id": "Ball-Alpheus-M", "display_name": "Ball, Alpheus M." }, { "name": { "family": "Fahs", "given": "John Louis" }, "id": "Fahs-John-Louis", "display_name": "Fahs, John Louis" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2X6M-P768", "abstract": "No abstract." }, { "name": "Baxter, Warren Phelps", "degree": "Masters", "year": "1926", "title": "The Interionic Attraction Theory of Ionized Solutes. Testing the Theory of Alcohol Solvents and by Solubility Experiments at Higher Temperature", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11112004-144145", "creators": [ { "name": { "family": "Baxter", "given": "Warren Phelps" }, "id": "Baxter-Warren-Phelps", "display_name": "Baxter, Warren Phelps" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3QH4-R578", "abstract": "No abstract.\r\n" }, { "name": "Carter, James Maurice", "degree": "Bachelors", "year": "1926", "title": "Catalytic Effect of Ruthenium Compound on the Reduction of Perchloric Acid by Hydrobromic Acid", "advisor": "Yost, Don M.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12302004-142437", "creators": [ { "name": { "family": "Carter", "given": "James Maurice" }, "id": "Carter-James-Maurice", "display_name": "Carter, James Maurice" } ], "advisors": [ { "name": { "family": "Yost", "given": "Don M." }, "id": "Yost-D-M", "role": "advisor", "display_name": "Yost, Don M." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3QJZ-MK77", "abstract": "No abstract." }, { "name": "Friauf, James Byron", "degree": "PhD", "year": "1926", "title": "The Crystal Structure of MgZn\u2082", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechETD:etd-11112004-102634", "creators": [ { "name": { "family": "Friauf", "given": "James Byron" }, "id": "Friauf-James-Byron", "display_name": "Friauf, James Byron" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A7KS-CZ31", "abstract": "[See Abstract in scanned thesis]." }, { "name": "Hendricks, Sterling Brown", "degree": "PhD", "year": "1926", "title": "Crystal Structure Determinations", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechETD:etd-06042004-135746", "creators": [ { "name": { "family": "Hendricks", "given": "Sterling Brown" }, "id": "Hendricks-Sterling-Brown", "display_name": "Hendricks, Sterling Brown" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BXG4-P850", "abstract": "No Abstract." }, { "name": "House, Harvey W.", "degree": "Masters", "year": "1926", "title": "The Activation of Sawdust Carbon for Decolorization", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11112004-111421", "creators": [ { "name": { "family": "House", "given": "Harvey W." }, "id": "House-Harvey-W", "display_name": "House, Harvey W." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HYWP-K634", "abstract": "No abstract." }, { "name": "Kirkpatrick, L. Merle", "degree": "PhD", "year": "1926", "title": "I. The Crystal Structure of Sodium Periodate. II. The Space Group Symmetry of Sodium Nitrate. III. The Crystal Structure of the Cubic Modification of Telluric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052004-134335", "creators": [ { "name": { "family": "Kirkpatrick", "given": "L. Merle" }, "id": "Kirkpatrick-L-Merle", "display_name": "Kirkpatrick, L. Merle" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/C0Z7-DP75", "abstract": "No Abstract." }, { "name": "Prescott, Charles Holden Jr.", "degree": "PhD", "year": "1926", "title": "The High Temperature Equilibrium Between Zirconium and Carbon", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102004-141753", "creators": [ { "name": { "family": "Prescott", "given": "Charles Holden Jr." }, "id": "Prescott-Charles-Holden-Jr", "display_name": "Prescott, Charles Holden Jr." } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/KR4H-HF27", "abstract": "No abstract." }, { "name": "Schott, Hermann Franz", "degree": "Bachelors", "year": "1926", "title": "The Molal Reduction Potential of a Selenium and the Free Energy of Selenious Acids From Equilibrium Measurements", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11222004-144046", "creators": [ { "name": { "family": "Schott", "given": "Hermann Franz" }, "id": "Schott-Hermann-Franz", "display_name": "Schott, Hermann Franz" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6VJG-TD52", "abstract": "No abstract." }, { "name": "Valby, Edgar Peterson", "degree": "Bachelors", "year": "1926", "title": "The Ionization Constant of Para Cyanobenzoic Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-145203", "creators": [ { "name": { "family": "Valby", "given": "Edgar Peterson" }, "id": "Valby-Edgar-Peterson", "display_name": "Valby, Edgar Peterson" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZFK9-ZQ29", "abstract": "No abstract." }, { "name": "Voelker, Joachim Frank", "degree": "Bachelors", "year": "1926", "title": "Acrolein and Certain of its Derivatives", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11292004-142602", "creators": [ { "name": { "family": "Voelker", "given": "Joachim Frank" }, "id": "Voelker-Joachim-Frank", "display_name": "Voelker, Joachim Frank" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XRXX-CE73", "abstract": "In connection with a theory as to the mechanism of alcoholic fermentation, certain of the unknown trioses were desired in order that their properties might be studied. These compounds which were of particular interest were:Due to the fact that perchloric acid resembles sulfuric acid in many respects without having many of the disadvantages of use possessed by the latter, the devising of a cheaper means of producing it would be well warranted by its increased use in both analytical and industrial work. The present work was undertaken with the above idea in view and consisted in studying quantitatively the reaction taking place between nitric oxide (NO), nitric acid, and ammonium perchlorate.
\r\n\r\nAnhydrous perchloric acid is an unstable compound, decomposing spontaneously after a few weeks even when kept in the dark. It is a violently reacting oxidizing agent for many organic substances but aqueous solutions of the acid are not affected by light and are not active oxidizing agents.
\r\n\r\nPerchloric acid solutions (60% strength being the standard commercial form of the acid) are strong, mono-basic solutions which are stable up to the 60% strength and have high boiling points. The salts which the acid forms are nearly all soluble, the potassium, rubidium, caesium and thallium perchlorates being the only ones which are only slightly soluble. This would recommend it over sulfuric acid in many cases where insoluble salts of the latter prevent its use or cause it to seriously interfere on this account in analytical determinations. Also the difference in the solubilities of the potassium and sodium salts permits an easy separation of the perchlorates of these two metals. The maximum boiling point of aqueous solutions at atmospheric pressure is 203\u00b0 C., which corresponds to a constant boiling mixture having a perchloric acid content of 72.3%. Below 160\u00b0C. the distillate contains less than 1% of perchloric acid. Most perchlorates are deliquescent except ammonium, potassium, lead and mercury salts.
\r\n\r\nThere have been a number of processes devised for the production of perchloric acid, some of which are only of theoretical importance, but the following methods are the ones which have been used to some extent commercially:
\r\n\r\n(a) The mixing of dry NaClO4 or KClO4 with H2SO4 and distilling the mixture under diminished pressure. The distillation process is a troublesome and expensive one and redistillation must take place to remove the H2SO4 and obtain a pure acid \u2013 the product containing 88-89% HClO4. HCl can be substituted for H2SO4 being precipitated from the solution. The HCl can then be distilled off from the filtrate and an approximately 95% HClO4 acid obtained. However, there are small amounts of NaClO4 still remaining which require distillation under reduced pressure to effect their removal.
\r\n\r\n(b) The electrolytic oxidation of HCl in dilute solution is the method used in this country at the present time for commercial production. However the resulting liquir contains HCl, chloric acids and chlorine in addition to the HClO4. Also the acid obtained is quite dilute and must be concentrated for commercial use.
\r\n\r\nThe above methods are expensive to operate due to the necessity of purification and concentration of the acid resulting from the reaction used, and the use of NH4ClO4 as a source of HClO4 has been advocated as the best means of overcoming the above objections. NH4ClO4 can be obtained comparatively cheaply and when purified and the ammonium radical oxidized by oxides of nitrogen, there are no non-volatile impurities remaining in the product. All gases and volatile liquids can be easily distilled off at atmospheric pressure and any further concentration of the product can be accomplished at the same time although no such amount of concentration will be required as in (b) cited above.
\r\n\r\nInvestigation of the possibilities of the above method is the object of the present work which is a continuation of the work begun at the Institute in 1921 by R.W. Stenzel and continued in the following year by A.W. Knight and in 1924 by V.A. Kalichevsky.
\r\n" }, { "name": "Allen, William Head", "degree": "Bachelors", "year": "1925", "title": "Oxidation of Valeric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12072004-160451", "creators": [ { "name": { "family": "Allen", "given": "William Head" }, "id": "Allen-William-Head", "display_name": "Allen, William Head" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ZK8H-KX74", "abstract": "No abstract." }, { "name": "Banks, Sydney Allen", "degree": "Bachelors", "year": "1925", "title": "A Study of a Grid Failure in Lead Storage Batteries", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-12092004-111648", "creators": [ { "name": { "family": "Banks", "given": "Sydney Allen" }, "id": "Banks-Sydney-Allen", "display_name": "Banks, Sydney Allen" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/X0K9-4V54", "abstract": "No abstract." }, { "name": "Dalton, Robert Hennah", "degree": "Bachelors", "year": "1925", "title": "A System of Qualitative Analysis for Tellurium, Molybdenum, Iridium, Rhodium and the Copper Group Elements", "advisor": "Noyes, Arthur A.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072024-173813001", "creators": [ { "name": { "family": "Dalton", "given": "Robert Hennah" }, "id": "Dalton-Robert-Hennah", "display_name": "Dalton, Robert Hennah" } ], "advisors": [ { "name": { "family": "Noyes", "given": "Arthur A." }, "id": "Noyes-A-A", "role": "advisor", "display_name": "Noyes, Arthur A." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/fy0b-7v23", "abstract": "No abstract." }, { "name": "Diack, Samuel Latta", "degree": "Bachelors", "year": "1925", "title": "The Reduction of Tungstic Oxide to Tungsten", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12102004-142411", "creators": [ { "name": { "family": "Diack", "given": "Samuel Latta" }, "id": "Diack-Samuel-Latta", "display_name": "Diack, Samuel Latta" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/MY81-ET78", "abstract": "No abstract." }, { "name": "Dillon, Robert Troutman", "degree": "Bachelors", "year": "1925", "title": "The Addition of a Halogen Hydride to 3-Heptene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-12062004-162616", "creators": [ { "name": { "family": "Dillon", "given": "Robert Troutman" }, "id": "Dillon-Robert-Troutman", "display_name": "Dillon, Robert Troutman" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WGN6-SW81", "abstract": "The purpose of this study is to determine the relative affinity for electrons of the ethyl and propyl groups and thereby to check the indications of the ionization constants of certain acids and amines. The ionization constants of methyl, ethyl and propyl amines and acetic, propionic and butyric acids, indicate that the ethyl group has a smaller affinity for electrons than either the methyl or the propyl group. Lucas and Moyse have shown this to be true with respect to the methyl group and it is the intent of this work to investigate the evidence with respect to the propyl group.
\r\n\r\nTwo theories regarding the electronic character of carbon union have been proposed. The first is the alternate polarity theory which has been supported and worked on by Cuy. The second is the displacement theory which has been proposed by Lewis and has been used by Latimer and Rodebush in accounting for the ionization constants of some acids of phosphorus. The latter theory has also been worked on in this laboratory by Lucas and Jameson, Lucas, Simpson and Carter and Lucas and Moyse.
\r\n\r\nAccording to the alternate polarity theory the carbon atoms in aliphatic chain tend to become arranged alternately positive and negative. Therefore, 3-heptene (minus the hydrogen atoms) would appear to be:
\r\n[See Abstract for chemical formula].
\r\nAs may be seen C-3 is preponderantly negative while C-4 is positive. Therefore, when a strong polar compound such as hydrogen bromide is added to this unsaturated hydrocarbon, the positive hydrogen will go to C-3, while the bromine will go to C-4. The theory consequently predicts the formation of 4-bromo-heptane on the addition of hydrogen bromide to 3-heptene.
The ionization constant, Ka of propionic acid is 1.35 x 10-5 and of butyric acid is 1.65 x 10-5, while Kb of ethyl amine is 5.6 x 10-4 and of proyl amine is 4.7 x 10-4. These values indicate that the propyl group has a greater affinity for electrons than the ethyl group. The validity of this apparent difference in affinity for electrons forms the basic assumption on which the displacement theory is based. This difference results in the displacement of the electronic orbits in the chain, which may be represented by a displacement of the average position of the electron pair. Therefore, 3-heptene (minus the hydrogen atoms) would appear to be:
\r\n[See Abstract for chemical formula].
\r\nConsideration of the preceding diagram indicates that C-3 is essentially positive in comparison to C-4. When hydrogen bromide is added to this hydrocarbon the theory predicts the formation of 3-bromo-heptane. This is opposite to that predicted by the first theory.
A factor which must be considered in dealing with this problem is that of symmetry of the molecule. Reference to innumerable organic compounds shows that the tendency towards this symmetrical formation is exceedingly great. In the addition of hydrogen bromide to 2-pentene as well s to 3-heptene, as mentioned above, the two theories predict different products. In the case of 2-pentene, the symmetrical form is predicted by the displacement theory, and this isomer in the work of Lucas and Moyse was found to be formed in excess. However, in the case of 3-heptene the unsymmetrical form is predicted. Therefore if the unsymmetrical form is produced in excess the evidence shows unquestionably the agreement of the electron affinities of the ethyl and propyl groups with the indications of the ionization constants. It also shows the factor of symmetry to be of minor importance compared to that of electron affinity. On the other hand, if the symmetrical form is produced in excess the evidence shows that the factor of symmetry is not of minor importance.
\r\n" }, { "name": "Emmett, Paul Hugh", "degree": "PhD", "year": "1925", "title": "I. The Reduction of Nickelous and Ferric Oxides by Hydrogen. II. The Catalytic Synthesis of Water Vapor on the Presence of Metallic Nickel", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10262017-143242550", "creators": [ { "name": { "family": "Emmett", "given": "Paul Hugh" }, "id": "Emmett-Paul-Hugh", "display_name": "Emmett, Paul Hugh" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5PHZ-9J45", "abstract": "A study has been made by a flow method of the combination of hydrogen and\r\noxygen in contact with reduced nickel, using oxygen concentrations up to 5%.
\r\n\r\n1. At all temperatures at which any water formation could be detected it\r\nwas found that superficial oxidation of the nickel readily took place. At the\r\nlower temperatures this oxidation eventually covered the whole surface, with\r\nthe result that the rate of catalysis suddenly decreased to a small value.
\r\n\r\n2. When hydrogen was passed over a catalyst superficially oxidized in\r\nthis way, the rate of reduction accelerated auto-catalytically, in conformity\r\nwith the previous observation that the reduction of ordinary nickel oxide is\r\nan interfacial reaction, that is, a reaction whose rate depends on the area of\r\ncontact between the two solid phases. However, the maximum rates of reduction\r\nso obtained were always very small in comparison with the rates of the\r\nhydrogen-oxygen catalysis at the same temperature.
\r\n\r\n3. It was found that under certain conditions the rate of reduction\r\nwas considerably increased by the presence of oxygen in the hydrogen.
\r\n\r\n4. Arguments are presented to show that the area of contact between the\r\nnickel oxide and the nickel, and therefore also the rate of reduction, are\r\nvery much greater in the catalytic process than in the reduction of a completely\r\noxidized surface by hydrogen alone.
\r\n\r\n5. The conclusion is reached that the catalytic water formation can be\r\nlargely and perhaps entirely accounted for on the theory of successive oxidation\r\nand reduction of the catalyst.
\r\n\r\nIn conclusion we wish to record our indebtedness to the Carnegie Institution\r\nof Washington for financial aid in this investigation from a grant made to \r\nProf. A. A. Noyes.
\r\n" }, { "name": "Ferkel, Albert Jefferson", "degree": "Bachelors", "year": "1925", "title": "The Extraction and Precipitation of Pectin", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062024-184852993", "creators": [ { "name": { "family": "Ferkel", "given": "Albert Jefferson" }, "id": "Ferkel-Albert-Jefferson", "display_name": "Ferkel, Albert Jefferson" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ehz1-ee02", "abstract": "No abstract." }, { "name": "Hart, Edward Whipple", "degree": "Bachelors", "year": "1925", "title": "The Bromination of Para-Cresol in the Presence of Strong Acids", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062024-211921874", "creators": [ { "name": { "family": "Hart", "given": "Edward Whipple" }, "id": "Hart-Edward-Whipple", "display_name": "Hart, Edward Whipple" } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/dm40-6b05", "abstract": "No abstract." }, { "name": "Hess, Ben Ewart", "degree": "Bachelors", "year": "1925", "title": "A Method for the Recovery of Alumina and other Valuable Constituents from Clay", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062024-224911379", "creators": [ { "name": { "family": "Hess", "given": "Ben Ewart" }, "id": "Hess-Ben-Ewart", "display_name": "Hess, Ben Ewart" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vqd3-jm20", "abstract": "No abstract." }, { "name": "Pauling, Linus Carl", "degree": "PhD", "year": "1925", "title": "The Determination With X-Rays of the Structures of Crystals", "advisor": "Dickinson, Roscoe Gilkey", "url": "https://resolver.caltech.edu/CaltechETD:etd-05142003-141307", "creators": [ { "name": { "family": "Pauling", "given": "Linus Carl" }, "id": "Pauling-Linus-Carl", "display_name": "Pauling, Linus Carl" } ], "advisors": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-R-G", "role": "advisor", "display_name": "Dickinson, Roscoe Gilkey" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/F7V6-4P98", "abstract": "No Abstract." }, { "name": "Prentice, Leland Busby", "degree": "Bachelors", "year": "1925", "title": "Dehydration of Alcohol by Potassium Carbonate", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:10172011-143206819", "creators": [ { "name": { "family": "Prentice", "given": "Leland Busby" }, "id": "Prentice-Leland-Busby", "display_name": "Prentice, Leland Busby" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ADR8-HW51", "abstract": "No Abstract." }, { "name": "Ranney, Kenneth Wyckoff", "degree": "Bachelors", "year": "1925", "title": "A Fusion Method for the Production of Sodium Fluoride", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072024-161746447", "creators": [ { "name": { "family": "Ranney", "given": "Kenneth Wyckoff" }, "id": "Ranney-Kenneth-Wyckoff", "display_name": "Ranney, Kenneth Wyckoff" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3vz0-2w58", "abstract": "No abstract." }, { "name": "Raymond, Albert L.", "degree": "PhD", "year": "1925", "title": "The Mechanism of Alcoholic Fermentation", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-11052004-164657", "creators": [ { "name": { "family": "Raymond", "given": "Albert L." }, "id": "Raymond-Albert-L", "display_name": "Raymond, Albert L." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/P58Q-KP97", "abstract": "The alcoholic fermentation of sugar containing materials is one of the oldest biochemical processes of which we have historical record. On the other hand, only in recent years have we acquired much evidence as to the mechanism by which alcohol and carbon dioxide are formed from the sugar. Although Pasteur proved conclusively that fermentation is closely associated with the life of certain organisms, yet it was not until Buchner showed that fermentation may take place in the absence of living cells that the importance of organic catalysts was realized. It was these researchers of Buchner which made possible the intelligent investigation of this important mechanism.
\r\n\r\nIn the several years which have passed since this memorable discovery, and enormous amount of work has been done in the field and many data have accumulated. Many theories have also been advanced to explain the confusing results which have been obtained, but objections have been raised to all that have so far been presented. On reviewing these theories, however, it seemed possible by a slight modification of some of them to account for a large proportion of the available facts in a modified theory. Since modified theory suggests the advisability of a number of experimental investigations, it would seem of value to give an account of it at the present time, together with an outline of possible modes of experimental attack and a statement of the meager results already obtained.
\r\n\r\nThe development of the new theory is made more intelligible by first discussing the older theories most intimately involved, and by then attempting to show how they may perhaps be correlated. In discussing those theories which have been advanced it is of course necessary to include a summary of the evidence on which they are based; but no attempt will be made to include information other than that which is directly involved. It is hoped that no omissions of unfavorable facts have been made. The following discussion will be confined to the process of fermentation as accomplished by enzyme systems, and will not touch upon the complex question of the mode of action of the living organisms.
" }, { "name": "Shafer, Edgar Esterly, Jr.", "degree": "Bachelors", "year": "1925", "title": "The Benzoylation of Malic Acid", "advisor": "Lucas, Howard J.", "url": "https://resolver.caltech.edu/CaltechTHESIS:08072024-201041930", "creators": [ { "name": { "family": "Shafer", "given": "Edgar Esterly, Jr." }, "id": "Shafer-Edgar-Esterly-Jr.", "display_name": "Shafer, Edgar Esterly, Jr." } ], "advisors": [ { "name": { "family": "Lucas", "given": "Howard J." }, "id": "Lucas-H-J", "role": "advisor", "display_name": "Lucas, Howard J." } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/vqh5-gw80", "abstract": "No abstract." }, { "name": "Sheffield, Harold Clough", "degree": "Bachelors", "year": "1925", "title": "A Method for the Production of Barium Hydroxide from Barytes", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:08082024-160329147", "creators": [ { "name": { "family": "Sheffield", "given": "Harold Clough" }, "id": "Sheffield-Harold-Clough", "display_name": "Sheffield, Harold Clough" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/tdct-qz72", "abstract": "The inertness of barytes has led to many experiments\r\nand patents for its reduction. It was decided to effect\r\nthe reduction of the barytes in a cement kiln with carbon. The temperature\r\nof the greatest yield with the least water insoluble material\r\nis between 1000\u00b0C and 1100\u00b0C and with a minimum period of heating.\r\nThe yield is about 87% of the original barytes. The resulting\r\nBaS is quenched with water and ground to 20 mesh. The leaching\r\nis very quickly accomplished and the temperature of the solution\r\nis raised 80\u00b0C to bring more material into solution. The \r\nsolution is then filtered, a theoretical amount of CuO\r\nadded and the mixture boiled. The resulting CuS is filtered\r\noff and CuO regenerated by roasting. The Ba(OH)2 solution\r\nis evaporated down and the solid precipitated out by cooling.\r\nThe material is in the form of Ba(OH)28H2O, and \r\nmust be heated to a dark red heat to drive off all the water of crystallization." }, { "name": "Simpson, Thomas Patrick", "degree": "Bachelors", "year": "1925", "title": "A Study of the Unsaturation of 2-Bromo Butane", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08082024-161604927", "creators": [ { "name": { "family": "Simpson", "given": "Thomas Patrick" }, "id": "Simpson-Thomas-Patrick", "display_name": "Simpson, Thomas Patrick" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/q12t-z316", "abstract": "No abstract." }, { "name": "Stewart, Earl Deloris", "degree": "Bachelors", "year": "1925", "title": "The Sandmeyer Reaction (Nitrile) with P-Toluidin-Meta-Sulfonic Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:08082024-181856789", "creators": [ { "name": { "family": "Stewart", "given": "Earl Deloris" }, "id": "Stewart-Earl-Deloris", "display_name": "Stewart, Earl Deloris" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zwan-w729", "abstract": "No abstract." }, { "name": "White, Ernest Croel", "degree": "PhD", "year": "1925", "title": "The Initial Decomposition Rate of Nitrogen Pentoxide", "advisor": "Tolman, Richard Chace", "url": "https://resolver.caltech.edu/CaltechETD:etd-07162004-145619", "creators": [ { "name": { "family": "White", "given": "Ernest Croel" }, "id": "White-Ernest-Croel", "display_name": "White, Ernest Croel" } ], "advisors": [ { "name": { "family": "Tolman", "given": "Richard Chace" }, "id": "Tolman-R-C", "role": "advisor", "display_name": "Tolman, Richard Chace" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/PVPC-1N90", "abstract": "No Abstract." }, { "name": "Alles, Gordon Albert", "degree": "Masters", "year": "1924", "title": "Experiments on the Chemical Behaviour of Insulin", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-135943", "creators": [ { "name": { "family": "Alles", "given": "Gordon Albert" }, "id": "Alles-Gordon-Albert", "display_name": "Alles, Gordon Albert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/4VRT-8N60", "abstract": "No Abstract." }, { "name": "Badger, Richard McLean", "degree": "PhD", "year": "1924", "title": "The Ammonia, Carbon, Hydrogen Cyanide, Hydrogen Equilibrium, and the Free Energy of Hydrogen Cyanide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05132003-153829", "creators": [ { "name": { "family": "Badger", "given": "Richard McLean" }, "id": "Badger-Richard-McLean", "display_name": "Badger, Richard McLean" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/2ZMQ-YC04", "abstract": "No abstract." }, { "name": "Baxter, Warren Phelps", "degree": "Bachelors", "year": "1924", "title": "The Precipitation of Iron as a Basic Acetate", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-142344", "creators": [ { "name": { "family": "Baxter", "given": "Warren Phelps" }, "id": "Baxter-Warren-Phelps", "display_name": "Baxter, Warren Phelps" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/X6WW-PV88", "abstract": "No Abstract." }, { "name": "Farnham, Harold Hurst", "degree": "Bachelors", "year": "1924", "title": "Oxidation of Butyric Acid with Chromic Anhydride and Sulfuric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232004-142709", "creators": [ { "name": { "family": "Farnham", "given": "Harold Hurst" }, "id": "Farnham-Harold-Hurst", "display_name": "Farnham, Harold Hurst" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/414Y-PZ45", "abstract": "No Abstract." }, { "name": "Hastings, Robert Clinton", "degree": "Bachelors", "year": "1924", "title": "An Investigation of the Effect of Varying Viscosity and Velocity on the Transfer of Heat Under Conditions of Straight Line Flow in Circular Pipes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232004-144102", "creators": [ { "name": { "family": "Hastings", "given": "Robert Clinton" }, "id": "Hastings-Robert-Clinton", "display_name": "Hastings, Robert Clinton" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/3QPD-7B19", "abstract": "No Abstract." }, { "name": "Hough, Frederic Allen", "degree": "Bachelors", "year": "1924", "title": "The Dissociation Pressure of Stannous Sulfate", "advisor": "Smith, David F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232004-144719", "creators": [ { "name": { "family": "Hough", "given": "Frederic Allen" }, "id": "Hough-Frederic-Allen", "display_name": "Hough, Frederic Allen" } ], "advisors": [ { "name": { "family": "Smith", "given": "David F." }, "id": "Smith-D-F", "role": "advisor", "display_name": "Smith, David F." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/5NDY-QS02", "abstract": "No Abstract." }, { "name": "Jameson, Archibald Yule", "degree": "Bachelors", "year": "1924", "title": "The Rearrangement of 1-Bromobutane", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262004-135347", "creators": [ { "name": { "family": "Jameson", "given": "Archibald Yule" }, "id": "Jameson-Archibald-Yule", "display_name": "Jameson, Archibald Yule" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/1TX9-VR87", "abstract": "No Abstract." }, { "name": "Jenkins, Grant Vincent", "degree": "Bachelors", "year": "1924", "title": "A Study of the Bromination of Paracresol in Water Solution and in Hydrochloric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04262004-140048", "creators": [ { "name": { "family": "Jenkins", "given": "Grant Vincent" }, "id": "Jenkins-Grant-Vincent", "display_name": "Jenkins, Grant Vincent" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/V00G-WY31", "abstract": "No Abstract." }, { "name": "Kalichevsky, Vladimir Anatole", "degree": "Bachelors", "year": "1924", "title": "Manufacturing of Perchloric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052006-154839", "creators": [ { "name": { "family": "Kalichevsky", "given": "Vladimir Anatole" }, "id": "Kalichevsky-Vladimir-Anatole", "display_name": "Kalichevsky, Vladimir Anatole" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/8R89-GH11", "abstract": "The object of this research was to study quantitatively possibilities of a continuous process of production of perchloric acid from nitrogen peroxide and ammonium perchlorate. Perchloric acid has many properties which make it an important acid in industrial and analytical work and its use would be much greater if its cost of production could be lowered. It is a strong monobasic acid, stable in solutions (up to 60%), has a high boiling point. There are relatively few insoluble salts (potassium, rubidium, caesium, and thallium perchlorates are only highly soluble) and the difference in solubilities of potassium and sodium perchlorates give an easy method of separation of these two metals in analytical work." }, { "name": "Magill, Paul Lafrone", "degree": "Bachelors", "year": "1924", "title": "Equilibrium in the System Hydrogen, Water Vapor and the Oxides of Tin", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06072004-150521", "creators": [ { "name": { "family": "Magill", "given": "Paul Lafrone" }, "id": "Magill-Paul-Lafrone", "display_name": "Magill, Paul Lafrone" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/GHDG-PP88", "abstract": "No Abstract." }, { "name": "Mayer, Joseph Edward", "degree": "Bachelors", "year": "1924", "title": "The Free Energy of Aqueous Sulfuric Acid", "advisor": "Smith, David F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06102004-135443", "creators": [ { "name": { "family": "Mayer", "given": "Joseph Edward" }, "id": "Mayer-Joseph-Edward", "display_name": "Mayer, Joseph Edward" } ], "advisors": [ { "name": { "family": "Smith", "given": "David F." }, "id": "Smith-D-F", "role": "advisor", "display_name": "Smith, David F." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/TX6K-AK35", "abstract": "No Abstract." }, { "name": "Miller, Palmer", "degree": "Bachelors", "year": "1924", "title": "The Electromotive-Force of Cells Containing Stannous Sulphate and Stannic Oxide", "advisor": "Smith, David F.", "url": "https://resolver.caltech.edu/CaltechETD:etd-06142004-145236", "creators": [ { "name": { "family": "Miller", "given": "Palmer" }, "id": "Miller-Palmer", "display_name": "Miller, Palmer" } ], "advisors": [ { "name": { "family": "Smith", "given": "David F." }, "id": "Smith-D-F", "role": "advisor", "display_name": "Smith, David F." } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/H0XD-1T68", "abstract": "No Abstract." }, { "name": "Moyse, Hollis Weaver", "degree": "Bachelors", "year": "1924", "title": "The Saturation of 2 Pentene with Hydrogen Bromide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06162004-133650", "creators": [ { "name": { "family": "Moyse", "given": "Hollis Weaver" }, "id": "Moyse-Hollis-Weaver", "display_name": "Moyse, Hollis Weaver" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/ABQD-8M14", "abstract": "No Abstract." }, { "name": "Schuhmann, Reinhardt", "degree": "PhD", "year": "1924", "title": "I. The Free Energy of Antimony and the Reduction Potential of Antimony. II. The Activity of Perchloric Acid in Aqueous Solution. III. The Free Energy and Heat Content of Arsenic Trioxide and the Reduction Potential of Arsenic", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06252004-110943", "creators": [ { "name": { "family": "Schuhmann", "given": "Reinhardt" }, "id": "Schuhmann-Reinhardt", "display_name": "Schuhmann, Reinhardt" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/63T8-VE76", "abstract": "No Abstract." }, { "name": "Swift, Ernest Haywood", "degree": "PhD", "year": "1924", "title": "A New Method for the Separation of Gallium from Other Elements", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05142003-144844", "creators": [ { "name": { "family": "Swift", "given": "Ernest Haywood" }, "id": "Swift-Ernest-Haywood", "display_name": "Swift, Ernest Haywood" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/WC3B-5D45", "abstract": "No Abstract." }, { "name": "Tracy, Willard Harmon", "degree": "Bachelors", "year": "1924", "title": "The Rate of Oxidation of Hydriodic Acid by Sulphuric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-07012004-111626", "creators": [ { "name": { "family": "Tracy", "given": "Willard Harmon" }, "id": "Tracy-Willard-Harmon", "display_name": "Tracy, Willard Harmon" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/MSN0-6E90", "abstract": "No Abstract." }, { "name": "Wolochow, David", "degree": "Bachelors", "year": "1924", "title": "The Manufacture of Tungstic Acid from Scheelite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-07202004-104651", "creators": [ { "name": { "family": "Wolochow", "given": "David" }, "id": "Wolochow-David", "display_name": "Wolochow, David" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/DAGK-9119", "abstract": "No Abstract." }, { "name": "Alcock, Joseph Rodney", "degree": "Bachelors", "year": "1923", "title": "A Method for the Preparation of Oxalic Acid From Sawdust", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02042005-103712", "creators": [ { "name": { "family": "Alcock", "given": "Joseph Rodney" }, "id": "Alcock-Joseph-Rodney", "display_name": "Alcock, Joseph Rodney" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/256R-2144", "abstract": "This investigation was undertaken to find the best method of preparing oxalic acid from sawdust, either by one of the methods described in the literature or a modification of it. The first work consisted in following the procedure recommended by a previous experimenter in order to become acquainted with the methods which are now used and to discover their weak points. The procedures used commercially, and the experimental work of Thorn, described in \"Utilization of Wood Waste\" by E. Hubbard form the basis of the work. No recent literature could be found on the subject, the work of Thorn having been done nearly forty years before. Various commercial processes use slightly different methods; one uses KOH alone in the fusion and precipitates MgC2O4 by adding MgCl2 to the K2C2O4 solution; in another a preliminary fusion is carried on in a vacuum at 180\u00b0, followed by the regular fusion yielding a nearly colorless product. A process similar to that outlined by Thorn is also used.
\r\n\r\nThe heating of sawdust with KOH results in the production of oxalic acid. Since NaOH is much cheaper, it is desirable to substitute it for KOH as far as possible. Thorn found that a mixture containing 40% KOH and 60% NaOH by weight gave almost as good a yield, when heated in thin layers, as pure KOH. The yield dropped off rapidly with a decreasing KOH percentage below 40%. He also found that the most satisfactory melt was made by using one part of sawdust to two parts of lye, striking a balance between large percentage yield from lye with more sawdust, and more organic impurities which are hard to remove if more sawdust is used. Soft wood gives a better yield than hardwood, and pure sawdust gives a better one than lignose left after treating cellulose with HCl.
" }, { "name": "Baier, Willard Ewing", "degree": "Bachelors", "year": "1923", "title": "The Extraction of Orange Oil with Volatile Solvents", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082005-155830", "creators": [ { "name": { "family": "Baier", "given": "Willard Ewing" }, "id": "Baier-Willard-Ewing", "display_name": "Baier, Willard Ewing" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/YTJZ-YV74", "abstract": "Citrus oils are used largely by confectioners, bakers, and manufacturers of soft drinks for flavoring. In 1916, 98% of the citrus oils used in this country were imported. The relatively small amount of oils produced here are obtained from the cull fruit by two general methods, the expression or pressure method and by some form of the distillation method, either vacuum distillation of the dry peel or steam distillation under various pressures. The expression method gives a much superior oil as compared with the oil obtained by distillation. However the expression method has the disadvantage that a considerable amount of oil is left in the pulp after the squeezing process. In the plant of the Exchange Orange Products Co. at San Dimas, California, where orange oil is produced, this remaining oil is recovered in a less valuable form by a subsequent steam distillation.
\r\n\r\nThe object of this investigation was to study the method of solvent extraction as a possible means of obtaining all of the oil in a good condition. A satisfactory solvent was to be found and its use studied as extensively as time permitted.
" }, { "name": "Evans, Bernard Gwynne", "degree": "Bachelors", "year": "1923", "title": "An Investigation into the Possibilities of the Electrolytic Production of Methyl Alcohol from Formaldehyde", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02172005-162819", "creators": [ { "name": { "family": "Evans", "given": "Bernard Gwynne" }, "id": "Evans-Bernard-Gwynne", "display_name": "Evans, Bernard Gwynne" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/XZTB-YR70", "abstract": "No abstract." }, { "name": "Hopper, Basil", "degree": "Bachelors", "year": "1923", "title": "Methods for the Production of Lithium Carbonate from Lipidolite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082005-164225", "creators": [ { "name": { "family": "Hopper", "given": "Basil" }, "id": "Hopper-Basil", "display_name": "Hopper, Basil" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/CCFS-JG79", "abstract": "[Introduction] The object of this investigation has been to determine a method to extract lithium from its ores in order to produce Li2CO3 which is used in medicine. Lithium salts command very good prices (averaging about $1.50 per pound) and a simple method of production would form a successful commercial enterprise. Lithium occurs in lepidolite (a lithium mica) and in amblygonite and other moderately rare minerals. In Southern California there are deposits of lepidolite with which this work has been conducted.
\r\n\r\nThe metal belongs to the alkali group but shows many properties characteristic of the alkaline-earths. It acts vigorously with water, hydrogen, nitrogen and oxygen, thus resembling the alkalies. The relative insolubility of the hydroxide, carbonate and phosphate, makes it resemble the alkaline-earths. Lithium gives a very characteristic spectrum which makes it easy to test for traces with a hand spectroscope.
" }, { "name": "Kuffel, George Cole", "degree": "Bachelors", "year": "1923", "title": "The Production of Caustic Soda Solution from Trona", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-113025", "creators": [ { "name": { "family": "Kuffel", "given": "George Cole" }, "id": "Kuffel-George-Cole", "display_name": "Kuffel, George Cole" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/R9VQ-3S68", "abstract": "This problem concerns itself with the possibility of producing a reasonably pure concentrated caustic soda solution using trona as a starting material. It involves a carbonation process, purification of raw material and causticization with lime. Since soda ash costs a little less than three times what trona costs, the process has good commercial possibilities.\r\n" }, { "name": "Nies, Henry Todd", "degree": "Bachelors", "year": "1923", "title": "The Extraction of Gallium from Zinc Ores", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-164254", "creators": [ { "name": { "family": "Nies", "given": "Henry Todd" }, "id": "Nies-Henry-Todd", "display_name": "Nies, Henry Todd" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/A9T6-E248", "abstract": "The discovery of small amounts of gallium in zinc ores showed the possibility of its presence in a small quantity of zinc ore residues on hand at the Institute. Germanium had been previously extracted from the ore, and later, part of the zinc was recovered. During this work, the presence of gallium was shown by spectroscopic tests, and indium was at the same time shown to be absent.
\r\n\r\nIn the present investigation, the reactions of different gallium compounds were studied and the action of various reagents on the residues observed, with a view toward the development of a distinctive test for gallium and finally toward the separation and purification of gallium from the residues. The residues consisted of approximately eighty liters of saturated zinc sulfate solution, containing small quantities of gallium together with various impurities.
" }, { "name": "Raymond, Albert L.", "degree": "Masters", "year": "1923", "title": "The Crystal Structure of Hexamethylene-Tetramine", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02252005-092152", "creators": [ { "name": { "family": "Raymond", "given": "Albert L." }, "id": "Raymond-Albert-L", "display_name": "Raymond, Albert L." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/A6QY-FJ79", "abstract": "No abstract." }, { "name": "Alles, Gordon Albert", "degree": "Bachelors", "year": "1922", "title": "A New Acridine Dye", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-140311", "creators": [ { "name": { "family": "Alles", "given": "Gordon Albert" }, "id": "Alles-Gordon-Albert", "display_name": "Alles, Gordon Albert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/BDX6-MF14", "abstract": "No Abstract." }, { "name": "Ames, Paul Russell", "degree": "Bachelors", "year": "1922", "title": "The Specific Heat Capacity of Heavy Petroleum Products", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-141328", "creators": [ { "name": { "family": "Ames", "given": "Paul Russell" }, "id": "Ames-Paul-Russell", "display_name": "Ames, Paul Russell" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/5C9C-MH72", "abstract": "No abstract." }, { "name": "Beman, Willard Jarvis", "degree": "Bachelors", "year": "1922", "title": "The Lowig Process for Caustic Soda Using Trona as a Raw Material", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-143549", "creators": [ { "name": { "family": "Beman", "given": "Willard Jarvis" }, "id": "Beman-Willard-Jarvis", "display_name": "Beman, Willard Jarvis" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6J5Q-Z168", "abstract": "No Abstract." }, { "name": "Bozorth, Richard Milton", "degree": "PhD", "year": "1922", "title": "Ionization in Mixtures of Salt Solutions. Activities of Ions from the Solubilities of Salts in Solutions of One Another. The Crystal Structure of Lead Molybdate. The Crystal Structure of Potassium Cyanide. The Crystal Structure of Ammonium Silicofluoride. The Crystal Structure of Cadmium Iodide. Monograph on the Separation of Isotopes", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04142004-153349", "creators": [ { "name": { "family": "Bozorth", "given": "Richard Milton" }, "id": "Bozorth-Richard-Milton", "display_name": "Bozorth, Richard Milton" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/QSQ5-A228", "abstract": "No Abstract." }, { "name": "Bridgeford, Frank Robert", "degree": "Bachelors", "year": "1922", "title": "A Process for the Utilization of Pyrite Ash", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-160316", "creators": [ { "name": { "family": "Bridgeford", "given": "Frank Robert" }, "id": "Bridgeford-Frank-Robert", "display_name": "Bridgeford, Frank Robert" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/P747-5S86", "abstract": "No Abstract." }, { "name": "Burks, Jesse Carhart", "degree": "Bachelors", "year": "1922", "title": "Semi-Works Development of a Germanium Extraction Process", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechETD:etd-04192004-161549", "creators": [ { "name": { "family": "Burks", "given": "Jesse Carhart" }, "id": "Burks-Jesse-Carhart", "display_name": "Burks, Jesse Carhart" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/TE5X-TQ90", "abstract": "No Abstract." }, { "name": "Gillies, Robert W.", "degree": "Bachelors", "year": "1922", "title": "An Attempt to Dehydrogenate Cottonseed Oil", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-04232004-143458", "creators": [ { "name": { "family": "Gillies", "given": "Robert W." }, "id": "Gillies-Robert-W", "display_name": "Gillies, Robert W." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/6E4J-V604", "abstract": "No Abstract." }, { "name": "Hill, James Ewing", "degree": "Bachelors", "year": "1922", "title": "The Distribution of Picric Acid Between Water and Benzene and the Effect on the Equilibrium of Added Sodium and Hydrogen Chlorides", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-132447", "creators": [ { "name": { "family": "Hill", "given": "James Ewing" }, "id": "Hill-James-Ewing", "display_name": "Hill, James Ewing" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/DZW2-0R55", "abstract": "This investigation was undertaken in order to study the distribution of picric acid between the immiscible solvents water and benzene at different concentrations, and to determine the effect upon this equilibrium of the addition of successive amounts to sodium chloride and hydrogen chloride to the aqueous phase.
\r\n\r\nData of this character is very similar to that relating to the effect of added electrolytes upon the solubility of slightly soluble salts and the theoretical conclusions which may be drawn are of a similar nature. The distribution results have, however, advantages over the solubility data: (1) in the former the activity may be varied over a considerable range, while in the latter it is fixed at an arbitrary value by the solubility of the salt; (2) the degree of ionization of the electrolyte used in the distribution experiments may be more accurately determined, for in the case of slightly soluble salts the range over which their concentration may be measured is very limited.
\r\n\r\nPicric acid was chosen for these experiments because its degree of ionization is that of a typical electrolyte and because it is one of the very few highly ionized substances which distribute themselves in a convenient ration between water and the more miscible solvent.
\r\n\r\nThe distribution of picric acid between water and benzene in the absence of added electrolytes has been studied by Walden (1) Kuriloff (2), and by Rothmund and Druker (3). The work of the latter investigators only is of sufficient accuracy to warrant careful study. Recently Eherenfeld (4) obtained some preliminary data regarding the effect of added salts upon the distribution ratio. The results of these investigations will be compared with the data obtained in this, after that data has been presented.
" }, { "name": "Knight, Alfred Wheelock", "degree": "Bachelors", "year": "1922", "title": "Perchloric Acid from Ammonium Perchlorate and Oxides of Nitrogen", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-05052004-140206", "creators": [ { "name": { "family": "Knight", "given": "Alfred Wheelock" }, "id": "Knight-Alfred-Wheelock", "display_name": "Knight, Alfred Wheelock" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/MTDD-R892", "abstract": "No Abstract." }, { "name": "Maurer, Frederic Andrew", "degree": "Bachelors", "year": "1922", "title": "A Study of the Production of Sodium Perchlorate Electrolytically", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02242005-114700", "creators": [ { "name": { "family": "Maurer", "given": "Frederic Andrew" }, "id": "Maurer-Frederic-Andrew", "display_name": "Maurer, Frederic Andrew" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/N86F-JR54", "abstract": "The purpose of this work is to investigate the electrolytic production of perchlorate from chloride, and particularly to determine which anode materials serve best under the rigorous conditions imposed. In order that one may better understand what follows, it is necessary to briefly summarize the existing theory of the electrolytic formation of chlorate and perchlorate." }, { "name": "Reynolds, Maynard Stuckey", "degree": "Bachelors", "year": "1922", "title": "The Utilization of a Deposit of Magnesite Located Near Porterville, California as a Source of Raw Material for the Manufacture of C.P. Epsom Salts", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06242004-141108", "creators": [ { "name": { "family": "Reynolds", "given": "Maynard Stuckey" }, "id": "Reynolds-Maynard-Stuckey", "display_name": "Reynolds, Maynard Stuckey" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/K4AH-1W74", "abstract": "No Abstract." }, { "name": "Ritchie, Charles Fisher", "degree": "Bachelors", "year": "1922", "title": "A Colorimetric Determination of Hydrocyanic Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:06112015-155708716", "creators": [ { "name": { "family": "Ritchie", "given": "Charles Fisher" }, "id": "Ritchie-Charles-Fisher", "display_name": "Ritchie, Charles Fisher" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/WNXG-ZT76", "abstract": "The object of this investigation is to devise a rapid,\r\nfairly accurate, colorimetric analysis for HCN to be used in field work\r\nfor determining instantaneous concentrations of the gas under fumigating\r\ncanvas. A large amount of money is expended yearly by the citrus industry\r\nof this state in attempting to control and to eradicate the scale\r\npests. Although fumigation with HCN has been practiced tor many years,\r\nthe progress made has been anything but satisfactory. The greater portion of the work has always been carried on by contractors, who in a large number of cases have been very unscrupulous. The materials\r\nand labor are very expensive and the growers have been satisfied to\r\nadhere to beaten paths and hope for the best results on scale kill\r\nwith the least attendant foliage injury. One familiar with fumigating,\r\neither from the grower's or the operator's viewpoint, knows that very\r\nwidely varying results are obtained, even under what are apparently\r\nidentical condition. Even after discounting for the dishonesty of\r\nsome operators and the prejudices of the grower, there is still a large variance between desired or expected results and those actually obtained." }, { "name": "Ritchie, Charles Fisher", "degree": "Bachelors", "year": "1922", "title": "An Investigation on the Production of Sodium Thiosulfate from Trona", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-06242004-143142", "creators": [ { "name": { "family": "Ritchie", "given": "Charles Fisher" }, "id": "Ritchie-Charles-Fisher", "display_name": "Ritchie, Charles Fisher" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/Y01W-T284", "abstract": "No Abstract." }, { "name": "Smith, David Frederick", "degree": "PhD", "year": "1922", "title": "The Condition of Bismuth Salts in Aqueous Solutions and the Molar Electrode-Potential of Bismuth", "advisor": "Pauling, Linus", "url": "https://resolver.caltech.edu/CaltechTHESIS:08062024-172939090", "creators": [ { "name": { "family": "Smith", "given": "David Frederick" }, "id": "Smith-David-Frederick", "display_name": "Smith, David Frederick" } ], "advisors": [ { "name": { "family": "Pauling", "given": "Linus" }, "id": "Pauling-L", "role": "advisor", "display_name": "Pauling, Linus" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/vskt-t918", "abstract": "No abstract." }, { "name": "Vesper, Howard Gockley", "degree": "Bachelors", "year": "1922", "title": "The Preparation of Carbon Monosulphide and Hydrocyanic Acid by the Use of Activated Carbon", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-07162004-142151", "creators": [ { "name": { "family": "Vesper", "given": "Howard Gockley" }, "id": "Vesper-Howard-Gockley", "display_name": "Vesper, Howard Gockley" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemeng" ], "doi": "10.7907/HXNR-JN80", "abstract": "No Abstract." }, { "name": "Warner, Lester Orville", "degree": "Bachelors", "year": "1922", "title": "The Reaction Between Nitrogen and Methane in the Silent Electric Discharge", "advisor": "Lacey, William Noble", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232024-203144641", "creators": [ { "name": { "family": "Warner", "given": "Lester Orville" }, "id": "Warner-Lester-Orville", "display_name": "Warner, Lester Orville" } ], "advisors": [ { "name": { "family": "Lacey", "given": "William Noble" }, "id": "Lacey-W-N", "role": "advisor", "display_name": "Lacey, William Noble" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/576e-8q34", "abstract": "No abstract." }, { "name": "Clarke, Philip Seymour", "degree": "Bachelors", "year": "1921", "title": "The Extracting of Germanium from Crude Oxide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02032005-111330", "creators": [ { "name": { "family": "Clarke", "given": "Philip Seymour" }, "id": "Clarke-Philip-Seymour", "display_name": "Clarke, Philip Seymour" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XZ1Y-JE25", "abstract": "Since the discovery of germanium in certain American zinc ores, notably that of Joplin, Mo., several procedures have been suggested for the extraction of the germanium. These procedures, however, were simple distillations of the zinc ore with hydrochloric acid carried out in the laboratory on a small scale. The cost of the materials and the character of the reagents required obviously would cause such procedures to be impracticable on a large scale.
\r\n\r\nIn the present investigation, the reactions of germanium compounds and the actions of different reagents on the sample were observed with the view toward developing a method of extraction that would be applicable on and industrial scale. For this purpose, a ten-pound sample of germanium-bearing zinc oxide was furnished by the New Jersey Zinc Co. with the accompanying information that germanium was present in the sample to the extent of 0.25% GeO2.
" }, { "name": "Simpson, Charles Fillmore", "degree": "Bachelors", "year": "1921", "title": "Some Silver Salts of Brominate Phenols and Napthols. The Action of Potassium and Butyl Alcohol on Amines", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02082005-164843", "creators": [ { "name": { "family": "Simpson", "given": "Charles Fillmore" }, "id": "Simpson-Charles-Fillmore", "display_name": "Simpson, Charles Fillmore" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/3EKX-NW09", "abstract": "No abstract." }, { "name": "Stamm, Alfred Joaquin", "degree": "Bachelors", "year": "1921", "title": "A Study of the Nature of the Adsorptive Property of Fuller's Earth", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07292024-185226060", "creators": [ { "name": { "family": "Stamm", "given": "Alfred Joaquin" }, "id": "Stamm-Alfred-Joaquin", "display_name": "Stamm, Alfred Joaquin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/azp4-y170", "abstract": "No abstract." }, { "name": "Stenzel, Richard Werner", "degree": "Bachelors", "year": "1921", "title": "A Method for the Preparation of Perchloric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-02092005-084840", "creators": [ { "name": { "family": "Stenzel", "given": "Richard Werner" }, "id": "Stenzel-Richard-Werner", "display_name": "Stenzel, Richard Werner" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/Z1NE-DB82", "abstract": "Perchloric Acid is a substance resembling sulfuric acid in many respects. It is a strong acid, very stable in solution, and has a high boiling point. It possesses some advantages over sulfuric acid, such as being monobasic, and having relatively few insoluble salts. (K, Rb, Cs, and Tl perchlorates are only slightly soluble.) Hence a cheap way of making perchloric acid would be highly advantageous to the chemical industry. The present methods of its production are rather expensive, employing the electrolytic production of sodium perchlorate and the distillation of the latter with sulfuric acid under reduced pressure. The product, a 60% perchloric acid is now sold for $7 to $8 per pound. Ammonium perchlorate is obtainable at a fairly low cost, (about 2O [cents] per pound) and might be used as a basis for the cheaper preparation of perchloric acid.
\r\n\r\nObviously the most direct method of accomplishing this would be the replacement of the NH4 radical in NH4ClO4 by H. It is proposed in this paper to find whether the ammonium ion in ammonium perchlorate solution can be oxidized by means of the oxides of nitrogen, producing only perchloric acid solution and gaseous products. The ideal reaction would be: (I) 2NH4ClO4 + N2O3 = 2N2 + 2HClO4 + 3H2O. This leaves no reaction products from which the perchloric acid need be purified, and hence it is desired to approach in practice this equation as closely as possible.
\r\n" }, { "name": "Dickinson, Roscoe Gilkey", "degree": "PhD", "year": "1920", "title": "I. The Crystal Structures of Wulfenite and Scheelite. II. The Crystal Structures of Sodium Chlorate and Sodium Bromate", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechETD:etd-08112004-160640", "creators": [ { "name": { "family": "Dickinson", "given": "Roscoe Gilkey" }, "id": "Dickinson-Roscoe-Gilkey", "display_name": "Dickinson, Roscoe Gilkey" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/XY4V-FK91", "abstract": "In the study of the crystal structures of wulfenite and scheelite a number of possible sources of difficulty came to light which either would not be encountered or could be avoided in the study of sodium chlorate by the Bragg method. Large crystals could be obtained without serious difficulty and on these any desired face could be ground, a necessary precaution that could not be taken with the borrowed specimens of the previous research. This would eliminate gross ambiguities as to the amount of absorption suffered by the X-ray beam, and also permit definition of the relative areas of crystal operating in the successive orders of reflection. On the interpretive side, although the various atoms involved differ in atomic number sufficiently for their effects to be easily distinguishable, they are all included within a sufficiently limited range so that their contributions to the amplitude of the reflected wave would be expected to be sufficiently near proportional to their atomic numbers. It seemed advisable to make measurements on sodium bromate also since this salt is completely isomorphous with the chlorate." }, { "name": "House, Harvey Walter", "degree": "Bachelors", "year": "1920", "title": "The Dehydrogenation of Cotton Seed Oil", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232024-204630794", "creators": [ { "name": { "family": "House", "given": "Harvey Walter" }, "id": "House-Harvey-Walter", "display_name": "House, Harvey Walter" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/h8am-bw96", "abstract": "No abstract." }, { "name": "Beuschlein, Warren L.", "degree": "Bachelors", "year": "1919", "title": "The Electrolytic Reduction of Sodium Nitrate to Sodium Nitrite", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07192024-212532240", "creators": [ { "name": { "family": "Beuschlein", "given": "Warren L." }, "id": "Beuschlein-Warren-L", "display_name": "Beuschlein, Warren L." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/kxfg-f833", "abstract": "No abstract." }, { "name": "Kirschman, H. Darwin", "degree": "Masters", "year": "1919", "title": "The Vapor Pressure of Hydrogen Chloride and Hydrogen Bromide Above their Aqueous Solutions at 25", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07262024-213658242", "creators": [ { "name": { "family": "Kirschman", "given": "H. Darwin" }, "id": "Kirschman-H-Darwin", "display_name": "Kirschman, H. Darwin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/xym2-hn54", "abstract": "No abstract." }, { "name": "Capra, Frank Russell", "degree": "Bachelors", "year": "1918", "title": "The Equivalent Conductance of Solutions of Picric Acid", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:09102015-160736564", "creators": [ { "name": { "family": "Capra", "given": "Frank Russell" }, "id": "Capra-Frank-Russell", "display_name": "Capra, Frank Russell" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "None", "given": "None" }, "display_name": "None, None" } ], "option_major": [ "chemistry" ], "doi": "10.7907/6Z0C-0639", "abstract": "Picric acid possesses the property, which is rare among strong electrolytes, of having a convenient distribution ratio between water and certain organic solvents such as benzene, chloroform, etc. Because of this property, picric acid offers peculiar advantages for studying the well known deviations of strong electrolytes from the law of mass action, for; by means of distribution experiments, the activities of picric acid in various aqueous solutions may be compared.
\r\n\r\nIn order to interpret the results of such distribution experiments, it is necessary to know the degree of ionization of picric acid in aqueous solutions.
\r\n\r\nAt least three series of determinations of the equivalent conductance of picric acid have been published, but the results are not concordant; and therefore, the degree of ionization cannot be calculated with any degree of certainty.
\r\n\r\nThe object of the present investigation was to redetermine the conductance of picric acid solutions in order to obtain satisfactory data from which the degrees of ionization of its solutions might be calculated.
\r\n\r\n" }, { "name": "Flory, Robert Weybright", "degree": "Bachelors", "year": "1918", "title": "I. Action of Hydrogen Peroxide on Aromatic Compounds. II. An Attempt to Prepare Di-Para-Di-Amino-Para-Diphenylbenzene", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07092024-150922588", "creators": [ { "name": { "family": "Flory", "given": "Robert Weybright" }, "id": "Flory-Robert-Weybright", "display_name": "Flory, Robert Weybright" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/zka7-6m70", "abstract": "No abstract." }, { "name": "Hainsworth, William Richard", "degree": "Masters", "year": "1918", "title": "Equilibria Investigation of the Bucher Process for Nitrogen Fixation", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07242024-153823595", "creators": [ { "name": { "family": "Hainsworth", "given": "William Richard" }, "id": "Hainsworth-William-Richard", "display_name": "Hainsworth, William Richard" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/a17y-hn74", "abstract": "No abstract." }, { "name": "Hartley, Joseph Frederick", "degree": "Bachelors", "year": "1918", "title": "An Equipment for Determining the Relative Viscosity of Aqueous Solutions", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07242024-153450069", "creators": [ { "name": { "family": "Hartley", "given": "Joseph Frederick" }, "id": "Hartley-Joseph-Frederick", "display_name": "Hartley, Joseph Frederick" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/my4k-wt64", "abstract": "No abstract." }, { "name": "Kirschman, H. Darwin", "degree": "Bachelors", "year": "1918", "title": "The Vapor Pressure of Hydrogen Chloride Above its Aqueous Solution", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232024-203714594", "creators": [ { "name": { "family": "Kirschman", "given": "H. Darwin" }, "id": "Kirschman-H-Darwin", "display_name": "Kirschman, H. Darwin" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/zdvc-9r83", "abstract": "No abstract." }, { "name": "Nutt, Donovan", "degree": "Bachelors", "year": "1918", "title": "The Equilibrium Between Cuprous and Cupric Ions and Copper", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07232024-204159052", "creators": [ { "name": { "family": "Nutt", "given": "Donovan" }, "id": "Nutt-Donovan", "display_name": "Nutt, Donovan" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/nxx1-4431", "abstract": "No abstract." }, { "name": "Steele, James P.", "degree": "Bachelors", "year": "1918", "title": "The Silver Salts of Tetrabromphenol", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07192024-224641502", "creators": [ { "name": { "family": "Steele", "given": "James P." }, "id": "Steele-James-P", "display_name": "Steele, James P." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/cjev-mb95", "abstract": "No abstract." }, { "name": "Sticht, Robert Carl, Jr.", "degree": "Bachelors", "year": "1918", "title": "The Specific Electrode Potential of Bismuth", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07192024-214358601", "creators": [ { "name": { "family": "Sticht", "given": "Robert Carl, Jr." }, "id": "Sticht-Robert-Carl-Jr.", "display_name": "Sticht, Robert Carl, Jr." } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemeng" ], "doi": "10.7907/2wr9-sr76", "abstract": "No abstract." }, { "name": "Kemp, Archie Reed", "degree": "Bachelors", "year": "1917", "title": "The Determination of Silver in Organic Compounds. The Silver Salts of Pentabromophenol", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07082024-223136719", "creators": [ { "name": { "family": "Kemp", "given": "Archie Reed" }, "id": "Kemp-Archie-Reed", "display_name": "Kemp, Archie Reed" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/k6gy-t596", "abstract": "No abstract." }, { "name": "Manning, Paul DeVries", "degree": "Masters", "year": "1917", "title": "The Equilibrium in a Process for the Production of Sodium Cyanide", "advisor": "Unknown, Unknown", "url": "https://resolver.caltech.edu/CaltechTHESIS:07052024-203247999", "creators": [ { "name": { "family": "Manning", "given": "Paul DeVries" }, "id": "Manning-Paul-DeVries", "display_name": "Manning, Paul DeVries" } ], "advisors": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "committee": [ { "name": { "family": "Unknown", "given": "Unknown" }, "display_name": "Unknown, Unknown" } ], "option_major": [ "chemistry" ], "doi": "10.7907/jjaf-m922", "abstract": "[Introduction]: The normally large demand for supplies of the various nitrogenous products of the industries has been greatly increased as a result of the war. The importation of nitrates to the United States from Chile would be stopped in case of a naval blockade. The problem of assuring an adequate supply of such materials is, therefore, a very pertinent one. This may best be solved by the improvement of the present commercial processes for the fixation of atmospheric nitrogen and by the development of new processes, not at present successful commercially. Apparently, the most\r\npromising known process of the latter class is based upon the formation of sodium cyanide by passing nitrogen gas over a mixture of sodium carbonate and carbon in the presence of a suitable\r\ncatalyzer at high temperatures." } ]